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PF00389 2-Hacid_DH; <br>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.. 
PF00198 2-oxoacid dehydrogenases acyltransferase (catalytic domain)<br>These proteins contain one to three copies of a lipoyl binding domain followed by the catalytic domain.. 
PF04029 2-phosphosulpholactate phosphatase<br>Thought to catalyse 2-phosphosulpholactate = sulpholactate + phosphate. Probable magnesium cofactor.  Involved in the second step of coenzyme M biosynthesis.  Inhibited by vanadate in Methanococcus jannaschii.  Also known as the ComB family  .. 
PF03171 2OG-Fe(II) oxygenase superfamily<br>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  catalysing the reaction: Procollagen L-proline + 2-oxoglutarate + O2 <=> procollagen trans- 4-hydroxy-L-proline + succinate + CO2.  The full enzyme consists of a alpha2 beta2 complex with the alpha subunit contributing most of the parts of the active site  . The family also includes lysyl hydrolases, isopenicillin synthases and AlkB.. 
PF01073 3-beta hydroxysteroid dehydrogenase/isomerase family<br>Pfam-B_504 (release 3.0). 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 precursors into the corresponding 4-ene-ketosteroids necessary for the formation of all classes of steroid hormones.. 
PF04419 4F5 protein family<br>Members of this family are short proteins that are rich in aspartate, glutamate, lysine and arginine. Although the function of these proteins is unknown, they are found to be ubiquitously expressed  .. 
PF03061 Thioesterase superfamily<br>Pfam-B_2758 (release 6.4). This family contains a wide variety of enzymes, principally thioesterases. This family includes 4HBT (EC 3.1.2.23) which catalyses the final step in the  biosynthesis of 4-hydroxybenzoate from 4-chlorobenzoate in the soil dwelling microbe Pseudomonas CBS-3. This family includes various cytosolic long-chain acyl-CoA  thioester hydrolases. Long-chain acyl-CoA hydrolases hydrolyse palmitoyl-CoA to CoA and palmitate, they also catalyse the hydrolysis of other  long chain fatty acyl-CoA thioesters.. 
PF02872 5_nucleotidaseC; <br>5'-nucleotidase, C-terminal domain. Pfam-B_1318 (release 3.0). 
PF00003 7 transmembrane sweet-taste receptor of 3 GCPR<br>This is a domain of seven transmembrane regions that forms the C-terminus of some subclass 3 G-coupled-protein receptors. It is often associated with a downstream cysteine-rich linker domain, NCD3G Pfam:PF07562, which is the human sweet-taste receptor, and the N-terminal domain, ANF_receptor Pfam:PF01094. The seven TM regions assemble in such a way as to produce a docking pocket into which such molecules as cyclamate and lactisole have been found to bind and consequently confer the taste of sweetness  .. 
PF01661 DUF27;A1pp; <br>Pfam-B_434 (release 4.1). This domain is an ADP-ribose binding module.  It is found in a number of otherwise unrelated proteins.  It is found at the C-terminus of the macro-H2A histone protein Swiss:Q02874. This domain is found in the non-structural proteins of several types of ssRNA viruses such as NSP3 from alphaviruses Swiss:P03317. This domain is also found on its own in a family of proteins from bacteria Swiss:P75918, archaebacteria Swiss:O59182 and eukaryotes Swiss:Q17432.. 
PF02177 A4_EXTRA;<br>Amyloid A4 N-terminal heparin-binding. Alignment kindly provided by SMART. This N-terminal domain of APP, amyloid precursor protein, is the heparin-binding domain of the protein. this region is also responsible for stimulation of neurite outgrowth. The structure reveals both a highly charged basic surface that may interact with glycosaminoglycans in the brain and an abutting hydrophobic surface that is proposed to play an important functional role such as in dimerisation or ligand-binding. Structural similarities with cysteine-rich growth factors, taken together with its known growth-promoting properties, suggest the APP N-terminal domain could function as a growth factor in vivo  .. 
PF00962 Adenosine/AMP deaminase<br>
PF01490 Transmembrane amino acid transporter protein<br>Pfam-B_419 (release 4.0). This transmembrane region is found in many amino acid transporters  including UNC-47 and MTR. UNC-47 encodes a vesicular amino butyric acid (GABA) transporter, (VGAT). UNC-47 is predicted to have 10 transmembrane  domains Swiss:P34579  . MTR is a N system amino acid transporter system protein involved in methyltryptophan resistance Swiss:P38680. Other members of this family include proline transporters and amino acid permeases.. 
PF00004 ATPase family associated with various cellular activities (AAA)<br>AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes  .. 
PF00696 aakinase; <br>Amino acid kinase family. Pfam-B_100 (release 2.1). This family includes kinases that phosphorylate a variety of amino acid substrates, as well as uridylate kinase and carbamate kinase. This family includes: Aspartokinase EC:2.7.2.4, Swiss:P00561. Acetylglutamate kinase EC:2.7.2.8, Swiss:Q07905. Glutamate 5-kinase EC:2.7.2.11, Swiss:P07005. Uridylate kinase EC:2.7.4.-, Swiss:P29464. Carbamate kinase EC:2.7.2.2, Swiss:O96432.. 
PF03109 ABC1 family<br>Pfam-B_339 (release 6.5). 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 cytochrome b mRNA translation defect and is essential for the electron transfer in the bc 1 complex   and E. coli AarF is required for ubiquinone production  . It has been  suggested that members of the ABC1 family are novel chaperonins  . These proteins are unrelated to the ABC transporter proteins.. 
PF01842 ACT domain<br>This family of domains generally have a regulatory role. ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. Pairs of ACT domains bind specifically to a particular amino acid leading to regulation of the linked enzyme.  The ACT domain is found in: D-3-phosphoglycerate dehydrogenase EC:1.1.1.95 Swiss:P08328, which is inhibited by serine  . Aspartokinase EC:2.7.2.4 Swiss:P53553, which is regulated by lysine. Acetolactate synthase small regulatory subunit Swiss:P00894, which is inhibited by valine. Phenylalanine-4-hydroxylase EC:1.14.16.1 Swiss:P00439, which is regulated by phenylalanine. Prephenate dehydrogenase EC:4.2.1.51 Swiss:P21203. formyltetrahydrofolate deformylase EC:3.5.1.10, Swiss:P37051, which is activated by methionine and inhibited by glycine. GTP pyrophosphokinase EC:2.7.6.5 Swiss:P11585. 
PF04083 abhydro_lipase; <br>Partial alpha/beta-hydrolase lipase region. Pfam-B_267 (release 7.3);. This family corresponds to a N-terminal part of an alpha/beta hydrolase domain.. 
PF00583 Acetyltransf; <br>Acetyltransferase (GNAT) family. MRC-LMB Genome group. This family contains proteins with N-acetyltransferase functions such as Elp3-related proteins.. 
PF01648 4'-phosphopantetheinyl transferase superfamily<br>Pfam-B_1679 (release 4.1) & Pfam-B_3672 (Release 7.5). Members of this family transfers the 4'-phosphopantetheine (4'-PP) moiety from coenzyme A (CoA) to the invariant serine of Pfam:PF00550. This post-translational modification renders holo-ACP capable of acyl group activation via thioesterification of the cysteamine thiol of 4'-PP  . This superfamily consists of two subtypes: The ACPS type such as Swiss:P24224 and the Sfp type such as Swiss:P39135. The structure of the Sfp type is known  , which shows the active site accommodates a magnesium ion. The most highly conserved regions of the alignment are involved in binding the magnesium ion.. 
PF01064 Activin types I and II receptor domain<br>Pfam-B_338 (release 3.0). This Pfam entry consists of both TGF-beta receptor types. This is an alignment of the hydrophilic cysteine-rich  ligand-binding domains, Both receptor types, (type I and II) posses a 9 amino acid cysteine box, with the the consensus CCX{4-5}CN. The type I receptors also possess 7 extracellular residues preceding the cysteine box.. 
PF00441 Acyl-CoA_dh;<br>Acyl-CoA dehydrogenase, C-terminal domain. C-terminal domain of Acyl-CoA dehydrogenase is an all-alpha, four helical up-and-down bundle.. 
PF01757 DUF33;<br>Acyltransferase family. Pfam-B_708 (release 4.2). 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.. 
PF00928 Adaptor complexes medium subunit family<br>Pfam-B_1007 (release 3.0). This family also contains members which are coatomer subunits.. 
PF00107 adh_zinc; <br>Zinc-binding dehydrogenase. 
PF02682 DUF213; <br>Allophanate hydrolase subunit 1. This family is the first subunit of allophanate hydrolase.. 
PF03915 Actin interacting protein 3<br>Wood V, Griffiths-Jones SR. Pfam-B_38461 (release 7.2). 
PF00842 Ala_racemase; <br>Alanine racemase, C-terminal domain. Pfam-B_1496 (release 2.1). 
PF01168 UPF0001;<br>Alanine racemase, N-terminal domain. 
PF01315 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain<br>
PF02738 Molybdopterin-binding domain of aldehyde dehydrogenase<br>
PF00248 aldo_ket_red; <br>Aldo/keto reductase family. This family includes a number of K+ ion channel beta chain regulatory domains - these are reported to have oxidoreductase activity  .. 
PF01263 Aldose 1-epimerase<br>
PF03155 ALG6, ALG8 glycosyltransferase family<br>Pfam-B_3941 (release 6.5). 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 membrane prior to the transfer of the oligosaccharide moiety to the target asparagine residues. This oligosaccharide is composed of Glc(3)Man(9)GlcNAc(2). The addition of the three glucose residues is the final series of steps in the synthesis of the oligosaccharide precursor. Alg6 transfers the first glucose residue, and Alg8 transfers the second one  . In the human alg6 gene, a C->T transition, which causes Ala333 to be replaced with Val, has been identified as the cause of a congenital disorder of glycosylation, designated as type Ic OMIM:603147  .. 
PF00245 alk_phosphatase; <br>Alkaline phosphatase. 
PF02806 alpha-amylase_C; <br>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 between beta strand 3 and alpha helix 3, and a  carboxyl-terminal Greek key beta-barrel domain.. 
PF05111 Ameloblastin precursor (Amelin)<br>Pfam-B_6419 (release 7.7). This family consists of several mammalian Ameloblastin precursor (Amelin) proteins. Matrix proteins of tooth enamel consist mainly of amelogenin but also of non-amelogenin proteins, which, although their volumetric percentage is low, have an important role in enamel mineralisation. One of the non-amelogenin proteins is ameloblastin, also known as amelin and  sheathlin. Ameloblastin (AMBN) is one of the enamel sheath proteins which  is though to have a role in determining the prismatic structure of growing enamel crystals  .. 
PF01510 N-acetylmuramoyl-L-alanine amidase<br>Pfam-B_735 (release 4.0). This family includes zinc amidases that have N-acetylmuramoyl-L-alanine amidase activity EC:3.5.1.28. This enzyme domain cleaves the amide bond between N-acetylmuramoyl and L-amino acids in bacterial cell walls (preferentially: D-lactyl-L-Ala).  The structure is known for the bacteriophage T7 structure and shows that two of the conserved histidines are zinc binding.. 
PF01520 N-acetylmuramoyl-L-alanine amidase<br>Pfam-B_888 (release 4.0). This enzyme domain cleaves the amide bond between N-acetylmuramoyl and L-amino acids in bacterial cell walls.. 
PF01593 Flavin containing amine oxidoreductase<br>Pfam-B_606 (release 4.1)b. This family consists of various amine oxidases, including maze polyamine oxidase (PAO)   and various flavin containing monoamine oxidases (MAO). The aligned region includes the flavin binding site of these enzymes. The family also contains phytoene dehydrogenases and related enzymes. In vertebrates MAO plays an important role regulating the intracellular levels of amines via there oxidation; these include various neurotransmitters, neurotoxins and trace amines  . In lower eukaryotes such as aspergillus and in bacteria the main role of amine oxidases is to provide a source of ammonium  . PAOs in plants, bacteria and protozoa oxidase spermidine and spermine to an aminobutyral, diaminopropane and hydrogen peroxide and are involved in the catabolism of polyamines  .  Other members of this family include tryptophan 2-monooxygenase, putrescine oxidase, corticosteroid binding proteins and antibacterial glycoproteins.. 
PF00501 AMP-binding enzyme<br>
PF05195 Aminopeptidase P, N-terminal domain<br>This domain is structurally very similar   to the creatinase N-terminal domain (Pfam:PF01321). However, little or no sequence similarity exists between the two families.. 
PF03098 Animal haem peroxidase<br>
PF01821 Anaphylotoxin-like domain<br>C3a, C4a and C5a anaphylatoxins are protein fragments generated enzymatically in serum during activation of complement molecules C3, C4, and C5. They induce smooth muscle contraction. These fragments are homologous to a three-fold repeat in fibulins.. 
PF01094 Receptor family ligand binding region<br>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.. 
PF00023 ank; <br>Swissprot_feature_table. Ankyrins are multifunctional adaptors that link specific proteins to the membrane-associated, spectrin- actin cytoskeleton. This repeat-domain is a 'membrane-binding' domain of up to 24 repeated units, and it mediates most of the protein's binding activities. Repeats 13-24 are especially active, with known sites of interaction for the Na/K ATPase, Cl/HCO(3) anion exchanger, voltage-gated sodium channel, clathrin heavy chain and L1 family cell adhesion molecules. The ANK repeats are found to form a contiguous spiral stack such that ion transporters like the anion exchanger associate in a large central cavity formed by the ANK repeat spiral, while clathrin and cell adhesion molecules associate with specific regions outside this cavity   .. 
PF00191 annexin; <br>This family of annexins also includes giardin that has been shown to function as an annexin  .. 
PF03861 ANTAR domain<br>ANTAR (AmiR and NasR transcription antitermination regulators) is an RNA-binding domain found in bacterial transcription antitermination regulatory proteins. The majority of the  domain consists of a coiled-coil. . 
PF04729 Anti-silence; <br>ASF1 like histone chaperone. Pfam-B_3167 (release 7.5). This family includes the yeast and human ASF1 protein.  These proteins have histone chaperone activity  .  ASF1 participates in both the replication-dependent and replication-independent pathways.  The structure three-dimensional has been determined as a a compact immunoglobulin-like beta sandwich fold topped by three helical linkers  .. 
PF02822 Antistasin family<br>Members of this family are inhibitors of trypsin family proteases. This domain is highly disulphide bonded. The domain is also found in some large extracellular proteins in multiple copies.. 
PF00847 AP2-domain; <br>Pfam-B_409 (release 3.0). This 60 amino acid residue domain can bind to DNA   and is found in transcription factor proteins.. 
PF02424 ApbE family<br>Pfam-B_1963 (release 5.4). This prokaryotic family of lipoproteins are related to ApbE from Salmonella typhimurium. ApbE is involved in thiamine synthesis  . More specifically is may be involved in the conversion of aminoimidazole ribotide (AIR) to 4-amino-5-hydroxymethyl-2-methyl pyrimidine (HMP).. 
PF04049 Anaphase promoting complex subunit 8 / Cdc23 <br>Pfam-B_13808 (release 7.3);. The anaphase-promoting complex is composed of eight protein  subunits, including BimE (APC1), CDC27 (APC3), CDC16 (APC6),  and CDC23 (APC8).. 
PF04106 Autophagy protein Apg5 <br>Pfam-B_12134 (release 7.3);. Apg5 is directly required for the import of  aminopeptidase I via the cytoplasm-to-vacuole targeting  pathway  .. 
PF04602 arab_transf; <br>Mycobacterial cell wall arabinan synthesis protein. Pfam-B_4670 (release 7.5). Arabinosyltransferase is involved in arabinogalactan (AG) biosynthesis pathway in mycobacteria. AG is a component of the   macromolecular assembly of the mycolyl-AG-peptidoglycan complex of the cell wall. This enzyme has important clinical applications as it is believed to be the target of the antimycobacterial drug Ethambutol  .. 
PF03079 ARD/ARD' family<br>Pfam-B_2276 (release 6.4). 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  Swiss:Q9ZFE7, but bind different metal ions: ARD binds Ni2+, ARD' binds Fe2+. ARD and ARD' can be experimentally interconverted by removal of the bound metal ion and reconstitution with the appropriate metal ion.  The two enzymes share the same substrate, 1,2-dihydroxy-3-keto-5-(methylthio)pentene, but yield different products. ARD' yields the alpha-keto precursor of methionine (and formate), thus forming part of the ubiquitous methionine salvage  pathway that converts 5'-methylthioadenosine (MTA) to methionine. This pathway is responsible for the tight control of the concentration of MTA, which is a powerful inhibitor of polyamine biosynthesis and transmethylation reactions [1,2]. ARD yields methylthiopropanoate, carbon monoxide and formate, and thus prevents the conversion of MTA to methionine. The role of the ARD catalysed reaction is unclear: methylthiopropanoate is cytotoxic, and carbon monoxide can activate guanylyl cyclase, leading to increased intracellular cGMP levels [1,2]. This family also contains other members, whose functions are not well characterised.. 
PF01412 Putative GTPase activating protein for Arf<br>Ponting CP, Schultz J, Bork P. 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.. 
PF01388 ARID/BRIGHT DNA binding domain<br>This domain is know as ARID for AT-Rich Interaction Domain  , and also known as the BRIGHT domain  .. 
PF04683 ARM_1; <br>Proteasome complex subunit Rpn13 ubiquitin receptor. Pfam-B_4497 (release 7.5). This family was thought originally to be involved in cell-adhesion [1,2], but the members are now known to be proteasome subunit Rpn13, a novel ubiquitin receptor. The 26S proteasome is a huge macromolecular protein-degradation machine consisting of a proteolytically active 20S core, in the form of four disc-like proteins, and one or two 19S regulatory particles. The regulatory particle(s) sit on the top and or bottom of the core, de-ubiquitinate the substrate peptides, unfold them and guide them into the narrow channel through the centre of the core. Rpn13 and its homologues dock onto the regulatory particle through the N-terminal region which binds Rpn2. The C-terminal part of the domain binds de-ubiquitinating enzyme Uch37/UCHL5 and enhances its isopeptidase activity. Rpn13 binds ubiquitin via a conserved amino-terminal region called the pleckstrin-like receptor for ubiquitin, termed Pru, domain  . The domain forms two contiguous anti-parallel beta-sheets with a configuration similar to the pleckstrin-homology domain (PHD) fold  . Rpn13's ability to bind ubiquitin and the proteasome subunit Rpn2/S1 simultaneously supports evidence of its role as a ubiquitin receptor. Finally, when complexed to di-ubiquitin, via the Pru, and Uch37 via the C-terminal part, it frees up the distal ubiquitin for de-ubiquitination by the Uch37  .. 
PF00514 Armadillo_seg; <br>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.. 
PF00339 arrestin; <br>Arrestin (or S-antigen), N-terminal domain. Ig-like beta-sandwich fold.  Scop reports duplication with C-terminal domain.. 
PF02752 arrestin_C; <br>Arrestin (or S-antigen), C-terminal domain. Ig-like beta-sandwich fold.  Scop reports duplication with N-terminal domain.. 
PF04959 Arsenite-resistance protein 2<br>Pfam-B_5269 (release 7.6). Arsenite is a carcinogenic compound which can act as a co-mutagen by  inhibiting DNA repair. Arsenite-resistance protein 2 is thought to play a role in arsenite resistance  .. 
PF01037 ASNC_trans_reg; <br>Pfam-B_773 (release 3.0). The AsnC family is a family of similar bacterial transcription regulatory  proteins.. 
PF05118 Aspartyl/Asparaginyl beta-hydroxylase<br>Pfam-B_2775 (release 7.7). Iron (II)/2-oxoglutarate (2-OG)-dependent oxygenases catalyse oxidative reactions in a range of metabolic processes.  Proline 3-hydroxylase hydroxylates proline at position 3, the first of a 2-OG oxygenase catalysing oxidation of a free alpha-amino acid. The structure of proline 3-hydroxylase contains the conserved motifs present in other 2-OG oxygenases including a jelly roll strand core and residues binding iron and 2-oxoglutarate, consistent with divergent evolution within the extended family.  This family represent the arginine, asparagine and proline hydroxylases. The aspartyl/asparaginyl beta-hydroxylase (EC:1.14.11.16) specifically hydroxylates one aspartic or asparagine residue in certain epidermal growth factor-like domains of a number of proteins  .. 
PF01177 Asp/Glu/Hydantoin racemase<br>This family contains aspartate racemase, maleate isomerases EC:5.2.1.1  , glutamate racemase, hydantoin racemase and arylmalonate decarboxylase EC:4.1.1.76  .. 
PF01400 Astacin (Peptidase family M12A)<br>The members of this family are enzymes that cleave peptides. These proteases require zinc for catalysis. Members of this family contain two conserved disulphide bridges, these are joined 1-4 and 2-3.  Members of this family have an amino terminal propeptide which is cleaved to give the active protease domain.  All other linked domains are found to the carboxyl terminus of this domain. This family includes: Astacin Swiss:P07584, a digestive enzyme from Crayfish. Meprin, Swiss:Q16819, a multiple domain membrane component that is constructed from a homologous alpha and beta chain. Proteins involved in morphogenesis such as Swiss:P13497, and Tolloid from drosophila Swiss:P25723.. 
PF02178 AT hook motif<br>Alignment kindly provided by SMART. At hooks are DNA binding motifs with a preference for A/T rich regions.. 
PF03029 ATP-bind; <br>Conserved hypothetical ATP binding protein. Pfam-B_1301 (release 6.4) & Pfam-B_2154 (Release 8.0). Members of this family are found in a range of archaea and eukaryotes and have hypothesised ATP binding activity.. 
PF00306 ATP synthase alpha/beta chain, C terminal domain<br>Pfam-B_15 (release 1.0). 
PF02874 ATP synthase alpha/beta family, beta-barrel domain<br>This family includes the ATP synthase alpha and beta subunits the ATP synthase associated with flagella.. 
PF04718 ATPsynth_g; <br>Mitochondrial ATP synthase g subunit. Pfam-B_5977 (release 7.5). The Fo sector of the ATP synthase is a membrane bound complex which mediates proton transport.  It is composed of nine different polypeptide subunits (a, b, c, d, e, f, g F6, A6L). The function of subunit g is currently unknown.  The conserved region covers all but the very N-terminus of the member sequences. No prokaryotic members have been identified thus far  .. 
PF03768 Attacin, N-terminal region<br>Pfam-B_2791 (release 7.0). This family includes attacin and sarcotoxin, but not  diptericin (which share similarity to the C-terminal region of attacin).  All members of this family are insect antibacterial proteins which are induced by the fat body and subsequently released into secreted into the hemolymph where they act synergistically  to kill the invading microorganism  .. 
PF03797 Autotransporter beta-domain<br>Secretion of protein products occurs by a number of different pathways in bacteria.  One of these pathways known as the type V pathway was first described for the IgA1 protease  . The protein component that mediates secretion through the outer membrane is contained within the secreted protein itself, hence the proteins secreted in this way are called autotransporters. This family corresponds to the presumed integral membrane beta-barrel domain that transports the protein. This domain is found at the C terminus of the proteins it occurs in.  The N terminus contains the variable passenger domain that is translocated across the membrane.  Once the passenger domain is exported it is cleaved auto-catalytically in some proteins, in others a different protease is used and in some cases no cleavage occurs  .. 
PF03547 Auxin_eff; <br>Membrane transport protein. TIGRFAMs, Griffiths-Jones SR. TIGRFAMs & Pfam-B_5261 (Release 7.5). This family includes auxin efflux carrier proteins and other transporter proteins from all domains of life.. 
PF02310 B12 binding domain<br>Pfam-B_359 (release 5.2). This domain binds to B12 (adenosylcobamide)[1-3], it is found in several enzymes, such as glutamate mutase Swiss:Q05488, methionine synthase Swiss:Q99707 and methylmalonyl-CoA mutase Swiss:P22033. It contains a conserved DxHxxGx(41)SxVx(26)GG motif, which is important for B12 binding  .. 
PF02607 B12 binding domain<br>This B12 binding domain is found in methionine synthase EC:2.1.1.13 Swiss:Q99707, and other shorter proteins that bind to B12. This domain is always found to the N-terminus of Pfam:PF02310. The structure of this domain is known  , it is a  4 helix bundle. Many of the conserved residues in this domain are involved in B12 binding, such as those in the MXXVG motif.. 
PF02362 B3 DNA binding domain<br>Pfam-B_582 (release 5.2). This is a family of plant transcription factors with various roles in development, the aligned region corresponds the B3 DNA binding domain as described in   this domain is found in VP1/AB13 transcription factors  .  Some proteins also have a second AP2 DNA binding domain Pfam:PF00847 such as RAV1 Swiss:Q9ZWM9  . DNA binding activity was demonstrated by  .. 
PF01313 Bacterial export proteins, family 3<br>Pfam-B_898 (release 3.0). This family includes the following members;     FliQ, MopD, HrcS, Hrp, YopS and SpaQ All of these members export proteins, that do not possess signal  peptides, through the membrane.  Although the proteins that these exporters move may be different, the exporters are thought to  function in similar ways  .. 
PF02673 Bacitracin resistance protein BacA<br>Bacitracin resistance protein (BacA) is a putative undecaprenol kinase. BacA confers resistance to bacitracin, probably by phosphorylation of undecaprenol  .. 
PF01011 Bacterial_PQQ;<br>Pfam-B_1319 (release 3.0). The family represent a single repeat of a beta propeller. This propeller has been found in several enzymes which utilise pyrrolo-quinoline quinone as a prosthetic group.. 
PF03704 BAD; <br>Bacterial transcriptional activator domain. Found in the DNRI/REDD/AFSR family of regulators. This region of AFSR (Swiss:P25941) along with the C terminal region is capable of independently directing actinorhodin production. This family contains TPR repeats.. 
PF01426 BAH domain<br>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  .. 
PF01145 SPFH domain / Band 7 family<br>This family has been called SPFH  , Band 7 or PHB domain. Recent phylogenetic analysis has shown this domain to be a slipin or Stomatin-like integral membrane domain conserved from protozoa to mammals.. 
PF03594 Benzoate membrane transport protein<br>TIGRFAMs, Griffiths-Jones SR. 
PF02944 BESS motif<br>The BESS motif is named after the proteins in which it is found (BEAF  , Suvar(3)7   and Stonewall  ). The motif is 40 amino acid residues long and is composed of two predicted alpha helices. Based on the protein in which it is found and the presence of conserved positively charged residues it is predicted to be a DNA binding domain. This domain appears to be specific to drosophila.. 
PF02369 Bacterial Ig-like domain (group 1)<br>This family consists of bacterial domains with an Ig-like fold. Members of this family are found in bacterial surface proteins such as intimins and invasins involved in pathogenicity. . 
PF02785 Biotin carboxylase C-terminal domain<br>Biotin carboxylase is a component of the acetyl-CoA carboxylase multi-component enzyme which catalyses the first committed step  in fatty acid synthesis in animals, plants and bacteria. Most of the active site residues reported in reference   are in  this C-terminal domain.. 
PF02012 BNR/Asp-box repeat<br>Members of this family contain multiple BNR (bacterial neuraminidase repeat) repeats or Asp-boxes. The repeats are short, however the repeats are never found closer than 40 residues together suggesting that the repeat is structurally longer. These repeats are found in many glycosyl hydrolases as well as other extracellular proteins of unknown function.. 
PF00528 BPD_transp; <br>Binding-protein-dependent transport system inner membrane component. LMB bacterial genome group and Prosite. The alignments cover the most conserved region of the proteins, which is thought to be located in a cytoplasmic loop between two transmembrane domains. The members of this family have a variable number of transmembrane helices.. 
PF02237 Biotin protein ligase C terminal domain<br>The function of this structural domain is unknown.  It is found to the C terminus of the biotin protein ligase catalytic domain Pfam:PF01317. . 
PF03099 BPL_LipA_LipB; <br>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 form cellular metabolites.  Biotin protein ligase (BPL) is the enzyme responsible for attaching biotin to a specific lysine at the active site of biotin enzymes. Each organism probably has only one BPL.  Biotin attachment is a two step reaction that results in the formation of an amide linkage between the carboxyl group of biotin and the epsilon-amino group of the modified lysine  . Lipoate-protein ligase A (LPLA) catalyses the formation of an amide linkage between lipoic acid and a specific lysine residue in lipoate dependent enzymes  . The unusual biosynthesis pathway of lipoic acid is mechanistically intertwined with attachment of the cofactor  .. 
PF02485 Core-2/I-Branching enzyme<br>Pfam-B_842 (release 5.4). This is a family of two different beta-1,6-N-acetylglucosaminyltransferase enzymes, I-branching enzyme (eg Swiss:Q06430) and core-2 branching enzyme (eg Swiss:Q02742). I-branching enzyme is responsible for the production of the blood group I-antigen during embryonic development  . Core-2 branching enzyme forms crucial side-chain branches in  O-glycans  .. 
PF00533 BRCA1 C Terminus (BRCT) domain<br>
PF04089 BRICHOS domain<br>The BRICHOS domain is about 100 amino acids long. It is found in a variety of proteins implicated in dementia, respiratory distress and cancer. Its exact function is unknown; roles that have been proposed for it include (a) in targeting of the protein to the secretory pathway, (b) intramolecular chaperone-like function, and (c) assisting the specialised intracellular protease processing system  . This C-terminal domain is embedded in the endoplasmic reticulum lumen, and binds to the N-terminal, transmembrane, SP_C, Pfam:PF08999, provided that it is in non-helical conformation. Thus the Brichos domain of proSP-C is a chaperone that induces alpha-helix formation of an aggregation-prone TM region  .. 
PF04427 Brix domain<br>
PF03097 BRO1-like domain<br>This domain is found in a number proteins including Rhophilin Swiss:Q61085 and BRO1 Swiss:P48582.  It is known to have a role in endosomal targeting.  ESCRT-III subunit Snf7 binds to a conserved hydrophobic patch in the BRO1 domain that is required for protein complex formation and for the protein-sorting function of BRO1  .. 
PF00439 bromodomain; <br>Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine  .. 
PF03909 BSD domain  <br>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.. 
PF03092 BT1 family<br>Pfam-B_1804 (release 6.4). Members of this family are transmembrane proteins. Several are Leishmania putative proteins that are thought to be pteridine transporters. One such protein Swiss:Q25272, previously termed (and is still annotated as) ORFG, was shown to encode a biopterin transport protein using null mutants  , thus being subsequently renamed BT1. The significant similarity of ORFG/BT1 to Trypanosoma brucei ESAG10 (a putative transmembrane protein and another member  of this family) was previously noted  . This family also contains five putative Arabidopsis thaliana proteins of unknown function. In addition, it also contains two predicted  prokaryotic proteins (from the cyanobacteria Synechocystis and  Synechococcus).. 
PF00651 BTB/POZ domain<br>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 (Pfam:PF00096) proteins and in proteins that contain the Pfam:PF01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation  . The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer.  The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule  . POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT [4,5,6]. The POZ or BTB domain is also known as BR-C/Ttk or ZiN.. 
PF03437 BtpA family<br>Pfam-B_4453 (release 6.6). The BtpA protein is tightly associated with the thylakoid membranes, where it stabilises the reaction centre proteins of photosystem I.. 
PF03131 bZIP Maf transcription factor<br>Mifsud W, Eberhardt R. Pfam-B_482 (release 6.5). Maf transcription factors contain a conserved basic region leucine zipper (bZIP) domain, which mediates their dimerisation and DNA binding property  . Thus, this family is probably related to Pfam:PF00170. This family also includes the DNA_binding domain of Skn-1 (Swiss:P34707), this domain lacks the leucine zipper found in other bZip domains, and binds DNA is a monomer [2,3].. 
PF00168 C2 domain<br>Swissprot_feature_table. 
PF02743 Cache; <br>
PF04857 CAF1 family ribonuclease<br>Pfam-B_1567 (release 7.5). 
PF03135 CagE, TrbE, VirB family, component of type IV transporter system<br>Pfam-B_843 (release 6.5). This family includes the Helicobacter pylori protein CagE  Swiss:Q48252, which together with other proteins from the cag pathogenicity island (PAI), encodes a type IV transporter secretion system.  The precise role of CagE is not known, but studies in animal models have shown that it is essential for pathogenesis in Helicobacter pylori induced gastritis and peptic ulceration  . Indeed, the expression of the cag PAI has been shown to be essential for stimulating human gastric epithelial cell apoptosis in vitro  . Similar type IV transport systems are also found in other bacteria. This family includes the TrbE Swiss:P54910 and VirB Swiss:P05353  proteins from the respective trb and Vir conjugal transfer systems in Agrobacterium tumefaciens. Homologues of VirB proteins from other species are also members of this family, e.g. VirB from Brucella suis Swiss:Q9RPY1.. 
PF02515 CAIB-BAIF;<br>CoA-transferase family III. Pfam-B_887 (release 5.4). CoA-transferases are found in organisms from all lines of descent. Most of these enzymes belong to two well-known enzyme families, but recent work on unusual biochemical pathways of anaerobic bacteria has revealed the existence of a third family of CoA-transferases. The members of this enzyme family differ in sequence and reaction mechanism from CoA-transferases of the other families. Currently known enzymes of the new family are a formyl-CoA: oxalate CoA-transferase, a succinyl-CoA: (R)-benzylsuccinate CoA-transferase, an (E)-cinnamoyl-CoA: (R)-phenyllactate CoA-transferase, and a butyrobetainyl-CoA: (R)-carnitine CoA-transferase. In addition, a large number of proteins of unknown or differently annotated function from Bacteria, Archaea and Eukarya apparently belong to this enzyme family. Properties and reaction mechanisms of the CoA-transferases of family III are described and compared to those of the previously known CoA-transferases.. 
PF02888 Calmodulin binding domain<br>Psi-blast P70604/413-489. 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 Ca2+-binding protein calmodulin (CaM)  . CaM binds to the SK channel through this the CaM-binding domain (CaMBD), which is located in an intracellular region of the alpha-subunit immediately carboxy-terminal to the pore. Channel opening is triggered when Ca2+ binds the EF hands in the N-lobe of CaM. The structure of this domain complexed with CaM is known  . This domain forms an elongated dimer with a CaM molecule bound at each end; each CaM wraps around three alpha-helices, two from one CaMBD subunit and one from the other.. 
PF01302 CAP-Gly domain<br>Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of Caenorhabditis elegans F53F4.3 protein Swiss:Q20728 CAP-Gly domain was recently solved  . The domain contains three beta-strands. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove  .. 
PF01039 Carboxyl transferase domain<br>Pfam-B_299 (release 3.0). All of the members in this family are biotin dependent carboxylases.  The carboxyl transferase domain carries out the following reaction; transcarboxylation from biotin to an acceptor molecule. There are two recognised types of carboxyl transferase. One of them uses acyl-CoA and the other uses 2-oxoacid as the acceptor molecule of carbon dioxide.  All of the members in this family utilise acyl-CoA as the acceptor molecule.. 
PF00755 Choline/Carnitine o-acyltransferase<br>Pfam-B_438 (release 2.1). 
PF03378 CAS/CSE protein, C-terminus<br>Pfam-B_3786 (release 6.6). 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 and proliferation [2,3]. Apoptosis is inhibited in CAS-depleted cells, while the expression of CAS correlates to the degree of cellular proliferation.  Like CSE1, it is essential for the mitotic checkpoint in the cell cycle (CAS depletion blocks the cell in the G2 phase), and has been shown to be associated with the microtubule network and the mitotic spindle  , as is the protein MEK, which is thought to regulate the intracellular localisation (predominantly nuclear vs. predominantly cytosolic) of CAS. In the nucleus, CAS acts as a nuclear transport factor in the importin pathway  . The importin pathway mediates the nuclear transport of several proteins that are necessary for mitosis and further progression. CAS is therefore thought to affect the cell cycle through its effect on the nuclear transport of these proteins  . Since apoptosis also requires the nuclear import of several proteins (such as P53 and transcription factors), it has been suggested that CAS also enables apoptosis by facilitating the nuclear import of at least a subset of these essential proteins  .. 
PF00690 Na_K_ATPase_N; <br>Cation transporter/ATPase, N-terminus. Pfam-B_138 (release 2.1). Members of this families are involved in Na+/K+, H+/K+, Ca++ and Mg++ transport.. 
PF01545 Cation efflux family<br>Pfam-B_232 (release 4.0). 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.. 
PF04586 Caudo_protease; <br>Caudovirus prohead protease. Pfam-B_4836 (release 7.5). Family of Caudovirus prohead proteases also found in a number of bacteria possibly as the result of horizontal transfer. . 
PF01607 Chitin_bind_2; <br>Chitin binding Peritrophin-A domain. This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include [1-3]. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains  .. 
PF00942 Cellulose_bind; CBD_3; <br>Cellulose binding domain. Pfam-B_1126 (release 3.0). 
PF02018 CBD_6; CBM_4; <br>Carbohydrate binding domain. This family includes diverse carbohydrate binding domains.. 
PF03422 Carbohydrate binding module (family 6)<br>Pfam-B_1231 (release 6.6). 
PF00571 CBS domain<br>
PF02754 DUF224; <br>Cysteine-rich domain. The key element of this family is the CX31-38CCX33-34CXXC sequence motif normally found at the C-terminus in archaeal and bacterial Hdr-like proteins  . There may be one or two copies, and the motif is probably an iron-sulfur binding cluster. In some instances one of the cysteines is replaced by an aspartate, and aspartate can in principle also function as a ligand of an iron-sulfur cluster  . The family includes a subunit from heterodisulphide reductase and a subunit from glycolate oxidase   Swiss:P52074 and glycerol-3-phosphate dehydrogenase.. 
PF03379 CcmB protein<br>Pfam-B_3059 (release 6.6). CcmB is the product of one of a cluster of Ccm genes that are necessary for cytochrome c biosynthesis in eubacteria. Expression of these proteins is induced when the organisms are grown under anaerobic conditions with nitrate or nitrite as the final electron acceptor. CcmB is required for the export of haem to the periplasm.. 
PF04103 CD20-like family<br>Pfam-B_1979 (rel 7.3), Pfam-B_10092 (rel 9.0). 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 single beta subunit, and two disulfide-linked gamma subunits. The alpha subunit of Fc epsilon RI and most Fc receptors are homologous members of the Ig superfamily. By contrast, the beta and gamma subunits from Fc epsilon RI are not homologous to the Ig superfamily. Both molecules have four putative transmembrane segments and a probably topology where both amino- and carboxy termini protrude into the cytoplasm  . This family also includes LR8 like proteins from humans, mice and rats. The function of the human LR8 protein is unknown although it is known to be strongly expressed in the lung fibroblasts  . This family also includes sarcospan is a transmembrane component of dystrophin-associated glycoprotein. Loss of the sarcoglycan complex and sarcospan alone is sufficient to cause muscular dystrophy. The role of the sarcoglycan complex and sarcospan is thought to be to strengthen the dystrophin axis connecting the basement membrane with the cytoskeleton  .. 
PF05179 Cdc73; <br>RNA pol II accessory factor, Cdc73 family. Pfam-B_6394 (release 7.7). 
PF01066 CDP-alcohol phosphatidyltransferase<br>Pfam-B_651 (release 3.0). 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.. 
PF00150 cellulase; <br>Cellulase (glycosyl hydrolase family 5). 
PF04218 CENP-B N-terminal DNA-binding domain<br>Centromere Protein B (CENP-B) is a DNA-binding protein localised 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 dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure  .. 
PF04734 Neutral/alkaline non-lysosomal ceramidase<br>Pfam-B_3385 (release 7.5). This family represents a group of neutral/alkaline ceramidases found in both bacteria and eukaryotes [1,2,3].. 
PF03859 CG-1 domain<br>Pfam-B_18451 (Release 7.1). 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 associated with CAMTA proteins (for CAlModulin -binding Transcription Activator) that are transcription factors containing a calmodulin -binding domain and ankyrins (ANK) motifs  .. 
PF00307 actinin-binding; <br>Calponin homology (CH) domain. The CH domain is found in both cytoskeletal proteins and signal transduction proteins  .  The CH domain is involved in actin binding in some members of the family.  However in calponins there is evidence that the CH domain is not involved in its actin binding activity  .  Most member proteins have from two to four copies of the CH domain, however some proteins such as calponin and Swiss:P15498 have only a single copy.. 
PF04420 CHD5-like protein<br>Members of this family are probably coiled-coil proteins that are similar to the CHD5 (Congenital heart disease 5) protein. In Saccharomyces cerevisiae this protein localises to the ER and is thought to play a homeostatic role  .. 
PF03067 Chitin binding domain<br>Pfam-B_2364 (release 6.4). This domain is found associated with a wide variety of cellulose binding domain. This domain however is a chitin binding domain. This domain is found in isolation in baculoviral spheroidins and spindolins, protein of unknown function.. 
PF00379 insect_cuticle; <br>Insect cuticle protein. Many insect cuticular proteins include a 35-36 amino acid motif known as the R&R consensus. The extensive conservation of this region led to the suggestion that it functions to bind chitin. Provocatively, it has no sequence similarity to the well-known cysteine-containing chitin-binding domain found in chitinases and some peritrophic membrane proteins. Chitin binding has been shown experimentally for this region  . Thus arthropods have two distinct classes of chitin binding proteins, those with the chitin-binding domain found in lectins, chitinases and peritrophic membranes (cysCBD) and those with the cuticular protein chitin-binding domain (non-cysCBD)  .. 
PF04968 CHORD <br>Pfam-B_1217 (release 7.0). CHORD represents a Zn binding domain. Silencing of the  C. elegans CHORD-containing gene results in semisterility and embryo lethality, suggesting an essential function of  the wild-type gene in nematode development  . . 
PF02017 CIDE-N domain<br>This domain is found in CAD nuclease Swiss:O76075 , ICAD Swiss:O00273 the inhibitor of CAD nuclease. The two proteins interact through this domain.. 
PF02487 CLN3 protein<br>Pfam-B_1060 (release 5.4). 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 (Swiss:Q13286) has been implicated in Juvenile neuronal ceroid  lipofuscinosis (Batten disease)  .. 
PF02861 Clp amino terminal domain<br>Pfam-B_102 (release 6.0). This short domain is found in one or two copies at the amino terminus of ClpA and ClpB proteins from bacteria and eukaryotes. The function of these domains is uncertain but they may form a protein binding site  .. 
PF02353 Mycolic acid cyclopropane synthetase<br>Pfam-B_862 (release 5.2). This family consist of Cyclopropane-fatty-acyl-phospholipid synthase or CFA synthase EC:2.1.1.79 this enzyme catalyse the reaction: S-adenosyl-L-methionine + phospholipid olefinic fatty acid <=> S-adenosyl-L-homocysteine + phospholipid cyclopropane fatty acid.. 
PF00780 CNH domain<br>Alignment kindly provided by SMART. Domain found in NIK1-like kinase, mouse citron and yeast ROM1, ROM2. Unpublished observations.. 
PF00027 Cyclic nucleotide-binding domain<br>
PF02629 DUF184; <br>This domain has a Rossmann fold and is found in a number of proteins including succinyl CoA synthetases, malate and ATP-citrate ligases.. 
PF01144 Coenzyme A transferase<br>
PF02514 cobN-Mg_chel; <br>CobN/Magnesium Chelatase. Pfam-B_647 (release 5.4). This family contains a domain common to the cobN protein and to magnesium protoporphyrin chelatase. CobN is implicated in the conversion of hydrogenobyrinic acid a,c-diamide to cobyrinic acid  . Magnesium protoporphyrin chelatase is involved in chlorophyll biosynthesis  .. 
PF02492 CobW/HypB/UreG, nucleotide-binding domain<br>Pfam-B_428 (release 4.0) & Pfam-B_1247 (release 5.4). This domain is found in HypB, a hydrogenase expression / formation protein, and  UreG a urease accessory protein.  Both these proteins contain a P-loop nucleotide binding motif [2,3]. HypB has GTPase activity  and is a guanine nucleotide binding protein  . It is not known whether UreG binds GTP or some other nucleotide. Both enzymes are involved in nickel binding. HypB can store nickel and is required for nickel dependent hydrogenase expression  . UreG is required for functional incorporation of the urease nickel metallocenter.  GTP hydrolysis may required by these proteins for nickel incorporation into other nickel proteins  . This family of domains also contains P47K (Swiss:P31521), a Pseudomonas  chlororaphis protein needed for nitrile hydratase expression, and the  cobW gene product (Swiss:P29937), which may be involved in cobalamin biosynthesis in Pseudomonas denitrificans  .. 
PF00135 Carboxylesterase family<br>
PF01484 Nematode cuticle collagen N-terminal domain<br>Pfam-B_200 (release 4.0). The function of this domain is unknown. It is found in the N-terminal region of nematode cuticle collagens, see Pfam:PF01391. Cuticle is a tough elastic structure secreted by hypodermal cells and is primarily composed of collagen proteins  .. 
PF01391 Collagen triple helix repeat (20 copies)<br>Members of this family belong to the collagen superfamily  . Collagens are generally extracellular structural proteins involved in formation of connective tissue structure. The alignment contains 20 copies of the G-X-Y repeat that forms a triple helix.  The first position of the repeat is glycine, the second and third positions can be any residue but are frequently proline and hydroxyproline.  Collagens are post translationally modified by proline hydroxylase to form the hydroxyproline residues. Defective hydroxylation is the cause of scurvy. Some members of the collagen superfamily are not involved in connective tissue structure but share the same triple helical structure.. 
PF03772 Competence protein<br>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 [1,4]. These proteins may transport DNA across the cell membrane. These proteins contain a highly conserved motif in the amino terminal transmembrane region that has two histidines that may form a metal binding site.. 
PF05071 Complex1_17_2kD; <br>NADH ubiquinone oxidoreductase subunit NDUFA12. This family contains the 17.2 kD subunit of complex I (NDUFA12) and its homologues.  The family also contains a second related eukaryotic protein of unknown function, e.g. Swiss:Q9BV02.. 
PF00329 complex1_30Kd; <br>Respiratory-chain NADH dehydrogenase, 30 Kd subunit. 
PF02950 Conotoxin<br>Pfam-B_529 (release 6.4). Conotoxins are small snail toxins that block ion channels.. 
PF05019 Coenzyme Q (ubiquinone) biosynthesis protein Coq4<br>Pfam-B_14948 (release 7.6). Coq4p was shown to peripherally associate with the matrix face of the mitochondrial inner membrane. The putative mitochondrial- targeting sequence present at the amino-terminus of the polypeptide efficiently imported it to mitochondria. The function of Coq4p is unknown, although its presence is required to maintain a steady-state level of Coq7p, another component of the Q biosynthetic pathway  .  The overall structure of Coq4 is alpha helical and shows resemblance to haemoglobin/myoglobin (information from TOPSAN).. 
PF03471 Transporter associated domain<br>This small domain is found in a family of proteins with the Pfam:PF01595 domain and two CBS domains with this domain found at the C-terminus of the proteins, the domain is also found at the C terminus of some Na+/H+ antiporters. This domain is also found in CorC that is involved in Magnesium and cobalt efflux.  The function of this domain is uncertain but might be involved in modulating transport of ion substrates.. 
PF02389 Cornifin (SPRR) family<br>Pfam-B_1215 (release 5.2). 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 the SPRR gene family resides in the structure of the central segments of the encoded polypeptides that are built up from tandemly repeated units of either eight (SPRR1 and SPRR3) or nine (SPRR2) amino acids with the general consensus XKXPEPXX where X is any amino acid  . . 
PF02628 Cytochrome oxidase assembly protein<br>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 (Swiss:P40086).. 
PF02936 Cytochrome c oxidase subunit IV<br>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 member of this family is called COX VI Swiss:P26310. The yeast protein Swiss:P53077 appears to be the yeast COX IV subunit.. 
PF03626 Prokaryotic Cytochrome C oxidase subunit IV <br>Pfam-B_3217 (release 7.0). Cytochrome c oxidase (COX) is a multi-subunit enzyme complex that catalyses the final step of electron transfer through the respiratory chain on the mitochondrial inner membrane. This family is composed of cytochrome c oxidase subunit 4 from prokaryotes.. 
PF02937 Cytochrome c oxidase subunit VIc<br>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.. 
PF02935 Cytochrome c oxidase subunit VIIc<br>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 is called COX VIII Swiss:P04039.. 
PF04516 CP2 transcription factor<br>Pfam-B_2156 (release 7.5). This family represents a conserved region in the CP2 transcription factor family.. 
PF00118 cpn60_TCP1; <br>TCP-1/cpn60 chaperonin family. This family includes members from the HSP60 chaperone family and  the TCP-1 (T-complex protein) family.. 
PF02787 Carbamoyl-phosphate synthetase large chain, oligomerisation domain<br>Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a  heterodimer of a small and large chain.  . 
PF04969 CS domain<br>Pfam-B_1217 (release 7.0). The CS and CHORD (Pfam:PF04968) are fused into a single polypeptide chain in metazoans but are found in separate proteins in plants; this is thought to be indicative of an interaction between CS and CHORD  . It has been suggested that the CS domain is a binding module for HSP90, implying that CS domain-containing proteins are involved in recruiting heat shock proteins to multiprotein assemblies  . Two CS domains are found at the C-terminus of Ubiquitin carboxyl-terminal hydrolase 19 (USP19) (Swiss:O94966), these domains may play a role in the interaction of USP19 with cellular inhibitor of apoptosis 2  .. 
PF00988 Carbamoyl-phosphate synthase small chain, CPSase domain<br>Pfam-B_345 (release 3.0). The carbamoyl-phosphate synthase domain is in the amino terminus of  protein. Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from  glutamine or ammonia and bicarbonate.  This  important enzyme initiates both the urea cycle and the biosynthesis  of arginine and/or pyrimidines  . The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a  heterodimer of a small and large chain.  The small chain promotes the hydrolysis of glutamine to ammonia, which is used by the large chain to synthesise carbamoyl phosphate. See Pfam:PF00289. The small chain has a GATase domain in the carboxyl terminus. See Pfam:PF00117.. 
PF03178 CPSF A subunit region<br>Pfam-B_1224 (release 6.5). 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 pre-mRNA. CPSF has also been found to be necessary for splicing of single-intron pre-mRNAs  . The function of the aligned region is unknown but may be involved in RNA/DNA binding.. 
PF00313 'Cold-shock' DNA-binding domain<br>
PF04442 Cytochrome c oxidase assembly protein CtaG/Cox11<br>Cytochrome c oxidase assembly protein is essential for the assembly of functional cytochrome oxidase protein.\.  In eukaryotes it is an integral protein of the mitochondrial inner membrane. Cox11 is essential for the insertion of Cu(I) ions to form the CuB site. This is essential for the stability of other structures in subunit I, for example haems a and a3, and the magnesium/manganese centre.  Cox11 is probably only required in sub-stoichiometric amounts relative to the structural units  . The C terminal region of the protein is known to form a dimer.  Each monomer coordinates one Cu(I) ion via three conserved cysteine residues (111, 208 and 210) in Saccharomyces cerevisiae (Swiss:P19516).  Met 224 is also thought to play a role in copper transfer or stabilising the copper site  .. 
PF01148 Cytidylyltrans; <br>Cytidylyltransferase family. Pfam-B_921 (release 3.0). The members of this family are integral membrane protein cytidylyltransferases. The family includes phosphatidate cytidylyltransferase EC:2.7.7.41 as well as Sec59 from yeast.  Sec59 is a dolichol kinase EC:2.7.1.108.. 
PF04145 Ctr copper transporter family<br>Pfam-B_3006 (release 7.3). 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 high-affinity copper transport proteins (Ctr proteins) mediates copper uptake at the plasma membrane.  A series of clustered methionine residues in the hydrophilic extracellular domain, and an MXXXM motif in the second transmembrane domain, are important for copper uptake. These methionine probably coordinate copper during the process of metal transport.. 
PF00394 Multicopper oxidase<br>Many of the proteins in this family contain multiple similar  copies of this plastocyanin-like domain.. 
PF03712 Copper type II ascorbate-dependent monooxygenase, C-terminal domain<br>The N and C-terminal domains of members of this family adopt the same PNGase F-like fold.. 
PF01082 Copper type II ascorbate-dependent monooxygenase, N-terminal domain<br>The N and C-terminal domains of members of this family adopt the same PNGase F-like fold.. 
PF02845 CUE domain<br>Alignment kindly provided by SMART. CUE domains have been shown to bind ubiquitin [3-4]. It has been suggested that CUE domains are related to Pfam:PF00627   and this has been confirmed by the structure of the domain  . CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2  .. 
PF00190 Seedstore_11s;Cupin; <br>This family represents the conserved barrel domain of the 'cupin' superfamily   ('cupa' is the Latin term for a small barrel). This family contains 11S and 7S plant seed storage proteins, and germins.  Plant seed storage proteins provide the major nitrogen source for the developing plant.. 
PF04889 Cwf15/Cwc15 cell cycle control protein<br>Pfam-B_6589 (release 7.6). This family represents Cwf15/Cwc15 (from Schizosaccharomyces pombe and Saccharomyces cerevisiae respectively) and their homologues. The function of these proteins is unknown, but they form part of the spliceosome and are thus thought to be involved in mRNA splicing  . . 
PF04677 CwfJ_N_1; <br>Protein similar to CwfJ C-terminus 1. This region is found in the N terminus of Schizosaccharomyces pombe protein CwfJ (Swiss:Q09909).  CwfJ is part of the Cdc5p complex involved in mRNA splicing  .. 
PF04676 CwfJ_N_2; <br>Protein similar to CwfJ C-terminus 2. This region is found in the N terminus of Schizosaccharomyces pombe protein CwfJ (Swiss:Q09909).  CwfJ is part of the Cdc5p complex involved in mRNA splicing  .. 
PF01705 CX module<br>This domain has no known function. It is found in several C. elegans proteins. The domain contains 6 conserved cysteines that probably form three disulphide bridges.. 
PF04673 cyclase_polyket; <br>Polyketide synthesis cyclase. Pfam-B_5596 (release 7.5). This family represents a number of cyclases involved in polyketide synthesis in a number of actinobacterial species.. 
PF00134 cyclin; <br>Cyclin, N-terminal domain. Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a Uracil-DNA glycosylase that is related to other cyclins  . Cyclins contain two domains of similar all-alpha fold, of which this family corresponds with the N-terminal domain.. 
PF02276 Photosynthetic reaction centre cytochrome C subunit<br>Pfam-B_5109 (release 5.2). Photosynthesis in purple bacteria is dependent on light-induced electron transfer in the reaction centre (RC), coupled to the uptake  of protons from the cytoplasm. The RC contains a cytochrome molecule which re-reduces the oxidised electron donor.. 
PF05038 cytochr_b558a; <br>Cytochrome Cytochrome b558 alpha-subunit. Pfam-B_5327 (release 7.7). Cytochrome b-245 light chain (p22-phox) is one of the key electron transfer elements of the NADPH oxidase in phagocytes  .. 
PF01820 Dala_Dala_ligas; <br>D-ala D-ala ligase N-terminus. This family represents the N-terminal region of the D-alanine--D-alanine ligase enzyme EC:6.3.2.4 which is thought to be involved in substrate binding  . D-Alanine is one of the central molecules of the cross-linking step of peptidoglycan assembly. There are three enzymes involved in the D-alanine branch of peptidoglycan biosynthesis: the pyridoxal phosphate-dependent D-alanine racemase (Alr), the ATP-dependent D-alanine:D-alanine ligase (Ddl), and the ATP-dependent D-alanine:D-alanine-adding enzyme (MurF)  .. 
PF01113 DapB; <br>Dihydrodipicolinate reductase, N-terminus. Dihydrodipicolinate reductase (DapB) reduces the alpha,beta-unsaturated  cyclic imine, dihydro-dipicolinate.  This reaction is the  second committed step in the biosynthesis of L-lysine and its precursor meso-diaminopimelate, which are critical for both  protein and cell wall biosynthesis. The N-terminal domain of DapB binds the dinucleotide NADPH.. 
PF01682 DB module<br>This domain has no known function. It is found in several C. elegans proteins. The domain contains 12 conserved cysteines that probably form six disulphide bridges. This domain is found associated with ig Pfam:PF00047 and fn3 Pfam:PF00041 domains, as well as in some lipases Pfam:PF00657.. 
PF05011 Lariat debranching enzyme, C-terminal domain<br>Pfam-B_9676 (release 7.6). This presumed domain is found at the C-terminus of lariat debranching enzyme. This domain is always found in association with Pfam:PF00149.. 
PF03107 DC1;<br>Pfam-B_16 (release 6.5). 
PF00383 dCMP_cyt_deam;<br>Cytidine and deoxycytidylate deaminase zinc-binding region. 
PF05026 Dcp2, box A domain<br>Pfam-B_10622 (release 7.6). This domain is always found to the amino terminal side of Pfam:PF00293.  This domain is specific to mRNA decapping protein 2 and this region has been termed Box A  .  Removal of the cap structure is catalysed by the Dcp1-Dcp2 complex  .. 
PF03607 Doublecortin<br>
PF03455 dDENN domain<br>This region is always found associated with Pfam:PF02141. 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 similar to members of the Rho/Rac/Cdc42 GEF family  .. 
PF02791 DDT domain<br>The DDT domain is named after (DNA binding homeobox and Different  Transcription factors) and is approximately 60 residues in length   . Along with the WHIM motifs, it comprises an entirely alpha  helical module found in diverse eukaryotic chromatin proteins  .  Based on the structure of Ioc3, this module is inferred to  interact with nucleosomal linker DNA and the SLIDE domain of ISWI  proteins   . The resulting complex forms a protein ruler that  measures out the spacing between two adjacent nucleosomes  .  In particular, the DDT domain, in combination with the WHIM1 and WHIM2 motifs form the SLIDE domain binding pocket  .. 
PF00270 DEAD/DEAH box helicase<br>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 splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.. 
PF00531 death; <br>
PF04626 Dec-1 protein, C terminal region<br>The defective chorion-1 gene (dec-1) in Drosophila encodes follicle cell proteins necessary for proper eggshell assembly. Multiple products of the dec-1 gene are formed by alternative RNA splicing and proteolytic processing  . Cleavage products include S80 (80 kDa) which is incorporated into the eggshell, and further proteolysis of S80 gives S60 (60 kDa). Alternative splicing generates different carboxyl terminal ends in different protein isoforms, so this is region is the most C terminal region that is present in the main isoforms.. 
PF02141 DENN (AEX-3) domain<br>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  .. 
PF00610 Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP)<br>Ponting C, Schultz J, Bork P, Martemyanov K, Thorner J. The DEP domain   is responsible for mediating intracellular protein targeting and regulation of protein stability in the cell [2-3]. The DEP domain is present in a number of signaling molecules, including Regulator of G protein Signaling (RGS) proteins, and has been implicated in membrane targeting [4-5]. New findings in yeast, however, demonstrate a major role for a DEP domain in mediating the interaction of an RGS protein to the C-terminal tail of a GPCR, thus placing RGS in close proximity with its substrate G protein alpha subunit [6-7].. 
PF02272 DHHA1 domain<br>This domain is often found adjacent to the DHH domain Pfam:PF01368 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 e.g. Swiss:P00957, suggesting that this domain may have an RNA binding function. The domain is about 60 residues long and contains a conserved GG motif.. 
PF04922 DIE2/ALG10 family<br>Pfam-B_9570 (release 7.6). The ALG10 protein from Saccharomyces cerevisiae encodes the alpha-1,2 glucosyltransferase of the endoplasmic reticulum. This protein has been characterised in rat as potassium channel regulator 1  .. 
PF01843 DIL domain<br>The DIL domain has no known function.. 
PF03018 disease_resp; <br>Dirigent-like protein. Pfam-B_835 (release 6.4). This family contains a number of proteins which are induced during disease response in plants. Members of this family are involved in lignification.. 
PF02377 Dishevelled specific domain<br>Pfam-B_1381 (release 5.2). This domain is specific to the signaling protein dishevelled. The domain is found adjacent to the PDZ domain Pfam:PF00595, often in conjunction with DEP (Pfam:PF00610) and DIX (Pfam:PF00778).. 
PF02916 DNA polymerase processivity factor<br>
PF01965 ThiJ; <br>The family includes the protease PfpI Swiss:Q51732  . This domain is also found in transcriptional regulators such as Swiss:Q9RJG8. This N-terminal region of the full-length AdpA proteins is necessary for dimerisation of the molecule.. 
PF00751 DM-domain; <br>DM DNA binding domain. The DM domain is named after dsx and mab-3  . dsx contains a single amino-terminal DM domain, whereas mab-3 contains two amino-terminal domains.  The DM domain has a pattern of conserved zinc chelating residues C2H2C4  . The dsx DM domain has been shown to dimerise and bind palindromic DNA  .. 
PF01068 DNA_ligase; <br>ATP dependent DNA ligase domain. Pfam-B_788 (release 3.0). This domain belongs to a more diverse superfamily, including Pfam:PF01331 and Pfam:PF01653  .. 
PF04679 ATP dependent DNA ligase C terminal region        <br>This region is found in many but not all ATP-dependent DNA ligase enzymes  (EC:6.5.1.1).  It is thought to constitute part of the catalytic core of ATP dependent DNA ligase  .. 
PF04675 DNA ligase N terminus<br>This region is found in many but not all ATP-dependent DNA ligase enzymes (EC:6.5.1.1).  It is thought to be involved in DNA binding and in catalysis. In human DNA ligase I (Swiss:P18858), and in Saccharomyces cerevisiae (Swiss:P04819), this region was necessary for catalysis, and separated from the amino terminus by targeting elements. In vaccinia virus (Swiss:P16272) this region was not essential for catalysis, but deletion decreases the affinity for nicked DNA and decreased the rate of strand joining at a step subsequent to enzyme-adenylate formation  .. 
PF00875 DNA photolyase<br>Pfam-B_777 (release 3.0). This domain binds a light harvesting cofactor.. 
PF00136 DNA polymerase family B<br>This region of DNA polymerase B appears to consist of more than one structural domain, possibly including elongation, DNA-binding and dNTP binding activities.. 
PF03104 DNA_pol_B_exo;<br>DNA polymerase family B, exonuclease domain. This domain has 3' to 5' exonuclease activity and adopts a ribonuclease H type fold.. 
PF04081 DNA polymerase delta, subunit 4 <br>Pfam-B_25322 (release 7.3);. 
PF00772 DnaB-like helicase N terminal domain<br>Pfam-B_1000 (release 2.1). The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerisation of the N-terminal domain has been observed and may occur during the enzymatic cycle. This N-terminal domain is required both for interaction with other proteins in the primosome and for DnaB helicase activity  .. 
PF03796 DnaB-like helicase C terminal domain<br>Pfam-B_1000 (release 2.1). The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerisation of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.. 
PF00226 DnaJ domain<br>DnaJ domains (J-domains) are associated with hsp70 heat-shock system and it is thought that this domain mediates the interaction.  DnaJ-domain is therefore part of a chaperone (protein folding) system. The T-antigens, although not in Prosite are confirmed as DnaJ containing domains from literature  .. 
PF03351 DOMON domain<br>Aravind L, Coggill P. 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 up to 11 strands and is secreted to the extracellular compartment. The beta-strand folding produces a hydrophobic pocket which appears to bind soluble haem. This is consistent with the predominant architectures where the protein is associated with cytochromes or enzymatic domains whose activity involves redox or electron transfer reactions potentially as a direct participant in the electron transfer process. The DOMON domain superfamily, of which this is just one member, shows (1) multiple hydrophobic residues that contribute to the hydrophobic core of the strands of the beta-sandwich, and small residues found at the boundaries of strands and loops, (2) a strongly conserved charged residue (usually arginine/lysine) at the end of strand 9, which possibly stabilises the loop between 9 and 10, and (3) a polar residue (usually histidine, lysine or arginine), that interacts or coordinates with ligands  . The suggested superfamily includes both haem- and sugar-binding members: the haem-binding families being the ethyl-Benzoate dehydrogenase family EB_dh, Pfam:PF09459, the cellobiose dehydrogenase family CBDH and this family, and the sugar-binding families being the xylanases, CBM_4_9, Pfam:PF02018. The common feature of the superfamily is the 11-beta-strand structure, although the first and eleventh strands are not well conserved either within families or between families.. 
PF04124 Dor1-like family <br>Pfam-B_12640 (release 7.3);. 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  .. 
PF04173 TQO small subunit DoxD<br>Swiss:P97207 is a subunit of the terminal quinol oxidase present in the plasma  membrane of Acidianus ambivalens, with calculated molecular mass of 20.4 kDa  . Thiosulphate:quinone oxidoreductase (TQO) is one of the early steps in elemental sulphur oxidation.  A novel TQO enzyme was purified from the thermo-acidophilic archaeon Acidianus ambivalens and shown to consist of a large subunit (DoxD) and a smaller subunit (DoxA). The DoxD- and DoxA-like two subunits are fused together in a single polypeptide in Swiss:Q8AAF0.. 
PF00930 DPPIV_N_term; <br>Dipeptidyl peptidase IV (DPP IV) N-terminal region. Pfam-B_1017 (release 3.0). This family is an alignment of the region to the N-terminal side of the active site. The Prosite motif does not correspond to this Pfam entry.. 
PF05186 Dpy-30 motif<br>Pfam-B_13490 (release 7.7). 
PF01414 Delta serrate ligand<br>Ponting CP, Schultz J, Bork P. 
PF01666 DX module<br>This domain has no known function. It is found in several C. elegans proteins. The domain contains 6 conserved cysteines that probably form three disulphide bridges.. 
PF00782 Dual specificity phosphatase, catalytic domain<br>Alignment kindly provided by SMART. 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  .. 
PF00035 Double-stranded RNA binding motif<br>Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localisation of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.. 
PF01951 DUF101; <br>Archease protein family (MTH1598/TM1083). This archease family of proteins  , has two SHS2 domains  , with one inserted into another. It is predicted to be an enzyme  . It is predicted to act as a chaperone in DNA/RNA metabolism  . . 
PF02575 DUF149;<br>YbaB/EbfC DNA-binding family. This is a family of DNA-binding proteins. Members of this family form homodimers which bind DNA via a tweezer-like structure [1-3]. The conformation of the DNA is changed when bound to these proteins  . In bacteria, these proteins may play a role in DNA replication-recovery following DNA damage  .. 
PF02580 DUF154;<br>D-Tyr-tRNA(Tyr) deacylase. This family comprises of several D-Tyr-tRNA(Tyr) deacylase proteins. Cell growth inhibition by several d-amino acids can be explained by an in vivo  production of d-aminoacyl-tRNA molecules. Escherichia coli and yeast cells express an enzyme, d-Tyr-tRNA(Tyr) deacylase, capable of recycling such d-aminoacyl-tRNA molecules into free tRNA and d-amino acid. Accordingly, upon inactivation of the genes of the above deacylases, the toxicity of d-amino acids increases. Orthologues of the deacylase are found in many cells  .. 
PF02583 DUF156;<br>Metal-sensitive transcriptional repressor. This is a family of metal-sensitive repressors, involved in resistance to metal ions. Members of this family bind copper, nickel or cobalt ions via conserved cysteine and histidine residues. In the absence of metal ions, these proteins bind to promoter regions and repress transcription. When bound to metal ions they are unable to bind DNA, leading to transcriptional derepression [1-5].. 
PF02588 Uncharacterized BCR, YitT family COG1284<br>This is probably a bacterial ABC transporter permease (personal obs:Yeats C).. 
PF02639 Uncharacterized BCR, YaiI/YqxD family COG1671<br>
PF02641 Uncharacterized ACR, COG1993<br>
PF02958 DUF227;<br>Pfam-B_2081 (release 6.4). This family includes ecdysteroid 22-kinase, an enzyme responsible for the phosphorylation of ecdysteroids (insect growth and moulting hormones) at C-22, to form physiologically inactive ecdysteroid 22-phosphates  .. 
PF02995 Protein of unknown function (DUF229)<br>Pfam-B_1566 (release 6.4). 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. The Go annotation for the protein indicates that it is involved in nematode larval development and has a positive regulation on growth rate.. 
PF01697 DUF23;<br>Glycosyltransferase family 92. Pfam-B_1694 (release 4.1). Members of this family act as galactosyltransferases, belonging to glycosyltransferase family 92 [1,2]. The aligned region contains several conserved cysteine residues and several charged residues that may be catalytic residues. This is supported by the inclusion of this family in the GT-A glycosyl transferase superfamily.. 
PF02996 DUF232;<br>Pfam-B_1664 (release 6.4). This family comprises of several prefoldin subunits. The biogenesis of the cytoskeletal proteins actin and tubulin involves interaction of nascent chains of each of the two proteins with the oligomeric protein prefoldin (PFD) and their subsequent transfer to the cytosolic chaperonin CCT (chaperonin containing TCP-1). Electron microscopy shows that eukaryotic PFD, which has a similar structure to its archaeal counterpart, interacts with unfolded actin along the tips of its projecting arms. In its PFD-bound state, actin seems to acquire a conformation similar to that adopted when it is bound to CCT  .. 
PF03080 DUF239; Glucoamylase;<br>Domain of unknown function (DUF239). Pfam-B_913 (release 6.4). This is a family of plant and bacterial proteins, a small number of which are putative carboxy-terminal peptidases (see for example Swiss:Q9XIN9).. 
PF03087 Arabidopsis protein of unknown function<br>Pfam-B_1563 (release 6.5). This family represents a number of Arabidopsis proteins. Their functions are unknown.. 
PF03103 Domain of unknown function (DUF243)<br>Pfam-B_1157 (release 6.5). This family of uncharacterised proteins is only found in fly proteins. It is found associated with YLP motifs Pfam:PF02757 in some proteins.. 
PF03140 Plant protein of unknown function<br>Pfam-B_1292 (release 6.5). The function of the plant proteins constituting this family is unknown.. 
PF03141 DUF248;<br>Putative S-adenosyl-L-methionine-dependent methyltransferase. Mifsud W, Moxon SJ, Eberhardt R. Pfam-B_1462 (release 6.5). This family is a putative S-adenosyl-L-methionine (SAM)-dependent methyltransferase [1,2].. 
PF03164 DUF254; <br>Trafficking protein Mon1. Members of this family have been called SAND proteins   although these proteins do not contain a SAND domain.  In Saccharomyces cerevisiae a protein complex of Mon1 and Ccz1 functions with the small GTPase Ypt7 to mediate vesicle trafficking to the vacuole  . The Mon1/Ccz1 complex is conserved in eukaryotic evolution and members of this family (previously known as DUF254) are distant homologues to domains of known structure that assemble into cargo vesicle adapter (AP) complexes  .   describes orthologues in Fugu rubripes.. 
PF03194 DUF259; <br>Pfam-B_2902 (release 6.5). This family contains the N terminal region of several LUC7 protein homologues and only contains eukaryotic proteins. LUC7 has been shown to be a U1 snRNA associated protein   with a role in splice site recognition  . The family also contains human and mouse LUC7 like (LUC7L) proteins   and human cisplatin resistance-associated overexpressed protein (CROP)  .. 
PF01657 DUF26;<br>Salt stress response/antifungal. Pfam-B_980 (release 4.1). This domain is often found in association with the kinase domains Pfam:PF00069 or Pfam:PF07714. In many proteins it is duplicated. It contains six conserved cysteines which are involved in disulphide bridges  . It has a role in salt stress response   and has antifungal activity  .. 
PF03195 Protein of unknown function DUF260<br>Pfam-B_2998 (release 6.5). 
PF03268 Caenorhabditis protein of unknown function, DUF267<br>Pfam-B_4201 (release 6.5). 
PF03269 Caenorhabditis protein of unknown function, DUF268<br>Pfam-B_4252 (release 6.5). 
PF03312 Protein of unknown function (DUF272)<br>Mifsud W, Pollington J. Pfam-B_3609 (release 6.5). This family of proteins is restricted to C.elegans and has no known function. The protein contains a ubiquitin fold. The GO annotation for the protein indicates that it has a function in nematode larval development.. 
PF03409 DUF274; Glycoprotein_Ce;<br>Transmembrane glycoprotein. Pfam-B_4416 (release 6.6). This family of proteins has some GO annotations for positive regulation of growth rate and nematode larval development. This is probably a family of membrane glycoproteins  .. 
PF03357 DUF279; SNF7; ESCRT-III; <br>Mifsud W, Moxon SJ, Mistry J, Wood V. Pfam-B_1641 (release 6.6). This family of proteins are involved in protein sorting and transport from the endosome to the vacuole/lysosome in eukaryotic cells. Vacuoles/lysosomes play an important role in the degradation of both lipids and cellular proteins. In order to perform this degradative function, vacuoles/lysosomes contain numerous hydrolases which have been transported in the form of inactive precursors via the biosynthetic pathway and are proteolytically activated upon delivery to the vacuole/lysosome. The delivery of transmembrane proteins, such as activated cell surface receptors to the lumen of the vacuole/lysosome, either for degradation/downregulation, or in the case of hydrolases, for proper localisation, requires the formation of multivesicular bodies (MVBs).  These late endosomal structures are formed by invaginating and budding of the limiting membrane into the lumen of the compartment. During this process, a subset of the endosomal membrane proteins is sorted into the forming vesicles. Mature MVBs fuse with the vacuole/lysosome, thereby releasing cargo containing vesicles into its hydrolytic lumen for degradation. Endosomal proteins that are not sorted into the intralumenal MVB vesicles are either recycled back to the plasma membrane or Golgi complex, or remain in the limiting membrane of the MVB and are thereby transported to the limiting membrane of the vacuole/lysosome as a consequence of fusion. Therefore, the MVB sorting pathway plays a critical role in the decision between recycling and degradation of membrane proteins  . A few archaeal sequences are also present within this family.. 
PF03380 Caenorhabditis protein of unknown function, DUF282<br>Pfam-B_2840 (release 6.6). 
PF03368 DUF283; dsRNA_bind;<br>Dicer dimerisation domain. 
PF03382 Mycoplasma protein of unknown function, DUF285<br>Pfam-B_2864 (release 6.6). This region appears distantly related to leucine rich repeats.. 
PF01060 Worm_family_2; <br>Transthyretin-like family. This family called family 2 in  , has weak similarity to transthyretin (formerly called pre-albumin) which transports thyroid hormones.\.      The specific function of this protein is unknown.. 
PF03478 Protein of unknown function (DUF295)<br>Pfam-B_790 (release 7.0). This family of proteins are found in plants.  The function of the proteins is unknown.. 
PF03556 DUF298;<br>Pfam-B_3021 (release 7.0). This domain binds to cullins and to Rbx-1, components of an E3 ubiquitin ligase complex for neddylation [1-3]. Neddylation is the process by which the C-terminal glycine of the ubiquitin-like protein Nedd8 is covalently linked to lysine residues in a protein through an isopeptide bond. The structure of this domain is composed entirely of alpha helices [1,2].. 
PF03619 DUF300;<br>Organic solute transporter Ostalpha. Pfam-B_3382 (release 7.0). This family is a transmembrane organic solute transport protein. In vertebrates these proteins form a complex with Ostbeta, and function as bile transporters  . In plants they may transport brassinosteroid-like compounds and act as regulators of cell death  .. 
PF03703 DUF304;<br>Domain found in uncharacterised family of membrane proteins. 1-3 copies found in each protein, with each copy flanked by transmembrane helices. Members of this family have a PH domain like structure  .. 
PF03713 Domain of unknown function (DUF305)<br>Domain found in small family of bacterial secreted proteins with no known function. Also found in Paramecium bursaria chlorella virus 1.  This domain is short and found in one or two copies. The domain has a conserved HH motif that may be functionally important.  This domain belongs to the ferritin superfamily. It contains two sequence similar repeats each of which is composed of two alpha helices.. 
PF03754 Domain of unknown function (DUF313) <br>Pfam-B_2540 (release 7.0). Family of proteins from Arabidopsis thaliana with uncharacterised function.. 
PF03761 Domain of unknown function (DUF316) <br>Pfam-B_2972 (release 7.0). This family of proteins with unknown function are from Caenorhabditis elegans. The protein has GO references indicating the protein is a positive regulator of growth rate and is also involved in nematode larval development.. 
PF03777 Small secreted domain (DUF320)  <br>Small domain found in a family of secreted streptomyces proteins. It occurs singly or as a pair. Many of the domains have two cysteines that may form a disulphide bridge.. 
PF03860 Domain of Unknown Function (DUF326) <br>This family is a small cysteine-rich repeat. The cysteines mostly follow a C-X(2)-C-X(3)-C-X(2)-C-X(3) pattern,  though they often appear at other positions in the repeat as well.. 
PF03935 DUF338; <br>Beta-glucan synthesis-associated protein (SKN1). This family consists of the beta-glucan synthesis-associated proteins KRE6 and SKN1. Beta1,6-Glucan is a key component of the yeast cell wall, interconnecting cell wall proteins, beta1,3-glucan, and chitin. It has been postulated that the synthesis of beta1,6-glucan begins in the endoplasmic reticulum with the formation of protein-bound primer structures and that these primer structures are extended in the Golgi complex by two putative glucosyltransferases that are functionally redundant, Kre6 and Skn1. This is followed by maturation steps at the cell surface and by coupling to other cell wall macromolecules  . . 
PF03990 Domain of unknown function (DUF348)     <br>This domain normally occurs as tandem repeats; however it is found as a single copy in the S. cerevisiae DNA-binding nuclear protein YCR593 (Swiss:P25357).  This protein is involved in sporulation part of the  SET3C complex, which is required to repress early/middle sporulation genes during meiosis ( ). The bacterial proteins are likely to be involved in a cell wall function as they are found in conjunction  with the Pfam:PF07501 domain, which is involved in various cell surface processes.. 
PF03993 Domain of Unknown Function (DUF349)<br>This domain is found singly or as up to five tandem repeats in a small set of  bacterial proteins. There are two or three alpha-helices, and possibly a beta-strand.. 
PF04008 DUF355; <br>Adenosine specific kinase. The structure of a member of this family from the hyperthermophilic archaeon Pyrobaculum aerophilum contains a modified histidine residue which is interpreted as stable phosphorylation  . In vitro binding studies confirmed that adenosine and AMP but not ADP or ATP bind to the protein  .. 
PF04013 DUF358;<br>Putative SAM-dependent RNA methyltransferase. This family is likely to be an S-adenosyl-L-methionine (SAM)-dependent RNA methyltransferase  .. 
PF04020 Membrane protein of unknown function<br>These proteins a predicted transmembrane proteins with probably four transmembrane spans. The function of these bacterial proteins is unknown. The sequences do not appear to contain any conserved polar residues that could form an active site.. 
PF04037 Domain of unknown function (DUF382) <br>Pfam-B_10232 (release 7.3);. This domain is specific to the human splicing factor 3b subunit 2 and it's orthologues. Splicing factor 3b subunit 2 or SAP145 is a suppressor of U2 snRNA mutations. Pre-mRNA splicing is catalysed by a large ribonucleoprotein complex called the spliceosome. Spliceosomes are multi-component enzymes that catalyse pre-mRNA splicing and form step-wise by the ordered interaction of UsnRNPs and non-snRNP proteins with short conserved regions of the pre-mRNA at the 5' and 3' splice sites and branch site  .. 
PF04075 Domain of unknown function (DUF385) <br>TIGRFAMs (release 2.0);. Family of Mycobacterium tuberculosis proteins.. 
PF04087 Domain of unknown function (DUF389) <br>TIGRFAMs (release 2.0);. Family of hypothetical bacterial proteins with  an undetermined function.. 
PF04155 DUF398; <br>Pfam-B_3296 (release 7.3). This family consists of the ground-like domain and is specific to C.elegans. It has been proposed that the ground-like domain containing proteins may bind and modulate the activity of Patched-like membrane molecules, reminiscent of the modulating activities of neuropeptides  .  . 
PF04241 Protein of unknown function (DUF423)<br>This family of proteins with unknown function is a possible integral membrane protein from Caenorhabditis elegans. This family of proteins has GO references indicating the protein is involved in nematode larval development and is a positive regulator of growth rate.. 
PF04255 Protein of unknown function (DUF433)<br>
PF01862 DUF44;<br>Pyruvoyl-dependent arginine decarboxylase (PvlArgDC). Methanococcus jannaschii contains homologues of most genes required for spermidine polyamine biosynthesis. Yet genomes from neither this organism nor any other euryarchaeon have orthologues of the pyridoxal 5'-phosphate- dependent ornithine or arginine decarboxylase genes, required to produce putrescine. Instead,these organisms have a new class of arginine decarboxylase (PvlArgDC) formed by the self-cleavage of a proenzyme into a 5-kDa subunit and a 12-kDa subunit that contains a reactive pyruvoyl group. Although this extremely thermostable enzyme has no significant sequence similarity to previously characterised proteins, conserved active site residues are similar to those of the pyruvoyl-dependent histidine decarboxylase enzyme, and its subunits form a similar (alpha-beta)(3) complex. Homologues of PvlArgDC are found in several bacterial genomes, including those of Chlamydia spp., which have no agmatine ureohydrolase enzyme to convert agmatine (decarboxylated arginine) into putrescine. In these intracellular pathogens, PvlArgDC may function analogously to pyruvoyl-dependent histidine decarboxylase; the cells are proposed to import arginine and export agmatine, increasing the pH and affecting the host cell's metabolism. Phylogenetic analysis of Pvl- ArgDC proteins suggests that this gene has been recruited from the euryarchaeal polyamine biosynthetic pathway to function as a degradative enzyme in bacteria  .. 
PF04332 Protein of unknown function (DUF475)<br>Predicted to be an integral membrane protein with multiple membrane spans.. 
PF04720 Protein of unknown function (DUF506) <br>Pfam-B_4111 (release 7.5). Family of uncharacterised plant proteins.. 
PF04784 Protein of unknown function, DUF547<br>Pfam-B_3926 (release 7.5). Family of uncharacterised proteins from C. elegans and A. thaliana. . 
PF04484 Family of unknown function (DUF566) <br>Pfam-B_3992 (release 7.5). Family of related proteins that is plant specific.. 
PF04526 Protein of unknown function (DUF568)<br>Pfam-B_4977 (release 7.5). Family of uncharacterised plant proteins.. 
PF04502 Family of unknown function (DUF572) <br>Pfam-B_3967 (release 7.5). Family of eukaryotic proteins with undetermined function.. 
PF04504 Protein of unknown function, DUF573<br>Pfam-B_2087 (release 7.5). 
PF04535 Domain of unknown function (DUF588)<br>Pfam-B_1439 (release 7.5). This family of plant proteins contains a domain that may have a catalytic activity.  It has a conserved arginine and aspartate that could form an active site. These proteins are predicted to contain 3 or 4 transmembrane helices.. 
PF01883 Domain of unknown function DUF59<br>This family has an alpha/beta topology, with 13 conserved hydrophobic residues at its core and a putative active site containing a highly conserved cysteine  . Members of this family are involved in a range of physiological functions. The family includes PaaJ (PhaH) Swiss:O84984 from Pseudomonas putida. PaaJ forms a complex with PaaG (PhaF) Swiss:O84982, PaaI (PhaG) Swiss:O84983 and PaaK (PhaI) Swiss:O84985, which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid  . It also includes PaaD Swiss:P76080 from Escherichia coli, a member of a multicomponent oxygenase involved in phenylacetyl-CoA hydroxylation  . It is found near the N-terminus of the chloroplast scaffold protein HCF101 Swiss:Q8LD16, involved in the assembly of [4Fe-4S] clusters and their transfer to apoproteins  .. 
PF04547 DUF590; <br>Calcium-activated chloride channel. Pfam-B_2735 (release 7.5). The family carries eight putative transmembrane domains, and, although it has no similarity to other known channel proteins, it is clearly a calcium-activated ionic channel. It is expressed in various secretory epithelia, the retina and sensory neurons, and mediates receptor-activated chloride currents in diverse physiological processes  .. 
PF04576 DUF593;<br>Mifsud W, Eberhardt R. Pfam-B_2802 (release 7.5). This domain binds to zein proteins, Pfam:PF01559  . Zein proteins are seed storage proteins.. 
PF04642 Protein of unknown function, DUF601<br>Pfam-B_5475 (release 7.5). This family represents a conserved region found in several uncharacterised plant proteins.. 
PF04641 DUF602;<br>Mifsud W, Pollington J. Pfam-B_5482 (release 7.5). It is vital for effective cell-replication that replication is not stalled at any point by, for instance, damaged bases. Replication termination factor 2 (Rtf2) stabilizes the replication fork stalled at the site-specific replication barrier RTS1 by preventing replication restart until completion of DNA synthesis by a converging replication fork initiated at a flanking origin. The RTS1 element terminates replication forks that are moving in the cen2-distal direction while allowing forks moving in the cen2-proximal direction to pass through the region. Rtf2 contains a C2HC2 motif related to the C3HC4 RING-finger motif, and would appear to fold up, creating a RING finger-like structure but forming only one functional Zn2+ ion-binding site  . This domain is also found at the N-terminus of peptidyl-prolyl cis-trans isomerase 4, a divergent cyclophilin family  .. 
PF04652 Vta1 like<br>Mifsud W, Mistry J, Wood V. Pfam-B_5537 (release 7.5). Vta1 (VPS20-associated protein 1) is a positive regulator of Vps4.  Vps4 is an ATPase that is required in the multivesicular body (MVB) sorting pathway to dissociate the endosomal sorting complex required for transport (ESCRT).  Vta1 promotes correct assembly of Vps4 and stimulates its ATPase activity through its conserved Vta1/SBP1/LIP5 region  .. 
PF04678 Protein of unknown function, DUF607<br>Pfam-B_5620 (release 7.5). This family represents a conserved region found in several uncharacterised eukaryotic proteins.. 
PF04685 Protein of unknown function, DUF608<br>Pfam-B_5657 (release 7.5). This family represents a conserved region with a pankaryotic distribution in a number of uncharacterised proteins.. 
PF04727 DUF609; <br>Pfam-B_3095 (release 7.5). This family represents a conserved domain which is found in a number of eukaryotic proteins including CED-12, ELMO I and ELMO II. ELMO1 is a component of signalling pathways that regulate phagocytosis and cell migration and is the mammalian orthologue of the C. elegans gene, ced-12. CED-12 is required for the engulfment of dying cells and cell migration. In mammalian cells, ELMO1 interacts with Dock180 as part of the CrkII/Dock180/Rac pathway responsible for phagocytosis and cell migration. ELMO1 is ubiquitously expressed, although its expression is highest in the spleen, an organ rich in immune cells  . ELMO1 has a PH domain and a polyproline sequence motif at its C terminus which are not present in this alignment.. 
PF04747 Protein of unknown function, DUF612<br>Pfam-B_3614 (release 7.5). This family includes several uncharacterised proteins from Caenorhabditis elegans.. 
PF04749 DUF614; <br>Pfam-B_3635 (release 7.5). This family includes Swiss:Q9NZF1, the Placenta-specific gene 8 protein.. 
PF04759 Protein of unknown function, DUF617<br>Pfam-B_3842 (release 7.5). This family represents a conserved region in a number of uncharacterised plant proteins.. 
PF04818 DUF618;<br>RNA polymerase II-binding domain.. Mifsud W, Eberhardt R. Pfam-B_3687 (release 7.6). This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase II [1,2].. 
PF04789 Protein of unknown function (DUF621)<br>Pfam-B_6219 (release 7.5). Family of uncharacterised proteins. Some (such as Swiss:O01625) are annotated as having possible G-protein-coupled receptor-like activity.. 
PF04802 DUF625; SMK-1_Ce; <br>Component of IIS longevity pathway SMK-1. Pfam-B_6319 (release 7.5). SMK-1 is a component of the IIs longevity pathway which regulates aging in C.elegans. Specifically, SMK-1 influences DAF-16-dependant regulation of the aging process by regulating the transcriptional specificity of DAF-16 activity  . SMK-1 plays a role in longevity by modulating the transcriptional specificity of DAF-16  .. 
PF04783 Protein of unknown function (DUF630)<br>Pfam-B_2481 (release 7.6). This region is sometimes found at the N-terminus of putative plant bZIP proteins.  Its function is not known. Structural modelling suggests this domain may bind nucleic acids  .. 
PF01683 EB module<br>This domain has no known function. It is found in several C. elegans proteins. The domain contains 8 conserved cysteines that probably form four disulphide bridges. This domain is found associated with kunitz domains Pfam:PF00014.. 
PF04782 Protein of unknown function (DUF632)<br>Pfam-B_2481 (release 7.6). This plant protein may be a leucine zipper, but there is no experimental evidence for this.. 
PF04826 DUF634;<br>Pfam-B_2700 (release 7.6). This domain contains armadillo-like repeats  . Proteins containing this domain interact with numerous other proteins, through these interactions they are involved in a wide variety of processes including carcinogenesis  , control of cellular ageing and survival  , regulation of circadian rhythm   and lysosomal sorting of G protein-coupled receptors  .. 
PF04859 Plant protein of unknown function (DUF641)<br>Pfam-B_6069 (release 7.6). Plant protein of unknown function.. 
PF04884 Vitamin B6 photo-protection and homoeostasis<br>Mifsud W, Eberhardt R. Pfam-B_6523 (release 7.6). In plants, this domain plays a role in auxin-transport, plant growth and development [1,2] and appears to be expressed by all cells in the plant as well as in plastids. The family has been shown to play a role in vitamin B6 photo-protection and homoeostasis in plants  .. 
PF04900 DUF652; <br>Mifsud W, Wood V, Mistry J. Pfam-B_6634 (release 7.6). Fcf1 is a nucleolar protein involved in pre-rRNA processing  . Depletion of yeast Fcf1 and Fcf2 leads to a decrease in synthesis of the 18S rRNA and results in a deficit in 40S ribosomal subunits  .. 
PF04949 DUF662;<br>Transcriptional activator. Pfam-B_6952 (release 7.6). This family of proteins may act as a transcriptional activator. It plays a role in stress response in plants  .. 
PF04950 Protein of unknown function (DUF663)<br>Pfam-B_5147 (release 7.6). This family contains several uncharacterised eukaryotic proteins.. 
PF05057 Putative serine esterase (DUF676)<br>Pfam-B_5941 (release 7.7). This family of proteins are probably serine esterase type enzymes with an alpha/beta hydrolase fold.. 
PF05097 Protein of unknown function (DUF688)<br>Pfam-B_6331 (release 7.7). This family contains several uncharacterised proteins found in Arabidopsis thaliana.. 
PF05108 Protein of unknown function (DUF690)<br>Pfam-B_6322 (release 7.7). This family contains several uncharacterised bacterial membrane proteins.. 
PF05127 DUF699;<br>Pfam-B_884 (release 7.7). This domain contains a P-loop (Walker A) motif, suggesting that it has ATPase activity, and a Walker B motif. In tRNA(Met) cytidine acetyltransferase (TmcA) it may function as an RNA helicase motor (driven by ATP hydrolysis) which delivers the wobble base to the active centre of the GCN5-related N-acetyltransferase (GNAT) domain  . It is found in the bacterial exodeoxyribonuclease V alpha chain (RecD), which has 5'-3' helicase activity. It is structurally similar to the motor domain 1A in other SF1 helicases  .. 
PF05129 DUF701; <br>Transcription elongation factor Elf1 like. Pfam-B_8884 (release 7.7). This family of short proteins contains a putative zinc binding domain with four conserved cysteines.  Swiss:P36053 has been identified as a transcription elongation factor in Saccharomyces cerevisiae  .. 
PF05197 DUF714; <br>Pfam-B_9855 (release 7.7). TRIC (trimeric intracellular cation) channels are differentially expressed in intracellular stores in animal cell types. TRIC subtypes contain three proposed transmembrane segments, and form homo-trimers with a bullet-like structure. Electrophysiological measurements with purified TRIC preparations identify a monovalent cation-selective channel  .. 
PF01031 dynamin_2; <br>Dynamin central region. Pfam-B_220 (release 3.0). This region lies between the GTPase domain, see Pfam:PF00350, and the pleckstrin  homology (PH) domain, see Pfam:PF00169.. 
PF03028 Dynein heavy chain and region D6 of dynein motor<br>Pfam-B_928 (release 6.4). 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 also involved in cilia and flagella movement. The dynein subunit consists of at least two heavy chains and a number of intermediate and light chains  . The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This C-terminal domain carries the D6 region of the dynein motor where the P-loop has been lost in evolution but the general structure of a potential ATP binding site appears to be retained  .. 
PF04261 Dyp_perox_fam; <br>Dyp-type peroxidase family . TIGRFAMs (release 2.0);. This family of dye-decolourising peroxidases lack a typical heme-binding region.. 
PF02221 ML domain<br>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 (Swiss:P49278). It has been implicate in lipid recognition, particularly in the recognition of pathogen related products. A mutation in Npc2 (Swiss:Q15668) causes a rare form of Niemann-Pick type C2 disease. This domain has a similar topology to immunoglobulin domains.. 
PF03271 EB1-like C-terminal motif<br>Pfam-B_1529 (release 6.5). 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 Pfam:PF00307. The human EB1 protein was originally discovered as a protein interacting with the C-terminus of the APC protein. This interaction is often disrupted in colon cancer, due to deletions affecting the  APC C-terminus. Several EB1 orthologues are also included in this family.  The interaction between EB1 and APC has been shown to have a potent synergistic effect on microtubule polymerisation. Neither of EB1 or APC alone has this effect. It is thought that EB1 targets APC to the + ends of microtubules, where APC promotes microtubule polymerisation. This process is regulated by APC phosphorylation by Cdc2, which disrupts APC-EB1 binding. Human EB1 protein can functionally substitute for the yeast EB1 homologue Mal3. In addition, Mal3 can substitute for human EB1 in promoting microtubule polymerisation with APC.. 
PF05009 EBNA-3;<br>Epstein-Barr virus nuclear antigen 3 (EBNA-3). Pfam-B_4674 (release 7.6). This family contains EBNA-3A, -3B, and -3C which are latent infection nuclear proteins important for Epstein-Barr virus (EBV)-induced B-cell immortalisation and the immune response to EBV infection  .. 
PF00679 Elongation factor G C-terminus<br>Pfam-B_40 (release 2.1). 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.. 
PF03764 Elongation factor G, domain IV<br>Pfam-B_40 (release 2.1). 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.. 
PF00036 efhand; EF_hand_1;<br>The EF-hands can be divided into two classes: signaling proteins and buffering/transport proteins.  The first group is the largest and includes the most well-known members of the family such as calmodulin, troponin C and S100B. These proteins typically undergo a calcium-dependent conformational change which opens a target binding site.  The latter group is represented by calbindin D9k and do not undergo calcium dependent conformational changes.. 
PF04189 eIF3_gamma; <br>Pfam-B_8933 (release 7.3);. eIF-3 is a multi-subunit complex that stimulates translation initiation in vitro at several different steps. This family corresponds to the gamma subunit if eIF3 [1,2]. The Yeast protein Gcd10p has also been shown to be part of a complex with the methyltransferase Gcd14p that is involved in modifying tRNA  .. 
PF03610 PTS system fructose IIA component<br>TIGRFAMs, Griffiths-Jones SR. 
PF01448 ELM2 domain<br>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 Pfam:PF00249. ELM2 is also found associated with an ARID DNA binding domain Pfam:PF01388 in Swiss:O82364. This suggests that ELM2 may also be involved in DNA binding, or perhaps is a protein-protein interaction domain.. 
PF02990 Endomembrane protein 70<br>Pfam-B_1312 (release 6.4). 
PF01223 Endonuclease; <br>DNA/RNA non-specific endonuclease. 
PF00812 Ephrin<br>Pfam-B_1390 (release 2.1). 
PF05139 Erythromycin esterase<br>This family includes erythromycin esterase enzymes [1,2] that confer resistance to the erythromycin antibiotic.. 
PF04800 ETC_CI_21; <br>ETC complex I subunit conserved region. Pfam-B_6275 (release 7.5). Family of pankaryotic NADH-ubiquinone oxidoreductase subunits (EC:1.6.5.3) (EC:1.6.99.3) from complex I of the electron transport chain initially identified in Neurospora crassa as a 21 kDa protein  .. 
PF04716 ETC_CI_29_9;<br>ETC complex I subunit conserved region. Pfam-B_4159 (release 7.5). Family of eukaryotic NADH-ubiquinone oxidoreductase subunits (EC:1.6.5.3) (EC:1.6.99.3) from complex I of the electron transport chain initially identified in Neurospora crassa as a 29.9 kDa protein. The conserved region is found at the N-terminus of the member proteins  .. 
PF04621 PEA3 subfamily ETS-domain transcription factor N terminal domain<br>The N terminus of the PEA3 transcription factors is implicated in transactivation and in inhibition of DNA binding  . Transactivation is potentiated by activation of the Ras/MAP kinase and protein kinase A signalling cascades.  The N terminal region contains conserved MAP kinase phosphorylation sites  .. 
PF04777 Erv1 / Alr family<br>Pfam-B_5005 (release 7.6). Biogenesis of Fe/S clusters involves a number of essential mitochondrial  proteins. Erv1p of Saccharomyces cerevisiae mitochondria is  required for the maturation of Fe/S proteins in the cytosol. The ALR  (augmenter of liver regeneration) represents a mammalian orthologue of yeast Erv1p. Both Erv1p and full-length ALR are located in the  mitochondrial intermembrane an d it thought to operate downstream of  the mitochondrial ABC transporter  .  . 
PF03372 Endonuclease/Exonuclease/phosphatase family<br>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 e.g Swiss:P27695, DNase I proteins EC:3.1.21.1 e.g. Swiss:P24855, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56 Swiss:O43426, Sphingomyelinase EC:3.1.4.12 Swiss:P11889 and Nocturnin Swiss:O35710.. 
PF02609 Exonuclease VII small subunit<br>This family consist of exonuclease VII, small subunit EC:3.1.11.6 This enzyme catalyses exonucleolytic cleavage in either 5'->3' or 3'->5'  direction to yield 5'-phosphomononucleotides.  This exonuclease VII enzyme is composed of one large subunit and 4 small ones  .. 
PF00929 Exonuclease; Exonuc_X-T;<br>Pfam-B_1153 (release 3.0). This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.; . 
PF03016 Exostosin family<br>Pfam-B_2031 (release 6.4). The EXT family is a family of tumour suppressor genes.  Mutations of EXT1 Swiss:Q16394 on 8q24.1, EXT2 Swiss:Q93063 on 11p11-13, and EXT3 on 19p have been associated with the autosomal dominant disorder known as hereditary multiple exostoses (HME). This is the most common known skeletal dysplasia. The chromosomal locations of other EXT genes suggest association with other forms of neoplasia.  EXT1 and EXT2 have both been shown to encode a heparan sulphate polymerase with both D-glucuronyl (GlcA) and N-acetyl-D-glucosaminoglycan (GlcNAC) transferase activities  . The nature of the defect in heparan sulphate biosynthesis in HME is unclear.. 
PF03124 EXS family<br>Pfam-B_605 (release 6.5). 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 cerevisiae, and sequences that are thought to be murine leukaemia virus (MLV)  receptors (XPR1). N-terminus portions from these proteins are aligned in the SPX  Pfam:PF03105 family. The previously noted similarity between SYG1 and MLV receptors over their whole sequences   is thus borne out in Pfam:PF03105 and this family. While the N-termini aligned in Pfam:PF03105 are thought to be involved in signal transduction, the role of the C-terminus sequences aligned in this family is not known. This region of similarity contains several predicted transmembrane helices. This family also includes the ERD1 (ERD: ER retention  defective) yeast proteins Swiss:P16151.  ERD1 proteins are involved in the localisation of endogenous endoplasmic reticulum (ER) proteins. erd1 null mutants secrete such proteins even though they possess the C-terminal HDEL ER lumen localisation label sequence. In addition, null mutants also exhibit defects in the Golgi-dependent processing of several glycoproteins, which led to the suggestion that the sorting of luminal ER proteins actually occurs in the Golgi, with subsequent return of these proteins to the ER via  `salvage' vesicles  .. 
PF04554 Extensin-like region<br>Pfam-B_1707 (release 7.5). 
PF00646 F-box domain<br>This domain is approximately 50 amino acids long, and is usually found in the N-terminal half of a variety of proteins. Two motifs that are commonly found associated with the F-box domain are the leucine rich repeats (LRRs; Pfam:PF00560 and Pfam:PF07723) and the WD repeat (Pfam:PF00400). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression  .. 
PF00754 F5/8 type C domain<br>Pfam-B_478 (release 2.1). This domain is also known as the discoidin (DS) domain family  .. 
PF00487 Fatty acid desaturase<br>
PF02913 FAD linked oxidases, C-terminal domain<br>This domain has a ferredoxin-like fold.. 
PF01565 FAD binding domain <br>Pfam-B_352 (release 4.0). This family consists of various enzymes that use FAD as a co-factor, most of the enzymes are similar to oxygen oxidoreductase. One of the enzymes Vanillyl-alcohol oxidase (VAO) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110  . The FAD molecule is covalently bound in the known structure, however the residue that links to the FAD is not in the alignment. VAO catalyses the oxidation of a wide variety of substrates, ranging form aromatic amines to 4-alkylphenols. Other members of this family include D-lactate dehydrogenase, this enzyme catalyses the conversion of D-lactate to pyruvate using FAD as a co-factor; mitomycin radical oxidase, this enzyme oxidises the reduced form of mitomycins and is involved in mitomycin resistance. This family includes MurB an UDP-N-acetylenolpyruvoylglucosamine reductase enzyme EC:1.1.1.158.  This enzyme is involved in the biosynthesis of peptidoglycan  .. 
PF00970 Cyt_reductase; <br>Oxidoreductase FAD-binding domain. Pfam-B_143 (release 3.0). 
PF03441 FAD binding domain of DNA photolyase<br>
PF03101 FAR1 DNA-binding domain<br>Pfam-B_2535 (release 6.4). This domain contains a WRKY like fold and is therefore most likely a zinc binding DNA-binding domain.. 
PF04300 F-box associated region<br>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. Swiss:Q9UK22 is involved in binding to N-glycosylated proteins.. 
PF00611 Fes/CIP4, and EFC/F-BAR homology domain<br>Ponting C, Schultz J, Bork P. Alignment extended from  . Highly alpha-helical.  The cytosolic endocytic adaptor proteins in fungi carry this domain at the N-terminus; several of these have been referred to as muniscin proteins  . These N-terminal BAR, N-BAR, and EFC/F-BAR domains are found in proteins that regulate membrane trafficking events by inducing membrane tubulation. The domain dimerises into a curved structure that binds to liposomes and either senses or induces the curvature of the membrane bilayer to cause biophysical changes to the shape of the bilayer; it also thereby recruits other trafficking factors, such as the GTPase dynamin. Most EFC/F-BAR domain-family members localise to actin-rich structures  .. 
PF00111 fer2; <br>2Fe-2S iron-sulfur cluster binding domain. 
PF01799 fer2_2; <br>[2Fe-2S] binding domain. 
PF04324 fer2_BFD; <br>BFD-like [2Fe-2S] binding domain. The two Fe ions are each coordinated by two conserved cysteine residues. This domain occurs alone in small proteins such as Bacterioferritin-associated ferredoxin (BFD, Swiss:P13655).  The function of BFD is not known, but it may may be a general redox and/or regulatory component involved in the iron storage or mobilisation functions of bacterioferritin in bacteria  .  This domain is also found in nitrate reductase proteins in association with Nitrite and sulphite reductase 4Fe-4S domain (Pfam:PF01077), Nitrite/Sulfite reductase ferredoxin-like half domain (Pfam:PF03460) and Pyridine nucleotide-disulphide oxidoreductase (Pfam:PF00070). It is also found in NifU nitrogen fixation proteins, in association with NifU-like N terminal domain (Pfam:PF01592) and NifU-like domain (Pfam:PF01106).. 
PF00037 fer4; <br>4Fe-4S binding domain. Superfamily includes proteins containing  domains which bind to iron-sulfur clusters. Members  include bacterial ferredoxins, various dehydrogenases, and various reductases.  Structure of the domain is an alpha-antiparallel beta sandwich.. 
PF00210 ferritin; <br>Ferritin-like domain. This family contains ferritins and other ferritin-like proteins such as members of the DPS family and bacterioferritins.. 
PF01839 FG-GAP repeat<br>This family contains the extracellular repeat that is found in up to seven copies in alpha integrins.  This repeat has been predicted to fold into a beta propeller structure  . The repeat is called the FG-GAP repeat after two conserved motifs in the repeat  .  The FG-GAP repeats are found in the N terminus of integrin alpha chains, a region that has been shown to be important for ligand binding  . A putative Ca2+ binding motif is found in some of the repeats.. 
PF02181 Formin Homology 2 Domain<br>Alignment kindly provided by SMART. 
PF02661 Fic/DOC family<br>This family consists of the Fic (filamentation induced by cAMP) protein and doc (death on curing).  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 and cAMP are involved in a regulatory mechanism of cell division via folate metabolism  .  This family contains a central conserved motif HPFXXGNG in most members.  The exact molecular function of these proteins is uncertain.  P1 lysogens of Escherichia coli carry the prophage as a stable low copy number plasmid. The frequency with which viable cells cured of prophage are produced is about 10(-5) per cell per generation  .  A significant part of this remarkable stability can be attributed to a plasmid-encoded mechanism that causes death of cells that have lost P1  . In other words, the lysogenic cells appear to be addicted to the presence of the prophage. The plasmid withdrawal response depends on a gene named doc (death on curing) that is represented by this family  . Doc induces a reversible growth arrest of E. coli cells by targetting the protein synthesis machinery. Doc hosts the C-terminal domain of its antitoxin partner Phd (prevents host death) through fold complementation, a domain that is intrinsically disordered in solution but that folds into an alpha-helix on binding to Doc  .This domain forms complexes with Phd antitoxins containing Pfam:PF02604.. 
PF00254 FKBP; <br>FKBP-type peptidyl-prolyl cis-trans isomerase. 
PF01003 Flavivirus capsid protein C<br>Pfam-B_156 (release 3.0)  . Flaviviruses are small enveloped viruses with virions comprised of 3 proteins called C, M and E.  Multiple copies of the C protein  form the nucleocapsid, which contains the ssRNA molecule.. 
PF02832 Flavivirus glycoprotein, immunoglobulin-like domain<br>Pfam-B_146 (release 3.0). 
PF00869 Flavivirus glycoprotein, central and dimerisation domains<br>Pfam-B_146 (release 3.0). 
PF00949 Flavi_helicase; <br>Peptidase S7, Flavivirus NS3 serine protease . Pfam-B_199 (release 3.0). The viral genome is a positive strand RNA that encodes a single  polyprotein precursor. Processing of the polyprotein precursor into mature proteins is carried out by the host signal peptidase and by NS3 serine  protease, which requires NS2B (Pfam:PF01002) as a cofactor  . . 
PF01004 Flavivirus envelope glycoprotein M<br>Pfam-B_156 (release 3.0)  . Flaviviruses are small enveloped viruses with virions comprised of 3 proteins called C, M and E. The envelope glycoprotein M is made as a precursor, called prM. The precursor portion of the protein is the signal peptide for the proteins entry into the membrane. prM is cleaved to form M in a late-stage cleavage event. Associated with this cleavage is a change in the infectivity and fusion activity of the virus.. 
PF00948 Flavivirus non-structural Protein NS1 <br>Pfam-B_157 (release 3.0). The NS1 protein is well conserved amongst the flaviviruses. It contains 12 cysteines, and undergoes glycosylation in a similar manner to other NS proteins.  Mutational analysis has strongly  implied a role for NS1 in the early stages of RNA replication.. 
PF01005 Flavivirus non-structural protein NS2A<br>Pfam-B_156 (release 3.0). NS2A is a hydrophobic protein about 25 kDa is size.  NS2A is  cleaved from NS1 by a membrane bound host protease  .  NS2A has been found to associate with the dsRNA within the vesicle packages.  It has also been found that NS2A associates with the  known replicase components and so NS2A has been postulated to be part of this replicase complex  . . 
PF01002 Flavivirus non-structural protein NS2B<br>Pfam-B_156 (release 3.0). Flaviviruses encode a single polyprotein. This is cleaved into three structural and seven non-structural proteins. All, but two, are cleaved by the NS2B-NS3 protease complex.. 
PF01613 Flavin reductase like domain<br>Pfam-B_710 (release 4.1). This is a flavin reductase family consisting of enzymes known to be flavin reductases as well as various oxidoreductase and monooxygenase components. VlmR is a flavin reductase that functions in a two-component enzyme system to provide isobutylamine N-hydroxylase with reduced flavin and may be involved in the synthesis of valanimycin  . SnaC is a flavin reductase that provides reduced flavin for the oxidation of pristinamycin IIB to pristinamycin IIA as catalysed by SnaA, SnaB heterodimer  .  This flavin reductase region characterised by enzymes of the family is present in the C-terminus of potential FMN proteins from Synechocystis sp. suggesting it is a flavin reductase domain  .. 
PF00258 flavodoxin; <br>
PF04500 FLYWCH zinc finger domain<br>Mutations in the mod(mdg4) gene have effects on variegation (PEV), the properties of insulator sequences, correct path-finding of growing nerve cells, meiotic pairing of chromosomes, and apoptosis. The  occurrence of FLYWCH motifs in mod(mdg4) gene product and other proteins is discussed in  .. 
PF03358 NADPH-dependent FMN reductase<br>Pfam-B_2010 (release 6.6). 
PF02434 Fringe-like<br>Pfam-B_1900 (release 5.4). 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 through glycosylation by FNG. The xenopus homologue, lunatic fringe, has been implicated in a variety of functions.. 
PF01534 Frizzled/Smoothened family membrane region<br>Pfam-B_949 (release 4.0). 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 (Swiss:P18537) are receptors for Wnt (mediating the beta-catenin signalling pathway)  , but also the planar cell polarity (PCP) pathway and the Wnt/calcium pathway. The predominantly alpha-helical Cys-rich ligand-binding region (CRD) of Frizzled is both necessary and sufficient for Wnt binding  .  The smoothened receptor mediates hedgehog signalling  .. 
PF01827 DUF38; <br>Pfam-B_67 (release 4.2). This presumed domain is likely to be a protein-protein interaction module  . It is found in many proteins from C. elegans. The domain is found associated with the F-box Pfam:PF00646. This domain is named FTH after FOG-2 homology domain  .. 
PF01913 Formylmethanofuran-tetrahydromethanopterin formyltransferase<br>This enzyme EC:2.3.1.101 is involved in archaebacteria in the formation of methane from carbon dioxide. N-terminal distal lobe of alpha+beta ferredoxin-like fold. SCOP reports fold duplication with C-terminal proximal lobe.. 
PF02741 FTR, proximal lobe<br>The FTR (Formylmethanofuran--tetrahydromethanopterin formyltransferase) enzyme EC:2.3.1.101 is involved in archaebacteria in the formation of methane from carbon dioxide. C-terminal proximal lobe of alpha+beta ferredoxin-like fold. SCOP reports fold duplication with N-terminal distal lobe.. 
PF01728 FtsJ-like methyltransferase<br>Pfam-B_1791 (release 4.1). This family consists of FtsJ from various bacterial and archaeal sources FtsJ is a methyltransferase, but actually has no effect on cell division. FtsJ's substrate is the 23S rRNA. The 1.5 A crystal structure of FtsJ in complex with its cofactor S-adenosylmethionine revealed that FtsJ has a methyltransferase fold. This family also includes the N terminus of flaviviral NS5 protein. It has been hypothesised that the N-terminal domain of NS5 is a methyltransferase involved in viral RNA capping  .. 
PF02687 DUF214; <br>FtsX-like permease family. This is a family of predicted permeases and hypothetical transmembrane proteins. Swiss:P57382 has been shown to transport lipids targeted to the outer membrane across the inner membrane. Both Swiss:P57382 and Swiss:O54500 have been shown to require ATP. This region contains three transmembrane helices.. 
PF04082 Fungal specific transcription factor domain <br>Pfam-B_306 (release 7.3);. 
PF01363 FYVE zinc finger<br>Pfam-B_655 (release 3.0). The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn++ ions  . The FYVE finger has eight potential zinc coordinating cysteine positions.  Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue.  We have included members which do not conserve these histidine residues but are clearly related.. 
PF01392 Fz domain<br>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 [1,2,3,4].  The domain contains 10 conserved cysteines.. 
PF01585 G7; <br>Pfam-B_585 (release 4.1). 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.. 
PF01019 Gamma-glutamyltranspeptidase<br>Pfam-B_878 (release 3.0). 
PF04114 Gaa1-like, GPI transamidase component <br>Pfam-B_12685 (release 7.3);. 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  synthesised proteins. . 
PF01590 GAF domain<br>This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyse ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalysed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyses the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region. This domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54.. 
PF01140 gag_MA;<br>Matrix protein (MA), p15. Pfam-B_229 (release 3.0). The matrix protein, p15, is encoded by the gag gene. MA is involved in pathogenicity  .. 
PF01141 gag_p12; <br>Gag polyprotein, inner coat protein p12. Pfam-B_821 (release 3.0). 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  .. 
PF02140 Galactose binding lectin domain<br>
PF03127 GAT domain<br>The GAT domain is responsible for binding of GGA proteins to several members of the ARF family including ARF1   and ARF3. The GAT domain stabilises membrane bound ARF1 in its GTP bound state, by interfering with GAP proteins  .. 
PF00320 GATA zinc finger<br>This domain uses four cysteine residues to coordinate a zinc ion. This domain binds to DNA. Two GATA zinc fingers are found in the GATA transcription factors.  However there are several proteins which only contains a single copy of the domain.. 
PF00117 Glutamine amidotransferase class-I<br>
PF02934 PET112_N; <br>GatB/GatE catalytic domain. This domain is found in the GatB and GatE proteins  .. 
PF02637 DUF186;<br>This domain is found in GatB. It is about 140 amino acid residues long.  This domain is found at the C terminus of GatB Swiss:O30509 which transamidates Glu-tRNA to Gln-tRNA.. 
PF03615 GCM motif protein<br>
PF03074 Glutamate-cysteine ligase<br>Pfam-B_541 (release 6.4). 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. The eukaryotic enzyme is a dimer of a heavy chain and a light chain with all the catalytic activity exhibited by the heavy chain (this family).. 
PF03009 Glycerophosphoryl diester phosphodiesterase family<br>Pfam-B_4008 (release 6.4). 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 been noted  . This family appears to have weak but not significant matches to mammalian phospholipase C Pfam:PF00388, which suggests that this family may adopt a TIM barrel fold.. 
PF00626 Gelsolin repeat<br>
PF01408 Oxidoreductase family, NAD-binding Rossmann fold<br>Pfam-B_342 (release 3.0). This family of enzymes utilise NADP or NAD. This family is called the GFO/IDH/MOCA family in swiss-prot.. 
PF02894 Oxidoreductase family, C-terminal alpha/beta domain<br>Pfam-B_342 (release 3.0). This family of enzymes utilise NADP or NAD. This family is called the GFO/IDH/MOCA family in swiss-prot.. 
PF00990 DUF9; <br>Pfam-B_112 (release 3.0). This domain is found linked to a wide range of non-homologous domains in a variety of bacteria. It has been shown to be homologous to the adenylyl cyclase catalytic domain   and has diguanylate cyclase activity  . This observation correlates with the functional information available on two GGDEF-containing proteins, namely diguanylate cyclase and phosphodiesterase A of Acetobacter xylinum, both of which regulate the turnover of cyclic diguanosine monophosphate.. 
PF03321 GH3 auxin-responsive promoter<br>Pfam-B_3652 (release 6.5). 
PF00288 GHMP_kinases; <br>GHMP kinases N terminal domain. This family includes homoserine kinases, galactokinases and mevalonate kinases.. 
PF00594 gla; <br>Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain. This  domain is  responsible for the high-affinity binding of calcium ions. This domain contains post-translational modifications of many glutamate residues by Vitamin K-dependent carboxylation to form gamma-carboxyglutamate (Gla).. 
PF00208 E_L_F_V_dh; GLFV_dehydrog; <br>Glutamate/Leucine/Phenylalanine/Valine dehydrogenase. 
PF00042 globin; <br>Structure_superposition. 
PF04898 Glutamate synthase central domain<br>Pfam-B_455 (release 7.6). The central domain of glutamate synthase connects the amino terminal amidotransferase domain with the FMN-binding domain and has an alpha / beta overall topology  .  This domain appears to be a rudimentary form of the FMN-binding TIM barrel according to SCOP.. 
PF04960 Glutaminase<br>This family of enzymes deaminates glutamine to glutamate EC:3.5.1.2.. 
PF04488 Glycosyltransferase sugar-binding region containing DXD motif   <br>The DXD motif is a short conserved motif found in many families of glycosyltransferases, which add a range of different sugars to other  sugars, phosphates and proteins.  DXD-containing glycosyltransferases all  use nucleoside diphosphate sugars as donors and require divalent cations,  usually manganese.  The DXD motif is expected to play a carbohydrate  binding role in sugar-nucleoside diphosphate and manganese dependent  glycosyltransferases  .. 
PF00722 glycosyl_hydro9; <br>Glycosyl hydrolases family 16. Pfam-B_759 (release 2.1). 
PF00704 glycosyl_hydro8; <br>Glycosyl hydrolases family 18. Pfam-B_574 (release 2.1). 
PF02055 O-Glycosyl hydrolase family 30<br>
PF01055 Glycosyl_hydr15; <br>Glycosyl hydrolases family 31 . Pfam-B_369 (release 3.0). Glycosyl hydrolases are key enzymes of carbohydrate metabolism. Family 31 comprises of enzymes that are, or similar to, alpha- galactosidases.. 
PF01532 Glycosyl hydrolase family 47<br>Pfam-B_958 (release 4.0). 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).. 
PF03200 Mannosyl oligosaccharide glucosidase<br>Pfam-B_2589 (release 6.5). 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 glucosidase EC:3.2.1.106 is the first enzyme in the N-linked oligosaccharide processing pathway.. 
PF03648 Glyco_hydro_67; <br>Glycosyl hydrolase family 67 N-terminus. Alpha-glucuronidases, components of an ensemble of enzymes central to the recycling of photosynthetic biomass, remove the alpha-1,2 linked 4-O-methyl glucuronic acid from xylans. This family represents the N-terminal region of alpha-glucuronidase. The N-terminal domain forms a two-layer sandwich, each layer being formed by a beta sheet of five strands. A further two helices  form part of the interface with the central, catalytic, module (Pfam:PF07488)  . . 
PF03663 Glycosyl hydrolase family 76 <br>Family of alpha-1,6-mannanases.. 
PF03644 Glycosyl hydrolase family 85 <br>Family of endo-beta-N-acetylglucosaminidases.  These enzymes work on a broad spectrum of substrates.. 
PF04101 Glycosyltransferase family 28 C-terminal domain<br>Pfam-B_1105 (release 6.4). The glycosyltransferase family 28 includes  monogalactosyldiacylglycerol synthase (Swiss:P93115, EC 2.4.1.46) and UDP-N-acetylglucosamine transferase (Swiss:P74657, EC 2.4.1.-). Structural analysis suggests the C-terminal domain contains the UDP-GlcNAc binding site.. 
PF00852 Fucosyl_transf; <br>Glycosyltransferase family 10 (fucosyltransferase). Pfam-B_1677 (release 2.1). 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  .. 
PF00982 TrehaloseP_syn;<br>Glycosyltransferase family 20. Pfam-B_1035 (release 3.0). Members of this family belong to glycosyl transferase family 20  . OtsA (Trehalose-6-phosphate synthase) is homologous to regions in the subunits of yeast trehalose-6-phosphate synthase/phosphate complex,  .. 
PF01755 LPS_glycoyl_T; <br>Glycosyltransferase family 25 (LPS biosynthesis protein). Pfam-B_1857 (release 4.1). Members of this family belong to Glycosyltransferase family 25   This is a family of glycosyltransferases involved in lipopolysaccharide (LPS) biosynthesis. These enzymes catalyse the transfer of various sugars onto the growing LPS chain during its biosynthesis.. 
PF00777 Sialyltransf; <br>Glycosyltransferase family 29 (sialyltransferase). Pfam-B_1020 (release 2.1). Members of this family belong to glycosyltransferase family 29  .. 
PF03360 Glyco_tranf_43;<br>Glycosyltransferase family 43. Pfam-B_1447 (release 6.6). 
PF01501 Glycosyl transferase family 8<br>Pfam-B_730 (release 4.0) & Pfam-B_5903 (Release 7.5). This family includes enzymes that transfer sugar residues to donor molecules. Members of this family are involved in lipopolysaccharide biosynthesis and glycogen synthesis. This family includes Lipopolysaccharide galactosyltransferase Swiss:P27128, lipopolysaccharide glucosyltransferase 1 Swiss:P27129, and glycogenin glucosyltransferase Swiss:P46976.. 
PF00535 glycosyl_transf_2;<br>Glycosyl transferase family 2. MRC-LMB Genome group. 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.. 
PF00953 Glycosyl transferase family 4<br>Pfam-B_534 (release 3.0). 
PF00903 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily<br>Pfam-B_1207 (release 3.0) & Pfam-B_5495 (Release 8.0). 
PF04464 glyphos_transf; <br>CDP-Glycerol:Poly(glycerophosphate) glycerophosphotransferase . Wall-associated teichoic acids are a heterogeneous class of phosphate-rich polymers that are covalently linked to the cell wall peptidoglycan of gram-positive bacteria. They consist of a main chain of phosphodiester-linked polyols and/or sugar moieties attached to peptidoglycan via a linkage unit. CDP-glycerol:poly(glycerophosphate) glycerophosphotransferase is responsible for the polymerisation of the main chain of the teichoic acid by sequential transfer of glycerol-phosphate  units from CDP-glycerol to the linkage unit lipid  .. 
PF00958 GMP synthase C terminal domain<br>Pfam-B_1137 (release 3.0). 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 Swiss:P49915 EC:6.3.5.2. In prokaryotes this domain mediates dimerisation. Eukaryotic GMP synthases are monomers. This domain in eukaryotes includes several large insertions that may form globular domains.. 
PF01825 Latrophilin/CL-1-like GPS domain<br>Domain present in latrophilin/CL-1, sea urchin REJ and polycystin.. 
PF02893 GRAM domain<br>Alignment kindly provided by SMART. The GRAM domain is found in in glucosyltransferases, myotubularins and other putative membrane-associated proteins.. 
PF03514 GRAS domain family<br>Pfam-B_393 (release 7.0). Proteins in the GRAS (GAI, RGA, SCR) family are known as  major players in gibberellin (GA) signaling, which regulates various aspects of plant growth and development  .  Mutation of the SCARECROW (SCR) gene results in a radial  pattern defect, loss of a ground tissue layer, in the root.  The PAT1 protein is involved in phytochrome A signal  transduction  . A sequence, structure and evolutionary  analysis showed that the GRAS family emerged in bacteria  and belongs to the Rossmann-fold, AdoMET (SAM)-dependent  methyltransferase superfamily  . All bacterial, and a subset  of plant GRAS proteins, are predicted to be active and function  as small-molecule methylases. Several plant GRAS proteins  lack one or more AdoMet (SAM)-binding residues while  preserving their substrate-binding residues. Although GRAS   proteins are implicated to function as transcriptional factors,  the above analysis suggests that they instead might either   modify or bind small molecules  .. 
PF01465 GRIP domain<br>The GRIP (golgin-97, RanBP2alpha,Imh1p and p230/golgin-245) domain is found in many large coiled-coil proteins. It has been shown to be sufficient for targeting to the Golgi. The GRIP domain contains a completely conserved tyrosine residue. At least some of these domains have been shown to bind to GTPase Arl1, see structures in [4,5].. 
PF02946 GTF2I-like repeat<br>Pfam-B_101 (release 6.4). 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 [1,2].. 
PF01018 GTP1/OBG<br>Pfam-B_875 (release 3.0). The N-terminal domain of Swiss:P20964 has the OBG fold, which is formed by three glycine-rich regions inserted into a small 8-stranded beta-sandwich these regions form six left-handed collagen-like helices packed and H-bonded together.. 
PF00009 Elongation factor Tu GTP binding domain<br>This domain contains a P-loop motif, also found in several other families such as Pfam:PF00071, Pfam:PF00025 and Pfam:PF00063. Elongation factor Tu consists of three structural domains, this plus two C-terminal beta barrel domains.. 
PF03144 Elongation factor Tu domain 2<br>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 other proteins such as elongation factor G and translation initiation factor IF-2. This domain is structurally related to Pfam:PF03143, and in fact has weak sequence matches to this domain.. 
PF03143 Elongation factor Tu C-terminal domain<br>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 Pfam:PF00889  .. 
PF01493 DUF14; <br>Pfam-B_428 (release 4.0). This domain is found in glutamate synthase, tungsten formylmethanofuran dehydrogenase subunit c (FwdC) and molybdenum formylmethanofuran dehydrogenase subunit c (FmdC). A repeated G-XX-G-XXX-G motif is seen in the alignment.. 
PF02756 GYR motif<br>The GYR motif is found in several drosophila proteins. Its function is unknown, however the presence of completely conserved tyrosine residues may suggest it could be a substrate for tyrosine kinases.. 
PF03457 Helicase associated domain<br>This short domain is found in multiple copies in bacterial helicase proteins. The domain is predicted to contain 3 alpha helices.  The function of this domain may be to bind nucleic acid.. 
PF04408 Helicase associated domain (HA2)<br>This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding.. 
PF04774 Hyaluronan / mRNA binding family<br>Pfam-B_2044 (release 7.6). This family includes the HABP4 family of hyaluronan-binding proteins, and the PAI-1 mRNA-binding protein, PAI-RBP1.  HABP4 has been observed to bind hyaluronan (a glucosaminoglycan), but it is not known whether this is its primary role in vivo.  It has also been observed to bind RNA, but with a lower affinity than that for hyaluronan  . PAI-1 mRNA-binding protein specifically binds the mRNA of type-1 plasminogen activator inhibitor (PAI-1), and is thought to be involved in regulation of mRNA stability  . However, in both cases, the sequence motifs predicted to be important for ligand binding are not conserved throughout the family, so it is not known whether members of this family share a common function.. 
PF02183 Homeobox associated leucine zipper<br>Alignment kindly provided by SMART & Pfam-B_1492 (Release 7.5). 
PF00672 DUF5;<br>Pfam-B_113 (release 2.1). 
PF04849 HAP1 N-terminal conserved region<br>Pfam-B_4571 (release 7.6). This family represents an N-terminal conserved region found in several huntingtin-associated protein 1 (HAP1) homologues. HAP1 binds to huntingtin in a polyglutamine repeat-length-dependent manner. However, its possible role in the pathogenesis of Huntington's disease is unclear [1-3]. This family also includes a similar N-terminal conserved region from hypothetical protein products of ALS2CR3 genes found in the human juvenile amyotrophic lateral sclerosis critical region 2q33-2q34  .. 
PF02184 HAT (Half-A-TPR) repeat<br>Alignment kindly provided by SMART. The HAT (Half A TPR) repeat is found in several RNA processing proteins  .. 
PF02518 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase<br>SMART, Griffiths-Jones SR. This family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90.. 
PF00955 Anion_Exchanger; <br>HCO3- transporter family. Pfam-B_1004 (release 3.0). This family contains Band 3 anion exchange proteins that exchange CL-/HCO3- such as Swiss:P48751. This family also includes cotransporters of Na+/HCO3- such as Swiss:O15153.. 
PF01966 HD domain<br>HD domains are metal dependent phosphohydrolases.. 
PF00271 helicase_C; <br>Helicase conserved C-terminal domain. The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.. 
PF02602 Uroporphyrinogen-III synthase HemD<br>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: Hydroxymethylbilane <=> uroporphyrinogen-III + H(2)O.  Some members of this family are multi-functional proteins possessing other enzyme activities related to porphyrin biosynthesis, such as Swiss:Q59294 with Pfam:PF00590, however the aligned region corresponds with the uroporphyrinogen-III synthase EC:4.2.1.75 activity only. Uroporphyrinogen-III synthase is the fourth enzyme in the heme pathway  . Mutant forms of the Uroporphyrinogen-III synthase gene cause congenital erythropoietic porphyria in humans a recessive inborn error of metabolism also known as Gunther disease  .. 
PF00173 heme_1; <br>Cytochrome b5-like Heme/Steroid binding domain. This family includes heme binding domains from a diverse range of proteins. This family also includes proteins that bind to steroids. The family includes progesterone receptors such as Swiss:O00264 [1,2]. Many members of this subfamily are membrane anchored by an N-terminal transmembrane alpha helix. This family also includes a domain in some chitin synthases.  There is no known ligand for this domain in the chitin synthases.. 
PF01814 Hemerythrin HHE cation binding domain<br>Iteration of the HHE family ( ) found it to be related to Hemerythrin. It also demonstrated that what has been described as a single domain ( ) in fact consists of two cation binding domains. Members of this family occur all across nature and are involved in a variety of processes. For instance, in Nereis diversicolor Swiss:P80255 binds Cadmium so as to protect the organism from toxicity ( ). However Hemerythrin is classically described as Oxygen-binding through two attached Fe2+ ions. And the bacterial Swiss:Q7WX96 is a regulator of response to NO, which suggests yet another set-up for its metal ligands ( ). In Staphylococcus aureus P72360 has been noted to be important when the organism switches to living in environments with low oxygen concentrations ( ); perhaps this protein acts as an oxygen store or scavenger.. 
PF00353 hemolysinCabind; <br>Hemolysin-type calcium-binding repeat (2 copies). 
PF00132 hexapep; <br>Bacterial transferase hexapeptide (six repeats). 
PF03129 Anticodon binding domain<br>This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases   it is probably the anticodon binding domain  .. 
PF03578 HGWP repeat<br>Pfam-B_220 (release 7.0). This short (30 amino acids) repeat is found in a number of plant proteins. It contains a conserved HGWP motif, hence its name. The function of these proteins is unknown.. 
PF00633 Helix-hairpin-helix motif<br>The helix-hairpin-helix DNA-binding motif is found to be duplicated in the central domain of RuvA  . The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain  .. 
PF01079 Hint module<br>Pfam-B_766 (release 3.0). This is an alignment of the Hint module in the Hedgehog proteins. It does not include any Inteins which also possess the Hint module. . 
PF01634 ATP phosphoribosyltransferase<br>Pfam-B_1142 (release 4.1). 
PF00512 signal; <br>His Kinase A (phospho-acceptor) domain. Dimerisation and phospho-acceptor domain of histidine kinases.. 
PF00850 Histone deacetylase domain<br>Pfam-B_343 (release 3.0). Histones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism.  Histone deacetylases catalyse the removal of the acetyl group. Histone deacetylases are related to other proteins  .. 
PF00010 Helix-loop-helix DNA-binding domain<br>
PF00403 Heavy-metal-associated domain<br>
PF00368 HMG-CoA_red1;<br>Hydroxymethylglutaryl-coenzyme A reductase. The HMG-CoA reductases catalyse the conversion of HMG-CoA to mevalonate, which is the rate-limiting step in the synthesis of isoprenoids like cholesterol. Probably because of the critical role of this enzyme in cholesterol homeostasis, mammalian HMG-CoA reductase is heavily regulated at the transcriptional, translational, and post-translational levels  .. 
PF02301 MAD2; <br>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 a spindle checkpoint protein which prevents progression of the cell cycle upon detection of a defect in mitotic spindle integrity.. 
PF00104 hormone_rec; <br>Ligand-binding domain of nuclear hormone receptor. This all helical domain is involved in binding the hormone in these receptors.. 
PF03241 4-hydroxyphenylacetate 3-hydroxylase C terminal<br>Pfam-B_3148 (release 6.5). HpaB Swiss:Q57160 encodes part of the 4-hydroxyphenylacetate 3-hydroxylase from Escherichia coli  . HpaB is part of a heterodimeric enzyme that also requires HpaC. The enzyme is NADH-dependent and uses FAD as the redox chromophore. This family also includes PvcC Swiss:O30372 may play a role in one of the proposed hydroxylation steps of pyoverdine chromophore biosynthesis  . . 
PF02185 Hr1 repeat<br>Alignment kindly provided by SMART. 
PF00570 HRDC domain<br>The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain cause human disease. It is interesting to note that the RecQ helicase in Deinococcus radiodurans has three tandem HRDC domains  .. 
PF03878 Hrf1; <br>YIF1 (Yip1 interacting factor) is an integral membrane protein that is required for membrane fusion of ER derived vesicles  . It also plays a role in the biogenesis of ER derived COPII transport vesicles  .. 
PF02793 Hormone receptor domain<br>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. . 
PF01381 Helix-turn-helix<br>This large family of DNA binding helix-turn helix proteins includes Cro Swiss:P03036 and CI Swiss:P03034. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteristic of the whole family  .. 
PF01402 Ribbon-helix-helix protein, copG family<br>The structure of this protein repressor, which is the shortest reported to date and the first isolated from a plasmid, has a homodimeric ribbon-helix-helix arrangement  . The helix-turn-helix-like structure is involved in dimerisation and not DNA binding as might have been expected  .. 
PF02954 Bacterial regulatory protein, Fis family<br>
PF04005 Hus1-like protein<br>Pfam-B_12502 (release 7.3). 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, and could function as a sliding clamp during checkpoint control. . 
PF03810 IBN_NT; <br>Importin-beta N-terminal domain. 
PF01485 IBR domain<br>The IBR (In Between Ring fingers) domain is often found to occur between pairs of ring fingers (Pfam:PF00097).  This domain has also been called the C6HC domain and DRIL (for double RING finger linked) domain  .  Proteins that contain two Ring fingers and an IBR domain (these proteins are also termed RBR family proteins) are thought to exist in all eukaryotic organisms.  RBR family members play roles in protein quality control and can indirectly regulate transcription  .  Evidence suggests that RBR proteins are often parts of cullin-containing ubiquitin ligase complexes.  The ubiquitin ligase Parkin is an RBR family protein whose mutations are involved in forms of familial Parkinson's disease   .. 
PF01614 Bacterial transcriptional regulator<br>Pfam-B_755 (release 4.1). 
PF04760 Translation initiation factor IF-2, N-terminal region<br>This conserved feature at the N-terminus of bacterial translation initiation factor IF2 has recently had its structure solved.  It shows structural similarity to the tRNA anticodon Stem Contact Fold domains of the methionyl-tRNA and glutaminyl-tRNA synthetases, and a similar fold is also found in the B5 domain of the phenylalanine-tRNA synthetase.. 
PF05198 Translation initiation factor IF-3, N-terminal domain<br>Pfam-B_629 (release 2.1). 
PF05004 Interferon-related developmental regulator (IFRD)<br>Pfam-B_4730 (release 7.6). Interferon-related developmental regulator (IFRD1) is the human homologue of the rat early response protein PC4 and its murine homologue TIS7  .  The exact function of IFRD1 is unknown but it has been shown that PC4 is necessary to muscle differentiation and that it might have a role in signal transduction. This family also contains IFRD2 and its murine equivalent SKMc15 which are highly expressed soon after gastrulation and in the hepatic primordium, suggesting an involvement in early hematopoiesis  .. 
PF00817 impB/mucB/samB family<br>Pfam-B_1349 (release 2.1). These proteins are involved in UV protection (Swiss).. 
PF04836 Interferon-related protein conserved region<br>Pfam-B_4453 (release 7.6). Family of proteins thought to be involved in regulating gene activity in the proliferative and/or differentiative pathways induced by NGF  .. 
PF04762 IKI3 family<br>Members of this family are components of the elongator multi-subunit component of a novel RNA polymerase II holoenzyme for transcriptional elongation  . This region contains WD40 like repeats.. 
PF00478 IMP dehydrogenase / GMP reductase domain<br>This family is involved in biosynthesis of guanosine nucleotide. Members of this family contain a TIM barrel  structure. In the inosine monophosphate dehydrogenases 2 CBS domains Pfam:PF00571 are inserted in the TIM barrel  . This family is a member of the common phosphate binding site TIM barrel family.. 
PF03941 Inner centromere protein, ARK binding region<br>Wood V, Griffiths-Jones SR. Pfam-B_67765 (release 7.2). 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 segregation with cell division in yeast.. 
PF04179 Initiator tRNA phosphoribosyl transferase <br>Pfam-B_16986 (release 7.3);. This enzyme (EC:2.4.2.-) modifies exclusively the initiator tRNA in position 64 using 5'-phosphoribosyl-1'-pyrophosphate as the  modification donor. As the initiator tRNA participates both in the  initiation and elongation of translation, the 2'-O-ribosyl phosphate  modification discriminates the initiator tRNAs from the elongator  tRNAs  .. 
PF02022 Integrase Zinc binding domain<br>Integrase mediates integration of a DNA copy of the viral genome into the host chromosome.  Integrase is composed of three domains.  This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain Pfam:PF00665. The carboxyl terminal domain is a  DNA binding domain Pfam:PF00552.. 
PF00520 ion_trans; <br>Ion transport protein. Pfam-B_33 (release 1.0). This family contains Sodium, Potassium, Calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is  repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane. A bacterial structure of the protein is known for the last two helices but is not the Pfam family due to it lacking the first four helices. 
PF03770 Inositol polyphosphate kinase <br>Pfam-B_1382 (release 7.0). ArgRIII has has been demonstrated to be an inositol polyphosphate kinase  . . 
PF00612 IQ calmodulin-binding motif<br>Ponting C, Schultz J, Bork P. Calmodulin-binding motif.. 
PF01007 Inward rectifier potassium channel<br>Pfam-B_18 (release 3.0). 
PF02174 PTB domain (IRS-1 type)<br>
PF02922 isoamylase_N; Isoamylase_N; <br>Carbohydrate-binding module 48 (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.. 
PF00857 Isochorismatase family<br>Pfam-B_566 (release 3.0). This family are hydrolase enzymes.. 
PF02373 jmjC; <br>JmjC domain, hydroxylase. The JmjC domain belongs to the Cupin superfamily  . JmjC-domain proteins may be protein hydroxylases that catalyse a novel histone modification  . This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalysing hydroxylation  .. 
PF02099 Josephin<br>
PF02214 K_tetra;<br>Pfam-B_27 (Release 5.2). In voltage-gated K+ channels this domain is responsible for subfamily-specific assembly of alpha-subunits into functional tetrameric channels  . In KCTD1 (Swiss:Q719H9) this domain functions as a transcriptional repressor  . It also mediates homomultimerisation of KCTD1 and interaction of KCTD1 with the transcription factor AP-2-alpha [2-3].. 
PF02705 K+_trans; <br>K+ potassium transporter. Pfam-B_677 (release 5.5). This is a family of K+ potassium transporters that are conserved across phyla, having both bacterial (KUP) Swiss:P30016  , yeast (HAK)  Swiss:P50505  , and plant (AtKT) Swiss:O22397   sequences as members.. 
PF01920 KE2; <br>This family includes prefoldin subunits that are not detected by Pfam:PF02996.. 
PF01344 Kelch motif<br>The kelch motif was initially discovered in Kelch (Swiss:Q04652). In this protein there are six copies of the motif.  It has been shown that Swiss:Q04652 is related to Galactose Oxidase   for which a structure has been solved  . The kelch motif forms a beta sheet.  Several of these sheets associate to form a beta propeller structure as found in Pfam:PF00064, Pfam:PF00400 and Pfam:PF00415.. 
PF00013 KH-domain; KH; <br>KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.. 
PF00109 Beta-ketoacyl synthase, N-terminal domain<br>The structure of beta-ketoacyl synthase is similar to that of the  thiolase family (Pfam:PF00108) and also chalcone synthase. The active site of beta-ketoacyl synthase is located between the N and C-terminal domains.  The N-terminal domain contains most of  the structures involved in dimer formation and also the active site  cysteine  .. 
PF02801 ketoacyl-synt_C; <br>Beta-ketoacyl synthase, C-terminal domain. The structure of beta-ketoacyl synthase is similar to that of the  thiolase family (Pfam:PF00108) and also chalcone synthase. The active site of beta-ketoacyl synthase is located between the N and C-terminal domains.. 
PF00225 kinesin; <br>Kinesin motor domain. 
PF00467 L24;Ribosomal_L24;<br>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.. 
PF01352 KRAB box<br>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 [2,3].  The KRAB domain is generally encoded by two exons.  The regions coded by the two exons are known as KRAB-A and KRAB-B. The A box plays an important role in repression by binding to corepressors, while the B box is thought to enhance this repression brought about by the A box. KRAB-containing proteins are thought to have critical functions in cell proliferation and differentiation, apoptosis and neoplastic transformation  .. 
PF05178 Krr1; <br>Pfam-B_8372 (release 7.7). The yeast member of this family (Kri1p) is found to be required for 40S ribosome biogenesis in the nucleolus  .. 
PF02735 ku; <br>Ku70/Ku80 beta-barrel domain. The Ku heterodimer (composed of Ku70 Swiss:P12956 and Ku80 Swiss:P13010) 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-binding beta-barrel domain. This domain is found in both the Ku70 Swiss:P12956 and Ku80 Swiss:P13010 proteins that form a DNA binding heterodimer  .. 
PF03730 Ku70/Ku80 C-terminal arm<br>The Ku heterodimer (composed of Ku70 Swiss:P12956 and Ku80 Swiss:P13010) 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. This alpha helical region embraces the beta-barrel domain Pfam:PF02735 of the opposite subunit  .. 
PF03731 Ku70/Ku80 N-terminal alpha/beta domain<br>The Ku heterodimer (composed of Ku70 Swiss:P12956 and Ku80 Swiss:P13010) 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 terminal alpha/beta domain. This domain only makes a small contribution to the dimer interface.  The domain comprises a six stranded beta sheet of the Rossman fold  .. 
PF00014 Kunitz/Bovine pancreatic trypsin inhibitor domain<br>Indicative of a protease inhibitor, usually a serine protease inhibitor. Structure is a disulfide rich  alpha+beta fold. BPTI (bovine pancreatic trypsin  inhibitor) is an extensively studied model structure. Certain family members are similar to the tick  anticoagulant peptide (TAP, Swiss:P17726). This is a  highly selective inhibitor of factor Xa in the blood  coagulation pathways  . TAP molecules are highly  dipolar  , and are arranged to form a twisted two- stranded antiparallel beta-sheet followed by an alpha  helix  .. 
PF03521 Kv21channel; <br>Kv2 voltage-gated K+ channel. 
PF02828 L27 domain<br>Alignment kindly provided by SMART. The L27 domain is found in receptor targeting proteins Lin-2 and Lin-7.. 
PF02448 L71 family<br>Pfam-B_1976 (release 5.4). This family of insect proteins are each about 100 amino acids long and have 6 conserved cysteine residues. They all have a predicted signal peptide and are probably excreted. The function of the proteins is unknown  .. 
PF00753 lactamase_B; <br>Metallo-beta-lactamase superfamily. 
PF02652 L-lactate permease<br>L-lactate permease is an integral membrane protein probably involved in L-lactate transport  .. 
PF03798 LAG1;<br>Pfam-B_1398 (release 7.0). 
PF03161 LAGLIDADG DNA endonuclease family<br>Pfam-B_3225 (release 6.5). This is a family of site-specific DNA endonucleases encoded by DNA mobile elements. Similar to Pfam:PF00961, the members of this family are also LAGLIDADG endonucleases.. 
PF04916 Laminin_A; <br>Pfam-B_5721 (release 7.6). Phospholipase B (PLB) catalyses the hydrolytic cleavage of both acylester bonds of glycerophospholipids.  This family of PLB enzymes has been identified in mammals, flies and nematodes but not in yeast  .  In Drosophila this protein was named LAMA for laminin ancestor since it is expressed in the neuronal and glial precursors that surround the lamina  .. 
PF04031 Las1-like <br>Pfam-B_10636 (release 7.3);. Las1 is an essential nuclear protein involved in cell  morphogenesis and cell surface growth  .. 
PF00057 ldl_recept_a;<br>Low-density lipoprotein receptor domain class A. Swissprot_feature_table. 
PF02987 LEA; <br>Late embryogenesis abundant protein. Pfam-B_106 (release 6.4). 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.. 
PF04004 Leo1-like protein<br>Pfam-B_11226 (release 7.3). Members of this family are part of the Paf1/RNA polymerase II complex [1,2]. The Paf1 complex probably functions during the elongation phase of transcription  . The Leo1 subunit of the yeast Paf1-complex binds RNA and contributes to complex recruitment. The subunit acts by co-ordinating co-transcriptional chromain modifications and helping recruitment of mRNA 3prime-end processing factors  .. 
PF00060 lig_chan; <br>Ligand-gated ion channel. This family includes the four transmembrane regions of the ionotropic glutamate receptors and NMDA receptors.. 
PF02900 Catalytic LigB subunit of aromatic ring-opening dioxygenase<br>
PF03893 Lipase 3 N-terminal region<br>N terminal region to Pfam:PF01764, found on a subset of Lipase 3 containing proteins. . 
PF01764 Lipase (class 3)<br>Pfam-B_893 (release 4.2). 
PF04571 lipin_N; <br>lipin, N-terminal conserved region. Pfam-B_4929 (release 7.5). Mutations in the lipin gene lead to fatty liver dystrophy in mice.  The protein has been shown to be phosphorylated by the TOR Ser/Thr protein kinases in response to insulin stimulation. The conserved region is found at the N-terminus of the member proteins [1,2].. 
PF03180 NLPA lipoprotein<br>Pfam-B_1418 (release 6.5). This family of bacterial lipoproteins contains several antigenic members, that may be involved in bacterial virulence. Their precise function is unknown. However they are probably distantly related to Pfam:PF00497 which are solute binding proteins.. 
PF02190 ATP-dependent protease La (LON) domain<br>Alignment kindly provided by SMART. This domain has been shown to be part of the PUA superfamily  .. 
PF00560 LRR; <br>CAUTION: This Pfam may not find all Leucine Rich Repeats in a protein.  Leucine Rich Repeats are short sequence motifs present in a number of proteins with diverse functions and cellular locations.  These repeats are usually involved in protein-protein interactions. Each Leucine Rich Repeat is composed of a beta-alpha unit. These units form elongated non-globular structures. Leucine Rich Repeats are often flanked by cysteine rich domains.. 
PF01463 Leucine rich repeat C-terminal domain<br>Leucine Rich Repeats Pfam:PF00560 are short sequence motifs present in a number of proteins with diverse functions and cellular locations. Leucine Rich Repeats are often flanked by cysteine rich domains. This domain is often found at the C-terminus of tandem leucine rich repeats.. 
PF04180 Low temperature viability protein <br>Pfam-B_15065 (release 7.3);. The low-temperature viability protein LTV1 is involved in ribosome  biogenesis 40S subunit production  .. 
PF02123 Viral RNA-directed RNA-polymerase<br>IPR001795 & Pfam-B_6212 (release 8.0) & Pfam-B_9867 (release 8.0). This family includes RNA-dependent RNA polymerase proteins  (RdRPs) from Luteovirus, Totivirus and Rotavirus.. 
PF01476 PG_binding_2; <br>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  .. 
PF03466 LysR substrate binding domain<br>The structure of this domain is known and is similar to the periplasmic binding proteins  .. 
PF03816 Cell envelope-related transcriptional attenuator domain<br>TIGRFAMs, Griffiths-Jones SR. 
PF02847 MA3 domain<br>Alignment kindly provided by SMART. Domain in DAP-5, eIF4G, MA-3 and other proteins.  Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains  .. 
PF01454 MAGE family<br>Prodom_3141 (release 99.1). The MAGE (melanoma antigen-encoding gene) family are expressed in a wide variety of tumours but not in normal cells, with the exception of the male germ cells, placenta, and, possibly, cells of the developing embryo. The cellular function of this family is unknown.  This family also contains the yeast protein, Nse3.  The Nse3 protein is part of the Smc5-6 complex [2-3]. Nse3 has been demonstrated to be important for meiosis .. 
PF00390 Malic enzyme, N-terminal domain<br>
PF03949 malic_N; <br>Malic enzyme, NAD binding domain. 
PF00629 MAM domain<br>An extracellular domain found in many receptors.. 
PF03999 Microtubule associated protein (MAP65/ASE1 family)<br>Pfam-B_12512 (release 7.3). 
PF00917 MATH domain<br>Pfam-B_1602 (release 3.0). This motif has been called the Meprin And TRAF-Homology (MATH) domain. This domain is hugely expanded in the nematode C. elegans  .. 
PF01429 Methyl-CpG binding domain<br>The Methyl-CpG binding domain (MBD) binds to DNA that contains one or more symmetrically methylated CpGs  .  DNA methylation in animals is associated with alterations in chromatin structure and silencing of gene expression. MBD has negligible non-specific affinity for DNA. In vitro foot-printing with MeCP2 showed the MBD can protect a 12 nucleotide region surrounding a methyl CpG pair  . MBDs are found in several Methyl-CpG binding proteins and also DNA demethylase  .. 
PF03062 MBOAT, membrane-bound O-acyltransferase family<br>Pfam-B_2359 (release 6.4). 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  .. 
PF02820 mbt;<br>Pfam-B_526 (Release 6.2). The function of this repeat is unknown, but is found in a number of nuclear proteins such as drosophila sex comb on midleg protein Swiss:Q9VHA0. The repeat is found in up to four copies as in Swiss:Q9UHJ3. The repeat contains a completely conserved glutamate at its amino terminus that may be important for function.. 
PF02470 mce; <br>Pfam-B_475 (release 5.4). This family of proteins contains the mce (mammalian cell entry) proteins from Mycobacterium tuberculosis. The archetype (Rv0169), was isolated as being necessary for colonisation of, and survival within, the macrophage  . This family contains proteins of  unknown function from other bacteria.. 
PF05053 Menin<br>Pfam-B_5848 (release 7.7). MEN1, the gene responsible for multiple endocrine neoplasia type 1, is a tumour suppressor gene that encodes a protein called Menin which may be an atypical GTPase stimulated by nm23 .. 
PF00149 STphosphatase; <br>Calcineurin-like phosphoesterase. This family includes a diverse range of phosphoesterases  , including protein phosphoserine phosphatases, nucleotidases, sphingomyelin phosphodiesterases and 2'-3' cAMP phosphodiesterases as well as nucleases such as bacterial SbcD Swiss:P13457 or yeast MRE11 Swiss:P32829. The most conserved regions in this superfamily centre around the metal chelating residues.. 
PF01420 Type I restriction modification DNA specificity domain<br>This domain is also known as the target recognition domain (TRD). Restriction-modification (R-M) systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification.  The host genome is protected from cleavage by methylation of specific nucleotides in the target sites.  In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity subunit (this family), two modification (M) subunits and two restriction (R) subunits  .. 
PF01795 DUF36; UPF0117;<br>MraW methylase family. Pfam-B_1376 (release 4.2). Members of this family are probably SAM dependent methyltransferases based on Swiss:P18595  . This family appears to be related to Pfam:PF01596.. 
PF05060 N-acetylglucosaminyltransferase II (MGAT2)<br>Pfam-B_6001 (release 7.7). UDP-N-acetyl-D-glucosamine:alpha-6-D-mannoside beta-1,2-N- acetylglucosaminyltransferase II (EC 2.4.1.143) (GnT II/MGAT2) is a Golgi resident enzyme that catalyses an essential step in the biosynthetic pathway leading from high mannose to complex N-linked oligosaccharides  . Mutations in the MGAT2 gene lead to congenital disorder of glycosylation (CDG IIa). CDG IIa patients have an increased bleeding tendency,  unrelated to coagulation factors  .. 
PF02142 Methylglyoxal_synth; <br>Pfam-B_220 (Release 4.4). This domain composes the whole protein of methylglyoxal synthetase and the domain is also found in Carbamoyl phosphate synthetase (CPS) where it forms a regulatory domain that binds to the  allosteric effector ornithine. This family also includes inosicase. The known structures in this family show a common phosphate binding site  .. 
PF01769 Divalent cation transporter<br>
PF00993 Class II histocompatibility antigen, alpha domain<br>Pfam-B_1288 (release 3.0). 
PF00969 Class II histocompatibility antigen, beta domain<br>Pfam-B_331 (release 3.0). 
PF02816 MHCK_EF2_kinase;<br>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 [1,2] and Elongation Factor-2 kinase and a bifunctional ion channel  . This family is known as the alpha-kinase family  . The structure of the kinase domain   revealed unexpected similarity to eukaryotic protein kinases in the catalytic core as well as to metabolic enzymes with ATP-grasp domains.. 
PF02854 MIF4G domain<br>Alignment kindly provided by SMART. 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 and DNA  .. 
PF02815 MIR domain<br>Ponting CP (EMBL archive). The MIR (protein mannosyltransferase, IP3R and RyR) domain is a domain that may have a ligand transferase function  .. 
PF04212 MIT (microtubule interacting and transport) domain<br>The MIT domain forms an asymmetric three-helix bundle   and binds ESCRT-III (endosomal sorting complexes required for transport) substrates  .. 
PF00153 mito_carr;<br>Mitochondrial carrier protein. 
PF03637 Mob1/phocein family<br>Pfam-B_1830 (release 7.0). 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 structural motifs; however MOB1 is a member of a conserved gene family and shares sequence similarity with a nonessential yeast gene, MOB2. Mob1 is a phosphoprotein in vivo and a substrate for the Mps1p kinase in vitro. Conditional alleles of MOB1 cause a late nuclear division arrest at restrictive temperature  . This family also includes phocein Swiss:Q9QYW3, a rat protein that by yeast two hybrid interacts with striatin  .. 
PF00994 Probable molybdopterin binding domain<br>Pfam-B_1258 (release 3.0). This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor. The domain is presumed to bind molybdopterin. The structure of this domain is known, and it forms an alpha/beta structure. In the known structure of Gephyrin this domain mediates trimerisation  .. 
PF03454 MoeA C-terminal region (domain IV)<br>This domain is found in  proteins involved in biosynthesis of molybdopterin cofactor however the exact molecular function of this domain is uncertain. The structure of this domain is known   and forms an incomplete beta barrel.. 
PF03453 MoeA N-terminal region (domain I and II)<br>This family contains two structural domains. One of these contains the conserved DGXA motif. This region is found in proteins involved in biosynthesis of molybdopterin cofactor however the exact molecular function of this region is uncertain.. 
PF02493 MORN repeat<br>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;6:11-22).\. A MORN-repeat protein has been identified in the parasite Toxoplasma gondiis a dynamic component of cell division apparatus in Toxoplasma gondii  .  It has been hypothesised to functions as a linker protein between certain membrane regions and the parasite's cytoskeleton  .. 
PF03476 MOSC N-terminal beta barrel domain<br>Aravind L, Anantharaman V. This domain is found to the N-terminus of Pfam:PF03473. The function of this domain is unknown, however it is predicted to adopt a beta barrel fold.. 
PF04643 motilin_assoc; <br>Motilin/ghrelin-associated peptide. Pfam-B_5485 (release 7.5). This family represents a peptide sequence that lies C-terminal to motilin/ghrelin on the respective precursor peptide. Its function is unknown.. 
PF04644 motilin_ghrelin; <br>Pfam-B_5485 (release 7.5). Motilin is a gastrointestinal regulatory polypeptide produced by motilin cells in the duodenal epithelium. It is released into the general circulation at about 100-min intervals during the inter-digestive state and is the most important factor in controlling the inter-digestive migrating contractions. Motilin also stimulates endogenous release of the endocrine pancreas  . This family also includes ghrelin, a growth hormone secretagogue synthesised by endocrine cells in the stomach. Ghrelin stimulates growth hormone secretagogue receptors in the pituitary. These receptors are distinct from the growth hormone-releasing hormone receptors, and thus provide a means of controlling pituitary growth hormone release by the gastrointestinal system  .. 
PF01398 Mov34; JAMM;<br>JAB1/Mov34/MPN/PAD-1 ubiquitin protease. Pfam-B_738 (release 3.0). Members of this family are found in proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. This family is also known as the MPN domain   and PAD-1-like domain  , JABP1 domain   or JAMM domain  .  These are metalloenzymes that function as the ubiquitin isopeptidase/ deubiquitinase in the ubiquitin-based signaling and protein turnover pathways in eukaryotes  . Versions of the domain in prokaryotic  cognates of the ubiquitin-modification pathway are predicted to have  a similar role  . . 
PF01853 MOZ/SAS family<br>Pfam-B_3994 (Release 4.3). This region of these proteins has been suggested to be homologous to acetyltransferases  .. 
PF04117 Mpv17 / PMP22 family <br>Pfam-B_8493 (release 7.3);. 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 synthesised on free cytosolic ribosomes and then directed to the peroxisome membrane by specific targeting information  . Mpv17 is a closely related peroxisomal protein. In mouse, the Mpv17 protein is involved in the development of early-onset glomerulosclerosis  .  More recently a homolog of Mpv17 in S. cerevisiae has been been found to be an integral membrane protein of the inner mitochondrial membrane where it has been proposed to have a role in ethanol metabolism and tolerance during heat-shock  . Defects in MPV17 is associated with mitochondrial DNA depletion syndrome (MDDS) and Navajo neurohepatopathy (NNH)   .  MDDS is a clinically heterogeneous group of disorders characterised by a reduction in mitochondrial DNA (mtDNA) copy number. Primary mtDNA depletion is inherited as an autosomal recessive trait and may affect single organs, typically muscle or liver, or multiple tissues.  Individuals with the hepatocerebral form of mitochondrial DNA depletion syndrome have early progressive liver failure and neurologic abnormalities, hypoglycemia, and increased lactate in body fluids.  NNH is an autosomal recessive disease that is prevalent among Navajo children in the South Western states of America.  The major clinical features are hepatopathy, peripheral neuropathy, corneal anesthesia and scarring, acral mutilation, cerebral leukoencephalopathy, failure to thrive, and recurrent metabolic acidosis with intercurrent infections. Infantile, childhood, and classic forms of NNH have been described. Mitochondrial DNA depletion was detected in the livers of patients, suggesting a primary defect in mtDNA maintenance  .. 
PF03587 Mra1; Nep1; <br>EMG1/NEP1 methyltransferase. Pfam-B_3290 (release 7.0). Members of this family are essential for 40S ribosomal biogenesis.  The structure of EMG1 has revealed that it is a novel member of the superfamily of alpha/beta knot fold methyltransferases  .. 
PF03022 Major royal jelly protein<br>Pfam-B_1099 (release 6.4). 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 protein of drosophila  which controls pigmentation of the adult cuticle and larval mouth  parts.. 
PF04707 MSF1; <br>Pfam-B_5792 (release 7.5). This family includes a conserved region found in the PRELI protein and yeast YLR168C gene MSF1 product. The function of this protein is unknown, though it is thought to be involved in intra-mitochondrial protein sorting. This region is also found in a number of other eukaryotic proteins.. 
PF00635 MSP_domain; <br>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.. 
PF03820 Tricarboxylate carrier<br>TIGRFAMs, Griffiths-Jones SR. 
PF00249 myb_DNA-binding; <br>Myb-like DNA-binding domain. This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family  .. 
PF02736 Myosin N-terminal SH3-like domain<br>Pfam-B_110 (Release 5.5). 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.. 
PF00784 MyTH4 domain<br>Alignment kindly provided by SMART. Domain in myosin and kinesin tails, present twice in myosin-VIIa, and also present in 3 other myosins.. 
PF03485 N-Arg; <br>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 recognition  .. 
PF01699 Na_Ca_Ex; <br>Sodium/calcium exchanger protein. Pfam-B_1680 (release 4.1). This is a family of sodium/calcium exchanger integral membrane proteins. This family covers the integral membrane regions of the proteins. Sodium/calcium exchangers regulate intracellular Ca2+ concentrations in many cells; cardiac myocytes, epithelial cells, neurons retinal rod photoreceptors and smooth muscle cells  . Ca2+ is moved into or out of the cytosol depending on Na+ concentration  .  In humans and rats there are 3 isoforms; NCX1 NCX2 and NCX3   see Swiss:Q01728, Swiss:P48768 and Swiss:P70549 respectively.. 
PF00999 Sodium/hydrogen exchanger family<br>Pfam-B_312 (release 3.0). Na/H antiporters are key transporters in maintaining the pH of actively metabolising cells. The molecular mechanisms of antiport are unclear. These antiporters contain 10-12 transmembrane regions (M) at the amino-terminus and a large cytoplasmic region at the carboxyl terminus.\. The transmembrane regions M3-M12 share identity with other members of the family.  The M6 and M7 regions are highly conserved. Thus, this is thought to be the region that is involved in the transport of sodium and hydrogen ions.  The cytoplasmic region has little similarity throughout the family.. 
PF02690 Na+/Pi-cotransporter<br>Pfam-B_509 (release 5.5). 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-cotransporters protein allows re-absorption of filtered Pi in the  proximal tubule  .. 
PF02445 Quinolinate synthetase A protein<br>Pfam-B_1915 (release 5.4). Quinolinate synthetase catalyses the second step of the de novo biosynthetic pathway of pyridine nucleotide formation. In particular, quinolinate synthetase is involved in the condensation of dihydroxyacetone phosphate and iminoaspartate to form quinolinic acid  . This synthesis requires two enzymes, a FAD-containing "B protein" and an "A protein".. 
PF03822 NAF domain<br>
PF05089 Alpha-N-acetylglucosaminidase (NAGLU) tim-barrel domain<br>Pfam-B_6295 (release 7.7). Alpha-N-acetylglucosaminidase, a lysosomal enzyme required for the stepwise degradation of heparan sulfate  . Mutations on the alpha-N-acetylglucosaminidase (NAGLU) gene can lead to Mucopolysaccharidosis type IIIB (MPS IIIB; or Sanfilippo syndrome type B) characterised by neurological dysfunction but relatively mild somatic manifestations  . The structure shows that the enzyme is composed of three domains.  This central domain has a tim barrel fold  .. 
PF02365 No apical meristem (NAM) protein<br>Pfam-B_530 (release 5.2). This is a family of no apical meristem (NAM) proteins these are plant development proteins.  Mutations in NAM result in the failure to develop a shoot apical meristem in petunia embryos  .  NAM is indicated as having a role in determining positions of meristems and primordial  . One member of this family NAP (NAC-like, activated by AP3/PI) is encoded by the target genes of the AP3/PI transcriptional activators and functions in the transition between growth by cell division and cell expansion in stamens and petals  .. 
PF04095 Nicotinate phosphoribosyltransferase (NAPRTase) family<br>Pfam-B_5038 (release 7.3) & Pfam-B_5422 (Release 7.5). Nicotinate phosphoribosyltransferase (EC:2.4.2.11) is the rate limiting enzyme that catalyses the first reaction in  the NAD salvage synthesis. This family also includes Pre-B cell enhancing factor that is a cytokine Swiss:P43490. This family is related to Quinolinate phosphoribosyltransferase Pfam:PF01729.. 
PF04970 NC;<br>Lecithin retinol acyltransferase. Pfam-B_3758 (release 7.0). The full-length members of this family, eg Swiss:P53816, are representatives of a novel class II tumour-suppressor family, designated as H-REV107-like. This domain is the catalytic N-terminal proline-rich region of the protein. The downstream region is a putative C-terminal transmembrane domain which is found to be crucial for cellular localisation, but not necessary for the enzyme activity  .  H-REV107-like proteins are homologous to lecithin retinol acyltransferase (LRAT), an enzyme that catalyses the transfer of the sn-1 acyl group of phosphatidylcholine to all-trans-retinol and forming a retinyl ester  .. 
PF04904 NAB conserved region 1 (NCD1)<br>Pfam-B_6188 (release 7.6). Nab1 and Nab2 are co-repressors that specifically interact with and repress transcription mediated by the three members of the NGFI-A (Egr-1, Krox24, zif/268) family of transcription  factors  . This region consists of the N-terminal NAB conserved region 1, which  interacts with the EGR1 inhibitory domain (R1)  .  It may also mediate multimerisation.. 
PF04905 NAB conserved region 2 (NCD2)<br>Pfam-B_6188 (release 7.6). Nab1 and Nab2 are co-repressors that specifically interact with and repress transcription mediated by the three members of the NGFI-A (Egr-1, Krox24, zif/268) family of transcription  factors  . This family consists of NAB conserved region 2, near the C-terminus of the protein.  It is necessary for transcriptional repression by the Nab  proteins  .  It is also required for transcription activation by Nab  proteins at Nab-activated promoters  .. 
PF03096 Ndr family<br>Pfam-B_2481 (release 6.4). 
PF03102 NeuB family<br>Pfam-B_2572 (release 6.4). 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 been observed in prokaryotes; eukaryotes synthesise the 9-phosphate form, Neu5Ac-9-P, and utilise ManNAc-6-P instead of ManNAc. Such eukaryotic enzymes are not present in this family  . This family also contains SpsE spore coat polysaccharide biosynthesis proteins.. 
PF02931 Neurotransmitter-gated ion-channel ligand binding domain<br>This family is the extracellular ligand binding domain of these ion channels  .  This domain forms a pentameric arrangement in the known structure.. 
PF01436 NHL repeat<br>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 Pfam:PF00400.  The repeats have a catalytic activity in Swiss:P10731, proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats  . Swiss:Q13049 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats  .. 
PF03031 NLI interacting factor-like phosphatase<br>Pfam-B_1405 (release 6.4). This family contains a number of NLI interacting factor isoforms (eg. Swiss:Q9PTJ8) and also an N-terminal regions of RNA polymerase II CTC phosphatase (Swiss:Q9Y5BO) and FCP1 serine phosphatase (Swiss:Q9PT70). This region has been identified as the minimal phosphatase domain  .. 
PF04923 Ninjurin <br>Pfam-B_5824 (release 7.6). Ninjurin (nerve injury-induced protein) is involved in nerve regeneration and in the formation and function in some tissues  .. 
PF02613 Nitrate reductase delta subunit<br>This family is the delta subunit of the nitrate reductase enzyme, The delta subunit is not part of the nitrate reductase enzyme but is most likely needed for assembly of the multi-subunit enzyme complex  .  In the absence of the delta subunit the core alpha beta enzyme complex is unstable  .  The delta subunit is essential for enzyme activity in vivo and in vitro  .  The nitrate reductase enzyme, EC:1.7.99.4 catalyse the conversion of nitrite to nitrate via the reduction of an acceptor.\.    The nitrate reductase enzyme is composed of three subunits  .\.    Nitrate is the most widely used alternative electron acceptor after oxygen  . This family also now contains the family TorD, a family of cytoplasmic chaperone proteins; like many prokaryotic molybdoenzymes, the TMAO reductase (TorA) of Escherichia coli requires the insertion of a bis(molybdopterin guanine dinucleotide) molybdenum (bis(MGD)Mo) cofactor in its catalytic site to be active and translocated to the periplasm. The TorD chaperone increases apoTorA activation up to four-fold, allowing maturation of most of the apoprotein.   Therefore TorD is involved in the first step of TorA maturation to make it competent to receive the cofactor  .. 
PF00877 NlpC/P60 family<br>Pfam-B_292 (release 3.0) & Pfam-B_9022 (Release 8.0). The function of this domain is unknown. It is found in several lipoproteins.. 
PF04981 NMD3 family <br>The NMD3 protein is involved in nonsense mediated mRNA decay. This amino terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway  .. 
PF01234 NNMT/PNMT/TEMT family<br>
PF04147 Nop14-like family <br>Pfam-B_8521 (release 7.3);. Emg1 and Nop14 are novel proteins whose interaction is  required for the maturation of the 18S rRNA and for 40S  ribosome production  .. 
PF04153 NOT; <br>NOT2 / NOT3 / NOT5 family. Pfam-B_2131 (release 7.3). 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.. 
PF04065 Not1 N-terminal domain, CCR4-Not complex component <br>Pfam-B_8081 (release 7.3);. 
PF03060 NPD;<br>Nitronate monooxygenase. Pfam-B_2634 (release 6.4). Nitronate monooxygenase (NMO), formerly referred to as 2-nitropropane dioxygenase (NPD) (EC:1.13.11.32), is an FMN-dependent enzyme that uses molecular oxygen to oxidize (anionic) alkyl nitronates and, in the case of the enzyme from Neurospora crassa, (neutral) nitroalkanes to the corresponding carbonyl compounds and nitrite. Previously classified as 2-nitropropane dioxygenase [1,2,3], but it is now recognized that this was the result of the slow ionization of nitroalkanes to their nitronate (anionic) forms  . The enzymes from the fungus Neurospora crassa and the yeast Williopsis saturnus var. mrakii (formerly classified as Hansenula mrakii) contain non-covalently bound FMN as the cofactor. Active towards linear alkyl nitronates of lengths between 2 and 6 carbon atoms and, with lower activity, towards propyl-2-nitronate. The enzyme from N. crassa can also utilize neutral nitroalkanes, but with lower activity. One atom of oxygen is incorporated into the carbonyl group of the aldehyde product. The reaction appears to involve the formation of an enzyme-bound nitronate radical and an a-peroxynitroethane species, which then decomposes, either in the active site of the enzyme or after release, to acetaldehyde and nitrite.. 
PF05021 NPL4 family<br>Pfam-B_13681 (release 7.6). The HRD4 gene was identical to NPL4, a gene previously implicated in nuclear transport. Using a diverse set of substrates and direct ubiquitination assays, analysis revealed that HRD4/NPL4 is required for a poorly characterised step in ER-associated degradation after ubiquitination of target proteins but before their recognition by the 26S proteasome  . Npl4p physically associates with Cdc48p via Ufd1p to form a Cdc48p-Ufd1p-Npl4p complex. The Cdc48-Ufd1-Npl4 complex functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation or even more specific processing.. 
PF01909 DUF76;<br>Nucleotidyltransferase domain. Members of this family belong to a large family of nucleotidyltransferases  . This family includes kanamycin nucleotidyltransferase (KNTase) which is a plasmid-coded enzyme responsible for some types of bacterial resistance to aminoglycosides. KNTase in-activates antibiotics by catalysing the addition of a nucleotidyl group onto the drug.. 
PF01759 UNC-6/NTR/C345C module<br>Sequence similarity between netrin UNC-6 and C345C complement protein family members, and hence the existence of the UNC-6 module, was first reported in  . Subsequently, many additional members of the family were identified on the basis of sequence similarity between the C-terminal domains of netrins, complement proteins C3, C4, C5, secreted frizzled-related proteins, and type I pro-collagen C-proteinase enhancer proteins (PCOLCEs), which are homologous with the N-terminal domains of tissue inhibitors of metalloproteinases (TIMPs).  The TIMPs are classified as a separate family in Pfam (Pfam:PF00965)  . This expanded domain family has been named as the NTR module  .. 
PF04142 Nucleotide-sugar transporter<br>Pfam-B_2311 (release 7.3). This family of membrane proteins transport nucleotide sugars from the cytoplasm into golgi vesicles.  Swiss:P78382 transports CMP-sialic acid, Swiss:P78381 transports UDP-galactose and Swiss:Q9Y2D2 transports UDP-GlcNAc.. 
PF04096 Nucleoporin autopeptidase<br>Pfam-B_5132 (release 7.3);. 
PF01733 Nucleoside transporter<br>Pfam-B_2135 (release 4.1). 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 own de novo synthesis pathways  . Also in this family is mouse and human nucleolar protein HNP36 Swiss:Q14542 a protein of unknown function; although it has been hypothesised to be a plasma membrane nucleoside transporter  .. 
PF04880 NUDE protein, C-terminal conserved region<br>Pfam-B_6501 (release 7.6). This family represents the C-terminal conserved region of the NUDE proteins. NUDE proteins are involved in nuclear migration  .. 
PF00293 mutT; <br>
PF03826 OAR domain<br>
PF03137 OATP_C;<br>Organic Anion Transporter Polypeptide (OATP) family. Pfam-B_626 (release 6.5). 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 and substrate specificity. Since the numbering of different OATPs in particular species was based originally on the order of discovery, similarly numbered OATPs in humans and rats did not necessarily correspond in function, tissue distribution and substrate specificity (in spite of the name, some OATPs also transport organic cations and neutral molecules). Thus, Tamai et al.   initiated the current scheme of using digits for rat OATPs and letters for human ones. Prostaglandin transporter (PGT) proteins (e.g. Swiss:Q92959) are also considered to be OATP family members. In addition, the methotrexate transporter OATK (Swiss:P70502) is closely related to OATPs. This family also includes several predicted proteins from Caenorhabditis elegans and Drosophila melanogaster. This similarity was not previously noted.  Note: Members of this family are described (in the Swiss-Prot database) as belonging to the SLC21 family of transporters.. 
PF05005 Janus/Ocnus family (Ocnus)<br>Pfam-B_4799 (release 7.6). This family is comprised of the Ocnus, Janus-A and Janus-B proteins. These proteins have been found to be testes specific in Drosophila melanogaster  . . 
PF00215 Orotidine 5'-phosphate decarboxylase / HUMPS family<br>This family includes Orotidine 5'-phosphate decarboxylase enzymes EC:4.1.1.23 that are involved in the final step of pyrimidine biosynthesis. The family also includes enzymes such as hexulose-6-phosphate synthase. This family appears to be distantly related to Pfam:PF00834.. 
PF04084 Origin recognition complex subunit 2 <br>Pfam-B_7065 (release 7.3);. 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  . . 
PF03392 Insect pheromone-binding family, A10/OS-D<br>Pfam-B_3032 (release 6.6). 
PF04756 OST3 / OST6 family<br>The proteins in this family are part of a complex of eight ER proteins that transfers core oligosaccharide from dolichol carrier to Asn-X-Ser/Thr motifs  . This family includes both OST3 and OST6, each of which contains four predicted transmembrane helices. Disruption of OST3 and OST6 leads to a defect in the assembly of the complex. Hence, the function of these genes seems to be essential for recruiting a fully active complex necessary for efficient N-glycosylation  .. 
PF01010 oxidored_q1_C; <br>NADH-Ubiquinone oxidoreductase (complex I) subunit C-terminus. Pfam-B_41 (release 3.0). This sub-family represents a carboxyl terminal extension of Pfam:PF00361. It includes subunit 5 from chloroplasts, and bacterial subunit L.  This sub-family is part of complex I which catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane.. 
PF01483 P; <br>Proprotein convertase P-domain. A unique feature of the eukaryotic subtilisin-like proprotein convertases is the presence of an additional highly conserved sequence of approximately 150 residues (P domain) located immediately downstream of the catalytic domain.. 
PF04062 ARP2/3 complex ARPC3 (21 kDa) subunit<br>Pfam-B_6413 (release 7.3);. The seven component ARP2/3 actin-organising complex is involved in actin assembly and function.. 
PF02331 Apoptosis preventing protein<br>Pfam-B_13247 (release 5.2). This viral protein functions to block the host apoptotic response  caused by infection by the virus. The apoptosis preventing protein (or early 35kD protein, P35) acts by blocking caspase protease  activity.. 
PF02225 PA domain<br>Pfam-B_259 (release 5.2). 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 Swiss:O22925 and members of the RZF family Swiss:O43567. It has been suggested that this domain forms a lid-like structure that covers the active site in active proteases, and is involved in protein recognition in vacuolar sorting receptors  .. 
PF00291 S_T_dehydratase; <br>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 Swiss:P04968, tryptophan synthase beta chain EC:4.2.1.20 Swiss:P00932, threonine synthase EC:4.2.99.2 Swiss:P04990, cysteine synthase EC:4.2.99.8 P11096, cystathionine beta-synthase EC:4.2.1.22 Swiss:P35520, 1-aminocyclopropane-1-carboxylate deaminase EC:4.1.99.4 Swiss:P76316.. 
PF00024 apple; Apple;PAN; <br>The PAN domain   contains a conserved core of three disulphide bridges.  In some members of the family there is an additional fourth disulphide bridge the links the N and C termini of the domain. The domain is found in diverse proteins, in some they mediate protein-protein interactions, in others they mediate protein-carbohydrate interactions.. 
PF01569 PAP2 superfamily<br>Pfam-B_486 (release 4.0). This family includes the enzyme type 2 phosphatidic acid phosphatase (PAP2), Glucose-6-phosphatase EC:3.1.3.9, Phosphatidylglycerophosphatase B EC:3.1.3.27 and bacterial acid phosphatase EC:3.1.3.2. The family also includes a variety of haloperoxidases [1,2] that function by oxidising halides in the presence of hydrogen peroxide to form the corresponding hypohalous acids.. 
PF03828 Cid1 family poly A polymerase<br>Griffiths-Jones SR, Wood V, Mistry J. This domain is found in poly(A) polymerases and has been shown to have polynucleotide adenylyltransferase activity     . Proteins in this family have been located to both the nucleus and the cytoplasm.. 
PF04928 Poly(A) polymerase central domain<br>Pfam-B_1341 (release 7.6). The central domain of Poly(A) polymerase shares structural similarity with the allosteric activity domain of ribonucleotide reductase R1, which comprises a four-helix bundle and a three-stranded mixed beta- sheet. Even though the two enzymes bind ATP, the ATP-recognition motifs are different.. 
PF05028 PARG; <br>Poly (ADP-ribose) glycohydrolase (PARG). Pfam-B_5996 (release 7.6). Poly(ADP-ribose) glycohydrolase (PARG), is a ubiquitously expressed exo-  and endoglycohydrolase which mediates oxidative and excitotoxic neuronal death  .. 
PF01734 Patatin-like phospholipase<br>Pfam-B_2206 (release 4.1). This family consists of various patatin glycoproteins from plants. The patatin protein accounts for up to 40% of  the total soluble protein in potato tubers  . Patatin is a storage protein but it also has the enzymatic activity of lipid acyl hydrolase, catalysing the cleavage of fatty acids from membrane lipids  . Members of this family have been found also in vertebrates.. 
PF02460 Patched family<br>Pfam-B_2400 (release 5.4). The transmembrane protein Patched Swiss:P18502 is a receptor for the morphogene Sonic Hedgehog. This protein associates with the smoothened protein to transduce hedgehog signals.. 
PF02170 ZAP;<br>This domain is named PAZ after the proteins Piwi  Argonaut and Zwille. This domain is found in two families of proteins that are involved in post-transcriptional gene silencing. These are the Piwi family and the Dicer family, that includes the Carpel factory protein. The function of the domains is unknown but has been suggested to mediate complex formation between proteins of the Piwi and Dicer families by hetero-dimerisation. The three-dimensional structure of this domain has been solved [2-4]. The PAZ domain is composed of two subdomains. One subdomain is similar to the OB fold, albeit with a different topology. The OB-fold is well known as a single-stranded nucleic acid binding fold. The second subdomain is composed of a beta-hairpin followed by an alpha-helix. The PAZ domains shows low-affinity nucleic acid binding and appears to interact with the 3' ends of single-stranded regions of RNA in the cleft between the two subdomains. PAZ can bind the characteristic two-base 3' overhangs of siRNAs, indicating that although PAZ may not be a primary nucleic acid binding site in Dicer or RISC, it may contribute to the specific and productive incorporation of siRNAs and miRNAs into the RNAi pathway.. 
PF00564 OPR;<br>Alignment kindly provided by SMART. 
PF00786 P21-Rho-binding domain<br>Alignment kindly provided by SMART. Small domains that bind Cdc42p- and/or Rho-like small GTPases. Also known as the Cdc42/Rac interactive binding (CRIB).. 
PF01161 Phosphatidylethanolamine-binding protein<br>Prosite & Pfam-B_5394 (Release 7.5). 
PF01399 PCI domain<br>This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15)  .. 
PF03462 PCRF domain<br>This domain is found in peptide chain release factors.. 
PF02153 Prephenate dehydrogenase<br>PSI-BLAST P20692/1-290. Members of this family are prephenate dehydrogenases EC:1.3.1.12 involved in tyrosine biosynthesis.. 
PF04166 Pyridoxal phosphate biosynthetic protein PdxA<br>TIGRFAMs (release 2.0);. In Escherichia coli the coenzyme pyridoxal 5'-phosphate is synthesised  de novo by a pathway that is thought to involve the condensation of 4-(phosphohydroxy)-L-threonine and 1-deoxy-D-xylulose, catalysed by  the enzymes PdxA and PdxJ, to form either pyridoxine (vitamin B6) or pyridoxine 5'-phosphate  .. 
PF00934 PE family<br>Pfam-B_253 (release 3.0). This family named after a PE motif near to the amino terminus of the domain.  The PE family of proteins all contain an amino-terminal region of about 110 amino acids.  The carboxyl terminus of this family are variable and fall into several classes.  The largest class of PE proteins is the highly repetitive PGRS class which have a high glycine content. The function of these proteins is uncertain but it has been suggested that they may be related to antigenic variation of Mycobacterium tuberculosis  .. 
PF01095 Pectinesterase<br>
PF04710 Pellino<br>Pfam-B_5882 (release 7.5). Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase [1,2,3].. 
PF02452 PemK-like protein<br>Pfam-B_2134 (release 5.4). PemK is a growth inhibitor in E. coli known to bind to the promoter  region of the Pem operon, auto-regulating synthesis. This Pfam family consists of the PemK protein in addition to ChpA, ChpB and other PemK-like proteins. . 
PF01804 Penicillin amidase<br>Pfam-B_1410 (release 4.2). Penicillin amidase or penicillin acylase EC:3.5.1.11 catalyses the hydrolysis of benzylpenicillin to phenylacetic acid and 6-aminopenicillanic acid (6-APA) a key intermediate in the the synthesis of penicillins  . Also in the family is cephalosporin acylase Swiss:P07662 and  Swiss:P29958 aculeacin A acylase which are involved in the synthesis of related peptide antibiotics.. 
PF01469 Pentapeptide repeats (8 copies)<br>These repeats are found in many mycobacterial proteins.  These repeats are most common in the Pfam:PF00823 family of proteins, where they are found in the MPTR subfamily of PPE proteins. The function of these repeats is unknown. The repeat can be approximately described as XNXGX, where X can be any amino acid. These repeats are similar to Pfam:PF00805  , however it is not clear if these two families are structurally related.. 
PF00391 PEP-utilising enzyme, mobile domain<br>This domain is a "swivelling" beta/beta/alpha domain which is thought to be mobile in all proteins known to contain it.. 
PF05131 Pep3/Vps18/deep orange family<br>Pfam-B_6057 (release 7.7). This region is found in a number of protein identified as involved in golgi function and vacuolar sorting. The molecular function of this region is unknown.  The members of this family contain a C-terminal ring finger domain.. 
PF03051 Pept_C1-like; <br>Peptidase C1-like family. Pfam-B_2136 (release 6.4). This family is closely related to the Peptidase_C1 family  Pfam:PF00112, containing several prokaryotic and eukaryotic aminopeptidases and bleomycin hydrolases.. 
PF00112 Cys-protease; <br>Papain family cysteine protease. 
PF01650 Peptidase C13 family<br>Pfam-B_1302 (release 4.1). Members of this family are asparaginyl peptidases  . The blood fluke parasite Schistosoma mansoni has at least five Clan CA cysteine peptidases in its digestive tract including cathepsins B (2 isoforms), C, F and L. All have been recombinantly expressed as active enzymes, albeit in various stages of activation  . In addition, a Clan CD peptidase, termed asparaginyl endopeptidase or 'legumain' has been identified.  This has formerly been characterised as a 'haemoglobinase', but this term is probably incorrect  .  Two cDNAs have been described for Schistosoma mansoni legumain; one encodes an active enzyme whereas the active site cysteine residue encoded by the second cDNA is substituted by an asparagine residue.  Both forms have been recombinantly expressed  .. 
PF00863 Peptidase family C4<br>Pfam-B_232 (release 3.0). This peptidase is present in the nuclear inclusion protein of potyviruses.. 
PF02902 Ulp1_C; <br>Ulp1 protease family, C-terminal catalytic domain. This domain contains the catalytic triad Cys-His-Asn.. 
PF03416 Peptidase family C54<br>
PF01433 Peptidase family M1<br>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 Swiss:P09960, this enzyme also has an aminopeptidase activity  .. 
PF01431 Peptidase family M13<br>Mammalian enzymes are typically type-II membrane anchored enzymes which are known, or believed to activate or inactivate oligopeptide (pro)-hormones such as opioid peptides. The family also contains a bacterial member believed to be involved with milk protein cleavage.. 
PF05193 Peptidase M16 inactive domain<br>Peptidase M16 consists of two structurally related domains. One is the active peptidase, whereas the other is inactive. The two domains hold the substrate like a clamp  .. 
PF02789 Cytosol aminopeptidase family, N-terminal domain<br>Pfam-B_990 (release 3.0). 
PF02127 Aminopeptidase I zinc metalloprotease (M18)<br>
PF01546 CO_pept_M20; <br>Peptidase family M20/M25/M40. Pfam-B_253 (release 4.0). 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.. 
PF00814 Glycoprotease; <br>Glycoprotease family. Pfam-B_1670 (release 2.1) & Pfam-B_4550 (Release 7.5). The Peptidase M22 proteins are part of the HSP70-actin superfamily ( ). The region represented here is an insert into the fold and is not found in the rest of the family (beyond the Peptidase M22 family). Included in this family are the Rhizobial NodU proteins and the HypF regulator. This region also contains the histidine dyad believed to coordinate the metal ion and hence provide catalytic activity. Interestingly the histidines are not well conserved, and there is a lack of experimental  evidence to support peptidase activity as a general  property of this family. There also appear to be instances of this domain outside of the HSP70-actin superfamily (e.g. Swiss:Q9ZM49).. 
PF04389 Peptidase family M28<br>
PF01551 Peptidase_M37;<br>Peptidase family M23. Pfam-B_291 (release 4.0). Members of this family are zinc metallopeptidases with a range of specificities. The peptidase family M23 is included in this family, these are Gly-Gly endopeptidases. Peptidase family M23 are also endopeptidases. This family also includes some bacterial lipoproteins such as Swiss:P33648 for which no proteolytic activity has been demonstrated. This family also includes leukocyte cell-derived chemotaxin 2 (LECT2) proteins.  LECT2 is a liver-specific protein which is thought to be linked to hepatocyte growth although the exact function of this protein is unknown.. 
PF01434 Peptidase family M41<br>
PF02163 Peptidase family M50<br>
PF02897 Prolyl oligopeptidase, N-terminal beta-propeller domain<br>This unusual 7-stranded beta-propeller domain protects the catalytic triad of prolyl oligopeptidase (see Pfam:PF00326), excluding larger peptides and proteins from proteolysis in the cytosol.. 
PF04080 Per1-like <br>Pfam-B_12918 (release 7.3);. PER1 is required for GPI-phospholipase A2 activity and is involved in lipid remodelling of GPI-anchored proteins  .. 
PF04695 Peroxisomal membrane anchor protein (Pex14p) conserved region<br>Pfam-B_4121 (release 7.5). Family of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes.  Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N-terminus of the protein [1,2].. 
PF00294 pfkB; <br>pfkB family carbohydrate kinase. This family includes a variety of carbohydrate and pyrimidine kinases.. 
PF00169 PH domain<br>PH stands for pleckstrin homology.. 
PF05065 Phage capsid family <br>Pfam-B_3186 (release 7.7) & Pfam-B_9481 (release 10.0). Family of bacteriophage hypothetical proteins and capsid proteins. . 
PF02899 Phage_integr_N;<br>Phage integrase, N-terminal SAM-like domain. 
PF04860 Phage portal protein<br>Pfam-B_6050 (release 7.6). Bacteriophage portal proteins form a dodecamer and is located at a  five-fold vertex of the viral capsid.  The portal complex forms a channel through which the viral DNA is packaged into the capsid, and exits during  infection.  The portal protein is though to rotate during DNA packaging   . Portal proteins from different phage show little sequence homology, so  this family does not represent all portal proteins.. 
PF05119 Phage_sml_term; <br>Phage terminase, small subunit. TIGRFAMs (release 2.0);. 
PF03354 Phage_terminase; <br>Pfam-B_3931 (release 6.5). The majority of the members of this family are bacteriophage proteins, several of which are thought to be terminase large subunit proteins. There are also a number of bacterial proteins of unknown function.. 
PF00628 PHD-finger<br>PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains  .  Several PHD fingers have been identified as binding modules of methylated histone H3  .. 
PF01384 Phosphate transporter family<br>Pfam-B_923 (release 3.0). This family includes PHO-4 from Neurospora crassa which is a is a Na(+)-phosphate symporter  . This family also contains the leukaemia virus receptor Swiss:Q08344.. 
PF01663 Type I phosphodiesterase / nucleotide pyrophosphatase<br>Pfam-B_994 (release 4.1) & Pfam-B_6150 (Release 8.0). This family consists of phosphodiesterases, including human plasma-cell membrane glycoprotein PC-1 / alkaline phosphodiesterase i / nucleotide pyrophosphatase (nppase). These enzymes catalyse the cleavage of phosphodiester and phosphosulfate bonds in NAD,  deoxynucleotides and nucleotide sugars  . Also in this family is ATX an autotaxin, tumour cell motility-stimulating protein which  exhibits type I phosphodiesterases activity  . The alignment encompasses the active site [3,4]. Also present with in this family is 60-kDa Ca2+-ATPase form  F. odoratum  .. 
PF02811 PHP_C; <br>The PHP (Polymerase and Histidinol Phosphatase) domain is a putative phosphoesterase domain.. 
PF02972 phycoerythr_ab; <br>Phycoerythrin, alpha/beta chain. This family represents the non-globular alpha and beta chain components of phycoerythrin.  The structure is a long beta-hairpin and a single alpha-helix.. 
PF05023 Phytochelatin synthase<br>Pfam-B_9299 (release 7.6). Phytochelatin synthase is the enzyme responsible for the synthesis of heavy-metal-binding peptides (phytochelatins) from glutathione and related thiols  . The crystal structure of a member of this family shows it to possess a papain fold  . The enzyme catalyses the deglycination of a GSH donor molecule  . The enzyme contains a catalytic triad of cysteine, histidine and aspartate residues.. 
PF02567 Phenazine biosynthesis-like protein<br>
PF00454 Phosphatidylinositol 3- and 4-kinase<br>Prosite & Pfam-B_6771 (Rlease 7.6). Some members of this family probably do not have lipid kinase activity and are protein kinases, e.g. Swiss:P42345  .. 
PF00792 Phosphoinositide 3-kinase C2<br>SMART, Griffiths-Jones SR. Alignment kindly provided by SMART. Phosphoinositide 3-kinase region postulated to contain a C2 domain. Outlier of Pfam:PF00168 family. . 
PF00640 Phosphotyrosine interaction domain (PTB/PID)<br>
PF04987 Phosphatidylinositolglycan class N (PIG-N)<br>Pfam-B_5307 (release 7.6). Phosphatidylinositolglycan class N (PIG-N) is a mammalian homologue of the yeast protein MCD4P and is expressed in the endoplasmic reticulum  . PIG-N is essential for glycosylphosphatidylinositol anchor synthesis. Glycosylphosphatidylinositol (GPI)-anchored proteins are cell surface-localised proteins that serve many important cellular functions  .. 
PF01850 PIN domain<br>
PF04696 pinin_SDK_memA; <br>pinin/SDK/memA/ protein conserved region. Pfam-B_4141 (release 7.5). Members of this family have very varied localisations within the eukaryotic cell. pinin is known to localise at the desmosomes and is implicated in anchoring intermediate filaments to the desmosomal plaque  .  SDK2/3 is a dynamically localised nuclear protein thought to be involved in modulation of alternative pre-mRNA splicing  .  memA is a tumour marker preferentially expressed in human melanoma cell lines.  A common feature of the members of this family is that they may all participate in regulating protein-protein interactions  .. 
PF01504 Phosphatidylinositol-4-phosphate 5-Kinase<br>Pfam-B_571 (release 4.0). This family contains a region from the common kinase core found in the type I phosphatidylinositol-4-phosphate 5-kinase (PIP5K) family as described in  . The family consists of various type I, II and III PIP5K enzymes. PIP5K catalyses the formation of phosphoinositol-4,5-bisphosphate via the  phosphorylation of phosphatidylinositol-4-phosphate a precursor in the  phosphinositide signaling pathway.. 
PF02171 Piwi domain<br>This domain is found in the protein Piwi and its relatives.  The function of this domain is the dsRNA guided hydrolysis of ssRNA. Determination of the crystal structure of Argonaute reveals that PIWI is an RNase H domain, and identifies Argonaute as Slicer, the enzyme that cleaves mRNA in the RNAi RISC complex  .  In addition, Mg+2 dependence and production of 3'-OH and 5' phosphate products are shared characteristics of RNaseH and RISC. The PIWI domain core has a tertiary structure belonging to the RNase H family of enzymes.  RNase H fold proteins all have a five-stranded mixed beta-sheet surrounded by helices. By analogy to RNase H enzymes which cleave single-stranded RNA guided by the DNA strand in an RNA/DNA hybrid, the PIWI domain can be inferred to cleave single-stranded RNA, for example mRNA, guided by double stranded siRNA. . 
PF00801 PKD domain<br>This domain was first identified in the Polycystic kidney disease protein PKD1. This domain has been predicted to contain an Ig-like fold  .. 
PF01477 PLAT/LH2 domain<br>This domain is found in a variety of membrane or lipid associated proteins. It is called the PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology) domain.  The known structure of pancreatic lipase shows this domain binds to procolipase Pfam:PF01114, which mediates membrane association. So it appears possible that this domain mediates membrane attachment via other protein binding partners.\. The structure of this domain is known for many members of the family and is composed of a beta sandwich.. 
PF00614 Phospholipase D Active site motif<br>Ponting C, Schultz J, Bork P. Alignment kindly provided by SMART. Phosphatidylcholine-hydrolysing phospholipase D (PLD) isoforms are activated by ADP-ribosylation factors (ARFs). PLD produces phosphatidic acid from phosphatidylcholine, which may be essential for the formation of certain types of transport vesicles or may be constitutive vesicular transport to signal transduction pathways.  PC-hydrolysing PLD is a homologue of cardiolipin synthase, phosphatidylserine synthase, bacterial PLDs, and viral proteins. Each of these appears to possess a domain duplication which is apparent by the presence of two motifs containing well-conserved histidine, lysine, and/or asparagine residues which may contribute to the active site. aspartic acid.  An E. coli endonuclease (nuc) and similar proteins appear to be PLD homologues but possess only one of these motifs. The profile contained here represents only the putative active site regions, since an accurate multiple alignment of the repeat units has not been achieved.. 
PF01690 Potato leaf roll virus readthrough protein<br>Pfam-B_1335 (release 4.1). This family consists mainly of the potato leaf roll virus  readthrough protein. This is generated via a readthrough  of open reading frame 3 a coat protein allowing transcription of open reading frame 5 to give an extended coat protein  with a large c-terminal addition or read through domain  . The readthrough protein is thought to play a role in the  circulative aphid transmission of potato leaf roll virus  . Also in the family is open reading frame 6 from beet western yellows virus and potato leaf roll virus both luteovirus and an unknown protein from cucurbit aphid-borne yellows virus a closterovirus.. 
PF03126 Plus-3 domain<br>This domain is about 90 residues in length and is often found associated with the Pfam:PF02213 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 charged residues, hence this domain has been named the plus-3 domain. It is found in yeast Rtf1 which may be a transcription elongation factor  .. 
PF04043 Plant invertase/pectin methylesterase inhibitor<br>This domain inhibits pectin methylesterases (PMEs) and invertases through formation of a non-covalent 1:1 complex  . It has been implicated in the regulation of fruit development, carbohydrate metabolism and cell wall extension (see  ). It may also be involved in inhibiting microbial pathogen PMEs. It has been observed that it is often expressed as a large inactive preprotein  . It is also found at the N-termini of PMEs predicted from DNA sequences (personal obs:C Yeats), suggesting that both PMEs and their inhibitor are expressed as a single polyprotein and subsequently processed. It has two disulphide bridges and is mainly alpha-helical  .. 
PF04721 PNGase; <br>Domain of unknown function (DUF750) . Pfam-B_4045 (release 7.5). This family of proteins with unknown function shows similarity to PNG-1, a enzyme responsible for de-N-glycosylation of misfolded glycoproteins in the cytosol  . However, unlike PNG-1, this protein does not contain a catalytic triad in its transglutaminase domain  .. 
PF03726 Polyribonucleotide nucleotidyltransferase, RNA binding domain<br>This family contains the RNA binding domain of Polyribonucleotide nucleotidyltransferase (PNPase) PNPase is involved in mRNA degradation in a 3'-5' direction.. 
PF01357 Pollen_allergen; <br>This family contains allergens lol PI, PII and PIII from Lolium perenne.. 
PF01522 Polysac_deacet;Polysacc_deacet; <br>Polysaccharide deacetylase. Pfam-B_502 (release 4.0). This domain is found in polysaccharide deacetylase. This family of polysaccharide deacetylases includes NodB (nodulation protein B from  Rhizobium) which is a chitooligosaccharide deacetylase  . It also includes chitin deacetylase from yeast  , and endoxylanases which hydrolyses glucosidic bonds in xylan  .. 
PF04831 Popeye protein conserved region<br>Pfam-B_3905 (release 7.6). The function of Popeye proteins is not well understood. They are predominantly expressed in cardiac and skeletal muscle. This family represents a conserved region which includes three potential transmembrane domains  .. 
PF01558 Pyruvate ferredoxin/flavodoxin oxidoreductase<br>Pfam-B_350 (release 4.0). This family includes a region of the large protein pyruvate-flavodoxin oxidoreductase and the whole pyruvate ferredoxin oxidoreductase gamma subunit protein.  It is not known whether the  gamma subunit has a catalytic or regulatory role. Pyruvate oxidoreductase (POR) catalyses the final step in the fermentation of carbohydrates in anaerobic microorganisms  . This involves the oxidative decarboxylation of pyruvate with the participation of thiamine followed by the transfer of an acetyl moiety to coenzyme A for the synthesis of acetyl-CoA  . The family also includes  pyruvate flavodoxin oxidoreductase as encoded by the nifJ gene in cyanobacterium which is required for growth on molecular nitrogen when iron is limited  . . 
PF01855 Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg<br>Pfam-B_323 (release 4.2). This family includes the N terminal structural domain of the pyruvate ferredoxin oxidoreductase. This domain binds thiamine diphosphate, and along with domains II and IV, is involved in inter subunit contacts  . The family also includes pyruvate flavodoxin oxidoreductase as encoded by the nifJ gene in cyanobacterium which is required for growth on molecular nitrogen when iron is limited  .. 
PF04151 Bacterial pre-peptidase C-terminal domain<br>
PF01577 Poty_P1; <br>Potyvirus P1 protease. Pfam-B_364 (release 4.1). The potyviridae family positive stand RNA viruses with genome  encoding a polyprotein. members include zucchini yellow mosaic virus, and turnip mosaic viruses which cause considerable losses of crops  worldwide. This family consists of a C terminus region from various plant potyvirus P1 proteins (found at the N terminus of the polyprotein). The C terminus of P1 is a serine-type protease responsible for  autocatalytic cleavage between P1 and the helper component protease  Pfam:PF00851 [1,2]. The entire P1 protein may be involved in virus-host interactions  .. 
PF03291 mRNA capping enzyme<br>Pfam-B_4078 (release 6.5) & Pfam-B_3482 (Release 7.5). This family of enzymes are related to Pfam:PF03919.. 
PF00481 Protein phosphatase 2C<br>Protein phosphatase 2C is a Mn++ or Mg++ dependent protein serine/threonine phosphatase.. 
PF00823 PPE family<br>Pfam-B_297 (release 3.0). This family named after a PPE motif near to the amino terminus of the domain.  The PPE family of proteins all contain an amino-terminal region of about 180 amino acids.  The carboxyl terminus of this family are variable, and on the basis of this region fall into at least three groups.  The MPTR subgroup has tandem copies of a motif NXGXGNXG. The second subgroup contains a conserved motif at about position 350. The third group are only related in the amino terminal region. The function of these proteins is uncertain but it has been suggested that they may be related to antigenic variation of Mycobacterium tuberculosis  .. 
PF01535 DUF17; <br>Pfam-B_874 (release 4.0). 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 Swiss:P32522 that may be involved in RNA stabilisation  . This domain occurs in crp1 that is involved in RNA processing  .  This repeat is associated with a predicted plant protein Swiss:O49549 that has a domain organisation similar to the human BRCA1 protein. The repeat has been called PPR  .. 
PF04193 PQ loop repeat <br>TIGRFAMs (release 2.0);. 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 localisation of cystinosin to lysosomes  . However, the PQ motif appears not to be a general lysosome-targeting motif. It is thought likely to possess a more general function. Most probably this involves a glutamine residue  .. 
PF05033 Pre-SET motif<br>This protein motif is a zinc binding motif  .  It  contains 9 conserved cysteines that coordinate three zinc ions. It is thought that this region plays a structural role in stabilising SET domains.. 
PF00156 Phosphoribosyl transferase domain<br>This family includes a range of diverse phosphoribosyl transferase enzymes.  This family includes: Adenine phosphoribosyl-transferase EC:2.4.2.7, Swiss:P07672. Hypoxanthine-guanine-xanthine phosphoribosyl-transferase Swiss:P51900. Hypoxanthine phosphoribosyl-transferase EC:2.4.2.8 Swiss:P36766. Ribose-phosphate pyrophosphokinase i EC:2.7.6.1 Swiss:P09329. Amidophosphoribosyltransferase EC:2.4.2.14 Swiss:P00496. Orotate phosphoribosyl-transferase EC:2.4.2.10 Swiss:P11172. Uracil phosphoribosyl-transferase EC:2.4.2.9 Swiss:P25532. Xanthine-guanine phosphoribosyl-transferase EC:2.4.2.22 Swiss:P00501.  In Arabidopsis, At the very N-terminus of this domain is the P-Loop NTPase domain  .. 
PF00377 prion; <br>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 normal cellular protein, and the other is the infectious form which can change the normal prion protein into the infectious form. It has been found that the prion alpha-helical domain is also found in the Doppel protein.. 
PF00227 proteasome; <br>The proteasome is a multisubunit structure that degrades proteins. Protein degradation is an essential component of regulation because proteins can become misfolded, damaged, or unnecessary. Proteasomes and their homologues vary greatly in complexity: from HslV (heat shock locus v), which is encoded by 1 gene in bacteria, to the eukaryotic 20S proteasome, which is encoded by more than 14 genes  . Recently evidence of two novel groups of bacterial proteasomes was proposed. The first is Anbu, which is sparsely distributed among cyanobacteria and proteobacteria  . The second is call beta-proteobacteria proteasome homologue (BPH)  .. 
PF03371 PRP38 family<br>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 180 amino acids in length. PRP38 is a unique component of the U4/U6.U5 tri-small nuclear ribonucleoprotein (snRNP) particle and is necessary for an essential step late in spliceosome maturation  . . 
PF01789 PsbP<br>Pfam-B_1303 (release 4.2). This family consists of the 23 kDa subunit of oxygen evolving system of  photosystem II or PsbP from various plants (where it is encoded by the  nuclear genome) and Cyanobacteria. The 23 KDa PsbP protein is required for PSII to be fully operational in  vivo, it increases the affinity of the water oxidation site for Cl- and  provides the conditions required for high affinity binding of Ca2+  .. 
PF01416 PseudoU_synt;<br>tRNA pseudouridine synthase. Howe K, Griffiths-Jones SR. Involved in the formation of pseudouridine at the anticodon stem and loop of transfer-RNAs Pseudouridine is an isomer of uridine (5-(beta-D-ribofuranosyl) uracil, and id the most abundant modified nucleoside found in  all cellular RNAs. The TruA-like proteins also exhibit a conserved sequence with a strictly conserved aspartic acid, likely involved in catalysis.. 
PF01437 Plexin_repeat;<br>
PF04046 PSP<br>Pfam-B_PSP (release 7.3);. Proline rich domain found in numerous spliceosome associated proteins.. 
PF04468 PSP1 C-terminal conserved region<br>This region is present in both eukaryotes and eubacteria. The yeast PSP1 protein is involved in  suppressing mutations in the DNA polymerase alpha subunit in yeast  .. 
PF04024 PspC domain<br>This family includes Phage shock protein C (PspC) that is thought to be a transcriptional regulator. The presumed domain is 60 amino acid residues in length.. 
PF04886 PT repeat<br>Pfam-B_517 (release 7.6). This short repeat is composed on the tetrapeptide XPTX. This repeat is found in a variety of proteins, however it is not clear if these repeats are homologous to each other. The alignment represents nine copies of this repeat.. 
PF01329 Pterin 4 alpha carbinolamine dehydratase<br>Pterin 4 alpha carbinolamine dehydratase is also known as DCoH (dimerisation cofactor of hepatocyte nuclear factor 1-alpha).. 
PF03095 Phosphotyrosyl phosphate activator (PTPA) protein<br>Pfam-B_2456 (release 6.4). 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 relatively low when compared to the better recognised phosphoserine/ threonine protein phosphorylase activity. The specific biological role of PTPA is unknown, Basal expression of PTPA depends on the activity of a ubiquitous transcription factor, Yin Yang 1 (YY1). The tumour suppressor protein p53 can inhibit PTPA expression through an unknown mechanism that negatively controls YY1  .. 
PF02302 PTS system, Lactose/Cellobiose specific IIB subunit<br>Pfam-B_9339 (release 5.2). The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. The lactose/cellobiose-specific family are one of four structurally and functionally distinct group IIB PTS system cytoplasmic enzymes. The fold of IIB cellobiose shows similar structure to mammalian tyrosine phosphatases.  This family also contains the fructose specific IIB subunit.. 
PF01472 PUA domain<br>The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, was detected in archaeal and eukaryotic pseudouridine synthases, archaeal archaeosine synthases, a family of predicted ATPases that may be involved in RNA modification, a family of predicted archaeal and bacterial rRNA methylases. Additionally, the PUA domain was detected in a family of eukaryotic proteins that also contain a domain homologous to the translation initiation factor eIF1/SUI1; these proteins may comprise a novel type of translation factors. Unexpectedly, the PUA domain was detected also in bacterial and yeast glutamate kinases; this is compatible with the demonstrated role of these enzymes in the regulation of the expression of other genes  .  It is predicted that the PUA domain is an RNA binding domain.. 
PF01480 PWI domain<br>
PF00787 PX domain<br>Alignment kindly provided by SMART & iterated. PX domains bind to phosphoinositides.. 
PF02194 PXA domain<br>Alignment kindly provided by SMART. This domain is associated with PX domains Pfam:PF00787.. 
PF00070 pyr_redox; <br>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.. 
PF02852 pyr_redox_dim; <br>Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain. This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases.. 
PF01729 QRPTase; <br>Quinolinate phosphoribosyl transferase, C-terminal domain. Pfam-B_2063 (release 4.1). Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase EC:2.4.2.19 is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide [1,2]. The QA substrate is bound between the C-terminal domain of one subunit, and the N-terminal domain of the other.  The C-terminal domain has a 7 beta-stranded TIM barrel-like fold.. 
PF02749 Quinolinate phosphoribosyl transferase, N-terminal domain<br>Pfam-B_2063 (release 4.1). Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase EC:2.4.2.19 is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide [1,2]. The QA substrate is bound between the C-terminal domain of one subunit, and the N-terminal domain of the other.  The N-terminal domain has an alpha/beta hammerhead fold.. 
PF01424 R3H domain<br>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.. 
PF03834 Binding domain of DNA repair protein Ercc1 (rad10/Swi10)<br>TIGRFAMs, Griffiths-Jones SR, Coggill PC. Ercc1 and XPF (xeroderma pigmentosum group F-complementing protein) are two structure-specific endonucleases of a class of seven containing an ERCC4 domain.  Together they form an obligate complex that functions primarily in nucleotide excision repair (NER), a versatile pathway able to detect and remove a variety of DNA lesions induced by UV light and environmental carcinogens, and secondarily in DNA interstrand cross-link repair and telomere maintenance. This domain in fact binds simultaneously to both XPF and single-stranded DNA; this ternary complex explains the important role of Ercc1 in targeting its catalytic XPF partner to the NER pre-incision complex  .. 
PF04423 Rad50 zinc hook motif<br>The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.. 
PF04055 Radical SAM superfamily<br>Radical SAM proteins catalyse diverse reactions, including unusual methylations, isomerisation, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation.. 
PF02145 Rap/ran-GAP<br>
PF04078 Cell differentiation family, Rcd1-like <br>Pfam-B_5278 (release 7.3);. Two of the members in this family have been characterised as being  involved in regulation of Ste11 regulated sex genes [1,2]. Mammalian Rcd1 is a novel transcriptional cofactor that mediates retinoic acid-induced cell differentiation  .. 
PF05177 RCSD region<br>Proteins contain this region include C.elegans UNC-89. This region is found repeated in UNC-89 and shows conservation in prolines, lysines and glutamic acids. Proteins with RCSD are involved in muscle M-line assembly, but the function of this region RCSD is not clear.. 
PF01030 Receptor L domain<br>Pfam-B_244 (release 3.0). 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.. 
PF02010 REJ domain<br>The REJ (Receptor for Egg Jelly) domain is found in PKD1 Swiss:P98161, and the sperm receptor for egg jelly Swiss:Q26627.  The function of this domain is unknown. The domain is 600 amino acids long so is probably composed of multiple structural domains. There are six completely conserved cysteine residues that may form disulphide bridges. This region contains tandem PKD-like domains.. 
PF03432 Relaxase/Mobilisation nuclease domain <br>Pfam-B_4002 (release 6.6). Relaxases/mobilisation proteins are required for the horizontal transfer of genetic information contained on plasmids that occurs during bacterial conjugation. The relaxase, in conjunction with several auxiliary proteins, forms the relaxation complex or relaxosome. Relaxases nick duplex DNA in a specific manner by catalysing  trans-esterification .    . 
PF03090 Replicase family<br>Pfam-B_2424 (release 6.4). This is a family of bacterial plasmid DNA replication initiator proteins. Pfam: PF01051 is a similar family.  These RepA proteins exist as monomers and dimers in equilibrium: monomers bind directly to repeated DNA sequences and thus activate replication; dimers repress repA transcription by binding an inversely repeated DNA operator. Dimer dissociation can occur spontaneously or be mediated by Hsp70 chaperones.. 
PF03248 Rer1 family<br>Pfam-B_3358 (release 6.5). 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  .. 
PF02453 Reticulon<br>Pfam-B_2196 (release 5.4). 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.. 
PF04527 Drosophila Retinin like protein<br>Pfam-B_4914 (release 7.5). Family of Drosophila proteins related to the C-terminal region of the Drosophila Retinin protein. Conserved region is found towards the C-terminus of the member proteins.. 
PF03732 Retrotransposon gag protein <br>Pfam-B_3194 (release 7.0). 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  .. 
PF01694 Rhomboid family<br>Pfam-B_1399 (release 4.1). This family contains integral membrane proteins that are related to Drosophila rhomboid protein Swiss:P20350. Members of this family are found in bacteria and eukaryotes.\. Rhomboid promotes the cleavage of the membrane-anchored TGF-alpha-like growth factor Spitz, allowing it to activate the Drosophila EGF receptor.  Analysis has shown that Rhomboid-1 is an intramembrane serine protease     (EC:3.4.21.105).  Parasite-encoded rhomboid enzymes are also important for invasion of host cells by Toxoplasma and the malaria parasite  .. 
PF05104 Ribosome receptor lysine/proline rich region<br>Pfam-B_3249 (release 7.7). This highly conserved region is found towards the C-terminus of the transmembrane domain  . The function is unclear.. 
PF00636 Ribonuclease III domain<br>
PF04597 Ribophorin I<br>Ribophorin I is an essential subunit of oligosaccharyltransferase (OST), which is also known as Dolichyl-diphosphooligosaccharide--protein glycosyltransferase, (EC:2.4.1.119).  OST catalyses the transfer of an oligosaccharide from dolichol pyrophosphate to selected asparagine residues of nascent polypeptides as they are translocated into the lumen of the rough endoplasmic reticulum.  Ribophorin I and OST48 are though to be responsible for OST catalytic activity  . Both yeast and mammalian proteins are glycosylated but the sites are not conserved.  Glycosylation may contribute towards general solubility but is unlikely to be involved in a specific biochemical function   Most family members are predicted to have a transmembrane helix at the C terminus of this region.. 
PF01775 Ribosomal L18ae/LX protein domain<br>This family includes eukaryotic L18ae as well as archaebacterial specific LX.  Ribosomal protein L18ae forms part of the 60S ribosomal subunit.. 
PF00828 Ribosomal protein L18e/L15<br>Pfam-B_1295 (release 2.1). This family includes eukaryotic L18 as well as prokaryotic L15.. 
PF01907 Ribosomal protein L37e<br>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.. 
PF00347 L6;<br>Ribosomal protein L6. 
PF02482 Ribosomal_S30;<br>Sigma 54 modulation protein / S30EA ribosomal protein. Pfam-B_869 (release 5.4). This Pfam family contains the sigma-54 modulation protein family and the S30AE family of ribosomal proteins which includes the light- repressed protein (lrtA) (Swiss:P47908)  .. 
PF01201 Ribosomal protein S8e<br>
PF00652 Ricin-type beta-trefoil lectin domain<br>
PF00355 Rieske [2Fe-2S] domain<br>Prosite & Pfam-B_31 (release 4.1). The rieske domain has a [2Fe-2S] centre. Two conserved cysteines coordinate one Fe ion, while the other Fe ion is coordinated by two conserved histidines. In hyperthermophilic archaea there is a SKTPCX(2-3)C motif at the C-terminus. The cysteines in this motif form a disulphide bridge, which stabilises the protein  .. 
PF00866 Ring hydroxylating beta subunit<br>Pfam-B_771 (release 3.0). This subunit has a similar structure to NTF-2 and scytalone dehydratase.. 
PF04068 Possible Fer4-like domain in RNase L inhibitor, RLI<br>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, Pfam:PF00037. Also often found adjacent to the DUF367 domain Pfam:PF04034 in uncharacterised proteins. The RNase L system plays a major role in the anti-viral and anti-proliferative activities of interferons  , and could possibly play a more general role in the regulation of RNA stability in mammalian cells.  Inhibitory activity requires concentration-dependent association of RLI with RNase L  .. 
PF04437 RINT-1 / TIP-1 family<br>This family includes RINT-1, a Rad50 interacting protein which participates in radiation induced checkpoint control  , as well as the TIP-1 protein from yeast that seems to be involved in a complex with Sec20p that is required for golgi transport  .. 
PF01163 RIO1 family<br>This is a family of atypical serine kinases which are found in archaea, bacteria and eukaryotes.\.       Activity of Rio1 is vital in Saccharomyces cerevisiae for the processing of ribosomal RNA, as well as for proper cell cycle progression and chromosome maintenance.  The structure of RIO1 has been determined  .. 
PF01000 RNA polymerase Rpb3/RpoA insert domain<br>Pfam-B_172 (release 3.0). Members of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal. 
PF04997 RNA polymerase Rpb1, domain 1<br>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 domain, domain 1, represents  the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand [1,2]. . 
PF00623 RNA polymerase Rpb1, domain 2<br>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 domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion [1,2].. 
PF04983 RNA polymerase Rpb1, domain 3<br>Pfam-B_288 (release 4.2). 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 domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking [1,2].. 
PF05000 RNA polymerase Rpb1, domain 4<br>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 domain, domain 4, represents the funnel domain.  The funnel contain the binding site for some elongation factors [1,2].. 
PF04998 RNA polymerase Rpb1, domain 5<br>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 domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound [1,2].. 
PF04992 RNA polymerase Rpb1, domain 6<br>Pfam-B_288 (release 4.2). 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 domain, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module [1,2].  This family appears to be specific to the largest subunit of RNA polymerase II.. 
PF05001 RNA polymerase Rpb1 C-terminal repeat <br>The repetitive C-terminal domain (CTD) of Rpb1 (RNA polymerase Pol II) plays a critical role in the regulation of gene expression. The activity of the CTD is dependent on its state of phosphorylation  .. 
PF04565 RNA polymerase Rpb2, domain 3<br>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). Domain 3, s also known as the fork domain and is proximal to catalytic site  .. 
PF04567 RNA polymerase Rpb2, domain 5<br>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). Domain 5, is also known as the external 2 domain  .. 
PF00562 RNA polymerase Rpb2, domain 6<br>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 domain represents the hybrid binding domain and the wall domain  .  The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex.  This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion .  This domain is also involved in binding to Rpb1 and Rpb3  .  Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).. 
PF04560 RNA polymerase Rpb2, domain 7<br>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).  Rpb2 is the second largest subunit of the RNA polymerase.  This domain comprised of the structural domains anchor and clamp  . The clamp region (C-terminal) contains a zinc-binding motif  . The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription  .. 
PF03874 RNA polymerase Rpb4<br>This family includes the Rpb4 protein.  This family also includes C17 (aka CGRP-RCP) is an essential subunit of RNA polymerase III. C17 forms a subcomplex with C25   which is likely to be the counterpart of subcomplex Rpb4/7 in Pol II  .. 
PF01351 Ribonuclease HII<br>
PF01138 3' exoribonuclease family, domain 1<br>This family includes 3'-5' exoribonucleases.  Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction.  The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA.  Three of its five protein components, Swiss:P46948 Swiss:Q12277 and Swiss:P25359 contain a copy of this domain  . Swiss:Q10205, a hypothetical protein from S. pombe appears to belong to an uncharacterised subfamily. This subfamily is found in both eukaryotes and archaebacteria.. 
PF03725 3' exoribonuclease family, domain 2<br>This family includes 3'-5' exoribonucleases.  Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction.  The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA.  Three of its five protein components, Swiss:P46948 Swiss:Q12277 and Swiss:P25359 contain a copy of this domain  . Swiss:Q10205, a hypothetical protein from S. pombe appears to belong to an uncharacterised subfamily. This subfamily is found in both eukaryotes and archaebacteria.. 
PF02755 RPEL repeat<br>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 Swiss:Q9VZY2 contains a Pfam:PF02037 domain that is also implicated in DNA binding.. 
PF04059 rrm_2; <br>RNA recognition motif 2. Pfam-B_4981 (release 7.3);. 
PF01137 RCT; <br>RNA 3'-terminal phosphate cyclase. RNA cyclases are a family of RNA-modifying enzymes that are conserved in all cellular organisms. They catalyse the ATP-dependent conversion of the 3'-phosphate to the 2',3'-cyclic phosphodiester at the end of  RNA, in a reaction involving formation of the covalent AMP-cyclase  intermediate  . The structure of RTC demonstrates that RTCs are  comprised two domain.  The larger domain contains an insert domain of approximately 100 amino acids  . . 
PF05189 RNA 3'-terminal phosphate cyclase (RTC), insert domain<br>RNA cyclases are a family of RNA-modifying enzymes that are conserved in all cellular organisms. They catalyse the ATP-dependent conversion of the 3'-phosphate to the 2',3'-cyclic phosphodiester at the end of  RNA, in a reaction involving formation of the covalent AMP-cyclase  intermediate  . The structure of RTC demonstrates that RTCs are  comprised two domain.  The larger domain contains an insert domain of approximately 100 amino acids  . . 
PF00301 rubredoxin; <br>
PF02759 RUN domain<br>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 signalling pathways. The domain is comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases  .. 
PF00853 Runt domain<br>
PF00665 Integrase core domain<br>Pfam-B_10 (release 2.1). 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 Pfam:PF02022.  This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain Pfam:PF00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyses the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site  .. 
PF00077 rvp; <br>Retroviral aspartyl protease. Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases such as pepsins, cathepsins, and renins (Pfam:PF00026).. 
PF00078 rvt; RVT; <br>Reverse transcriptase (RNA-dependent DNA polymerase). Published_alignment and HMM_iterative_training. A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.. 
PF03501 Plectin/S10 domain<br>Pfam-B_2138 (release 7.0). 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.. 
PF01479 S4 domain<br>The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation  . The S4 domain probably mediates binding to RNA.. 
PF04382 SAB domain<br>This presumed domain is found in proteins containing FERM domains Pfam:PF00373.  This domain is found to bind to both spectrin and actin, hence the name SAB (Spectrin and Actin Binding) domain.. 
PF03399 SAC3/GANP/Nin1/mts3/eIF-3 p25 family<br>Pfam-B_2845 (release 6.6) & Pfam-B_4388 (release 7.5). This large family includes diverse proteins involved in large complexes. The alignment contains one highly conserved negatively charged residue and one highly conserved positively charged residue that are probably important for the function of these proteins.  The family includes the yeast nuclear export factor Sac3 Swiss:P46674, and mammalian GANP/MCM3-associated proteins, which facilitate the nuclear localisation of MCM3, a protein that associates with chromatin in the G1 phase of the cell-cycle.  The 26S protease (or 26S proteasome) is responsible for degrading ubiquitin conjugates. It consists of 19S regulatory complexes associated with the ends of 20S proteasomes. The 19S regulatory complex is composed of about 20 different polypeptides and confers ATP-dependence and substrate specificity to the 26S enzyme.  The conserved region occurs at the C-terminal of the Nin1-like regulatory subunit [4,5,6].  This family includes several eukaryotic translation initiation factor 3 subunit 11 (eIF-3 p25) proteins. Eukaryotic initiation factor 3 (eIF3) is a multisubunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilisation of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits  .. 
PF03435 Saccharopine dehydrogenase <br>Pfam-B_4166 (release 6.6) & Pfam-B_6325 (Release 7.5). 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.  The saccharopine dehydrogenase can also function as a saccharopine reductase.. 
PF00536 SAM_1;<br>SAM domain (Sterile alpha motif). It has been suggested that SAM is an evolutionarily conserved protein binding domain that is involved in the regulation of numerous developmental processes in diverse eukaryotes. The SAM domain can potentially function as a protein interaction module through its ability to homo- and heterooligomerise with other SAM domains.. 
PF02198 Sterile alpha motif (SAM)/Pointed domain<br>Alignment kindly provided by SMART. 
PF01342 SAND domain<br>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  . This region is also found in the putative transcription factor RegA from the multicellular green alga Volvox cateri.  This region of RegA is known as the VARL domain  .. 
PF02037 SAP domain<br>The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins.. 
PF05184 Saposin-like type B, region 1<br>
PF03489 Surfactant_B;<br>Saposin-like type B, region 2. 
PF04499 SIT4 phosphatase-associated protein<br>Pfam-B_2011 (release 7.5). This family includes a conserved region from a group of yeast proteins that associate with the SIT4 phosphatase. This association is required for SIT4's role in G1 cyclin transcription and for bud formation. This family also includes homologous regions from other eukaryotes.. 
PF04000 Sas10/Utp3/C1D family<br>Pfam-B_6555 (release 7.3). This family contains Utp3 and LCP5 which are components of the U3 ribonucleoprotein complex   . It also includes the human C1D protein and Saccharomyces cerevisiae YHR081W (rrp47), an exosome-associated protein required for the 3' processing of stable RNAs  , and Sas10 which has been identified as a regulator of chromatin silencing  . This family also includes the human protein Neuroguidin an initiation factor 4E (eIF4E) binding protein  .. 
PF01547 SBP_bacterial_1; <br>Bacterial extracellular solute-binding protein. Pfam-B_269 (release 4.0). This family also includes the bacterial extracellular solute-binding protein family POTD/POTF.. 
PF00497 Bacterial extracellular solute-binding proteins, family 3<br>
PF04144 SCAMP family<br>Pfam-B_1298 (release 7.3). 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 cytoplasmic tail. SCAMPs probably function in endocytosis by recruiting EH-domain proteins to the N-terminal NPF repeats but may have additional functions mediated by their other sequences  .. 
PF02023 SCAN domain<br>Pfam-B_1614 (Release 5.0). The SCAN domain   (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found in several Pfam:PF00096 proteins. The domain has been shown to be able to mediate homo- and hetero-oligomerisation  .. 
PF02404 Stem cell factor<br>Pfam-B_2598 (release 5.4). 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 identified  . . 
PF00188 SCP;<br>Cysteine-rich secretory protein family. This is a large family of cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins (CAP) that are found in a wide range of organisms, including prokaryotes   and non-vertebrate eukaryotes  , The nine subfamilies of the mammalian CAP 'super'family include: the human glioma pathogenesis-related 1 (GLIPR1), Golgi associated pathogenesis related-1 (GAPR1) proteins, peptidase inhibitor 15 (PI15), peptidase inhibitor 16 (PI16), cysteine-rich secretory proteins (CRISPs), CRISP LCCL domain containing 1 (CRISPLD1), CRISP LCCL domain containing 2 (CRISPLD2), mannose receptor like and the R3H domain containing like proteins.  Members are most often secreted and have an extracellular endocrine or paracrine function and are involved in processes including the regulation of extracellular matrix and branching morphogenesis, potentially as either proteases or protease inhibitors; in ion channel regulation in fertility; as tumour suppressor or pro-oncogenic genes in tissues including the prostate; and in cell-cell adhesion during fertilisation. The overall protein structural conservation within the CAP 'super'family results in fundamentally similar functions for the CAP domain in all members, yet the diversity outside of this core region dramatically alters the target specificity and, thus, the biological consequences  . The Ca++-chelating function   would fit with the various signalling processes (e.g. the CRISP proteins) that members of this family are involved in, and also the sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how Swiss:Q91055 blocks the Ca++ transporting ryanodine receptors.. 
PF03803 Scramblase <br>Pfam-B_3893 (release 7.0). 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 in the redistribution of phospholipids after cell activation or injury  .. 
PF01390 SEA domain<br>Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain  .. 
PF04091 Exocyst complex subunit Sec15-like <br>Pfam-B_7871 (release 7.3);. 
PF04815 Sec23/Sec24 helical domain<br>Pfam-B_3055 (release 7.3). COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is composed of five alpha helices.. 
PF04811 Sec23/Sec24 trunk domain<br>COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is known as the trunk domain and has an alpha/beta vWA fold and forms the dimer interface.. 
PF04136 Sec34-like family <br>Pfam-B_16464 (release 7.3);. 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  .. 
PF02889 Sec63 Brl domain<br>This domain (also known as the Brl domain) is required for assembly of functional endoplasmic reticulum translocons  .. 
PF04048 Sec8 exocyst complex component specific domain<br>Pfam-B_9576 (release 7.3);. 
PF00856 SET domain<br>SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases)  .  A subset of SET domains have been called PR domains.  These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction  .  The SET domain consists of two regions known as SET-N and SET-C.  SET-C forms an unusual and conserved knot-like structure of probably functional importance.  Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure  .. 
PF03749 Sugar fermentation stimulation protein<br>This family contains Sugar fermentation stimulation proteins. Which is probably a regulatory factor involved in maltose metabolism. SfsA has been shown to bind DNA   and it contains a helix-turn-helix motif that probably binds DNA at its C-terminus.. 
PF05002 SGS domain <br>This domain was thought to be unique to the SGT1-like proteins  , but is also found in calcyclin binding proteins.. 
PF03983 SLA1 homology domain 1, SHD1 <br>Pfam-B_ (release 7.2). NPFXD peptides specifically interact with the SHD1 domain. NPFXD is a clathrin-facilitated endocytic targeting signal. NPFXD was originally discovered in the cytoplasmic  domain of the furin-like protease Kex2p  . Sla1 is thought to function as an endocytic adaptor  .  . 
PF04925 SHQ1 protein<br>Pfam-B_11411 (release 7.6). S. cerevisiae SHQ1 protein is required for SnoRNAs of the box H/ACA Quantitative accumulation (unpublished).. 
PF01549 DUF18;ShTK; <br>Pfam-B_662 (release 4.0). This domain of is found in several C. elegans proteins. The domain is 30 amino acids long and rich in cysteine residues. There are 6 conserved cysteine positions in the domain that form three disulphide bridges.  The domain is found in the potassium channel inhibitor ShK in sea anemone   .. 
PF04542 sigma70_r2; <br>Region 2 of sigma-70 is the most conserved region of the entire protein.  All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant.  The core binding helix, interacts with the  clamp domain of the largest polymerase subunit, beta prime [1,2]. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation [1,2]. . 
PF04545 sigma70_r4;<br>Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif  . Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.. 
PF03145 Seven in absentia protein family<br>Pfam-B_1854 (release 6.5). 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 in the transformation of the R7 precursor cell to a non- neuronal cell type. The Sina protein contains an N-terminal RING finger domain Pfam:PF00097. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that thus Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologues of Sina have also been identified. The human homologue Siah-1   also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation [2,3]. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is described in Pfam:PF00097, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologues, whose similarity was noted previously, this family also includes putative homologues from Caenorhabditis elegans, Arabidopsis thaliana.. 
PF04938 Survival motor neuron (SMN) interacting protein 1 (SIP1)<br>Pfam-B_5071 (release 7.6). Survival motor neuron (SMN) interacting protein 1 (SIP1) interacts with SMN protein and plays a crucial role in the biogenesis of spliceosomes. There is evidence that the protein is linked to spinal muscular atrophy (SMA) and amyotrophic lateral sclerosis(ALS) in humans .. 
PF03530 Calcium-activated SK potassium channel<br>
PF02437 SKI/SNO/DAC family<br>Pfam-B_2013 (release 5.4). 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 myogenic differentiation  . Sno, a Ski proto-oncogene homologue, is expressed in two isoforms and plays a role in the response to proliferation stimuli. Dachshund also contains this domain.  It is involved in various aspects of development [2,3].. 
PF01466 Skp1 family, dimerisation domain<br>
PF03931 Skp1 family, tetramerisation domain<br>
PF00395 S-layer homology domain<br>
PF01423 Sm; <br>The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins  . Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings.. 
PF02463 RecF/RecN/SMC N terminal domain<br>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 by a hinge in the middle.  The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics  .\.  This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.. 
PF04158 Sof1-like domain <br>Pfam-B_9404 (release 7.3);. Sof1 is essential for cell growth and is a component of  the nucleolar rRNA processing machinery  . . 
PF01033 Somatomedin B domain<br>
PF03700 Sorting nexin, N-terminal domain <br>Pfam-B_29150 (release 7.0) . 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.. 
PF04130 Spc97 / Spc98 family<br>Pfam-B_3531 (release 7.3). 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. This family of proteins includes the grip motif 1 and grip moti 2  . Members of this family all form components of the gamma-tubulin complex, GCP  .. 
PF04435 DUF545; <br>Domain of unknown function (DUF545)  . Pfam-B_429 (release 7.5). Family of uncharacterised C. elegans proteins. The region represented by this family can is found to be repeated up to four time in some proteins.. 
PF04014 SpoVT_AbrB;<br>Antidote-toxin recognition MazE. MazE is the antidote to the toxin MazF of E. coli. MazE-MazF in E. coli is a regulated prokaryotic chromosomal addiction module. MazE antidote is degraded by the ClpPA protease of the bacterial proteasome. MazE-MazF is thought to play a role in programmed cell death when cells suffer nutrient deprivation  , and MazE-MazF modules have also been implicated in the bacteriostatic effects of other addiction modules  . MazF toxin functions as an mRNA interferase, cleaving mRNAs at ACA sequences to inhibit protein synthesis leading to cell growth arrest  .. 
PF00622 SPRY domain<br>Alignment kindly provided by SMART. SPRY Domain is named from SPla and the RYanodine Receptor.  Domain of unknown function. Distant homologues are domains in butyrophilin/marenostrin/pyrin homologues.. 
PF03105 SPX domain<br>Pfam-B_502 (release 6.5). 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 subunit and inhibits transduction of the mating pheromone signal  . This finding suggests that all the members of this family are involved in G-protein associated signal transduction. The N-termini of several proteins involved in the regulation of phosphate transport, including the putative phosphate level sensors PHO81 Swiss:P17442 from Saccharomyces cerevisiae and NUC-2 Swiss:Q01317 from Neurospora crassa, are also members of this family [see 4,5].  The SPX domain of S. cerevisiae low-affinity phosphate transporters Pho87 and Pho90 auto-regulates uptake and prevents efflux. This SPX dependent inhibition is mediated by the physical interaction with Spl2   NUC-2 contains several ankyrin repeats Pfam:PF00023. Several members of this family are annotated as XPR1 proteins: the xenotropic and polytropic retrovirus receptor confers susceptibility to infection with murine leukaemia viruses (MLV)  .  The similarity between SYG1, phosphate regulators and XPR1 sequences has been previously noted, as has the additional similarity to several predicted proteins, of unknown function, from Drosophila melanogaster, Arabidopsis thaliana, Caenorhabditis elegans, Schizosaccharomyces pombe, and Saccharomyces cerevisiae [1,2]. In addition, given the similarities between XPR1 and SYG1 and phosphate regulatory proteins, it has been proposed that XPR1 might be involved in G-protein associated signal transduction and may itself function as a phosphate sensor  .. 
PF03125 C. elegans Sre G protein-coupled chemoreceptor<br>Pfam-B_352 (release 6.5). Caenorhabditis elegans Sre proteins are candidate chemosensory receptors. There are four main recognised groups of such receptors: Odr-10, Sra, Sro, and Srg. Sre (this family), Sra Pfam:PF02117 and Srb Pfam:PF02175 comprise the Sra group. All of the above receptors are thought to be G protein-coupled seven transmembrane domain proteins [1,2]. The existence of several different chemosensory receptors underlies the fact that in spite of having only 20-30 chemosensory neurones, C. elegans detects hundreds of different chemicals, with the ability to discern individual chemicals among combinations  .. 
PF04086 Signal recognition particle, alpha subunit, N-terminal<br>Pfam-B_7342 (release 7.3);. 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 the endoplasmic reticulum (ER)  membrane  . SRP binds hydrophobic signal sequences as  they emerge from the ribosome, and arrests translation.. 
PF00448 SRP54-type protein, GTPase domain<br>This family includes relatives of the G-domain of the SRP54 family of proteins.. 
PF02881 SRP54-type protein, helical bundle domain<br>
PF02978 Signal peptide binding domain<br>
PF00436 Single-strand binding protein family<br>This family includes single stranded binding proteins and also the primosomal replication protein N (PriB). PriB forms a complex with PriA, PriC and ssDNA.. 
PF04503 Single-stranded DNA binding protein, SSDP<br>Pfam-B_2031 (release 7.5). This is a family of eukaryotic single-stranded DNA binding proteins with specificity to a pyrimidine-rich element found in the promoter region of the alpha2(I) collagen gene.. 
PF05030 SSXT protein (N-terminal region)<br>Pfam-B_4900 (release 7.6). The SSXT or SS18 protein is involved in synovial sarcoma in humans.  A SYT-SSX fusion gene resulting from the chromosomal translocation t(X;18) (p11;q11) is characteristic of synovial sarcomas. This translocation fuses the SSXT (SYT) gene from chromosome 18 to either of two homologous genes  at Xp11, SSX1 or SSX2  .. 
PF01852 START domain<br>Alignment kindly provided by SMART. 
PF01740 SpoIIAA; <br>The STAS (after Sulphate Transporter and AntiSigma factor antagonist) domain is found in the C terminal region of Sulphate transporters and bacterial antisigma factor antagonists. It has been suggested that this domain may have a general NTP binding function  .. 
PF03015 Male sterility protein<br>Pfam-B_1115 (release 6.4). 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.. 
PF02544 3-oxo-5-alpha-steroid 4-dehydrogenase <br>Pfam-B_1713 (release 5.4). 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)-steroid + reduced acceptor.  The Steroid 5-alpha-reductase enzyme is responsible for the formation of dihydrotestosterone, this hormone promotes the differentiation of male external genitalia and the prostate during fetal development  .  In humans mutations in this enzyme can cause a form of male pseudohermaphorditism in which the external genitalia and prostate fail to develop normally  . A related enzyme is also found in plants is Swiss:Q38944 (DET2) a steroid reductase from Arabidopsis.  Mutations in this enzyme cause defects in light-regulated development  .. 
PF02910 succ_DH_flav_C;<br>Fumarate reductase flavoprotein C-term. This family contains fumarate reductases, succinate dehydrogenases and L-aspartate oxidases.. 
PF00884 Sulfatase<br>Pfam-B_784 (release 3.0) & Pfam-B_7393 (Release 8.0). 
PF00685 Sulfotransfer; <br>Sulfotransferase domain. Pfam-B_87 (release 2.1) & Pfam-B_1885 (Release 7.5). 
PF03567 Sulfotransfer2; <br>Sulfotransferase family. Pfam-B_3050(7.0),Pfam-B_5394(7.7),Pfam-B_7836(10.0),Pfam-B_5040(7.5). This family includes a variety of sulfotransferase enzymes. Chondroitin 6-sulfotransferase catalyses the transfer of sulfate to position 6 of the N-acetylgalactosamine residue of chondroitin. This family also includes Heparan sulfate 2-O-sulfotransferase (HS2ST) and Heparan sulfate 6-sulfotransferase (HS6ST).  Heparan sulfate (HS) is a co-receptor for a number of growth factors, morphogens, and adhesion proteins. HS biosynthetic modifications may determine the strength and outcome of HS-ligand interactions. Mice that lack HS2ST undergo developmental failure only after midgestation,the most dramatic effect being the complete failure of kidney development  .  Heparan sulphate 6- O -sulfotransferase (HS6ST) catalyses the transfer of sulphate from adenosine 3'-phosphate, 5'-phosphosulphate to the 6th position of the N -sulphoglucosamine residue in heparan sulphate  .. 
PF04935 Surfeit locus protein 6<br>Pfam-B_5497 (release 7.6). The surfeit locus protein SURF-6 is shown to be a component of the  nucleolar matrix and has a strong binding capacity for nucleic acids  .. 
PF01805 Surp module<br>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  .. 
PF02201 SWIB/MDM2 domain<br>This family includes the SWIB domain and the MDM2 domain  . The p53-associated protein (MDM2) is an inhibitor of the p53 tumour suppressor gene binding the transactivation domain and down regulating the ability of p53 to activate transcription. This family contains the  p53 binding domain of MDM2  .. 
PF04434 SWIM zinc finger<br>This domain is found in bacterial, archaeal and eukaryotic proteins. It is predicted to be organised into two N-terminal beta-strands and a C-terminal alpha helix, thus possibly adopting a fold similar to that of the C2H2 zinc finger (Pfam:PF00096). SWIM is thought to be a versatile domain that can interact with DNA or proteins in different contexts  .. 
PF04433 SWIRM domain<br>This SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in chromosomal proteins.  It contains a helix-turn helix motif and binds to DNA  .. 
PF00804 Syntaxin<br>Pfam-B_1158 (release 2.1). Syntaxins are the prototype family of SNARE proteins. They usually consist of three main regions - a C-terminal transmembrane region, a central SNARE domain which is characteristic of and conserved in all syntaxins (Pfam:PF05739), and an N-terminal domain that is featured in this entry. This domain varies between syntaxin isoforms; in syntaxin 1A (Swiss:O35526) it is found as three alpha-helices with a left-handed twist. It may fold back on the SNARE domain to allow the molecule to adopt a 'closed' configuration that prevents formation of the core fusion complex - it thus has an auto-inhibitory role. The function of syntaxins is determined by their localisation. They are involved in neuronal exocytosis, ER-Golgi transport and Golgi-endosome transport, for example. They also interact with other proteins as well as those involved in SNARE complexes. These include vesicle coat proteins, Rab GTPases, and tethering factors  .. 
PF00907 T-box<br>Pfam-B_363 (release 3.0). The T-box encodes a 180 amino acid domain that binds to DNA. Genes encoding T-box proteins are found in a wide range of animals, but not in other kingdoms such as plants. Family members are all thought to bind to the DNA consensus sequence TCACACCT. they are found exclusively in the nucleus, and perform DNA-binding and transcriptional activation/repression roles. They are generally required for development of the specific tissues they are expressed in, and mutations in T-box genes are implicated in human conditions such as DiGeorge syndrome and X-linked cleft palate, which feature malformations  .. 
PF04719 hTAFII28-like protein conserved region<br>Pfam-B_4085 (release 7.5). The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex.  The conserved region is found at the C-terminal of most member proteins.  The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits.  The conserved region contains four alpha helices and three loops arranged as in histone H3 [1,2].. 
PF04177 TAP42-like family<br>Pfam-B_5735 (release 7.3);. 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  .. 
PF03943 TAP C-terminal domain<br>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 nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate nuclear shuttling  . The structure of the C-terminal domain is composed of four helices  . The structure is related to the UBA domain.. 
PF03134 TB2/DP1, HVA22 family<br>Pfam-B_837 (release 6.5). This family includes members from a wide variety of eukaryotes. It includes the TB2/DP1 (deleted in polyposis) protein  (e.g. Swiss:Q00765), which in humans is deleted in severe forms of familial adenomatous polyposis, an autosomal dominant oncological inherited disease. The family also includes the plant protein of known similarity to TB2/DP1, the HVA22 abscisic acid-induced protein (e.g. Swiss:Q07764), which is thought to be a regulatory protein.. 
PF00352 Transcription factor TFIID (or TATA-binding protein, TBP)<br>
PF03148 Tektin family<br>Pfam-B_3069 (release 6.5). 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, organised as longitudinal polymers of tektin heterodimers with axial periodicity matching tubulin. Tektin polypeptides consist of several alpha-helical regions that are  predicted to form coiled coils. Indeed, tektins share considerable structural similarities with intermediate filament proteins. Possible functional roles for tektins are: stabilisation of tubulin protofilaments; attachment of A and B-tubules in ciliary/flagellar microtubule doublets and C-tubules in centrioles; binding of axonemal components  .. 
PF01397 Terpene synthase, N-terminal domain<br>Pfam-B_728 (release 3.0). It has been suggested that this gene family be designated tps (for terpene synthase)  .  It has been split into six subgroups on the basis of phylogeny, called tpsa-tpsf. tpsa includes vetispiridiene synthase Swiss:Q39979, 5-epi- aristolochene synthase, Swiss:Q40577 and (+)-delta-cadinene synthase Swiss:P93665. tpsb includes (-)-limonene synthase, Swiss:Q40322. tpsc includes kaurene synthase A, Swiss:O04408. tpsd includes taxadiene synthase, Swiss:Q41594, pinene synthase, Swiss:O24475 and myrcene synthase, Swiss:O24474. tpse includes kaurene synthase B. tpsf includes linalool synthase.. 
PF00440 tetR; <br>Bacterial regulatory proteins, tetR family. 
PF03850 Transcription factor Tfb4<br>This family appears to be distantly related to the VWA domain.. 
PF02269 TFIID-18; <br>Transcription initiation factor IID, 18kD subunit. Pfam-B_3681 (release 5.2). 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 fold  . 
PF03847 TFIID_A; <br>Transcription initiation factor TFIID subunit A. 
PF04494 TFIID_WDA; <br>WD40 associated region in TFIID subunit. Pfam-B_9152 (release 7.5). This region, possibly a domain is found in subunits of transcription factor TFIID.  The function of this region is unknown.. 
PF04253 Transferrin receptor-like dimerisation domain<br>This domain is involved in dimerisation of the transferrin receptor as shown in its crystal structure.. 
PF02824 TGS domain<br>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 spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly  beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role  . . 
PF00763 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain<br>Pfam-B_882 (release 2.1). 
PF02882 Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain<br>Pfam-B_882 (release 2.1). 
PF00899 ThiF_family;<br>Pfam-B_59 (release 3.0). This family contains a repeated domain in ubiquitin activating enzyme E1 and members of the bacterial ThiF/MoeB/HesA family.. 
PF02597 DUF170;<br>ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer Swiss:O32583. 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 activation process. Sulphur is transferred from ThiI to ThiS in a reaction catalysed by IscS  . MoaD, Swiss:P30748 a protein involved sulphur transfer in molybdopterin synthesis, is about the same length and shows limited sequence similarity to ThiS. Both have the conserved GG at the COOH end.. 
PF01833 IPT/TIG domain<br>This family consists of a domain that has an immunoglobulin like fold. These domains are found in cell surface receptors such as Met and Ron as well as in intracellular transcription factors where it is involved in DNA binding. CAUTION: This family does not currently recognise a significant number of members.. 
PF04280 Tim44-like domain<br>TIGRFAMs (release 2.0);. 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 the mitochondrial inner membrane both by electrostatic interactions and by penetrating the polar head group region  .  This family includes the C-terminal region of Tim44 that has been shown to form a stable proteolytic fragment in yeast.  This region is also found in a set of smaller bacterial proteins. The molecular function of the bacterial members of this family is unknown but transport seems likely. The crystal structure of the C terminal of Tim44 has revealed a large hydrophobic pocket which might play an important role in interacting with the acyl chains of lipid molecules in the mitochondrial membrane  .. 
PF04176 TIP41-like family <br>Pfam-B_12821 (release 7.3);. The TOR signalling pathway activates a cell-growth program in response to nutrients  . TIP41 interacts with TAP42 and negatively regulates the TOR signaling pathway  .. 
PF01582 TIR domain<br>Pfam-B_571 (release 4.1). The Toll/interleukin-1 receptor (TIR) homology domain is an intracellular signalling domain found in MyD88, interleukin 1 receptor and the Toll receptor. It contains three highly-conserved regions, and mediates protein-protein interactions between the Toll-like receptors (TLRs) and signal-transduction components. TIR-like motifs are also found in plant proteins thought to be involved in resistance to disease. When activated, TIR domains recruit cytoplasmic adaptor proteins MyD88 (Swiss:Q99836) and TOLLIP (Toll interacting protein, Swiss:Q9H0E2). In turn, these associate with various kinases to set off signalling cascades  .. 
PF03920 TLE_N-terminal; <br>Groucho/TLE N-terminal Q-rich domain. The N-terminal domain of the Grouch/TLE co-repressor proteins are involved in oligomerisation.. 
PF05154 TM2 domain<br>This family is composed of a pair of transmembrane alpha helices connected by a short linker.  The function of this domain is unknown, however it occurs in a wide range or protein contexts.. 
PF03348 TMS_TDE; <br>Serine incorporator (Serinc). Pfam-B_3473 (release 6.5). This is a family of eukaryotic membrane proteins which incorporate serine into membranes and facilitate the synthesis of the serine-derived lipids phosphatidylserine and sphingolipid  .  Members of this family contain 11 transmembrane domains and form intracellular complexes with key enzymes involved in serine and sphingolipid biosynthesis  .. 
PF03459 TOBE domain<br>The TOBE domain   (Transport-associated OB) always occurs  as a dimer as the C-terminal strand of each domain is supplied by the partner. Probably involved in the recognition of small ligands such as molybdenum (eg Swiss:P46930) and sulfate (Swiss:P16676). Found in ABC transporters immediately  after the ATPase domain.. 
PF04265 Thiamin pyrophosphokinase, vitamin B1 binding domain<br>TIGRFAMs (release 2.0);. Family of thiamin pyrophosphokinase (EC:2.7.6.2). Thiamin pyrophosphokinase (TPK) catalyses the transfer of a pyrophosphate group from ATP to vitamin B1 (thiamin) to form the coenzyme thiamin pyrophosphate (TPP). Thus, TPK is important for the formation of a coenzyme required for central metabolic functions. The structure of thiamin pyrophosphokinase suggest that the enzyme may operate by a mechanism of pyrophosphoryl transfer similar to those described for pyrophosphokinases functioning in nucleotide biosynthesis  .. 
PF04263 Thiamin pyrophosphokinase, catalytic domain<br>TIGRFAMs (release 2.0);. Family of thiamin pyrophosphokinase (EC:2.7.6.2). Thiamin pyrophosphokinase (TPK) catalyses the transfer of a pyrophosphate group from ATP to vitamin B1 (thiamin) to form the coenzyme thiamin pyrophosphate (TPP). Thus, TPK is important for the formation of a coenzyme required for central metabolic functions. The structure of thiamin pyrophosphokinase suggest that the enzyme may operate by a mechanism of pyrophosphoryl transfer similar to those described for pyrophosphokinases functioning in nucleotide biosynthesis  .. 
PF00515 TPR;<br>Tetratricopeptide repeat. Alignment kindly provided by SMART. 
PF01938 DUF90;<br>
PF00486 trans_reg_C; <br>Transcriptional regulatory protein, C terminal. Pfam-B_94 (release 1.0). 
PF02458 Transferase family<br>Pfam-B_1540 (release 5.4). This family includes a number of transferase enzymes. These include anthranilate N-hydroxycinnamoyl/benzoyltransferase that catalyses the first committed reaction of phytoalexin biosynthesis  . Deacetylvindoline 4-O-acetyltransferase EC:2.3.1.107 catalyses the last step in vindoline biosynthesis is also a member of this family  . The motif HXXXD is probably part of the active site. The family also includes trichothecene 3-O-acetyltransferase.. 
PF01336 Aspartyl_tRNA_N; tRNA_anti;<br>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 Pfam:PF00152). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [2,3]. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain.. 
PF01841 Transglutaminase-like superfamily<br>This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterised transglutaminase, the human blood clotting factor XIIIa'  . On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase  , it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease.  . 
PF00927 1005; Transglutamin_C; <br>Transglutaminase family, C-terminal ig like domain. Pfam-B_1005 (release 3.0). 
PF02779 transketolaseD2; transket_pyr; <br>Transketolase, pyrimidine binding domain. This family includes transketolase enzymes, pyruvate dehydrogenases, and branched chain alpha-keto acid decarboxylases.. 
PF02780 transketolaseD3; transketolase_C;<br>Transketolase, C-terminal domain. The C-terminal domain of transketolase has been proposed as a regulatory molecule binding site  .. 
PF00335 transmembrane4; <br>
PF00905 Penicillin binding protein transpeptidase domain<br>The active site serine (residue 337 in Swiss:P14677) is conserved in all members of this family.. 
PF01609 Transposase_11;<br>Transposase DDE domain. Pfam-B_1013 (release 4.1). Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction  . This family contains transposases for  IS4 Swiss:P03835  ,  IS421 Swiss:P11901  , IS5377 Swiss:Q45620, IS427  , IS402  , IS1355 Swiss:O69604, IS5, which was original isolated in bacteriophage lambda  .. 
PF02371 Transposase_19; <br>Transposase IS116/IS110/IS902 family. Pfam-B_280 (release 5.2). Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. This region is often found with Pfam:PF01548. The exact function of this region is uncertain. This family contains a HHH motif suggesting a DNA-binding function.. 
PF01526 Transposase_7;<br>Tn3 transposase DDE domain. Pfam-B_885 (release 4.0). This family includes transposases of Tn3, Tn21, Tn1721, Tn2501, Tn3926 transposons from E-coli.  The specific binding of the Tn3 transposase to DNA has been demonstrated. Sequence analysis has suggested that the invariant triad of Asp689, Asp765, Glu895 (numbering as in Tn3) may correspond to the D-D-35-E motif previously implicated in the catalysis of numerous transposases  .. 
PF01548 Transposase_9;<br>Pfam-B_646 (release 4.0). Transposase proteins are necessary for efficient DNA transposition.  This family includes an amino-terminal region of the pilin gene inverting protein (PIVML) and members of the IS111A/IS1328/IS1533 family of transposases.. 
PF00579 tRNA synthetases class I (W and Y)<br>MRC-LMB Genome group. 
PF01409 tRNA synthetases class II core domain (F)<br>Other tRNA synthetase sub-families are too dissimilar to be included.  This family includes only phenylalanyl-tRNA synthetases. This is the core catalytic domain.. 
PF01588 Putative tRNA binding domain<br>Pfam-B_482 (release 4.1). This domain is found in prokaryotic methionyl-tRNA synthetases,  prokaryotic phenylalanyl tRNA synthetases the yeast GU4 nucleic-binding  protein (G4p1 or p42, ARC1)  , human tyrosyl-tRNA synthetase  , and endothelial-monocyte activating polypeptide II.  G4p1 binds specifically to tRNA form a complex with methionyl-tRNA  synthetases  . In human tyrosyl-tRNA synthetase this domain may direct tRNA to the active site of the enzyme  . This domain may perform a common function in tRNA aminoacylation  .. 
PF03250 Tropomodulin<br>Pfam-B_3359 (release 6.5). 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 domains  . The amino terminal domain contains the tropomyosin binding function  .. 
PF00992 Troponin<br>Pfam-B_62 (release 3.0). Troponin (Tn) contains three subunits, Ca2+ binding (TnC), inhibitory (TnI), and tropomyosin binding (TnT).  this Pfam contains members of the TnT subunit. Troponin is a complex of three proteins, Ca2+ binding (TnC), inhibitory (TnI), and tropomyosin binding (TnT).  The troponin complex regulates Ca++ induced muscle contraction. This family includes troponin T and troponin I.  Troponin I binds to actin and troponin T binds to tropomyosin.. 
PF00234 tryp_alpha_amyl; <br>Protease inhibitor/seed storage/LTP family. This family is composed of trypsin-alpha amylase inhibitors, seed  storage proteins and lipid transfer proteins from plants.. 
PF00089 trypsin;<br>
PF02210 TSPN; TSP_N;<br>Pfam-B_4211 (release 12.0) . This family includes the Thrombospondin N-terminal-like domain, a Laminin G subfamily.. 
PF03133 Tubulin-tyrosine ligase family<br>Pfam-B_682 (release 6.5). 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 modification cycle involves a specific carboxypeptidase and the activity of the tubulin-tyrosine ligase (TTL)  . The true physiological function of TTL has so far not been established. Tubulin-tyrosine ligase (TTL) catalyses the ATP-dependent post-translational addition of a tyrosine to the carboxy terminal end of detyrosinated alpha-tubulin. In normally cycling cells, the tyrosinated form of tubulin predominates. However, in breast cancer cells, the detyrosinated form frequently predominates, with a correlation to tumour aggressiveness  . On the other hand, 3-nitrotyrosine has been shown to be incorporated, by TTL, into the carboxy terminal end of detyrosinated alpha-tubulin. This reaction is not reversible by the carboxypeptidase enzyme. Cells cultured in 3-nitrotyrosine rich medium showed evidence of altered microtubule structure and function, including altered cell morphology, epithelial barrier dysfunction, and apoptosis  .  Bacterial homologs of TTL are predicted to form peptide tags. Some of these are fused to a 2-oxoglutarate Fe(II)-dependent  dioxygenase domain  .. 
PF01167 Tub family<br>
PF03953 tubulin_C; <br>Tubulin C-terminal domain. This family includes the tubulin alpha, beta and gamma chains. Members of this family are involved in polymer formation. Tubulins are GTPases. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea. Tubulin is the major component of microtubules. (The FtsZ GTPases have been split into their won family).. 
PF00567 Tudor domain<br>Alignment kindly provided by SMART. 
PF04906 Tweety<br>Pfam-B_5713 (release 7.6). The tweety (tty) gene has not been characterised at the protein level. However, it is thought to form a membrane protein with five potential membrane-spanning regions. A number of potential functions have been suggested in  .. 
PF04564 U-box domain<br>Pfam-B_2801 (release 7.5). This domain is related to the Ring finger Pfam:PF00097 but lacks the zinc binding residues  .. 
PF00627 UBA/TS-N domain<br>This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin and the ubiquitination pathway. The structure of the UBA domain consists of a compact three helix bundle  . This domain is found at the N terminus of EF-TS hence the name TS-N.  The structure of EF-TS is known and this domain is implicated in its interaction with EF-TU  . The domain has been found in non EF-TS proteins such as alpha-NAC Swiss:P70670 and MJ0280 Swiss:Q57728  .. 
PF01040 CytC_assmbly_fac; COX10_ctaB_cyoE;<br>UbiA prenyltransferase family. Pfam-B_1357 (release 3.0). 
PF00240 Ubiquitin family<br>This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites  .. 
PF00789 UBX domain<br>SMART, Mistry J, Wood V. Alignment kindly provided by SMART. This domain is present in ubiquitin-regulatory proteins and is a general Cdc48-interacting module  .. 
PF00443 UCH-2;<br>Ubiquitin carboxyl-terminal hydrolase. 
PF03456 uDENN domain<br>This region is always found associated with Pfam:PF02141. It is predicted to form an all beta domain  .. 
PF03167 Uracil DNA glycosylase superfamily<br>
PF02809 Ubiquitin interaction motif<br>This motif is called the ubiquitin interaction motif. One of the proteins containing this motif is a receptor for poly-ubiquitination chains for the proteasome  . This motif has a pattern of conservation characteristic of an alpha helix.. 
PF01027 UPF0005;<br>Inhibitor of apoptosis-promoting Bax1. Pfam-B_1376 (release 3.0) & Pfam-B_5704 (release 7.5). Programmed cell-death involves a set of Bcl-2 family proteins, some of which inhibit apoptosis (Bcl-2 and Bcl-XL) and some of which promote it (Bax and Bak). Human Bax inhibitor, BI-1, is an evolutionarily conserved integral membrane protein containing multiple membrane-spanning segments predominantly localised to intracellular membranes. It has 6-7 membrane-spanning domains. The C termini of the mammalian BI-1 proteins are comprised of basic amino acids resembling some nuclear targeting sequences, but otherwise the predicted proteins lack motifs that suggest a function. As plant BI-1 appears to localise predominantly to the ER, we hypothesized that plant BI-1 could also regulate cell death triggered by ER stress  . BI-1 appears to exert its effect through an interaction with calmodulin  . The budding yeast member of this family has been found unexpectedly to encode a BH3 domain-containing protein (Ybh3p) that regulates the mitochondrial pathway of apoptosis in a phylogenetically conserved manner  .. 
PF03684 Uncharacterised protein family (UPF0179)<br>The function of this family is unknown, however the proteins contain two cysteine clusters that may be iron sulphur redox centres.. 
PF03699 Uncharacterised protein family (UPF0182)<br>This family contains uncharacterised integral membrane proteins.. 
PF03676 Uncharacterised protein family (UPF0183)<br>This family of proteins includes Lin-10 from C. elegans. . 
PF03671 UPF0185; <br>Ubiquitin fold modifier 1 protein. This is a family of short ubiquitin-like proteins, that is like neither type-1 or type-2. It is a ubiquitin-fold modifier 1 (Ufm1) that is synthesised in a precursor form of 85 amino-acid residues. In humans the enzyme for Ufm1 is Uba5 and the conjugating enzyme is Ufc1. Prior to activation by Uba5 the extra two amino acids at the C-terminal region of the human pro-Ufm1 protein are removed to expose Gly whose residue is necessary for conjugation to target molecule(s). The mature Ufm1 is conjugated to yet unidentified endogenous proteins, . While Ubiquitin and many Ubls possess the conserved C-terminal di-glycine that is adenylated by each specific E1 or E1-like enzyme, respectively, in an ATP-dependent manner, Ufm1(1-83) possesses a single glycine at its C-terminus, which is followed by a Ser-Cys dipeptide in the precursor form of Ufm1. The C-terminally processed Ufm1(1-83) is specifically activated by Uba5, an E1-like enzyme, and then transferred to its cognate Ufc1, an E2-like enzyme  .. 
PF00179 Ubiquitin-conjugating enzyme<br>Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine [4, 5].. 
PF02814 UreE;<br>UreE urease accessory protein, N-terminal domain. Pfam-B_6279 (release 6.1). UreE is a urease accessory protein. Urease Pfam:PF00449 hydrolyses  urea into ammonia and carbamic acid.. 
PF04192 Utp21 specific WD40 associated putative domain <br>Pfam-B_16350 (release 7.3);. Utp21 is a subunit of U3 snoRNP, which is essential for  synthesis of 18S rRNA.. 
PF02151 UvrB/uvrC motif<br>
PF05008 Vesicle transport v-SNARE protein N-terminus<br>Pfam-B_5492 (release 7.6). V-SNARE proteins are required for protein traffic between eukaryotic organelles. The v-SNAREs on transport vesicles interact with t-SNAREs on target membranes in order to facilitate this  .  This domain is the N-terminal half of the V-Snare proteins.. 
PF00790 VHS domain<br>Alignment kindly provided by SMART. Domain present in VPS-27, Hrs and STAM.. 
PF00654 voltage_CLC; <br>Voltage gated chloride channel. wublastp P37020/1-588. This family of ion channels contains 10 or 12 transmembrane helices. Each protein forms a single pore. It has been shown that some members of this family form homodimers. In terms of primary structure, they are unrelated to known cation channels or other types of anion channels. Three ClC subfamilies are found in animals. ClC-1 (Swiss:P35523) is involved in setting and restoring the resting membrane potential of skeletal muscle, while other channels play important parts in solute concentration mechanisms in the kidney  . These proteins contain two Pfam:PF00571 domains.. 
PF04840 Vps16, C-terminal region<br>Pfam-B_6003 (release 7.6). This protein forms part of the Class C vacuolar protein sorting (Vps) complex. Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast  . The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole.  It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport  .  The role of VPS16 in this complex is not known.. 
PF04841 Vps16, N-terminal region<br>Pfam-B_6003 (release 7.6). This protein forms part of the Class C vacuolar protein sorting (Vps) complex. Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast  . The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole.  It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport  .  The role of VPS16 in this complex is not known.. 
PF03635 Vacuolar protein sorting-associated protein 35 <br>Pfam-B_3569 (release 7.0). 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 Vps5, Vps17, Vps26 and Vps29.  Vps35 contains a central region of weaker sequence similarity, thought to indicate the presence of at least three domains .. 
PF04129 Vps52 / Sac2 family <br>Pfam-B_10164 (release 7.3);. Vps52 complexes with Vps53 and Vps54 to form a multi- subunit complex involved in regulating membrane trafficking events  .. 
PF04100 Vps53-like, N-terminal <br>Pfam-B_5601 (release 7.3);. Vps53 complexes with Vps52 and Vps54 to form a multi- subunit complex involved in regulating membrane trafficking events  .. 
PF02204 Vacuolar sorting protein 9 (VPS9) domain<br>Alignment kindly provided by SMART. This domain acts as a GDP-GTP exchange factor (GEF). It activates Rab GTPases by stimulating the release of GDP and allowing GTP to bind  .. 
PF03302 Giardia variant-specific surface protein<br>Pfam-B_4536 (release 6.5). 
PF00092 vwa; <br>von Willebrand factor type A domain. 
PF00094 vwd; <br>von Willebrand factor type D domain. Swiss:P17554 contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods.. 
PF00095 wap; <br>WAP-type (Whey Acidic Protein) 'four-disulfide core'. Swissprot_feature_table. 
PF00400 G-beta; <br>WD domain, G-beta repeat. Pfam-B_2 (release 1.0). 
PF00568 WH1 domain<br>Alignment kindly provided by SMART. 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 mGluR5 bind a protein called homer, which is a WH1 domain homologue   . A subset of WH1 domains has been termed a "EVH1" domain   and  appear to bind a polyproline motif.. 
PF02205 WH2 motif<br>Alignment kindly provided by SMART. The WH2 motif (for Wiskott Aldrich syndrome homology region 2) has been shown in WASP Swiss:P42768 and Scar1 (mammalian homologue) to be the region that interacts with actin.. 
PF02467 Transcription factor WhiB<br>Pfam-B_2249 (release 5.4). WhiB is a putative transcription factor in Actinobacteria, required for differentiation and sporulation.. 
PF02019 WIF domain<br>The WIF domain is found in the RYK tyrosine kinase receptors Swiss:P34925 and WIF the Wnt-inhibitory- factor. The domain is extracellular and contains two conserved cysteines that may form a disulphide bridge.  This domain is Wnt binding in WIF, and it has been suggested that RYK may also bind to Wnt  . The WIF domain is a member of the immunoglobulin superfamily, and it comprises nine beta-strands and two alpha-helices, with two of the beta-strands (6 and 9) interrupted by four and six residues of irregular secondary structure, respectively. Considering that the activity of Wnts depends on the presence of a palmitoylated cysteine residue in their amino-terminal polypeptide segment, Wnt proteins are lipid-modified and can act as stem cell growth factors, it is likely that the WIF domain recognises and binds to Wnts that have been activated by palmitoylation and that the recognition of palmitoylated Wnts by WIF-1 is effected by its WIF domain rather than by its EGF domains. A strong binding affinity for palmitoylated cysteine residues would further explain the remarkably high affinity of human WIF-1 not only for mammalian Wnts, but also for Wnts from Xenopus and Drosophila  .. 
PF03106 WRKY DNA -binding domain<br>Pfam-B_85 (release 6.5). 
PF02206 Domain of unknown function<br>Alignment kindly provided by SMART. 
PF00397 WW_rsp5_WWP; <br>The WW domain is a protein module with two highly conserved tryptophans that binds proline-rich peptide motifs in vitro.. 
PF02825 WWE domain<br>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  .. 
PF02706 wzz; <br>Chain length determinant protein. Pfam-B_1977 (release 5.5). This family includes proteins involved in lipopolysaccharide (lps) biosynthesis. This family comprises the whole length of chain length determinant protein (or wzz protein) that confers a modal distribution of chain length on the O-antigen component of lps  . This region is also found as part of bacterial tyrosine kinases such as Swiss:P38134.. 
PF03254 Xyloglucan fucosyltransferase<br>Pfam-B_3419 (release 6.5). Plant cell walls are crucial for development, signal transduction, and disease resistance in plants. Cell walls are made of cellulose, hemicelluloses, and pectins. Xyloglucan (XG), the principal load-bearing hemicellulose of dicotyledonous plants, has a terminal fucosyl residue. This fucosyltransferase adds this residue  .. 
PF05181 XPA;<br>XPA protein C-terminus. 
PF01286 XPA; <br>XPA protein N-terminal. 
PF00102 Protein-tyrosine phosphatase<br>Swissprot_feature_table. 
PF04893 DUF649; <br>Pfam-B_5598 (release 7.6). The Yip1 integral membrane domain contains four transmembrane alpha helices. The domain is characterised by the motifs DLYGP and GY. The Yip1 protein is a golgi protein involved in vesicular transport that interacts with GTPases  .. 
PF03226 Yippee;<br>Yippee zinc-binding/DNA-binding /Mis18, centromere assembly. Pfam-B_2930 (release 6.5). This family includes both Yippee-type proteins and Mis18 kinetochore proteins.\. Yippee are putative zinc-binding/DNA-binding proteins. Mis18 are proteins involved in the priming of centromeres for recruiting CENP-A. Mis18-alpha and beta form part of a small complex with Mis18-binding protein. Mis18-alpha is found to interact with DNA de-methylases through a Leu-rich region located at its carboxyl terminus  .. 
PF02757 YLP motif<br>The YLP motif is found in several drosophila proteins. Its function is unknown, however the presence of completely conserved tyrosine residues and its presence in Swiss:Q15303 may suggest it could be a substrate for tyrosine kinases.. 
PF04146 YT521-B; <br>Pfam-B_1386 (release 7.3). A protein of the YTH family has been shown to selectively remove transcripts of meiosis-specific genes expressed in mitotic cells  .  It has been speculated that in higher eukaryotic YTH-family members may be involved in similar mechanisms to suppress gene regulation during gametogenesis or general silencing.  The rat protein Swiss:Q9QY02 YT521-B is a tyrosine-phosphorylated nuclear protein, that interacts with the nuclear transcriptosomal component scaffold attachment factor B, and the 68-kDa Src substrate associated during mitosis, Sam68. In vivo splicing assays demonstrated that YT521-B modulates alternative splice site selection in a concentration-dependent manner  . The YTH domain has been identified as part of the PUA superfamily  .. 
PF00643 B-box zinc finger<br>
PF02892 BED zinc finger<br>
PF01530 Zinc finger, C2HC type<br>This is a DNA binding zinc finger domain.. 
PF00097 Zinc finger, C3HC4 type (RING finger)<br>Swissprot_feature_table. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid  . Many proteins containing a RING finger play a key role in the ubiquitination pathway  .. 
PF00642 Zinc finger C-x8-C-x5-C-x3-H type (and similar)<br>
PF00098 Zinc knuckle<br>Overington and HMM_iterative_training. The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag  proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.. 
PF02008 CXXC zinc finger domain<br>This domain contains eight conserved cysteine residues that bind to two zinc ions.  The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterised by two repeats  , and shows a peculiar internal duplication in which the second unit is inserted into the first one  . Each of these units is  characterised by four conserved cysteines, displaying a CXXCXXCX(n)C motif that chelate a Zn+2 ion. The DNA binding interface has been  identified by NMR  . In eukaryotes, the CXXC domain is found in stramenopiles, plants and metazoans. Plants possess  a mono-CXXC domain that is present in distinct chromatin proteins   . Structural comparisons show that the mono-CXXC is homologous  to the structural-zinc binding domain of medium chain  dehydrogenases  .. 
PF01529 DHHC palmitoyltransferase<br>Pfam-B_945 (release 4.0). This family includes the well known DHHC zinc binding domain as well as three of the four conserved transmembrane regions found in this family of palmitoyltransferase enzymes.. 
PF04438 HIT zinc finger<br>This presumed zinc finger contains up to 6 cysteine residues that could coordinate zinc. The domain is named after the HIT protein Swiss:P46973. This domain is also found in the Thyroid receptor interacting protein 3 (TRIP-3) Swiss:Q15649 that specifically interact with the ligand binding domain of the thyroid receptor.. 
PF02891 MIZ/SP-RING zinc finger<br>This domain has SUMO (small ubiquitin-like modifier) ligase activity and is involved in DNA repair and chromosome organisation   .. 
PF01753 MYND finger<br>
PF05020 NPL4 family, putative zinc binding region<br>Pfam-B_13681 (release 7.6). 
PF04810 Sec23/Sec24 zinc finger<br>COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is found to be zinc binding domain.. 
PF02148 Zn-finger in ubiquitin-hydrolases and other protein<br>
PF04704 Zfx / Zfy transcription activation region<br>Zfx and Zfy are transcription factors implicated in mammalian sex  determination. This region is found N terminal to multiple copies of a C2H2 Zinc finger  (Pfam:PF00096).  This region has been shown to activate transcription when fused to a GAL4 DNA binding domain  .. 
PF02535 ZIP Zinc transporter<br>Pfam-B_1189 (release 5.4) & Pfam-B_1903 (Release 7.5). 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 plant  .  Also found within this family are  C. elegans proteins of unknown function which are annotated as being similar to human growth arrest inducible gene product, although this protein in not found within this family.. 
PF00246 Zn_carbOpept; <br>Zinc carboxypeptidase. Prosite & Pfam-B_4832 (Release 7.5). 
PF00100 zona_pellucida; <br>Zona pellucida-like domain. Swissprot_feature_table. 
PF01262 AlaDh_PNT; <br>Alanine dehydrogenase/PNT, C-terminal domain. Pfam-B_4166 (release 6.6). This family now also contains the lysine 2-oxoglutarate reductases. . 
PF05222 Alanine dehydrogenase/PNT, N-terminal domain<br>This family now also contains the lysine 2-oxoglutarate reductases. . 
PF05218 Protein of unknown function (DUF713)<br>Moxon SJ, Pollington J. Pfam-B_6651 (release 7.7). This family contains several proteins of unknown function from C.elegans. The GO annotation suggests that this protein is involved in nematode development and has a positive regulation on growth rate.. 
PF05210 Sprouty protein (Spry)<br>Pfam-B_6527 (release 7.7). This family consists of eukaryotic Sprouty protein homologues. Sprouty proteins have been revealed as inhibitors of the Ras/mitogen-activated protein kinase (MAPK) cascade, a pathway crucial for developmental processes initiated by activation of various receptor tyrosine kinases  . The sprouty gene has found to be expressed in the the brain, cochlea, nasal organs, teeth, salivary gland, lungs, digestive tract, kidneys and limb buds in mice  .. 
PF05216 UNC-50 family<br>Pfam-B_6607 (release 7.7). Gmh1p (Swiss:P36125) from S. cerevisiae is located in the Golgi membrane and interacts with ARF exchange factors  .. 
PF00702 haloacid dehalogenase-like hydrolase<br>Pfam-B_566 (release 2.1). This family is structurally different from the alpha/beta hydrolase family (Pfam:PF00561). This family includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases. The structure of the family consists of two domains. One is an inserted four helix bundle, which is the least well conserved region of the alignment, between residues 16 and 96 of Swiss:P24069. The rest of the fold is composed of the core alpha/beta domain  . Those members with the characteristic DxD triad at the N-terminus are probably phosphatidylglycerolphosphate (PGP) phosphatases involved in cardiolipin biosynthesis in the mitochondria  .. 
PF04227 Indigoidine synthase A like protein<br>Indigoidine is a blue pigment synthesised by Erwinia chrysanthemi implicated in pathogenicity and protection from oxidative stress. IdgA is involved in indigoidine biosynthesis, but its specific function is unknown  . The recommended name for this protein is now pseudouridine-5'-phosphate glycosidase.. 
PF04613 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD  <br>UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase (EC 2.3.1.-) catalyses an early step in lipid A biosynthesis: UDP-3-O-(3-hydroxytetradecanoyl)glucosamine + (R)-3-hydroxytetradecanoyl- [acyl carrier protein] -> UDP-2,3-bis(3-hydroxytetradecanoyl)glucosamine + [acyl carrier protein]  . Members of this family also contain a hexapeptide repeat (Pfam:PF00132).  This family constitutes the non-repeating region of LPXD proteins.. 
PF00244 14-3-3 protein<br>
PF02826 2-Hacid_DH_C; <br>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 Pfam:PF00389.. 
PF02834 2_5_ligase; 2_5_RNA_ligase;<br>LigT like Phosphoesterase. Members of this family are bacterial and archaeal RNA ligases that are able to ligate tRNA half molecules containing 2',3'-cyclic phosphate and 5' hydroxyl termini to products containing the 2',5' phosphodiester linkage. Each member of this family contains an internal duplication, each of which contains an HXTX motif that defines the family. The structure of a related protein is known  . They belong to the 2H phosphoesterase superfamily  . They share a common active site, characterised by two conserved histidines, with vertebrate myelin-associated 2',3' phosphodiesterases, plant Arabidopsis thaliana CPDases and several several bacteria and virus proteins.. 
PF03475 3-alpha domain<br>Aravind L, Anantharaman V. This small triple helical domain has been predicted to assume a topology similar to helix-turn-helix domains. These domains are found at the C-terminus of proteins related to Swiss:P32157.. 
PF01612 3_5_exonuclease; 3_5_exonuc;<br>Pfam-B_659 (release 4.1). 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-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D).  Werner syndrome is a human genetic disorder causing premature aging; the WRN protein has helicase activity in the 3'-5' direction [4,5].  The FFA-1 protein is required for formation of a replication foci and also has helicase activity; it is a homologue of the WRN protein  . RNase D is a 3'-5' exonuclease involved in tRNA processing. Also found in this family is the autoantigen PM/Scl thought to be involved in polymyositis-scleroderma overlap syndrome.. 
PF00803 3A/RNA2 movement protein family<br>Pfam-B_1054 (release 2.1) & Pfam-B_6332 (release 7.5). This family includes movement proteins from various viruses. The 3A protein is found in bromoviruses and Cucumoviruses. The genome of these viruses contain 3 RNA segments.  The third segment (RNA 3) contains two proteins, the coat protein and the 3A protein. The function of the 3A protein is uncertain but has been shown to be involved in cell-to- cell movement of the virus  . The family also includes movement proteins from Dianthoviruses.. 
PF02829 3H domain<br>This domain is predicted to be a small molecule binding domain, based on its occurrence with other domains  . The domain is named after its three conserved histidine residues.. 
PF00725 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain<br>Pfam-B_743 (release 2.1). This family also includes lambda crystallin. Some proteins include two copies of this domain.. 
PF02737 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain<br>Pfam-B_743 (release 2.1). This family also includes lambda crystallin.. 
PF02446 4A_glucanotrans; 4a_glucanotrans; <br>4-alpha-glucanotransferase. Pfam-B_1924 (release 5.4). These enzymes EC:2.4.1.25 transfer a segment of a (1,4)-alpha-D-glucan to a new 4-position in an acceptor, which may be glucose or (1,4)-alpha-D-glucan  .. 
PF01812 5-formyltetrahydrofolate cyclo-ligase family<br>Pfam-B_1555 (release 4.2). 5-formyltetrahydrofolate cyclo-ligase or methenyl-THF synthetase EC:6.3.3.2 catalyses the interchange of 5-formyltetrahydrofolate  (5-FTHF) to 5-10-methenyltetrahydrofolate, this requires ATP and Mg2+  . 5-FTHF is used in chemotherapy where it is clinically known as Leucovorin  .. 
PF02739 5'-3' exonuclease, N-terminal resolvase-like domain<br>Pfam-B_716 (release 3.0). 
PF01367 5_3_exonuclease; <br>5'-3' exonuclease, C-terminal SAM fold. Pfam-B_716 (release 3.0). 
PF03491 Serotonin (5-HT) neurotransmitter transporter, N-terminus<br>
PF02096 60Kd inner membrane protein<br>
PF00428 60s_ribosomal;<br>60s Acidic ribosomal protein. Pfam-B_151 (release 1.0). This family includes archaebacterial L12, eukaryotic P0, P1 and P2.. 
PF01591 6-phosphofructo-2-kinase<br>Pfam-B_717 (release 4.1). This enzyme occurs as a bifunctional enzyme with fructose-2,6-bisphosphatase. The bifunctional enzyme catalyses both the synthesis and degradation of fructose-2,6-bisphosphate, a potent regulator of glycolysis  . This enzyme contains a P-loop motif.. 
PF00393 6-phosphogluconate dehydrogenase, C-terminal domain<br>This family represents the C-terminal all-alpha domain of 6-phosphogluconate dehydrogenase.\.  The domain contains two structural repeats of 5 helices each.. 
PF02495 7kD viral coat protein<br>Pfam-B_2886 (release 5.4). This family consists of a 7kD coat protein from carlavirus  and potexvirus  .. 
PF02294 7kD DNA-binding domain<br>Pfam-B_8148 (release 5.2). This family contains members of the hyper-thermophilic archaebacterium  7kD DNA-binding/endoribonuclease P2 family. There are five 7kD DNA-binding proteins, 7a-7e, found as monomers in the cell. Protein 7e shows the  tightest DNA-binding ability.. 
PF00001 7 transmembrane receptor (rhodopsin family)<br>This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins  .. 
PF00002 7 transmembrane receptor (Secretin family)<br>This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs).They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognised. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97 (Swiss:P48960); calcium-independent receptors for latrotoxin (such as Swiss:O94910), and brain-specific angiogenesis inhibitors (such as Swiss:O14514) amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins (e.g. Swiss:P83119). Other than the typical seven-transmembrane region, characteristic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling  .. 
PF02949 7tm Odorant receptor<br>Pfam-B_436 (release 6.4). This family is composed of 7 transmembrane receptors, that are probably drosophila odorant receptors.. 
PF00207 Alpha-2-macroglobulin family<br>This family includes the C-terminal region of the alpha-2-macroglobulin family.. 
PF01835 MG2 domain<br>This is the MG2 (macroglobulin) domain of alpha-2-macroglobulin  .. 
PF01356 Alpha amylase inhibitor<br>
PF02137 Adenosine-deaminase (editase) domain<br>Adenosine deaminases acting on RNA (ADARs) can deaminate adenosine to form inosine. In long double-stranded RNA, this process is non-specific; it occurs site-specifically in RNA transcripts. The former is important in defence against viruses, whereas the latter may affect splicing or untranslated regions. They are primarily nuclear proteins, but a longer isoform of ADAR1 is found predominantly in the cytoplasm. ADARs are derived from the Tad1-like tRNA deaminases that are present across eukaryotes. These in turn belong to the nucleotide/nucleic acid deaminase superfamily and are characterized by a distinct insert between the two conserved cysteines that are involved in binding zinc  .. 
PF00324 aa_permeases; <br>
PF03306 Alpha-acetolactate decarboxylase<br>Pfam-B_3661 (release 6.5). 
PF04611 Mating type protein A alpha Y mating type dependent binding region <br>This region is important for the mating type dependent binding of Y protein to the A alpha Z protein of another mating type in Schizophyllum commune  .. 
PF03417 Peptidase_C45; <br>Acyl-coenzyme A:6-aminopenicillanic acid acyl-transferase. 
PF02496 ABA/WDS induced protein<br>Pfam-B_2496 (release 5.4). This is a family of plant proteins induced by water deficit stress (WDS)  , or abscisic acid (ABA) stress and ripening  . . 
PF00950 ABC 3 transport family<br>Pfam-B_1591 (release 2.1). 
PF01061 ABC-2 type transporter<br>Pfam-B_865 (release 3.0) & Pfam-B_31 (release 15.0). 
PF00664 ABC transporter transmembrane region<br>Pfam-B_2 (release 2.1). This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (Pfam:PF00005) have two such regions.. 
PF00005 ABC transporter<br>ABC transporters for a large family of proteins responsible for translocation of a variety of compounds across biological membranes.  ABC transporters are the largest family of proteins in many completely sequenced bacteria. ABC transporters are composed of two copies of this domain and two copies of a transmembrane domain Pfam:PF00664.  These four domains may belong to a single polypeptide as in Swiss:P13569, or belong in different polypeptide chains.. 
PF00561 abhydrolase; <br>alpha/beta hydrolase fold. MRC-LMB Genome group. This catalytic domain is found in a very wide range of enzymes.. 
PF03806 AbgT putative transporter family<br>TIGRFAMs, Griffiths-Jones SR. 
PF02230 abhydrolase_2; <br>Phospholipase/Carboxylesterase. Pfam-B_1382 (release 5.2). This family consists of both phospholipases   and carboxylesterases with broad substrate specificity, and is structurally related to  alpha/beta hydrolases Pfam:PF00561  .. 
PF02517 CAAX protease self-immunity<br>Pfam-B_1073 (release 5.4). Members of this family are probably proteases (after a isoprenyl group is attached to the Cys residue in the C-terminal CAAX motif of a protein to attach it to the membrane, the AAX tripeptide being removed by one of the CAAX prenyl proteases).  The family contains the Swiss:Q03530 CAAX prenyl protease. The proteins contain a highly conserved Glu-Glu motif at the amino end of the alignment. The alignment also contains two histidine residues that may be involved in zinc binding  . While they are involved in membrane anchoring of proteins in eukaryotes, little is known about their function in prokaryotes. In some known bacteriocin loci, Abi genes have been found downstream of bacteriocin structural genes where they are probably involved in self-immunity. Investigation of the bacteriocin-like loci in the Gram positive bacteria locus from Lactobacillus sakei 23K confirmed that the bacteriocin-like genes (sak23Kalphabeta) exhibited antimicrobial activity when expressed in a heterologous host and that the associated Abi gene (sak23Ki) conferred immunity against the cognate bacteriocin.  Interestingly, the immunity genes from three similar systems conferred a high degree of cross-immunity against each other's bacteriocins, suggesting the recognition of a common receptor. Site-directed mutagenesis demonstrated that the conserved motifs constituting the putative proteolytic active site of the Abi proteins are essential for the immunity function of Sak23Ki - thus a new concept in self-immunity  .. 
PF03992 Antibiotic biosynthesis monooxygenase<br>This domain is found in monooxygenases involved in the biosynthesis of several antibiotics by Streptomyces species. It's occurrence as a repeat in Streptomyces coelicolor SCO1909 (Swiss:Q9X9W3) is  suggestive that the other proteins function as  multimers. There is also a conserved histidine which is likely to be an active site residue.. 
PF00887 Acyl CoA binding protein<br>Pfam-B_864 (release 3.0). 
PF03255 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit<br>Pfam-B_1935 (release 6.5). Acetyl co-enzyme A carboxylase carboxyltransferase is composed of an alpha and beta subunit.. 
PF00871 Acetokinase family<br>Pfam-B_1595 (release 2.1). This family includes acetate kinase, butyrate kinase and 2-methylpropanoate kinase.. 
PF02550 Acetyl-CoA_hydro; <br>Acetyl-CoA hydrolase/transferase N-terminal domain. This family contains several enzymes which take part in pathways involving acetyl-CoA. Acetyl-CoA hydrolase EC:3.1.2.1 (Swiss:P32316) catalyses the formation of acetate from acetyl-CoA, CoA transferase (CAT1) EC:2.8.3.- (Swiss:P38946) produces succinyl-CoA, and acetate-CoA transferase EC:2.8.3.8 (Swiss:Q59323) utilises acyl-CoA and acetate to form acetyl-CoA.. 
PF00797 Acetyltransf2; <br>Pfam-B_575 (release 2.1). Arylamine N-acetyltransferase (NAT) is a cytosolic enzyme of approximately 30kDa. It facilitates the transfer of an acetyl group from Acetyl Coenzyme A on to a wide range of arylamine, N-hydroxyarylamines and hydrazines. Acetylation of these compounds generally results in inactivation. NAT is found in many species from Mycobacteria (M. tuberculosis, M. smegmatis etc) to man. It was the first enzyme to be observed to have polymorphic activity amongst human individuals. NAT is responsible for the inactivation of Isoniazid (a drug used to treat Tuberculosis) in humans. The NAT protein has also been shown to be involved in the breakdown of folic acid.. 
PF00328 acid_phosphat; Acid_phosphat_A;<br>Histidine phosphatase superfamily (branch 2). The histidine phosphatase superfamily is so named because catalysis centres on a conserved His residue that is transiently phosphorylated during the catalytic cycle.  Other conserved residues contribute to a 'phosphate pocket' and interact with the phospho group of substrate before, during and after its transfer to the His residue. Structure and sequence analyses show that different families contribute different additional residues to the 'phosphate pocket' and, more surprisingly, differ in the position, in sequence and in three dimensions, of a catalytically essential acidic residue.  The superfamily may be divided into two main branches.The smaller branch 2 contains predominantly eukaryotic proteins.  The catalytic functions in members include phytase, glucose-1-phosphatase and multiple inositol polyphosphate phosphatase.  The in vivo roles of the mammalian acid phosphatases in branch 2 are not fully understood, although activity against lysophosphatidic acid and tyrosine-phosphorylated proteins has been demonstrated.. 
PF03767 acid_phosphat_B;<br>HAD superfamily, subfamily IIIB (Acid phosphatase). Pfam-B_2784 (release 7.0). This family proteins includes acid phosphatases and a number of vegetative storage proteins. . 
PF00330 aconitase; <br>Aconitase family (aconitate hydratase). 
PF00694 Aconitase C-terminal domain<br>Pfam-B_224 (release 2.1). Members of this family usually also match to Pfam:PF00330. This domain undergoes conformational change in the enzyme mechanism  .. 
PF01756 Acyl-CoA oxidase<br>Pfam-B_598 (release 4.2). This is a family of Acyl-CoA oxidases EC:1.3.3.6. Acyl-coA oxidase converts acyl-CoA into trans-2- enoyl-CoA  .. 
PF00873 AcrB/AcrD/AcrF family<br>Pfam-B_578 (release 3.0). Members of this family are integral membrane proteins. Some are involved in drug resistance. AcrB cooperates with a membrane fusion protein, AcrA, and an outer  membrane channel TolC. The structure shows the AcrB forms a  homotrimer  .. 
PF05058 ActA Protein<br>Pfam-B_5981 (release 7.7). The ActA family is found in Listeria and is associated with motility. ActA protein acts as a scaffold to assemble and activate host cell actin cytoskeletal factors at the bacterial surface, resulting in directional actin polymerisation and propulsion of the bacterium through the cytoplasm of the host cell [1,2]. . 
PF00976 Corticotropin ACTH domain<br>Pfam-B_1057 (release 3.0). 
PF00022 actin; <br>
PF01643 Acyl-ACP thioesterase<br>Pfam-B_928 (release 4.1). This family consists of various acyl-acyl carrier protein (ACP) thioesterases (TE) these terminate fatty acyl group extension via  hydrolysing an acyl group on a fatty acid  .. 
PF02770 Acyl-CoA dehydrogenase, middle domain<br>Central domain of Acyl-CoA dehydrogenase has a beta-barrel fold.. 
PF02771 Acyl-CoA dehydrogenase, N-terminal domain<br>The N-terminal domain of Acyl-CoA dehydrogenase is an all-alpha  domain.. 
PF02551 Acyl-CoA thioesterase<br>This family represents the thioesterase II domain.  Two copies of this domain are found in a number of acyl-CoA thioesterases.. 
PF00698 Acyl_transf; <br>Acyl transferase domain. Pfam-B_250 (release 2.1). 
PF02273 Acyl transferase<br>Pfam-B_5787 (release 5.2). This bacterial family of Acyl transferases (or myristoyl-acp-specific thioesterases) catalyse the first step in the bioluminescent fatty acid reductase system.. 
PF00708 Acylphosphatase<br>Pfam-B_686 (release 2.1). 
PF01553 Acyltransferase<br>Pfam-B_128 (release 4.0) & Pfam-B_5069 (Release 7.5). This family contains acyltransferases involved in phospholipid biosynthesis and other proteins of unknown function  .  This family also includes tafazzin Swiss:Q16635, the Barth syndrome gene  .. 
PF02805 Metal binding domain of Ada<br>The Escherichia coli Ada protein repairs O6-methylguanine residues and methyl phosphotriesters in DNA by direct transfer of the methyl group to a cysteine residue. This domain contains four conserved cysteines that form a zinc binding site [1,2]. One of these cysteines is a methyl group acceptor. The methylated domain can then specifically bind to the ada box on a DNA duplex  .. 
PF01602 Adaptin N terminal region<br>Pfam-B_491 (release 4.0). This family consists of the N terminal region of various alpha,  beta and gamma subunits of the AP-1, AP-2 and AP-3 adaptor protein complexes. The adaptor protein (AP) complexes are involved in the formation of clathrin-coated pits and vesicles  . The N-terminal region of the various adaptor proteins (APs) is constant by comparison to the C-terminal which is variable within members of the AP-2 family ; and it has been proposed that this constant region interacts with another uniform component of the coated vesicles  .. 
PF03352 Methyladenine glycosylase<br>Pfam-B_3953 (release 6.5). The DNA-3-methyladenine glycosylase I is constitutively expressed and is specific for the alkylated 3-methyladenine DNA. . 
PF02438 adeno_100; <br>Pfam-B_1583 (release 5.4). The late 100kD protein is a non-structural viral protein involved in the transport of hexon from the cytoplasm to the nucleus.. 
PF03052 Adenoviral protein L1 52/55-kDa<br>Pfam-B_2151 (release 6.4). The adenoviral protein L1 52/55-kDa is expressed in both the early and late stages of infection which suggests that it could play multiple roles in the viral life cycle.  The L1 52/55 kDa protein interacts with the viral IVa2 protein and is required for DNA packaging   . L1 53/55-kDa is required to mediate stable association between the viral DNA and empty capsid  .. 
PF02703 Early E1A protein<br>Pfam-B_1193 (release 5.5). 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 genome at the start of the infection process as  well as some cellular genes  .. 
PF01691 Adenovirus E1B 19K protein / small t-antigen<br>Pfam-B_1569 (release 4.1). This family consists of adenovirus E1B 19K protein or small t-antigen. The E1B 19K protein inhibits E1A induced apoptosis and hence prolongs the viability of the host cell  . It can also inhibit apoptosis mediated by tumour necrosis factor alpha and Fas antigen  . E1B 19K blocks apoptosis by interacting with and inhibiting the p53-inducible and death- promoting Bax protein  .  The E1B region of adenovirus encodes two proteins E1B 19K the small t-antigen as found in this family and E1B 55K the large t-antigen which is not found in this family; both of these proteins inhibit E1A induced apoptosis  .. 
PF01696 Adenovirus EB1 55K protein / large t-antigen<br>Pfam-B_1728 (release 4.1). This family consists of adenovirus E1B 55K protein or large t-antigen. E1B 55K binds p53 the tumour suppressor protein converting it from a transcriptional activator which responds to damaged DNA in to an unregulated repressor of genes with a p53 binding site  .  This protects the virus against p53 induced host antiviral responses and prevents apoptosis as induced by the adenovirus E1A protein  .  The E1B region of adenovirus encodes two proteins E1B 55K the large t-antigen as found in this family and E1B 19K Pfam:PF01691 the small t-antigen which is not found in this family; both of these proteins inhibit E1A induced apoptosis.  This family shows distant similarities to the pectate lyase superfamily.. 
PF04623 Adenovirus E1B protein N-terminus<br>This family constitutes the amino termini of E1B 55 kDa (Pfam:PF01696). E1B 55K binds p53 the tumour suppressor protein converting it from a transcriptional activator which responds to damaged DNA in to an unregulated repressor of genes with a p53 binding site  . This protects the virus against p53 induced host antiviral responses and prevents apoptosis as induced by the by the adenovirus E1A protein  . The role of the N terminus in the function of E1B is not known.. 
PF04834 Early E3 14.5 kDa protein<br>Pfam-B_4148 (release 7.6). The E3B 14.5 kDa was first identified in Human adenovirus type 5. It is an integral membrane protein oriented with its C terminus in the cytoplasm.  It functions to down-regulate the epidermal growth factor receptor and prevent tumour necrosis factor cytolysis.  It achieves this through the interaction with E3 10.4 kDa protein [1,2].. 
PF03307 Adenovirus 15.3kD protein in E3 region<br>Pfam-B_3512 (release 6.5). 
PF02440 Adenovirus E3 region protein CR1<br>Pfam-B_1854 (release 5.4). 
PF02439 Adenovirus E3 region protein CR2<br>Pfam-B_1854 (release 5.4). Early region 3 (E3) of human adenoviruses (Ads) codes for proteins that appear to control viral interactions with the host  . This region called CR2 (conserved region 1)   is found in Adenovirus type 19 (a subgroup D virus) 49 Kd protein in the E3 region. CR2 is also found in the 20.1 Kd protein of subgroup B adenoviruses. The function of this 50 amino acid region is unknown.. 
PF03376 Adenovirus E3B protein<br>Pfam-B_3736 (release 6.6). 
PF04528 Adenovirus early E4 34 kDa protein conserved region<br>Pfam-B_4904 (release 7.5). Conserved region found in the Adenovirus E4 34 kDa protein.. 
PF00541 adeno_fiber; <br>Adenoviral fibre protein (knob domain). Specific  attachment of adenovirus is achieved through interactions  between host-cell receptors and the adenovirus fibre protein and is  mediated by the globular carboxy-terminal domain of the adenovirus fibre protein, termed the carboxy-terminal knob domain.. 
PF00608 adeno_fiber2; <br>Adenoviral fibre protein (repeat/shaft region). There is no separation between signal and noise. Specific attachment of adenovirus is achieved through interactions between host-cell receptors and the adenovirus fibre protein and is mediated by the globular carboxy-terminal domain of the adenovirus fibre protein, rather than the 'shaft' region represented by this family. The alignment of this family contains two copies of a fifteen residue repeat found in the 'shaft' region of adenoviral fibre proteins.. 
PF04881 Adenovirus GP19K<br>Pfam-B_6142 (release 7.6). This 19 kDa glycoprotein binds the major histocompatibility (MHC) class I antigens in the endoplasmic reticulum (ER).  The ER retention signal at the C-terminus of GP19K causes retention of the complex in the ER, preventing lysis of the cell by cytotoxic T lymphocytes  .. 
PF01065 Hexon, adenovirus major coat protein, N-terminal domain<br>Pfam-B_885 (release 3.0). Hexon is the major coat protein from adenovirus type 2. Hexon forms a homo-trimer.  The 240 copies of the hexon trimer are organised so that 12 lie on each of the 20 facets. The central 9 hexons in a facet are cemented together by 12 copies of polypeptide IX.  The penton complex, formed by the peripentonal hexons and base hexon (holding in place a fibre), lie at each of the 12 vertices  . The N and C-terminal domains adopt the same PNGase F-like fold although they are significantly different in length.. 
PF03678 Hexon, adenovirus major coat protein, C-terminal domain<br>Pfam-B_885 (release 3.0). Hexon is the major coat protein from adenovirus type 2. Hexon forms a homo-trimer.  The 240 copies of the hexon trimer are organised so that 12 lie on each of the 20 facets. The central 9 hexons in a facet are cemented together by 12 copies of polypeptide IX.  The penton complex, formed by the peripentonal hexons and base hexon (holding in place a fibre), lie at each of the 12 vertices  . The N and C-terminal domains adopt the same PNGase F-like fold although they are significantly different in length.. 
PF02456 Adenovirus IVa2 protein<br>Pfam-B_1982 (release 5.4). IVa2 protein can interact with the adenoviral packaging signal and that this interaction involves DNA sequences that have previously been demonstrated to be required for packaging  . During the course of lytic infection, the adenovirus major late promoter (MLP) is induced to high levels after replication of viral DNA has started. IVa2 is a transcriptional activator of the major late promoter  . . 
PF01686 Adenovirus penton base protein<br>Pfam-B_1180 (release 4.1). This family consists of various adenovirus penton base proteins, from both the Mastadenoviradae having mammalian hosts and the Aviadenoviradae having avian hosts. The penton base is a major structural protein forming part of the penton which consists of a base and a fibre, the pentons hold a morphologically prominent position at the vertex capsomer in the adenovirus particle  . In mammalian adenovirus there is only one tail on each base where as in avian adenovirus there are two  .. 
PF03955 Adenovirus hexon-associated protein (IX)<br>Hexon (PF01065) is the major coat protein from  adenovirus type 2. Hexon forms a homo-trimer.  The 240 copies of the hexon trimer are organised so that 12 lie on each of the 20 facets. The central 9 hexons in a facet are cemented together  by 12 copies of polypeptide IX.. 
PF03910 Adenovirus minor core protein PV<br>
PF01310 Adenovirus hexon associated protein, protein VIII<br>Pfam-B_1405 (release 3.0). See Pfam:PF01065. This family represents Hexon.. 
PF02459 Adenoviral DNA terminal protein<br>Pfam-B_1602 (release 5.4). This protein is covalently attached to the terminii of replicating DNA in vivo  .. 
PF03228 Adenoviral core protein VII<br>Pfam-B_3049 (release 6.5). The function of this protein is unknown. It has a conserved amino terminus of 50 residues followed by a positively charged tail, suggesting it may interact with nucleic acid. The major core protein of the adenovirus, protein VII, was found to be associated with viral DNA throughout infection. The precursor to protein VII were shown to be in vivo and in vitro acceptors of ADP-ribose. The ADP-ribosylated core proteins were assembled into mature virus particles. ADP-ribosylation of adenovirus core proteins may have a role in virus decapsidation.. 
PF04439 Streptomycin adenylyltransferase<br>Also known as Aminoglycoside 6- adenylyltransferase (EC:2.7.7.-), this protein confers resistance to aminoglycoside antibiotics.. 
PF01928 Adenylate_cyc_2; <br>These sequences are functionally identified as members of the adenylate cyclase family, which catalyses the conversion of ATP to 3',5'-cyclic AMP and pyrophosphate.  Six distinct non-homologous classes of AC have been identified.  The structure of three classes of adenylyl cyclases have been solved  .. 
PF01295 Adenylate_cycla; <br>Adenylate cyclase, class-I. 
PF00709 Adenylosuccinate synthetase<br>Pfam-B_690 (release 2.1). 
PF00106 short chain dehydrogenase<br>This family contains a wide variety of dehydrogenases.. 
PF04619 Dr-family adhesin<br>This family of adhesins bind to the Dr blood group antigen component of decay-accelerating factor.  This mediates adherence of uropathogenic Escherichia coli to the urinary tract.  This family contains both fimbriated and afimbriated adherence structures  .  This protein also confers the phenotype of mannose-resistant hemagglutination, which can be inhibited by chloramphenicol.  The N terminal portion of the protein is though to be responsible for chloramphenicol sensitivity  .. 
PF03257 Mycoplasma adhesin P1<br>Pfam-B_4117 (release 6.5). This family corresponds to a short 100 residue region found in adhesins from Mycoplasmas.. 
PF00406 adenylatekinase; <br>
PF05191 Adenylate kinase, active site lid<br>Comparisons of adenylate kinases have revealed  a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain, is clearly  structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely  structural function  .. 
PF05221 S-adenosyl-L-homocysteine hydrolase<br>Pfam-B_157 (release 2.1). 
PF00670 AdoHcyase; <br>S-adenosyl-L-homocysteine hydrolase, NAD binding domain. Pfam-B_157 (release 2.1). 
PF03747 ADP-ribosyl_GH;<br>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 surprisingly the family also includes jellyfish crystallins  , these proteins appear to have lost the presumed active site residues.. 
PF04587 ADP-specific Phosphofructokinase/Glucokinase conserved region<br>Pfam-B_4731 (release 7.5). In archaea a novel type of glycolytic pathway exists that is deviant from the classical Embden-Meyerhof pathway. This pathway utilises two novel proteins: an ADP-dependent Glucokinase and an ADP-dependent Phosphofructokinase.  This conserved region is present at the C-terminal of both these proteins.  Interestingly this family contains sequences from higher eukaryotes. [1,2,3]. . 
PF01117 Aerolysin toxin<br>This family represents the pore forming lobe of aerolysin.. 
PF05110 AF-4 proto-oncoprotein<br>Pfam-B_6407 (release 7.7). This family consists of AF4 (Proto-oncogene AF4) and FMR2 (Fragile X E mental retardation syndrome) nuclear proteins. These proteins have been linked to human diseases such as acute lymphoblastic leukaemia and mental retardation  . The family also contains a Drosophila AF4 protein homologue Lilliputian which contains an AT-hook domain.  Lilliputian represents a novel pair-rule gene that acts in cytoskeleton regulation, segmentation and morphogenesis in Drosophila  .. 
PF03969 AFG1-like ATPase<br>This family of proteins contains a P-loop motif and are predicted to be ATPases.. 
PF01314 AFOR; <br>Aldehyde ferredoxin oxidoreductase, domains 2 & 3. Aldehyde ferredoxin oxidoreductase (AOR) catalyses the reversible  oxidation of aldehydes to their corresponding carboxylic acids  with their accompanying reduction of the redox protein ferredoxin.  This family is composed of two structural domains that bind the  tungsten cofactor via DXXGL(C/D) motifs. In addition to maintaining specific binding interactions with the cofactor, another role for domains 2 and 3 may be to regulate substrate access to AOR  .. 
PF02730 Aldehyde ferredoxin oxidoreductase, N-terminal domain<br>Aldehyde ferredoxin oxidoreductase (AOR) catalyses the reversible oxidation of aldehydes to their corresponding carboxylic acids with their accompanying reduction of the redox protein ferredoxin. This domain interacts with the tungsten cofactor  .. 
PF02420 Insect antifreeze protein repeat<br>This family of extracellular proteins is involved in stopping the formation of ice crystals at low temperatures. The proteins are composed of a 12 residue repeat that forms a structural repeat. The structure of the repeats is a beta helix  . Each repeat contains two cys residues that form a disulphide bridge.. 
PF03756 AfsA_repeat; <br>A-factor biosynthesis hotdog domain. The AfsA family are key enzymes in A-factor biosynthesis, which is essential for streptomycin production and resistance. This domain is distantly related to the thioester dehydratase FabZ family and therefore has a HotDog domain  .. 
PF04671 Erythrocyte membrane-associated giant protein antigen 332 <br>Pfam-B_4587 (release 7.5). To date many different Plasmodium antigens recognised by the hyperimmune system human sera have been cloned, sequenced and characterised.  The majority contain tandemly repeated amino acid sequences which make up a considerable portion of the protein sequence. It has been suggested that these repeat-containing antigens may provide an immunological 'smokescreen' to the parasite in order to evade the human immune system. This repeat is found exclusively in the Plasmodium falciparum Ag332 protein and occupies most of its length  .. 
PF01453 Agglutinin; MMBL2; MMBL; Agglutinin;<br>D-mannose binding lectin. Prodom_2511 (release 99.1). These proteins include mannose-specific lectins from plants  as well as bacteriocins from bacteria  .. 
PF05039 agouti; <br>Pfam-B_5381 (release 7.7). The agouti protein regulates pigmentation in the mouse hair follicle producing a black hair with a subapical yellow band. A highly homologous protein agouti signal protein (ASIP)is present in humans and is expressed at highest levels in adipose tissue where it may play a role in energy homeostasis and possibly human pigmentation    .. 
PF04647 Accessory gene regulator B<br>Pfam-B_5200 (release 7.5). The arg locus consists of two transcripts: RNAII and RNAIII. RNAII encodes four genes (agrA, B, C, and D) whose gene products assemble a quorum sensing system.  AgrB and AgrD are essential for the production of the autoinducing peptide which functions as a signal for quorum sensing.  AgrB is a transmembrane protein  .. 
PF04730 Agrobacterium VirD5 protein<br>Pfam-B_3261 (release 7.5). The virD operon in Agrobacterium encodes a site-specific endonuclease, and a number of other poorly characterised products. This family represents the VirD5 protein.. 
PF00578 AhpC/TSA family<br>MRC-LMB Genome group. This family contains proteins related to alkyl hydroperoxide reductase (AhpC) and thiol specific antioxidant (TSA). . 
PF02626 DUF183; <br>Allophanate hydrolase subunit 2. This domain forms the second subunit of allophanate hydrolase. In yeast urea amidolyase (Swiss:P32528) this domain is found between Pfam:PF00289 and Pfam:PF00364.. 
PF01808 AICARFT/IMPCHase bienzyme<br>Pfam-B_1613 (release 4.2). 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-carboxamide  ribonucleotide formyltransferase EC:2.1.2.3 (AICARFT), this enzyme catalyses the formylation of AICAR with 10-formyl-tetrahydrofolate to yield FAICAR and tetrahydrofolate  . This is catalysed by a pair of C-terminal deaminase fold domains in the protein  , where the active site is formed by the dimeric interface of two monomeric units  . The last  step is catalysed by the N-terminal IMP (Inosine monophosphate)  cyclohydrolase domain EC:3.5.4.10 (IMPCHase), cyclizing FAICAR  (5-formylaminoimidazole-4-carboxamide ribonucleotide) to IMP  . . 
PF04548 AIG1 family<br>Pfam-B_1846 (release 7.5). Arabidopsis protein AIG1 appears to be involved in plant resistance to bacteria.. 
PF00731 AIR carboxylase<br>Pfam-B_462 (release 2.1). Members of this family catalyse the decarboxylation of 1-(5-phosphoribosyl)-5-amino-4-imidazole-carboxylate (AIR). This family catalyse the sixth step of de novo purine biosynthesis. Some members of this family contain two copies of this domain.. 
PF00586 AIR synthase related protein, N-terminal domain<br>MRC-LMB Genome Group. This family includes Hydrogen expression/formation protein  HypE Swiss:P24193, AIR synthases Swiss:P08178 EC:6.3.3.1, FGAM synthase Swiss:P35852 EC:6.3.5.3 and selenide, water dikinase Swiss:P16456 EC:2.7.9.3. The N-terminal domain of AIR synthase forms the dimer interface of the protein, and is suggested as a putative ATP binding domain  .. 
PF02769 AIR synthase related protein, C-terminal domain<br>MRC-LMB Genome Group. This family includes Hydrogen expression/formation protein  HypE Swiss:P24193, AIR synthases Swiss:P08178 EC:6.3.3.1, FGAM synthase Swiss:P35852 EC:6.3.5.3 and selenide, water dikinase Swiss:P16456 EC:2.7.9.3. The function of the C-terminal domain of AIR synthase is unclear, but the cleft formed between N and C domains is postulated as a sulphate binding site  .. 
PF04988 A-kinase anchoring protein 95 (AKAP95)<br>Pfam-B_5366 (release 7.6). A-kinase (or PKA)-anchoring protein AKAP95 is implicated in mitotic  chromosome condensation by acting as a targeting molecule for the  condensin complex. The protein contains two zinc fingers which are thought to mediate the binding of AKAP95 to DNA  .. 
PF02983 AL_protease; <br>Alpha-lytic protease prodomain. 
PF00490 Delta-aminolevulinic acid dehydratase<br>
PF00171 aldedh; <br>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 Swiss:P00352 EC:1.2.1.3. Succinate-semialdehyde dehydrogenase Swiss:P25526 EC:1.2.1.16. Lactaldehyde dehydrogenase Swiss:P25553 EC:1.2.1.22. Benzaldehyde dehydrogenase Swiss:P43503 EC:1.2.1.28. Methylmalonate-semialdehyde dehydrogenase Swiss:Q02252 EC:1.2.1.27. Glyceraldehyde-3-phosphate dehydrogenase Swiss:P81406 EC:1.2.1.9. Delta-1-pyrroline-5-carboxylate dehydrogenase Swiss:P30038 EC: 1.5.1.12. Acetaldehyde dehydrogenase Swiss:P17547 EC:1.2.1.10. Glutamate-5-semialdehyde dehydrogenase Swiss:P07004 EC:1.2.1.41. This family also includes omega crystallin Swiss:P30842 an eye lens protein from squid and octopus that has little aldehyde dehydrogenase activity.. 
PF01081 KDPG and KHG aldolase<br>This family includes the following members: 4-hydroxy-2-oxoglutarate aldolase (KHG-aldolase) Phospho-2-dehydro-3-deoxygluconate  aldolase (KDPG-aldolase). 
PF00596 Aldolase_class_II; <br>Class II Aldolase and Adducin N-terminal domain. MRC-LMB Genome Group. This family includes class II aldolases and adducins which have not been ascribed any enzymatic function.. 
PF03752 DUF312; <br>Short repeats of unknown function. This set of repeats is found in a small family of secreted proteins of no known function, though they are possibly involved in signal transduction. ALF stands for Alanine-rich (AL) - conserved Phenylalanine (F).. 
PF05208 ALG3 protein<br>Pfam-B_3416 (release 7.7). The formation of N-glycosidic linkages of glycoproteins involves the ordered assembly of the common Glc3Man9GlcNAc2 core-oligosaccharide on the lipid carrier dolichyl pyrophosphate. Whereas early mannosylation steps occur on the cytoplasmic side of the endoplasmic reticulum with GDP-Man as donor, the final reactions from Man5GlcNAc2-PP-Dol to Man9GlcNAc2-PP-Dol on the lumenal side use Dol-P-Man  . ALG3 gene encodes the Dol-P-Man:Man5GlcNAc2-PP-Dol mannosyltransferase.. 
PF03561 Allantoicase repeat<br>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 =  (-)-ureidoglycolate + urea.. 
PF04864 Allinase<br>Pfam-B_4527 (release 7.6). Allicin is a thiosulphinate that gives rise to dithiines, allyl sulphides and ajoenes, the three groups of active compounds in Allium species. Allicin is synthesised from sulfoxide cysteine derivatives by alliinase (EC:4.4.1.4), whose C-S lyase activity cleaves C(beta)-S(gamma) bonds. It is thought that this enzyme forms part of a primitive plant defence system.. 
PF04030 D-arabinono-1,4-lactone oxidase <br>Pfam-B_33547 (release 7.3);. This domain is specific to D-arabinono-1,4-lactone oxidase EC:1.1.3.- , which is involved in the final step of the  D-erythroascorbic acid biosynthesis pathway  .. 
PF00128 alpha-amylase; <br>Alpha amylase, catalytic domain. Alpha amylase is classified as family 13 of the glycosyl hydrolases. The structure is an 8 stranded alpha/beta barrel containing the  active site, interrupted by a ~70 a.a. calcium-binding domain  protruding between beta strand 3 and alpha helix 3, and a  carboxyl-terminal Greek key beta-barrel domain.. 
PF02903 alpha-amylase_N; <br>Alpha amylase, N-terminal ig-like domain. 
PF02296 Alpha adaptin AP2, C-terminal domain<br>Pfam-B_8859 (release 5.2). 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.. 
PF02883 Adaptin C-terminal domain<br>Pfam-B_8859 (release 5.2). 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 in alpha, beta and gamma adaptins.. 
PF00944 Alpha_core; <br>Alphavirus core protein . Pfam-B_266 (release 3.0). Also known as coat protein C and capsid protein C. This makes the literature very confusing.  Alphaviruses consist of a nucleoprotein core, a lipid membrane which envelopes the core, and glycoprotein spikes protruding from the lipid membrane.. 
PF01589 Alphavirus E1 glycoprotein<br>Pfam-B_587 (release 4.1). E1 forms a heterodimer with E2 Pfam:PF00943.  The virus spikes are made up of 80 trimers of these heterodimers (sindbis virus)  .. 
PF00943 Alphavirus E2 glycoprotein<br>Pfam-B_308 (release 3.0). E2 forms a heterodimer with E1.  The virus spikes are made up of 80 trimers of these heterodimers (sindbis virus)  .. 
PF01563 Alphavirus E3 glycoprotein<br>Pfam-B_285 (release 4.0). This protein is found in some alphaviruses as a virion associated spike protein  .. 
PF03229 Alphavirus glycoprotein J<br>Pfam-B_3350 (release 6.5). 
PF01120 Alpha-L-fucosidase<br>
PF02232 Alpha trans-inducing protein (Alpha-TIF) <br>Pfam-B_1799 (release 5.2). Alpha-TIF, a virion protein (VP16), is involved in transcriptional activation of viral immediate early (IE) promoters (alpha genes). Specificity of Swiss:P23990 for IE genes is conferred by the  400 residue N-terminal, the 80 residue C-terminal is responsible for transcriptional activation  .. 
PF02430 Apical membrane antigen 1<br>Pfam-B_2016 (release 5.4). Apical membrane antigen 1 (AMA-1) is a Plasmodium asexual blood-stage antigen. It has been suggested that positive selection operates on the AMA-1 gene in regions coding for antigenic sites  .. 
PF03913 Amb V Allergen<br>
PF02948 Amelogenin<br>Pfam-B_402 (release 6.4). Amelogenins play a role in biomineralisation. 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 organisation and mineralisation of developing enamel. They are found in the extracellular matrix. Mutations in X-chromosomal amelogenin can cause Amelogenesis imperfecta  .. 
PF04709 Anti-Mullerian hormone, N terminal region<br>Anti-Mullerian hormone, AMH is a signalling molecule involved in male and female sexual differentiation  .  Defects in synthesis or action of AMH cause persistent Mullerian duct syndrome (PMDS), a rare form of male pseudohermaphroditism  . This family represents the N terminal part of the protein, which is not thought to be essential for activity  .\.  AMH contains a TGF-beta domain (Pfam:PF00019), at the C terminus.. 
PF01425 Amidase<br>Pfam-B_191 (release 2.1). 
PF01832 Amidase_4; <br>Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase. Pfam-B_888 (release 4.0). This family includes Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase EC:3.2.1.96. As well as the flageller protein J Swiss:P75942 that has been shown to hydrolyse peptidoglycan  .. 
PF02274 Amidinotransferase<br>Pfam-B_5784 (release 5.2) and Pfam-B_1850 (release 5.5). This family contains glycine (EC:2.1.4.1) and inosamine  (EC:2.1.4.2) amidinotransferases, enzymes involved in creatine and streptomycin biosynthesis respectively.  This family also includes arginine deiminases, EC:3.5.3.6. These enzymes catalyse the reaction: arginine + H2O <=> citrulline + NH3. Also found in this family is the Streptococcus anti tumour glycoprotein    (Swiss:P16962).. 
PF01979 Adenine_deam;<br>Amidohydrolase family. This family of enzymes are a a large metal dependent hydrolase superfamily  . The family includes Adenine deaminase EC:3.5.4.2 that hydrolyses adenine to form hypoxanthine and ammonia. Adenine deaminases reaction is important for adenine utilisation as a purine and also as a nitrogen source  . This family also includes dihydroorotase and N-acetylglucosamine-6-phosphate deacetylases, EC:3.5.1.25 These enzymes catalyse the reaction N-acetyl-D-glucosamine 6-phosphate +  H2O <=> D-glucosamine 6-phosphate + acetate. This family includes the catalytic domain of urease alpha subunit  . Dihydroorotases (EC:3.5.2.3) are also included [4-5]. . 
PF04909 Amidohydrolase<br>Pfam-B_4687 (release 7.6). These proteins are amidohydrolases that are related to Pfam:PF01979  .. 
PF00155 aminotran_1; aminotran_1_2; <br>Aminotransferase class I and II. 
PF00202 aminotran_3; <br>Aminotransferase class-III. 
PF01063 AA_transferase_C4;aminotran_4; <br>Aminotransferase class IV. Pfam-B_607 (release 3.0). The D-amino acid transferases (D-AAT) are required by bacteria to  catalyse the synthesis of D-glutamic acid and D-alanine, which are  essential constituents of bacterial cell wall and are the building block for other D-amino acids.  Despite the difference in the structure of the substrates, D-AATs and L-ATTs have strong similarity.. 
PF00266 aminotran_5; <br>Aminotransferase class-V. This domain is found in amino transferases, and other enzymes including cysteine desulphurase EC:4.4.1.-.. 
PF02293 AmiS/UreI family transporter<br>This family includes UreI and proton gated urea channel as well as putative amide transporters  .. 
PF02461 Ammonia monooxygenase<br>Pfam-B_2301 (release 5.4). Ammonia monooxygenase plays a key role in the nitrogen cycle and degrades a wide range of hydrocarbons and halogenated hydrocarbons.. 
PF00909 Ammonium Transporter Family<br>Pfam-B_596 (release 3.0). 
PF05145 Putative ammonia monooxygenase<br>This family are annotated by COGS as putative ammonia monooxygenase enzymes.. 
PF04896 Ammonia monooxygenase/methane monooxygenase, subunit C<br>Pfam-B_6611 (release 7.6). Ammonia monooxygenase plays a key role in the nitrogen cycle and degrades a wide range of hydrocarbons and halogenated hydrocarbons. This family represents the AmoC subunit. It also includes the particulate methane monooxygenase subunit PmoC from methanotrophic bacteria [1,2].. 
PF03782 AMOP domain<br>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  .. 
PF04739 5'-AMP-activated protein kinase beta subunit, interation domain<br>This region is found in the beta subunit of the 5'-AMP-activated protein kinase complex, and its yeast homologues Sip1, Sip2 and Gal83, which are found in the SNF1 kinase complex  . This region is sufficient for interaction of this subunit with the kinase complex, but is not solely responsible for the interaction, and the interaction partner is not known  .  The isoamylase N-terminal domain (Pfam:PF02922) is sometimes found in proteins belonging to this family.. 
PF02166 Androgen receptor<br>
PF03139 Vanadium/alternative nitrogenase delta subunit<br>Pfam-B_1227 (release 6.5). The nitrogenase complex EC:1.18.6.1 catalyses the conversion of molecular nitrogen to ammonia (nitrogen fixation) as follows: 8 reduced ferredoxin + 8 H(+) + N(2) + 16 ATP <=> 8 oxidised ferredoxin + 2 NH(3) + 16 ADP + 16 phosphate. The complex is hexameric, consisting of 2 alpha, 2 beta, and 2 delta subunits. This family represents the delta subunit of a group of nitrogenases that do not utilise molybdenum (Mo) as a cofactor, but instead use either vanadium (V nitrogenases), or iron (alternative nitrogenases). V nitrogenases are encoded by vnf operons, and alternative nitrogenases by anf operons. The delta subunits are VnfG and AnfG, respectively.. 
PF00212 Atrial natriuretic peptide<br>
PF03452 Anp1<br>Pfam-B_4441 (release 6.6). The members of this family (Anp1, Van1 and Mnn9) are membrane proteins required for proper Golgi function. These proteins co-localise within the cis Golgi, and that they are physically associated in two distinct  complexes .. 
PF03374 Phage antirepressor protein KilAC domain<br>Pfam-B_3485 (release 6.6). This domain was called the KilAC domain by Iyer and colleagues  .. 
PF04715 Anthranilate synthase component I, N terminal region<br>Anthranilate synthase (EC:4.1.3.27) catalyses the first step in the  biosynthesis of tryptophan.  Component I catalyses the formation of  anthranilate using ammonia and chorismate.  The catalytic site lies in the adjacent region, described in the chorismate binding enzyme family  (Pfam:PF00425). This region is involved in feedback inhibition by tryptophan  .  This family also contains a region of Para-aminobenzoate synthase component I (EC 4.1.3.-).. 
PF03497 Anthrax toxin LF subunit<br>
PF02522 Aminoglycoside 3-N-acetyltransferase<br>Pfam-B_1432 (release 5.4). This family consists of bacterial aminoglycoside 3-N-acetyltransferases EC:2.3.1.81, these catalyse the reaction: Acetyl-Co + a 2-deoxystreptamine antibiotic <=> CoA + N3'-acetyl-2-deoxystreptamine antibiotic.\.      The enzyme can use a range of antibiotics with 2-deoxystreptamine rings as acceptor for its acetyltransferase activity, this inactivates and confers resistance to gentamicin, kanamycin, tobramycin, neomycin and apramycin amongst others.. 
PF03230 Antirestriction protein<br>Pfam-B_3190 (release 6.5). This family includes various protein that are involved in antirestriction. The ArdB protein Swiss:Q47057 efficiently inhibits restriction by members of the three known families of type I systems of E. coli  .. 
PF03589 Antitermination protein<br>
PF01786 Alternative oxidase<br>Pfam-B_1154 (release 4.2). The alternative oxidase is used as a second terminal oxidase  in the mitochondria, electrons are transfered directly from reduced ubiquinol to oxygen forming water  . This is not coupled to ATP synthesis and is not inhibited by cyanide, this pathway is a single step process  . In rice the transcript levels of the alternative oxidase are increased by low temperature  .. 
PF01261 AP_endonulease2; <br>Xylose isomerase-like TIM barrel. Prosite & Pfam-B_3980 (Release 7.5). This TIM alpha/beta barrel structure is found in xylose isomerase (Swiss:P19148) and in endonuclease IV (Swiss:P12638, EC:3.1.21.2).  This domain is also found in the N termini of bacterial myo-inositol catabolism proteins. These are involved in the myo-inositol catabolism pathway, and is required for growth on myo-inositol in Rhizobium leguminosarum bv. viciae  .. 
PF01636 Phosphotransferase enzyme family<br>Pfam-B_840 (release 4.1). This family consists of bacterial antibiotic resistance proteins, which confer resistance to various aminoglycosides they include: aminoglycoside 3'-phosphotransferase or kanamycin kinase / neomycin-kanamycin phosphotransferase and streptomycin 3''-kinase or streptomycin 3''-phosphotransferase. The aminoglycoside phosphotransferases inactivate aminoglycoside antibiotics via phosphorylation  . This family also includes homoserine kinase. This family is related to fructosamine kinase Pfam:PF03881.. 
PF02558 Ketopantoate reductase PanE/ApbA<br>This is a family of 2-dehydropantoate 2-reductases also known as  ketopantoate reductases, EC:1.1.1.169.  The reaction catalysed by this  enzyme is: (R)-pantoate + NADP(+) <=> 2-dehydropantoate + NADPH.  AbpA catalyses the NADPH reduction of ketopantoic acid to pantoic acid in the alternative pyrimidine biosynthetic (APB) pathway  .  ApbA and PanE are allelic  .  ApbA, the ketopantoate reductase enzyme is required for  the synthesis of thiamine via the APB biosynthetic pathway  .. 
PF03256 Anaphase-promoting complex, subunit 10 (APC10)<br>Pfam-B_4273 (release 6.5). 
PF04110 Ubiquitin-like autophagy protein Apg12 <br>Pfam-B_9471 (release 7.3);. In yeast, 15 Apg proteins coordinate the formation of autophagosomes.  Autophagy is a bulk degradation process induced by starvation in eukaryotic cells  . The Apg12 system is one of the ubiquitin-like protein conjugation systems conserved in eukaryotes. It was first discovered in yeast during systematic analyses of the apg mutants defective in autophagy. Covalent attachment of Apg12-Apg5 is essential for autophagy [2,3,4].. 
PF04108 Autophagy protein Apg17 <br>Pfam-B_71163 (release 7.3);. Apg17 is required for activating Apg1 protein kinases  .. 
PF04111 Autophagy protein Apg6<br>Pfam-B_11747 (release 7.3);. 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 associated with the membrane or in a retrieval step of the  carboxypeptidase Y sorting pathway  .. 
PF04109 Autophagy protein Apg9 <br>Pfam-B_12479 (release 7.3);. 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 targeting and autophagic vesicles, possibly serving as a  marker for a specialised compartment essential for these  vesicle-mediated alternative targeting pathways  .. 
PF04655 Aminoglycoside/hydroxyurea antibiotic resistance kinase<br>Pfam-B_4369 (release 7.5). The aminoglycoside phosphotransferases achieve inactivation of their antibiotic substrates by phosphorylation utilising ATP. Likewise hydroxyurea is inactivated by phosphorylation of the hydroxy group in the hydroxylamine moiety [1,2,3].. 
PF00807 Apidaecin<br>Pfam-B_1489 (release 2.1). These antibacterial peptides are found in bees. These heat-stable, non-helical peptides are active against a wide range of plant-associated bacteria and some human pathogens  . The Pfam alignment includes the propeptide and apidaecin sequence.. 
PF04711 Apolipoprotein A-II (ApoA-II)<br>Apolipoprotein A-II (ApoA-II) is the second major apolipoprotein of high density lipoprotein in human plasma.\.  Mature ApoA-II is present as a dimer of two 77-amino acid chains joined by a disulphide bridge  . ApoA-II regulates many steps in HDL metabolism, and its role in coronary heart disease is unclear  . In bovine serum, the ApoA-II homologue is present in almost free form.\.        Bovine ApoA-II shows antimicrobial activity against Escherichia coli and yeasts in phosphate buffered saline (PBS)  .. 
PF04691 Apolipoprotein C-I (ApoC-1)<br>Apolipoprotein C-I (ApoC-1) is a water-soluble protein component of plasma lipoprotein.  It solubalises lipids and regulates lipid metabolism.  ApoC-1 transfers among HDL (high density lipoprotein), VLDL (very low-density lipoprotein) and chylomicrons.  ApoC-1 activates lecithin:choline acetyltransferase (LCAT), inhibits cholesteryl ester transfer protein, can inhibit hepatic lipase and phospholipase 2 and can stimulate cell growth. ApoC-1 delays the clearance of beta-VLDL by inhibiting its uptake via the LDL receptor-related pathway  . ApoC-1 has been implicated in hypertriglyceridemia  , and Alzheimer's disease  .. 
PF01333 Apocytochrome_F; <br>Apocytochrome F, C-terminal. Pfam-B_1294 (release 3.0). This is a sub-family of cytochrome C.  See Pfam:PF00034.. 
PF01442 Apolipoprotein A1/A4/E domain<br>Prodom_1521 (release 99.1). These proteins contain several 22 residue repeats which form a pair of alpha helices. This family includes: Swiss:P02647 Apolipoprotein A-I. Swiss:P06727 Apolipoprotein A-IV. Swiss:P02649 Apolipoprotein E.. 
PF01583 Adenylylsulphate kinase<br>Pfam-B_578 (release 4.1). Enzyme that catalyses the phosphorylation of adenylylsulphate to 3'-phosphoadenylylsulfate.  This domain contains an ATP binding P-loop motif.. 
PF03440 Aerolysin/Pertussis toxin (APT) domain<br>This family represents the N-terminal domain of aerolysin and pertussis toxin and has a type-C lectin like fold.. 
PF02610 L-arabinose isomerase<br>This is a family of L-arabinose isomerases, AraA, EC:5.3.1.4.  These enzymes catalyse the reaction: L-arabinose <=> L-ribulose.  This reaction is the first step in the pathway of L-arabinose utilisation as a carbon source after entering the cell L-arabinose is converted into  L-ribulose by the L-arabinose isomerases enzyme  .. 
PF02311 AraC-like ligand binding domain<br>Pfam-B_12588 (release 5.2). This family represents the arabinose-binding and dimerisation  domain of the bacterial gene regulatory protein AraC. The domain is found in conjunction with the helix-turn-helix (HTH)  DNA-binding motif Pfam:PF00165. This domain is distantly related to the Cupin domain Pfam:PF00190.. 
PF03869 Arc-like DNA binding domain<br>Arc repressor act by he cooperative binding of two Arc repressor dimers to a 21-base-pair operator site.  Each Arc dimer uses an antiparallel beta-sheet to recognise bases in the major groove  .. 
PF04659 Archaeal flagella protein <br>Pfam-B_4437 (release 7.5). Family of archaeal flaD and flaE proteins.  Conserved region found at N-terminus of flaE but towards the C-terminus of flaD  . . 
PF01917 Archaebacterial flagellin<br>Enright A & COG3354 & COG3353. Members of this family are the proteins that form the flagella in archaebacteria.. 
PF01637 Archaeal_ATPase; <br>Pfam-B_1507 (release 4.1). This family contain a conserved P-loop motif that is involved in binding ATP. This family is almost exclusively found in archaebacteria and particularly in Methanococcus jannaschii that encodes sixteen members of this family.. 
PF00798 Arenavirus glycoprotein<br>Pfam-B_1047 (release 2.1). 
PF00843 Arenavirus nucleocapsid protein<br>Pfam-B_1333 (release 2.1). 
PF00025 arf; <br>ADP-ribosylation factor family. Pfam combines a number of different Prosite families together. 
PF01316 Arginine repressor, DNA binding domain<br>
PF02863 Arginine repressor, C-terminal domain<br>
PF00491 arginase; <br>
PF00764 Arginosuccinate synthase<br>Pfam-B_888 (release 2.1). This family contains a PP-loop motif  .. 
PF01960 ArgJ family<br>Members of the ArgJ family catalyse the first EC:2.3.1.1 and fifth steps EC:2.3.1.35 in arginine biosynthesis. . 
PF03308 ArgK protein<br>Pfam-B_3540 (release 6.5). 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.. 
PF02374 Anion-transporting ATPase<br>Pfam-B_1201 (release 5.2). 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. . 
PF02040 Arsenical pump membrane protein<br>
PF03960 ArsC family<br>This family is related to glutaredoxins Pfam:PF00462.. 
PF01129 NAD:arginine ADP-ribosyltransferase<br>
PF02497 Art_glycop; <br>Arterivirus glycoprotein. Pfam-B_787 (release 5.4). This is a family of structural glycoproteins from arterivirus that corresponds to open reading frame 4 (ORF4) of the virus.. 
PF01481 Arte_nucleocap;<br>Arterivirus nucleocapsid protein. Prodom_2418 (release 99.1). 
PF01606 Arterivirus envelope protein<br>Pfam-B_664 (release 4.1). This family consists of viral envelope proteins from the arterivirus genus; this includes porcine reproductive and  respiratory virus (PRRSV) envelope protein GP3 and lactate  dehydrogenase elevating virus (LDV) structural glycoprotein. Arteriviruses consists of positive ssRNA and do not have a DNA stage.. 
PF00951 Arteri_glycop; <br>Arterivirus GL envelope glycoprotein. Pfam-B_425 (release 3.0). Arteriviruses encode 4 envelope proteins, Gl, Gs, M and N. Gl   envelope protein, is encoded in ORF5, and is 30- 45 kDa in size. Gl is heterogenously glycosylated with N-acetyllactosamine in  a cell-type-specific manner. The Gl glycoprotein expresses the  neutralisation determinants.. 
PF01097 Defensin; Arthro_defensin; <br>
PF04161 Arv1-like family <br>Pfam-B_9351 (release 7.3);. Arv1 is a transmembrane protein with potential zinc-binding motifs. ARV1 is a novel mediator of eukaryotic sterol homeostasis  .. 
PF01731 Arylesterase<br>Pfam-B_2101 (release 4.1). This family consists of arylesterases (Also known as serum paraoxonase) EC:3.1.1.2. These enzymes hydrolyse organophosphorus esters such as paraoxon and are found in the liver and blood. They confer resistance to organophosphate toxicity  . Human arylesterase (PON1) Swiss:P27169 is associated with HDL and may protect against LDL oxidation  .. 
PF00858 Amiloride-sensitive sodium channel<br>Pfam-B_415 (release 3.0). 
PF01671 African swine fever virus multigene family 360 protein<br>Pfam-B_1174 (release 4.1). The multigene family 360 protein are found within the African swine fever virus (ASF) genome which consist of dsDNA and has similar structural features to the poxyviruses  . The biological function of this family is not known  . Although Swiss:Q65137 is a major structural protein  .. 
PF05170 AsmA family<br>The AsmA gene, whose product is involved in the assembly of outer membrane proteins in Escherichia coli  . AsmA mutations were isolated as extragenic suppressors of an OmpF assembly mutant  . AsmA may have a role in LPS biogenesis  .. 
PF00733 Asparagine synthase<br>Pfam-B_443 (release 2.1). This family is always found associated with Pfam:PF00310. Members of this family catalyse the conversion of aspartate to asparagine.. 
PF03590 Aspartate-ammonia ligase<br>TIGRFAMs, Griffiths-Jones SR. 
PF00026 asp; <br>Eukaryotic aspartyl protease. Aspartyl (acid) proteases include pepsins, cathepsins, and renins.  Two-domain structure, probably arising from ancestral duplication.  This family does not include the retroviral nor retrotransposon proteases (Pfam:PF00077), which are much smaller and appear to be homologous to a single domain of the eukaryotic asp proteases.. 
PF02261 Aspartate decarboxylase<br>Pfam-B_3879 (release 5.2). Decarboxylation of aspartate is the major route of beta-alanine  production in bacteria, and is catalysed by the enzyme aspartate decarboxylase EC:4.1.1.11 which requires a pyruvoyl group for its activity. It is synthesised initially as a proenzyme which is then proteolytically cleaved to an alpha (C-terminal) and beta (N-terminal) subunit and a pyruvoyl group. This family contains both chains of aspartate decarboxylase.. 
PF00710 Asparaginase<br>Pfam-B_652 (release 2.1). 
PF01112 Asparaginase<br>
PF04958 Arginine N-succinyltransferase beta subunit<br>Arginine N-succinyltransferase EC:2.3.1.109 catalyses the transfer of succinyl-CoA to arginine to produce succinylarginine. This is the first step in arginine catabolism by the arginine succinyltransferase pathway.. 
PF04996 Succinylarginine dihydrolase<br>This enzyme transforms N(2)-succinylglutamate into succinate and glutamate. This is the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway.. 
PF04952 Aste_AspA; <br>Succinylglutamate desuccinylase / Aspartoacylase family. COG2988 & Pfam-B_15640 (release 10.0). 
PF03115 Astrovirus capsid protein precursor<br>Pfam-B_2957 (release 6.5). This product is encoded by astrovirus ORF2, one of the three astrovirus ORFs (1a, 1b, 2). The 87kD precursor protein undergoes an intracellular cleavage to form a 79kD protein. Subsequently, extracellular trypsin cleavage yields the three proteins forming the infectious virion  .. 
PF04377 Arginine-tRNA-protein transferase, C terminus<br>This family represents the C terminal region of the enzyme  arginine-tRNA-protein transferase (EC 2.3.2.8), which catalyses the post-translational conjugation of arginine to the N terminus of a protein. In eukaryotes, this functions as part of the N-end rule pathway  of protein degradation by conjugating a destabilising amino acid to the amino terminal aspartate or glutamate of a protein, targeting the protein for ubiquitin-dependent proteolysis.  N terminal cysteine is sometimes  modified  .. 
PF04376 Arginine-tRNA-protein transferase, N terminus<br>This family represents the N terminal region of the enzyme  arginine-tRNA-protein transferase (EC 2.3.2.8), which catalyses the post-translational conjugation of arginine to the N terminus of a protein. In eukaryotes, this functions as part of the N-end rule pathway  of protein degradation by conjugating a de-stabilising amino acid to the amino terminal aspartate or glutamate of a protein, targeting the protein for ubiquitin-dependent proteolysis.  N terminal cysteine is sometimes  modified  . In S cerevisiae, Cys20, 23, 94 and/or 95 are thought to be important  for activity  .  Of these, only Cys 94 appears to be completely conserved in this family.. 
PF03078 ATHILA ORF-1 family<br>Pfam-B_2240 (release 6.4). ATHILA is a group of Arabidopsis thaliana retrotransposons    belonging to the Ty3/gypsy family of the long terminal repeat (LTR) class of eukaryotic retrotransposons[2,3]. The central region of ATHILA retrotransposons contains two or three open reading frames (ORFs). This family represents the ORF1 product. The function of ORF1 is unknown.. 
PF03477 ATP cone domain<br>
PF02222 ATP-grasp domain<br>Pfam-B_157 (release 5.2). 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.. 
PF00217 ATP:guanido phosphotransferase, C-terminal catalytic domain<br>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.. 
PF02807 ATP:guanido phosphotransferase, N-terminal domain<br>The N-terminal domain has an all-alpha fold.. 
PF01747 ATP-sulfurylase<br>Pfam-B_494 (release 4.2). This domain is the catalytic domain of ATP-sulfurylase or sulfate adenylyltransferase EC:2.7.7.4 some of which are part of a bifunctional polypeptide chain associated with adenosyl phosphosulphate (APS) kinase Pfam:PF01583. Both enzymes are required for PAPS (phosphoadenosine-phosphosulfate) synthesis from inorganic sulphate  . ATP sulfurylase catalyses the synthesis of adenosine-phosphosulfate APS from ATP and inorganic sulphate  .. 
PF00231 ATP synthase<br>
PF05176 ATP10 protein<br>ATP 10 is essential for the assembly of a functional mitochondrial ATPase complex  .. 
PF00895 ATP synthase protein 8<br>Pfam-B_446 (release 3.0). 
PF00119 ATP synthase A chain<br>
PF00006 ATP synthase alpha/beta family, nucleotide-binding domain<br>This family includes the ATP synthase alpha and beta subunits, the ATP synthase associated with flagella and the termination factor Rho.. 
PF00430 ATP synthase B/B' CF(0)<br>Pfam-B_137 (release 1.0). Part of the CF(0) (base unit) of the  ATP synthase. The base unit is thought to translocate protons through membrane  (inner membrane in mitochondria, thylakoid membrane in plants, cytoplasmic membrane in bacteria). The B subunits are thought to interact with the stalk of the CF(1) subunits.  This domain should not be confused with the ab CF(1) proteins (in the head of the ATP synthase) which are found in Pfam:PF00006. 
PF00137 ATP synthase subunit C<br>
PF01813 ATP synthase subunit D <br>Pfam-B_1304 (release 4.2). 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  .. 
PF00401 ATP synthase, Delta/Epsilon chain, long alpha-helix domain<br>Pfam-B_114 (release 1.0). Part of the ATP synthase CF(1). These subunits are part of the head unit of the ATP synthase. This subunit is called epsilon in bacteria and delta in  mitochondria.  In bacteria the delta (D) subunit is equivalent to the mitochondrial Oligomycin sensitive subunit, OSCP (Pfam:PF00213).. 
PF02823 ATP synthase, Delta/Epsilon chain, beta-sandwich domain<br>Pfam-B_114 (release 1.0). Part of the ATP synthase CF(1). These subunits are part of the head unit of the ATP synthase. The subunit is called epsilon in bacteria and delta in mitochondria.  In bacteria the delta (D) subunit is equivalent to the mitochondrial Oligomycin sensitive subunit, OSCP (Pfam:PF00213).. 
PF04627 ATP-synt_E;<br>Mitochondrial ATP synthase epsilon chain. This family constitutes the mitochondrial ATP synthase epsilon subunit.  This is not to be confused with the bacterial epsilon subunit, which is homologous to the mitochondrial delta subunit (Pfam:PF00401 and Pfam:PF02823) The epsilon subunit is located in the extrinsic membrane section F1, which is the catalytic site of ATP synthesis.  The epsilon subunit was not well ordered in the crystal structure of bovine F1  , but it is known to be located in the stalk region of F1  . E subunit is thought to be involved in the regulation of ATP synthase, since a null mutation increased oligomycin sensitivity and decreased inhibition by inhibitor protein IF1  .. 
PF01990 ATP synthase (F/14-kDa) subunit<br>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  .. 
PF04911 ATP synthase j chain<br>
PF02038 ATP1G1/PLM/MAT8 family<br>
PF03899 ATP synthase I chain<br>
PF03154 Atrophin-1 family<br>Pfam-B_3427 (release 6.5). 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. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins [1,2]. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity  .. 
PF03769 Attacin, C-terminal region<br>Pfam-B_2791 (release 7.0). This family includes attacin, sarcotoxin and diptericin.  All members of this family are insect antibacterial proteins which are induced by the fat body and subsequently released into secreted into the hemolymph where they act synergistically to kill the invading microorganism  .. 
PF03472 Autoinducer binding domain<br>This domain is found a a large family of transcriptional regulators.  This domain specifically binds to autoinducer molecules.. 
PF00765 Autoinducer synthetase<br>Pfam-B_881 (release 2.1). 
PF03987 Autophagy_C; <br>Autophagocytosis associated protein, active-site domain . Pfam-B_10019 (release 7.3). Autophagocytosis is a starvation-induced process responsible for transport of cytoplasmic proteins to the vacuole. The cysteine residue within the HPC motif is the putative active-site residue for recognition of the Apg5 subunit of the autophagosome complex  .. 
PF03986 Autophagocytosis associated protein (Atg3), N-terminal domain <br>Pfam-B_10019 (release 7.3). 
PF02309 AUX/IAA family<br>Pfam-B_801 (release 5.2). Transcription of the AUX/IAA family of genes is rapidly induced by the plant hormone auxin. Some members of this family are longer and contain an N terminal DNA binding domain, such as Swiss:O64965. The function of this region is uncertain.. 
PF02041 Auxin binding protein<br>
PF02519 Auxin responsive protein<br>Pfam-B_1263 (release 5.4). This family consists of the protein products of the ARG7 auxin responsive genes family none of which have any identified functional role. . 
PF03708 Avian retrovirus envelope protein, gp85 <br>Pfam-B_3651 (release 7.0). Family of a vain specific viral glycoproteins that forms a  receptor-binding gp85 polypeptide that is linked through disulfide  to a membrane-spanning gp37 spike.  Gp85 confers a high degree of subgroup  specificity for interaction with distinct cell receptors  .. 
PF01382 Avidin family<br>
PF03377 Xanthomonas avirulence protein, Avr/PthA<br>Pfam-B_3936 (release 6.6). 
PF03591 AzlC protein<br>TIGRFAMs, Griffiths-Jones SR. 
PF02216 B domain<br>Pfam-B_1782 (release 5.2). This family contains the B domain of Staphylococcal protein A, which specifically binds to the Fc portion of immunoglobulin G.. 
PF04182 B-block binding subunit of TFIIIC<br>Pfam-B_68239 (release 7.3);. Yeast transcription factor IIIC (TFIIIC) is a multi-subunit protein complex that interacts with two control elements of class III promoters called the A and B blocks. This family represents the subunit within TFIIIC involved in B-block binding  .. 
PF02246 Protein L b1 domain<br>Pfam-B_3438 (release 5.2). Protein L is a bacterial protein with immunoglobulin (Ig) light  chain-binding properties. It contains a number of homologous b1 repeats towards the N-terminus. These repeats have been found to  be responsible for the interaction of protein L with Ig light  chains  .. 
PF03483 S3_4;<br>Pfam-B_1005 (release 7.0). This domain is found in tRNA synthetase beta subunits as well as in some non tRNA synthetase proteins.. 
PF03484 tRNA synthetase B5 domain<br>Pfam-B_1005 (release 7.0). This domain is found in phenylalanine-tRNA synthetase beta subunits.. 
PF01603 Protein phosphatase 2A regulatory B subunit (B56 family)<br>Pfam-B_984 (release 4.1). 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 enzyme to act on a diverse array of substrates is largely controlled by the nature of its regulatory B subunit. There are multiple families of B subunits (See also Pfam:PF01240), this family is called the B56 family  .. 
PF02043 Bacteriochlorophyll C binding protein<br>
PF00216 Bacterial DNA-binding protein<br>
PF00308 bac_dnaA; <br>Bacterial dnaA  protein. 
PF01311 Bacterial export proteins, family 1<br>Pfam-B_1442 (release 3.0). This family includes the following members;     FliR, MopE, SsaT, YopT, Hrp, HrcT and SpaR All of these members export proteins, that do not possess signal  peptides, through the membrane.  Although the proteins that these exporters move may be different, the exporters are thought to  function in similar ways  .. 
PF01312 FlhB HrpN YscU SpaS Family<br>Pfam-B_1200 (release 3.0). This family includes the following members:   FlhB, HrpN, YscU, SpaS, HrcU SsaU and YopU. All of these proteins export peptides using the type III secretion system.  The peptides exported are quite diverse.. 
PF05088 Bacterial NAD-glutamate dehydrogenase<br>Pfam-B_6291 (release 7.7). This family consists of several bacterial proteins which are closely related to NAD-glutamate dehydrogenase found in Streptomyces clavuligerus. Glutamate dehydrogenases (GDHs) are a broadly distributed group of enzymes that catalyse the reversible oxidative deamination of glutamate to  ketoglutarate and ammonia  .. 
PF01152 Globin;<br>Bacterial-like globin. This family of heme binding proteins are found mainly in bacteria. However they can also be found in some protozoa and plants as well.. 
PF00296 bac_luciferase; <br>Luciferase-like monooxygenase. 
PF01036 Bacteriorhodopsin-like protein<br>Pfam-B_1412 (release 3.0). The bacterial opsins are retinal-binding proteins that provide light- dependent ion transport and sensory functions to a family of halophilic bacteria [2,3]. They are integral membrane proteins believed to contain seven transmembrane (TM) domains, the last of which contains the attachment point for retinal (a conserved lysine). This family also includes distantly related proteins that do not contain the retinal binding lysine and so cannot function as opsins.  Some fungal examples are: Swiss:O74870, Swiss:P25619, Swiss:P38079, Swiss:Q12117.. 
PF01103 Bac_suface_Ag; <br>Pfam-B_1201 (release 3.0). This entry includes the following surface antigens;    D15 antigen from H.influenzae,    OMA87 from P.multocida,    OMP85 from N.meningitidis and N.gonorrhoeae. The family also includes a number of eukaryotic proteins that are members of the UPF0140 family. There also appears to be a relationship to Pfam:PF03865 (personal obs: C Yeats). In eukaryotes, it appears that these proteins are not surface antigens; S. cerevisiae YNL026W (SAM50, Swiss:P53969) is an essential component of the Sorting and Assembly Machinery (SAM) of the mitochondrial outer membrane. The protein was localised to the mitochondria  .. 
PF01338 Bacillus thuringiensis toxin<br>
PF01654 Bacterial Cytochrome Ubiquinol Oxidase<br>Pfam-B_1148 (release 4.1). This family are the alternative oxidases found in many bacteria which oxidise ubiquinol and reduce oxygen as part of the electron transport chain. This family is the subunit I of the oxidase E. coli has two copies of the oxidase, bo and bd', both of which are represented here In some nitrogen fixing bacteria, e.g. Klebsiella pneumoniae this oxidase is responsible for removing oxygen in microaerobic conditions, making the oxidase required for nitrogen fixation. This subunit binds a single b-haem, through ligands at His186 and Met393 (using SW:P11026 numbering). In addition His19 is a ligand for the haem b found in subunit II. 
PF00936 Bact_microcomp; Bac_microcomp; <br>Pfam-B_1071 (release 3.0). Bacterial microcompartments are primitive organelles composed entirely of protein subunits. The prototypical bacterial microcompartment is the carboxysome, a protein shell for sequestering carbon fixation reactions. These proteins for hexameric structure  .. 
PF02397 Bact_transf; <br>Bacterial sugar transferase. Pfam-B_1538 (release 5.4). This Pfam family represents a conserved region from a number of  different bacterial sugar transferases, involved in diverse  biosynthesis pathways.. 
PF01721 Class II bacteriocin<br>Pfam-B_1954 (release 4.1). The bacteriocins are small peptides that inhibit the growth of various bacteria. Bacteriocins of lactic acid  bacteria may inhibit their target cells by permeabilising the cell  membrane  .. 
PF04798 Baculovirus 19 kDa protein conserved region<br>Pfam-B_6291 (release 7.5). Family of Baculovirus proteins of approximate mass 19 kDa. . 
PF04631 Baculovirus hypothetical protein<br>Pfam-B_5343 (release 7.5). This family includes several hypothetical baculoviral proteins, with predicted molecular weights of approximately 44 kD.. 
PF04786 ssDNA binding protein <br>Pfam-B_6251 (release 7.5). Family of Baculovirus ssDNA binding proteins.. 
PF04639 Baculoviral E56 protein, specific to ODV envelope<br>Pfam-B_5446 (release 7.5). This family represents the E56 protein, which is localises to the occlusion derived virus (ODV) envelope, but not to the budded virus (BV) envelope  .. 
PF04850 Baculovirus E66 occlusion-derived virus envelope protein<br>Pfam-B_4624 (release 7.6). 
PF03258 Baculovirus FP protein<br>Pfam-B_4275 (release 6.5). The FP protein is missing in baculovirus (Few Polyhedra) mutants  .. 
PF04700 Structural glycoprotein p40/gp41 conserved region<br>Pfam-B_4278 (release 7.5). Family of viral structural glycoproteins  .. 
PF03273 Baculovirus gp64 envelope glycoprotein family<br>Pfam-B_4223 (release 6.5). This family includes the gp64 glycoprotein from baculovirus as well as other viruses e.g. Swiss:P28970.. 
PF04735 Baculovirus DNA helicase<br>Pfam-B_3393 (release 7.5). 
PF04838 Baculoviridae late expression factor 5 <br>Pfam-B_5141 (release 7.6). 
PF05073 Baculovirus P24 capsid protein<br>Pfam-B_6005 (release 7.7). Baculovirus P24 is associated with nucleocapsids of budded and polyhedra-derived virions [1,2].. 
PF04766 Nucleopolyhedrovirus p26 protein<br>Pfam-B_6066 (release 7.5). Family of Baculovirus p26 proteins. . 
PF05214 Baculo_P33; <br>Pfam-B_6583 (release 7.7). This family consists of a series of Baculovirus P33 protein homologues of unknown function.. 
PF02961 Barrier to autointegration factor<br>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.. 
PF05112 Baculo_P47; <br>Baculovirus P47 protein. Pfam-B_6441 (release 7.7). This family consists of several Baculovirus P47 proteins which is one of the primary components of Baculovirus encoded RNA polymerase, which  initiates transcription from late and very late promoters  .. 
PF04878 Baculo_P48; <br>Baculovirus P48 protein. Pfam-B_6510 (release 7.6). 
PF04583 Baculoviridae p74 conserved region<br>Pfam-B_4744 (release 7.5). Baculoviruses are distinct from other virus families in that there are two viral phenotypes: budded virus (BV) and occlusion-derived virus (ODV). BVs disseminate viral infection throughout the tissues of the host and ODVs transmit baculovirus between insect hosts.  GFP tagging experiments implicate p74 as an ODV envelope protein [1,2].. 
PF04513 Baculovirus polyhedron envelope protein, PEP, C terminus <br>Polyhedra are large crystalline occlusion bodies containing  nucleopolyhedrovirus virions, and surrounded by an electron-dense  structure called the polyhedron envelope or polyhedron calyx.  The  polyhedron envelope (associated) protein PEP is thought to be an  integral part of the polyhedron envelope. PEP is concentrated at the surface of polyhedra, and is thought to be important for the proper  formation of the periphery of polyhedra.  It is thought that PEP may  stabilise polyhedra and protect them from fusion or aggregation  .. 
PF04512 Baculovirus polyhedron envelope protein, PEP, N terminus<br>Polyhedra are large crystalline occlusion bodies containing  nucleopolyhedrovirus virions, and surrounded by an electron-dense  structure called the polyhedron envelope or polyhedron calyx.  The  polyhedron envelope (associated) protein PEP is thought to be an  integral part of the polyhedron envelope. PEP is concentrated at the surface of polyhedra, and is thought to be important for the proper  formation of the periphery of polyhedra.  It is thought that PEP may  stabilise polyhedra and protect them from fusion or aggregation  .. 
PF04501 Baculovirus major capsid protein VP39<br>This family constitutes the 39 kDa major capsid protein of the Baculoviridae  .. 
PF04913 Baculovirus Y142 protein<br>Pfam-B_6688 (release 7.6). 
PF04684 BAF1 / ABF1 chromatin reorganising factor<br>ABF1 is a sequence-specific DNA binding protein involved in transcription  activation, gene silencing and initiation of DNA replication. ABF1 is known to remodel chromatin, and it is proposed that it mediates its effects on  transcription and gene expression by modifying local chromatin architecture  . These functions require a conserved stretch of 20 amino acids in the  C-terminal region of ABF1 (amino acids 639 to 662 S. cerevisiae  (Swiss:P14164))  .  The N-terminal two thirds of the protein are  necessary for DNA binding, and the N-terminus (amino acids 9 to 91 in S.  cerevisiae) is thought to contain a novel zinc-finger motif which may  stabilise the protein structure  .. 
PF02179 BAG domain<br>Alignment kindly provided by SMART. Domain present in Hsp70 regulators.. 
PF02923 Restriction endonuclease BamHI<br>
PF00373 Band_41; <br>This domain is the central structural domain of the FERM domain.. 
PF03114 BAR domain<br>BAR domains are dimerisation, lipid binding and curvature sensing modules found in many different protein families. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysin, endophilin, BRAP and Nadrin. BAR domains are also frequently found alongside domains that determine lipid specificity, like Pfam:PF00169 and Pfam:PF00787 domains in beta centaurins and sorting nexins respectively.. 
PF01337 Barstar (barnase inhibitor)<br>
PF00967 Barwin family<br>
PF04865 Baseplate J-like protein<br>Pfam-B_4777 (release 7.6). The P2 bacteriophage J protein lies at the edge of the baseplate. This family also includes a number of bacterial homologues, which are thought to have been horizontally transferred.. 
PF01586 Myogenic Basic domain<br>Pfam-B_427 (release 4.1). 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 specific DNA binding  . With 12 residues of the basic domain involved in DNA binding  . The basic domain forms an extended alpha helix in the structure.. 
PF02028 BCCT family transporter<br>
PF02327 Bacteriochlorophyll A protein<br>Pfam-B_38317 (release 5.2). Bacteriochlorophyll A protein is involved in the energy transfer system of green photosynthetic bacteria. The protein forms a homotrimer, with each monomer unit containing seven molecules of bacteriochlorophyll A.. 
PF00452 Apoptosis regulator proteins, Bcl-2 family<br>
PF04538 Brain expressed X-linked like family <br>Pfam-B_3086 (release 7.5). This is a family of transcription elongation factors which includes those referred to as Bex proteins as well as those named TCEAL7. Bex1 was shown to be a novel link between neurotrophin signalling, the cell cycle, and neuronal differentiation, suggesting it might function by coordinating internal cellular states with the ability of cells to respond to external signals  . TCEAL7 has been shown negatively to regulate the NF-kappaB pathway, hence being important in ovarian cancer as it one of the genes frequently downregulated in this cancer. A closely related protein, TFIIS/TCEA, found in Pfam:PF07500 is involved in transcription elongation and transcript fidelity. TFIIS/TCEA promotes 3' endoribonuclease activity of RNA polymerase II (pol II) and allows pol II to bypass transcript pause or 'arrest' during elongation process. It is thus possible that BEX is also acting in this way  .. 
PF04714 BCL7, N-terminal conserver region<br>Pfam-B_5900 (release 7.5). Members of the BCL family have significant sequence similarity at their N-terminus, represented in this family. The function of BCL7 proteins is unknown. They may be involved in early development. In addition, BCL7B is commonly hemizygously deleted in patients with Williams syndrome  .. 
PF01869 BadF/BadG/BcrA/BcrD ATPase family<br>Enright A & Pfam-B_5854 (Release 7.5). This family includes the BadF Swiss:O07462 and BadG Swiss:O07463 proteins that are two subunits of Benzoyl-CoA reductase, that may be involved in ATP hydrolysis. The family also includes an activase subunit from the enzyme 2-hydroxyglutaryl-CoA dehydratase Swiss:P11568. The protein Swiss:O66634 contains two copies of this region suggesting that the family may structurally dimerise. This family appears to be related to Pfam:PF00370.. 
PF03170 Bacterial cellulose synthase subunit<br>Pfam-B_3954 (release 6.5). This family includes bacterial proteins involved in cellulose synthesis. Cellulose synthesis has been identified in several bacteria. In Agrobacterium tumefaciens, for instance, cellulose has a pathogenic role: it allows the bacteria to bind tightly to their host plant cells.  While several enzymatic steps are involved in cellulose synthesis, potentially the only step unique to this pathway is that catalysed by cellulose synthase. This enzyme is a multi subunit complex. This family encodes a subunit that is thought to bind the positive effector cyclic di-GMP. This subunit is found in several different bacterial cellulose synthase enzymes. The first recognised sequence for this subunit is BcsB. In the AcsII cellulose synthase, this subunit and the subunit corresponding to BcsA are found in the same protein. Indeed, this alignment only includes the C-terminal half of the AcsAII synthase (Swiss:Q59167), which corresponds to BcsB.. 
PF02138 Beige/BEACH domain<br>
PF00407 Bet_v_I; <br>Pathogenesis-related protein Bet v I family. This family is named after Bet v 1, the major birch pollen allergen. This protein belongs to family 10 of plant pathogenesis-related proteins (PR-10), cytoplasmic proteins of 15-17 kd that are wide-spread among dicotyledonous plants  . In recent years, a number of diverse plant proteins with low sequence similarity to Bet v 1 was identified. A classification by sequence similarity yielded several subfamilies related to PR-10  : - Pathogenesis-related proteins PR-10: These proteins were identified as major tree pollen allergens in birch and related species (hazel, alder), as plant food allergens expressed in high levels in fruits, vegetables and seeds (apple, celery, hazelnut), and as pathogenesis-related proteins whose expression is induced by pathogen infection, wounding, or abiotic stress. Hyp-1 (Swiss:Q8H1L1), an enzyme involved in the synthesis of the bioactive naphthodianthrone hypericin in St. John's wort (Hypericum perforatum) also belongs to this family. Most of these proteins were found in dicotyledonous plants. In addition, related sequences were identified in monocots and conifers. - Cytokinin-specific binding proteins: These legume proteins bind cytokinin plant hormones  . - (S)-Norcoclaurine synthases are enzymes catalysing the condensation of dopamine and 4-hydroxyphenylacetaldehyde to (S)-norcoclaurine, the first committed step in the biosynthesis of benzylisoquinoline alkaloids such as morphine  . -Major latex proteins and ripening-related proteins are proteins of unknown biological function that were first discovered in the latex of opium poppy (Papaver somniferum) and later found to be upregulated during ripening of fruits such as strawberry and cucumber  . The occurrence of Bet v 1-related proteins is confined to seed plants with the exception of a cytokinin-binding protein from the moss Physcomitrella patens (Swiss:Q9AXI3).. 
PF03494 Beta-amyloid peptide (beta-APP)<br>
PF00144 beta-lactamase; <br>Prosite and Pfam-B_106 (Release 7.5). This family appears to be distantly related to Pfam:PF00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.. 
PF01212 Beta-eliminating lyase<br>
PF02929 Beta galactosidase small chain<br>Pfam-B_592 (Release 6.3). This domain comprises the small chain of dimeric beta-galactosidases EC:3.2.1.23.  This domain is also found in single chain beta-galactosidase.. 
PF02180 Bcl-2 homology region 4<br>Alignment kindly provided by SMART. 
PF02368 Bacterial Ig-like domain (group 2)<br>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.. 
PF04775 Acyl-CoA thioester hydrolase/BAAT N-terminal region<br>Pfam-B_2191 (release 7.6). This family consists of the amino termini of acyl-CoA thioester hydrolase and bile acid-CoA:amino acid N-acetyltransferase (BAAT)  .  This region is not thought to contain the active site of either enzyme.  Thioesterase isoforms have been identified in peroxisomes, cytoplasm and mitochondria, where they are thought to have distinct functions in lipid metabolism  .  For example, in peroxisomes, the hydrolase acts on bile-CoA esters  .. 
PF03496 Binary_toxA;<br>ADP-ribosyltransferase exoenzyme. This is a family of bacterial and viral bi-glutamic acid ADP-ribosyltransferases, where, in Swiss:Q93Q17, E403 is the catalytic residue and E401 contributes to the transfer of ADP-ribose to the target protein. In clostridial species it is actin that is being ADP-ribosylated; this result is lethal and dermonecrotic in infected mammals.. 
PF03495 Clostridial binary toxin B/anthrax toxin PA<br>The N-terminal region of this family contains a  calcium-binding motif that may be an EF-hand.. 
PF02084 Bindin<br>
PF00351 biopterin_H; <br>Biopterin-dependent aromatic amino acid hydroxylase. This family includes phenylalanine-4-hydroxylase, the phenylketonuria disease protein.. 
PF00364 biotin_req_enzy; biotin_lipoyl; <br>Biotin-requiring enzyme. This family covers two Prosite entries, the conserved lysine residue binds biotin in one group and lipoic acid in the other. Note that the HMM does not currently recognise the Glycine cleavage system H proteins.. 
PF03744 6-carboxyhexanoate--CoA ligase<br>This family contains the enzyme 6-carboxyhexanoate--CoA ligase EC:6.2.1.14. This enzyme is involved in the first step of biotin synthesis, where it converts pimelate into pimeloyl-CoA  . The enzyme requires magnesium as a cofactor and forms a homodimer  .. 
PF02632 BioY family<br>A number of bacterial genes are involved in bioconversion of pimelate into dethiobiotin  . BioY is a component of the BioMNY transport system involved in biotin uptake in prokaryotes  .. 
PF00653 Inhibitor of Apoptosis domain<br>BIR stands for 'Baculovirus Inhibitor of apoptosis protein Repeat'. It is found repeated in inhibitor of apoptosis proteins (IAPs), and in fact it is also known as IAP repeat. These domains characteristically have a number of invariant residues, including 3 conserved cysteines and one conserved histidine that coordinate a zinc ion. They are usually made up of 4-5 alpha helices and a three-stranded beta-sheet. BIR is also found in other proteins known as BIR-domain-containing proteins (BIRPs), such as Survivin (Swiss:O15392)  .. 
PF04197 Birnavirus RNA dependent RNA polymerase (VP1)<br>Pfam-B_2204 (release 7.3). Birnaviruses are dsRNA viruses. This family corresponds to the RNA dependent RNA polymerase. This protein is also known as VP1. All of the birnavirus VP1 proteins contain conserved RdRp motifs that reside in the catalytic "palm" domain of all classes of polymerases. However, the birnavirus RdRps lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RdRps  .. 
PF01766 Birnavirus VP2 protein<br>Pfam-B_946 (release 4.2). VP2 is the major structural protein of birnaviruses  . The large RNA segment of birnaviruses codes for a polyprotein (N-VP2-VP4-VP3-C)  .. 
PF01767 Birnavirus VP3 protein<br>Pfam-B_946 (release 4.2). VP3 is a minor structural component of the virus. The large RNA segment of birnaviruses codes for a polyprotein (N-VP2-VP4-VP3-C)  .. 
PF01768 Birnavirus VP4 protein<br>Pfam-B_946 (release 4.2). VP4 is a viral protease  . The large RNA segment of birnaviruses codes for a polyprotein (N-VP2-VP4-VP3-C)  .. 
PF03042 Birnavirus VP5 protein<br>Pfam-B_1772 (release 6.4). 
PF03493 Calcium-activated BK potassium channel alpha subunit<br>
PF04940 Sensors of blue-light using FAD<br>The BLUF domain has been shown to bind FAD in the AppA protein (Swiss:Q53119). AppA is  involved in the repression of photosynthesis genes in response to blue-light.. 
PF02608 Basic membrane protein<br>This is a family of basic membrane lipoproteins form Borrelia and various putative lipoproteins form other bacteria.  All of these proteins are  outer membrane proteins and are thus antigenic in nature when possessed by the pathogenic members of the family.  One protein Swiss:032436 is a transcriptional activator  .. 
PF01722 BolA-like protein<br>Pfam-B_1996 (release 4.1). This family consist of the morphoprotein BolA from E. coli and its various homologues. In E. coli over expression of this protein causes round morphology and may be involved in  switching the cell between elongation and septation systems during  cell division  . The expression of BolA is growth rate regulated and is induced during the transition into the the stationary phase  . BolA is also induced by stress during early stages of  growth   and may have a general role in stress response.  It has also been suggested that BolA can induce the transcription of penicillin binding proteins 6 and 5 [2,1].. 
PF02044 Bombesin-like peptide<br>
PF02414 Borrelia ORF-A<br>Pfam-B_1805 (release 5.4). This protein is encoded by an open reading frame in plasmid borne DNA repeats of Borrelia species. This protein is known as ORF-A  . The function of this putative protein is unknown.. 
PF03183 Borrelia repeat protein<br>Pfam-B_2029 (release 6.5). 
PF00228 Bowman-Birk serine protease inhibitor family<br>
PF02653 Branched-chain amino acid transport system / permease component<br>COG0559 & Pfam-B_654 (Release 7.5). This is a large family mainly comprising high-affinity branched-chain amino acid transporter proteins such as E. coli LivH Swiss:P08340 and LivM  Swiss:P22729 both of which are form the LIV-I transport system  . Also found with in this family are proteins from the galactose transport system permease   and a ribose transport system  .. 
PF00634 BRCA2_repeat;<br>The alignment covers only the most conserved region of the repeat.. 
PF02498 BRO; <br>BRO family, N-terminal domain. Pfam-B_1235 (release 5.4). This family includes the N-terminus of baculovirus BRO and ALI motif proteins. The function of BRO proteins is unknown.  It has been suggested that BRO-A and BRO-C are DNA binding proteins that influence host DNA replication and/or transcription  . This Pfam domain does not include the characteristic invariant alanine, leucine, isoleucine motif of the ALI proteins  .. 
PF03032 Brevenin/esculentin/gaegurin/rugosin family<br>Pfam-B_1232 (release 6.4). This family contains a number of defence peptides secreted from the skin of amphibians, including the opiate-like dermorphins and deltorphins, and the antimicrobial  dermoseptins and temporins. The alignment for this family includes the signal peptide.. 
PF01318 Bromo_CP; <br>Bromovirus coat protein. 
PF01573 Bromovirus movement protein<br>Pfam-B_508 (release 4.1). 
PF04450 Peptidase of plants and bacteria<br>Pfam-B_5066 (release 7.5). These basic secretory proteins (BSPs) are believed to be part of the plants defence mechanism against pathogens  . . 
PF00779 BTK motif<br>Alignment kindly provided by SMART. 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  .. 
PF04514 Bluetongue virus non-structural protein NS2<br>This family includes NS2 proteins from other members of the Orbivirus genus.  NS2 is a non-specific single-stranded RNA-binding protein that forms large homomultimers and accumulates in viral inclusion bodies of infected cells. Three RNA binding regions have been identified in Bluetongue virus serotype 17 (Swiss:P33473) at residues 2-11, 153-166 and 274-286  . NS2 multimers also possess nucleotidyl phosphatase activity  . The precise function of NS2 is not known, but it may be involved in the transport and condensation of viral mRNAs  .. 
PF04426 Bul1 C terminus<br>This family contains the C terminus of Saccharomyces cerevisiae Bul1. Bul1 binds the ubiquitin ligase Rsp5, via an N terminal PPSY motif (157-160 in Swiss:P48524)  .  The complex containing Bul1 and Rsp5 is involved in  intracellular trafficking of the general amino acid permease Gap1  , degradation of Rog1 in cooperation with Bul2 and GSK-3  , and  mitochondrial inheritance  . Bul1 may contain HEAT repeats.. 
PF04425 Bul1 N terminus<br>This family contains the N terminus of Saccharomyces cerevisiae Bul1. Bul1 binds the ubiquitin ligase Rsp5, via an N terminal PPSY motif (157-160 in Swiss:P48524)  .  The complex containing Bul1 and Rsp5 is involved in  intracellular trafficking of the general amino acid permease Gap1  , degradation of Rog1 in cooperation with Bul2 and GSK-3  , and  mitochondrial inheritance  . Bul1 may contain HEAT repeats.. 
PF03557 Bunyavirus glycoprotein G1<br>Pfam-B_653 (release 7.0). 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-structural protein (NSm). The L segment codes for an RNA polymerase.  This family contains the G1 glycoprotein which is the viral attachment protein  .. 
PF03563 Bunyavirus glycoprotein G2<br>Pfam-B_1048 (release 7.0). 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-structural protein (NSm). The L segment codes for an RNA polymerase.  This family contains the G2 glycoprotein which interacts with the Pfam:PF03557 G1 glycoprotein  .. 
PF01104 Bunyavirus non-structural protein NS-s<br>Pfam-B_880 (release 3.0). The NS-s protein is encoded by the S RNA. This segment also encodes for the N protein.  These two proteins are encoded by overlapping reading frames.. 
PF03231 Bunyavirus non-structural protein NS-S<br>Pfam-B_3018 (release 6.5). This family represents the Bunyavirus NS-S family. 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-structural protein (NSm). The L segment codes for an RNA polymerase.. 
PF00952 Bunyavirus nucleocapsid (N) protein<br>Pfam-B_587 (release 3.0). The bunyaviruses are enveloped viruses with a genome consisting of 3 ssRNA segments (called L, M and S). The nucleocapsid protein  is encode on the small (S) genomic RNA. The N protein is the major  component of the nucleocapsids.  This protein is thought to  interact with the L protein, virus RNA and/or other N proteins.. 
PF04196 Bunyavirus RNA dependent RNA polymerase<br>Pfam-B_2559 (release 7.3). The bunyaviruses are enveloped viruses with a genome consisting of 3 ssRNA segments (called L, M and S). The nucleocapsid protein is encode on the small (S) genomic RNA. The L segment codes for an RNA polymerase. This family contains the RNA dependent RNA polymerase on the L segment.. 
PF03181 BURP domain<br>Pfam-B_1432 (release 6.5). The BURP domain is found at the C-terminus of several different plant proteins. It was named after the proteins in which it was first  identified: the BNM2 clone-derived protein from Brassica napus Swiss:O65009; USPs and USP-like proteins Swiss:P21746 Swiss:P21747 Swiss:Q06765  Swiss:O24482; RD22 from Arabidopsis thaliana Swiss:Q08298; and PG1beta from Lycopersicon esculentum Swiss:Q40161. This domain is around 230 amino acid residues long. It possesses the following conserved features: two phenylalanine residues at its N-terminus; two cysteine residues; and four repeated cysteine-histidine motifs, arranged as: CH-X(10)-CH-X(25-27)-CH-X(25-26)-CH, where X can be any amino acid  . The function of this domain is unknown.. 
PF03309 Bvg_acc_factor;<br>Type III pantothenate kinase. Pfam-B_3452 (release 6.5). Type III pantothenate kinase catalyses the phosphorylation of pantothenate (Pan), the first step in the universal pathway of CoA biosynthesis.. 
PF04681 Blastomyces yeast-phase-specific protein<br>Pfam-B_5640 (release 7.5). The molecular function of this protein is not known. Its expression is specific to the high temperature, unicellular yeast morphology (as opposed to the lower temperature, multicellular mycelium form)  .. 
PF00170 bZIP;<br>bZIP transcription factor. The Pfam entry includes the basic region and the leucine zipper region.. 
PF00386 C1q domain<br>C1q is  a subunit of the C1 enzyme complex that activates the serum complement system.. 
PF01413 C-terminal tandem repeated domain in type 4 procollagen<br>Ponting CP, Schultz J, Bork P. Duplicated domain in C-terminus of type 4 collagens. Mutations in alpha-5 collagen IV are associated with X-linked Alport syndrome.. 
PF03595 C4dic_mal_tran;<br>Voltage-dependent anion channel. This family of transporters has ten alpha helical transmembrane segments  .  The structure of a bacterial homologue of SLAC1 shows it to have a trimeric arrangement. The pore is composed of five helices with a conserved Phe residue involved in gating. One homologue, Mae1 from the yeast Schizosaccharomyces pombe, functions as a malate uptake transporter; another, Ssu1 from Saccharomyces cerevisiae and other fungi including Aspergillus fumigatus, is characterised as a sulfite efflux pump; and TehA from Escherichia coli is identified as a tellurite resistance protein by virtue of its association in the tehA/tehB operon. In plants, this family is found in the stomatal guard cells functioning as an anion-transporting pore  . Many homologues are incorrectly annotated as tellurite resistance or dicarboxylate transporter (TDT) proteins.. 
PF01681 C6 domain<br>This domain of unknown function is found in the C. elegans protein Swiss:Q19522. It is presumed to be an extracellular domain.  The C6 domain contains six conserved cysteine residues in most copies of the domain. However some copies of the domain are missing cysteine residues 1 and 3 suggesting that these form a disulphide bridge.. 
PF03596 Cadmium resistance transporter<br>TIGRFAMs, Griffiths-Jones SR. 
PF00028 cadherin; <br>Swissprot_feature_table. 
PF01049 Cadherin_C_term; <br>Cadherin cytoplasmic region. Pfam-B_257 (release 3.0). Cadherins are vital in cell-cell adhesion during tissue differentiation.  Cadherins are linked to the cytoskeleton by catenins. Catenins bind to the cytoplasmic tail of the   cadherin.  Cadherins cluster to form foci of homophilic binding units.  A key determinant to the strength of the  binding that it is mediated by cadherins is the juxtamembrane region of the cadherin.  This region induces clustering  and also binds to the protein p120ctn  .. 
PF03507 CagA exotoxin<br>Pfam-B_918 (release 7.0). 
PF03524 cagX; <br>Conjugal transfer protein. PRINTS & Pfam-B_5812 (Release 7.5). This family includes type IV secretion system CagX conjugation protein. Other members of this family are involved in conjugal transfer to plant cells of T-DNA.. 
PF03185 Calcium-activated potassium channel, beta subunit<br>Pfam-B_2176 (release 6.5). 
PF00214 Calcitonin / CGRP / IAPP family<br>
PF04847 Calcipressin<br>Pfam-B_4547 (release 7.6). Calcipressin is also known as calcineurin-binding protein, since it inhibits calcineurin-mediated transcriptional modulation by binding to calcineurin's catalytic domain  .. 
PF02029 Caldesmon<br>
PF05042 Caleosin related protein<br>Pfam-B_5163 (release 7.7). This family contains plant proteins related to caleosin. Caleosins contain calcium-binding domains and have an oleosin-like association with lipid  bodies. Caleosins are present at relatively low levels and are mainly bound to microsomal membrane fractions at the early stages of seed development. As the seeds mature, overall levels of caleosins increased dramatically and they were associated almost exclusively with storage lipid bodies  . This family is probably related to EF hands Pfam:PF00036.. 
PF00915 Calicivirus coat protein<br>Pfam-B_202 (release 3.0). 
PF01067 Calpain large subunit, domain III<br>Pfam-B_852 (release 3.0). The function of the domain III and I are currently unknown. Domain II is a cysteine protease and domain IV is a calcium binding domain. Calpains are believed to participate in intracellular signaling pathways mediated by calcium ions.. 
PF00748 Calpain inhibitor<br>Pfam-B_543 (release 2.1). This region is found multiple times in calpain inhibitor proteins.. 
PF00402 calponin; <br>Calponin family repeat. 
PF00262 calreticulin; <br>
PF01216 Calsequestrin<br>
PF03160 Calx-beta domain<br>
PF01213 CAP; <br>Adenylate cyclase associated (CAP) N terminal. 
PF04451 Capsid_Iridovir; <br>Large eukaryotic DNA virus major capsid protein. DOMO:DM04206; Iyer L. This family includes the major capsid protein of iridoviruses, chlorella virus and Spodoptera ascovirus, which are all dsDNA viruses with no RNA stage. This is the most abundant structural protein and can account for up to 45% of virion protein  .  In Chlorella virus PBCV-1 the major capsid protein is a glycoprotein  . The four families of large eukaryotic DNA viruses, Poxviridae, Asfarviridae, Iridoviridae, and Phycodnaviridae, are referred to collectively as nucleocytoplasmic large DNA viruses or NCLDV. The virions of different NCLDV have dramatically different structures. The major capsid proteins of iridoviruses and phycodnaviruses, both of which have icosahedral capsids surrounding an inner lipid membrane, showed a high level of sequence conservation. A more limited, but statistically significant sequence similarity was observed between these proteins and the major capsid protein (p72) of ASFV, which also has an icosahedral capsid. It was surprising, however, to find that all of these proteins shared a conserved domain with the poxvirus protein D13L, which is an integral virion component thought to form a scaffold for the formation of viral crescents and immature virion  .. 
PF05159 Capsule polysaccharide biosynthesis protein<br>This family includes export proteins involved in capsule polysaccharide biosynthesis, such as KpsS Swiss:P42218 and LipB Swiss:P57038.. 
PF00194 carb_anhydrase; <br>Eukaryotic-type carbonic anhydrase. 
PF02977 Carboxypeptidase A inhibitor<br>
PF00619 Caspase recruitment domain<br>Ponting C, Schultz J, Bork P. Motif contained in proteins involved in apoptotic signaling. Predicted to possess a DEATH (Pfam:PF00531) domain-like fold .. 
PF01623 Carlavirus putative nucleic acid binding protein<br>Pfam-B_808 (release 4.1). This family of carlavirus nucleic acid binding proteins includes a motif for a potential C-4 type zinc finger this has four highly conserved cysteine residues and is a conserved feature of the carlaviruses 3' terminal ORF  . These proteins may function as viral transcriptional regulators. The carlavirus family includes garlic latent virus and potato virus S and M, these viruses are positive strand, ssRNA with no DNA stage.. 
PF00997 casein_kappa; <br>Pfam-B_1298 (release 3.0). 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 (caseinomacropeptide). Caseinomacropeptide is responsible for increased efficiency of digestion, prevention of neonate hypersensitivity to ingested proteins, and inhibition of gastric pathogens.. 
PF00363 caseins; <br>
PF00302 Chloramphenicol acetyltransferase<br>
PF03123 CAT RNA binding domain<br>P39805/1-60 Psi-blast. This RNA binding domain is found at the amino terminus of transcriptional antitermination proteins such as BglG, SacY and LicT. These proteins control the expression of sugar metabolising operons in Gram+ and Gram- bacteria. This domain has been called the CAT (Co-AntiTerminator) domain. It binds as a dimer   to short Ribonucleotidic Anti-Terminator (RAT) hairpin, each monomer interacting symmetrically with both strands of the RAT hairpin  . In the full-length protein, CAT is followed by two phosphorylatable PTS regulation domains (Pfam:PF00874) that modulate the RNA binding activity of CAT. Upon activation, the dimeric proteins bind to RAT targets in the nascent mRNA, thereby preventing abortive dissociation of the RNA polymerase from the DNA template  .. 
PF00199 catalase; <br>
PF00666 Cathelicidin<br>Pfam-B_276 (release 2.1). A novel protein family, showing a conserved proregion and a variable carboxyl-terminal antimicrobial domain. This region shows similarity to cystatins.. 
PF04731 Caudal like protein activation region<br>This family consists of the amino termini of proteins belonging to the caudal-related homeobox protein family.  This region is thought to mediate transcription activation.  The level of activation caused by mouse Cdx2  (Swiss:P43241) is affected by phosphorylation at serine 60 via the mitogen-activated protein kinase pathway  .  Caudal family proteins are involved in the transcriptional regulation of multiple genes expressed in the intestinal epithelium, and are important in differentiation and maintenance of the intestinal epithelial lining. Caudal proteins always have a homeobox DNA binding domain (Pfam:PF00046).. 
PF00689 Na_K_ATPase_C;<br>Cation transporting ATPase, C-terminus. Pfam-B_137 (release 2.1). Members of this families are involved in Na+/K+, H+/K+, Ca++ and Mg++ transport. This family represents 5 transmembrane helices.. 
PF03310 Caulimovirus DNA-binding protein<br>Pfam-B_3746 (release 6.5). 
PF03233 Caulimo_AT; <br>Aphid transmission protein. Pfam-B_3118 (release 6.5). This protein is found in various caulimoviruses. It codes for an 18 kDa protein (PII), which is dispensable for infection but which is required for aphid transmission of the virus  . This protein interacts with the PIII protein  .. 
PF01693 Caulimo_VI;<br>Caulimovirus viroplasmin. Pfam-B_1373 (release 4.1). This family consists of various caulimovirus viroplasmin proteins.  The viroplasmin protein is encoded by gene VI and is the main component of viral inclusion bodies or viroplasms  . Inclusions are the site of viral assembly, DNA synthesis and accumulation  . Two domains exist within gene VI corresponding approximately to the 5' third and middle third of gene VI, these influence systemic infection in a light-dependent manner  .. 
PF04771 Chicken anaemia virus VP-3 protein<br>Pfam-B_2147 (release 7.6). This protein is found in the nucleus of infected cells and may act as a transcriptional regulator.  It induces apoptosis, and is also known as apoptin [SwissProt annotation for Swiss:P54094].. 
PF01146 Caveolin<br>All three known Caveolin forms have the FEDVIAEP caveolin 'signature motif' within their hydrophilic N-terminal domain. Caveolin 2 (Cav-2) is co-localised and co-expressed with Cav-1/VIP21, forms heterodimers with it and needs Cav-1 for proper membrane localisation. Cav-3 has greater protein sequence similarity to Cav-1 than to Cav-2. Cellular processes caveolins are involved in include vesicular transport, cholesterol homeostasis, signal transduction, and tumour suppression  .. 
PF02275 Linear amide C-N hydrolases, choloylglycine hydrolase family<br>Pfam-B_5806 (release 5.2). This family includes several hydrolases which cleave carbon-nitrogen bonds, other than peptide bonds, in linear amides.  These include choloylglycine hydrolase (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. This domain forms the alpha-subunit for members from vertebral species, see family NAAA-beta, Pfam:PF15508.. 
PF03914 CBF/Mak21 family<br>Wood V, Griffiths-Jones SR. Pfam-B_3822 (release 7.2). 
PF02312 Core binding factor beta subunit<br>Pfam-B_12381 (release 5.2). 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 been show to have a structure related to the OB fold  .. 
PF02045 CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B<br>
PF00808 Archael_histone; Arch_histone; <br>Histone-like transcription factor (CBF/NF-Y) and archaeal histone. Pfam-B_1351 (Rel 2.1) & Pfam-B_3673 (Rel 7.5) & Pfam-B_2078 (Rel 8.0). This family includes archaebacterial histones and histone like transcription factors from eukaryotes.. 
PF01656 CBIA;<br>CobQ/CobB/MinD/ParA nucleotide binding domain. Pfam-B_782 (release 4.1). This family consists of various cobyrinic acid a,c-diamide synthases. These include CbiA Swiss:P29946 and CbiP Swiss:Q05597 from  S.typhimurium  , and CobQ Swiss:Q52686 from R. capsulatus  . These amidases catalyse amidations to various side chains of  hydrogenobyrinic acid or cobyrinic acid a,c-diamide in the biosynthesis  of cobalamin (vitamin B12) from uroporphyrinogen III. Vitamin B12 is an important cofactor and an essential nutrient for many  plants and animals and is primarily produced by bacteria  . The family also contains dethiobiotin synthetases as well as the plasmid partitioning proteins of the MinD/ParA family  .. 
PF02570 Precorrin-8X methylmutase<br>This is a family Precorrin-8X methylmutases also known as Precorrin  isomerase, CbiC/CobH,  EC:5.4.1.2.  This enzyme catalyses the reaction: Precorrin-8X <=> hydrogenobyrinate.  This enzyme is part of the Cobalamin (vitamin B12) biosynthetic pathway and catalyses a methyl rearrangement  [1,2].. 
PF01888 CbiD<br>CbiD is essential for cobalamin biosynthesis in both S. typhimurium and B. megaterium, no functional role has been ascribed to the protein. The CbiD protein has a putative S-AdoMet binding site. It is possible that CbiD might have the same role as CobF in undertaking the C-1 methylation and deacylation reactions required during the ring contraction process  .. 
PF01890 CbiG; <br>Cobalamin synthesis G C-terminus. Members of this family are involved in cobalamin synthesis.  The gene encoded by Swiss:P72862 has been designated cbiH but in fact represents a fusion between cbiH and cbiG. As other multi-functional proteins involved in cobalamin biosynthesis catalyse adjacent steps in the pathway, including CysG, CobL (CbiET), CobIJ and CobA-HemD, it is therefore possible that CbiG catalyses a reaction step adjacent to CbiH. In the anaerobic pathway such a step could be the formation of a gamma lactone, which is thought to help to mediate the anaerobic ring contraction process  . Within the cobalamin synthesis pathway CbiG catalyses the both the opening of the lactone ring and the extrusion of the two-carbon fragment of cobalt-precorrin-5A from C-20 and its associated methyl group (deacylation) to give cobalt-precorrin-5B  . This family is the C-terminal region, and the mid- and N-termival parts are conserved independently in other families.. 
PF02571 Precorrin-6x reductase CbiJ/CobK<br>This family consists of Precorrin-6x reductase EC:1.3.1.54. This enzyme catalyses the reaction: precorrin-6Y + NADP(+)  <=> precorrin-6X + NADPH.  CbiJ and CobK both catalyse the reduction of macocycle in the colbalmin biosynthesis pathway [1,2].. 
PF01891 Cobalt uptake substrate-specific transmembrane region<br>This family of proteins forms part of the cobalt-transport complex in prokaryotes, CbiMNQO. CbiMNQO and NikMNQO are the most widespread groups of microbial transporters for cobalt and nickel ions and are unusual uptake systems as they consist of eg two transmembrane components (CbiM and CbiQ), a small membrane-bound component (CbiN) and an ATP-binding protein (CbiO) but no extracytoplasmic solute-binding protein. Similar components constitute the nickel transporters with some variability in the small membrane-bound component, either NikN or NikL, which are not similar to CbiN at the sequence level. CbiM is the substrate-specific component of the complex and is a seven-transmembrane protein  . The CbiMNQO and NikMNQO systems form part of the coenzyme B12 biosynthesis pathway  . The NikM protein is Pfam:PF10670.. 
PF02553 Cobalt transport protein component CbiN<br>CbiN is part of the active cobalt transport system involved in  uptake of cobalt in to the cell involved with cobalamin biosynthesis (vitamin B12).  It has been suggested that CbiN may function as the periplasmic binding protein component of the active cobalt transport  system  .. 
PF02361 Cobalt transport protein<br>Pfam-B_673 (release 5.2). This family consists of various cobalt transport proteins Most of which are found in Cobalamin (Vitamin B12) biosynthesis operons.  In Salmonella the cbiN cbiQ (product CbiQ in this family) and cbiO are likely to form an active cobalt transport system  .. 
PF01903 CbiX<br>The function of CbiX is uncertain, however it is found in cobalamin biosynthesis operons and so may have a related function. Some CbiX proteins contain a striking histidine-rich region at their C-terminus, which suggests that it might be involved in metal chelation  .. 
PF02262 CBL proto-oncogene N-terminal domain 1<br>Pfam-B_3949 (release 5.2). 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 is known to bind to phosphorylated tyrosine residues. Cbl_N is comprised of 3 structural domains of which this is the first - a four helix bundle.. 
PF02761 CBL proto-oncogene N-terminus, EF hand-like domain<br>Pfam-B_3949 (release 5.2). 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 is known to bind to phosphorylated tyrosine residues. The so called N-terminal domain is actually 3 structural domains, of which this is the central EF hand domain.. 
PF02762 CBL proto-oncogene N-terminus, SH2-like domain<br>Pfam-B_3949 (release 5.2). 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 is known to bind to phosphorylated tyrosine residues. The so called N-terminal domain is actually 3 structural domains, of which this is the C-terminal SH2 domain.. 
PF00734 CBD_fungal; CBD_1; <br>Fungal cellulose binding domain. Pfam-B_444 (release 2.1). 
PF02013 CBD_5; <br>Cellulose or protein binding domain. PSI-BLAST P10476/668-713. This domain is found in two distinct sets of proteins with different functions. Those found in aerobic bacteria bind cellulose (or other carbohydrates); but in anaerobic fungi they are protein binding domains, referred to as dockerin domains or docking domains. They are believed to be responsible for the assembly of a multiprotein cellulase/hemicellulase complex, similar to the cellulosome found in certain anaerobic bacteria.. 
PF03425 Carbohydrate binding domain (family 11)<br>
PF03426 Carbohydrate binding domain (family 15)<br>
PF03424 CBM_28;<br>Carbohydrate binding domain (family 17/28). 
PF03427 Carbohydrate binding domain (family 19)<br>
PF00553 CBD_1; CBD_2; <br>Cellulose binding domain. Two tryptophan residues are involved in cellulose binding. Cellulose binding domain found in bacteria.. 
PF00686 CBD_2; CBD_4; <br>Starch binding domain. Pfam-B_111 (release 2.1). 
PF03370 PRS; <br>Putative phosphatase regulatory subunit. Pfam-B_2433 (release 6.6). 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 Swiss:O08541 has been shown to interact with glycogen synthase, phosphorylase kinase, phosphorylase a: these three enzymes have key roles in the regulation of glycogen metabolism. PTG also binds the catalytic subunit of protein phosphatase 1 (PP1C) and localises it to glycogen.  Subsets of similar interactions have been observed with several other members of this family, such as the yeast PIG1, PIG2, GAC1 and GIP2 proteins. While the precise function of these proteins is not known, they may serve a scaffold function, bringing together the key enzymes in glycogen metabolism. This family is a carbohydrate binding domain.. 
PF03423 Carbohydrate binding domain (family 25)<br>
PF02839 CBD_7; CBM_5; <br>Carbohydrate binding domain. This short domain is found in many different glycosyl hydrolase enzymes and is presumed to have a carbohydrate binding function. The domain has six aromatic groups that may be important for binding.. 
PF04942 CC domain<br>Pfam-B_4563 (release 7.5). This short domain contains four conserved cysteines that probably for two disulphide bonds. The domain is named after the characteristic CC motif.. 
PF01845 CcdB protein<br>
PF04995 Heme exporter protein D (CcmD)<br>The CcmD protein is part of a C-type cytochrome biogenesis operon  .  The exact function of this protein is uncertain. It has been proposed that CcmC, CcmD and CcmE interact directly with each other, establishing a cytoplasm to periplasm haem delivery pathway for cytochrome c maturation  . This protein is found fused to CcmE in Swiss:P52224. These proteins contain a predicted transmembrane helix.. 
PF03100 CcmE<br>Pfam-B_2583 (release 6.4). CcmE is the product of one of a cluster of Ccm genes that are necessary for cytochrome c biosynthesis in eubacteria. Expression of these proteins is induced when the organisms are grown under anaerobic conditions with nitrate or nitrite as the final electron acceptor.. 
PF03918 Cytochrome C biogenesis protein<br>Members of this family include NrfF, CcmH, CycL, Ccl2.. 
PF03597 Cytochrome oxidase maturation protein cbb3-type<br>TIGRFAMs, Griffiths-Jones SR. 
PF03150 Di-haem cytochrome c peroxidase<br>Pfam-B_3135 (release 6.5). This is a family of distinct cytochrome c peroxidases (CCPs) that contain two haem groups. Similar to other cytochrome c peroxidases, they reduce hydrogen peroxide to water using c-type haem as an oxidisable substrate. However, since they possess two, instead of one, haem prosthetic groups, bacterial CCPs reduce hydrogen peroxide without the need to generate semi-stable free radicals. The two haem groups have significantly different redox potentials. The high potential (+320 mV) haem feeds electrons from electron shuttle proteins to the low potential (-330 mV) haem, where peroxide is reduced (indeed, the low potential site is known as the peroxidatic site)  . The CCP protein itself is structured into two domains, each containing one c-type haem group, with a calcium-binding site at the domain interface. This family also includes MauG proteins, whose similarity to di-haem CCP was previously recognised  .. 
PF04505 CD225;<br>Interferon-induced transmembrane protein. Pfam-B_2070 (release 7.5). This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression  .. 
PF01130 CD36 family<br>Pfam-B_1229 (release 3.0). 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.. 
PF04549 CD47 transmembrane region<br>Pfam-B_2739 (release 7.5). This family represents the transmembrane region of CD47 leukocyte antigen [1-2].. 
PF03234 Cdc37;CDC37; <br>Cdc37 N terminal kinase binding. Pfam-B_3345 (release 6.5). Cdc37 is a molecular chaperone required for the activity of numerous eukaryotic protein kinases.  This domain corresponds to the N terminal domain which binds predominantly to protein kinases   and is found N terminal to the Hsp (Heat shocked protein) 90-binding domain Pfam:PF08565.  Expression of a construct consisting of only the N-terminal domain of Saccharomyces pombe Cdc37 results in cellular viability.  This indicates that interactions with the cochaperone Hsp90 may not be essential for Cdc37 function  .. 
PF02724 CDC45-like protein<br>Pfam-B_1919 (release 5.5). CDC45 is an essential gene required for initiation of DNA replication in S. cerevisiae (Swiss:Q08032), forming a complex with MCM5/CDC46. Homologues of CDC45 have been identified in  human  , mouse and smut fungus (Swiss:Q99107) among others. . 
PF02933 cdc48_2; <br>Cell division protein 48 (CDC48), domain 2. Pfam-B_799 (release 5.2). This domain has a double psi-beta barrel fold and includes VCP-like  ATPase and N-ethylmaleimide sensitive fusion protein N-terminal  domains.  Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at the C-terminus. The VAT-N domain found in AAA ATPases Pfam:PF00004 is a substrate  185-residue recognition domain  .. 
PF02359 VAT-Nn; cdc48_N; <br>Cell division protein 48 (CDC48), N-terminal domain. Pfam-B_799 (release 5.2). This domain has a double psi-beta barrel fold and includes VCP-like  ATPase and N-ethylmaleimide sensitive fusion protein N-terminal  domains.  Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at the N-terminus. The VAT-N domain found in AAA ATPases Pfam:PF00004 is a substrate  185-residue recognition domain  .. 
PF03381 DUF284; <br>LEM3 (ligand-effect modulator 3) family / CDC50 family. Pfam-B_2846 (release 6.6). Members of this family have been predicted to contain transmembrane helices. The family member LEM3 (Swiss:P42838) is a ligand-effect modulator, mutation of which increases glucocorticoid receptor activity in response to dexamethasone and also confers increased activity on other intracellular receptors including the progesterone, oestrogen and mineralocorticoid receptors. LEM3 is thought to affect a downstream step in the glucocorticoid receptor pathway. Factors that modulate ligand responsiveness are likely to contribute to the context-specific actions of the glucocorticoid receptor in mammalian cells  . The products of genes YNR048w (Swiss:P53740), YNL323w (Swiss:P42838) and YCR094w (Swiss:P25656) (CDC50) show redundancy of function and are involved in regulation of transcription via CDC39  . CDC39 (also known as NOT1) is normally a negative regulator of transcription either by affecting the general RNA polymerase II machinery or by altering chromatin structure  . One function of CDC39 is to block activation of the mating response pathway in the absence of pheromone, and mutation causes arrest in G1 by activation of the pathway  . It may be that the cold-sensitive arrest in G1 noticed in CDC50 mutants   may be due to inactivation of CDC39.  The effects of LEM3 on glucocorticoid receptor activity may also be due to effects on transcription via CDC39.. 
PF02611 CDP-diacylglycerol pyrophosphatase<br>This is a family of CDP-diacylglycerol pyrophosphatases, EC:3.6.1.26.  This enzyme catalyses the reaction CDP-diacylglycerol + H2O <=> CMP + phosphatidate.. 
PF03598 CO dehydrogenase/acetyl-CoA synthase complex beta subunit<br>TIGRFAMs, Griffiths-Jones SR. 
PF03599 CO dehydrogenase/acetyl-CoA synthase delta subunit<br>TIGRFAMs, Griffiths-Jones SR. 
PF02234 Cyclin-dependent kinase inhibitor<br>Pfam-B_1698 (release 5.2) & Pfam-B_5787 (Release 8.0). Cell cycle progression is negatively controlled by cyclin-dependent  kinases inhibitors (CDIs). CDIs are involved in cell cycle arrest at the G1 phase.. 
PF03261 Cyclin-dependent kinase 5 activator protein<br>Pfam-B_4160 (release 6.5). 
PF05174 Cysteine-rich D. radiodurans N terminus<br>This domain is found individually and at the N terminus of a few multi-domain proteins. . 
PF03498 Cytolethal distending toxin A/C family<br>
PF00272 cecropin; <br>
PF02927 celD_N; <br>N-terminal ig-like domain of cellulase. 
PF03500 Cellulose synthase subunit D<br>
PF03552 Cellulose synthase<br>Pfam-B_1346 (release 7.0). Cellulose, an aggregate of unbranched polymers of beta-1,4-linked glucose residues, is the major component of wood and thus paper, and is synthesised by plants, most algae, some bacteria and fungi, and even some animals. The genes that synthesise cellulose in higher plants differ greatly from the well-characterised genes found in Acetobacter and Agrobacterium sp. More correctly designated as 'cellulose synthase catalytic subunits', plant cellulose synthase (CesA) proteins are integral membrane proteins, approximately 1,000 amino acids in length.  There are a number of highly conserved residues, including several motifs shown to be necessary for processive glycosyltransferase activity  .. 
PF03040 CemA family<br>Pfam-B_1775 (release 6.4). Members of this family are probable integral membrane proteins.  Their molecular function is unknown. CemA proteins are found in the inner envelope membrane of chloroplasts but not in the thylakoid membrane  . A cyanobacterial member of this family has been implicated in CO2 transport, but is probably not a CO2 transporter itself  . They are predicted to be haem-binding however this has not been proven experimentally  .. 
PF03879 Cgr1 family<br>Members of this family are coiled-coil proteins that are involved in pre-rRNA processing  .. 
PF04752 ChaC-like protein<br>Pfam-B_3722 (release 7.5). The ChaC protein is thought to be associated with the putative ChaA Ca2+/H+ cation transport protein in Escherichia coli. Its function is not known. This family also includes homologues regions from several other bacterial and eukaryotic proteins.. 
PF00195 Chal_stil_synt; <br>Chalcone and stilbene synthases, N-terminal domain. The C-terminal domain of Chalcone synthase is reported to be structurally similar to domains in thiolase and beta-ketoacyl synthase.\.   The differences in activity are accounted for by differences in this N-terminal domain.. 
PF02797 Chal_stil_syntC; <br>Chalcone and stilbene synthases, C-terminal domain. This domain of chalcone synthase is reported to be structurally  similar to domains in thiolase and beta-ketoacyl synthase.   The differences in activity are accounted for by differences  in the N-terminal domain.. 
PF02431 Chalcone-flavanone isomerase<br>Pfam-B_2073 (release 5.4). 
PF03502 Nucleoside-specific channel-forming protein, Tsx<br>
PF03924 CHASE domain<br>This domain is found in the extracellular portion of receptor-like proteins - such as serine/threonine kinases and adenylyl cyclases [1,2].  Predicted to be a ligand binding domain  .. 
PF03173 Putative carbohydrate binding domain<br>Pfam-B_8666 (release 6.5). This domain represents the N terminal domain in chitobiases and beta-hexosaminidases EC:3.2.1.52. It is composed of a beta sandwich structure that is similar in structure to the cellulose binding domain of cellulase from Cellulomonas fimi  .  This suggests that this may be a carbohydrate binding domain.. 
PF03174 Chitobiase/beta-hexosaminidase C-terminal domain<br>Pfam-B_8666 (release 6.5). This short domain represents the C terminal domain in chitobiases and beta-hexosaminidases EC:3.2.1.52. It is composed of a beta sandwich structure  . The function of this domain is unknown.. 
PF01339 CheB methylesterase<br>
PF04509 CheC-like family<br>The restoration of pre-stimulus levels of the chemotactic response regulator, CheY-P, is important for allowing bacteria to respond to new environmental stimuli.  The members of this family, CheC, CheX, CheA and FliY are CheY-P phosphatase [1,2]. CheC appears to be primarily involved in restoring normal CheY-P levels, whereas FliY seems to act on CheY-P constitutively. CheD enhances the activity of CheC 5-fold, which is normally relatively low [1,2].  In some cases, the region represented by this entry is present as multiple copies.. 
PF03975 CheD chemotactic sensory transduction<br>This chemotaxis protein stimulates methylation of MCP proteins  . The chemotaxis machinery of Bacillus subtilis is similar to that of the well characterised system of Escherichia coli. However, B. subtilis contains several chemotaxis genes not found in the E. coli genome, such as CheC and CheD, indicating that the B. subtilis chemotactic system is more complex. CheD plays an important role in chemotactic sensory transduction for many organisms. CheD deamidates other B. subtilis chemoreceptors including McpB and McpC. Deamidation by CheD is required for B. subtilis chemoreceptors to effectively transduce signals to the CheA kinase  . The structure of a complex between the signal-terminating phosphatase, CheC, and the receptor-modifying deamidase, CheD, reveals how CheC mimics receptor substrates to inhibit CheD and how CheD stimulates CheC phosphatase activity. CheD resembles other cysteine deamidases from bacterial pathogens that inactivate host Rho-GTPases. Phospho-CheY, the intracellular signal and CheC target, stabilises the CheC-CheD complex and reduces availability of CheD  . A model is proposed whereby CheC acts as a CheY-P-induced regulator of CheD; CheY-P would cause CheC to sequester CheD from the chemoreceptors, inducing adaptation of the chemotaxis system  .. 
PF01739 CheR methyltransferase, SAM binding domain<br>Pfam-B_694 (release 4.2). CheR proteins are part of the chemotaxis signaling mechanism in bacteria. CheR methylates the chemotaxis receptor at specific glutamate residues. CheR is an S-adenosylmethionine- dependent methyltransferase - the C-terminal domain (this one) binds SAM.. 
PF03705 CheR methyltransferase, all-alpha domain<br>Pfam-B_694 (release 4.2). CheR proteins are part of the chemotaxis signaling mechanism in bacteria. CheR methylates the chemotaxis receptor at specific glutamate residues. CheR is an S-adenosylmethionine- dependent methyltransferase.. 
PF01584 CheW-like domain<br>Pfam-B_579 (release 4.1). CheW proteins are part of the chemotaxis signaling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and other related proteins that are involved in chemotaxis.  The CheW-like regulatory domain in CheA   binds to CheW, suggesting that these domains can interact with each other.. 
PF01111 Cyclin-dependent kinase regulatory subunit<br>
PF04344 Chemotaxis phosphatase, CheZ<br>This family represents the bacterial chemotaxis phosphatase, CheZ. This protein forms a dimer characterised by a long four-helix bundle, composed of two helices from each monomer. CheZ dephosphorylates CheY in a reaction that is essential to maintain a continuous chemotactic response to environmental changes. It is thought that CheZ's conserved residue Gln 147 orientates a water molecule for nucleophilic attack at the CheY active site.. 
PF00187 chitin_binding; <br>Chitin recognition protein. 
PF01644 Chitin_synth; <br>Pfam-B_892 (release 4.1). This region is found commonly in chitin synthases classes I, II and III. Chitin a linear homopolymer of GlcNAc residues, it is an important component of the cell wall of fungi and is synthesised on the cytoplasmic surface of the cell membrane by membrane bound chitin synthases  .. 
PF03142 Chitin synthase<br>Pfam-B_1787 (release 6.5). 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).. 
PF03503 Chlamydia cysteine-rich outer membrane protein 3<br>PRINTS, Griffiths-Jones SR. 
PF03504 Chlamydia cysteine-rich outer membrane protein 6<br>PRINTS, Griffiths-Jones SR. 
PF01308 Chlamydia_OMP; <br>Chlamydia major outer membrane protein. Pfam-B_1429 (release 3.0). The major outer membrane protein of Chlamydia contains four symmetrically spaced variable domains (VDs I to IV).  This protein is believed to be an integral part to the pathogenesis, possibly adhesion. Along with the lipopolysaccharide, the major out membrane  protein (MOMP) makes up the surface of the elementary body cell.   The MOMP is the protein used to determine the different serotypes.. 
PF00504 chloroa_b-bind;<br>Chlorophyll A-B binding protein. Pfam-B_54 (release 1.0) & Pfam-B_5772 (Release 7.5). 
PF02962 5-carboxymethyl-2-hydroxymuconate isomerase<br>
PF04428 Choline kinase N terminus<br>Found N terminal to choline/ethanolamine kinase regions (Pfam:PF01633) in some plant and fungal choline kinase enzymes (EC:2.7.1.32).  This region is only found in some members of the choline kinase family, and is therefore unlikely to contribute to catalysis.. 
PF01633 Choline/ethanolamine kinase<br>Pfam-B_1165 (release 4.1). Choline kinase catalyses the committed step in the synthesis of phosphatidylcholine by the CDP-choline pathway  . This alignment covers the protein kinase portion of the protein. The divergence of this family makes it very difficult to create a model that specifically predicts choline/ethanolamine kinases only. However if [add Pfam ID here for Choline_kinase_C] is also present then it is definitely a member of this family. . 
PF04345 Chorismate lyase<br>Chorismate lyase catalyses the first step in ubiquinone synthesis, i.e. the removal of pyruvate from chorismate, to yield 4-hydroxybenzoate.. 
PF01723 Chorion; <br>Pfam-B_1914 (release 4.1). This family consists of the chorion superfamily proteins classes A, B, CA, CB and high-cysteine HCB from silk,  gypsy and polyphemus moths. The chorion proteins make up the moths egg shell a complex extracellular structure  .. 
PF03964 Chorion family 2<br>The chorion genes of Drosophila are amplified in  response to developmental signals in the follicle  cells of the ovary . . 
PF00425 chorismate_bind; <br>chorismate binding enzyme. Pfam-B_164 (release 1.0). This family includes the catalytic regions of the chorismate binding enzymes anthranilate synthase, isochorismate synthase, aminodeoxychorismate synthase and para-aminobenzoate synthase.. 
PF01817 Chorismate_mut; <br>Chorismate mutase type II. Chorismate mutase EC:5.4.99.5 catalyses the conversion of chorismate to prephenate in the pathway of tyrosine and phenylalanine biosynthesis. This enzyme is negatively regulated by tyrosine, tryptophan and phenylalanine [2,3].. 
PF01264 Chorismate_synth;<br>
PF02417 Chromate transporter<br>Pfam-B_1872 (release 5.4). Members of this family probably act as chromate transporters [1,2].  Members of this family are found in both bacteria and archaebacteria.  The proteins are composed of one or two copies of this region. The alignment contains two conserved motifs, FGG and PGP.. 
PF00385 chromo; <br>Chromo (CHRromatin Organisation MOdifier) domain. 
PF01393 Chromo shadow domain<br>This domain is distantly related to Pfam:PF00385. This domain is always found in association with a chromo domain.. 
PF00878 CIMR_repeat;<br>Cation-independent mannose-6-phosphate receptor repeat. Pfam-B_764 (release 3.0). The cation-independent mannose-6-phosphate receptor contains 15 copies of a repeat.. 
PF02464 Competence-damaged protein<br>Pfam-B_2197 (release 5.4). 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 the  cin operon.. 
PF04162 Circo_coat; <br>Gyrovirus capsid protein (VP1). Pfam-B_1772 (release 7.3). Gyroviruses are small circular single stranded viruses. This family includes the VP1 protein from the chicken anaemia virus which is the viral capsid protein.. 
PF02443 Circo_ORF2; <br>Circovirus capsid protein. Pfam-B_1890 (release 5.4). Circoviruses are small circular single stranded viruses.  This family is the capsid protein from viruses such as porcine circovirus   and beak and feather disease virus Swiss:Q9YUC8. These proteins are about 220 amino acids long.. 
PF04487 CITED<br>Pfam-B_3987 (release 7.5). CITED, CBP/p300-interacting transactivator with ED-rich tail,  are characterised by a conserved 32-amino acid sequence at  the C-terminus. CITED proteins do not bind DNA directly  and are thought to function as transcriptional co-activators  . . 
PF04223 Citrate lyase, alpha subunit (CitF)<br>In citrate-utilising prokaryotes, citrate lyase EC:4.1.3.6 cleaves intracellular citrate into acetate and oxaloacetate, and is organised as a functional complex consisting of alpha, beta, and gamma subunits. The gamma subunit serves as an acyl carrier protein (ACP), and has a 2'-(5''-phosphoribosyl)-3'-dephospho-CoA prosthetic group. The citrate lyase is active only if this prosthetic group is acetylated; this acetylation is catalysed by an acetate:SH-citrate lyase ligase. The alpha subunit substitutes citryl for the acetyl group to form citryl-S-ACP. The beta subunit completes the reaction by cleaving the citryl to yield oxaloacetate and (regenerated) acetyl-S-ACP. This family represents the alpha subunit EC:2.8.3.10.. 
PF01874 ATP:dephospho-CoA triphosphoribosyl transferase <br>The citG gene is found in a gene cluster with citrate lyase subunits  .  The function of the CitG protein was elucidated as ATP:dephospho-CoA triphosphoribosyl transferase [2-3].. 
PF03600 Citrate transporter<br>
PF00285 citrate_synt; <br>
PF03802 Apo-citrate lyase phosphoribosyl-dephospho-CoA transferase<br>
PF01214 Casein kinase II regulatory subunit<br>
PF03805 Cytoadherence-linked asexual protein<br>Clag (cytoadherence linked asexual gene) is a malaria surface protein which has been shown to be involved in the binding of Plasmodium falciparum infected erythrocytes to host endothelial cells, a process termed cytoadherence. The cytoadherence phenomenon is associated with the sequestration of infected erythrocytes in the blood vessels of the brain, cerebral malaria. Clag is a multi-gene family in Plasmodium falciparum with at least 9 members identified to date.  Orthologous proteins in the rodent malaria species Plasmodium chabaudi (Lawson D Unpubl. obs.) suggest that the gene family is found in other malaria species and may play a more generic role in cytoadherence.. 
PF01217 Clathrin_adapt_s;<br>Clathrin adaptor complex small chain. 
PF00637 Clathrin_repeat; <br>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.. 
PF01086 Clathrin light chain<br>
PF01394 Clathrin propeller repeat<br>Clathrin is the scaffold protein of the basket-like coat that surrounds coated vesicles.  The soluble assembly unit, a triskelion, contains three heavy chains and three light chains in an extended three-legged structure.  Each leg contains one heavy and one light chain.  The N-terminus of the heavy chain is known as the globular domain, and is composed of seven repeats which form a beta propeller  .. 
PF03505 Clostridium enterotoxin<br>
PF03515 Colicin-like bacteriocin tRNase domain<br>The C-terminal region of colicin-like bacteriocins is either a pore-forming or an endonuclease-like domain. Cloacin and Pyocins have similar structures and activities to the colicins from E coli and the klebicins from Klebsiella spp. Colicins E5 and D cleave the anticodon loops of distinct tRNAs of Escherichia coli both in vivo and in vitro  . The full-length molecule has an N-terminal translocation domain and a middle, double alpha-helical region which is receptor-binding  .. 
PF03513 Cloacin immunity protein<br>
PF01785 Closterovirus coat protein<br>Pfam-B_1309 (release 4.2) & Pfam-B_6985 (release 8.0). This family consist of coat proteins from closteroviruses a member of the closteroviridae.  The viral coat protein encapsulates and protects the viral genome. Both the large cp1 and smaller cp2 coat protein originate from the same primary transcript  .  Members of the closteroviridae include Sugar beet  yellow virus and Grapevine leafroll-associated virus,  closteroviruses have a positive strand ssRNA genome with no DNA  stage during replication. . 
PF00574 Clp protease<br>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. Swiss:P48254 has lost all of these active site residues and is therefore inactive. Swiss:P42379 contains two large insertions, Swiss:P42380 contains one large insertion.. 
PF01093 Clusterin<br>
PF03026 Influenza C virus M1 protein<br>Pfam-B_1290 (release 6.4). This family represents the matrix 1 protein of influenza C virus. The protein is the product of a spliced mRNA. Small quantities of the unspliced mRNA are found in the cell additionally encoding the M2 protein (see Pfam:PF03021).. 
PF03021 Influenza C virus M2 protein<br>Pfam-B_1092 (release 6.4). Influenza C virus M1 protein is encoded by a spliced mRNA.  The unspliced mRNA is also found in small quantities and can encode  the protein represented by this family.. 
PF02543 Carbamoyltransferase<br>Pfam-B_1740 (release 5.4). This family consists of NodU from Rhizobium and CmcH from Nocardia lactamdurans.  NodU a Rhizobium nodulation protein involved in the synthesis of nodulation factors has 6-O-carbamoyltransferase-like activity  .  CmcH is involved in cephamycin (antibiotic) biosynthesis and has 3-hydroxymethylcephem carbamoyltransferase activity  , EC:2.1.3.7 catalysing the reaction: Carbamoyl phosphate + 3-hydroxymethylceph-3-EM-4-carboxylate <=> phosphate + 3-carbamoyloxymethylcephem.. 
PF04989 Cephalosporin hydroxylase<br>Members of this family are about 220 amino acids long. The CmcI protein Swiss:O85726 is presumed to represent the cephalosporin-7--hydroxylase  . However this has not been experimentally verified. . 
PF02627 Carboxymuconolactone decarboxylase family<br>Carboxymuconolactone decarboxylase (CMD) EC:4.1.1.44 is involved in protocatechuate catabolism. In some bacteria a gene fusion event leads to expression of CMD with a hydrolase involved in the same pathway  . In these bifunctional proteins (e.g. Swiss:O67982) CMD represents the C-terminal domain, Pfam:PF00561 represents the  N-terminal domain. . 
PF00795 Nitrilase;<br>Carbon-nitrogen hydrolase. Pfam-B_1042 (release 2.1) & Pfam-B_5155 (Release 7.5). This family contains hydrolases that break carbon-nitrogen bonds  .  The family includes: Nitrilase EC:3.5.5.1 Swiss:Q42965, Aliphatic amidase EC:3.5.1.4 Swiss:Q01360, Biotidinase EC:3.5.1.12 Swiss:P43251, Beta-ureidopropionase EC:3.5.1.6 Swiss:Q03248.  Nitrilase-related proteins generally have a conserved E-K-C catalytic triad, and are multimeric alpha-beta-beta-alpha sandwich proteins  .. 
PF01110 Ciliary neurotrophic factor<br>
PF03450 CO dehydrogenase flavoprotein C-terminal domain<br>
PF00473 Corticotropin-releasing factor family<br>
PF02552 CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit<br>This family consists of Carbon monoxide dehydrogenase I/II beta subunit  EC:1.2.99.2 and acetyl-CoA synthase epsilon subunit.  Carbon monoxide beta subunit catalyses the reaction: CO + H2O + acceptor <=> CO2 + reduced  acceptor.. 
PF01121 UPF0038;<br>Dephospho-CoA kinase. This family catalyses the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form Coenzyme A EC:2.7.1.24. This enzyme uses ATP in its reaction.. 
PF02035 Coagulin<br>
PF04733 Coatomer epsilon subunit<br>Pfam-B_3343 (release 7.5). This family represents the epsilon subunit of the coatomer complex, which is involved in the regulation of intracellular protein trafficking between the endoplasmic reticulum and the Golgi complex  .. 
PF04053 Coatomer WD associated region <br>Pfam-B_1269 (release 7.3);. This region is composed of WD40 repeats.. 
PF02572 ATP:corrinoid adenosyltransferase BtuR/CobO/CobP<br>This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin adenosyltransferase, EC:2.5.1.17, involved in cobalamin (vitamin B12) biosynthesis.  These enzymes catalyse the adenosylation reaction: ATP + cob(I)alamin + H2O <=> phosphate + diphosphate + adenosylcobalamin.. 
PF01122 Eukaryotic cobalamin-binding protein<br>
PF03186 CobD/Cbib protein<br>Pfam-B_2468 (release 6.5). This family includes CobD proteins from a number of bacteria, in Salmonella this protein is called Cbib. Salmonella CobD is a different protein  . This protein is involved in cobalamin biosynthesis and is probably an enzyme responsible for the conversion of adenosylcobyric acid to adenosylcobinamide or adenosylcobinamide phosphate  .. 
PF02654 Cobalamin-5-phosphate synthase<br>This is family of Colbalmin-5-phosphate synthases, CobS, from bacteria. The CobS enzyme catalyses the synthesis of AdoCbl-5'-p from AdoCbi-GDP  and alpha-ribazole-5'-P  .  This enzyme is involved in the cobalamin (vitamin B12) biosynthesis pathway in particular the nucleotide loop  assembly stage in conjunction with CobC, CobU and CobT  .. 
PF02283 COBU; <br>Cobinamide kinase / cobinamide phosphate guanyltransferase. Pfam-B_7022 (release 5.2). This family is composed of a group of bifunctional cobalamin  biosynthesis enzymes which display cobinamide kinase and cobinamide phosphate guanyltransferase activity. The crystal structure of the enzyme reveals the molecule to be a trimer with a propeller-like shape  .. 
PF00241 cofilin_ADF; <br>Cofilin/tropomyosin-type actin-binding protein. Severs actin filaments and binds to actin monomers.. 
PF00963 Cohesin domain<br>Cohesin domains interact with a complementary domain, termed the dockerin domain.  The cohesin-dockerin interaction is the crucial interaction for complex formation in the cellulosome  .. 
PF01410 Fibrillar collagen C-terminal domain<br>Ponting CP, Schultz J, Bork P. Pfam-B_464 (release 3.0). Found at C-termini of fibrillar collagens: Ephydatia muelleri procollagen EMF1 alpha, vertebrate collagens alpha(1)III, alpha(1)II, alpha(2)V etc.. 
PF01024 Colicin pore forming domain<br>
PF03857 Colicin immunity protein<br>Colicin immunity proteins are plasmid-encoded proteins necessary for protecting the cell against colicins. Colicins are toxins released by bacteria during times of stress  .. 
PF01320 Colicin immunity protein / pyocin immunity protein<br>
PF02674 Colicin V production protein<br>Colicin V production protein is required in E. Coli for colicin V production from plasmid pColV-K30  . This protein is coded for in the purF operon. . 
PF01114 Colipase, N-terminal domain<br>SCOP reports duplication of common fold with Colipase  C-terminal domain.. 
PF00325 crp; <br>Bacterial regulatory proteins, crp family. 
PF02740 Colipase, C-terminal domain<br>SCOP reports duplication of common fold with Colipase  N-terminal domain.. 
PF03047 COMC family<br>Pfam-B_2107 (release 6.4). This family consists exclusively of streptococcal competence stimulating peptide precursors, which are generally up to 50 amino acid residues long. In all the members of this family, the leader sequence is cleaved after two conserved glycine residues; thus the leader sequence is of the double- glycine type  . Competence stimulating peptides (CSP) are small (less than 25 amino acid residues) cationic peptides. The N-terminal amino acid residue is negatively charged, either glutamate or aspartate. The C-terminal end is positively charged. The third residue is also positively charged: a highly conserved arginine  . A few COMC proteins and their precursors (not included in this family) do not fully follow the above description. In particular: the leader sequence in the CSP precursor from Streptococcus sanguis NCTC 7863 Swiss:O33758 is not of the double-glycine type; the CSP from Streptococcus gordonii NCTC 3165 Swiss:O33645 does not have a negatively charged N-terminus residue and has a lysine instead of arginine at the third position.  Functionally, CSP act as pheromones, stimulating competence for genetic transformation in streptococci. In streptococci, the (CSP mediated) competence response requires exponential cell growth at a critical density, a relatively simple requirement when compared to the stationary-phase requirement of Haemophilus, or the late-logarithmic- phase of Bacillus  . All bacteria induced to competence by a particular CSP are said to belong to the same pherotype, because each CSP is recognised by a specific receptor (the signalling domain of a histidine kinase ComD). Pherotypes are not necessarily species-specific. In addition, an organism may change pherotype. There are two possible mechanisms for pherotype switching: horizontal gene transfer, and accumulation of point mutations. The biological significance of pherotypes and pherotype switching is not definitively determined. Pherotype switching occurs frequently enough in naturally competent streptococci to suggest that it may be an important contributor to genetic exchange between different bacterial species  . The family Antibacterial16, streptolysins from group A streptococci, has been merged into this family. . 
PF02247 Large coat protein<br>Pfam-B_2294 (release 5.2). This family contains the large coat protein (LCP)   of the  comoviridae viral family.. 
PF02248 Small coat protein<br>Pfam-B_2294 (release 5.2). This family contains the small coat protein (SCP)   of the  comoviridae viral family.. 
PF01257 complex1_24kD; Complex1_24kDa;<br>Thioredoxin-like [2Fe-2S] ferredoxin. 
PF00346 complex1_49Kd; <br>Respiratory-chain NADH dehydrogenase, 49 Kd subunit. 
PF01512 Respiratory-chain NADH dehydrogenase 51 Kd subunit<br>Pfam-B_780 (release 4.0). 
PF00668 DUF4;<br>Pfam-B_130 (release 2.1). This domain is found in many multi-domain enzymes which synthesise peptide antibiotics. This domain catalyses a condensation reaction to form peptide bonds in non- ribosomal peptide biosynthesis. It is usually found to the carboxy side of a phosphopantetheine binding domain (Pfam:PF00550). It has been shown that mutations in the HHXXXDG motif abolish activity suggesting this is part of the active site  .. 
PF00029 connexin; <br>
PF03508 Gap junction alpha-1 protein (Cx43)<br>
PF03509 Gap junction alpha-8 protein (Cx50)<br>
PF03601 Conserved hypothetical protein 698<br>TIGRFAMs, Griffiths-Jones SR. 
PF03602 Conserved hypothetical protein 95<br>TIGRFAMs, Griffiths-Jones SR. 
PF04234 CopC domain<br>CopC is a bacterial blue copper protein that binds 1 atom of copper per  protein molecule.  Along with CopA, CopC mediates copper resistance by sequestration of copper in the periplasm  .. 
PF00127 copper-bind; <br>Copper binding proteins, plastocyanin/azurin family. 
PF00649 Copper fist DNA binding domain<br>
PF01218 Coproporphyrinogen III oxidase<br>
PF03232 Ubiquinone biosynthesis protein COQ7<br>Pfam-B_3545 (release 6.5). Members of this family contain two repeats of about 90 amino acids, that contains two conserved motifs. One of these DXEXXH may be part of an enzyme active site.. 
PF04803 Cor1/Xlr/Xmr conserved region<br>Pfam-B_6320 (release 7.5). Cor1 is a component of the chromosome core in the meiotic prophase chromosomes  .  Xlr is a lymphoid cell specific protein  . Xlm is abundantly transcribed in testis in a tissue-specific and developmentally regulated manner.\.      The protein is located in the nuclei of spermatocytes, early in the prophase of the first meiotic division, and later becomes concentrated in the XY nuclear subregion where it is in particular associated with the axes of sex chromosomes  .. 
PF01544 CorA-like Mg2+ transporter protein<br>Pfam-B_944 (release 4.0) & Pfam-B_3206 (release 7.5). The CorA transport system is the primary Mg2+ influx system of Salmonella typhimurium and Escherichia coli.  CorA is virtually ubiquitous in the Bacteria and Archaea.  There are also eukaryotic relatives of this protein. The family includes the MRS2 protein Swiss:Q01926 from yeast that is thought to be an RNA splicing protein  .  However its membership of this family suggests that its effect on splicing is due to altered magnesium levels in the cell.. 
PF03311 Cornichon protein<br>Pfam-B_3813 (release 6.5). 
PF04694 Coronavirus ORF3 protein<br>Pfam-B_5763 (release 7.5). 
PF03262 Coronavirus 6B/7B protein<br>Pfam-B_4476 (release 6.5). 
PF02398 Coronavirus protein 7<br>Pfam-B_1574 (release 5.4). This is a family of proteins from coronavirus which may function in  viral assembly. . 
PF03187 Corona nucleocapsid I protein<br>Pfam-B_2926 (release 6.5). 
PF01635 Coronavirus M matrix/glycoprotein<br>Pfam-B_845 (release 4.1). This family consists of various coronavirus matrix proteins which are transmembrane glycoproteins. The M protein or E1 glycoprotein is The coronavirus M protein is implicated in virus assembly  . The E1 viral membrane protein is required for formation of the viral  envelope and is transported via the Golgi complex  .. 
PF04753 Coronavirus non-structural protein NS2<br>Pfam-B_3747 (release 7.5). 
PF05213 Coronavirus NS2A protein<br>Pfam-B_6568 (release 7.7). This family contains a number of corona virus non-structural proteins of unknown function. The family also includes a polymerase protein fragment from Berne virus and does not seem to be related to the Pfam:PF04753 Coronavirus NS2 family. This family is part of the 2H phosphoesterase superfamily  .. 
PF03053 ORF3b coronavirus protein<br>Pfam-B_2130 (release 6.4). Members of this family are non-structural proteins, approximately 250 amino acid residues long. They are found in transmissible gastroenteritis coronavirus (TGEV) and porcine respiratory coronavirus (PRCV) isolates. These proteins are found on the same mRNA as another product, designated ORF3a. While ORF3a/b has been implicated in TGEV and PRCV pathogenesis, its precise role remains unclear (see [2,3]).. 
PF03905 Coronavirus_NS4; <br>Coronavirus non-structural protein NS4. 
PF00937 Coronavirus nucleocapsid protein<br>Pfam-B_267 (release 3.0). 
PF01600 Coronavirus S1 glycoprotein<br>The coronavirus spike glycoprotein forms the characteristic 'corona' after which the group is named. The Spike glycoprotein is translated as a large polypeptide that is subsequently cleaved to S1 and S2 Pfam:PF01601  .. 
PF01601 Coronavirus S2 glycoprotein<br>The coronavirus spike glycoprotein forms the characteristic 'corona' after which the group is named. The Spike glycoprotein is translated as a large polypeptide that is subsequently cleaved to S1 Pfam:PF01600 and S2  .. 
PF00115 Cytochrome C and Quinol oxidase polypeptide I<br>Pfam-B_23 (release 1.0) and Prosite. 
PF05051 Cytochrome C oxidase copper chaperone (COX17)<br>Moxon SJ, Mistry J, Wood V. Pfam-B_5838 (release 7.7). Cox17 is essential for the assembly of functional cytochrome c oxidase (CCO) and for delivery of copper ions to the mitochondrion for insertion into the enzyme in yeast  . The structure of Cox17   shows the protein to have an unstructured N-terminal region followed by two helices and several unstructured C-terminal residues. The Cu(I) binding site has been modelled as two-coordinate with ligation by conserved residues Cys23 and Cys26.. 
PF00431 CUB domain<br>Pfam-B_136 (release 1.0). 
PF00116 Cytochrome C oxidase subunit II, periplasmic domain<br>
PF02790 Cytochrome C oxidase subunit II, transmembrane domain<br>The N-terminal domain of cytochrome C oxidase contains two transmembrane alpha-helices.. 
PF00510 Cytochrome c oxidase subunit III<br>Pfam-B_78 (release 1.0). 
PF02284 Cytochrome c oxidase subunit Va<br>Pfam-B_7466 (release 5.2). 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.. 
PF01215 Cytochrome c oxidase subunit Vb<br>
PF02046 Cytochrome c oxidase subunit VIa<br>
PF02297 Cytochrome oxidase c subunit VIb<br>Pfam-B_9188 (release 5.2). 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.. 
PF02238 Cytochrome c oxidase subunit VIIa<br>Pfam-B_3023 (release 5.2). 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.. 
PF02285 Cytochrome oxidase c subunit VIII<br>Pfam-B_6423 (release 5.2). 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.. 
PF02672 CP12 domain<br>
PF01383 CpcD/allophycocyanin linker domain<br>Pfam-B_887 (release 3.0). 
PF00166 cpn10; <br>Chaperonin 10 Kd subunit. This family contains GroES and Gp31-like chaperonins. Gp31 is a functional co-chaperonin that is required for the folding and assembly of Gp23, a major capsid protein, during phage morphogenesis  . . 
PF05205 Cps15; <br>COMPASS (Complex proteins associated with Set1p) component shg1. The Shg1 subunit is one of the eight subunits of the COMPASS complex, complex associated with SET1, conserved in yeasts and in other eukaryotes up to humans. It is associated with the region of the Set1 protein that is N-terminal to the C-terminus, ie Set1-560-900. The function of Shg1 seems to be to slightly inhibit histone 3 lysine 4 (H3K4) di- and tri-methylation, and it is a pioneer protein. The COMPASS complex functions to methylate the fourth lysine of Histone 3 and for silencing of genes close to the telomeres of chromosomes  .. 
PF00289 CPSase; <br>Carbamoyl-phosphate synthase L chain, N-terminal domain. Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from  glutamine or ammonia and bicarbonate.  This  important enzyme initiates both the urea cycle and the biosynthesis  of arginine and/or pyrimidines  . The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a  heterodimer of a small and large chain.  The small chain promotes the hydrolysis of glutamine to ammonia, which is used by the large chain to synthesise carbamoyl phosphate. See Pfam:PF00988. The small chain has a GATase domain in the carboxyl terminus. See Pfam:PF00117.. 
PF02786 CPSase; <br>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 biosynthesis  of arginine and/or pyrimidines  . The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a  heterodimer of a small and large chain.  The small chain promotes the hydrolysis of glutamine to ammonia, which is used by the large chain to synthesise carbamoyl phosphate. See Pfam:PF00988. The small chain has a GATase domain in the carboxyl terminus. See Pfam:PF00117. The ATP binding domain (this one) has an ATP-grasp fold.. 
PF00650 CRAL/TRIO domain<br>
PF03765 CRAL/TRIO, N-terminal domain<br>This all-alpha domain is found to the N-terminus of Pfam:PF00650.. 
PF02537 CrcB-like protein<br>CRCB is a putative integral membrane protein possibly involved in chromosome condensation. Over expression in E. coli also leads to  camphor resistance  . . 
PF01321 Creatinase/Prolidase N-terminal domain<br>This family includes the N-terminal non-catalytic domains from creatinase and prolidase. The exact function of this domain is uncertain.. 
PF00030 crystall; <br>Beta/Gamma crystallin. Swissprot_feature_table. The alignment comprises two Greek key motifs since the similarity between them is very low.. 
PF02633 Creatinine amidohydrolase<br>Creatinine amidohydrolase (EC:3.5.2.10), or creatininase, catalyses  the hydrolysis of creatinine to creatine  . . 
PF03858 Crustacean neurohormone H<br>These proteins are referred to as precursor-related peptides as they are typically co-transcribed and translated with the CHH neurohormone (Pfam:PF01147).  However, in some species this neuropeptide is synthesised as a separate protein. Furthermore, neurohormone H can undergo proteolysis to give rise to 5 different neuropeptides  .  . 
PF01147 Crustacean CHH/MIH/GIH neurohormone family<br>
PF00525 crystallin; <br>Alpha crystallin A chain, N terminal. Pfam-B_97 (release 1.0). 
PF03783 Curli production assembly/transport component CsgG<br>CsgG is an outer membrane-located lipoprotein that is highly resistant to protease digestion. During curli assembly, an adhesive surface fibre, CsgG is required to maintain the stability of CsgA and CsgB  .. 
PF02599 Global regulator protein family<br>This is a family of global regulator proteins. This protein is a RNA-binding protein and a global regulator of carbohydrate metabolism genes facilitating mRNA decay  .  In E. coli CsrA binds the CsrB RNA molecule to form the Csr regulatory system which has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis  . In other bacteria such as Erwinia caratovara RmsA has been shown to regulate the production of virulence determinants, such extracellular enzymes  . RmsA binds to RmsB regulatory RNA.. 
PF02554 Carbon starvation protein CstA<br>This family consists of Carbon starvation protein CstA a predicted membrane protein.\.   It has been suggested that CstA is involved in peptide utilisation  .. 
PF00859 CTF/NF-I family transcription modulation region<br>Pfam-B_362 (release 3.0). 
PF01467 Cytidylyltransf; <br>Cytidylyltransferase. This family includes: Cholinephosphate cytidylyltransferase Swiss:P49585. Glycerol-3-phosphate cytidylyltransferase Swiss:P27623.. 
PF02348 Cytidylyl_trans; <br>Cytidylyltransferase. Pfam-B_886 (release 5.2). 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-octulosonate, 2) acylneuraminate cytidylyltransferase EC:2.7.7.43, [1,2], catalysing  the reaction:- CTP + N-acylneuraminate <=> diphosphate + CMP-N-acylneuraminate. NeuAc cytydilyltransferase of Mannheimia haemolytica has been characterised describing kinetics and regulation by substrate charge, energetic charge and amino-sugar demand .. 
PF04808 Citrus tristeza virus (CTV) P23 protein <br>Pfam-B_2595 (release 7.6). This family consists of protein P23 from the citrus tristeza virus, which is a member of the Closteroviridae.\.  CTV viruses produce more positive than negative RNA strands, and P23 controls this asymmetrical RNA accumulation. Amino acids 42-180 are essential for function and are thought to contain RNA-binding and zinc finger domains  .. 
PF01179 Copper amine oxidase, enzyme domain<br>Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyse the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ). This family corresponds to the catalytic domain of the enzyme. . 
PF02727 Copper amine oxidase, N2 domain<br>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 Pfam:PF01179. Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyse the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ).. 
PF02728 Copper amine oxidase, N3 domain<br>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 Pfam:PF01179. Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyse the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ).. 
PF02298 Plastocyanin-like domain<br>Pfam-B_398 (release 5.2). This family represents a domain found in flowering plants related to the copper binding protein plastocyanin. Some members of this family (eg  Swiss:P93328) may not bind copper due to the lack of key residues.. 
PF03263 Cucumovirus protein 2B<br>Pfam-B_4373 (release 6.5). This protein may be a viral movement protein.. 
PF00760 Cucumovirus coat protein<br>Pfam-B_867 (release 2.1). 
PF02376 CUT domain<br>Pfam-B_770 (release 5.2). 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 (eg Swiss:P10180).. 
PF00888 Cullin family<br>Pfam-B_1149 (release 3.0). 
PF03091 CutA1 divalent ion tolerance protein<br>Pfam-B_2307 (release 6.4). 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 variety of divalent cations other than copper. The cutA locus consists of two operons, of one and two genes. The CutA1 protein is a cytoplasmic protein, encoded by the single-gene operon and has been linked to divalent cation tolerance. It has no recognised structural motifs  . This family also contains putative proteins from eukaryotes (human and Drosophila).. 
PF03932 CutC family<br>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 between 200 and 300 amino acids in length are found in both eukaryotes and bacteria.. 
PF01083 Cutinase<br>
PF01473 Putative cell wall binding repeat<br>These repeats are characterised by conserved aromatic residues and glycines are found in multiple tandem copies in a number of proteins.  The CW repeat is 20 amino acid residues long. The exact domain boundaries may not be correct. It has been suggested that these repeats in Swiss:P15057 might be responsible for the specific recognition of choline-containing cell walls  . Similar but longer repeats are found in the glucosyltransferases and glucan-binding proteins of oral streptococci and shown to be involved in glucan binding   as well as in the related dextransucrases of Leuconostoc mesenteroides.  Repeats also occur in toxins of Clostridium difficile and other clostridia, though the ligands are not always known.. 
PF04122 Putative cell wall binding repeat 2<br>This repeat is found in multiple tandem copies in proteins including  amidase enhancers   and adhesins  .. 
PF03638 CXC;<br>Tesmin/TSO1-like CXC domain, cysteine-rich domain. Pfam-B_1144 (release 7.0). 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 Swiss:Q9Y4I5   and TSO1 Swiss:Q9LE32  . This family is called a CXC domain in  .. 
PF03128 CXCXC repeat<br>Pfam-B_252 (release 6.5). This repeat contains the conserved pattern CXCXC where X can be any amino acid.  The repeat is found in up to five copies in Vascular endothelial growth factor C  . In the salivary glands of the dipteran Chironomus tentans, a specific messenger ribonucleoprotein (mRNP) particle, the Balbiani ring (BR) granule, can be visualised during its assembly on the gene and during its nucleocytoplasmic transport. This repeat is found over 70 copies in the balbiani ring protein 3 Swiss:Q03376. It is also found in some silk proteins  .. 
PF02560 Cyanate lyase C-terminal domain<br>Cyanate lyase (also known as cyanase) EC:4.2.1.104 is responsible for the hydrolysis of cyanate, allowing organisms that possess the enzyme to overcome the toxicity of environmental cyanate. This enzyme is composed of two domains, an N-terminal helix-turn-helix and this structurally unique C-terminal domain  .. 
PF04199 Putative cyclase<br>Pfam-B_1440 (release 7.3). Proteins in this family are thought to be cyclase enzymes.  They are found in proteins involved in antibiotic synthesis.  However they are also found in organisms that do not make antibiotics pointing to a wider role for these proteins. The proteins contain a conserved motif HXGTHXDXPXH that is likely to form part of the active site.. 
PF02984 cyclin_C; <br>Cyclin, C-terminal domain. Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 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-terminal domain.. 
PF03784 Cyclotide family<br>This family contains a set of cyclic peptides with a variety of activities. The structure consists of a distorted triple-stranded beta-sheet and a cysteine-knot arrangement of the disulfide bonds  . Cyclotides can be separated into two subfamilies, namely bracelet and moebius. The bracelet cyclotide subfamily tends to contain a larger number of positively charged residues and has a bracelet-like circularisation of the backbone  . The moebius cyclotide subfamily contains a backbone twist due to a cis-Pro peptide bond and may conceptually be regarded as a molecular Moebius strip  .. 
PF00548 Cys-protease-3C; <br>3C cysteine protease (picornain 3C). Picornaviral proteins are expressed as a single polyprotein which is cleaved by the viral 3C cysteine protease.. 
PF00007 Cystine-knot domain<br>Published_alignment enriched with PDOC00234 members.. The family comprises glycoprotein hormones and the C-terminal domain of various extracellular proteins.  It is believed to be involved in disulfide-linked dimerisation.. 
PF01053 Cys/Met metabolism PLP-dependent enzyme<br>Pfam-B_366 (release 3.0). 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/OAS sulfhydrylase,  O-succinylhomoserine sulfhydrylase All of these members participate is slightly different reactions. All these enzymes use PLP (pyridoxal-5'-phosphate) as a cofactor.. 
PF00839 cys_rich_FGFR; <br>Cysteine rich repeat. Pfam-B_297 (release 3.0). 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).. 
PF00031 cystatin; <br>Very diverse family.  Attempts to define separate sub-families failed.  Typically, either the N-terminal or C-terminal end is very divergent.  But splitting into two domains would make very short families. All members except Swiss:Q03196 and Swiss:Q10993 are found. Pfam:PF00666 are related to this family but have not been included.. 
PF01578 CytC_asm; <br>Cytochrome C assembly protein. Pfam-B_114 (release 4.1) Pfam-B_8014 (Release 8.0). This family consists of various proteins involved in cytochrome c assembly from mitochondria and bacteria; CycK from Rhizobium ,  CcmC from E. coli and Paracoccus denitrificans [2,1] and orf240 from wheat mitochondria  .  The members of this family are probably integral membrane proteins with six predicted transmembrane helices. It has been proposed that members of this family comprise a membrane component of an  ABC (ATP binding cassette) transporter complex. It is also proposed  that this transporter is necessary for transport of some component  needed for cytochrome c assembly. One member CycK contains a putative heme-binding motif  , orf240 also contains a putative heme-binding motif and is a proposed  ABC transporter with c-type heme as its proposed substrate  . However it seems unlikely that all members of this family transport heme nor c-type apocytochromes because CcmC in the putative CcmABC transporter transports neither  .. 
PF02224 Cytidylate kinase<br>Pfam-B_1582 (release 5.2). Cytidylate kinase EC:2.7.4.14 catalyses the phosphorylation of cytidine 5'-monophosphate (dCMP) to cytidine 5'-diphosphate (dCDP) in the presence of ATP or GTP.. 
PF01265 Cytochrome c/c1 heme lyase<br>
PF02322 Cytochrome oxidase subunit II<br>Pfam-B_997 (release 5.2). This Family consists of cytochrome bd type terminal oxidases that catalyses Quinol dependent, Na+ independent oxygen uptake  .  Members of this family are integral membrane proteins andi  contain a protohaem IX centre B558. One member of the family  Swiss:O05192 is implicated in having an important role in micro-aerobic nitrogen fixation in the enteric bacterium Klebsiella  pneumoniae  .. 
PF00283 cytochr_b559; <br>Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits. 
PF00284 cytochr_b559a; <br>Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit. This family is the lumenal portion of cytochrome b559 alpha chain, matches to this family should be accompanied by a match to the Pfam:PF00283 family also. The Prosite pattern pattern matches the transmembrane region of the cytochrome b559 alpha and beta subunits.. 
PF02335 cytochr_c552; <br>Pfam-B_19175 (release 5.2). Cytochrome c552 (cytochrome c nitrite reductase) is a crucial enzyme  in the nitrogen cycle catalysing the reduction of nitrite to ammonia. The crystal structure of cytochrome c552 reveals it to be a dimer, with with 10 close-packed type c haem groups.. 
PF03188 Cytochrome_B561; <br>Eukaryotic cytochrome b561. Pfam-B_2927 (release 6.5) & Pfam-B_7165 (Release 8.0). Cytochrome b561 is a secretory vesicle-specific electron transport protein. It is an integral membrane protein, that binds two heme groups non-covalently.  This is a eukaryotic family. Members of the 'prokaryotic cytochrome b561' family can be found in Pfam: PF01292.. 
PF00032 cytochrome_b_C; <br>Cytochrome b(C-terminal)/b6/petD. 
PF00033 cytochrome_b_N; <br>Cytochrome b(N-terminal)/b6/petB. 
PF00034 cytochrome_c; <br>The Pfam entry does not include all Prosite members.  The cytochrome 556 and cytochrome c' families are not included. All these are now in a new clan together. The C-terminus of DUF989, Pfam:PF06181, has now been merged into this family.. 
PF02167 Cytochrome_C1; <br>Cytochrome C1 family. 
PF01322 Cytochrome_C_2; <br>
PF02085 Cytochrome_CIII; <br>Class III cytochrome C family. 
PF03264 Cytochrome_NNT; <br>NapC/NirT cytochrome c family, N-terminal region. Pfam-B_1404 (release 6.5). Within the NapC/NirT family of cytochrome c proteins, some members, such as NapC Swiss:P33932 and NirT Swiss:P24038, bind four haem groups, while others, such as TorC Swiss:P33226, bind five haems. This family aligns the common N-terminal region that contains four haem-binding C-X(2)-CH motifs.. 
PF01801 Cytomegalo_gL; <br>Cytomegalovirus glycoprotein L . Pfam-B_1420 (release 4.2). Glycoprotein L from cytomegalovirus serves a chaperone for the correct folding and surface expression of glycoprotein H  (gH)  . Glycoprotein L is a member of the heterotrimeric gCIII complex of  glycoprotein which also includes gH and gO and has an essential  role in viral fusion  .. 
PF02239 D1_heme; <br>Cytochrome D1 heme domain. Pfam-B_3322 (release 5.2). 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 iron of the active site in the oxidised  state  .. 
PF02109 DAD family<br>Members of this family are thought to be integral membrane proteins.  Some members of this family have been shown to cause apoptosis if mutated  , these proteins are known as DAD for defender against death.  The family also includes the epsilon subunit of the oligosaccharyltransferase that is involved in N-linked glycosylation  .. 
PF00130 DAG_PE-bind; C1;<br>Phorbol esters/diacylglycerol binding domain (C1 domain). This domain is also known as the Protein kinase C conserved region 1 (C1) domain.. 
PF03982 Diacylglycerol acyltransferase <br>Pfam-B_11378 (release 7.2). The terminal step of triacylglycerol (TAG) formation is catalysed by the enzyme diacylglycerol acyltransferase (DAGAT) [1,2].. 
PF01219 Prokaryotic diacylglycerol kinase<br>
PF00609 DAGKa; <br>Diacylglycerol kinase accessory domain. Ponting C, Schultz J, Bork P. 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.. 
PF00781 DAGKc; <br>Diacylglycerol kinase catalytic domain. Alignment kindly provided by SMART. Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. The catalytic domain is assumed from the finding of bacterial homologues. YegS is the Escherichia coli protein in this family whose crystal structure reveals an active site in the inter-domain cleft formed by four conserved sequence motifs, revealing a novel metal-binding site. The residues of this site are conserved across the family  .. 
PF00793 DAHP_synthetase;<br>DAHP synthetase I family. Pfam-B_1032 (release 2.1). Members of this family catalyse the first step in aromatic amino acid biosynthesis from chorismate. E-coli has three related synthetases, which are inhibited by different aromatic amino acids. This family also includes KDSA which has very similar catalytic activity but is involved in the first step of liposaccharide biosynthesis. The enzyme is also part of the shikimate pathway, EC:2.5.1.54.. 
PF01474 Class-II DAHP synthetase family<br>Prodom_1974 (release 99.1). Members of this family are aldolase enzymes that catalyse the first step of the shikimate pathway.. 
PF02733 Dak1 domain<br>This is the kinase domain of the dihydroxyacetone kinase family EC:2.7.1.29. . 
PF02734 DAK2 domain<br>This domain is the predicted phosphatase domain of the dihydroxyacetone kinase family.. 
PF03045 DAN domain<br>Pfam-B_1968 (release 6.4). 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, Cerberus and Gremlin. The gremlin protein is an antagonist of bone morphogenetic protein signaling.  It is postulated that all members of this family antagonise different TGF beta Pfam:PF00019 ligands  . Recent work shows that the DAN protein is not an efficient antagonist of  BMP-2/4 class signals, we found that DAN was able to interact with  GDF-5 in a frog embryo assay, suggesting that DAN may regulate signaling by the GDF-5/6/7 class of BMPs in vivo  .. 
PF01266 FAD dependent oxidoreductase<br>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.. 
PF01678 Diaminopimelate epimerase<br>Pfam-B_2089 (release 4.1). Diaminopimelate epimerase contains two domains of the same alpha/beta fold, both contained in this family.. 
PF05173 Dihydrodipicolinate reductase, C-terminus<br>Dihydrodipicolinate reductase (DapB) reduces the alpha,beta-unsaturated cyclic imine, dihydro-dipicolinate.  This  reaction is the second committed step in the biosynthesis of L-lysine and its precursor meso-diaminopimelate, which are critical for both protein and cell wall biosynthesis. The C-terminal domain of DapB has been proposed to be the substrate- binding domain.. 
PF03344 Daxx Family<br>Pfam-B_3933 (release 6.5). The Daxx protein (also known as the Fas-binding protein) is thought  to play a role in apoptosis, but precise role played by Daxx remains to be determined. Daxx forms a complex with Axin. . 
PF02277 Phosphoribosyltransferase<br>Pfam-B_5739 (release 5.2). This family of proteins represent the nicotinate-nucleotide- dimethylbenzimidazole phosphoribosyltransferase (NN:DBI PRT) enzymes involved in dimethylbenzimidazole synthesis. This function is essential to de novo cobalamin (vitamin B12) production in bacteria. Nicotinate mononucleotide (NaMN):5,6-dimethylbenzimidazole (DMB) phosphoribosyltransferase (CobT) from Salmonella enterica plays a central role in the synthesis of alpha-ribazole-5'-phosphate, an intermediate for the lower ligand of cobalamin  .. 
PF03880 YxiN_DEAD; <br>DbpA RNA binding domain   . This RNA binding domain is found at the C-terminus of a number of DEAD helicase proteins  .  It is sufficient to confer specificity  for hairpin 92 of 23S rRNA, which is part of the ribosomal A-site. However, several members of this family lack specificity for 23S rRNA. These can proteins can generally be distinguished by a basic region that extends beyond this domain [Karl Kossen, unpublished data].. 
PF04290 Tripartite ATP-independent periplasmic transporters, DctQ component<br>The function of the members of this family is unknown, but DctQ homologues are invariably found in the tripartite ATP-independent periplasmic transporters  . . 
PF03605 Dcu; <br>Anaerobic c4-dicarboxylate membrane transporter. TIGRFAMs, Griffiths-Jones SR. 
PF03606 C4-dicarboxylate anaerobic carrier<br>TIGRFAMs, Griffiths-Jones SR. 
PF03184 CENP-B; DDE;<br>DDE superfamily endonuclease. Pfam-B_2254 (release 6.5). This family of proteins are related to Pfam:PF00665 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 contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction. Interestingly this family also includes the CENP-B protein. This domain in that protein appears to have lost the metal binding residues and is unlikely to have endonuclease activity. Centromere Protein B (CENP-B) is a DNA-binding protein localised to the centromere.. 
PF02862 DDHD domain<br>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 phosphoesterase domains. This domain is found in retinal degeneration B proteins, as well as a family of probable phospholipases. It has been shown that this domain is found in a longer C terminal region that binds to PYK2 tyrosine kinase. These proteins have been called N-terminal domain-interacting receptor (Nir1, Nir2 and Nir3)  . This suggests that this region is involved in functionally important interactions in other members of this family.. 
PF03345 Oligosaccharyltransferase 48 kDa subunit beta<br>Pfam-B_3520 (release 6.5). Members of this family are involved in asparagine-linked protein glycosylation. In particular, dolichyl-diphosphooligosaccharide-protein glycosyltransferase (DDOST), also known as oligosaccharyltransferase EC:2.4.1.119, transfers the high-mannose sugar GlcNAc(2)-Man(9)-Glc(3) from a dolichol-linked donor to an asparagine acceptor in a consensus Asn-X-Ser/Thr motif. In most eukaryotes, the DDOST complex is composed of three subunits, which in humans are described as a 48kD subunit, ribophorin I, and ribophorin II. However, the yeast DDOST appears to consist of six subunits (alpha, beta, gamma, delta, epsilon, zeta). The yeast beta subunit is a 45kD polypeptide, previously discovered as the Wbp1 protein, with known sequence similarity to the human 48kD subunit and the other orthologues. This family includes the 48kD-like subunits from several eukaryotes; it also includes the yeast DDOST beta subunit Wbp1.. 
PF04625 DEC-1 protein, N-terminal region<br>The defective chorion-1 gene (dec-1) in Drosophila encodes follicle cell proteins necessary for proper eggshell assembly. Multiple products of the dec-1 gene are formed by alternative RNA splicing and proteolytic processing  .  Cleavage products include S80 (80 kDa) which is incorporated into the eggshell, and further proteolysis of S80 gives S60 (60 kDa).. 
PF04624 DEC-1_REPEAT;<br>The defective chorion-1 gene (dec-1) in Drosophila encodes follicle cell proteins necessary for proper eggshell assembly. Multiple products of the dec-1 gene are formed by alternative RNA splicing and proteolytic processing  . Cleavage products include S80 (80 kDa) which is incorporated into the eggshell, and further proteolysis of S80 gives S60 (60 kDa). This repeat is usually found in 12 copies in the central region of the protein. Its function is unknown.  Length polymorphisms of Dec-1 have been observed in wild-type strains, and are caused by changes in the numbers of the first five repeats  .. 
PF02352 Decorin binding protein<br>Pfam-B_800 (release 5.2). This family consists of decorin binding proteins from Borrelia.  The decorin binding protein of Borrelia  burgdorferi the lyme disease spirochetes adheres to the  proteoglycan decorin found on collagen fibres  .. 
PF01335 Death effector domain<br>
PF00711 Beta defensin<br>Pfam-B_675 (release 2.1). The beta defensins are antimicrobial peptides implicated in the resistance of epithelial surfaces to microbial colonisation  .. 
PF00879 Defensin propeptide<br>Pfam-B_517 (release 3.0). 
PF00323 defensins; <br>
PF01041 DegT_DnrJ_EryC1_fam;<br>DegT/DnrJ/EryC1/StrS aminotransferase family. Pfam-B_239 (release 3.0). The members of this family are probably all pyridoxal-phosphate-dependent aminotransferase enzymes with a variety of molecular functions. The family includes StsA Swiss:P72454, StsC Swiss:P77952  and StsS  . The aminotransferase activity was demonstrated for purified StsC protein as the L-glutamine:scyllo-inosose aminotransferase EC:2.6.1.50, which catalyses the first amino transfer in the biosynthesis of the streptidine subunit of streptomycin  .. 
PF02286 Dehydratase large subunit<br>Pfam-B_7927 (release 5.2). This family contains the large subunit of the trimeric diol dehydratases and glycerol dehydratases. These enzymes are produced by some enterobacteria in response to growth substances.. 
PF02288 Dehydratase medium subunit<br>Pfam-B_7081 (release 5.2). This family contains the medium subunit of the trimeric diol dehydratases and glycerol dehydratases. These enzymes are produced by some enterobacteria in response to growth substances.. 
PF02287 Dehydratase small subunit<br>Pfam-B_6588 (release 5.2). This family contains the small subunit of the trimeric diol dehydratases and glycerol dehydratases. These enzymes are produced by some enterobacteria in response to growth substances.. 
PF00257 dehydrin; <br>Prosite & Pfam-B_3306 (Release 7.5). 
PF02336 denso_VP4; <br>Pfam-B_19701 (release 5.2). Four different translation initiation sites of the densovirus capsid protein mRNA give rise to four viral  proteins, VP1 to VP4. This family represents VP4.. 
PF01791 DeoC/LacD family aldolase<br>This family includes diverse aldolase enzymes.  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, see examples Swiss:Q57843 and Swiss:P76143.  The family also includes tagatose 1,6-diphosphate aldolase (EC:4.1.2.40) is part of the tagatose-6-phosphate pathway of galactose-6-phosphate degradation  .. 
PF00455 deoR; DeoR;<br>DeoR C terminal sensor domain. The sensor domains of the DeoR are catalytically inactive versions of the ISOCOT fold, but retain the substrate binding site  . DeorC  senses diverse sugar derivatives such as deoxyribose nucleoside  (DeoR), tagatose phosphate (LacR), galactosamine (AgaR), myo-inositol (Bacillus IolR) and L-ascorbate (UlaR)  ,  ,  .. 
PF04511 Der1-like family<br>Pfam-B_1901 (release 7.5). 
PF01880 Desulfoferrodoxin<br>Desulfoferrodoxins contains two types of iron: an Fe-S4 site very similar to that found in desulforedoxin from Desulfovibrio gigas and an octahedral coordinated high-spin ferrous site most probably with nitrogen/oxygen-containing ligands. Due to this rather unusual combination of active centres, this novel protein is named desulfoferrodoxin  .. 
PF04598 DFNA5; <br>Pfam-B_5153 (release 7.5). The precise function of this protein is unknown. A deletion/insertion mutation is associated with an autosomal dominant non-syndromic hearing impairment form  . In addition, this protein has also been found to contribute to acquired etoposide resistance in melanoma cells  . This family also includes the gasdermin protein  . 
PF04127 dfp;<br>DNA / pantothenate metabolism flavoprotein. Pfam-B_6559 (release 7.3);. The DNA/pantothenate metabolism flavoprotein (EC:4.1.1.36) affects synthesis of DNA, and pantothenate metabolism.. 
PF05035 2-keto-3-deoxy-galactonokinase<br>2-keto-3-deoxy-galactonokinase EC:2.7.1.58 catalyses the second step in D-galactonate degradation.. 
PF00926 3,4-dihydroxy-2-butanone 4-phosphate synthase<br>Pfam-B_1148 (release 3.0). 
PF00701 Dihydrodipicolinate synthetase family<br>Pfam-B_557 (release 2.1). This family has a TIM barrel structure.. 
PF01368 DHH family<br>Pfam-B_1245 (release 3.0). It is predicted that this family of proteins all perform a phosphoesterase function. It included the single stranded DNA exonuclease RecJ.. 
PF02833 DHHA2 domain<br>This domain is often found adjacent to the DHH domain Pfam:PF01368 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 its amino terminus.. 
PF01180 DHOdehase; <br>Dihydroorotate dehydrogenase. 
PF01761 3-dehydroquinate synthase<br>Pfam-B_1327 (release 4.2). The 3-dehydroquinate synthase EC:4.6.1.3 domain is present in isolation in various bacterial 3-dehydroquinate  synthases and also present as a domain in the pentafunctional AROM polypeptide Swiss:P07547  . 3-dehydroquinate (DHQ) synthase catalyses the formation of  dehydroquinate (DHQ) and orthophosphate from 3-deoxy-D-arabino heptulosonic 7 phosphate  . This reaction is part of the shikimate pathway which is involved  in the biosynthesis of aromatic amino acids.  . 
PF01487 Type I 3-dehydroquinase<br>Pfam-B_2492 (release 4.0). Type I 3-dehydroquinase, (3-dehydroquinate dehydratase or DHQase.) Catalyses the cis-dehydration of 3-dehydroquinate via a covalent imine intermediate giving dehydroshikimate. Dehydroquinase functions in the shikimate pathway which is involved in the biosynthesis of aromatic amino acids. Type II 3-dehydroquinase catalyses the trans-dehydration of 3-dehydroshikimate see Pfam:PF01220.. 
PF01220 Dehydroquinase class II<br>
PF04706 dickkopf_N; <br>Dickkopf N-terminal cysteine-rich region. Pfam-B_5838 (release 7.5). Dickkopf proteins are a class of Wnt antagonists. They possess two conserved cysteine-rich regions. This family represents the N-terminal one  . The C-terminal region has been found to share significant sequence similarity to the colipase fold, Pfam:PF01114, Pfam:PF02740  .. 
PF05086 Dict_REP; <br>Dictyostelium (Slime Mold) REP protein. Pfam-B_6278 (release 7.7). This family consists of REP proteins from Dictyostelium (Slime molds). REP protein is likely involved in transcription regulation and control of DNA replication, specifically amplification of plasmid at low copy numbers. The formation of homomultimers may be required for their regulatory activity  .. 
PF04562 Dict_spore_N;<br>Dictyostelium spore coat protein, N terminus. The Dictyostelium spore coat is a polarised extracellular matrix composed of glycoproteins and cellulose. Four of the major coat glycoproteins exist as a multi-protein complex within the prespore vesicles before secretion.  Of these, SP96 and SP70 are members of this family. The presence of SP96 and SP70 in the complex is necessary for the cellulose binding activity of the complex, which is in turn necessary for normal spore coat assembly  . The function of this region of these proteins is not known.. 
PF00186 DiHfolate_red; <br>Dihydrofolate reductase. 
PF02966 Mitosis protein DIM1<br>
PF05163 DinB family<br>DNA damage-inducible (din) genes in Bacillus subtilis are coordinately regulated and together compose a global regulatory network that has been termed the SOS-like or SOB regulon. This family includes DinB from B. subtilis  .. 
PF00775 Dioxygenase; <br>Pfam-B_1018 (release 2.1). 
PF04444 Catechol dioxygenase N terminus<br>This family consists of the N termini of catechol, chlorocatechol or  hydroxyquinol 1,2-dioxygenase proteins.  This region is always found  adjacent to the dioxygenase domain (Pfam:PF00775).. 
PF01866 Putative diphthamide synthesis protein<br>Swiss:Q16439 is a candidate tumour suppressor gene  . DPH2 from yeast Swiss:P32461  , which confers resistance to diphtheria toxin has been found to be involved in diphthamide synthesis. Diphtheria toxin inhibits eukaryotic protein synthesis by ADP-ribosylating diphthamide, a posttranslationally modified histidine residue present in EF2.  The exact function of the members of this family is unknown.. 
PF02763 Diphtheria toxin, C domain<br>N-terminal catalytic (C) domain - blocks protein synthesis by transfer of ADP-ribose from NAD to a diphthamide residue of EF-2.. 
PF01324 Diphtheria_tox; <br>Diphtheria toxin, R domain. C-terminal receptor binding (R) domain - binds to cell surface receptor, permitting the toxin to enter the cell by receptor  mediated endocytosis.. 
PF02764 Diphtheria toxin, T domain<br>Central domain of diphtheria toxin is the translocation (T) domain.   pH induced conformational change in this domain triggers insertion  into the endosomal membrane and facilitates the transfer of the  catalytic domain into the cytoplasm.. 
PF00200 disintegrin; <br>
PF05141 Pyoverdine/dityrosine biosynthesis protein<br>DIT1 is involved in synthesising dityrosine  . Dityrosine is a sporulation-specific component of the yeast ascospore wall that is essential for the resistance of the spores to adverse environmental conditions. Pyoverdine biosynthesis protein PvcA is involved in the biosynthesis of pyoverdine, a cyclized isocyano derivative of tyrosine [2,3]. It has a modified Rossmann fold  .. 
PF04977 Septum formation initiator<br>DivIC from B. subtilis is necessary for both vegetative and sporulation septum formation  . These proteins are mainly composed of an amino terminal coiled-coil.. 
PF05103 DivIVA protein<br>The Bacillus subtilis divIVA1 mutation causes misplacement of the septum during cell division, resulting in the formation of small, circular, anucleate mini-cells  . Inactivation of divIVA produces a mini-cell phenotype, whereas overproduction of DivIVA results in a filamentation phenotype  . These proteins appear to contain coiled-coils.. 
PF00778 DAX; <br>Alignment kindly provided by SMART. 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 Swiss:O35625  . The axin DIX domain also interacts with the dishevelled DIX domain  .  The DIX domain has also been called the DAX domain.. 
PF01738 Dienelactone hydrolase family<br>Pfam-B_757 (release 4.2). 
PF04914 DltD C-terminal region<br>Pfam-B_6216 (release 7.6). DltD is and integral membrane protein involved in the biosynthesis of D-alanyl-lipoteichoic acid.  This is important in controlling the net ionic charge in lipoteichoic acid (LTA). This family is found in bacteria of the Bacillus/Clostridium group. DltD binds Dcp and ligates it with D-alanine.  DltD does not ligate acyl carrier protein (ACP) with D-alanine.   It also has thioesterase activity for mischarged D-alanyl-acyl carrier protein (ACP). DltD is thought to be responsible for discriminating between Dcp involved in the D-alanylation of LTA, and ACP involved in fatty acid biosynthesis  . This family consists of the C-terminal region of DltD.. 
PF04918 DltD_central; <br>Pfam-B_6216 (release 7.6). DltD is and integral membrane protein involved in the biosynthesis of D-alanyl-lipoteichoic acid.  This is important in controlling the net ionic charge in lipoteichoic acid (LTA). This family is found in bacteria of the Bacillus/Clostridium group. DltD binds Dcp and ligates it with D-alanine.  DltD does not ligate acyl carrier protein (ACP) with D-alanine.   It also has thioesterase activity for mischarged D-alanyl-acyl carrier protein (ACP). DltD is thought to be responsible for discriminating between Dcp involved in the D-alanylation of LTA, and ACP involved in fatty acid biosynthesis  . This family consists of the central region of DltD.. 
PF04915 DltD N-terminal region<br>Pfam-B_6216 (release 7.6). DltD is and integral membrane protein involved in the biosynthesis of D-alanyl-lipoteichoic acid.  This is important in controlling the net ionic charge in lipoteichoic acid (LTA). This family is found in bacteria of the Bacillus/Clostridium group. DltD binds Dcp and ligates it with D-alanine.  DltD does not ligate acyl carrier protein (ACP) with D-alanine.  It also has thioesterase activity for mischarged D-alanyl-acyl carrier protein (ACP). DltD is thought to be responsible for discriminating between Dcp involved in the D-alanylation of LTA, and ACP involved in fatty acid biosynthesis  . This family consists of the N-terminal region of DltD.. 
PF03474 DMRTA motif<br>This region is found to the C-terminus of the Pfam:PF00751  . DM-domain proteins with this motif are known as DMRTA proteins. The function of this region is unknown.. 
PF00885 6,7-dimethyl-8-ribityllumazine synthase<br>Pfam-B_1503 (release 3.0). This family includes the beta chain of 6,7-dimethyl-8- ribityllumazine synthase EC:2.5.1.9, an enzyme involved in riboflavin biosynthesis. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function for example Swiss:O28856.. 
PF04976 DMSO reductase anchor subunit (DmsC)<br>The terminal electron transfer enzyme Me2SO reductase of Escherichia coli is a heterotrimeric enzyme composed of a membrane extrinsic catalytic dimer (DmsAB) and a membrane intrinsic polytopic anchor subunit (DmsC)  .. 
PF03989 DNA gyrase C-terminal domain, beta-propeller<br>This repeat is found as 6 tandem copies at the C-termini of GyrA and ParC DNA gyrases. It is predicted to form 4 beta strands and to probably form a  beta-propeller structure  . This region has been shown to bind DNA non-specifically and may stabilise the DNA-topoisomerase complex  .. 
PF00204 DNA_topoisoII; <br>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.. 
PF00986 DNA gyrase B subunit, carboxyl terminus<br>Pfam-B_332 (release 3.0). The amino terminus of eukaryotic and prokaryotic DNA topoisomerase II are similar, but they have a different carboxyl terminus. The amino-terminal portion of the DNA gyrase B  protein is thought to catalyse the ATP-dependent super-coiling of  DNA. See Pfam:PF00204. The carboxyl-terminal end supports the  complexation with the DNA gyrase A protein and the ATP-independent  relaxation. This family also contains Topoisomerase IV. This is a bacterial enzyme that is closely related to DNA gyrase,  .. 
PF03603 DNA polymerase III psi subunit<br>TIGRFAMs, Griffiths-Jones SR. 
PF01653 DNA_ligase_N; <br>NAD-dependent DNA ligase adenylation domain. Pfam-B_1334 (release 4.1). DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilising either ATP or NAD(+) as a cofactor  . This domain is the catalytic adenylation domain.  The NAD+ group is covalently attached to this domain at the lysine in the KXDG motif of this domain. This enzyme- adenylate intermediate is an important feature of the proposed catalytic mechanism  .. 
PF03120 NAD-dependent DNA ligase OB-fold domain<br>Pfam-B_1334 (release 4.1). DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilising either ATP or NAD(+) as a cofactor  . This family is a small domain found after the adenylation domain Pfam:PF01653 in NAD dependent ligases  . OB-fold domains generally are involved in nucleic acid binding. . 
PF03119 NAD-dependent DNA ligase C4 zinc finger domain<br>Pfam-B_1334 (release 4.1). DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilising either ATP or NAD(+) as a cofactor  . This family is a small zinc binding motif that is presumably DNA binding  . IT is found only in NAD dependent DNA ligases  .. 
PF00145 C-5 cytosine-specific DNA methylase<br>
PF01119 DNA mismatch repair protein, C-terminal domain<br>This family represents the C-terminal domain of the  mutL/hexB/PMS1 family.  This domain has a ribosomal S5  domain 2-like fold.. 
PF02499 Probable DNA packing protein, C-terminus<br>Pfam-B_1283 (release 5.4). This family includes proteins that are probably involved in DNA packing in herpesvirus. This domain is found at the C-terminus of the protein.. 
PF02500 Probable DNA packing protein, N-terminus <br>Pfam-B_1179 (release 5.4). This family includes proteins that are probably involved in DNA packing in herpesvirus. This domain is normally found at the N-terminus of the protein.. 
PF00712 DNA polymerase III beta subunit, N-terminal domain<br>Pfam-B_631 (release 2.1). A dimer of the beta subunit of DNA polymerase beta forms a ring which encircles duplex DNA.  Each monomer contains three domains of identical topology and DNA clamp fold.. 
PF02767 DNA polymerase III beta subunit, central domain<br>Pfam-B_631 (release 2.1). A dimer of the beta subunit of DNA polymerase beta forms a ring which encircles duplex DNA.  Each monomer contains three domains of identical topology and DNA clamp fold.. 
PF02768 DNA polymerase III beta subunit, C-terminal domain<br>Pfam-B_631 (release 2.1). A dimer of the beta subunit of DNA polymerase beta forms a ring which encircles duplex DNA.  Each monomer contains three domains of identical topology and DNA clamp fold.. 
PF04364 DNA polymerase III chi subunit, HolC<br>The DNA polymerase III holoenzyme (EC:2.7.7.7) is the polymerase responsible for the replication of the Escherichia coli chromosome.  The holoenzyme is composed of the DNA polymerase III core, the sliding clamp, and the DnaX clamp loading complex. The DnaX complex contains either either the tau or gamma product of gene dnax, complexed to delta.delta' and to chi psi. Chi forms a 1:1 heterodimer with psi.\. The chi psi complex functions by increasing the affinity of tau and gamma for delta.delta' allowing a functional clamp-loading complex to form at physiological subunit concentrations.  Psi is responsible for the interaction with DnaX (gamma/tau), but psi is insoluble unless it is in a complex with chi  .. 
PF00476 DNA polymerase family A<br>
PF03175 DNA polymerase type B, organellar and viral<br>Pfam-B_236 (release 6.5). Like Pfam:PF00136, members of this family are also DNA polymerase type B proteins. Those included here are found in plant and fungal mitochondria, and in viruses.. 
PF04042 DNA polymerase alpha/epsilon subunit B<br>Pfam-B_12632 (release 7.3) and Pfam-B_5821 (release 7.3). This family contains a number of DNA polymerase subunits.\.      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.  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 consists of at least four subunits in mammalian cells as well as in yeast.  The largest subunit of DNA polymerase epsilon is responsible for polymerase epsilon is responsible for polymerase activity. In mouse, the DNA polymerase epsilon subunit B is the second largest subunit of the DNA polymerase. A part of the N-terminal was found to be responsible for the interaction with SAP18.  Experimental evidence suggests that this subunit may recruit histone deacetylase to the replication fork to modify the chromatin structure  .. 
PF04931 DNA_pol_V; <br>Pfam-B_10566 (release 7.6). This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localised exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.. 
PF00336 DNA polymerase (viral) C-terminal domain<br>Pfam-B_107 (release 1.0). 
PF00242 DNA polymerase (viral) N-terminal domain<br>Pfam-B_107 (release 1.0). 
PF04104 Eukaryotic and archaeal DNA primase, large subunit<br>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 in yeast), and the large subunit Pri2 (58 kDa in the yeast S. cerevisiae)  .  The large subunit of DNA primase forms interactions with the small subunit and the structure implicates that it is not directly involved in catalysis, but plays roles in correctly positioning the primase/DNA complex, and in the transfer of RNA to DNA polymerase  .. 
PF01896 Eukaryotic and archaeal DNA primase small subunit<br>DNA primase synthesises the RNA primers for the Okazaki fragments in lagging strand DNA synthesis. DNA primase is a heterodimer of large and small subunits.  This family also includes baculovirus late expression factor 1 or LEF-1 proteins. Baculovirus LEF-1 is a DNA primase enzyme  .  Bacterial DNA primase adopts a different fold to archaeal and eukaryotic primases.. 
PF03604 DNA directed RNA polymerase, 7 kDa subunit<br>
PF00521 DNA gyrase/topoisomerase IV, subunit A<br>Pfam-B_55 (release 1.0). 
PF01556 DnaJ_C;<br>DnaJ C terminal domain. Pfam-B_342 (release 4.0). This family consists of the C terminal region form the DnaJ protein.  It is always found associated with Pfam:PF00226 and Pfam:PF00684. DnaJ is a chaperone associated with the Hsp70 heat-shock system involved in protein folding and renaturation after stress. The two C-terminal domains CTDI and this, CTDII, are necessary for maintaining the J-domains in their specific relative positions  .. 
PF00684 DnaJ central domain<br>Pfam-B_89 (release 2.1). The central cysteine-rich (CR) domain of DnaJ proteins contains four repeats of the motif CXXCXGXG where X is any amino acid. The isolated cysteine rich domain folds in zinc dependent fashion. Each set of two repeats binds one unit of zinc.  Although this domain has been implicated in substrate binding, no evidence of specific interaction between the isolated DNAJ cysteine rich domain and various hydrophobic peptides has been found  .. 
PF03265 Deoxyribonuclease II<br>Pfam-B_4508 (release 6.5). 
PF01712 Deoxynucleoside kinase<br>Pfam-B_1744 (release 4.1). This family consists of various deoxynucleoside kinases cytidine EC:2.7.1.74, guanosine EC:2.7.1.113, adenosine EC:2.7.1.76  and thymidine kinase EC:2.7.1.21 (which also phosphorylates deoxyuridine  and deoxycytosine.) These enzymes catalyse the production of  deoxynucleotide 5'-monophosphate from a deoxynucleoside.  Using ATP and yielding ADP in the process.. 
PF00404 celCC;<br>Dockerin type I repeat. The dockerin repeat is the binding partner of the cohesin domain Pfam:PF00963. The cohesin-dockerin interaction is the crucial interaction for complex formation in the cellulosome  . The dockerin repeats, each bearing homology to the EF-hand calcium-binding loop bind calcium  .. 
PF04118 Dopey, N-terminal<br>Pfam-B_17466 (release 7.3);. DopA is the founding member of the Dopey family and is required for correct cell morphology and spatiotemporal organisation of multicellular structures  in the filamentous fungus Aspergillus nidulans. DopA homologues are found in mammals.  S. cerevisiae DOP1 is essential for viability and, affects cellular morphogenesis  .. 
PF04556 DpmII;<br>DpnII restriction endonuclease. Members of this family are type II restriction enzymes (EC:3.1.21.4).  They recognise the double-stranded unmethylated sequence GATC and cleave before G-1  . http://rebase.neb.com/rebase/enz/DpnII.html. 
PF04244 DUF426; <br>Deoxyribodipyrimidine photo-lyase-related protein. This family appears to be related to Pfam:PF00875.. 
PF05219 DREV methyltransferase<br>Pfam-B_6662 (release 7.7). 
PF02635 DsrE/DsrF-like family<br>DsrE is a small soluble protein involved in intracellular sulfur  reduction  . This family also includes DsrF.. 
PF01916 Deoxyhypusine synthase<br>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 synthase (DS) EC:1.1.1.249. The modified version of eIF-5A, and DS, are required for eukaryotic cell proliferation  .. 
PF01323 DSBA-like thioredoxin domain<br>This family contains a diverse set of proteins with a thioredoxin-like structure Pfam:PF00085. This family also includes 2-hydroxychromene-2-carboxylate (HCCA) isomerase enzymes catalyse one step in prokaryotic polyaromatic hydrocarbon (PAH) catabolic pathways [2,3,4].  This family also contains members with functions other than HCCA isomerisation, such as Kappa family GSTs (e.g. Swiss:P24473), whose similarity to HCCA isomerases was not previously recognised.  The sequence Swiss:O07298 has been annotated as a dioxygenase but is almost certainly an HCCA isomerase enzyme. Similarly, the sequence Swiss:Q9ZI67 has been annotated as a dehydrogenase, but is most probably also an HCCA isomerase enzyme. In addition, the Rhizobium leguminosarum Swiss:Q52782 protein has been annotated as a putative glycerol-3-phosphate transfer protein, but is also most likely to be an HCCA isomerase enzyme (see  ).. 
PF02600 Disulfide bond formation protein DsbB<br>This family consists of disulfide bond formation protein DsbB from bacteria.\.   The DsbB protein oxidises the periplasmic protein DsbA which in turn oxidises cysteines in other periplasmic proteins in order to make disulfide bonds  .  DsbB acts as a redox potential transducer across the cytoplasmic membrane and is an integral membrane protein  . DsbB posses six cysteines four of which are necessary for it proper function in vivo  .. 
PF02683 Cytochrome C biogenesis protein transmembrane region<br>This family consists of the transmembrane (i.e. non-catalytic) region of Cytochrome C biogenesis proteins also known as disulphide interchange  proteins.  These proteins posses a protein disulphide isomerase like domain that is not found within the aligned region of this family.. 
PF01984 DUF122; <br>Double-stranded DNA-binding domain. This domain is believed to bind double-stranded DNA   of 20 bases length.. 
PF04077 DsrH like protein<br>DsrH  is involved in oxidation of intracellular sulphur in the phototrophic sulphur bacterium Chromatium vinosum D  .. 
PF05160 DSS1/SEM1 family<br>Pfam-B_22209 (release 7.7). This family contains the breast cancer tumour suppressor BRCA2-interacting protein DSS1 and its homologue SEM1, both of which are short acidic proteins.  DSS1 has been shown to be a conserved component of the Rae1 mediated mRNA export pathway in Schizosaccharomyces pombe  .. 
PF00908 dTDP-4-dehydrorhamnose 3,5-epimerase<br>Pfam-B_540 (release 3.0). This family catalyse the isomerisation of dTDP-4-dehydro-6-deoxy -D-glucose with dTDP-4-dehydro-6-deoxy-L-mannose. The EC number of this enzyme is 5.1.3.13.. 
PF03942 DTW domain<br>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.. 
PF01950 DUF100; <br>Fructose-1,6-bisphosphatase. This is a family of bacterial and archaeal fructose-1,6-bisphosphatases (FBPases).  FBPase catalyses the hydrolysis of D-fructose-1,6-bisphosphate (FBP) to D-fructose-6-phosphate (F6P) and orthophosphate and is an essential regulatory enzyme in the glyconeogenic pathway.. 
PF01954 Protein of unknown function DUF104<br>This family includes short archaebacterial proteins of unknown function.\.       Archaeoglobus fulgidus has twelve copies of this protein, with several being clustered together in the genome.. 
PF01955 DUF105; <br>Adenosylcobinamide amidohydrolase. This prokaryotic protein family includes CbiZ which converts adenosylcobinamide (AdoCbi) to adenosylcobyric acid (AdoCby), an intermediate of the de novo coenzyme B12 biosynthetic route  .. 
PF01956 DUF106; Methyltrn_RNA_3;<br>Integral membrane protein DUF106. This archaebacterial protein family has no known function. Members are predicted to be integral membrane proteins.. 
PF01957 DUF107; <br>NfeD-like C-terminal, partner-binding. NfeD-like proteins are widely distributed throughout prokaryotes and are frequently associated with genes encoding stomatin-like proteins (slipins). There appear to be three major groups: an ancestral group with only an N-terminal serine protease domain and this C-terminal beta sheet-rich domain which is structurally very similar to the OB-fold domain, associated with its neighbouring slipin cluster; a second major group with an additional middle, membrane-spanning domain, associated in some species with eoslipin and in others with yqfA; a final 'artificial' group which unites truncated forms lacking the protease region and associated with their ancestral gene partner, either yqfA or eoslipin. This NefD, C-terminal, domain appears to be the major one for relating to the associated protein. NfeD homologues are clearly reliant on their conserved gene neighbour which is assumed to be necessary for function, either through direct physical interaction or by functioning in the same pathway, possibly involve with lipid-rafts  .. 
PF01958 Domain of unknown function DUF108<br>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 Swiss:Q19527.. 
PF01959 DUF109; <br>3-dehydroquinate synthase (EC 4.6.1.3). 3-Dehydroquinate synthase is an enzyme in the common pathway of aromatic amino acid biosynthesis that catalyses the conversion of  3-deoxy-D-arabino-heptulosonic acid 7-phosphate (DAHP) into 3-dehydroquinic acid  . This synthesis of aromatic amino acids is an essential metabolic function for most prokaryotic as well as lower eukaryotic cells, including plants. The pathway is absent in humans; therefore, DHQS represents a potential target for the development of novel and selective antimicrobial agents. Owing to the threat posed by the spread of pathogenic bacteria resistant to many currently used antimicrobial drugs, there is clearly a need to develop new anti-infective drugs acting at novel targets. A further potential use for DHQS inhibitors is as herbicides  .. 
PF01345 Domain of unknown function DUF11<br>Pfam-B_1553 (release 3.0). A domain of unknown function found in multiple copies in several archaebacterial proteins.. 
PF01969 Protein of unknown function DUF111<br>This prokaryotic family has no known function.. 
PF01970 DUF112;<br>Tripartite tricarboxylate transporter TctA family. This family, formerly known as DUF112, is a family of bacterial and archaeal tripartite tricarboxylate transporters of the extracytoplasmic solute binding receptor-dependent transporter group of families, distinct from the ABC and TRAP-T families  . TctA is part of the tripartite TctABC system which, as characterised in S. typhimurium  , is a secondary carrier that depends for activity on the extracytoplasmic tricarboxylate-binding receptor TctC as well as two integral membrane proteins, TctA and TctB. complete three-component systems are found only in bacteria. TctA is a large transmembrane protein with up to 12 predicted membrane spanning regions in bacteria and up to 11 such in archaea, with the N-terminal within the cytoplasm. TctA is thought to be a permease, and in most other bacteria functions without TctB and TctC molecules  .. 
PF01972 DUF114;<br>Serine dehydrogenase proteinase. This family of archaebacterial proteins, formerly known as DUF114, has been found to be a serine dehydrogenase proteinase distantly related to ClpP proteinases that belong to the serine proteinase superfamily. The family has a catalytic triad of Ser, Asp, His residues, which shows an altered residue ordering compared with the ClpP proteinases but similar to that of the carboxypeptidase clan  .. 
PF01973 DUF115;<br>Protein of unknown function DUF115. This family of archaebacterial proteins has no known function.. 
PF01976 Protein of unknown function DUF116<br>This archaebacterial protein has no known function. The protein contains seven conserved cysteines and may also be an integral membrane protein.. 
PF01978 DUF118; <br>Sugar-specific transcriptional regulator TrmB. One member of this family, TrmB, has been shown to be a sugar-specific transcriptional regulator of the trehalose/maltose ABC transporter   in Thermococcus litoralis.. 
PF01982 DUF120; <br>Domain of unknown function DUF120. This domain is a CTP-dependent riboflavin kinase (RFK), found in archaea, that catalyses the phosphorylation of riboflavin to form flavin mononucleotide in riboflavin biosynthesis EC:2.7.1.26. Its structure resembles a RIFT barrel, structurally similar to but topologically distinct from bacterial and eukaryotic examples. The N-terminal is a winged helix-turn-helix DNA-binding domain, and the C-terminal half is most similar in sequence to a group of cradle-loop barrels. Swiss:O28174 has this domain attached to Pfam:PF00325.. 
PF01983 DUF121;<br>Guanylyl transferase CofC like. Coenzyme F420 is a hydride carrier cofactor that functions during methanogenesis.  This family of proteins represents CofC, a nucleotidyl transferase that is involved in coenzyme F420 biosynthesis.  CofC has been shown to catalyse the formation of lactyl-2-diphospho-5'-guanosine from 2-phospho-L-lactate and GTP  .. 
PF01986 Domain of unknown function DUF123<br>
PF01987 DUF124;<br>Mitochondrial biogenesis AIM24. In eukaryotes, this domain is involved in mitochondrial biogenesis  . Its function in prokaryotes in unknown.. 
PF01988 DUF125;<br>This family includes the vacuolar Fe2+/Mn2+ uptake transporter Swiss:P47818, Ccc1   and the vacuolar iron transporter VIT1 Swiss:Q9ZUA5.. 
PF01989 Protein of unknown function DUF126<br>This archaebacterial protein family has no known function.. 
PF01994 DUF127;<br>tRNA ribose 2'-O-methyltransferase, aTrm56. This family is an aTrm56 that catalyses the 2'-O-methylation of the cytidine residue in archaeal tRNA, using S-adenosyl-L-methionine. Biochemical assays showed that aTrm56 forms a dimer and prefers the L-shaped tRNA to the lambda form as its substrate    .  aTrm56 consists of the SPOUT domain, which contains the characteristic deep trefoil knot for AdoMet binding, and a unique C-terminal beta-hairpin  .. 
PF01995 Domain of unknown function DUF128<br>This archaebacterial protein family has no known function. The domain is found duplicated in Swiss:O27611. Many of these are attached to an N-terminal winged helix domain suggesting these are transcriptional regulators and that this domain has a ligand binding function.. 
PF01996 DUF129; <br>F420-0:Gamma-glutamyl ligase. F420-0:Gamma-glutamyl ligase (EC:6.3.2.-) is an enzyme involved in F420 biosynthesis pathway.  It catalyses the GTP-dependent successive addition of multiple gamma-linked L-glutamates to the L-lactyl phosphodiester of 7,8-didemethyl-8-hydroxy-5-deazariboflavin (F420-0). This reaction produces polyglutamated F420 derivatives.  GTP + F420-0 + n L-glutamate -> GDP + phosphate + F420-n. 
PF02343 DUF130; R03H10.4; <br>TRA-1 regulated protein R03H10.4. Pfam-B_814 (release 5.2). This family of proteins represents the protein product of the gene R03H10.4 which is located near a sequence that matches the TRA-1 binding consensus. TRA-1 is a transcription factor which controls sexual differentiation in C.elegans. R03H10.4 shows male-enriched reporter gene expression and acts as a direct target of TRA-1 regulation  .. 
PF01998 Protein of unknown function DUF131<br>This archaebacterial protein family has no known function. The proteins are predicted to contain two transmembrane helices.. 
PF02001 Protein of unknown function  DUF134<br>This family of archaeal proteins has no known function.. 
PF02006 Protein of unknown function DUF137<br>This family of archaeal proteins has no known function.. 
PF02363 DUF139; <br>Cysteine rich repeat. Pfam-B_602 (release 5.2). This Cysteine repeat C-X3-C-X3-C is repeated in sequences of  this family, 34 times in Swiss:O17970. The function of these repeats is unknown as is the function of the proteins in which they  occur.  Most of the sequences in this family are from C. elegans.. 
PF02405 DUF140;<br>Pfam-B_1126 (release 5.2). This domain functions as a permease. In Swiss:Q7DD59 it is involved in L-glutamate import into the cell  . In Swiss:Q8L4R0 it is involved in lipid transfer within the cell  .. 
PF02408 DUF141; <br>Pfam-B_1716 (release 5.4). This is a family of hypothetical C. elegans proteins.  The aligned region has no known function nor do any of the proteins which possess it. However, this domain is related to the CUB domain.. 
PF02410 DUF143;<br>Oligomerisation domain. Pfam-B_1798 (release 5.4). In yeasts, this domain is required for the oligomerisation of ATP synthase subunit 9 into a ring structure  .. 
PF02413 DUF144; <br>Caudovirales tail fibre assembly protein. Pfam-B_1800 (release 5.4). This family contains bacterial and phage tail fibre assembly proteins  . E.coli contains several members of this family although the function of these proteins is uncertain.. 
PF02415 DUF145; Chlamydia_PMP; <br>Chlamydia polymorphic membrane protein (Chlamydia_PMP) repeat. This family contains several Chlamydia polymorphic membrane proteins. Chlamydia pneumoniae is an obligate intracellular bacterium and a common human pathogen causing infection of the upper and lower respiratory tract. Common for the Pmps are the tetrapeptide GGA(I/V/L) motif repeated several times in the N-terminal part. The C-terminal half is characterised by conserved tryptophans and a carboxy-terminal phenylalanine. A signal peptide leader sequence is predicted in 20 C. pneumoniae Pmps, which indicates an outer membrane localisation. Pmp10 and Pmp11 contain a signal peptidase II cleavage site suggesting lipid modification. The C. pneumoniae pmp genes represent 17.5% of the chlamydia-specific coding capacity and they are all transcribed during chlamydial growth but the function of Pmps remains unknown  . This family shows some similarity to Pfam:PF05594 and hence is likely to also form a beta-helical structure (personal obs:C Yeats).. 
PF02457 DUF147; <br>DisA bacterial checkpoint controller nucleotide-binding. Pfam-B_1846 (release 5.4). The DisA protein is a bacterial checkpoint protein that dimerises into an octameric complex. The protein consists of three distinct domains. This domain is the first and is a globular, nucleotide-binding region; the next 146-289 residues constitute the DisA-linker family, Pfam:PF10635, that consists of an elongated bundle of three alpha helices (alpha-6, alpha-10, and alpha-11), one side of which carries an additional three helices (alpha7-9), which thus forms a spine like-linker between domains 1 and 3. The C-terminal residues, of domain 3, are represented by family HHH, Pfam:PF00633, the specific DNA-binding domain. The octameric complex thus has structurally linked nucleotide-binding and DNA-binding HhH domains and the nucleotide-binding domains are bound to a cyclic di-adenosine phosphate such that DisA is a specific di-adenylate cyclase. The di-adenylate cyclase activity is strongly suppressed by binding to branched DNA, but not to duplex or single-stranded DNA, suggesting a role for DisA as a monitor of the presence of stalled replication forks or recombination intermediates via DNA structure-modulated c-di-AMP synthesis  .. 
PF02520 Domain of unknown function DUF148<br>Pfam-B_1103 (release 5.4). This domain has no known function nor do any of the proteins that possess it.  In one member of this family Swiss:Q23614 the aligned region is repeated twice.. 
PF02576 Uncharacterised BCR, YhbC family COG0779<br>
PF02577 DUF151;<br>Bifunctional nuclease. This family is a bifunctional nuclease, with both DNase and RNase activity  . It forms a wedge-shaped dimer, with each monomer being triangular in shape. A large groove at the thick end of the wedge contains a possible active site  .. 
PF02578 DUF152; Cu_oxidase_4; <br>Multi-copper polyphenol oxidoreductase laccase. Laccases are multi-copper oxidoreductases able to oxidise a wide variety of phenolic and non-phenolic compounds and are widely distributed among both prokaryotes and eukaryotes. There are two main active catalytic sites with conserved histidines that are capable of binding four copper atoms  .. 
PF02579 DUF153;<br>Dinitrogenase iron-molybdenum cofactor. This family contains several NIF (B, Y and X) proteins which are iron-molybdenum cofactors (FeMo-co) in the dinitrogenase enzyme which catalyses the reduction of dinitrogen to ammonium. Dinitrogenase is a hetero-tetrameric (alpha(2)beta(2)) enzyme which contains the iron-molybdenum cofactor (FeMo-co) at its active site  .. 
PF02582 Uncharacterised ACR, YagE family COG1723<br>
PF02585 DUF158; <br>GlcNAc-PI de-N-acetylase. Members of this family are related to PIG-L an N-acetylglucosaminylphosphatidylinositol de-N-acetylase (EC:3.5.1.89) that catalyses the second step in GPI biosynthesis  .. 
PF02586 Uncharacterised ACR, COG2135<br>
PF01519 Protein of unknown function DUF16<br>Pfam-B_764 (release 4.0). The function of this protein is unknown.  It appears to only occur in Mycoplasma pneumoniae. The crystal structure revealed that this domain is composed of two separated homotrimeric coiled-coils  .. 
PF02589 Uncharacterised ACR, YkgG family COG1556<br>
PF02590 DUF163; <br>Predicted SPOUT methyltransferase. This family of proteins are predicted to be SPOUT methyltransferases  .. 
PF02591 Putative zinc ribbon domain<br>Structural modelling suggests this domain may bind nucleic acids  .. 
PF02592 Uncharacterized ACR, YhhQ family COG1738<br>
PF02593 DUF166;<br>Thymidylate synthase. This family catalyses the synthesis of thymidine monophosphate (dTMP) from deoxyuridine monophosphate (dUMP). The physiological co-substrate has not yet been identified  .. 
PF02594 Uncharacterised ACR, YggU family COG1872<br>
PF02596 Uncharacterised ArCR, COG2043<br>
PF02598 DUF171;<br>Putative RNA methyltransferase. This family has a TIM barrel-like fold with a deep C-terminal trefoil knot. The arrangement of its hydrophilic and hydrophobic surfaces are opposite to that of the classic TIM barrel proteins. It is likely to bind RNA  , and may function as a methyltransferase [2,3].. 
PF02604 DUF172; PhdYeFM;<br>Antitoxin Phd_YefM, type II toxin-antitoxin system. Members of this family act as antitoxins in type II toxin-antitoxin systems  .  When bound to their toxin partners, they can bind DNA via the N-terminus and repress the expression of operons containing genes encoding the toxin and the antitoxin  .  This domain complexes with Txe toxins containing Pfam:PF06769, Fic/DOC toxins containing Pfam:PF02661 and YafO toxins containing Pfam:PF13957.. 
PF02616 DUF173; <br>ScpA and ScpB participate in chromosomal partition during cell division. It may act via the formation of a condensin-like complex containing smc that pull DNA away from mid-cell into both cell halves. These proteins are part of the Kleisin superfamily.. 
PF02617 DUF174; <br>ATP-dependent Clp protease adaptor protein ClpS. In the bacterial cytosol, ATP-dependent protein degradation is performed by several different chaperone-protease pairs, including ClpAP. ClpS directly influences the ClpAP machine by binding to the N-terminal domain of the chaperone ClpA. The degradation of ClpAP substrates, both SsrA-tagged proteins and ClpA itself, is specifically inhibited by ClpS. ClpS modifies ClpA substrate specificity, potentially redirecting degradation by ClpAP toward aggregated proteins  .. 
PF02618 DUF175; ADC_lyase;<br>This family of proteins is found in bacteria. Proteins in this family are typically between 332 and 389 amino acids in length. This family was previously incorrectly annotated and names as aminodeoxychorismate lyase. The structure of Swiss:P28306 was solved by X-ray crystallography.. 
PF02620 Uncharacterized ACR, COG1399<br>
PF02621 DUF178;<br>Menaquinone biosynthesis. This family includes two enzymes which are involved in menaquinone biosynthesis. One which catalyses the conversion of cyclic de-hypoxanthine futalosine to 1,4-dihydroxy-6-naphthoate, and one which may be involved in the conversion of chorismate to futalosine  . These enzymes comprise two domains with alpha/beta structures, a large domain and a small domain. A pocket between the two domains may form the active site, a conserved histidine located within this pocket could be the catalytic base  .. 
PF02622 Uncharacterized ACR, COG1678<br>
PF02623 DUF180; <br>The protein BSU35380 from Bacillus subtilis (renamed FliW) was characterised as being a flagellar assembly factor. Experimental characterisation was also carried out in Treponema pallidum (TP0658).  In Campylobacter jejuni, Cj1075 has been shown to be involved in motility and flagellin biosynthesis. The two paralogues in Helicobacter pylori (HP1154 and HP1377) were found to be able to bind to flagellin. FliW proteins are involved in flagellar assembly  . FliW is part of a three-part feedback loop: in Bacillus subtilis FliW inhibits CsrA (an RNA-binding protein) which inhibits FliC translation; hence FliW is required for FliC (flagellin) production  .. 
PF02624 DUF181; <br>
PF02636 DUF185;<br>Putative S-adenosyl-L-methionine-dependent methyltransferase. This family is a putative S-adenosyl-L-methionine (SAM)-dependent methyltransferase [1,2]. In eukaryotes it plays a role in mitochondrial complex I activity  .. 
PF02638 Glycosyl hydrolase like GH101<br>
PF01579 Domain of unknown function (DUF19)<br>Pfam-B_402 (release 4.1). This presumed domain has no known function. It is found in one or two copies in several Caenorhabditis elegans proteins.  It is roughly 130 amino acids long. The domain contains 12 conserved cysteines which suggests that the domain is an extracellular domain and that these cysteines form six intradomain disulphide bridges.  The GO annotation for this protein indicates that it has a function in nematode larval development and has a positive regulation of growth rate.. 
PF02643 Uncharacterized ACR, COG1430<br>Two structures have been solved for members of this large (>500 members) family of bacterial proteins present mostly in environmental bacteria and metagenomes (distant homologues are also present in several Plasmodium species).  TOPSAN analysis for pdb:3pjy shows that there is much similarity with the other solved structure, pdb:3m7a, solved for UniProt:Q2GA55 (Saro_0823), a homologue of Thermotoga maritima TM1668, UniProt:Q9X1Z6., The homologue in Caulobacter crescentus (CC1388), UniProt:Q9A8G6, is associated with CspD, a cold shock protein (CC1387), UniProt:Q9A8G7. However, the genomic context of UniProt:Q2GA55 is most conserved with a putative xylose isomerase, suggesting a possible role in extracellular sugar processing. Saro_0821, UniProt:Q2GA57, is annotated as an AMP-dependent synthetase and ligase. PDB:3m7a structure corresponds to the C-terminal (27-165) fragment of the YP_496102 (Saro_0823) protein and it is structurally unique, as the best hits from Dali have a Z-score of 3.8 (1nt0, 2j1t, 3kq4) and it is thus a likely candidate for a new fold. Interestingly, many of the top Dali hits are involved in sugar metabolism. There are no obvious active site-like cavities on the protein surface of 3m7a (http://www.topsan.org/Proteins/JCSG/).. 
PF02645 DUF194; <br>Uncharacterised protein, DegV family COG1307. The structure of this protein revealed a bound fatty-acid molecule in a pocket between the two protein domains. The structure indicates that this family has the molecular function of fatty-acid binding and may play a role in the cellular functions of fatty acid transport or metabolism  .. 
PF02646 DUF195; <br>This family contains several bacterial RmuC DNA recombination proteins. The function of the RMUC protein is unknown but it is suspected that it is either a structural protein that protects DNA against nuclease action, or is itself involved in DNA cleavage at the regions of DNA secondary structures  . 
PF02649 DUF198;<br>Type I GTP cyclohydrolase folE2. This is a family of prokaryotic proteins with type I GTP cyclohydrolase activity. GTP cyclohydrolase I is the first enzyme of the de novo tetrahydrofolate biosynthetic pathway present in bacteria, fungi, and plants, and encoded in Escherichia coli by the folE gene; it is also the first enzyme of the biopterin (BH4) pathway in Homo sapiens . The invariate, highly conserved glutamate residue at position 216 in Swiss:Q5F9K6 is likely to be the substrate ligand and the metal ligand is likely to be the cysteine at position 147. The enzyme is Zinc 2+ dependent  .. 
PF02650 DUF199; <br>WhiA C-terminal HTH domain. This domain is found at the C-terminus of the sporulation regulator WhiA.  It is predicted to form a DNA-binding helix-turn-helix structure  .  The WhiA protein also contains two N-terminal domains that are distant homologues of LAGLIDADG homing endonucleases  .. 
PF02655 DUF201; <br>
PF02656 Domain of unknown function (DUF202)<br>This family consists of hypothetical proteins some of which are putative membrane proteins.  No functional information or experimental verification of function is known.  This domain is around 100 amino acids long.. 
PF02659 Domain of unknown function DUF<br>This family consists of hypothetical transmembrane proteins non of which have any known function, the aligned region is 180 amino acids long.. 
PF02660 DUF205;<br>Glycerol-3-phosphate acyltransferase. This family of enzymes catalyses the transfer of an acyl group from acyl-ACP to glycerol-3-phosphate to form lysophosphatidic acid  ].. 
PF02675 DUF206; AdoMetDC; <br>S-adenosylmethionine decarboxylase . This family contains several S-adenosylmethionine decarboxylase proteins from bacterial and archaebacterial species. S-adenosylmethionine decarboxylase (AdoMetDC), a key enzyme in the biosynthesis of spermidine and spermine, is first synthesised as a proenzyme, which is cleaved post translationally to form alpha and beta subunits. The alpha subunit contains a covalently bound pyruvoyl group derived from serine that is essential for activity [1,2].. 
PF02676 DUF207; <br>Methyltransferase TYW3. The methyltransferase TYW3 (tRNA-yW- synthesising protein 3) has been identified in yeast to be involved in wybutosine (yW) biosynthesis  .  yW is a complexly modified guanosine residue that contains a tricyclic base and is found at the 3' position adjacent the anticodon of phenylalanine tRNA.  TYW3 is an N-4 methylase that methylates yW-86 to yield yW-72 in an Ado-Met-dependent manner  .. 
PF02677 Uncharacterized BCR, COG1636<br>
PF02678 DUF209;<br>This family consists of Pirin proteins from both eukaryotes and prokaryotes. The function of Pirin is unknown but the gene coding for this protein is known to be expressed in all tissues in the human body although it is expressed most strongly in the liver and heart. Pirin is known to be a nuclear protein, exclusively localised within the nucleoplasma and predominantly concentrated within dot-like subnuclear structures  . A tomato homologue of human Pirin has been found to be induced during programmed cell death  . Human Pirin interacts with Bcl-3 and NFI   and hence is probably involved in the regulation of DNA transcription and replication. It appears to be an Fe(II)-containing member of the Cupin superfamily.. 
PF01595 Domain of unknown function DUF21<br>Pfam-B_618 (release 4.1). 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 Swiss:Q54318 that does not contain this domain. This domain is found in the N-terminus of the proteins adjacent to two intracellular CBS domains Pfam:PF00571.. 
PF02679 DUF210;<br>(2R)-phospho-3-sulfolactate synthase (ComA). In methanobacteria (2R)-phospho-3-sulfolactate synthase (ComA) catalyses the first step of the biosynthesis of coenzyme M from phosphoenolpyruvate (P-enolpyruvate). This novel enzyme catalyses the stereospecific Michael addition of sulfite to P-enolpyruvate, forming L-2-phospho-3-sulfolactate (PSL). It is suggested that the ComA-catalysed reaction is analogous to those reactions catalysed by beta-elimination enzymes that proceed through an enolate intermediate  .. 
PF02680 Uncharacterized ArCR, COG1888<br>
PF02681 Divergent PAP2 family<br>This family is related to the Pfam:PF01569 family (personal obs: C Yeats).. 
PF02697 Uncharacterized ACR, COG1753<br>Structural modelling suggests this domain may bind nucleic acids  .. 
PF02698 DUF218 domain<br>
PF01629 Domain of unknown function DUF22<br>Pfam-B_1137 (release 4.1). This domain is found in 1 to 3 copies in archaebacterial proteins.  The function of the domain is unknown. This family appears to be expanded in Archaeoglobus fulgidus.. 
PF02713 Domain of unknown function DUF220<br>Pfam-B_1412 (release 5.5). This is family consists of a region in several Arabidopsis thaliana hypothetical proteins none of which have any known function. The aligned  region contains two cysteine residues.. 
PF02714 Domain of unknown function DUF221<br>Pfam-B_1596 (release 5.5). This family consists of hypothetical transmembrane proteins none of which have any function, the aligned region is at 538 residues at maximum length.. 
PF02720 Domain of unknown function (DUF222)<br>Pfam-B_1711 (release 5.5). This family is often found associated to the N-terminus of the HNH endonuclease domain Pfam:PF01844. The function of this domain is uncertain. This family has been called the 13E12 repeat family  .. 
PF02721 Domain of unknown function DUF223<br>Pfam-B_1714 (release 5.5). 
PF02890 Borrelia family of unknown function DUF226<br>Pfam-B_1255 (release 6.0). This family of proteins are found in Borrelia.  The proteins are about 190 amino acids long and have no known function.. 
PF02989 Lyme disease proteins of unknown function<br>Pfam-B_1298 (release 6.4). 
PF03003 Poxvirus proteins of unknown function<br>Pfam-B_1300 (release 6.4). 
PF03008 Archaea bacterial proteins of unknown function<br>Pfam-B_1430 (release 6.4). 
PF03057 Protein of unknown function<br>Pfam-B_488 (release 6.4). This family represents the C-terminal region of a number of C. elegans proteins of unknown function.. 
PF03072 MG032/MG096/MG288 family 1<br>Pfam-B_2298 (release 6.4). This family consists entirely of mycoplasmal proteins. Their function is unknown. Another related family, Pfam:PF03086, also consists entirely of mycoplasmal proteins of the MG032/MG096/MG288 family. Some proteins, such as Swiss:P75072, are included in both families, but of course differ in the aligned residues.. 
PF01638 DUF24;<br>HxlR-like helix-turn-helix. Pfam-B_1509 (release 4.1). HxlR, a member of this family, is a DNA-binding protein that acts as a positive regulator of the formaldehyde-inducible hxlAB operon in Bacillus subtilis.. 
PF03086 MG032/MG096/MG288 family 2<br>Pfam-B_2385 (release 6.4). This family consists entirely of mycoplasmal proteins. Their function is unknown. Another related family, Pfam:PF03072, also consists entirely of mycoplasmal proteins of the MG032/MG096/MG288 family. Some proteins, such as Swiss:P75072, are included in both families, but of course differ in the aligned residues.. 
PF03112 Uncharacterized protein family (ORF7) DUF<br>Pfam-B_2667 (release 6.5). Several members of this family are Borrelia burgdorferi plasmid proteins of uncharacterized function.. 
PF03136 DUF245; Proteosome_20S;<br>Pfam-B_3042 (release 6.5). Pupylation is a novel protein modification system found in some bacteria  . This family of proteins are the enzyme that can conjugate proteins of the Pup family to lysine residues in target proteins marking them for degradation. The archetypal protein in this family is PafA (proteasome accessory factor) from Mycobacterium tuberculosis  . It has been suggested that these proteins are related to gamma-glutamyl-cysteine synthetases  .. 
PF03158 Multigene family 530 protein<br>Pfam-B_2304 (release 6.5). Members of this family are multigene family 530 proteins from African swine fever viruses. These proteins may be involved in promoting survival of infected macrophages  .. 
PF03151 DUF250; <br>Triose-phosphate Transporter family. Pfam-B_3234 (release 6.5). This family includes transporters with a specificity for triose phosphate  .. 
PF03159 DUF251; <br>XRN 5'-3' exonuclease N-terminus. Pfam-B_2349 (release 6.5). 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 necessary for 5' to 3' exonuclease function. The family also contains several Xrn1 and Xrn2 proteins. The 5'-3' exoribonucleases Xrn1p and Xrn2p/Rat1p function in the degradation and processing of several classes of RNA in Saccharomyces cerevisiae. Xrn1p is the main enzyme catalysing cytoplasmic mRNA degradation in multiple decay pathways, whereas Xrn2p/Rat1p functions in the processing of rRNAs and small nucleolar RNAs (snoRNAs) in the nucleus  .. 
PF03162 DUF252; <br>Tyrosine phosphatase family. Pfam-B_3756 (release 6.5). This family is closely related to the Pfam:PF00102 and Pfam:PF00782 families.. 
PF03190 DUF255;<br>Protein of unknown function, DUF255. Pfam-B_2331 (release 6.5). 
PF03192 Pyrococcus protein of unknown function, DUF257<br>Pfam-B_2788 (release 6.5). 
PF03193 Protein of unknown function, DUF258<br>Pfam-B_2832 (release 6.5). 
PF03196 Protein of unknown function, DUF261<br>Pfam-B_2687 (release 6.5). 
PF03235 Protein of unknown function DUF262<br>Pfam-B_3462 (release 6.5). 
PF03237 DUF264; <br>Terminase-like family. Pfam-B_3575 (release 6.5). This family represents a group of terminase proteins.. 
PF03266 DUF265;<br>Pfam-B_4081 (release 6.5). This domain is found across all species from bacteria to human, and the function was determined first in a hyperthermophilic bacterium to be an NTPase  . The structure of one member-sequence represents a variation of the RecA fold, and implies that the function might be that of a DNA/RNA modifying enzyme  . The sequence carries both a Walker A and Walker B motif which together are characteristic of ATPases or GTPases. The protein exhibits an increased expression profile in human liver cholangiocarcinoma when compared to normal tissue  .. 
PF03270 Protein of unknown function, DUF269<br>Pfam-B_4172 (release 6.5). Members of this family may be involved in nitrogen fixation, since they are found within nitrogen fixation operons.. 
PF03189 DUF270; <br>Pfam-B_2323 (release 6.5). 
PF03407 DUF271; <br>Nucleotide-diphospho-sugar transferase. Pfam-B_4460 (release 6.6). Proteins in this family have been been predicted to be nucleotide-diphospho-sugar transferases.. 
PF03314 Protein of unknown function, DUF273<br>Pfam-B_3636 (release 6.5). 
PF03434 DUF276 <br>Pfam-B_4450 (release 6.6). This family is specific to Borrelia burgdorferi.  The protein is encoded on extra-chromosomal DNA.\.     This domain has no known function.. 
PF03353 DUF278; Lin-8_Ec; Lin-8_Ce; <br>Ras-mediated vulval-induction antagonist. Pfam-B_3924 (release 6.5). LIN-8 is a nuclear protein, present at the sites of transcriptional repressor complexes, which interacts with LIN-35 Rb.Lin35 Rb is a product of the class B synMuv gene lin-35 which silences genes required for vulval specification through chromatin modification and remodelling  . The biological role of the interaction has not yet been determined however predictions have been made. The interaction shows that class A synMuv genes control vulval induction through the transcriptional regulation of gene expression. LIN-8 normally functions as part of a protein complex however when the complex is absent, other family members can partially replace LIN-8 activity  .. 
PF01709 DUF28;<br>Transcriptional regulator. Pfam-B_1741 (release 4.1). This is a family of transcriptional regulators. In mammals, it activates the transcription of mitochondrially-encoded COX1  . In bacteria, it negatively regulates the quorum-sensing response regulator by binding to its promoter region  .. 
PF03436 Domain of unknown function (DUF281) <br>Pfam-B_4313 (release 6.6). This family of worm domain has no known function. The boundaries of the presumed domain are rather uncertain.. 
PF03383 DUF286; <br>Caenorhabditis serpentine receptor-like protein, class xa. Pfam-B_2888 (release 6.6). This family contains various Caenorhabditis proteins, some of which are annotated as being serpentine receptors, mainly of the xa class.. 
PF03384 Drosophila protein of unknown function, DUF287<br>Pfam-B_2926 (release 6.6). 
PF03385 Protein of unknown function, DUF288<br>Pfam-B_3134 (release 6.6). 
PF01062 Worm_family_8;DUF289; <br>Bestrophin, RFP-TM, chloride channel. Bestrophin is a 68-kDa basolateral plasma membrane protein expressed in retinal pigment epithelial cells (RPE). It is encoded by the VMD2 gene, which is mutated in Best macular dystrophy, a disease characterised by a depressed light peak in the electrooculogram  .  VMD2 encodes a 585-amino acid protein with an approximate mass of 68 kDa which has been designated bestrophin. Bestrophin shares homology with the Caenorhabditis elegans RFP gene family, named for the presence of a conserved arginine (R), phenylalanine (F), proline (P), amino acid sequence motif.  Bestrophin is a plasma membrane protein, localised to the basolateral surface of RPE cells consistent with a role for bestrophin in the generation or regulation of the EOG light peak. Bestrophin and other RFP family members represent a new class of chloride channels, indicating a direct role for bestrophin in generating the light peak  . The VMD2 gene underlying Best disease was shown to represent the first human member of the RFP-TM protein family. More than 97% of the disease-causing mutations are located in the N-terminal RFP-TM domain implying important functional properties  . The bestrophins are four-pass transmembrane chloride-channel proteins  , and the RFP-TM or bestrophin domain extends from the N-terminus through approximately 350 amino acids and contains all of the TM domains as well as nearly all reported disease causing mutations  . Interestingly, the RFP motif is not conserved evolutionarily back beyond Metazoa, neither is it in plant members.. 
PF01724 Domain of unknown function DUF29<br>Pfam-B_2003 (release 4.1). This family consists of various hypothetical proteins from cyanobacteria, none of which are functionally described. The aligned region is approximately 120-140 amino acids long corresponding to almost the entire length of the proteins in the family. Swiss:Q2RPE2, PDB:3fcn, is a small protein that has a novel all-alpha fold. The N-terminal helical hairpin is likely to function as a dimerisation module. This protein is a member of PFam family PF01724. The function of this protein is unknown. One protein sequence contains a fusion of this protein and a DnaB domain, suggesting a possible role in DNA helicase activity (hypothetical). Dali hits have low Z and high rmsd, suggesting probably only topological similarities (not functional relevance) (details derived from TOPSAN). The family has several highly conserved sequence motifs, including YD/ExD, DxxNVxEEIE, and CPY/F/W, as well as conserved tryptophans.. 
PF03442 DUF291;<br>Carbohydrate binding domain X2. This domain binds to cellulose and to bacterial cell walls. It is found in glycosyl hydrolases and in scaffolding proteins of cellulosomes (multiprotein glycosyl hydrolase complexes). In the cellulosome it may aid cellulose degradation by anchoring the cellulosome to the bacterial cell wall and by binding it to its substrate  . This domain has an Ig-like fold  .. 
PF03398 DUF292; <br>Regulator of Vps4 activity in the MVB pathway. Pfam-B_3833 (release 6.6). ESCRT-I, -II, and -III are endosomal sorting complexes required for transporting proteins and carry out cargo sorting and vesicle formation in the multivesicular bodies, MVBs, pathway. These complexes are transiently recruited from the cytoplasm to the endosomal membrane where they bind transmembrane proteins previously marked for degradation by mono-ubiquitination. Assembly of ESCRT-III, a complex composed of at least four subunits (Vps2, Vps24, Vps20, Snf7), is intimately linked with MVB vesicle formation, its disassembly being an essential step in the MVB vesicle formation, a reaction that is carried out by Vps4, an AAA-type ATPase. The family Ist1 is a regulator of Vps4 activity; by interacting with Did2 and Vps4, Ist1 appears to regulate the recruitment and oligomerisation of Vps4. Together Ist1, Did2, and Vta1 form a network of interconnected regulatory proteins that modulate Vps4 activity, thereby regulating the flow of cargo through the MVB pathway  .. 
PF03444 DUF293;<br>Winged helix-turn-helix transcription repressor, HrcA DNA-binding. This domain is always found with a pair of CBS domains Pfam:PF00571.. 
PF03445 Putative nucleotidyltransferase DUF294<br>This domain is found associated with Pfam:PF00571.  This region is uncharacterised, however it seems to be similar to Pfam:PF01909, conserving the DXD motif.\. 
PF03479 Domain of unknown function (DUF296)<br>Pfam-B_796 (release 7.0) & Dlakic M. This putative domain is found in proteins that contain AT-hook motifs Pfam:PF02178, which strongly suggests a DNA-binding function for the proteins as a whole. There are three highly conserved histidine residues, eg at 117, 119 and 133 in Swiss:Q46QL5, which should be a structurally conserved metal-binding unit, based on structural comparison with known metal-binding structures. The proteins should work as trimers.. 
PF03537 DUF297; Glyco_hydro_114; GHL7;<br>Glycoside-hydrolase family GH114. This family is recognised as a glycosyl-hydrolase family, number 114.  It is endo-alpha-1,4-polygalactosaminidase, a rare enzyme. It is proposed to be TIM-barrel, the most common structure amongst the catalytic domains of glycosyl-hydrolases  .. 
PF03618 DUF299;<br>Kinase/pyrophosphorylase. Pfam-B_3403 (release 7.0). This family of regulatory proteins has ADP-dependent kinase and inorganic phosphate-dependent pyrophosphorylase activity [1-3].. 
PF03625 Domain of unknown function DUF302 <br>Domain is found in an undescribed set of proteins. Normally occurs uniquely within a sequence, but is found as a tandem repeat (Swiss:Q9X8B8). Shows interesting phylogenetic distribution with majority of examples in bacteria and archaea, but also in in D.melanogaster (e.g. Swiss:Q9VA18).. 
PF03629 Domain of unknown function (DUF303) <br>Pfam-B_3622 (release 7.0). Distribution of this domain seems limited to prokaryotes and viruses. . 
PF03733 Domain of unknown function (DUF307)<br>Domain occurs as one or more copies in a small family of putative membrane proteins.. 
PF03729 RUF1; <br>Short repeat of unknown function (DUF308). Family of short repeats that occurs in a limited number of membrane proteins. It may divide further in short repeats of around 7-10 residues of the pattern G-#-X(2)-#(2)-X  (#=hydrophobic).. 
PF03745 Domain of unknown function (DUF309)<br>This domain is found in eubacterial and archaebacterial proteins of unknown function. The proteins contain a motif HXXXEXX(W/Y) where X can be any amino acid. This motif is likely to be functionally important and may be involved in metal binding.. 
PF01732 Putative peptidase (DUF31)<br>Pfam-B_2152 (release 4.1). This domain has no known function. It is found in various hypothetical proteins and putative lipoproteins from mycoplasmas. It appears to be related to the superfamily of trypsin peptidases and so may have a peptidase function.. 
PF03750 Protein of unknown function (DUF310)<br>This family contains a number of archaeal proteins that are completely uncharacterised. The proteins are between 130 and 160 amino acids long. Their C-terminus contains several conserved residues.. 
PF03759 DUF315; <br>PRONE (Plant-specific Rop nucleotide exchanger). Pfam-B_3610 (release 7.0). This is a functional guanine exchange factor (GEF) of plant Rho GTPase  .. 
PF03773 Predicted permease<br>This family of integral membrane proteins are predicted to be permeases of unknown specificity.. 
PF03778 Protein of unknown function (DUF321) <br>Pfam-B_876 (release 7.0). This family may be related to the FARP (FMRFamide) family, Pfam:PF01581.  Currently this repeat was only detectable in Arabidopsis thaliana. . 
PF03780 DUF322;<br>The alkaline shock protein Asp23 was identified as an alkaline shock protein   that was expressed in a sigmaB-dependent manner in Staphylococcus aureus.. 
PF03781 DUF323; <br>Sulfatase-modifying factor enzyme 1. This domain is found in eukaryotic proteins   required for post-translational sulfatase modification (SUMF1).  These proteins are associated with the rare disorder multiple sulfatase deficiency (MSD)  . The protein product of the SUMF1 gene is FGE, formylglycine (FGly),-generating enzyme, which is a sulfatase.  Sulfatases are enzymes essential for degradation and remodelling of sulfate esters, and formylglycine (FGly), the key catalytic in the active site, is unique to sulfatases  . FGE is localised to the endoplasmic reticulum (ER) and interacts with and modifies the unfolded form of newly synthesised sulfatases. FGE is a single-domain monomer with a surprising paucity of secondary structure that adopts a unique fold which is stabilised by two Ca2+ ions. The effect of all mutations found in MSD patients is explained by the FGE structure, providing a molecular basis for MSD. A redox-active disulfide bond is present in the active site of FGE. An oxidised cysteine residue, possibly cysteine sulfenic acid, has been detected that may allow formulation of a structure-based mechanism for FGly formation from cysteine residues in all sulfatases  . In Mycobacteria and Treponema denticola this enzyme functions as an iron(II)-dependent oxidoreductase [5,6].. 
PF03787 DUF324; <br>COG1332, COG1567, COG1367. The molecular function of these proteins is not yet known.  However, they have been identified and called the RAMP (Repair Associated Mysterious Proteins) superfamily. The members of this family have no known function they are around 300 amino acids in length and have several conserved motifs.. 
PF03804 Viral domain of unknown function<br>
PF03885 Protein of unknown function (DUF327)<br>The proteins in this family are around 140-170 residues in length. The proteins contain many conserved residues. with the most conserved motifs found in the central and C-terminal region. The function of these proteins is unknown.. 
PF03883 Protein of unknown function (DUF328)<br>Members of this family are functionally uncharacterised. They are about 250 amino acids in length.. 
PF03884 Domain of unknown function (DUF329)<br>The function of this short domain is unknown it contains four conserved cysteines and may therefore be involved in zinc binding.. 
PF03886 Protein of unknown function (DUF330)<br>The proteins in this family are uncharacterised. The proteins are 170-190 amino residues in length.. 
PF03889 Domain of unknown function<br>Members of this family are uncharacterised proteins from a number of bacterial species.  The proteins range in size from 50-70 residues.. 
PF03891 Domain of unknown function (DUF333)<br>This small domain of about 70 residues is found in a number of bacterial proteins.  It is found at the N-terminus the of Swiss:O28332 protein. The proteins containing this domain are uncharacterised.. 
PF03904 Domain of unknown function (DUF334)<br>Staphylococcus aureus plasmid proteins with no characterised function.. 
PF03928 Domain of unknown function (DUF336)<br>This family contains uncharacterised sequences, including several GlcG proteins. The alignment contains many conserved motifs that are suggestive of cofactor binding and  enzymatic activity.. 
PF03929 DUF337;<br>PepSY-associated TM helix. 
PF03937 DUF339; TPR_div1;<br>Flavinator of succinate dehydrogenase. This family includes the highly conserved mitochondrial and bacterial proteins Sdh5/SDHAF2/SdhE. Both yeast and human Sdh5/SDHAF2 interact with the catalytic subunit of the succinate dehydrogenase (SDH) complex, a component of both the electron transport chain and the tricarboxylic acid cycle.\. Sdh5 is required for SDH-dependent respiration and for Sdh1 flavination (incorporation of the flavin adenine dinucleotide cofactor). Mutational inactivation of Sdh5 confers tumor susceptibility in humans  . Bacterial homologues of Sdh5, termed SdhE, are functionally conserved being required for the flavinylation of SdhA and succinate dehydrogenase activity. Like Sdh5, SdhE interacts with SdhA. Furthermore, SdhE was characterised as a FAD co-factor chaperone that directly binds FAD to facilitate the flavinylation of SdhA. Phylogenetic analysis demonstrates that SdhE/Sdh5 proteins evolved only once in an ancestral alpha-proteobacteria prior to the evolution of the mitochondria and now remain in subsequent descendants including eukaryotic mitochondria and the alpha, beta and gamma proteobacteria  .  This family was previously annotated in Pfam as being a divergent TPR repeat but structural evidence has indicated this is not true.. 
PF01784 DUF34;<br>NIF3 (NGG1p interacting factor 3). Pfam-B_1006 (release 4.2). This family contains several NIF3 (NGG1p interacting factor 3) protein homologues. NIF3 interacts with the yeast transcriptional coactivator NGG1p which is part of the ADA complex, the exact function of this interaction is unknown [1,2].. 
PF03956 Membrane protein of unknown function (DUF340)<br>Members of this family contain a conserved core of four predicted transmembrane segments.  Some members have an additional pair of N-terminal transmembrane helices. The functions of the proteins in this family are unknown.. 
PF03959 DUF341; <br>Serine hydrolase (FSH1). This is a family of serine hydrolases  .. 
PF03961 Protein of unknown function (DUF342)<br>This family of bacterial proteins has no known function. The proteins are in the region of 500-600 amino acid residues in length.. 
PF03966 DUF343; <br>Trm112p-like protein. The function of this family is uncertain. 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 conservation.  Trm112p is required for tRNA methylation in S. cerevisiae and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W  . The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast  . The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices  .. 
PF03976 DUF344; <br>Polyphosphate kinase 2 (PPK2). Inorganic polyphosphate (polyP) plays a role in metabolism and regulation and has been proposed to serve as a energy source in a pre-ATP world.  In prokaryotes, the synthesis and utilisation of polyP are catalysed by PPK1, PPK2 and polyphosphatases.  Proteins with a single PPK2 domain catalyse polyP-dependent phosphorylation of ADP to ATP, whereas proteins containing 2 fused PPK2 domains phosphorylate AMP to ADP.\.       The structure of PPK2 from Pseudomonas aeruginosa has revealed a a 3-layer alpha/beta/alpha sandwich fold with an alpha-helical lid similar to the structures of microbial thymidylate kinases  .. 
PF03978 DUF345; <br>Borrelia burgdorferi REV protein. Pfam-B_26177 (release 7.2). This family consists of several REV proteins from Borrelia burgdorferi (Lyme disease spirochete). The function of REV is unknown although it known that gene is induced during the ingesting of host blood suggesting a role in the metabolic activation of borreliae to adapt to physiological stimuli  .. 
PF03984 Repeat of unknown function (DUF346)  <br>This repeat was found as seven tandem copies in one protein. It is predicted to be composed of beta-strands. Thus it is likely that it forms a beta-propeller structure. It is found in association with BNR repeats, which also form a  beta-propeller.. 
PF03988 Repeat of Unknown Function (DUF347) <br>This repeat is found as four tandem repeats in a family of bacterial membrane proteins. Each repeat contains two transmembrane regions and a conserved tryptophan.. 
PF01796 DUF35 OB-fold domain<br>Pfam-B_1390 (release 4.2). This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is approximately 70 amino acids long. The domain is duplicated in Swiss:O53566.  The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain and a C-terminal OB fold domain represented in this entry.  OB-folds are frequently found to bind nucleic acids suggesting this domain might bind to DNA or RNA.. 
PF03994 Domain of Unknown Function (DUF350) <br>This domain occurs in a small set of of bacterial proteins. It has two transmembrane regions, and often occurs as tandem repeats. The are no conserved catalytic residues.. 
PF03995 DUF351;<br>Peptidase inhibitor family I36. This domain is currently only found in a small set of S. coelicolor secreted proteins. There are four conserved cysteines that probably form two disulphide bonds. Proteins 2SCK31.15C (Swiss:Q9ADK5) and SCO3675 (Swiss:Q9X8V7) also have probable beta-propellers at their C-termini. This family includes Swiss:P01077 a known peptidase inhibitor of known structure. This protein has a crystallin like fold Pfam:PF00030 and is distantly related by sequence.  It is not known whether other members of this family are peptidase inhibitors.. 
PF04001 DUF352; <br>Transcription factor Vhr1. Vhr1 is a transcription factor which regulates the biotin-dependent expression of transporters VHT1 and BIO5  .. 
PF04007 Protein of unknown function (DUF354)<br>Members of this family are around 350 amino acids in length. They are found in archaebacteria and have no known function.. 
PF04009 Protein of unknown function (DUF356)<br>Members of this family are around 120 amino acids in length and are found in some archaebacteria.  The function of this family is unknown.  However it contains a conserved motif IHPPAH that may be involved in its function.. 
PF04010 Protein of unknown function (DUF357)<br>Members of this family are short (less than 100 amino acid) proteins found in archaebacteria.  The function of these proteins is unknown.. 
PF04019 Protein of unknown function (DUF359)<br>This family of archaebacterial proteins are about 170 amino acids in length.  They have no known function. The most conserved portion of the protein contains the sequence GEEDL that may be important for its function.. 
PF04021 DUF361; Type_III_signal; <br>Class III signal peptide. This family of archaeal proteins contains.  an amino terminal motif QXSXEXXXL that has been suggested to be part of a class III signal sequence. With the Q being the +1 residue of the signal peptidase cleavage site  . Two members of this family are cleaved by a type IV pilin-like signal peptidase.. 
PF04015 Domain of unknown function (DUF362) <br>Domain that is sometimes present in iron-sulphur proteins.. 
PF04016 Domain of unknown function (DUF364)<br>This domain of unknown function has a PLP-dependent transferase-like fold. Its genomic context suggests that it may have a role in anaerobic vitamin B12 biosynthesis. This domain is often found at the C-terminus of proteins containing DUF4213, Pfam:PF13938.. 
PF04033 Domain of unknown function (DUF365)<br>Archaeal domain of unknown function.. 
PF04017 Domain of unknown function (DUF366)<br>Archaeal domain of unknown function.. 
PF04034 Domain of unknown function (DUF367)<br>
PF04018 Domain of unknown function (DUF368)<br>Predicted transmembrane domain of unknown function.  Family members have between 6 and 9 predicted transmembrane segments.. 
PF04126 DUF369;<br>This domain has a cyclophilin-like fold, consisting of an eight-stranded beta-barrel with an alpha helix located between the beta-2 and beta-3 strands and a 310 helix located between the beta-7 and beta-8 strands. The catalytic site found in human cyclophilin is not conserved in this domain, suggesting a different function for this domain [1,2].. 
PF01809 DUF37;<br>Pfam-B_1485 (release 4.2). This domain has haemolytic activity  . It is found in short (73-103 amino acid) proteins and contains three conserved cysteine residues.. 
PF04025 Domain of unknown function (DUF370)<br>Bacterial domain of unknown function.. 
PF04027 Domain of unknown function (DUF371)<br>Archaeal domain of unknown function.. 
PF04036 Domain of unknown function (DUF372)<br>Domain of unknown function.. 
PF04123 Domain of unknown function (DUF373)<br>Archaeal domain of unknown function.  Predicted to be an integral membrane protein with six transmembrane regions.. 
PF04028 Domain of unknown function (DUF374)<br>Bacterial domain of unknown function.. 
PF04041 Domain of unknown function (DUF377)<br>This family contains many hypothetical proteins, some of which are predicted to be glycosyl hydrolases. This family was noted to belong to the Beta fructosidase superfamily in  .. 
PF04070 Domain of unknown function (DUF378)<br>Predicted transmembrane domain of unknown function.  The majority of the family have two predicted transmembrane regions.. 
PF04038 Domain of unknown function (DUF381)<br>Archaeal domain of unknown function.  Strongly conserved YPLM motif.. 
PF04063 Domain of unknown function (DUF383)<br>
PF04064 Domain of unknown function (DUF384)<br>
PF04074 Domain of unknown function (DUF386)<br>TIGRFAMs (release 2.0);. This family consists of conserved hypothetical proteins,  typically about 150 amino acids in length, with no known  function.. 
PF04079 Putative transcriptional regulators (Ypuh-like)<br>TIGRFAMs (release 2.0);. This family of conserved bacterial proteins are thought to possibly be helix-turn-helix type transcriptional regulators.. 
PF04076 DUF388; <br>Bacterial OB fold (BOF) protein. TIGRFAMs (release 2.0);. Proteins in this family form an OB-fold.  Analysis of the predicted binding site of BOF family proteins implies that they lack nucleic acid-binding properties  .  They contain an predicted N-terminal signal peptide which indicates that they localise in the periplasm where they may function to bind proteins, small molecules, or other typical OB-fold ligands  . As hypothesised for the distantly related OB-fold containing bacterial enterotoxins, the loss of nucleotide-binding function and the rapid evolution of the BOF ligand-binding site may be associated with the presence of BOF proteins in mobile genetic elements and their potential role in bacterial pathogenicity  .. 
PF01837 Domain of unknown function DUF39<br>Pfam-B_7373 (release 4.0). This presumed domain is about is about 360 residues long. The function of this domain is unknown. It is found in some proteins that have two C-terminal CBS Pfam:PF00571 domains. There are also proteins that contain two inserted Fe4S domains near the C-terminal end of the domain.  The protein Swiss:O26943 has been misannotated as an inosine monophosphate dehydrogenase based on the similarity to the CBS domains.. 
PF04094 Protein of unknown function (DUF390)<br>Pfam-B_1698 (release 7.3). This is a family of long proteins currently only found in the rice genome. They have no known function. However they may be some kind of transposable element.. 
PF04134 Protein of unknown function, DUF393<br>Members of this family have two highly conserved cysteine residues near their N-terminus. The function of these proteins is unknown.. 
PF04143 DUF395;<br>Pfam-B_2577 (release 7.3). This is an integral membrane protein. It is predicted to have a function in the transport of sulphur-containing molecules  .  It contains several conserved glycines and an invariant cysteine that is probably an important functional residue.. 
PF04148 DUF396; <br>Transmembrane adaptor Erv26. Pfam-B_22900 (release 7.3);. Erv26 is an integral membrane protein that is packed into COPII vesicles and cycles between the ER and Golgi compartments.  It directs pro-alkaline phosphatase into endoplasmic reticulum-derived COPII transport vesicles  .. 
PF04149 Domain of unknown function (DUF397)<br>Pfam-B_3066 (release 7.3). The function of this family is unknown. It has been suggested that some members of this family are regulators of transcription. In  particular, it is thought that this may regulator of antibiotic production in Streptomyces coelicolor  .  . 
PF04187 Protein of unknown function, DUF399<br>No function is known for any member of this family.. 
PF04165 Protein of unknown function (DUF401) <br>TIGRFAMs (release 2.0);. Members if this family are predicted to have 10 transmembrane  regions.. 
PF04167 Protein of unknown function (DUF402)<br>Family member FomD is a predicted protein from a fosfomycin biosynthesis gene cluster in Streptomyces wedmorensis  .  Its function is unknown.. 
PF04168 DUF403;<br>A predicted alpha-helical domain with a conserved ER motif.. An uncharacterized alpha helical domain containing a highly  conserved ER motif and typically found as a tandem duplication.  Contextual analysis suggests that it functions in a distinct peptide  synthesis/modification system comprising of a transglutaminase,  a peptidase of the NTN-hydrolase superfamily, an active and inactive  circularly permuted ATP-grasp domains and a transglutaminase fused  N-terminal to a circularly permuted COOH-NH2 ligase domain  .. 
PF04175 Protein of unknown function (DUF406) <br>TIGRFAMs (release 2.0);. Members of this family appear to be found only in gamma proteobacteria. The function of this protein family is undetermined. Solution of the structures of the two members of this family investigated bear some resemblance to that of the single domain enzyme pterin-4a-carbinolamine dehydratase, PDC. Although the residues of PCDs involved in binding of metabolite are not conserved in the two structures under study, they do correspond to a surface-region structurally aligned with residues that are highly conserved, eg Glu 89, suggesting that this region is also involved in binding of a ligand, thereby possibly constituting a catalytic site of a yet uncharacterised enzyme specific for gamma proteobacteria.. 
PF04174 DUF407;<br>A circularly permuted ATPgrasp . An ATP-grasp family that is present both as catalytically active  and inactive versions. Contextual analysis suggests that  it functions in a distinct peptide synthesis/modification system  that additionally contains a transglutaminase, an NTN-hydrolase,  the Alpha-E domain, and a transglutaminase fused N-terminal to a  circularly permuted COOH-NH2 ligase. The inactive forms are often  fused N-terminal to the Alpha-E domain  .. 
PF04181 DUF408; <br>Pfam-B_22202 (release 7.3);. This family includes the human RPAP2 (RNAP II associated polypeptide) protein and the yeast Rtr1 protein  . It has been suggested that this family of proteins are regulators of core RNA polymerase II function  .. 
PF04188 DUF409; <br>Mannosyltransferase (PIG-V)). Pfam-B_9248 (release 7.3);. This is a family of eukaryotic ER membrane proteins that are involved in the synthesis of glycosylphosphatidylinositol (GPI), a glycolipid that anchors many proteins to the eukaryotic cell surface.  Proteins in this family are involved in transferring the second mannose in the biosynthetic pathway of GPI    .. 
PF04190 Protein of unknown function (DUF410) <br>Pfam-B_12495 (release 7.3);. This family of proteins is from Caenorhabditis elegans and has no known function. The protein has some GO references indicating that the protein has a positive regulation of growth rate and is involved in nematode larval development.. 
PF04214 Protein of unknown function, DUF<br>The function of the members of this bacterial protein family is unknown. Some members may be involved in conferring cation resistance.. 
PF04217 Protein of unknown function, DUF412<br>This family consists of bacterial uncharacterised proteins.. 
PF04219 Protein of unknown function, DUF<br>
PF04220 DUF414;<br>Der GTPase activator (YihI). YihI activates the GTPase activity of Der, a 50S ribosomal subunit stability factor  .  The stimulation is specific to Der as YihI does not stimulate the GTPase activity of Era or ObgE. The interaction of YihI with Der requires only the C-terminal 78 amino acids of YihI  . A yihI deletion mutant is viable and shows a shorter lag period, but the same post-lag growth rate as a wild-type strain. yihI is expressed during the lag period. Overexpression of yihI inhibits cell growth and biogenesis of the 50S ribosomal subunit  . YihI is an unusual, highly hydrophilic protein with an uneven distribution of charged residues, resulting in an N-terminal region with high pI and a C-terminal region with low pI  .. 
PF04222 Protein of unknown function (DUF416)<br>This is a bacterial protein family of unknown function.  Proteins in this family adopt an alpha helical structure.  Genome context analysis has suggested a high probability of a functional association with histidine kinases, which implicates proteins in this family to play a role in signalling (information from TOPSAN 2Q9R).. 
PF04224 Protein of unknown function, DUF417<br>This family of uncharacterised proteins appears to be restricted to proteobacteria.. 
PF04235 Protein of unknown function (DUF418)<br>Probable integral membrane protein.. 
PF04237 DUF419;<br>YjbR has a CyaY-like fold  . 
PF04238 Protein of unknown function (DUF420)<br>Predicted membrane protein with four transmembrane helices.. 
PF04239 Protein of unknown function (DUF421)<br>
PF04240 Protein of unknown function (DUF422)<br>Predicted to be an integral membrane protein.. 
PF04242 Protein of unknown function (DUF424)<br>This is a family of uncharacterised proteins.. 
PF04248 Domain of unknown function (DUF427)<br>
PF04250 Protein of unknown function (DUF429)<br>
PF01861 Protein of unknown function DUF43<br>This family includes archaebacterial proteins of unknown function.  All the members are 350-400 amino acids long.. 
PF04254 Protein of unknown function (DUF432)<br>Archaeal protein of unknown function.. 
PF04256 Protein of unknown function (DUF434)<br>
PF04258 DUF435; <br>Signal peptide peptidase. The members of this family are membrane proteins. In some proteins this region is found associated with Pfam:PF02225. This family corresponds with Merops subfamily A22B, the type example of which is signal peptide peptidase. There is a sequence-similarity relationship with Pfam:PF01080.. 
PF04260 Protein of unknown function (DUF436) <br>TIGRFAMs (release 2.0);. Family of bacterial proteins with undetermined function. . 
PF04266 DUF437; <br>The ASCH domain adopts a beta-barrel fold similar to the Pfam:PF01472 domain  .  It is thought to function as an RNA-binding domain during coactivation, RNA-processing and possibly during prokaryotic translation regulation  .. 
PF04282 Family of unknown function (DUF438)<br>
PF04283 DUF439;<br>Chemotaxis signal transduction system protein F from archaea. This is a family of proteins that are archaea-specific components of the bacterial-like chemotaxis signal transduction system of archaea. In H. salinarum, the CheF proteins interact with the chemotaxis proteins CheY, CheD and CheC2 as well as the flagella-accessory proteins FlaCE and FlaD, and are essential for any tactic response. CheF probably functions at the interface between the bacterial-like chemotaxis signal transduction system and the archaeal flagellar apparatus.. 
PF04269 Protein of unknown function, DUF440<br>This family consists of uncharacterised bacterial proteins.. 
PF04284 Protein of unknown function (DUF441)<br>Predicted to be an integral membrane protein.. 
PF04273 Putative phosphatase (DUF442)<br>TIGRFAMs (release 2.0);. Although this domain is uncharacterised it seems likely that it performs a phosphatase function.. 
PF04276 Protein of unknown function (DUF443) <br>TIGRFAMs (release 2.0);. Family of uncharacterised proteins.. 
PF04285 Protein of unknown function (DUF444)<br>Bacterial protein of unknown function.  One family member (Swiss:Q97LI1) is predicted to contain a von Willebrand factor (vWF) type A domain (Smart:VWA).. 
PF04286 Protein of unknown function (DUF445)<br>Predicted to be a membrane protein.. 
PF04287 tRNA pseudouridine synthase C<br>This family is suggested to be the catalytic domain of tRNA pseudouridine synthase C by association. The structure has been solved for one member, as PDB:2HGK, which by inference is designated in this way.. 
PF04289 Protein of unknown function (DUF447)<br>Archaeal protein of unknown function.. 
PF04296 Protein of unknown function (DUF448)<br>
PF01863 Protein of unknown function DUF45<br>This protein has no known function.  Members are found in some archaebacteria, as well as Helicobacter pylori.  The proteins are 190-240 amino acids long, with the C terminus being the most conserved region, containing three conserved histidines.  This motif is similar to that found in Zinc proteases, suggesting that this family may also be proteases.. 
PF04313 DUF450; <br>Type I restriction enzyme R protein N terminus (HSDR_N). This family consists of a number of N terminal regions found in type I restriction enzyme R (HSDR) proteins. Restriction and modification (R/M) systems are found in a wide variety of prokaryotes and are thought to protect the host bacterium from the uptake of foreign DNA  . Type I restriction and modification systems are encoded by three genes: hsdR, hsdM, and hsdS. The three polypeptides, HsdR, HsdM, and HsdS, often assemble to give an enzyme (R2M2S1) that modifies hemimethylated DNA and restricts unmethylated DNA  .. 
PF04301 Protein of unknown function (DUF452)<br>
PF04303 DUF453;<br>PrpF is a protein found in the 2-methylcitrate pathway. It is structurally similar to DAP epimerase and proline racemase. This protein is likely to acts to isomerise trans-aconitate to cis-aconitate  .. 
PF04304 Protein of unknown function (DUF454)<br>Predicted membrane protein.. 
PF04305 Protein of unknown function (DUF455)<br>
PF04306 Protein of unknown function (DUF456)<br>This family is a putative membrane protein that contains glycine zipper motifs  .. 
PF04307 Predicted membrane-bound metal-dependent hydrolase (DUF457)<br>Family of predicted membrane-bound metal-dependent hydrolases, based on Swiss:Q97LP7. May act as phospholipases.. 
PF04308 Protein of unknown function (DUF458) <br>Family of uncharacterised eubacterial proteins.. 
PF04311 Protein of unknown function (DUF459)<br>Putative periplasmic protein.. 
PF01864 Putative integral membrane protein DUF46<br>This archaebacterial protein has no known function. It contains several predicted transmembrane regions, suggesting it is an integral membrane protein.. 
PF04312 Protein of unknown function (DUF460)<br>Archaeal protein of unknown function.. 
PF04314 Protein of unknown function (DUF461)<br>Putative membrane or periplasmic protein.. 
PF04315 Protein of unknown function, DUF462<br>This family consists of bacterial proteins of uncharacterised function.. 
PF04317 YcjX-like family, DUF463<br>These proteins possess a P-loop motif.. 
PF04327 Protein of unknown function (DUF464)<br>
PF04325 Protein of unknown function (DUF465)<br>Family members are found in small bacterial proteins, and also in the heavy chains of eukaryotic myosin and kinesin, C terminal of the motor domain (Myosin Pfam:PF00063, Kinesin Pfam:PF00225). Members of this family may form coiled coil structures.. 
PF04328 Protein of unknown function (DUF466)<br>Small bacterial protein of unknown function. Structural modelling suggests this domain may bind nucleic acids  .. 
PF04326 DUF467; AAA_div; <br>Divergent AAA domain. This family is related to the Pfam:PF00004 family, and presumably has the same function (ATP-binding).. 
PF04318 Protein of unknown function (DUF468) <br>These conserved ORFs probably are probably not translated into protein [Personal communication, Val Wood].. 
PF04320 Protein with unknown function (DUF469)<br>Family of bacteria protein with no known function.. 
PF01865 DUF47; <br>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 Swiss:O30498. However, the function of this protein is also unknown (Pit stands for Phosphate transport). It is probably distantly related to Pfam:PF01895 (personal obs:Yeats C).. 
PF04322 Protein of unknown function (DUF473)<br>Family of uncharacterised Archaeal proteins.. 
PF04536 DUF477; Repair_PSII; Phosphatase;<br>TLP18.3, Psb32 and MOLO-1 founding proteins of phosphatase. COG1512 & Pfam-B_18715 (release 10.0). This family has a Rossmann-like fold. It has phosphatase activity  .. 
PF04334 Protein of unknown function (DUF478)<br>This family contains uncharacterised protein encoded on Trypanosoma kinetoplast minicircles.. 
PF04336 Protein of unknown function, DUF479<br>This family includes several bacterial proteins of uncharacterised function.. 
PF01867 DUF48;<br>CRISPR associated protein Cas1. Clustered regularly interspaced short palindromic repeats (CRISPRs) are a family of DNA direct repeats found in many prokaryotic genomes. This family of proteins corresponds to Cas1, a CRISPR-associated protein.  Cas1 may be involved in linking DNA segments to CRISPR  .. 
PF04337 Protein of unknown function, DUF480<br>This family consists of several proteins of uncharacterised function.. 
PF04338 Protein of unknown function, DUF481<br>This family includes several proteins of uncharacterised function.. 
PF04339 Protein of unknown function, DUF482<br>This family contains several proteins of uncharacterised function.. 
PF04467 Protein of unknown function (DUF483)<br>Family of uncharacterised prokaryotic proteins.. 
PF04340 Protein of unknown function, DUF484<br>This family consists of several proteins of uncharacterised function.. 
PF04341 Protein of unknown function, DUF485<br>This family includes several putative integral membrane proteins.. 
PF04342 Protein of unknown function, DUF486<br>This family contains several proteins of uncharacterised function.. 
PF04343 Protein of unknown function, DUF488<br>This family includes several proteins of uncharacterised function.. 
PF04356 Protein of unknown function (DUF489)<br>Protein of unknown function, cotranscribed with purB in Escherichia coli, but with function unrelated to purine biosynthesis  .. 
PF04357 Family of unknown function (DUF490)<br>
PF04361 Protein of unknown function (DUF494)<br>Members of this family of uncharacterised proteins are often named Smg.. 
PF04362 DUF495; <br>Bacterial Fe(2+) trafficking. This is a family of bacterial Fe(2+) trafficking proteins.. 
PF04363 Protein of unknown function (DUF496)<br>
PF04365 Protein of unknown function (DUF497)<br>
PF04430 Protein of unknown function (DUF498/DUF598)<br>This is a large family of uncharacterised proteins found in all domains of life.  The structure shows a novel fold with three beta sheets.  A dimeric form is found in the crystal structure. It was suggested that the cleft in between the two monomers might bing nucleic acid  .. 
PF00674 DUP family<br>Pfam-B_99 (release 2.1). This family consists of several yeast proteins of unknown functions.  Swiss-prot annotates these as belonging to the DUP family. Several members of this family contain an internal duplication of this region.. 
PF04465 Protein of unknown function (DUF499)<br>Family of uncharacterised hypothetical prokaryotic proteins.. 
PF04366 Family of unknown function (DUF500)<br>Proteins in this family often also contain an SH3 domain (Pfam:PF00018), or a FYVE zinc finger (Pfam:PF01363).. 
PF04417 Protein of unknown function (DUF501)<br>Family of uncharacterised bacterial proteins.. 
PF04367 Protein of unknown function (DUF502)<br>Predicted to be an integral membrane protein.. 
PF04456 Protein of unknown function (DUF503)<br>Family of hypothetical bacterial proteins.. 
PF04457 Protein of unknown function (DUF504)<br>Family of uncharacterised proteins.. 
PF04458 Protein of unknown function (DUF505)<br>Family of uncharacterised prokaryotic proteins.. 
PF04368 Protein of unknown function (DUF507)<br>Bacterial protein of unknown function.. 
PF04370 Domain of unknown function (DUF508) <br>This is a family of uncharacterised proteins from C. elegans.. 
PF01871 DUF51; <br>This family consists of several AMMECR1 as well as several uncharacterised proteins. The contiguous gene deletion syndrome AMME is characterised by Alport syndrome, midface hypoplasia, mental retardation and elliptocytosis and is caused by a deletion in Xq22.3, comprising several genes including COL4A5, FACL4 and AMMECR1  . This family contains sequences from several eukaryotic species as well as archaebacteria and it has been suggested that the AMMECR1 protein may have a basic cellular function, potentially in either the transcription, replication, repair or translation machinery  .. 
PF04459 Protein of unknown function (DUF512)<br>Family of uncharacterised prokaryotic proteins.. 
PF04375 DUF513; <br>This family consists of several bacterial HemX proteins. The hemX gene is not essential for haem synthesis in B. subtilis. HemX is a polytopic membrane protein which by an unknown mechanism down-regulates the level of HemA  .. 
PF04415 Protein of unknown function (DUF515)    <br>Family of hypothetical Archaeal proteins.. 
PF04414 DUF516; <br>D-aminoacyl-tRNA deacylase. Several aminoacyl-tRNA synthetases have the ability to transfer the D-isomer of their amino acid onto their cognate tRNA. D-aminoacyl-tRNA deacylases hydrolyse the ester bond between the polynucleotide and the D-amino acid, thereby preventing the accumulation of such mis-acylated and metabolically inactive tRNA molecules.. 
PF04378 DUF519;<br>Ribosomal RNA small subunit methyltransferase D, RsmJ. RsmJ is the tenth to be found of the ten methyltransferases required for full methylation of 16S ribosomal RNA (rRNA). It specifically methylates m(2)G1516. A strain of E.coli lacking RsmJ due to deletion of the rsmJ(yhiQ) gene is missing the methyl group at G1516 and exhibits a cold-sensitive phenotype.. 
PF04461 Protein of unknown function (DUF520)<br>Family of uncharacterised proteins.. 
PF04412 Protein of unknown function (DUF521)<br>Family of hypothetical proteins.. 
PF04463 Protein of unknown function (DUF523)<br>Family of uncharacterised bacterial proteins.. 
PF04411 Protein of unknown function (DUF524)<br>This domain has been identified as a member of the PD-(D/E)XK nuclease superfamily through transitive meta profile searches  .  The domain has two additional beta-strands inserted to the core fold after the first core alpha-helix.\.       It has been speculated that it could function as s methylation-dependent restriction  .. 
PF04379 Protein of unknown function (DUF525)<br>Members of this family include the bacterial protein ApaG and the C termini of some F-box proteins (Pfam:PF00646).  F-box proteins contain a carboxyl-terminal domain that interacts with protein substrates  , so this family may be involved in protein-protein interaction.  The function of ApaG proteins is unknown, but mutations in the Salmonella typhimurium ApaG homologue corD gives a phenotype of low-level cobalt resistance and decreased magnesium efflux by effects on the CorA magnesium transport system  .. 
PF04380 DUF526;<br>Membrane fusogenic activity. BMFP consists of two structural domains, a coiled-coil C-terminal domain via which the protein self-associates as a trimer, and an N-terminal domain disordered at neutral pH but adopting an amphipathic alpha-helical structure in the presence of phospholipid vesicles, high ionic strength, acidic pH or SDS. BMFP interacts with phospholipid vesicles though the predicted amphipathic alpha-helix induced in the N-terminal half of the protein and promotes aggregation and fusion of vesicles in vitro.. 
PF04384 DUF528;<br>Iron-sulphur cluster assembly. This family of proteins is likely to be involved in the assembly of iron-sulphur clusters. It may function as an adaptor protein. In Escherichia coli Swiss:P0C0L9 forms part of the isc operon, which encodes genes involved in iron-sulphur cluster assembly. Its structure is entirely alpha helical, and it contains a modified wing-helix structure, usually found in DNA-binding proteins. It binds to Fe2+ and Fe3+ ions and to the cysteine desulfurase IscS, the same surface of the protein is involved in both binding to iron and to IscS [1,2].. 
PF04385 DUF529; <br>Domain of unknown function, DUF529. This family represents a repeated region found in several Theileria parva proteins. The repeat is normally about 70 residues long and contains a conserved aromatic  residue in the middle. . 
PF04409 Protein of unknown function (DUF530)<br>Family of hypothetical archaeal proteins.. 
PF04407 Protein of unknown function (DUF531)<br>Family of hypothetical archaeal proteins.. 
PF04391 Protein of unknown function (DUF533)<br>Some family members may be secreted or integral membrane proteins.. 
PF04392 DUF534; <br>ABC transporter substrate binding protein. This family contains many hypothetical proteins and some ABC transporter substrate binding proteins.. 
PF04393 Protein of unknown function (DUF535)<br>Family member Shigella flexneri VirK (Swiss:Q99QA5) is a virulence protein required for the expression, or correct membrane localisation of IcsA  (VirG) on the bacterial cell surface  ,  . This family also includes Pasteurella haemolytica lapB (Swiss:P32181),  which is thought to be membrane-associated.. 
PF04394 Protein of unknown function, DUF536<br>Pfam-B_2107 (release 7.3). This family aligns the C-terminal region from several bacterial proteins of unknown function that may be involved in a theta-type replication mechanism.. 
PF04398 Protein of unknown function, DUF538<br>Pfam-B_2637 (release 7.3). This family consists of several plant proteins of unknown function.. 
PF04400 Protein of unknown function (DUF539)<br>Putative periplasmic protein.. 
PF01877 DUF54;<br>PH1010 Swiss:O58738 is composed of five alpha-helices (1-5) and eight beta-strands (1-8) with the following topology: beta-1, alpha-1, beta-2, beta-3, alpha-2, alpha-3, beta-4, beta-5, alpha-4, beta-6, alpha-5, beta-7, beta-8. The first six beta-strands (1-6) form a slightly twisted antiparallel beta-sheet and face five alpha-helices on one side. The last two beta-strands form an antiparallel beta-sheet in the C-terminus. PH1010 forms a characteristic homodimer structure in the crystal.\.       Dimerisation of the molecule is crucial for function. The structure resembles that of some ribosomal proteins such as the 50S ribosomal protein L5  . Although the structure resembles that of the RRM-type RNA-binding domain of the ribosomal L5 protein, the residues involved in RNA-binding in the L5 protein are not conserved in this family  . Despite this, these proteins bind to double-stranded RNA in a non-sequence specific manner  .. 
PF04402 DUF541; <br>Protein of unknown function (DUF541). Members of this family have so far been found in bacteria and mouse SwissProt or TrEMBL entries.  However possible family members have also been identified in translated rat (Genbank:AW144450) and human (Genbank:AI478629) ESTs. A mouse family member has been named SIMPL (signalling molecule that associates with mouse pelle-like kinase).  SIMPL appears to facilitate and/or regulate complex formation between IRAK/mPLK (IL-1 receptor-associated kinase) and IKK (inhibitor of kappa-B kinase) containing complexes, and thus regulate NF-kappa-B activity  . Separate experiments demonstrate that a mouse family member (named LaXp180) binds the Listeria monocytogenes surface protein ActA, which is a virulence factor that induces actin polymerisation. It may also bind stathmin, a protein involved in signal transduction and in the regulation of microtubule dynamics  . In bacteria its function is unknown, but it is thought to be located in the periplasm or outer membrane.. 
PF04418 Domain of unknown function (DUF543)<br>This family of short eukaryotic proteins has no known function. Most of the members of this family are only 80 amino acid residues long.  However the Arabidopsis homologue is over 300 residues long.  The presumed domain contains a conserved amino terminal cysteine and a conserved motif GXGXGXG in the carboxy terminal half that may be functionally important.. 
PF04424 Protein of unknown function (DUF544)     <br>Eukaryotic protein of unknown function.. 
PF04440 DUF546; <br>Dysbindin (Dystrobrevin binding protein 1). Pfam-B_3919 (release 7.5). Dysbindin is an evolutionary conserved 40-kDa coiled-coil-containing protein that binds to alpha- and beta-dystrobrevin in muscle and brain. Dystrophin and alpha-dystrobrevin are co-immunoprecipitated with dysbindin, indicating that dysbindin is DPC-associated in muscle. Dysbindin co-localises with alpha-dystrobrevin at the sarcolemma and is up-regulated in dystrophin-deficient muscle. In the brain, dysbindin is found primarily in axon bundles and especially in certain axon terminals, notably mossy fibre synaptic terminals in the cerebellum and hippocampus. Dysbindin may have implications for the molecular pathology of Duchenne muscular dystrophy and may provide an alternative route for anchoring dystrobrevin and the DPC to the muscle membrane  . Genetic variation in the  human dysbindin gene is also thought to be associated with Schizophrenia  .. 
PF04445 DUF548;<br>Putative SAM-dependent methyltransferase. This is a family of putative SAM-dependent methyltransferases.. 
PF04446 DUF549; <br>tRNAHis guanylyltransferase. The Thg1 protein from Saccharomyces cerevisiae is responsible for adding a GMP residue to the 5' end of tRNA His  . The catalytic domain Thg1 contains a RRM (ferredoxin) fold palm domain, just like the viral RNA-dependent RNA polymerases, reverse transcriptases, family A and B DNA polymerases, adenylyl cyclases,  diguanylate cyclases (GGDEF domain) and the predicted polymerase of the CRISPR system  . Thg1 possesses an active site with three  acidic residues that chelate Mg++ cations  . Thg1 catalyzes  polymerization similar to the 5'-3' polymerases   .. 
PF01878 DUF55;<br>This domain was formerly known as DUF55.  Crystal structures have shown that this domain is part of the PUA superfamily. This domain has been named EVE and is thought to be RNA-binding  .. 
PF04447 Protein of unknown function (DUF550)<br>This family is found in a range of Proteobacteria and a few P-22 dsDNA virus particles. The function is currently not known.. 
PF04448 Protein of unknown function (DUF551)   <br>This family represents the carboxy terminus of a protein of unknown  function, found in dsDNA viruses with no RNA stage, including  bacteriophages lambda and P22, and also in some Escherichia coli prophages.. 
PF04472 Protein of unknown function (DUF552)<br>Family of uncharacterised proteins.. 
PF04473 Transglutaminase-like domain<br>This family of uncharacterised archaeal proteins are related to Transglutaminase-like domains. This family has previously been called DUF553 and UPF0252.. 
PF04474 Protein of unknown function (DUF554)<br>Family of uncharacterised prokaryotic proteins.  Multiple predicted transmembrane regions suggest that the region is membrane associated. . 
PF04475 Protein of unknown function (DUF555)<br>Family of uncharacterised, hypothetical archaeal proteins. . 
PF04476 Protein of unknown function (DUF556)<br>Family of uncharacterised, hypothetical prokaryotic proteins.. 
PF04452 DUF558; <br>RNA methyltransferase. RNA methyltransferases modify nucleotides during ribosomal RNA maturation in a site-specific manner.  The Escherichia coli member is specific for U1498 methylation   .. 
PF04480 Protein of unknown function (DUF559)<br>
PF04575 Protein of unknown function (DUF560)<br>Pfam-B_4010 (release 7.5). Family of hypothetical bacterial proteins. . 
PF04481 Protein of unknown function (DUF561)<br>Protein of unknown function found in a cyanobacterium, and the chloroplasts of algae.. 
PF04763 Protein of unknown function (DUF562)<br>Pfam-B_6057 (release 7.5). Family of uncharacterised proteins.. 
PF04577 Protein of unknown function (DUF563)<br>Pfam-B_4026 (release 7.5). Family of uncharacterised proteins.. 
PF04483 Protein of unknown function (DUF565)<br>Predicted transmembrane protein found in plants, chloroplasts and cyanobacteria.  This family is also known as YCF20.. 
PF04525 DUF567;<br>Pfam-B_4998 (release 7.5). The structure of this family has been solved. It comprises a 12-stranded beta barrel with a central C-terminal alpha helix. This helix is thought to be a transmembrane helix. It is structurally similar to the C-terminal domain of the Tubby protein  . In plants it plays a role in defense against pathogens  .. 
PF04601 Protein of unknown function (DUF569)<br>Pfam-B_4902 (release 7.5). Family of hypothetical proteins. Some family members contain a two copies of the region.. 
PF01881 DUF57;<br>CRISPR associated protein Cas6. This group of families is one of several protein families that are always found associated with prokaryotic CRISPRs, themselves a family of clustered regularly interspaced short palindromic repeats, DNA repeats found in nearly half of all bacterial and archaeal genomes. These DNA repeat regions have a remarkably regular structure: unique sequences of constant size, called spacers, sit between each pair of repeats  . It has been shown that the CRISPRs are virus-derived sequences acquired by the host to enable them to resist viral infection. The Cas proteins from the host use the CRISPRs to mediate an antiviral response. After transcription of the CRISPR, a complex of Cas proteins termed Cascade cleaves a CRISPR RNA precursor in each repeat and retains the cleavage products containing the virus-derived sequence. Assisted by the helicase Cas3, these mature CRISPR RNAs then serve as small guide RNAs that enable Cascade to interfere with virus proliferation  . Cas5 contains an endonuclease motif, whose inactivation leads to loss of resistance, even in the presence of phage-derived spacers  .. 
PF04489 Protein of unknown function (DUF570)    <br>Protein of unknown function, found in herpesvirus and cytomegalovirus.. 
PF04672 DUF574;<br>S-adenosyl methyltransferase. Pfam-B_4601 (release 7.5). This family contains a SAM (S-adenosyl methyltransferase) domain, with a central beta sheet with 3 alpha-helices on both sides. Crystal packing analysis of the structure PDB:3giw from Swiss:Q82L35 suggests that a monomer is the solution state oligomeric form. An unidentified ligand (UNL, cyan) was found at the putative active site surrounded by the residues His57, His170, Phe171, Tyr216 and Met22 . The UNL is likely to be a phenylalanine or phenylalanine-like molecule. (details derived from TOPSAN).. 
PF04746 Protein of unknown function (DUF575)<br>Pfam-B_6048 (release 7.5). Family of uncharacterised proteins.  Contains several chlamydial members. . 
PF04507 Protein of unknown function, DUF576<br>Pfam-B_2120 (release 7.5). This family contains several uncharacterised staphylococcal proteins.. 
PF04510 Family of unknown function (DUF577)<br>Pfam-B_3938 (release 7.5). Family of Arabidopsis thaliana proteins.  Many of these members contain a repeated region.. 
PF04669 DUF579;<br>Polysaccharide biosynthesis. Pfam-B_4574 (release 7.5). This family of proteins plays a role in xylan biosynthesis in plant cell walls. Its precise role in xylan biosynthesis is unknown [1,2]. Its function in other organisms is unknown.. 
PF01882 Protein of unknown function DUF58<br>This family of prokaryotic proteins have no known function. Swiss:P71138 a protein of unknown function in the family has been misannotated as alpha-dextrin 6-glucanohydrolase.. 
PF04515 DUF580; <br>Plasma-membrane choline transporter. Mifsud W, Pollington J. Pfam-B_2258 (release 7.5). This family represents a high-affinity plasma-membrane choline transporter in C.elegans which is thought to be rate-limiting for ACh synthesis in cholinergic nerve terminals  .. 
PF04570 Protein of unknown function (DUF581)<br>Pfam-B_4765 (release 7.5). Family of uncharacterised proteins.. 
PF04518 DUF582;<br>Effector from type III secretion system. Mifsud W, Eberhardt R. Pfam-B_2447 (release 7.5). This is a family of effector proteins which are secreted by the type III secretion system [1,2]. The precise function of this family is unknown.. 
PF04519 DUF583;<br>Polymer-forming cytoskeletal. Pfam-B_2455 (release 7.5). This is a family of bactofilins, a functionally diverse class of cytoskeletal, polymer-forming, proteins that is widely conserved among bacteria. In the example species C. crescentus, two bactofilins assemble into a membrane-associated laminar structure that shows cell-cycle-dependent polar localisation and acts as a platform for the recruitment of a cell wall biosynthetic enzyme involved in polar morphogenesis. Bactofilins display distinct subcellular distributions and dynamics in different bacterial species, suggesting that they are versatile structural elements that have adopted a range of different cellular functions.. 
PF04520 DUF584;<br>Senescence regulator. Pfam-B_2571 (release 7.5). This protein regulates the expression of proteins associated with leaf senescence in plants [1,2].. 
PF04522 Protein of unknown function (DUF585)<br>This region represents the N terminus of bromovirus 2a protein, and is always found N terminal to a predicted RNA-dependent RNA polymerase region (Pfam:PF00978).. 
PF04532 Protein of unknown function (DUF587)<br>This family consists of the N termini of some human herpesvirus U58 proteins, and some cytomegalovirus UL87 proteins. This region is always found N terminal to the Pfam family UL87 (Pfam:PF03043), which has no known function.. 
PF04569 Protein of unknown function<br>Pfam-B_2799 (release 7.5). This family represents a conserved region in a number of uncharacterised plant proteins.. 
PF04574 Protein of unknown function (DUF592)<br>This region is found in some SIR2 family proteins (Pfam:PF02146).. 
PF04578 Protein of unknown function, DUF594<br>Pfam-B_2859 (release 7.5). 
PF04591 Protein of unknown function, DUF596<br>Pfam-B_5061 (release 7.5). This family contains several uncharacterised proteins.. 
PF04640 DUF597; <br>PLATZ transcription factor. Mifsud W, Riaño-Pachón D, Mistry J. Pfam-B_5458 (release 7.5). Plant AT-rich sequence and zinc-binding proteins (PLATZ) are zinc dependant DNA binding proteins.  They bind to AT rich sequences and functions in transcriptional repression  .. 
PF04654 Protein of unknown function, DUF599<br>Pfam-B_5550 (release 7.5). This family includes several uncharacterised proteins.. 
PF00892 DUF6;<br>EamA-like transporter family. Pfam-B_177 (release 3.0). This family includes many hypothetical membrane proteins of unknown function.\.       Many of the proteins contain two copies of the aligned region. The family used to be known as DUF6.. 
PF04634 Protein of unknown function, DUF600<br>Pfam-B_5411 (release 7.5). This conserved region is found in several uncharacterised proteins from Gram positive bacteria.. 
PF04645 Protein of unknown function, DUF603<br>Pfam-B_5498 (release 7.5). This family includes several uncharacterised proteins from Borrelia species.. 
PF04646 Protein of unknown function, DUF604<br>Pfam-B_5503 (release 7.5). This family includes a conserved region found in several uncharacterised plant proteins.. 
PF04657 Protein of unknown function, DUF606<br>Pfam-B_5554 (release 7.5). This family includes several uncharacterised bacterial proteins.. 
PF01886 Protein of unknown function DUF61<br>Protein found in Archaebacteria. These proteins have no known  function.. 
PF04748 DUF610; div_psaccdeacet; <br>Divergent polysaccharide deacetylase. Pfam-B_5949 (release 7.5). This family is divergently related to Pfam:PF01522 (personal obs:Yeats C).. 
PF04764 Protein of unknown function (DUF613)<br>Pfam-B_6084 (release 7.5). Family of chloroplast proteins of unknown function.  Some members have two copies of the conserved region.. 
PF04751 Protein of unknown function (DUF615)<br>This family of bacterial proteins has no known function.. 
PF04765 Protein of unknown function (DUF616)<br>Pfam-B_6152 (release 7.5). Family of uncharacterised proteins.. 
PF04768 Protein of unknown function (DUF619)<br>This region of unknown function is found at the C-terminus of Neurospora crassa acetylglutamate synthase (amino-acid acetyltransferase, EC: 2.3.1.1) (Swiss:Q12643).  It is also found C-terminal to the amino acid kinase  region (Pfam:PF00696) in some fungal acetylglutamate kinase enzymes.. 
PF01887 DUF62;<br>S-adenosyl-l-methionine hydroxide adenosyltransferase. This is a family of proteins, previously known as DUF62, found in archaebacteria and bacteria. The structure of proteins in this family is similar to that of a bacterial fluorinating enzyme  . S-adenosyl-l-methionine hydroxide adenosyltransferases utilises a rigorously conserved amino acid side chain triad (Asp-Arg-His) which may have a role in activating water to hydroxide ion  . This family used to be known as DUF62.. 
PF04788 Protein of unknown function (DUF620)<br>Pfam-B_6213 (release 7.5). Family of uncharacterised proteins.. 
PF04822 DUF622;<br>Mifsud W, Eberhardt R. Pfam-B_3835 (release 7.6). This domain is named takusan, which is a Japanese word meaning 'many'. Members of this family regulate synaptic activity  .. 
PF04844 DUF623;<br>Transcriptional repressor, ovate. Mifsud W, Eberhardt R. Pfam-B_4487 (release 7.6). This is a family of transcriptional repressors. In plants, these proteins are important regulators of growth and development [1,2].. 
PF04854 Protein of unknown function, DUF624<br>Pfam-B_4640 (release 7.6). This family includes several uncharacterised bacterial proteins.. 
PF04776 Protein of unknown function (DUF626)<br>Pfam-B_2357 (release 7.6). Protein of unknown function, currently only identified in Brassicaceae.. 
PF04781 Protein of unknown function (DUF627)<br>Pfam-B_2475 (release 7.6). This family represents the N-terminal region of several plant proteins of unknown function.. 
PF04780 Protein of unknown function (DUF629)<br>Pfam-B_2475 (release 7.6). This family represents a region of several plant proteins of unknown  function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.. 
PF01889 Membrane protein of unknown function DUF63<br>Proteins found in Archaebacteria of unknown function. These proteins are probably transmembrane proteins.. 
PF04816 Family of unknown function (DUF633) <br>Pfam-B_5077 (release 7.6). This family of proteins are uncharacterised have no known function.. 
PF04827 DUF635; <br>Plant transposon protein. Pfam-B_2859 (release 7.6). This family contains plant transposases which are putative members of the PIF / Ping-Pong family   .. 
PF04828 DUF636; <br>Glutathione-dependent formaldehyde-activating enzyme. Pfam-B_2779 (release 7.6). 
PF04830 Possible hemagglutinin (DUF637)<br>Pfam-B_2732 (release 7.6). This family represents a conserved region found in a bacterial protein which may be a hemagglutinin or hemolysin.. 
PF04829 DUF638;<br>Pre-toxin domain with VENN motif. Pfam-B_2732 (release 7.6). This family represents a conserved region found in many bacterial porlymorphic toxins which is located before the C-terminal toxin modules   .. 
PF04842 Plant protein of unknown function (DUF639)<br>Pfam-B_6010 (release 7.6). Plant protein of unknown function.. 
PF04852 Protein of unknown function (DUF640)<br>Pfam-B_6053 (release 7.6). This family represents a conserved region found in plant  proteins including Resistance protein-like protein (Swiss:O49468).. 
PF04862 Protein of unknown function (DUF642)<br>Pfam-B_4723 (release 7.6). This family represents a duplicated conserved region found in a number of uncharacterised plant proteins, potentially in the stem. There is a conserved CGP sequence motif.. 
PF04867 Protein of unknown function (DUF643)<br>Pfam-B_6086 (release 7.6). Protein of unknown function found in Borrelia burgdorferi, the Lyme disease spirochete.. 
PF04870 DUF644;<br>Mifsud W, Eberhardt R. Pfam-B_4889 (release 7.6). This family of proteins plays a role in the moulting cycle of nematodes, which involves the synthesis of a new collagen-rich cuticle underneath the existing cuticle and the subsequent removal of the old cuticle  .. 
PF04875 Protein of unknown function, DUF645<br>Mifsud W, Eberhardt R, Haft D. Pfam-B_4997 (release 7.6). This family includes several uncharacterised proteins from Vibrio cholerae. There is some doubt regarding the existence of these proteins, they are encoded by open reading frames contained within a repeated region in the Vibrio superintegron.. 
PF04883 DUF646;<br>Bacteriophage HK97-gp10, putative tail-component. Pfam-B_6160 (release 7.6). This family of proteins is found in the caudovirales.  It may be a tail component.. 
PF04890 Family of unknown function (DUF648) <br>Pfam-B_5530 (release 7.6). Family of hypothetical Chlamydia proteins.  This family may well comprise of two domains, as some members only match the N-terminus. . 
PF04894 Archaeal protein of unknown function (DUF650)<br>Pfam-B_6199 (release 7.6). This family represents the amino terminal region of an archaeal protein of unknown function.. 
PF04895 Archaeal protein of unknown function (DUF651)<br>Pfam-B_6199 (release 7.6). This family represents the carboxy terminal region of an archaeal protein of unknown function.. 
PF04910 DUF654;<br>Transcriptional repressor TCF25. Mifsud W, Eberhardt R. Pfam-B_6652 (release 7.6). Members of this family are transcriptional repressors. They may act by increasing histone deacetylase activity at promoter regions  .. 
PF04919 Protein of unknown function (DUF655)<br>Pfam-B_6697 (release 7.6). This family includes several uncharacterised archaeal proteins. This protein appears to contain two HHH motifs.. 
PF04920 Family of unknown function (DUF656) <br>Pfam-B_5777 (release 7.6). A family of hypothetical proteins from Beet necrotic yellow vein virus.. 
PF04936 Protein of unknown function (DUF658)<br>Pfam-B_5062 (release 7.6). Protein of unknown function found in Lactococcus lactis bacteriophages.. 
PF04937 Protein of unknown function (DUF 659)<br>Pfam-B_5061 (release 7.6). Transposase-like protein with no known function.. 
PF04939 DUF660; <br>Ribosome biogenesis regulatory protein (RRS1). Pfam-B_6906 (release 7.6). This family consists of several eukaryotic ribosome biogenesis regulatory (RRS1) proteins. RRS1 is a nuclear protein that is essential for the maturation of 25 S rRNA and the 60 S ribosomal subunit assembly in Saccharomyces cerevisiae  .. 
PF04978 Protein of unknown function (DUF664)<br>Pfam-B_5281 (release 7.6). This family is commonly found in Streptomyces coelicolor and is of unknown  function. These proteins contain several conserved histidines at their N-terminus that may form a metal binding site.. 
PF05006 Protein of unknown function (DUF666)<br>Pfam-B_5319 (release 7.6). This family contains several uncharacterised viral proteins.. 
PF05018 Protein of unknown function (DUF667)<br>This family of proteins are highly conserved in eukaryotes. Some proteins in the family are annotated as transcription factors. However, there is currently no support for this in the literature.. 
PF05003 Protein of unknown function (DUF668)<br>Pfam-B_4700 (release 7.6). Uncharacterised plant protein.. 
PF05037 Protein of unknown function (DUF669)<br>Pfam-B_5014 (release 7.7). Members of this family are found in various phage proteins.. 
PF05050 DUF672;<br>Methyltransferase FkbM domain. Pfam-B_5811 (release 7.7). This family has members from bacteria to human, and appears to be a methyltransferase.. 
PF05054 Protein of unknown function (DUF673)<br>Pfam-B_5918 (release 7.7). Family of uncharacterised viral proteins.. 
PF05056 Protein of unknown function (DUF674)<br>Pfam-B_5937 (release 7.7). This family is found in Arabidopsis thaliana and contains several uncharacterised proteins.. 
PF05055 Protein of unknown function (DUF677)<br>Pfam-B_5920 (release 7.7). This family consists of AT14A like proteins from Arabidopsis thaliana. At14a has a small domain that has sequence similarities to integrins from fungi, insects and humans. Transcripts of At14a are found in all  Arabidopsis tissues and localises partly to the plasma membrane  .. 
PF05077 Protein of unknown function (DUF678)<br>Pfam-B_6127 (release 7.7). This family contains several poxvirus proteins of unknown function.. 
PF05078 Protein of unknown function (DUF679)<br>Pfam-B_6129 (release 7.7). This family contains several uncharacterised plant proteins.. 
PF05079 Protein of unknown function (DUF680)<br>Pfam-B_6131 (release 7.7). This family contains several uncharacterised proteins which seem to be found exclusively in Rhizobium loti.. 
PF05080 Protein of unknown function (DUF681)<br>Pfam-B_6137 (release 7.7). This family contains several uncharacterised beak and feather disease virus proteins.. 
PF05081 Protein of unknown function (DUF682)<br>Pfam-B_6152 (release 7.7). This family consists if several uncharacterised baculovirus proteins.. 
PF05082 DUF683;<br>Moxon SJ, Eberhardt R. Pfam-B_6161 (release 7.7). This family contains several uncharacterised bacterial proteins. These proteins are found in nitrogen fixation operons so are likely to play some role in this process. They consist of two alpha helices which are joined by a four residue linker. The helices form an antiparallel bundle and cross towards their termini. They are likely to form a rod-like dimer  . They have structural similarity to the regulatory protein Rop, Pfam:PF01815.. 
PF05075 Protein of unknown function (DUF684)<br>Moxon SJ, Pollington J. Pfam-B_6081 (release 7.7). This family contains several uncharacterised proteins from Caenorhabditis elegans. The GO annotation suggests that the protein is involved in nematode larval development and has a positive regulation on growth rate.. 
PF05085 Protein of unknown function (DUF685)<br>Pfam-B_6261 (release 7.7). This family consists of several uncharacterised proteins from Borrelia burgdorferi (Lyme disease spirochete). There is some evidence to suggest that the proteins may be outer surface proteins.. 
PF05092 DUF686;<br>Pfam-B_6313 (release 7.7). This is a family of dsDNA Baculovirus proteins. It is required for the infectivity of the OBs or occlusion bodies. It is a structural protein of the ODV envelope required only in the first steps of per os larva infection, as viruses being produced in cells expressing the gene for this protein but not containing it in their genomes are able to produce successful infections. Baculoviruses are large DNA viruses that infect arthropods, mainly members of the order Lepidoptera. In their life cycle, they produce two kinds of particles, a budded, non-occluded virus (BV), which buds out of the infected cell and is responsible for the cell-to-cell transmission of the virus, and an occluded form, the occlusion body (OB), which is responsible for protecting the virus between encounters with larvae. A variable number of virions are included in the para-crystalline structure of the OB, mainly constituted by the virus-encoded polyhedrin protein; these virions are called occlusion body-derived virions or ODVs. . 
PF05095 Protein of unknown function (DUF687)<br>Pfam-B_6321 (release 7.7). This family contains several uncharacterised Chlamydia proteins.. 
PF05093 DUF689; <br>Cytokine-induced anti-apoptosis inhibitor 1, Fe-S biogenesis. Pfam-B_6320 (release 7.7), Wood V. Anamorsin, subsequently named CIAPIN1 for cytokine-induced anti-apoptosis inhibitor 1, in humans is the homologue of yeast Dre2, a conserved soluble eukaryotic Fe-S cluster protein, that functions in cytosolic Fe-S protein biogenesis. It is found in both the cytoplasm and in the mitochondrial intermembrane space (IMS)  .  CIAPIN1 is found to be up-regulated in hepatocellular cancer, is considered to be a downstream effector of the receptor tyrosine kinase-Ras signalling pathway, and is essential in mouse definitive haematopoiesis  . Dre2 has been found to interact with the yeast reductase Tah18, forming a tight cytosolic complex implicated in the response to high levels of oxidative stress  .. 
PF05148 DUF691; Methyltransf_hyp; <br>Hypothetical methyltransferase. Pfam-B_6432 (release 7.7). This family consists of several uncharacterised eukaryotic proteins which  are related to methyltransferases Pfam:PF01209.. 
PF05114 Protein of unknown function (DUF692)<br>Pfam-B_6476 (release 7.7). This family consists of several uncharacterised bacterial proteins.. 
PF05113 Protein of unknown function (DUF693)<br>Pfam-B_6473 (release 7.7). This family consists of several uncharacterised proteins from Borrelia  burgdorferi (Lyme disease spirochete).. 
PF05107 Family of unknown function (DUF694) <br>TIGRFAMs (release 2.0);. Family of hypothetical bacterial proteins.. 
PF05117 Family of unknown function (DUF695) <br>TIGRFAMs (release 2.0);. Family of uncharacterised bacterial proteins.. 
PF05128 Domain of unknown function (DUF697) <br>TIGRFAMs (release 2.0);. Family of bacterial hypothetical proteins that is sometimes associated with GTPase domains.. 
PF01901 Protein of unknown function  DUF70<br>Archaebacterial proteins of unknown function. Members of this family may be transmembrane proteins. . 
PF05142 Domain of unknown function (DUF702) <br>Members of this family are found in various putative zinc finger proteins.. 
PF05152 Protein of unknown function (DUF705)<br>Pfam-B_6448 (release 7.7). This family contains several uncharacterised Baculovirus proteins. . 
PF05153 Family of unknown function (DUF706) <br>Pfam-B_2804 (release 7.7). Family of uncharacterised eukaryotic function.  Some members have a described putative function, but a common theme is not evident.. 
PF05212 Protein of unknown function (DUF707)<br>Pfam-B_6598 (release 7.7). This family consists of several uncharacterised proteins from Arabidopsis thaliana.. 
PF05166 DUF709; <br>This family of proteins formerly called DUF709 includes the E. coli gene ycgL. Homologues of YcgL are found in gammaproteobacteria. The structure of this protein shows a novel alpha/beta/alpha sandwich structure  .. 
PF01902 DUF71; ATP_bind4;<br>This family of proteins probably binds ATP. This domain is about 200 amino acids long with a strongly conserved motif SGGKD at the N terminus.In some members of this family e.g. Swiss:Q12429, this domain is associated with Pfam:PF01042. . 
PF05164 DUF710; <br>Cell division protein ZapA. ZapA is a cell division protein which interacts with FtsZ.  FtsZ is part of a mid-cell cytokinetic structure termed the Z-ring that recruits a hierarchy of fission related proteins early in the bacterial cell cycle.  The interaction of FtsZ with ZapA drives its polymerisation and promotes FtsZ filament bundling thereby contributing to the spatio-temporal tuning of the Z-ring   .. 
PF05167 Uncharacterised ACR (DUF711)<br>The proteins in this family are functionally uncharacterised. The proteins are around 450 amino acids long. It is likely that this family represents a group of glycerol-3-phosphate dehydrogenases.. 
PF05168 DUF712; <br>
PF05206 DUF715; <br>Methyltransferase TRM13. Pfam-B_10143 (release 7.7). This is a family of eukaryotic proteins which are responsible for 2'-O-methylation of tRNA at position 4  .  TRM13 shows no sequence similarity to other known methyltransferases.. 
PF01904 Protein of unknown function DUF72<br>The function of this family is unknown.. 
PF01905 DUF73;<br>CRISPR-associated negative auto-regulator DevR/Csa2. This group of families is one of several protein families that are always found associated with prokaryotic CRISPRs, themselves a family of clustered regularly interspaced short palindromic repeats, DNA repeats found in nearly half of all bacterial and archaeal genomes. These DNA repeat regions have a remarkably regular structure: unique sequences of constant size, called spacers, sit between each pair of repeats  . It has been shown that the CRISPRs are virus-derived sequences acquired by the host to enable them to resist viral infection. The Cas proteins from the host use the CRISPRs to mediate an antiviral response. After transcription of the CRISPR, a complex of Cas proteins termed Cascade cleaves a CRISPR RNA precursor in each repeat and retains the cleavage products containing the virus-derived sequence. Assisted by the helicase Cas3, these mature CRISPR RNAs then serve as small guide RNAs that enable Cascade to interfere with virus proliferation  . Cas5 contains an endonuclease motif, whose inactivation leads to loss of resistance, even in the presence of phage-derived spacers  . This family used to be known as DUF73. DevR appears to be negative auto-regulator within the system  .. 
PF01906 DUF74;<br>Putative heavy-metal-binding. From comparative structural analysis, this family is likely to be a heavy-metal binding domain. The domain oligomerises as a pentamer. The domain is about 100 amino acids long and is found in prokaryotes.. 
PF01910 Domain of unknown function DUF77<br>Enright A, Ouzounis C, Cerutti L. Domain of unknown function.  The crystal structure of two of these members shows that this domain has a ferredoxin like fold and is  likely to exists as at least homodimers.  Sulphate ions are  are located at the dimer interfaces, which are thought to confer additional stability.  Although the function of this domain remains to be identified, its structure suggests a role in  protein-protein interactions possibly regulated by the binding of small-molecule ligands  .. 
PF01918 DUF78; <br>Alba is a novel chromosomal protein that coats archaeal DNA without compacting it.. 
PF01923 DUF80;<br>Cobalamin adenosyltransferase. Cobalamin adenosyltransferase This family contains the gene products of PduO and EutT which are both cobalamin adenosyltransferases. PduO is a protein with ATP:cob(I)alamin adenosyltransferase activity. The main role of this protein is the conversion of inactive cobalamins to AdoCbl for 1,2-propanediol degradation  .The EutT enzyme appears to be an adenosyl transferase, converting CNB12 to AdoB12  .. 
PF01925 DUF81;<br>Sulfite exporter TauE/SafE. Enright A & Pfam-B_3578 (Release 7.5). This is a family of integral membrane proteins where the alignment appears to contain two duplicated modules of three transmembrane helices. The proteins are involved in the transport of anions across the cytoplasmic membrane   during taurine metabolism as an exporter of sulfoacetate  . This family used to be known as DUF81.. 
PF01927 DUF82;<br>RNAse domain of the PIN fold   with an inserted Zinc Ribbon at the C terminus  .. 
PF01930 DUF83;<br>Domain of unknown function DUF83. This domain has no known function.  The domain contains three conserved cysteines at its C terminus.. 
PF01931 DUF84;<br>Protein of unknown function DUF84. The function of this prokaryotic protein family is unknown.. 
PF01934 Protein of unknown function DUF86<br>The function of members of this family is unknown.. 
PF01935 Domain of unknown function DUF87<br>The function of this prokaryotic domain is unknown. It contains several conserved aspartates and histidines that could be metal ligands.. 
PF01936 DUF88;<br>These domains are found in the eukaryotic proteins typified by the Nedd4-binding protein 1 and the bacterial YacP-like proteins (Nedd4-BP1, YacP nucleases; NYN domains). The NYN domain shares a common protein fold with two other previously characterized groups of nucleases, namely the PIN (PilT N-terminal) and FLAP/5' --> 3' exonuclease superfamilies. These proteins share a common set of 4 acidic conserved residues that are predicted to constitute their active site. Based on the conservation of the acidic residues and structural elements Aravind and colleagues suggest that PIN and NYN domains are likely to bind only a single metal ion, unlike the FLAP/5' --> 3' exonuclease superfamily, which binds two metal ions.  Based on conserved gene neighborhoods Aravind and colleagues infer that the bacterial members are likely to be components of the processome/degradsome that process tRNAs or ribosomal RNAs.. 
PF01937 Protein of unknown function DUF89<br>This family has no known function.. 
PF01939 Protein of unknown function DUF91<br>The function of this prokaryotic protein is unknown.. 
PF01940 Integral membrane protein DUF92<br>Members of this family have several predicted transmembrane helices.  The function of these prokaryotic proteins is unknown.. 
PF01941 DUF93; <br>S-adenosylmethionine synthetase (AdoMet synthetase). This family consists of several archaebacterial S-adenosylmethionine synthetase C(AdoMet synthetase or MAT) (EC 2.5.1.6). S-Adenosylmethionine (AdoMet) occupies a central role in the metabolism of all cells. The biological roles of AdoMet include acting as the primary methyl group donor, as a precursor to the polyamines, and as a progenitor of a 5'-deoxyadenosyl radical. S-Adenosylmethionine synthetase catalyses the only known route of AdoMet biosynthesis. The synthetic process occurs in a unique reaction in which the complete triphosphate chain is displaced from ATP and a sulfonium ion formed. MATs from various organisms contain ~400-amino acid polypeptide chains  . . 
PF01944 Integral membrane protein DUF95<br>Members of this family have several predicted transmembrane regions.  The function of this family is unknown.. 
PF01947 Protein of unknown function (DUF98)<br>This is a family of uncharacterised proteins.. 
PF01949 Protein of unknown function DUF99<br>The function of this archaebacterial protein family is unknown.. 
PF01207 UPF0034;<br>Dihydrouridine synthase (Dus). Members of this family catalyse the reduction of the 5,6-double bond of a uridine residue on tRNA.  Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archae.  Most dihydrouridines are found in the D loop of t-RNAs.  The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap.  Dus 1 (Swiss:Q9HGN6) from Saccharomyces cerevisiae acts on pre-tRNA-Phe, while Dus 2 (Swiss:P53720) acts on pre-tRNA-Tyr and pre-tRNA-Leu.  Dus 1 is active as a single subunit, requiring NADPH or NADH, and is stimulated by the presence of FAD  .  Some family members may be targeted to the mitochondria and even have a role in mitochondria  .. 
PF00692 dUTPase<br>Pfam-B_127 (release 2.1). dUTPase hydrolyses dUTP to dUMP and pyrophosphate.. 
PF02670 1-deoxy-D-xylulose 5-phosphate reductoisomerase<br>This is a family of 1-deoxy-D-xylulose 5-phosphate reductoisomerases.  This enzyme catalyses the formation of 2-C-methyl-D-erythritol 4-phosphate from 1-deoxy-D-xylulose-5-phosphate in the presence of NADPH  . This reaction is part of the terpenoid biosynthesis pathway.. 
PF00350 dynamin; <br>
PF04912 Dynamitin <br>Pfam-B_5757 (release 7.6). Dynamitin is a subunit of the microtubule-dependent motor complex and in implicated in cell adhesion by binding to macrophage-enriched myristoylated alanine-rice C kinase substrate (MacMARCKS)  .. 
PF01221 Dynein light chain type 1 <br>
PF00519 E1; <br>Papillomavirus helicase. Pfam-B_48 (release 1.0). This protein is a DNA helicase that is required for initiation of viral DNA replication.  This protein forms a complex with the E2 protein Pfam:PF00508.. 
PF00122 E1-E2 ATPase<br>
PF00676 E1_dehydrog; <br>Dehydrogenase E1 component. Pfam-B_117 (release 2.1). This family uses thiamine pyrophosphate as a cofactor. This family includes pyruvate dehydrogenase, 2-oxoglutarate dehydrogenase and 2-oxoisovalerate dehydrogenase.. 
PF00524 E1_N; <br>E1 Protein, N terminal domain. Pfam-B_98 (release 1.0). 
PF00511 E2_C; <br>E2 (early) protein, C terminal. Pfam-B_87 (release 1.0). 
PF00508 E2_N; <br>E2 (early) protein, N terminal. Pfam-B_76 (release 1.0). 
PF02319 E2F/DP family winged-helix DNA-binding domain<br>Pfam-B_8420 (release 5.2). 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 association with TDP1/2, the heterodimer having increased binding efficiency. The crystal structure of an E2F4-DP2-DNA complex shows  that the DNA-binding domains of the E2F and DP proteins both have a fold related to the winged-helix DNA-binding motif. Recognition of the central c/gGCGCg/c sequence of the consensus DNA-binding site is symmetric, and amino acids that contact these bases are conserved among all known E2F and DP proteins.. 
PF02817 e3_binding; <br>This family represents a small domain of the E2 subunit of 2-oxo-acid dehydrogenases responsible for the binding of the E3 subunit.. 
PF00518 Early Protein (E6)<br>Pfam-B_57 (release 1.0). 
PF00527 E7 protein, Early protein<br>Pfam-B_95 (release 1.0). 
PF00563 DUF2; <br>Alignment kindly provided by SMART. This domain is found in diverse bacterial signaling proteins.  It is called EAL after its conserved residues. The EAL domain is a good candidate for a diguanylate phosphodiesterase function  . The domain contains many conserved acidic residues  that could participate in metal binding and might form the phosphodiesterase active site  .. 
PF04157 EAP30/Vps36 family<br>Pfam-B_8830 (release 7.3);. This family includes EAP30 as well as the Vps36 protein. Vps36 is involved in Golgi to endosome trafficking.  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 transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity  .. 
PF01309 EAV_env_prot; <br>Equine arteritis virus small envelope glycoprotein . Pfam-B_656 (release 3.0). Equine arteritis virus small envelope glycoprotein (Gs) is a  class I transmembrane protein which adopts a number of different conformations. . 
PF02905 EBNA1; <br>Epstein Barr virus nuclear antigen-1, DNA-binding domain. This domain has a ferredoxin-like fold.. 
PF00378 Enoyl-CoA hydratase/isomerase family<br>This family contains a diverse set of enzymes including: Enoyl-CoA hydratase (Swiss:Q13011). Napthoate synthase (Swiss:P27290). Carnitate racemase (Swiss:P31551). 3-hydoxybutyryl-CoA dehydratase (Swiss:P52046). Dodecanoyl-CoA delta-isomerase (Swiss:P42126).. 
PF04736 Eclosion hormone<br>Eclosion hormone is an insect neuropeptide that triggers the performance of ecdysis behaviour, which causes shedding of the old cuticle at the end of a molt  ,  .. 
PF02963 Restriction endonuclease EcoRI<br>
PF03974 Ecotin<br>Pfam-B_54504 (release 7.2). Ecotin is a broad range serine protease inhibitor, which forms homodimers. The C-terminal region contains the dimerisation motif  . Interestingly, the binding sites show a fluidity of protein contacts binding sites show a fluidity of protein contacts derived from ecotin's  innate flexibility in fitting itself to proteases while [4,5].. 
PF00736 EF1BD; <br>EF-1 guanine nucleotide exchange domain. Pfam-B_488 (release 2.1). This family is the guanine nucleotide exchange domain of EF-1 beta and EF-1 delta chains.. 
PF00647 EF1G_domain;<br>Elongation factor 1 gamma, conserved domain. 
PF00889 Elongation factor TS<br>Pfam-B_1408 (release 3.0). 
PF01132 Elongation factor P (EF-P) OB domain<br>
PF04863 Alliinase EGF-like domain<br>Pfam-B_4527 (release 7.6). Allicin is a thiosulphinate that gives rise to dithiines, allyl sulphides and ajoenes, the three groups of active compounds in Allium species. Allicin is synthesised from sulfoxide cysteine derivatives by alliinase (EC:4.4.1.4), whose C-S lyase activity cleaves C(beta)-S(gamma) bonds. It is thought that this enzyme forms part of a primitive plant defence system. This family represents the  N-terminal EGF-like domain  .. 
PF01303 Egg lysin (Sperm-lysin)<br>Pfam-B_1464 (release 3.0). Egg lysin creates a hole in the envelope of the egg thereby allowing  the sperm to pass through the envelope and fuse with the egg.. 
PF00971 EIAV coat protein, gp90<br>Pfam-B_210 (release 3.0). Equine infectious anaemia (EIAV). EIAV belongs to the family Retroviridae. EIAV gp90 is hypervariable in the carboxyl-end region and more stable in the amino-end region.  This variability is a pathogenicity factor that allows the evasion of the host's immune response.. 
PF01176 Translation initiation factor 1A / IF-1<br>This family includes both the eukaryotic translation factor eIF-1A and the bacterial translation initiation factor IF-1.. 
PF05091 Eukaryotic translation initiation factor 3 subunit 7 (eIF-3)<br>Pfam-B_6311 (release 7.7). This family is made up of eukaryotic translation initiation factor 3 subunit 7 (eIF-3 zeta/eIF3 p66/eIF3d). Eukaryotic initiation factor 3 is a multi-subunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilisation of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits. These functions and the complex nature of eIF3 suggest multiple interactions with many components of the translational machinery  . The gene coding for the protein has been implicated in cancer in mammals  .. 
PF01287 Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold<br>eIF5A, previously thought to be an initiation factor, has been shown to be required for peptide chain elongation in yeast  .. 
PF01873 eIF5_eIF2B; <br>Domain found in IF2B/IF5. This family includes the N terminus of eIF-5 Swiss:P55010, and the C terminus of eIF-2 beta Swiss:P20042. This region corresponds to the whole of the archaebacterial eIF-2 beta homologue. The region contains a putative zinc binding C4 finger.. 
PF01912 eIF6; <br>This family includes eukaryotic translation initiation factor 6 as well as presumed archaebacterial homologues.. 
PF03608 PTS system enzyme II sorbitol-specific factor<br>TIGRFAMs, Griffiths-Jones SR. 
PF03609 PTS system sorbose-specific iic component<br>TIGRFAMs, Griffiths-Jones SR. 
PF03612 EIIBC-GUT; <br>Sorbitol phosphotransferase enzyme II N-terminus. TIGRFAMs, Griffiths-Jones SR, Yeats C. 
PF03611 PTS system sugar-specific permease component<br>This family includes bacterial transmembrane proteins with a putative sugar-specific permease function, including and analogous to the IIC component of the PTS system. It has been suggested that this permease may form part of an L-ascorbate utilisation pathway, with proposed specificity for 3-keto-L-gulonate (formed by hydrolysis of L-ascorbate) . This family includes the IIC component of the galactitol specific GAT family PTS system.. 
PF03613 PTS system mannose/fructose/sorbose family IID component<br>TIGRFAMs, Griffiths-Jones SR. 
PF04873 Ethylene insensitive 3<br>Pfam-B_4883 (release 7.6). Ethylene insensitive 3 (EIN3) proteins are a family of plant DNA-binding proteins that regulate transcription in response to the gaseous plant hormone ethylene, and are essential for ethylene-mediated responses including the triple response, cell growth inhibition, and accelerated senescence. . 
PF03317 ELF protein<br>Pfam-B_3282 (release 6.5). This is a family of hypothetical proteins from cereal crops.. 
PF02323 Egg-laying hormone precursor    <br>Pfam-B_953 (release 5.2). This family consists of egg-laying hormone (ELH) precursor and atrial gland peptides form little and California sea hare. The family also includes ovulation prohormone precursor from great pond snail. This family thus represents a conserved gastropoda ovulation and  egg production prohormone.  Note that many of the proteins present  are further cleaved to give individual peptides  . Neuropeptidergic bag cells of the marine mollusk Aplysia californica synthesise an egg-laying hormone (ELH) precursor protein which is  cleaved to generate several bioactive peptides including ELH,  bag cell peptides (BCP) and acidic peptide (AP)  .. 
PF00964 Elicitin<br>Elicitins form a novel class of plant necrotic proteins which are secreted by Phytophthora and Pythium fungi, parasites of many economically important crops. These proteins induce leaf necrosis in infected plants and elicit an incompatible hypersensitive-like reaction, leading to the development of a systemic acquired resistance against a range of fungal and bacterial plant pathogens  .. 
PF03789 ELK domain <br>Pfam-B_3136 (release 7.0). This domain is required for the nuclear localisation of these proteins  .  All of these proteins are members of the Tale/Knox homeodomain family, a subfamily within homeobox Pfam:PF00046. . 
PF01151 GNS1_SUR4; <br>Members of this family are involved in long chain fatty acid elongation systems that produce the 26-carbon precursors for ceramide and  sphingolipid synthesis  .  Predicted to be integral membrane proteins, in eukaryotes they are probably located on the endoplasmic reticulum.   Yeast ELO3 (Swiss:P40319) affects plasma membrane H+-ATPase activity, and may act on a glucose-signaling pathway that controls the expression of several genes that are transcriptionally regulated by glucose such as PMA1  .. 
PF02488 Merozoite Antigen<br>Pfam-B_924 (release 5.4). This family represents the immunodominant surface antigen of Theileria parasites including equi merozoite antigen-1 (EMA-1) and equi merozoite antigen-2 (EMA-2)  . The protein shows variation at a putative glycosylation site, a potential mechanism for host immune response evasion  .. 
PF01105 emp24/gp25L/p24 family/GOLD<br>Pfam-B_803 (release 3.0). Members of this family are implicated in bringing cargo forward from the ER and binding to coat proteins by their cytoplasmic domains.  This domain corresponds closely to the beta-strand rich GOLD domain described in  .\.  The GOLD domain is always found combined with lipid- or membrane-association domains  .. 
PF04493 Endonuc_V; <br>Endonuclease V is specific for single-stranded DNA or for duplex DNA that contains uracil or that is damaged by a variety of agents  .. 
PF02945 endonuclease_7; <br>Recombination endonuclease VII. 
PF04231 Endonuclease_I;<br>Bacterial periplasmic or secreted endonuclease I (EC:3.1.21.1) E. coli endonuclease I (EndoI) is a sequence independent endonuclease located in the periplasm. It is inhibited by different RNA species.  It is thought to normally generate double strand breaks in DNA, except in the presence of high salt concentrations and RNA, when it generates single strand breaks in DNA. Its biological role is unknown  .  Other family members are known to be extracellular  .  This family also includes a non-specific, Mg2+ activated ribonuclease precursor (Swiss:Q03091)  .. 
PF04667 endosulfine; <br>cAMP-regulated phosphoprotein/endosulfine conserved region. Pfam-B_4454 (release 7.5). Conserved region found in both cAMP-regulated phosphoprotein 19 (ARPP-19) and Alpha/Beta endosulfine. No function has yet been assigned to ARPP-19.  Endosulfine is the endogenous ligand for the ATP-dependent potassium (K ATP) channels which occupy a key position in the control of insulin release from the pancreatic beta cell by coupling cell polarity to metabolism.  In both cases the region occupies the majority of the protein [1,2]. . 
PF00322 endothelin; <br>
PF00555 endotoxin; <br>This family contains insecticidal toxins produced by Bacillus species of bacteria.  During spore formation the bacteria produce crystals of this protein.  When an insect ingests these proteins they are activated by proteolytic cleavage.  The N terminus is cleaved in all of the proteins and a C terminal extension is cleaved in some members.  Once activated the  endotoxin binds to the gut epithelium and causes cell lysis leading to death.  This activated region of the delta endotoxin is composed of three structural domains.  The N-terminal helical domain is involved in membrane insertion and pore formation.  The second and third domains are involved in receptor binding.. 
PF03944 endotoxin_C; <br>This family contains insecticidal toxins produced by Bacillus species of bacteria.  During spore formation the bacteria produce crystals of this protein.  When an insect ingests these proteins they are activated by proteolytic cleavage.  The N terminus is cleaved in all of the proteins and a C terminal extension is cleaved in some members.  Once activated the  endotoxin binds to the gut epithelium and causes cell lysis leading to death.  This activated region of the delta endotoxin is composed of three structural domains.  The N-terminal helical domain is involved in membrane insertion and pore formation.  The second and third domains are involved in receptor binding.. 
PF03945 endotoxin_N; <br>delta endotoxin, N-terminal domain. This family contains insecticidal toxins produced by Bacillus species of bacteria.  During spore formation the bacteria produce crystals of this protein.  When an insect ingests these proteins they are activated by proteolytic cleavage.  The N terminus is cleaved in all of the proteins and a C terminal extension is cleaved in some members.  Once activated the  endotoxin binds to the gut epithelium and causes cell lysis leading to death.  This activated region of the delta endotoxin is composed of three structural domains.  The N-terminal helical domain is involved in membrane insertion and pore formation.  The second and third domains are involved in receptor binding.. 
PF03272 Viral enhancin protein<br>Pfam-B_4236 (release 6.5). 
PF03386 Early nodulin 93 ENOD93 protein<br>Pfam-B_2931 (release 6.6). 
PF00113 enolase; <br>Enolase, C-terminal TIM barrel domain. 
PF03952 enolase_N; <br>Enolase, N-terminal domain. 
PF03735 ENT domain<br>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 function.  This domain has a completely conserved histidine residue that may be functionally important.. 
PF01375 Enterotoxin_A; <br>Heat-labile enterotoxin alpha chain. 
PF01376 Enterotoxin_B; <br>Heat-labile enterotoxin beta chain. 
PF02048 Enterotoxin_HS;<br>Heat-stable enterotoxin ST. This family consists of the heat stable enterotoxin ST from Escherichia coli. ST is a small peptide of 18 or 19 amino acid residues produced by enterotoxigenic E. coli and is one of the causes of acute diarrhoea in infants and travellers in developing countries. ST triggers a biological response by binding to a membrane-associated guanylyl cyclase C which is located on intestinal epithelial cell membranes  .. 
PF01417 ENTH domain<br>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.. 
PF00429 ENV_polyprotein; <br>ENV polyprotein (coat polyprotein). Pfam-B_145 (release 1.0). 
PF00811 Ependymin<br>Pfam-B_1391 (release 2.1). 
PF01404 EPH_lbd; <br>Ephrin receptor ligand binding domain. The Eph receptors, which bind to ephrins Pfam:PF00812 are a large family of receptor tyrosine kinases.  This family represents the amino terminal domain which binds the ephrin ligand  .. 
PF01370 NAD dependent epimerase/dehydratase family<br>Pfam-B_93 (release 3.0). This family of proteins utilise NAD as a cofactor. The proteins in this family use nucleotide-sugar substrates for a variety of chemical reactions.. 
PF02350 UDP-N-acetylglucosamine 2-epimerase<br>Pfam-B_888 (release 5.2) & Pfam-B_4862 (Release 7.5). 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 such as Swiss:O35826 and Swiss:Q9Z0P6 in this instance Pfam matches only the N-terminal half of the protein suggesting that the additional C-terminal part (when compared to mono-functional members of this family) is responsible for the UPD-N-acetylmannosamine kinase activity of these enzymes. This hypothesis is further supported by the assumption that the C-terminal part of Swiss:O35826 is the kinase domain  .. 
PF00758 Erythropoietin/thrombopoietin<br>Pfam-B_990 (release 2.1). 
PF00275 EPSP_syntase; <br>EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase). 
PF03736 EPTP domain<br>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.  The architecture and structural features of this repeat make it a likely member 7-bladed beta-propeller fold  .. 
PF01133 Enhancer of rudimentary<br>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 Swiss:P05990.. 
PF00810 ER lumen protein retaining receptor<br>Pfam-B_1387 (release 2.1). 
PF02732 ERCC4 domain<br>This domain is a family of nucleases. The family includes EME1 which is an essential component of a Holliday junction resolvase [2-3].  EME1 interacts with MUS81 to form a DNA structure-specific endonuclease.. 
PF04404 ERF superfamily<br>The DNA single-strand annealing proteins (SSAPs), such as RecT, Red-beta, ERF and Rad52, function in RecA-dependent and RecA-independent DNA recombination pathways. This family includes proteins related to ERF  .. 
PF03463 eRF1 domain 1<br>The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known  . The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site  . This family also includes other proteins for which the precise molecular function is unknown.  Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification.. 
PF03464 eRF1 domain 2<br>The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known  . The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site  . This family also includes other proteins for which the precise molecular function is unknown.  Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification.. 
PF03465 eRF1 domain 3<br>The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known  . The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site  . This family also includes other proteins for which the precise molecular function is unknown.  Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification.. 
PF03734 ErfK_YbiS_YhnG; <br>L,D-transpeptidase catalytic domain. This family of proteins are found in a range of bacteria. It has been shown that this domain can act as an L,D-transpeptidase that gives rise to an alternative pathway for peptidoglycan cross-linking  .  This gives bacteria resistance to beta-lactam antibiotics that inhibit PBPs which usually carry out the cross-linking reaction.  The conserved region contains a conserved histidine and cysteine, with the cysteine thought to be an active site residue.  Several members of this family contain peptidoglycan binding domains.  The molecular structure of YkuD protein shows this domain has a novel tertiary fold consisting of a beta-sandwich with two mixed sheets, one containing five strands and the other, six strands. The two beta-sheets form a cradle capped by an alpha-helix. This family was formerly called the ErfK/YbiS/YcfS/YnhG family, but is now named after the first protein of known structure.. 
PF03694 UPF0143; <br>This is a family of integral membrane proteins, which may contain four  transmembrane helices.  Members of this family are thought to be involved  in sterol C-4 demethylation. In S. cerevisiae they may tether Erg26p  (sterol dehydrogenase/decarboxylase) and Erg27p (3-ketoreductase) to the  endoplasmic reticulum or may facilitate interaction between these proteins  .  The family contains a conserved arginine and histidine that may be  functionally important.. 
PF04622 ERG2 and Sigma1 receptor like protein<br>This family consists of the fungal C-8 sterol isomerase and mammalian sigma1 receptor. C-8 sterol isomerase (delta-8--delta-7 sterol isomerase), catalyses a  reaction in ergosterol biosynthesis, which results in unsaturation at C-7  in the B ring of sterols  . Sigma 1 receptor is a low molecular mass mammalian protein located in the  endoplasmic reticulum  , which interacts with endogenous steroid  hormones, such as progesterone and testosterone  .  It also binds the  sigma ligands, which are are a set of chemically unrelated drugs including haloperidol, pentazocine, and ditolylguanidine  .   Sigma1 effectors are not well understood, but sigma1 agonists have been observed to affect NMDA  receptor function, the alpha-adrenergic system and opioid analgesia.. 
PF01222 Ergosterol biosynthesis ERG4/ERG24 family<br>
PF00769 Ezrin/radixin/moesin family<br>Pfam-B_851 (release 2.1). This family of proteins contain a band 4.1 domain (Pfam:PF00373), at their amino terminus.  This family represents the rest of these proteins.. 
PF04137 Endoplasmic Reticulum Oxidoreductin 1 (ERO1)<br>Pfam-B_4729 (release 7.3);. Members of this family are required for the formation of disulphide bonds in the ER [1,2].. 
PF03238 ESAG protein<br>Pfam-B_3037 (release 6.5). Expression-site-associated gene (ESAG) proteins are thought  to be involved in VSG activation. This family includes ESAG 117A Swiss:P04477 as well as ESAG IM Swiss: Q26705.. 
PF03433 ESPA; <br>EspA-like secreted protein . Pfam-B_4100 (release 6.6). EspA is the prototypical member of this family. EspA, together with EspB, EspD and Tir are exported by a type III secretion system.  These proteins are essential for attaching and effacing lesion formation. EspA is a structural protein and a major component of a large, transiently expressed, filamentous surface organelle which forms a direct link between the bacterium and the host cell [1,2].. 
PF04806 EspF protein repeat<br>Pfam-B_3518 (release 7.6). The enteropathogenic Escherichia coli EspF secreted protein induces host cell apoptosis. Its proline-rich structure suggests that it may act by binding to SH3 domains or EVH1 domains of host cell signalling proteins  . . 
PF00756 Putative esterase<br>Pfam-B_476 (release 2.1) & Pfam-B_4968 (Release 7.5). This family contains Esterase D Swiss:P10768. However it is not clear if all members of the family have the same function.  This family is related to the Pfam:PF00135 family.. 
PF01684 ET module<br>This domain has no known function. It is found in several C. elegans proteins. The domain contains 8-10 conserved cysteines that probably form 4-5 disulphide bridges. By inspection of the conservation of cysteines it looks like cysteines 1,2,3,4,9 and 10 are always present and that sometimes the pair 5 and 8 or the pair 6 and 7 are missing. This suggests that cysteines 5/8 and 6/7 make disulphide bridges. . 
PF00766 Electron transfer flavoprotein FAD-binding domain<br>Pfam-B_853 (release 2.1) & Pfam-B_1321 (release 3.0). This domain found at the C-terminus of electron transfer flavoprotein alpha chain and binds to FAD  . The fold consists of a five-stranded parallel beta sheet as the core of the domain, flanked by alternating helices.  A small part of this domain is donated by the beta chain  .. 
PF01012 ETF_beta; <br>Electron transfer flavoprotein domain. Pfam-B_1321 (release 3.0). This family includes the homologous domain shared between the alpha and beta subunits of the electron transfer flavoprotein  .. 
PF05187 ETFD; <br>Electron transfer flavoprotein-ubiquinone oxidoreductase. Pfam-B_2305 (release 7.7). Electron-transfer flavoprotein-ubiquinone oxidoreductase (ETF-QO) in the inner mitochondrial membrane accepts electrons from electron-transfer flavoprotein which is located in the mitochondrial matrix and reduces ubiquinone in the mitochondrial membrane. The two redox centres in the protein, FAD and a [4Fe4S] cluster, are present in a 64-kDa monomer  . . 
PF00178 Ets-domain<br>
PF03318 Clostridium epsilon toxin ETX/Bacillus mosquitocidal toxin MTX2<br>Pfam-B_3569 (release 6.5). This family appears to be distantly related to Pfam:PF01117.. 
PF01459 Euk_porin; <br>Prodom_3211 (release 99.1) & Pfam-B__3211 (release 7.5). 
PF04346 Ethanolamine utilisation protein, EutH<br>EutH is a bacterial membrane protein whose molecular function is unknown. It has been suggested that it may act as an ethanolamine transporter, responsible for carrying ethanolamine from the periplasm to the cytoplasm  .. 
PF03319 Ethanolamine utilisation protein EutN/carboxysome<br>Pfam-B_3053 (release 6.5). The crystal structure of EutN contains a central five-stranded beta-barrel, with an alpha-helix at the open end of this barrel (PDB:2HD3). The structure also contains three additional beta-strands, which help the formation of a tight hexamer, with a hole in the center. this suggests that EutN forms a pore, with an opening of 26 Angstrom in diameter on one face and 14 Angstrom on the other face  . EutN is involved in the cobalamin-dependent degradation of ethanolamine  .. 
PF02472 Biopolymer transport protein ExbD/TolR<br>Pfam-B_2343 (release 5.4). This group of proteins are membrane bound transport proteins essential for ferric ion uptake in bacteria  . The Pfam family consists of ExbD, and TolR which are involved in TonB-dependent transport of various  receptor bound substrates including colicins  .. 
PF01541 Exci_endo_N; <br>GIY-YIG catalytic domain. Pfam-B_489 (release 4.0). This domain called GIY-YIG is found in the amino terminal region of excinuclease abc subunit c (uvrC), bacteriophage T4 endonucleases segA, segB, segC, segD and segE; it is also found in putative endonucleases encoded by group I introns of fungi and phage.  The structure of I-TevI a GIY-YIG endonuclease, reveals a novel alpha/beta-fold with a central three-stranded antiparallel beta-sheet flanked by three helices  . The most conserved and putative catalytic residues are located on a shallow, concave surface and include a metal coordination site.. 
PF03081 Exo70 exocyst complex subunit<br>Pfam-B_2462 (release 6.4). 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 complex is involved in the late stages of exocytosis, and is localised at the tip of the bud, the major site of exocytosis in yeast  . Exo70 interacts with the Rho3 GTPase  . This interaction mediates one of the three known functions of Rho3 in cell polarity: vesicle docking and fusion with the plasma membrane (the other two functions are regulation of actin polarity and transport of exocytic vesicles from the mother cell to the bud)  . In humans, the functions of Exo70 and the exocyst complex are less well characterised: Exo70 is expressed in several tissues and is thought to also be involved in exocytosis  .. 
PF04257 Exodeoxyribonuclease V, gamma subunit <br>TIGRFAMs (release 2.0);. The Exodeoxyribonuclease V enzyme is a multi-subunit enzyme comprised of the proteins RecB, RecC (this family) and  RecD.  This enzyme plays an important role in homologous genetic recombination, repair of double strand DNA breaks resistance to UV irradiation and chemical DNA-damage. The enzyme (EC:3.1.11.5) catalyses ssDNA or dsDNA-dependent ATP hydrolysis, hydrolysis of ssDNA or dsDNA and unwinding of dsDNA  . This family consists of two AAA domains.. 
PF02601 Exonuclease_VII; <br>Exonuclease VII, large subunit. This family consist of exonuclease VII, large subunit EC:3.1.11.6 This enzyme catalyses exonucleolytic cleavage in either 5'->3' or 3'->5'  direction to yield 5'-phosphomononucleotides.  This exonuclease VII enzyme is composed of one large subunit and 4 small ones  .. 
PF02095 Extensin; <br>Extensin-like protein repeat. 
PF01267 F-actin capping protein alpha subunit<br>
PF00469 Negative factor, (F-Protein) or Nef<br>Pfam-B_128 (release 1.0). Nef protein accelerates virulent progression of AIDS by its interaction with cellular proteins involved in signal transduction and host cell activation. Nef has been shown to  bind specifically to a subset of the Src kinase family.. 
PF03807 NADP oxidoreductase coenzyme F420-dependent<br>TIGRFAMs, Griffiths-Jones SR. 
PF01115 F-actin capping protein, beta subunit<br>
PF01116 Fructose-bisphosphate aldolase class-II<br>
PF03405 Fatty acid desaturase<br>
PF04116 Fatty_acid_hyrd; <br>Fatty acid hydroxylase superfamily. Pfam-B_7847 (release 7.3) & DOMO:DM04600 & Pfam-B_905 (release 4.1);. This superfamily includes fatty acid and carotene hydroxylases and sterol desaturases.  Beta-carotene hydroxylase is involved in zeaxanthin synthesis by hydroxylating beta-carotene, but the enzyme may be involved in other pathways  .  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 two copies of a HXHH motif.  Members of this family are integral membrane proteins.. 
PF02504 Fatty acid synthesis protein<br>Pfam-B_1671 (release 5.4). The plsX gene is part of the bacterial fab gene cluster which encodes several key fatty acid biosynthetic enzymes  . The exact function of the plsX protein in fatty acid synthesis is unknown.. 
PF01557 Fumarylacetoacetate (FAA) hydrolase family<br>Pfam-B_641 (release 4.0) & Pfam-B_1228 (release 4.1). 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 tyrosine catabolic pathway, it hydrolyses  fumarylacetoacetate into fumarate and acetoacetate which then join the  citric acid cycle  . Mutations in FAA cause type I tyrosinemia in humans this is an inherited disorder mainly affecting the liver leading to  liver cirrhosis, hepatocellular carcinoma, renal tubular damages and  neurologic crises amongst other symptoms  . The enzymatic defect causes the toxic accumulation of phenylalanine/tyrosine catabolites  . The E. coli W enzyme HHDD isomerase/OPET decarboxylase contains two copies of this domain and functions in fourth and fifth steps of the homoprotocatechuate pathway; here it decarboxylates OPET to HHDD and isomerises this to OHED.  The final products of this pathway are pyruvic acid and succinic  semialdehyde. This family also includes 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 in E. coli Swiss:P77608 is involved in the phenylpropionic acid pathway of E. coli and catalyses the conversion of 2-hydroxy pentadienoate to 4-hydroxy-2-keto-pentanoate and uses a Mn2+ co-factor  . OHED hydratase encoded by hpcG in E. coli Swiss:P42270 is involved  in the homoprotocatechuic acid (HPC) catabolism  . XylI in P. putida Swiss:P49155 is a 4-Oxalocrotonate decarboxylase  .. 
PF00667 FAD_binding; <br>Pfam-B_180 (release 2.1). This domain is found in sulfite reductase, NADPH cytochrome P450 reductase, Nitric oxide synthase and methionine synthase reductase.. 
PF00890 FAD binding domain<br>Pfam-B_255 (release 3.0). This family includes members that bind FAD.  This family includes the flavoprotein subunits from succinate and fumarate dehydrogenase, aspartate oxidase and the alpha subunit of adenylylsulphate reductase.. 
PF01494 FAD binding domain<br>Pfam-B_549 (release 4.0). This domain is involved in FAD binding in a number of enzymes.. 
PF00941 dehydrog_molyb; <br>FAD binding domain in molybdopterin dehydrogenase. Pfam-B_1112 (release 3.0). 
PF01687 FAD_Synth; <br>Pfam-B_1221 (release 4.1). This family represents the C-terminal region of the bifunctional riboflavin biosynthesis protein known as RibC in Bacillus subtilis.  The RibC protein from Bacillus subtilis has both flavokinase and flavin adenine dinucleotide synthetase (FAD-synthetase) activities. RibC plays an essential role in the flavin metabolism  .  This domain is thought to have kinase activity  .. 
PF04703 FaeA-like protein<br>Pfam-B_5784 (release 7.5). This family represents a number of fimbrial protein transcription regulators found in Gram-negative bacteria. These proteins are thought to facilitate binding of the leucine-rich regulatory protein to regulatory elements, possibly by inhibiting deoxyadenosine methylation of these elements by deoxyadenosine methylase [1,2].. 
PF02106 Fanconi; <br>Fanconi anaemia group C protein. 
PF03511 Fanconia; <br>Fanconi anaemia group A protein. 
PF01149 Formamidopyrimidine-DNA glycosylase N-terminal domain<br>Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidised purines from damaged DNA. This family is the N-terminal domain contains eight beta-strands, forming a beta-sandwich with two alpha-helices parallel to its edges  .. 
PF04750 FAR-17a/AIG1-like protein<br>Pfam-B_3664 (release 7.5). This family includes the hamster androgen-induced FAR-17a protein (Swiss:Q60534)  ,  and its human homologue, the AIG1 protein (Swiss:Q9NVV5)  . The function of these proteins is unknown. This family also includes homologous regions from a number of other metazoan proteins.. 
PF01581 FMRFamide related peptide family<br>Pfam-B_666 (release 4.1). The neuroactive peptide Phe-Met-Arg-Phe-NH2 (FMRF-amide) has a variety of effects on both mammalian and invertebrate tissues  .. 
PF02469 Fasciclin domain<br>Pfam-B_562 (release 5.4). 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  .. 
PF02259 FAT domain<br>(Keith and Schreiber, Science 270:50). The FAT domain is named after FRAP, ATM and TRRAP.. 
PF02260 FATC domain<br>(Keith and Schreiber, Science 270:50). The FATC domain is named after FRAP, ATM, TRRAP C-terminal  . The solution structure of the FATC domain suggests it plays a role in redox-dependent structural and cellular stability  .. 
PF00316 Fructose-1-6-bisphosphatase<br>
PF03320 Bacterial fructose-1,6-bisphosphatase, glpX-encoded<br>Pfam-B_3515 (release 6.5). 
PF02634 FdhD/NarQ family<br>A pan-bacterial lineage of proteins. Nitrate assimilation protein,  NarQ,   and FdhD (Swiss:P32177) are required for formate  dehydrogenase activity. Structurally, they possess a deaminase fold with a characteristic binding pocket, suggesting that they  might bind a nucleotide or related molecule allosterically to  regulate the formate dehydrogenase catalytic subunit  .. 
PF04216 Protein involved in formate dehydrogenase formation<br>The function of these proteins is unknown. They may possibly be involved in the formation of formate dehydrogenase.. 
PF03147 Ferredoxin-fold anticodon binding domain<br>This is the anticodon binding domain found in some phenylalanyl tRNA synthetases.  The domain has a ferredoxin fold [1,2].. 
PF00465 Iron-containing alcohol dehydrogenase <br>
PF02742 Iron dependent repressor, metal binding and dimerisation domain<br>This family includes the Diphtheria toxin repressor.. 
PF01325 Iron dependent repressor, N-terminal DNA binding domain<br>This family includes the Diphtheria toxin repressor. DNA binding is through a helix-turn-helix motif.. 
PF02906 Iron only hydrogenase large subunit, C-terminal domain<br>
PF02256 Iron hydrogenase small subunit<br>Pfam-B_3750 (release 5.2). This family represents the small subunit of the Fe-only hydrogenases EC:1.18.99.1. The subunit is comprised of alternating random coil and alpha helical structures that encompasses the large subunit in a novel protein fold  .. 
PF01032 FecCD_family;<br>FecCD transport family. Pfam-B_377 (release 3.0). This is a sub-family of bacterial binding protein-dependent transport systems family. This Pfam entry contains the inner components of this multicomponent transport system.. 
PF04773 FecR protein<br>Pfam-B_3234 (release 7.5). FecR is involved in regulation of iron dicitrate transport. In the absence of citrate FecR inactivates FecI. FecR is probably a sensor that recognises iron dicitrate in the periplasm.. 
PF02388 FemAB family<br>Pfam-B_1214 (release 5.2). The femAB operon codes for two nearly identical approximately 50-kDa proteins involved in the formation of the Staphylococcal pentaglycine interpeptide bridge in peptidoglycan  . These proteins are also considered as a factor influencing the level of methicillin resistance  .. 
PF04023 FeoA domain<br>This family includes FeoA a small protein, probably involved in Fe2+ transport  . This presumed short domain is also found at the C-terminus of a variety of metal dependent transcriptional regulators.  This suggests that this domain may be metal-binding. In most cases this is likely to be either iron or manganese.. 
PF02421 FeoB; <br>Ferrous iron transport protein B. Escherichia coli has an iron(II) transport system (feo) which may make an important contribution to the iron supply of the cell under anaerobic conditions  . FeoB has been identified as part of this transport system. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent  .. 
PF00142 fer4_NifH; <br>4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family. 
PF01794 Ferric reductase like transmembrane component<br>Pfam-B_728 (release 4.2). This family includes a common region in the transmembrane proteins mammalian cytochrome B-245 heavy chain (gp91-phox), ferric reductase transmembrane component in yeast and respiratory burst oxidase from mouse-ear cress. This may be a family of flavocytochromes capable of moving electrons across the plasma membrane  . The Frp1 protein Swiss:Q04800 from S. pombe is a ferric reductase component and is required for cell surface ferric reductase activity, mutants in frp1 are deficient in ferric iron uptake  . Cytochrome B-245 heavy chain Swiss:P04839 is a FAD-dependent dehydrogenase it is also has electron transferase activity which reduces molecular oxygen to superoxide anion, a precursor in the production of microbicidal oxidants  . Mutations in the sequence of cytochrome B-245 heavy chain (gp91-phox) lead to the X-linked chronic granulomatous disease. The bacteriocidal ability of phagocytic cells is reduced and is characterised by the absence of a functional plasma membrane associated NADPH oxidase  .  The chronic granulomatous disease gene codes for the beta chain of cytochrome B-245 and cytochrome B-245 is missing from patients with the disease  .. 
PF00762 Ferrochelatase<br>Pfam-B_879 (release 2.1). 
PF04060 Putative Fe-S cluster<br>This family includes a domain with four conserved cysteines that probably form an Fe-S redox cluster.. 
PF02941 FeThRed; FeThRed_beta; <br>Ferredoxin thioredoxin reductase variable alpha chain. 
PF02943 FeThRed_alpha; <br>Ferredoxin thioredoxin reductase catalytic beta chain. 
PF01846 FF domain<br>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  .. 
PF05013 N-formylglutamate amidohydrolase<br>Formylglutamate amidohydrolase (FGase) catalyses the terminal reaction in the five-step pathway for histidine utilisation in Pseudomonas putida. By this action, N-formyl-L-glutamate (FG) is hydrolysed to produce L-glutamate plus formate  .. 
PF00167 Fibroblast growth factor<br>Fibroblast growth factors are a family of proteins involved in growth and differentiation in a wide range of contexts. They are found in a wide range of organisms, from nematodes to humans  . Most share an internal core region of high similarity, conserved residues in which are involved in binding with their receptors. On binding, they cause dimerisation of their tyrosine kinase receptors leading to intracellular signalling. There are currently four known tyrosine kinase receptors for fibroblast growth factors.  These receptors can each bind several different members of this family.  Members of this family have a beta trefoil structure. Most have N-terminal signal peptides and are secreted. A few lack signal sequences but are secreted anyway; still others also lack the signal peptide but are found on the cell surface and within the extracellular matrix. A third group remain intracellular  . They have central roles in development, regulating cell proliferation, migration and differentiation. On the other hand, they are important in tissue repair following injury in adult organisms  .. 
PF00370 FGGY; <br>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.. 
PF02782 FGGY family of carbohydrate kinases, C-terminal domain<br>This domain adopts a ribonuclease H-like fold and is structurally related to the N-terminal domain.. 
PF00498 FHA domain<br>The FHA (Forkhead-associated) domain is a phosphopeptide binding motif  .. 
PF00771 FHIPEP family<br>Pfam-B_983 (release 2.1). 
PF01269 Fibrillarin<br>
PF00147 fibrinogen_C; <br>Fibrinogen beta and gamma chains, C-terminal globular domain. 
PF03516 Filaggrin<br>
PF00038 filament; <br>Intermediate filament protein. 
PF04732 filament_head; <br>Intermediate filament head (DNA binding) region. This family represents the N-terminal head region of intermediate  filaments.  Intermediate filament heads bind DNA  .  Vimentin heads are  able to alter nuclear architecture and chromatin distribution, and the liberation of heads by HIV-1 protease liberates may play an important role in HIV-1 associated cytopathogenesis and carcinogenesis  .   Phosphorylation of the head region can affect filament stability  .  The head has been shown to interaction with the rod domain of the same protein  .. 
PF00630 Filamin/ABP280 repeat<br>
PF01611 Filovirus glycoprotein<br>Pfam-B_1023 (release 4.1). This family includes an extracellular region from the envelope glycoprotein of Ebola and Marburg viruses. This region is also produced as a separate transcript that gives rise to a non-structural, secreted glycoprotein, which is produced in large amounts and has an unknown function  . Processing of this protein may be involved in viral pathogenicity  .. 
PF02097 Filoviridae VP35<br>
PF00419 Fimbrial protein<br>Pfam-B_196 (release 1.0) & Jackhmmer:B2PIN3. 
PF04449 CS1 type fimbrial major subunit<br>Fimbriae, also known as pili, form filaments radiating from the surface of the bacterium to a length of 0.5-1.5 micrometres. They enable the cell to colonise host epithelia. This family constitutes the major subunits of CS1 like pili, including CS2 and CFA1 from Escherichia coli, and also the Cable type II pilin major subunit from Burkholderia cepacia  . The major subunit of CS1 pili is called CooA.  Periplasmic CooA is mostly complexed with the assembly protein CooB.  In addition, a small pool of CooA multimers, and CooA-CooD complexes exists, but the functional significance is unknown  . A member of this family has also been identified in Salmonella typhi and Salmonella enterica  .. 
PF02432 Fibrimal; <br>Fimbrial, major and minor subunit. Pfam-B_2036 (release 5.4). Fimbriae (also know as pili) are polar filaments found on the bacterial surface, allowing colonisation of the host. This family consists of the minor and major fimbrial subunits.. 
PF05182 Fip1 motif<br>Pfam-B_4652 (release 7.7). This short motif is about 40 amino acids in length.  In the Fip1 protein that is a component of a yeast pre-mRNA polyadenylation factor that directly interacts with poly(A) polymerase  . This region of Fip1 is needed for the interaction with the Th1 subunit of the complex and for specific polyadenylation of the cleaved mRNA precursor  .. 
PF02433 Cytochrome C oxidase, mono-heme subunit/FixO<br>Pfam-B_2045 (release 5.4). The bacterial oxidase complex, fixNOPQ or cytochrome cbb3, is thought to be required for respiration in endosymbiosis. FixO is a membrane bound mono-heme constituent of the fixNOPQ complex.. 
PF01346 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase<br>Pfam-B_402 (release 3.0). This family is only found at the amino terminus of Pfam:PF00254. This domain is of unknown function.. 
PF04620 Flagellar filament outer layer protein Flaa<br>Periplasmic flagella are the organelles of spirochete mobility, and are structurally different from the flagella of other motile bacteria. They reside inside the cell within the periplasmic space, and confer mobility in viscous gel-like media such connective tissue  . The flagella are composed of an outer sheath of FlaA proteins and a core filament of FlaB proteins. Each species usually has several FlaA protein species  .. 
PF03646 FlaG protein<br>Pfam-B_2985 (release 7.0). Although important for flagella the exact function of this protein is unknown.. 
PF03614 Repressor of phase-1 flagellin<br>
PF05149 Paraflagellar rod protein<br>Pfam-B_6464 (release 7.7). This family consists of several eukaryotic paraflagellar rod component proteins. The eukaryotic flagellum represents one of the most complex macromolecular structures found in any organism and contains more than 250 proteins  . In addition to its locomotive role, the flagellum is probably involved in nutrient uptake since receptors for host low-density lipoproteins are localised on the flagellar membrane as well as on the flagellar pocket membrane  .. 
PF00700 Bacterial flagellin C-terminal helical region<br>Pfam-B_41 (release 2.1). Flagellins polymerise to form bacterial flagella.\.     There is some similarity between this family and Pfam:PF00669, particularly the motif NRFXSXIXXL. It has been suggested that these two regions associate   and this is shown to be correct as structurally this family forms an extended helix that interacts with Pfam:PF00700.. 
PF00669 Bacterial flagellin N-terminal helical region<br>Pfam-B_37 (release 2.1). Flagellins polymerise to form bacterial flagella. This family includes flagellins and hook associated protein 3. Structurally this family forms an extended helix that interacts with Pfam:PF00700.. 
PF01350 Flavivirus non-structural protein NS4A<br>Pfam-B_211 (release 3.0). Flaviviruses encode a single polyprotein. This is cleaved into three structural and seven non-structural proteins. The NS4A protein is small and poorly conserved among the Flaviviruses. NS4A contains multiple hydrophobic potential membrane spanning regions  .  NS4A has only been found in cells infected by Kunjin virus  .. 
PF01349 Flavivirus non-structural protein NS4B<br>Pfam-B_211 (release 3.0). Flaviviruses encode a single polyprotein.\.      This is cleaved into three structural and seven non-structural proteins. The NS4B protein is small and poorly conserved among the Flaviviruses. NS4B contains multiple hydrophobic potential membrane spanning regions  .  NS4B may form membrane components of the viral replication complex and could be involved in membrane localisation of NS3 and Pfam:PF00972  .. 
PF00972 Flavivirus RNA-directed RNA polymerase<br>Pfam-B_200 (release 3.0). Flaviviruses produce a polyprotein from the ssRNA genome. This protein is also known as NS5. This RNA-directed RNA polymerase possesses a number of short regions and motifs homologous to other RNA-directed RNA polymerases  .. 
PF01570 Flavivirus polyprotein propeptide<br>Pfam-B_304 (release 4.1). The flaviviruses are small enveloped animal viruses containing a single positive strand genomic RNA  .  The genome encodes one large ORF a polyprotein which undergos proteolytic processing into mature viral  peptide chains. This family consists of a propeptide region of approximately 90 amino acid length.. 
PF02525 NADHdh_2; <br>Flavodoxin-like fold. Pfam-B_1456 (release 5.4). 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 and protect cells against damage by free radicals and reactive oxygen species  .\.     This enzyme uses a FAD co-factor.  The equation for this reaction is:- NAD(P)H + acceptor <=> NAD(P)(+) + reduced acceptor. This enzyme is also involved in the bioactivation of prodrugs used in chemotherapy  . The family also includes acyl carrier protein phosphodiesterase EC:3.1.4.14. This enzyme converts holo-ACP to apo-ACP by hydrolytic cleavage of the phosphopantetheine residue from ACP  . This family is related to Pfam:PF03358 and Pfam:PF00258.. 
PF02441 Flavoprotein<br>Pfam-B_1622 (release 5.4). This family contains diverse flavoprotein enzymes. This family includes epidermin biosynthesis protein, EpiD Swiss:P30197, which has been shown to be a flavoprotein that binds FMN  . This enzyme catalyses the removal of two reducing equivalents from the cysteine residue of the C-terminal meso-lanthionine of epidermin to form a --C==C-- double bond. This family also includes the B chain of dipicolinate synthase a small polar molecule that accumulates to high concentrations in bacterial endospores, and is thought to play a role in spore heat resistance, or the maintenance of heat resistance  . dipicolinate synthase catalyses the formation of dipicolinic acid from dihydroxydipicolinic acid. This family also includes phenyl-acrylic acid decarboxylase Swiss:P33751 (EC:4.1.1.-)  .. 
PF00460 flg_bb_rod; <br>Flagella basal body rod protein. 
PF02120 Flagellar hook-length control protein FliK<br>This is the C terminal domain of FliK. FliK controls the length of the flagellar hook by directly measuring the hook length as a molecular ruler  .  This family also includes YscP of the Yersinia type III secretion system, and equivalent proteins in other pathogenic bacterial type III secretion systems.. 
PF03963 Flagellar hook capping protein - N-terminal region<br>FlgD is known to be absolutely required for hook assembly, yet it has not been detected in the mature flagellum  . It appears to act as a hook-capping protein to enable assembly of hook protein subunits  .  FlgD regulates the assembly of the hook cap structure to prevent leakage of hook monomers into the medium and hook monomer polymerisation and also plays a role in determination of the correct hook length, with the help of the FliK protein  .  This family represents the N-terminal conserved region of FlgD. A recent crystal structure showed that this region was likely to be flexible and was cleaved off during crystallisation  .. 
PF02107 Flagellar L-ring protein<br>
PF02119 Flagellar P-ring protein<br>
PF04316 Anti-sigma-28 factor, FlgM<br>FlgM binds and inhibits the activity of the transcription factor sigma 28. Inhibition of sigma 28 prevents the expression of genes from flagellar transcriptional class 3, which include genes for the filament and chemotaxis.  Correctly assembled basal body-hook structures export FlgM, relieving inhibition of sigma 28 and allowing expression of class 3 genes. NMR studies show that free FlgM is mostly unfolded, which may facilitate its export. The C terminal half of FlgM adopts a tertiary structure when it binds to sigma 28.  All mutations in FlgM that prevent sigma 28 inhibition affect the C-terminal domain and is the region thought to constitute the binding domain. A minimal binding domain has been identified between Glu 64 and Arg 88 in Salmonella typhimurium (Swiss:P26477).  The N-terminal portion remains unstructured and may be necessary for recognition by the export machinery  .. 
PF05130 FlgN protein<br>This family includes the FlgN protein and export chaperone involved in flagellar synthesis  .. 
PF02465 Flagellar hook-associated protein 2 N-terminus<br>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  . This alignment covers the N-terminal region of this family of proteins.. 
PF02049 Flagellar hook-basal body complex protein FliE<br>
PF01706 FliG-C; <br>FliG C-terminal domain. FliG is a component of the flageller rotor, present in about 25 copies per flagellum.  This domain functions specifically in motor rotation.. 
PF02108 Flagellar assembly protein FliH<br>
PF02050 Flagellar FliJ protein<br>
PF03748 Flagellar basal body-associated protein FliL<br>This FliL protein controls the rotational direction of the flagella during chemotaxis  . FliL is a cytoplasmic membrane protein associated with the basal body  .. 
PF02154 Flagellar motor switch protein FliM<br>
PF04347 Flagellar biosynthesis protein, FliO<br>FliO is an essential component of the flagellum-specific protein export apparatus  . It is an integral membrane protein. Its precise molecular function is unknown.. 
PF00813 FliP family<br>Pfam-B_1679 (release 2.1). 
PF02561 Flagellar protein FliS<br>FliS is coded for by the FliD operon and is transcribed in conjunction with FliD and FliT, however this protein has no known function.. 
PF01698 Floricaula / Leafy protein<br>Pfam-B_1633 (release 4.1). This family consists of various plant development proteins which are homologues of floricaula (FLO)  and Leafy (LFY) proteins which are floral meristem identity proteins. Mutations in the sequences of these proteins affect  flower and leaf development.. 
PF00624 Flocculin repeat<br>Pfam-B_51 (release 2.1). This short repeat is rich in serine and threonine residues.. 
PF05202 Recombinase Flp protein<br>
PF04964 Flp/Fap pilin component<br>
PF03930 Flp;<br>Recombinase Flp protein N-terminus. 
PF02662 Methyl-viologen-reducing hydrogenase, delta subunit<br>This family consist of methyl-viologen-reducing hydrogenase, delta subunit / heterodisulphide reductase.  No specific functions have been assigned to this  subunit.  The aligned region corresponds to almost the entire delta chain sequence and contains 4 conserved cysteine residues.  However, in  two Archaeoglobus sequences this region corresponds to only the C-terminus of these proteins Swiss:O29030 and Swiss:029595.. 
PF02947 flt3_lig; <br>The flt3 ligand is a short chain cytokine with a 4 helical bundle fold.. 
PF04772 Influenza B matrix protein 2 (BM2)<br>Pfam-B_2165 (release 7.6). M2 is synthesised in the late phase of infection and incorporated into the virion.  It may be phosphorylated in vivo.  The function of BM2 is unknown  .. 
PF02942 Influenza B non-structural protein (NS1)<br>Pfam-B_198 (Release 6.4). A specific region of the influenza B virus NS1 protein, which includes part of its effector domain, blocks the covalent linkage of ISG15 Swiss:Q64339 to its target proteins both in vitro and in infected cells. Of the several hundred proteins induced by interferon (IFN) alpha/beta, the ubiquitin-like ISG15 protein is one of the most predominant. Influenza A virus employs a different strategy: its NS1 protein does not bind the ISG15 protein, but little or no ISG15 protein is produced during infection  .. 
PF03506 Influenza C non-structural protein (NS1)<br>Pfam-B_980 (release 7.0). The influenza C virus genome consists of seven single-stranded RNA segments. The shortest RNA segment  encodes a 286 amino acid  non-structural protein NS1  . This protein contains 6 conserved cysteines that may be functionally important, perhaps binding to a metal ion.. 
PF03555 Influenza C non-structural protein (NS2)<br>Pfam-B_346 (release 7.0). The influenza C virus genome consists of seven single-stranded RNA segments. The shortest RNA segment  encodes a 286 amino acid  non-structural protein NS1 Pfam:PF03506 as well as the NS2 protein. The NS2 protein is only about 60 amino acids in length and of unknown function.. 
PF00598 Influenza Matrix protein (M1)<br>This protein forms a continuous shell on the inner side of the lipid bilayer, but its function is unclear.. 
PF00599 Influenza Matrix protein (M2)<br>This protein spans the viral membrane with an extracellular amino-terminus external and a cytoplasmic carboxy-terminus.. 
PF00506 flu_virus_nuc;<br>Influenza virus nucleoprotein. Pfam-B_10 (release 1.0). 
PF00600 Influenza non-structural protein (NS1)<br>NS1 is a homodimeric RNA-binding protein that is required for viral replication. NS1 binds polyA tails of mRNA keeping them in the nucleus. NS1 inhibits pre-mRNA splicing by tightly binding to a specific stem-bulge of U6 snRNA.. 
PF00601 Influenza non-structural protein (NS2)<br>NS2 may play a role in promoting normal replication of the genomic RNAs by preventing the replication of short-length RNA species  . . 
PF00603 Influenza RNA-dependent RNA polymerase subunit PA<br>
PF00602 Influenza RNA-dependent RNA polymerase subunit PB1<br>Two GTP binding sites exist in this protein  .. 
PF00604 Influenza RNA-dependent RNA polymerase subunit PB2<br>PB2 can bind 5' end cap structure of RNA  .. 
PF03069 Acetamidase/Formamidase family<br>Pfam-B_2541 (release 6.4). This family includes amidohydrolases of formamide EC:3.5.1.49 and acetamide. Swiss:Q50228 forms a homotrimer suggesting all the members of this family also do.. 
PF01070 FMN-dependent dehydrogenase<br>Pfam-B_829 (release 3.0). 
PF00743 Flavin-binding monooxygenase-like<br>Pfam-B_437 (release 2.1). 
PF00039 Fibronectin type I domain<br>Swissprot_feature_table. 
PF00040 Fibronectin type II domain<br>
PF00041 Fibronectin type III domain<br>Swissprot_feature_table. 
PF02986 Fibronectin binding repeat<br>Griffiths-Jones SR, Schwarz-Linek U. Pfam-B_2661 (release 6.4). The ability of bacteria to bind fibronectin is thought to enable the colonisation of wound tissue and blood clots.  The fibronectin binding repeat is found in bacterial fibronectin binding proteins and serum opacity factor.  Bacterial fibronectin binding proteins are surface proteins that covalently link to the bacterial cell wall, mediate adherence of the bacteria to host cells   and trigger the fibronectin/integrin-mediated uptake of bacteria by host cells  . Each fibronectin binding repeat is an array of short motifs that bind to fibronectin type I domains  . Fibronectin binding repeats are natively unfolded in the absence of fibronectin and are thought to adopt a well-defined conformation (tandem beta-zipper) upon binding  .. 
PF03274 Foamy virus BEL 1/2 protein<br>Pfam-B_4337 (release 6.5). 
PF03408 Foamy virus envelope protein  <br>Pfam-B_4411 (release 6.6). Expression of the envelope (Env) glycoprotein is essential for viral  particle egress.  This feature is unique to the Spumavirinae, a  subclass of the Retroviridae.. 
PF03623 Focal adhesion targeting region<br>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 targeting' (FAT) region is necessary and sufficient for localising FAK to focal adhesions. The crystal structure of FAT shows it forms a four-helix bundle that resembles those found in two other proteins involved in cell adhesion, alpha-catenin and vinculin  . The binding of FAT to the focal adhesion protein, paxillin, requires the integrity of the helical bundle, whereas binding to another focal adhesion protein, talin, does not.. 
PF02980 Restriction endonuclease FokI, catalytic domain<br>
PF02981 Restriction endonuclease FokI, recognition domain<br>
PF01770 Reduced folate carrier<br>Pfam-B_1123 (release 4.2). The reduced folate carrier (a transmembrane glycoprotein) transports reduced folate into mammalian cells via the carrier mediated mechanism (as opposed to the receptor mediated mechanism) it also transports cytotoxic folate analogues used in chemotherapy  , such as methotrexate (MTX). Mammalian cells have an absolute requirement for exogenous folates which are needed for growth, and biosynthesis of macromolecules  .. 
PF03024 Folate receptor family<br>Pfam-B_1966 (release 6.4). 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-anchor. The proteins contain 16 conserved cysteines that form eight disulphide bridges.. 
PF02152 Dihydroneopterin aldolase<br>This enzyme EC:4.1.2.25 catalyses the conversion of 7,8-dihydroneopterin to 6-hydroxymethyl-7,8-dihydropterin in the biosynthetic pathway of tetrahydrofolate.. 
PF00250 FKH;<br>
PF01226 Formate/nitrite transporter<br>
PF02971 formiminotr; <br>Formiminotransferase domain. 
PF02911 formyl_trans_C; <br>Formyl transferase, C-terminal domain. 
PF00551 formyl_transf; <br>This family includes the following members. Glycinamide ribonucleotide transformylase catalyses the third step in de novo purine biosynthesis, the transfer of a formyl group to 5'-phosphoribosylglycinamide. Formyltetrahydrofolate deformylase produces formate from formyl- tetrahydrofolate. Methionyl-tRNA formyltransferase transfers a formyl group onto the amino terminus of the acyl moiety of the methionyl aminoacyl-tRNA. Inclusion of the following members is supported by PSI-blast. HOXX_BRAJA (P31907) contains a related domain of unknown function. PRTH_PORGI (P46071) contains a related domain of unknown function. Y09P_MYCTU (Q50721) contains a related domain of unknown function.. 
PF01491 Frataxin-like domain<br>This family contains proteins that have a domain related to the globular C-terminus of Frataxin the protein that is mutated in Friedreich's ataxia.  This domain is found in a family of bacterial proteins.\.   The function of this domain is currently unknown. It has been suggested that this family is involved in iron transport.. 
PF03197 Bacteriophage FRD2 protein<br>Pfam-B_2816 (release 6.5). 
PF04422 Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term<br>Coenzyme F420 hydrogenase (EC:1.12.99.1) reduces the low-potential two-electron acceptor coenzyme F420.  This family contains the N termini of F420 hydrogenase and dehydrogenase beta subunits  ,  .  The N terminus of Methanobacterium formicicum formate dehydrogenase beta chain (EC:1.2.1.2, Swiss:P06130) is also a member of this family  . This region is often found in association with the 4Fe-4S binding domain, fer4 (Pfam:PF00037).. 
PF03881 Fructosamine kinase<br>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.. 
PF04961 Formiminotransferase-cyclodeaminase<br>Members of this family are thought to be Formiminotransferase- cyclodeaminase enzymes EC:4.3.1.4. This domain is found in  the C-terminus of the bifunctional animal members of the family.. 
PF01268 Formate--tetrahydrofolate ligase<br>
PF03239 Iron permease FTR1 family<br>Pfam-B_3227 (release 6.5). 
PF02491 FtsA;<br>SHS2 domain inserted in FTSA. FtsA is essential for bacterial cell division, and co-localises to  the septal ring with FtsZ. The SHS2 domain is inserted in to the RNAseH fold of FtsA  , and is involved in protein-protein  interaction  .. 
PF01580 FtsK/SpoIIIE family<br>Pfam-B_458 (release 4.1). FtsK has extensive sequence similarity to wide variety of proteins from prokaryotes and plasmids  , termed the FtsK/SpoIIIE family.  This domain contains a putative ATP binding P-loop motif. It is found in the FtsK cell division protein from E. coli Swiss:P46889 and the stage III sporulation protein E SpoIIIE Swiss:P21458 which has roles in regulation of prespore specific gene expression in B. subtilis. A mutation in FtsK causes a temperature sensitive block in cell division and it is involved in peptidoglycan synthesis or modification  . The SpoIIIE protein is implicated in intercellular chromosomal DNA transfer  .. 
PF04999 Cell division protein FtsL<br>In Escherichia coli, nine gene products are known to be essential for assembly of the division septum. One of these, FtsL, is a bitopic membrane protein whose precise function is not understood. It has been proposed that FtsL interacts with the DivIC protein Pfam:PF04977  , however this interaction may be indirect  .. 
PF03799 Cell division protein FtsQ<br>Pfam-B_1605 (release 7.0). FtsQ is one of several cell division proteins.  FtsQ interacts with other Fts proteins, reviewed in  .  The precise function of FtsQ is unknown.. 
PF01098 Cell cycle protein<br>This entry includes the following members;    FtsW, RodA, SpoVE. 
PF03867 Fushi tarazu (FTZ), N-terminal region<br>This region contains the important motif (LXXLL) necessary for the interaction of FTZ with the nuclear receptor FTZ-F1. FTZ is thought to represents a category of LXXLL motif-dependent co-activators for nuclear receptors.. 
PF02952 fucose_iso_C; <br>L-fucose isomerase, C-terminal domain. Pfam-B_9303 (Release 8.0). 
PF02300 Fumarate reductase subunit C<br>Pfam-B_11568 (release 5.2). Fumarate reductase is a membrane-bound flavoenzyme consisting of  four subunits, A-B. A and B comprise the membrane-extrinsic catalytic domain and C and D link the catalytic centres to the electron-transport chain. This family consists of the 15kD hydrophobic subunit C.. 
PF02313 Fumarate reductase subunit D<br>Pfam-B_12414 (release 5.2). Fumarate reductase is a membrane-bound flavoenzyme consisting of  four subunits, A-B. A and B comprise the membrane-extrinsic catalytic domain and C and D link the catalytic centres to the electron-transport chain. This family consists of the 13kD hydrophobic subunit D.. 
PF03630 Fumble <br>Pfam-B_3299 (release 7.0). Fumble is required for cell division in Drosophila.  Mutants lacking fumble exhibit abnormalities in bipolar spindle organisation, chromosome segregation, and contractile ring formation. Analyses have demonstrated that encodes three protein isoforms, all of which contain a domain with  high similarity to the pantothenate kinases of A. nidulans and mouse . A role of fumble in membrane synthesis has been proposed .. 
PF04930 FUN14 family<br>Pfam-B_8237 (release 7.5). This family of short proteins are found in eukaryotes and some archaea.  Although the function of these proteins is not known they may contain transmembrane helices.. 
PF01475 Ferric uptake regulator family<br>Prodom_2003 (release 99.1). This family includes metal ion uptake regulator proteins, that bind to the operator DNA and controls transcription of metal ion-responsive genes.  This family is also known as the FUR family.. 
PF00757 Furin-like cysteine rich region<br>
PF04632 Fusaric acid resistance protein family<br>Pfam-B_5345 (release 7.5). This family includes a conserved region found in two proteins associated with fusaric acid resistance, Swiss:P24128 from Burkholderia cepacia  and Swiss:Q48403 from Klebsiella oxytoca. These proteins are likely to be membrane transporter proteins.. 
PF00523 fusion_gly; <br>Fusion glycoprotein F0. Pfam-B_102 (release 1.0). 
PF01621 Cell fusion glycoprotein K<br>Pfam-B_1083 (release 4.1). This protein is probably an integral membrane bound glycoprotein that is involved in viral fusion with the host cell  . . 
PF02663 FwdE;<br>FmdE, Molybdenum formylmethanofuran dehydrogenase operon . This entry represents the FmdE protein that is encode by the molybdenum formylmethanofuran dehydrogenase operon.  FmdE does not co-purify with the molybdenum isozyme that is formed by FmdC and FmdB  .  The domain is typically found as a single copy, but is repeated in some sequence two to three times.  It is also common place to find this domain co-occurs with a zinc-beta ribbon domain, suggesting that is may bind nucleic acid and be involved in transcription regulation.. 
PF04186 FxsA cytoplasmic membrane protein <br>This is a bacterial family of cytoplasmic membrane proteins. It includes two transmembrane regions. The molecular function of FxsA is unknown, but in Escherichia coli its over-expression has been shown to alleviate the exclusion of phage T7 in those cells with an F plasmid.. 
PF04799 fzo_mitofusin; <br>fzo-like conserved region. Pfam-B_6217 (release 7.5). Family of putative transmembrane GTPase.  The fzo protein is a mediator of mitochondrial fusion  . This conserved region is also found in the  human mitofusin protein  .. 
PF01125 G10 protein<br>
PF00503 G-protein alpha subunit<br>G proteins couple receptors of extracellular signals to intracellular signaling pathways. The G protein alpha subunit binds guanyl nucleotide and is a weak GTPase. A set of residues that are unique to G-alpha as compared to its ancestor the Arf-like family form a ring  of residues centered on the nucleotide binding site  . A Ggamma is  found fused to an inactive Galpha in the Dictyostelium protein gbqA   .. 
PF00631 G_protein_gamma; <br>G-protein gamma like domains (GGL) are found in the gamma subunit of the heterotrimeric G protein complex and in regulators of G protein signaling (RGS) proteins  . It is also found fused to an inactive  Galpha in the Dictyostelium protein gbqA  . G-gamma likely shares a common origin with the helical N-terminal unit of G-beta  . All organisms that posses a G-beta possess a G-gamma  .. 
PF04466 G2P; <br>Phage terminase large subunit. Initiation of packaging of double-stranded viral DNA involves the specific interaction of the prohead with viral DNA in a process mediated by a phage-encoded terminase protein. The terminase enzymes are usually hetero-oligomers composed of a small and a large subunit.  This region is found on the large subunit and possess an endonuclease and ATPase activity that require Mg2+ and a neutral or slightly basic reaction.  This region is also found in bacterial sequences [1,2].. 
PF04309 Glycerol-3-phosphate responsive antiterminator<br>Intracellular glycerol is usually converted to glycerol-3-phosphate in an  ATP-requiring phosphorylation reaction catalysed by glycerol kinase (GlpK) glycerol-3-phosphate activates the antiterminator GlpP  .. 
PF00479 G6PD; <br>Glucose-6-phosphate dehydrogenase, NAD binding domain. 
PF02781 Glucose-6-phosphate dehydrogenase, C-terminal domain<br>
PF01468 GA module<br>Pfam-B_895 (release 4.0). The GA (protein G-related Albumin-binding) module is composed of three alpha helices  . This module is found in a range of bacterial cell surface proteins. The GA module from Swiss:Q51911 shows a strong affinity for albumin.. 
PF02938 GAD domain<br>This domain is found in some members of the GatB and aspartyl tRNA synthetases.. 
PF02337 Retroviral GAG p10 protein<br>Pfam-B_959 (release 5.2). 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 with the virus envelope  glycoproteins in most mammalian retroviruses and may be involved in  virus particle assembly, transport and budding  . Some of the GAG polyproteins have alternate cleavage sites leading to  the production of alternative and longer cleavage products (e.g. p19  Swiss:P21411) the alignment of this family only covers the approximately  N-terminal (GAG) 100 amino acid region of homology to p10.. 
PF00540 gag_p17; <br>gag gene protein p17 (matrix protein). The matrix protein forms an icosahedral shell associated with the inner membrane of the mature immunodeficiency virus.. 
PF02228 gag_p19; <br>Major core protein p19. Pfam-B_1307 (release 5.2). p19 is a component of the inner protein layer of the viral  nucleocapsid.. 
PF00607 gag_p24; <br>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.. 
PF02093 Gag P30 core shell protein<br>According to Swiss-Prot annotation this protein is the viral core shell protein. P30 is essential for viral assembly  .. 
PF03276 Spumavirus gag protein<br>Pfam-B_1878 (release 6.5). 
PF00337 Galactoside-binding lectin<br>This family contains galactoside binding lectins.\.   The family also includes enzymes such as human eosinophil lysophospholipase (Swiss:Q05315, EC:3.1.1.5).. 
PF03902 Gal4-like dimerisation domain<br>
PF01762 Galactosyltransferase<br>Pfam-B_885 (release 4.2). This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferas e Swiss:O43825   and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase  Swiss:O54904  .  Specific galactosyltransferases transfer galactose to GlcNAc terminal  chains in the synthesis of the lacto-series oligosaccharides types 1  and 2  .. 
PF02709 Galactosyl_T_2; Glyco_transf_2C;<br>N-terminal domain of galactosyltransferase. Pfam-B_834 (release 5.5). This is the N-terminal domain of a family of galactosyltransferases from a wide range of Metazoa with three related galactosyltransferases activities, all three of which are possessed by one sequence in some cases.  EC:2.4.1.90, N-acetyllactosamine synthase; EC:2.4.1.38, Beta-N-acetylglucosaminyl-glycopeptide beta-1,4- galactosyltransferase; and EC:2.4.1.22 Lactose synthase. Note that N-acetyllactosamine synthase is a component of Lactose synthase along with alpha-lactalbumin, in the absence of alpha-lactalbumin EC:2.4.1.90 is the catalysed reaction.. 
PF01296 Galanin<br>
PF02052 Gallidermin<br>
PF02744 GalP_UDP_trans_C; <br>Galactose-1-phosphate uridyl transferase, C-terminal domain. SCOP reports fold duplication with N-terminal domain.  Both involved in Zn and Fe binding.. 
PF01087 Galactose-1-phosphate uridyl transferase, N-terminal domain<br>SCOP reports fold duplication with C-terminal domain.  Both involved in Zn and Fe binding.. 
PF00304 Gamma-thionin family<br>
PF04410 Gar1/Naf1 RNA binding region<br>Gar1 is a small nucleolar RNP that is required for pre-mRNA processing and pseudouridylation  . It is co-immunoprecipitated with the H/ACA families of snoRNAs. This family represents the conserved central region of Gar1. This region is necessary and sufficient for normal cell growth, and specifically binds two snoRNAs snR10 and snR30. This region is also necessary for nucleolar targeting, and it is thought that the protein is co-transported to the nucleolus as part of a nucleoprotein complex  . In humans, Gar1 is also component of telomerase in vivo  .  Naf1 is an essentail protein that plays a role in ribosome biogenesis, modification of spliceosomal small nuclear RNAs and telomere synthesis, and is homologous to Gar1  .. 
PF01071 GARS; <br>Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain. Pfam-B_916 (release 3.0). Phosphoribosylglycinamide synthetase catalyses the second step in  the de novo biosynthesis of purine. The reaction catalysed by Phosphoribosylglycinamide synthetase is the ATP- dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide. This domain is related to the ATP-grasp domain of biotin  carboxylase/carbamoyl phosphate synthetase (see Pfam:PF02786).. 
PF02843 Phosphoribosylglycinamide synthetase, C domain<br>Pfam-B_916 (release 3.0). Phosphoribosylglycinamide synthetase catalyses the second step in the de novo biosynthesis of purine. The reaction catalysed by Phosphoribosylglycinamide synthetase is the ATP- dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide. This domain is related to the C-terminal domain of biotin carboxylase/carbamoyl phosphate synthetase (see Pfam:PF02787).. 
PF02844 Phosphoribosylglycinamide synthetase, N domain<br>Pfam-B_916 (release 3.0). Phosphoribosylglycinamide synthetase catalyses the second step in the de novo biosynthesis of purine. The reaction catalysed by Phosphoribosylglycinamide synthetase is the ATP- dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide. This domain is related to the N-terminal domain of biotin carboxylase/carbamoyl phosphate synthetase (see Pfam:PF00289).. 
PF03198 GAS1; <br>Glucanosyltransferase. Pfam-B_2209 (release 6.5). This is a family of glycosylphosphatidylinositol-anchored beta(1-3)glucanosyltransferases. The active site residues in the Aspergillus fumigatus example Swiss:B0XT72 are the two glutamate residues at 160 and 261  .. 
PF02187 Growth-Arrest-Specific Protein 2 Domain<br>Alignment kindly provided by SMART. 
PF00741 Gas vesicle protein<br>Pfam-B_545 (release 2.1). 
PF01304 Gas vesicles protein GVPc repeated domain<br>
PF02704 Gibberellin regulated protein<br>Pfam-B_1221 (release 5.5). This is the GASA gibberellin regulated cysteine rich protein family.  The expression of these proteins is up-regulated by the plant hormone gibberellin, most of these proteins have some role in plant development. There are 12 cysteine residues conserved within the alignment giving the potential for these proteins to posses 6 disulphide bonds.. 
PF00918 Gastrin/cholecystokinin family<br>Pfam-B_1542 (release 3.0). 
PF00310 Glutamine amidotransferases class-II<br>Prosite & Pfam-B_5381 (Release 7.5) & Pfam-B_455 (release 7.6). 
PF04572 Alpha 1,4-glycosyltransferase conserved region<br>Pfam-B_4980 (release 7.5). The glycosphingolipids (GSL) form part of eukaryotic cell membranes. They consist of a hydrophilic carbohydrate moiety linked to a hydrophobic ceramide tail embedded within the lipid bilayer of the membrane. Lactosylceramide, Gal1,4Glc1Cer (LacCer), is the common synthetic precursor to the majority of GSL found in vertebrates. Alpha 1.4-glycosyltransferases utilise UDP donors and transfer the sugar to a beta-linked acceptor. This region appears to be confined to higher eukaryotes. No function has been yet assigned to this region  .  . 
PF02263 Guanylate-binding protein, N-terminal domain<br>Pfam-B_4308 (release 5.2) & Pfam-B_9065 (release 8.0). 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 Guanylate-binding protein, C-terminal domain<br>Pfam-B_4308 (release 5.2). 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.. 
PF02425 Paralytic/GBP/PSP peptide<br>Pfam-B_2690 (release 5.4). This family includes insect peptides that are short (23 amino acids) and contain 1 disulphide bridge.  The family includes growth-blocking peptide (GBP) of Pseudaletia separata and the paralytic peptides from Manduca sexta, Heliothis virescens, and Spodoptera exigua   as well as plasmatocyte-spreading peptide (PSP1)  . These peptides function to halt metamorphosis from larvae to pupae.. 
PF02526 Glycophorin-binding protein<br>Pfam-B_1047 (release 5.4). This family contains glycophorin binding proteins from P. falciparum the malarial parasite  . Glycophorin is a cell surface protein of erythrocytes. The Glycophorin binding protein contains a tandem 38 residue repeat. In Swiss:P02895 the repeat occurs 11 times.. 
PF04551 GcpE protein<br>Pfam-B_1482 (release 7.5). In a variety of organisms, including plants and several eubacteria, isoprenoids are synthesised by the mevalonate-independent 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway. Although different enzymes of this pathway have been described, the terminal biosynthetic steps of the MEP pathway have not been fully elucidated. GcpE gene of Escherichia coli is involved in this pathway  .. 
PF02155 Glucocorticoid receptor<br>
PF04107 Glutamate-cysteine ligase family 2(GCS2)<br>Also known as gamma-glutamylcysteine synthetase and gamma-ECS (EC:6.3.2.2). This enzyme catalyses the first and rate limiting step in de novo glutathione biosynthesis. Members of this family are found in archaea, bacteria and plants. May and Leaver   discuss the possible evolutionary origins of glutamate-cysteine ligase enzymes in different organisms and suggest that it evolved independently in different eukaryotes, from an ancestral bacterial enzyme. They also state that Arabidopsis thaliana gamma-glutamylcysteine synthetase is structurally unrelated to mammalian, yeast and Escherichia coli homologues. In plants, there are separate cytosolic and chloroplast forms of the enzyme.. 
PF01597 Glycine cleavage H-protein<br>Pfam-B_988 (release 4.1). This is a family of glycine cleavage H-proteins, part of the glycine  cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. A lipoyl group is attached to a completely conserved lysine residue. The H protein shuttles the methylamine group of glycine from the P protein to the T protein.. 
PF01571 Aminomethyltransferase folate-binding domain<br>Pfam-B_933 (release 4.0). This is a family of glycine cleavage T-proteins, part of the glycine  cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl transferase. . 
PF04295 D-galactarate dehydratase / Altronate hydrolase, C terminus<br>Family members include the C termini of D-galactarate dehydratase  (EC:4.2.1.42) which is thought to catalyse the reaction  D-galactarate = 5-keto-4-deoxy-D-glucarate + H2O,   and altronate  hydrolase (altronic acid hydratase, EC:4.2.1.7), which catalyses D-altronate = 2-keto-2-deoxygluconate + H2O  . As purified, both enzymes are catalytically inactive in the absence of  added Fe2+, Mn2+, and beta-mercaptoethanol.  Synergistic activation of altronate hydrolase activity is seen in the presence of both iron and manganese ions, suggesting that the enzyme may have two ion binding sites. Mn2+ appears to be part of the enzyme active centre, but the function of  the single bound Fe2+ ion is unknown.  The hydratase has no Fe-S core  .. 
PF01150 GDA1_CD39_NTPase; <br>GDA1/CD39 (nucleoside phosphatase) family. 
PF02347 Glycine cleavage system P-protein<br>Pfam-B_840 (release 5.2). This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources.  The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1.2.10 (GDC)  also annotated as glycine cleavage system or glycine synthase. GDC consists of four proteins P, H, L and T  .  The reaction catalysed by this protein is:-  Glycine + lipoylprotein <=> S-aminomethyldihydrolipoylprotein + CO2. 
PF00996 GDP dissociation inhibitor<br>Pfam-B_1220 (release 3.0). 
PF02351 GDNF/GAS1 domain<br>Pfam-B_889 (release 5.2). This cysteine rich domain is found in multiple copies in GNDF and GAS1 proteins. GDNF and neurturin (NTN) receptors are potent survival factors for sympathetic, sensory and central nervous system neurons  .  GDNF and neurturin promote neuronal survival by signaling through similar multicomponent receptors that consist of a common receptor tyrosine kinase and a member of a GPI-linked family of receptors that determines ligand specificity  .. 
PF02212 Dynamin GTPase effector domain<br>Alignment kindly provided by SMART. 
PF04807 Geminivirus AC4/5 conserved region<br>Pfam-B_3520 (release 7.6). 
PF00799 Geminivirus_AL1;<br>Geminivirus Rep catalytic domain. Pfam-B_286 (release 2.1). The AL1 proteins encodes the replication initiator protein (Rep) of geminiviruses, which is a replicon-specific initiator enzyme and is an essential component of the replisome  . For geminivirus Rep protein, this N-terminal region is crucial for origin recognition and DNA cleavage and nucleotidyl transfer  .. 
PF01440 Geminivirus AL2 protein<br>Prodom_1117 (release 99.1). Geminiviruses are small, ssDNA-containing plant viruses. Geminiviruses contain three ORFs (designated AL1, AL2, and AL3) that overlap and are specified by multiple polycistronic mRNAs. The AL2 gene product transactivates expression of TGMV coat protein gene  , and BR1 movement protein.. 
PF01407 Geminivirus AL3 protein<br>Pfam-B_1874 (release 3.0). Geminiviruses are small, ssDNA-containing plant viruses. Geminiviruses contain three ORFs (designated AL1, AL2, and AL3) that overlap and are specified by multiple polycistronic mRNAs. The AL3 protein comprises approximately 0.05% of the cellular proteins and is present in the soluble and organelle fractions  . AL3 may form oligomers  . Immunoprecipitation of AL3 in a baculovirus expression system extracts expressing both AL1 Pfam:PF00799 and AL3 showed that the two proteins also complex with each other  . The AL3 protein is involved in viral replication.. 
PF00845 Geminivirus BL1 movement protein<br>Pfam-B_1535 (release 2.1). Geminiviruses encode two movement proteins that are essential for systemic infection of their host but dispensable for replication and encapsidation.. 
PF01492 Geminivirus C4 protein<br>Pfam-B_453 (release 4.0). This family consists of the N terminal region of geminivirus C4 or AC4 proteins.  In Tomato yellow leaf curl geminivirus (TYLCV) the C4 protein is necessary for efficient spreading of the virus in tomato plants  .. 
PF00844 Geminivirus coat protein/nuclear export factor BR1 family<br>Pfam-B_1430 (release 2.1). It has been shown that the 104 N-terminal amino acids of the maize streak virus coat protein bind DNA non- specifically  . This family also includes various geminivirus movement proteins that are nuclear export factors or shuttles. One member BR1 facilitates the export of both ds and ss DNA form the nucleus  .. 
PF01708 Geminivirus putative movement protein <br>Pfam-B_1771 (release 4.1). This family consists of putative movement proteins from Maize streak and wheat dwarf virus.. 
PF01524 Geminivirus V1 protein<br>Pfam-B_893 (release 4.0). Disruption of the V1 gene in Tomato yellow leaf curl virus (TYLCV) stopped its ability to systemically infect tomato plants, suggesting that the V1 gene product is required for successful infection of the host  .. 
PF02053 Gene 66 (IR5) protein<br>
PF03323 Bacillus/Clostridium GerA spore germination protein<br>Pfam-B_3821 (release 6.5). 
PF00196 Bacterial regulatory proteins, luxR family<br>
PF01353 Green fluorescent protein<br>
PF05165 GGDN family<br>I have named this protein family of unknown function GGDN after the most conserved motif. The proteins are 200-270 amino acids in length.. 
PF01134 Glucose inhibited division protein A<br>Prosite & Pfam-B_4007 (Release 8.0). 
PF02527 rRNA small subunit methyltransferase G<br>Pfam-B_1265 (release 5.4). This is a family of bacterial glucose inhibited division proteins these are probably involved in the regulation of cell devision  . GidB has been shown to be a methyltransferase G specific to the rRNA small subunit [2, 3]. Previously identified as a glucose-inhibited division protein B that appears to be present and in a single copy in all complete eubacterial genomes so far sequenced. GidB specifically methylates the N7 position of a guanosine in 16S rRNA  .. 
PF03227 Gamma interferon inducible lysosomal thiol reductase (GILT)<br>Pfam-B_1477 (release 6.5). This family includes the two characterised human gamma-interferon-inducible lysosomal thiol reductase (GILT) sequences: Swiss:P13284   and Swiss:Q9UL08  . It also contains several other eukaryotic putative proteins with similarity to GILT  . The aligned region contains three conserved cysteine residues. In addition, the two GILT sequences possess a C-X(2)-C motif that is shared by some of the other sequences in the family. This motif is thought to be associated with disulphide bond reduction.. 
PF03359 Guanylate-kinase-associated protein (GKAP) protein<br>Pfam-B_1892 (release 6.6). 
PF03275 UDP-galactopyranose mutase<br>Pfam-B_4203 (release 6.5). 
PF02812 E_L_F_V_dh; GLFV_dehydrog_N; <br>Glu/Leu/Phe/Val dehydrogenase, dimerisation domain. 
PF00120 gln-synt; <br>Glutamine synthetase, catalytic domain. 
PF03951 gln-synt_N; <br>Glutamine synthetase, beta-Grasp domain. 
PF03710 Glutamate-ammonia ligase adenylyltransferase<br>Conserved repeated domain found in GlnE proteins. These proteins  adenylate and deadenylate glutamine synthases: ATP + {L-Glutamate:ammonia ligase (ADP-forming)} = Diphosphate + Adenylyl-{L-Glutamate:Ammonia ligase  (ADP-forming)}. The family is related to the  Pfam:PF01909 domain.. 
PF03616 Sodium/glutamate symporter<br>TIGRFAMs, Griffiths-Jones SR. 
PF01744 GLTT repeat (6 copies)<br>Pfam-B_681 (release 4.2). This short repeat of unknown function is found in multiple copies in several C. elegans proteins. The repeat is five residues long and consists of XGLTT where X can be any amino acid.. 
PF02686 Glu-tRNAGln amidotransferase C subunit<br>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 correct Gln-tRANGln via transmidation of the misacylated Glu-tRNAGln  .  This activity supplements the lack  of glutaminyl-tRNA synthetase activity in gram-positive eubacterteria, cyanobacteria, Archaea, and organelles  .. 
PF05096 Glutamine cyclotransferase<br>This family of enzymes EC:2.3.2.5 catalyse the cyclization of free L-glutamine and N-terminal glutaminyl residues in proteins to pyroglutamate (5-oxoproline) and pyroglutamyl residues respectively  . This family includes plant and bacterial enzymes and seems unrelated to the mammalian enzymes.. 
PF04262 glu_cys_ligase; <br>Glutamate-cysteine ligase . TIGRFAMs (release 2.0);. Family of bacterial f glutamate-cysteine ligases (EC:6.3.2.2) that carry out the first step of the glutathione biosynthesis pathway.. 
PF01645 Conserved region in glutamate synthase<br>Pfam-B_719 (release 4.1). This family represents a region of the glutamate synthase protein.  This region is expressed as a separate subunit in the glutamate synthase alpha subunit from archaebacteria, or part of a large multidomain enzyme in other organisms. The aligned region of these proteins contains a putative FMN binding site and Fe-S cluster.. 
PF02364 1,3-beta-glucan synthase component <br>Pfam-B_686 (release 5.2). 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-glucan polymer that is a major component of the fungal cell wall  . The reaction catalysed is:- UDP-glucose + {(1,3)-beta-D-glucosyl}(N) <=> UDP + {(1,3)-beta-D-glucosyl}(N+1).. 
PF02685 Glucokinase<br>This is a family of glucokinases or glucose kinases EC:2.7.1.2. These enzymes phosphorylate glucose using ATP as a donor to give glucose-6-phosphate and ADP.. 
PF01182 Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase<br>
PF00462 glutaredoxin; <br>Prosite & Pfam-B_3081 (Release 8.0). 
PF04399 Glutaredoxin 2, C terminal domain<br>Glutaredoxins are a multifunctional family of glutathione-dependent disulphide oxidoreductases.  Unlike other glutaredoxins, glutaredoxin 2 (Grx2) cannot reduce ribonucleotide reductase.  Grx2 has significantly higher catalytic activity in the reduction of mixed disulphides with glutathione (GSH) compared with other glutaredoxins. The active site residues (Cys9-Pro10-Tyr11-Cys12, in Escherichia coli Grx2, Swiss:P39811), which are found at the interface between the N- and C-terminal domains are identical to other glutaredoxins, but there is no other similarity between glutaredoxin 2 and other glutaredoxins. Grx2 is structurally similar to glutathione-S-transferases (GST), but there is no obvious sequence similarity. The inter-domain contacts are mainly hydrophobic, suggesting that the two domains are unlikely to be stable on their own.  Both domains are needed for correct folding and activity of Grx2. It is thought that the primary function of Grx2 is to catalyse reversible glutathionylation of proteins with GSH in cellular redox regulation including the response to oxidative stress.. 
PF03157 High molecular weight glutenin subunit<br>Pfam-B_2180 (release 6.5). 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 high molecular weight subunits are classified as elastomeric proteins, because the glutenin network can withstand significant deformations without breaking, and return to the original conformation when the stress is removed. Elastomeric proteins differ considerably in amino acid sequence, but they are all polymers whose subunits consist of elastomeric domains, composed of repeated motifs, and non-elastic domains that mediate cross-linking between the subunits. The elastomeric domain motifs are all rich in glycine residues in addition to other hydrophobic residues.  High molecular weight glutenin subunits have an extensive central elastomeric domain, flanked by two terminal non-elastic domains that form disulphide cross-links. The central elastomeric domain is characterised by the following three repeated motifs: PGQGQQ, GYYPTS[P/L]QQ, GQQ. It possesses overlapping beta-turns within and between the repeated motifs, and assumes a regular helical secondary structure with a diameter of approx. 1.9 nm and a pitch of approx. 1.5 nm [see 1, fig.2].. 
PF00745 GlutR; <br>Glutamyl-tRNAGlu reductase, dimerisation domain. Pfam-B_544 (release 2.1). 
PF05201 Glutamyl-tRNAGlu reductase, N-terminal domain<br>
PF02595 DUF168; <br>Glycerate kinase family. This is family of Glycerate kinases.. 
PF01228 Glycine radical<br>
PF00232 glycosyl_hydro1; <br>Glycosyl hydrolase family 1. 
PF00331 glycosyl_hydro3; <br>Glycosyl hydrolase family 10. 
PF00457 glycosyl_hydro6; <br>Glycosyl hydrolases family 11. 
PF01109 Granulocyte-macrophage colony-stimulating factor<br>
PF01670 Glycosyl hydrolase family 12<br>Pfam-B_1736 (release 4.1). 
PF01373 Glycosyl_hydr22; <br>Glycosyl hydrolase family 14. This family are beta amylases.. 
PF00723 glycosyl_hydr10;<br>Glycosyl hydrolases family 15. Pfam-B_771 (release 2.1). In higher organisms this family is represented by phosphorylase kinase subunits.. 
PF00332 glycosyl_hydro4; <br>Glycosyl hydrolases family 17. 
PF00182 chitinase_1; <br>
PF00703 glycosyl_hydro7;<br>Glycosyl hydrolases family 2. Pfam-B_572 (release 2.1). This family contains beta-galactosidase, beta-mannosidase and beta-glucuronidase activities.. 
PF00728 glycosyl_hydr11; <br>Glycosyl hydrolase family 20, catalytic domain. Pfam-B_877 (release 2.1). This domain has a TIM barrel fold.. 
PF02838 glycosyl_hydr11; <br>Glycosyl hydrolase family 20, domain 2. Pfam-B_877 (release 2.1). This domain has a zincin-like fold.. 
PF01183 Glycosyl_hydr18;<br>Glycosyl hydrolases family 25. 
PF02156 Glycosyl hydrolase family 26<br>
PF00295 PG; <br>Glycosyl hydrolases family 28. Glycosyl hydrolase family 28 includes polygalacturonase EC:3.2.1.15 as well as rhamnogalacturonase A(RGase A), EC:3.2.1.-.  These enzymes is important in cell wall metabolism.. 
PF02836 glycosyl_hydro7; <br>Glycosyl hydrolases family 2, TIM barrel domain. Pfam-B_572 (release 2.1). This family contains beta-galactosidase, beta-mannosidase and beta-glucuronidase activities.. 
PF02837 glycosyl_hydro7; <br>Glycosyl hydrolases family 2, sugar binding domain. Pfam-B_572 (release 2.1). This family contains beta-galactosidase, beta-mannosidase and beta-glucuronidase activities and has a jelly-roll fold.. 
PF00933 glycosyl_hydr14;<br>Glycosyl hydrolase family 3 N terminal domain. Pfam-B_1151 (release 3.0). 
PF00251 glycosyl_hydro2; Glyco_hydro_32; <br>Glycosyl hydrolases family 32 N-terminal domain. This domain corresponds to the N-terminal domain of glycosyl hydrolase family 32 which forms a five bladed beta propeller structure  .. 
PF01301 Glycosyl_hydr17; <br>Glycosyl hydrolases family 35. 
PF01074 Glycosyl_hydr16;<br>Glycosyl hydrolases family 38 N-terminal domain. Pfam-B_731 (release 3.0). Glycosyl hydrolases are key enzymes of carbohydrate metabolism.. 
PF01229 Glycosyl_hydr19;<br>Glycosyl hydrolases family 39. 
PF01915 glycosyl_hydr14; <br>Glycosyl hydrolase family 3 C-terminal domain. Pfam-B_1151 (release 3.0). This domain is involved in catalysis and may be involved in binding beta-glucan  . This domain is found associated with Pfam:PF00933.. 
PF02056 Family 4 glycosyl hydrolase<br>
PF02449 Beta-galactosidase<br>Pfam-B_2131 (release 5.4). This group of beta-galactosidase enzymes belong to the glycosyl hydrolase 42 family. The enzyme catalyses the hydrolysis of terminal, non-reducing terminal beta-D-galactosidase residues.. 
PF04616 Glycosyl hydrolases family 43<br>Pfam-B_5336 (release 7.5). The glycosyl hydrolase family 43 contains members that are arabinanase.  Rabinanases hydrolyses the alpha-1,5-linked  L-arabinofuranoside backbone of plant cell wall arabinans.  The structure of arabinanase Arb43A from Cellvibrio japonicus reveals a five-bladed beta-propeller fold. A long V-shaped  groove, partially enclosed at one end, forms a single extended  substrate-binding surface across the face of the propeller  .. 
PF02015 Glycosyl hydrolase family 45<br>
PF01374 Glycosyl_hydr23; <br>Glycosyl hydrolase family 46. This family are chitosanase enzymes.. 
PF02011 Glycosyl hydrolase family 48<br>Members of this family are endoglucanase EC:3.2.1.4 and exoglucanase EC:3.2.1.91 enzymes that cleave cellulose or related substrate.. 
PF03718 Glycosyl hydrolase family 49<br>Family of dextranase (EC 3.2.1.11) and isopullulanase (EC 3.2.1.57). Dextranase hydrolyses alpha-1,6-glycosidic bonds in dextran polymers.. 
PF03512 Glycosyl hydrolase family 52<br>
PF01630 Hyaluronidase<br>Pfam-B_1150 (release 4.1). 
PF03065 Glycosyl hydrolase family 57<br>Pfam-B_2506 (release 6.4). This family includes alpha-amylase (EC:3.2.1.1), 4--glucanotransferase (EC:2.4.1.-) and amylopullulanase enzymes.. 
PF02057 Glycosyl hydrolase family 59<br>
PF01341 Glycosyl_hydr21; <br>Glycosyl hydrolases family 6. 
PF03443 Glycosyl hydrolase family 61<br>Although weak endoglucanase activity has been demonstrated in several members of this family [1-3], they lack the clustered conserved catalytic acidic amino acids present in most glycoside hydrolases. Many members of this family lack measurable cellulase activity on their own, but enhance the activity of other cellulolytic enzymes. They are therefore unlikely to be true glycoside hydrolases  .. 
PF03664 Glycosyl hydrolase family 62 <br>Family of alpha -L-arabinofuranosidase (EC 3.2.1.55).  This enzyme hydrolysed aryl alpha-L-arabinofuranosides and  cleaves arabinosyl side chains from arabinoxylan and arabinan. . 
PF03633 Glyco_hydro_65c; <br>Glycosyl hydrolase family 65, C-terminal domain . Pfam-B_3470 (release 7.0). This family of glycosyl hydrolases contains vacuolar acid trehalase and maltose phosphorylase.Maltose phosphorylase (MP)  is a dimeric enzyme that catalyses the conversion of maltose and  inorganic phosphate into beta-D-glucose-1-phosphate and glucose.  The C-terminal domain forms a two layered jelly roll motif.  This domain is situated at the base of the catalytic domain, however its function remains unknown  .. 
PF03632 Glycosyl hydrolase family 65 central catalytic domain<br>Pfam-B_3470 (release 7.0). This family of glycosyl hydrolases contains vacuolar acid trehalase and maltose phosphorylase.Maltose phosphorylase (MP) is a dimeric enzyme that catalyses the conversion of maltose and inorganic phosphate into beta-D-glucose-1-phosphate and glucose. The central domain is the catalytic domain, which binds a phosphate ion that is proximal the the highly conserved Glu.  The arrangement of the phosphate and the glutamate is thought to cause nucleophilic attack on the anomeric carbon atom  .  The catalytic domain also forms the majority of the dimerisation interface.. 
PF03636 Glyco_hydro_65n; <br>Glycosyl hydrolase family 65, N-terminal domain . Pfam-B_3470 (release 7.0). This family of glycosyl hydrolases contains vacuolar acid trehalase and maltose phosphorylase.Maltose phosphorylase (MP)  is a dimeric enzyme that catalyses the conversion of maltose and  inorganic phosphate into beta-D-glucose-1-phosphate and glucose.  This domain is believed to be essential for catalytic activity   although its precise function remains unknown.. 
PF02435 Levansucrase/Invertase<br>Pfam-B_2011 (release 5.4). This Pfam family consists of the glycosyl hydrolase 68 family, including several bacterial levansucrase enzymes, and invertase from zymomonas.. 
PF00840 glycosyl_hydr13; <br>Glycosyl hydrolase family 7. Pfam-B_1478 (release 2.1). 
PF02324 Gluco_S_transf; <br>Glycosyl hydrolase family 70. Pfam-B_965 (release 5.2). Members of this family belong to glycosyl hydrolase family 70   Glucosyltransferases or sucrose 6-glycosyl transferases (GTF-S) catalyse the transfer of D-glucopyramnosyl units from sucrose  onto acceptor molecules  , EC:2.4.1.5.  This family roughly corresponds to the N-terminal catalytic domain of the enzyme. Members of this family also contain the Putative cell wall binding domain Pfam:PF01473, which corresponds with the C-terminal glucan-binding domain.. 
PF03659 Glycosyl hydrolase family 71 <br>Family of alpha-1,3-glucanases. . 
PF03662 Glycosyl hydrolase family 79, N-terminal domain <br>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 matrices. Hence, cleavage of heparan sulfate (HS) affects the integrity and functional state of tissues and thereby fundamental normal and pathological phenomena involving cell migration and response to changes in the extracellular micro-environment.  Heparanase degrades HS at specific intra-chain sites. The enzyme is synthesised as a latent approximately 65 kDa protein that is processed at the N-terminus into a highly active approximately 50 kDa form.  Experimental evidence suggests that heparanase may facilitate both tumour cell invasion and neovascularization, both critical steps in cancer progression. The enzyme is also involved in cell migration associated with inflammation and autoimmunity  .. 
PF01270 Glycosyl_hydr20; <br>Glycosyl hydrolases family 8. 
PF03639 Glycosyl hydrolase family 81 <br>Family of eukaryotic beta-1,3-glucanases. Within the Aspergillus fumigatus protein Swiss:Q9UVV0 two perfectly conserved Glu residues (E550 or E554) have been proposed as putative nucleophiles of the active site of the Engl1 endoglucanase, while the proton donor would be D475. The endo-beta-1,3-glucanase activity is essential for efficient spore release  .. 
PF00759 glycosyl_hydr12; <br>Glycosyl hydrolase family 9. Pfam-B_843 (release 2.1). 
PF03808 Glycosyl transferase WecB/TagA/CpsF family<br>TIGRFAMs, Griffiths-Jones SR. 
PF01531 Glycosyl transferase family 11<br>Pfam-B_935 (release 4.0). This family contains several fucosyl transferase enzymes.. 
PF01793 Glycolipid 2-alpha-mannosyltransferase<br>Pfam-B_1324 (release 4.2). This is a family of alpha-1,2 mannosyl-transferases involved in N-linked and O-linked glycosylation of proteins.  Some of the enzymes in this family have been shown to be involved in O- and N-linked glycan modifications in the Golgi  .. 
PF03076 Equine arteritis virus GP3<br>Pfam-B_687 (release 6.4). This protein is encoded by ORF3 of equine arteritis virus. The function is unknown.. 
PF04724 Glyco_tranf_17; <br>Glycosyltransferase family 17. Pfam-B_5914 (release 7.5). This family represents beta-1,4-mannosyl-glycoprotein beta-1,4-N-acetylglucosaminyltransferase (EC:2.4.1.144). This enzyme transfers the bisecting GlcNAc to the core mannose of complex N-glycans. The addition of this residue is regulated during development and has functional consequences for receptor signalling, cell adhesion, and tumour progression [1,2].. 
PF03033 Glycosyltransferase family 28 N-terminal domain<br>Pfam-B_1105 (release 6.4) & Pfam-B_2764 (release 7.5). The glycosyltransferase family 28 includes  monogalactosyldiacylglycerol synthase (Swiss:P93115, EC 2.4.1.46) and UDP-N-acetylglucosamine transferase (Swiss:P74657, EC 2.4.1.-). This N-terminal domain contains the acceptor binding site and likely membrane association site. This family also contains a large number of proteins that probably have quite distinct activities.. 
PF04666 GnT_IV_N; Glyco_transf_55; <br>N-Acetylglucosaminyltransferase-IV (GnT-IV) conserved region. Pfam-B_4541 (release 7.5). The complex-type of oligosaccharides are synthesised through elongation by glycosyltransferases after trimming of the precursor oligosaccharides transferred to proteins in the endoplasmic reticulum. N-Acetylglucosaminyltransferases (GnTs) take part in the formation of branches in the biosynthesis of complex-type sugar chains. In vertebrates, six GnTs, designated as GnT-I to -VI, which catalyse the transfer of GlcNAc to the core mannose residues of Asn-linked sugar chains, have been identified. GnT-IV (EC:2.4.1.145) catalyses the transfer of GlcNAc from UDP-GlcNAc to the GlcNAc1-2Man1-3 arm of core oligosaccharide [Gn2(22)core oligosaccharide] and forms GlcNAc1-4(GlcNAc1-2)Man1-3 structure on the core oligosaccharide (Gn3(2,4,2)core oligosaccharide).  In some members the conserved region occupies all but the very for N-terminal, where there is a signal sequence on all members. For other members the conserved region does not occupy the entire protein but is still to the N-terminus of the protein  .. 
PF03414 Glycosyltransferase family 6<br>Pfam-B_4383 (release 6.6). 
PF01075 Heptosyltranf;<br>Glycosyltransferase family 9 (heptosyltransferase). Pfam-B_839 (release 3.0). Members of this family belong to glycosyltransferase family 9  .  Lipopolysaccharide is a major component of the outer leaflet of the outer membrane in Gram-negative bacteria. It is composed of three domains; lipid A, Core oligosaccharide and the O-antigen. All of these enzymes transfer heptose to the lipopolysaccharide core.. 
PF00274 glycolytic_enzy; <br>Fructose-bisphosphate aldolase class-I. 
PF01102 Glycophorin A<br>
PF00606 Herpesvirus Glycoprotein B<br>This family of proteins contains a transmembrane region.. 
PF00802 Pneumovirus attachment glycoprotein G<br>Pfam-B_1049 (release 2.1). This family includes attachment proteins from respiratory synctial virus.  Glycoprotein G has not been shown to have any neuraminidase or hemagglutinin activity (Swiss-Prot). The amino terminus is thought to be cytoplasmic, and the carboxyl terminus extracellular.  The extracellular region contains four completely conserved cysteine residues.. 
PF02885 glycosyl_transf_3; <br>Glycosyl transferase family, helical bundle domain. MRC-LMB Genome group. This family includes anthranilate phosphoribosyltransferase (TrpD), thymidine phosphorylase.  All these proteins can transfer a phosphorylated ribose substrate.. 
PF00534 glycosyl_transf_1; <br>Glycosyl transferases group 1. MRC-LMB Genome group. Mutations in this domain of Swiss:P37287 lead to disease  (Paroxysmal Nocturnal haemoglobinuria). Members of this family transfer activated sugars to a variety  of substrates, including glycogen, Fructose-6-phosphate and lipopolysaccharides. Members of this family transfer UDP, ADP,  GDP or CMP linked sugars. The eukaryotic glycogen synthases may be distant members of this family.. 
PF00591 glycosyl_transf_3; <br>Glycosyl transferase family, a/b domain. MRC-LMB Genome group. This family includes anthranilate phosphoribosyltransferase (TrpD), thymidine phosphorylase.  All these proteins can transfer a phosphorylated ribose substrate.. 
PF04413 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase)<br>Members of this family transfer activated sugars to a variety of substrates, including glycogen, fructose-6-phosphate and lipopolysaccharides.  Members of the family transfer UDP, ADP, GDP or CMP linked sugars.  The Glycos_transf_N region is flanked at the N-terminus by a signal peptide and at the C-terminus by Glycos_transf_1 (Pfam:PF00534).  The eukaryotic  glycogen synthases may be distant members of this bacterial  family  .. 
PF01153 Glypican<br>
PF05199 GMC oxidoreductase<br>Pfam-B_891 (release 2.1). This domain found associated with Pfam:PF00732.. 
PF00732 GMC_oxred; <br>Pfam-B_891 (release 2.1). This family of proteins bind FAD as a cofactor.. 
PF00446 Gonadotropin-releasing hormone<br>
PF03071 GNT-I family<br>Pfam-B_2207 (release 6.4). 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 complex or hybrid-type N-linked oligosaccharides. The enzyme is an integral membrane protein localised to the Golgi  apparatus, and is probably distributed in all tissues. The catalytic domain is located at the C-terminus  .. 
PF02447 GntP family permease<br>Pfam-B_1928 (release 5.4). This is a family of integral membrane permeases that are involved in gluconate uptake. E. coli contains several members of this family including GntU Swiss:P46858 a low affinity transporter   and GntT Swiss:P39835 a high affinity transporter  .. 
PF00392 gntR; <br>Bacterial regulatory proteins, gntR family. Prosite & Pfam-B_6405 (Release 8.0). This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector-binding/oligomerisation domain. The GntR-like proteins include the following sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA, DevA, DasR [1-2]  . Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships  . The DasR regulator has been shown to be a global regulator of primary metabolism and development in Streptomyces coelicolor  .. 
PF02188 GoLoco motif<br>Alignment kindly provided by SMART. 
PF04178 Got1/Sft2-like family <br>Pfam-B_7371 (release 7.3) & Pfam-B_8991 (release 14.0). 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  .  This is a family of sequences derived from eukaryotic proteins. They are similar to a region of a SNARE-like protein required for traffic through the Golgi complex, SFT2 protein (Swiss:P38166)  . This is a conserved protein with four putative transmembrane helices, thought to be involved in vesicular transport in later Golgi compartments  .. 
PF00516 Envelope glycoprotein GP120<br>Pfam-B_44 (release 1.0). The entry of HIV requires interaction of viral GP120 with Swiss:P01730 and a chemokine receptor on the cell surface.. 
PF03010 GP4<br>Pfam-B_1094 (release 6.4). GP4 is a minor membrane-associated glycoproteins. This family contains envelope protein GP4 from equine arteritis virus.. 
PF00517 Retroviral envelope protein<br>Pfam-B_44 (release 1.0). This family includes envelope protein from a variety of retroviruses. It includes the GP41 subunit of the envelope protein complex from human and simian immunodeficiency viruses (HIV and SIV) which mediate membrane fusion during viral entry. The family also includes bovine immunodeficiency virus, feline immunodeficiency virus and Equine infectious anaemia (EIAV). The family also includes the Gp36 protein from mouse mammary tumour virus (MMTV) and human endogenous retroviruses (HERVs).. 
PF02925 Bacteriophage scaffolding protein D<br>
PF00044 gpdh; <br>Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain. Eddy SR, Griffiths-Jones SR. GAPDH is a tetrameric NAD-binding enzyme involved in glycolysis and glyconeogenesis. N-terminal domain is a Rossmann NAD(P) binding fold.. 
PF02800 gpdh_C; <br>Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain. Eddy SR, Griffiths-Jones SR. GAPDH is a tetrameric NAD-binding enzyme involved in glycolysis and glyconeogenesis. C-terminal domain is a mixed alpha/antiparallel beta fold.. 
PF05024 N-acetylglucosaminyl transferase component (Gpi1)<br>Pfam-B_4796 (release 7.6). Glycosylphosphatidylinositol (GPI) represents an important anchoring  molecule for cell surface proteins.The first step in its synthesis is the transfer of N-acetylglucosamine (GlcNAc) from UDP-N-acetylglucosamine to  phosphatidylinositol (PI). This chemically simple step is genetically  complex because three or four genes are required in both yeast  (GPI1, GPI2 and GPI3) and mammals (GPI1, PIG A, PIG H and PIG C), respectively  .. 
PF04113 Gpi16 subunit, GPI transamidase component<br>Pfam-B_7012 (release 7.3);. 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  synthesised proteins.  Gpi16 is an essential N-glycosylated transmembrane glycoprotein. Gpi16 is largely found on the lumenal side of the ER. It has a single C-terminal transmembrane domain and a small  C-terminal, cytosolic extension with an ER retrieval motif  .. 
PF02831 gpW<br>gpW is a 68 residue protein known to be present in  phage particles. Extracts of phage-infected cells lacking gpW contain DNA-filled heads, and active tails, but no infectious virions. gpW is required for the addition of gpFII to the head, which is, in turn, required for the attachment of tails. Since gpFII and tails are known to be attached at the connector, gpW is also likely to assemble at this site. The addition of gpW to filled heads increases the DNase resistance of the packaged DNA, suggesting that gpW either forms a plug at the connector to prevent ejection of the DNA, or binds directly to the DNA. The large number of positively charged residues in gpW (its calculated pI is 10.8) is consistent with a role in DNA interaction  .. 
PF04965 Gene 25-like lysozyme<br>This family includes the phage protein Gene 25 from T4 which is a structural component of the outer wedge of the baseplate that has acidic lysozyme activity  . The family also includes relatives from bacteria that are also presumably lysozymes.. 
PF05084 Granule antigen protein (GRA6)<br>Pfam-B_6204 (release 7.7). This family contains the granule antigen protein GRA6 which is found in the parasitic protozoa Toxoplasma gondii and Neospora caninum. GRA6 protein plays an important role in the antigenicity and pathogenicity in these organisms  .. 
PF00267 Gram-ve_porins; <br>
PF00746 Gram positive anchor<br>Pfam-B_457 (release 2.1). 
PF01271 Granin (chromogranin or secretogranin)<br>
PF00396 granulin; <br>
PF04495 GRASP55/65 PDZ-like domain <br>Pfam-B_3985 (release 7.5). GRASP55 (Golgi re-assembly stacking protein of 55 kDa) and GRASP65 (a 65 kDa) protein are highly homologous. GRASP55 is a component of the Golgi stacking machinery. GRASP65, an N-ethylmaleimide- sensitive membrane protein required for the stacking of Golgi cisternae in a cell-free system  .  This region appears to be related to the PDZ domain.. 
PF04723 Glycine reductase complex selenoprotein A<br>Found in clostridia, this protein contains one active site selenocysteine and catalyses the reductive deamination of glycine, which is coupled to the esterification of orthophosphate resulting in the formation of ATP  . A member of this family may also exist in Treponema denticola  .. 
PF01272 Transcription elongation factor, GreA/GreB, C-term<br>This domain has an FKBP-like fold.. 
PF03449 Transcription elongation factor, N-terminal<br>This domain adopts a long alpha-hairpin structure.. 
PF01184 GPR1/FUN34/yaaH family<br>The Ady2 protein in (Swiss:P25613) is required for acetate in Saccharomyces cerevisiae, and is probably an acetate transporter. A homologue in Yarrowia lipolytica (GPR1) has a role in acetic acid sensitivity.. 
PF01025 GrpE<br>Pfam-B_817 (release 3.0). 
PF02955 Prokaryotic glutathione synthetase, ATP-grasp domain<br>
PF02951 GTS_N; <br>Prokaryotic glutathione synthetase, N-terminal domain. 
PF03917 Eukaryotic glutathione synthase, ATP binding domain<br>Pfam-B_2922 (release 6.5). 
PF03199 Eukaryotic glutathione synthase<br>Pfam-B_2922 (release 6.5). 
PF00255 Glutathione peroxidase<br>
PF03738 Glutathionylspermidine synthase preATP-grasp<br>This region contains the Glutathionylspermidine synthase enzymatic activity EC:6.3.1.8. This is the C-terminal region in bienzymes such as Swiss:P43675. Glutathionylspermidine (GSP) synthetases of Trypanosomatidae and Escherichia coli couple hydrolysis of ATP (to ADP and Pi) with formation of an amide bond between spermidine and the glycine carboxylate of glutathione (gamma-Glu-Cys-Gly). In the pathogenic trypanosomatids, this reaction is the penultimate step in the biosynthesis of the antioxidant metabolite, trypanothione (N1,N8-bis-(glutathionyl)spermidine), and is a target for drug design  . This region, the pre-ATP grasp region, probably carries the substrate-binding site  .. 
PF00437 GSPII_E;<br>Type II/IV secretion system protein. Prosite & Pfam-B_2215 (Release 8.0). This family contains both type II and type IV Swiss:P54907 pathway secretion proteins from bacteria. Swiss:P07169 VirB11 ATPase is a subunit of the Agrobacterium tumefaciens transfer DNA (T-DNA) transfer system, a type IV secretion pathway required for delivery of T-DNA and effector proteins to plant cells during infection  . . 
PF05157 GSPII_E_N;<br>Type II secretion system (T2SS), protein E, N-terminal domain. This domain is found at the N-terminus of members of the Type II secretion system protein E. Proteins in this subfamily are typically involved in Type 4 pilus biogenesis (eg Swiss:Q9X4G8), though some are involved in other processes; for instance aggregation in Myxococcus xanthus (Swiss:Q9RF11)  . The structure of this domain is now known [2,3].. 
PF00482 GSPII_F;<br>Type II secretion system (T2SS), protein F. The original family covered both the regions found by the current model. The splitting of the family has allowed the related FlaJ_arch (archaeal FlaJ family) to be merged with it. Proteins with this domain in form a platform for the machiney of the Type II secretion system, as well as the Type 4 pili and the archaeal flagella  . This domain seems to show some similarity to PF00664 but this may just be due to similarities in the TM helices (personal obs: C Yeats).. 
PF00263 Bac_GSPproteins; GSPII_III; Secretin; Secretin_C; <br>Bacterial type II and III secretion system protein. 
PF01203 T2SP_N; GSPII_N;<br>Type II secretion system (T2SS), protein N. Members of the T2SN family are involved in the Type II protein secretion system. The precise function of these proteins is unknown.. 
PF03958 NolW-like; GSPII_III_N; <br>Bacterial type II/III secretion system short domain. This is a short, often repeated, domain found in bacterial type II/III secretory system proteins.\.    All previous NolW-like domains fall into this family.. 
PF02501 GSPII_IJ;<br>Type II secretion system (T2SS), protein I. Pfam-B_2607 (release 5.4). The Type II secretion system, also called Secretion-dependent pathway (SDP), is responsible for the transport of proteins across the outer membrane first exported to the periplasm by the Sec or Tat translocon in Gram-negative (diderm) bacteria. As members of the T2SJ family, members of the T2SI family are pseudopilins containing prepilin signal sequences  .. 
PF03934 GspK;<br>Type II secretion system (T2SS), protein K. Members of this family are involved in the Type II protein secretion system. The T2SK family includes proteins such as ExeK, PulK, OutX  and XcpX.. 
PF05134 GspL;<br>Type II secretion system (T2SS), protein L. Pfam-B_6494 (release 7.7). This family consists of Type II secretion system protein L sequences from several Gram-negative (diderm) bacteria. The Type II secretion system, also called Secretion-dependent pathway (SDP), is responsible for extracellular secretion of a number of different proteins, including proteases and toxins. This pathway supports secretion of proteins across the cell envelope in two distinct steps, in which the second step, involving translocation through the outer membrane, is assisted by at least 13 different gene products. T2SL is predicted to contain a large cytoplasmic domain represented by this family and has been shown to interact with the autophosphorylating cytoplasmic membrane protein T2SE. It is thought that the tri-molecular complex of T2SL, T2SE (Pfam:PF00437) and T2SM (Pfam:PF04612) might be involved in regulating the opening and closing of the secretion pore and/or transducing energy to the site of outer membrane translocation  .. 
PF04612 GspM;<br>Type II secretion system (T2SS), protein M. Pfam-B_5302 (release 7.5). This family of membrane proteins consists of Type II secretion system protein M sequences from several Gram-negative (diderm) bacteria. The precise function of these proteins is unknown, though in Vibrio cholerae, the T2SM (EpsM) protein interacts with the T2SL (EpsL) protein, and also forms homodimers  .. 
PF00043 gluts; GST;<br>Glutathione S-transferase, C-terminal domain. Eddy SR, Griffiths-Jones SR. GST conjugates reduced glutathione to a variety of targets including S-crystallin from squid, the eukaryotic elongation factor 1-gamma, the HSP26 family of stress-related proteins and auxin-regulated proteins in plants.  Stringent starvation proteins in E. coli are also included in the alignment but are not known to have GST activity.\. The glutathione molecule binds in a cleft between N and  C-terminal domains. The catalytically important residues are proposed  to reside in the N-terminal domain  . In plants, GSTs are encoded by  a large gene family (48 GST genes in Arabidopsis) and can be divided  into the phi, tau, theta, zeta, and lambda classes  .. 
PF02798 gluts; <br>Glutathione S-transferase, N-terminal domain. Eddy SR, Griffiths-Jones SR. 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 factors 1-gamma. Not known to have GST  activity; similarity not previously recognised. * HSP26 family of stress-related proteins. including auxin-regulated  proteins in plants and stringent starvation proteins in E. coli.  Not known to have GST activity. Similarity not previously recognised. The glutathione molecule binds in a cleft between N and C-terminal domains - the catalytically important residues are proposed to reside in the N-terminal domain  .. 
PF00735 GTP_CDC; <br>Pfam-B_440 (release 2.1). Members of this family include CDC3, CDC10, CDC11 and CDC12/Septin.  Members of this family bind GTP. As regards the septins, these are polypeptides of 30-65kDa with three characteristic GTPase motifs (G-1, G-3 and G-4) that are similar to those of the Ras family. The G-4 motif is strictly conserved with a unique septin consensus of AKAD. Most septins are thought to have at least one coiled-coil region, which in some cases is necessary for intermolecular interactions that allow septins to polymerise to form rod-shaped complexes. In turn, these are arranged into tandem arrays to form filaments. They are multifunctional proteins, with roles in cytokinesis, sporulation, germ cell development, exocytosis and apoptosis  .. 
PF00925 GTP cyclohydrolase II<br>Pfam-B_1147 (release 3.0). GTP cyclohydrolase II catalyses the first committed step in the biosynthesis of riboflavin.. 
PF01227 GTP_cyclohydro_I; <br>GTP cyclohydrolase I. This family includes GTP cyclohydrolase enzymes and a family of related bacterial proteins including Swiss:Q46920.. 
PF04670 Gtr1/RagA G protein conserved region<br>Pfam-B_4577 (release 7.5). GTR1 was first identified in S. cerevisiae as a suppressor of a mutation in RCC1.\.      Biochemical analysis revealed that Gtr1 is in fact a G protein of the Ras family.       The RagA/B proteins are the human homologues of Gtr1.     Included in this family is the human Rag C, a novel protein that has been shown to interact with RagA/B [1,2,3,4].. 
PF04138 GtrA-like protein<br>Members of this family are predicted to be integral membrane proteins with three or four transmembrane spans.  They are involved in the synthesis of cell surface polysaccharides. The GtrA family are a subset of this family. GtrA is predicted to be an integral membrane protein with 4 transmembrane spans.  It is involved is in O antigen modification by Shigella flexneri bacteriophage X (SfX), but does not determine the specificity of glucosylation.  Its function remains unknown, but it may play a role in translocation of undecaprenyl phosphate linked glucose (UndP-Glc) across the cytoplasmic membrane  . Another member of this family is a DTDP-glucose-4-keto-6-deoxy-D-glucose reductase, which catalyses the conversion of dTDP-4-keto-6-deoxy-D-glucose to dTDP-D-fucose, which is involved in the biosynthesis of the serotype-specific polysaccharide antigen of Actinobacillus actinomycetemcomitans Y4 (serotype b) . This family also includes the teichoic acid glycosylation protein, GtcA, which is a serotype-specific protein in some Listeria innocua and monocytogenes strains.  Its exact function is not known, but it is essential for decoration of cell wall teichoic acids with glucose and galactose  .. 
PF00211 guanylate_cyc; <br>Adenylate and Guanylate cyclase catalytic domain. 
PF00625 Guanylate kinase<br>
PF02058 Guanylin precursor<br>
PF05120 Gas vesicle protein G <br>These proteins are involved in the formation of gas vesicles ( ).. 
PF05121 Gas vesicle protein K  <br>These proteins are involved in the formation of gas vesicles ( ).. 
PF02213 GYF domain<br>Alignment kindly provided by SMART. 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 Swiss:O95400.. 
PF02895 Signal transducing histidine kinase, homodimeric domain<br>This helical bundle domain is the homodimer interface  of the signal transducing histidine kinase family.. 
PF03030 Inorganic H+ pyrophosphatase<br>Pfam-B_1050 (release 6.4). The H+ pyrophosphatase is an transmembrane proton pump involved in establishing the H+ electrochemical potential difference between the vacuole lumen and the cell cytosol. Vacuolar-type H(+)-translocating inorganic pyrophosphatases have long been considered to be restricted to plants and to a few species of photo-trophic bacteria. However, in recent investigations, these pyrophosphatases have been found in organisms as disparate as thermophilic Archaea and parasitic protists  .. 
PF01725 Ham1 family<br>Pfam-B_2030 (release 4.1). This family consists of the HAM1 protein Swiss:P47119 and hypothetical archaeal bacterial and C. elegans proteins. HAM1 controls 6-N-hydroxylaminopurine (HAP) sensitivity and mutagenesis in S. cerevisiae Swiss:P47119  . The HAM1 protein protects the cell from HAP, either on the level of deoxynucleoside triphosphate or the DNA level by a yet unidentified set of reactions  .. 
PF04388 Hamartin protein<br>This family includes the hamartin protein which is thought to function as a tumour suppressor.  The hamartin protein interacts with the tuberin protein Pfam:PF03542. Tuberous sclerosis complex (TSC) is an autosomal dominant disorder and is characterised by the presence of hamartomas in many organs, such as brain, skin, heart, lung, and kidney. It is caused by mutation either TSC1 or TSC2 tumour suppressor gene. TSC1 encodes a protein, hamartin, containing two coiled-coil regions, which have been shown to mediate binding to tuberin. The TSC2 gene codes for tuberin Pfam:PF03542. These two proteins function within the same pathway(s) regulating cell cycle, cell growth, adhesion, and vesicular trafficking  .. 
PF01567 Hantavirus glycoprotein G1<br>Pfam-B_399 (release 4.0). 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 Hantavirus glycoprotein G2<br>Pfam-B_401 (release 4.0). 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. . 
PF00846 Hantavirus nucleocapsid protein<br>Pfam-B_310 (release 3.0). 
PF03866 Hydrophobic abundant protein (HAP)        <br>Expression of HAP is thought to be developmentally regulated and possibly involved in spherule cell wall formation  .   . 
PF01543 Hepatitis C virus capsid protein<br>
PF01542 Hepatitis C virus core protein<br>The viral core protein forms the internal viral coat that encapsidates the genomic RNA and is enveloped in a host cell-derived lipid membrane. The core protein has been shown, by yeast two-hybrid assay to interact with cellular DEAD box helicases  . The N terminus of the core protein is involved in transcriptional repression  .. 
PF01539 Hepatitis C virus envelope glycoprotein E1<br>
PF01560 Hepatitis C virus non-structural protein E2/NS1<br>The hypervariable region of the E2/NS1 region of hepatitis C virus varies greatly between viral isolates. E2 is thought to encode a structurally unconstrained envelope protein  .. 
PF01538 Hepatitis C virus non-structural protein NS2<br>The viral genome is translated into a single polyprotein of about 3000 amino acids. Generation of the mature non-structural proteins relies on the activity of viral proteases.  Cleavage at the NS2/NS3 junction is accomplished by a metal-dependent autoprotease encoded within NS2 and the N-terminus of NS3 [1,2].. 
PF02907 HCV_NS3; <br>Hepatitis C virus NS3 protease. Griffiths-Jones SR, Knutson S. Hepatitis C virus NS3 protein is a serine protease which has a trypsin-like fold.  The non-structural (NS) protein NS3 is one of the NS proteins involved in replication of the HCV genome. NS2-3 proteinase, a zinc-dependent enzyme, performs a single proteolytic cut to release the N-terminus of NS3.  The action of NS3 proteinase (NS3P), which resides in the N-terminal one-third of the NS3 protein, then yields all remaining non-structural proteins.  The C-terminal two-thirds of the NS3 protein contain a helicase. The functional relationship between the proteinase and helicase domains is unknown. NS3 has a structural zinc-binding site and requires cofactor NS4A.. 
PF01006 Hepatitis C virus non-structural protein NS4a<br>Pfam-B_315 (release 3.0). NS4a forms an integral part of the NS3 serine protease, as  it is required in a number of cases as a cofactor of cleavage [1,3]. It has also been reported that NS4a interacts with NS4b and NS3 to form a multi-subunit replicase complex  .. 
PF01001 Hepatitis C virus non-structural protein NS4b<br>Pfam-B_315 (release 3.0). No precise function has been assigned to NS4b.  However, it is known that NS4b interacts with NS4a and NS3 to form a large replicase complex to direct the viral RNA replication  .. 
PF01506 Hepatitis C virus non-structural 5a protein membrane anchor<br>The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR, Swiss:P19525 [1,2].  The N-terminal region of the NS5a protein has been used in the construction of the alignment for this family.  The C-terminal region has not been included because it is too heterogeneous.. 
PF04618 HD-ZIP protein N terminus<br>This family consists of the N termini of plant homeobox-leucine zipper proteins. Its function is unknown.. 
PF02329 Histidine carboxylase PI chain<br>Pfam-B_19599 (release 5.2). Histidine carboxylase catalyses the formation of histamine from histidine. Cleavage of the proenzyme PI chain yields two subunits,  alpha and beta, which arrange as a hexamer (alpha beta)6. . 
PF02924 Bacteriophage lambda head decoration protein D<br>
PF01517 Hepatitis delta virus delta antigen<br>Pfam-B_808 (release 4.0). The hepatitis delta virus (HDV) encodes a single protein, the hepatitis delta antigen (HDAg).  The central region of this protein has been shown to bind RNA  .  Several interactions are also mediated by a coiled-coil region at the N terminus of the protein  .. 
PF02985 HEAT repeat<br>The HEAT repeat family is related to armadillo/beta-catenin-like  repeats (see Pfam:PF00514).. 
PF03130 PBS lyase HEAT-like repeat<br>Pfam-B_172 (release 6.5). This family contains a short bi-helical repeat that is related to Pfam:PF02985. Cyanobacteria and red algae harvest light energy using macromolecular complexes known as phycobilisomes (PBS), peripherally attached to the photosynthetic membrane. The major components of PBS are the phycobiliproteins. These heterodimeric proteins are covalently attached to phycobilins: open-chain tetrapyrrole chromophores, which function as the photosynthetic light-harvesting pigments. Phycobiliproteins differ in sequence and in the nature and number of attached phycobilins to each of their subunits. This family includes the lyase enzymes that specifically attach particular phycobilins to apophycobiliprotein subunits. The most comprehensively studied of these is the CpcE/F lyase Swiss:P31967 Swiss:P31968, which attaches phycocyanobilin (PCB) to the alpha subunit of apophycocyanin  . Similarly, MpeU/V attaches phycoerythrobilin to phycoerythrin II, while CpeY/Z is thought to be involved in phycoerythrobilin (PEB) attachment to phycoerythrin (PE) I (PEs I and II differ in sequence and in the number of attached molecules of PEB: PE I has five, PE II has six)  . All the reactions of the above lyases involve an apoprotein cysteine SH addition to a terminal delta 3,3'-double bond.  Such a reaction is not possible in the case of phycoviolobilin (PVB), the phycobilin of alpha-phycoerythrocyanin (alpha-PEC). It is thought that in this case, PCB, not PVB, is first added to apo-alpha-PEC, and is then isomerised to PVB. The addition reaction has been shown to occur in the presence of either of the components of alpha-PEC-PVB lyase PecE or PecF (or both). The isomerisation reaction occurs only when both PecE and PecF components are present, i.e. the PecE/F phycobiliprotein lyase is also a phycobilin isomerase  . Another member of this family is the NblB protein Swiss:Q9Z3G5, whose similarity to the phycobiliprotein lyases was previously noted  .  This constitutively expressed protein is not known to have any lyase activity. It is thought to be involved in the coordination of PBS degradation with environmental nutrient limitation. It has been suggested that the similarity of NblB to the phycobiliprotein lyases is due to the ability to bind tetrapyrrole phycobilins via the common repeated motif  .. 
PF00632 HECT-domain (ubiquitin-transferase)<br>The name HECT comes from Homologous to the E6-AP Carboxyl Terminus.. 
PF03451 HELP motif<br>The founding member of the EMAP protein family is the 75 kDa Echinoderm Microtubule-Associated Protein, so-named for its abundance in sea urchin, sand dollar and starfish eggs. The Hydrophobic EMAP-Like Protein (HELP) motif was identified initially in the human EMAP-Like Protein 2 (EML2) and subsequently in the entire EMAP Protein family.  The HELP motif is approximately 60-70 amino acids in length and is conserved amongst metazoans. Although the HELP motif is hydrophobic, there is no evidence that EMAP-Like Proteins are membrane-associated. All members of the EMAP-Like Protein family, identified to-date, are constructed with an amino terminal HELP motif followed by a WD domain  .  In C. elegans, EMAP-Like Protein-1 (ELP-1) is required for touch sensation indicating that ELP-1 may play a role in mechanosensation  .  The localization of ELP-1 to microtubules and adhesion sites implies that ELP-1 may transmit forces between the body surface and the touch receptor neurons.. 
PF03996 Hemagglutinin esterase<br>Pfam-B_505 (release 5.5). 
PF02710 Hemagglutinin domain of haemagglutinin-esterase-fusion glycoprotein<br>Pfam-B_505 (release 5.5). 
PF00509 Haemagglutinin<br>Pfam-B_26 (release 1.0). Hemagglutinin from influenza virus causes membrane fusion of the viral membrane with the host membrane. Fusion occurs after the host cell internalises the virus by endocytosis.  The drop of pH causes release of a hydrophobic fusion peptide and a large conformational change leading to membrane fusion.. 
PF01126 Heme_oxygnease;<br>
PF00372 hemocyanin; <br>Hemocyanin, copper containing domain. This family includes arthropod hemocyanins and insect larval storage proteins.. 
PF03723 hemocyanin_C; <br>Hemocyanin, ig-like domain. This family includes arthropod hemocyanins and insect larval storage proteins.. 
PF03722 hemocyanin_N; <br>Hemocyanin, all-alpha domain. This family includes arthropod hemocyanins and insect larval storage proteins.. 
PF00045 hemopexin; <br>Hemopexin is a heme-binding protein that transports heme to the liver. Hemopexin-like repeats occur in vitronectin and some matrix metallopeptidases family (matrixins). The HX repeats of some matrixins bind tissue inhibitor of metallopeptidases (TIMPs).. 
PF05171 Haemin-degrading HemS.ChuX domain<br>The Yersinia enterocolitica O:8 periplasmic binding-protein- dependent transport system consisted of four proteins: the periplasmic haemin-binding protein HemT, the haemin permease protein HemU, the ATP-binding hydrophilic protein HemV and the haemin-degrading protein HemS (this family). The structure for HemS has been solved and consists of a tandem repeat of this domain.. 
PF00906 Hepatitis core antigen<br>Pfam-B_8 (release 3.0). The core antigen of hepatitis viruses possesses a carboxyl terminus rich in arginine. On this basis it was predicted that the core antigen would bind DNA  . There is some experimental evidence to support this  .. 
PF01771 Herpesvirus alkaline exonuclease<br>Pfam-B_822 (release 4.2). This family includes various alkaline exonucleases from members of the herpesviridae. Alkaline exonuclease  appears to have an important role in the replication of herpes simplex virus  .. 
PF04793 BRRF1-like protein<br>Pfam-B_6247 (release 7.5). Family of herpesvirus proteins including Epstein-barr virus protein BBRF1.   . 
PF05109 Herpes virus major outer envelope glycoprotein (BLLF1)<br>Pfam-B_6348 (release 7.7). This family consists of the BLLF1 viral late glycoprotein, also termed  gp350/220. It is the most abundantly expressed glycoprotein in the viral  envelope of the Herpesviruses and is the major antigen responsible for  stimulating the production of neutralising antibodies in vivo  .. 
PF04633 Herpesvirus BMRF2 protein<br>Pfam-B_5353 (release 7.5). 
PF04682 Herpesvirus BTRF1 protein conserved region<br>Pfam-B_4518 (release 7.5). Herpesvirus protein.. 
PF04929 Herpes DNA replication accessory factor <br>Pfam-B_5837 (release 7.6). Replicative DNA polymerases are capable of polymerising tens of thousands of nucleotides without dissociating from their DNA templates. The high processivity of these polymerases is dependent upon accessory proteins that bind to the catalytic subunit of the polymerase or to the substrate.  The Epstein-Barr virus (EBV) BMRF1 protein is an essential component of the viral DNA polymerase and is absolutely required for lytic virus replication  . BMRF1 is also a transactivator  .  This family is predicted to have a UL42 like structure  .. 
PF01673 Herpesvirus putative major envelope glycoprotein<br>Pfam-B_1084 (release 4.1). This family consists of probable major envelope glycoproteins from members of the herpesviridae including herpes simplex  virus, human cytomegalovirus and varicella-zoster virus. Members of the herpesviridae have a dsDNA genome and do not have a RNA stage during there replication. . 
PF02480 Alphaherpesvirus glycoprotein E<br>Pfam-B_849 (release 5.4). Glycoprotein E (gE) of Alphaherpesvirus forms a complex with  glycoprotein I (gI) (Pfam:PF01688), functioning as an immunoglobulin G (IgG) Fc binding protein. gE is involved in virus spread but is not essential for propagation  .. 
PF01688 Alphaherpesvirus glycoprotein I<br>Pfam-B_1222 (release 4.1). This family consists of glycoprotein I form various members of the  alphaherpesvirinae these include herpesvirus, varicella-zoster virus and pseudorabies virus. Glycoprotein I (gI) is important during natural  infection, mutants lacking gI produce smaller lesions at the site of infection and show reduced neuronal spread  . gI forms a heterodimeric complex with gE; this complex displays Fc receptor activity (binds to  the Fc region of immunoglobulin)  . Glycoproteins are also important  in the production of virus-neutralising antibodies and cell mediated  immunity  . The alphaherpesvirinae have a dsDNA gnome and have no RNA stage during viral replication.. 
PF01528 Herpesvirus glycoprotein M<br>Pfam-B_929 (release 4.0). The herpesvirus glycoprotein M (gM) is an integral membrane protein predicted to contain 8 transmembrane segments  . Glycoprotein M is not essential for viral replication  .. 
PF01537 Herpesvirus glycoprotein D/GG/GX domain<br>Pfam-B_603 (release 4.0). This domain is found in several Herpes viruses glycoproteins. This is a family includes glycoprotein-D (gD or gIV) which is common to herpes simplex virus types 1 and 2, as well as equine herpes, bovine herpes and Marek's disease virus. Glycoprotein-D has been found on the viral envelope and the plasma membrane of infected cells. and gD immunisation can produce an immune response to bovine herpes virus (BHV-1). This response is stronger than that of the other major glycoproteins gB (gI) and gC (gIII) in BHV-1.  Glycoprotein G (gG)is one of the seven external glycoproteins of HSV1 and HSV2. This family also contains the glycoprotein GX, (gX), initially identified in Pseudorabies virus.. 
PF02489 Herpesvirus glycoprotein H<br>Pfam-B_1142 (release 5.4). Herpesvirus glycoprotein H (gH) is a virion associated envelope glycoprotein  . Complex formation between gH and gL has been demonstrated in both virions and infected cells  .. 
PF02689 Helicase<br>Pfam-B_607 (release 5.5). 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.. 
PF03324 Herpesvirus DNA helicase/primase complex associated protein<br>Pfam-B_3676 (release 6.5) & Pfam-B_4951 (release 14.0). This family includes  HSV UL8, EHV-1 54, VZV 52 AND HCMV 102.. 
PF03585 Herpesvirus ICP4-like protein C-terminal region<br>Pfam-B_1422 (release 7.0). The immediate-early protein ICP4 (infected-cell polypeptide 4) is required for efficient transcription of early and late viral genes and is thus essential for productive infection.  ICP4 is a large phosphoprotein that binds DNA in a sequence specific manner as a homodimer.  ICP4 represses transcription from LAT, ICP4 and ORF-P that have high-affinity a ICP4 binding site that spans the transcription initiation site. ICP4 proteins have two highly conserved regions, this family contains the C-terminal region that probably acts as an enhancer for the N-terminal region  .. 
PF03584 Herpesvirus ICP4-like protein N-terminal region<br>Pfam-B_1422 (release 7.0). The immediate-early protein ICP4 (infected-cell polypeptide 4) is required for efficient transcription of early and late viral genes and is thus essential for productive infection.  ICP4 is a large phosphoprotein that binds DNA in a sequence specific manner as a homodimer.  ICP4 represses transcription from LAT, ICP4 and ORF-P that have high-affinity a ICP4 binding site that spans the transcription initiation site. ICP4 proteins have two highly conserved regions, this family contains the N-terminal region that contains sites for DNA binding and homodimerisation  .. 
PF03361 Herpes virus intermediate/early protein 2/3<br>Pfam-B_2178 (release 6.6). These viral sequences are similar to UL117 protein of human  and chimpanzee cytomegalovirus, and to intermediate/early  proteins 2 and 3 of certain herpes viruses. UL117 is thought  to be a glycoprotein that is expressed at early and late times after infection  . This region is close to the C-terminus of the protein and may be a transmembrane region  .. 
PF03363 Herpesvirus leader protein<br>Pfam-B_1664 (release 6.6). 
PF03122 Herpes virus major capsid protein<br>Pfam-B_600 (release 6.5). 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 the hexamers form the edges and 20 faces  .. 
PF04797 Herpesvirus dUTPase protein<br>Pfam-B_6280 (release 7.5). 
PF02399 Origin of replication binding protein<br>Pfam-B_1518 (release 5.4). This Pfam family represents the herpesvirus origin of replication binding protein, probably involved in DNA replication.. 
PF03325 Herpesvirus polymerase accessory protein<br>Pfam-B_3097 (release 6.5). The same proteins are also known as polymerase processivity factors.. 
PF04846 Herpesvirus pp38 phosphoprotein<br>Pfam-B_4545 (release 7.6). This protein represents a conserved region found in most herpesvirus pp38 phosphoproteins.. 
PF04637 Herpesvirus phosphoprotein 85 (HHV6-7 U14/HCMV UL25)<br>Pfam-B_5418 (release 7.5). This family includes UL25 proteins from HCMV, as well as U14 proteins from HHV 6 and HHV7. These 85 kD phosphoproteins appear to act as structural antigens, but their precise function is otherwise unknown.. 
PF03326 Herpesvirus transcription activation factor (transactivator)<br>Pfam-B_3658 (release 6.5). This family includes EBV BRLF1 and similar ORF 50 proteins from other herpesviruses.. 
PF04843 Herpesvirus tegument protein, N-terminal conserved region<br>Pfam-B_3992 (release 7.6). 
PF04523 Herpes virus tegument protein U30<br>This family is named after the human herpesvirus protein, but has been characterised in cytomegalovirus as UL47. Cytomegalovirus UL47 is a component of the tegument, which is a protein layer surrounding the viral capsid. UL47 co-precipitates with UL48 and UL69 tegument proteins, and the major capsid protein UL86.  A UL47-containing complex is thought to be involved in the release of viral DNA from the disassembling virus particle  .. 
PF04541 Herpesvirus virion protein U34    <br>The virion proteins in this family include membrane phosphoprotein-like proteins such as UL34, Epstein-Barr and R50, from dsDNA viruses, no RNA stage, Herpesvirales. The family Herpes_BFRF1, Pfam:PF05900, has been merged in.. 
PF04533 Herpes virus U44 protein<br>This is a family of proteins from dsDNA beta-herpesvirinae and gamma-herpesvirinae viruses. The function is not known, and the proteins are named variously as U44, BSRF1, UL71, and M71. The family BSRF1 has been merged into this.. 
PF04529 Herpesvirus U59 protein   <br>The proteins in this family have no known function.  Cytomegalovirus UL88 is also a member of this family.. 
PF03580 Herpesvirus UL14-like protein<br>Pfam-B_2982 (release 7.0). This is a family of Herpesvirus proteins including UL14. UL14 protein is a minor component of the virion tegument   and is expressed late in infection. UL14 protein can influence the intracellular localisation patterns of a number of proteins belonging to the capsid or the DNA encapsidation machinery  .. 
PF04559 Herpesvirus UL17 protein<br>UL17 protein is required for DNA cleavage and packaging in herpes viruses. It has been shown to associate with immature B-type capsids  , and is required for the the localisation of capsids and capsid proteins to the intranuclear sites where viral DNA is cleaved and packaged  . In the virion, UL17 is a component of the tegument, which is a protein layer surrounding the viral capsid  .. 
PF04544 Herpesvirus egress protein UL20<br>UL20 is predicted to be a transmembrane protein with multiple membrane spans.  It is involved in the trans-cellular transport of enveloped virions, and is therefore important for viral egress.  However, UL20 operates in different cellular compartments and different stages of egress in pseudorabies virus and herpes simplex virus.  This is thought to be due to differences in egress pathways between these two viruses  .. 
PF01646 Herpes virus protein UL24<br>Pfam-B_946 (release 4.1). This family consists of various herpes virus proteins; the gene 20 product, U49 protein, UL24 protein and BXRF1. The UL24 gene (product of the 24th ORF) is not essential for virus  replication, mutants with lesions in UL24 show a reduced ability to  replicate in tissue culture and have reduced thymidine kinase activity as the UL24 gene overlaps with thymidine kinase  .. 
PF02760 HIN-200/IF120x domain<br>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 Pfam:PF02758.. 
PF03369 Herpesvirus UL3 protein<br>Pfam-B_2492 (release 6.6). 
PF02718 Herpesvirus UL31-like protein<br>Pfam-B_1786 (release 5.5). This is a family of Herpesvirus proteins including UL31 (Swiss:P10215), UL53 (Swiss:P16794), and the  product of ORF 69 in some strains (e.g. Swiss:O36420). The proteins in this family have no known function.. 
PF03581 Herpesvirus UL33-like protein<br>Pfam-B_1115 (release 7.0). This is a family of Herpesvirus proteins including UL33 Swiss:P10217 ,UL51 Swiss:P16792. The proteins in this  family are involved in packaging viral DNA.. 
PF03586 Herpesvirus UL36 tegument protein<br>Pfam-B_3425 (release 7.0). The UL36 open reading frame (ORF) encodes the largest herpes simplex virus type 1 (HSV-1) protein, a 270-kDa polypeptide designated VP1/2, which is also a component of the virion tegument. A null mutation in the UL36 gene of herpes simplex virus type 1 results in accumulation of unenveloped DNA-filled capsids in the cytoplasm of infected cells  . This family only covers a small central part of this large protein.. 
PF03277 Herpesvirus UL4 family<br>Pfam-B_4461 (release 6.5). 
PF05072 Herpesvirus UL43 protein<br>Pfam-B_5928 (release 7.7). UL43 genes are expressed with true-late (gamma2) kinetics and have been identified as a virion tegument component  .. 
PF03387 Herpesvirus UL46 protein<br>Pfam-B_2545 (release 6.6). 
PF03362 Herpesvirus UL47 protein<br>Pfam-B_2182 (release 6.6). 
PF04823 Herpes_UL49; <br>Herpesvirus UL49 tegument protein. Pfam-B_3850 (release 7.6). 
PF04540 Herpesvirus UL51 protein<br>UL51 protein is a virion protein. In pseudorabies virus, UL51 (Swiss:Q85227) was identified as a component of the capsid  . In herpes simplex virus type 1 there is evidence for post-translational modification of UL51  .. 
PF04537 Herpesvirus UL55 protein<br>In infected cells, UL55 is associated with the nuclear matrix, and found adjacent to compartments containing the capsid protein ICP35.  UL55 was not detected in assembled virions. It is thought that UL55 may play a role in virion assembly or maturation  .. 
PF04534 Herpesvirus UL56 protein<br>In herpes simplex virus type 2, UL56 is thought to be a tail-anchored type II membrane protein involved in vesicular trafficking.  The C terminal hydrophobic region is required for association with the cytoplasmic membrane, and the N terminal proline-rich region is important for the translocation of UL56 to the Golgi apparatus and cytoplasmic vesicles  .. 
PF01763 Herpesvirus UL6 like<br>Pfam-B_878 (release 4.2). 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  .. 
PF01677 Herpesvirus UL7 like<br>Pfam-B_1086 (release 4.1). This family consists of various functionally undefined proteins from the herpesviridae and UL7 from bovine herpes virus [1,2]. UL7 is not essential for virus replication in cell culture, and is found localised in the cytoplasm of infected cells accumulated around the nucleus but could not be detected in purified virions  .  Members of the herpesviridae have a dsDNA genome and do not have a RNA stage during there replication.. 
PF03554 gpUL73; <br>UL73 viral envelope glycoprotein  . Pfam-B_3001 (release 7.0). This family groups together the viral proteins BLRF1, U46, 53, and  UL73.  The UL73-like envelope glycoproteins, which associates in a  high molecular mass complex with its counterpart, gM, induce neutralising antibody responses in the host.  These glycoprotein are  highly  polymorphic, particularly in the N-terminal region  .. 
PF01802 Herpesvirus VP23 like capsid protein<br>Pfam-B_1435 (release 4.2). This family consist of various capsid proteins from members  of the herpesviridae. The capsid protein VP23 in herpes simplex virus forms a triplex together with VP19C these fit between and link together adjacent capsomers as formed by VP5 and VP26  . VP3 along with the scaffolding proteins helps to form normal capsids by defining the curvature of the shell and size of the particle  .. 
PF03327 Herpesvirus capsid shell protein VP19C<br>Pfam-B_3451 (release 6.5). 
PF01521 HesB-like;HesB; <br>Iron-sulphur cluster biosynthesis. Pfam-B_518 (release 4.0). This family is involved in iron-sulphur cluster biosynthesis  . Its members include proteins that are involved in nitrogen fixation such as the HesB and HesB-like proteins    .. 
PF02444 HEV_ORF2; <br>Hepatitis E virus ORF-2 (Putative capsid protein). Pfam-B_1896 (release 5.4). The Hepatitis E virus (HEV) genome is a single-stranded, positive-sense RNA molecule of approximately 7.5 kb  . Three open reading frames (ORF) were identified within the HEV genome: ORF1 encodes non-structural proteins, ORF2 encodes the putative structural protein(s)  , and ORF3 encodes a protein of unknown function. ORF2 contains a consensus signal peptide sequence at its amino terminus and a capsid-like region with a high content of basic amino acids similar to that seen with other virus capsid proteins  .. 
PF02455 Hexon-associated protein (IIIa)<br>Pfam-B_2076 (release 5.4). The major capsid protein of the adenovirus strain is also known  as a hexon. This is a family of hexon-associated proteins (protein IIIa).. 
PF00349 hexokinase; <br>Hexokinase (EC:2.7.1.1) 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.. 
PF03727 hexokinase2; <br>Hexokinase (EC:2.7.1.1) 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.. 
PF03559 NDP-hexose 2,3-dehydratase<br>Pfam-B_1070 (release 7.0). This family includes a range of proteins from antibiotic production pathways. The family includes gra-ORF27 Swiss:Q9ZA32 product that probably functions at an early step, most likely as a dTDP-4-keto-6- deoxyglucose-2,3-dehydratase  . Its homologues include dnmT from the daunorubicin biosynthetic gene cluster in S. peucetius  , a similar gene from the daunomycin biosynthetic cluster in Streptomyces sp. strain C5 Swiss:Q53880   , eryBVI from the erythromycin cluster in S. erythraea and snoH from the nogalamycin cluster in S. nogalater. The proteins in this family are composed of two copies of a 200 amino acid long unit that may be a structural domain.. 
PF04209 homogentisate 1,2-dioxygenase<br>TIGRFAMs (release 2.0);. 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 forms a hexamer arrangement comprised of a dimer of trimers. The active site iron ion is  coordinated near the interface between the trimers  .. 
PF01085 Hedgehog amino-terminal signalling domain<br>Pfam-B_1424 (release 3.0). For the carboxyl Hint module, see Pfam:PF01079. Hedgehog is a family of secreted signal molecules required for embryonic cell differentiation.. 
PF00730 Endonuclease_3; <br>HhH-GPD superfamily base excision DNA repair protein. Pfam-B_854 (release 2.1). This family contains a diverse range of structurally related DNA repair proteins. The superfamily is called the HhH-GPD family after its hallmark Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate  . This includes endonuclease III, EC:4.2.99.18 and MutY an A/G-specific adenine glycosylase, both have a C terminal 4Fe-4S cluster. The family also includes 8-oxoguanine DNA glycosylases such as Swiss:P53397. The methyl-CPG binding protein MBD4 Swiss:Q9Z2D7 also contains a related domain   that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II EC:3.2.2.21 and other members of the AlkA family.. 
PF03753 Human herpesvirus 6 immediate early protein <br>Pfam-B_1006 (release 7.0). The proteins in this family are poorly characterised, but an investigation  has indicated that the immediate early protein is required the down-regulation of MHC class I expression in dendritic cells. Human herpesvirus 6 immediate early protein is also referred to as U90.. 
PF03486 HI0933-like protein<br>
PF04588 Hypoxia induced protein conserved region<br>Pfam-B_4868 (release 7.5). This family is found in proteins thought to be involved in the response to hypoxia.  Family members mostly come from diverse eukaryotic organisms however eubacterial members have been identified.  This region is found at the N-terminus of the member proteins which are predicted to be transmembrane  .. 
PF01355 High potential iron-sulfur protein<br>
PF00713 Hirudin<br>Pfam-B_707 (release 2.1). 
PF02098 Tick histamine binding protein<br>
PF00977 Histidine biosynthesis protein<br>Pfam-B_1089 (release 3.0). Proteins involved in steps 4 and 6 of the histidine biosynthesis pathway are contained in this family. Histidine is formed by several complex and distinct biochemical reactions catalysed by eight enzymes.  The enzymes in this Pfam entry are called His6 and His7 in eukaryotes and HisA and HisF in prokaryotes. The structure of HisA is known to be a TIM barrel fold.  In some archaeal HisA proteins the TIM barrel is composed of two tandem repeats of a half barrel e.g. Swiss:P05325  . This family belong to the common phosphate binding site TIM barrel family  .. 
PF00815 Histidinol dehydrogenase<br>Pfam-B_1358 (release 2.1). 
PF00125 histone; <br>Core histone H2A/H2B/H3/H4. 
PF01230 HIT domain<br>Prosite & Pfam-B_8474 (Release 8.0). 
PF00816 H-NS histone family<br>Pfam-B_1651 (release 2.1). 
PF01870 DUF50;<br>Archaeal holliday junction resolvase (hjc). This family of archaebacterial proteins are holliday junction resolvases (hjc gene)  . The Holliday junction is an essential intermediate of homologous recombination. This protein is the archaeal equivalent of RuvC but is not sequence similar.. 
PF02110 Hydroxyethylthiazole kinase family<br>
PF03865 HlyB; <br>Haemolysin secretion/activation protein ShlB/FhaC/HecB. This family represents a group of sequences that are related to ShlB from Serratia marcescens. ShlB is an outer membrane protein pore involved in the Type Vb or Two-partner secretion system where it is functions to secrete and activate the haemolysin ShlA. The activation of ShlA occurs during secretion when ShlB imposes a conformational change in the inactive haemolysin to form the active protein  . . 
PF02794 RTX toxin acyltransferase family<br>Pfam-B_1230 (Pfam 6.0). Members of this family are enzymes EC:2.3.1.-. involved in fatty acylation of the protoxins (HlyA) at lysine residues, thereby converting them to the active toxin. Acyl-acyl carrier protein (ACP) is the essential acyl donor.  This family show a number of conserved residues that are possible candidates for participation in acyl transfer. Site-directed mutagenesis of the single conserved histidine residue in Swiss:P06736 resulted in complete inactivation of the enzyme  .. 
PF00529 HlyD family secretion protein<br>MRC-LMB Genome group. 
PF03201 H2-forming N5,N10-methylene-tetrahydromethanopterin dehydrogenase<br>Pfam-B_2929 (release 6.5). 
PF01101 HMG14 and HMG17<br>
PF00505 HMG_box; MaoC_dehydrat_N;<br>HMG (high mobility group) box. Pfam-B_8 (release 1.0). 
PF01154 HMG_CoA_synt; <br>Hydroxymethylglutaryl-coenzyme A synthase N terminal. 
PF00682 HMGL-like<br>Pfam-B_71 (release 2.1). This family contains a diverse set of enzymes.  These include various aldolases and a region of pyruvate carboxylase. . 
PF00423 Haemagglutinin-neuraminidase<br>Pfam-B_171 (release 1.0). 
PF04814 Hepatocyte nuclear factor 1 (HNF-1), N terminus<br>Pfam-B_2624 (release 7.6). This family consists of the N terminus of homeobox-containing transcription factor HNF-1.  This region contains a dimerisation sequence   and an  acidic region that may be involved in transcription activation. Mutations and the common Ala/Val 98 polymorphism in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3)  .. 
PF04813 Hepatocyte nuclear factor 1 (HNF-1), alpha isoform C terminus<br>Pfam-B_2624 (release 7.6). This family consists of an alternative C terminus of homeobox-containing transcription factor HNF-1, found in the HNF-1A isoform.  Different isoforms of HNF-1 are generated by the differential use of polyadenylation sites and by alternative splicing.\. The C-terminal region of HNF-1 is responsible for the activation of transcription, and HNF-1A, which has this C-terminal extension, transactivates less well than the B and C isoforms  . Mutations and polymorphisms in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3)  .. 
PF04812 Hepatocyte nuclear factor 1 (HNF-1), beta isoform C terminus<br>Pfam-B_2624 (release 7.6). This family consists of a region found within the alpha isoform and at  the C terminus of the beta isoform of the homeobox-containing transcription factor of HNF-1.  Different isoforms of HNF-1 are generated by the differential use of polyadenylation sites and by alternative  splicing.  The C-terminal region of HNF-1 is responsible for the  activation of transcription  . Mutations and polymorphisms in HNF-1  cause the type 3 form of maturity-onset diabetes of the young (MODY3)  .. 
PF01844 HNH endonuclease<br>
PF01848 Hok/gef family<br>
PF05102 holin_BlyA; <br>TIGRFAMs (release 2.0);. BlyA, a small holin found in Borrelia circular plasmids that is  encoded by a prophage.  BlyA contains two largely hydrophobic  helices and a highly charged C-terminus and is membrane  associated  .. 
PF05204 Homing endonuclease<br>Homing endonucleases are encoded by mobile DNA elements that are found inserted within host genes in all domains of life.. 
PF05203 Hom_end-associated Hint<br>Homing endonucleases are encoded by mobile DNA elements that are found inserted within host genes in all domains of life. The crystal structure of the homing nuclease PI-Sce   revealed two domains: an endonucleolytic centre resembling the C-terminal domain of Drosophila melanogaster Hedgehog protein, and a  a second domain containing the protein-splicing active site. This Domain corresponds to the latter protein-splicing domain.. 
PF00046 homeobox; <br>
PF00742 Homoserine dehydrogenase<br>Pfam-B_459 (release 2.1). 
PF00103 hormone; <br>Somatotropin hormone family. 
PF00123 hormone2; <br>This family contains glucagon, GIP, secretin and VIP.. 
PF00159 hormone3; <br>Pancreatic hormone peptide. 
PF00220 hormone4; <br>Neurohypophysial hormones, N-terminal Domain. C-terminal is in hormone5. 
PF00184 hormone5; <br>Neurohypophysial hormones, C-terminal Domain. N-terminal Domain is in hormone5. 
PF00236 hormone6; <br>Glycoprotein hormone. 
PF04617 Hox9 activation region    <br>This family constitutes the N termini of the paralogous homeobox proteins HoxA9, HoxB9, HoxC9 and HoxD9.  The N terminal region is found to act as a transcription activation region. Btg1 and Btg2 - the B-cell translocation gene products - may function as cofactors for Hoxb9-mediated transcription. The Btg proteins modulate Hoxb9 transcriptional activity by recruiting a multiprotein Ccr4-like complex  .. 
PF01856 Helicobacter outer membrane protein<br>Pfam-B_395 (release 4.2). This family seems confined to Helicobacter. It is predicted to be an outer membrane protein based on its pattern of alternating hydrophobic amino acids similar to porins  .. 
PF02521 Putative outer membrane protein<br>Pfam-B_1230 (release 5.4). This family consists of putative outer membrane proteins from  Helicobacter pylori (campylobacter pylori). . 
PF03328 HpcH/HpaI aldolase/citrate lyase family<br>Pfam-B_3076 (release 6.5) & Pfam-B_2811 (release 14.0). This family includes 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase and 4-hydroxy-2-oxovalerate aldolase.. 
PF04982 HPP family<br>These proteins are integral membrane proteins with four transmembrane spanning helices. The most conserved region of the alignment is a motif HPP. The function of these proteins is uncertain but they may be transporters.. 
PF01288 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK)<br>
PF02603 Hpr_kinase; <br>HPr Serine kinase N terminus. This family represents the N-terminal region of Hpr Serine/threonine kinase PtsK.  This kinase is the sensor in a multicomponent phospho-relay system in control of carbon catabolic repression in bacteria  .  This kinase in unusual in that it recognises the tertiary structure of its target and is a member of a novel family unrelated to any previously described protein phosphorylating enzymes  . X-ray analysis of the full-length crystalline enzyme from Staphylococcus xylosus at a resolution of 1.95 A shows the enzyme to consist of two clearly separated domains that are assembled in a hexameric structure resembling a three-bladed propeller. The blades are formed by two N-terminal domains each, and the compact central hub assembles the C-terminal kinase domains  .. 
PF01627 Hpt domain<br>Pfam-B_971 (release 4.1). The histidine-containing phosphotransfer (HPt) domain is a novel protein module with an active histidine residue that mediates phosphotransfer reactions in the two-component signaling systems. A multistep phosphorelay involving the HPt domain has been suggested for these signaling pathways. The crystal structure of the HPt domain of the anaerobic sensor kinase ArcB has been determined  . The domain consists of six alpha helices containing a four-helix bundle-folding. The pattern of sequence similarity of the HPt domains of ArcB and components in other signaling systems can be interpreted in light of the three-dimensional structure and supports the conclusion that the HPt domains have a common structural motif both in prokaryotes and eukaryotes. In S. cerevisiae ypd1p this domain has been shown to  contain a binding surface for Ssk1p (response regulator receiver domain containing protein Pfam:PF00072)  .. 
PF01628 HrcA protein C terminal domain<br>Pfam-B_1133 (release 4.1). HrcA is found to negatively regulate the transcription of heat shock genes [1,2]. HrcA contains an amino terminal helix-turn-helix domain, however this corresponds to the carboxy terminal domain.. 
PF04877 HrpZ;<br>Pfam-B_6141 (release 7.6). HrpZ from the plant pathogen Pseudomonas syringae binds to lipid bilayers and forms a cation-conducting pore in vivo.  This pore-forming activity may allow nutrient release or delivery of virulence factors during bacterial colonisation of host plants  . The family of hairpinN proteins, Harpin, has been merged into this family. HrpN is a virulence determinant which elicits lesion formation in Arabidopsis and tobacco and triggers systemic resistance in Arabidopsis  .. 
PF02218 Repeat in HS1/Cortactin<br>Pfam-B_5631 (Release 5.2). The function of this repeat is unknown. Seven copies are found in cortactin Swiss:Q14247 and four copies are found in HS1 Swiss:P14317. The repeats are always found amino terminal to an SH3 domain Pfam:PF00018.. 
PF00447 HSF-type DNA-binding<br>
PF00011 Hsp20/alpha crystallin family<br>
PF01430 Hsp33 protein<br>Hsp33 is a molecular chaperone, distinguished from all other known chaperones by its mode of functional regulation. Its activity is redox regulated. Hsp33 is a cytoplasmically localised protein with highly reactive cysteines that respond quickly to changes in the redox environment. Oxidising conditions like H2O2 cause disulfide bonds to form in Hsp33, a process that leads to the activation of its chaperone function  .. 
PF00012 Hsp70 protein<br>Hsp70 chaperones help to fold many proteins. Hsp70 assisted folding involves repeated cycles of substrate binding and release.  Hsp70 activity is ATP dependent. Hsp70 proteins are made up of two regions: the amino terminus is the ATPase domain and the carboxyl terminus is the substrate binding region.. 
PF00183 Hsp90 protein<br>
PF04119 Heat shock protein 9/12<br>Pfam-B_14318 (release 7.3);. These heat shock proteins (Hsp9 and Hsp12) are strongly expressed, an increase of 100 fold, upon entry into stationary phase in yeast [1,2].. 
PF04213 Htaa; <br>This domain is found in HtaA, a secreted protein implicated in iron acquisition and transport  .. 
PF00126 Bacterial regulatory helix-turn-helix protein, lysR family<br>
PF04967 HTH DNA binding domain<br>
PF01022 HTH_ArsR_family;<br>Bacterial regulatory protein, arsR family. Pfam-B_139 (release 3.0). Members of this family contains a DNA binding 'helix-turn-helix' motif. This family includes other proteins which are not included in the Prosite definition.. 
PF01418 Helix-turn-helix domain, rpiR family<br>Pfam-B_3373 (release 2.1). This domain contains a helix-turn-helix motif  . The best characterised member of this family is Swiss:P39266. RpiR is a regulator of the expression of rpiB gene.. 
PF02796 Helix-turn-helix domain of resolvase<br>
PF00165 HTH_2; <br>Bacterial regulatory helix-turn-helix proteins, AraC family. In the absence of arabinose, the N-terminal arm of AraC  binds to the DNA binding domain (Pfam:PF00165) and helps to hold the two DNA binding domains in a relative  orientation that favours DNA looping. In the presence of arabinose, the arms bind over the arabinose on the dimerisation domain, thus freeing the DNA-binding domains. The freed DNA-binding domains are then able to assume a conformation suitable for binding to the adjacent DNA sites that are utilised when AraC activates transcription, and  hence AraC ceases looping the DNA when arabinose is added [1-2].. 
PF04204 Homoserine O-succinyltransferase <br>TIGRFAMs (release 2.0);. 
PF04955 HupE / UreJ protein<br>This family of proteins are hydrogenase / urease accessory proteins.  The alignment contains many conserved histidines that are likely to be involved in nickel binding. The members usually have five membrane-spanning regions.. 
PF01455 HupF/HypC family<br>Prodom_3112 (release 99.1). 
PF04809 HupH hydrogenase expression protein, C-terminal conserved region<br>Pfam-B_3701 (release 7.6). This family represents a C-terminal conserved region found in these bacterial proteins necessary for hydrogenase synthesis. Their precise function is unknown  .. 
PF01750 Hydrogenase maturation protease<br>Pfam-B_548 (release 4.2). The family consists of hydrogenase maturation proteases. In E. coli HypI the hydrogenase maturation protease is involved in processing of HypE the large subunit of hydrogenases 3, by cleavage of its C-terminal  .. 
PF01968 Hydantoinase; <br>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  .. 
PF02538 Hydantoinase B/oxoprolinase<br>This family includes N-methylhydaintoinase B which converts hydantoin to N-carbamyl-amino acids, and 5-oxoprolinase (Swiss:P97608) EC:3.5.2.9 which catalyses the formation of L-glutamate from  5-oxo-L-proline. These enzymes are part of the oxoprolinase family and are related to Pfam:PF01968.. 
PF01185 Fungal hydrophobin<br>
PF01155 Hydrogenase expression/synthesis hypA family<br>Four conserved cysteines lie either side of the least conserved region.. 
PF01924 Hydrogenase formation hypA family<br>HypD is involved in hydrogenase formation. It contains many possible metal binding residues, which may bind to nickel. Transposon Tn5 insertions into hypD resulted in R. leguminosarum mutants that lacked any hydrogenase activity in symbiosis with peas  .. 
PF02494 HYR domain<br>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 uncertain it may be involved in cell adhesion  .. 
PF01608 I/LWEQ domain<br>I/LWEQ domains bind to actin. It has been shown that the I/LWEQ domains from mouse talin Swiss:P26039 and yeast Sla2p Swiss:P33338 interact with F-actin  . I/LWEQ domains can be placed into four major groups based on sequence similarity: (1) Metazoan talin; (2) Dictyostelium TalA/TalB Swiss:P54633 and SLA110; (3) metazoan Hip1p Swiss:O00291; and (4) yeast Sla2p Swiss:P33338. The domain has four conserved blocks, the name of the domain is derived from the initial conserved amino acid of each of the four blocks  .. 
PF04568 Mitochondrial ATPase inhibitor, IATP<br>ATP synthase inhibitor prevents the enzyme from switching to ATP hydrolysis during collapse of the electrochemical gradient, for example during oxygen deprivation   ATP synthase inhibitor forms a one to one complex with the F1 ATPase, possibly by binding at the alpha-beta interface.  It is thought to inhibit ATP synthesis by preventing the release of ATP  . The minimum inhibitory region for bovine inhibitor (Swiss:P01096) is from residues 39 to 72  . The inhibitor has two oligomeric states, dimer (the active state) and tetramer. At low pH , the inhibitor forms a dimer via antiparallel coiled coil interactions between the C terminal regions of two monomers.\. At high pH, the inhibitor forms tetramers and higher oligomers by coiled coil interactions involving the N terminus and inhibitory region, thus preventing the inhibitory activity  .. 
PF01749 Importin beta binding domain<br>Pfam-B_544 (release 4.2). This family consists of the importin alpha (karyopherin alpha), importin beta (karyopherin beta) binding domain. The domain mediates  formation of the importin alpha beta complex; required for classical  NLS import of proteins into the nucleus, through the nuclear pore  complex and across the nuclear envelope. Also in the alignment is the NLS of importin alpha which overlaps with the IBB domain  .. 
PF03617 IBV 3A protein <br>Pfam-B_3183 (release 7.0). The gene product of gene 3 from Avian infectious bronchitis virus. Currently, the function of this protein remains unknown.. 
PF03622 IBV 3B protein <br>Pfam-B_3190 (release 7.0). Product of ORF 3B from Avian infectious bronchitis virus (IBV). Currently, the function of this protein remains unknown  .. 
PF03620 IBV 3C protein<br>Pfam-B_3232 (release 7.0). Product of ORF 3C from Avian infectious bronchitis virus (IBV). Currently, the function of this protein remains unknown.. 
PF04629 Islet cell autoantigen ICA69, C-terminal domain<br>Pfam-B_5314 (release 7.5). This family includes a 69 kD protein which has been identified as an islet cell autoantigen in type I diabetes mellitus  . Its precise function is unknown.. 
PF03921 ICAM_N-terminal;<br>Intercellular adhesion molecule (ICAM), N-terminal domain. ICAMs normally functions to promote intercellular adhesion and  signalling. However, The N-terminal domain of the receptor binds to the  rhinovirus 'canyon' surrounding the icosahedral 5-fold axes,  during the viral attachment process  . This family is a family that is part of the Ig superfamily and is therefore related to the family ig (Pfam:PF00047). . 
PF00818 Ice nucleation protein repeat<br>Pfam-B_2 (release 3.0). 
PF00656 ICE_p20; <br>
PF00463 Isocitrate lyase family<br>
PF03517 ICln_channel;<br>Regulator of volume decrease after cellular swelling. Griffiths-Jones SR, Coggill P. ICln is a ubiquitously expressed multi-functional protein that plays a critical role in regulating volume decrease in cells after cellular swelling. In plants, ICln induces Cl- currents [1,4,5], thus regulating Cl- homoeostasis in eukaryotes [2,3]. Structurally, the fold resembles a pleckstrin homology fold, on of whose roles is to recruit and tether their host protein to the cell membrane; and although the surface charges of the ICln fold are not equivalent to those of the PH domain, ICln can be phosphorylated in vitro and the PH-nature of the domain may be the part involving it in the transposition from cytosol to cell membrane during cytotonic swelling  .. 
PF04140 Isoprenylcysteine carboxyl methyltransferase (ICMT) family <br>Pfam-B_15304 (release 7.3) & Pfam-B_5114 (Release 8.0). The isoprenylcysteine o-methyltransferase (EC:2.1.1.100) family carry out carboxyl methylation of cleaved eukaryotic proteins that terminate in a CaaX motif. In Saccharomyces cerevisiae this methylation is carried out by Ste14p, an integral endoplasmic reticulum membrane protein. Ste14p is the founding member of the isoprenylcysteine carboxyl methyltransferase (ICMT) family, whose members share significant sequence homology  .. 
PF03971 Monomeric isocitrate dehydrogenase<br>NADP(+)-dependent isocitrate dehydrogenase (ICD) is an important enzyme of the intermediary metabolism, as it controls the carbon flux within the citric acid cycle and supplies the cell with 2-oxoglutarate EC:1.1.1.42 and NADPH for biosynthetic purposes  .. 
PF01231 Indoleamine 2,3-dioxygenase<br>
PF02479 IE68; <br>Herpesvirus immediate early protein. Pfam-B_2276 (release 5.4). This regulatory protein is expressed from an immediate early gene in the cell cycle of herpesvirus. The protein is known by various names  including IE-68, US1, ICP22 and IR4.. 
PF01008 Initiation factor 2 subunit family<br>Pfam-B_1302 (release 3.0). This family includes initiation factor 2B alpha, beta and delta subunits from eukaryotes, initiation factor 2B subunits 1 and 2 from archaebacteria and some proteins of unknown function from prokaryotes. Initiation factor 2 binds to Met-tRNA, GTP and the small ribosomal subunit. Members of this family have also been characterised as 5-methylthioribose- 1-phosphate isomerases, an enzyme of the methionine salvage pathway. The  crystal structure of Ypr118w, a non-essential, low-copy number gene  product from Saccharomyces cerevisiae, reveals a dimeric protein with  two domains and a putative active site cleft  .. 
PF00707 IF3; <br>Translation initiation factor IF-3, C-terminal domain. Pfam-B_629 (release 2.1). 
PF01652 Eukaryotic initiation factor 4E<br>Pfam-B_1315 (release 4.1). 
PF00932 IF_C_term; IF_tail;<br>The lamin-tail domain (LTD), which has an immunoglobulin (Ig) fold, is found in Nuclear Lamins, Chlo1887 from Chloroflexus, and several bacterial proteins where it occurs with membrane associated  hydrolases of the metallo-beta-lactamase,synaptojanin, and  calcineurin-like phosphoesterase superfamilies  .. 
PF00714 Interferon gamma<br>Pfam-B_615 (release 2.1). 
PF00047 Immunoglobulin domain<br>Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases.  Immunoglobulin-like domains may be involved in protein-protein and protein-ligand interactions. The Pfam alignments do not include the first and last strand of the immunoglobulin-like domain.. 
PF02395 IGA1; <br>Immunoglobulin A1 protease. Pfam-B_540 (release 5.2). 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 IgA proteases Swiss:O32555 from E. coli O157:H7 cleaves human coagulation factor V   and Swiss:O88093 is a hemoglobin protease from E. coli EB1  .. 
PF00219 Insulin-like growth factor binding protein<br>
PF01378 B domain<br>This domain is found as a tandem repeat in Streptococcal cell surface proteins, such as the IgG binding protein G.. 
PF00475 Imidazoleglycerol-phosphate dehydratase<br>
PF00218 Indole-3-glycerol phosphate synthase<br>
PF05049 Interferon-inducible GTPase (IIGP)<br>Pfam-B_5519 (release 7.7). Interferon-inducible GTPase (IIGP) is thought to play a role in in intracellular defence. IIGP is predominantly associated with the Golgi apparatus and also localises to the endoplasmic reticulum and exerts a distinct role in IFN-induced intracellular membrane trafficking or processing  .. 
PF00340 interleukin-1; <br>This family includes interleukin-1 and interleukin-18.. 
PF00726 Interleukin 10<br>Pfam-B_885 (release 2.1). 
PF03039 Interleukin-12 alpha subunit<br>Pfam-B_2071 (release 6.4). Interleukin 12 (IL-12) is a disulphide-bonded heterodimer consisting of a 35kDa alpha subunit (e.g. Swiss:P29459) and a 40kDa beta subunit (e.g. Swiss:P29460). It is involved in the stimulation and maintenance of Th1 cellular immune responses, including the normal host defence against various intracellular pathogens, such as Leishmania, Toxoplasma, measles virus and HIV. IL-12 also has an important role in pathological Th1 responses, such as in inflammatory bowel disease and multiple sclerosis. Suppression of IL-12 activity in such diseases may have therapeutic benefit.  On the other hand, administration of recombinant IL-12 may have therapeutic benefit in conditions associated with pathological Th2 responses [1,2].. 
PF02372 Interleukin 15<br>Pfam-B_2545 (release 5.4). Interleukin-15 (IL-15) is a cytokine that possesses a variety of biological functions, including stimulation and maintenance of cellular immune responses  .. 
PF02394 Interleukin-1 propeptide<br>Pfam-B_1500 (release 5.2). 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.. 
PF00715 Interleukin 2<br>Pfam-B_709 (release 2.1). 
PF02059 Interleukin-3<br>
PF00727 Interleukin 4<br>Pfam-B_833 (release 2.1). 
PF02025 Interleukin 5<br>
PF00489 IL-6; <br>Interleukin-6/G-CSF/MGF family. 
PF01415 Interleukin 7/9 family<br>Ponting CP, Schultz J, Bork P. 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 response remains unclear.. 
PF00048 il8; <br>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.. 
PF01787 Ilarvirus coat protein<br>Pfam-B_1131 (release 4.2). This family consists of various coat proteins from the ilarviruses part of the Bromoviridae, members include apple mosaic virus and prune dwarf virus. The ilarvirus coat protein is required to initiate replication of the viral genome in host plants  .  Members of the Bromoviridae have a positive stand ssRNA genome with no DNA stage in there replication.. 
PF01450 Acetohydroxy acid isomeroreductase, catalytic domain<br>Prodom_2380 (release 99.1). Acetohydroxy acid isomeroreductase catalyses the conversion of acetohydroxy acids into dihydroxy valerates. This reaction is the second in the synthetic pathway of the essential branched side chain amino acids valine and isoleucine.. 
PF00920 Dehydratase family<br>Pfam-B_1309 (release 3.0). 
PF05046 Mitochondrial large subunit ribosomal protein (Img2)<br>Pfam-B_17929 (release 7.6). This family of proteins have been identified as part of the mitochondrial large ribosomal subunit in yeast  .. 
PF04156 IncA protein<br>Pfam-B_2718 (release 7.3). Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is non-fusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA, is functionally associated with the homotypic fusion of inclusions  . This family probably includes members of the wider Inc family rather than just IncA.. 
PF02387 IncFII RepA protein family<br>Pfam-B_1209 (release 5.2). This protein is plasmid encoded and found to be essential for plasmid replication  .. 
PF02974 Protease inhibitor Inh<br>The Inh inhibitor is secreted into the periplasm where its presumed physiological function is to protect periplasmic proteins against the action of secreted proteases  . A range of proteases including A, B and C from E. chrysanthemi, alkaline protease from Pseudomonas aeruginosa and the 50 kDa protease from Serratia marcescens are inhibited.. 
PF00876 Ogre; <br>Pfam-B_779 (release 3.0). This family includes the drosophila proteins Ogre and shaking-B, and the C. elegans proteins Unc-7 and Unc-9. Members of this family are integral membrane proteins which are involved in the formation of gap junctions  . This family has been named the Innexins  .. 
PF01658 Myo-inositol-1-phosphate synthase<br>Pfam-B_959 (release 4.1). This is a family of myo-inositol-1-phosphate synthases. Inositol-1-phosphate catalyses the conversion of glucose-6- phosphate to inositol-1-phosphate, which is then dephosphorylated  to inositol  . Inositol phosphates play an important role in  signal transduction.. 
PF00459 inositol_P; <br>Inositol monophosphatase family. 
PF03488 Ins_beta_nem; <br>Nematode insulin-related peptide beta type. 
PF03811 Ins_element1; HTH_Tnp_IS1;<br>InsA N-terminal domain. This appears to be a short zinc binding domain found in IS1 InsA family protein. It is found at the N-terminus of the protein and may be a DNA-binding domain.. 
PF00049 ins; <br>Insulin/IGF/Relaxin family. Superfamily includes insulins; relaxins; insulin-like growth factor; and bombyxin. All are secreted regulatory hormones. Disulfide rich, all-alpha fold. Alignment includes B chain, linker (which is processed out of the final product), and A chain.. 
PF00552 integrase; Integrase;<br>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 Pfam:PF00665. This domain is the carboxyl terminal domain that is a non-specific DNA binding domain  .. 
PF02920 integrase_DNA; <br>DNA binding domain of tn916 integrase. 
PF00357 integrin_A; <br>Integrin alpha cytoplasmic region. This family contains the short intracellular region of integrin alpha chains.. 
PF00362 integrin_B; <br>Integrin, beta chain. Integrins have been found in animals and their homologues have also been found in cyanobacteria, probably due to horizontal gene transfer  .  The sequences repeats have been trimmed due to an overlap with EGF.. 
PF00143 interferon; <br>Interferon alpha/beta domain. 
PF03487 Interleukin_13; <br>
PF01348 Type II intron maturase<br>Pfam-B_105 (release 3.0). Group II introns use intron-encoded reverse transcriptase, maturase and DNA endonuclease activities for site-specific insertion into DNA  .  Although this type of intron is self splicing in vitro they require a maturase protein for splicing in vivo. It has been shown that a specific region of the aI2 intron is needed for the maturase function  . This region was found to be conserved in group II introns and called domain X  .. 
PF03519 Invasion protein B family<br>
PF04741 InvH outer membrane lipoprotein<br>Pfam-B_3503 (release 7.5). This family represents the Salmonella outer membrane lipoprotein InvH. The molecular function of this protein is unknown, but it is required for the localisation to outer membrane of InvG, which is involved in a type III secretion apparatus mediating host cell invasion [1,2].. 
PF00904 Involucrin repeat<br>Pfam-B_1158 (release 3.0). 
PF02121 Phosphatidylinositol transfer protein<br>Along with the structurally unrelated Sec14p family (found in Pfam:PF00650), this family can bind/exchange one molecule of phosphatidylinositol (PI) or phosphatidylcholine (PC) and thus aids their transfer between different membrane compartments. There are three sub-families - all share an N-terminal PITP-like domain, whose sequence is highly conserved. It is described as consisting of three regions. The N-terminal region is thought to bind the lipid and contains two helices and an eight-stranded, mostly antiparallel beta-sheet. An intervening loop region, which is thought to play a role in protein-protein interactions, separates this from the C-terminal region, which exhibits the greatest sequence variation and may be involved in membrane binding. PITP alpha (Swiss:Q00169) has a 16-fold greater affinity for PI than PC. Together with PITP beta (Swiss:P48739), it is expressed ubiquitously in all tissues  .. 
PF03278 IpaB/EvcA family<br>Pfam-B_4003 (release 6.5). This family includes IpaB, which is an invasion plasmid antigen from  Shigella  , as well as EvcA from E. coli Swiss:Q9ZNF1. Members of this family seem to be involved in pathogenicity of some enterobacteria. However the exact function of this component is not clear.. 
PF04979 Protein phosphatase inhibitor 2 (IPP-2)<br>Pfam-B_5306 (release 7.6). Protein phosphotase inhibitor 2 (IPP-2) is a phosphoprotein conserved among all eukaryotes, and it appears in both the nucleus and cytoplasm of tissue culture cells .. 
PF01715 IPP transferase<br>Pfam-B_1875 (release 4.1). This is a family of IPP transferases EC:2.5.1.8 also known as  tRNA delta(2)-isopentenylpyrophosphate transferase. These enzymes modify both cytoplasmic and mitochondrial tRNAs  at A(37) to give isopentenyl A(37)  .. 
PF01745 Isopentenyl transferase<br>Pfam-B_2229 (release 4.1). Isopentenyl transferase / dimethylallyl transferase synthesises isopentenyladensosine 5'-monophosphate, a cytokinin that induces shoot formation on host plants  infected with the Ti plasmid  .. 
PF00605 Interferon regulatory factor transcription factor<br>This family of transcription factors are important in the regulation of interferons in response to infection by virus and in the regulation of interferon-inducible genes. Three of the five conserved tryptophan residues bind to DNA.. 
PF04120 iron_permease; <br>Low affinity iron permease . Pfam-B_71435 (release 7.3);. 
PF02060 Slow voltage-gated potassium channel<br>
PF00180 isodh; <br>Isocitrate/isopropylmalate dehydrogenase. 
PF04279 Intracellular septation protein A <br>TIGRFAMs (release 2.0);. 
PF01128 UPF0007;<br>2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase. Members of this family are enzymes which catalyse the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from cytidine triphosphate and 2-C-methyl-D-erythritol 4-phosphate (MEP)  .. 
PF01695 IstB;<br>IstB-like ATP binding protein. Pfam-B_982 (release 4.1). This protein contains an ATP/GTP binding P-loop motif. It is found associated with IS21 family insertion sequences  .  The function of this protein is unknown, but it may perform a transposase function  .. 
PF02189 Immunoreceptor tyrosine-based activation motif<br>Alignment kindly provided by SMART. 
PF01156 Inosine-uridine preferring nucleoside hydrolase<br>
PF04183 IucA / IucC family<br>Pfam-B_1982 (release 7.3). IucA and IucC catalyse discrete steps in biosynthesis of the siderophore aerobactin from N epsilon-acetyl-N epsilon-hydroxylysine and citrate  . This family represents the N-terminal region.  The C-terminal region appears to be related to iron transporter proteins.. 
PF01419 Jacalin-like lectin domain<br>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 (Swiss:P15501).. 
PF02375 jmjN; <br>
PF03957 JNK; <br>Jun-like transcription factor. 
PF01486 K-box region<br>Pfam-B_25 (release 4.0). The K-box region is commonly found associated with SRF-type transcription factors see Pfam:PF00319. The K-box is a possible coiled-coil structure  . Possible role in multimer formation  .. 
PF02960 K1 glycoprotein<br>Pfam-B_345 (release 6.4). 
PF02149 Kinase associated domain 1<br>
PF02524 KID_repeat; <br>Pfam-B_1382 (release 5.4). This is family contains the KID repeat as found in Borrelia spirochete RepA / Rep+ proteins.  The function of these proteins is unknown. RepA and related Borrelia proteins have been suggested to play an important genus-wide role in the biology of the Borrelia  .. 
PF00050 kazal; <br>Kazal-type serine protease inhibitor domain. Usually indicative of serine protease inhibitors. However, kazal-like domains are also seen in the extracellular part of agrins, which are not known to be protease inhibitors. Kazal domains often occur in tandem arrays. Small alpha+beta fold containing three disulphides. Alignment also includes a single domain from transporters in the OATP/PGT family Swiss:P46721.. 
PF03522 K-Cl Co-transporter type 1 (KCC1)<br>
PF03520 KCNQ1_channel; <br>KCNQ voltage-gated potassium channel. This family matches to the C-terminal tail of KCNQ type potassium channels.. 
PF03812 2-keto-3-deoxygluconate permease<br>TIGRFAMs, Griffiths-Jones SR. 
PF03814 Potassium-transporting ATPase A subunit<br>TIGRFAMs, Griffiths-Jones SR. 
PF02669 K+-transporting ATPase, c chain<br>This family consists of K+-transporting ATPase, c chain, KdpC. KdpC forms strong interactions with the KdpA subunit, serving to assemble and stabilise the Kdp complex  .  It has been suggested that KdpC could be one of the connecting links between the energy providing subunit KdpB and the K+-transporting subunit KdpA  .  The K+ transport system actively transports K+ ions via ATP hydrolysis.. 
PF02702 Osmosensitive K+ channel His kinase sensor domain<br>This is a family of KdpD sensor kinase proteins that regulate the kdpFABC operon responsible for potassium transport  .  The aligned region corresponds to the N-terminal cytoplasmic part of the protein which may be  the sensor domain responsible for sensing turgor pressure  .. 
PF04962 KduI/IolB family<br>COG3717 & Pfam-B_11840 (release 10.0). This family includes the 5-keto 4-deoxyuronate isomerase enzyme EC:5.3.1.17 that is involved in pectin degradation. This family aldo includes bacterial Myo-inositol catabolism (IolB) proteins. The Bacillus subtilis inositol operon (iolABCDEFGHIJ) is involved in myo-inositol catabolism. Glucose repression of the iol operon induced by inositol is exerted through catabolite repression mediated by CcpA and the iol induction system mediated by IolR  . The exact function of IolB is unknown. Members of this family possess a Cupin like structure.. 
PF02422 Keratin<br>Pfam-B_1920 (release 5.4). This family represents avian keratin proteins  , found in feathers, scale and claw.. 
PF01500 Keratin, high sulfur B2 protein<br>Pfam-B_706 (release 4.0). High sulfur proteins are cysteine-rich proteins synthesised during the differentiation of hair matrix cells, and form hair fibres in association with hair keratin intermediate filaments  . This family has been divided up into four regions, with the second region containing 8 copies of a short repeat  . This family is also known as B2 or KAP1.. 
PF04579 Keratin, high-sulphur matrix protein<br>Pfam-B_4676 (release 7.5). Family of Keratin, high-sulfur matrix proteins.  The keratin products of mammalian epidermal derivatives such as wool and hair consist of microfibrils embedded in a rigid matrix of other proteins. The matrix proteins include the high-sulphur and high-tyrosine keratins, having molecular weights of 6-20 kDa, whereas microfibrils contain the larger, low-sulphur keratins (40-56 kDa)  .. 
PF03882 KicB killing factor<br>The kicA and kicB genes are found upstream of mukB. It has been suggested that the kicB gene encodes a killing factor and the kicA gene codes for a protein that suppresses the killing function of the kicB gene product  . It was also demonstrated that KicA and KicB can function as a post-segregational killing system, when the genes are transferred from the E. coli chromosome onto a plasmid  .. 
PF04383 KilA-N domain<br>The amino-terminal module of the D6R/N1R proteins defines a novel, conserved DNA-binding domain (the KilA-N domain) that is found in a wide range of proteins of large bacterial and eukaryotic DNA viruses. The KilA-N domain family also includes the previously defined APSES domain. The KilA-N and APSES domains may also share a common fold with the nucleic acid-binding modules of the LAGLIDADG nucleases and the amino-terminal domains of the tRNA endonuclease  .. 
PF02172 KIX domain<br>Pfam-B_4149 (Release 4.2). 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.. 
PF03037 Kinetoplastid membrane protein 11<br>Pfam-B_1062 (release 6.4). Kinetoplastid membrane protein 11 is a major cell surface glycoprotein  of the parasite Leishmania donovani.. 
PF03790 KNOX1 domain <br>Pfam-B_533 (release 7.0). The MEINOX region is comprised of two domains, KNOX1 and KNOX2.  KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerisation  . . 
PF03791 KNOX2 domain <br>Pfam-B_533 (release 7.0). The MEINOX region is comprised of two domains, KNOX1 and KNOX2.  KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerisation  . . 
PF00051 kringle; <br>Swissprot_feature_table. Kringle domains have been found in plasminogen, hepatocyte growth factors, prothrombin, and apolipoprotein A. Structure is disulfide-rich, nearly all-beta.. 
PF00197 Trypsin and protease inhibitor<br>
PF02442 L1L_F9_C19; <br>Lipid membrane protein of large eukaryotic DNA viruses. Pfam-B_1868 (release 5.4), Iyer L. The four families of large eukaryotic DNA viruses, Poxviridae, Asfarviridae, Iridoviridae, and Phycodnaviridae, referred to collectively as nucleocytoplasmic large DNA viruses or NCLDV, have all been shown to have a lipid membrane, in spite of the major differences in virion structure. The paralogous genes L1R and F9L encode membrane proteins that have a conserved domain architecture, with a single, C-terminal transmembrane helix, and an N-terminal, multiple-disulfide-bonded domain. The conservation of the myristoylated, disulfide-bonded protein L1R/F9L in most of the NCLDV correlates with the conservation of the thiol-disulfide oxidoreductase E10R which, in vaccinia virus, is required for the formation of disulfide bonds in L1R and F9L  .. 
PF05047 Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain <br>Pfam-B_9461 (release 7.6). The proteins in this family are located in the  mitochondrion. The family includes ribosomal protein L51, and S25. This family also includes mitochondrial NADH-ubiquinone oxidoreductase B8 subunit (CI-B8) EC:1.6.5.3. It is not known whether all members of this family form part of the NADH-ubiquinone oxidoreductase and whether they are also all ribosomal proteins.. 
PF04604 Type-A lantibiotic<br>Pfam-B_4608 (release 7.5). Lantibiotics are antibiotic peptides distinguished by the presence of the rare thioether amino acids lanthionine and/or methyl-lanthionine. They are produced by Gram-positive bacteria as gene-encoded precursor peptides and undergo post-translational modification to generate the mature peptide. Based on their structural and functional features lantibiotics are currently divided into two major groups: the flexible amphiphilic type-A and the rather rigid and globular type-B. Type-A lantibiotics act primarily by pore formation in the bacterial membrane by a mechanism involving the interaction with specific docking molecules such as the membrane precursor lipid II  .. 
PF02502 Ribose/Galactose Isomerase<br>Pfam-B_1105 (release 5.4). This family of proteins contains the sugar isomerase enzymes ribose  5-phosphate isomerase B (rpiB), galactose isomerase subunit A (LacA) and galactose isomerase subunit B (LacB). . 
PF00356 lacI; <br>Bacterial regulatory proteins, lacI family. 
PF02450 LACT;<br>Lecithin:cholesterol acyltransferase. Pfam-B_2099 (release 5.4). Lecithin:cholesterol acyltransferase (LCAT) is involved in extracellular metabolism of plasma lipoproteins, including cholesterol.. 
PF04369 Lactococcin-like family<br>Family of bacteriocins from lactic acid bacteria.. 
PF01306 LacY proton/sugar symporter<br>This family is closely related to the sugar transporter family.. 
PF00961 Intron_maturase; <br>LAGLIDADG endonuclease. 
PF02264 LamB porin<br>Pfam-B_4810 (release 5.2). Maltoporin (LamB protein) forms a trimeric structure which facilitates the diffusion of maltodextrins across the outer membrane of Gram-negative bacteria. The membrane channel is formed by an antiparallel  beta-barrel  .. 
PF03746 LamB/YcsF family<br>This family includes LamB. The lam locus of Aspergillus nidulans consists of two divergently transcribed genes, lamA and lamB, involved in the utilisation of lactams such as 2-pyrrolidinone. Both genes are under the control of the positive regulatory gene amdR and are subject to carbon and nitrogen metabolite repression  . The exact molecular function of the proteins in this family is unknown.. 
PF02061 Lambda Phage CIII<br>The CIII protein from bacteriophage lambda is an inhibitor of the FtsH peptidase  .. 
PF00052 laminin_B; <br>Laminin B (Domain IV). Swissprot_feature_table. 
PF00053 Laminin EGF-like (Domains III and V)<br>Swissprot_feature_table. This family is like Pfam:PF00008 but has 8 conserved  cysteines instead of six.. 
PF00054 laminin_G; Laminin_G; <br>Swissprot_feature_table. 
PF00055 laminin_Nterm;<br>Laminin N-terminal (Domain VI). Swissprot_feature_table. 
PF01299 Lysosome-associated membrane glycoprotein (Lamp)<br>
PF05147 Lanthionine synthetase C-like protein<br>Pfam-B_6095 (release 7.7). Lanthionines are thioether bridges that are putatively generated by dehydration of Ser and Thr residues followed by addition of cysteine residues within the peptide. This family contains the lanthionine synthetase C-like proteins 1 and 2 which are related to the bacterial lanthionine synthetase components C (LanC). LANCL1 (P40 seven-transmembrane-domain protein) and LANCL2 (testes-specific adriamycin sensitivity protein) are thought to be peptide-modifying enzyme components in eukaryotic cells. Both proteins are produced in large quantities in the brain and testes and may have role in the immune surveillance of these organs  . Lanthionines are found in lantibiotics, which are peptide-derived, post-translationally modified antimicrobials produced by several bacterial strains  . This region contains seven internal repeats.. 
PF04738 Lantibiotic dehydratase, C terminus<br>Lantibiotics are ribosomally synthesised antimicrobial agents derived from ribosomally synthesised peptides  .  They are produced by bacteria of the Firmicutes phylum, and include mutacin, subtilin, and nisin.  Lantibiotic peptides contain thioether bridges termed lanthionines that are thought to be generated by dehydration of serine and threonine residues followed by addition of cysteine residues  .  This family constitutes the C-terminus of the enzyme proposed to catalyse the dehydration step  , .. 
PF04737 Lantibiotic dehydratase, N terminus<br>Lantibiotics are ribosomally synthesised antimicrobial agents derived from ribosomally synthesised peptides  .  They are produced by bacteria of the Firmicutes phylum, and include mutacin, subtilin, and nisin.  Lantibiotic peptides contain thioether bridges termed lanthionines that are thought to be generated by dehydration of serine and threonine residues followed by addition of cysteine residues  .  This family constitutes the N-terminus of the enzyme proposed to catalyse the dehydration step  , .. 
PF00500 late_protein_L1; <br>Pfam-B_69 (release 1.0). 
PF00513 late_protein_L2; <br>Pfam-B_39 (release 1.0). 
PF02354 Latrophilin Cytoplasmic C-terminal region<br>Pfam-B_874 (release 5.2). 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 coupled receptors that are involved in  secretion  .  Latrophilin mRNA is present only in neuronal  tissue  .  Lactrophillin interacts with G-alpha O  .. 
PF01273 Lipid_binding_gp; <br>LBP / BPI / CETP family, N-terminal domain. The N and C terminal domains of the LBP/BPI/CETP family are structurally similar.. 
PF02886 Lipid_binding_gp; <br>LBP / BPI / CETP family, C-terminal domain. The N and C terminal domains of the LBP/BPI/CETP family are structurally similar.. 
PF03815 LCCL domain<br>TIGRFAMs, Griffiths-Jones SR. 
PF04072 Leucine carboxyl methyltransferase<br>Pfam-B_5898 (release 7.3);. Family of leucine carboxyl methyltransferases EC:2.1.1.- . This family may need divides a the full alignment contains a significantly shorter mouse sequence.. 
PF04792 V antigen (LcrV) protein<br>Pfam-B_6155 (release 7.5). Yersinia pestis, the aetiologic agent of plague, secretes a set of environmentally regulated, plasmid pCD1-encoded virulence proteins termed Yops and V antigen (LcrV) by a type III secretion mechanism. LcrV is a multifunctional protein that has been shown to act at the level of secretion control by binding the Ysc inner-gate protein LcrG and to modulate the host immune response by altering cytokine production.  LcrV is also necessary for full induction of low-calcium response (LCR) stimulon virulence gene transcription.  Family members are not confined to Yersinia pestis [1,2].   . 
PF00056 ldh; <br>lactate/malate dehydrogenase, NAD binding domain. L-lactate dehydrogenases are metabolic enzymes which catalyse the conversion of L-lactate to pyruvate, the last step in anaerobic glycolysis. L-2-hydroxyisocaproate dehydrogenases are also members of the family.  Malate dehydrogenases catalyse the interconversion of malate to oxaloacetate. The enzyme participates in the citric acid cycle. L-lactate dehydrogenase is also found as a lens crystallin in bird and crocodile eyes. N-terminus (this family) is a Rossmann NAD-binding fold. C-terminus is an unusual alpha+beta fold.. 
PF02615 ldh_2;<br>Malate/L-lactate dehydrogenase. This family consists of bacterial and archaeal Malate/L-lactate dehydrogenase. L-lactate dehydrogenase, EC:1.1.1.27, catalyses  the reaction (S)-lactate + NAD(+) <=> pyruvate + NADH. Malate dehydrogenase, EC:1.1.1.37 and EC:1.1.1.82, catalyses the reactions: (S)-malate + NAD(+) <=> oxaloacetate  + NADH, and (S)-malate + NADP(+) <=> oxaloacetate + NADPH respectively.. 
PF02866 ldh_C; <br>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 members of the family.  Malate dehydrogenases catalyse the interconversion of malate to oxaloacetate. The enzyme participates in the citric acid cycle. L-lactate dehydrogenase is also found as a lens crystallin in bird and crocodile eyes.. 
PF00058 ldl_recept_b; <br>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  .. 
PF03760 LEA-group1; <br>Late embryogenesis abundant (LEA) group 1 . Pfam-B_1549 (release 7.0). Family members are conserved along the entire coding region,  especially within the hydrophobic internal 20 amino acid motif, which may be repeated.. 
PF03168 Late embryogenesis abundant protein<br>Mifsud W, Griffiths-Jones SR. Pfam-B_3080 (release 6.5). 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.  This family represents a group of LEA proteins that appear to be distinct from those in Pfam:PF02987. The family DUF1511, Pfam:PF07427, has now been merged into this family.. 
PF03242 Late embryogenesis abundant protein<br>Pfam-B_3170 (release 6.5). Members of this family are similar to late embryogenesis abundant proteins.\.    Members of the family have been isolated in a number of different screens.  However, the molecular function of these proteins remains obscure.. 
PF00059 lectin_c; <br>Lectin C-type domain. Swissprot_feature_table. This family includes both long and short form C-type. 
PF03041 lef-2; <br>Pfam-B_1773 (release 6.4). The lef-2 gene (for late expression factor 2) from baculovirus is required for expression of late genes. This gene has been shown to be specifically required for expression from the vp39 and polh promoters  .  LEF-1 is a DNA primase and there is some evidence to suggest that LEF-2 may bind to both DNA and LEF-1  .. 
PF03388 Legume-like lectin family<br>Pfam-B_2789 (release 6.6). Lectins are structurally diverse proteins that bind to specific carbohydrates. This family includes the VIP36 Swiss:P49256 and ERGIC-53 Swiss:P49257 lectins. These two proteins were the first recognised members of a family of animal lectins similar (19-24%) to the leguminous plant lectins  . The alignment for this family aligns residues lying towards the N-terminus, where the similarity of VIP36 and ERGIC-53 is greatest. However, while Fiedler and Simons   identified these proteins as a new family of animal lectins, our alignment also includes yeast sequences. ERGIC-53 is a 53kD protein, localised to the intermediate region between the endoplasmic reticulum and the Golgi apparatus (ER-Golgi-Intermediate Compartment, ERGIC). It was identified as a calcium-dependent, mannose-specific lectin  . Its dysfunction has been associated with combined factors V and VIII deficiency OMIM:227300 OMIM:601567, suggesting an important and substrate-specific role for ERGIC-53 in the glycoprotein- secreting pathway [2,3]. . 
PF00139 lectin_legB; <br>Legume lectin domain. 
PF03954 lectin_N; <br>Hepatic lectin, N-terminal domain. 
PF05098 Late expression factor 4 (LEF-4)<br>Pfam-B_6330 (release 7.7). Late expression factor 4 (LEF-4) is one of the Baculovirus late expression factor proteins. LEF-4 carries out all the enzymatic functions related to  mRNA capping  .. 
PF04941 Late expression factor 8 (LEF-8)<br>Pfam-B_5130 (release 7.6). Late expression factor 8 (LEF-8) is one of the primary components of RNA polymerase produced by polyhedrosis viruses. LEF-8 shows homology to the  second largest subunit of prokaryotic DNA-directed RNA polymerase .. 
PF05094 Late expression factor 9 (LEF-9)<br>Pfam-B_6326 (release 7.7). Late expression factor 9 (LEF-9) is one of the primary components of RNA polymerase produced by baculoviruses. LEF-9 is homologous to the largest beta-subunit of prokaryotic DNA-directed RNA polymerase  .. 
PF05150 Legionella pneumophila major outer membrane protein precursor<br>Pfam-B_6492 (release 7.7). This family consists of major outer membrane protein precursors from Legionella pneumophila.. 
PF03020 LEM domain<br>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 Swiss:Q62733, Emerin Swiss:P50402 and Man1.. 
PF04011 LemA family<br>The members of this family are related to the LemA protein Swiss:P71452  . LemA contains an amino terminal predicted transmembrane helix. It has been predicted that the small amino terminus is extracellular  . The exact molecular  function of this protein is uncertain.. 
PF02998 Lentiviral Tat protein<br>Pfam-B_1519 (release 6.4). This family contains retroviral transactivating (Tat) proteins [1,2], from a variety of Lentiviruses.. 
PF02024 Leptin<br>
PF03588 Leucyl/phenylalanyl-tRNA protein transferase<br>TIGRFAMs, Griffiths-Jones SR. 
PF01819 Levivirus coat protein<br>The Levivirus coat protein forms the bacteriophage coat that encapsidates the viral RNA.  180 copies of this protein form the virion shell. The MS2 bacteriophage coat protein controls two distinct processes: sequence-specific RNA encapsidation and repression of replicase translation-by binding to an RNA stem-loop structure of 19 nucleotides containing the initiation codon of the replicase gene. The binding of a coat protein dimer to this hairpin shuts off synthesis of the viral replicase, switching the viral replication cycle to virion assembly rather than continued replication  .. 
PF01726 LexA DNA binding domain<br>Pfam-B_1975 (release 4.1). This is the DNA binding domain of the LexA SOS regulon  repressor which prevents expression of DNA repair proteins. The aligned region contains a variant form of the helix-turn-helix DNA  binding motif  . This domain is found associated with Pfam:PF00717 the auto-proteolytic  domain of LexA EC:3.4.21.88.. 
PF01790 Prolipoprotein diacylglyceryl transferase<br>
PF00556 Antenna complex alpha/beta subunit<br>
PF04991 LicD family<br>Pfam-B_5278 (release 7.6). The LICD family of proteins show high sequence similarity and are involved in phosphorylcholine metabolism. There is evidence to show that LicD2 mutants have a reduced ability to take up choline, have decreased ability to adhere to host cells and are less virulent  . These proteins are part of the nucleotidyltransferase superfamily  .. 
PF01291 LIF / OSM family<br>
PF00549 ligase-CoA; <br>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.. 
PF00412 LIM domain<br>This family represents two copies of the LIM structural domain.. 
PF01803 LIM-domain binding protein<br>Pfam-B_1352 (release 4.2). The LIM-domain binding protein, binds to the LIM domain Pfam:PF00412 of LIM homeodomain proteins which are transcriptional regulators of development. Nuclear LIM interactor (NLI) / LIM domain-binding protein 1 (LDB1) Swiss:P70662 is located in the nuclei of neuronal cells during development, it is co-expressed with Isl1 in early motor neuron differentiation and has a suggested role in the Isl1 dependent development of motor neurons  . It is suggested that these proteins act synergistically to enhance transcriptional efficiency by acting as co-factors for LIM homeodomain and Otx class transcription factors both of which have essential roles in development  . The Drosophila protein Chip Swiss:O18353 is required for segmentation and activity of a remote wing margin enhancer  . Chip is a ubiquitous chromosomal factor required for normal expression of diverse genes at many stages of development  . It is suggested that Chip cooperates with different LIM domain proteins and other factors to structurally support remote enhancer-promoter interactions  .. 
PF00538 linker_histone; <br>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.. 
PF04454 Encapsulating protein for peroxidase<br>The Linocin_M18 is found in eubacteria and archaea [1,2]. These proteins, referred to as encapsulins, form nanocompartments within the bacterium which contain ferritin-like proteins or peroxidases, enzymes involved in oxidative-stress response. These enzymes are targeted to the interior of encapsulins via unique C-terminal extensions  .. 
PF03583 Secretory lipase <br>Pfam-B_3085 (release 7.0). These lipases are expressed and secreted during the infection cycle of these pathogens.  In particular, C. albicans has  a large number of different lipases, possibly reflecting broad  lipolytic activity, which may contribute to the persistence and  virulence of C. albicans in human tissue  .. 
PF03279 Bacterial lipid A biosynthesis acyltransferase<br>Pfam-B_1803 (release 6.5). 
PF00151 lipase; <br>
PF01674 Lipase (class 2)<br>Pfam-B_968 (release 4.1). This family consists of hypothetical C. elegans proteins and lipases. Lipases or triacylglycerol acylhydrolases hydrolyse ester bonds in triacylglycerol giving diacylglycerol, monoacylglycerol, glycerol  and free fatty acids  . Swiss:P37957 is a extracellular lipase from B. subtilis 168  .. 
PF03280 Proteobacterial lipase chaperone protein<br>Pfam-B_4313 (release 6.5). 
PF00657 GDSL-like Lipase/Acylhydrolase<br>Prosite & Pfam-B_543 (Release 7.5). 
PF00061 lipocalin; <br>Lipocalin / cytosolic fatty-acid binding protein family. Prosite and HMM_iterative_training. Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The family also encompasses the enzyme prostaglandin D synthase (EC:5.3.99.2). Alignment subsumes both the lipocalin and fatty acid binding protein signatures from PROSITE. This is supported on structural and functional grounds. The structure is an eight-stranded beta barrel.. 
PF00820 Borrelia lipoprotein<br>Pfam-B_1321 (release 2.1). This family of lipoproteins is found in Borrelia spirochetes.  The function of these proteins is uncertain.. 
PF03202 Putative mycoplasma lipoprotein, C-terminal region<br>Pfam-B_2205 (release 6.5). 
PF03260 Lepidopteran low molecular weight (30 kD) lipoprotein<br>Pfam-B_4108 (release 6.5). 
PF03330 Lipoprotein_13;<br>Rare lipoprotein A (RlpA)-like double-psi beta-barrel. Pfam-B_3255 (release 6.5). Rare lipoprotein A (RlpA) contains a conserved region that has the  double-psi beta-barrel (DPBB) fold [3,4]. The function of RlpA is not well understood, but it has been shown to act as a prc mutant suppressor in Escherichia coli  . The DPBB fold is often an enzymatic domain. The members of this family are quite diverse, and if catalytic this family may contain several different functions. Another example of this domain is found in the N terminus of pollen allergen.. 
PF03640 Secreted repeat of unknown function<br>This family occurs as tandem repeats in a set of lipoproteins. The alignment contains a Y-X4-D motif.. 
PF04791 LMBR1-like membrane protein<br>Pfam-B_6189 (release 7.5). Members of this family are integral membrane proteins that are around 500 residues in length. LMBR1 is not involved in preaxial polydactyly, as originally thought  . Vertebrate members of this family may play a role in limb development  . A member of this family has been shown to be a lipocalin membrane receptor  . 
PF03923 Uncharacterized lipoprotein<br>The function of this presumed lipoprotein is unknown. The family includes E. coli YajG Swiss:P36671.. 
PF04200 Lipoprotein associated domain<br>Pfam-B_3382 (release 7.3). This presumed domain is about 100 amino acids in length. It is found in lipoprotein of unknown function and is greatly expanded in Mycoplasma pulmonis.  The domain is found in up to five copies in some proteins. This family also includes the Mycoplasma arthritidis MAA2 variable surface protein. MAA2 is implicated in in cytoadherence and virulence and has been shown to exhibit both size and phase variability  .. 
PF00921 Borrelia lipoprotein<br>Pfam-B_1509 (release 3.0). This family of lipoproteins is found in Borrelia spirochetes.  The function of these proteins is uncertain.. 
PF00938 Lipoprotein; <br>Pfam-B_1076 (release 3.0). This family of lipoproteins is Mycoplasma specific.. 
PF01298 Transferrin binding protein-like solute binding protein<br>Pfam-B_893 (release 3.0). This family of proteins are distantly related to other families of solute binding proteins.. 
PF01441 Lipoprotein<br>Prodom_1149 (release 99.1). Members of this family are lipoproteins that are probably involved in evasion of the host immune system by pathogens.. 
PF01540 Adhesin lipoprotein<br>Pfam-B_615 (release 4.0). This family consists of the p50 and variable adherence-associated antigen (Vaa) adhesins from Mycoplasma hominis. M. hominis is a mycoplasma associated with human urogenital diseases, pneumonia, and septic arthritis  . An adhesin is a cell surface molecule that mediates adhesion to other cells or to the surrounding surface or substrate. The Vaa antigen is a 50-kDa surface lipoprotein that has four tandem repetitive DNA sequences encoding a periodic peptide structure, and is highly immunogenic in the human host  . p50 is also a 50-kDa lipoprotein, having three repeats A,B and C, that may be a tetramer of 191-kDa in its native environment  .. 
PF02030 Hypothetical lipoprotein (MG045 family)<br>This family includes hypothetical lipoproteins, the amino terminal part of this protein is related to Pfam:PF01547, a family of solute binding proteins. This suggests this family also has a solute binding function.. 
PF03305 Mycoplasma MG185/MG260 protein<br>Pfam-B_4433 (release 6.5). Most of the aligned regions in this family are found towards the middle of the member proteins.. 
PF00305 lipoxygenase; <br>
PF04778 LMP repeated region<br>Pfam-B_2380 (release 7.6). This family consists of a repeated sequence element found in the LMP group of surface-located membrane proteins of Mycoplasma hominis.  The the number of repeats in the protein affects the tendency of cells to spontaneously  aggregate.  Agglutination may be an important factor in colonisation. Non-agglutinating microorganisms might easily be distributed whereas  aggregation might provide a better chance to avoid an antibody response since some of the epitopes may be buried  .. 
PF01451 Low molecular weight phosphotyrosine protein phosphatase<br>Prodom_2132 (release 99.1). 
PF03548 Outer membrane lipoprotein carrier protein LolA<br>TIGRFAMs, Griffiths-Jones SR. 
PF03550 Outer membrane lipoprotein LolB<br>TIGRFAMs, Griffiths-Jones SR. 
PF04728 Lipoprotein leucine-zipper<br>This is leucine-zipper is found in the enterobacterial outer membrane lipoprotein LPP. It is likely that this domain oligomerises and is involved in protein-protein interactions. As such it is a bundle of alpha-helical coiled-coils, which are known to play key roles in mediating specific protein-protein interactions for in molecular recognition and the assembly of multi-protein complexes.. 
PF02169 LPP20 lipoprotein<br>This family contains the LPP20 lipoprotein, which is a non-essential class of lipoprotein  .. 
PF04348 LppC putative lipoprotein<br>This family includes several bacterial outer membrane antigens, whose molecular function is unknown.. 
PF02684 Lipid-A-disaccharide synthetase<br>This is a family of lipid-A-disaccharide synthetases, EC:2.4.2.128. These enzymes catalyse the reaction: UDP-2,3-bis(3-hydroxytetradecanoyl) glucosamine + 2,3-bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl  1-phosphate <=> UDP + 2,3-bis(3-hydroxytetradecanoyl)-D-glucosaminyl-1,6 -beta-D-2,3-bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl 1-phosphate. These enzymes catalyse the fist disaccharide step in the synthesis of  lipid-A-disaccharide.. 
PF03331 UDP-3-O-acyl N-acetylglycosamine deacetylase<br>Pfam-B_3666 (release 6.5). The enzymes in this family catalyse the second step in the biosynthetic pathway for lipid A.. 
PF02606 Tetraacyldisaccharide-1-P 4'-kinase<br>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)-D -glucosaminyl-(beta-D-1,6)-2,3-bis(3-hydroxytetradecanoyl)-D-glucosam inyl  beta-phosphate <=> ADP + 2,3,2',3'-tetrakis(3-hydroxytetradecanoyl)-D- glucosaminyl-1,6-beta-D-glucosamine 1,4'-bisphosphate.  This enzyme is  involved in the synthesis of lipid A portion of the bacterial  lipopolysaccharide layer (LPS)  . The family contains a P-loop motif at the N terminus.. 
PF03788 LrgA family<br>This family is uncharacterised. It contains the protein LrgA that has been hypothesised to export murein hydrolases  .. 
PF04172 LrgB-like family <br>TIGRFAMs (release 2.0);. The two products of the lrgAB operon are potential membrane proteins, and LrgA and LrgB are both thought to control of murein hydrolase activity and penicillin tolerance  .. 
PF01462 Leucine rich repeat N-terminal domain<br>Leucine Rich Repeats Pfam:PF00560 are short sequence motifs present in a number of proteins with diverse functions and cellular locations. Leucine Rich Repeats are often flanked by cysteine rich domains. This domain is often found at the N-terminus of tandem leucine rich repeats.. 
PF01816 Leucine rich repeat variant<br>The function of this repeat is unknown. It has an unusual structure of two helices. One is an alpha helix, the other is the much rarer 3-10 helix.. 
PF05083 LST-1 protein<br>Pfam-B_6166 (release 7.7). B144/LST1 is a gene encoded in the human major histocompatibility complex that produces multiple forms of alternatively spliced mRNA and encodes peptides fewer than 100 amino acids in length. B144/LST1 is strongly expressed in dendritic cells. Transfection of B144/LST1 into a variety of cells induces morphologic changes including the production of long, thin filopodia  .. 
PF00677 Lumazine binding domain<br>Pfam-B_291 (release 2.1). This domain binds to derivatives of lumazine  in some proteins. Some proteins have lost the residues involved in binding lumazine.. 
PF00894 Luteovirus coat protein<br>Pfam-B_123 (release 3.0). 
PF02122 Luteo_ORF2; <br>This family contains polyprotein processing endopeptidases from RNA viruses.. 
PF04662 Luteovirus P0 protein<br>Pfam-B_4444 (release 7.5) & Pfam-B_3579 (release 10.0). This family of proteins may be involved in suppression of PTGS a plant defence mechanism  .. 
PF01659 Luteovirus putative VPg genome linked protein<br>Pfam-B_970 (release 4.1). This family consists of several putative genome linked proteins.  The genomic RNA of luteoviruses are linked to virally encoded genome proteins (VPg).  Open reading frame 4 is thought to encode the VPg  in Soybean dwarf luteovirus  . Luteoviruses have isometric capsids that contain a positive stand ssRNA genome, they have no DNA stage during their replication.. 
PF04443 Acyl-protein synthetase, LuxE<br>LuxE is an acyl-protein synthetase found in bioluminescent bacteria.  LuxE catalyses the formation of an acyl-protein thioester from a fatty acid and a protein.\.       This is the second step in the bioluminescent fatty acid reduction system, which converts tetradecanoic acid to the aldehyde substrate of the luciferase-catalysed bioluminescence reaction   A conserved cysteine found at position 364 in Photobacterium phosphoreum LuxE (Swiss:Q52100) is thought to be acylated during the transfer of the acyl group from the synthetase subunit to the reductase.  The carboxyl terminal of the synthetase is though to act as a flexible arm to transfer acyl groups between the sites of activation and reduction  . This family also includes Vibrio cholerae RBFN protein (Swiss:Q06961), which is involved in the biosynthesis of the O-antigen component 3-deoxy-L-glycero-tetronic acid.. 
PF02664 S-Ribosylhomocysteinase (LuxS)<br>This family consists of the LuxS protein involved in autoinducer AI2  synthesis and its hypothetical relatives. S-ribosylhomocysteinase (LuxS) catalyses the cleavage of the thioether bond in S-ribosylhomocysteine (SRH) to produce homocysteine and 4,5-dihydroxy-2,3-pentanedione (DPD), the precursor of type II bacterial quorum sensing molecule. . 
PF00206 lyase_1; <br>
PF02278 Polysaccharide lyase family 8, super-sandwich domain<br>Pfam-B_4840 (release 5.2). This family consists of a group of secreted bacterial lyase enzymes EC:4.2.2.1 capable of acting on hyaluronan and chondroitin in the extracellular matrix of host tissues, contributing to the invasive capacity of the pathogen.. 
PF02884 Polysaccharide lyase family 8, C-terminal beta-sandwich domain<br>Pfam-B_4840 (release 5.2). This family consists of a group of secreted bacterial lyase enzymes EC:4.2.2.1 capable of acting on hyaluronan and chondroitin in the extracellular matrix of host tissues, contributing to the invasive capacity of the pathogen.. 
PF00062 lys; <br>C-type lysozyme/alpha-lactalbumin family. Overington and HMM_iterative_training. Alpha-lactalbumin is the regulatory subunit of lactose synthase, changing the substrate specificity of galactosyltransferase from N-acetylglucosamine to glucose. C-type lysozymes are secreted bacteriolytic enzymes that cleave the peptidoglycan of bacterial cell walls. Structure is a multi-domain, mixed alpha and beta fold, containing four conserved disulfide bonds.. 
PF01810 LysE type translocator<br>Pfam-B_1537 (release 4.2) & Pfam-B_7916 (Release 8.0). This family consists of various hypothetical proteins and an l-lysine exporter LysE Swiss:P94633 from Corynebacterium glutamicum which is proposed  to be the first of a novel family of translocators  . LysE exports l-lysine from the cell into the surrounding medium and is predicted to span the membrane six times  . The physiological function of the exporter is to excrete excess l-Lysine as a result of natural flux imbalances or peptide hydrolysis; and also after artificial deregulation of  l-Lysine biosynthesis as used by the biotechnology. industry for the production of l-lysine  .. 
PF03641 Possible lysine decarboxylase<br>Pfam-B_741 (release 7.0). The members of this family share a highly conserved motif PGGXGTXXE that is probably functionally important. This family includes proteins annotated as lysine decarboxylases, although the evidence for this is not clear.. 
PF02402 Lysis protein<br>Pfam-B_1555 (release 5.4). 
PF04971 Lysis protein S <br>Pfam-B_7633 (release 7.0). The lysis S protein is a cytotoxic protein forming holes in membranes causing cell lysis. The action of Lysis S is independent of the  proportion of acidic phospholipids in the membrane  .. 
PF01186 Lysyl oxidase <br>
PF02401 LytB protein<br>Pfam-B_1515 (release 5.4). The mevalonate-independent 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway for isoprenoid biosynthesis is essential in many eubacteria, plants, and the malaria parasite. The LytB gene is involved in the trunk line of the MEP pathway.. 
PF04397 LytTr DNA-binding domain<br>This domain is found in a variety of bacterial transcriptional regulators. The domain binds to a specific DNA sequence pattern (see  ). . 
PF02370 M protein repeat<br>Pfam-B_208 (release 5.2). This short repeat is found in multiple copies in bacterial M proteins. The M proteins bind to IgA and are closely associated with virulence. The M protein has been postulated to be a major group A Streptococcal (GAS) virulence factor because of its contribution to the bacterial resistance to opsonophagocytosis  .. 
PF03855 M-factor<br>The M-factor is a pheromone produce upon nitrogen starvation.  The production of M-factor is increased by the pheromone signal. The protein undergoes post-translational modification, to remove the C-terminal signal peptide, the carboxy-terminal cysteine residue is carboxy-methylated  and S-alkylated, with a farnesyl residue  .. 
PF05034 MAAL; <br>Methylaspartate ammonia-lyase N-terminus. Methylaspartate ammonia-lyase EC:4.3.1.2 catalyses the second step of fermentation of glutamate. It is a homodimer. This family represents the N-terminal region of Methylaspartate ammonia-lyase. This domain is structurally related to Pfam:PF03952  . This domain is associated with the catalytic domain Pfam:PF07476.. 
PF03281 Mab-21 protein<br>Pfam-B_4530 (release 6.5). This family contains Mab-21 and Mab-21 like proteins.  In C. elegans these proteins are required for several aspects of embryonic development [2-3].. 
PF01823 MAC/Perforin domain<br>The membrane-attack complex (MAC) of the complement system forms transmembrane channels. These channels disrupt the phospholipid bilayer of target cells, leading to cell lysis and death. A number of proteins participate in the assembly of the MAC. Freshly activated C5b binds to C6 to form a C5b-6 complex, then to C7 forming the C5b-7 complex. The C5b-7 complex binds to C8, which is composed of three chains (alpha, beta, and gamma), thus forming the C5b-8 complex. C5b-8 subsequently binds to C9 and acts as a catalyst in the polymerisation of C9. Active MAC has a subunit composition of C5b-C6-C7-C8-C9{n}. Perforin is a protein found in cytolytic T-cell and killer cells. In the presence of calcium, perforin polymerises into transmembrane tubules and is capable of lysing, non-specifically, a variety of target cells. There are a number of regions of similarity in the sequences of complement components C6, C7, C8-alpha, C8-beta, C9 and perforin.  The X-ray crystal structure of a MACPF domain reveals that it shares a common fold with bacterial cholesterol dependent cytolysins (Pfam:PF01289) such as perfringolysin O. Three key pieces of evidence suggests that MACPF domains and CDCs are homologous: Functional similarity (pore formation), conservation of three glycine residues at a hinge in both families and conservation of a complex core fold  . . 
PF03523 Macrophage scavenger receptor<br>
PF03817 Malonate transporter MadL subunit<br>TIGRFAMs, Griffiths-Jones SR. 
PF03818 Malonate/sodium symporter MadM subunit<br>TIGRFAMs, Griffiths-Jones SR. 
PF02545 Maf-like protein<br>Maf is a putative inhibitor of septum formation   in eukaryotes,  bacteria, and archaea.. 
PF02792 Mago nashi protein<br>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 Swiss:Q9Y5S9  . An RNAi knockout of the C. elegans homologue causes masculinization of the germ line (Mog phenotype) hermaphrodites, suggesting it is involved in hermaphrodite germ-line sex determination  . Mago nashi has been found to be part of the exon-exon junction complex that binds 20 nucleotides upstream of exon-exon junctions  .. 
PF03082 Male accessory gland secretory protein<br>Pfam-B_256 (release 6.4). The accessory gland of male insects is a genital tissue that secretes many components of the ejaculatory fluid, some of which affect the female's receptivity to courtship and her rate of oviposition.  This protein is expressed exclusively in the male accessory glands of adult Drosophila melanogaster. The proteins are transferred to the female fly during copulation and are rapidly altered in the female genital tract  .. 
PF04112 Mak10 subunit, NatC N(alpha)-terminal acetyltransferase<br>Pfam-B_9176 (release 7.3);. NatC N(alpha)-terminal acetyltransferases contains Mak10p,  Mak31p and Mak3p subunits.  All three subunits are associated  with each other to form the active complex  .  . 
PF04874 Mak16 protein C-terminal region<br>Pfam-B_4960 (release 7.6). The precise function of this eukaryotic protein family is unknown. The yeast orthologues have been implicated in cell cycle progression and biogenesis of 60S ribosomal subunits. The Schistosoma mansoni Mak16 has been shown to target protein transport to the nucleolus  .. 
PF01274 Malate synthase<br>
PF02330 Mitochondrial glycoprotein<br>Pfam-B_17905 (release 5.2). 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 interactions  .. 
PF02157 Mannose-6-phosphate receptor<br>This family includes both Cation-dependent and cation independent mannose-6-phosphate receptors.. 
PF01232 Mannitol_dh_N; <br>Mannitol dehydrogenase Rossmann domain. 
PF01050 Mannose-6-phosphate isomerase<br>Pfam-B_899 (release 3.0). All of the members of this Pfam entry belong to family 2 of the mannose-6-phosphate isomerases. The type II phosphomannose isomerases are bifunctional  enzymes. This Pfam entry covers the isomerase domain.  The guanosine diphospho-D-mannose pyrophosphorylase domain is in another Pfam entry, see Pfam:PF00483.. 
PF05007 Mannosyltransferase (PIG-M)<br>Pfam-B_5638 (release 7.6). PIG-M has a DXD motif. The DXD motif is found in many glycosyltransferases that utilise nucleotide sugars. It is thought that the motif is involved in the binding of a manganese ion that is required for association of the enzymes with nucleotide sugar substrates  .. 
PF01575 MaoC_like;<br>Pfam-B_297 (release 4.0). The maoC gene is part of a operon with maoA which is involved in the synthesis of monoamine oxidase  .  The MaoC protein is found to share similarity with a wide variety of enzymes; estradiol 17 beta-dehydrogenase 4, peroxisomal hydratase-dehydrogenase-epimerase, fatty acid synthase beta subunit. Several bacterial proteins that are composed solely of this domain have (R)-specific enoyl-CoA hydratase activity  . This domain is also present in the NodN nodulation protein N.. 
PF03642 MAP domain<br>Pfam-B_1396 (release 7.0). This presumed 110 amino acid residue domain is found in multiple copies in MAP (MHC class II analogue protein) Swiss:Q9Z4J2  . The protein has been found in a wide range of extracellular matrix proteins  .. 
PF02991 MAP1_LC3;<br>Autophagy protein Atg8 ubiquitin like. Pfam-B_1384 (release 6.4). 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  . Autophagy is generally known as a process involved in the degradation of bulk cytoplasmic components that are non-specifically sequestered into an autophagosome, where they are sequestered into double-membrane vesicles and delivered to the degradative organelle, the lysosome/vacuole, for breakdown and eventual recycling of the resulting macromolecules. The yeast proteins are involved in the autophagosome, and Atg8 binds Atg19, via its N-terminus and the C-terminus of Atg19.. 
PF00414 Neuraxin and MAP1B repeat<br>
PF01124 FLAP;<br>This family is has been called MAPEG (Membrane Associated Proteins in Eicosanoid and Glutathione metabolism). It includes proteins such as Prostaglandin E synthase. This enzyme  catalyses the synthesis of PGE2 from PGH2 (produced by cyclooxygenase from arachidonic acid). Because of structural similarities in the active sites of FLAP, LTC4 synthase and PGE synthase, substrates for each enzyme can compete with one another and modulate synthetic activity.. 
PF01914 UPF0056; <br>MarC family integral membrane protein. Integral membrane protein family that includes the antibiotic resistance protein MarC.  These proteins may be transporters.. 
PF02063 MARCKS family<br>
PF02124 Marek's disease glycoprotein A<br>
PF01047 MarR family<br>Pfam-B_269 (release 3.0). The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR.  A large number of compounds induce transcription of the mar operon.  This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds  . The structure of MarR is known   and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif.. 
PF02064 MAS20 protein import receptor<br>
PF04769 Mating-type protein MAT alpha 1<br>This family includes Saccharomyces cerevisiae mating type protein alpha 1 (Swiss:P01365).  Mat alpha 1 is a transcription activator which activates mating-type alpha-specific genes.\.     MAT alpha 1 and MCM 1 bind cooperatively to PQ elements upstream of alpha-specific genes  .\. Alpha 1 interacts in vivo with STE12, linking expression of alpha-specific genes to the alpha-pheromone (Pfam:PF04648) response pathway  .. 
PF01554 UPF0013; <br>Pfam-B_163 (release 4.0). 
PF01824 MatK/TrnK amino terminal region<br>Pfam-B_30 (release 4.2). The function of this region is unknown.. 
PF00661 Viral matrix protein<br>Pfam-B_128 (release 2.1). Found in Morbillivirus and paramyxovirus, pneumovirus.. 
PF03819 MazG nucleotide pyrophosphohydrolase domain<br>
PF04837 MbeB-like, N-term conserved region<br>Pfam-B_3854 (release 7.6). This family represents an N-terminal conserved region of MbeB/MobB proteins. These proteins are essential for specific plasmid transfer.. 
PF04899 MbeD/MobD like <br>Pfam-B_5673 (release 7.6). The MbeD and MobD proteins are plasmid encoded, and are involved in the plasmids mobilisation and transfer in the presence of conjugative plasmids  .. 
PF03621 MbtH-like protein<br>Yeats C, Eberhardt R. This domain is found in the MbtH protein Swiss:O05821 as well as at the N terminus of the antibiotic synthesis protein NIKP1. MbtH and its homologues were first noted in gene clusters involved in non-ribosomal peptides and other secondary metabolites by Quadri et al  . This domain is about 70 amino acids long and contains 3 fully conserved tryptophan residues  .  The structure of the PA2412 protein shows it adopts a beta-beta-beta-alpha-alpha topology with the short C-terminal helix forming the tip of an overall arrowhead shape  . MbtH proteins have been shown to be required for the synthesis of antibiotics, siderophores and glycopeptidolipids [3-6].. 
PF02289 Cyclohydrolase (MCH)<br>Pfam-B_6511 (release 5.2). Methenyl tetrahydromethanopterin cyclohydrolase EC:3.5.4.27 is involved in methanogenesis in bacteria and archaea, producing methane from  carbon monoxide or carbon dioxide.. 
PF00493 MCM2/3/5 family<br>
PF00015 Methyl-accepting chemotaxis protein (MCP) signalling domain<br>Blast MCP1_ECOLI/361-421. This domain is thought to transduce the signal to CheA since it is highly conserved in very diverse MCPs.. 
PF02993 Minor capsid protein VI<br>Pfam-B_1634 (release 6.4). 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  .. 
PF02249 Methyl-coenzyme M reductase alpha subunit, C-terminal domain<br>Pfam-B_2706 (release 5.2). Methyl-coenzyme M reductase (MCR) is the enzyme responsible for  microbial formation of methane. It is a hexamer composed of 2 alpha (this family), 2 beta (Pfam:PF02241), and 2 gamma (Pfam:PF02240) subunits with two identical nickel porphinoid active sites  . The C-terminal domain is comprised of an all-alpha multi-helical bundle.. 
PF02745 Methyl-coenzyme M reductase alpha subunit, N-terminal domain<br>Pfam-B_2706 (release 5.2). Methyl-coenzyme M reductase (MCR) is the enzyme responsible for  microbial formation of methane. It is a hexamer composed of 2 alpha (this family), 2 beta (Pfam:PF02241), and 2 gamma (Pfam:PF02240) subunits with two identical nickel porphinoid active sites  . The N-terminal domain has a ferredoxin-like fold.. 
PF02241 Methyl-coenzyme M reductase beta subunit, C-terminal domain<br>Pfam-B_2692 (release 5.2). Methyl-coenzyme M reductase (MCR) is the enzyme responsible for microbial formation of methane. It is a hexamer composed of 2 alpha (Pfam:PF02249), 2 beta (this family), and 2 gamma (Pfam:PF02240) subunits with two identical nickel porphinoid active sites  . The C-terminal domain of MCR beta has an all-alpha fold with buried central helix.. 
PF02783 Methyl-coenzyme M reductase beta subunit, N-terminal domain<br>Pfam-B_2692 (release 5.2). Methyl-coenzyme M reductase (MCR) is the enzyme responsible for  microbial formation of methane. It is a hexamer composed of 2 alpha (Pfam:PF02249), 2 beta (this family), and 2 gamma (Pfam:PF02240) subunits with two identical nickel porphinoid active sites  . The N-terminal domain has an alpha/beta ferredoxin-like fold.. 
PF02505 Methyl-coenzyme M reductase operon protein D<br>Pfam-B_2115 (release 5.4). Methyl coenzyme M reductase (MCR) catalyses the final step in methanogenesis. MCR is composed of three subunits, alpha  (Pfam:PF02249), beta (Pfam:PF02241) and gamma (Pfam:PF02240)  . Genes encoding the beta (mcrB) and gamma (mcrG) subunits are separated by two open reading frames coding for two proteins C and D  . The function of proteins C and D (this  family) is unknown.. 
PF02240 Methyl-coenzyme M reductase gamma subunit<br>Pfam-B_2713 (release 5.2). Methyl-coenzyme M reductase (MCR) is the enzyme responsible for  microbial formation of methane. It is a hexamer composed of 2 alpha (Pfam:PF02249), 2 beta (Pfam:PF02241), and 2 gamma (this family)  subunits with two identical nickel porphinoid active sites  .. 
PF02315 Methanol dehydrogenase beta subunit<br>Pfam-B_12628 (release 5.2). Methanol dehydrogenase (MDH) is a bacterial periplasmic quinoprotein that oxidises methanol to formaldehyde. MDH is a tetramer of two alpha and two beta subunits. This family contains the small beta subunit.. 
PF04349 Periplasmic glucan biosynthesis protein, MdoG<br>This family represents MdoG, a protein that is necessary for the synthesis of periplasmic glucans. The function of MdoG remains unknown. It has been suggested that it may catalyse the addition of branches to a linear glucan backbone.. 
PF02975 Me-amine-deh_L; <br>Methylamine dehydrogenase, L chain. 
PF04934 MED6; <br>MED6 mediator sub complex component. Pfam-B_4045 (release 7.6). Component of RNA polymerase II holoenzyme and mediator sub complex.. 
PF03525 Meiotic recombination protein rec114<br>
PF03243 Alkylmercury lyase<br>Pfam-B_3505 (release 6.5). Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate.. 
PF02065 Melibiase<br>Glycoside hydrolase families GH27, GH31 and GH36 form the glycoside hydrolase clan GH-D. Glycoside hydrolase family 36 can be split into 11 families, GH36A to GH36K  . This family includes enzymes from GH36A-B and GH36D-K and from GH27.. 
PF01372 Melittin<br>
PF02964 Methane monooxygenase, hydrolase gamma chain<br>
PF03203 MerC mercury resistance protein<br>Pfam-B_2720 (release 6.5). 
PF05052 MerE protein<br>Pfam-B_5840 (release 7.7). The prokaryotic MerE (or URF-1) protein is part of the mercury resistance operon. The protein is thought not to have any direct role in conferring mercury resistance to the organism but may be a mercury resistance transposon [1,2]. . 
PF00376 merR; <br>MerR family regulatory protein. Prosite & Pfam-B_3021 (Release 7.5). 
PF02411 MerT mercuric transport protein<br>Pfam-B_1796 (release 5.4). MerT is an mercuric transport integral membrane protein and  is responsible for transport of the Hg2+ iron from periplasmic  MerP (also part of the transport system) to mercuric reductase (MerE).. 
PF02475 Met-10+ like-protein<br>Pfam-B_2239 (release 5.4). The methionine-10 mutant allele of N. crassa codes for a protein of unknown function, Swiss:O27901. However, homologous proteins have been found in yeast (Swiss:P38793) suggesting this protein may be involved in methionine biosynthesis, transport and/or utilisation  .. 
PF02965 Vitamin B12 dependent methionine synthase, activation domain<br>Griffiths-Jones SR, Eberhardt R. 
PF03724 DUF306;<br>Small domain family found in proteins of of unknown function. Some are secreted (e.g. Swiss:O25998) and implicated in motility in bacteria. Also occurs in Leishmania spp. as an essential gene.  Over-expression in L.amazonensis increases virulence (Swiss:O43987;  ). A pair of cysteine residues show correlated conservation, suggesting that they form a disulphide bond.. 
PF01676 Metalloenzyme superfamily<br>Pfam-B_1926 (release 4.1). This family includes phosphopentomutase Swiss:P07651 and 2,3-bisphosphoglycerate-independent phosphoglycerate mutase, Swiss:P37689. This family is also related to Pfam:PF00245  . The alignment contains the most conserved residues that are probably involved in metal binding and catalysis.. 
PF02066 Metallothionein family 11<br>
PF01439 Metallothionein<br>Prodom_1611 (release 99.1). Members of this family are metallothioneins. These proteins are cysteine rich proteins that bind to heavy metals. Members of this family appear to be closest to Class II metallothioneins, seed Pfam:PF00131.. 
PF02067 Metallothionein family 5<br>
PF02068 Plant PEC family metallothionein<br>
PF02069 Prokaryotic metallothionein<br>
PF00131 metalthio; <br>
PF01717 Methionine_synt; <br>Cobalamin-independent synthase, Catalytic domain. Pfam-B_1909 (release 4.1). This is a family of vitamin-B12 independent methionine synthases or 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferases, EC:2.1.1.14 from bacteria and plants. Plants are the only higher eukaryotes that have the required enzymes for methionine synthesis  . This enzyme catalyses the last step in the production of methionine by transferring a methyl group from 5-methyltetrahydrofolate to homocysteine  . The aligned region makes up the carboxy region of the approximately 750 amino acid protein except in some hypothetical archaeal proteins present in the family, where this region corresponds to the entire length. This domain contains the catalytic residues of the enzyme  .. 
PF01035 Methlytrans; Methyltrans; Methyltransf_1; <br>6-O-methylguanine DNA methyltransferase, DNA binding domain. Pfam-B_1191 (release 3.0). This domain is a 3 helical bundle.. 
PF02870 Methlytrans; Methyltrans; <br>6-O-methylguanine DNA methyltransferase, ribonuclease-like domain. Pfam-B_1191 (release 3.0). 
PF00891 Methyltransf;<br>Pfam-B_152 (release 3.0). This family includes a range of O-methyltransferases. These enzymes utilise S-adenosyl methionine.. 
PF01596 O-methyltransferase<br>Pfam-B_749 (release 4.1). Members of this family are O-methyltransferases. The family includes catechol o-methyltransferase Swiss:P21964, caffeoyl-CoA O-methyltransferase Swiss:Q43095 and a family of bacterial O-methyltransferases that may be involved in antibiotic production  .. 
PF02390 Putative methyltransferase <br>Pfam-B_1023 (release 5.2). This is a family of putative methyltransferases. The aligned  region contains the GXGXG S-AdoMet binding site suggesting  a putative methyltransferase activity.. 
PF03737 Demethylmenaquinone methyltransferase<br>Members of this family are demethylmenaquinone methyltransferases that convert dimethylmenaquinone (DMK) to menaquinone (MK) in the final step of menaquinone biosynthesis. This region is also found at the C-terminus of the DlpA protein Swiss:Q48806.. 
PF03492 Methytransf_6;<br>SAM dependent carboxyl methyltransferase. Pfam-B_1148 (release 7.0). This family of plant methyltransferases contains enzymes that act on a variety of substrates including salicylic acid, jasmonic acid and 7-Methylxanthine. Caffeine is synthesised through sequential three-step methylation of xanthine derivatives at positions 7-N, 3-N, and 1-N.  The protein 7-methylxanthine methyltransferase (designated as CaMXMT) catalyses the second step to produce theobromine  .. 
PF02086 D12 class N6 adenine-specific DNA methyltransferase<br>
PF01340 Met Apo-repressor, MetJ<br>
PF04648 Yeast mating factor alpha hormone<br>The hormone is excreted into the culture medium by haploid cells of the alpha mating type and acts on cells of the opposite mating type (type A). It inhibits DNA synthesis in type A cells synchronising them with type alpha, and so mediates the conjugation process.. 
PF04202 Foot protein 3<br>Pfam-B_1860 (release 7.3). Mytilus foot protein-3 (Mfp-3) is a highly polymorphic protein family located in the byssal adhesive plaques of blue mussels.. 
PF01078 Magnesium chelatase, subunit ChlI<br>Pfam-B_616 (release 3.0). Magnesium-chelatase is a three-component enzyme that  catalyses the insertion of Mg2+ into protoporphyrin IX. This is the first unique step in the synthesis of  (bacterio)chlorophyll.  Due to this, it is thought that  Mg-chelatase has an important role in channelling inter- mediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weight between 38-42 kDa.. 
PF05043 Mga helix-turn-helix domain<br>Pfam-B_5126 (release 7.7). M regulator protein trans-acting positive regulator (Mga) is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions  . This domain is found in the centre of the Mga proteins.  This family also contains a number of bacterial RofA transcriptional regulators that seem to be largely restricted to streptococci.  These proteins have been shown to regulate the expression of important bacterial adhesins  . This is presumably a DNA-binding domain.. 
PF05220 MgpC protein precursor<br>Pfam-B_6685 (release 7.7). This family contains several Mycoplasma MgpC like-proteins.. 
PF02308 MgtC family<br>The MgtC protein is found in an operon with the Mg2+ transporter protein MgtB.  The function of MgtC and its homologues is not known.. 
PF03448 MgtE intracellular N domain<br>This domain is found at the N-terminus of eubacterial magnesium transporters of the MgtE family Pfam:PF01769. This domain is an intracellular domain that has an alpha-helical structure. The crystal structure of the MgtE transporter   shows two of 5 magnesium ions are in the interface between the N domain and the CBS domains. In the absence of magnesium there is a large shift between the N and CBS domains.. 
PF03165 MH1 domain<br>Pfam-B_519 (release 3.0). The MH1 (MAD homology 1) domain is found at the amino terminus of MAD related proteins such as Smads. This domain is separated from the MH2 domain by a non-conserved linker region. The crystal structure of the MH1 domain shows that a highly conserved 11 residue beta hairpin is used to bind the DNA consensus sequence GNCN in the major groove, shown to be vital for the transcriptional activation of target genes. Not all examples of MH1 can bind to DNA however.  Smad2 cannot bind DNA and has a large insertion within the hairpin that presumably abolishes DNA binding. A basic helix (H2) in MH1 with the nuclear localisation signal KKLKK has been shown to be essential for Smad3 nuclear import. Smads also use the MH1 domain to interact with transcription factors such as Jun, TFE3, Sp1, and Runx [1,3].. 
PF03166 MH2 domain<br>Pfam-B_519 (release 3.0). This is the MH2 (MAD homology 2) domain found at the carboxy terminus of MAD related proteins such as Smads. 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 and provides specificity and selectivity to Smad function and also is critical for mediating interactions in Smad oligomers. Unlike MH1, MH2 does not bind DNA. The well-studied MH2 domain of Smad4 is composed of five alpha helices and three loops enclosing a beta sandwich. Smads are involved in the propagation of TGF-beta signals by direct association with the TGF-beta receptor kinase which phosphorylates the last two Ser of a conserved 'SSXS' motif located at the C-terminus of MH2 [1-3].. 
PF00129 Class I Histocompatibility antigen, domains alpha 1 and 2<br>
PF03707 SPNTR; <br>Bacterial signalling protein N terminal repeat. Found as an N terminal triplet tandem repeat in bacterial signalling proteins. Family includes CoxC (Swiss:Q9KX27) and CoxH (Swiss:Q9KX23) from P.carboxydovorans. Each repeat contains two transmembrane helices. Domain is also described as the MHYT domain  .. 
PF02426 Muconolactone delta-isomerase<br>Pfam-B_2784 (release 5.4). This small enzyme forms a homodecameric complex, that catalyses the third step in the catabolism of catechol to succinate- and acetyl-coa in the beta-ketoadipate pathway EC:5.3.3.4. The protein has a ferredoxin-like fold according to SCOP.. 
PF03526 Colicin E1 (microcin) immunity protein<br>
PF04687 Microvirus H protein (pilot protein)<br>A single molecule of H protein is found on each of the 12 spikes on the microvirus shell.  H is involved in the ejection of the phage DNA, and at  least one copy is injected into the host's periplasmic space along with the ssDNA viral genome  . Part of H is thought to lie outside the shell, where it recognises lipopolysaccharide from virus-sensitive strains  .  Part of H may lie  within the capsid, since mutations in H can influence the DNA ejection  mechanism by affecting the DNA-protein interactions  .  H may span the  capsid through the hydrophilic channels formed by G proteins  .. 
PF04726 Microvirus J protein<br>This small protein is involved in DNA packaging, interacting with DNA via its hydrophobic carboxyl terminus.  In bacteriophage phi-X174, J is present in 60 copies, and forms an S-shaped polypeptide chain without any secondary structure.  It is thought to interact with DNA through simple charge interactions  .. 
PF04517 Microvirus lysis protein (E), C terminus<br>E protein causes host cell lysis by inhibiting MraY, a peptidoglycan biosynthesis enzyme.  This leads to cell wall failure at septation  . The N terminal transmembrane region matches the signal peptide model and must be omitted from the family.. 
PF04478 Mid2 like cell wall stress sensor<br>This family represents a region near the C terminus of Mid2, which contains a transmembrane region. The remainder of the protein sequence is serine-rich and of low complexity, and is therefore impossible to align accurately. Mid2 is thought to act as a mechanosensor of cell wall stress.  The C-terminal cytoplasmic region of Mid2 is known to interact with Rom2, a guanine nucleotide exchange factor (GEF) for Rho1, which is part of the cell wall integrity signalling pathway []1.. 
PF01187 Macrophage migration inhibitory factor (MIF)<br>
PF03775 MinC;<br>Septum formation inhibitor MinC, C-terminal domain. In Escherichia coli Swiss:P06138 assembles into a Z ring at midcell while assembly at polar sites is prevented by the min system. MinC Swiss:P18196 a component of this system, is an inhibitor of FtsZ assembly that is positioned within the cell by interaction with MinDE. MinC is an oligomer, probably a dimer  . The C terminal half of MinC is the most conserved and interacts with MinD.  The N terminal half is thought interact with FtsZ.. 
PF05209 Septum formation inhibitor MinC, N-terminal domain<br>In Escherichia coli Swiss:P06138 assembles into a Z ring at midcell while assembly at polar sites is prevented by the min system. MinC Swiss:P18196 a component of this system, is an inhibitor of FtsZ assembly that is positioned within the cell by interaction with MinDE. MinC is an oligomer, probably a dimer  . The C terminal half of MinC is the most conserved and interacts with MinD.  The N terminal half is thought to interact with FtsZ.. 
PF03776 Septum formation topological specificity factor MinE<br>The E. coli minicell locus was shown to code for three gene products (MinC, MinD, and MinE) whose coordinate action is required for proper placement of the division septum. The minE gene codes for a topological specificity factor that, in wild-type cells, prevents the division inhibitor from acting at internal division sites while permitting it to block septation at polar sites  .. 
PF00230 Major intrinsic protein<br>MIP (Major Intrinsic Protein) family proteins exhibit essentially two distinct types of channel properties: (1) specific water transport by the aquaporins, and (2) small neutral solutes transport, such as glycerol by the glycerol facilitators  .. 
PF03094 Mlo family<br>Pfam-B_2483 (release 6.4). A family of plant integral membrane proteins, first discovered in barley. Mutants lacking wild-type Mlo proteins show broad spectrum resistance to the powdery mildew fungus, and dysregulated cell death control, with spontaneous cell death in response to developmental or abiotic stimuli. Thus wild-type Mlo proteins are thought to be inhibitors of cell death whose deficiency lowers the threshold required to trigger the cascade of events that result in plant cell death. Mlo proteins are localised in the plasma membrane and possess seven transmembrane regions; thus the Mlo family is the only major higher plant family to possess 7 transmembrane domains. It has been suggested that Mlo proteins function as G-protein coupled receptors in plants  ; however the molecular and biological functions of Mlo proteins remain to be fully determined.. 
PF03304 Lipoprotein_12; <br>Mlp lipoprotein family. Pfam-B_1663 (release 6.5). The Mlp (for Multicopy Lipoprotein) family of lipoproteins is found in Borrelia species  . This family were previously known as 2.9 lipoprotein genes  . These surface expressed genes may represent new candidate vaccinogens for Lyme disease  . Members of this family generally are downstream of four ORFs called A,B,C and D that are involved in hemolytic activity. . 
PF03562 MltA specific insert domain<br>Pfam-B_1127 (release 7.0). This beta barrel domain is found inserted in the MltA a murein degrading transglycosylase enzyme  . This domain may be involved in peptidoglycan binding.. 
PF01642 Methylmalonyl-CoA mutase<br>Pfam-B_1611 (release 4.1). The enzyme methylmalonyl-CoA mutase is a member of a class of enzymes that uses coenzyme B12 (adenosylcobalamin) as a cofactor. The enzyme induces the formation of an adenosyl radical from the cofactor. This radical then initiates a free-radical rearrangement of its substrate, succinyl-CoA, to methylmalonyl-CoA  .. 
PF03972 MmgE/PrpD family<br>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.. 
PF02406 MmoB/DmpM family <br>Pfam-B_1148 (release 5.2). This family consists of monooxygenase components such as MmoB methane monooxygenase (EC:1.14.13.25) regulatory protein B. When MmoB is present at low concentration it converts methane monooxygenase from an oxidase to a hydroxylase and stabilises intermediates required for the activation of dioxygen  . Also found in this family is DmpM or Phenol hydroxylase (EC:1.14.13.7) protein component P2, this protein lacks redox co-factors and is required for optimal turnover of Phenol hydroxylase  .. 
PF03176 MMPL family<br>Pfam-B_357 (release 6.5). 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, although it has been suggested that they may be involved in lipid transport  .. 
PF01926 50S ribosome-binding GTPase<br>The full-length GTPase protein is required for the complete activity of the protein of interacting with the 50S ribosome and binding of both adenine and guanine nucleotides, with a preference for guanine nucleotide.. 
PF01054 Mouse mammary tumour virus superantigen<br>Pfam-B_518 (release 3.0). The mouse mammary tumour 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.. 
PF05067 Manganese containing catalase<br>Catalases are important antioxidant metalloenzymes that catalyse disproportionation of hydrogen peroxide, forming dioxygen and water. Two families of catalases are known, one having a heme cofactor, and this family that is a structurally distinct family containing non-heme manganese  .. 
PF03962 Mnd1 family<br>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  .. 
PF04039 Domain related to MnhB subunit of Na+/H+ antiporter<br>Possible subunit of Na+/H+ antiporter  ,  . Predicted integral membrane protein, usually four transmembrane regions in this domain.  Often found in bacterial NADH dehydrogenase subunit.. 
PF01899 DUF68; <br>Na+/H+ ion antiporter subunit. Subunit of a Na+/H+ Prokaryotic antiporter complex ( , ).. 
PF03404 Mo-co oxidoreductase dimerisation domain<br>This domain is found in molybdopterin cofactor (Mo-co) oxidoreductases.  It is involved in dimer formation, and has an Ig-fold structure  .. 
PF01967 MoaC family<br>Members of this family are involved in molybdenum cofactor biosynthesis. However their molecular function is not known.. 
PF02391 MoeA; MoeE;<br>Pfam-B_1056 (release 5.2). This family contains the MoaE protein that is involved in biosynthesis of molybdopterin  . Molybdopterin, the universal component of the pterin molybdenum cofactors, contains a dithiolene group serving to bind Mo. Addition of the dithiolene sulfurs to a molybdopterin precursor requires the activity of the converting factor. Converting factor contains the MoaE and MoaD proteins.. 
PF01076 Plasmid recombination enzyme<br>Pfam-B_717 (release 3.0). With some plasmids, recombination can occur in a site specific  manner that is independent of RecA.  In such cases, the  recombination event requires another protein called Pre. Pre is a plasmid recombination enzyme.  This protein is  also known as Mob (conjugative mobilisation).. 
PF03389 MobA/MobL family<br>Pfam-B_3424 (release 6.6). This family includes of the MobA protein from the E. coli plasmid RSF1010, and the MobL protein from the Thiobacillus ferrooxidans plasmid PTF1. These sequences are mobilisation proteins, which are essential for specific plasmid transfer.. 
PF03205 Molybdopterin guanine dinucleotide synthesis protein B<br>Pfam-B_2446 (release 6.5). This protein contains a P-loop.. 
PF04698 MOBP; MOBP_C-Myrip;<br>Rab effector MyRIP/melanophilin C-terminus. Pfam-B_4174 (release 7.5). This domain is found at the C-terminus of the Rab effector proteins MyRIP and melanophilin.. 
PF05161 MOFRL family<br>MOFRL(multi-organism fragment with rich Leucine) family exists in bacteria and eukaryotes. The function of this domain is not clear, although it  exists in some putative enzymes such as reductases and kinases.. 
PF04603 Ran-interacting Mog1 protein<br>Pfam-B_4771 (release 7.5). Segregation of nuclear and cytoplasmic processes facilitates regulation of many eukaryotic cellular functions such as gene expression and cell cycle progression. Trafficking through the nuclear pore requires a number of highly conserved soluble factors that escort macromolecular substrates into and out of the nucleus. The Mog1 protein has been shown to interact with RanGTP which stimulates guanine nucleotide release, suggesting Mog1 regulates the nuclear transport functions of Ran. The human homologue of Mog1 is thought to be alternatively spliced [1,2,3,4].  . 
PF04879 Molybdopterin oxidoreductase Fe4S4 domain<br>This domain is found in formate dehydrogenase H for which the structure is known. The first domain (residues 1 to 60, 448 to 476, and 499 to 540), comprising two small antiparallel sheets and four helices, coordinates the Fe4S4 cluster just below the protein surface  .. 
PF00384 molybdopterin; <br>Molybdopterin oxidoreductase. Prosite & Pfam-B_2803 (Release 7.5). 
PF01568 Molydopterin dinucleotide binding domain<br>Pfam-B_129 (release 4.0). This domain is found in various molybdopterin - containing  oxidoreductases and tungsten formylmethanofuran dehydrogenase  subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase  subunit (FmdD); where the domain constitutes almost the entire subunit. The formylmethanofuran dehydrogenase catalyses the first step in methane formation from CO2 in methanogenic archaea and has a  molybdopterin dinucleotide cofactor  . This domain corresponds to the C-terminal domain IV in dimethyl sulfoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both  molybdopterin guanine dinucleotide molecules  .. 
PF04744 Monooxygenase subunit B protein<br>Pfam-B_6020 (release 7.5). Family of membrane associated monooxygenases (EC 1.13.12.-) which utilise O(2) to oxidise their substrate.  Family members include both ammonia and methane monooxygenases involved in the oxidation of their respective substrates.  These enzymes are multi-subunit  complexes.  This family represents the B subunit of the enzyme; the A subunit is thought to contain the active site. [1,2]. . 
PF03473 MOSC domain<br>Aravind L, Anantharaman V. 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 conserved cysteine and occur either as stand-alone forms such as Swiss:P32157, or fused to other domains such as NifS-like catalytic domain in Molybdenum cofactor sulfurase. The MOSC domain is predicted to be a sulfur-carrier domain that receives sulfur abstracted by the pyridoxal phosphate-dependent NifS-like enzymes, on its conserved cysteine, and delivers it for the formation of diverse sulfur-metal clusters.. 
PF02722 Major Outer Sheath Protein C-terminal region<br>Pfam-B_653 (release 5.5). This is a family of spirochete major outer sheath protein C-terminal  regions. These proteins are present on the bacterial cell surface.  In T. denticola the major outer sheath protein (Msp) binds immobilised laminin and  fibronectin supporting the hypothesis that Msp mediates the extracellular matrix binding activity of T. denticola  .. 
PF02707 MOSP; <br>Major Outer Sheath Protein N-terminal region. Pfam-B_653 (release 5.5). This is a family of spirochete major outer sheath protein N-terminal regions. These proteins are present on the bacterial cell surface.  In T. denticola the major outer sheath protein (Msp) binds immobilised laminin and  fibronectin supporting the hypothesis that Msp mediates the extracellular matrix binding activity of T. denticola  .. 
PF01618 MotA/TolQ/ExbB proton channel family<br>Pfam-B_1099 (release 4.1). This family groups together integral membrane proteins that appear to be involved translocation of proteins across a membrane. These proteins are probably proton channels.  MotA is an essential component of the flageller motor that uses a proton gradient to generate rotational motion in the flageller  . ExbB is part of the TonB-dependent transduction complex.  The TonB complex uses the proton gradient across the inner bacterial membrane to transport large molecules across the outer bacterial membrane.. 
PF04006 Mpp10 protein<br>Pfam-B_12513 (release 7.3). 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 cerevisiae, depletion of Mpp10, a U3 snoRNP-specific protein, halts 18S rRNA production and impairs cleavage at the three U3 snoRNP-dependent sites  .. 
PF05172 MPPN;<br>Nup53/35/40-type RNA recognition motif. Members of this family belong to the nucleor pore complex, NPC, the only gateway between the nucleus and the cytoplasm. The NPC consists of several subcomplexes each one of which is made up of multiple copies of several individual Nup, Nic or Sec protein subunits. In yeast, this Nup or nucleoporin subunit is numbered Nup53, Nup40 in Schizo. pombe and in vertebrates as Nup35. This subunit forms part of the inner ring within the membrane and interacts directly with Nup-Ndc1, considered to be an anchor for the NPC in the pore membrane  . This region of the Nup is the RNA-recognition region  .. 
PF01188 Mandelate racemase / muconate lactonizing enzyme, C-terminal domain<br>C-terminal domain is TIM barrel fold, dehydratase-like domain. Manganese is associated with this domain.. 
PF02746 Mandelate racemase / muconate lactonizing enzyme, N-terminal domain<br>SCOP reports fold similarity with enolase N-terminal domain.. 
PF04152 Mer11_DNA_bind; <br>Mre11 DNA-binding presumed domain . Pfam-B_3909 (release 7.3);. The Mre11 complex is a multi-subunit 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 on its own or in combination with Nbs1  .. 
PF04085 rod shape-determining protein MreC<br>TIGRFAMs (release 2.0);. MreC (murein formation C) is involved in the rod shape  determination in E. coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped.. 
PF04093 rod shape-determining protein MreD<br>MreD (murein formation D) is involved in the rod shape  determination in E. coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped.. 
PF03919 mRNA capping enzyme, C-terminal domain<br>
PF01331 mRNA capping enzyme, catalytic domain<br>This family represents the ATP binding catalytic domain of the mRNA capping enzyme.. 
PF02940 mRNA capping enzyme, beta chain<br>The beta chain of mRNA capping enzyme has triphosphatase activity.  The function of the capping enzyme also depends on the guanylyltransferase activity conferred by the alpha chain (see Pfam:PF01331). 
PF02349 Major surface glycoprotein<br>Pfam-B_864 (release 5.2). This is a novel repeat in Pneumocystis carinii Major surface glycoprotein (MSG) some members of the alignment have up to nine  repeats of this family, the repeats containing several conserved  cysteines.  The MSG of P. carinii is an important protein in  host-pathogen interactions  . Surface glycoprotein A Swiss:O59920 from Pneumocystis carinii is a main target for the host immune system, this protein  is implicated in the attachment of Pneumocystis carinii to the host alveolar epithelial cells, alveolar macrophages,  host surfactant and possibly accounts in part for the hypoxia seen in Pneumocystis carinii pneumonia (PCP)  .. 
PF04066 Multiple resistance and pH regulation protein F (MrpF / PhaF)<br>Members of the PhaF / MrpF family are predicted to be an integral membrane proteins with three transmembrane regions, involved in regulation of pH. PhaF is part of a potassium efflux system involved in pH regulation.\.       It is also involved in symbiosis in Rhizobium meliloti  .  MrpF is part of a Na+/H+ antiporter complex, also involved in pH homeostasis.  MrpF is thought to be an efflux system for Na+ and cholate  . The Mrp system in Bacilli may also have primary energisation capacities  .. 
PF04471 Restriction endonuclease<br>Prokaryotic family found in type II restriction enzymes containing the hallmark (D/E)-(D/E)XK active site. Presence of catalytic residues implicates this region in the enzymatic cleavage of DNA [1,2].. 
PF00924 UPF0003;<br>Mechanosensitive ion channel. Pfam-B_1136 (release 3.0). Two members of  this protein family: Swiss:Q57634 and Swiss:Q58543 of M. jannaschii have been functionally characterised. Both proteins form mechanosensitive (MS) ion channels upon  reconstitution into liposomes and functional examination by the patch-clamp technique. Therefore this family are likely to also be MS channel proteins.. 
PF00985 Merozoite Surface Antigen 2 (MSA-2) family<br>Pfam-B_1052 (release 3.0). 
PF01741 Large-conductance mechanosensitive channel, MscL<br>
PF01716 Manganese-stabilising protein / photosystem II polypeptide<br>Pfam-B_1814 (release 4.1). This family consists of the 33 KDa photosystem II polypeptide from the oxygen evolving complex (OEC) of plants and cyanobacteria. The protein is also known as the manganese-stabilising protein as it is associated with the manganese complex of the OEC and may provide the ligands for the complex  .. 
PF03429 Major surface protein 1B<br>Pfam-B_4414 (release 6.6). The major surface protein (MSP1) of the cattle pathogen Anaplasma is a heterodimer comprised of MSP1a and MSP1b.  This family is the MSP1b chain.  There MSP1 proteins are putative adhesins for bovine erythrocytes. . 
PF04421 Mss4 protein<br>
PF03940 Male specific sperm protein<br>This family of drosophila proteins are typified by the repetitive motif C-G-P.. 
PF05063 MT-A70 <br>Pfam-B_3025 (release 7.7). MT-A70 is the S-adenosylmethionine-binding subunit of human mRNA:m6A  methyl-transferase (MTase), an enzyme that sequence-specifically methylates adenines in pre-mRNAs. . 
PF01993 methylene-5,6,7,8-tetrahydromethanopterin dehydrogenase<br>This enzyme family is involved in formation of methane from carbon dioxide EC:1.5.99.9. The enzyme requires coenzyme F420  .. 
PF02536 mTERF<br>Pfam-B_1422 (release 5.4). 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 possessing three putative leucine zippers one of which is bipartite. The protein binds DNA as a monomer  .  The leucine zippers are not implicated in a dimerisation role as in other leucine zippers  .. 
PF02219 Methylenetetrahydrofolate reductase<br>Pfam-B_2407 (release 5.2). This family includes the 5,10-methylenetetrahydrofolate reductase EC:1.7.99.5 from bacteria and  methylenetetrahydrofolate reductase EC: 1.5.1.20 from eukaryotes. The structure for this domain is known   to be a TIM barrel.. 
PF05068 Mannitol repressor<br>The mannitol operon of Escherichia coli, encoding the mannitol-specific enzyme II of the phosphotransferase system (MtlA) and mannitol phosphate dehydrogenase (MtlD) contains an additional downstream open reading frame which encodes the mannitol repressor (MtlR).. 
PF03083 Sugar efflux transporter for intercellular exchange<br>Pfam-B_623 (release 6.4). 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 proteins is unknown, they are almost certainly transmembrane proteins. This family contains a region of two transmembrane helices that is found in two copies in most members of the family. This family also contains specific sugar efflux transporters that are essential for the maintenance of animal blood glucose levels, plant nectar production, and plant seed and pollen development. In many organisims it meditaes gluose transport; in Arabidopsis it is necessary for pollen viability; and two of the rice homologues are specifically exploited by bacterial pathogens for virulence by means of direct binding of a bacterial effector to the SWEET promoter  .. 
PF03821 Golgi 4-transmembrane spanning transporter<br>TIGRFAMs, Griffiths-Jones SR. 
PF04208 Tetrahydromethanopterin S-methyltransferase, subunit A <br>TIGRFAMs (release 2.0);. The N5-methyltetrahydromethanopterin: coenzyme M (EC:2.1.1.86) of Methanosarcina mazei Go1 is a membrane-associated,  corrinoid-containing protein that uses a transmethylation reaction to drive an energy-conserving sodium ion pump  .. 
PF04211 Tetrahydromethanopterin S-methyltransferase, subunit C <br>TIGRFAMs (release 2.0);. The N5-methyltetrahydromethanopterin: coenzyme M (EC:2.1.1.86) of Methanosarcina mazei Go1 is a membrane-associated,  corrinoid-containing protein that uses a transmethylation reaction to drive an energy-conserving sodium ion pump  .. 
PF04207 Tetrahydromethanopterin S-methyltransferase, subunit D <br>TIGRFAMs (release 2.0);. The N5-methyltetrahydromethanopterin: coenzyme M (EC:2.1.1.86) of Methanosarcina mazei Go1 is a membrane-associated,  corrinoid-containing protein that uses a transmethylation reaction to drive an energy-conserving sodium ion pump  .. 
PF04206 Tetrahydromethanopterin S-methyltransferase, subunit E <br>TIGRFAMs (release 2.0);. The N5-methyltetrahydromethanopterin: coenzyme M (EC:2.1.1.86) of Methanosarcina mazei Go1 is a membrane-associated,  corrinoid-containing protein that uses a transmethylation reaction to drive an energy-conserving sodium ion pump  . . 
PF04210 Tetrahydromethanopterin S-methyltransferase, subunit G <br>TIGRFAMs (release 2.0);. The N5-methyltetrahydromethanopterin: coenzyme M (EC:2.1.1.86) of Methanosarcina mazei Go1 is a membrane-associated,  corrinoid-containing protein that uses a transmethylation reaction to drive an energy-conserving sodium ion pump  .. 
PF02007 Tetrahydromethanopterin S-methyltransferase MtrH subunit<br>The enzyme tetrahydromethanopterin S-methyltransferase EC:2.1.1.86 is composed of eight subunits  . The enzyme is a membrane- associated enzyme complex which catalyses an energy-conserving, sodium-ion-translocating step in methanogenesis from hydrogen and carbon dioxide  . . 
PF05175 Methyltransferase small domain<br>This domain is found in ribosomal RNA small subunit methyltransferase C (eg Swiss:P44453) as well as other  methyltransferases (eg Swiss:Q53742).. 
PF02416 mttA/Hcf106 family<br>Pfam-B_1826 (release 5.4). Members of this protein family are involved in a sec independent translocation mechanism. This pathway has been called the DeltapH pathway in chloroplasts  . Members of this family in E.coli are involved in export of redox proteins with a "twin arginine" leader motif  .. 
PF02316 Mu_DNA_bind;<br>Mu DNA-binding domain. Pfam-B_12856 (release 5.2). This family consists of MuA-transposase and repressor protein CI. These proteins contain homologous DNA-binding domains at their N-termini which compete for the same DNA site within the Mu bacteriophage genome.. 
PF02914 Mu_transposase;<br>Bacteriophage Mu transposase. 
PF03888 MucB_ResB; <br>Members of this family are regulators of the anti-sigma E protein  RseD.. 
PF03108 MuDR;<br>MuDR family transposase. Pfam-B_271 (release 6.5). This region is found in plant proteins that are presumed to be the transposases for Mutator transposable elements [1,2]. These transposons contain two ORFs. The molecular function of this region is unknown.. 
PF04310 MukB N-terminal<br>This family represents the N-terminal region of MukB, one of a group of bacterial proteins essential for the movement of nucleoids from mid-cell towards the cell quarters (i.e. chromosome partitioning).  The structure of the N-terminal domain consists of an antiparallel six-stranded beta sheet surrounded by one helix on one side and by five helices on the other side  . It contains an exposed Walker A loop in an unexpected helix-loop-helix motif (in other proteins, Walker A motifs generally adopt a P loop conformation as part of a strand-loop-helix motif embedded in a conserved topology of alternating helices and (parallel) beta strands) .. 
PF04288 MukE-like family<br>Bacterial protein involved in chromosome partitioning, MukE. 
PF00893 DUF7; SMR;<br>Small Multidrug Resistance protein. Pfam-B_1082 (release 3.0). This family is the Small Multidrug Resistance (SMR) family. Several members have been shown to export a range of toxins, including ethidium bromide (  and quaternary ammonium compounds  , through coupling with proton influx  .. 
PF01225 FPGS; <br>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 (Swiss:P17952), MurD (Swiss:P14900), MurE (Swiss:P22188),  MurF (Swiss:P11880), Mpl (Swiss:P37773) and FolC (Swiss:P08192). MurC, MurD, Mure and MurF catalyse consecutive steps in the synthesis of peptidoglycan.  Peptidoglycan consists of a sheet of two sugar derivatives, with one of these N-acetylmuramic acid attaching to a small pentapeptide.  The pentapeptide is is made of L-alanine, D-glutamic acid, Meso-diaminopimelic acid and D-alanyl alanine.  The peptide moiety is synthesised by successively adding these amino acids to UDP-N-acetylmuramic acid. MurC transfers the L-alanine, MurD transfers the D-glutamate, MurE transfers the diaminopimelic acid, and MurF transfers the D-alanyl alanine. This family also includes Folylpolyglutamate synthase that transfers glutamate to folylpolyglutamate.. 
PF02875 FPGS; <br>Mur ligase family, glutamate ligase domain. This family contains a number of related ligase enzymes which have EC numbers 6.3.2.*. This family includes: MurC (Swiss:P17952), MurD (Swiss:P14900), MurE (Swiss:P22188),  MurF (Swiss:P11880), Mpl (Swiss:P37773) and FolC (Swiss:P08192). MurC, MurD, Mure and MurF catalyse consecutive steps in the synthesis of peptidoglycan.  Peptidoglycan consists of a sheet of two sugar derivatives, with one of these N-acetylmuramic acid attaching to a small pentapeptide.  The pentapeptide is is made of L-alanine, D-glutamic acid, Meso-diaminopimelic acid and D-alanyl alanine.  The peptide moiety is synthesised by successively adding these amino acids to UDP-N-acetylmuramic acid. MurC transfers the L-alanine, MurD transfers the D-glutamate, MurE transfers the diaminopimelic acid, and MurF transfers the D-alanyl alanine. This family also includes Folylpolyglutamate synthase that transfers glutamate to folylpolyglutamate.. 
PF02873 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain<br>Pfam-B_1092 (release 5.2). Members of this family are UDP-N-acetylenolpyruvoylglucosamine reductase enzymes EC:1.1.1.158. This enzyme is involved in the biosynthesis of peptidoglycan.. 
PF02976 DNA mismatch repair enzyme MutH<br>
PF01624 MutS;MutS_N;<br>Pfam-B_800 (release 4.1). This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with Pfam:PF00488, Pfam:PF05188, Pfam:PF05192 and Pfam:PF05190. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein  . The aligned region corresponds with globular domain I, which is involved in DNA binding, in Thermus aquaticus MutS as characterised in  .. 
PF05188 MutS domain II<br>Pfam-B_800 (release 4.1). This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with Pfam:PF00488, Pfam:PF01624, Pfam:PF05192 and Pfam:PF05190. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair;  other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and  recombination. Human MSH has been implicated in non-polyposis colorectal  carcinoma (HNPCC) and is a mismatch binding protein  .  This domain corresponds to domain II in Thermus aquaticus MutS as characterised in  , and has similarity resembles RNAse-H-like domains (see Pfam:PF00075).. 
PF05192 MutS domain III<br>This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with Pfam:PF00488, Pfam:PF05188, Pfam:PF01624 and Pfam:PF05190. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein  . The aligned region corresponds with domain III, which is central to the structure of Thermus aquaticus MutS as characterised in  .   . 
PF05190 MutS family domain IV<br>This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with Pfam:PF01624, Pfam:PF05188, Pfam:PF05192 and Pfam:PF00488. The mutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair;  other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and  recombination. Human MSH has been implicated in non-polyposis colorectal  carcinoma (HNPCC) and is a mismatch binding protein  . The aligned region corresponds in part with globular domain IV,  which is involved in DNA binding, in Thermus aquaticus MutS as characterised in  .. 
PF00488 mutS;MutS_C;<br>This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with Pfam:PF01624, Pfam:PF05188, Pfam:PF05192 and Pfam:PF05190. The mutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair;  other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and  recombination. Human MSH has been implicated in non-polyposis colorectal  carcinoma (HNPCC) and is a mismatch binding protein  . The aligned region corresponds with domain V of  Thermus aquaticus MutS as characterised in  , which contains a Walker A motif, and is structurally similar to the ATPase domain of ABC transporters.. 
PF03023 MviN-like protein<br>Pfam-B_1348 (release 6.4). Deletion of the mviN virulence gene in Salmonella enterica serovar. Typhimurium greatly reduces virulence in a mouse model of typhoid-like disease  . Open reading frames encoding homologues of MviN have since been identified in a variety of bacteria  , including pathogens and non-pathogens and plant-symbionts.  In the nitrogen-fixing symbiont Rhizobium tropici, mviN is required for motility. The MviM protein is predicted to be membrane-associated.. 
PF02344 Myc leucine zipper domain<br>Pfam-B_829 (release 5.2). This family consists of the leucine zipper dimerisation domain found in both cellular c-Myc proto-oncogenes and viral v-Myc oncogenes.  Dimerisation via the leucine zipper motif with other basic helix-loop-helix-leucine zipper (b/HLH/lz) proteins such as  Max Swiss:P25912 is required for efficient DNA binding.  The Myc-Max dimer is a transactivating complex activating expression of growth related genes promoting cell proliferation. The dimerisation is facilitated via interdigitating leucine residues  every 7th position of the alpha helix.  Like charge repulsion of  adjacent residues in this region perturbs the formation of homodimers  with heterodimers being promoted by opposing charge attractions.. 
PF01056 Myc_N_term; <br>Myc amino-terminal region. Pfam-B_387 (release 3.0). The myc family belongs to the basic helix-loop-helix leucine zipper class of transcription factors, see Pfam:PF00010. Myc forms a heterodimer with Max, and this complex regulates cell growth through direct activation of genes involved in cell replication  . Mutations in the C-terminal 20 residues of this domain cause unique changes in the induction of apoptosis, transformation, and G2 arrest  .. 
PF01669 Myelin basic protein<br>Pfam-B_1868 (release 4.1). 
PF01275 Myelin proteolipid protein (PLP or lipophilin)<br>
PF00063 myosin_head; <br>Myosin head (motor domain). Blastp MYSA_HUMAN/1-840. 
PF01576 Myosin_tail; <br>Pfam-B_356 (release 4.1). The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types  . This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then  assemble into the macromolecular thick filament  . The coiled-coil region provides the structural backbone the thick filament  . . 
PF00819 Myotoxin<br>Pfam-B_1337 (release 2.1). 
PF02384 N-6 DNA Methylase<br>Pfam-B_508 (release 5.2). Restriction-modification (R-M) systems protect a bacterial  cell against invasion of foreign DNA by endonucleolytic  cleavage of DNA that lacks a site specific modification. The R-M system is a complex containing three polypeptides: M (this family), S (Pfam:PF01420), and R  . This family consists of N-6 adenine-specific DNA methylase EC:2.1.1.72 from Type I and Type IC restriction systems. These methylases have the same sequence specificity as their corresponding restriction enzymes.. 
PF01555 DNA methylase<br>Pfam-B_164 (release 4.0). Members of this family are DNA methylases. The family contains both N-4 cytosine-specific DNA methylases and N-6 Adenine-specific DNA methylases.. 
PF04245 37-kD nucleoid-associated bacterial protein<br>
PF01235 Sodium:alanine symporter family<br>
PF03390 Na_citrate; <br>2-hydroxycarboxylate transporter family. Pfam-B_3683 (release 6.6). The 2-hydroxycarboxylate transporter family is a family of secondary transporters found exclusively in the bacterial kingdom. They function in the metabolism of the di- and tricarboxylates malate and citrate, mostly in fermentative pathways involving decarboxylation of malate or oxaloacetate  .. 
PF03553 Na+/H+ antiporter family<br>Pfam-B_620 (release 7.0). This family includes integral membrane proteins, some of which are NA+/H+ antiporters  .. 
PF00287 Sodium / potassium ATPase beta chain<br>
PF00939 Sodium:sulfate symporter transmembrane region<br>Pfam-B_1100 (release 3.0). There are also some members in this family that do not match the Prosite motif, and belong to the subfamily  SODIT1.. 
PF04902 Conserved region in Nab1<br>Pfam-B_6188 (release 7.6). Nab1 and Nab2 are co-repressors that specifically interact with and repress transcription mediated by the three members of the NGFI-A (Egr-1, Krox24, zif/268) family of transcription  factors  . This C-terminal region is found only in the Nab1 subfamily.. 
PF01849 NAC domain<br>
PF00175 oxidored_fad; NAD_binding; <br>Oxidoreductase NAD-binding domain . Xanthine dehydrogenases, that also bind FAD/NAD, have essentially no similarity.. 
PF03446 NAD binding domain of 6-phosphogluconate dehydrogenase<br>The NAD binding domain of 6-phosphogluconate dehydrogenase adopts a Rossmann fold.. 
PF03447 Homoserine dehydrogenase, NAD binding domain<br>Pfam-B_459 (release 2.1). This domain adopts a Rossmann NAD binding fold.  The C-terminal domain of homoserine dehydrogenase contributes a single helix to this structural domain, which is not included in the Pfam model.. 
PF01210 NAD_Gly3P_dh; <br>NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus. NAD-dependent glycerol-3-phosphate dehydrogenase (GPDH) catalyses the interconversion of dihydroxyacetone phosphate and L-glycerol-3-phosphate. This family represents the N-terminal NAD-binding domain  .. 
PF01513 DUF15; <br>Pfam-B_797 (release 4.0). Members of this family include ATP-NAD kinases EC:2.7.1.23, which catalyses the phosphorylation of NAD to NADP utilising ATP and other nucleoside triphosphates as well as inorganic polyphosphate as a source of phosphorus. Also includes NADH kinases EC:2.7.1.86.. 
PF02540 NAD synthase<br>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.. 
PF00146 NADH dehydrogenase<br>
PF02477 Nairo_nucleocap; <br>Nucleocapsid N protein. Pfam-B_2892 (release 5.4). The nucleoprotein of the ssRNA negative-strand Nairovirus is an internal part of the virus particle. . 
PF04131 nanE; <br>Putative N-acetylmannosamine-6-phosphate epimerase. This family represents a putative ManNAc-6-P-to-GlcNAc-6P epimerase in the N-acetylmannosamine (ManNAc) utilisation pathway found mainly in pathogenic bacteria.. 
PF04660 Nanovirus coat protein<br>Pfam-B_4486 (release 7.5). Family of conserved Nanoviral coat proteins  .. 
PF00956 NAP_family; <br>Nucleosome assembly protein (NAP). Pfam-B_1009 (release 3.0). NAP proteins are involved in moving histones into the nucleus, nucleosome assembly and chromatin fluidity.  They affect the transcription of many genes.. 
PF03892 Nitrate reductase cytochrome c-type subunit (NapB)<br>The napB gene encodes a dihaem cytochrome c, the small subunit of a heterodimeric periplasmic nitrate reductase  .. 
PF03927 NapD protein<br>Uncharacterized protein involved in formation of periplasmic nitrate reductase.. 
PF03059 Nicotianamine synthase protein<br>Pfam-B_2173 (release 6.4). Nicotianamine synthase EC:2.5.1.43 catalyses the trimerisation of S-adenosylmethionine to yield one molecule of nicotianamine. Nicotianamine has an important role in plant iron uptake mechanisms.  Plants adopt two strategies (termed I and II) of iron acquisition.  Strategy I is adopted by all higher plants except graminaceous plants, which adopt strategy II [1,2]. In strategy I plants, the role of nicotianamine is not fully determined: possible roles include the formation of more stable complexes with ferrous than with ferric ion, which might serve as a sensor of the physiological status of iron within a plant, or which might be involved in the transport of iron  . In strategy II (graminaceous) plants, nicotianamine is the key intermediate (and nicotianamine synthase the key enzyme) in the synthesis of the mugineic family (the only known family in plants) of phytosiderophores. Phytosiderophores are iron chelators whose secretion by the roots is greatly increased in instances of iron deficiency  . The 3D structures of five example NAS from Methanothermobacter thermautotrophicus reveal the monomer to consist of a five-helical bundle N-terminal domain on top of a classic Rossmann fold C-terminal domain. The N-terminal domain is unique to the NAS family, whereas the C-terminal domain is homologous to the class I family of SAM-dependent methyltransferases. An active site is created at the interface of the two domains, at the rim of a large cavity that corresponds to the nucleotide binding site such as is found in other proteins adopting a Rossmann fold  .. 
PF04159 NB glycoprotein<br>Pfam-B_1501 (release 7.3). The NB glycoprotein is found in Influenza type B virus.  Its function is unknown.. 
PF00931 NB-ARC domain<br>
PF04485 nblA; <br>Phycobilisome degradation protein nblA . In the cyanobacterium Synechococcus PCC 7942 (Swiss:P35087) , nblA triggers degradation of light-harvesting phycobiliproteins in response to  deprivation nutrients including nitrogen, phosphorus and sulphur.  The  mechanism of nblA function is not known, but it has been hypothesised that nblA may act by disrupting phycobilisome structure, activating a protease or tagging phycobiliproteins for proteolysis. Members of this family have also been identified in the chloroplasts of some red algae.. 
PF03801 HEC/Ndc80p family<br>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.. 
PF00334 Nucleoside diphosphate kinase<br>
PF05031 Iron Transport-associated domain <br>This domain is involved in the transport of iron, possibly as a siderophore.. 
PF00880 Nebulin_repeat; <br>Pfam-B_1603 (release 3.0). 
PF04299 DUF449; Neg_reg; <br>Putative FMN-binding domain. In Bacillus subtilis, family member Swiss:P21341 (PAI 2/ORF-2) was found to be essential for growth  . The SUPERFAMILY database finds that this domain is related to FMN-binding domains, suggesting this protein is also FMN-binding.. 
PF00960 Neocarzinostatin family<br>
PF03391 Nepovirus coat protein, central domain<br>Pfam-B_3589 (release 6.6). The members of this family are derived from nepoviruses. Together with comoviruses and picornaviruses, nepoviruses are classified in the picornavirus superfamily of plus strand single-stranded RNA viruses. This family aligns several nepovirus coat protein sequences. In several cases, this is found at the C-terminus of the RNA2-encoded viral polyprotein. The coat protein consists of three trapezoid-shaped beta-barrel domains, and forms a pseudo T = 3 icosahedral capsid structure  .. 
PF03688 Nepovirus coat protein, C-terminal domain<br>Pfam-B_3589 (release 6.6). The members of this family are derived from nepoviruses. Together with comoviruses and picornaviruses, nepoviruses are classified in the picornavirus superfamily of plus strand single-stranded RNA viruses. This family aligns several nepovirus coat protein sequences. In several cases, this is found at the C-terminus of the RNA2-encoded viral polyprotein. The coat protein consists of three trapezoid-shaped beta-barrel domains, and forms a pseudo T = 3 icosahedral capsid structure  .. 
PF03689 Nepovirus coat protein, N-terminal domain<br>Pfam-B_3589 (release 6.6). The members of this family are derived from nepoviruses. Together with comoviruses and picornaviruses, nepoviruses are classified in the picornavirus superfamily of plus strand single-stranded RNA viruses. This family aligns several nepovirus coat protein sequences. In several cases, this is found at the C-terminus of the RNA2-encoded viral polyprotein. The coat protein consists of three trapezoid-shaped beta-barrel domains, and forms a pseudo T = 3 icosahedral capsid structure  .. 
PF00064 neur; <br>Overington and HMM_iterative_training. Neuraminidases cleave sialic acid residues from glycoproteins. Belong to the sialidase family - but this alignment does not generalise to the other sialidases. Structure is a 6-sheet beta propeller.. 
PF02932 Neurotransmitter-gated ion-channel transmembrane region<br>This family includes the four transmembrane helices that form the ion channel.. 
PF02158 Neuregulin family<br>
PF03823 Neurokinin B<br>TIGRFAMs, Griffiths-Jones SR. 
PF00243 Nerve growth factor family<br>
PF02979 Nitrile hydratase, alpha chain<br>
PF02211 Nitrile hydratase beta subunit<br>Pfam-B_5347 (release 5.2). Nitrile hydratases EC:4.2.1.84 are unusual metalloenzymes that catalyse the hydration of nitriles to their corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and they contain one iron atom per alpha beta unit  . . 
PF01292 Prokaryotic cytochrome b561<br>This family includes cytochrome b561 and related proteins, in addition to the nickel-dependent hydrogenases b-type cytochrome subunit.  Cytochrome b561 is a secretory vesicle-specific electron transport protein. It is an integral membrane protein, that binds two heme groups non-covalently.  This is a  prokaryotic family.  Members of the 'eukaryotic cytochrome b561' family can be found in Pfam: PF03188.. 
PF04097 NIC;<br>Pfam-B_5541 (release 7.3);. Nup93/Nic96 is a component of the nuclear pore complex.  It is required for the correct assembly of the nuclear pore complex  .  In Saccharomyces cerevisiae, Nic96 has been shown to be involved in the distribution and cellular concentration of the GTPase Gsp1  . The structure of Nic96 has revealed a mostly alpha helical structure  .. 
PF03824 High-affinity nickel-transport protein<br>High affinity nickel transporters involved in the incorporation of nickel into H2-uptake hydrogenase   and urease   enzymes. Essential for the expression of catalytically active hydrogenase and urease. Ion uptake is dependent on proton motive force.  HoxN in Alcaligenes eutrophus is thought to be an integral membrane protein with seven transmembrane helices  . The family also includes a cobalt transporter.. 
PF00374 Nickel-dependent hydrogenase<br>
PF04891 NifQ<br>Pfam-B_6173 (release 7.6). NifQ is involved in early stages of the biosynthesis of the iron-molybdenum cofactor (FeMo-co)  , which is an integral part of the active site of dinitrogenase  .  The conserved C-terminal cysteine residues may be  involved in metal binding  .. 
PF01106 NifU; NifU-like; <br>Pfam-B_1206 (release 3.0). 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  .. 
PF01592 NifU-like N terminal domain<br>Pfam-B_772 (release 4.1). This domain is found in NifU in combination with Pfam:PF01106. This domain is found on isolated in several bacterial species such as Swiss:O53156. The nif genes are responsible for nitrogen fixation.  However this domain is found in bacteria that do not fix nitrogen, so it may have a broader significance in the cell than nitrogen fixation. These proteins appear to be scaffold proteins for iron-sulfur clusters  .. 
PF03206 Nitrogen fixation protein NifW<br>Pfam-B_2891 (release 6.5). Nitrogenase is a complex metalloenzyme composed of two proteins designated the Fe-protein and the MoFe-protein. Apart from these two proteins, a number of accessory proteins are essential for the maturation and assembly of nitrogenase. Even though experimental evidence suggests that these accessory proteins are required for nitrogenase activity, the exact roles played by many of these proteins in the functions of nitrogenase are unclear  .\.  Using yeast two-hybrid screening it has been shown that NifW can interact with itself as well as NifZ  .. 
PF04319 NifZ domain<br>Pfam-B_6057 (release 7.3). This short protein is found in the nif (nitrogen fixation) operon.  Its function is unknown but is probably involved in nitrogen fixation or regulating some component of this process. This 75 residue region is presumed to be a domain.  It is found in isolation in some members and in the amino terminal half of the longer NifZ proteins.. 
PF01077 Nitrite and sulphite reductase 4Fe-4S domain<br>Pfam-B_1092 (release 3.0). Sulphite and nitrite reductases are vital in the biosynthetic assimilation of sulphur and nitrogen, respectfully.  They are also both important for the dissimilation of oxidised anions for energy transduction.. 
PF03460 Nitrite/Sulfite reductase ferredoxin-like half domain<br>Sulfite and Nitrite reductases are key to both biosynthetic assimilation of sulfur and nitrogen and dissimilation of oxidised anions for energy transduction  . Two copies of this repeat are found in Nitrite and Sulfite reductases and form a single structural domain.. 
PF02665 Nitrate reductase gamma subunit<br>This family is the gamma subunit of the nitrate reductase enzyme, the gamma subunit is a b-type cytochrome that receives electrons from the quinone pool  .\.      It then transfers these via the iron-sulfur clusters of the beta subunit to the molybdenum cofactor found in the alpha subunit  .  The nitrate reductase enzyme, EC:1.7.99.4 catalyses the conversion of nitrite to nitrate via the reduction of an acceptor.  The nitrate reductase enzyme is composed of three subunits  .  Nitrate is the most widely used alternative electron acceptor after oxygen  .. 
PF02087 Nitrophorin<br>
PF00881 Nitroreductase family<br>Pfam-B_481 (release 3.0). The nitroreductase family comprises a group of FMN- or FAD-dependent and NAD(P)H-dependent enzymes able to metabolize nitrosubstituted compounds.. 
PF05211 Neuraminyllactose-binding hemagglutinin precursor (NLBH)<br>Pfam-B_6567 (release 7.7). This family is comprised of several flagellar sheath adhesin proteins also called neuraminyllactose-binding hemagglutinin precursor (NLBH) or N-acetylneuraminyllactose-binding fibrillar hemagglutinin receptor-binding subunits. NLBH is found exclusively in Helicobacter which are gut colonising bacteria and bind to sialic acid rich macromolecules present on the gastric epithelium  .. 
PF04170 NlpE N-terminal domain<br>This family represents a bacterial outer membrane lipoprotein that is necessary for signalling by the Cpx pathway  . This pathway responds to cell envelope disturbances and increases the expression of periplasmic protein folding and degradation factors. While the molecular function of the NlpE protein is unknown, it may be involved in detecting bacterial adhesion to abiotic surfaces. In Escherichia coli and Salmonella typhi, NlpE is also known to confer copper tolerance in copper-sensitive strains of Escherichia coli, and may be involved in copper efflux and delivery of copper to copper-dependent enzymes  .. 
PF04973 Nicotinamide mononucleotide transporter<br>Members of this family are integral membrane proteins that are involved in transport of nicotinamide mononucleotide [1,2].. 
PF01233 Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain<br>The N and C-terminal domains of NMT are structurally similar, each adopting an acyl-CoA N-acyltransferase-like fold.. 
PF02799 Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain<br>The N and C-terminal domains of NMT are structurally similar, each adopting an acyl-CoA N-acyltransferase-like fold.. 
PF02070 Neuromedin U<br>
PF03980 Nnf1 <br>NNF1 is an essential yeast gene that is necessary for chromosome  segregation.  It is associated with the spindle poles   and forms  part of a kinetochore subcomplex called MIND  .. 
PF02898 Nitric oxide synthase, oxygenase domain<br>
PF02474 Nodulation protein A (NodA)<br>Pfam-B_2183 (release 5.4). Rhizobia nodulation (nod) genes control the biosynthesis of Nod factors required for infection and nodulation of their legume hosts. Nodulation  protein A (NodA) is a N-acetyltransferase involved in production of Nod factors that stimulate mitosis in various plant protoplasts.. 
PF01798 Putative snoRNA binding domain<br>Pfam-B_1362 (release 4.2). 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) Swiss:Q12499 from yeast is the protein component of a ribonucleoprotein protein required for pre-18s rRNA processing and is suggested to function with Nop1p in a snoRNA complex  . Nop56p Swiss:O00567 and Nop5p interact with Nop1p and are required for ribosome biogenesis  . Prp31p Swiss:p49704 is required for pre-mRNA splicing in S. cerevisiae  .. 
PF02451 Nodulin<br>Pfam-B_2163 (release 5.4). Nodulin is a plant protein of unknown function. It is induced during nodulation in legume roots after rhizobium infection.. 
PF01189 Nol1_Nop2_Sun;<br>NOL1/NOP2/sun family. 
PF04135 Nucleolar RNA-binding protein, Nop10p family<br>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  snoRNAs (H/ACA snoRNPs).  Nop10p is probably necessary for the stability of these RNPs  .. 
PF05048 Periplasmic copper-binding protein (NosD)<br>Pfam-B_5499 (release 7.7). NosD is a periplasmic protein which is thought to insert copper into the exported reductase apoenzyme (NosZ)  . This region forms a parallel beta helix domain.. 
PF04054 CCR4-Not complex component, Not1<br>Pfam-B_13503 (release 7.3);. The Ccr4-Not complex is a global regulator of transcription that  affects genes positively and negatively and is thought to regulate  transcription factor TFIID  . . 
PF00066 notch; <br>Swissprot_feature_table. The LNR (Lin-12/Notch repeat) domain is found in three tandem copies in Notch related proteins. The structure of the domain has been determined by NMR   and was shown to contain three disulphide bonds and coordinate a calcium ion.  Three repeats are also found in the PAPP-A peptidase  .. 
PF03000 NPH3 family<br>Pfam-B_1584 (release 6.4). Phototropism of Arabidopsis thaliana seedlings in response to a blue light source is initiated by nonphototropic hypocotyl 1 (NPH1), a light-activated serine-threonine protein kinase. Mutations in NPH3 disrupt early signaling occurring downstream of the NPH1 photoreceptor. The NPH3 gene encodes a NPH1-interacting protein. NPH3 is a member of a large protein family, apparently specific to higher plants, and may function as an adapter or scaffold protein to bring together the enzymatic components of a NPH1-activated phosphorelay  .. 
PF03116 NQR2, RnfD, RnfE family<br>Pfam-B_2882 (release 6.5). This family of bacterial proteins includes a sodium-translocating  NADH-ubiquinone oxidoreductase (i.e. a respiration linked sodium  pump). In Vibrio cholerae, it negatively regulates the expression of virulence factors through inhibiting  (by an unknown mechanism) the transcription of the transcriptional activator ToxT  . The family also includes proteins involved in nitrogen fixation, RnfD and RnfE. The similarity of these proteins to NADH-ubiquinone oxidoreductases was previously noted  .. 
PF01566 Natural resistance-associated macrophage protein<br>Pfam-B_624 (release 4.0). The natural resistance-associated macrophage protein (NRAMP) family consists of Nramp1, Nramp2, and yeast proteins Smf1 and Smf2. The NRAMP family is a novel family of functional related proteins defined by a conserved hydrophobic core of ten transmembrane domains  . This family of membrane proteins are divalent cation transporters. Nramp1 is an integral membrane protein expressed exclusively in cells of the immune system and is recruited to the membrane of a phagosome upon phagocytosis  . By controlling divalent cation concentrations Nramp1 may regulate the interphagosomal replication of bacteria  . Mutations in Nramp1 may genetically predispose an individual to susceptibility to diseases including leprosy and tuberculosis conversely this might however provide protection form rheumatoid arthritis  . Nramp2 is a multiple divalent cation transporter for Fe2+, Mn2+ and Zn2+ amongst others it is expressed at high levels in the intestine; and is major transferrin-independent iron uptake system in mammals  . The yeast proteins Smf1 and Smf2 may also transport divalent cations  .. 
PF03813 Nrap protein<br>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 localised in the nucleolus  . Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript  .. 
PF03916 Polysulphide reductase, NrfD<br>NrfD is an integral transmembrane protein with loops in both the  periplasm and the cytoplasm.  NrfD is thought to participate in  the transfer of electrons, from the quinone pool into the terminal  components of the Nrf pathway  . . 
PF02723 Non-structural protein NS3/Small envelope protein E<br>Pfam-B_1913 (release 5.5) & Pfam-B_7381 (release 8.0). This is a family of small non-structural proteins, well conserved among Coronavirus strains. This protein is also found in murine hepatitis virus as small envelope protein E (e.g. Swiss:O72008).. 
PF02071 Aromatic-di-Alanine (AdAR) repeat <br>This repeat is found in NSF attachment proteins. Its structure is similar to that found in TPR repeats Pfam:PF00515.. 
PF05064 Nsp1-like C-terminal region<br>Pfam-B_3555 (release 7.7). This family probably forms a coiled-coil  .  This important region of Nsp1 is involved in binding Nup82  .. 
PF03146 Agrin NtA domain<br>Agrin is a multidomain heparan sulphate proteoglycan, that is a key organiser for the induction of postsynaptic specialisations at the neuromuscular junction. Binding of agrin to basement membranes requires the amino terminal (NtA) domain  . This region mediates high affinity interaction with the coiled-coil domain of laminins. The binding of agrin to laminins via the NtA domain is subject to tissue-specific regulation. The NtA domain-containing form of agrin is expressed in non-neuronal cells or in neurons that project to non-neuronal cell such as motor neurons. The structure of this domain is an OB-fold  .. 
PF02136 Nuclear transport factor 2 (NTF2) domain<br>This family includes the NTF2-like Delta-5-3-ketosteroid isomerase proteins.. 
PF00483 ADP_glu_Plase;<br>Nucleotidyl transferase. This family includes a wide range of enzymes which transfer nucleotides onto phosphosugars.. 
PF05014 Nucleoside 2-deoxyribosyltransferase<br>Nucleoside 2-deoxyribosyltransferase EC:2.4.2.6 catalyses the cleavage of the glycosidic bonds of 2`-deoxyribonucleosides  .. 
PF03825 Nucleoside H+ symporter<br>TIGRFAMs, Griffiths-Jones SR. 
PF02321 Outer membrane efflux protein<br>The OEP family (Outer membrane efflux protein) form trimeric channels that allow export of a variety of substrates in Gram negative bacteria.\.    Each member of this family is composed of two repeats. The trimeric channel is composed of a 12 stranded all beta sheet barrel that spans the outer membrane, and a long all helical barrel that spans the periplasm.. 
PF02265 Nuclease; <br>Pfam-B_2480 (release 5.2). This family contains both S1 and P1 nucleases (EC:3.1.30.1) which cleave RNA and single stranded DNA with no base specificity.. 
PF03066 Nucleoplasmin<br>Pfam-B_2930 (release 6.4). 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.. 
PF03177 Nucleoporin;<br>Non-repetitive/WGA-negative nucleoporin C-terminal. Pfam-B_1212 (release 6.5). This is the C-termainl half of 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. Two nucleoporin classes are known: one is characterised by the FG repeat Pfam:PF03093; the other is represented by this family, and lacks any repeats. RNA undergoing nuclear export first encounters the basket of the nuclear pore and many nucleoporins are accessible on the basket side of the pore  .. 
PF01773 Nucleoside_tra2; <br>Na+ dependent nucleoside transporter N-terminus. This family consists of nucleoside transport proteins. Swiss:Q62773 is a purine-specific Na+-nucleoside cotransporter localised to the bile canalicular membrane  . Swiss:Q62674 is a a Na+-dependent nucleoside transporter selective for pyrimidine nucleosides and adenosine it also transports the anti-viral nucleoside analogues AZT and ddC  . This alignment covers the N terminus of this family. 
PF03800 Nuf2 family<br>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 has been included in this family that has previously not been identified as a member of this family, Swiss:Q9C953. The match is not strong, but in common with other members of this family contains coiled-coil to the C terminus of this region.. 
PF04121 Nuclear pore protein 84 / 107 <br>Pfam-B_13117 (release 7.3);. Nup84p forms a complex with five proteins, of which Nup120p,  Nup85p, Sec13p, and a Sec13p homologues. This Nup84p complex in  conjunction with Sec13-type proteins is required for correct  nuclear pore biogenesis  .. 
PF01029 NusB family<br>The NusB protein is involved in the regulation of rRNA biosynthesis by transcriptional antitermination. . 
PF02357 Transcription termination factor nusG<br>Pfam-B_697 (release 5.2). 
PF04277 Oxaloacetate decarboxylase, gamma chain <br>TIGRFAMs (release 2.0);. 
PF03977 OadB_MmdB;<br>Na+-transporting oxaloacetate decarboxylase beta subunit. Members of this family are integral membrane proteins. The decarboxylation reactions they catalyse are coupled to the vectorial transport of Na+ across the cytoplasmic membrane, thereby creating a sodium ion motive force that is used for ATP synthesis  .. 
PF04225 Opacity-associated protein A LysM-like domain<br>This family includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonisation, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [1,2]. This is a LysM-like domain.. 
PF03373 Octapeptide repeat<br>This octapeptide repeat is found in several bacterial proteins. The function of this repeat is unknown.. 
PF02317 NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain<br>Pfam-B_9653 (release 5.2). This group of enzymes act on the CH-NH substrate bond using NAD(+) or NADP(+) as an acceptor. The Pfam family consists mainly of octopine and nopaline dehydrogenases from Ti plasmids.. 
PF02101 Ocular albinism type 1 protein<br>
PF02100 Ornithine decarboxylase antizyme<br>IPR002993 & Pfam-B_34796 (release 7.7). This family consists of ornithine decarboxylase antizyme proteins. The polyamine biosynthetic enzyme ornithine decarboxylase (ODC) is degraded by the 26 S proteasome via a ubiquitin-independent pathway. Its degradation is greatly accelerated by association with the polyamine-induced regulatory protein antizyme 1 (AZ1)  .. 
PF02423 ODC_Mu_crystall; <br>Ornithine cyclodeaminase/mu-crystallin family. Pfam-B_1960 (release 5.4). This family contains the bacterial Ornithine cyclodeaminase enzyme EC:4.3.1.12, which catalyses the deamination of ornithine to proline  . This family also contains mu-Crystallin the major component of the eye lens in several Australian marsupials, mRNA for this protein has also been found in human retina  .. 
PF02159 Oestrogen receptor<br>
PF04664 Opioid growth factor receptor (OGFr) conserved region<br>Pfam-B_4529 (release 7.5). Opioid peptides act as growth factors in neural and non-neural cells and tissues, in addition to serving in neurotransmission/neuromodulation in the nervous system. The Opioid growth factor receptor is an integral membrane protein associated with the nucleus. The conserved region is situated at the N-terminus of the member proteins with a series of imperfect repeats lying immediately to its C-terminus  .. 
PF04680 OGFr_repeat; <br>Opioid growth factor receptor repeat. Pfam-B_4529 (release 7.5). Proline-rich repeat found only in a human opioid growth factor receptor  . . 
PF04606 Ogr/Delta-like zinc finger<br>Pfam-B_5059 (release 7.5). This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes  . The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F  . This family also includes zinc fingers in recombinase proteins.. 
PF01276 Orn/Lys/Arg decarboxylase, major domain<br>
PF03711 Orn/Lys/Arg decarboxylase, C-terminal domain<br>
PF03709 Orn/Lys/Arg decarboxylase, N-terminal domain<br>This domain has a flavodoxin-like fold, and is termed the "wing" domain because of its position in the overall 3D  structure.. 
PF01277 Oleosin<br>
PF02191 Olfactomedin-like domain<br>Alignment kindly provided by SMART. 
PF00691 OmpA family<br>Pfam-B_166 (release 2.1). The Pfam entry also includes MotB and related proteins which are not included in the Prosite family.. 
PF01389 OmpA-like transmembrane domain<br>The structure of OmpA transmembrane domain shows that it consists of an eight stranded beta barrel  . This family includes some other distantly related outer membrane proteins with low scores.. 
PF03938 Outer membrane protein (OmpH-like)<br>This family includes outer membrane proteins such as OmpH among others. Skp (OmpH) has been characterised as a molecular chaperone that interacts with unfolded proteins as they emerge in the periplasm from the Sec translocation machinery  .. 
PF01278 Omptin family<br>The omptin family is a family of  serine proteases.. 
PF03922 OmpW family<br>This family includes outer membrane protein W (OmpW) proteins from a variety of bacterial species. This protein may form the receptor for S4 colicins in E. coli  .. 
PF03532 OMS28 porin<br>
PF02462 Opacity family porin protein<br>Pfam-B_2356 (release 5.4). Pathogenic Neisseria spp. possess a repertoire of phase-variable Opacity proteins that mediate various pathogen--host cell interactions  . These proteins are integral membrane proteins related to other porins.. 
PF01160 Vertebrate endogenous opioids neuropeptide<br>
PF04966 Carbohydrate-selective porin, OprB family<br>
PF03573 Peptidase_S43; <br>outer membrane porin, OprD family. This family includes outer membrane proteins related to OprD. OprD has been described as a serine type peptidase  . However the proposed catalytic residues are not conserved suggesting that many of these proteins are not peptidases.. 
PF03169 OPT oligopeptide transporter protein<br>Pfam-B_3048 (release 6.5). The OPT family of oligopeptide transporters is distinct from the ABC Pfam:PF00005 and PTR Pfam:PF00854 transporter families. OPT transporters were first recognised in fungi (Candida albicans and Schizosaccharomyces pombe), but this alignment also includes orthologues from Arabidopsis thaliana. OPT transporters are thought to have 12-14 transmembrane domains and contain the following motif: SPYxEVRxxVxxxDDP  .. 
PF04069 Substrate binding domain of ABC-type glycine betaine transport system<br>Part of a high affinity multicomponent binding-protein-dependent transport system involved in bacterial osmoregulation.  This domain is often fused to the permease component of the transporter complex.  Family members are often integral membrane proteins or predicted to be attached to the membrane by a lipid anchor. Glycine betaine is involved in protection from high osmolarity environments for example in Bacillus subtilis  . The family member OpuBC is closely related, and involved in choline transport.  Choline is necessary for the biosynthesis of glycine betaine  .  L-carnitine is important for osmoregulation in Listeria monocytogenes. Family also contains proteins binding l-proline (ProX), histidine (HisX) and taurine (TauA).. 
PF01718 Orbivirus non-structural protein NS1, or hydrophobic tubular protein<br>Pfam-B_1752 (release 4.1). This family consists of orbivirus non-structural protein NS1,  or hydrophobic tubular protein. NS1 has no specific function in  virus replication, it is however thought to play a role in  transport of mature virus particles from virus inclusion bodies  to the cell membrane  . Orbivirus are part of the larger reoviridae which have a dsRNA genome of at least 10 segments encoding at least 10 viral proteins  ; orbivirus found in this family include  bluetongue virus, and African horsesickness virus.. 
PF01616 Orbivirus NS3<br>Pfam-B_1029 (release 4.1). The function of this Orbivirus non structural protein is uncertain.   However it may play a role on release of the virus from infected cells  .. 
PF00898 Orbivirus outer capsid protein VP2<br>Pfam-B_1525 (release 2.1). VP2 acts as an anchor for VP1 and VP3. VP2 contains a non-specific  DNA and RNA binding domain in the N-terminus  .. 
PF01700 Orbivirus VP3 (T2) protein<br>Pfam-B_1622 (release 4.1). 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 found in the family is structural core protein VP2 from   broadhaven virus which is similar to VP3 in bluetongue  virus  . Orbivirus are part of the larger reoviridae which have a  dsRNA genome of 10-12 linear segments  ; orbivirus found in this family include bluetongue virus and epizootic hemorrhagic  disease virus. . 
PF05059 Orbivirus VP4 core protein<br>Pfam-B_5992 (release 7.7). Orbiviruses are double stranded RNA retroviruses of which the bluetongue virus is a member. The core of bluetongue virus (BTV) is a multienzyme complex composed of two major proteins (VP7 and VP3) and three minor proteins (VP1, VP4 and VP6) in addition to the viral genome. VP4 has been shown to perform all RNA capping activities and has both methyltransferase type 1 and type 2 activities associated with it  .. 
PF00901 Orbivirus outer capsid protein VP5<br>Pfam-B_1525 (release 2.1). cryoelectron microscopy indicates that VP5 is a trimer implying that there are 360 copies of VP5 per virion  . . 
PF01516 Orbivirus helicase VP6<br>Pfam-B_765 (release 4.0). The VP6 protein a minor protein in the core of the virion is probably the viral helicase  .. 
PF00897 Orbivirus inner capsid protein VP7<br>Pfam-B_1523 (release 2.1). In BTV, 260 trimers of VP7 are found in the core. The major proteins of the core are VP7 and VP3. VP7 forms an outer layer around VP3  .. 
PF02072 Prepro-orexin<br>
PF03827 Orexin receptor type 2<br>
PF02999 Mlp; Orf-D; <br>Borrelia orf-D family. Pfam-B_1511 (release 6.4). Borrelia burgdorferi supercoiled plasmids encode multicopy tandem open reading frames called Orf-A, Orf-B, Orf-C and Orf-D. This family corresponds to Orf-D. The putative product of this gene has no known function.. 
PF04160 Orf-X; <br>Pfam-B_3014 (release 7.3). 
PF04061 ORMDL family <br>Pfam-B_4871 (release 7.3);. Evidence form   suggests that ORMDLs are involved in protein folding in the ER.  Orm proteins have been identified as negative regulators of sphingolipid synthesis that form a conserved complex with serine palmitoyltransferase, the first and rate-limiting enzyme in sphingolipid production. This novel and conserved protein complex, has been termed the SPOTS complex (serine palmitoyltransferase, Orm1/2, Tsc3, and Sac1).. 
PF02784 Pyridoxal-dependent decarboxylase, pyridoxal binding domain<br>These pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates This domain has a TIM barrel fold.. 
PF00278 Pyridoxal-dependent decarboxylase, C-terminal sheet domain<br>These pyridoxal-dependent decarboxylases act on ornithine, lysine,  arginine and related substrates.  . 
PF02088 Ornatin<br>
PF02250 35kD major secreted virus protein <br>Pfam-B_3549 (release 5.2). This family of orthopoxvirus secreted proteins (also known as T1 and  A41) interact with members of both the CC and CXC superfamilies of  chemokines. It has been suggested that these secreted proteins  modulate leukocyte influx into virus-infected tissues  .. 
PF00213 ATP synthase delta (OSCP) subunit<br>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 Pfam:PF00401.. 
PF02566 OsmC-like protein<br>Pfam-B_2694 (release 7.0). Osmotically inducible protein C (OsmC) (Swiss:P23929) is a stress -induced protein found in E. Coli. This family also contains a organic hydroperoxide detoxification protein (Swiss:O68390) that  has a novel pattern of oxidative stress regulation  .. 
PF03207 Borrelia outer surface protein D (OspD)<br>Pfam-B_2915 (release 6.5). 
PF02471 OspEF; <br>Borrelia outer surface protein E. Pfam-B_962 (release 5.4). This is a family of outer surface proteins (Osp) from the Borrelia spirochete  . The family includes OspE, and OspEF-related proteins (Erp)  . These proteins are coded for on different circular plasmids in the Borrelia genome.. 
PF03968 OstA-like protein<br>This family of proteins are mostly uncharacterised. However the family does include E. coli OstA Swiss:P31554 that has been characterised as an organic solvent tolerance protein  .. 
PF04453 Organic solvent tolerance protein<br>Family involved in organic solvent tolerance in bacteria. The region contains several highly conserved, potentially catalytic, residues  .. 
PF00865 Osteopontin<br>Pfam-B_1593 (release 2.1). 
PF00185 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain<br>
PF02729 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain<br>
PF02338 OTU-like cysteine protease<br>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 and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases.. 
PF00724 oxidored_FMN; <br>NADH:flavin oxidoreductase / NADH oxidase family. Pfam-B_642 (release 2.1). 
PF00174 oxidored_molyb; <br>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.. 
PF00148 oxidored_nitro; <br>Nitrogenase component 1 type Oxidoreductase. 
PF00361 oxidored_q1; <br>NADH-Ubiquinone/plastoquinone (complex I), various chains. Pfam-B_4 (release 1.0). 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.. 
PF00662 oxidored_q1_N; <br>NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus. Pfam-B_22 (release 2.1). This sub-family represents an amino terminal extension of Pfam:PF00361. Only NADH-Ubiquinone chain 5 and eubacterial chain L are in this family. This sub-family is part of complex I which catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane.. 
PF00420 oxidored_q2; <br>NADH-ubiquinone/plastoquinone oxidoreductase chain 4L. Pfam-B_193 (release 1.0). 
PF00499 oxidored_q3; <br>NADH-ubiquinone/plastoquinone oxidoreductase chain 6. Pfam-B_61 (release 1.0). 
PF00507 oxidored_q4; <br>NADH-ubiquinone/plastoquinone oxidoreductase, chain 3. Pfam-B_68 (release 1.0). 
PF01059 oxidored_q5_N;<br>NADH-ubiquinone oxidoreductase chain 4, amino terminus. Pfam-B_381 (release 3.0). 
PF01058 oxidored_q6; <br>NADH ubiquinone oxidoreductase, 20 Kd subunit. Pfam-B_1345 (release 3.0). 
PF01237 Oxysterol-binding protein <br>
PF00543 Nitrogen regulatory protein P-II<br>P-II modulates the activity of glutamine synthetase.. 
PF04275 Phosphomevalonate kinase <br>TIGRFAMs (release 2.0);. Phosphomevalonate kinase (EC:2.7.4.2) catalyses the  phosphorylation of 5-phosphomevalonate into 5-diphosphomevalonate,  an essential step in isoprenoid biosynthesis via the mevalonate  pathway  . This family represents the animal type of the  enzyme. The other is the ERG8 type, found in plants and fungi, and some bacteria (see Pfam:PF00288).. 
PF04699 p16_Arc; <br>ARP2/3 complex 16 kDa subunit (p16-Arc). Pfam-B_4180 (release 7.5). The Arp2/3 protein complex has been implicated in the control of actin polymerisation.  The human complex consists of seven subunits which include the actin related proteins Arp2 and Arp3, and five others referred to as p41-Arc, p34-Arc, p21-Arc, p20-Arc, and p16-Arc.  The precise function of p16-Arc is currently unknown.  Its structure consists of a single domain containing a bundle of seven alpha helices [1,2].. 
PF00864 ATP P2X receptor<br>Pfam-B_1590 (release 2.1). 
PF04045 p34-Arc; <br>Arp2/3 complex, 34 kD subunit p34-Arc. Pfam-B_9846 (release 7.3);. Arp2/3 protein complex has been implicated in the control of actin polymerisation in cells. The human complex consists of seven subunits which include the actin related Arp2 and Arp3, and five others referred to as p41-Arc, p34-Arc, p21-Arc, p20-Arc, and p16-Arc  .  This family represents the p34-Arc subunit.. 
PF00067 Cytochrome P450<br>Overington and HMM_iterative_training. Cytochrome P450s are haem-thiolate proteins   involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyse regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures  .. 
PF00870 P53 DNA-binding domain<br>Pfam-B_782 (release 3.0). This family contains one anomalous member, viz: Zea mays (Q6JAD8). This sequence is identical to human P53 and would appear to be a a human contaminant within the Zea mays sampling effort.. 
PF04636 PA26 p53-induced protein (sestrin)<br>Pfam-B_5416 (release 7.5). PA26 is a p53-inducible protein. Its function is unknown. It has similarity to Pfam:PF04636 in its N-terminus.. 
PF02251 Proteasome activator pa28 alpha subunit<br>Pfam-B_2837 (release 5.2). PA28 activator complex (also known as 11s regulator of 20S proteasome) is a ring shaped hexameric structure of alternating alpha and beta subunits. This family represents the alpha subunit. The activator complex binds to the 20S proteasome ana simulates peptidase activity in and ATP-independent manner.. 
PF02252 Proteasome activator pa28 beta subunit<br>Pfam-B_2809 (release 5.2). PA28 activator complex (also known as 11s regulator of 20S proteasome) is a ring shaped hexameric structure of alternating alpha and beta subunits. This family represents the beta subunit. The activator complex binds to the 20S proteasome ana simulates peptidase activity in and ATP-independent manner.. 
PF05138 Phenylacetic acid catabolic protein<br>This family includes proteins such as PaaA and PaaC that are part of a catabolic pathway of phenylacetic acid  . These proteins may form part of a dioxygenase complex.. 
PF02758 PAAD_DAPIN;<br>PAAD/DAPIN/Pyrin domain. This domain is predicted to contain 6 alpha helices and to have the same fold as the Pfam:PF00531 domain.  This similarity may mean that this is a protein-protein interaction domain.. 
PF00658 Poly-adenylate binding protein, unique domain<br>The region featured in this family is found towards the C-terminus of poly(A)-binding proteins (PABPs). These are eukaryotic proteins that, through their binding of the 3' poly(A) tail on mRNA, have very important roles in the pathways of gene expression. They seem to provide a scaffold on which other proteins can bind and mediate processes such as export, translation and turnover of the transcripts. Moreover, they may act as antagonists to the binding of factors that allow mRNA degradation, regulating mRNA longevity. PABPs are also involved in nuclear transport. PABPs interact with poly(A) tails via RNA-recognition motifs (Pfam:PF00076)  . Note that the PABP C-terminal region is also found in members of the hyperplastic discs protein (HYD) family of ubiquitin ligases that contain HECT domains - these are also included in this family.. 
PF03068 Protein-arginine deiminase (PAD)<br>Pfam-B_2195 (release 6.4). 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-arginine + H2O <=> Protein L-citrulline + NH3. Several types are recognised (and included in the family) on the basis of molecular mass, substrate specificity, and tissue localisation. The expression of type I PAD is known to be under the control of oestrogen  .. 
PF04371 Porphyromonas-type peptidyl-arginine deiminase<br>Peptidyl-arginine deiminase (PAD) enzymes catalyse the deimination of the guanidino group from carboxy-terminal arginine residues of various peptides to produce ammonia.  PAD from Porphyromonas gingivalis (PPAD) appears to be evolutionarily unrelated to mammalian PAD (Pfam:PF03068), which is a metalloenzyme.  PPAD is thought to belong to the same superfamily as aminotransferase and arginine deiminase, and to form an alpha/beta propeller structure. This family has previously been named PPADH (Porphyromonas peptidyl-arginine deiminase homologues)  . The predicted catalytic residues in PPAD (Swiss:Q9RQJ2) are Asp130, Asp187, His236, Asp238 and Cys351  . These are absolutely conserved with the exception of Asp187 which is absent in two family members.  PPAD is also able to catalyse the deimination of free L-arginine, but has primarily peptidyl-arginine specificity.  It may have a FMN cofactor  .. 
PF03551 Transcriptional regulator PadR-like family<br>Pfam-B_1014 (release 7.0). Members of this family are transcriptional regulators that appear to be related to the Pfam:PF01047 family. This family includes PadR Swiss:Q9EXE6 a protein that is involved in negative regulation of phenolic acid metabolism.. 
PF03283 Pectinacetylesterase<br>Pfam-B_1589 (release 6.5). 
PF03403 Platelet-activating factor acetylhydrolase, isoform II<br>Pfam-B_3469 (release 6.6). 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. Three known PAF-AHs are the brain heterotrimeric PAF-AH Ib, whose catalytic beta and gamma subunits are aligned in Pfam:PF02266, the extracellular, plasma PAF-AH (pPAF-AH), and the intracellular PAF-AH isoform II (PAF-AH II). This family aligns pPAF-AH and PAF-AH II, whose similarity was previously noted.. 
PF03985 Paf1 <br>Pfam-B_ (release 7.3). 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 [1,2]. . 
PF02671 Paired amphipathic helix repeat<br>Pfam-B_281 (release 5.4). This family contains the paired amphipathic helix repeat. The family contains the yeast SIN3 gene Swiss:P22579 (also known as SDI1) that is a negative regulator of the yeast HO gene  . This repeat may be distantly related to the helix-loop-helix motif, which mediate protein-protein interactions.. 
PF00221 PAL;<br>Aromatic amino acid lyase. This family includes proteins with phenylalanine ammonia-lyase, EC:4.3.1.24, histidine ammonia-lyase, EC:4.3.1.3, and tyrosine aminomutase, EC:5.4.3.6, activities [1-3].. 
PF02089 Palmitoyl protein thioesterase<br>
PF02569 Pantoate-beta-alanine ligase<br>Pantoate-beta-alanine ligase, also know as pantothenate  synthase, (EC:6.3.2.1) catalyses the formation of pantothenate from pantoate and alanine  .. 
PF02548 Ketopantoate hydroxymethyltransferase<br>Ketopantoate hydroxymethyltransferase (EC:2.1.2.11) is the first enzyme in the pantothenate biosynthesis pathway.. 
PF02711 E4 protein<br>Pfam-B_1589 (release 5.5). This is is a family of Papillomavirus proteins, E4, coded for by  ORF4. A splice variant, E1--E4, exists but neither the function of E4 or E1--E4 is known  .. 
PF04755 PAP_fibrillin<br>Pfam-B_3698 (release 7.5). This family identifies a conserved region found in a number of plastid lipid-associated proteins (PAPs), and in a number of putative fibrillin proteins.. 
PF04926 Poly(A) polymerase predicted RNA binding domain<br>Pfam-B_1341 (release 7.6). Based on its similarity structurally to the RNA recognition motif this domain is thought to be RNA binding  .. 
PF04795 PAPA-1-like conserved region<br>Pfam-B_6501 (release 7.5). Family of proteins with a conserved region found in PAPA-1, a PAP-1 binding protein. . 
PF03333 Adhesin biosynthesis transcription regulatory protein<br>Pfam-B_3068 (release 6.5). This family includes PapB, DaaA, FanA, FanB, and AfaA.. 
PF03628 PapG chaperone-binding domain <br>Pfam-B_3074 (release 7.0). PapG, the adhesin of the P-pili, is situated at the tip and  is only a minor component of the whole pilus structure.  A two-domain structure has been postulated for PapG; a carbohydrate  binding N-terminus and chaperone binding C-terminus (this domain). The chaperone-binding domain is highly conserved, and is essential  for the correct assembly of the pili structure when aided by the  chaperone molecule PapD [1,2]. . 
PF03627 PapG carbohydrate binding domain<br>Pfam-B_3074 (release 7.0). PapG, the adhesin of the P-pili, is situated at the tip and is only a minor component of the whole pilus structure.  A two-domain structure has been postulated for PapG; a carbohydrate binding N-terminus (this domain) and chaperone binding C-terminus. The carbohydrate-binding domain interacts with the receptor glycan [1,2].. 
PF03025 Papillomavirus E5<br>Pfam-B_1916 (release 6.4). The E5 protein from papillomaviruses is about 80 amino acids long.  The proteins are contain three regions that are predicted to be transmembrane alpha helices.  The function of this protein is unknown.. 
PF02380 T-antigen specific domain<br>Pfam-B_1131 (release 5.2). This domain represents a conserved region in papovavirus small and middle T-antigens. It is found as the N-terminal domain in the small T-antigen, and is centrally located in the middle T-antigen.. 
PF01507 Phosphoadenosine phosphosulfate reductase family<br>Pfam-B_590 (release 4.0). This domain is found in phosphoadenosine phosphosulfate (PAPS) reductase enzymes or PAPS sulfotransferase. PAPS reductase is part of the adenine  nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases  . The enzyme uses thioredoxin as an electron  donor for the reduction of PAPS to phospho-adenosine-phosphate (PAP) [1,2]. It is also found in NodP nodulation protein P from Rhizobium which has ATP sulfurylase activity (sulfate adenylate transferase)  .   . 
PF03285 Paralemmin<br>Pfam-B_4064 (release 6.5). 
PF01508 Paramecium surface antigen domain<br>This domain is a cysteine rich extracellular repeat found in surface antigens of Paramecium.  The domain contains 8 cysteine residues. . 
PF03210 Paramyx_P_V;<br>Paramyxovirus P/V phosphoprotein C-terminal. Pfam-B_2037 (release 6.5). Paramyxoviridae 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 proteins present in the infected cell but not in the virus particle. This family includes phosphoprotein P and the non-structural phosphoprotein V from different paramyxoviruses.  Phosphoprotein P is essential for the activity of the RNA polymerase complex which it forms with another subunit, L Pfam:PF00946. Although all the catalytic activities of the polymerase are associated with the L subunit, its function requires specific interactions with phosphoprotein P  . The P and V phosphoproteins are amino co-terminal, but diverge at their C-termini. This difference is generated by an RNA-editing mechanism in which one or two non-templated G residues are inserted into P-gene-derived mRNA. In measles virus and Sendai virus, one G residue is inserted and the edited transcript encodes the V protein. In mumps, simian virus type 5 and Newcastle disease virus, two G residues are inserted, and the edited transcript codes for the P protein  . Being phosphoproteins, both P and V are rich in serine and threonine residues over their whole lengths. In addition, the V proteins are rich in cysteine residues at the C-termini  . This C-terminal region of the P phosphoprotein is likely to be the nucleocapsid-binding domain, and is found to be intrinsically disordered and thus liable to induced folding  .. 
PF00946 Paramyx_RNA_pol;<br>Mononegavirales RNA dependent RNA polymerase . Pfam-B_586 (release 3.0). Members of the Mononegavirales including the Paramyxoviridae, like other non-segmented negative strand RNA viruses, have an RNA-dependent RNA polymerase composed of two subunits, a large protein L and a phosphoprotein P.\.   This is a protein family of the L protein. The L protein confers the RNA polymerase activity on the complex. The P protein acts as a transcription factor  .. 
PF01692 Paramyxovirus non-structural protein c<br>Pfam-B_1202 (release 4.1). This family consist of the C proteins (C', C, Y1, Y2)  found in Paramyxovirinae; human parainfluenza, and sendai virus. The C proteins effect viral RNA synthesis having both a positive and negative effect during the course of infection  . Paramyxovirus have a negative strand ssRNA genome of 15.3kb  form which six mRNAs are transcribed, five of these are monocistronic.\.   The P/C mRNA is polycistronic and has two overlapping open reading  frames P and C, C encodes the nested C proteins C', C, Y1 and Y2  .. 
PF00973 Paramyx_ncap;<br>Paramyxovirus nucleocapsid protein. Pfam-B_158 (release 3.0). The nucleocapsid protein is referred to as NP.  NP is is the major structural component of the nucleocapsid. The protein is approx. 58 kDa. 2600 NP molecules go to tightly encapsidate the RNA. NP interacts with several other viral encoded proteins, all of which are involved in controlling replication. {NP-NP, NP-P, NP-(PL), and NP-V}[1,2,3].. 
PF02725 Non-structural protein C<br>Pfam-B_1636 (release 5.5). This family consists of the polymerase accessory protein C from members of the paramyxoviridae.. 
PF01806 Paramyxovirinae P phosphoprotein C-terminal region<br>Pfam-B_1628 (release 4.1), Karlin D. The subfamily Paramyxovirinae of the family Paramyxoviridae now contains as main genera the Rubulaviruses, avulaviruses, respiroviruses, Henipavirus-es and morbilliviruses.  Protein P is the best characterised, structurally of the replicative complex of N, P and L proteins and consists of two functionally distinct moieties, an N-terminal PNT, and a C-terminal PCT  . The P protein is an essential part of the viral RNA polymerase complex formed from the P and L proteins  . P protein plays a crucial role in the enzyme by positioning L onto the N/RNA template through an interaction with the C-terminal domain of N. Without P, L is not functional.The C-terminal part of P (PCT) is only functional as an oligomer and forms with L the polymerase complex. PNT is poorly conserved and unstructured in solution while PCT contains the oligomerisation domain (PMD) that folds as a homotetrameric coiled coil (40) containing the L binding region and a C-terminal partially folded domain, PX (residues 474 to 568), identified as the nucleocapsid binding site. Interestingly, PX is also expressed as an independent polypeptide in infected cells. PX has a C-subdomain (residues 516 to 568) that consists of three {alpha}-helices arranged in an antiparallel triple-helical bundle linked to an unfolded flexible N-subdomain (residues 474 to 515).. 
PF01279 Parathyroid hormone family<br>
PF02195 ParB-like nuclease domain<br>Alignment kindly provided by SMART. 
PF00644 Poly(ADP-ribose) polymerase catalytic domain<br>Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a  carboxyl 40 kDa fragment is still catalytically active  .. 
PF02877 Poly(ADP-ribose) polymerase, regulatory domain<br>Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a  carboxyl 40 kDa fragment is still catalytically active  .. 
PF01358 Poly A polymerase regulatory subunit<br>
PF00740 Parvovirus coat protein VP2<br>Pfam-B_436 (release 2.1) & Pfam-B_445 (release 3.0). This protein, together with VP1 forms a capsomer. Both of these proteins are formed from the same transcript using alternative splicing.\.     As a result, VP1 and VP2 differ only in the N-terminal region of VP1.\.    VP2 is involved in packaging the viral DNA.. 
PF01057 Parvovirus non-structural protein NS1<br>Pfam-B_400 (release 3.0). This family also contains the NS2 protein. Parvoviruses encode two non-structural proteins, NS1 and NS2. The mRNA for NS2 contains the coding sequence for the first 87 amino acids of NS1, then by an alternative splicing mechanism mRNA from a different reading frame, encoding the last 78 amino acids, makes up the full length of the NS2 mRNA  . NS1, is the major non-structural protein.  It is essential for DNA replication.  It is an 83-kDa nuclear phosphoprotein.  It has DNA helicase and ATPase activity  .  . 
PF00989 PAS fold<br>Sequences from SMART alignment. The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs  . The PAS fold appears in archaea, eubacteria and eukarya.. 
PF03793 PASTA domain<br>This domain is found at the C termini of several Penicillin-binding proteins and bacterial serine/threonine kinases  . It binds the beta-lactam stem, which implicates it in sensing D-alanyl-D-alanine - the PBP transpeptidase substrate. It is a small globular fold consisting of 3 beta-sheets and an alpha-helix. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain.. 
PF00292 'Paired box' domain<br>
PF03535 Paxillin family<br>
PF03717 Penicillin-binding Protein dimerisation domain<br>This domain is found at the N terminus of Class B High Molecular Weight Penicillin-Binding Proteins. Its function has not been precisely defined, but is strongly implicated in PBP polymerisation. The domain forms a largely disordered 'sugar tongs' structure.. 
PF01395 PBP/GOBP family<br>Pfam-B_1765 (release 3.0). The olfactory receptors of terrestrial animals exist in an aqueous environment, yet detect odorants that are primarily hydrophobic. The aqueous solubility of hydrophobic odorants is thought to be greatly enhanced via odorant binding proteins which exist in the extracellular fluid surrounding the odorant receptors  . This family is composed of pheromone binding proteins (PBP), which are male-specific and associate with pheromone-sensitive neurons and general-odorant binding proteins (GOBP).. 
PF00427 Phycobilisome Linker polypeptide<br>Pfam-B_159 (release 1.0). 
PF03792 PBX;<br>Pfam-B_3021 (release 7.0). The PBC domain is a member of the TALE (three-amino-acid loop extension) superclass of homeodomain proteins   . . 
PF02229 Transcriptional Coactivator p15 (PC4)<br>Pfam-B_6534 (release 5.2). p15 has a bipartite structure composed of an amino-terminal  regulatory domain and a carboxy-terminal cryptic DNA-binding  domain  . The DNA-binding activity of the carboxy-terminal is disguised by the amino-terminal p15 domain. Activity is  controlled by protein kinases that target the regulatory domain.. 
PF01851 Proteasome/cyclosome repeat<br>
PF01135 Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)<br>
PF00705 PCNA; <br>Proliferating cell nuclear antigen, N-terminal domain. Pfam-B_598 (release 2.1). 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 Proliferating cell nuclear antigen, C-terminal domain<br>Pfam-B_598 (release 2.1). 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.. 
PF02429 Peridinin-chlorophyll A binding protein<br>Pfam-B_2945 (release 5.4). Peridinin-chlorophyll-protein, a water-soluble light-harvesting complex that has a blue-green absorbing carotenoid as its main pigment, is present in most photosynthetic dinoflagellates. These proteins are composed of two similar repeated domains. These domains constitute a scaffold with pseudo-twofold symmetry surrounding a hydrophobic cavity filled by two lipid, eight peridinin, and two chlorophyll a molecules  .. 
PF01884 PcrB family<br>This family contains proteins that are related to PcrB Swiss:Q53726. The function of these proteins is unknown.. 
PF04194 Programmed cell death protein 2, C-terminal putative domain <br>Pfam-B_19053 (release 7.3);. 
PF04868 Retinal cGMP phosphodiesterase, gamma subunit<br>Pfam-B_4858 (release 7.6). Retinal rod and cone cGMP phosphodiesterases function as the effector enzymes in the vertebrate visual transduction cascade. This family represents the inhibitory gamma subunit  , which is also expressed outside retinal tissues and has been shown to interact with the G-protein-coupled receptor kinase 2 signalling system to regulate the epidermal growth factor- and thrombin-dependent stimulation of p42/p44 mitogen-activated protein kinase in human embryonic kidney 293 cells  .. 
PF00233 PDEase; <br>3'5'-cyclic nucleotide phosphodiesterase. 
PF02112 cAMP phosphodiesterases class-II<br>
PF00341 PDGF/VEGF domain<br>
PF04692 Platelet-derived growth factor, N terminal region<br>This family consists of the amino terminal regions of platelet-derived  growth factor (PDGF, Pfam:PF00341) A and B chains.. 
PF00800 Prephenate dehydratase<br>Pfam-B_1095 (release 2.1). This protein is involved in Phenylalanine biosynthesis. This protein catalyses the decarboxylation of prephenate to phenylpyruvate.. 
PF03740 Pyridoxal phosphate biosynthesis protein PdxJ<br>Members of this family belong to the PdxJ family that catalyses the condensation of 1-deoxy-d-xylulose-5-phosphate (DXP) and 1-amino-3-oxo-4-(phosphohydroxy)propan-2-one to form pyridoxine 5'-phosphate (PNP). This reaction is involved in de novo synthesis of pyridoxine (vitamin B6) and pyridoxal phosphate  .. 
PF00595 PDZ domain (Also known as DHR or GLGF)<br>PDZ domains are found in diverse signaling proteins.. 
PF00544 pec_lyase; <br>This enzyme forms a right handed beta helix structure. Pectate lyase is an enzyme involved in the maceration and  soft rotting of plant tissue. . 
PF05041 Pecanex protein (C-terminus)<br>Pfam-B_5192 (release 7.7). This family consists of C terminal region of the pecanex protein homologues. The pecanex protein is a maternal-effect neurogenic gene found in Drosophila  .. 
PF03211 Pectate lyase<br>Pfam-B_2273 (release 6.5). 
PF04191 Phospholipid methyltransferase <br>Pfam-B_14367 (release 7.3);. The S. cerevisiae phospholipid methyltransferase (EC:2.1.1.16) has a broad substrate specificity of unsaturated phospholipids  .. 
PF03965 Pencillinase_R;<br>Penicillinase repressor. DOMO_DM03102 & Pfam-B_5099 (release 14.0). The penicillinase repressor negatively regulates  expression of the penicillinase gene. The N-terminal region of this protein is involved in operator recognition, while the C-terminal is responsible for dimerisation of the  protein  . . 
PF00805 Pentapeptide repeats (8 copies)<br>These repeats are found in many cyanobacterial proteins. The repeats were first identified in hglK  . The function of these repeats is unknown. The structure of this repeat has been predicted to be a beta-helix  . The repeat can be approximately described as A(D/N)LXX, where X can be any amino acid.. 
PF00354 pentaxin; <br>Pentaxins are also known as pentraxins.. 
PF02896 PEP-utilising enzyme, TIM barrel domain<br>
PF01327 Polypeptide deformylase<br>
PF01562 Reprolysin family propeptide<br>Pfam-B_117 (release 4.0). This region is the propeptide for members of peptidase family M12B.  The propeptide contains a sequence motif similar to the "cysteine switch" of the matrixins. This motif is found at the C terminus of the alignment but is not well aligned.. 
PF03413 Pep_M4_propep;<br>Peptidase propeptide and YPEB domain. This region is likely to have an protease inhibitory function (personal obs:C Yeats). This model is likely to miss some members of this family as the separation from signal to noise is not clear. The name is derived from Peptidase & Bacillus subtilis YPEB. . 
PF00311 Phosphoenolpyruvate carboxylase<br>
PF00821 Phosphoenolpyruvate carboxykinase<br>Pfam-B_1309 (release 2.1). Catalyses the formation of phosphoenolpyruvate by decarboxylation of  oxaloacetate.. 
PF01293 Phosphoenolpyruvate carboxykinase<br>
PF01195 Peptidyl-tRNA hydrolase<br>
PF03564 Peptidase_A16; Peptidase_A16_N; <br>Protein of unknown function (DUF1759). This is a family of proteins of unknown function. Most of the members are gag-polyproteins.. 
PF03566 Peptidase family A21<br>
PF02160 Cauliflower mosaic virus peptidase (A3)<br>
PF01828 Peptidase A4 family<br>
PF01829 Peptidase A6 family<br>
PF01252 SPASE_II; <br>Signal peptidase (SPase) II. 
PF01640 Peptidase C10 family<br>Pfam-B_1522 (release 4.1). This family represents just the active peptide part of these proteins. Residues 1-120 are not part of the model as they form the pro-peptide, which before cleavage blocks the active site from the substrate.  The catalytic residues of histidine and cysteine are brought close together at the active site by the folding of the active peptide.. 
PF03415 Clostripain family<br>
PF01088 UCH; <br>Ubiquitin carboxyl-terminal hydrolase, family 1. 
PF01470 Pyroglutamyl peptidase<br>
PF01831 Peptidase C16 family<br>
PF00648 Cys_protease_2;<br>Calpain family cysteine protease. 
PF01478 Peptidase_C20; <br>Type IV leader peptidase family. Peptidase A24, or the prepilin peptidase as it is also known, processes the N-terminus of the prepilins  . The processing is essential for the correct formation of the pseudopili of type IV bacterial protein secretion. The enzyme is found across eubacteria and archaea  .. 
PF03510 Endoptase_C24; <br>2C endopeptidase (C24) cysteine protease family. 
PF01364 Peptidase family C25<br>Pfam-B_516 (release 3.0). 
PF03785 Peptidase family C25, C terminal ig-like domain<br>Pfam-B_516 (release 3.0). 
PF03412 Peptidase C39 family<br>Lantibiotic and non-lantibiotic bacteriocins are synthesised as precursor peptides containing N-terminal extensions (leader peptides) which are cleaved off during maturation. Most non-lantibiotics and also some lantibiotics have leader peptides of the so-called double-glycine type. These leader peptides share consensus sequences and also a common processing site with two conserved glycine residues in positions -1 and -2. The double- glycine-type leader peptides are unrelated to the N-terminal signal sequences which direct proteins across the cytoplasmic membrane via the sec pathway. Their processing sites are also different from typical signal peptidase cleavage sites, suggesting that a different processing enzyme is involved. Peptide bacteriocins are exported across the cytoplasmic membrane by a dedicated ATP-binding cassette (ABC) transporter. The ABC transporter is the maturation protease  and its proteolytic domain resides in the N-terminal part of the protein  .  This peptidase domain is found in a wide range of ABC transporters, however the presumed catalytic cysteine and histidine are not conserved in all members of this family.. 
PF00770 Adenovirus endoprotease<br>Pfam-B_900 (release 2.1). This family of adenovirus thiol endoproteases specifically cleave Gly-Ala peptides in viral precursor peptides.. 
PF03568 Peptidase family C50<br>
PF03421 Peptidase_C55; <br>YopJ Serine/Threonine acetyltransferase. The Yersinia effector YopJ inhibits the innate immune response by blocking MAP kinase and NFkappaB signaling pathways.  YopJ is a serine/threonine acetyltransferase which regulates signalling pathways by blocking phosphorylation   .  Specifically, YopJ has been shown to block phosphorylation of active site residues  .  It has also been shown that YopJ acetyltransferase is activated by eukaryotic host cell inositol hexakisphosphate  . This family was previously incorrectly annotated in Pfam as being a peptidase family.. 
PF03290 Pox_I7L_G1L; <br>Vaccinia virus I7 processing peptidase. Pfam-B_4082 (release 6.5). 
PF00851 Helper component proteinase<br>Pfam-B_326 (release 3.0). This protein is found in genome polyproteins of potyviruses.. 
PF01830 Peptidase C7 family<br>
PF03569 Peptidase family C8<br>
PF01707 Peptidase family C9<br>
PF00413 matrixin; <br>The members of this family are enzymes that cleave peptides. These proteases require zinc for catalysis.. 
PF00675 Insulinase;<br>Insulinase (Peptidase family M16). Pfam-B_88 (release 2.1). 
PF00883 Cytosol aminopeptidase family, catalytic domain<br>Pfam-B_990 (release 3.0). The two associated zinc ions and the active site are entirely enclosed within the C-terminal catalytic domain in leucine  aminopeptidase.. 
PF01401 Angiotensin-converting enzyme<br>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 peptidase domain, both of these are catalytically active. Most members are secreted membrane bound ectoenzymes.. 
PF00557 pep_M24; <br>Metallopeptidase family M24. This family contains metallopeptidases.  It also contains non-peptidase homologues such as the N terminal domain of Spt16 which is a histone H3-H4 binding module  .. 
PF01742 Clostridial neurotoxin zinc protease<br>Pfam-B_407 (release 4.2). These toxins are zinc proteases that block neurotransmitter release by proteolytic cleavage of synaptic proteins such as synaptobrevins, syntaxin and SNAP-25.. 
PF02073 Thermophilic metalloprotease (M29)<br>
PF01432 Peptidase family M3<br>This is the Thimet oligopeptidase family, large family of mammalian and bacterial oligopeptidases that cleave medium sized peptides. The group also contains mitochondrial intermediate peptidase which is encoded by nuclear DNA but functions within the mitochondria to remove the leader sequence.. 
PF02074 Carboxypeptidase Taq (M32) metallopeptidase<br>
PF02102 Deuterolysin metalloprotease (M35) family<br>
PF02128 Fungalysin metallopeptidase (M36)<br>
PF01447 Thermolysin metallopeptidase, catalytic domain<br>
PF03410 Protein_G1; <br>Pfam-B_4417 (release 6.6). Protein G1, named after the vaccinia virus protein, is a glycoprotein expressed by many Poxviridae.. 
PF01427 Peptidase_M45; <br>D-ala-D-ala dipeptidase. 
PF01435 Peptidase family M48<br>
PF03571 Peptidase family M49<br>
PF02868 Thermolysin metallopeptidase, alpha-helical domain<br>
PF04951 D-aminopeptidase<br>Bacillus subtilis DppA is a binuclear zinc-dependent, D-specific aminopeptidase. The structure reveals that DppA is a new example of a 'self-compartmentalising protease', a family of proteolytic complexes. Proteasomes are the most extensively studied representatives of this family. The DppA enzyme is composed of identical 30 kDa subunits organised in a decamer with 52 point-group symmetry. A 20 A wide channel runs through the complex, giving access to a central chamber holding the active sites. The structure shows DppA to be a prototype of a new family of metalloaminopeptidases characterised by the SXDXEG key sequence  . The only known substrates are D-ala-D-ala and D-ala-gly-gly.. 
PF02031 Streptomyces extracellular neutral proteinase (M7) family<br>
PF01457 Leishmanolysin<br>Prodom_3085 (release 99.1). 
PF01752 Collagenase<br>This family of enzymes break down collagens.. 
PF00768 D-alanyl-D-alanine carboxypeptidase<br>Pfam-B_864 (release 2.1). 
PF02113 D-Ala-D-Ala carboxypeptidase 3 (S13) family<br>
PF02129 X-Pro dipeptidyl-peptidase (S15 family)<br>IPR000383 & Pfam-B_2704 (Release 7.5). 
PF00716 Assemblin (Peptidase family S21)<br>Pfam-B_729 (release 2.1). 
PF00717 Peptidase S24-like<br>Pfam-B_616 (release 2.1). 
PF03572 Peptidase_S41;<br>Peptidase family S41. 
PF03574 Peptidase family S48<br>
PF03575 Peptidase family S51<br>
PF03576 Peptidase_T4;<br>Peptidase family S58 . 
PF00082 subtilase; <br>Subtilases are a family of serine proteases. They appear to have independently and convergently evolved an Asp/Ser/His catalytic triad, like that found in the trypsin serine proteases (see Pfam:PF00089). Structure is an alpha/beta fold containing a 7-stranded parallel beta sheet, order 2314567.. 
PF00326 Prolyl_oligopep;<br>Prolyl oligopeptidase family. 
PF03418 Peptidase_U3; Peptidase_M63; <br>Germination protease. 
PF01136 Peptidase family U32<br>
PF03577 Peptidase_U34; <br>Peptidase family C69. 
PF03419 Sporulation factor SpoIIGA <br>
PF03411 Peptidase_U6; <br>Penicillin-insensitive murein endopeptidase. 
PF01343 Peptidase_U7; <br>Peptidase family S49. Pfam-B_707 (release 2.1). 
PF03420 Prohead core protein protease<br>
PF03036 perilipin; <br>Pfam-B_1154 (release 6.4). The perilipin family includes lipid droplet-associated protein  (perilipin) and adipose differentiation-related protein  (adipophilin).. 
PF01497 Periplasmic binding protein<br>Pfam-B_461 (release 4.0). This family includes bacterial periplasmic binding proteins.  Several of which are involved in iron transport.. 
PF00532 periplasmic_binding_like; <br>Periplasmic binding proteins and sugar binding domain of LacI family. MRC-LMB Genome group. This family includes the periplasmic binding proteins, and the LacI  family transcriptional regulators. The periplasmic binding  proteins are the primary receptors for chemotaxis and transport of many sugar based solutes.  The LacI family of proteins consist of  transcriptional regulators related to the lac repressor. In this case, generally the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain (Pfam:PF00356).. 
PF00141 Peroxidase<br>Prosite; PfamB-105, Release 14.0;. 
PF01328 Peroxidase, family 2<br>The peroxidases in this family do not have similarity to other peroxidases.. 
PF04088 Peroxin 13, N-terminal region<br>Pfam-B_8055 (release 7.3);. Both termini of the Peroxin-13 are oriented to  the cytosol. Peroxin-13 is required for peroxisomal  association of peroxin-14  .. 
PF04882 Peroxin-3<br>Pfam-B_6513 (release 7.6). Peroxin-3 is a peroxisomal protein. It is thought to be involve in membrane vesicle assembly prior to the translocation of matrix proteins  .. 
PF03212 Pertactin<br>Pfam-B_2005 (release 6.5). 
PF02917 Pertussis toxin, subunit 1<br>
PF02918 Pertussis toxin, subunit 2 and 3, C-terminal domain<br>
PF02529 Cytochrome B6-F complex subunit 5<br>Pfam-B_1348 (release 5.4). This family consists of cytochrome B6-F complex subunit 5 (PetG). The cytochrome bf complex found in green plants, eukaryotic algae and cyanobacteria, connects photosystem I to photosystem II in the electron  transport chain, functioning as a plastoquinol:plastocyanin/cytochrome c6 oxidoreductase  .  PetG or subunit 5 is associated with the bf complex and the absence of PetG affects either the assembly or stability of the  cytochrome bf complex in  Chlamydomonas reinhardtii  .. 
PF05115 Cytochrome B6-F complex subunit VI (PetL)<br>Pfam-B_6510 (release 7.7). This family consists of several Cytochrome B6-F complex subunit VI (PetL) proteins found in several plant species. PetL is one of the small subunits which make up The cytochrome b(6)f complex. PetL is strictly required neither for the accumulation nor for the function of cytochrome b6f; in its absence, however, the complex becomes unstable in vivo in aging cells and labile in vitro.  It has been suggested that the N-terminus of the protein is likely to lie in the thylakoid lumen  .. 
PF03742 PetN <br>Pfam-B_3260 (release 7.0). PetN is a small hydrophobic protein, crucial for cytochrome b6-f complex assembly and/or stability. . 
PF04614 Pex19 protein family<br>
PF04757 Pex2 / Pex12 amino terminal region<br>This region is found at the N terminal of a number of known and predicted peroxins including Pex2, Pex10 and Pex12. This conserved region is usually associated with a C terminal ring finger (Pfam:PF00097) domain.. 
PF03011 PFEMP DBL domain<br>Pfam-B_822 (release 6.4). PfEMP1 (Plasmodium falciparum erythrocyte membrane protein) has been identified as the rosetting ligand of the malaria parasite P.  falciparum [1,2].  Rosetting is the adhesion of infected erythrocytes with uninfected erythrocytes in the vasculature of the infected organ, and is associated with severe malaria. PfEMP1 interacts with Complement Receptor One on uninfected erythrocytes to form rosettes  . The extreme variation within these proteins and the grouping of var genes implies that var gene recombination preferentially occurs within var gene groups. These groups reflect a functional diversification that has evolved to cope with the varying conditions of transmission and host immune response met by the parasite  . A recombination hotspot was uncovered between Duffy-binding-like (DBL) subdomains  . Solution of the crystal structure of the N-terminal and first DBL region of PfEMP1 from the VarO variant of the PfEMP1 protein is found to be directly implicated in rosetting as the heparin-binding site  .. 
PF00365 Phosphofructokinase<br>
PF02901 Pyruvate formate lyase<br>
PF01471 Putative peptidoglycan binding domain<br>Pfam-B_2277 (release 4.0). This domain is composed of three alpha helices  .  This domain is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation  .  This domain may have a general peptidoglycan binding function.  This family is found N-terminal to the catalytic domain of matrixins  . The domain is found to bind peptidoglycan experimentally  .. 
PF00300 PGAM;<br>Histidine phosphatase superfamily (branch 1). The histidine phosphatase superfamily is so named because catalysis centres on a conserved His residue that is transiently phosphorylated during the catalytic cycle.  Other conserved residues contribute to a 'phosphate pocket' and interact with the phospho group of substrate before, during and after its transfer to the His residue. Structure and sequence analyses show that different families contribute different additional residues to the 'phosphate pocket' and, more surprisingly, differ in the position, in sequence and in three dimensions, of a catalytically essential acidic residue.  The superfamily may be divided into two main branches.  The larger branch 1 contains a wide variety of catalytic functions, the best known being fructose 2,6-bisphosphatase (found in a bifunctional protein with 2-phosphofructokinase) and cofactor-dependent phosphoglycerate mutase.  The latter is an unusual example of a mutase activity in the superfamily: the vast majority of members appear to be phosphatases.  The bacterial regulatory protein phosphatase SixA is also in branch 1 and has a minimal, and possible ancestral-like structure, lacking the large domain insertions that contribute to binding of small molecules in branch 1 members.. 
PF00342 Phosphoglucose isomerase<br>Phosphoglucose isomerase catalyses the interconversion of glucose-6-phosphate and fructose-6-phosphate.. 
PF00162 Phosphoglycerate kinase<br>
PF00408 PGM_PMM; <br>Phosphoglucomutase/phosphomannomutase, C-terminal domain. 
PF02878 Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I<br>
PF02879 Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II<br>
PF02880 Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III<br>
PF04608 Phosphatidylglycerophosphatase A<br>Pfam-B_5195 (release 7.5). This family represents a family of bacterial phosphatidylglycerophosphatases (EC:3.1.3.27), known as PgpA. It appears that bacteria possess several phosphatidylglycerophosphatases, and thus, PgpA is not essential in Escherichia coli  .. 
PF03334 Na+/H+ antiporter subunit<br>Pfam-B_3611 (release 6.5). This family includes PhaG from Rhizobium meliloti Swiss:Q9ZNG0, MnhG from Staphylococcus aureus Swiss:Q9ZNG0, YufB from Bacillus subtilis Swiss:O05227.. 
PF02304 Scaffold protein B<br>Pfam-B_9648 (release 5.2). This is a family of proteins from single-stranded DNA bacteriophages.  Scaffold proteins B and D are required for procapsid formation.  Sixty copies of the internal scaffold protein B are found in the procapsid.. 
PF04717 phage_base_V; <br>Phage-related baseplate assembly protein. Pfam-B_5996 (release 7.5). Family of phage baseplate assembly proteins responsible for forming the small spike at the end of the tail  . Also found in bacteria, probably the result of horizontal transmission.. 
PF03864 Phage major capsid protein E<br>Major capsid protein E is involved with the stabilisation of the condensed form of the DNA molecule in phage heads  .. 
PF05125 Phage major capsid protein, P2 family <br>TIGRFAMs (release 2.0);. 
PF05144 Phage replication protein CRI  <br>TIGRFAMs (release 2.0);. The phage replication protein CRI, is also known as Gene II, is essential for DNA replication. . 
PF02303 Helix-destabilising protein<br>Pfam-B_9239 (release 5.2). This family contains the bacteriophage helix-destabilising protein, or single-stranded DNA binding protein, required for DNA synthesis.. 
PF02305 Capsid protein (F protein)<br>Pfam-B_10357 (release 5.2). This is a family of proteins from single-stranded DNA bacteriophages. Protein F is the major capsid component, sixty copies of which are found in the virion.. 
PF03335 Phage tail fibre repeat<br>Pfam-B_3576 (release 6.5). 
PF03406 Phage tail fibre repeat<br>Pfam-B_854 (release 6.6). This repeat is found in the tail fibres of phage. For example protein K Swiss:Q37842  . The repeats are about 40 residues long.. 
PF02306 Major spike protein (G protein)<br>Pfam-B_8833 (release 5.2). This is a family of proteins from single-stranded DNA bacteriophages. Five G proteins, each a tight beta barrel, from twelve surface spikes. . 
PF04688 Phage lysis protein, holin<br>This family constitutes holin proteins from the dsDNA Siphidoviridae group bacteriophages.  Most bacteriophages require an endolysin and a holin for host lysis.  During late gene expression, holins accumulate and oligomerise in the host cell membrane.  They then suddenly trigger to permeablise the membrane, which causes lysis by allowing endolysin to attach the peptidoglycan.  There are thought to be at least 35 different families of holin genes  .. 
PF04531 Bacteriophage holin<br>Pfam-B_2644 (release 7.5). This family of holins is found in several staphylococcal and streptococcal bacteriophages. Holins are a diverse family of proteins that cause bacterial membrane lysis during late-protein synthesis. It is thought that the temporal precision of holin-mediated lysis may occur through the buildup of a holin oligomer which causes the lysis  .. 
PF04550 Phage holin family 2 <br>Pfam-B_61235 (release 7.0). Holins are a diverse family of proteins that cause bacterial membrane lysis during late-protein synthesis. It is thought that the temporal precision of holin-mediated lysis may occur through the buildup of a holin oligomer which causes the lysis  .. 
PF05106 Phage holin family (Lysis protein S)<br>TIGRFAMs (release 2.0);. This family represents one of a large number of mutually dissimilar families of phage holins. Holins act against the host cell membrane to allow lytic enzymes of the phage to reach the bacterial cell wall.  This family includes the product of the S gene of phage lambda.. 
PF05105 Holin; <br>TIGRFAMs (release 2.0);. Phage holins and lytic enzymes are both necessary for bacterial  lysis and virus dissemination.This family also includes TcdE/UtxA  involved in toxin secretion in Clostridium difficile  .. 
PF00589 Phage integrase family<br>MRC-LMB Genome group. Members of this family cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment. The catalytic site residues in CRE recombinase  (Swiss:P06956) are Arg-173, His-289, Arg-292 and Tyr-324.. 
PF03245 Bacteriophage Rz lysis protein<br>Pfam-B_3219 (release 6.5). This protein is involved in host lysis. This family is not considered to be a peptidase according to the MEROPs database. This family Rz and the Rz1 protein (Pfam:PF06085) represent a unique example of two genes located in different reading frames in the same nucleotide sequence, which encode different proteins that are both required in the same physiological pathway  .. 
PF00959 Phage lysozyme<br>This family includes lambda phage lysozyme and E. coli endolysin.. 
PF03863 Phage maturation protein<br>
PF04233 Phage Mu protein F like protein<br>Members of this family are found in double-stranded DNA bacteriophages, and in some bacteria.  A member of this family is required for viral head  morphogenesis in bacteriophage SPP1 (Swiss:Q38577).  This family is  possibly a minor head protein. This family may be related to the family TT_ORF1 (Pfam:PF02956).. 
PF05136 Phage portal protein, lambda family <br>TIGRFAMs (release 2.1);. This protein forms a hole, or portal, that enables DNA passage  during packaging and ejection.  It also forms the junction between  the phage capsid and the tail proteins. . 
PF05133 Phage portal protein, SPP1 Gp6-like<br>TIGRFAMs (release 2.0);. This protein forms a hole, or portal, that enables DNA passage during packaging and ejection.  It also forms the junction between the phage head (capsid) and the tail proteins. During SPP1 morphogenesis, Gp6 participates in the procapsid assembly reaction [1,2]. This family also includes the old Pfam family Phage_min_cap (PF05126).. 
PF05135 Phage_QLRG;<br>Phage gp6-like head-tail connector protein. TIGRFAMs (release 2.1);. This family of proteins contain head-tail connector proteins related to gp6 from bacteriophage HK97  . A structure of this protein shows similarity to gp15 a well characterised connector component of bacteriophage SPP1  .. 
PF04492 Bacteriophage replication protein O      <br>Replication protein O is necessary for the initiation of bacteriophage DNA replication.  Protein O interacts with the lambda replication origin, and also with replication protein P to form an oligomer  . It is speculated that the N-terminal half interacts with the replication origin while the C terminal half mediates protein-protein interaction (annotation of Swiss: P14815).. 
PF04984 Phage tail sheath protein<br>This family includes a variety of phage tail sheath proteins.. 
PF04630 Phage major tail protein<br>Pfam-B_5341 (release 7.5). 
PF05100 Phage minor tail protein L <br>TIGRFAMs (release 2.0);. 
PF04761 Lactococcus bacteriophage putative transcription regulator<br>Pfam-B_3898 (release 7.5). This family represents a number of putative transcription repressor proteins found in several Lactococcus bacteriophages. Horizontal transfer may account for the presence of similar proteins in Lactococcus  .. 
PF04985 Phage tail tube protein FII<br>The major structural components of the contractile tail of bacteriophage P2 are proteins FI and FII, which are believed to be the tail sheath and tube proteins, respectively.. 
PF05155 Phage X family   <br>TIGRFAMs (release 2.1);. This family is the product of Gene X.  The function of this protein is unknown.. 
PF02912 tRNA-synt_2_N; <br>Aminoacyl tRNA synthetase class II, N-terminal domain. 
PF02332 Methane/Phenol/Toluene Hydroxylase<br>Pfam-B_15166 (release 5.2) & Pfam-B_3223 (Release 7.5). Bacterial phenol hydroxylase is a multicomponent enzyme that catabolises phenol and some of its methylated derivatives. This Pfam family contains both the P1 and P3 polypeptides of phenol hydroxylase and the alpha and beta chain of methane hydroxylase protein A.. 
PF04663 Phenol hydroxylase conserved region<br>Pfam-B_4509 (release 7.5). Under aerobic conditions, phenol is usually hydroxylated to catechol and degraded via the meta or ortho pathways. Two types of phenol hydroxylase are known: one is a multi-component enzyme the other is a single-component monooxygenase.  This region is found in both types of enzymes [1,2].. 
PF04674 Phosphate-induced protein 1 conserved region<br>Pfam-B_4596 (release 7.5). Family of conserved plant proteins.  Conserved region identified in a phosphate-induced protein of unknown function  .. 
PF03831 PhnA protein<br>TIGRFAMs, Griffiths-Jones SR. 
PF02562 PhoH-like protein<br>PhoH is a cytoplasmic protein and predicted ATPase that is  induced by phosphate starvation.. 
PF02114 Phosducin<br>
PF00068 phoslip; <br>Overington and HMM_iterative_training. Phospholipase A2 releases fatty acids from the second carbon group of glycerol. Perhaps the best known members are secreted snake venoms, but also found in secreted pancreatic and membrane-associated forms. Structure is all-alpha, with two core disulfide-linked helices and a calcium-binding loop. This alignment represents the major family of PLA2s. A second minor family, defined by the honeybee venom PLA2 PDB:1POC and related sequences from Gila monsters (Heloderma), is not recognised. This minor family conserves the core helix pair but is substantially different elsewhere. The PROSITE pattern PA2_HIS, specific to the first core helix, recognises both families.. 
PF04185 Phosphoesterase family<br>Pfam-B_1803 (release 7.3). This family includes both bacterial phospholipase C enzymes EC:3.1.4.3, but also eukaryotic acid phosphatases EC:3.1.3.2.. 
PF04272 Phospholamban<br>TIGRFAMs (release 2.0);. 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+) pump and regulating the flow of Ca ions across the sarcoplasmic reticulum membrane during muscle contraction and relaxation  . Phospholamban is thought to form a pentamer in the membrane  .. 
PF00922 Vesiculovirus phosphoprotein<br>Pfam-B_1160 (release 3.0). 
PF00343 phosphorylase; <br>Carbohydrate phosphorylase. The members of this family catalyse the formation of  glucose 1-phosphate from one of the following polyglucoses;   glycogen, starch, glucan or maltodextrin.. 
PF00124 photoRC; <br>Photosynthetic reaction centre protein. 
PF01895 DUF65; <br>This family contains phosphate regulatory proteins including PhoU. PhoU proteins are known to play a role in the regulation of phosphate uptake. The PhoU domain is composed of a three helix bundle  . The PhoU protein contains two copies of this domain. The domain binds to an iron cluster via its conserved E/DXXXD motif.. 
PF00502 Phycobilisome protein<br>Pfam-B_10 (release 1.0). 
PF02333 Phytase<br>Pfam-B_14843 (release 5.2). Phytase is a secreted enzyme which hydrolyses phytate to release inorganic phosphate. This family appears to represent a novel enzyme that shows phytase activity   and has been shown to have a six- bladed propeller folding architecture  .. 
PF04833 phytochel_synth; Phytochel_synth;<br>Pfam-B_4078 (release 7.6). Family of plant proteins are designated COBRA-like (COBL) proteins.  The 12 Arabidopsis members of the family are all GPI-liked  . Some members of this family are annotated as phytochelatin synthase, but these annotations are incorrect  .. 
PF00360 phytochrome; Phytochrome;<br>Phytochromes are red/far-red photochromic biliprotein photoreceptors which regulate plant development. They are widely represented in both photosynthetic and non-photosynthetic bacteria and are known in a variety of fungi. Although sequence similarities are low, this domain is structurally related to Pfam:PF01590  , which is generally located immediately N-terminal to this domain.  Compared with Pfam:PF01590, this domain carries an additional tongue-like hairpin loop between the fifth beta-sheet and the sixth alpha-helix which functions to seal the chromophore pocket and stabilise the photoactivated far-red-absorbing state (Pfr)  . The tongue carries a conserved PRxSF motif, from which an arginine finger points into the chromophore pocket close to ring D forming a salt bridge with a conserved aspartate residue  .. 
PF03284 Phenazine biosynthesis protein A/B<br>Pfam-B_4020 (release 6.5). 
PF00388 Phosphatidylinositol-specific phospholipase C, X domain<br>This associates with Pfam:PF00387 to form a single structural unit.. 
PF00387 Phosphatidylinositol-specific phospholipase C, Y domain<br>This associates with Pfam:PF00388 to form a single structural unit.. 
PF02192 PI3-kinase family, p85-binding domain<br>Alignment kindly provided by SMART. 
PF00794 PI3-kinase family, ras-binding domain<br>Alignment kindly provided by SMART. 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 Pfam:PF00788 domains  (unpublished observation).. 
PF00613 Phosphoinositide 3-kinase family, accessory domain (PIK domain)<br>Ponting C, Schultz J, Bork P. 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.. 
PF02226 Picornavirus coat protein (VP4)<br>Pfam-B_345 (release 5.2). VP1, VP2, VP3 and VP4 for the basic unit that forms the icosahedral coat of picornaviruses. Five symmetry-related N termini of coat protein VP4 form a ten-stranded, antiparallel beta barrel around the base of the icosahedral fivefold axis  .. 
PF00947 Picornavirus core protein 2A<br>Pfam-B_138 (release 3.0). This protein is a protease, involved in cleavage of the polyprotein.. 
PF01552 Picornavirus 2B protein<br>Pfam-B_214 (release 4.0). Poliovirus infection leads to drastic alterations in membrane permeability late during infection. Proteins 2B and 2BC enhance membrane permeability [1,2].. 
PF00345 pili_assembly; Pili_assembly_N;<br>Pili and flagellar-assembly chaperone, PapD N-terminal domain. C2 domain-like beta-sandwich fold. This domain is the n-terminal part of the PapD chaperone protein for pilus and flagellar assembly.. 
PF02753 pili_assembly_C; Pili_assembly_C;<br>Pili assembly chaperone PapD, C-terminal domain. Ig-like beta-sandwich fold. This domain is the C-terminal part of the pilus and flagellar-assembly chaperone protein PapD.. 
PF00114 pilin; <br>Pilin (bacterial filament). Proteins with only the short N-terminal methylation site are not separated from the noise.\.     The Prosite pattern detects those better.. 
PF05137 Fimbrial assembly protein (PilN)<br>
PF04350 Pilus assembly protein, PilO<br>PilO proteins are involved in the assembly of pilin. However, the precise function of this family of proteins is not known.. 
PF04351 Pilus assembly protein, PilP<br>The PilP family are periplasmic proteins involved in the biogenesis of type IV pili  .. 
PF04697 pinin_SDK_N; <br>pinin/SDK conserved region. Pfam-B_4141 (release 7.5). SDK2/3 is localised in nuclear speckles where as pinin is known to localise at the desmosomes where it is thought to be involved in anchoring intermediate filaments to the desmosomal plaque [1,2]. The role of SDK2/3 in the nucleus is thought to be concerned with modulation of alternative pre-mRNA splicing  . pinin has also been implicated as a tumour suppressor.  The conserved region is found at the N-terminus of the member proteins  .. 
PF00224 Pyruvate kinase, barrel domain<br>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.. 
PF02887 Pyruvate kinase, alpha/beta domain<br>As well as being found in pyruvate kinase this family is found as an isolated domain in some bacterial proteins.. 
PF02827 cAMP-dependent protein kinase inhibitor<br>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 its regulatory chains.. 
PF02173 pKID domain<br>Pfam-B_1547 (Release 4.2). CBP and P300 bind to the pKID (phosphorylated kinase-inducible-domain) domain of CREB  .. 
PF03832 PkinA_anch; <br>This short motif is names after three conserved residues found in a WXSXK motif in protein kinase A anchoring proteins.. 
PF00069 pkinase; <br>Protein kinase domain. 
PF00433 pkinase_C; <br>Protein kinase C terminal domain. Pfam-B_135 (release 1.0). 
PF02253 Phospholipase A1<br>Pfam-B_3500 (release 5.2). Phospholipase A1 is a bacterial outer membrane bound acyl hydrolase with a broad substrate specificity EC:3.1.1.32. It has been proposed  that Ser164 is the active site for Swiss:P00631  .. 
PF01735 Lysophospholipase catalytic domain<br>Pfam-B_2127 (release 4.1). 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 Pfam:PF00168.  Phospholipase B enzymes catalyse the release of fatty acids from lysophsopholipids and are capable in vitro of hydrolysing all  phospholipids extractable form yeast cells  .  Cytosolic phospholipase A2 associates with natural membranes in response to physiological increases in Ca2+ and selectively hydrolyses arachidonyl phospholipids  , the aligned region corresponds the the carboxy-terminal Ca2+-independent catalytic  domain of the protein as discussed in  .. 
PF02988 Phospholipase A2 inhibitor<br>Pfam-B_1254 (release 6.4). 
PF00321 plant_thionins; <br>
PF01307 Plant viral movement protein<br>Pfam-B_881 (release 3.0). This family includes several known plant viral movement proteins (e.g. Swiss:Q85292) from a number of different ssRNA plant virus families including potexviruses, hordeiviruses and carlaviruses. . 
PF04819 Plant_viral_rep; <br>Family of unknown function (DUF716) . Pfam-B_5106 (release 7.6). This family is equally distributed in both metazoa and plants. Annotation associated with Swiss:Q9SLW7 suggest that it may be  involved in response to viral attack in plants.  However, no clear function has been assigned to this family.. 
PF05015 Plasmid maintenance system killer protein<br>Several plasmids with proteic killer gene systems have been reported. All of them encode a stable toxin and an unstable antidote. Upon loss of the plasmid, the less stable inhibitor is inactivated more rapidly than the toxin, allowing the toxin to be activated. The activation of those systems result in cell filamentation and cessation of viable cell production. It has been verified that both the stable killer and the unstable inhibitor of the systems are short polypeptides. This family corresponds to the toxin.. 
PF01672 Putative plasmid partition protein<br>Pfam-B_1163 (release 4.1). This family consists of conserved hypothetical proteins from Borrelia burgdorferi the lyme disease spirochaete, some of which are putative plasmid partition proteins  .. 
PF05016 Plasmid stabilisation system protein<br>Members of this family are involved in plasmid stabilisation. The exact molecular function of this protein is not known. This family also encompasses RelE/ParE described in  .. 
PF00681 Plectin_repeat;<br>Pfam-B_68 (release 2.1). This family includes repeats from plectin, desmoplakin, envoplakin and bullous pemphigoid antigen.. 
PF01523 Putative modulator of DNA gyrase<br>Pfam-B_845 (release 4.0). tldD and pmbA were found to suppress mutations in letD and inhibitor of DNA gyrase. Therefore it has been hypothesised that the TldD and PmbA proteins modulate the activity of DNA gyrase  . It has also been suggested that PmbA may be involved in secretion  .. 
PF03332 Eukaryotic phosphomannomutase<br>Pfam-B_3713 (release 6.5). 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.. 
PF03901 PMP; <br>Alg9-like mannosyltransferase family. DOMO:DM04662 & Pfam-B_7750 (Release 8.0). Members of this family are mannosyltransferase enzymes [1-2].  At least some members are localised in endoplasmic reticulum and involved in GPI anchor biosynthesis [3-4].. 
PF00822 PMP22; <br>PMP-22/EMP/MP20/Claudin family. Pfam-B_1393 (release 2.1). 
PF01625 Peptide methionine sulfoxide reductase<br>Pfam-B_1111 (release 4.1). This enzyme repairs damaged proteins.  Methionine sulfoxide in proteins is reduced to methionine.. 
PF02366 Dolichyl-phosphate-mannose-protein mannosyltransferase  <br>Pfam-B_556 (release 5.2). This is a family of Dolichyl-phosphate-mannose-protein mannosyltransferase proteins EC:2.4.1.109.  These proteins are responsible for O-linked glycosylation of proteins, they catalyse the reaction:- Dolichyl phosphate D-mannose + protein <=> dolichyl phosphate + O-D-mannosyl-protein.\. 
PF03393 Pneumovirus matrix protein<br>Pfam-B_3641 (release 6.6). 
PF03246 Pneumovirus nucleocapsid protein<br>Pfam-B_3020 (release 6.5). 
PF03438 Pneumovirus NS1 protein<br>Pfam-B_3221 (release 6.6). This non-structural protein is one of two found in pneumoviruses. The protein is about 140 amino acids in length. The NS1 protein appears to be important for efficient replication but not essential  . The NS1 protein has been shown by yeast two-hybrid to interact with the viral P protein  . This protein is also known as the 1C protein. It has also been shown that NS1 can potently inhibit transcription and RNA replication  .. 
PF02478 Pneumovirus phosphoprotein<br>Pfam-B_2290 (release 5.4). This family represents the phosphoprotein of Paramyxoviridae,  a putative RNA polymerase alpha subunit that may function in template binding.. 
PF01048 Phosphorylase superfamily<br>Pfam-B_1190 (release 3.0). Members of this family include: purine nucleoside phosphorylase (PNP) Uridine phosphorylase (UdRPase) 5'-methylthioadenosine phosphorylase (MTA phosphorylase). 
PF02233 NAD(P) transhydrogenase beta subunit<br>Pfam-B_2220 (release 5.2). 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 Pfam:PF01262. Pyridine  nucleotide transhydrogenase catalyses the reduction of NAD+ to NADPH. A complete loss of activity occurs upon  mutation of Gly314 in  E. coli  .. 
PF03833 DNA polymerase II large subunit DP2<br>TIGRFAMs, Griffiths-Jones SR. 
PF01620 Ribonuclease (pollen allergen)<br>Pfam-B_1050 (release 4.1). This family contains grass pollen proteins of group V. Swiss:Q40963 has been shown to possess ribonuclease activity  .. 
PF01190 Pollen proteins Ole e I like<br>
PF00659 POLO box duplicated region<br>
PF02563 Polysaccharide biosynthesis/export protein<br>COGs & Pfam-B_1505 (Release 7.5). This is a family of periplasmic proteins involved in polysaccharide biosynthesis and/or export.. 
PF01743 Poly A polymerase head domain<br>Pfam-B_814 (release 4.2). This family includes nucleic acid independent RNA polymerases, such as Poly(A) polymerase, which adds the poly (A) tail to mRNA EC:2.7.7.19. This family also includes the tRNA nucleotidyltransferase that adds the CCA to the 3' of the tRNA EC:2.7.7.25. This family is part of the nucleotidyltransferase superfamily.. 
PF01518 Sigma NS protein<br>Pfam-B_803 (release 4.0). This viral protein has a poly(C)-dependent poly(G) polymerase activity  . . 
PF00738 Polyhedrin<br>Pfam-B_423 (release 2.1). These proteins are found in occlusion bodies in various viruses. The polyhedrin protein protects the virus.. 
PF03364 Polyketide cyclase / dehydrase and lipid transport<br>Mifsud W, Mistry J, Wood V. Pfam-B_1457 (release 6.6). This family contains polyketide cylcases/dehydrases which are enzymes involved in polyketide synthesis. The family also includes proteins which are involved in the binding/transport of lipids.. 
PF01736 Polyomavirus agnoprotein<br>Pfam-B_1917 (release 4.1). This family consist of the DNA binding protein or agnoprotein from various polyomaviruses. This protein is highly basic and can bind single stranded and double stranded DNA  . Mutations in the agnoprotein produce smaller viral plaques, hence its function is not essential for growth in tissue  culture cells but something has slowed in the normal replication  cycle  . There is also evidence suggesting that the agnogene and agnoprotein act as regulators of structural protein synthesis  .. 
PF00718 Polyomavirus coat protein<br>Pfam-B_748 (release 2.1). 
PF00761 Polyomavirus coat protein<br>Pfam-B_871 (release 2.1). 
PF00348 Polyprenyl synthetase<br>
PF01943 Polysaccharide biosynthesis protein<br>Members of this family are integral membrane proteins  . Many members of the family are implicated in production of polysaccharide. The family includes RfbX part of the O antigen biosynthesis operon  . The family includes SpoVB from Bacillus subtilis Swiss:Q00758, which is involved in spore cortex biosynthesis  .. 
PF02719 Polysaccharide biosynthesis protein<br>Pfam-B_1536 (release 5.5). This is a family of diverse bacterial polysaccharide biosynthesis  proteins including the CapD protein (Swiss:P39853)  , WalL protein (Swiss:O86159) mannosyl-transferase (Swiss:O05349)   and several putative epimerases (e.g. WbiI Swiss:O69130).. 
PF02530 Porin subfamily<br>Pfam-B_1122 (release 5.4). This family consists of porins from the alpha subdivision of Proteobacteria the members of this family are related to Pfam:PF00267. The porins form large aqueous channels in the cell membrane allowing the selective entry of hydrophilic compounds this so called 'molecular sieve' is found in the cell walls of gram negative bacteria.   . 
PF01379 Porphobilinogen deaminase, dipyromethane cofactor binding domain<br>
PF03900 Porphobilinogen deaminase, C-terminal domain<br>
PF00280 Potato inhibitor I family<br>
PF00767 Potyvirus coat protein<br>Pfam-B_868 (release 2.1). 
PF00157 pou; <br>Pou domain - N-terminal to homeobox domain. 
PF05061 Poxvirus A11 Protein<br>Pfam-B_5994 (release 7.7). Family of conserved Chordopoxvirinae A11 family proteins. Conserved region spans entire protein in the majority of family members.. 
PF04651 Poxvirus A12 protein<br>Pfam-B_5523 (release 7.5). 
PF04848 Poxvirus A22 protein<br>Pfam-B_4558 (release 7.6). 
PF04584 Poxvirus A28 family<br>Pfam-B_4756 (release 7.5). Family of conserved Poxvirus A28 family proteins. Conserved region spans entire protein in the majority of family members.. 
PF04665 Poxvirus A32 protein<br>Pfam-B_5586 (release 7.5). The A32 protein is thought to be involved in viral DNA packaging.. 
PF04948 Poxvirus A51 protein <br>Pfam-B_6937 (release 7.6). 
PF04924 Poxvirus A6 protein <br>Pfam-B_5792 (release 7.6). 
PF04745 VITF-3 subunit protein<br>Pfam-B_6036 (release 7.5). Family of Chordopoxvirus proteins composing one of the two subunits that make up VITF-3, a virally encoded complex necessary for intermediate stage transcription  .. 
PF04835 A9 protein conserved region<br>Pfam-B_4431 (release 7.6). Family of Chordopoxvirus A9 proteins. . 
PF04508 Viral A-type inclusion protein repeat <br>The repeat is found in the A-type inclusion protein of the Poxvirus family  .  . 
PF03286 Pox virus Ag35 surface protein<br>Pfam-B_4295 (release 6.5). 
PF03336 Poxvirus C4/C10 protein<br>Pfam-B_3519 (release 6.5). 
PF03287 Poxvirus C7/F8A protein<br>Pfam-B_4089 (release 6.5). 
PF04701 Pox virus D2 protein<br>Pfam-B_5832 (release 7.5). 
PF00874 BglG_antitermin;<br>Pfam-B_772 (release 3.0). The PRD domain (for PTS Regulation Domain), is the phosphorylatable regulatory domain found in bacterial transcriptional antiterminator such as BglG, SacY and LicT, as well as in activators such as MtlR and LevR. The PRD is phosphorylated on one or two conserved histidine residues. PRD-containing proteins are involved in the regulation of catabolic operons in Gram+ and Gram- bacteria and are often characterised by a short N-terminal effector domain that binds to either RNA (CAT-RBD for antiterminators Pfam:PF03123) or DNA (for activators), and a duplicated PRD module which is phosphorylated by the sugar phosphotransferase system (PTS) in response to the availability of carbon source. The phosphorylations modify the conformation and stability of the dimeric proteins and thereby the RNA- or DNA-binding activity of the effector domain. The structure of the LicT PRD domains has been solved in both the active (pdb:1h99,  ) and inactive state (pdb:1tlv  ), revealing massive structural rearrangements upon activation.. 
PF04580 Chordopoxvirinae D3 protein <br>Pfam-B_4684 (release 7.5). Chordopoxvirinae D3 protein conserved region.  Region occupies entire length of D3 protein.. 
PF03288 Poxvirus D5 protein-like<br>Pfam-B_4009 (release 6.5). This family includes D5 from Poxviruses which is necessary for viral DNA replication, and is a nucleic acid independent nucleoside triphosphatase. Members of this family are also found outside of poxviruses. This domain is a DNA-binding winged HTH domain.. 
PF04805 E10-like protein conserved region<br>Pfam-B_6357 (release 7.5). Family of poxvirus proteins.. 
PF04497 Pox_E2;<br>Pfam-B_3979 (release 7.5). This family of proteins is restricted to Poxviridae.  It contains a number of differently named uncharacterised proteins.. 
PF04656 Pox virus E6 protein<br>Pfam-B_4392 (release 7.5). Family of pox virus E6 proteins.. 
PF03394 Poxvirus E8 protein<br>Pfam-B_3759 (release 6.6). 
PF04943 Poxvirus F11 protein<br>Pfam-B_6911 (release 7.6). The protein F11 is an early virus protein.. 
PF03337 Poxvirus F12L protein<br>Pfam-B_3082 (release 6.5). 
PF04596 Poxvirus protein F15<br>Pfam-B_5182 (release 7.5). 
PF04708 Poxvirus F16 protein<br>Pfam-B_5863 (release 7.5). 
PF04767 DNA-binding 11 kDa phosphoprotein<br>Pfam-B_6128 (release 7.5). Family of poxvirus proteins required for virus morphogenesis. Protein function necessary for proteolytic processing of the major viral structural proteins, P4a and P4b  . . 
PF04599 Poxvirus G5 protein<br>Pfam-B_5216 (release 7.5). This protein has been predicted to be related to the FEN-1 endonuclease  .. 
PF04787 Late protein H7<br>Pfam-B_6266 (release 7.5). Family of poxvirus late H7 proteins.. 
PF03289 Poxvirus protein I1<br>Pfam-B_4306 (release 6.5). 
PF04661 Poxvirus I3 ssDNA-binding protein<br>Pfam-B_5571 (release 7.5). 
PF04713 Poxvirus protein I5<br>Pfam-B_5901 (release 7.5). 
PF04595 Poxvirus I6-like family<br>Pfam-B_5073 (release 7.5) & Pfam-B_6224 (release 8.0). This family includes I6 proteins as well as the related F5L proteins.. 
PF03338 Poxvirus J1 protein<br>Pfam-B_3556 (release 6.5). 
PF03339 Poxvirus L3/FP4 protein<br>Pfam-B_3380 (release 6.5). 
PF00485 Phosphoribulokinase / Uridine kinase family<br>In Arabidopsis the region carries two binding domains, a phosphoribosylpyrophosphate-binding domain and, at the very C-terminus, a uracil-binding domain.. 
PF04872 Poxvirus L5 protein family<br>Pfam-B_6088 (release 7.6). This family includes variola (smallpox) and vaccinia virus L5 proteins. However, not all  proteins in this family are called L5.  L5 is thought to contain a  metal-binding region  .. 
PF03356 Viral late protein H2<br>Pfam-B_3929 (release 6.5). All Members of this family show similarity to the vaccinia virus late protein H2. This protein is often referred to by its gene name of H2R. Members from this family all belong to the viral taxon Poxviridae.. 
PF04887 Poxvirus M2 protein<br>Pfam-B_6168 (release 7.6). This family includes M2 protein from variola virus.  The function of this protein is not known.. 
PF03341 Poxvirus mRNA capping enzyme, small subunit<br>Pfam-B_3728 (release 6.5). The small subunit of the poxvirus mRNA capping enzyme has been found to have a structure which suggests that it started life as an RNA cap 2-prime O-methyltransferase. It has subsequently evolved to a catalytically inactive form that has been retained in order to help stabilise the large subunit, D1, and to enhance its methyltransferase activity through an allosteric mechanism  .. 
PF03213 Poxvirus P35 protein<br>Pfam-B_2785 (release 6.5). 
PF03395 Poxvirus P4A protein<br>Pfam-B_2985 (release 6.6). 
PF03292 Poxvirus P4B major core protein<br>Pfam-B_4215 (release 6.5). 
PF03296 Poxvirus poly(A) polymerase nucleotidyltransferase domain<br>Pfam-B_4019 (release 6.5). 
PF03294 RNA polymerase-associated transcription specificity factor, Rap94<br>Pfam-B_4535 (release 6.5). 
PF03340 Poxvirus rifampicin resistance protein<br>Pfam-B_3377 (release 6.5). 
PF03293 Poxvirus DNA-directed RNA polymerase, 18 kD subunit<br>Pfam-B_4188 (release 6.5). 
PF03396 Poxvirus DNA-directed RNA polymerase, 35 kD subunit<br>Pfam-B_3921 (release 6.6). 
PF04490 Poxvirus T4 protein, C terminus<br>This family of poxvirus proteins are thought to be retained in the endoplasmic reticulum.  M-T4 of myxoma virus (Swiss:O55698) is thought to protect infected lymphocytes from apoptosis and modulate the inflammatory response to virus infection  .. 
PF04491 Poxvirus T4 protein, N terminus<br>This family of poxvirus proteins are thought to be secreted or retained in the endoplasmic reticulum if the protein also contains an additional C terminal region (Pfam:PF04490).  M-T4 of myxoma virus (Swiss:O55698) is thought to protect infected lymphocytes from apoptosis and modulate the inflammatory response to virus infection  .. 
PF03295 Poxvirus trans-activator protein A1 C-terminal<br>Pfam-B_4259 (release 6.5). 
PF03355 Viral Trans-Activator Protein <br>Pfam-B_3956 (release 6.5). These proteins function as a trans-activator of viral late  genes.. 
PF04441 Poxvirus early transcription factor (VETF), large subunit <br>Pfam-B_3920 (release 7.5). The poxvirus early transcription factor (VETF), in addition to  the viral RNA polymerase, is required for efficient transcription of early genes in vitro. VETF is a heterodimeric protein that binds  specifically to early gene promoters. The heterodimer is comprised of an 82 kDa (this family) subunit and a 70 kDa subunit. . 
PF04947 Poxvirus Late Transcription Factor VLTF3 like <br>Members of this family are approximately 26 KDa, and are involved in trans-activator of late transcription  .. 
PF04498 Poxvirus nucleic acid binding protein VP8/L4R<br>The 25 kDa product of Vaccinia virus gene L4R is also known as VP8.  VP8 is found in the cores of Vaccinia virions and is essential for the formation of transcriptionally competent viral particles.  It binds both single stranded and double stranded DNA and RNA with similar affinities.  Binding is thought to involve cooperative interactions between protein subunits. The protein is proteolytically cleaved during viral assembly at an Ala-Gly-Ala site. Possible roles for VP8 include packaging and maintaining the DNA genome in a transcribable configuration; binding ssDNA during transcription initiation; and cooperation with I8R protein to unwind early promoter regions.  VP8 may also function in either transcription elongation or release of mRNA molecules from viral particles  .. 
PF04395 Poxvirus B22R protein<br>Pfam-B_3510 (release 7.3). This is highly conserved C-rich, central region of poxvirus proteins from eg, Fowlpox virus, Myxoma virus, Lumpy skin disease, Variola virus and other members of the Poxviridae family of double-stranded, no-RNA stage poxviruses. There are three pairs of conserved cysteine residues.. 
PF00550 pp-binding; <br>Phosphopantetheine attachment site. A 4'-phosphopantetheine prosthetic group is attached through a serine. This prosthetic group acts as a a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups. This domain forms a four helix bundle. This family includes members not included in Prosite. The inclusion of these members is supported by sequence analysis and functional evidence. The related domain of Swiss:P19828 has the attachment serine replaced by an alanine.. 
PF02503 Polyphosphate kinase middle domain<br>Pfam-B_2701 (release 5.4). Polyphosphate kinase (Ppk) catalyses the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate molecules.. 
PF03012 Phosphoprotein<br>Pfam-B_1336 (release 6.4). This family includes the M1 phosphoprotein non-structural RNA polymerase alpha subunit, which is thought to be a  component of the active polymerase, and may be involved in template binding.. 
PF02818 PPAK motif<br>These motifs are found in the PEVK region of titin.. 
PF01326 PPDK_N_term; <br>Pyruvate phosphate dikinase, PEP/pyruvate binding domain. This enzyme catalyses the reversible conversion of ATP to AMP, pyrophosphate and phosphoenolpyruvate (PEP).. 
PF01239 Protein prenyltransferase alpha subunit repeat<br>Both farnesyltransferase (FT) and geranylgeranyltransferase 1 (GGT1) recognise a CaaX motif on their substrates where 'a' stands for preferably aliphatic residues, whereas GGT2 recognises a completely different motif. Important substrates for FT include, amongst others, many members of the Ras superfamily. GGT1 substrates include some of the other small GTPases and GGT2 substrates include the Rab family  .. 
PF02541 Ppx/GppA phosphatase family<br>This family consists of the N-terminal region of exopolyphosphatase (Ppx) EC:3.6.1.11 and guanosine pentaphosphate phospho-hydrolase (GppA) EC:3.6.1.40.. 
PF04403 Paraquat-inducible protein A<br>Paraquat is a superoxide radical-generating agent.  The promoter for the  pqiA gene is also inducible by other known superoxide generators  . This is predicted to be a family of integral membrane proteins, possibly  located in the inner membrane. This family is related to NADH dehydrogenase subunit 2 (Pfam:PF00361).. 
PF01502 Phosphoribosyl-AMP cyclohydrolase<br>Pfam-B_782 (release 4.0). This enzyme catalyses the third step in the histidine biosynthetic pathway. It requires Zn ions for activity.. 
PF01503 Phosphoribosyl-ATP pyrophosphohydrolase<br>Pfam-B_784 (release 4.0). This enzyme catalyses the second step in the histidine biosynthetic pathway.. 
PF03208 PRA1 family protein<br>Pfam-B_2976 (release 6.5) & Pfam-B_8147 (Release 8.0). This family includes the PRA1 (Prenylated rab acceptor) protein which is a Rab guanine dissociation inhibitor (GDI) displacement factor  .  This family also includes the glutamate transporter EAAC1 interacting protein GTRAP3-18  .. 
PF00697 N-(5'phosphoribosyl)anthranilate (PRA) isomerase<br>Pfam-B_247 (release 2.1). 
PF03967 Photosynthetic reaction centre, H-chain N-terminal region<br>The family corresponds the N-terminal cytoplasmic domain.. 
PF00432 prenyltrans; <br>Prenyltransferase and squalene oxidase repeat. Pfam-B_130 (release 1.0). 
PF01080 Presenilin<br>Pfam-B_789 (release 3.0). Mutations in presenilin-1 are a major cause of early onset Alzheimer's disease  .  It has been found that presenilin-1 (Swiss:P49768) binds to beta-catenin in-vivo  . This family also contains SPE proteins from C.elegans.. 
PF03991 Prion_octopep;<br>Copper binding octapeptide repeat. This repeat is found at the amino terminus of prion proteins.  It has been shown to bind to copper.. 
PF03063 Prismane/CO dehydrogenase family<br>Pfam-B_2956 (release 6.4). This family includes both hybrid-cluster proteins and the beta chain of carbon monoxide dehydrogenase. The hybrid-cluster proteins contain two Fe/S centres - a [4Fe-4S] cubane cluster, and a hybrid [4Fe-2S-2O] cluster.  The physiological role of this protein is as yet unknown, although a role in nitrate/nitrite respiration has been suggested  . The prismane protein from Escherichia coli was shown to contain hydroxylamine reductase activity (NH2OH + 2e + 2 H+ -> NH3 + H2O). This activity is rather low. Hydroxylamine reductase activity was also found in CO-dehydrogenase in which the active site Ni was replaced by Fe  .  The CO dehydrogenase contains a Ni-3Fe-2S-3O centre.. 
PF00484 Carbonic anhydrase<br>Prosite & Pfam-B_9319 (Release 8.0). This family includes carbonic anhydrases as well as a family of non-functional homologues related to YbcF.. 
PF01619 Proline dehydrogenase<br>Pfam-B_1092 (release 4.1). 
PF00160 pro_isomerase; <br>Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD. The peptidyl-prolyl cis-trans isomerases, also known as cyclophilins, share this domain of about 109 amino acids. Cyclophilins have been found in all organisms studied so far and catalyse peptidyl-prolyl isomerisation during which the peptide bond preceding proline (the peptidyl-prolyl bond) is stabilised in the cis conformation.  Mammalian cyclophilin A (CypA) is a major cellular target for the immunosuppressive drug cyclosporin A (CsA).  Other roles for cyclophilins may include chaperone and cell signalling function  .. 
PF00235 profilin; <br>
PF02161 Progesterone receptor<br>
PF02244 Carboxypeptidase activation peptide<br>Pfam-B_2335 (release 5.2). Carboxypeptidases are found in abundance in pancreatic secretions.  The pro-segment moiety (activation peptide) accounts for up to a  quarter of the total length of the peptidase, and is responsible  for modulation of folding and activity of the pro-enzyme.. 
PF04352 ProQ/FINO family<br>COG3109 & Pfam-B_7673 (release 7.7). This family includes ProQ, which is required for full activation of the osmoprotectant transporter, ProQ, in Escherichia coli. This family includes several bacterial fertility inhibition (FINO) proteins. The conjugative transfer of F-like plasmids is repressed by FinO, an RNA binding protein. FinO interacts with the F-plasmid encoded traJ mRNA and its antisense RNA, FinP, stabilising FinP against endonucleolytic degradation and facilitating sense-antisense RNA recognition  .. 
PF02428 Potato type II proteinase inhibitor family<br>Pfam-B_2913 (release 5.4). Members of this family are proteinase inhibitors that contain eight cysteines that form four disulphide bridges. The structure of the proteinase-inhibitor complex is known  .. 
PF00260 protamine_P1; <br>
PF00841 protamine_P2; <br>Pfam-B_1350 (release 2.1). This protein also known as protamine P2 can substitute for histones in the chromatin of sperm (Swiss). The alignment contains both the sequence of the mature P2 protein and its propeptide.. 
PF03247 Prothymosin/parathymosin family<br>Pfam-B_3463 (release 6.5). 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  . . 
PF05044 Prox1;<br>Homeo-prospero domain. Pfam-B_5293 (release 7.7). Prospero is a large drosophila transcription factor protein that is expressed in all neural lineages of drosophila embryos.  It is needed for correct expression of several neural proteins and in determining the cell fates of neural stem cells. Homologues of prospero are found in a wide range of animals including humans with the highest level of similarity being found in the C-terminal 160 amino acids. This region was identified as containing an atypical homeobox domain followed by a prospero domain.  However, the structure shows that these two regions form a single stable structural domain as defined here  .  This homeo-prospero domain binds to DNA.. 
PF02840 Prp18 domain<br>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 sequences of Prp18 that have been evolutionarily conserved. The core structure consists of five alpha-helices that adopt a novel fold. The most highly conserved region of Prp18, a nearly invariant stretch of 19 aa, forms part of a loop between two alpha-helices and may interact with the U5 small nuclear ribonucleoprotein particles  .. 
PF02340 PRRSV putative envelope protein<br>Pfam-B_939 (release 5.2). This family consists of a conserved probable envelope protein  or ORF2 in porcine reproductive and respiratory syndrome virus (PRRSV) also in the family is a minor structural protein from lactate dehydrogenase-elevating virus.. 
PF01366 Herpesvirus processing and transport protein<br>Pfam-B_1171 (release 3.0). The members of this family are associate with capsid intermediates during packaging of the virus.. 
PF02666 Phosphatidylserine decarboxylase<br>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 the biosynthesis of aminophospholipids by converting  phosphatidylserine to phosphatidylethanolamine  .. 
PF04230 Polysaccharide pyruvyl transferase<br>Pyruvyl-transferases involved in peptidoglycan-associated polymer  biosynthesis.  CsaB in Bacillus anthracis is necessary for the non-covalent anchoring of proteins containing an SLH (S-layer homology) domain to peptidoglycan-associated pyruvylated polysaccharides.  WcaK and AmsJ are involved in the biosynthesis of colanic acid in Escherichia coli and of amylovoran in Erwinia amylovora  .. 
PF00223 psaA_psaB;<br>Photosystem I psaA/psaB protein. 
PF02531 PsaD<br>Pfam-B_1336 (release 5.4). This family consists of PsaD from plants and cyanobacteria. PsaD is an extrinsic polypeptide of photosystem I (PSI) and is required for native assembly of PSI reaction clusters and is implicated in the  electrostatic binding of ferredoxin within the reaction centre  . PsaD forms a dimer in solution which is bound by PsaE however PsaD is monomeric in its native complexed PSI environment  .. 
PF02605 Photosystem I reaction centre subunit XI<br>Pfam-B_1741 (release 5.4). This family consists of the photosystem I reaction centre subunit XI, PsaL, from plants and bacteria.  PsaL is one of the smaller subunits in photosystem I with only two transmembrane alpha helices and interacts closely with PsaI  .. 
PF00737 PSBH; <br>Photosystem II 10 kDa phosphoprotein. Pfam-B_465 (release 2.1). This protein is phosphorylated in a light dependent reaction.. 
PF02532 Photosystem II reaction centre I protein (PSII 4.8 kDa protein)<br>Pfam-B_1731 (release 5.4). This family consists of various Photosystem II (PSII) reaction centre I proteins or PSII 4.8 kDa proteins, PsbI, from the chloroplast genome of many plants and Cyanobacteria. PsbI is a small, integral membrane component of PSII the role of which is not clear  .  Synechocystis mutants lacking  PsbI have 20-30% loss of PSII activity however the PSII complex is not  destabilised  .. 
PF01788 PsbJ<br>Pfam-B_1227 (release 4.2). This family consists of the photosystem II reaction centre protein PsbJ from plants and Cyanobacteria.  In Synechocystis sp. PCC 6803 PsbJ regulates the number of  photosystem II centres in thylakoid membranes, it is a predicted 4kDa protein with one membrane spanning domain  .. 
PF02533 Photosystem II 4 kDa reaction centre component<br>Pfam-B_1331 (release 5.4). This family consists of various photosystem II 4 kDa reaction centre components (PsbK) from plant and Cyanobacteria.  The photosystem II reaction centre is responsible for catalysing the core photosynthesis reaction the light-induced splitting of water and the consequential release of dioxygen.  In C. reinhardtii the psbK product is required for the stable assembly and/or stability of the photosystem II complex  .. 
PF02419 PsbL protein<br>Pfam-B_1884 (release 5.4). This family consists of the photosystem II reaction centre protein PsbJ from plants and Cyanobacteria. The function of this small  protein is unknown. Interestingly the mRNA for this protein requires a post-transcriptional modification of an ACG triplet to form an AUG initiator codon [1,2].. 
PF05151 Photosystem II reaction centre M protein (PsbM)<br>Pfam-B_6558 (release 7.7). This family consists of several Photosystem II reaction centre M proteins (PsbM) from plants and cyanobacteria. During the photosynthetic light reactions in the thylakoid membranes of cyanobacteria, algae, and plants, photosystem II (PSII), a multi-subunit membrane protein complex, catalyses oxidation of water to molecular oxygen and reduction of plastoquinon  .. 
PF02468 psbN; <br>Photosystem II reaction centre N protein (psbN). Pfam-B_2222 (release 5.4). This is a family of small proteins encoded on the chloroplast genome. psbN is involved in photosystem II during photosynthesis, but its exact role is unknown.. 
PF04725 Photosystem II 10 kDa polypeptide PsbR<br>This protein is associated with the oxygen-evolving complex of photosystem II.  Its function in photosynthesis is not known.  The C-terminal hydrophobic region functions as a thylakoid transfer signal but is not removed  .. 
PF01405 PSBT; <br>Photosystem II reaction centre T protein. Pfam-B_1880 (release 3.0). The exact function of this protein is unknown. It probably consists of a single transmembrane spanning helix. The Swiss:P37256 protein, appears to be (i) a novel photosystem II subunit and (ii) required for maintaining optimal photosystem II activity under adverse growth conditions  .. 
PF03912 PsbW; <br>Psb28 is a 13 kDa soluble protein that is directly assembled in dimeric PSII supercomplexes.  The negatively charged N-terminal region is essential for this process  . This protein was formerly known as PsbW, but PsbW is now reserved for Pfam:PF07123.. 
PF00849 YABO;<br>RNA pseudouridylate synthase. Pfam-B_421 (release 3.0). 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 Swiss:P33643, a pseudouridylate synthase that converts specific uracils to pseudouridine in 23S rRNA. RluA from E. coli converts bases in both rRNA and tRNA  .. 
PF00796 Photosystem I reaction centre subunit VIII<br>Pfam-B_528 (release 2.1). 
PF02427 Photosystem I reaction centre subunit IV / PsaE<br>Pfam-B_1594 (release 5.4). PsaE is a 69 amino acid polypeptide from photosystem I present on the stromal side of the thylakoid membrane  . The structure is comprised of a well-defined five-stranded beta-sheet similar to SH3 domains  .. 
PF02507 Photosystem I reaction centre subunit III<br>Pfam-B_2122 (release 5.4). Photosystem I (PSI) is an integral membrane protein complex that  uses light energy to mediate electron transfer from plastocyanin to ferredoxin. Subunit III (or PSI-F) is one of at least 14 different subunits that compose the PSI complex.. 
PF03244 Photosystem I reaction centre subunit VI<br>Pfam-B_3007 (release 6.5). Photosystem I (PSI) is an integral membrane protein complex that uses light energy to mediate electron transfer from plastocyanin to ferredoxin.. 
PF01701 Photosystem I reaction centre subunit IX / PsaJ<br>Pfam-B_1599 (release 4.1). This family consists of the photosystem I reaction centre subunit IX or PsaJ from various organisms including Synechocystis sp. (strain pcc 6803), Pinus thunbergii (green pine) and Zea mays (maize). PsaJ Swiss:P19443 is a small 4.4kDa, chloroplastal encoded, hydrophobic subunit of the photosystem I reaction complex its function is not yet fully understood  . PsaJ can be cross-linked to PsaF Swiss:P12356 and has a single predicted transmembrane domain it has a proposed role in maintaining PsaF in the correct orientation to allow for fast electron transfer from soluble donor proteins to P700+  .. 
PF01241 Photosystem I psaG / psaK<br>
PF00421 Photosystem II protein<br>Pfam-B_182 (release 1.0). 
PF04012 PspA/IM30 family<br>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 in many Gram-negative pathogenic bacteria and its homologue in plants, VIPP1, plays a critical role in thylakoid biogenesis, essential for photosynthesis. Activation of transcription by the enhancer-dependent bacterial sigma(54) containing RNA polymerase occurs through ATP hydrolysis-driven protein conformational changes enabled by activator proteins that belong to the large AAA(+) mechanochemical protein family. It has been shown that PspA directly and specifically acts upon and binds to the AAA(+) domain of the PspF transcription activator  .. 
PF04839 Plastid and cyanobacterial ribosomal protein (PSRP-3 / Ycf65)<br>Pfam-B_2979 (release 7.6). This small acidic protein is found in 30S ribosomal subunit of cyanobacteria and plant plastids.\.       In plants it has been named plastid-specific ribosomal protein 3 (PSRP-3), and in cyanobacteria it is named Ycf65.  Plastid-specific ribosomal proteins may mediate the effects of nuclear factors on plastid translation.  The acidic PSRPs are thought to contribute to protein-protein interactions in the 30S subunit, and are not thought to bind RNA  .. 
PF03034 Phosphatidyl serine synthase<br>Pfam-B_1414 (release 6.4). 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 (phosphotidylcholine or phosphotidylethanolamine) by L-serine.. 
PF01515 Phosphate acetyl/butaryl transferase<br>Pfam-B_799 (release 4.0). This family contains both phosphate acetyltransferase and phosphate butaryltransferase.  These enzymes catalyse the transfer of an acetyl or butaryl group to orthophosphate.. 
PF02126 Phosphotriesterase family<br>
PF00809 DHPS; <br>Pterin binding enzyme. Pfam-B_1411 (release 2.1) and Pfam-B_3423 (release 6.6). This family includes a variety of pterin binding enzymes that all adopt a TIM barrel fold. The family includes dihydropteroate synthase EC:2.5.1.15 as well as a group methyltransferase enzymes including methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) Swiss:Q46389 that catalyses a key step in the Wood-Ljungdahl pathway of carbon dioxide fixation. It transfers the N5-methyl group from methyltetrahydrofolate (CH3-H4folate) to a cob(I)amide centre in another protein, the corrinoid iron-sulfur protein. MeTr is a member of a family of proteins that includes methionine synthase and methanogenic enzymes that activate the methyl group of methyltetra-hydromethano(or -sarcino)pterin  .. 
PF01091 PTN_MK; <br>PTN/MK heparin-binding protein family, C-terminal domain. 
PF05196 PTN/MK heparin-binding protein family, N-terminal domain<br>
PF04387 Protein tyrosine phosphatase-like protein, PTPLA<br>Pfam-B_1525 (release 7.3). This family includes the mammalian protein tyrosine phosphatase-like protein, PTPLA. A significant variation of PTPLA from other protein tyrosine phosphatases is the presence of proline instead of catalytic arginine at the active site. It is thought that PTPLA proteins have a role in the development, differentiation, and maintenance of a number of tissue types  .. 
PF01242 6-pyruvoyl tetrahydropterin synthase<br>6-Pyruvoyl tetrahydrobiopterin synthase catalyses the conversion of dihydroneopterin triphosphate to 6-pyruvoyl tetrahydropterin, the second of three enzymatic steps in the synthesis of tetrahydrobiopterin from GTP. The functional enzyme is a hexamer of identical subunits  .. 
PF00854 POT family<br>Pfam-B_571 (release 3.0). The POT (proton-dependent oligopeptide transport) family all appear to be proton dependent transporters  .. 
PF00381 PTS HPr component phosphorylation site<br>
PF01885 DUF60; <br>RNA 2'-phosphotransferase, Tpt1 / KptA family. Tpt1 catalyses the last step of tRNA splicing in yeast.  It transfers the splice junction 2'-phosphate from ligated tRNA to NAD, to produce ADP-ribose 1"-2"-cyclic phosphate.  This is presumed to be followed by a transesterification step to release the RNA.\.     The first step of this reaction is similar to that catalysed by some bacterial toxins.\.        E. coli KptA and mouse Tpt1 are likely to use the same reaction mechanism  .. 
PF00358 phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1<br>
PF00359 Phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2<br>
PF00367 phosphotransferase system, EIIB<br>
PF02378 Phosphotransferase system, EIIC <br>Pfam-B_639 (release 5.2). The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. The sugar-specific permease of the PTS consists of three domains (IIA, IIB and IIC). The IIC domain catalyses the transfer of a phosphoryl group from IIB to the sugar substrate.. 
PF02255 PTS system, Lactose/Cellobiose specific IIA subunit<br>Pfam-B_3710 (release 5.2). The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a  variety of metabolic and transcriptional processes.  The lactose/cellobiose-specific family are one of four structurally and functionally distinct group IIA PTS system enzymes. This family of proteins normally function as a homotrimer, stabilised by a centrally located metal ion  . Separation into subunits is thought to occur after phosphorylation. . 
PF03714 Bacterial pullanase-associated domain<br>Domain is found in pullanase - carbohydrate de-branching - proteins. It is found both to the N or the C terminii of of the alpha-amylase active site region. This domain contains several conserved aromatic residues that are suggestive of a carbohydrate binding function.. 
PF03829 PTS system glucitol/sorbitol-specific IIA component<br>TIGRFAMs, Griffiths-Jones SR. 
PF03830 PTS system sorbose subfamily IIB component<br>TIGRFAMs, Griffiths-Jones SR. 
PF03209 PUCC protein<br>Pfam-B_2839 (release 6.5). This protein is required for high-level transcription of the PUC operon.. 
PF00806 Pumilio-family RNA binding repeat<br>Puf repeats (aka PUM-HD, Pumilio homology domain) are necessary and sufficient for sequence specific RNA binding in fly Pumilio and worm FBF-1 and FBF-2. Both proteins function as translational repressors in early embryonic development by binding sequences in the 3' UTR of target mRNAs (e.g. the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA).  Other proteins that contain Puf domains are also plausible RNA binding proteins. Swiss:P47135, for instance, appears to also contain a single RRM domain by HMM analysis. Puf domains usually occur as a tandem repeat of 8 domains. The Pfam model does not necessarily recognise all 8 repeats in all sequences; some sequences appear to have 5 or 6 repeats on initial analysis, but further analysis suggests the presence of additional divergent repeats.  Structures of PUF repeat proteins show they consist of a two helix structure [3,4].. 
PF02245 Methylpurine-DNA glycosylase (MPG)<br>Pfam-B_3352 (release 5.2). 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.. 
PF04845 PurA ssDNA and RNA-binding protein<br>Pfam-B_4535 (release 7.6). This family represents most of the length of the protein.. 
PF02700 UPF0062; PurC;<br>Phosphoribosylformylglycinamidine (FGAM) synthase. This family forms a component of the de novo purine biosynthesis pathway. . 
PF00855 PWWP domain<br>The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif  . The domain binds to Histone-4 methylated at lysine-20, H4K20me, suggesting that it is methyl-lysine recognition motif. Removal of two conserved aromatic residues in a hydrophobic cavity created by this domain within the full-length protein, Pdp1, abolishes the interaction o f the protein with H4K20me3. In fission yeast, Set9 is the sole enzyme that catalyses all three states of H4K20me, and Set9-mediated H4K20me is required for efficient recruitment of checkpoint protein Crb2 to sites of DNA damage. The methylation of H4K20 is involved in a diverse array of cellular processes, such as organising higher-order chromatin, maintaining genome stability, and regulating cell-cycle progression  .. 
PF02436 Conserved carboxylase domain<br>Pfam-B_628 (release 5.2). This domain represents a conserved region in pyruvate carboxylase  (PYC), oxaloacetate decarboxylase alpha chain (OADA), and  transcarboxylase 5s subunit. The domain is found adjacent to the  HMGL-like domain (Pfam:PF00682) and often close to the biotin_lipoyl domain (Pfam:PF00364) of biotin requiring enzymes. . 
PF03013 Pyrimidine dimer DNA glycosylase<br>Pfam-B_1388 (release 6.4). Pyrimidine dimer DNA glycosylases excise pyrimidine dimers by hydrolysis of the glycosylic bond of the 5' pyrimidine, followed by the intra-pyrimidine phosphodiester bond. Pyrimidine dimers are the major UV-lesions of DNA.. 
PF01948 Aspartate carbamoyltransferase regulatory chain, allosteric domain<br>The regulatory chain is involved in allosteric regulation of aspartate carbamoyltransferase. The N-terminal domain has ferredoxin-like fold, and provides the  regulatory chain dimerisation interface.. 
PF02748 Aspartate carbamoyltransferase regulatory chain, metal binding domain<br>The regulatory chain is involved in allosteric regulation of aspartate carbamoyltransferase. The C-terminal metal binding domain has a rubredoxin-like fold and  provides the interface with the catalytic chain.. 
PF01243 Pyridoxamine 5'-phosphate oxidase<br>
PF00282 pyridoxal_deC; <br>Pyridoxal-dependent decarboxylase conserved domain. 
PF00719 Inorganic pyrophosphatase<br>Pfam-B_613 (release 2.1). 
PF02547 Queuosine biosynthesis protein<br>Queuosine (Q) biosynthesis protein, or S-adenosylmethionine:tRNA -ribosyltransferase-isomerase, is required for the synthesis of the queuosine precursor (oQ). It catalyses the transfer and isomerisation of the ribose moiety from AdoMet to the 7-aminomethyl group of 7-deazaguanine (preQ1-tRNA) to form epoxyqueuosine (oQ-tRNA).  Q is a hypermodified nucleoside usually found at the first position of the anticodon of asparagine, aspartate, histidine, and tyrosine tRNAs [1,2]. In Streptococcus gordonii , QueA has been shown to play a role in the regulation of arginine deiminase genes  .. 
PF00788 Ras association (RalGDS/AF-6) domain<br>Alignment kindly provided by SMART. RasGTP effectors (in cases of AF6, canoe and RalGDS); putative RasGTP effectors in other cases. Recent evidence (not yet in MEDLINE) shows that some RA domains do NOT bind RasGTP. Predicted structure   similar to that determined  , and that of the RasGTP-binding domain of Raf kinase.. 
PF03528 Rabaptin<br>
PF02144 Repair protein Rad1/Rec1/Rad17<br>
PF03215 Rad17 cell cycle checkpoint protein<br>Pfam-B_2764 (release 6.5). 
PF04824 Conserved region of Rad21 / Rec8 like protein<br>Pfam-B_2686 (release 7.6). This family represents a conserved region found in eukaryotic  cohesins of the Rad21, Rec8 and Scc1 families.  Members of this family  mediate sister chromatid cohesion during mitosis and meiosis, as part of  the cohesin complex  . Cohesion is necessary for homologous recombination (including double-strand break repair) and correct chromatid segregation.  These proteins may also be involved in chromosome condensation.  Dissociation at the metaphase to  anaphase transition causes loss of cohesion and chromatid segregation  .. 
PF04825 N terminus of Rad21 / Rec8 like protein<br>Pfam-B_2686 (release 7.6). This family represents a conserved N-terminal region found in eukaryotic  cohesins of the Rad21, Rec8 and Scc1 families.  Members of this family  mediate sister chromatid cohesion during mitosis and meiosis, as part of  the cohesin complex  . Cohesion is necessary for homologous recombination (including double-strand break repair) and correct chromatid segregation.  These proteins may also be involved in chromosome condensation.  Dissociation at the metaphase to  anaphase transition causes loss of cohesion and chromatid segregation  .. 
PF03835 Rad4 transglutaminase-like domain<br>
PF04098 Rad52/22 family double-strand break repair protein<br>The DNA single-strand annealing proteins (SSAPs), such as RecT, Red-beta, ERF and Rad52, function in RecA-dependent and RecA-independent DNA recombination pathways. This family includes proteins related to Rad52  . These proteins contain two helix-hairpin-helix motifs  .. 
PF04139 Rad9<br>Pfam-B_28077 (release 7.3);. Rad9 is required for transient cell-cycle arrests and transcriptional induction of DNA repair in response to DNA damage.  It contains a Bcl-2 homology domain 3 (BH3)  .. 
PF04002 RadC; DUF2466;<br>RadC-like JAB domain. A family of proteins present widely across the bacteria. This family was named initially with reference to the E. coli radC102 mutation which suggested that RadC was involved in repair of DNA lesions  . However the relevant mutation has subsequently been shown to be in recG, where radC is in fact an allele of recG  . In addition, a personal communication from Claverys, J-P, et al, indicates a total failure of all attempts to characterise a radiation-related function for RadC in Streptococcus pneumoniae, suggesting that it is not involved in repair of DNA lesions, in recombination during transformation, in gene conversion, nor in mismatch repair. Computational analysis, however, provides a possible function. The RadC-like family belong to the JAB superfamily  of metalloproteins  . The domain shows fusions to an N-terminal  Helix-hairpin-Helix (HhH) domain in most instances. Other domain combinations include fusions to the anti-restriction module ArdC, the DinG/RAD3-like superfamily II helicases and the DNAG-like primase. In some bacteria, closely related DinG/Rad3- like superfamily II helicases are fused to a 3'-5' exonuclease in the  same position as the RadC-like JAB domain. These conserved domain  associations lead to the hypothesis that the RadC-like JAB domains  might function as a nuclease  .. 
PF04712 Radial spokehead-like protein<br>Pfam-B_5891 (release 7.5). This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene  .. 
PF03089 Recombination activating protein 2<br>Pfam-B_4702 (release 6.5). 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 by RAG1 and RAG2 in  developing lymphocytes.  Defects in RAG2 in humans are a cause of severe combined immunodeficiency B cell negative and Omenn syndrome.. 
PF04901 Receptor activity modifying family <br>Pfam-B_5615 (release 7.6). The calcitonin-receptor-like receptor can function as either a calcitonin-gene-related peptide or an adrenomedullin receptor. The receptors function is modified by receptor-activity-modifying  protein or RAMP. RAMPs are single-transmembrane-domain proteins  . . 
PF00638 RanBP1 domain<br>
PF03085 Rhoptry-associated protein 1 (RAP-1)<br>Pfam-B_1750 (release 6.4). Members of this family are found in Babesia species. Though not in this Pfam family, rhoptry-associated proteins are also found in Plasmodium falciparum. Indeed, animal infection with Babesia may produce a pattern similar to human malaria  . Rhoptry organelles form part of the apical complex in apicomplexan parasites. Rhoptry-associated proteins are antigenic, and generate partially protective immune responses in infected mammals. Thus RAPs are among the targeted vaccine antigens for babesial (and malarial) parasites. However, RAP-1 proteins are encoded by by a multigene family; thus RAP-1 proteins are polymorphic, with  B and T cell epitopes that are conserved among strains, but not across species [1,2,5]. Antibodies to Babesia RAP-1 may also be helpful in the  serological detection of Babesia infections  .. 
PF00071 ras; <br>Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head.  See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices  .. 
PF00616 GTPase-activator protein for Ras-like GTPase<br>Ponting C, Schultz J, Bork P. All alpha-helical domain that accelerates the GTPase activity of Ras, thereby "switching" it into an "off" position.. 
PF03836 RasGAP C-terminus<br>
PF00617 RasGEF domain<br>Ponting C, Schultz J, Bork P. Guanine nucleotide exchange factor for Ras-like small GTPases.. 
PF00618 RasGEFN; <br>RasGEF N-terminal motif. Ponting C, Schultz J, Bork P. A subset of guanine nucleotide exchange factor for Ras-like small  GTPases appear to possess this motif/domain N-terminal to the RasGef (Cdc25-like) domain.. 
PF01858 Retinoblastoma-associated protein A domain<br>This domain has the cyclin fold   as predicted  .. 
PF01857 Retinoblastoma-associated protein B domain<br>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 groove on the B domain  .  The B domain has a cyclin fold. . 
PF02196 Raf-like Ras-binding domain<br>Alignment kindly provided by SMART. 
PF02033 Ribosome-binding factor A<br>
PF05025 RbsD / FucU transport protein family<br>Pfam-B_4828 (release 7.6). The Escherichia coli high-affinity ribose-transport system consists of six proteins encoded by the rbs operon (rbsD, rbsA, rbsC, rbsB, rbsK and rbsR). Of the six components, RbsD is the only one whose function is unknown although it is thought that it somehow plays a critical role in  PtsG-mediated ribose transport  . This family also includes FucU a protein from the fucose biosynthesis operon that is presumably also involved in fucose transport by similarity to RbsD.. 
PF02341 RbcX protein<br>Pfam-B_948 (release 5.2). The RBCX protein has been identified as having a possible  chaperone-like function  .  The rbcX gene is juxtaposed to and cotranscribed with rbcL and rbcS encoding RuBisCO in Anabaena sp. CA  . RbcX has been shown to possess a chaperone-like  function assisting correct folding of RuBisCO in E. coli expression  studies and is needed for RuBisCO to reach its maximal activity  .. 
PF00415 Regulator of chromosome condensation (RCC1) repeat<br>
PF04381 Putative exonuclease, RdgC<br>Members of the RdgC family may have exonuclease activity. RdgC is required for efficient pilin variation in Neisseria gonorrhoeae, suggesting that it may be involved in recombination reactions  . In Escherichia coli, RdgC is required for growth in recombination-deficient exonuclease-depleted strains.  Under these conditions, RdgC may act as an exonuclease to remove collapsed replication forks, in the absence of the normal repair mechanisms  .. 
PF05183 RNA dependent RNA polymerase<br>Pfam-B_2226 (release 7.7). This family of proteins are eukaryotic RNA dependent RNA polymerases. These proteins are involved in post transcriptional gene silencing where they are thought to amplify dsRNA templates.. 
PF00154 recA; <br>recA bacterial DNA recombination protein. RecA is a DNA-dependent ATPase and functions in DNA repair systems.  RecA protein catalyses an ATP-dependent DNA strand-exchange reaction that is the central step in the repair of dsDNA breaks by homologous recombination  .. 
PF02565 RecO;<br>Recombination protein O C terminal. Recombination protein O (RecO) is involved in DNA repair and Pfam:PF00470 pathway recombination.. 
PF02132 RecR protein<br>
PF03837 RecT family<br>The DNA single-strand annealing proteins (SSAPs), such as RecT, Red-beta, ERF and Rad52, function in RecA-dependent and RecA-independent DNA recombination pathways. This family includes proteins related to RecT  .. 
PF03838 Recombination protein U<br>TIGRFAMs, Griffiths-Jones SR. 
PF02631 RecX family<br>RecX is a putative bacterial regulatory protein  . The gene  encoding RecX is found downstream of recA, and is thought to interact with the RecA protein.   . 
PF02014 Reeler domain<br>
PF04221 DUF415; <br>RelE and RelB form a toxin-antitoxin system. RelE represses translation, probably through binding ribosomes ( ,  ). RelB stably binds RelE, presumably deactivating it.. 
PF03763 Remorin, C-terminal region <br>Pfam-B_1798 (release 7.0). Remorins are plant-specific plasma membrane-associated proteins. In tobacco remorin co-purifies with lipid rafts. Most remorins have a variable, proline-rich C-half and a more conserved N-half that is predicted to form coiled coils. Consistent with this, circular dichroism studies have demonstrated that much of the protein is alpha-helical. Remorins exist in plasma membrane preparations as oligomeric structures and form filaments in vitro. The proteins can bind polyanions including the extracellular matrix component oligogalacturonic acid (OGA). In vitro, remorin in plasma membrane preparations is phosphorylated (principally on threonine residues) in the presence of OGA and thus co-purifies with a protein kinases(s). The biological functions of remorins are unknown but roles as components of the membrane/cytoskeleton are possible.. 
PF03766 Remorin, N-terminal region <br>Pfam-B_1798 (release 7.0). Remorins are plant-specific plasma membrane-associated proteins. In tobacco remorin co-purifies with lipid rafts. Most remorins have a variable, proline-rich C-half and a more conserved N-half that is predicted to form coiled coils. Consistent with this, circular dichroism studies have demonstrated that much of the protein is alpha-helical. Remorins exist in plasma membrane preparations as oligomeric structures and form filaments in vitro. The proteins can bind polyanions including the extracellular matrix component oligogalacturonic acid (OGA). In vitro, remorin in plasma membrane preparations is phosphorylated (principally on threonine residues) in the presence of OGA and thus co-purifies with a protein kinases(s). The biological functions of remorins are unknown but roles as components of the membrane/cytoskeleton are possible. . 
PF01244 Renal_dipeptase; <br>Membrane dipeptidase (Peptidase family M19). 
PF01664 Reovirus viral attachment protein sigma 1<br>Pfam-B_1003 (release 4.1). This family consists of the reovirus sigma 1 hemagglutinin, cell attachment protein. This glycoprotein is a minor capsid  protein and also determines the serotype-specific humoral immune response. Sigma 1 consist of a fibrous tail and a globular head. The head has important roles in the cell attachment function of sigma 1  and determinant of the type-specific humoral immune response  . Reovirus is part of the orthoreovirus group of retroviruses with, a dsRNA genome. Also present in this family is bacteriophage SF6  Lysozyme Swiss:P21270.. 
PF04582 Reovirus sigma C capsid protein<br>Pfam-B_2922 (release 7.5). 
PF00979 Reovirus outer capsid protein, Sigma 3<br>Pfam-B_1049 (release 3.0). Sigma 3 is the major outer capsid protein of reovirus  . Sigma 3 is encoded by genome segment 4.  Sigma 3 binds to  double stranded RNA and associates with polypeptide u1 and  its cleavage product u1C to form the outer shell of the virion. The Sigma 3 protein possesses a zinc-finger motif and an RNA-binding domain in the N and C termini respectively. This protein is also thought to play a role in pathogenesis.  . 
PF01446 Rep; <br>Prodom_1565 (release 99.1). Replication proteins (rep) are involved in plasmid replication. The Rep protein binds to the plasmid DNA and nicks it at the double strand origin  (dso) of replication.  The 3'-hydroxyl end created is extended by the host DNA replicase, and the 5' end is displaced during synthesis. At the end of one replication round, Rep introduces a second single stranded break at the dso and ligates the ssDNA extremities generating one double-stranded plasmid and one circular ssDNA form. Complementary strand synthesis of the circular ssDNA is usually initiated at the single-stranded origin by the host RNA polymerase  .. 
PF04057 Rep-A_protein_1;<br>Replication factor-A protein 1, N-terminal domain. Pfam-B_6000 (release 7.3);. 
PF01719 Plasmid replication protein<br>Pfam-B_1901 (release 4.1). This family consists of various bacterial plasmid replication (Rep)  proteins. These proteins are essential for replication of plasmids, the Rep proteins are topoisomerases that nick the positive stand at the plus origin of replication and also at the single-strand conversion sequence  .. 
PF01051 RepB_protein; <br>Initiator Replication protein. Pfam-B_313 (release 3.0). This protein is an initiator of plasmid replication. RepB possesses nicking-closing (topoisomerase I) like activity. It is also able to perform a strand transfer reaction on ssDNA that contains its target. This family also includes RepA which is an E.coli protein involved in plasmid replication. The RepA protein binds to DNA repeats that flank the repA gene [3,4].. 
PF02486 Replication initiation factor<br>Pfam-B_2164 (release 5.4) & COG2946. Plasmid replication is initiated by the replication initiation factor (REP). This family represents a probable topoisomerase that makes a  sequence-specific single-stranded nick in the plasmid DNA at the origin of replication. Human proteins also belong to this family,  including myelin transcription factor 2 (Swiss:O15150) and cerebrin-50 (Swiss:Q16301)  .. 
PF04796 Plasmid encoded RepA protein<br>Pfam-B_6223 (release 7.5). Family of plasmid encoded proteins involved in plasmid replication.  The role of RepA in the replication process is not clearly understood  .. 
PF01421 Reprolysin (M12B) family zinc metalloprotease <br>The members of this family are enzymes that cleave peptides. These proteases require zinc for catalysis.  Members of this family are also known as adamalysins. Most members of this family are snake venom endopeptidases, but there are also some mammalian proteins such as Swiss:P78325, and fertilin Swiss:Q28472.  Fertilin and closely related proteins appear to not have some active site residues and may not be active enzymes.. 
PF05140 ResB-like family <br>Pfam-B_1866 (release 7.7). This family includes both ResB and cytochrome c biogenesis  proteins [1,2].  Mutations in ResB indicate that they are  essential for growth  .  ResB is predicted to be a  transmembrane protein  .. 
PF04851 Type III restriction enzyme, res subunit<br>Pfam-B_4631 (release 7.6). 
PF00239 recombinase; resolvase; <br>Resolvase, N terminal domain. Prosite & Pfam-B_3830 (Release 7.5). The N-terminal domain of the resolvase family (this family) contains the active site and the dimer interface.  The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase - see Pfam:PF02796.. 
PF00072 response_reg; <br>Response regulator receiver domain. This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain.. 
PF02813 Retroviral M domain<br>Retroviruses contain a small protein, MA (matrix), which forms a protein lining immediately beneath the phospholipid membrane of the mature virus particle. MA is located in the N-terminal region of the Gag precursor polyprotein. The N-terminal segment of MA proteins directs the Gag protein to the plasma membrane where budding takes place, and has been called the M domain.  This domain forms an alpha helical bundle structure.. 
PF00424 REV protein (anti-repression trans-activator protein)<br>Pfam-B_169 (release 1.0). 
PF00472 RF-1 domain<br>This domain is found in peptide chain release factors such as RF-1 (Swiss:P07011) and RF-2 (Swiss:P07012), and a number of smaller proteins of unknown function such as Swiss:P40711. This domain contains the peptidyl-tRNA hydrolase activity. The domain contains a highly conserved motif GGQ, where the glutamine is thought to coordinate the water that mediates the hydrolysis.. 
PF04506 Rft protein<br>
PF04589 RFX1 transcription activation region      <br>The RFX family is a family of winged-helix DNA binding proteins.  RFX1 is a regulatory factor essential for expression of MHC class II genes. This region is to found N terminal to the RFX DNA binding region  (Pfam:PF02257) in some mammalian RFX proteins, and is thought to activate  transcription when associated with DNA.  Deletion analysis has identified  the region 233-351 in human RFX1 (Swiss:P22670) as being required for  maximal activation  .. 
PF02257 RFX DNA-binding domain<br>Pfam-B_3682 (release 5.2). RFX is a regulatory factor which binds to the X box of MHC class II genes and is essential for their expression. The DNA-binding domain of RFX is the central domain of the protein and binds ssDNA as either a monomer or homodimer  . It recognize X-boxes (DNA of the sequence 5'-GTNRCC(0-3N)RGYAAC-3', where N is any nucleotide, R is a purine and Y is a pyrimidine) using a highly conserved 76-residue DNA-binding domain (DBD)  .. 
PF03214 Reversibly glycosylated polypeptide<br>Pfam-B_2662 (release 6.5). 
PF05045 Rhamnan synthesis protein F<br>Pfam-B_5448 (release 7.7). This family consists of a group of proteins which are related to the Streptococcus rhamnose-glucose polysaccharide assembly protein (RgpF). Rhamnan backbones are found in several O polysaccharides of phytopathogenic bacteria and are regarded as pathogenic factors  .. 
PF00615 Regulator of G protein signaling domain<br>Ponting C, Schultz J, Bork P. RGS family members are GTPase-activating proteins for heterotrimeric G-protein alpha-subunits.. 
PF00974 Rhabd_glycop;<br>Rhabdovirus spike glycoprotein. Pfam-B_167 (release 3.0). Frequently abbreviated to G protein.  The glycoprotein spike is made up of a trimer of G proteins. Channel formed by glycoprotein spike is thought to function in a similar manner to Influenza virus M2 protein channel, thus allowing a signal to pass across the viral membrane to signal for viral uncoating.. 
PF03342 Rhabdovirus M1 matrix protein (M1 polymerase-associated protein)<br>Pfam-B_3629 (release 6.5). 
PF04785 Rhabdovirus matrix protein M2<br>Pfam-B_2486 (release 7.6). M protein is involved in condensing and targeting the ribonucleoprotein (RNP) coil to the plasma membrane.  M interacts specifically with the transmembrane spike protein (G) is important for the incorporation of G  protein into budding virions  .. 
PF03397 Rhabdovirus matrix protein<br>Pfam-B_3980 (release 6.6). 
PF00945 Rhabd_nucleocap;<br>Rhabdovirus nucleocapsid protein. Pfam-B_477 (release 3.0). The Nucleocapsid (N) Protein is said to have a "tight" structure. The carboxyl end of the N-terminal domain possesses an RNA binding domain. Sequence alignments show 2 regions of reasonable conservation,  approx. 64-103 and 201-329  .  A whole functional protein is required  for encapsidation to take place  .. 
PF03216 Rhabdovirus nucleoprotein<br>Pfam-B_2146 (release 6.5). 
PF02484 Rhabd_NV; <br>Rhabdovirus Non-virion protein. Pfam-B_2189 (release 5.4). 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  .. 
PF00554 Rel homology domain (RHD)<br>Proteins containing the Rel homology domain (RHD) are eukaryotic transcription factors. The RHD is composed of two structural domains. This is the N-terminal domain that is similar to that found in P53. The C-terminal domain has an immunoglobulin-like fold (See Pfam:PF01833) that binds to DNA.. 
PF02115 RHO protein GDP dissociation inhibitor<br>
PF00581 Rhodanese-like domain<br>MRC-LMB Genome group. 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.. 
PF00620 RhoGAP domain<br>Ponting C, Schultz J, Bork P. GTPase activator proteins towards Rho/Rac/Cdc42-like small GTPases.. 
PF00621 RhoGEF domain<br>Alignment kindly provided by SMART. Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases Also called Dbl-homologous (DH) domain. It appears that Pfam:PF00169 domains invariably occur C-terminal to RhoGEF/DH domains.. 
PF03527 RHS protein<br>
PF00073 rhv; <br>picornavirus capsid protein. Overington and HMM_iterative_training. CAUTION: This alignment is very weak.  It can not be generated by clustalw. If a representative set is used for a seed, many so-called members are not recognised.  The family should probably be split up into sub-families. Capsid proteins of picornaviruses. Picornaviruses are non-enveloped plus-strand ssRNA animal viruses with icosahedral capsids. They include rhinovirus (common cold) and poliovirus. Common structure is an 8-stranded beta sandwich. Variations (one or two extra strands) occur.. 
PF02267 ADP-ribosyl cyclase<br>Pfam-B_3719 (release 5.2). ADP-ribosyl cyclase EC:3.2.2.5 (also know as cyclic ADP-ribose  hydrolase or CD38) synthesises cyclic-ADP ribose, a second messenger for glucose-induced insulin secretion.. 
PF01872 RibD C-terminal domain<br>Enright A & Pfam-B_6425 (Release 8.0). The function of this domain is not known, but it is thought to be involved in riboflavin biosynthesis. This domain is found in the C terminus of RibD/RibG Swiss:P25539, in combination with Pfam:PF00383, as well as in isolation in some archaebacterial proteins Swiss:P95872.  This family appears to be related to Pfam:PF00186.. 
PF05062 RICH domain<br>Pfam-B_277 (release 7.7). This presumed domain is about 85 residues in length and very rich in charged residues, hence the name RICH (Rich In CHarged residues). It is found in secreted proteins such as PspC Swiss:Q9KK19, SpsA Swiss:O33742 and IgA FC receptor Swiss:P27951 from Streptococcus agalactiae. This domain could be involved in bacterial adherence or cell wall binding.. 
PF01042 DUF10;UPF0076; ribonuc_L-PSP; <br>Endoribonuclease L-PSP. Pfam-B_797 (release 3.0). Endoribonuclease active on single-stranded mRNA.  Inhibits protein synthesis by cleavage of mRNA  .  Previously thought to inhibit protein synthesis initiation  . This protein may also be involved in the regulation of purine biosynthesis  . YjgF (renamed RidA) family members are enamine/imine deaminases. They hydrolyze reactive intermediates released by PLP-dependent enzymes, including threonine dehydratase  . YjgF also prevents inhibition of transaminase B (IlvE) in Salmonella  .. 
PF00317 ribonucleo_red; ribonuc_red_lg; <br>Ribonucleotide reductase, all-alpha domain. 
PF02867 ribonuc_red_lgC; <br>Ribonucleotide reductase, barrel domain. 
PF00268 ribonuc_red; ribonuc_red_sm; <br>Ribonucleotide reductase, small chain. 
PF00545 ribonuclease; <br>This enzyme hydrolyses RNA and oligoribonucleotides.. 
PF03631 Ribonuclease_BN;<br>Virulence factor BrkB. Pfam-B_4424 (release 7.0). This family acts as a virulence factor. In Bordetella pertussis, Swiss:Q45339 is essential for resistance to complement-dependent killing by serum  . This family was originally predicted to be ribonuclease BN  , but this prediction has since been shown to be incorrect  .. 
PF00825 Ribonuclease P<br>Pfam-B_1558 (release 2.1). 
PF00445 ribonuclease_T2; <br>Ribonuclease T2 family. 
PF00687 L1; <br>Ribosomal protein L1p/L10e family. Pfam-B_115 (release 2.1). This family includes prokaryotic L1 and eukaryotic L10.. 
PF00466 L10;<br>Ribosomal protein L10. 
PF00298 L11; <br>Ribosomal protein L11, RNA binding domain. 
PF03946 L11; <br>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.. 
PF00542 L12; <br>Ribosomal protein L7/L12 C-terminal domain. 
PF00572 L13;<br>Ribosomal protein L13. 
PF01294 Ribosomal protein L13e<br>
PF00238 L14; <br>Ribosomal protein L14p/L23e. 
PF01929 Ribosomal protein L14<br>This family includes the eukaryotic ribosomal protein L14.. 
PF00827 Ribosomal L15<br>Pfam-B_1567 (release 2.1). 
PF00252 L16;<br>Ribosomal protein L16p/L10e. 
PF01196 Ribosomal protein L17<br>
PF00861 Ribosomal L18p/L5e family<br>Pfam-B_495 (release 3.0) & Pfam-B_741 (release 4.1). This family includes ribosomal proteins from the large subunit. This family includes L18 from bacteria and L5 from eukaryotes. It has been shown that the amino terminal 93 amino acids of Swiss:P09895 are necessary and sufficient to bind 5S rRNA in vitro  . Suggesting that the entire family has a function in rRNA binding.. 
PF01245 Ribosomal protein L19<br>
PF01280 Ribosomal protein L19e<br>
PF00181 L2;<br>Ribosomal Proteins L2, RNA binding domain. 
PF00453 L20;<br>Ribosomal protein L20. 
PF01157 L21e;<br>Ribosomal protein L21e. 
PF00829 Ribosomal prokaryotic L21 protein<br>Pfam-B_1297 (release 2.1). 
PF00237 L22; <br>Ribosomal protein L22p/L17e. This family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes.. 
PF01776 Ribosomal L22e protein family<br>
PF00276 L23;<br>Ribosomal protein L23. 
PF03939 Ribosomal protein L23, N-terminal domain<br>The N-terminal domain appears to be specific to the  eukaryotic ribosomal proteins L25, L23, and L23a.. 
PF01246 Ribosomal protein L24e<br>
PF01386 Ribosomal L25p family<br>Ribosomal protein L25 is an RNA binding protein, that binds 5S rRNA. This family includes Ctc from B. subtilis Swiss:P14194, which is induced by stress.. 
PF01016 Ribosomal L27 protein<br>Pfam-B_1340 (release 3.0). 
PF01777 Ribosomal L27e protein family<br>The N-terminal region of the eukaryotic ribosomal L27 has the KOW motif.  C-terminal region is represented by this family. . 
PF00830 Ribosomal L28 family<br>Pfam-B_1561 (release 2.1). The ribosomal 28 family includes L28 proteins from bacteria and chloroplasts.  The L24 protein from yeast Swiss:P36525 also contains a region of similarity to prokaryotic L28 proteins.  L24 from yeast is also found in the large ribosomal subunit. 
PF01778 Ribosomal L28e protein family<br>
PF00831 Ribosomal L29 protein<br>Pfam-B_1296 (release 2.1). 
PF01779 Ribosomal L29e protein family<br>
PF03947 L2;<br>Ribosomal Proteins L2, C-terminal domain. 
PF00297 L3;<br>Ribosomal protein L3. 
PF00327 L30;<br>Ribosomal protein L30p/L7e. This family includes prokaryotic L30 and eukaryotic L7.. 
PF01197 Ribosomal protein L31<br>
PF01198 Ribosomal protein L31e<br>
PF01655 Ribosomal protein L32<br>Pfam-B_1346 (release 4.1). This family includes ribosomal protein L32 from eukaryotes and archaebacteria.. 
PF01783 Ribosomal L32p protein family<br>
PF00471 L33; <br>Ribosomal protein L33. 
PF00468 L34; <br>Ribosomal protein L34. 
PF01199 Ribosomal protein L34e<br>
PF01247 Ribosomal protein L35Ae<br>
PF01632 Ribosomal protein L35<br>Pfam-B_1156 (release 4.1). 
PF00444 L36;<br>Ribosomal protein L36. 
PF01158 L36e; <br>Ribosomal protein L36e. 
PF01780 Ribosomal L37ae protein family<br>This ribosomal protein is found in archaebacteria and eukaryotes. It contains four conserved cysteine residues that may bind to zinc.. 
PF01781 Ribosomal L38e protein family<br>
PF00832 Ribosomal L39 protein<br>Pfam-B_1293 (release 2.1). 
PF00573 L1e; Ribosomal_L1e;<br>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  .. 
PF01020 Ribosomal L40e family<br>Pfam-B_884 (release 3.0). Bovine L40 has been identified as a secondary RNA binding protein  . L40 is fused to a ubiquitin protein  .. 
PF05162 Ribosomal protein L41<br>
PF00935 L44;<br>Ribosomal protein L44. Pfam-B_1065 (release 3.0). 
PF00281 L5;<br>Ribosomal protein L5. 
PF00673 L5_C;<br>ribosomal L5P family C-terminus. Pfam-B_69 (release 2.1). This region is found associated with Pfam:PF00281.. 
PF01159 L6e; <br>Ribosomal protein L6e . 
PF03868 Ribosomal protein L6, N-terminal domain<br>
PF01248 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family<br>This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD118  .. 
PF03948 Ribosomal protein L9, C-terminal domain<br>
PF01281 Ribosomal_L9; <br>Ribosomal protein L9, N-terminal domain. 
PF00338 S10;<br>Ribosomal protein S10p/S20e. This family includes small ribosomal subunit S10 from prokaryotes and S20 from eukaryotes.. 
PF00411 S11;<br>Ribosomal protein S11. 
PF00164 S12; Ribosomal_S12;<br>Ribosomal protein S12/S23. This protein is known as S12 in bacteria and archaea and S23 in eukaryotes.. 
PF00416 S13;<br>Ribosomal protein S13/S18. This family includes ribosomal protein S13 from prokaryotes and S18 from eukaryotes.. 
PF00253 S14;<br>Ribosomal protein S14p/S29e. This family includes both ribosomal S14 from prokaryotes and S29 from eukaryotes.. 
PF00312 S15; <br>Ribosomal protein S15. 
PF00886 Ribosomal protein S16<br>Pfam-B_1025 (release 3.0). 
PF00366 S17; <br>Ribosomal protein S17. 
PF00833 Ribosomal_S17; <br>Pfam-B_1566 (release 2.1). 
PF01084 S18;<br>Ribosomal protein S18. Pfam-B_712 (release 3.0). 
PF00203 S19;<br>Ribosomal protein S19. 
PF01090 S19e; <br>Ribosomal protein S19e. 
PF00318 S2;<br>Ribosomal protein S2. 
PF01649 Ribosomal protein S20<br>Pfam-B_1685 (release 4.1). Bacterial ribosomal protein S20 interacts with 16S rRNA  .. 
PF01165 S21; <br>Ribosomal protein S21. 
PF01249 Ribosomal protein S21e <br>
PF01282 Ribosomal protein S24e<br>
PF03297 S25 ribosomal protein<br>Pfam-B_4038 (release 6.5). 
PF01283 Ribosomal protein S26e<br>
PF01599 Ribosomal protein S27a<br>Pfam-B_638 (release 4.1). This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesised as a C-terminal extension of ubiquitin (CEP). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis  .  The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins  .. 
PF01667 Ribosomal protein S27<br>Pfam-B_1929 (release 4.1). 
PF01200 Ribosomal protein S28e<br>
PF04758 Ribosomal protein S30<br>
PF00189 S3_C;<br>Ribosomal protein S3, C-terminal domain. This family contains a central domain Pfam:PF00013, hence the amino and carboxyl terminal domains are stored separately. This is a minimal carboxyl-terminal domain.\.   Some are much longer.. 
PF01015 Ribosomal S3Ae family<br>Pfam-B_1334 (release 3.0). 
PF00163 S4;<br>Ribosomal protein S4/S9 N-terminal domain. This family includes small ribosomal subunit S9 from prokaryotes and S16 from metazoans.  This domain is predicted to bind to ribosomal RNA  .  This domain is composed of four helices in the known structure.  However the domain is discontinuous in sequence and the alignment for this family contains only the first three helices.. 
PF00900 Ribosomal family S4e<br>Pfam-B_1205 (release 3.0). 
PF00333 S5; <br>Ribosomal protein S5, N-terminal domain. 
PF03719 Ribosomal protein S5, C-terminal domain<br>
PF01250 Ribosomal protein S6<br>
PF01092 S6e; <br>Ribosomal protein S6e. 
PF00177 S7; <br>Ribosomal protein S7p/S5e. This family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes.. 
PF01251 Ribosomal protein S7e<br>
PF00410 S8; <br>Ribosomal protein S8. 
PF00380 S9;<br>Ribosomal protein S9/S16. This family includes small ribosomal subunit S9 from prokaryotes and S16 from eukaryotes.. 
PF00834 Ribulose-phosphate 3 epimerase family<br>Pfam-B_1291 (release 2.1). This enzyme catalyses the conversion of D-ribulose 5-phosphate into D-xylulose 5-phosphate.. 
PF02009 Rifin/stevor family<br>Several multicopy gene families have been described in Plasmodium falciparum, including the stevor family of subtelomeric open reading frames and the rif interspersed repetitive elements. Both families contain three predicted transmembrane segments. It has been proposed that stevor and rif are members of a larger superfamily that code for variant surface antigens  .. 
PF02197 Regulatory subunit of type II PKA R-subunit<br>Alignment kindly provided by SMART. 
PF01782 RimM N-terminal domain<br>The RimM protein is essential for efficient processing of 16S rRNA  . The RimM protein was shown to have affinity for free ribosomal 30S subunits but not for 30S subunits in the 70S ribosomes  .  This N-terminal domain is found associated with a PRC-barrel domain  . . 
PF00848 Ring hydroxylating alpha subunit (catalytic domain)<br>Pfam-B_407 (release 3.0). This family is the catalytic domain of aromatic-ring- hydroxylating dioxygenase systems.  The active site contains a non-heme ferrous ion coordinated by three ligands.. 
PF00161 Ribosome inactivating protein<br>
PF04957 Ribosome modulation factor<br>This protein associates with 70s ribosomes and converts them to a dimeric form (100S ribosomes) which appear during the transition from the exponential growth phase to the stationary phase of Escherichia coli cells.. 
PF04321 RmlD substrate binding domain<br>L-rhamnose is a saccharide required for the virulence of some bacteria. Its precursor, dTDP-L-rhamnose, is synthesised by four different enzymes the final one of which is RmlD.\.    The RmlD substrate binding domain is responsible for binding a sugar nucleotide [1,2].. 
PF03035 Calicivirus putative RNA polymerase/capsid protein<br>Pfam-B_1282 (release 6.4). 
PF00680 RNA dependent RNA polymerase<br>Pfam-B_32 (release 2.1). 
PF00978 RNA_dep_RNApol2; <br>RNA dependent RNA polymerase. Pfam-B_13 (release 3.0). This family may represent an RNA dependent RNA polymerase. The family also contains the following proteins:     2A protein from bromoviruses     putative RNA dependent RNA polymerase from tobamoviruses     Non structural polyprotein from togaviruses. 
PF00910 RNA helicase<br>Pfam-B_11 (release 3.0). 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.. 
PF00940 DNA-dependent RNA polymerase<br>Pfam-B_1108 (release 3.0). This is a family of single chain RNA polymerases.. 
PF03118 Bacterial RNA polymerase, alpha chain C terminal domain<br>Pfam-B_172 (release 3.0). The alpha subunit of RNA polymerase consists of two independently folded domains, referred to as amino-terminal and carboxyl terminal domains.  The amino terminal domain is involved in the interaction with the other subunits of the RNA polymerase.  The carboxyl-terminal domain interacts with the DNA and activators.  The amino acid sequence of the alpha subunit is conserved in prokaryotic and chloroplast RNA  polymerases.  There are three regions of particularly strong  conservation, two in the amino-terminal and one in the carboxyl- terminal  .. 
PF05066 RNA_pol_delta;<br>HB1, ASXL, restriction endonuclease HTH domain. A winged helix-turn-helix domain present in the plant HB1, vertebrate ASXL, the H. pylori restriction endonuclease HpyAIII(HgrA), the RNA polymerase delta subunit(RpoE) of Gram positive bacteria and several restriction endonucleases  . The domain is distinguished by the presence of a conserved one-turn helix between helix-3 and the preceding conserved turn. Its diverse architectures in eukaryotic species with extensive gene body methylation is suggestive of a chromatin function. The genetic interaction of the HARE-HTH containing ASXL with the methyl cytosine hydroxylating Tet2 protein is suggestive of a role for the domain in discriminating sequences with DNA modifications such as  hmC  . Bacterial versions include fusions to diverse restriction  endonucleases, and a DNA glycosylase where it may play a similar  role in detecting modified DNA. Certain bacterial version of the  HARE-HTH domain show fusions to the helix-hairpin-helix domain of  the RNA polymerase alpha subunit and the HTH domains found in  regions 3 and 4 of the sigma factors  . These versions are  predicted to function as a novel inhibitor of the binding of RNA  polymerase to transcription start sites, similar to the Bacillus delta protein [2,3].. 
PF04090 RNA polymerase I specific initiation factor<br>Pfam-B_43469 (release 7.3);. 
PF01193 RNA polymerase Rpb3/Rpb11 dimerisation domain<br>Pfam-B_172 (release 3.0). The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer.  The dimerisation domain of the alpha subunit/Rpb3 is interrupted by an insert domain (Pfam:PF01000).  Some of the alpha subunits also contain iron-sulphur binding domains (Pfam:PF00037).  Rpb11 is found as a continuous domain.  Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp.. 
PF02150 RNA polymerases M/15 Kd subunit<br>
PF01194 RNA polymerases N / 8 kDa subunit<br>
PF04990 RNA polymerase Rpb1, domain 7<br>Pfam-B_288 (release 4.2). 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 domain, domain 7, represents a mobile module of the RNA polymerase. Domain 7 forms a substantial interaction with the lobe domain of Rpb2 (Pfam:PF04561) [1,2].. 
PF04563 RNA polymerase beta subunit<br>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 domain forms one of the two distinctive lobes of the Rpb2 structure.  This domain is also known as the protrusion domain  .  The other lobe (Pfam:PF04561) is nested within this domain.. 
PF04561 RNA polymerase Rpb2, domain 2<br>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). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure.  This domain is also known as the lobe domain  .  DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble  .  Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).. 
PF04566 RNA polymerase Rpb2, domain 4<br>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). Domain 4, is also known as the external 2 domain  .. 
PF01191 RNA_pol_H; <br>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.. 
PF03871 RNA polymerase Rpb5, N-terminal domain<br>Rpb5 has a bipartite structure which includes a eukaryote-specific  N-terminal domain and a C-terminal domain resembling the archaeal RNAP  subunit H [1,2].  The N-terminal domain is involved in DNA binding and is  part of the jaw module in the RNA pol II structure  .  This module is important for positioning the downstream DNA.. 
PF01192 RNA polymerase Rpb6 <br>Rpb6 is an essential subunit in the eukaryotic polymerases Pol I, II and III. This family also contains the bacterial equivalent to Rpb6, the omega subunit.  Rpb6 and omega are structurally conserved and both function in polymerase assembly  .. 
PF03876 RNA_pol_Rpb7_N;<br>SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397. Rpb7 bind to Rpb4 to form a heterodimer.  This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation .  This family includes the homologs from RNA polymerase I and III.  In RNA polymerase I, Rpa43 is at least one of the subunits contacted by the transcription factor TIF-IA  . The N terminus of Rpb7p/Rpc25p/MJ0397 has a SHS2 domain that is involved in protein-protein interaction  .. 
PF03870 RNA polymerase Rpb8<br>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.. 
PF05158 RNA polymerase Rpc34 subunit<br>Subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of yeast RNA Pol III is part of a subcomplex of  three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and is  therefore participates in Pol III recruitment  . . 
PF05132 RNA polymerase III RPC4<br>Pfam-B_18856 (release 7.7). Specific subunit for Pol III, the tRNA specific polymerase.. 
PF03431 RNA replicase, beta-chain <br>Pfam-B_4422 (release 6.6). This family is of Leviviridae RNA replicases.  The replicase is also known as RNA dependent RNA polymerase.    . 
PF01876 DUF53; <br>This protein is part of the RNase P complex that is involved in tRNA maturation  .. 
PF01900 DUF69; <br>tRNA processing enzyme ribonuclease P (RNase P) consists of an RNA molecule associated with at least eight protein subunits, hPop1, Rpp14, Rpp20, Rpp25, Rpp29, Rpp30, Rpp38, and Rpp40  . This protein is known as Pop5 in eukaryotes.. 
PF00074 rnaseA; <br>Pancreatic ribonuclease. Overington and HMM_iterative_training. Ribonucleases. Members include pancreatic RNAase A and angiogenins. Structure is an alpha+beta fold -- long curved beta sheet and three helices.. 
PF00075 rnaseH; RnaseH;<br>Swissprot; SCOP and HMM_iterative_training. 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.. 
PF00773 RNB domain<br>Pfam-B_1009 (release 2.1). This domain is the catalytic domain of ribonuclease II  .. 
PF02508 Rnf-Nqr subunit, membrane protein<br>Pfam-B_1638 (release 5.4). This is a family of integral membrane proteins including  Rhodobacter-specific nitrogen fixation (rnf) proteins RnfA and RnfE   and Na+-translocating NADH:ubiquinone oxidoreductase  (Na+-NQR) subunits NqrD and NqrE. . 
PF03259 Roadblock/LC7 domain<br>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 dynein. It is proposed that roadblock/LC7 family members may modulate specific dynein functions  . This family also includes Swiss:Q9Y2Q5 Golgi-associated MP1 adapter protein and MglB from Myxococcus xanthus Swiss:Q50883, a protein involved in gliding motility  . However the family also includes members from non-motile bacteria such as Streptomyces coelicolor, suggesting that the protein may play a structural or regulatory role.. 
PF00480 ROK family<br>
PF02027 Glyco_hydro_41; <br>RolB/RolC glucosidase family. This family of proteins includes RolB and RolC.  RolC  releases cytokinins from glucoside conjugates  . Whereas RolB hydrolyses indole glucosides  .. 
PF01815 Rop protein<br>
PF00980 Rotavirus major capsid protein VP6<br>Pfam-B_1047 (release 3.0). 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 possesses the ability to interact with VP2, VP4 and VP7 [1,2].. 
PF01525 Rotavirus NS26<br>Pfam-B_762 (release 4.0). Gene 11 product is a non-structural phosphoprotein designated as NS26  .. 
PF02509 Rotavirus non-structural protein 35<br>Pfam-B_1677 (release 5.4). Rotavirus non-structural protein 35 (NS35) is a basic protein which possesses RNA-binding activity and is essential for genome replication  .. 
PF00981 Rotavirus RNA-binding Protein 53 (NS53)<br>Pfam-B_1048 (release 3.0). This protein is also known as NSP1. NS53 is encoded by gene 5.  It is made in low levels in the infected cells and is a component of early replication.  The protein is known to accumulate on the cytoskeleton of the infected cell.  NS53 is an RNA binding protein that contains a characteristic cysteine rich region  .. 
PF04866 Rotavirus non-structural protein 6<br>Pfam-B_4831 (release 7.6). 
PF01665 Rotavirus non-structural protein NSP3<br>Pfam-B_1010 (release 4.1). 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; a basic region which binds ssRNA, a region containing heptapeptide repeats mediating oligomerisation and a leucine zipper motif  . NSP3 may play a central role in replication and assembly of genomic RNA structures  . Rotaviruses have a dsRNA genome and are a major cause cause of acute gastroenteritis in the young of many species  . The rotavirus non-structural protein NSP3 is a sequence-specific RNA binding protein that binds the nonpolyadenylated 3' end of the rotavirus mRNAs. NSP3 also interacts with the translation initiation factor eIF4GI and competes with the poly(A) binding protein  .. 
PF01452 Rotavirus non structural protein<br>Prodom_2202 (release 99.1). This protein has been called NSP4, NSP5, NS28, and NCVP5. The final steps in the assembly of rotavirus occur in the lumen of the endoplasmic reticulum (ER). Targeting of the immature inner capsid particle (ICP) to this compartment is mediated by the cytoplasmic tail of NSP4, located in the ER membrane.. 
PF05087 Rotavirus VP2 protein<br>Pfam-B_6280 (release 7.7). Rotavirus particles consist of three concentric proteinaceous capsid layers. The innermost capsid (core) is made of VP2. The genomic RNA and the two minor proteins VP1 and VP3 are encapsidated within this layer  . The N-terminus of rotavirus VP2 is necessary for the encapsidation of VP1 and VP3  .. 
PF00639 PPIC-type PPIASE domain<br>Rotamases increase the rate of protein folding by catalysing the interconversion of cis-proline and trans-proline.. 
PF03428 Replication protein C N-terminal domain<br>Pfam-B_4463 (release 6.6). Replication protein C is involved in the early stages of viral DNA replication.. 
PF03055 Retinal pigment epithelial membrane protein<br>Pfam-B_947 (release 6.4). 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 related neoxanthin cleavage enzyme in plants and lignostilbene-alpha,beta-dioxygenase in bacteria.. 
PF02318 RPH3A_effector; RPH3A_effect_N;<br>FYVE-type zinc finger. This FYVE-type zinc finger is found at the N-terminus of effector proteins including rabphilin-3A   and regulating synaptic membrane exocytosis protein 2  .. 
PF04390 DUF532; RplB;<br>Lipopolysaccharide-assembly. LptE (formerly known as RplB) is involved in lipopolysaccharide-assembly on the outer membrane of Gram-negative organisms. The lipopolysaccharide component of the outer bacterial membrane is transported from its source of origin to the outer membrane by a set of proteins constituting a transport machinery that is made up of LptA, LptB, LptC, LptD, LptE. LptD appears to be anchored in the outer membrane, and LptE forms a complex with it. This part of the machinery complex is involved in the assembly of lipopolysaccharide in the outer leaflet of the outer membrane  .. 
PF04032 DUF363; <br>RNAse P Rpr2/Rpp21/SNM1 subunit domain. This family contains a ribonuclease P subunit of humans and yeast.  Other members of the family include the probable archaeal homologues. This family includes SNM1  .  It is a subunit of RNase MRP (mitochondrial RNA processing), a ribonucleoprotein endoribonuclease that has roles in both mitochondrial DNA replication and nuclear 5.8S rRNA processing.  SNM1 is an RNA binding protein that binds the MRP RNA specifically  . This subunit possibly binds the precursor tRNA  .. 
PF01765 Ribosome recycling factor<br>Pfam-B_949 (release 4.2). The ribosome recycling factor (RRF / ribosome release factor) dissociates the ribosome from the mRNA after termination of translation, and is  essential bacterial growth  . Thus ribosomes are "recycled" and ready for another round of protein synthesis.. 
PF00076 rrm; <br>RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain). Published_alignment . The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins.  The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins (Swiss:P05455) have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins (Swiss:P05455) are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.. 
PF00398 Ribosomal RNA adenine dimethylase<br>
PF04353 Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ<br>This family includes bacterial transcriptional regulators that are thought to act through an interaction with the conserved region 4 of the sigma(70) subunit of RNA polymerase. The Pseudomonas aeruginosa homologue, AlgQ, positively regulates virulence gene expression and is associated with the mucoid phenotype observed in Pseudomonas aeruginosa isolates from cystic fibrosis patients.. 
PF03873 Anti sigma-E protein RseA, C-terminal domain<br>Sigma-E is important for the induction of proteins  involved in heat shock response. RseA binds sigma-E via its N-terminal domain, sequestering sigma-E and  preventing transcription from heat-shock promoters  . The C-terminal domain is located in the periplasm, and may interact with other protein that signal  periplasmic stress.. 
PF03872 Anti sigma-E protein RseA, N-terminal domain<br>Sigma-E is important for the induction of proteins  involved in heat shock response. RseA binds sigma-E via its N-terminal domain, sequestering sigma-E and  preventing transcription from heat-shock promoters  . The C-terminal domain is located in the periplasm, and may interact with other protein that signal  periplasmic stress.. 
PF04246 Positive regulator of sigma(E), RseC/MucC<br>This bacterial family of integral membrane proteins represents a positive regulator of the sigma(E) transcription factor, namely RseC/MucC. The sigma(E) transcription factor is up-regulated by cell envelope protein misfolding, and regulates the expression of genes that are collectively termed ECF (devoted to Extra-Cellular Functions)  . In Pseudomonas aeruginosa, de-repression of sigma(E) is associated with the alginate-overproducing phenotype characteristic of chronic respiratory tract colonisation in cystic fibrosis patients. The mechanism by which RseC/MucC positively regulates the sigma(E) transcription factor is unknown. RseC is also thought to have a role in thiamine biosynthesis in Salmonella typhimurium  . In addition, this family also includes an N-terminal part of RnfF, a Rhodobacter capsulatus protein, of unknown function, that is essential for nitrogen fixation. This protein also contains an ApbE domain Pfam:PF02424, which is itself involved in thiamine biosynthesis. . 
PF03113 Respiratory synctial virus non-structural protein NS2<br>Pfam-B_2717 (release 6.5). The molecular structure and function of the NS2 protein is not known. However, mutants lacking the NS2 grow at slower rates when compared to the wild-type. Nevertheless, NS2 is not essential for viral replication  .. 
PF04479 RTA1 like protein<br>This family is comprised of fungal proteins with multiple transmembrane regions.  RTA1 (Swiss:P53047) is involved in resistance to 7-aminocholesterol  , while RTM1 (Swiss:P40113) confers resistance to an an unknown toxic chemical in molasses  .  These proteins may bind to the toxic substance, and thus prevent toxicity.  They are not thought to be involved in the efflux of xenobiotics  .. 
PF02334 Replication terminator protein<br>Pfam-B_12997 (release 5.2). The bacterial replication terminator protein (RTP) plays a role in  the termination of DNA replication by impeding replication fork movement. Two RTP dimers bind to the two inverted repeat regions at the termination site.. 
PF02382 RTX N-terminal domain<br>Pfam-B_833 (release 5.2). The RTX family of bacterial toxins are a group of cytolysins and cytotoxins. This Pfam family represents the N-terminal domain which is found in association with a glycine-rich repeat domain and  hemolysinCabind Pfam:PF00353.. 
PF00016 Ribulose bisphosphate carboxylase large chain, catalytic domain<br>The C-terminal domain of RuBisCO large chain is the catalytic domain adopting a TIM barrel fold.. 
PF02788 Ribulose bisphosphate carboxylase large chain, N-terminal domain<br>The N-terminal domain of RuBisCO large chain adopts a  ferredoxin-like fold.. 
PF00101 Ribulose bisphosphate carboxylase, small chain<br>
PF02915 Rubrerythrin<br>This domain has a ferritin-like fold.. 
PF01330 RuvA; <br>RuvA N terminal domain. The N terminal domain of RuvA has an OB-fold structure. This domain forms the RuvA tetramer contacts  .. 
PF02075 Crossover junction endodeoxyribonuclease RuvC<br>
PF02042 RWP-RK domain<br>Pfam-B_9740 (Release 5.1). This domain is named RWP-RK after a conserved motif at the C terminus of the presumed domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development  .. 
PF01365 RIH domain<br>Ponting CP (EMBL alignments). 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 Swiss:P21817 and the inositol-1,4,5- trisphosphate receptor Swiss:Q14571. This domain may form a binding site for IP3  .. 
PF02026 RyR domain<br>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.. 
PF00575 S1 RNA binding domain<br>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.. 
PF00438 S-AdoMet_synt; <br>S-adenosylmethionine synthetase, N-terminal domain. The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold.. 
PF02772 S-AdoMet_syntD2; <br>S-adenosylmethionine synthetase, central domain. The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold.. 
PF02773 S-AdoMet_syntD3; <br>S-adenosylmethionine synthetase, C-terminal domain. The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold.. 
PF02574 Homocysteine S-methyltransferase<br>This is a family of related homocysteine S-methyltransferases enzymes: 5-methyltetrahydrofolate--homocysteine S-methyltransferases  also known EC:2.1.1.13,  ; Betaine--homocysteine S-methyltransferase  (vitamin B12 dependent), EC:2.1.1.5,  ; and Homocysteine  S-methyltransferase, EC:2.1.1.10,  .. 
PF04689 DNA binding protein S1FA<br>S1FA is a DNA-binding protein found in plants that specifically  recognises the negative promoter element S1F  .. 
PF05116 Sucrose-6F-phosphate phosphohydrolase<br>Pfam-B_6442 (release 7.7). This family consists of Sucrose-6F-phosphate phosphohydrolase proteins found in plants and cyanobacteria. Sucrose-6(F)-phosphate phosphohydrolase catalyses the final step in the pathway of sucrose biosynthesis  .. 
PF01023 S_100_domain; <br>S-100/ICaBP type calcium binding domain. Pfam-B_242 (release 3.0). The S-100 domain is a subfamily of the EF-hand calcium binding proteins.. 
PF05124 S-layer like family, C-terminal region <br>TIGRFAMs (release 2.0);. 
PF05123 S-layer like family, N-terminal region <br>TIGRFAMs (release 2.0);. 
PF00954 S-locus glycoprotein family<br>Pfam-B_357 (release 3.0). In Brassicaceae, self-incompatible plants have a self/non-self  recognition system.  This is sporophytically controlled by  multiple alleles at a single locus (S). S-locus glycoproteins, as well as S-receptor kinases, are in linkage with the S-alleles  .. 
PF00526 S_mold_repeat; <br>Dictyostelium (slime mold) repeat. Pfam-B_96 (release 1.0). 
PF00277 SAA_proteins; <br>Serum amyloid A protein. 
PF04455 LOR/SDH bifunctional enzyme conserved region <br>Lysine-oxoglutarate reductase/Saccharopine dehydrogenase (LOR/SDH) is a bifunctional enzyme.  This conserved region is commonly found immediately  N-terminal to Saccharop_dh (Pfam:PF03435) in eukaryotes [1,2].. 
PF04092 SRS domain<br>Pfam-B_1675 (release 7.3). Toxoplasma gondii is a persistent protozoan parasite capable of infecting almost any warm-blooded vertebrate. The surface of Toxoplasma is coated with a family of developmentally regulated glycosylphosphatidylinositol (GPI)-linked proteins (SRSs), of which SAG1 is the prototypic member. SRS proteins mediate attachment to host cells and interface with the host immune response to regulate the virulence of the parasite. SAG1 is composed of two disulphide linked SRS domains. These have 6 cysteines that form 1-6,2-5 and 3-4 pairings. The structure of the immunodominant SAG1 antigen reveals a homodimeric configuration  . The SRS domain is found in a single copy in the SAG2 proteins. This family of surface antigens are found in other apicomplexans.. 
PF01259 SAICAR synthetase<br>Pfam-B_1426 (release 3.0). Also known as Phosphoribosylaminoimidazole-succinocarboxamide  synthase.. 
PF03534 Sal_SpvB; <br>Salmonella virulence plasmid 65kDa B protein. 
PF03538 Sal_vir_VRP1; <br>Salmonella virulence plasmid 28.1kDa A protein. 
PF01758 Sodium Bile acid symporter family<br>Pfam-B_697 (release 4.2). This family consists of Na+/bile acid co-transporters. These transmembrane proteins function in the liver in the uptake of bile acids from portal blood plasma a process mediated by the co-transport of Na+  . Also in the family is ARC3 from S. cerevisiae Swiss:Q06598 this is a putative transmembrane protein involved in resistance to arsenic compounds  .. 
PF03536 Sal_vir_VRP3; <br>Salmonella virulence-associated 28kDa protein. 
PF01536 Adenosylmethionine decarboxylase<br>Pfam-B_600 (release 4.0). This is a family of S-adenosylmethionine decarboxylase (SAMDC) proenzymes.  In the biosynthesis of polyamines SAMDC produces decarboxylated S-adenosylmethionine, which serves as the aminopropyl moiety necessary for spermidine and spermine biosynthesis from putrescine  . The Pfam alignment contains both the alpha and beta chains that are cleaved to form the active enzyme.. 
PF02199 SAPA; <br>Saposin A-type domain. Alignment kindly provided by SMART. 
PF03058 Sar8.2 family<br>Pfam-B_2148 (release 6.4). Members of this family are found in Solanaceae plants, a taxonomic group (family) that includes pepper and tobacco plant species.  Synthesis of these proteins is induced by tobacco mosaic virus (TMV) and salicylic acid  ; indeed they are thought to be involved in the development of systemic acquired resistance (SAR) after an initial hypersensitive response to microbial infection [1,2]. SAR is characterised by long-lasting resistance to infection by a wide range of pathogens, extending to plant tissues distant from the initial infection site  .. 
PF04790 sarcoglycan; <br>Sarcoglycan complex subunit protein. Pfam-B_6135 (release 7.5). The dystrophin glycoprotein complex (DGC) is a membrane-spanning complex that links the interior cytoskeleton to the extracellular matrix in muscle.\.   The sarcoglycan complex is a subcomplex within the DGC and is composed of several muscle-specific, transmembrane proteins (alpha-, beta-, gamma-, delta- and zeta-sarcoglycan). The sarcoglycans are asparagine-linked glycosylated proteins with single transmembrane domains.  This family contains beta, gamma and delta members [1,2].. 
PF03343 SART-1 family<br>Mifsud W, Mistry J, Wood V. Pfam-B_3690 (release 6.5). SART-1 is a protein involved in cell cycle arrest and pre-mRNA splicing   .  It has been shown to be a component of U4/U6 x U5 tri-snRNP complex in human, Schizosaccharomyces pombe and Saccharomyces cerevisiae  .  SART-1 is a known tumour antigen in a range of cancers recognised by T cells  .. 
PF00269 Small, acid-soluble spore proteins, alpha/beta type<br>
PF04259 Small, acid-soluble spore protein, gamma-type <br>TIGRFAMs (release 2.0);. The SASP family is a family of small, glutamine and asparagine-rich  peptides that store amino acids in the spores of Bacillus subtilis  and related bacteria. . 
PF03898 Satellite_CP; <br>Satellite tobacco necrosis virus coat protein. 
PF03110 SBP domain<br>Pfam-B_737 (release 6.5). SBP domains (for SQUAMOSA-pROMOTER BINDING PROTEIN) are found in plant proteins.  It is a sequence specific DNA-binding domain  . Members of family probably function as transcription factors involved in the control of early flower development  . The domain contains 10 conserved cysteine and histidine residues that probably are zinc ligands.. 
PF00496 Bacterial extracellular solute-binding proteins, family 5 Middle<br>The borders of this family are based on the PDBSum definitions of the domain edges for Swiss:P06202.. 
PF03480 Bacterial extracellular solute-binding protein, family 7<br>Pfam-B_808 (release 7.0). This family of proteins is involved in binding extracellular solutes for transport across the bacterial cytoplasmic membrane. This family includes Swiss:P37735, a C4-dicarboxylate-binding protein   and the sialic acid-binding protein SiaP. The structure of the SiaP receptor has revealed an overall topology similar to ATP binding cassette ESR (extracytoplasmic solute receptors) proteins  .  Upon binding of sialic acid, SiaP undergoes domain closure about a hinge region and kinking of an alpha-helix hinge component  .. 
PF01297 Lipoprotein_4; SBP_bac_9;<br>Periplasmic solute binding protein family. Pfam-B_1416 (release 3.0). This family includes periplasmic solute binding proteins such as TroA that interacts with an ATP-binding cassette transport system in Treponema pallidum.. 
PF04405 Domain of Unknown function (DUF542)  <br>This domain is always found in conjunction with the HHE domain (Pfam:PF03794) at the  N-terminus.. 
PF02667 Short chain fatty acid transporter<br>This family consists of two sequences annotated as short chain fatty acid transporters, however, there are no references giving details of experimental characterisation of this function.. 
PF04486 SchA/CurD like domain<br>Members of this family have only been identified in species of the Streptomyces genus.  Two family members are known to be part of gene clusters involved in the synthesis of polyketide-based spore pigments, homologous to clusters involved in the synthesis of polyketide antibiotics.  The function of this protein is unknown, but it has been speculated to contain a NAD(P) binding site  . Many of these proteins contain two copies of this presumed domain.. 
PF02630 SCO1/SenC<br>This family is involved in  biogenesis of respiratory and  photosynthetic systems. SCO1 (Swiss:P23833) is required for a  post-translational step in the accumulation of subunits COXI and COXII of cytochrome c oxidase  . SenC (Swiss:Q52720) is required for optimal  cytochrome c oxidase activity and maximal induction of genes encoding the light-harvesting and reaction centre complexes of R. capsulatus  .  . 
PF02036 SCP-2 sterol transfer family<br>Pfam-B_1050 (Release 5.1). This domain is involved in binding sterols. It is found in the SCP2 protein Swiss:P22307, as well as the C terminus of Swiss:P51659 the enzyme estradiol 17 beta-dehydrogenase EC:1.1.1.62. The UNC-24 protein Swiss:Q17372 contains an SPFH domain Pfam:PF01145  .  . 
PF00375 Sodium:dicarboxylate symporter family<br>
PF02982 Scytalone_DH; <br>Scytalone dehydratase. Scytalone dehydratases are structurally related to the NTF2 family (see Pfam:PF02136).. 
PF03313 Serine dehydratase alpha chain<br>L-serine dehydratase (EC:4.2.1.13) is a found as a heterodimer of alpha and beta chain or as a fusion of the two chains in a single protein. This enzyme catalyses the deamination of serine to form pyruvate. This enzyme is part of the gluconeogenesis pathway.. 
PF03315 Serine dehydratase beta chain<br>L-serine dehydratase (EC:4.2.1.13) is a found as a heterodimer of alpha and beta chain or as a fusion of the two chains in a single protein. This enzyme catalyses the deamination of serine to form pyruvate. This enzyme is part of the gluconeogenesis pathway.. 
PF01127 Succinate dehydrogenase/Fumarate reductase transmembrane subunit<br>Prosite & Structural domain. This family includes a transmembrane protein from both the Succinate dehydrogenase and Fumarate reductase complexes.. 
PF02810 SEC-C motif<br>The SEC-C motif found in the C-terminus of the SecA protein, in the middle of some SWI2 ATPases and also solo in several proteins. The motif is predicted to chelate zinc with the  CXC and C[HC] pairs that constitute the most conserved feature of the motif. It is predicted to be a potential nucleic acid binding domain.. 
PF00995 Sec1 family<br>Pfam-B_530 (release 3.0). 
PF03908 Sec20<br>Wood V, Griffiths-Jones SR. Sec20 is a membrane glycoprotein associated with secretory pathway.. 
PF03911 Sec61beta family<br>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. It consists of a single putative transmembrane helix, preceded by a short stretch containing various charged residues; this arrangement may help determine orientation in the cell membrane  .. 
PF03839 Translocation protein Sec62<br>TIGRFAMs, Griffiths-Jones SR. 
PF01369 Sec7 domain<br>Pfam-B_1629 (release 3.0). The Sec7 domain is a guanine-nucleotide-exchange-factor (GEF) for the Pfam:PF00025 family  .. 
PF01043 SecA_protein; SecA;<br>SecA preprotein cross-linking domain. Pfam-B_507 (release 3.0). The SecA ATPase is involved in the insertion and retraction of preproteins through the plasma membrane.  This domain has been found to cross-link to preproteins, thought to  indicate a role in  preprotein binding.  The pre-protein cross-linking domain is comprised of two sub domains that are inserted within the ATPase domain  .  . 
PF02556 Preprotein translocase subunit SecB<br>This family consists of preprotein translocase subunit SecB. SecB is required for the normal export of envelope proteins out of the  cell cytoplasm  .. 
PF02355 Protein export membrane protein<br>Pfam-B_844 (release 5.2). This family consists of various prokaryotic SecD and SecF protein export membrane proteins. This SecD and SecF proteins are part of the multimeric protein export complex comprising SecA, D, E, F, G, Y, and YajC  . SecD and SecF are required to maintain a proton motive force  .. 
PF00584 SecE/Sec61-gamma subunits of protein translocation complex<br>SecE is part of the SecYEG complex in bacteria which  translocates proteins from the cytoplasm. In eukaryotes the complex, made from Sec61-gamma and Sec61-alpha  translocates protein from the cytoplasm to the ER.  Archaea have a similar complex.. 
PF03840 Preprotein translocase SecG subunit<br>TIGRFAMs, Griffiths-Jones SR. 
PF04856 Securin sister-chromatid separation inhibitor<br>Pfam-B_4643 (release 7.6). Securin is also known as pituitary tumour-transforming gene product. Over-expression of securin is associated with a number of tumours, and it has been proposed that this may be due to erroneous chromatid separation leading to chromosome gain or loss  .. 
PF00344 secY;<br>
PF04628 Sedlin, N-terminal conserved region<br>Pfam-B_5308 (release 7.5). Mutations in this protein are associated with the X-linked spondyloepiphyseal dysplasia tarda syndrome (OMIM:313400)  . This family represents an N-terminal conserved region.. 
PF00477 seed_protein; <br>Small hydrophilic plant seed protein. 
PF03841 L-seryl-tRNA selenium transferase<br>TIGRFAMs, Griffiths-Jones SR. 
PF04593 Selenoprotein P, C terminal region<br>SelP is the only known eukaryotic selenoprotein that contains multiple selenocysteine (Sec) residues, and accounts for more than 50% of the selenium content of rat and human plasma  . It is thought to be glycosylated  . SelP may have antioxidant properties.  It can attach to epithelial cells, and may protect vascular endothelial cells against peroxynitrite toxicity  . The high selenium content of SelP suggests that it may be involved in selenium intercellular transport or storage  . The promoter structure of bovine SelP suggest that it may be involved in countering heavy metal intoxication, and may also have a developmental function  . The N terminal region always contains one Sec residue, and this is separated from the C terminal region (9-16 sec residues) by a histidine-rich sequence  .  The large number of Sec residues in the C-terminal portion of SelP suggest CC that it may be involved in selenium transport or storage. However, it is also possible that this region has a redox function  .. 
PF04592 Selenoprotein P, N terminal region<br>SelP is the only known eukaryotic selenoprotein that contains multiple selenocysteine (Sec) residues, and accounts for more than 50% of the selenium content of rat and human plasma  .  It is thought to be glycosylated  .  SelP may have antioxidant properties.  It can attach to epithelial cells, and may protect vascular endothelial cells against peroxynitrite toxicity  . The high selenium content of SelP suggests that it may be involved in selenium intercellular transport or storage  . The promoter structure of bovine SelP suggest that it may be involved in countering heavy metal intoxication, and may also have a developmental function  . The N-terminal region of SelP can exist independently of the C terminal region.  Zebrafish selenoprotein Pb (Swiss:Q98SV0) lacks the C terminal Sec-rich region, and a protein encoded by the rat SelP gene and lacking this region has also been reported  . N-terminal region contains a conserved SecxxCys motif, which is similar to the CysxxCys found in thioredoxins.  It is speculated that the N terminal region may adopt a thioredoxin fold and catalyse redox reactions  . The N-terminal region also contains a His-rich region, which is thought to mediate heparin binding.  Binding to heparan proteoglycans could account for the membrane binding properties of SelP  .  The function of the bacterial members of this family is uncharcterised.. 
PF01641 DUF25;<br>Pfam-B_1539 (release 4.1). Methionine sulfoxide reduction is an important process, by which cells regulate biological processes and cope with oxidative stress. MsrA, a protein involved in the reduction of methionine sulfoxides in proteins, has been known for four decades and has been extensively characterised with respect to structure and function. However, recent studies revealed that MsrA is only specific for methionine-S-sulfoxides. Because oxidised methionines occur in a mixture of R and S isomers in vivo, it was unclear how stereo-specific MsrA could be responsible for the reduction of all protein methionine sulfoxides. It appears that a second methionine sulfoxide reductase, SelR , evolved that is specific for methionine-R-sulfoxides, the activity that is different but complementary to that of MsrA. Thus, these proteins, working together, could reduce both stereoisomers of methionine sulfoxide. This domain is found both in SelR proteins and fused with the peptide methionine sulfoxide reductase enzymatic domain Pfam:PF01625. The domain has two conserved cysteine and histidines. The domain binds both selenium and zinc  . The final cysteine is found to be replaced by the rare amino acid selenocysteine in some members of the family  . This family has methionine-R-sulfoxide reductase activity  .. 
PF01403 Sema domain<br>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 Swiss:P08581 the hepatocyte growth factor receptor and Swiss:P51805. 
PF01118 Semialdehyde dehydrogenase, NAD binding domain<br>Pfam-B_1079 (release 3.0). This Pfam entry contains the following members: N-acetyl-glutamine semialdehyde dehydrogenase (AgrC) Aspartate-semialdehyde dehydrogenase. 
PF02774 Semialdehyde dehydrogenase, dimerisation domain<br>Pfam-B_1079 (release 3.0). This Pfam entry contains the following members: N-acetyl-glutamine semialdehyde dehydrogenase (AgrC) Aspartate-semialdehyde dehydrogenase. 
PF03925 SeqA protein<br>The binding of SeqA protein to hemimethylated GATC sequences is important in the negative modulation of chromosomal initiation at oriC, and in the formation of SeqA foci necessary for Escherichia coli chromosome segregation  . SeqA tetramers are able to aggregate or multimerise in a reversible, concentration-dependent manner  . Apart from its function in the control of DNA replication, SeqA may also be a specific transcription factor  .. 
PF04360 Serglycin <br>Serglycin is the most prevalent proteoglycan produced in haemopoietic cells. Serglycin is a proteinase resistant secretory granule  proteoglycan  .. 
PF00450 serine_carbpept; <br>Serine carboxypeptidase. 
PF00079 serpin; <br>Serpin (serine protease inhibitor). Overington and HMM_iterative_training. Structure is a multi-domain fold containing a bundle of helices and a beta sandwich.. 
PF02403 Seryl-tRNA synthetase N-terminal domain<br>Pfam-B_518 (release 5.4). This domain is found associated with the Pfam tRNA synthetase class II domain (Pfam:PF00587) and represents the N-terminal domain of seryl-tRNA synthetase.. 
PF01445 Viral small hydrophobic protein<br>Prodom_1504 (release 99.1). The SH (small hydrophobic) protein is a membrane protein of uncertain function  .. 
PF00017 SH2 domain<br>Swissprot_feature_table. 
PF00018 SH3;<br>SH3 (Src homology 3) domains are often indicative of a protein involved in  signal transduction related to cytoskeletal organisation. First described in the Src cytoplasmic tyrosine kinase Swiss:P12931. The structure is a partly opened beta barrel.. 
PF04908 SH3-binding, glutamic acid-rich protein<br>Pfam-B_6650 (release 7.6). 
PF03579 Small hydrophobic protein<br>Pfam-B_1121 (release 7.0). The small hydrophobic integral membrane protein, SH (previously designated 1A) is found to have a variety of glycosylated forms [1,2]. This protein is a component of the mature virion  .   . 
PF01488 Shikimate / quinate 5-dehydrogenase<br>Pfam-B_336 (release 4.0). This family contains both shikimate and quinate dehydrogenases. Shikimate 5-dehydrogenase catalyses the conversion of  shikimate to 5-dehydroshikimate. This reaction is part of  the shikimate pathway which is involved in the biosynthesis of aromatic amino acids. Quinate 5-dehydrogenase catalyses the conversion of  quinate to 5-dehydroquinate. This reaction is part of the quinate pathway where quinic acid is exploited as a source of carbon in prokaryotes and microbial eukaryotes. Both the shikimate and quinate pathways share two common pathway metabolites 3-dehydroquinate and dehydroshikimate.. 
PF00464 Serine hydroxymethyltransferase<br>
PF04917 Bacterial shufflon protein, N-terminal constant region<br>Pfam-B_6667 (release 7.6). This family represents the high-similarity N-terminal 'constant region' shared by shufflon proteins.. 
PF02973 sialidase_N; <br>Sialidase, N-terminal domain. 
PF03482 sic; <br>Pfam-B_5 (Release 7.0). 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  .. 
PF00158 sigma54;<br>Sigma-54 interaction domain. 
PF00309 sigma54_AID; <br>Sigma-54 factor, Activator interacting domain (AID) . The sigma-54 holoenzyme is an enhancer dependent  form of the RNA polymerase.  The AID is necessary for activator interaction  .  In addition, the AID also inhibits  transcription initiation in the sigma-54 holoenzyme prior to  interaction with the activator  .. 
PF04963 sigma54_CBD; <br>Sigma-54 factor, core binding domain. This domain makes a direct interaction with the core RNA polymerase, to form an enhancer dependent holoenzyme  . The centre of this domain contains a very weak similarity to a helix-turn-helix motif which may represent the other DNA binding domain.. 
PF04552 sigma54_DBD; <br>Sigma-54, DNA binding domain. This DNA binding domain is based on peptide fragmentation data.  This domain is proximal to DNA in the promoter/holoenzyme complex.  Furthermore this region contains a putative helix-turn-helix motif.  At the C-terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins  . . 
PF04546 sigma70_ner; <br>Sigma-70, non-essential region. The domain is found in the primary vegetative sigma factor.  The function of this domain is unclear and can be removed without loss of function.. 
PF03979 sigma70_r1_1; <br>Sigma-70 factor, region 1.1. Region 1.1 modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [1,2]. Region 1.1 is also involved in promoter binding  . 
PF00140 sigma70_r1_2; <br>Sigma-70 factor, region 1.2. 
PF04539 sigma70_r3; <br>Region 3 forms a discrete compact three helical domain within the sigma-factor.  Region is not normally involved in the recognition of promoter DNA, but as some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role.  Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme  .. 
PF03084 Reoviral Sigma1/Sigma2 family<br>Pfam-B_1759 (release 6.4). Reoviruses are double-stranded RNA viruses. They lack a membrane envelope and their capsid is organised in two concentric icosahedral layers: an inner core and an outer capsid layer. The sigma1 protein is found in the outer capsid, and the sigma2 protein is found in the core. There are four other kinds of protein (besides sigma2) in the core, termed lambda 1-3, mu2. Interactions between sigma2 and lambda 1 and lambda 3 are thought to initiate core formation, followed by mu2 and lambda2  . Sigma1 is a trimeric protein, and is positioned at the 12 vertices of the icosahedral outer capsid layer. Its N-terminal fibrous tail, arranged as a triple coiled coil, anchors it in the virion, and a C-terminal globular head interacts with the cellular receptor  .  These two parts form by separate trimerisation events. The N-terminal fibrous tail forms on the polysome, without the involvement of ATP or chaperones. The post- translational assembly of the C-terminal globular head involves the chaperone activity of Hsp90, which is associated with  phosphorylation of Hsp90 during the process  . Sigma1 protein acts as a cell attachment protein, and determines viral virulence, pathways of spread, and tropism. Junctional adhesion molecule has been identified as a receptor for sigma1  . In type 3  reoviruses, a small region, predicted to form a beta sheet, in the N-terminal tail was found to bind target cell surface sialic acid (i.e. sialic acid acts as a co-receptor) and promote apoptosis  . The sigma1 protein also binds to the lambda2 core protein  .. 
PF02454 Sigma 1s protein<br>Pfam-B_2133 (release 5.4). The reoviral gene S1 encodes for haemagglutinin (sigma 1 protein), an outer capsid protein and a major factor in determining virus-host cell interactions. Sigma 1s is one of two translation products of the S1 gene.. 
PF03842 Silicon transporter<br>TIGRFAMs, Griffiths-Jones SR. 
PF04801 Sin-like protein conserved region<br>Pfam-B_6302 (release 7.5). Family of higher eukaryotic proteins.  SIN was identified as a protein that interacts specifically with SXL (sex lethal) in a yeast two-hybrid assay.\.   The interaction is mediated by one of the SXL RNA binding domains  .. 
PF04954 Siderophore-interacting protein<br>
PF02146 Sir2 family<br>This region is characteristic of Silent information regulator 2 (Sir2) proteins, or sirtuins. These are protein deacetylases that depend on nicotine adenine dinucleotide (NAD). They are found in many subcellular locations, including the nucleus, cytoplasm and mitochondria. Eukaryotic forms play in important role in the regulation of transcriptional repression. Moreover, they are involved in microtubule organisation and DNA damage repair processes  .. 
PF04247 Invasion gene expression up-regulator, SirB<br>SirB up-regulates Salmonella typhimurium invasion gene transcription. It is, however, not essential for the expression of these genes. Its function is unknown  .. 
PF01380 SIS domain<br>SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars.  Presumably the SIS domains bind to the end-product of the pathway.. 
PF05185 Skb1; <br>PRMT5 arginine-N-methyltransferase. Pfam-B_4050 (release 7.7). The human homologue of yeast Skb1 (Shk1 kinase-binding protein 1) is PRMT5, an arginine-N-methyltransferase   .  These proteins appear to be key mitotic regulators. They play a role in Jak signalling in higher eukaryotes.. 
PF01202 Shikimate kinase<br>
PF02731 SKIP/SNW domain<br>This domain is found in chromatin proteins.. 
PF03217 Bacterial surface layer protein<br>Pfam-B_2530 (release 6.5). 
PF03843 Outer membrane lipoprotein Slp family<br>TIGRFAMs, Griffiths-Jones SR. 
PF01464 Transglycosylase SLT domain<br>Prodom_3175 (release 99.1). This family is distantly related to Pfam:PF00062. Members are found in phages, type II, type III and type IV secretion systems (reviewed in  ).. 
PF02258 Shiga-like toxin beta subunit<br>Pfam-B_3684 (release 5.2). This family represents the B subunit of shiga-like toxin (SLT or verotoxin) produced by some strains of E.coli associated with hemorrhagic colitis and hemolytic uremic syndrome. SLT's are  composed of one enzymatic A subunit and five cell binding B subunits.. 
PF04102 SlyX<br>The SlyX protein has no known function.  It is short less than 80 amino acids and is found close to the slyD gene. The SlyX protein has a conserved PPH(Y/W) motif at its C-terminus. The protein may be a coiled-coil structure.. 
PF02481 SMF; <br>DNA recombination-mediator protein A. Pfam-B_2252 (release 5.4). The SMF family, of DNA processing chain A, dprA, are a group of bacterial proteins. In H. pylori, dprA is required for natural chromosomal and plasmid transformation  . It has now been shown that DprA is found to bind cooperatively to single-stranded DNA (ssDNA) and to interact with RecA. In the process, DprA-RecA-ssDNA filaments are produced and these filaments catalyse the homology-dependent formation of joint molecules. While the E.coli SSB protein limits access of RecA to ssDNA, DprA alleviates this barrier. It is proposed that DprA is a new member of the recombination-mediator protein family, dedicated to natural bacterial transformation  .. 
PF03467 Smg-4/UPF3 family<br>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.. 
PF04927 Seed maturation protein<br>Pfam-B_6221 (release 7.6). Plant seed maturation protein.. 
PF04355 SmpA / OmlA family<br>Lipoprotein Bacterial outer membrane lipoprotein, possibly involved in in maintaining the structural integrity of the cell envelope  .  Lipid attachment site  is a conserved N terminal cysteine residue.  Sometimes found adjacent to  the OmpA domain (Pfam:PF00691).. 
PF01668 SmpB protein<br>Pfam-B_1766 (release 4.1). 
PF01713 Smr domain<br>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 Swiss:P23909 protein in the case of Smr proteins and with the N-terminal MutS related region of MutS2 Swiss:P94545  . This domain exhibits nicking endonuclease activity that might have a role in mismatch repair or genetic recombination. It shows no significant double strand cleavage or exonuclease activity  . The full-length Swiss:Q86UW6 also has the polynucleotide kinase activity.. 
PF00835 SNAP-25 family<br>Pfam-B_1606 (release 2.1). 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  .. 
PF00565 Staphylococcal nuclease homologue<br>Alignment kindly provided by SMART. Present in all three domains of cellular life. Four copies in the transcriptional coactivator p100: these, however, appear to lack the active site residues of Staphylococcal nuclease. Positions 14 (Asp-21), 34 (Arg-35), 39 (Asp-40), 42 (Glu-43) and 110 (Arg-87) [SNase numbering in parentheses] are thought to be involved in substrate-binding and catalysis.. 
PF00209 Sodium:neurotransmitter symporter family<br>
PF00176 SNF2 family N-terminal domain<br>This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1).. 
PF04855 SNF5 / SMARCB1 / INI1<br>Pfam-B_6054 (release 7.6). SNF5 is a component of the yeast SWI/SNF complex, which is an ATP-dependent nucleosome-remodelling complex that regulates the transcription of a subset of yeast genes. SNF5 is a key component of all SWI/SNF-class complexes  characterised so far  .  This family consists of the conserved region of SNF5, including a direct repeat motif.  SNF5 is essential for the assembly promoter targeting and chromatin remodelling activity of the SWI-SNF  complex  . SNF5 is also known as SMARCB1, for SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily b, member 1, and also INI1 for integrase interactor 1. Loss-of function mutations in SNF5 are thought to contribute to oncogenesis in malignant rhabdoid tumours (MRTs)  .. 
PF01174 UPF0030; <br>SNO glutamine amidotransferase family. This family and its amidotransferase domain was first described in  . It is predicted that members of this family are involved in the pyridoxine biosynthetic pathway, based on the proximity and co-regulation of the corresponding genes and physical interaction between the members of Pfam:PF01174 and Pfam:PF01680  .. 
PF00080 sodcu; <br>Copper/zinc superoxide dismutase (SODC). Overington and HMM_iterative_training. superoxide dismutases (SODs) catalyse the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen.  Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding  family is one. Defects in the human SOD1 gene cause familial amyotrophic lateral sclerosis (Lou Gehrig's disease). Structure is an eight-stranded beta sandwich, similar to the immunoglobulin fold.. 
PF00081 sodfe; <br>Iron/manganese superoxide dismutases, alpha-hairpin domain. Eddy SR, Griffiths-Jones SR. Overington and HMM_iterative_training. superoxide dismutases (SODs) catalyse the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen.  Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding  family is one. In humans, there is a cytoplasmic Cu/Zn SOD, and a mitochondrial Mn/Fe SOD. N-terminal domain is a long alpha antiparallel hairpin.  A small fragment of YTRE_LEPBI matches well - sequencing error?. 
PF02777 sodfe_C; <br>Iron/manganese superoxide dismutases, C-terminal domain. Eddy SR, Griffiths-Jones SR. Overington and HMM_iterative_training. superoxide dismutases (SODs) catalyse the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding  family is one. In humans, there is a cytoplasmic Cu/Zn SOD, and a mitochondrial Mn/Fe SOD. C-terminal domain is a mixed alpha/beta fold.. 
PF03002 Somatostatin/Cortistatin family<br>Pfam-B_1891 (release 6.4). 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 somatostatin, induces low-frequency waves in the cerebral cortex and antagonises the effects of acetylcholine on hippocampal and cortical measures of excitability  .. 
PF01680 UPF0019; <br>Pfam-B_2034 (release 4.1). Members of this family are enzymes involved in a new pathway of pyridoxine/pyridoxal 5-phosphate biosynthesis  . This family was formerly known as UPF0019.. 
PF02208 Sorbin homologous domain<br>Alignment kindly provided by SMART. 
PF04203 Sortase family<br>TIGRFAMs (release 2.0);. The founder member of this family is S.aureus sortase,  a transpeptidase that attaches surface proteins by the  threonine of an LPXTG motif to the cell wall  . . 
PF04832 SOUL heme-binding protein<br>Pfam-B_3872 (release 7.6). This family represents a group of putative heme-binding proteins  . Our family includes archaeal and bacterial homologues.. 
PF04267 Sarcosine oxidase, delta subunit family <br>TIGRFAMs (release 2.0);. Sarcosine oxidase is a hetero-tetrameric enzyme that contains both covalently bound FMN and non-covalently bound FAD and NAD(+).  This enzyme catalyses the oxidative demethylation of sarcosine to yield glycine, H2O2, and 5,10-CH2-tetrahydrofolate (H4folate) in a reaction requiring H4folate and O2 [1,2].. 
PF04268 Sarcosine oxidase, gamma subunit family <br>TIGRFAMs (release 2.0);. Sarcosine oxidase is a hetero-tetrameric enzyme that contains both covalently bound FMN and non-covalently bound FAD and NAD(+).  This enzyme catalyses the oxidative demethylation of sarcosine to yield glycine, H2O2, and 5,10-CH2-tetrahydrofolate (H4folate) in a reaction requiring H4folate and O2 [1,2].. 
PF03172 Sp100 domain<br>Pfam-B_3126 (release 6.5). 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 Pfam:PF01342.. 
PF03014 Structural protein 2<br>Pfam-B_1375 (release 6.4). 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.. 
PF02090 Salmonella surface presentation of antigen gene type M protein<br>
PF02510 Surface presentation of antigens protein<br>Pfam-B_1678 (release 5.4). Surface presentation of antigens protein (SPAN), also know as invasion protein invJ, is a Salmonella secretory pathway protein involved in presentation of determinants required for mammalian host cell invasion. . 
PF04573 Signal peptidase subunit<br>Pfam-B_4675 (release 7.5). Translocation of polypeptide chains across the endoplasmic reticulum membrane is triggered by signal sequences. During translocation of the nascent chain through the membrane, the signal sequence of most secretory and membrane proteins is cleaved off. Cleavage occurs by the signal peptidase complex (SPC) which consists of four subunits in yeast and five in mammals.  This family is common to yeast and mammals  [1,2].. 
PF05122 Mobile element transfer protein<br>This proteins are involved in transferring a group of integrating conjugative DNA elements, such as pSAM2 from Streptomyces ambofaciens ( ). Their precise role is not known. . 
PF03771 DUF317; <br>Domain of unknown function (DUF317). This a sequence family found in a set of bacterial proteins with no known function. This domain is currently only found in streptomyces bacteria.\.      Most proteins contain two copies of this domain.. 
PF00435 spectrin; <br>Pfam-B_1 (release 1.0). Spectrin repeat-domains are found in several proteins involved in cytoskeletal structure.  These include spectrin, alpha-actinin and dystrophin.  The sequence repeat used in this family is taken from the structural repeat in reference  . The spectrin domain- repeat forms a three helix bundle. The second helix is interrupted by proline in some sequences. The repeats are defined by a characteristic tryptophan (W) residue at position 17 in helix A and a leucine (L) at 2 residues from the carboxyl end of helix C. Although the domain occurs in ultiple repeats along sequences, the domains are actually stable on their own - ie they act, biophysically, like domains rather than repeats that along function when aggregated.. 
PF01564 Spermine/spermidine synthase<br>Pfam-B_798 (release 4.0). 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.. 
PF02819 spidertoxin; <br>This family of spider neurotoxins are thought to be calcium ion channel inhibitors.. 
PF02513 Spin/Ssty Family<br>Spindlin (Spin) is a novel maternal transcript present in the unfertilised egg and early embryo  . The Y-linked spermiogenesis -specific transcript (Ssty) is also expressed during gametogenesis  and forms part of this Pfam family. Members of this family contain three copies of this 50 residue repeat. The repeat is predicted to contain four beta strands.. 
PF05215 Spiralin<br>Pfam-B_6625 (release 7.7). This family consists of Spiralin proteins found in spiroplasma bacteria. Spiroplasmas are helically shaped pathogenic bacteria related to the  mycoplasmas. The surface of spiroplasma bacteria is crowded with the  membrane-anchored lipoprotein spiralin whose structure and function are  unknown although its cellular function is thought to be a structural and  mechanical one rather than a catalytic one  .. 
PF03533 SPO11 homologue<br>
PF05032 Spo12 family<br>Pfam-B_51047 (release 7.6). This family of proteins includes Spo12 from S. cerevisiae Swiss:P17123. The Spo12 protein plays a regulatory role in two of the most fundamental processes of biology, mitosis and meiosis, and yet its biochemical function remains elusive  . Spo12 is a nuclear protein  . Spo12 is a component of the FEAR (Cdc fourteen early anaphase release) regulatory network, that promotes Cdc14 release from the nucleolus during early anaphase  . The FEAR network is comprised of the polo kinase Cdc5, the separase Esp1, the kinetochore-associated protein Slk19, and Spo12  .. 
PF03907 Spo7-like protein<br>S. cerevisiae Spo7 Swiss:P18410 has an unknown function, but has a role in formation of a spherical nucleus and meiotic division  .. 
PF01052 SPOA_protein;<br>Surface presentation of antigens (SPOA). Pfam-B_408 (release 3.0). This family includes the C-terminal region of flagellar motor switch proteins FliN and FliM. It is associated with family FliM, Pfam:PF02154.. 
PF05036 Sporulation related domain<br>This 70 residue domain is composed of two 35 residue repeats found in proteins involved in sporulation and cell division such as FtsN, DedD, and CwlM.  This domain is involved in binding peptidoglycan  . Two tandem repeats fold into a pseudo-2-fold symmetric single-domain structure containing numerous contacts between the repeats  . FtsN is an essential cell division protein with a simple bitopic topology, a short N-terminal cytoplasmic segment fused to a large carboxy periplasmic domain through a single transmembrane domain. These repeats lay at the periplasmic C-terminus. FtsN localises to the septum ring complex.. 
PF03845 Spore germination protein<br>TIGRFAMs, Griffiths-Jones SR. 
PF00588 SpoU rRNA Methylase family<br>MRC-LMB Genome group. This family of proteins probably use S-AdoMet. . 
PF03862 spoVA;<br>Members of this family are all transcribed from the spoVA operon. These proteins are poorly characterised, but are thought to be involved in dipicolinic acid transport into the developing forespore during sporulation  .. 
PF04026 SpoVG<br>Stage V sporulation protein G. Essential for sporulation and specific to stage V sporulation in Bacillus megaterium and subtilis  . In B. subtilis, expression decreases after 30-60 minutes of cold shock  .. 
PF04293 SpoVR like protein<br>Family member Swiss:P37875 is Bacillus subtilis stage V sporulation protein R, which is involved in spore cortex formation  .  Little is known about cortex biosynthesis, except that it depends on several sigma E  controlled genes, including spoVR  .. 
PF04232 Stage V sporulation protein S (SpoVS)<br>In Bacillus subtilis this protein interferes with sporulation at an early stage and this inhibitory effect is overcome by SpoIIB and SpoVG.  SpoVS seems to play a positive role in allowing progression beyond stage V of sporulation.  Null mutations in the spoVS gene block sporulation at stage V, impairing the development of heat resistance and coat assembly  .. 
PF03539 Spumavirus aspartic protease (A9)<br>
PF03779 SPW repeat<br>A short repeat found in a small family  of membrane-bound proteins. This repeat contains a conserved SPW motif in the first of two transmembrane helices.. 
PF00494 Squalene/phytoene synthase<br>
PF00299 squash; <br>Squash family serine protease inhibitor. 
PF02117 Sra; 7TM_GCPR_Sra; <br>Serpentine type 7TM GPCR chemoreceptor Sra. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type  . Sra is part of the Sra superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'  .. 
PF02175 Srb; <br>Serpentine type 7TM GPCR chemoreceptor Srb. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type  . Srb is part of the Sra superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'  .. 
PF00530 Scavenger receptor cysteine-rich domain<br>These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.. 
PF00319 transcript_fact; <br>SRF-type transcription factor (DNA-binding and dimerisation domain). Prosite & Pfam-B_6396 (Release 8.0). 
PF02118 Srg family chemoreceptor<br>
PF02290 Signal recognition particle 14kD protein<br>Pfam-B_7955 (release 5.2). 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.. 
PF01922 SRP19 protein<br>The signal recognition particle (SRP) binds to the signal peptide of proteins as they are being translated. The binding of the SRP halts translation and the complex is then transported to the endoplasmic reticulum's cytoplasmic surface. The SRP then aids translocation of the protein through the ER membrane. The SRP is a ribonucleoprotein that is composed of a small RNA and several proteins. One of these proteins is the SRP19 protein   (Sec65 in yeast [2,3]).. 
PF00660 Seripauperin and TIP1 family<br>
PF05022 SRP40, C-terminal domain<br>Pfam-B_9034 (release 7.6). This presumed domain is found at the C-terminus of the S. cerevisiae SRP40 protein Swiss:P32583 and its homologues. SRP40/nopp40 is a chaperone involved in nucleocytoplasmic transport. SRP40 is also a suppressor of mutant AC40 subunit of RNA polymerase I and III.. 
PF04888 Secretion system effector C (SseC) like family <br>Pfam-B_5525 (release 7.6). SseC is a secreted protein that forms a complex together with SecB and SecD on the surface of Salmonella.  All these proteins are secreted by the type III secretion system  . Many mucosal pathogens use type III secretion systems for the injection of effector proteins into target cells.  SecB, SseC and SecD are inserted into the target cell membrane.  where they form a small pore or translocon [1,2]. In addition to SseC, this family includes the bacterial secreted proteins PopB, PepB, YopB and EspD which are thought to be directly involved in pore formation, and type III secretion system translocon.. 
PF00474 Sodium:solute symporter family<br>This family includes Swiss:P33413 which is not in the Prosite entry.  Membership of this family is supported by a significant blast score.. 
PF04686 Streptomyces sporulation and cell division protein, SsgA<br>Pfam-B_5645 (release 7.5). The precise function of SsgA is unknown. It has been found to be essential for spore formation, and to stimulate cell division  .. 
PF00720 Subtilisin inhibitor-like<br>Pfam-B_679 (release 2.1). 
PF04056 Ssl1-like<br>Pfam-B_13499 (release 7.3);. Ssl1-like proteins are 40kDa subunits of the Transcription factor II H complex.. 
PF04386 Stringent starvation protein B<br>Escherichia coli stringent starvation protein B (SspB), is thought to enhance the specificity of degradation of tmRNA-tagged proteins by the ClpXP protease.  The tmRNA tag, also known as ssrA, is an 11-aa peptide added to the C terminus of proteins stalled during translation, targets proteins for degradation by ClpXP and ClpAP.  SspB a cytoplasmic protein that specifically binds to residues 1-4 and 7 of the tag. Binding of SspB enhances degradation of tagged proteins by ClpX, and masks sequence elements important for ClpA interactions, inhibiting degradation by ClpA  . However, more recent work has cast doubt on the importance of SspB in wild-type cells  . SspB is encoded in an operon whose synthesis is stimulated by carbon, amino acid, and phosphate starvation.  SspB may play a special role during nutrient stress, for example by ensuring rapid degradation of the products of stalled translation, without causing a global increase in degradation of all ClpXP substrates  .. 
PF03531 Structure-specific recognition protein (SSRP1)<br>Griffiths-Jones SR, Mistry J. SSRP1 has been implicated in transcriptional initiation and elongation and in DNA replication and repair  . This domain belongs to the Pleckstrin homology fold superfamily.. 
PF04722 Ssu72-like protein<br>Pfam-B_5993 (release 7.5). The highly conserved and essential protein Ssu72 has intrinsic phosphatase activity and plays an essential role in the transcription cycle. Ssu72 was originally identified in a yeast genetic screen as enhancer of a defect caused by a mutation in the transcription initiation factor TFIIB  .  It binds to TFIIB and is also involved in mRNA elongation.  Ssu72 is further involved in both poly(A) dependent and independent termination. It is a subunit of the yeast cleavage and polyadenylation factor (CPF), which is part of the machinery for mRNA 3'-end formation.  Ssu72 is also essential for transcription termination of snRNAs   .. 
PF04184 ST7 protein<br>Pfam-B_2088 (release 7.3). The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene. The molecular function of this protein is uncertain.. 
PF03298 Stanniocalcin family<br>Pfam-B_4401 (release 6.5). 
PF02200 STE like transcription factor<br>Alignment kindly provided by SMART. 
PF02876 Staphylococcal/Streptococcal toxin, beta-grasp domain<br>
PF01123 Staphylococcal/Streptococcal toxin, OB-fold domain<br>
PF04022 Staphylocoagulase repeat<br>
PF02821 Staphylokinase/Streptokinase family<br>
PF01017 STAT; <br>STAT protein, all-alpha domain. Pfam-B_856 (release 3.0). STAT proteins (Signal Transducers and Activators of Transcription) are a family of transcription factors that are specifically activated to regulate gene transcription when cells encounter cytokines and growth factors. STAT proteins also include an SH2 domain Pfam:PF00017.. 
PF02864 STAT protein, DNA binding domain<br>Pfam-B_856 (release 3.0). 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. This family represents the DNA binding domain of STAT, which has an ig-like fold. STAT proteins also include an SH2 domain Pfam:PF00017.. 
PF02865 STAT_prot; <br>STAT protein, protein interaction domain. Pfam-B_856 (release 3.0). STAT proteins (Signal Transducers and Activators of Transcription) are a family of transcription factors that are specifically activated to regulate gene transcription when cells encounter cytokines and growth factors. STAT proteins also include an SH2 domain Pfam:PF00017.. 
PF03875 Statherin<br>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  . . 
PF00836 Stathmin family<br>Pfam-B_1551 (release 2.1). The Stathmin family of proteins play an important role in the regulation of the microtubule cytoskeleton.  They regulate microtubule dynamics by promoting depolymerization of microtubules and/or preventing polymerisation of tubulin heterodimers  .. 
PF02116 Fungal pheromone mating factor STE2 GPCR<br>
PF02076 Pheromone A receptor<br>
PF04885 Stigma-specific protein, Stig1<br>Pfam-B_6528 (release 7.6). This family represents the Stig1 cysteine rich plant protein. The STIG1 gene is developmentally regulated and expressed specifically in the stigmatic secretory zone  .. 
PF05217 STOP protein<br>Pfam-B_6629 (release 7.7). Neurons contain abundant subsets of highly stable microtubules that resist de-polymerising conditions such as exposure to the cold. Stable  microtubules are thought to be essential for neuronal development, maintenance, and function. STOP is a major factor responsible for the  intriguing stability properties of neuronal microtubules and is important  for synaptic plasticity. Additionally knowledge of STOPs function and properties may help in the treatment of neuroleptics in illnesses such as schizophrenia, currently thought to result from synaptic defects  .. 
PF03088 Strictosidine synthase<br>Pfam-B_1533 (release 6.5). 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.. 
PF04270 strep_his_triad; <br>Streptococcal histidine triad protein . TIGRFAMs (release 2.0);. All members of this family are proteins from Streptococcal species.  The proteins are characterised by having a HxxHxH motif that usually occurs multiple times throughout the protein.. 
PF02516 Oligosaccharyl transferase STT3 subunit<br>Pfam-B_1095 (release 5.4). This family consists of the oligosaccharyl transferase STT3 subunit and related proteins.  The STT3 subunit is part of the oligosaccharyl transferase (OTase) complex of proteins and is required for its activity  .  In eukaryotes, OTase transfers a lipid-linked core-oligosaccharide to selected asparagine residues in the ER  . In the archaea STT3 occurs alone, rather than in an OTase complex, and is required for N-glycosylation of asparagines [3-4].. 
PF03481 Putative GTP-binding controlling metal-binding<br>Structural investigation of this domain suggests that it might be a GTP-binding region that regulates metal binding and involves hydrolysis of ATP to AMP. It is found to the C-terminus of Pfam:PF01300.. 
PF01300 Telomere recombination<br>This domain has been shown to bind preferentially to dsRNA  . The domain is found in SUA5 Swiss:P32579 as well as HypF and YrdC Swiss:P45748. It has also been shown to be required for telomere recombniation in yeast.. 
PF00862 Sucrose synthase<br>Pfam-B_484 (release 3.0). Sucrose synthases catalyse the synthesis of sucrose from UDP-glucose and fructose. This family includes the bulk of the sucrose synthase protein.  However the carboxyl terminal region of the sucrose synthases belongs to the glycosyl transferase family Pfam:PF00534.. 
PF02657 UPF0050;<br>Fe-S metabolism associated domain. This family consists of the SufE-related proteins. These have been implicated in Fe-S metabolism and export  ).. 
PF05076 Suppressor of fused protein (SUFU)<br>Pfam-B_6089 (release 7.7). SUFU, encoding the human orthologue of Drosophila suppressor of fused,  appears to have a conserved role in the repression of Hedgehog signaling. SUFU exerts its repressor role by physically interacting with GLI proteins in both the cytoplasm and the nucleus  . SUFU has been found to be a tumour-suppressor gene that predisposes individuals to medulloblastoma by modulating the SHH signaling pathway  . Genomic contextual analysis of bacterial SUFU versions revealed that they are immunity proteins against diverse nuclease toxins in polymorphic toxin systems  . . 
PF04198 Putative sugar-binding domain<br>Pfam-B_1085 (release 7.3). This probable domain is found in bacterial transcriptional regulators such as DeoR and SorC. These proteins have an amino-terminal helix-turn-helix Pfam:PF00325 that binds to DNA. This domain is probably the ligand regulator binding region.  SorC is regulated by sorbose and other members of this family are likely to be regulated by other sugar substrates.. 
PF00083 sugar_tr; <br>Sugar (and other) transporter. Prosite hmmls-iteration. 
PF01253 Translation initiation factor SUI1<br>
PF03846 Cell division inhibitor SulA<br>TIGRFAMs, Griffiths-Jones SR. 
PF00916 Sulfate transporter family<br>Pfam-B_223 (release 3.0). Mutations in Swiss:P50443 lead to several human diseases.. 
PF03856 Beta-glucosidase (SUN family)<br>Members of this family include Nca3, Sun4 and Sim1. This is a family of yeast proteins, involved in a diverse set of functions (DNA replication, aging,  mitochondrial biogenesis and cell septation) . BGLA from Candida wickerhamii has been characterised as a Beta-glucosidase EC:3.2.1.21.. 
PF03439 Supt5;<br>Early transcription elongation factor of RNA pol II, NGN section. Spt5p and prokaryotic NusG are shown to contain a novel 'NGN' domain. The combined NGN and KOW motif regions of Spt5 form the binding domain with Spt4  .  Spt5 complexes with Spt4 as a 1:1 heterodimer snf this Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The Schizosaccharomyces pombe core Spt5-Spt4 complex is a heterodimer bearing a trypsin-resistant Spt4-binding domain within the Spt5 subunit  .. 
PF01975 Survival protein SurE<br>E. coli cells with the surE gene disrupted are found to survive poorly in stationary phase  .  It is suggested that SurE may be involved in stress response. Yeast also contains a member of the family Swiss:P38254.  Swiss:P30887 can complement a mutation in acid phosphatase, suggesting that members of this family could be phosphatases.. 
PF02104 SURF1 family<br>
PF02077 SURF4 family<br>
PF01617 Surface antigen<br>Pfam-B_1042 (release 4.1). This family includes a number of bacterial surface antigens expressed on the surface of pathogens.. 
PF00084 sushi; <br>Sushi domain (SCR repeat). Swissprot_feature_table. 
PF04099 Sybindin-like family <br>Pfam-B_3240 (release 7.3);. 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  .. 
PF02383 SacI homology domain<br>Pfam-B_1090 (release 5.2). This Pfam family represents a protein domain which shows homology to the yeast protein SacI Swiss:P32368. The SacI homology domain is most notably found at the amino terminal of the inositol  5'-phosphatase synaptojanin.. 
PF02078 Synapsin; Synapsin_N; <br>Synapsin, N-terminal domain. 
PF02750 Synapsin, ATP binding domain<br>Ca dependent ATP binding in this ATP grasp fold.  Function unknown.. 
PF00957 synaptobrevin; <br>Pfam-B_303 (release 3.0). 
PF01284 Synaptophysin; <br>Membrane-associating domain. MARVEL domain-containing proteins are often found in lipid-associating proteins - such as Occludin and MAL family proteins  . It may be part of the machinery of membrane apposition events, such as transport vesicle biogenesis.. 
PF01034 Syndecan domain<br>Pfam-B_1182 (release 3.0). Syndecans are transmembrane heparin  sulfate  proteoglycans  which  are   implicated  in  the binding of extracellular matrix components  and growth factors.. 
PF01387 Synuclein<br>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 plaques in Alzheimer's patients. . 
PF00837 Iodothyronine deiodinase<br>Pfam-B_1631 (release 2.1). Iodothyronine deiodinase converts thyroxine (T4) to 3,5,3'-triiodothyronine (T3).. 
PF03903 T4_tail_gp36; <br>
PF03906 Tail_fibre_T7; T7_tail_fibre; <br>Phage T7 tail fibre protein. The bacteriophage T7 tail complex consists of a conical  tail-tube surrounded by six kinked tail-fibres,  which are oligomers of the viral protein gp17.. 
PF02217 Origin of replication binding protein<br>Pfam-B_827 (release 5.2). This domain of large T antigen binds to the SV40 origin of DNA replication  . . 
PF05010 Transforming acidic coiled-coil-containing protein (TACC)<br>Pfam-B_4807 (release 7.6). This family contains the proteins TACC 1, 2 and 3 the genes for which are found concentrated in the centrosomes of eukaryotic and may play a conserved role in organising centrosomal microtubules. The human TACC proteins have been linked to cancer and TACC2 has been identified as a possible tumour suppressor (AZU-1)  .  The functional homologue (Alp7) in Schizosaccharomyces pombe has been shown to be required for organisation of bipolar spindles  .. 
PF02202 Tachykinin family<br>Alignment kindly provided by SMART. 
PF04972 TAD;<br>This domain is found in a family of osmotic shock protection proteins (e.g. Swiss:P27291). It is also found in some Secretins and a group of potential haemolysins. Its likely function is attachment to phospholipid membranes ( ).. 
PF02969 TATA box binding protein associated factor (TAF)<br>TAF proteins adopt a histone-like fold.. 
PF04658 TAFII55 protein conserved region<br>Pfam-B_4395 (release 7.5). The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex.   TAFII55 binds to TAFII250 and inhibits it acetyltransferase activity. The exact role of TAFII55 is currently unknown.  The conserved region is situated towards the N-terminus of the protein  .  . 
PF05069 tail_comp_S; <br>Phage virion morphogenesis family . TIGRFAMs (release 2.0);. Protein S of phage P2 is thought to be involved in tail completion and stable head joining.. 
PF02203 Tar ligand binding domain homologue<br>Alignment kindly provided by SMART. 
PF00539 Transactivating regulatory protein (Tat)<br>The retroviral Tat protein binds to the Tar RNA  .  This activates  transcriptional initiation and elongation from the LTR promoter. Binding is mediated by an arginine rich region.. 
PF01026 UPF0006;<br>Pfam-B_1370 (release 3.0). 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.. 
PF03430 Trans-activating transcriptional regulator <br>Pfam-B_4420 (release 6.6). This family of trans-activating transcriptional regulator (TATR), also known as intermediate early protein 1, are common to the  Nucleopolyhedroviruses.   . 
PF02668 Taurine catabolism dioxygenase TauD, TfdA family<br>This family consists of taurine catabolism dioxygenases of the TauD, TfdA family.  TauD from E. coli Swiss:P37610 is a alpha-ketoglutarate-dependent taurine dioxygenase  .  This enzyme catalyses the oxygenolytic release of sulfite from taurine  .  TfdA from Burkholderia sp. Swiss:Q45423 is a 2,4-dichlorophenoxyacetic acid/alpha-ketoglutarate dioxygenase  .\.       TfdA from Alcaligenes eutrophus JMP134 Swiss:P10088 is a 2,4-dichlorophenoxyacetate monooxygenase  . Also included are gamma-Butyrobetaine hydroxylase enzymes EC:1.14.11.1  .. 
PF01361 Tautomerase enzyme<br>This family includes the enzyme 4-oxalocrotonate tautomerase Swiss:Q01468 that catalyses the ketonisation of 2-hydroxymuconate to 2-oxo-3-hexenedioate.. 
PF02959 HTLV_tat;<br>Pfam-B_1456 (release 6.4). Human T-cell leukaemia virus type I (HTLV-I) is the etiological agent for adult T-cell leukaemia (ATL), as well as for tropical spastic paraparesis (TSP) and HTLV-I associate myelopathy (HAM). A biological understanding of the involvement of HTLV-I and in ATL has focused significantly on the workings of the virally-encoded 40 kDa phospho-oncoprotein, Tax. Tax is a transcriptional activator. Its ability to modulate the expression and function of many cellular genes has been reasoned to be a major contributory mechanism explaining HTLV-I-mediated transformation of cells. In activating cellular gene expression, Tax impinges upon several cellular signal-transduction pathways, including those for CREB/ATF and NF-kappaB  .. 
PF00683 TGF-bp; <br>Pfam-B_82 (release 2.1). 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.. 
PF00566 TBC;<br>Rab-GTPase-TBC domain. Alignment kindly provided by SMART. Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, implies that these domains are GTPase activator proteins of Rab-like small GTPases.. 
PF02970 Tubulin binding cofactor A<br>
PF03558 TBSV core protein P21/P22<br>Pfam-B_3028 (release 7.0). This protein is required for cell-to-cell movement in plants. Furthermore, the membrane-associated protein is dispensable for both replication and transcription  .. 
PF01840 TCL1/MTCP1 family<br>  & Pfam-B_7391 (Release 8.0). Two related oncogenes, TCL-1 Swiss:P56279 and MTCP-1 Swiss:P56278, are overexpressed in T cell prolymphocytic leukaemias as a result of chromosomal rearrangements that involve the translocation of one T cell receptor gene to either chromosome 14q32 or Xq28  . This family contains two repeated motifs that form a single globular domain  .. 
PF03634 TCP family transcription factor<br>Pfam-B_1979 (release 7.0). This is a family of TCP plant transcription factors.  TCP proteins were named after the first characterised members (TB1, CYC and PCFs) and they are involved in multiple developmental control pathways    .  This region contains a DNA binding basic-Helix-Loop-Helix (bHLP) structure   .. 
PF03645 Tctex-1 family<br>Pfam-B_2986 (release 7.0). 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. . 
PF00838 Translationally controlled tumour protein<br>Pfam-B_1548 (release 2.1). 
PF03347 Vibrio thermostable direct hemolysin<br>Pfam-B_3633 (release 6.5). 
PF01285 TEA/ATTS domain family<br>
PF03848 Tellurite resistance protein TehB<br>TIGRFAMs, Griffiths-Jones SR. 
PF02765 Telo_bind;<br>Telomeric single stranded DNA binding POT1/CDC13. This domain binds single stranded telomeric DNA and adopts an OB fold  .  It includes the proteins POT1 and CDC13 which have been shown to regulate telomere length, replication and capping [2-4].  POT1 is one component of the shelterin complex that protects telomere-ends from attack by DNA-repair mechanisms [5,6].. 
PF03070 TENA/THI-4/PQQC family<br>Pfam-B_2039 (release 6.4) & Pfam-B_7791 (release 7.7). Members of this family are found in all the three major phyla of life: archaebacteria, eubacteria, and eukaryotes. In Bacillus subtilis, TENA is one of a number of proteins that enhance the expression of extracellular enzymes, such as alkaline protease, neutral protease and levansucrase  .  The THI-4 protein, which is involved in thiamine biosynthesis, is also a member of this family. The C-terminal part of these proteins consistently show significant sequence similarity to TENA proteins. This similarity was first noted with the Neurospora crassa THI-4  . This family includes bacterial coenzyme PQQ synthesis protein C or PQQC proteins.  Pyrroloquinoline quinone (PQQ) is the prosthetic group of several bacterial enzymes,including methanol dehydrogenase of methylotrophs and the glucose dehydrogenase of a number of bacteria  . PQQC has been found to be required in the synthesis of PQQ but its function is unclear.  The exact molecular function of members of this family is uncertain.. 
PF04876 Tenuivirus major non-capsid protein<br>Pfam-B_6119 (release 7.6). This protein of unknown function accumulates in large amounts in tenuivirus infected cells.  It is found in all forms of the inclusion bodies that are formed after infection  .. 
PF03300 Tenuivirus non-structural protein NS4<br>Pfam-B_4315 (release 6.5). 
PF05099 Tellurite resistance protein TerB<br>This family contains the TerB tellurite resistance proteins from a a number of bacteria.. 
PF03741 Integral membrane protein TerC family<br>This family contains a number of integral membrane proteins that also contains the TerC protein. TerC has been implicated in resistance to tellurium. This protein may be involved in efflux of tellurium ions. The tellurite-resistant Escherichia coli strain KL53 was found during testing of the group of clinical isolates for antibiotics and heavy metal ion resistance  . Determinant of the tellurite resistance of the strain was located on a large conjugative plasmid. Analyses showed, the genes terB, terC, terD and terE are essential for conservation of the resistance. The members of the family contain a number of conserved aspartates that could be involved in binding to metal ions.. 
PF02342 TerD domain<br>The TerD domain is found in TerD family proteins that include the paralogous TerD, TerA, TerE, TerF and TerZ proteins    It is found in a stress response operon with TerB and TerC.  TerD has a maximum of two calcium binding sites {2] depending on the conservation of aspartates {2]. It has various fusions to nuclease domains, RNA binding domains, ubiquitin related domains, and metal binding domains. The ter gene products lie  at the center of membrane-linked metal recognition complexes  with regulatory ramifications encompassing phosphorylation- dependent signal transduction, RNA-dependent regulation,  biosynthesis of nucleoside-like metabolites and DNA processing linked to novel pathways  . . 
PF03592 Terminase_small; <br>Terminase small subunit . Pfam-B_3755 (release 7.0). Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA.  This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology.  The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site  .. 
PF03936 Terpene synthase family, metal binding domain<br>Pfam-B_728 (release 3.0). It has been suggested that this gene family be designated tps (for terpene synthase)  .  It has been split into six subgroups on the basis of phylogeny, called tpsa-tpsf. tpsa includes vetispiridiene synthase Swiss:Q39979, 5-epi- aristolochene synthase, Swiss:Q40577 and (+)-delta-cadinene synthase Swiss:P93665. tpsb includes (-)-limonene synthase, Swiss:Q40322. tpsc includes kaurene synthase A, Swiss:O04408. tpsd includes taxadiene synthase, Swiss:Q41594, pinene synthase, Swiss:O24475 and myrcene synthase, Swiss:O24474. tpse includes kaurene synthase B. tpsf includes linalool synthase.. 
PF02909 tetR_C; <br>Tetracyclin repressor, C-terminal all-alpha domain. 
PF03299 Transcription factor AP-2<br>Pfam-B_1736 (release 6.5). 
PF02559 CarD; TF_CarD; CarD_TRCF; CarD-CdnL_RID;<br>CarD-like/TRCF domain. CarD is a Myxococcus xanthus protein required for the activation of light- and starvation-inducible genes  . This family includes the presumed N-terminal domain, CdnL.\.      CarD interacts with the zinc-binding protein CarG to form a complex that regulates multiple processes in Myxococcus xanthus  .  This family also includes a domain to the N-terminal side of the DEAD helicase of TRCF (transcription-repair-coupling factor) proteins. TRCF displaces RNA polymerase stalled at a lesion, binds to the damage recognition protein UvrA, and increases the template strand repair rate during transcription  . This domain is involved in binding to the stalled RNA polymerase  . The family includes members otherwise referred to as CdnL, for CarD N-terminal like, whichdiffer functionally from CarD. The TRCF domain mentioned above is the RNA polymerase-interacting domain or RID  .. 
PF03529 Otx1 transcription factor<br>
PF03849 Transcription factor Tfb2<br>TIGRFAMs, Griffiths-Jones SR. 
PF03153 Transcription factor IIA, alpha/beta subunit<br>Pfam-B_3542 (release 6.5). 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 represented in Pfam:PF02268 and Pfam:PF02751, respectively. This family represents the precursor that yields both the alpha and beta subunits. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II. Together with TFIID, TFIIA binds to the promoter region; this is the first step in the formation of a pre-initiation complex (PIC). Binding of the rest of the transcription machinery follows this step  . After initiation, the PIC does not completely dissociate from the promoter. Some components, including TFIIA, remain attached and re-initiate a subsequent round of transcription.. 
PF02268 TFIIA_gamma; <br>Transcription initiation factor IIA, gamma subunit, helical domain. Pfam-B_4941 (release 5.2). Accurate transcription in vivo requires at least six  general transcription initiation factors, in addition to RNA  polymerase II. Transcription initiation factor IIA (TFIIA) is a multimeric protein which facilitates the binding of TFIID to the TATA box. The N-terminal domain of the gamma subunit is a 4 helix bundle.. 
PF02751 Transcription initiation factor IIA, gamma subunit<br>Pfam-B_4941 (release 5.2). Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II.  Transcription initiation factor IIA (TFIIA) is a multimeric protein which facilitates the binding of TFIID to the TATA box. The C-terminal domain of the gamma subunit is a 12 stranded beta-barrel.. 
PF02291 TFIID-31; <br>Transcription initiation factor IID, 31kD subunit. Pfam-B_6729 (release 5.2). 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 transcription activation.. 
PF03540 TFIID_30kD; <br>Transcription initiation factor TFIID 23-30kDa subunit. 
PF02002 TFIIE;<br>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 Swiss:P29083 and TFIIE-beta Swiss:P29084 and joins the pre-initiation complex after RNA polymerase II and TFIIF  . This family consists of the conserved amino terminal region of eukaryotic TFIIE-alpha   and proteins from archaebacteria that are presumed to be TFIIE-alpha subunits also Swiss:O29501  .. 
PF02186 TFIIE beta subunit core domain<br>General transcription factor TFIIE consists of two subunits, TFIIE alpha Pfam:PF02002 and TFIIE beta. TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The structure of the DNA binding core region has been solved   and has a winged helix fold.. 
PF02270 Transcription initiation factor IIF, beta subunit<br>Pfam-B_4519 (release 5.2). Accurate transcription in vivo requires at least six  general transcription initiation factors, in addition to RNA  polymerase II. Transcription initiation factor IIF (TFIIF) is a tetramer of two beta subunits associate with two alpha subunits which interacts directly with RNA polymerase II. The beta subunit  of TFIIF is required for recruitment of RNA polymerase II onto  the promoter.. 
PF01096 TFIIS; <br>Transcription factor S-II (TFIIS). 
PF04994 TfoX C-terminal domain<br>TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes  . This family corresponds to the C-terminal presumed domain of TfoX. The domain is found associated with Pfam:PF00383 in Swiss:Q9JZR1.  It is also found as an isolated domain in some proteins suggesting this is an autonomous domain.. 
PF04993 TfoX N-terminal domain<br>TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes  . This family corresponds to the N-terminal presumed domain of TfoX. The domain is found as an isolated domain in some proteins suggesting this is an autonomous domain.. 
PF00019 TGF-beta; <br>Transforming growth factor beta like domain. 
PF00688 TGF-beta propeptide<br>Pfam-B_110 (release 2.1). 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.. 
PF01702 Queuine tRNA-ribosyltransferase<br>Pfam-B_1643 (release 4.1). This is a family of queuine tRNA-ribosyltransferases EC:2.4.2.29, also known as tRNA-guanine transglycosylase and guanine insertion enzyme. Queuine tRNA-ribosyltransferase modifies tRNAs for asparagine,  aspartic acid, histidine and tyrosine with queuine.  It catalyses the exchange of guanine-34 at the wobble position with 7-aminomethyl-7-deazaguanine, and the addition of a cyclopentenediol  moiety to 7-aminomethyl-7-deazaguanine-34 tRNA; giving a hypermodified  base queuine in the wobble position [1,2]. The aligned region contains a zinc binding motif C-x-C-x2-C-x29-H,  and important tRNA and 7-aminomethyl-7deazaguanine binding residues  .. 
PF04858 TH1 protein<br>Pfam-B_6070 (release 7.6). TH1 is a highly conserved but uncharacterised metazoan protein.  No homologue has been identified in Caenorhabditis elegans  .  TH1 binds specifically to A-Raf kinase  .. 
PF00314 thaumatin; <br>
PF01946 Thi4 family<br>This family includes Swiss:P32318 a putative thiamine biosynthetic enzyme.. 
PF01964 ThiC family<br>ThiC is found within the thiamine biosynthesis operon. ThiC is involved in pyrimidine biosynthesis  . The precise catalytic function of ThiC is still not known. ThiC participates in the formation of 4-Amino-5-hydroxymethyl-2-methylpyrimidine from AIR, an intermediate in the de novo pyrimidine biosynthesis.. 
PF02568 Thiamine biosynthesis protein (ThiI)<br>ThiI is required for thiazole synthesis, required for thiamine biosynthesis  .. 
PF00975 Thioesterase domain<br>Pfam-B_180 (release 3.0). Peptide synthetases are involved in the non-ribosomal synthesis of peptide antibiotics.  Next to the operons encoding these enzymes, in almost all cases, are genes that encode proteins that have similarity to the type II fatty acid thioesterases of vertebrates.  There are also modules within the peptide synthetases that also share this similarity. With respect to antibiotic production, thioesterases are required for the addition of the last amino acid to the peptide antibiotic, thereby forming a cyclic antibiotic. Thioesterases (non-integrated) have molecular masses of 25-29 kDa.. 
PF01289 Thiol-activated cytolysin<br>
PF00108 thiolase; <br>Thiolase, N-terminal domain. Thiolase is reported to be structurally related to beta-ketoacyl  synthase (Pfam:PF00109), and also chalcone synthase.. 
PF02803 thiolase_C; <br>Thiolase, C-terminal domain. Thiolase is reported to be structurally related to beta-ketoacyl  synthase (Pfam:PF00109), and also chalcone synthase.. 
PF00085 thiored; <br>Thioredoxins are small enzymes that participate in redox reactions, via the reversible oxidation of an active centre disulfide bond. Some members with only the active site are not separated from the noise.. 
PF00585 Thr_dehydratase_C;<br>C-terminal regulatory domain of Threonine dehydratase. Threonine dehydratases Pfam:PF00291 all contain a carboxy terminal region.  This region may have a regulatory role. Some members contain two copies of this region. This family is homologous to the Pfam:PF01842 domain.. 
PF04163 Tht1-like nuclear fusion protein <br>Pfam-B_64620 (release 7.3);. 
PF02926 THUMP domain<br>The THUMP domain is named after after thiouridine synthases, methylases and PSUSs  . The THUMP domain consists of about 110 amino acid residues.  The structure of ThiI reveals that the THUMP has a fold unlike that of previously characterised RNA-binding domains  . It is predicted that this domain is an RNA-binding domain The THUMP domain probably functions by delivering a variety of RNA modification enzymes to their targets  .. 
PF02511 Thymidylate synthase complementing protein<br>Pfam-B_1648 (release 5.4). Thymidylate synthase complementing protein (Thy1) complements the thymidine growth requirement of the organisms in which it is found, but shows no homology to thymidylate synthase.. 
PF00303 thymidylat_synt; <br>Thymidylate synthase. Swiss:P28176 is not included as a member of this family, Although annotated as such there is no significant sequence similarity to other members.. 
PF02223 Thymidylate kinase<br>Pfam-B_484 (release 5.2). 
PF01290 Thymosin beta-4 family<br>
PF00086 thyroglobulin_1; <br>Thyroglobulin type-1 repeat. Swissprot_feature_table. Thyroglobulin type 1 repeats are thought to be involved in the control of proteolytic degradation  . The domain usually contains six conserved cysteines.  These form three disulphide bridges.  Cysteines 1 pairs with 2, 3 with 4 and 5 with 6.. 
PF04278 Tic22-like family<br>TIGRFAMs (release 2.0);. The preprotein translocation at the inner envelope membrane of  chloroplasts so far involves five proteins: Tic110, Tic55,  Tic40, Tic22 (this family) and Tic20. The molecular function of  these proteins has not yet been established  . . 
PF01826 Trypsin Inhibitor like cysteine rich domain<br>This family contains trypsin inhibitors as well as a domain found in many extracellular proteins. The domain typically contains ten cysteine residues that form five disulphide bonds. The cysteine residues that form the disulphide bonds are 1-7, 2-6, 3-5, 4-10 and 8-9.. 
PF00121 Triosephosphate isomerase<br>
PF02466 Tim17/Tim22/Tim23/Pmp24 family<br>Pfam-B_2241 (release 5.4) & Pfam-B_7792 (Release 8.0). 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. Tim17 and Tim23 are thought to form the translocation channel of the inner membrane.  This family includes Tim17, Tim22 and Tim23. This family also includes Pmp24 a peroxisomal protein. The involvement of this domain in the targeting of PMP24 remains to be proved. PMP24 was known as Pmp27 in  .. 
PF04821 Timeless protein<br>Pfam-B_3454 (release 7.6). The timeless gene in Drosophila melanogaster and its homologues in a number of other insects and mammals (including human) are involved in circadian rhythm control  . This family includes a related proteins from a number of fungal species.. 
PF05029 Timeless protein C terminal region<br>Pfam-B_5695 (release 7.6). The timeless (tim) gene is essential for circadian function in Drosophila. Putative homologues of Drosophila tim have been identified in both mice and humans (mTim and hTIM, respectively). Mammalian TIM is not the true orthologue of Drosophila TIM, but is the likely orthologue of a fly gene, timeout (also called tim-2)  . mTim has been shown to be essential for  embryonic development, but does not have substantiated circadian  function . Some family members contain a SANT domain in this region.. 
PF00965 Tissue inhibitor of metalloproteinase<br>Pfam-B_1239 (release 3.0). Members of this family are common in extracellular regions of vertebrate species. 
PF03549 Tir_receptor; <br>Translocated intimin receptor (Tir) intimin-binding domain. Griffiths-Jones SR, Moxon SJ. Intimin and its translocated intimin receptor (Tir) are bacterial proteins that mediate adhesion between mammalian cells and attaching and effacing (A/E) pathogens. A unique and essential feature of A/E bacterial pathogens is the formation of actin-rich pedestals beneath the intimately adherent bacteria and localised destruction of the intestinal brush border. The bacterial outer membrane adhesin, intimin, is necessary for the production of the A/E lesion and diarrhoea. The A/E bacteria translocate their own receptor for intimin, Tir, into the membrane of mammalian cells using the type III secretion system. The translocated Tir triggers additional host signalling events and actin nucleation, which are essential for lesion formation  . This family represents the Tir intimin-binding domain (Tir IBD) which is needed to bind intimin and support the predicted topology for Tir, with both N- and C-terminal regions in the mammalian cell cytosol  . . 
PF04553 Tis11B_C;<br>Tis11B like protein, N terminus. Members of this family always contain a tandem repeat of CCCH zinc fingers Pfam:PF00642.  Tis11B, Tis11D and their homologues are thought to be regulatory proteins involved in the response to growth factors.  The function of the N terminus is unknown.. 
PF01108 Tissue factor<br>This family is found in metazoa, and is very similar to the fibronectin type III domain.  The family is found in cytokine receptors, interleukin and interferon receptors and coagulation factor III proteins. It occurs multiple times, as does fn3, family Pfam:PF00041.. 
PF00265 Thymidine kinase<br>
PF00693 TK_herpes; <br>Thymidine kinase from herpesvirus. Pfam-B_186 (release 2.1). 
PF03219 TLC ATP/ADP transporter<br>Pfam-B_2261 (release 6.5). 
PF05017 TMP repeat<br>Pfam-B_1012 (release 7.6). This short repeat consists of the motif WXXh where X can be any residue and h is a hydrophobic residue. The repeat is name TMP after its occurrence in the  tape measure protein (TMP). Tape measure protein is a component of phage tail and probably forms a beta-helix. Truncated forms of TMP lead to shortened tail fibres  . This repeat is also found in non-phage proteins where it may play a structural role.. 
PF02581 Thiamine monophosphate synthase/TENI<br>Thiamine monophosphate synthase (TMP) (EC:2.5.1.3) catalyses the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5- (beta-hydroxyethyl)thiazole phosphate to yield thiamine  phosphate  . This Pfam family also includes the regulatory protein TENI (Swiss:P25053).. 
PF00721 Virus coat protein (TMV like)<br>Pfam-B_746 (release 2.1). This family contains coat proteins from tobamoviruses, hordeiviruses, Tobraviruses, Furoviruses and Potyviruses.. 
PF00229 TNF(Tumour Necrosis Factor) family <br>
PF00020 TNFR/NGFR cysteine-rich region<br>Swissprot_feature_table. 
PF01107 Tobamo_MP; <br>Viral movement protein (MP). Pfam-B_815 (release 3.0) & Pfam-B_1906 (release 4.1). This family includes a variety of movement proteins (MP)s. The MP is necessary for the initial cell-to-cell movement during the early stages of a viral infection.  This movement is active, and it is known that the MP interacts with the plasmodesmata and possesses the ability to bind to RNA to achieve its role  . This family also includes consists of virus movement proteins from the caulimovirus family. It has been suggested in cauliflower mosaic virus that these proteins mediated viral movement by modifying plasmodesmata and forming tubules in the channel that can accommodate the virus particles   and references therein. The family contains a conserved DXR motif that is probably functionally important.. 
PF04052 TolB amino-terminal domain<br>TolB is an essential periplasmic component of the tol-dependent translocation system. This function of this amino terminal domain is uncertain.. 
PF03349 Outer membrane protein transport protein (OMPP1/FadL/TodX)<br>Pfam-B_3708 (release 6.5). This family includes TodX from Pseudomonas putida F1 Swiss:Q51971 and TbuX from Ralstonia pickettii PKO1 Swiss:Q9RBW8. These are membrane proteins of uncertain function that are involved in toluene catabolism. Related proteins involved in the degradation of similar aromatic hydrocarbons are also in this family, such as CymD Swiss:O33458. This family also includes FadL involved in translocation of long-chain fatty acids across the outer membrane. It is also a receptor for the bacteriophage T2.. 
PF04281 Mitochondrial import receptor subunit Tom22 <br>TIGRFAMs (release 2.0);. The mitochondrial protein translocase family, which is responsible for movement of nuclear encoded pre-proteins into mitochondria, is very complex with at least 19 components. These proteins include several chaperone proteins, four proteins of the outer membrane translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins.  This family represents the Tom22 proteins  .  The N terminal region of Tom22 has been shown to have chaperone-like activity, and the C terminal region faces the intermembrane face  .. 
PF03220 Tombusvirus P19 core protein<br>Pfam-B_2714 (release 6.5). 
PF03544 TonB;<br>Gram-negative bacterial TonB protein C-terminal. The TonB_C domain is the well-characterised C-terminal region of the TonB receptor molecule. This protein is bound to an inner membrane-bound protein ExbB via a globular domain and has a flexible middle region that is likely to help in positioning the C-terminal domain into the iron-transporter barrel in the outer membrane  . TonB_C interacts with the N-terminal TonB box of the outer membrane transporter that binds the Fe3+-siderophore complex. The barrel of the transporter, consisting of 22 beta-sheets and an inside plug, binds the iron complex in the barrel entrance  .. 
PF00593 TonB_boxC; <br>TonB dependent receptor. This model now only covers the conserved part of the barrel structure.. 
PF01131 DNA topoisomerase<br>Pfam-B_505 (release 3.0). This subfamily of topoisomerase is divided on the basis that these enzymes preferentially relax  negatively supercoiled DNA, from a 5' phospho- tyrosine linkage in the enzyme-DNA covalent intermediate and has high affinity for single stranded DNA.. 
PF02919 Topoisomer_I_N; <br>Eukaryotic DNA topoisomerase I, DNA binding fragment. Pfam-B_1377 (release 3.0). Topoisomerase I promotes the relaxation of DNA superhelical tension by introducing a transient single-stranded break in duplex DNA and are vital for the processes of replication, transcription, and recombination  . This family may be more than one structural domain.. 
PF01028 Topoisomerase_I; <br>Eukaryotic DNA topoisomerase I, catalytic core. Pfam-B_1377 (release 3.0). Topoisomerase I promotes the relaxation of DNA superhelical tension by introducing a transient single-stranded break in duplex DNA and are vital for the processes of replication, transcription, and recombination  .. 
PF01751 Primase;<br>Pfam-B_500 (release 4.2). This is a conserved region from DNA primase. This corresponds to  the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins  . Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely  abolish DnaG type primase activity  . DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesises the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division  . This family also includes the atypical archaeal A subunit from type II DNA topoisomerases  . Type II DNA topoisomerases catalyse the relaxation of DNA supercoiling by causing transient double strand breaks.. 
PF01533 Tospovirus nucleocapsid protein<br>Pfam-B_950 (release 4.0). The tospovirus genome consists of three linear ssRNA segments, denoted L, M and S complexed with the nucleocapsid protein. The S RNA encodes the nucleocapsid protein and another non-structural protein  .. 
PF00087 toxin; toxin_1; <br>A family of venomous neurotoxins and cytotoxins. Structure is small, disulfide-rich, nearly all beta sheet.. 
PF00451 toxin_2; <br>Scorpion short toxin, BmKK2. Members of this family, which are found in various scorpion toxins, confer potassium channel blocking activity  .. 
PF00537 toxin_3; <br>Scorpion toxin-like domain . Pfam-B_8170 (release 8.0). This family contains both neurotoxins and plant defensins.  The mustard trypsin inhibitor, MTI-2, is plant defensin. It is a potent inhibitor of trypsin with no activity towards chymotrypsin. MTI-2 is toxic for Lepidopteran insects, but has low activity against aphids  .  Brazzein is plant defensin-like protein. It is pH-stable, heat-stable and intensely sweet protein  . The scorpion toxin (a neurotoxin) binds to sodium channels and inhibits the activation mechanisms of the channels, thereby blocking neuronal transmission. Scorpion toxins bind to sodium channels and inhibit the activation mechanisms of the channels, thereby blocking neuronal transmission. 
PF00706 toxin_4; <br>Pfam-B_589 (release 2.1). 
PF02079 Nuclear transition protein 1<br>
PF01254 Nuclear transition protein 2<br>
PF04406 Type IIB DNA topoisomerase<br>Type II DNA topoisomerases are ubiquitous enzymes that catalyse the ATP-dependent transport of one DNA duplex through a second DNA segment via a transient double-strand break.  Type II DNA topoisomerases are now subdivided into two sub-families, type IIA and IIB DNA topoisomerases.  TP6A_N is present in type IIB topoisomerase and is thought to be involved in DNA binding owing to its sequence similarity to E. coli catabolite activator protein (CAP)  . . 
PF00590 Tetrapyrrole (Corrin/Porphyrin) Methylases<br>MRC-LMB Genome group. This family uses S-AdoMet in the methylation of diverse substrates.  This family includes a related group of bacterial proteins of unknown function, including Swiss:P45528.\.   This family includes the methylase Dipthine synthase.. 
PF04201 Tumour protein D52 family<br>Pfam-B_2632 (release 7.3). 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 and cell proliferation. Two human homologues of hD52, hD53 and hD54, have also been identified, demonstrating the existence of a novel gene/protein family  . These proteins have an amino terminal coiled-coil that allows members to form homo- and heterodimers with each other  .. 
PF00205 TPP_enzymes; <br>Thiamine pyrophosphate enzyme, central domain. The central domain of TPP enzymes contains a 2-fold Rossman fold.. 
PF02775 TPP_enzymes_C; <br>Thiamine pyrophosphate enzyme, C-terminal TPP binding domain. 
PF02776 TPP_enzymes_N; <br>Thiamine pyrophosphate enzyme, N-terminal TPP binding domain. 
PF01963 TraB family<br>pAD1 is a hemolysin/bacteriocin plasmid originally identified in Enterococcus faecalis DS16. It encodes a mating response to a peptide sex pheromone, cAD1, secreted by recipient bacteria. Once the plasmid pAD1 is acquired, production of the pheromone ceases--a trait related in part to a determinant designated traB. However a related protein is found in C. elegans Swiss:Q94217, suggesting that members of the TraB family have some more general function. This family also includes the bacterial GumN protein. The family has a conserved GXXH motif close to the N-terminus, a conserved glutamate and a conserved arginine that may be catalytic. The family also includes a second conserved GXXH motif near the C-terminus.. 
PF02534 TRAG; TraG;<br>Type IV secretory system Conjugative DNA transfer. Pfam-B_1146 (release 5.4). These proteins contain a P-loop and walker-B site for nucleotide binding. TraG is essential for DNA transfer in bacterial conjugation.  These proteins are thought to mediate interactions between the DNA-processing (Dtr) and the mating pair formation (Mpf) systems  .  The C-terminus of this domain interacts with the relaxosome component TraM via the latter's tetramerisation domain. TraD is a hexameric ring ATPase that forms the cytoplasmic face of the conjugative pore  . The family contains a number of different DNA transfer proteins  .. 
PF00923 Transaldolase<br>Pfam-B_787 (release 3.0). 
PF00382 transcript_fac2; <br>Transcription factor TFIIB repeat. 
PF00405 transferrin; <br>
PF00868 Transglutaminas; Transglutamin_N; <br>Transglutaminase family. Pfam-B_783 (release 3.0). 
PF00912 Transglycosyl; <br>Pfam-B_558 (release 3.0). The penicillin-binding proteins are bifunctional proteins consisting of  transglycosylase and transpeptidase in the N- and C-terminus  respectively  . The transglycosylase domain catalyses the  polymerisation of murein glycan chains ( ).. 
PF00456 transketolase; <br>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 Swiss:P37941 EC:1.2.4.4.  Both these enzymes utilise thiamine pyrophosphate as a cofactor, suggesting there may be common aspects in their mechanism of catalysis.. 
PF01818 Bacteriophage translational regulator<br>The translational regulator protein regA is encoded by the T4 bacteriophage and binds to a region of messenger RNA (mRNA) that includes the initiator codon. RegA is unusual in that it represses the translation of about 35 early T4 mRNAs but does not affect nearly 200 other mRNAs  .. 
PF01997 DUF130;<br>Members of this family include Translin Swiss:Q15631 that interacts with DNA and forms a ring around the DNA. This family also includes Swiss:Q99598, that was found to interact with translin with yeast two-hybrid screen  .. 
PF02133 Permease for cytosine/purines, uracil, thiamine, allantoin<br>
PF04236 Tc5 transposase C-terminal domain<br>Pfam-B_2955 (release 6.5). 
PF00872 Transpo_mutator; <br>Transposase, Mutator family. Pfam-B_376 (release 3.0). 
PF00273 transport_prot; <br>Serum albumin family. 
PF01359 Transposase (partial DDE domain)<br>Pfam-B_394 (release 3.0). This family includes the mariner transposase  .. 
PF01610 Transposase_12;<br>Pfam-B_1015 (release 4.1). Transposase proteins are necessary for efficient DNA transposition. Contains transposases for IS204 (Swiss:Q50911)  , IS1001 (Swiss:Q06126)  , IS1096 (Swiss:Q50440)   and IS1165 Swiss:Q48788  .. 
PF01710 Transposase_14;<br>Pfam-B_1769 (release 4.1). Transposase proteins are necessary for efficient DNA transposition. This family includes insertion sequences from Synechocystis PCC 6803 three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily  .. 
PF01797 Transposase_17;<br>Transposase IS200 like. Pfam-B_1347 (release 4.2). Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS200 from E. coli.. 
PF01385 Transposase_2;<br>Probable transposase. Pfam-B_1210 (release 3.0) & Pfam-B_4602 (Release 7.5). This family includes IS891  , IS1136   and IS1341  . DUF1225, Pfam:PF06774, has now been merged into this family.. 
PF02992 Transposase family tnp2<br>Pfam-B_1531 (release 6.4). 
PF02994 L1 transposable element<br>Pfam-B_2299 (release 6.4). 
PF03017 TNP1/EN/SPM transposase<br>Pfam-B_1491 (release 6.4). 
PF03004 Plant transposase (Ptta/En/Spm family)<br>Pfam-B_1902 (release 6.4). Transposase proteins are necessary for efficient DNA transposition. This family includes various plant transposases from the Ptta and En/Spm families.. 
PF03050 Transposase_25;<br>Transposase IS66 family . Pfam-B_2526 (release 6.4). Transposase proteins are necessary for efficient DNA transposition. This family includes IS66 from Agrobacterium tumefaciens  .. 
PF03400 Transposase_27;<br>Pfam-B_2448 (release 6.6). Transposase proteins are necessary for efficient DNA transposition. This family represents bacterial IS1 transposases.. 
PF04195 Putative gypsy type transposon<br>Pfam-B_1755 (release 7.3). This family of plant genes are thought to be related to gypsy type transposons.. 
PF04693 Transposase_29;<br>Archaeal putative transposase ISC1217. Pfam-B_5730 (release 7.5). 
PF04740 LXG domain of WXG superfamily<br>Zhang D, Mifsud W, Aravind L. Pfam-B_3568 (release 7.5). This domain is present is the N-terminal region of a group of polymorphic toxin proteins in bacteria. It is predicted  to use Type VII secretion pathway to mediate export of bacterial toxins  .. 
PF04754 Putative transposase, YhgA-like<br>Pfam-B_3820 (release 7.5). This family of putative transposases includes the YhgA sequence from Escherichia coli (Swiss:P31667) and several prokaryotic homologues.. 
PF04986 Transposase_32;<br>Putative transposase. Pfam-B_5271 (release 7.6). Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases IS1294 and IS801. This is a rolling-circle transposase.. 
PF01498 Transposase_5;<br>Pfam-B_462 (release 4.0). Transposase proteins are necessary for efficient DNA transposition.  This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of C.elegans.  The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in  . Tc3 is a member of the Tc1/mariner family of transposable elements.. 
PF01527 Transposase_8;<br>Pfam-B_527 (release 4.0). 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.. 
PF03221 Transposase_Tc5;<br>Tc5 transposase DNA-binding domain. Pfam-B_2955 (release 6.5). 
PF02281 Transposase_Tn5;<br>Transposase Tn5 dimerisation domain. Pfam-B_5683 (release 5.2). Transposons are mobile DNA sequences capable of replication and insertion into the chromosome. Typically transposons code for  the transposase enzyme, which catalyses insertion, found between terminal inverted repeats. Tn5 has a unique method of self- regulation in which a truncated version of the transposase enzyme acts as an inhibitor  . The catalytic domain of the Tn5 transposon is found in Pfam:PF01609.  This domain mediates dimerisation in the known structure.. 
PF00576 HIUase/Transthyretin family<br>This family includes transthyretin that is a thyroid hormone-binding protein that transports thyroxine from the bloodstream to the brain.  However, most of the sequences listed in this family do not bind thyroid hormones. They are actually enzymes of the purine catabolism that catalyse the conversion of 5-hydroxyisourate (HIU) to OHCU [2,3].  HIU hydrolysis is the original function of the family and is conserved from bacteria to mammals; transthyretins arose by gene duplications in the vertebrate lineage  . HIUases are distinguished in the alignment from the conserved C-terminal YRGS sequence.. 
PF03896 TRAP-alpha; <br>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 the membrane  .. 
PF04051 TRAPP_Bet3; <br>Transport protein particle (TRAPP) component. Pfam-B_9946 (release 7.3) & Pfam-B_6495 (release 8.0). TRAPP plays a key role in the targeting and/or fusion of ER-to-Golgi transport vesicles with their acceptor compartment. TRAPP is a large multimeric protein that contains at least 10 subunits.  This family contains many TRAPP family proteins.  The Bet3 subunit is one of the better characterised TRAPP proteins and has a dimeric structure   with hydrophobic channels.  The channel entrances are located on a putative membrane-interacting surface that is distinctively flat, wide and decorated with positively charged residues.  Bet3 is proposed to localise TRAPP to the Golgi  .. 
PF04956 TrbC/VIRB2 family<br>Pfam-B_5261 (release 7.6) & Pfam-B_14627 (release 10.0). Conjugal transfer protein, TrbC has been identified as a subunit of the pilus precursor in bacteria. The protein undergoes three processing steps before gaining its mature cyclic structure . This family also contains several VIRB2 type IV secretion proteins. The virB2 gene encodes a putative type IV secretion system and is known to be a pathogenicity factor in Bartonella species  .. 
PF03743 Bacterial conjugation TrbI-like protein <br>Pfam-B_776 (release 7.0). Although not essential for conjugation, the TrbI protein greatly increase the conjugational efficiency  .. 
PF04610 TrbL/VirB6 plasmid conjugal transfer protein<br>Pfam-B_5275 (release 7.5) & COG3704. 
PF03461 TRCF domain<br>
PF03546 treacle; <br>Treacher Collins syndrome protein Treacle. 
PF00088 trefoil; <br>Trefoil (P-type) domain. Swissprot_feature_table. 
PF01204 Trehalase<br>Trehalase (EC:3.2.1.28) is known to recycle trehalose to glucose. Trehalose is a physiological hallmark of heat-shock response in yeast and protects of proteins and membranes against a variety of stresses. This family is found in conjunction with Pfam:PF07492 in fungi.. 
PF02358 Trehalose-phosphatase<br>Pfam-B_762 (release 5.2). This family consist of trehalose-phosphatases EC:3.1.3.12 these enzyme catalyse the de-phosphorylation of trehalose-6-phosphate to trehalose and orthophosphate.  The aligned region is present in  trehalose-phosphatases and comprises the entire length of the protein it is also found in the C-terminus of trehalose-6-phosphate synthase  EC:2.4.1.15 adjacent to the trehalose-6-phosphate synthase domain - Pfam:PF00982.  It would appear that the two equivalent genes in the  E. coli otsBA operon   otsA the trehalose-6-phosphate synthase and otsB trehalose-phosphatase (this family) have undergone gene fusion in most eukaryotes e.g. Swiss:P31688 and Swiss:P93653. Trehalose is a common disaccharide of bacteria, fungi and invertebrates that appears to play a major role in desiccation tolerance  .. 
PF03973 Triabin<br>Pfam-B_20829 (release 7.1). Triabin is a serine-protease inhibitor.. 
PF02080 TrkA;TrkA-C; <br>This domain is often found next to the Pfam:PF02254 domain.  The exact function of this domain is unknown. It has been suggested that it may bind an unidentified ligand  .  The domain is predicted to adopt an all beta structure  .. 
PF02254 KTN;TrkA-N; <br>Pfam-B_289 (Release 5.3). This domain is found in a wide variety of proteins. These protein include potassium channels Swiss:P31069, phosphoesterases Swiss:Q59027, and various other transporters.  This domain binds to NAD.. 
PF02386 Cation transport protein<br>Pfam-B_529 (release 5.2). 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 utilising ATP in the process.  TrkH a member of the family Swiss:P76769 from E. coli is a  hydrophobic membrane protein and determines the specificity and kinetics  of cation transport by the TrK system in E. coli  .. 
PF02005 N2,N2-dimethylguanosine tRNA methyltransferase<br>This enzyme EC:2.1.1.32 used S-AdoMet to methylate tRNA. The TRM1 gene of Saccharomyces cerevisiae is necessary for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNAs  . The enzyme is found in both eukaryotes and archaebacteria  . 
PF00133 tRNA synthetases class I (I, L, M and V)<br>Other tRNA synthetase sub-families are too dissimilar to be included.. 
PF00749 tRNA synthetases class I (E and Q), catalytic domain<br>Pfam-B_350 (release 2.1). Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only glutamyl and glutaminyl tRNA synthetases. In some organisms, a single glutamyl-tRNA synthetase aminoacylates both tRNA(Glu) and tRNA(Gln).. 
PF03950 tRNA synthetases class I (E and Q), anti-codon binding domain<br>Pfam-B_350 (release 2.1). Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only glutamyl and glutaminyl tRNA synthetases. In some organisms, a single glutamyl-tRNA synthetase aminoacylates both tRNA(Glu) and tRNA(Gln).. 
PF00750 tRNA synthetases class I (R)<br>Pfam-B_1276 (release 2.1). Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only arginyl tRNA synthetase.. 
PF01406 tRNA synthetases class I (C) catalytic domain<br>This family includes only cysteinyl tRNA synthetases.. 
PF01921 tRNA synthetases class I (K)<br>This family includes only lysyl tRNA synthetases from prokaryotes.. 
PF00152 tRNA synthetases class II (D, K and N) <br>
PF02081 Tryptophan RNA-binding attenuator protein<br>
PF00587 tRNA synthetase class II core domain (G, H, P, S and T)<br>MRC-LMB Genome group. Other tRNA synthetase sub-families are too dissimilar to be included. This domain is the core catalytic domain of tRNA synthetases and includes glycyl, histidyl, prolyl, seryl and threonyl tRNA synthetases.. 
PF01411 tRNA synthetases class II (A)<br>Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only alanyl-tRNA synthetases.. 
PF01974 tRNA intron endonuclease, catalytic C-terminal domain<br>Members of this family cleave pre tRNA at the 5' and 3' splice sites to release the intron EC:3.1.27.9.. 
PF02778 tRNA intron endonuclease, N-terminal domain<br>Members of this family cleave pre tRNA at the 5' and 3' splice sites to release the intron EC:3.1.27.9.. 
PF01746 tRNA (Guanine-1)-methyltransferase<br>Pfam-B_2049 (release 4.1). This is a family of tRNA (Guanine-1)-methyltransferases  EC:2.1.1.31. In E.coli K12 this enzyme catalyses the conversion of a guanosine residue to N1-methylguanine in position 37, next to the anticodon, in tRNA  .. 
PF03054 tRNA methyl transferase<br>Pfam-B_823 (release 6.4). 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  .. 
PF04558 Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1    <br>This is a region found N terminal to the catalytic domain of glutaminyl-tRNA synthetase (EC 6.1.1.18) in eukaryotes but not in Escherichia coli.\.       This region is thought to bind RNA in a non-specific manner, enhancing interactions between the tRNA and enzyme, but is not essential for enzyme function  .. 
PF04557 Glutaminyl-tRNA synthetase, non-specific RNA binding region part 2    <br>This is a region found N terminal to the catalytic domain of glutaminyl-tRNA synthetase (EC 6.1.1.18) in eukaryotes but not in Escherichia coli.\.   This region is thought to bind RNA in a non-specific manner, enhancing interactions between the tRNA and enzyme, but is not essential for enzyme function  .. 
PF02091 tRNA_synt_A;tRNA_synt_2e;<br>Glycyl-tRNA synthetase alpha subunit. 
PF02092 tRNA_synt_B; <br>Glycyl-tRNA synthetase beta subunit. 
PF00261 Tropomyosin<br>
PF03301 Tryptophan 2,3-dioxygenase<br>Pfam-B_4263 (release 6.5). 
PF04820 Tryptophan halogenase<br>Pfam-B_2531 (release 7.6). Tryptophan halogenase catalyses the chlorination of tryptophan to form 7-chlorotryptophan.  This is the first step in the biosynthesis of pyrrolnitrin, an antibiotic with broad-spectrum anti-fungal activity. Tryptophan halogenase is NADH-dependent  .. 
PF01371 Trp repressor protein<br>This protein binds to tryptophan and represses transcription of the Trp operon.. 
PF00290 trp_syntA; <br>Tryptophan synthase alpha chain. 
PF03222 Tryptophan/tyrosine permease family<br>Pfam-B_2873 (release 6.5). 
PF01509 TruB family pseudouridylate synthase (N terminal domain)<br>Pfam-B_792 (release 4.0). Members of this family are involved in modifying bases in RNA molecules.  They carry out the conversion of uracil bases to pseudouridine. This family includes TruB, a pseudouridylate synthase that specifically converts uracil 55 to pseudouridine in most tRNAs. This family also includes Cbf5p that modifies rRNA  .. 
PF01456 Tryp_mucin; <br>Mucin-like glycoprotein. Prodom_3102 (release 99.1) & Pfam-B_3837 (Release 8.0). This family of trypanosomal proteins resemble vertebrate mucins. The protein consists of three regions. The N and C terminii are conserved between all members of the family, whereas the central region is not well conserved and contains a large number of threonine residues which can be glycosylated  . Indirect evidence suggested that these genes might encode the core protein of parasite mucins, glycoproteins that were proposed to be involved in the interaction with, and invasion of, mammalian host cells. This family contains an N-terminal signal peptide.. 
PF00913 Trypanosome variant surface glycoprotein (A-type)<br>Pfam-B_1351 (release 3.0) & Pfam-B_2618 (release 8.0). The trypanosome parasite expresses these proteins to evade the immune response. This family includes a variety of surface proteins such as Trypanosoma brucei VSGs such as expression site associated gene (ESAG) 6 and 7  .. 
PF03249 Type specific antigen<br>Pfam-B_3060 (release 6.5). There are several antigenic variants in Rickettsia tsutsugamushi, and a type-specific antigen (TSA) of 56-kilodaltons located on the rickettsial surface is responsible for the variation [1,2]. TSA proteins are probably integral membrane proteins.. 
PF01166 TSC-22/dip/bun family<br>
PF04668 Twisted gastrulation (Tsg) protein conserved region<br>Pfam-B_4556 (release 7.5). Tsg was identified in Drosophila as being required to specify the dorsal-most structures in the embryo, for example amnioserosa. Biochemical experiments have revealed three key properties of Tsg: it can synergistically inhibit Dpp/BMP action in both Drosophila and vertebrates by forming a tripartite complete between itself, SOG/chordin and a BMP ligand; Tsg seems to enhance the Tld/BMP-1-mediated cleavage rate of SOG/chordin and may change the preference of site utilisation; Tsg can promote the dissociation of chordin cysteine-rich-containing fragments from the ligand to inhibit BMP signalling [1,2].  . 
PF04705 Thiostrepton-resistance methylase, N terminus<br>This region is found in some members of the SpoU-type rRNA methylase family (Pfam:PF00588).. 
PF00090 tsp_1; <br>Thrombospondin type 1 domain. 
PF02412 tsp_3;<br>Thrombospondin type 3 repeat. SwissProt & Pfam-B_2972 (Release 8.0). The thrombospondin repeat is a short aspartate rich repeat which binds to calcium ions. The repeat was initially identified in thrombospondin proteins that contained 7 of these repeats  . The repeat lacks defined secondary structure  .. 
PF03073 TspO/MBR family<br>Pfam-B_1882 (release 6.4). 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 intermediates from the cell. This reduces the activity of coproporphyrinogen III oxidase, which is thought to lead to the accumulation of a putative repressor molecule that inhibits the expression of specific photosynthesis genes. Several conserved aromatic residues are necessary for TspO function: they are thought to be involved in binding porphyrin intermediates  . In  , the rat mitochondrial peripheral benzodiazepine receptor (MBR) was shown to not only retain its structure within a bacterial outer membrane, but also to be able to functionally substitute for TspO in TspO- mutants, and to act in a similar manner to TspO in its in situ location: the outer mitochondrial membrane. The biological significance of MBR remains unclear, however. It is thought to be involved in a variety of cellular functions, including cholesterol transport in steroidogenic tissues.. 
PF02956 TT viral orf 1<br>Pfam-B_1612 (release 6.4). 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 unexplained hepatitis. ORF1 is a large 750 residue protein. The N-terminal half of this protein corresponds to the capsid protein.. 
PF02957 TT viral ORF2<br>Pfam-B_1489 (release 6.4) & Pfam-B_4693 (release 7.6). 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 unexplained hepatitis. ORF2 is a 150 residue protein. This family also includes the VP2 protein from the chicken anaemia virus which is a gyrovirus. Gyroviruses are small circular single stranded viruses. The proteins contain a set of conserved cysteine and histidine residues suggesting a zinc binding domain.. 
PF03542 Tuberin<br>Tuberous sclerosis complex (TSC) is an autosomal dominant disorder and is characterised by the presence of hamartomas in many organs, such as brain, skin, heart, lung, and kidney. It is caused by mutation either TSC1 or TSC2 tumour suppressor gene. The TSC2 gene codes for tuberin and interacts with hamartin Pfam:PF04388 , containing two coiled-coil regions, which have been shown to mediate binding to tuberin. These two proteins function within the same pathway(s) regulating cell cycle, cell growth, adhesion, and vesicular trafficking  .. 
PF00091 tubulin; <br>Tubulin/FtsZ family, GTPase domain. This family includes the tubulin alpha, beta and gamma chains, as well as the bacterial FtsZ family of proteins. Members of this family are involved in polymer formation. FtsZ is the polymer-forming protein of bacterial cell division. It is part of a ring in the middle of the dividing cell that is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ and tubulin are GTPases. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea. Tubulin is the major component of microtubules.. 
PF00418 tubulin-binding; <br>Tau and MAP protein, tubulin-binding repeat. This family includes the vertebrate proteins MAP2, MAP4 and Tau, as well as other animal homologs. MAP4 is present in many tissues but is usually absent from neurons; MAP2 and Tau are mainly neuronal. Members of this family have the ability to bind to and stabilise microtubules. As a result, they are involved in neuronal migration, supporting dendrite elongation, and regulating microtubules during mitotic metaphase. Note that Tau (Swiss:P10636) is involved in neurofibrillary tangle formation in Alzheimer's disease and some other dementias. This family features a C-terminal microtubule binding repeat that contains a conserved KXGS motif  .. 
PF01021 TYA transposon protein<br>Pfam-B_90 (release 3.0). Ty are yeast transposons.\.   A 5.7kb transcript codes for p3 a fusion protein of TYA and TYB.  The TYA protein is analogous to the gag protein of retroviruses. TYA a is cleaved to form 46kd protein which can form mature virion like particles  .. 
PF03251 Tymovirus 45/70Kd protein<br>Pfam-B_3418 (release 6.5). Tymoviruses are single stranded RNA viruses.  This family includes a protein of unknown function that has been named based on its molecular weight. Tymoviruses such as the ononis yellow mosaic tymovirus encode only three proteins. Of these two are overlapping this protein overlaps a larger ORF that is thought to be the polymerase  .. 
PF00983 Tymovirus coat protein<br>Pfam-B_1429 (release 2.1). 
PF00264 tyrosinase; <br>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 Pfam:PF00372.. 
PF03064 HSV U79 / HCMV P34<br>Pfam-B_2985 (release 6.4). This family represents herpes virus protein U79 and  cytomegalovirus early phosphoprotein P34 (UL112).. 
PF02134 UBACT_repeat;<br>Repeat in ubiquitin-activating (UBA) protein. 
PF01977 DUF117; UPF0096; <br>3-octaprenyl-4-hydroxybenzoate carboxy-lyase. This family has been characterised as 3-octaprenyl-4- hydroxybenzoate carboxy-lyase enzymes  . This enzyme catalyses the third reaction in ubiquinone biosynthesis. For optimal activity the carboxy-lase was shown to require Mn2+  .. 
PF01209 ubiE/COQ5 methyltransferase family<br>
PF03981 Ubiquinol-cytochrome C chaperone <br>Pfam-B_5272 (release 7.2). 
PF02271 Ubiquinol-cytochrome C reductase complex 14kD subunit<br>Pfam-B_4192 (release 5.2). The ubiquinol-cytochrome C reductase complex (cytochrome bc1 complex) is a respiratory multienzyme complex  . This Pfam family represents the 14kD (or VI) subunit of the complex which is not directly involved in electron transfer, but has a role in assembly of the complex  .. 
PF02320 Ubiquinol-cytochrome C reductase hinge protein<br>Pfam-B_11849 (release 5.2). The ubiquinol-cytochrome C reductase complex (cytochrome bc1 complex) is a respiratory multienzyme complex  . This Pfam family represents the 'hinge' protein of the complex which is thought to mediate formation of the cytochrome c1 and cytochrome c complex.. 
PF02921 Ubiquinol cytochrome reductase transmembrane region<br>Each subunit of the cytochrome bc1 complex provides a single helix (this family) to make up the transmembrane region of the complex.. 
PF02939 UcrQ family<br>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. . 
PF00984 UDP-glucose/GDP-mannose dehydrogenase family, central domain<br>Pfam-B_1105 (release 3.0). The UDP-glucose/GDP-mannose dehydrogenaseses are a small group of enzymes which possesses the ability to catalyse the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde  intermediate  .. 
PF03720 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain<br>Pfam-B_1105 (release 3.0). The UDP-glucose/GDP-mannose dehydrogenaseses are a small group of enzymes which possesses the ability to catalyse the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde  intermediate  .. 
PF03721 UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain<br>Pfam-B_1105 (release 3.0). The UDP-glucose/GDP-mannose dehydrogenaseses are a small group of enzymes which possesses the ability to catalyse the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde  intermediate  .. 
PF01704 UTP--glucose-1-phosphate uridylyltransferase<br>Pfam-B_1634 (release 4.1). 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 uridylyltransferase catalyses the interconversion of MgUTP + glucose-1-phosphate and UDP-glucose + MgPPi  . UDP-glucose is an important intermediate in mammalian carbohydrate interconversion involved in various metabolic roles depending on tissue type  . In Dictyostelium (slime mold) mutants in this enzyme abort the development cycle  . Also within the family is UDP-N-acetylglucosamine Swiss:Q16222 or AGX1   and two hypothetical proteins from Borrelia burgdorferi the lyme disease  spirochaete Swiss:O51893 and Swiss:O51036.. 
PF00201 UDP-glucoronosyl and UDP-glucosyl transferase<br>
PF03152 Ubiquitin fusion degradation protein UFD1<br>Pfam-B_3272 (release 6.5). Post-translational ubiquitin-protein conjugates are recognised for degradation by the ubiquitin fusion degradation (UFD) pathway. Several proteins involved in this pathway have been identified  . This family includes UFD1, a 40kD protein that is essential for vegetative cell viability  . The human UFD1 gene is expressed at high levels during embryogenesis, especially in the eyes and in the inner ear primordia and is thought to be important in the determination of ectoderm-derived structures, including neural crest cells. In addition, this gene is deleted in the CATCH-22 (cardiac defects, abnormal facies, thymic hypoplasia, cleft palate and hypocalcaemia with deletions on chromosome 22) syndrome. This clinical syndrome is associated with a variety of developmental defects, all characterised by microdeletions on 22q11.2. Two such developmental defects are the DiGeorge syndrome OMIM:188400, and the velo-cardio- facial syndrome OMIM:145410. Several of the abnormalities associated  with these conditions are thought to be due to defective neural crest cell differentiation  .. 
PF02512 UK_protein; <br>Virulence determinant. Pfam-B_2106 (release 5.4). 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  .. 
PF03044 UL16_UL94; <br>Herpesvirus UL16/UL94 family. Pfam-B_4392 (release 6.4). This family groups together HSV-1 UL16 Swiss:P10200, HSV-6 ORF11R Swiss:P24442, EHV-1 46 Swiss:P28970, HCMV UL94 Swiss:P16800, EBV BGLF2 Swiss:P03221 and VZV 44 Swiss:P09293. UL16 protein may play a role in capsid maturation including DNA  packaging/cleavage  . In immunofluorescence studies  , UL16 was localised to the nucleus of infected cells in areas containing high concentrations of HSV capsid proteins. These nuclear compartments have been described previously as viral assemblons   and are distinct from compartments containing replicating DNA. Localisation within assemblons argues for a role of UL16 encoded protein in capsid assembly or maturation  .. 
PF03252 UL21; <br>Pfam-B_3264 (release 6.5). The UL21 protein appears to be a dispensable component in herpesviruses  .. 
PF01499 UL25; <br>Herpesvirus UL25 family. Pfam-B_700 (release 4.0). The herpesvirus UL25 gene product is a virion component involved in virus penetration   and capsid assembly.  The product of the UL25 gene is required for packaging but not cleavage of replicated viral DNA  . This family includes a number of herpesvirus proteins: EHV-1 36, EBV BVRF1 Swiss:P03233, HCMV UL77 Swiss:P16726, ILTV ORF2 Swiss:P23987, and VZV gene 34 Swiss:P09287.. 
PF04496 UL35; <br>Herpesvirus UL35 family . Pfam-B_3981 (release 7.5). UL35 represents a true late gene which encodes a 12-kDa  capsid protein  .. 
PF03970 UL37;<br>Herpesvirus UL37 tegument protein. UL37 interacts with UL36, which is thought to be an important early step in tegumentation during virion morphogenesis in the cytoplasm  .. 
PF02282 UL42; <br>DNA polymerase processivity factor (UL42). Pfam-B_5119 (release 5.2). The DNA polymerase processivity factor (UL42) of herpes simplex virus forms a heterodimer with UL30 to create the viral DNA polymerase complex. UL42 functions to increase the processivity of polymerisation and makes little contribution to the catalytic activity of the  polymerase.. 
PF03117 UL49; <br>Pfam-B_2110 (release 6.5). Members of this family, found in several herpesviruses, include EBV BFRF2 Swiss:P14347 and other UL49 proteins (e.g. HCMVA UL49 Swiss:P16786, HSV6 U33 Swiss:P52441). There are eight conserved cysteine residues in this alignment, all lying towards the C-terminus. Their function is unknown.. 
PF03121 UL52_UL70; <br>Herpesviridae UL52/UL70 DNA primase. Pfam-B_203 (release 6.5). Herpes simplex virus type 1 DNA replication in host cells is known to be mediated by seven viral-encoded proteins, three of which form a heterotrimeric DNA helicase-primase complex. This complex consists of UL5, UL8, and UL52 subunits.  Heterodimers consisting of UL5 and UL52 have been shown to retain both helicase and primase activities. Nevertheless, UL8 is still essential for replication: though it lacks any DNA binding or catalytic activities, it is involved in the transport of UL5-UL52 and it also interacts with other replication proteins. The molecular mechanisms of the UL5-UL52 catalytic activities are not known. While UL5 is associated with DNA helicase activity and UL52 with DNA primase activity, the helicase activity requires the interaction of UL5 and UL52 [see 2,3]. It is not known if the primase activity can be maintained by UL52 alone. The region encompassed by residues 610-636 of HSV1 UL52 Swiss:P10236 is thought to contain a divalent metal cation binding motif. Indeed, this region contains several aspartate and  glutamate residues that might be involved in divalent cation binding. The biological significance of UL52-UL8 interaction is not known. Yeast two-hybrid analysis together with immunoprecipitation experiments  have shown that the HSV1 UL52 region between residues 366-914 is essential for this interaction, while the first 349 N-terminal residues are dispensable  .  This family also includes protein UL70 from cytomegalovirus (CMV, a subgroup of the Herpesviridae) strains (e.g. Swiss:P17149), which, by analogy with UL52, is thought to have DNA primase activity. Indeed, CMV  strains also possess a DNA helicase-primase complex, the other subunits  being protein UL105 (with known similarity to HSV1 UL5) and protein UL102.. 
PF03049 UL79; <br>Pfam-B_2433 (release 6.4). Members of this family are functionally uncharacterised proteins from herpesviruses. This family groups together HSV-6 U52 Swiss:P52469, HVS-1 18 Swiss:Q01003 and HCMV UL79 Swiss:P16752.. 
PF03043 UL87; <br>Herpesvirus UL87 family. Pfam-B_1736 (release 6.4). Members of this family are functionally uncharacterised. This family groups together EBV BcRF1 Swiss:P25215, HSV-6 U58 Swiss:P24437, HVS-1 24 Swiss:Q01007 and HCMV UL87 Swiss:P16730. The proteins range from 575 to 950 amino acids in length.. 
PF03048 2111; UL92; <br>Pfam-B_2111 (release 6.4). 
PF03038 UL95; <br>Pfam-B_2060 (release 6.4). Members of this family, found in several herpesviruses, include EBV BGLF3 Swiss:P03220 and other UL95 proteins (e.g. HCMV UL95 Swiss:P16801,  HVS-1 34 Swiss:Q01023, HSV6 U67 Swiss:P24444). Their function is unknown.. 
PF04817 Umbravirus long distance movement (LDM) family <br>Pfam-B_5103 (release 7.6). The long distance movement protein of Umbraviruses mediates the movement of viral RNA through the phloem of infected plants  .. 
PF00021 u-PAR/Ly-6 domain<br>This extracellular disulphide bond rich domain is related to Pfam:PF00087.. 
PF00919 Uncharacterized protein family UPF0004<br>Pfam-B_1257 (release 3.0). This family is the N terminal half of the Prosite family. The C-terminal half has been shown to be related to MiaB proteins [1,2]. This domain is a nearly always found in conjunction with Pfam:PF04055 and Pfam:PF01938 although its function is uncertain.. 
PF03649 Uncharacterised protein family (UPF0014)<br>
PF01169 Uncharacterized protein family UPF0016<br>This family contains integral membrane proteins of unknown function. Most members of the family contain two copies of a region that contains an EXGD motif. Each of these regions contains three predicted transmembrane regions.. 
PF01170 Putative RNA methylase family UPF0020<br>This domain is probably a methylase.  It is associated with the THUMP domain that also occurs with RNA modification domains  .. 
PF01171 UPF0021;ATP_bind3; <br>This family of proteins belongs to the PP-loop superfamily  .. 
PF01172 UPF0023; <br>Shwachman-Bodian-Diamond syndrome (SBDS) protein . This family is highly conserved in species ranging from archaea to vertebrates and plants. The family contains several Shwachman-Bodian-Diamond syndrome (SBDS) proteins from both mouse and humans. Shwachman-Diamond syndrome is an autosomal recessive disorder with clinical features that include pancreatic exocrine insufficiency, haematological dysfunction and skeletal abnormalities.  It is characterised by bone marrow failure and leukemia predisposition.  Members of this family play a role in RNA metabolism    .  In yeast these proteins have been shown to be critical for the release and recycling of the nucleolar shuttling factor Tif6 from pre-60S ribosomes, a key step in 60S maturation and translational activation of ribosomes  .  This data links defective late 60S subunit maturation to an inherited bone marrow failure syndrome associated with leukemia predisposition  .. 
PF01142 tRNA pseudouridine synthase D (TruD)<br>TruD is responsible for synthesis of pseudouridine from uracil-13 in transfer RNAs  .  The structure of TruD reveals an overall V-shaped molecule which contains an RNA-binding cleft  .. 
PF01139 UPF0027;<br>tRNA-splicing ligase RtcB. This family of RNA ligases (EC:6.5.1.3) join 2',3'-cyclic phosphate and 5'-OH ends. They catalyse the splicing of tRNA and may also participate in tRNA repair and recovery from stress-induced RNA damage [1-3].. 
PF01205 Uncharacterized protein family UPF0029<br>
PF01256 UPF0031; carb_kinase;<br>This family is related to Pfam:PF02110 and Pfam:PF00294 implying that it also is a carbohydrate kinase. (personal obs Yeats C).. 
PF00902 UPF0032; <br>Sec-independent protein translocase protein (TatC). Pfam-B_1212 (release 3.0). The bacterial Tat system has a remarkable ability to transport folded proteins even enzyme complexes across the cytoplasmic membrane. It is structurally and mechanistically similar to the Delta pH-driven thylakoidal protein import pathway. A functional Tat system or Delta pH-dependent pathway requires three integral membrane proteins: TatA/Tha4, TatB/Hcf106 and TatC/cpTatC. The TatC protein is essential for the function of both pathways. It might be involved in twin-arginine signal peptide recognition, protein translocation and proton translocation. Sequence analysis predicts that TatC contains six transmembrane helices (TMHs), and experimental data confirmed that N- and C-termini of TatC or cpTatC are exposed to the cytoplasmic or stromal face of the membrane. The cytoplasmic N-terminus and the first cytoplasmic loop region of the Escherichia coli TatC protein are essential for protein export. At least two TatC molecules co-exist within each Tat translocon  .. 
PF01206 UPF0033; SirA;<br>Sulfurtransferase TusA. This family includes the TusA sulfurtransferases  .. 
PF02381 UPF0040; <br>This small 70 amino acid domain is found duplicated in a family of bacterial proteins. These proteins may be DNA-binding transcription factors (Pers. comm. A Andreeva & A Murzin).. 
PF03650 UPF0041;<br>Uncharacterised protein family (UPF0041). 
PF03668 UPF0042; ATP_bind2; <br>P-loop ATPase protein family. This family contains an ATP-binding site and could be an ATPase (personal obs:C Yeats).. 
PF01985 UPF0044;<br>CRS1 / YhbY (CRM) domain. Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly.  GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants  .  A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing  .\.      In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity.  These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes  .  YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome   .. 
PF01894 Uncharacterised protein family UPF0047<br>This family has no known function. The alignment contains a conserved aspartate and histidine that may be functionally important.. 
PF01458 Uncharacterized protein family (UPF0051)<br>Prodom_3219 (release 99.1). 
PF01933 Uncharacterised protein family UPF0052<br>
PF02130 Uncharacterized protein family UPF0054<br>
PF01679 UPF0057;<br>Proteolipid membrane potential modulator. Pfam-B_2192 (release 4.1). Pmp3 is an evolutionarily conserved proteolipid in the plasma membrane which, in S. pombe, is transcriptionally regulated by the Spc1 stress MAPK (mitogen-activated protein kinases) pathway. It functions to modulate the membrane potential, particularly to resist high cellular cation concentration. In eukaryotic organisms, stress-activated mitogen-activated protein kinases play crucial roles in transmitting environmental signals that will regulate gene expression for allowing the cell to adapt to cellular stress. Pmp3-like proteins are highly conserved in bacteria, yeast, nematode and plants.. 
PF01893 Uncharacterised protein family UPF0058<br>This archaebacterial protein has no known function.. 
PF02694 Uncharacterised BCR, YnfA/UPF0060 family<br>
PF02696 Uncharacterized ACR, YdiU/UPF0061 family<br>
PF03401 UPF0065; Bug;<br>Tripartite tricarboxylate transporter family receptor. Pfam-B_3343 (release 6.6). These probable extra-cytoplasmic solute receptors are strongly overrepresented in several beta-proteobacteria  .  This family, formerly known as Bug - Bordetella uptake gene (bug) product - is a family of bacterial tripartite tricarboxylate receptors of the extracytoplasmic solute binding receptor-dependent transporter group of families, distinct from the ABC and TRAP-T families  . The TctABC system has been characterised in S. typhimurium  , and TctC is the extracytoplasmic tricarboxylate-binding receptor which binds the transporters TctA and TctB, two integral membrane proteins. Complete three-component systems are found only in bacteria  .. 
PF01980 Uncharacterised protein family UPF0066<br>
PF03006 UPF0073; <br>Haemolysin-III related. Pfam-B_1581 (release 6.4). Members of this family are integral membrane proteins.  This family includes a protein with hemolytic activity from Bacillus cereus  . It has been proposed that YOL002c encodes a Saccharomyces cerevisiae protein that plays a key role in metabolic pathways that regulate lipid and phosphate metabolism  . In eukaryotes, members are seven-transmembrane pass molecules found to encode functional receptors with a broad range of apparent ligand specificities, including progestin and adipoQ receptors, and hence have been named PAQR proteins  . The mammalian members include progesterone binding proteins  . Unlike the case with GPCR receptor proteins, the evolutionary ancestry of the members of this family can be traced back to the Archaea.. 
PF02082 UPF0074; <br>Transcriptional regulator. This family is related to Pfam:PF001022 and other transcription regulation families (personal obs: Yeats C).. 
PF03702 Uncharacterised protein family (UPF0075)<br>The proteins is this family are about 370 amino acids long and have no known function.. 
PF02367 Uncharacterised P-loop hydrolase UPF0079<br>This uncharacterised family contains a P-loop.. 
PF03652 Uncharacterised protein family (UPF0081)<br>
PF01868 DUF49;<br>Domain of unknown function UPF0086. This family consists of several archaeal and eukaryotic proteins. The archaeal proteins are found to be expressed within ribosomal operons and several of the sequences are described as ribonuclease P protein subunit p29 proteins.. 
PF03007 UPF0089;<br>Wax ester synthase-like Acyl-CoA acyltransferase domain. Pfam-B_1896 (release 6.4). This domain is found in wax ester synthase genes such as Swiss:Q8GGG1. In these proteins this domain catalyses the CoA dependent acyltransferase reaction with fatty alcohols to form wax esters  .. 
PF03653 Uncharacterised protein family (UPF0093)<br>
PF02016 UPF0094; Peptidase_U61; <br>Muramoyl-tetrapeptide carboxypeptidase hydrolyses a peptide bond between a di-basic amino acid and the C-terminal D-alanine in the tetrapeptide moiety in peptidoglycan. This cleaves the bond between an L- and a D-amino acid.\.       The function of this activity is in murein recycling. This family also includes the microcin c7 self-immunity protein Swiss:Q47511. This family corresponds to Merops family S66.. 
PF01981 DUF119;UPF0099; Pep-tRNA_hydrol; <br>Peptidyl-tRNA hydrolase PTH2. Peptidyl-tRNA hydrolases are enzymes that release tRNAs from peptidyl-tRNA during translation.. 
PF02021 Uncharacterised protein family UPF0102<br>The function of this family is unknown.. 
PF01875 DUF52; UPF0103; <br>This family contains members from all branches of life.  The molecular function of this protein is unknown, but Memo (mediator of ErbB2-driven cell motility) a human protein is included in this family  . It has been suggested that Memo controls cell migration by relaying extracellular chemotactic signals to the microtubule cytoskeleton  .. 
PF03706 Uncharacterised protein family (UPF0104)<br>This family of proteins are integral membrane proteins.  These proteins are uncharacterised but contain a conserved PG motif. Some members of this family are annotated as dolichol-P-glucose synthetase and contain a Pfam:PF00535 domain.. 
PF03656 UPF0108; <br>The Pam16 protein (Swiss:P42949) is the fifth essential subunit of the pre-sequence translocase-associated protein import motor (PAM)  .  In Saccharomyces cerevisiae, Pam16 is required for preprotein translocation into the matrix, but not for protein insertion into the inner membrane  .  Pam16 has a degenerate J domain.  J-domain proteins play important regulatory roles as co-chaperones, recruiting Hsp70 partners and accelerating the ATP-hydrolysis step of the chaperone cycle  .  Pam16's J-like domain strongly interacts with Pam18's J domain, leading to a productive interaction of Pam18 with mtHsp70 at the mitochondria import channel  .  Pam18 stimulates the ATPase activity of mtHsp70.. 
PF03657 Uncharacterised protein family (UPF0113)<br>
PF03350 Uncharacterized protein family, UPF0114<br>Pfam-B_3587 (release 6.5) & Pfam-B_10597 (release 10.0). 
PF01594 DUF20; <br>Domain of unknown function DUF20. Pfam-B_495 (release 4.1). This transmembrane region is found in putative permeases and  predicted transmembrane proteins it has no known function. It is not clear what source suggested that these proteins may be permeases and this information should be treated with caution.. 
PF03715 UPF0120; <br>At least one member, Noc2p from yeast, is required for a late step in 60S subunit export from the nucleus  . It has also been shown to co-precipitate with Nug1p, a nuclear GTPase also required for  ribosome nucleus export  . This family was formerly known as UPF0120.. 
PF03661 Uncharacterised protein family (UPF0121)<br>Uncharacterised integral membrane protein family.. 
PF04297 Putative helix-turn-helix protein, YlxM / p13 like<br>Members of this family are predicted to contain a helix-turn-helix motif,  for example residues 37-55 in Mycoplasma mycoides p13 (Swiss:O05290). Genes encoding family members are often part of operons that encode  components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway  .. 
PF03660 UPF0123; <br>This family of proteins the superfamily of PHD-finger proteins. At least one example, from mouse,  may act as a chromatin-associated protein . The S. pombe ini1 gene is essential, required for splicing  . It is localised in the nucleus, but not detected in the nucleolus and can be complemented by human ini1  .. 
PF03658 UPF0125;<br>RnfH family Ubiquitin. A member of the RnfH family of the ubiquitin superfamily. Members of this family strongly co-occur in two distinct gene neighborhood  contexts. In one it is associated with a START domain protein, a  membrane protein SmpA and the transfer mRNA binding protein SmpB.  This association suggests a possible role in the SmpB-tmRNA-based  tagging and degadation system of bacteria, which is interesting given that other members of the ubiquitin system are analogously involved  in protein-tagging and degradation across eukaryotes and various  prokaryotes. The second context in which the RnfH genes are present  is in a  membrane associated complex involved in transporting  electrons for various reductive reactions such as nitrogen  fixation  .. 
PF03458 UPF0126 domain<br>Domain always found as pair in bacterial membrane proteins of unknown function. This domain contains three transmembrane helices. The conserved glycines are suggestive of  an ion channel (C. Yeats unpublished obs.).. 
PF03673 Uncharacterised protein family (UPF0128)<br>The members of this family are about 240 amino acids in length.  The proteins are as yet uncharacterised.. 
PF03647 UPF0136; TMEM14; <br>Transmembrane proteins 14C. Pfam-B_2984 (release 7.0). This family of short membrane proteins are as yet uncharacterised.. 
PF03677 Uncharacterised protein family (UPF0137)<br>This family includes GP6-D a virulence plasmid encoded protein.. 
PF03669 Uncharacterised protein family (UPF0139)<br>
PF03686 Uncharacterised protein family (UPF0146)<br>The function of this family of proteins is unknown.. 
PF03685 Uncharacterised protein family (UPF0147)<br>This family of small proteins have no known function.. 
PF03695 Uncharacterised protein family (UPF0149)<br>The protein in this family are about 190 amino acids long.  The function of these proteins is unknown.. 
PF03681 Uncharacterised protein family (UPF0150)<br>This family of small proteins is uncharacterised. In Swiss:Q9A3L8 this domain is found next to a DNA binding helix-turn-helix domain Pfam:PF01402, which suggests that this is some kind of ligand binding domain. The structure of this domain suggests that these domains oligomerise and due to structural similarities may bind to RNA. The monomer adopts an alpha-beta-beta-beta-alpha fold and forms a homotetramer. Based on the properties and functions of structural homologues of the HB8 monomer, the protein is speculated to be involved in RNA metabolism, including RNA binding and cleavage  .. 
PF03692 UPF0153; FliB;<br>Putative zinc- or iron-chelating domain. This family of proteins contains 8 conserved cysteines. It has in the past been annotated as being one of the complex of proteins of the flagellar Fli complex.  However this was due to a mis-annotation of the original Salmonella LT2 Genbank entry of 'fliB'. With all its conserved cysteines it is possibly a domain that chelates iron or zinc ions.. 
PF03672 Uncharacterised protein family (UPF0154)<br>This family contains a set of short bacterial proteins of unknown function.. 
PF03693 Uncharacterised protein family (UPF0156)<br>This family of proteins are about 80 amino acids in length and their function is unknown. The proteins contain a conserved GRY motif. This family appears to be related to ribbon-helix-helix DNA-binding proteins.. 
PF04229 UPF0157;<br>This family has been suggested to belong to the nucleotidyltransferase superfamily  .  It occurs at the C-terminus of dephospho-CoA kinase (CoaE) in a number of cases, where it plays a role in the proper folding of the enzyme  .. 
PF03682 Uncharacterised protein family (UPF0158)<br>
PF03690 Uncharacterised protein family (UPF0160)<br>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 Pfam:PF01368.. 
PF03687 Uncharacterised protein family (UPF0164)<br>This family of uncharacterised proteins are only found in Treponema pallidum. They contain a putative signal peptide so may be secreted proteins.. 
PF03691 Uncharacterised protein family (UPF0167)<br>The proteins in this family are about 200 amino acids long and each contain 3 CXXC motifs.. 
PF03666 UPF0171;<br>Nitrogen Permease regulator of amino acid transport activity 3. This family, also known in yeasts as Rmd11, complexes with NPR2, Pfam:PF06218. This complex heterodimer is responsible for inactivating TORC1. an evolutionarily conserved protein complex that controls cell size via nutritional input signals, specifically, in response to amino acid starvation.. 
PF03665 Uncharacterised protein family (UPF0172)<br>In Chlamydomonas reinhardtii the protein TLA1 (truncated light-harvesting chlorophyll antenna size) apparently regulates genes that define the chlorophyll-a antenna size in the photosynthetic apparatus  . This family was formerly known as UPF0172.. 
PF02476 US2 family<br>Pfam-B_2256 (release 5.4). This is a family of unique short (US) region proteins from the  herpesvirus strain. The US2 family have no known function. . 
PF03683 Uncharacterised protein family (UPF0175)<br>This family contains small proteins of unknown function.. 
PF03698 Uncharacterised protein family (UPF0180)<br>The members of this family are small uncharacterised proteins.. 
PF03701 Uncharacterised protein family (UPF0181)<br>This family contains small proteins of about 50 amino acids of unknown function.\.       The family includes YoaH Swiss:P76260.. 
PF03670 Uncharacterised protein family (UPF0184)<br>
PF04050 Up-frameshift suppressor 2 <br>Pfam-B_14721 (release 7.3);. Transcripts harbouring premature signals for translation termination  are recognised and rapidly degraded by eukaryotic cells through a  pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3)  are required for nonsense-mediated mRNA decay  .. 
PF01255 UPF0015;UPP_synthetase; <br>Putative undecaprenyl diphosphate synthase. Previously known as uncharacterized protein family UPF0015, a single member of this family Swiss:O82827 has been identified as an undecaprenyl diphosphate synthase  .. 
PF00449 urease; <br>Urease alpha-subunit, N-terminal domain. The N-terminal domain is a composite domain and plays a major  trimer stabilising role by contacting the catalytic domain of the symmetry related alpha-subunit.. 
PF00699 Urease beta subunit<br>Pfam-B_405 (release 2.1). This subunit is known as alpha in Heliobacter.. 
PF00547 urease_gamma; <br>Urease, gamma subunit. Urease is a nickel-binding  enzyme that  catalyses the hydrolysis of  urea  to  carbon  dioxide and ammonia.. 
PF01774 UreD urease accessory protein<br>Pfam-B_1109 (release 4.2). UreD is a urease accessory protein. Urease Pfam:PF00449 hydrolyses  urea into ammonia and carbamic acid  . UreD is involved in  activation of the urease enzyme via the UreD-UreF-UreG-urease complex   and is required for urease nickel metallocenter assembly  .  See also UreF Pfam:PF01730, UreG Pfam:PF01495. . 
PF05194 UreE urease accessory protein, C-terminal domain<br>Pfam-B_6279 (release 6.1). UreE is a urease accessory protein. Urease Pfam:PF00449 hydrolyses  urea into ammonia and carbamic acid. The C-terminal region of members of this family contains a His rich Nickel binding site.. 
PF01730 UreF<br>Pfam-B_2037 (release 4.1). This family consists of the Urease accessory protein  UreF. The urease enzyme (urea amidohydrolase) hydrolyses urea into ammonia and carbamic acid  .  UreF is proposed to modulate the activation process of urease by eliminating the binding of nickel irons to  noncarbamylated protein  .. 
PF04115 Ureidoglycolate hydrolase <br>Pfam-B_9183 (release 7.3);. Ureidoglycolate hydrolase (EC:3.5.3.19) carried out the third step in the degradation of allantoin.. 
PF01014 Uricase<br>Pfam-B_1333 (release 3.0). 
PF01208 Uroporphyrinogen decarboxylase (URO-D)<br>
PF01175 Urocanase<br>
PF02083 Urotensin II<br>
PF02393 US22 like<br>Pfam-B_1016 (release 5.2). US22 proteins have been found across many animal DNA viruses and some vertebrates  . The name sake of this family US22  Swiss:P09722 is an early nuclear protein that is secreted from  cells  .  The US22 family may have a role in virus replication  and pathogenesis  . Domain analysis showed that US22 proteins\.       usually contain two copies of conserved modules which is  homologous to several other families like SMI1 and SYD (commonly  called SUKH superfamily)  . Bacterial operon analysis revealed that all bacterial SUKH members function as immunity proteins against various toxins. Thus US22 family is predicted to counter diverse anti-viral responses by interacting with specific host proteins  . . 
PF00577 Outer membrane usher protein<br>MRC-LMB Genome group and Prosite. In Gram-negative bacteria the biogenesis of fimbriae (or pili) requires a two- component assembly and transport system which is composed of a periplasmic chaperone and an outer membrane protein which has been termed a molecular 'usher' [1-3].  The usher protein is rather large (from 86 to 100 Kd) and seems to be mainly composed of membrane-spanning beta-sheets, a structure reminiscent of porins. Although the degree of sequence similarity of these proteins is not very high they share a number of characteristics. One of these is the presence of two pairs of cysteines, the first one located in the N-terminal part and the second at the C-terminal extremity that are probably involved in disulphide bonds. The best conserved region is located in the central part of these proteins [4-5].. 
PF04871 Uso1 / p115 like vesicle tethering protein, C terminal region<br>Pfam-B_6073 (release 7.6). Also known as General vesicular transport factor, Transcytosis associate protein (TAP) and Vesicle docking protein, this myosin-shaped molecule consists of an N-terminal globular head region, a coiled-coil tail which mediates dimerisation, and a short C-terminal acidic region  .  p115  tethers COP1 vesicles to the Golgi by binding the coiled coil proteins giantin (on the vesicles) and GM130 (on the Golgi), via its C-terminal  acidic region.  It is required for intercisternal transport in the golgi stack. This family consists of the acidic C-terminus, which binds to the golgins giantin and GM130.  p115 is thought to juxtapose two membranes by binding giantin with one acidic region, and GM130 with another  .. 
PF04869 Uso1 / p115 like vesicle tethering protein, head region<br>Pfam-B_6073 (release 7.6). Also known as General vesicular transport factor, Transcytosis associated protein (TAP) and Vesicle docking protein, this myosin-shaped molecule consists of an N-terminal globular head region, a coiled-coil tail which mediates dimerisation, and a short C-terminal acidic region  .  p115 tethers COP1 vesicles to the Golgi by binding the coiled coil proteins giantin (on the vesicles) and GM130 (on the Golgi), via its C-terminal acidic region.  It is required for intercisternal transport in the golgi stack.\. This family consists of part of the head region. The head region is highly conserved, but its function is unknown.  It does not seem to be essential for vesicle tethering  .  The N-terminal part of the head region, not within this family, contains context-detected Armadillo/beta-catenin-like repeats (Pfam:PF00514).. 
PF00582 Universal stress protein family<br>MRC-LMB Genome group. The universal stress protein UspA Swiss:P28242    is a small cytoplasmic  bacterial protein whose expression  is enhanced when the cell is exposed to stress agents. UspA enhances the rate of cell survival during  prolonged exposure to such conditions, and may provide a general "stress endurance" activity.  The crystal structure of Haemophilus influenzae UspA   reveals  an  alpha/beta fold similar to that of the Methanococcus jannaschii  MJ0577 protein, which binds ATP  , though UspA lacks ATP-binding activity.. 
PF03253 Urea transporter<br>Pfam-B_3193 (release 6.5). Members of this family transport urea across membranes. The family includes a bacterial homologue Swiss:Q9S408. . 
PF01099 Uterglobin; <br>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  .. 
PF03998 Utp11 protein<br>Pfam-B_6404 (release 7.3). 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 large RNP complex has been termed the small subunit (SSU) processome  .. 
PF04003 Dip2/Utp12 Family<br>Pfam-B_10105 (release 7.3). 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 Swiss:Q12220  .. 
PF04615 Utp14 protein<br>Pfam-B_5404 (release 7.4). 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 large RNP complex has been termed the small subunit (SSU) processome  .. 
PF03851 UV-endonuclease UvdE<br>TIGRFAMs, Griffiths-Jones SR. 
PF00580 UvrD/REP helicase N-terminal domain<br>MRC-LMB Genome group.. 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. Swiss:P23478, Swiss:P08394 have large insertions near to the carboxy-terminus relative to other members of the family.. 
PF02614 Glucuronate isomerase<br>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 D-galacturonate <=> D-tagaturonate.  It is not however  clear where the experimental evidence for this functional assignment came from and thus this family has no literature reference.. 
PF03786 D-mannonate dehydratase (UxuA)<br>UxuA (this family) and UxuB are required for hexuronate degradation.. 
PF03223 V-ATPase subunit C<br>Pfam-B_2945 (release 6.5). 
PF03179 Vacuolar (H+)-ATPase G subunit<br>Pfam-B_1274 (release 6.5). 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 in several organelles. They are also found in the plasma membranes of some specialised cells. V-ATPases consist of peripheral (V1) and membrane integral (V0) heteromultimeric complexes. The G subunit is part of the V1 subunit, but is also thought to be strongly attached to the V0 complex. It may be involved in the coupling of ATP degradation to H+ translocation.. 
PF03224 V-ATPase_H; <br>Pfam-B_2481 (release 6.5). The yeast Saccharomyces cerevisiae vacuolar H+-ATPase (V-ATPase) is a multisubunit complex responsible for acidifying organelles. It functions as an ATP dependent proton pump that transports protons across a lipid bilayer.  This domain corresponds to the N terminal domain of the H subunit of V-ATPase.  The N-terminal domain is required for the activation of the complex whereas the C-terminal domain is required for coupling ATP hydrolysis to proton translocation  .. 
PF01639 Viral family 110<br>Pfam-B_1518 (release 4.1). This family of viral proteins is known as the 110 family  . The function of members of this family is unknown. The family contains a central cysteine rich region with eight conserved cysteines. Some members of the family contains two copies of the cysteine rich region Swiss:P18560. . 
PF03402 Vomeronasal organ pheromone receptor family, V1R<br>Pfam-B_3057 (release 6.6). This family represents one of two known vomeronasal organ receptor families, the V1R family (after  ).. 
PF02830 V4R domain<br>The V4R (vinyl 4 reductase) domain is a predicted small molecular binding domain, that may bind to hydrocarbons  .. 
PF01496 V_ATPase_sub_a; <br>V-type ATPase 116kDa subunit family  . Pfam-B_446 (release 4.0). This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i.  The V-type ATPases family are proton pumps that acidify intracellular compartments  in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes  .  The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices  it has a hydrophilic amino terminal and a hydrophobic carboxy  terminal [1,2]. It has roles in proton transport and assembly of the V-type ATPase complex [1,2].  This subunit is encoded by two homologous gene in yeast VPH1 and STV1  .. 
PF02346 Chordopoxvirus fusion protein<br>Pfam-B_822 (release 5.2). This is a family of viral fusion proteins from the chordopoxviruses. Swiss:P26312 a 14-kDa Vaccinia Virus protein  has been demonstrated to function as a viral fusion protein mediating  cell fusion at endosmomal (low) pH  .. 
PF02691 Vacuolating cyotoxin<br>Pfam-B_436 (release 5.5). This family consists of Vacuolating cyotoxin proteins form Proteobacteria. These proteins are an important virulence determinate in H. pylori and induce cytoplasmic vacuolation in a variety of mammalian cell lines  .. 
PF03077 VACA; <br>Putative vacuolating cytotoxin. Pfam-B_2866 (release 6.4). This family contains a number of Helicobacter outer membrane proteins with multiple copies of this small conserved region.. 
PF04333 VacJ like lipoprotein<br>VacJ is required for the intercellular spreading of Shigella flexneri. It is attached to the outer membrane by a lipid anchor  .. 
PF04294 VanW like protein<br>Family members include vancomycin resistance protein W (VanW). Genes encoding members of this family have been found in vancomycin  resistance gene clusters vanB   and vanG  .  The function of VanW is  unknown.. 
PF02557 D-alanyl-D-alanine carboxypeptidase<br>
PF04892 VanZ like family <br>Pfam-B_5529 (release 7.6). This family contains several examples of the VanZ protein, but also contains examples of phosphotransbutyrylases  .. 
PF03490 Variant-surface-glycoprotein phospholipase C<br>
PF01992 ATP synthase (C/AC39) subunit<br>This family includes the AC39 subunit from vacuolar ATP synthase Swiss:P32366  , and the C subunit from archaebacterial ATP synthase  .  The family also includes subunit C from the Sodium transporting ATP synthase from Enterococcus hirae Swiss:P43456  .. 
PF01991 ATP synthase (E/31 kDa) subunit<br>This family includes the vacuolar ATP synthase E subunit  , as well as the archaebacterial ATP synthase E subunit  .. 
PF01505 Major Vault Protein repeat<br>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.. 
PF01847 von Hippel-Lindau disease tumour suppressor protein<br>VHL forms a ternary complex with the elonginB  Swiss:O44226 and elonginC Swiss:O13292 proteins. This complex binds Cul2, which then is involved in regulation of vascular endothelial growth factor Swiss:P15692 mRNA.. 
PF02209 Villin headpiece domain<br>Alignment kindly provided by SMART. 
PF04702 Vicilin N terminal region<br>This region is found in plant seed storage proteins, N-terminal to the Cupin domain (Pfam:PF00190). In Macadamia integrifolia (Swiss:Q9SPL4), this region is processed into peptides of approximately 50 amino acids containing a C-X-X-X-C-(10-12)X-C-X-X-X-C motif.  These peptides exhibit antimicrobial activity in vitro  .. 
PF00559 Retroviral Vif (Viral infectivity) protein<br>Human immunodeficiency virus type 1 (HIV-1) Vif is required for  productive infection of T lymphocytes and macrophages. Virions  produced in the absence of Vif have abnormal core morphology and  those produced in primary T cells carry immature core proteins  and low levels of mature capsid.. 
PF01044 Vinculin family<br>Pfam-B_1420 (release 3.0). 
PF02236 Vir_DNA_binding; <br>Viral DNA-binding protein, all alpha domain. Pfam-B_1651 (release 5.2). This family represents a domain of the viral DNA- binding protein, a multi functional protein involved in DNA  replication and transcription control.. 
PF03728 Vir_DNA_Zn_bind; <br>Viral DNA-binding protein, zinc binding domain. Pfam-B_1651 (release 5.2). This family represents the zinc binding domain of the viral DNA- binding protein, a multi functional protein involved in DNA  replication and transcription control.  Two copies of this domain  are found at the C-terminus of many members of the family.. 
PF00426 VP4;<br>Outer Capsid protein VP4 (Hemagglutinin). Pfam-B_161 (release 1.0). 
PF03225 Vir_Hsp90; <br>Viral heat shock protein Hsp90 homologue . Pfam-B_2880 (release 6.5). 
PF04530 Viral Beta C/D like family<br>Pfam-B_4973 (release 7.5). Family of ssRNA positive-strand viral proteins.  Conserved region found in the Beta C and Beta D transcripts.. 
PF00729 Viral coat protein (S domain)<br>Pfam-B_870 (release 2.1). 
PF00747 viral_DNA_bp; <br>ssDNA binding protein. Pfam-B_490 (release 2.1). This protein is found in herpesviruses and is needed for replication.. 
PF01443 Viral (Superfamily 1) RNA helicase<br>Prodom_1256 (release 99.1). Helicase activity for this family has been demonstrated   and NTPase activity  . This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis  .. 
PF04521 ssRNA positive strand viral 18kD cysteine rich protein<br>Pfam-B_2612 (release 7.5). 
PF00998 HCV_RdRP; Viral_RdRP; <br>Viral RNA dependent RNA polymerase. Pfam-B_315 (release 3.0). This family includes viral RNA dependent RNA polymerase enzymes from hepatitis C virus and various plant viruses.. 
PF02407 Putative viral replication protein<br>Pfam-B_1223 (release 5.2). This is a family of viral ORFs from various plant and animal ssDNA circoviruses.  Published evidence to  support the annotated function "viral replication  associated protein" has not be found.. 
PF05101 Type IV secretory pathway, VirB3-like protein<br>This family includes the Type IV secretory pathway VirB3 protein, that is found associated with bacterial inner and outer membranes  . The family also includes the conjugal transfer protein TrbD family that contains a nucleotide binding motif and may provide energy for the export of DNA or the export of other Trb proteins  .. 
PF04335 VirB8 protein<br>Pfam-B_1984 (release 7.3). VirB8 is a bacterial virulence protein with cytoplasmic, transmembrane, and periplasmic regions. It is thought that it is a primary constituent of a DNA transporter. The periplasmic region interacts with VirB9, VirB10, and itself  . This family also includes the conjugal transfer protein family TrbF, a family of proteins known to be involved in conjugal transfer.  The TrbF protein is thought to compose part of the pilus required for transfer  . This domain has a similar fold to the NTF2 protein.. 
PF00286 virus_P-coat; Virus_P-coat; <br>Family includes coat proteins from Potexviruses and carlaviruses.. 
PF01347 Lipoprotein amino terminal region<br>Pfam-B_1280 (release 3.0). This family contains regions from: Vitellogenin, Microsomal triglyceride transfer protein and apolipoprotein B-100.  These proteins are all involved in lipid transport  . This family contains the LV1n chain from lipovitellin, that contains two structural domains.. 
PF05090 Vitamin K-dependent gamma-carboxylase<br>Pfam-B_6307 (release 7.7). Using reduced vitamin K, oxygen, and carbon dioxide, gamma-glutamyl  carboxylase post-translationally modifies certain glutamates by adding carbon dioxide to the gamma position of those amino acids. In vertebrates, the modification of glutamate residues of target proteins is facilitated by an interaction between a propeptide present on target proteins and the gamma-glutamyl carboxylase  .. 
PF04649 Mycoplasma hyorhinis VlpA repeat <br>This repeat is found in the extracellular (C-terminal) region of the  variant surface antigen A (VlpA) of Mycoplasma hyorhinis. Mutations that change the number of repeats in the protein are involved in antigenic variation and immune evasion of this swine pathogen  .. 
PF01660 Viral methyltransferase<br>This RNA methyltransferase domain   is found in a wide range of ssRNA viruses, including Hordei-, Tobra-, Tobamo-, Bromo-, Clostero- and Caliciviruses.  This methyltransferase is involved in mRNA capping.  Capping of mRNA enhances its stability. This usually occurs in the nucleus.  Therefore, many viruses that replicate in the cytoplasm encode their own  .  This is a specific guanine-7-methyltransferase domain involved in viral mRNA cap0 synthesis. Specificity for guanine 7 position is shown by NMR in   and in vivo role in cap synthesis  .  Based on secondary structure prediction, the basic fold is believed to be similar to the common AdoMet-dependent methyltransferase fold  . A curious feature of this methyltransferase domain is that it together with flanking sequences seems to have guanylyltransferase activity coupled to the methyltransferase activity  . The domain is found throughout the so-called Alphavirus superfamily, (including alphaviruses and several other groups). It forms the defining, unique feature of this superfamily  .. 
PF00695 Major surface antigen from hepadnavirus<br>Pfam-B_168 (release 2.1). 
PF03762 Vitelline membrane outer layer protein I (VOMI) <br>Pfam-B_3481 (release 7.0). 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. Furthermore, the structure of VOMI has strong similarity  to the structure of the delta-endotoxin, as well as a  carbohydrate-binding site in the top region of the common fold  . . 
PF00434 Glycoprotein VP7<br>Pfam-B_116 (release 1.0). 
PF00522 VPR/VPX protein<br>Pfam-B_100 (release 1.0). 
PF03643 Vacuolar protein sorting-associated protein 26 <br>Pfam-B_4396 (release 7.0). 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 Vps5, Vps17, Vps29 and Vps35  . This family also contains Down syndrome critical region 3/A.. 
PF03997 VPS28 protein<br>Pfam-B_6317 (release 7.3). 
PF04133 Vacuolar protein sorting 55 <br>Pfam-B_25168 (release 7.3);. 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 are important for functioning membrane trafficking to the vacuole/lysosome of eukaryotic cells  .. 
PF00558 Vpu protein<br>The Vpu protein contains an N-terminal transmembrane spanning region and a C-terminal cytoplasmic region. The HIV-1 Vpu protein stimulates virus production by enhancing  the release of viral particles from infected cells. The VPU protein binds specifically to CD4.. 
PF03852 DNA mismatch endonuclease Vsr<br>TIGRFAMs, Griffiths-Jones SR. 
PF00093 vwc; <br>von Willebrand factor type C domain. The high cutoff was used to prevent overlap with Pfam:PF00094.. 
PF02020 IF5_eIF4_eIF2;<br>eIF4-gamma/eIF5/eIF2-epsilon. This domain of unknown function is found at the C-terminus of several translation initiation factors  .. 
PF03716 WCCH_motif; <br>Pfam-B_3194 (release 7.0). The WCCH motif is found in a retrotransposons and Gemini viruses. A specific function has not been associated to this motif  .. 
PF00458 WHEP-TRS domain<br>
PF00110 wnt family<br>Wnt genes have been identified in vertebrates and invertebrates but not in plants, unicellular eukaryotes or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families  .. 
PF01822 WSC domain<br>This domain may be involved in carbohydrate binding.. 
PF02165 Wilm's tumour protein<br>
PF03303 WTF protein<br>Pfam-B_4183 (release 6.5). This is a family of hypothetical Schizosaccharomyces pombe proteins. Their function is unknown.. 
PF04932 O-Antigen ligase<br>Pfam-B_5033 (release 7.6). This group of bacterial proteins is involved in the synthesis of O-antigen, a lipopolysaccharide found in the outer membrane in gram-negative bacteria. This family includes O-antigen ligases such as E. coli RfaL  .. 
PF00739 Trans-activation protein X<br>Pfam-B_458 (release 2.1). This protein is found in hepadnaviruses where it is indispensable for replication.. 
PF00860 xan_ur_permease; <br>Pfam-B_1593 (release 2.1). This family includes permeases for diverse substrates such as xanthine Swiss:P42086, uracil Swiss:P39766 and vitamin C Swiss:Q9UGH3.  However many members of this family are functionally uncharacterised and may transport other substrates. Members of this family have ten predicted transmembrane helices.. 
PF04921 XAP5, circadian clock regulator<br>Pfam-B_4702 (release 7.6). This protein is found in a wide range of eukaryotes. It is a nuclear protein and is suggested to be DNA binding [1,2]. In plants, this family is essential for correct circadian clock functioning by acting as a light-quality regulator coordinating the activities of blue and red light signalling pathways during plant growth - inhibiting growth in red light but promoting growth in blue light  .. 
PF02625 DUF182; <br>XdhC and CoxI family. This domain is often found in association with an NAD-binding region, related to TrkA-N (Pfam:PF02254; personal obs:C. Yeats). XdhC is  believed to be involved in the attachment of molybdenum to Xanthine Dehydrogenase ( ).. 
PF03894 D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase<br>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:4.1.2.22  . This family is distantly related to transketolases e.g. Pfam:PF02779.. 
PF03469 XH domain<br>The XH (rice gene X Homology) domain is found in a family of plant proteins including gene X Swiss:Q9SBW2.  The molecular function of these proteins is unknown.  However these proteins usually contain an XS domain that is also found in the PTGS protein SGS3. This domain contains a conserved glutamate residue that may be functionally important.. 
PF03468 XS domain<br>The XS (rice gene X and SGS3) domain is found in a family of plant proteins including gene X Swiss:Q9SBW2 and SGS3 Swiss:Q9LDX1.  SGS3 is thought to be involved in post-transcriptional gene silencing (PTGS). This domain contains a conserved aspartate residue that may be functionally important. The XS domain has recently been predicted to possess an RRM-like RNA-binding domain   by fold recognition.. 
PF04555 Restriction endonuclease XhoI<br>This family consists of type II restriction enzymes (EC:3.1.21.4) that recognise the double-stranded sequence CTCGAG and cleave after C-1.. 
PF00193 Extracellular link domain<br>Swissprot_feature_table. 
PF00867 XPG I-region<br>Pfam-B_776 (release 3.0). 
PF00752 XPG N-terminal domain<br>Pfam-B_491 (release 2.1). 
PF01834 XRCC1 N terminal domain<br>
PF02162 Rhodopsin_C; <br>XYPPX repeat (two copies). This repeat is found in a wide variety of proteins and generally consists of the motif XYPPX where X can be any amino acid. The family includes annexin VII Swiss:P24639, the carboxy tail of certain rhodopsins Swiss:Q17094. This family also includes plaque matrix proteins, however this motif is embedded in a ten residue repeat in Swiss:Q25460. The molecular function of this repeat is unknown. It is also not clear is all the members of this family share a common evolutionary ancestor due to its short length and biased amino acid composition.. 
PF04690 YABBY protein<br>Pfam-B_5698 (release 7.5). YABBY proteins are a group of plant-specific transcription involved in the specification of abaxial polarity in lateral organs [1,2].. 
PF03895 YadA; YadA_C;<br>YadA-like C-terminal region. This region represents the C-terminal 120 amino acids of a family of surface-exposed bacterial proteins. YadA, an adhesin from Yersinia, was the first member of this family to be characterised. UspA2 from Moraxella was second. The Eib immunoglobulin-binding proteins from E. coli were third, followed by the DsrA proteins of Haemophilus ducreyi and others. These proteins are homologous at their C-terminal and have predicted signal sequences, but they diverge elsewhere. The C-terminal 9 amino acids, consisting of alternating hydrophobic amino acids ending in F or W, comprise a targeting motif for the outer membrane of the Gram negative cell envelope. This region is important for oligomerisation  .. 
PF02699 DUF219; <br>Preprotein translocase subunit. 
PF04073 YbaK;<br>Aminoacyl-tRNA editing domain. This domain is found either on its own or in association with the tRNA synthetase class II core domain (Pfam:PF00587).  It is involved in the tRNA editing of mis-charged tRNAs including Cys-tRNA(Pro), Cys-tRNA(Cys), Ala-tRNA(Pro)[2-5].  The structure of this domain shows a novel fold  .. 
PF02392 Ycf4<br>Pfam-B_1026 (release 5.2). This family consists of hypothetical Ycf4 proteins from various chloroplast genomes.  It has been suggested that Ycf4 is involved in the assembly and/or stability of the photosystem I complex in chloroplasts  .. 
PF01737 YCF9; <br>Pfam-B_2211 (release 4.1). This family consists of the hypothetical protein product of the YCF9 gene from chloroplasts and  cyanobacteria. These proteins have no known function.. 
PF03795 YCII-related domain<br>
PF02182 G9a; YDG_SRA;<br>Iyer LM, Aravind L, SMART. Alignment kindly provided by SMART. The domain goes by several names including SAD  , SRA    and  YDG  . It adopts a beta barrel, modified PUA-like, fold that is  widely present in eukaryotic chromatin proteins and in bacteria  . Versions of this domain are known to bind hemi-methylated CpG  dinucleotides and also other 5mC containing dinucleotides. The  domain binds DNA by flipping out the methylated cytosine base from  the DNA double helix  .The conserved tyrosine and aspartate  residues and a glycine rich patch are critical for recognition of  the flipped out base   . Mammalian UHRF1 that contains this  domain plays an important role in maintenance of methylation at  CpG dinucleotides by recruiting DNMT1 to hemimethylated sites\. associated with replication forks  . The SAD/SRA domain has been combined with other domains involved in the ubiquitin pathway on multiple occasions and such proteins link recognition of DNA  methylation to chromatin-protein ubiquitination  . The domain is also found in species that lack DNA methylation, such as certain apicomplexans, suggestive of other DNA-binding modes or functions  . A highly derived and distinct version of the domain is also found in fungi where it is fused to AlkB-type 2OGFeDO domains  . In bacteria, the domain is usually fused or associated with restriction endonucleases, many of which target methylated or\. hemi-methylated DNA  .. 
PF04794 YdjC-like protein<br>Pfam-B_5925 (release 7.5). Family of YdjC-like proteins.  This region is possibly involved in the the cleavage of cellobiose-phosphate  .. 
PF00399 yeast_PIR; <br>Yeast PIR protein repeat. 
PF03366 YEATS family<br>Pfam-B_2273 (release 6.6). 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. 
PF03543 YerHae_surfAg; SurfAg;<br>Yersinia/Haemophilus virulence surface antigen. 
PF03545 Yers_vir_YopE; <br>Yersinia virulence determinant (YopE). 
PF03887 YfbU domain<br>This presumed domain is about 160 residues long.  It is found in archaebacteria and eubacteria.  In Swiss:Q9EUM2 it is associated with a helix-turn-helix domain. This suggests that this may be a ligand binding domain.. 
PF02542 YgbB family<br>The ygbB protein is a putative enzyme of deoxy-xylulose pathway (terpenoid biosynthesis)  .. 
PF02325 YGGT family<br>Pfam-B_983 (release 5.2). This family consists of a repeat found in conserved hypothetical integral membrane proteins.  The function of this region and the proteins which possess it is unknown.. 
PF04945 YHS domain<br>This short presumed domain is about 50 amino acid residues long.  It often contains two cysteines that may be functionally important.  This domain is found in copper transporting ATPases, some phenol hydroxylases and in a set of uncharacterised membrane proteins including Swiss:Q9CNI0. This domain is named after three of the most conserved amino acids it contains.  The domain may be metal binding, possibly copper ions. This domain is duplicated in some copper transporting ATPases.. 
PF03755 YicC_N-term; <br>YicC-like family, N-terminal region . Pfam-B_3743 (release 7.0). Family of bacterial proteins. Although poorly characterised, the members of this protein family have been demonstrated to play a role in stationary phase survival  . These proteins are  not essential during stationary phase  .. 
PF03853 YjeF-related protein N-terminus<br>TIGRFAMs, Griffiths-Jones SR. YjeF-N domain is a novel version of the Rossmann fold with a set of  catalytic residues and structural features that are different from the conventional dehydrogenases  . YjeF-N domain is fused to  Ribokinases in bacteria (YjeF), where they may be phosphatases, and to divergent Sm and the FDF domain in eukaryotes (Dcp3p and  FLJ21128)  , where they may be involved in decapping and catalyze  hydrolytic RNA-processing reactions  .. 
PF03739 Predicted permease YjgP/YjgQ family<br>Members of this family are predicted integral membrane proteins of unknown function.\.     They are about 350 amino acids long and contain about 6 transmembrane regions. They are predicted to be permeases although there is no verification of this.. 
PF02326 Plant ATP synthase F0<br>Pfam-B_984 (release 5.2). This family corresponds to subunit 8 (YMF19) of the F0 complex of plant and algae mitochondrial F-ATPases (EC:3.6.1.34).. 
PF01514 Secretory protein of YscJ/FliF family<br>Pfam-B_736 (release 4.0). This family includes proteins that are related to the YscJ lipoprotein, and the amino terminus of FliF, the flageller M-ring protein.  The members of the YscJ family are thought to be involved in secretion of several proteins.\.     The FliF protein ring is thought to be part of the export apparatus for flageller proteins, based on the similarity to YscJ proteins  .. 
PF04650 YSIRK type signal peptide<br>Pfam-B_3441 (release 7.5). Many surface proteins found in Streptococcus, Staphylococcus, and related lineages share apparently homologous signal sequences. A motif resembling [YF]SIRKxxxGxxS[VIA] appears at the start of the transmembrane domain. The GxxS motif appears perfectly conserved, suggesting a specific function and not just homology.  There is a strong correlation between proteins carrying this region at the N-terminus and those carrying the Gram-positive anchor domain with the LPXTG sortase processing site at the C-terminus.. 
PF02295 Adenosine deaminase z-alpha domain<br>Pfam-B_11136 (release 5.2). 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 region to B-DNA has been shown to be disfavoured by steric  hindrance  .  . 
PF01559 Zein seed storage protein<br>Pfam-B_181 (release 4.0). Zeins are seed storage proteins. They are unusually rich in glutamine, proline, alanine, and leucine residues and their sequences show a series of tandem repeats  .. 
PF01754 A20-like zinc finger<br>The A20 Zn-finger of bovine/human Rabex5/rabGEF1 is a Ubiquitin Binding Domain [5-6]. The zinc finger mediates self-association in A20. These fingers also mediate IL-1-induced NF-kappa B activation.. 
PF01428 AN1-like Zinc finger<br>Zinc finger at the C-terminus of An1 Swiss:Q91889, a ubiquitin-like protein in Xenopus laevis. The following pattern describes the zinc finger. C-X2-C-X(9-12)-C-X(1-2)-C-X4-C-X2-H-X5-H-X-C Where X can be any amino acid, and numbers in brackets indicate the number of residues.. 
PF00096 Zinc finger, C2H2 type<br>The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity  site for Sp1 binding to the wt1 promoter  .. 
PF00105 Zinc finger, C4 type (two domains)<br>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.. 
PF01396 Topoisomerase DNA binding C4 zinc finger<br>Pfam-B_1854 (release 3.0). 
PF02928 C5HC2 zinc finger<br>Predicted zinc finger with eight potential zinc ligand binding residues. This domain is found in Jumonji  . This domain may have a DNA binding function.. 
PF01807 CHC2 zinc finger<br>Pfam-B_755 (release 4.2). This domain is principally involved in DNA binding in DNA primases.. 
PF05207 CSL zinc finger<br>Pfam-B_12353 (release 7.7). This is a zinc binding motif which contains four cysteine residues which chelate zinc  .  This domain is often found associated with a Pfam:PF00226 domain.  This domain is named after the conserved motif of the final cysteine.. 
PF05180 DNL zinc finger<br>Pfam-B_9925 (release 7.7). The domain is named after a short C-terminal motif of D(N/H)L. This domain is a novel zinc-finger protein essential for protein  import into mitochondria  .. 
PF02701 Dof domain, zinc finger<br>Pfam-B_1250 (release 5.5). The Dof domain is a zinc finger DNA-binding domain, that shows resemblance to the Cys2 zinc finger  . . 
PF04770 ZF-HD protein dimerisation region<br>Pfam-B_2002 (release 7.6). This family of proteins has are plant transcription factors, and have been  named ZF-HD for zinc finger homeodomain proteins, on the basis of  similarity to proteins of known structure  .  This region is thought to  be involved in the formation of homo and heterodimers, and may form a zinc finger  .. 
PF01422 NF-X1 type zinc finger<br>This domain is presumed to be a zinc binding domain. The following pattern describes the zinc finger. C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C Where X can be any amino acid, and numbers in brackets indicate the number of residues. Two position can be either his or cys. This family includes Swiss:P40798, Swiss:Q12986 and Swiss:P53971. The zinc fingers in Swiss:Q12986 bind to DNA  .. 
PF00645 Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region<br>Poly(ADP-ribose) polymerase is an important regulatory component of the cellular response to DNA damage. The amino-terminal region of Poly(ADP-ribose) polymerase consists of two PARP-type zinc fingers.  This region acts as a DNA nick sensor.. 
PF00641 Zn-finger in Ran binding protein and others<br>
PF02135 TAZ zinc finger<br>The TAZ2 domain of CBP binds to other transcription factors such as the p53 tumour suppressor protein, E1A oncoprotein, MyoD, and GATA-1.  The zinc coordinating motif that is necessary for binding to target DNA sequences consists of HCCC.. 
PF02953 Tim10/DDP family zinc finger<br>Pfam-B_1207 (release 6.4). Putative zinc binding domain with four conserved cysteine residues.  This domain is found in the human disease protein Swiss:O60220.  Members of this family such as Tim9 and Tim10 are involved in mitochondrial protein import  .\.    Members of this family seem to be localised to the mitochondrial intermembrane space  .. 
PF02176 TRAF-type zinc finger<br>
PF02207 zf-UBR1; <br>Putative zinc finger in N-recognin (UBR box). Alignment kindly provided by SMART. This region is found in E3 ubiquitin ligases that recognise N-recognins  .. 
PF03470 XS zinc finger domain<br>This domain is a putative nucleic acid binding zinc finger found in proteins that also contain an XS domain.. 
PF01258 zf_dskA_traR; <br>Prokaryotic dksA/traR C4-type zinc finger. 
PF04071 DUF379; zf_like; <br>Cysteine-rich small domain. Probable metal-binding domain.. 
PF04354 ZipA, C-terminal FtsZ-binding domain<br>This family represents the ZipA C-terminal domain. ZipA is involved in septum formation in bacterial cell division. Its C-terminal domain binds FtsZ, a major component of the bacterial septal ring. The structure of this domain is an alpha-beta fold with three alpha helices and a beta sheet of six antiparallel beta strands. The major loops protruding from the beta sheet surface are thought to form a binding site for FtsZ  .. 
PF00172 Fungal Zn(2)-Cys(6) binuclear cluster domain<br>
PF00882 Zinc dependent phospholipase C<br>Pfam-B_1401 (release 3.0). 
PF04228 Putative neutral zinc metallopeptidase<br>Members of this family have a predicted zinc binding motif characteristic of neutral zinc metallopeptidases (Prosite:PDOC00129).. 
PF04298 Putative neutral zinc metallopeptidase<br>Zinc metallopeptidase zinc binding regions have been predicted in some  family members by a pattern match (Prosite:PS00142).. 
PF03854 ZnF_P11; <br>
PF03367 ZPR1; <br>ZPR1 zinc-finger domain. Pfam-B_1372 (release 6.6). 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 localised to the cytoplasm. But in proliferating cells treated with EGF or with other mitogens, ZPR1 accumulates in the nucleolus. ZPR1 interacts with the cytoplasmic domain of the inactive EGF receptor (EGFR) and is thought to inhibit the basal protein tyrosine kinase activity of EGFR. This interaction is disrupted when cells are treated with EGF, though by themselves, inactive EGFRs are not sufficient to sequester ZPR1 to the cytoplasm [1,2,3]. Upon stimulation by EGF, ZPR1 directly binds the eukaryotic translation elongation factor-1alpha (eEF-1alpha) to form ZPR1/eEF-1alpha complexes  . These move into the nucleus, localising particularly at the nucleolus. Indeed, the interaction between ZPR1 and eEF-1alpha has been shown to be essential for normal cellular proliferation  , and ZPR1 is thought to be involved in pre-ribosomal RNA expression  . The ZPR1 domain consists of an elongation initiation factor 2-like zinc finger and a double-stranded beta helix with a helical hairpin insertion. ZPR1 binds preferentially to GDP-bound eEF1A but does not directly influence the kinetics of nucleotide exchange or GTP hydrolysis  . The alignment for this family shows a domain of which there are two copies in ZPR1 proteins. This family also includes several hypothetical archaeal proteins (from both Crenarchaeota and Euryarchaeota), which only contain one copy of the aligned region. This similarity between ZPR1 and archaeal proteins was not previously noted.. 
PF00791 ZU5 domain<br>Alignment kindly provided by SMART. Domain present in ZO-1 and Unc5-like netrin receptors Domain of unknown function.. 
PF00569 Zinc finger, ZZ type<br>Alignment kindly provided by SMART. Zinc finger present in dystrophin, CBP/p300.  ZZ in dystrophin binds calmodulin.  Putative zinc finger; binding not yet shown. Four to six cysteine residues in its sequence are responsible for coordinating zinc ions, to reinforce the structure  .. 
PF04358 DsrC like protein<br>Family member Swiss:P45573 has been observed to co-purify with  Desulfovibrio vulgaris dissimilatory sulfite reductase  , and many  members of this family are annotated as the third (gamma) subunit of  dissimilatory sulphite reductase. However, this protein appears to be only loosely associated to the  sulfite reductase, which suggests that DsrC may not be an integral part of the dissimilatory sulphite reductase.  Members of this family are found in organisms such as E. coli and H. influenzae which do not contain  dissimilatory sulphite reductases but can synthesise assimilatory sirohaem  sulphite and nitrite reductases.  It is speculated that DsrC may be  involved in the assembly, folding or stabilisation of sirohaem proteins  .  The strictly conserved cysteine in the C terminus suggests that DsrC may have a catalytic function in the metabolism of sulphur compounds  .. 
PF04252 DUF431; <br>Predicted SAM-dependent RNA methyltransferase. This family of proteins are predicted to be alpha/beta-knot SAM-dependent RNA methyltransferases  .. 
PF04359 Protein of unknown function (DUF493)<br>
PF04205 FMN-binding domain<br>This conserved region includes the FMN-binding site of the NqrC protein   as well as the NosR and NirI regulatory proteins.. 
PF04432 Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus<br>Coenzyme F420 hydrogenase (EC:1.12.99.1) reduces the low-potential two-electron acceptor coenzyme F420. This family contains the C termini of F420 hydrogenase and dehydrogenase beta subunits  ,  .  The N terminus of Methanobacterium formicicum formate dehydrogenase beta chain (EC:1.2.1.2, Swiss:P06130) is also a member of this family  . This region is often found in association with the 4Fe-4S binding domain, fer4 (Pfam:PF00037).. 
PF04609 Methyl-coenzyme M reductase operon protein C<br>Methyl coenzyme M reductase (MCR) catalyses the final step in methanogenesis. MCR is composed of three subunits, alpha (Pfam:PF02249), beta (Pfam:PF02241) and gamma (Pfam:PF02240)  . Genes encoding the beta (mcrB) and gamma (mcrG) subunits are separated by two open reading frames coding for two proteins C and D  . The function of proteins C and D (this family) is unknown. This family nowalso includes family MtrC_related,. 
PF04607 Region found in RelA / SpoT proteins<br>This region of unknown function is found in RelA and SpoT of Escherichia coli, and their homologues in plants and in other eubacteria. RelA is a guanosine 3',5'-bis-pyrophosphate (ppGpp) synthetase (EC:2.7.6.5) while SpoT is thought to be a bifunctional enzyme catalysing both ppGpp  synthesis and degradation (ppGpp 3'-pyrophosphohydrolase, (EC:3.1.7.2))  . This region is often found in association with HD (Pfam:PF01966), a  metal-dependent phosphohydrolase, TGS (Pfam:PF02824) which is a possible  nucleotide-binding region, and the ACT regulatory domain (Pfam:PF01842).. 
PF04226 Transglycosylase associated protein<br>Bacterial protein, predicted to be an integral membrane protein. Some family members have been annotated as transglycosylase associated proteins, but no experimental evidence is provided.  This family was annotated based on the information in Swiss:P76011.. 
PF04264 YceI-like domain<br>E. coli YceI is a base-induced periplasmic protein  . The recent structure of a member of this family shows that it binds to polyisoprenoid  . The structure consists of an extended, eight-stranded, antiparallel beta-barrel that resembles the lipocalin fold.. 
PF04431 pec_lyase_N; <br>Pectate lyase, N terminus. This region is found N terminal to the pectate lyase domain (Pfam:PF00544) in some plant pectate lyase enzymes.. 
PF05223 NTF2-like N-terminal transpeptidase domain<br>The structure of this domain from MecA is known   Swiss:Q53707 and is found to be similar to that found in NTF2 Pfam:PF02136. This domain seems unlikely to have an enzymatic function, and its role remains unknown.. 
PF05224 NDT80 / PhoG like DNA-binding  family<br>This family includes the DNA-binding region of NDT80   as well as PhoG and its homologues. The family contains Swiss:Q05534 or VIB-1. VIB-1 is thought to be a regulator of conidiation in Neurospora crassa and shares a region of similarity to PHOG, a possible phosphate nonrepressible acid phosphatase in Aspergillus nidulans. It has been found that vib-1 is not the structural gene for nonrepressible acid phosphatase, but rather may regulate nonrepressible acid phosphatase activity  .. 
PF05225 helix-turn-helix, Psq domain<br>This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster  . In pipsqueak this domain binds to GAGA sequence  .. 
PF05226 CHASE2 domain<br>CHASE2 is an extracellular sensory domain, which is present in various classes of transmembrane receptors that are parts of signal transduction pathways in bacteria. Specifically, CHASE2 domains are found in histidine kinases, adenylate cyclases, serine/threonine kinases and predicted diguanylate cyclases/phosphodiesterases. Environmental factors that are recognised by CHASE2 domains are not known at this time  .. 
PF05227 CHASE3 domain<br>CHASE3 is an extracellular sensory domain, which is present in various classes of transmembrane receptors that are parts of signal transduction pathways in bacteria. Specifically, CHASE3 domains are found in histidine kinases, adenylate cyclases, methyl-accepting chemotaxis proteins and predicted diguanylate cyclases/phosphodiesterases. Environmental factors that are recognised by CHASE3 domains are not known at this time  .. 
PF05228 CHASE4 domain<br>CHASE4. This is an extracellular sensory domain, which is present in various classes of transmembrane receptors that are parts of signal transduction pathways in prokaryotes. Specifically, CHASE4 domains are found in histidine kinases in Archaea and in predicted diguanylate cyclases/phosphodiesterases in Bacteria. Environmental factors that are recognized by CHASE4 domains are not known at this time  .. 
PF05229 Spore Coat Protein U domain<br>This domain is found in a bacterial family of spore coat proteins  , as well as a family of secreted pili proteins involved in motility and biofilm formation ( ). This family is distantly related to fimbrial proteins.. 
PF05230 MASE2 domain<br>Predicted integral membrane sensory domain found in histidine kinases, diguanylate cyclases and other bacterial signaling proteins.. 
PF05231 MASE1<br>Predicted integral membrane sensory domain found in histidine kinases, diguanylate cyclases and other bacterial signaling proteins. This entry also includes members of the 8 transmembrane UhpB type (8TMR-UT) domain family  .. 
PF05232 Bacterial Transmembrane Pair family<br>This family represents a conserved pair of transmembrane helices. It appears to be found as two tandem repeats in a family of hypothetical proteins.. 
PF05233 PHB accumulation regulatory domain<br>The proteins this domain is found in are typically  involved in regulating polymer accumulation in bacteria, particularly poly-beta-hydroxybutyrate (PHB)  . The  N-terminal region is likely to be the DNA-binding domain (Pfam:PF07879) while this domain probably binds PHB (personal obs:C Yeats).. 
PF05234 UAF_rrn5; <br>UAF complex subunit Rrn10. The protein Rrn10 has been identified as a component of the Upstream Activating Factor (UAF), an RNA polymerase I (pol I) specific transcription stimulatory factor  . 
PF05235 CHAD domain<br>The CHAD domain is an alpha-helical domain functionally associated with the Pfam:PF01928 domains. It has conserved histidines that may chelate metals  .. 
PF05236 Transcription initiation factor TFIID component TAF4 family<br>This region of similarity is found in Transcription initiation factor TFIID component TAF4  .. 
PF05237 MoeZ/MoeB domain<br>This putative domain is found in the MoeZ protein and the MoeB protein. The domain has two CXXC motifs that are only partly conserved.. 
PF05238 CHL4;<br>Kinetochore protein CHL4 like. CHL4 is a protein involved in chromosome segregation  . It is a component of the central kinetochore which mediates the attachment of the centromere to the mitotic spindle  . CENP-N is one of the components that assembles onto the CENP-A-nucleosome-associated (NAC) centromere. The centromere, which is the basic element of chromosome inheritance, is epigenetically determined in mammals. CENP-A, the centromere-specific histone H3 variant, assembles an array of nucleosomes and it is this that seems to be the prime candidate for specifying centromere identity. CENP-A nucleosomes directly recruit a proximal CENP-A nucleosome associated complex (NAC) comprised of CENP-M, CENP-N and CENP-T, CENP-U(50), CENP-C and CENP-H. Assembly of the CENP-A NAC at centromeres is dependent on CENP-M, CENP-N and CENP-T. Additionally, there are seven other subunits which make up the CENP-A-nucleosome distal (CAD) centromere, CENP-K, CENP-L, CENP-O, CENP-P, CENP-Q, CENP-R and CENP-S, also assembling on the CENP-A NAC  .. 
PF05239 PRC-barrel domain<br>The PRC-barrel is an all beta barrel domain found in photosystem reaction centre subunit H of the purple bacteria and RNA metabolism proteins of the RimM group. PRC-barrels are approximately 80 residues long, and found widely represented in bacteria, archaea and plants.  This domain is also present at the carboxyl terminus of the pan-bacterial protein RimM, which is involved in ribosomal maturation and processing of 16S rRNA. A family of small proteins conserved in all known euryarchaea are composed entirely of a single stand-alone copy of the domain  .. 
PF05240 APOBEC-like C-terminal domain<br>This domain is found at the C-termini of the Apolipoprotein B mRNA editing enzyme.. 
PF05241 Emopamil binding protein <br>Pfam-B_7320 (release 7.7). Emopamil binding protein (EBP) is as a gene that encodes a non-glycosylated type I integral membrane protein of endoplasmic reticulum and shows high level expression in epithelial tissues. The EBP protein has emopamil binding domains, including the sterol acceptor site and the catalytic centre, which show Delta8-Delta7 sterol isomerase activity. Human sterol isomerase, a homologue of mouse EBP, is suggested not only to play a role in cholesterol biosynthesis, but also to affect lipoprotein internalisation. In humans, mutations of EBP are known to cause the genetic disorder of X-linked dominant chondrodysplasia punctata (CDPX2). This syndrome of humans is lethal in most males, and affected females display asymmetric hyperkeratotic skin and skeletal abnormalities  .. 
PF05242 Glycosylation-dependent cell adhesion molecule 1 (GlyCAM-1)<br>Pfam-B_7429 (release 7.7). This family consists of the lactophorin precursors proteose peptone component 3 (PP3) and glycosylation-dependent cell adhesion molecule 1 (GlyCAM-1). GlyCAM-1 functions as a ligand for L-selectin, a  saccharide-binding protein on the surface of circulating leukocytes, and mediates the trafficking of blood-born lymphocytes into secondary lymph  nodes. In this context, sulphatation of the carbohydrates of GlyCAM-1 has  been shown to be a critical structural requirement to be recognised by  L-selectin. GlyCAM-1 is also expressed in pregnant and lactating mammary glands of mouse and in an unknown site in the lung, in the bovine uterus  and rat cochlea  .. 
PF05244 Brucella outer membrane protein 2<br>Pfam-B_7448 (release 7.7). This family consists of several outer membrane proteins (2a and 2b) from brucella bacteria. Brucellae are Gram-negative, facultative intracellular bacteria that can infect many species of animals and man  .. 
PF05246 Protein of unknown function (DUF735)<br>Pfam-B_7611 (release 7.7). This family consists of several uncharacterised Borrelia burgdorferi (Lyme disease spirochete) proteins of unknown function.. 
PF05247 Flagellar transcriptional activator (FlhD)<br>Pfam-B_7623 (release 7.7). This family consists of several bacterial flagellar transcriptional activator (FlhD) proteins. FlhD combines with FlhC to form a regulatory complex in E. coli, this complex has been shown to be a global regulator  involved in many cellular processes as well as a flagellar transcriptional activator  .. 
PF05248 Adenovirus E3A<br>Pfam-B_7497 (release 7.7). 
PF05250 Uncharacterised protein family (UPF0193)<br>This family of proteins is functionally uncharacterised.. 
PF05251 Uncharacterised protein family (UPF0197)<br>This family of proteins is functionally uncharacterised.. 
PF05253 UPF0224; <br>U11-48K-like CHHC zinc finger. This zinc binding domain   has four conserved zinc chelating residues in a CHHC pattern. This domain is predicted to have an RNA-binding function  .. 
PF05254 Uncharacterised protein family (UPF0203)<br>This family of proteins is functionally uncharacterised.. 
PF05255 Uncharacterised protein family (UPF0220)<br>This family of proteins is functionally uncharacterised.. 
PF05256 Uncharacterised protein family (UPF0223)<br>This family of proteins is functionally uncharacterised.. 
PF05257 AXE; <br>Pfam-B_2845 (release 7.7). This domain corresponds to an amidase function.  Many of these proteins are involved in cell wall metabolism of bacteria. This domain is found at the N-terminus of Swiss:P43675, where is functions as a glutathionylspermidine amidase EC:3.5.1.78  . This domain is found to be the catalytic domain of PlyCA  .. 
PF05258 Protein of unknown function (DUF721)<br>Pfam-B_7527 (release 7.7). This family contains several actinomycete proteins of unknown function.. 
PF05259 Herpesvirus glycoprotein L<br>Pfam-B_7535 (release 7.7). This family consists of several herpesvirus glycoprotein L or UL1 proteins. Glycoprotein L is known to form a complex with glycoprotein H but the function of this complex is poorly understood  .. 
PF05261 TraM protein, DNA-binding<br>Pfam-B_7584 (release 7.7). The TraM protein is an essential part of the DNA transfer machinery of the conjugative resistance plasmid R1 (IncFII). On the basis of mutational  analyses, it was shown that the essential transfer protein TraM has at least two functions. First, a functional TraM protein was found to be  required for normal levels of transfer gene expression. Second, experimental evidence was obtained that TraM stimulates efficient site-specific single-stranded DNA cleavage at the oriT, in vivo. Furthermore, a specific interaction of the cytoplasmic TraM protein with the membrane protein TraD was demonstrated, suggesting that the TraM  protein creates a physical link between the relaxosomal nucleoprotein  complex and the membrane-bound DNA transfer apparatus  .. 
PF05262 Borrelia P83/100 protein<br>Pfam-B_6712 (release 7.7). This family consists of several Borrelia P83/P100 antigen proteins.. 
PF05263 Protein of unknown function (DUF722)<br>Pfam-B_6789 (release 7.7). This family contains several bacteriophage proteins of unknown function.. 
PF05264 Choristoneura fumiferana antifreeze protein (CfAFP)<br>Pfam-B_6800 (release 7.7). This family consists of several antifreeze proteins from the insect Choristoneura fumiferana (Spruce budworm). Antifreeze proteins (AFPs) and  antifreeze glycoproteins (AFGPs) are present in many organisms that must survive sub-zero temperatures. These proteins bind to seed ice crystals and inhibit their growth through an adsorption-inhibition mechanism  .. 
PF05265 Protein of unknown function (DUF723)<br>Pfam-B_6852 (release 7.7). This family contains several uncharacterised proteins from Neisseria meningitidis. These proteins may have a role in DNA-binding.. 
PF05266 Protein of unknown function (DUF724)<br>Pfam-B_6894 (release 7.7). This family contains several uncharacterised proteins found in Arabidopsis thaliana and other plants. This region is often found associated with Agenet domains and may contain coiled-coil.. 
PF05267 Protein of unknown function (DUF725)<br>Pfam-B_6905 (release 7.7). This family contains several Drosophila proteins of unknown function.. 
PF05268 Phage tail fibre adhesin Gp38<br>Pfam-B_7415 (release 7.7). This family contains several Gp38 proteins from T-even-like phages. Gp38,  together with a second phage protein, gp57, catalyses the organisation of  gp37 but is absent from the phage particle. Gp37 is responsible for  receptor recognition  .. 
PF05269 Bacteriophage CII protein<br>Pfam-B_7453 (release 7.7). This family consists of several phage CII regulatory proteins. CII plays a key role in the lysis-lysogeny decision in bacteriophage lambda and related phages  .. 
PF05270 Alpha-L-arabinofuranosidase B (ABFB)<br>Pfam-B_7464 (release 7.7). This family consists of several fungal alpha-L-arabinofuranosidase B proteins. L-Arabinose is a constituent of plant-cell-wall poly-saccharides. It is found in a polymeric form in L-arabinan, in which the backbone is  formed by 1,5-a- linked l-arabinose residues that can be branched via  1,2-a- and 1,3-a-linked l-arabinofuranose side chains. AbfB hydrolyses  1,5-a, 1,3-a and 1,2-a linkages in both oligosaccharides and  polysaccharides, which contain terminal non-reducing l-arabinofuranoses in side chains  .. 
PF05271 Tobravirus 2B protein<br>Pfam-B_7517 (release 7.7). This family consists of several tobravirus 2B proteins. It is known that the 2B protein is required for transmission by both Paratrichodorus  pachydermus and P. anemones nematodes  .. 
PF05272 Virulence-associated protein E<br>Pfam-B_6573 (release 7.7). This family contains several bacterial virulence-associated protein E like proteins. These proteins contain a P-loop motif.. 
PF05273 Poxvirus RNA polymerase 22 kDa subunit<br>Pfam-B_6584 (release 7.7). This family consists of several poxvirus DNA-dependent RNA polymerase 22 kDa subunits.. 
PF05274 Occlusion-derived virus envelope protein E25<br>Pfam-B_6633 (release 7.7). This family consists of several nucleopolyhedrovirus occlusion-derived virus envelope E25 proteins.. 
PF05275 Copper resistance protein B precursor (CopB)<br>Pfam-B_6721 (release 7.7). This family consists of several bacterial copper resistance proteins. Copper is essential and serves as cofactor for more than 30 enzymes yet a surplus of copper is toxic and leads to radical formation and oxidation of biomolecules. Therefore, copper homeostasis is a key requisite for every  organism. CopB serves to extrude copper when it approaches toxic levels  .. 
PF05276 SH3 domain-binding protein 5 (SH3BP5)<br>Pfam-B_6742 (release 7.7). This family consists of several eukaryotic SH3 domain-binding protein 5 or c-Jun N-terminal kinase (JNK)-interacting proteins (SH3BP5 or Sab). Sab binds to and serves as a substrate for JNK in vitro, and has been found to interact with the Src homology 3 (SH3) domain of Bruton's tyrosine kinase (Btk).  Inspection of the sequence of Sab reveals the presence of two putative mitogen-activated protein kinase interaction motifs (KIMs) similar to that found in the JNK docking domain of the c-Jun transcription factor, and four potential serine-proline JNK phosphorylation sites in the C-terminal half of the molecule  .. 
PF05277 Protein of unknown function (DUF726)<br>Pfam-B_6757 (release 7.7). This family consists of several uncharacterised eukaryotic proteins.. 
PF05278 Arabidopsis phospholipase-like protein (PEARLI 4)<br>Pfam-B_6763 (release 7.7). This family contains several phospholipase-like proteins from Arabidopsis thaliana which are homologous to PEARLI 4.. 
PF05279 Aspartyl beta-hydroxylase N-terminal region<br>Pfam-B_6767 (release 7.7). This family includes the N-terminal regions of the junctin, junctate and aspartyl beta-hydroxylase proteins. Junctate is an integral ER/SR membrane calcium binding protein, which comes from an alternatively spliced form of the same gene that generates aspartyl beta-hydroxylase and junctin  . Aspartyl beta-hydroxylase catalyses the post-translational hydroxylation of aspartic acid or asparagine residues contained within epidermal growth factor (EGF) domains of proteins  .. 
PF05280 Flagellar transcriptional activator (FlhC)<br>Pfam-B_6773 (release 7.7). This family consists of several bacterial flagellar transcriptional activator (FlhC) proteins. FlhC combines with FlhD to form a regulatory complex in E. coli, this complex has been shown to be a global regulator  involved in many cellular processes as well as a flagellar transcriptional activator  .. 
PF05281 Neuroendocrine protein 7B2 precursor (Secretogranin V)<br>Pfam-B_6776 (release 7.7). The neuroendocrine protein 7B2 has a critical role in the proteolytic conversion and activation of proPC2, the enzyme responsible for the proteolytic conversion of many peptide hormone precursors. The 7B2 protein acts as an intracellular binding protein for proPC2, facilitates its maturation, and is required for its enzymatic activity. Processing of many important peptide precursors does not occur in 7B2 nulls. 7B2 null mice exhibit a unique form of Cushing's disease with many atypical symptoms, such as hypoglycemia  .. 
PF05282 AAR2 protein<br>Pfam-B_6782 (release 7.7). This family consists of several eukaryotic AAR2-like proteins. The yeast protein AAR2 is involved in splicing pre-mRNA of the a1 cistron and other genes that are important for cell growth  .. 
PF05283 Multi-glycosylated core protein 24 (MGC-24)<br>Pfam-B_6825 (release 7.7). This family consists of several MGC-24 (or Cd164 antigen) proteins from  eukaryotic organisms. MGC-24/CD164 is a sialomucin expressed in many  normal and cancerous tissues. In humans, soluble and transmembrane forms of MGC-24 are produced by alternative splicing  .. 
PF05284 Protein of unknown function (DUF736)<br>Pfam-B_7619 (release 7.7). This family consists of several uncharacterised bacterial proteins of unknown function.. 
PF05285 SDA1<br>Pfam-B_6906 (release 7.7). This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus  .. 
PF05287 PMG protein<br>Pfam-B_7710 (release 7.7). This family consists of several mouse anagen-specific protein mKAP13 (PMG1 and PMG2). PMG1 and 2 contain characteristic repeats reminiscent of the keratin-associated proteins (KAPs). Both genes are expressed in growing hair follicles in skin as well as in sebaceous and eccrine sweat glands. Interestingly, expression is also detected in the mammary epithelium where it is limited to the onset of the pubertal growth phase and is independent of ovarian hormones. Their broad, developmentally controlled expression pattern, together with their unique amino acid composition, demonstrate that pmg-1 and pmg-2 constitute a novel KAP gene family participating in the differentiation of all epithelial cells forming the epidermal appendages  .. 
PF05288 Poxvirus A3L Protein<br>Pfam-B_7718 (release 7.7). This family consists of several poxvirus A3L or A2_5L proteins.. 
PF05289 Borrelia hemolysin accessory protein<br>Pfam-B_7729 (release 7.7). This family consists of several borrelia hemolysin accessory proteins (BLYB). BLYB was thought to be an accessory protein, which was proposed to comprise a hemolysis system but it is now thought that BlyA and BlyB function instead as a prophage-encoded holin or holin-like system  .. 
PF05290 Baculovirus immediate-early protein (IE-0)<br>Pfam-B_7745 (release 7.7). The Autographa californica multinucleocapsid nuclear polyhedrosis virus (AcMNPV) ie-1 gene product (IE-1) is thought to play a central role in stimulating early viral transcription. IE-1 has been demonstrated to activate several early viral gene promoters and to negatively regulate the promoters of two other AcMNPV regulatory genes, ie-0 and ie-2. It is thought that that IE-1 negatively regulates the expression of certain genes by binding directly, or as part of a complex, to promoter regions containing a specific IE-1-binding motif (5'-ACBYGTAA-3') near their mRNA start sites  .. 
PF05291 Bystin<br>Pfam-B_7767 (release 7.7). Trophinin and tastin form a cell adhesion molecule complex that potentially mediates an initial attachment of the blastocyst to uterine epithelial cells at the time of implantation. Trophinin and tastin bind to an intermediary cytoplasmic protein called bystin. Bystin may be involved in implantation and trophoblast invasion because bystin is found with trophinin and tastin in the cells at human implantation sites and also in the intermediate trophoblasts at invasion front in the placenta from early pregnancy  . This family also includes the yeast protein ENP1. ENP1 is an essential protein in Saccharomyces cerevisiae and is localised in the nucleus  . It is thought that ENP1 plays a direct role in the early steps of rRNA processing as enp1 defective yeast cannot synthesise 20S pre-rRNA and hence 18S rRNA, which leads to reduced formation of 40S ribosomal subunits  .. 
PF05292 Malonyl-CoA decarboxylase (MCD)<br>Pfam-B_7770 (release 7.7). This family consists of several eukaryotic malonyl-CoA decarboxylase (MLYCD) proteins. Malonyl-CoA, in addition to being an intermediate in the de novo synthesis of fatty acids, is an inhibitor of carnitine palmitoyltransferase I, the enzyme that regulates the transfer of long-chain fatty acyl-CoA into mitochondria, where they are oxidised. After exercise, malonyl-CoA decarboxylase participates with acetyl-CoA carboxylase in regulating the concentration of malonyl-CoA in liver and adipose tissue, as well as in muscle. Malonyl-CoA decarboxylase is regulated by AMP-activated protein kinase (AMPK)  .. 
PF05293 African swine fever virus (ASFV) L11L protein<br>Pfam-B_7869 (release 7.7). L11L is an integral membrane protein of the African swine fever virus (ASFV) which is expressed late in the virus replication cycle. The protein is thought to be non-essential for growth in vitro and for virus virulence in domestic swine  .. 
PF05294 toxin_5; <br>Scorpion short toxin. Pfam-B_7892 (release 7.7). This family contains various secreted scorpion short toxins and seems to be unrelated to Pfam:PF00451.. 
PF05295 Luciferase; <br>Luciferase/LBP N-terminal domain. Pfam-B_7906 (release 7.7). This family consists of a presumed N-terminal domain that is conserved between dinoflagellate luciferase and luciferin binding proteins. Luciferase is involved in catalysing the light emitting reaction in bioluminescence and luciferin binding protein (LBP) is known to bind to luciferin (the substrate for luciferase) to stop it reacting with the enzyme and therefore switching off the bioluminescence function. The expression of these two proteins is controlled by a circadian clock at the translational level, with synthesis and degradation occurring on a daily basis  . However This domain is not the catalytic part of the protein.  It has been suggested that this region may mediate an interaction between LBP and Luciferase or their association with the vacuolar membrane  .. 
PF05296 Mammalian taste receptor protein (TAS2R)<br>Pfam-B_1498 (release 7.7). This family consists of several forms of mammalian taste receptor proteins (TAS2Rs). TAS2Rs are G protein-coupled receptors expressed in subsets of taste receptor cells of the tongue and palate epithelia and are organised in the genome in clusters. The proteins are genetically linked to loci that influence bitter perception in mice and humans  .. 
PF05297 Herpesvirus latent membrane protein 1 (LMP1)<br>Pfam-B_5174 (release 7.7). This family consists of several latent membrane protein 1 or LMP1s mostly from Epstein-Barr virus. LMP1 of EBV is a 62-65 kDa plasma membrane protein possessing six membrane spanning regions, a short cytoplasmic N-terminus and a long cytoplasmic carboxy tail of 200 amino acids. EBV latent membrane protein 1 (LMP1) is essential for EBV-mediated transformation and has been associated with several cases of malignancies. EBV-like viruses in Cynomolgus monkeys (Macaca fascicularis) have been associated with high  lymphoma rates in immunosuppressed monkeys  . 
PF05298 Bombinin<br>Pfam-B_5347 (release 7.7). This family consists of Bombinin and Maximin proteins from Bombina maxima (Chinese red belly toad). Two groups of antimicrobial peptides have been isolated from skin secretions of Bombina maxima. Peptides in the first group, named maximins 1, 2, 3, 4 and 5, are structurally related to bombinin-like peptides (BLPs). Unlike BLPs, sequence variations in maximins occurred all through the molecules. In addition to the potent antimicrobial activity, cytotoxicity against tumour cells and spermicidal action of maximins, maximin 3 possessed a significant anti-HIV activity. Maximins 1 and 3 have been found to be toxic to mice. Peptides in the second group, termed maximins H1, H2, H3 and H4, are homologous with bombinin H peptides  .. 
PF05299 M61 glycyl aminopeptidase<br>Glycyl aminopeptidase is an unusual peptidase in that it has a preference for substrates with an N-terminal glycine or alanine. These proteins are found in Bacteria and in Archaea.. 
PF05300 Protein of unknown function (DUF737)<br>Pfam-B_6933 (release 7.7). This family consists of several uncharacterised mammalian proteins of unknown function.. 
PF05301 DUF738; <br>Touch receptor neuron protein Mec-17. Moxon SJ, Pollington JE. Pfam-B_6943 (release 7.7). Mec-17 is the protein product of one of the 18 genes required for the development and function of the touch receptor neuron for gentle touch. Mec-17 is specifically required for maintaining the differentiation of the touch receptor  . This family is conserved to higher eukaryotes.. 
PF05302 Protein of unknown function (DUF720)<br>Pfam-B_6980 (release 7.7). This family consists of several uncharacterised Chlamydia proteins of unknown function.. 
PF05303 Protein of unknown function (DUF727)<br>Pfam-B_7004 (release 7.7). This family consists of several uncharacterised eukaryotic proteins of unknown function.. 
PF05304 Protein of unknown function (DUF728)<br>Pfam-B_7223 (release 7.7). This family consists of several uncharacterised tobravirus proteins of unknown function.. 
PF05305 Protein of unknown function (DUF732)<br>Pfam-B_7356 (release 7.7). This family consists of several uncharacterised Mycobacterium tuberculosis and leprae proteins of unknown function.. 
PF05306 Protein of unknown function (DUF733)<br>Pfam-B_7392 (release 7.7). This family consists of several uncharacterised Drosophila melanogaster proteins of unknown function.. 
PF05307 Bundlin<br>Pfam-B_6974 (release 7.7). This family consists of several bundlin proteins from E. coli. Bundlin is a type IV pilin protein that is the only known structural component of  enteropathogenic Escherichia coli bundle-forming pili (BFP). BFP play a role in virulence, antigenicity, autoaggregation, and localised adherence  to epithelial cells  .. 
PF05308 DUF729;<br>Mitochondrial fission regulator. Moxon SJ, Eberhardt R. Pfam-B_6919 (release 7.7). In eukaryotes, this family of proteins induces mitochondrial fission [1,2].. 
PF05309 TraE protein<br>Pfam-B_7677 (release 7.7). This family consists of several bacterial sex pilus assembly and synthesis proteins (TraE). Conjugal transfer of plasmids from donor to recipient  cells is a complex process in which a cell-to-cell contact plays a key role. Many genes encoded by self-transmissible plasmids are required for various processes of conjugation, including pilus formation, stabilisation of mating pairs, conjugative DNA metabolism, surface exclusion and regulation of transfer gene expression  . The exact function of the TraE protein is unknown.. 
PF05310 Tenuivirus_NS3; <br>Tenuivirus movement protein. Pfam-B_7740 (release 7.7). This family of ssRNA negative-strand crop plant tenuivirus proteins appears to combine PV2  , NS2  , NS3, and PV3 proteins. Plant viruses encode specific proteins known as movement proteins (MPs) to control their spread through plasmodesmata (PD) in walls between cells as well as from leaf to leaf via vascular-dependent transport.  During this movement process, the virally encoded MPs interact with viral genomes for transport from the viral replication sites to the PDs in the walls of infected cells along the cytoskeleton and/or endoplasmic reticulum (ER) network. The virus is then thought to move through the PDs in the form of MP-associated ribonucleoprotein complexes or as virions  . The NS3 protein appears to function as an RNA silencing suppressor  .. 
PF05311 Baculovirus 33KDa late protein (PP31)<br>Pfam-B_7777 (release 7.7). Autographa californica nuclear polyhedrosis virus (AcMNPV) pp31 is a  nuclear phosphoprotein that accumulates in the virogenic stroma, which is the viral replication centre in the infected-cell nucleus, binds to DNA, and serves as a late expression factor  .. 
PF05313 Poxvirus P21 membrane protein<br>Pfam-B_7803 (release 7.7). The P21 membrane protein of vaccinia virus, encoded by the A17L (or A18L) gene, has been reported to localise on the inner of the two membranes of the intracellular mature virus (IMV). It has also been shown that P21 acts as a membrane anchor for the externally located fusion protein P14 (A27L gene)  . . 
PF05314 Baculovirus occlusion-derived virus envelope protein EC27<br>Pfam-B_7811 (release 7.7). This family consists of several baculovirus occlusion-derived virus envelope proteins (EC27 or E27). The ODV-E27 protein has distinct functional characteristics compared to cellular and viral cyclins. Depending on the cdk protein, and perhaps other viral or cellular proteins yet to be described, the kinase-EC27 complex may have either cyclin B- or  D-like activity  .. 
PF05315 ICEA Protein<br>Pfam-B_2792 (release 7.7). This family consists of several ICEA proteins from Helicobacter pylori. Helicobacter pylori infection causes gastritis and peptic ulcer disease, and is classified as a definite carcinogen of gastric cancer. ICEA1 is  speculated to be associated with peptic ulcer disease  .. 
PF05316 Yeast_VAR1; <br>Mitochondrial ribosomal protein (VAR1). Pfam-B_7802 (release 7.7). This family consists of the yeast mitochondrial ribosomal proteins VAR1. Mitochondria possess their own ribosomes responsible for the synthesis of a small number of proteins encoded by the mitochondrial genome. In yeast the two ribosomal RNAs and a single ribosomal protein, VAR1, are products of mitochondrial genes, and the remaining approximately 80 ribosomal  proteins are encoded in the nucleus  . VAR1 along with 15S rRNA are  necessary for the formation of mature 37S subunits  .. 
PF05317 Thermopsin<br>Pfam-B_7819 (release 7.7). This family consists of several thermopsin proteins from archaebacteria. Thermopsin is a thermostable acid protease which is capable of hydrolysing the following bonds: Leu-Val, Leu-Tyr, Phe-Phe, Phe-Tyr, and Tyr-Thr. The specificity of thermopsin is therefore similar to that of pepsin, that is, it prefers large hydrophobic residues at both sides of the scissile bond  .. 
PF05318 Tombusvirus movement protein<br>Pfam-B_4393 (release 7.7). This family consists of several Tombusvirus movement proteins. These proteins allow the virus to move from cell-to-cell and allow host-specific systemic spread  . . 
PF05320 Poxvirus DNA-directed RNA polymerase 19 kDa subunit<br>Pfam-B_6945 (release 7.7). This family contains several DNA-directed RNA polymerase 19 kDa polypeptides. The Poxvirus DNA-directed RNA polymerase (EC: 2.7.7.6)  catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time.. 
PF05321 Haemolysin expression modulating protein<br>Pfam-B_7025 (release 7.7). This family consists of haemolysin expression modulating protein (HHA) homologues. YmoA and Hha are highly similar bacterial proteins  downregulating gene expression in Yersinia enterocolitica and Escherichia  coli, respectively.. 
PF05322 NINE; <br>Pfam-B_7029 (release 7.7). This family consists of NINE proteins from several bacteriophages and from E. coli.. 
PF05323 Poxvirus A21 Protein<br>Pfam-B_7034 (release 7.7). This family consists of several poxvirus A21 proteins.. 
PF05324 Sperm antigen HE2<br>Pfam-B_7044 (release 7.7). This family consists of several variants of the human and chimpanzee sperm  antigen proteins (HE2 and EP2 respectively). The EP2 gene codes for a  family of androgen-dependent, epididymis-specific secretory proteins.The  EP2 gene uses alternative promoters and differential splicing to produce a family of variant messages.  The translated putative protein variants differ significantly from each other. Some of these putative proteins have  similarity to beta-defensins, a family of antimicrobial peptides  .. 
PF05325 Protein of unknown function (DUF730)<br>Pfam-B_7197 (release 7.7). This family consists of several uncharacterised Arabidopsis thaliana proteins of unknown function.. 
PF05326 Seminal vesicle autoantigen (SVA)<br>Pfam-B_7065 (release 7.7). This family consists of seminal vesicle autoantigen and prolactin-inducible (PIP) proteins. Seminal vesicle autoantigen (SVA) is specifically present in the seminal plasma of mice. This 19-kDa secretory glycoprotein suppresses the motility of spermatozoa by interacting with phospholipid. PIP, has several known functions. In saliva, this protein plays a role in host defence by binding to microorganisms such as Streptococcus. PIP is an aspartyl proteinase and it acts as a factor capable of suppressing T-cell apoptosis through its interaction with CD4  .. 
PF05327 RNA polymerase I specific transcription initiation factor RRN3<br>Pfam-B_7041 (release 7.7). This family consists of several eukaryotic proteins which are homologous to the yeast RRN3 protein. RRN3 is one of the RRN genes specifically required  for the transcription of rDNA by RNA polymerase I (Pol I) in Saccharomyces cerevisiae  .. 
PF05328 CybS<br>Pfam-B_7102 (release 7.7). This family consists of several eukaryotic succinate dehydrogenase [ubiquinone] cytochrome B small subunit, mitochondrial precursor (CybS) proteins. SDHD encodes the small subunit (cybS) of cytochrome b in succinate-ubiquinone oxidoreductase (mitochondrial complex II).  Mitochondrial complex II is involved in the Krebs cycle and in the aerobic electron transport chain. It contains four proteins. The catalytic core consists of a flavoprotein and an iron-sulfur protein; these proteins are anchored to the mitochondrial inner membrane by the large subunit of cytochrome b (cybL) and cybS, which together comprise the heme-protein cytochrome b. Mutations in the SDHD gene can lead to hereditary paraganglioma, characterised by the development of benign, vascularised tumours in the head and neck  .. 
PF05331 Protein of unknown function (DUF742)<br>Pfam-B_3675 (release 7.7). This family consists of several uncharacterised Streptomyces proteins as well as one from Mycobacterium tuberculosis. The function of these proteins is unknown.. 
PF05332 Protein of unknown function (DUF743)<br>Pfam-B_4046 (release 7.7). This family consists of several uncharacterised Calicivirus proteins of unknown function.. 
PF05334 Protein of unknown function (DUF719)<br>Pfam-B_7667 (release 7.7). This family consists of several eukaryotic proteins of unknown function.. 
PF05335 Protein of unknown function (DUF745)<br>Pfam-B_5169 (release 7.7). This family consists of several uncharacterised Drosophila melanogaster proteins of unknown function.. 
PF05336 Domain of unknown function (DUF718)<br>Pfam-B_7227 (release 7.7). This family consists of several uncharacterised bacterial proteins of unknown function.. 
PF05337 Macrophage colony stimulating factor-1 (CSF-1)<br>Pfam-B_7649 (release 7.7). Colony stimulating factor 1 (CSF-1) is a homodimeric polypeptide growth  factor whose primary function is to regulate the survival, proliferation, differentiation, and function of cells of the mononuclear phagocytic  lineage. This lineage includes mononuclear phagocytic precursors, blood monocytes, tissue macrophages, osteoclasts, and microglia of the brain, all of which possess cell surface receptors for CSF-1. The protein has also been linked with male fertility   and mutations in the Csf-1 gene have been found to cause osteopetrosis and failure of tooth eruption  .. 
PF05338 Protein of unknown function (DUF717)<br>Pfam-B_7144 (release 7.7). This family consists of several herpesvirus proteins of unknown function.. 
PF05339 Protein of unknown function (DUF739)<br>Pfam-B_7696 (release 7.7). This family contains several bacteriophage proteins. Some of the proteins in this family have been labeled putative cro repressor proteins.. 
PF05340 Protein of unknown function (DUF740)<br>Pfam-B_7873 (release 7.7). This family consists of several uncharacterised plant proteins of unknown function.. 
PF05341 Protein of unknown function (DUF708)<br>Pfam-B_7259 (release 7.7). This family consists of several uncharacterised nucleopolyhedrovirus proteins of unknown function.. 
PF05342 Peptidase_M26; <br>M26 IgA1-specific Metallo-endopeptidase N-terminal region. These peptidases, which cleave mammalian IgA, are found in Gram-positive bacteria. Often found associated  with Pfam:PF00746, they may be attached to the cell wall.. 
PF05343 M42 glutamyl aminopeptidase<br>These peptidases are found in Archaea and Bacteria. The example in Lactococcus lactis, PepA, aids growth on milk  .     Pyrococcus horikoshii contain a thermostable de-blocking  aminopeptidase member of this family used commercially for N-terminal protein sequencing  .. 
PF05344 Domain of Unknown Function (DUF746)<br>Yeats C, Eberhardt R. This is a short conserved region found in some transposons. Structural modelling suggests this domain may bind nucleic acids  .. 
PF05345 Putative Ig domain<br>This alignment represents the conserved core region of ~90 residue repeat found in several haemagglutinins and other cell surface proteins. Sequence similarities to  (Pfam:PF02494) and (Pfam:PF00801) suggest an Ig-like fold (personal obs:C. Yeats). So this family may be similar in function to the (Pfam:PF02639) and  (Pfam:PF02638) domains. This domain is also found in the WisP family of proteins of Tropheryma whipplei ( ).. 
PF05346 Eukaryotic membrane protein family<br>Pfam-B_13582 (release 7.8). This family is a family of eukaryotic membrane proteins.  It was previously annotated as including a putative receptor for human cytomegalovirus gH   but this has has since been disputed  . Analysis of the mouse Tapt1 protein (transmembrane anterior posterior transformation 1) has shown it to be involved in patterning of the vertebrate axial skeleton.. 
PF05347 Complex 1 protein (LYR family)<br>Pfam-B_15215 (release 7.8). Proteins in this family include an accessory subunit of the higher eukaryotic NADH dehydrogenase complex.  In Saccharomyces cerevisiae, the Isd11 protein (Swiss:Q6Q560) has been shown to play a role in Fe/S cluster biogenesis in mitochondria   . We have named this family LYR after a highly conserved tripeptide motif close to the N-terminus of these proteins.. 
PF05348 Proteasome maturation factor UMP1<br>Pfam-B_18845 (release 7.8). UMP1 is a short-lived chaperone present in the precursor form of the 20S proteasome and absent in the mature complex. UMP1 is required for the correct assembly and enzymatic activation of the proteasome. UMP1 seems to be degraded by the proteasome upon its formation. 
PF05349 GATA-type transcription activator, N-terminal <br>
PF05350 Glycogen synthase kinase-3 binding<br>Pfam-B_18811 (release 7.8). Glycogen synthase kinase-3 (GSK-3) sequentially phosphorylates four  serine residues on glycogen synthase (GS), in the sequence  SxxxSxxxSxxx-SxxxS(p), by recognising and phosphorylating the first  serine in the sequence motif SxxxS(P) (where S(p) represents a  phosphoserine). Interaction of GSK-3 with a peptide derived from GSK-3 binding protein (this family) prevents GSK-3 interaction with Axin. This interaction thereby inhibits the Axin-dependent phosphorylation of  beta-catenin by GSK-3  . . 
PF05351 GMP-PDE, delta subunit<br>Pfam-B_13828 (release 7.8). GMP-PDE delta subunit was originally identified as a fourth subunit of rod-specific cGMP phosphodiesterase (PDE)(EC:3.1.4.35).  The precise function of PDE delta subunit in the rod specific GMP-PDE complex is unclear. In addition, PDE delta subunit is not confined to photoreceptor cells but is widely distributed in different tissues.  PDE delta subunit is thought to be a specific soluble transport factor for certain prenylated proteins and Arl2-GTP a regulator of PDE-mediated transport  .. 
PF05352 Phage Connector (GP10)<br>Pfam-B_13828 (release 7.8). The head-tail connector of bacteriophage 29 is composed of 12  36  kDa subunits with 12 fold symmetry. It is the central component  of a rotary motor that packages the genomic dsDNA into pre-formed  proheads. This motor consists of the head-tail connector, surrounded  by a 29-encoded, 174-base, RNA and a viral ATPase protein [1,2].. 
PF05353 Delta Atracotoxin<br>Pfam-B_30981 (release 7.8). Delta atracotoxin produces potentially fatal neurotoxic symptoms in primates by slowing he inactivation of voltage-gated sodium channels  .  The structure of atracotoxin comprises a core beta region containing a triple-stranded a thumb-like extension protruding from the beta region and a C-terminal helix.  The beta region contains a cystine knot motif, a feature seen in other neurotoxic polypeptides  .. 
PF05354 Phage Head-Tail Attachment<br>Pfam-B_59968 (release 7.8). The phage head-tail attachment protein is required for the joining of phage heads and tails at the last step of morphogenesis  .. 
PF05355 Apolipoprotein C-II<br>Pfam-B_6456 (release 7.8). Apolipoprotein C-II (ApoC-II) is the major activator of lipoprotein lipase, a key enzyme in the regulation of triglyceride levels in human serum  .. 
PF05356 Phage Coat protein B <br>Pfam-B_51500 (release 7.8). The major coat protein in the capsid of filamentous bacteriophage forms a helical assembly of about 7000 identical protomers, with each protomer comprised of 46 amino acid, after the cleavage of the signal peptide.  Each protomer forms a slightly curved helix that combine to form a tubular structure that encapsulates the viral DNA  .. 
PF05357 Phage Coat Protein A<br>Pfam-B_7225 (release 7.8). Infection of Escherichia coli by filamentous bacteriophages is mediated  by the minor phage coat protein A and involves two distinct cellular receptors, the F' pilus and the periplasmic protein TolA.  These two receptors are contacted in a sequential manner, such that  binding of TolA by the extreme N-terminal domain is conditional on a  primary interaction of the second coat protein A domain with the F'  pilus  .. 
PF05358 DicB protein<br>DicB is part of the dic operon, which resides on cryptic prophage Kim. Under normal conditions, expression of dicB is actively repressed. When expression is induced, however, cell division rapidly ceases, and this division block is dependent on MinC with which it interacts  .. 
PF05359 Domain of Unknown Function (DUF748)<br>
PF05360 yiaA/B two helix domain<br>This domain consists of two transmembrane helices and a conserved linking section.. 
PF05361 PKC-activated protein phosphatase-1 inhibitor<br>Pfam-B_69711 (release 7.8). Contractility of vascular smooth muscle depends on phosphorylation of myosin light chains, and is modulated by hormonal control of myosin phosphatase activity. Signaling pathways activate kinases such as PKC or Rho-dependent kinases that phosphorylate the myosin phosphatase inhibitor protein called CPI-17. Phosphorylation of CPI-17 at Thr-38 enhances its inhibitory potency 1000-fold, creating a molecular switch for regulating contraction  .. 
PF05362 Lon protease (S16) C-terminal proteolytic domain<br>The Lon serine proteases must hydrolyse ATP to degrade protein substrates. In Escherichia coli, these proteases are involved in turnover of intracellular proteins, including abnormal proteins following heat-shock. The active site for protease activity resides in a C-terminal domain. The Lon proteases are classified as family S16 in Merops.. 
PF05363 Herpesvirus US12 family<br>Pfam-B_62991 (release 7.8). US12 a key factor in the evasion of cellular immune response against HSV-infected cells. Specific inhibition of the transporter associated with antigen processing (TAP) by US12 prevents peptide transport into the endoplasmic reticulum and subsequent loading of major histocompatibility complex (MHC) class I molecules  . US12 is comprised of three helices and is associated with cellular membranes  .. 
PF05364 SecIII_SopE; <br>Salmonella type III secretion SopE effector N-terminus. Pfam-B_18665 (release 7.8). Salmonella typhimurium employs a type III secretion system to inject bacterial toxins into the host cell cytosol. These toxins transiently activate Rho family GTP-binding protein-dependent signaling cascades to induce cytoskeletal rearrangements. SopE, one of these toxins, can activate Cdc42 in a Dbl-like fashion via its C-terminal GEP domain Pfam:PF07487  . This family represents the N-terminal region of SopE. The function of this domain is unknown.. 
PF05365 Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like<br>Pfam-B_18986 (release 7.8). The UQCRX/QCR9 protein is the 9/10 subunit of complex III, encoding a protein of about 7-kDa. Deletion of QCR9 results in the inability of cells  to grow on grow on-fermentable carbon source n yeast  .. 
PF05366 Sarcolipin<br>Pfam-B_33603 (release 7.8). Sarcolipin is a 31 amino acid integral membrane  protein that regulates Ca-ATPase activity in skeletal  muscle  .. 
PF05367 Phage endonuclease I<br>Pfam-B_22152 (release 7.8). The bacteriophage endonuclease I is a nuclease that is selective  for the structure of the four-way Holliday DNA  junction  .. 
PF05368 NmrA-like family<br>Pfam-B_25329 (release 7.8). NmrA is a negative transcriptional regulator involved in the post-translational modification of the transcription factor AreA. NmrA is part of a system controlling nitrogen metabolite repression in fungi  .  This family only contains a few sequences as iteration results in significant matches to other Rossmann fold families.. 
PF05369 Monomethylamine methyltransferase MtmB<br>Pfam-B_58618 (release 7.8). Monomethylamine methyltransferase of the archaebacterium Methanosarcina barkeri contains a novel amino acid, pyrrolysine, encoded by the termination codon UAG [1,2]. The structure reveals a homohexamer comprised of individual subunits with a TIM barrel fold  .. 
PF05370 Domain of unknown function (DUF749)<br>Pfam-B_54547 (release 7.8). Archaeal domain of unknown function.  This domain has been solved as part of a structural genomics project and comprises of segregated  helical and anti-parallel beta sheet regions.. 
PF05371 Phage major coat protein, Gp8<br>Pfam-B_31655 (release 7.8). Class I phage major coat protein Gp8 or B.  The coat protein  is largely alpha-helix with a slight curve  .   . 
PF05372 Delta lysin family<br>Pfam-B_45919 (release 7.8). Delta-lysin is a 26 amino acid, hemolytic peptide toxin secreted  by Staphylococcus aureus. It is thought that delta-toxin  forms an amphipathic helix upon binding to lipid bilayers  . The precise mode of action of delta-lysis is unclear.. 
PF05373 L-proline 3-hydroxylase, C-terminal<br>Pfam-B_32425 (release 7.8). Iron (II)/2-oxoglutarate (2-OG)-dependent oxygenases catalyse oxidative reactions in a range of metabolic processes.  Proline 3-hydroxylase  hydroxylates proline at position 3, the first of a 2-OG oxygenase catalysing oxidation of a free alpha-amino acid. The structure contains conserved motifs present in other 2-OG oxygenases including a  jelly roll strand core and residues binding iron and 2-oxoglutarate,  consistent with divergent evolution within the extended family.  The structure differs significantly from many other 2-OG oxygenases in possessing a discrete C-terminal helical domain.. 
PF05374 Mu-Conotoxin<br>Pfam-B_34209 (release 7.8). Mu-conotoxins are peptide inhibitors of voltage-sensitive sodium channels  .. 
PF05375 Pacifastin inhibitor (LCMII)<br>Pfam-B_35181 (release 7.8). Structures of members of this family show that they are comprised of a triple-stranded antiparallel beta-sheet connected by three disulfide bridges, which defines this as a novel family of serine protease inhibitors [1,2]. . 
PF05377 Flagella accessory protein C (FlaC)<br>Although archaeal flagella appear superficially similar to those of bacteria, they are quite distinct . In several archaea, the flagellin genes are followed immediately by the flagellar accessory genes flaCDEFGHIJ.  The gene products may have a role in translocation, secretion, or assembly of the flagellum. FlaC is a protein whose exact role is unknown but it has been shown to be membrane-associated (by immuno-blotting fractionated cells)  .. 
PF05378 Hydantoinase/oxoprolinase N-terminal region<br>This family is found at the N-terminus of the Pfam:PF01968 family.. 
PF05379 Carlavirus endopeptidase <br>A peptidase involved in auto-proteolysis of a polyprotein from the plant pathogen blueberry scorch carlavirus (BBScV) . Corresponds to Merops family C23. . 
PF05380 Pao retrotransposon peptidase <br>Corresponds to Merops family A17. These proteins are homologous to aspartic proteinases encoded by retroposons and retroviruses.. 
PF05381 Tymovirus endopeptidase<br>Corresponds to Merops family C21. The best-studied plant alpha-like virus proteolytic enzyme is the proteinase of turnip yellow mosaic virus (TYMV). The TYMV replicase protein undergoes auto-cleavage to yield two products.  The auto-peptidase activity has been mapped to the central part of this polyprotein.. 
PF05382 Bacteriophage peptidoglycan hydrolase <br>Pfam-B_6845 (Pfam7.8). At least one of the members of this family, the Pal protein from the pneumococcal bacteriophage Dp-1 Swiss:O03979 has been shown to be a N-acetylmuramoyl-L-alanine amidase  . According to the known modular structure of this and other peptidoglycan hydrolases from the pneumococcal system, the active site should reside at the N-terminal domain whereas the C-terminal domain binds to the choline residues of the cell wall teichoic acids [2,3].  This family appears to be related to Pfam:PF00877.. 
PF05383 La domain<br>This presumed domain is found at the N-terminus of La RNA-binding proteins as well as other proteins  . The function of this region is uncertain.. 
PF05384 Sensor protein DegS<br>This is small family of Bacillus DegS proteins.  The DegS-DegU two-component regulatory system of Bacillus subtilis controls various processes that characterise the transition from the exponential to the stationary growth phase, including the induction of extracellular degradative enzymes, expression of late competence genes and down-regulation of the sigma D regulon  . The family also contains one sequence Swiss:Q8R9D3 from Thermoanaerobacter tengcongensis which are described as sensory transduction histidine kinases.. 
PF05385 M_adenovirusE4; <br>Mastadenovirus early E4 13 kDa protein. This family consists of human and simian mastadenovirus early E4 13 kDa proteins. Human adenovirus type 9 (Ad9) is unique in eliciting exclusively estrogen-dependent mammary tumours in rats and in not requiring viral E1 region transforming genes for tumorigenicity. E4 codes for an oncoprotein essential for tumourigenesis by Ad9  .. 
PF05386 TEP1 N-terminal domain<br>This short sequence region is found in four copies at the N-terminus of the TEP1 telomerase component. The functional significance of the region is uncertain.  However the conservation of two histidines and a cysteine suggests it is a potential zinc binding domain.. 
PF05387 Chorion family 3<br>This family consists of several Drosophila chorion proteins S36 and S38. The chorion genes of Drosophila are amplified in response to developmental signals in the follicle cells of the ovary  .. 
PF05388 Carboxypeptidase Y pro-peptide<br>This family is found at the N terminus of several carboxypeptidase Y proteins and contains a signal peptide and pro-peptide regions [1,2].. 
PF05389 Negative regulator of genetic competence (MecA)<br>This family contains several bacterial MecA proteins. The development of competence in Bacillus subtilis is regulated by growth conditions and several regulatory genes. In complex media competence development is poor, and there is little or no expression of late competence genes. Mec  mutations permit competence development and late competence gene expression in complex media, bypassing the requirements for many of the competence regulatory genes. The mecA gene product acts negatively in the development of competence. Null mutations in mecA allow expression of a late competence gene comG, under conditions where it is not normally expressed, including in complex media and in cells mutant for several competence regulatory genes. Overexpression of MecA inhibits comG transcription [1,2,3].. 
PF05390 Yeast cell wall synthesis protein KRE9/KNH1<br>This family contains several KRE9 and KNH1 proteins which are involved in encoding cell surface O glycoproteins, which are required for beta -1,6-glucan synthesis in yeast  .. 
PF05391 Lsm interaction motif<br>This short motif is found at the C-terminus of Prp24 proteins and probably interacts with the Lsm proteins to promote U4/U6 formation  .. 
PF05392 Cytochrome C oxidase chain VIIB<br>
PF05393 Human adenovirus early E3A glycoprotein<br>This family consists of several early glycoproteins from human adenoviruses.. 
PF05394 Pseu_avirulence;<br>This family consists of several avirulence proteins from Pseudomonas syringae and Xanthomonas campestris.. 
PF05395 Protein phosphatase inhibitor 1/DARPP-32<br>This family consists of several mammalian protein phosphatase inhibitor 1 (IPP-1) and dopamine- and cAMP-regulated neuronal phosphoprotein (DARPP-32) proteins. Protein phosphatase inhibitor-1 is involved in signal transduction and is an endogenous inhibitor of protein phosphatase-1  . It has been demonstrated that DARPP-32, if phosphorylated, can inhibit protein-phosphatase-1  . DARPP-32 has a key role in many neurotransmitter pathways throughout the brain and has been shown to be involved in controlling receptors, ion channels and other physiological factors including the brain's response to drugs of abuse, such as cocaine, opiates and nicotine. DARPP-32 is reciprocally regulated by the two neurotransmitters that are most often implicated in schizophrenia - dopamine and glutamate. Dopamine activates DARPP-32 through the D1 receptor pathway and disables DARPP-32 through the D2 receptor. Glutamate, acting through the N-methyl-d-aspartate receptor, renders DARPP-32 inactive  . A mutant form of DARPP-32 has been linked with gastric cancers  .. 
PF05396 Phage T7 capsid assembly protein<br>
PF05397 GAL11;<br>Mediator complex subunit 15. GAL11 or MED15 is one of the up to 32 or subunits of the Mediator complex which is found from fungi to humans  . The Mediator complex interacts with RNA polymerase II and other general transcription factors to form the RNA polymerase II holoenzyme  , thereby affecting transcription through targetting of activators and repressors  . This family is found in fungi and the small metazoan starlet anemone.. 
PF05398 PufQ cytochrome subunit<br>This family consists of bacterial PufQ proteins. PufQ id required for bacteriochlorophyll biosynthesis serving a regulatory function in the formation of photosynthetic complexes  .. 
PF05399 Ectropic viral integration site 2A protein (EVI2A)<br>This family contains several mammalian ectropic viral integration site 2A (EVI2A) proteins. The function of this protein is unknown although it is thought to be a membrane protein and may function as an oncogene in retrovirus induced myeloid tumours [1,2].. 
PF05400 Flagellar protein FliT<br>This family contains several bacterial flagellar FliT proteins. The  flagellar proteins FlgN and FliT have been proposed to act as substrate specific export chaperones, facilitating incorporation of the enterobacterial hook-associated axial proteins (HAPs) FlgK/FlgL and FliD into the growing flagellum. In Salmonella typhimurium flgN and fliT mutants, the export of target HAPs is reduced, concomitant with loss of unincorporated flagellin into the surrounding medium  .  . 
PF05401 Nodulation protein S (NodS)<br>This family consists of nodulation S (NodS) proteins. The products of the rhizobial nodulation genes are involved in the biosynthesis of lipochitin oligosaccharides (LCOs), which are host-specific signal molecules required for nodule formation. NodS is an S-adenosyl-L-methionine (SAM)-dependent methyltransferase involved in N methylation of LCOs. NodS uses N-deacetylated chitooligosaccharides, the products of the NodBC proteins, as its methyl acceptors  .. 
PF05402 Coenzyme PQQ synthesis protein D (PqqD)<br>This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis [1,2].. 
PF05403 Plasmodium histidine-rich protein (HRPII/III)<br>This family consists of several histidine-rich protein II and III sequence from Plasmodium falciparum [1,2].. 
PF05404 Translocon-associated protein, delta subunit precursor (TRAP-delta)<br>Pfam-B_7178 (release 7.7). This family consists of several eukaryotic translocon-associated protein, delta subunit precursors (TRAP-delta or SSR-delta). The exact function of this protein is unknown [1,2].. 
PF05405 Mitochondrial ATP synthase B chain precursor (ATP-synt_B)<br>Pfam-B_7506 (release 7.7). The Fo sector of the ATP synthase is a membrane bound complex which mediates proton transport. It is composed of nine different polypeptide subunits (a, b, c, d, e, f, g F6, A6L)  .. 
PF05406 WGR domain<br>This domain is found in a variety of polyA polymerases as well as the E. coli molybdate metabolism regulator Swiss:P33345 and other proteins of unknown function. I have called this domain WGR after the most conserved central motif of the domain. The domain is found in isolation in proteins such as Swiss:Q9JN21 and is between 70 and 80 residues in length. I propose that this may be a nucleic acid binding domain.. 
PF05407 Rubella virus endopeptidase<br>Corresponds to Merops family C27. Required for processing of the rubella virus replication protein.. 
PF05408 Foot-and-mouth virus L-proteinase<br>Corresponds to Merops family C28. Protein fold of the peptidase unit for members of this family resembles that of papain. The leader proteinase of foot and mouth disease virus (FMDV) cleaves itself from the growing polyprotein and also cleaves the host translation initiation factor 4GI (eIF4G), thus inhibiting 5'-cap dependent translation.. 
PF05409 Coronavirus  endopeptidase C30<br>Corresponds to Merops family C30. These peptidases are involved in  viral polyprotein processing in replication.. 
PF05410 Porcine arterivirus-type cysteine proteinase alpha<br>Corresponds to Merops family C31. These peptidases are involved in viral polyprotein processing in replication.. 
PF05411 Equine arteritis virus putative proteinase<br>These proteins are characterised by a region that has been proposed to have peptidase activity involved in viral polyprotein processing in replication.. 
PF05412 Equine arterivirus Nsp2-type cysteine proteinase<br>Corresponds to Merops family C33. These peptidases are involved in viral polyprotein processing in replication.. 
PF05413 Putative closterovirus papain-like endopeptidase<br>Corresponds to Merops family C34. Putative closterovirus papain-like  endopeptidase from the apple chlorotic  leaf spot closterovirus.. 
PF05414 Peptidase_C35; <br>Viral domain of unknown function (DUF1717). This domain is found in viral proteins of unknown function.. 
PF05415 Beet necrotic yellow vein furovirus-type papain-like endopeptidase<br>Corresponds to Merops family C36. This protease involved in processing the viral polyprotein.. 
PF05416 Southampton virus-type processing peptidase<br>Corresponds to Merops family C37. Norwalk-like viruses (NLVs), including the Southampton virus, cause acute non-bacterial gastroenteritis in humans. The NLV genome encodes three open reading frames (ORFs). ORF1 encodes a polyprotein, which is processed by the viral protease into six proteins.. 
PF05417 Hepatitis E cysteine protease<br>Corresponds to MEROPs family C41. This papain-like protease cleaves the viral polyprotein encoded by ORF1 of the hepatitis E virus (HEV).. 
PF05418 Apovitellenin I (Apo-VLDL-II)<br>This family consists of several avian apovitellenin I sequences. As part of the avian reproductive effort, large quantities of triglyceride-rich very-low-density lipoprotein (VLDL) particles are transported by receptor-mediated endocytosis into the female germ cells. Although the oocytes are surrounded by a layer of granulosa cells harbouring high levels of active lipoprotein lipase, non-lipolysed VLDL is transported into the yolk. This is because VLDL particles from laying chickens are protected from lipolysis by apolipoprotein (apo)-VLDL-II, a potent dimeric lipoprotein lipase inhibitor  . Apo-VLDL-II is produced in the liver and secreted into the blood stream when induced by estrogen production in female birds.. 
PF05419 GUN4-like <br>In Arabidopsis, GUN4 is required for the functioning of the plastid mediated repression of nuclear transcription that is involved in controlling the levels of magnesium- protoporphyrin IX.  GUN4 binds the product and substrate of Mg-chelatase, an enzyme that produces Mg-Proto, and activates  Mg-chelatase. GUN4 is thought to participates in plastid-to-nucleus  signaling by regulating magnesium-protoporphyrin IX synthesis or  trafficking.. 
PF05420 BCSC_N; <br>Cellulose synthase operon protein C C-terminus (BCSC_C). Pfam-B_10335 (release 8.0). This family contains the C-terminal regions of several bacterial cellulose synthase operon C (BCSC) proteins. BCSC is involved in cellulose synthesis although the exact function of this protein is unknown  .. 
PF05421 Protein of unknown function (DUF751)<br>Pfam-B_10849 (release 8.0). This family contains several plant, cyanobacterial and algal proteins of unknown function. The family is exclusively found in phototrophic organisms and may therefore play a role in photosynthesis (personal obs:Moxon SJ).. 
PF05422 Stress-activated map kinase interacting protein 1 (SIN1)<br>Pfam-B_10677 (release 8.0). This family consists of several stress-activated map kinase interacting protein 1 (MAPKAP1 OR SIN1) sequences. The fission yeast Sty1/Spc1 mitogen-activated protein (MAP) kinase is a member of the eukaryotic stress-activated MAP kinase (SAPK) family. Sin1 interacts with Sty1/Spc1. Cells lacking Sin1 display many, but not all, of the phenotypes of cells lacking the Sty1/Spc1 MAP kinase including sterility, multiple stress sensitivity and a cell-cycle delay. Sin1 is phosphorylated after stress but this is not Sty1/Spc1-dependent  . . 
PF05423 Mycobacterium membrane protein<br>Pfam-B_10885 (release 8.0). This family contains several membrane proteins from Mycobacterium species.. 
PF05424 Duffy binding domain<br>Pfam-B_11112 (release 8.0). This domain is found in Plasmodium Duffy binding proteins. Plasmodium vivax and Plasmodium knowlesi merozoites invade human erythrocytes that express Duffy blood group surface determinants. The Duffy receptor family is localised in micronemes, an organelle found in all organisms of the phylum Apicomplexa  . This family is closely associated on PfEMP1 proteins with PFEMP, Pfam:PF03011.. 
PF05425 Copper resistance protein D<br>Pfam-B_19002 (release 8.0). Copper sequestering activity displayed by some bacteria is determined by copper-binding protein products of the copper resistance operon (cop). CopD, together with CopC, perform copper uptake into the cytoplasm  .. 
PF05426 Alginate lyase<br>Moxon SJ, Mistry J, Murzin A. Pfam-B_11800 (release 8.0). This family contains several bacterial alginate lyase proteins. Alginate is a family of 1-4-linked copolymers of beta -D-mannuronic acid (M) and alpha -L-guluronic acid (G). It is produced by brown algae and by some bacteria belonging to the genera Azotobacter and Pseudomonas. Alginate lyases catalyse the depolymerisation of alginates by beta -elimination, generating a molecule containing 4-deoxy-L-erythro-hex-4-enepyranosyluronate at the nonreducing end  .  This family adopts an all alpha fold  .. 
PF05427 Acidic fibroblast growth factor binding (FIBP) <br>Pfam-B_19083 (release 8.0). Acidic fibroblast growth factor (aFGF) intracellular binding  protein (FIBP) is a protein found mainly in the nucleus that is thought to be involved in the intracellular function of aFGF  .. 
PF05428 Corticotropin-releasing factor binding protein (CRF-BP)<br>Pfam-B_11928 (release 8.0). This family consists of several eukaryotic corticotropin-releasing factor binding proteins (CRF-BP or CRH-BP). Corticotropin-releasing hormone (CRH) plays multiple roles in vertebrate species. In mammals, it is the major hypothalamic releasing factor for pituitary adrenocorticotropin secretion, and is a neurotransmitter or neuromodulator at other sites in the central nervous system. In non-mammalian vertebrates, CRH not only acts as a neurotransmitter and hypophysiotropin, it also acts as a potent thyrotropin-releasing factor, allowing CRH to regulate both the adrenal and thyroid axes, especially in development. CRH-BP is thought to play an inhibitory role in which it binds CRH and other CRH-like ligands and prevents the activation of CRH receptors. There is however evidence that CRH-BP may also exhibit diverse extra and intracellular roles in a cell specific fashion and at specific times in development  .. 
PF05430 DUF752;<br>S-adenosyl-L-methionine-dependent methyltransferase. Moxon SJ, Eberhardt R. Pfam-B_12088 (release 8.0). This family is a S-adenosyl-L-methionine (SAM)-dependent methyltransferase. It is often found in association with Pfam:PF01266, where it is responsible for catalysing the transfer of a methyl group from S-adenosyl-L-methionine to 5-aminomethyl-2-thiouridine to form 5-methylaminomethyl-2-thiouridine [1,2].. 
PF05431 Toxin_P42; <br>Insecticidal Crystal Toxin, P42 . Pfam-B_19338 (release 8.0). Family of Bacillus insecticidal crystal toxins.  Strains of Bacillus that have this insecticidal activity use a binary toxin comprised of two proteins, P51 and P42 (this family).  Members of this family are highly conserved  between strains of different serotypes and phage groups  .. 
PF05432 Bone sialoprotein II (BSP-II)<br>Pfam-B_12103 (release 8.0). Bone sialoprotein (BSP) is a major structural protein of the bone matrix that is specifically expressed by fully-differentiated osteoblasts  . The expression of bone sialoprotein (BSP) is normally restricted to mineralised connective tissues of bones and teeth where it has been associated with mineral crystal formation. However, it has been found that ectopic expression of BSP occurs in various lesions, including oral and extraoral carcinomas, in which it has been associated with the formation of microcrystalline deposits and the metastasis of cancer cells to bone  . . 
PF05433 Glycine zipper 2TM domain<br>Pfam-B_13382 (Rel 8.0) & Pfam-B_6 (Rel 24.0). This family includes a putative two transmembrane alpha-helical region that contains glycine zipper motifs  . This family includes  several Rickettsia genus specific 17 kDa surface antigen proteins  .. 
PF05434 TMEM9; <br>Pfam-B_12447 (release 8.0). This family contains several eukaryotic transmembrane proteins which are homologous to human transmembrane protein 9 Swiss:Q9P0T7. The TMEM9 gene encodes a 183 amino-acid protein that contains an N-terminal signal peptide, a single transmembrane region, three potential N-glycosylation sites and three conserved cys-rich domains in the N-terminus, but no known functional domains. The protein is highly conserved between species from Caenorhabditis elegans to man and belongs to a novel family of transmembrane proteins. The exact function of TMEM9 is unknown although it has been found to be widely expressed and localised to the late endosomes and lysosomes  . Members of this family contain Pfam:PF03128 repeats in their N-terminal region.. 
PF05435 Phi-29 DNA terminal protein GP3<br>Pfam-B_14111 (release 8.0). This family consists of DNA terminal protein GP3 sequences from Phi-29 like bacteriophages. DNA terminal protein GP3 is linked to the 5' ends of both strands of the genome through a phosphodiester bond between the beta-hydroxyl group of a serine residue and the 5'-phosphate of the terminal deoxyadenylate. This protein is essential for DNA replication and is involved in the priming of DNA elongation  .. 
PF05436 Mating factor alpha precursor N-terminus<br>Pfam-B_12643 (release 8.0). This family contains the N-terminal regions of the Saccharomyces mating factor alpha precursor protein. All proteins in this family contain one or more copies Pfam:PF04648 further toward their C terminus.. 
PF05437 Branched-chain amino acid transport protein (AzlD)<br>Pfam-B_14345 (release 8.0). This family consists of a number of bacterial and archaeal branched-chain amino acid transport proteins. AzlD is known to be involved in conferring resistance to 4-azaleucine although its exact role is uncertain  .. 
PF05438 Thyrotropin-releasing hormone (TRH)<br>Pfam-B_14384 (release 8.0). This family consists of several thyrotropin-releasing hormone (TRH) proteins. Thyrotropin-Releasing Hormone (TRH; pyroGlu-His-Pro-NH2), originally isolated as a hypothalamic neuropeptide hormone, most likely acts also as a neuromodulator and/or neurotransmitter in the central nervous system (CNS). This interpretation is supported by the identification of a peptidase localised on the surface of neuronal cells which has been termed TRH-degrading ectoenzyme (TRH-DE) since it selectively inactivates TRH  . TRH has been used clinically for the treatment of spinocerebellar degeneration and disturbance of consciousness in humans  .. 
PF05439 Jumping translocation breakpoint protein (JTB)<br>Pfam-B_14502 (release 8.0). This family contains several jumping translocation breakpoint proteins or JTBs. Jumping translocation (JT) is an unbalanced translocation that comprises amplified chromosomal segments jumping to various telomeres. JTB, located at 1q21, has been found to fuse with the telomeric repeats of acceptor telomeres in a case of JT. hJTB (human JTB) encodes a trans-membrane protein that is highly conserved among divergent eukaryotic species. JT results in a hJTB truncation, which potentially produces an hJTB product devoid of the trans-membrane domain. hJTB is located in a gene-rich region at 1q21, called EDC (Epidermal Differentiation Complex)  . JTB has also been implicated in prostatic carcinomas  .. 
PF05440 Tetrahydromethanopterin S-methyltransferase subunit B<br>Pfam-B_15021 (release 8.0). The N5-methyltetrahydromethanopterin: coenzyme M (EC:2.1.1.86) of  Methanosarcina mazei Go1 is a membrane-associated, corrinoid-containing protein that uses a transmethylation reaction to drive an energy-conserving sodium ion pump  . . 
PF05443 ROS/MUCR transcriptional regulator protein<br>Pfam-B_1733 (release 8.0). This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti. This gene encodes a 15.5-kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid   and is necessary for succinoglycan production  . Sinorhizobium meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of alfalfa nodules. MucR from Sinorhizobium meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan  .. 
PF05444 Protein of unknown function (DUF753)<br>Pfam-B_1957 (release 8.0). This family contains sequences with are repeated in several uncharacterised proteins from Drosophila melanogaster.. 
PF05445 Poxvirus serine/threonine protein kinase<br>Pfam-B_1974 (release 8.0). 
PF05448 Acetyl xylan esterase (AXE1)<br>Pfam-B_4814 (release 8.0). This family consists of several bacterial acetyl xylan esterase proteins. Acetyl xylan esterases are enzymes that hydrolyse the ester linkages of the acetyl groups in position 2 and/or 3 of the xylose moieties of natural acetylated xylan from hardwood. These enzymes are one of the accessory enzymes which are part of the xylanolytic system, together with xylanases, beta-xylosidases, alpha-arabinofuranosidases and methylglucuronidases; these are all required for the complete hydrolysis of xylan  .. 
PF05449 Protein of unknown function (DUF754)<br>This domain appears to be found in a group of  prophage proteins.. 
PF05450 Nicastrin<br>Pfam-B_15452 (release 8.0). Nicastrin and presenilin are two major components of the gamma-secretase complex, which executes the intramembrane proteolysis of type I integral membrane proteins such as the amyloid precursor protein (APP) and Notch.  Nicastrin is synthesised in fibroblasts and neurons as an endoglycosidase-H-sensitive glycosylated precursor protein (immature nicastrin) and is then modified by complex glycosylation in the Golgi apparatus and by sialylation in the trans-Golgi network (mature nicastrin)  . A region featured in this family has a fold similar to human transferrin receptor (TfR, Swiss:P02786) and a bacterial aminopeptidase (Swiss:P80561). It is implicated in the pathogenesis of Alzheimer's disease  .. 
PF05451 Phytoreovirus nonstructural protein Pns10/11<br>Pfam-B_15695 (release 8.0). This family consists of Phytoreovirus nonstructural proteins Pns10 and Pns11. Genome segment S11 of rice gall dwarf virus (RGDV), a member of Phytoreovirus encodes a putative protein of 40 kDa that exhibits approximately 37% homology at the amino acid level to the nonstructural proteins Pns10 of rice dwarf and wound tumour viruses, which are other members of Phytoreovirus  .. 
PF05452 Clavanin<br>Pfam-B_15887 (release 8.0). This family consists of clavanin proteins from the haemocytes of the invertebrate Styela clava, a solitary tunicate. The family is made up of four alpha-helical antimicrobial peptides, clavanins A, B, C and D. The tunicate peptides resemble magainins in size, primary sequence and antibacterial activity. Synthetic clavanin A displays comparable antimicrobial activity to magainins and cecropins. The presence of alpha-helical antimicrobial peptides in the haemocytes of a urochordate suggests that such peptides are primeval effectors of innate immunity in the vertebrate lineage  .. 
PF05453 toxin_6; <br>BmTXKS1/BmP02 toxin family. Pfam-B_16009 (release 8.0). This family consists of toxin-like peptides that are isolated from the venom of Buthus martensii Karsch scorpion. The precursor consists of 60 amino acid residues, with a putative signal peptide of 28 residues and an extra residue, and a mature peptide of 31 residues with an amidated C-terminal. The peptides share close homology with other scorpion K+ channel toxins and should present a common three-dimensional fold - the Cysteine -Stabilised alphabeta (CSalphabeta) motif  . This family acts by blocking small conductance calcium activated potassium ion channels in their victim [1,2].. 
PF05454 Dystroglycan (Dystrophin-associated glycoprotein 1)<br>Pfam-B_15784 (release 8.0). Dystroglycan is one of the dystrophin-associated glycoproteins, which is encoded by a 5.5 kb transcript in human. The protein product is cleaved into two non-covalently associated subunits, [alpha] (N-terminal) and  [beta] (C-terminal). In skeletal muscle the dystroglycan complex works as a transmembrane linkage between the extracellular matrix and the cytoskeleton. [alpha]-dystroglycan is extracellular and binds to merosin ([alpha]-2 laminin) in the basement membrane, while [beta]-dystroglycan is a transmembrane protein and binds to dystrophin, which is a large rod-like cytoskeletal protein, absent in Duchenne muscular dystrophy patients. Dystrophin binds to intracellular actin cables. In this way, the dystroglycan complex, which links the extracellular matrix to the intracellular actin cables, is thought to provide structural integrity in muscle tissues. The dystroglycan complex is also known to serve as an agrin receptor in muscle, where it may regulate agrin-induced acetylcholine receptor clustering at the neuromuscular junction. There is also evidence which suggests the function of dystroglycan as a part of the signal transduction pathway because it is shown that Grb2, a mediator of the Ras-related signal pathway, can interact with the cytoplasmic domain of dystroglycan. In general, aberrant expression of dystrophin-associated protein complex underlies the pathogenesis of Duchenne muscular dystrophy, Becker muscular dystrophy and severe childhood autosomal recessive muscular dystrophy. Interestingly, no genetic disease has been described for either [alpha]- or [beta]-dystroglycan. Dystroglycan is widely distributed in non-muscle tissues as well as in muscle tissues. During epithelial morphogenesis of kidney, the dystroglycan complex is shown to act as a receptor for the basement membrane. Dystroglycan expression in mouse brain and neural retina has also been reported. However, the physiological role of dystroglycan in non-muscle tissues has remained unclear  . . 
PF05455 GvpH<br>Pfam-B_16017 (release 8.0). This family consists of archaeal GvpH proteins which are thought to be involved in gas vesicle synthesis  .. 
PF05456 EIF4EBP; <br>Eukaryotic translation initiation factor 4E binding protein (EIF4EBP). Pfam-B_5573 (release 8.0). This family consists of several eukaryotic translation initiation factor 4E binding proteins (EIF4EBP1 ,2 and 3). Translation initiation in eukaryotes is mediated by the cap structure (m7GpppN, where N is any nucleotide) present at the 5' end of all cellular mRNAs, except organellar. The cap is recognised by eukaryotic initiation factor 4F (eIF4F), which consists of three polypeptides, including eIF4E, the cap-binding protein subunit. The interaction of the cap with eIF4E facilitates the binding of the ribosome to the mRNA. eIF4E activity is regulated in part by translational repressors, 4E-BP1, 4E-BP2 and 4E-BP3 which bind to it and prevent its assembly into eIF4F  .. 
PF05458 Cd27 binding protein (Siva)<br>Pfam-B_5606 (release 8.0). Siva binds to the CD27 cytoplasmic tail. It has a DD homology region, a box-B-like ring finger, and a zinc finger-like domain. Overexpression of Siva in various cell lines induces apoptosis, suggesting an important role for Siva in the CD27-transduced apoptotic pathway  . Siva-1 binds to and inhibits BCL-X(L)-mediated protection against UV radiation-induced apoptosis. Indeed, the unique amphipathic helical region (SAH) present in Siva-1 is required for its binding to BCL-X(L) and sensitising cells to UV radiation. Natural complexes of Siva-1/BCL-X(L) are detected in HUT78 and murine thymocyte, suggesting a potential role for Siva-1 in regulating T cell homeostasis  . This family contains both Siva-1 and the shorter Siva-2 lacking the sequence coded by exon 2. It has been suggested that Siva-2 could regulate the function of Siva-1  .. 
PF05459 Herpesvirus transcriptional regulator family<br>Pfam-B_15401 (release 8.0). This family includes UL69 and IE63 that are transcriptional regulator proteins.. 
PF05460 ORC6; ORC6_1; <br>Origin recognition complex subunit 6 (ORC6). Pfam-B_16189 (release 8.0). This family consists of several eukaryotic origin recognition complex subunit 6 (ORC6) proteins.  Despite differences in their structure and sequences among eukaryotic replicators, ORC is a conserved feature of replication initiation in all eukaryotes. ORC-related genes have been identified in organisms ranging from S. pombe to plants to humans. 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  .. 
PF05461 Apolipoprotein L<br>Pfam-B_16464 (release 8.0). Apo L belongs to the high density lipoprotein family that plays a central role in cholesterol transport. The cholesterol content of membranes is important in cellular processes such as modulating gene transcription and signal transduction both in the adult brain and during neurodevelopment. There are six apo L genes located in close proximity to each other on chromosome 22q12 in humans. 22q12 is a confirmed high-susceptibility locus for schizophrenia and close to the region associated with velocardiofacial syndrome that includes symptoms of schizophrenia  .. 
PF05462 Dict_CAR; <br>Slime mold cyclic AMP receptor. Pfam-B_16614 (release 8.0). This family consists of cyclic AMP receptor (CAR) proteins from slime molds. CAR proteins are responsible for controlling development in Dictyostelium discoideum [1,2,3,4].. 
PF05463 Sclerostin (SOST)<br>Pfam-B_16740 (release 8.0). This family contains several mammalian sclerostin (SOST) proteins. SOST is thought to suppress bone formation. Mutations of the SOST gene lead to sclerosteosis, a progressive sclerosing bone dysplasia with an autosomal recessive mode of inheritance. Radiologically, it is characterised by a generalised hyperostosis and sclerosis leading to a markedly thickened and sclerotic skull, with mandible, ribs, clavicles and all long bones also being affected. Due to narrowing of the foramina of the cranial nerves, facial nerve palsy, hearing loss and atrophy of the optic nerves can occur. Sclerosteosis is clinically and radiologically very similar to van Buchem disease, mainly differentiated by hand malformations and a large stature in sclerosteosis patients  .. 
PF05464 Phi-29-like late genes activator (early protein GP4)<br>Pfam-B_16889 (release 8.0). This family consists of phi-29-like late genes activator (or early protein GP4). This protein is thought to be a positive regulator of late transcription and may function as a sigma like component of the host RNA polymerase  .. 
PF05465 Halobacterial gas vesicle protein C (GVPC) repeat<br>Pfam-B_17013 (release 8.0). This family consists of Halobacterium gas vesicle protein C sequences which are thought to confer stability to the gas vesicle membranes [1,2].. 
PF05466 Brain acid soluble protein 1 (BASP1 protein)<br>Pfam-B_16137 (release 8.0). This family consists of several brain acid soluble protein 1 (BASP1) or neuronal axonal membrane protein NAP-22. The BASP1 is a neuron enriched Ca(2+)-dependent calmodulin-binding protein of unknown function [1,2].. 
PF05467 Herpesvirus glycoprotein U47<br>Pfam-B_17115 (release 8.0). 
PF05470 eIF3c_N; <br>Eukaryotic translation initiation factor 3 subunit 8 N-terminus. Pfam-B_17447 (release 8.0). The largest of the mammalian translation initiation factors, eIF3, consists of at least eight subunits ranging in mass from 35 to 170 kDa. eIF3 binds to the 40 S ribosome in an early step of translation initiation and promotes the binding of methionyl-tRNAi and mRNA  .. 
PF05472 DNA replication terminus site-binding protein (Ter protein)<br>Pfam-B_17662 (release 8.0). This family contains several bacterial Ter proteins. The Ter protein specifically binds to DNA replication terminus sites on the host and plasmid genome and then blocks progress of the DNA replication fork  .. 
PF05473 UL45 protein<br>Pfam-B_17674 (release 8.0) & Pfam-B_16138 (release 10.0). This family consists several UL45 proteins. The herpes simplex virus UL45 gene encodes an 18 kDa virion envelope protein whose function remains unknown. It has been suggested that the 18 kDa UL45 gene product is required for efficient growth in the central nervous system at low doses and may play an important role under the conditions of a naturally acquired infection  . This family also contains several Varicellovirus UL45 or gene 15 proteins. The Equine herpesvirus 1 UL45 protein represents a type II membrane glycoprotein which has found to be non-essential for EHV-1 growth in vitro but deletion reduces the viruses' replication efficiency  .. 
PF05474 Semenogelin<br>Pfam-B_18147 (release 8.0). This family consists of several mammalian semenogelin (I and II) proteins. Freshly ejaculated human semen has the appearance of a loose gel in which the predominant structural protein components are the seminal vesicle secreted semenogelins (Sg)  .. 
PF05475 Chlamydia_vir; <br>Chlamydia virulence protein PGP3-D. Pfam-B_18238 (release 8.0). This family consists of Chlamydia virulence proteins which are thought to be required for growth within mammalian cells  .. 
PF05476 PET122<br>Pfam-B_18328 (release 8.0). The nuclear PET122 gene of S. cerevisiae encodes a mitochondrial-localised protein that activates initiation of translation of the mitochondrial mRNA from the COX3 gene, which encodes subunit III of cytochrome c oxidase  . . 
PF05477 Surfeit locus protein 2 (SURF2)<br>Pfam-B_18437 (release 8.0)  . Surfeit locus protein 2 is part of a group of at least six sequence unrelated genes (Surf-1 to Surf-6). The six Surfeit genes have been classified as housekeeping genes, being expressed in all tissue types tested and not containing a TATA box in their promoter region. The exact function of SURF2 is unknown  .. 
PF05478 Prominin<br>Pfam-B_18226 (release 8.0). The prominins are an emerging family of proteins that among the multispan membrane proteins display a novel topology. Mouse prominin and human prominin (mouse)-like 1 (PROML1) are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain  . The exact function of prominin is unknown although in humans defects in PROM1, the gene coding for prominin, cause retinal degeneration  .. 
PF05479 Photosystem I reaction centre subunit N (PSAN or PSI-N)<br>Pfam-B_18582 (release 8.0). This family contains several Photosystem I reaction centre subunit N (PSI-N) proteins. The protein has no known function although it is localised in the thylakoid lumen  . PSI-N is a small extrinsic subunit at the lumen side and is very likely involved in the docking of plastocyanin  .. 
PF05480 Staphylococcus haemolytic protein<br>Pfam-B_18620 (release 8.0). This family consists of several different short Staphylococcal proteins, it contains SLUSH A, B and C proteins as well as haemolysin and gonococcal growth inhibitor. Some strains of the coagulase-negative Staphylococcus lugdunensis produce a synergistic hemolytic activity (SLUSH), phenotypically similar to the delta-hemolysin of S. aureus  . Gonococcal growth inhibitor from Staphylococcus  act on the cytoplasmic membrane of the gonococcal cell causing cytoplasmic leakage and, eventually, death  .. 
PF05481 Mycobacterium 19 kDa lipoprotein antigen<br>Pfam-B_19467 (release 8.0). Most of the antigens of Mycobacterium leprae and M. tuberculosis that have been identified are members of stress protein families, which are highly conserved throughout many diverse species. Of the M. leprae and M. tuberculosis antigens identified by monoclonal antibodies, all except the 18-kDa M. leprae antigen and the 19-kDa M. tuberculosis antigen are strongly cross-reactive between these two species and are coded within very similar genes [1,2].. 
PF05482 Serendipity locus alpha protein (SRY-A)<br>Pfam-B_19519 (release 8.0). The Drosophila serendipity alpha (sry alpha) gene is specifically transcribed at the blastoderm stage, from nuclear cycle 11 to the onset of gastrulation, in all somatic nuclei  . SRY-A is required for the cellularisation of the embryo and is involved in the localisation of the actin filaments just prior to and during plasma membrane invagination  .. 
PF05483 Synaptonemal complex protein 1 (SCP-1)<br>Pfam-B_19633 (release 8.0). Synaptonemal complex protein 1 (SCP-1) is the major component of the transverse filaments of the synaptonemal complex. Synaptonemal complexes are structures that are formed between homologous chromosomes during meiotic prophase  .. 
PF05484 LRV protein FeS4 cluster<br>This Iron sulphur cluster is found at the N-terminus of some proteins containing Pfam:PF01816 repeats.. 
PF05485 THAP domain<br>The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes  .. 
PF05486 SRP9; <br>Signal recognition particle 9 kDa protein (SRP9). Pfam-B_7787 (release 8.0). This family consists of several eukaryotic SRP9 proteins. SRP9 together with the Alu-homologous region of 7SL RNA and SRP14 comprise the "Alu domain" of SRP, which mediates pausing of synthesis of ribosome associated nascent polypeptides that have been engaged by the targeting domain of SRP  . This family also contains the homologous fungal SRP21  .. 
PF05488 PAAR motif<br>This motif is found usually in pairs in a family of bacterial membrane proteins. It is also found as a triplet of tandem repeats comprising the entire length in a another family of hypothetical proteins.. 
PF05489 Tail_X; <br>Phage Tail Protein X. This domain is found in a family of phage tail proteins. Visual analysis suggests that it is related to Pfam:PF01476 (personal obs: C Yeats). The functional annotation of family members further confirms this hypothesis.. 
PF05491 Holliday junction DNA helicase ruvB C-terminus<br>Pfam-B_844 (release 8.0). The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein  . This family consists of the C-terminal region of the RuvB protein which is thought to be helicase DNA-binding domain. . 
PF05493 ATP synthase subunit H <br>Pfam-B_3341 (release 8.0). ATP synthase subunit H is an extremely hydrophobic  of approximately 9 kDa  .  This subunit may be required for assembly of vacuolar  ATPase  . . 
PF05494 Toluene tolerance, Ttg2 <br>Pfam-B_3575 (release 8.0). Toluene tolerance is mediated by increased cell membrane rigidity  resulting from changes in fatty acid and phospholipid compositions,  exclusion of toluene from the cell membrane, and removal of intracellular  toluene by degradation  .  Many proteins are involved in these processes.  This family is a transporter which shows similarity  to ABC transporters  .. 
PF05495 CHY zinc finger<br>Pfam-B_5537 (release 7.8). This family of domains are likely to bind to zinc ions. They contain many conserved cysteine and histidine residues. We have named this domain after the N-terminal motif CXHY. This domain can be found in isolation in some proteins, but is also often associated with Pfam:PF00097.  One of the proteins in this family (Swiss:P36078) is a mitochondrial intermembrane space protein called Hot13. This protein is involved in the assembly of small TIM complexes  .. 
PF05496 Holliday junction DNA helicase ruvB N-terminus<br>Pfam-B_844 (release 8.0). The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein  . This family contains the N-terminal region of the protein. . 
PF05497 Destabilase<br>Pfam-B_4147 (release 8.0). Destabilase is an endo-epsilon(gamma-Glu)-Lys isopeptidase, which cleaves  isopeptide bonds formed by transglutaminase (Factor XIIIa) between  glutamine gamma-carboxamide and the epsilon-amino group of lysine  .. 
PF05498 Rapid ALkalinization Factor (RALF) <br>Pfam-B_4453 (release 8.0). RALF, a 5-kDa ubiquitous polypeptide in plants, arrests root  growth and development  .. 
PF05499 DNA methyltransferase 1-associated protein 1 (DMAP1)<br>Pfam-B_38340 (release 8.0). DNA methylation can contribute to transcriptional silencing through several transcriptionally repressive complexes, which include methyl-CpG binding domain proteins (MBDs) and histone deacetylases (HDACs). The chief enzyme that maintains mammalian DNA methylation, DNMT1, can also establish a repressive transcription complex. The non-catalytic amino terminus of DNMT1 binds to HDAC2 and DMAP1 (for DNMT1 associated protein), and can mediate transcriptional repression. DMAP1 has intrinsic transcription repressive activity, and binds to the transcriptional co-repressor TSG101. DMAP1 is targeted to replication foci through interaction with the far N terminus of DNMT1 throughout S phase, whereas HDAC2 joins DNMT1 and DMAP1 only during late S phase, providing a platform for how histones may become deacetylated in heterochromatin following replication  .. 
PF05501 Domain of unknown function (DUF755) <br>Pfam-B_4891 (release 8.0). This family is predominated by ORFs from Circoviridae. The function of this family remains to be determined.. 
PF05502 Dynactin p62 family<br>Pfam-B_4912 (release 8.0). Dynactin is a multi-subunit complex and a required cofactor for most, or all, of the cellular processes powered by the microtubule-based motor cytoplasmic dynein. p62 binds directly to the Arp1 subunit of dynactin [1,2].. 
PF05503 Poxvirus G7-like <br>Pfam-B_4957 (release 8.0). 
PF05504 Spore germination B3/ GerAC like, C-terminal <br>Pfam-B_5052 (release 8.0). The GerAC protein of the Bacillus subtilis spore is required for the  germination response to L-alanine. Members of this family are thought to be located in the inner spore membrane. Although the function of this family is unclear, they are likely to encode the components of the  germination apparatus that respond directly to this germinant,  mediating the spore's response  .. 
PF05505 Ebola nucleoprotein<br>Pfam-B_8475 (release 8.0). This family consists of Ebola and Marburg virus nucleoproteins. These proteins are responsible for encapsidation of genomic RNA. It has been found that nucleoprotein DNA vaccines can offer protection from the virus  .. 
PF05506 Domain of unknown function (DUF756)<br>This domain is found, normally as a tandem repeat, at the C-terminus of bacterial phospholipase C proteins.. 
PF05507 Microfibril-associated glycoprotein (MAGP)<br>Pfam-B_8462 (release 8.0). This family consists of several mammalian microfibril-associated glycoprotein (MAGP) 1 and 2 proteins. MAGP1 and 2 are components of elastic fibres. MAGP-1 has been proposed to bind a C-terminal region of tropoelastin, the soluble precursor of elastin. MAGP-2 was found to interact with fibrillin-1 and -2, as well as fibulin-1, another component of elastic fibres this suggests that MAGP-2 may be important in the assembly of microfibrils  . . 
PF05508 RanGTP-binding protein<br>Pfam-B_37054 (release 8.0). The small Ras-like GTPase Ran plays an essential role in the transport of macromolecules in and out of the nucleus and has been implicated in spindle and nuclear envelope formation during mitosis in higher eukaryotes. The S. cerevisiae ORF YGL164c encoding a novel RanGTP-binding protein, termed Yrb30p was identified. The protein competes with yeast RanBP1 (Yrb1p) for binding to the GTP-bound form of yeast Ran (Gsp1p) and is, like Yrb1p, able to form trimeric complexes with RanGTP and some of the karyopherins  .. 
PF05509 TraY domain<br>Pfam-B_8963 (release 8.0). This family consists of several enterobacterial TraY proteins. TraY is involved in bacterial conjugation where it is required for efficient nick formation in the F plasmid  . These proteins have a ribbon-helix-helix fold and are likely to be DNA-binding proteins.. 
PF05510 sarcoglycan_2; <br>Sarcoglycan alpha/epsilon. Pfam-B_9181 (release 8.0). Sarcoglycans are a subcomplex of transmembrane proteins which are part of the dystrophin-glycoprotein complex. They are expressed in the skeletal, cardiac and smooth muscle. Although numerous studies have been conducted on the sarcoglycan subcomplex in skeletal and cardiac muscle, the manner of the distribution and localisation of these proteins along the nonjunctional sarcolemma is not clear  . This family contains alpha and epsilon members.. 
PF05511 Mitochondrial ATP synthase coupling factor 6<br>Pfam-B_9347 (release 8.0). Coupling factor 6 (F6) is a component of mitochondrial ATP synthase which is required for the interactions of the catalytic and proton-translocating segments  . . 
PF05512 AWPM-19-like family<br>Pfam-B_6960 (release 8.0). Members of this family are 19 kDa membrane proteins. The levels of the plant protein AWPM-19 increase dramatically when there is an increase level of abscisic acid.  The increase presence of this protein leads to greater tolerance of freezing  .. 
PF05513 TraA<br>Pfam-B_9521 (release 8.0). Conjugative transfer of a bacteriocin plasmid, pPD1, of Enterococcus faecalis is induced in response to a peptide sex pheromone, cPD1, secreted from plasmid-free recipient cells. cPD1 is taken up by a pPD1 donor cell and binds to an intracellular receptor, TraA. Once a recipient cell acquires pPD1, it starts to produce an inhibitor of cPD1, termed iPD1, which functions as a TraA antagonist and blocks self-induction in donor cells. TraA transduces the signal of cPD1 to the mating response  .. 
PF05514 HR-like lesion-inducing <br>Pfam-B_6954 (release 8.0). Family of plant proteins that are associated with the hypersensitive response (HR) pathway of defence against  plant pathogens  .. 
PF05515 Viral nucleic acid binding <br>Pfam-B_6916 (release 8.0). This family is common to ssRNA positive-strand viruses and are commonly described as nucleic acid binding  proteins (NABP).. 
PF05517 p25-alpha <br>Pfam-B_6873 (release 8.0). This family encodes a 25 kDa protein that is phosphorylated by a Ser/Thr-Pro kinase  .  It has been described as a brain specific protein, but it is found in Tetrahymena thermophila.. 
PF05518 Totivirus coat protein<br>Pfam-B_10221 (release 8.0). 
PF05520 Citrus tristeza virus P18 protein<br>Pfam-B_10309 (release 8.0). 
PF05521 Phage head-tail joining protein <br>Pfam-B_7008 (release 8.0). 
PF05522 Metallothionein;<br>Pfam-B_1360 (release 8.0). This family consists of metallothioneins from several worm and sea urchin species. Metallothioneins are low molecular weight, cysteine rich proteins known to be involved in heavy metal detoxification and homeostasis  .. 
PF05523 WxcM_C; <br>WxcM-like, C-terminal . Pfam-B_6950 (release 8.0). This family includes FdtA (Swiss:Q6T1W8) from Aneurinibacillus thermoaerophilus, which has been characterised as a dtdp-6-deoxy-3,4-keto-hexulose isomerase  . It also includes WxcM (Swiss:Q93S92) from Xanthomonas campestris (pv. campestris)  .. 
PF05524 PEP-utilising enzyme, N-terminal<br>Pfam-B_69291 (release 8.0). 
PF05525 Branched-chain amino acid transport protein<br>Pfam-B_1869 (release 8.0). This family consists of several bacterial branched-chain amino acid transport proteins which are responsible for the transport of leucine, isoleucine and valine via proton motive force  .. 
PF05526 Rhodococcus equi virulence-associated protein<br>Pfam-B_7324 (release 8.0). This family consists of several virulence-associated proteins from Rhodococcus equi. Rhodococcus equi is an important pulmonary pathogen of foals and is increasingly isolated from pneumonic infections and other infections in human immunodeficiency virus (HIV)-infected patients. Isolates from foals possess a large virulence plasmid, varying in size from 80 to 90 kb. Isolates lacking the plasmid are avirulent to foals. Little is known about the function of the plasmid apart from its encoding a virulence associated surface proteins  .. 
PF05527 Domain of unknown function (DUF758) <br>Pfam-B_6320 (release 8.0). Family of eukaryotic proteins with unknown function, which are induced by tumour necrosis factor.. 
PF05528 Coronavirus gene 5 protein<br>Pfam-B_7342 (release 8.0). Infectious bronchitis virus (IBV), a member of Coronaviridae family, has a single-stranded positive-sense RNA genome, which is 27 kb in length. Gene 5 contains two (5a and 5b) open reading frames. The function of the 5a and 5b proteins is unknown  .. 
PF05529 B-cell receptor-associated protein 31-like <br>Pfam-B_6449 (release 8.0). Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8.  Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31  .. 
PF05531 Nucleopolyhedrovirus P10 protein<br>Pfam-B_7343 (release 8.0) & Pfam-B_6199 (release 10.0). This family consists of several nucleopolyhedrovirus P10 proteins which are thought to be involved in the morphogenesis of the polyhedra  .. 
PF05532 CsbD-like<br>Pfam-B_6755 (release 8.0). CsbD is a bacterial general stress response protein.  It's expression is mediated by sigma-B, an alternative sigma factor  . The role of CsbD in stress response is  unclear.. 
PF05533 Beet yellows virus-type papain-like endopeptidase C42<br>Members of the Closteroviridae and Potyviridae families of plant positive-strand RNA viruses encode one or two papain-like leader proteinases, belonging to Merops peptidase family C42.. 
PF05534 HicB family<br>Pfam-B_6090 (release 8.0). This family consists of several bacterial HicB related proteins. The function of HicB is unknown although it is thought to be involved in pilus formation. It has been speculated that HicB performs a function antagonistic to that of pili and yet is necessary for invasion of certain niches  . . 
PF05535 Chromadorea ALT protein<br>Pfam-B_7314 (release 8.0). This family consists of several ALT protein homologues found in nematodes. Lymphatic filariasis is a major tropical disease caused by the mosquito borne nematodes Brugia and Wuchereria. About 120 million people are infected and at risk of lymphatic pathology such as acute lymphangitis and elephantiasis. Expression of alt-1 and alt-2 is initiated midway through development in the mosquito, peaking in the infective larva and declining sharply following entry into the host. ALT-1 and the closely related ALT-2 have been found to be strong candidates for a future vaccine against human filariasis  .. 
PF05536 Neurochondrin<br>Pfam-B_7411 (release 8.0). This family contains several eukaryotic neurochondrin proteins. Neurochondrin induces hydroxyapatite resorptive activity in bone marrow cells resistant to bafilomycin A1, an inhibitor of macrophage- and osteoclast-mediated resorption. Expression of the gene is localised to chondrocyte, osteoblast, and osteocyte in the bone and to the hippocampus and Purkinje cell layer of cerebellum in the brain  .. 
PF05537 Borrelia burgdorferi protein of unknown function (DUF759)<br>Pfam-B_7415 (release 8.0). This family consists of several uncharacterised proteins from the Lyme disease spirochete Borrelia burgdorferi.. 
PF05538 Campylobacter major outer membrane protein<br>Pfam-B_7418 (release 8.0). This family consists of Campylobacter major outer membrane proteins. The major outer membrane protein (MOMP), a putative porin and a multifunction surface protein of Campylobacter jejuni, may play an important role in the adaptation of the organism to various host environments  . . 
PF05539 Pneumovirinae attachment membrane glycoprotein G<br>Pfam-B_7428 (release 8.0). 
PF05540 Serpulina hyodysenteriae variable surface protein<br>Pfam-B_7432 (release 8.0). This family consists of several variable surface proteins from Serpulina hyodysenteriae.. 
PF05541 Entomopoxvirus spheroidin protein<br>Pfam-B_7488 (release 8.0). Entomopoxviruses (EPVs) are large (300-400 nm) oval-shaped viruses replicating in the cytoplasm of their insect host cells. At the end of their replicative cycle EPVs virions are occluded in a highly expressed protein called spheroidin. This protein forms large (5-20 mm long) oval-shaped occlusion bodies (OBs) called spherules. The infectious cycle of EPVs begins with the ingestion by the insect host of the spherules, their dissolution by the alkaline reducing conditions of the midgut fluid and the release of virions in the midgut lumen. The infective particles first replicate in midgut epithelial cells, then pass the gut barrier to colonise the internal tissues, mainly the fat body cells. Whilst spheroidin has been demonstrated to be non-essential for viral replication, it plays an essential role in the natural biological cycle of the virus in protecting virions from adverse environmental conditions (e.g. UV degradation) and thus improving transmission efficacy. In this respect, spheroidins are functionally similar to polyhedrins of baculoviruses or cypoviruses  .. 
PF05542 Protein of unknown function (DUF760)<br>Pfam-B_7508 (release 8.0). This family contains several uncharacterised plant proteins.. 
PF05543 Staphopain peptidase C47<br>Staphopains are one of four major families of  proteinases secreted by  the Gram-positive Staphylococcus aureus. These staphylococcal cysteine proteases are secreted as preproenzymes that are proteolytically cleaved to generate the mature enzyme.. 
PF05544 Proline racemase<br>Pfam-B_7562 (release 8.0). This family consists of proline racemase (EC 5.1.1.4) proteins which catalyse the interconversion of L- and D-proline in bacteria  . This family also contains several similar eukaryotic proteins including Swiss:Q9NCP4 a sequence with B-cell mitogenic properties which has been characterised as a co-factor-independent proline racemase  .. 
PF05545 Cbb3-type cytochrome oxidase component FixQ<br>Pfam-B_7570 (release 8.0). This family consists of several Cbb3-type cytochrome oxidase components (FixQ/CcoQ). FixQ is found in nitrogen fixing bacteria. Since nitrogen fixation is an energy-consuming process, effective symbioses depend on operation of a respiratory chain with a high affinity for O2, closely coupled to ATP production. This requirement is fulfilled by a special three-subunit terminal oxidase (cytochrome terminal oxidase cbb3), which was first identified in Bradyrhizobium japonicum as the product of the fixNOQP operon  .. 
PF05546 She9 / Mdm33 family<br>Pfam-B_35269 (Release 8.0). Members of this family are mitochondrial inner membrane proteins with a role in inner mitochondrial membrane organisation and biogenesis  .. 
PF05547 Immune inhibitor A peptidase M6<br>The insect pathogenic  Gram-positive Bacillus thuringiensis secretes immune inhibitor A, a metallopeptidase, which specifically cleaves host antibacterial proteins. A homologue of immune inhibitor A, PrtV, has been identified in the Gram-negative human pathogen Vibrio cholerae  .. 
PF05548 Gametolysin peptidase M11<br>In the unicellular biflagellated alga, Chlamydomonas reinhardtii, gametolysin, a zinc-containing metallo-protease, is responsible for the degradation of the cell wall. Homologues of gametolysin have also been reported in the simple multicellular organism, Volvox.. 
PF05549 Allexivirus 40kDa protein<br>Pfam-B_7591 (release 8.0). 
PF05550 Pestivirus Npro endopeptidase C53<br>Unique to pestiviruses, the N-terminal protein encoded by the bovine viral diarrhoea virus genome is a cysteine protease (Npro) responsible for  a self-cleavage that releases the N terminus of the core protein.  This unique protease is dispensable for viral replication, and its  coding region can be replaced by a ubiquitin gene directly fused in frame to the core. . 
PF05551 Naegl_SSU_RRNA; DUF1519;<br>Zinc-binding loop region of homing endonuclease. Pfam-B_7681 (release 8.0). This domain   is the short zinc-binding loops region of a number of much longer chain homing endonucleases. Such loops are probably stabilised by the zinc and may be viewed as small but separate domains. The common structural feature of these domains is that at least three zinc ligands lie very close to each other in the sequence and are not incorporated into regular secondary structural elements. The biological roles played by these small zinc-binding domains are presently unknown  .. 
PF05552 tm_helix; <br>This alignment represents a conserved transmembrane helix as well as some flanking sequence. It is often found in association with Pfam:PF00924.. 
PF05553 Cotton fibre expressed protein<br>Pfam-B_7657 (release 8.0). This family consists of several plant proteins of unknown function. Three of the sequences (from Gossypium hirsutum) in this family are described as cotton fibre expressed proteins  . The remaining sequences, found in Arabidopsis thaliana, are uncharacterised.. 
PF05554 Viral hemorrhagic septicemia virus non-virion protein<br>Pfam-B_7684 (release 8.0). This family consists of several viral hemorrhagic septicemia virus non-virion (Nv) proteins. The NV protein is a nonstructural protein absent from mature virions although it is present in infected cells. The function of this protein is unknown  .. 
PF05555 Coxiella burnetii protein of unknown function (DUF762)<br>Pfam-B_7710 (release 8.0). This family consists several of several uncharacterised proteins from the bacterium Coxiella burnetii. Coxiella burnetii is the causative agent of the Q fever disease.. 
PF05556 Calcineurin-binding protein (Calsarcin)<br>Pfam-B_7783 (release 8.0). This family consists of several mammalian calcineurin-binding proteins. The calcium- and calmodulin-dependent protein phosphatase calcineurin has been implicated in the transduction of signals that control the hypertrophy of cardiac muscle and slow fibre gene expression in skeletal muscle. Calsarcin-1 and calsarcin-2 are expressed in developing cardiac and skeletal muscle during embryogenesis, but calsarcin-1 is expressed specifically in adult cardiac and slow-twitch skeletal muscle, whereas calsarcin-2 is restricted to fast skeletal muscle. Calsarcins represent a novel family of sarcomeric proteins that link calcineurin with the contractile apparatus, thereby potentially coupling muscle activity to calcineurin activation  . Calsarcin-3, is expressed specifically in skeletal muscle and is enriched in fast-twitch muscle fibres. Like calsarcin-1 and calsarcin-2, calsarcin-3 interacts with calcineurin, and the Z-disc proteins alpha-actinin, gamma-filamin, and telethonin  .. 
PF05557 Mitotic checkpoint protein<br>Pfam-B_7761 (release 8.0). This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated  . . 
PF05558 DREPP plasma membrane polypeptide<br>Pfam-B_7798 (release 8.0). This family contains several plant plasma membrane proteins termed DREPPs as they are developmentally regulated plasma membrane polypeptides  .. 
PF05559 Protein of unknown function (DUF763)<br>Pfam-B_7805 (release 8.0). This family consists of several uncharacterised bacterial and archaeal proteins of unknown function.. 
PF05560 Bacillus thuringiensis P21 molecular chaperone protein<br>Pfam-B_7820 (release 8.0). This family contains several Bacillus thuringiensis P21 proteins. These proteins are thought to be molecular chaperones and have mosquitocidal properties [1,2].. 
PF05561 Borrelia burgdorferi protein of unknown function (DUF764)<br>Pfam-B_7823 (release 8.0). This family consists of proteins of unknown function from Borrelia burgdorferi (Lyme disease spirochete).. 
PF05562 Cold acclimation protein WCOR413<br>Pfam-B_7803 (release 8.0). This family consists of several WCOR413-like plant cold acclimation proteins.. 
PF05563 Sal_SpvD; <br>Salmonella plasmid virulence protein SpvD. Pfam-B_7864 (release 8.0). This family consists of several SpvD plasmid virulence proteins from different Salmonella species.. 
PF05564 Dormancy/auxin associated protein<br>Pfam-B_7941 (release 8.0). This family contains several plant dormancy-associated and auxin-repressed proteins the function of which are poorly understood  .. 
PF05565 Siphovirus Gp157<br>Pfam-B_7948 (release 8.0). This family contains both viral and bacterial proteins which are related to the Gp157 protein of the Streptococcus thermophilus SFi bacteriophages. It is thought that bacteria possessing the gene coding for this protein have an increased resistance to the bacteriophage .. 
PF05566 Orthopoxvirus interleukin 18 binding protein<br>Pfam-B_7955 (release 8.0). Interleukin-18 (IL-18) is a proinflammatory cytokine that plays a key role in the activation of natural killer and T helper 1 cell responses principally by inducing interferon-gamma (IFN-gamma). Several poxvirus genes encode proteins with sequence similarity to IL-18BPs. It has been shown that vaccinia, ectromelia and cowpox viruses secrete from infected cells a soluble IL-18BP (vIL-18BP) that may modulate the host antiviral response. The expression of vIL-18BPs by distinct poxvirus genera that cause local or general viral dissemination, or persistent or acute infections in the host, emphasises the importance of IL-18 in response to viral infections  .. 
PF05567 Neisseria PilC beta-propeller domain<br>Pfam-B_7966 (release 8.0). This family consists of several PilC protein sequences from Neisseria gonorrhoeae and N. meningitidis. PilC is a phase-variable protein associated with pilus-mediated adherence of pathogenic Neisseria to target cells  .\.  This domain has been shown to adopt a beta-propeller structure  .. 
PF05568 African swine fever virus J13L protein<br>Pfam-B_7998 (release 8.0). This family consists of several African swine fever virus J13L proteins.. 
PF05569 BlaR1 peptidase M56<br>Production of beta-Lactamase and penicillin-binding protein 2a (which mediate staphylococcal resistance to beta-lactam antibiotics) is regulated by a signal-transducing integral membrane protein       and a transcriptional repressor.  The signal transducer is a fusion protein with penicillin-binding and zinc metalloprotease domains.  The signal for protein expression is transmitted by site-specific proteolytic cleavage of both the transducer, which auto-activates, and the repressor, which is inactivated, unblocking gene transcription. Homologues to this peptidase domain, which corresponds to Merops family  M56, are also found in a number of other bacterial genome sequences.. 
PF05570 Circovirus protein of unknown function (DUF765)<br>Pfam-B_8063 (release 8.0). This family consists of several short (27-30aa) porcine and bovine circovirus ORF6 proteins of unknown function.. 
PF05571 Protein of unknown function (DUF766)<br>Pfam-B_8021 (release 8.0). This family consists of several eukaryotic proteins of unknown function.. 
PF05572 Peptidase_M46; <br>Pregnancy-associated plasma protein-A. Pregnancy-associated plasma protein A (PAPP-A) is a metallo-protease belonging to Merops family M43. It cleaves insulin-like growth factor (IGF) binding protein-4 (IGFBP-4), causing a dramatic reduction in its affinity for IGF-I and -II.  Through this mechanism, PAPP-A is a regulator of IGF bioactivity in several systems, including the human ovary and the cardiovascular system.. 
PF05573 NosL<br>Pfam-B_8116 (release 8.0). NosL is one of the accessory proteins of the nos (nitrous oxide reductase) gene cluster. NosL is a monomeric protein of 18,540 MW that specifically and stoichiometrically binds Cu(I). The copper ion in NosL is ligated by a Cys residue, and one Met and one His are thought to serve as the other ligands. It is possible that NosL is a copper chaperone involved in metallo-centre assembly  .. 
PF05575 Vibrio cholerae RfbT protein<br>Pfam-B_8029 (release 8.0). This family consists of several RfbT proteins from Vibrio cholerae. It has been found that genetic alteration of the rfbT gene is responsible for serotype conversion of Vibrio cholerae O1   and determines the difference between the Ogawa and Inaba serotypes, in that the presence of rfbT is sufficient for Inaba-to-Ogawa serotype conversion  .. 
PF05576 PS-10 peptidase S37<br>These serine proteases have been found in Streptomyces species.. 
PF05577 Serine carboxypeptidase S28<br>These serine proteases include several eukaryotic enzymes such as lysosomal Pro-X carboxypeptidase, dipeptidyl-peptidase II, and thymus-specific serine peptidase.. 
PF05578 Pestivirus NS3 polyprotein peptidase S31<br>These serine peptidases are involved in processing of the flavivirus polyprotein.. 
PF05579 Equine arteritis virus serine endopeptidase S32<br>Serine peptidases involved in processing nidovirus polyprotein.. 
PF05580 SpoIVB peptidase S55<br>The protein SpoIVB plays a key role in signalling in the final sigma-K checkpoint of Bacillus subtilis. . 
PF05581 Peptidase_S38; <br>Vibrio chemotaxis protein N terminus. This domain is found at the N terminus of several methyl-accepting chemotaxis proteins from Vibrio species.. 
PF05582 YabG peptidase U57<br>YabG is a protease involved in the proteolysis and maturation of SpoIVA and YrbA proteins, conserved with the cortex and/or coat assembly by Bacillus subtilis.. 
PF05584 Sulfolobus plasmid regulatory protein<br>Pfam-B_8140 (release 8.0). This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.. 
PF05585 Peptidase_A16; <br>Putative peptidase (DUF1758). This is a family of nematode proteins of unknown function. However, it seems likely that these proteins act as aspartic peptidases.. 
PF05586 Anthrax receptor C-terminus region<br>This region is found in the putatively cytoplasmic C-terminus of the anthrax receptor.. 
PF05587 Anthrax receptor extracellular domain<br>This region is found in the putatively extracellular N-terminal half of the anthrax receptor. It is  probably part of the Ig superfamily and most closely related to Pfam:PF01833 (personal obs: C Yeats).. 
PF05588 botulinum_HA-17; <br>Clostridium botulinum HA-17 protein. Pfam-B_8286 (release 8.0). This family consists of several Clostridium botulinum hemagglutinin (HA) subcomponents. Clostridium botulinum type D strain 4947 produces two different sizes of progenitor toxins (M and L) as intact forms without proteolytic processing. The M toxin is composed of neurotoxin (NT) and nontoxic-nonhemagglutinin (NTNHA), whereas the L toxin is composed of the M toxin and hemagglutinin (HA) subcomponents (HA-70, HA-17, and HA-33)  .. 
PF05589 Protein of unknown function (DUF768)<br>Pfam-B_8463 (release 8.0). This family consists of several uncharacterised hypothetical proteins from Rhizobium loti.. 
PF05590 Xylella fastidiosa protein of unknown function (DUF769)<br>Pfam-B_8396 (release 8.0). This family consists of several uncharacterised hypothetical proteins of unknown function from Xylella fastidiosa, the organism that causes Pierce's disease in plants.. 
PF05591 Protein of unknown function (DUF770)<br>Pfam-B_8473 (release 8.0). This family consists of several proteins of unknown function from various bacterial species.. 
PF05592 bac_rhamnosid;<br>Bacterial alpha-L-rhamnosidase. Pfam-B_8527 (release 8.0). This family consists of bacterial rhamnosidase A and B enzymes. L-Rhamnose is abundant in biomass as a common constituent of glycolipids and glycosides, such as plant pigments, pectic polysaccharides, gums or biosurfactants. Some rhamnosides are important bioactive compounds. For example, terpenyl glycosides, the glycosidic precursor of aromatic terpenoids, act as important flavouring substances in grapes. Other rhamnosides act as cytotoxic rhamnosylated terpenoids, as signal substances in plants or play a role in the antigenicity of pathogenic bacteria  .. 
PF05593 RHS Repeat<br>RHS proteins contain extended repeat regions. These repeats often appear to be involved in ligand binding (e.g.  ). Note that this model may not find all the repeats in a protein and that it covers  two RHS repeats.. 
PF05594 haemagg_repeats; <br>Haemagluttinin repeat. This highly divergent repeat occurs in number of proteins implicated in cell aggregation  . The Pfam alignment probably contains three such repeats (personal obs: C Yeats). These are likely to have a beta-helical structure.. 
PF05595 Domain of unknown function (DUF771) <br>Pfam-B_7023 (release 8.0). Family of uncharacterised ORFs found in  Bacteriophage and Lactococcus lactis. . 
PF05596 Taeniidae antigen<br>Pfam-B_8569 (release 8.0). This family consists of several antigen proteins from Taenia and Echinococcus (tapeworm) species.. 
PF05597 Poly(hydroxyalcanoate) granule associated protein (phasin)<br>Pfam-B_8339 (release 8.0). Polyhydroxyalkanoates (PHAs) are storage polyesters synthesised by various bacteria as intracellular carbon and energy reserve material. PHAs are accumulated as water-insoluble inclusions within the cells. This family consists of the phasins PhaF and PhaI which act as a transcriptional regulator of PHA biosynthesis genes. PhaF has been proposed to repress expression of the phaC1 gene and the phaIF operon  .. 
PF05598 Transposase domain (DUF772)<br>Pfam-B_8195 (release 8.0). This presumed domain is found at the N-terminus of many proteins found in transposons.. 
PF05599 Deltaretrovirus Tax protein<br>Pfam-B_8606 (release 8.0). This family consists of Rex/Tax proteins from human and simian T-cell leukaemia viruses. The exact function of these proteins is unknown. Tax is the viral transactivator; is it a nuclear phosphoprotein that interacts with CREB, coactivator CBP/p300 and PCAF to form a multiprotein complex, which activates viral LTR and stimulates virus expression. Tax is also involved in deregulated expression of numerous cellular genes leading to T-cell leukaemia. Rex is a nucleolar post transcriptional regulator that facilitates export to the cytoplasm of viral RNA not or incompletely spliced [personal communication, Dr. S Nicot].. 
PF05600 Protein of unknown function (DUF773)<br>Pfam-B_8595 (release 8.0). This family contains several eukaryotic sequences which are thought to be CDK5 activator-binding proteins, however, the function of this family is unknown.. 
PF05602 Cleft lip and palate transmembrane protein 1 (CLPTM1)<br>Pfam-B_8636 (release 8.0). This family consists of several eukaryotic cleft lip and palate transmembrane protein 1 sequences. Cleft lip with or without cleft palate is a common birth defect that is genetically complex. The nonsyndromic forms have been studied genetically using linkage and candidate-gene association studies with only partial success in defining the loci responsible for orofacial clefting. CLPTM1 encodes a transmembrane protein and has strong homology to two Caenorhabditis elegans genes, suggesting that CLPTM1 may belong to a new gene family  . This family also contains the human cisplatin resistance related protein CRR9p which is associated with CDDP-induced apoptosis  .. 
PF05603 Protein of unknown function (DUF775)<br>Pfam-B_8676 (release 8.0). This family consists of several eukaryotic proteins of unknown function.. 
PF05604 Protein of unknown function (DUF776)<br>Pfam-B_8747 (release 8.0). This family consists of several highly related mouse and human proteins of unknown function.. 
PF05605 Di19;<br>Drought induced 19 protein (Di19), zinc-binding. Pfam-B_8581 (release 8.0). This family consists of several drought induced 19 (Di19) like proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought  . This domain is a zinc-binding domain.. 
PF05606 Borrelia burgdorferi protein of unknown function (DUF777)<br>Pfam-B_8755 (release 8.0). This family consists of several hypothetical proteins of unknown function from Borrelia burgdorferi (Lyme disease spirochete).. 
PF05608 Protein of unknown function (DUF778)<br>Pfam-B_8777 (release 8.0). This family consists of several eukaryotic proteins of unknown function.. 
PF05609 Lamina-associated polypeptide 1C (LAP1C)<br>Pfam-B_8782 (release 8.0). This family contains rat LAP1C proteins and several uncharacterised highly related sequences from both mice and humans. LAP1s (lamina-associated polypeptide 1s) are type 2 integral membrane proteins with a single membrane-spanning region of the inner nuclear membrane  . LAP1s bind to both A- and B-type lamins and have a putative role in the membrane attachment and assembly of the nuclear lamina  .. 
PF05610 Protein of unknown function (DUF779)<br>Pfam-B_8830 (release 8.0). This family consists of several bacterial proteins of unknown function.. 
PF05611 Caenorhabditis elegans protein of unknown function (DUF780)<br>Pfam-B_8886 (release 8.0). This family consists of several short C. elegans proteins of unknown function.. 
PF05612 Mouse protein of unknown function (DUF781)<br>Pfam-B_8891 (release 8.0). This family consists of uncharacterised mouse proteins of unknown function.. 
PF05613 Human herpesvirus U15 protein<br>Pfam-B_8900 (release 8.0). 
PF05614 Circovirus protein of unknown function (DUF782)<br>Pfam-B_8909 (release 8.0). This family consists of porcine and bovine circovirus proteins of unknown function.. 
PF05615 DUF783; <br>Tho complex subunit 7. Pfam-B_8919 (release 8.0). The Tho complex is involved in transcription elongation and mRNA export from the nucleus.. 
PF05616 Neisseria meningitidis TspB protein<br>Pfam-B_8925 (release 8.0). This family consists of several Neisseria meningitidis TspB virulence factor proteins.. 
PF05617 DUF784;<br>Pfam-B_8935 (release 8.0). Both DUF784 and DUF1278 members are found to be expressed in the plant embryo sac and are regulated by the Myb98 transcription factor. Computational analysis has revealed that they are homologous to the plant prolamin superfamily (Protease inhibitor-seed storage-LTP family, Pfam:PF00234)  . In contrast to the typical prolamin members that have eight conserved Cys residues forming four pairs of disulfide bonds, both DUF784 and DUF1278 domains only contain six conserved Cys residues that may form three pairs of disulfide bonds. These two domains may have potential functions in lipid transfer or protection during plant embryo sac development and reproduction  .  This family has been merged with the DUF1278 family.. 
PF05618 DUF785;<br>Putative ATP-dependant zinc protease. Pfam-B_8936 (release 8.0). Proteins in this family are annotated as being ATP-dependant zinc proteases.. 
PF05619 Borrelia burgdorferi protein of unknown function (DUF787)<br>Pfam-B_9013 (release 8.0). This family consists of several hypothetical proteins of unknown function from Borrelia burgdorferi (Lyme disease spirochete). . 
PF05620 Protein of unknown function (DUF788)<br>Pfam-B_9014 (release 8.0). This family consists of several eukaryotic proteins of unknown function.. 
PF05621 Bacterial TniB protein<br>Pfam-B_9028 (release 8.0). This family consists of several bacterial TniB NTP-binding proteins. TniB is a probable ATP-binding protein   which is involved in Tn5053 mercury resistance transposition  .. 
PF05622 HOOK protein<br>Pfam-B_8981 (release 8.0). This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerisation and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes  , whereas both HOOK1 and HOOK2 are localised to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head  .. 
PF05623 Protein of unknown function (DUF789)<br>Pfam-B_9113 (release 8.0). This family consists of several plant proteins of unknown function.. 
PF05624 LISCH7; <br>Lipolysis stimulated receptor (LSR). Pfam-B_9152 (release 8.0). The lipolysis-stimulated receptor (LSR) is a lipoprotein receptor primarily expressed in the liver and activated by free fatty acids  .  It is thought to be involved in the clearance of triglyceride-rich lipoproteins, and has been shown in mice to be critical for liver and embryonic development  .. 
PF05625 PAXNEB protein<br>Moxon SJ, Mistry J, Wood V. Pfam-B_9269 (release 8.0). PAXNEB or PAX6 neighbour is found in several eukaryotic organisms.  PAXNED is an RNA polymerase II Elongator protein subunit  .  It is part of the HAP subcomplex of Elongator, which is a six-subunit component of the RNA polymerase II holoenzyme.  The HAP subcomplex is required for Elongator structural integrity and histone acetyltransferase activity  . This protein family has a P-loop motif. However its sequence has degraded in many members of the family.. 
PF05626 Protein of unknown function (DUF790)<br>Pfam-B_9309 (release 8.0). This family consists of several hypothetical archaeal proteins of unknown function.. 
PF05627 NOI; <br>Cleavage site for pathogenic type III effector avirulence factor Avr. Pfam-B_9342 (release 8.0). This domain is conserved in small families of otherwise unrelated proteins in both mono-cots and di-cots, suggesting that it has a conserved, plant-specific function. It is found both in the plant RIN4 (resistance R membrane-bound host-target protein) where it appears to contribute to the binding of the protein to both RCS (AvrRpt2 auto-cleavage site) and AvrB, the virulence factor from the infecting bacterium  . The cleavage site for the AvrRpt2 avirulence protein would appear to be the sequence motifs VPQFGDW and LPKFGEW, both of which are highly conserved within the domain  .. 
PF05628 Borrelia membrane protein P13<br>Pfam-B_8766 (release 8.0). This family consists of P13 proteins from Borrelia species. P13 is a 13kDa integral membrane protein which is post-translationally processed at both ends and modified by an unknown mechanism  .. 
PF05629 Nanovirus component 8 (C8) protein<br>Pfam-B_9354 (release 8.0). This family consists of a group of 17.4 kDa nanovirus proteins which are highly related to the faba bean necrotic yellows virus component 8 protein whose function is unknown  .. 
PF05630 Necrosis inducing protein (NPP1)<br>Pfam-B_9369 (release 8.0). This family consists of several NPP1 like necrosis inducing proteins from oomycetes, fungi and bacteria. Infiltration of NPP1 into leaves of Arabidopsis thaliana plants result in transcript accumulation of pathogenesis-related (PR) genes, production of ROS and ethylene, callose apposition, and HR-like cell death  . . 
PF05631 Protein of unknown function (DUF791)<br>Pfam-B_9328 (release 8.0). This family consists of several eukaryotic proteins of unknown function.. 
PF05632 Borrelia burgdorferi protein of unknown function (DUF792)<br>Pfam-B_9387 (release 8.0). This family consists of several hypothetical proteins from the Lyme disease spirochete Borrelia burgdorferi.. 
PF05633 Protein of unknown function (DUF793)<br>Pfam-B_9395 (release 8.0). This family consists of several plant proteins of unknown function.. 
PF05634 DUF794;<br>Moxon SJ, Eberhardt R, Barkan A. Pfam-B_9606 (release 8.0). This domain contains conserved cysteine and histidine residues  . It resembles zinc fingers, and binds to zinc  . This domain functions as an RNA-binding domain  .. 
PF05635 Ribosomal_S23p;<br>23S rRNA-intervening sequence protein. Moxon SJ, Eberhardt R. Pfam-B_9648 (release 8.0). This family consists of bacterial proteins encoded within an intervening sequence present within some 23S rRNA genes [1-3]. It folds into an anti-parallel four-helix bundle and forms homopentamers  .. 
PF05636 DUF795;<br>HIGH Nucleotidyl Transferase. Moxon SJ, Anantharaman V. Pfam-B_9692 (release 8.0). This family consists of HIGH Nucleotidyl Transferases. 
PF05637 galactosyl transferase GMA12/MNN10 family<br>Pfam-B_6000 (release 8.0). This family contains a number of glycosyltransferase enzymes that contain a DXD motif. This family includes a number of C. elegans homologues where the DXD is replaced by DXH. Some members of this family are included in glycosyltransferase family 34.. 
PF05638 Protein of unknown function (DUF796)<br>Pfam-B_9698 (release 8.0). This family consists of several bacterial proteins of unknown function.. 
PF05639 DUF797;<br>Pfam-B_9797 (release 8.0). This family consists of several short bacterial proteins formely known as (DUF797).  It was recently shown that Mycobacterium tuberculosis contains a small protein, Pup (Rv2111c), that is covalently conjugated to the e-NH2 groups of lysines on several target proteins (pupylation) such as the malonyl CoA acyl carrier protein (FabD)  . Pupylation of FabD was shown to result in its recruitment to the mycobacterial proteasome and subsequent degradation analogous to eukaryotic ubiquitin-conjugated proteins. Searches recovered Pup orthologs in all major actinobacteria lineages including the basal bifidobacteria and also sporadically in certain other bacterial lineages.   The Pup proteins were all between 50-90 residues in length and a multiple alignment shows that they all contain a conserved motif with a G [EQ] signature at the C-terminus. Thus, all of them are suitable for conjugation via the terminal glutamate or the deamidated glutamine (as shown in the case of the Mycobacterium Pup  ). The conserved globular core of Pup is predicted to form a bihelical unit with the extreme C-terminal 6-7 residues forming a tail in the extended conformation. Thus, Pup is structurally unrelated to the ubiquitin fold and has convergently evolved the function of protein modifier.. 
PF05640 DUF798; <br>Na,K-Atpase Interacting protein. Pfam-B_9801 (release 8.0). NKAIN (Na,K-Atpase INteracting) proteins are a family of evolutionary conserved transmembrane proteins that localise to neurons, that are critical for neuronal function, and that interact with the beta subunits, beta1 in vertebrates and beta in Drosophila, of Na,K-ATPase. NKAINs have highly conserved trans-membrane domains but otherwise no other characterised domains. NKAINs may function as subunits of pore or channel structures in neurons or they may affect the function of other membrane proteins. They are likely to function within the membrane bilayer  .. 
PF05641 Agenet domain<br>Pfam-B_2551 (release 8.0). This domain is related to the TUDOR domain Pfam:PF00567  . The function of the agenet domain is unknown. This family currently only matches one of the two Agenet domains in the FMR proteins  .. 
PF05642 Sporozoite P67 surface antigen<br>Pfam-B_8657 (release 8.0). This family consists of several Theileria P67 surface antigens. A stage specific surface antigen of Theileria parva, p67, is the basis for the development of an anti-sporozoite vaccine for the control of East Coast fever (ECF) in cattle. The antigen has been shown to contain five distinct linear peptide sequences recognised by sporozoite-neutralising murine monoclonal antibodies  .. 
PF05643 Putative bacterial lipoprotein (DUF799)<br>Pfam-B_9829 (release 8.0). This family consists of several bacterial proteins of unknown function. Some of the family members are described as putative lipoproteins.. 
PF05644 DUF800;<br>Mitochondrial and peroxisomal fission factor Mff. Moxon SJ, Eberhardt R. Pfam-B_9868 (release 8.0). This protein has a role in mitochondrial and peroxisomal fission  .. 
PF05645 RNA polymerase III subunit RPC82<br>Pfam-B_9884 (release 8.0). This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In Saccharomyces cerevisiae, the enzyme is composed of 15 subunits, ranging from 160 to about 10 kDa  .. 
PF05647 DUF801;<br>Tandem-repeating region of mucin, epiglycanin-like. Pfam-B_1480 (release 8.0) Pfam-B_13922 (release 26.0). The unusual mucin, epiglycanin, is membrane-bound at the C-terminus but has a long region of this tandem-repeat at the N-terminus  . It was the first mucin identified to be associated with the malignant behaviour of carcinoma cells  . Mouse Muc21/epiglycanin is thought to be a highly glycosylated molecule, which makes it likely that its function is dependent on its glycoforms. Cells expressing Muc21 are significantly less adherent to each other and to extracellular matrix components than control cells, and this loss of adhesion is mediated by the TR portion of Muc21  . This family also now contains the repeat that was the C. elegans protein of unknown function (DUF801).. 
PF05648 Peroxisomal biogenesis factor 11 (PEX11)<br>Pfam-B_2629 (release 8.0). This family consists of several peroxisomal biogenesis factor 11 (PEX11) proteins from several eukaryotic species. The PEX11 peroxisomal membrane proteins promote peroxisome division in multiple eukaryotes.. 
PF05649 Peptidase family M13<br>M13 peptidases are well-studied proteases found in a wide range of organisms including mammals and bacteria. In mammals they participate in processes such as cardiovascular development, blood-pressure  regulation, nervous control of respiration, and regulation of the function of neuropeptides in the central nervous system. In bacteria they may be used for digestion of milk. . 
PF05650 Domain of unknown function (DUF802)<br>This region is found as two or more repeats in a small number of hypothetical proteins.. 
PF05651 Putative sugar diacid recognition<br>This region is found in several proteins characterised as carbohydrate diacid regulators (e.g. Swiss:P36047). An HTH DNA-binding motif is found at the C-terminus of these proteins suggesting that this region includes the sugar recognition region.. 
PF05652 Scavenger mRNA decapping enzyme (DcpS) N-terminal<br>Pfam-B_9894 (release 8.0). This family consists of several scavenger mRNA decapping enzymes (DcpS) and is the N-terminal domain of these proteins. DcpS is a scavenger pyrophosphatase that hydrolyses the residual cap structure following 3' to 5' decay of an mRNA. The association of DcpS with 3' to 5' exonuclease exosome components suggests that these two activities are linked and there is a coupled exonucleolytic decay-dependent decapping pathway.. 
PF05653 DUF803;<br>Magnesium transporter NIPA. Moxon SJ, Eberhardt R. Pfam-B_9876 (release 8.0). NIPA (nonimprinted in Prader-Willi/Angelman syndrome) is a family of integral membrane proteins which function as magnesium transporters [1,2].. 
PF05655 Pseudomon_AvrD; <br>Pseudomonas avirulence D protein (AvrD). Pfam-B_9946 (release 8.0). This family consists of several avirulence D (AvrD) proteins primarily found in Pseudomonas syringae [1,2].. 
PF05656 Protein of unknown function (DUF805)<br>Pfam-B_2800 (release 8.0). This family consists of several bacterial proteins of unknown function.. 
PF05657 Protein of unknown function (DUF806)<br>Pfam-B_7291 (release 8.0). This family consists of several Siphovirus and Lactococcus proteins of unknown function. The viral sequences are thought to be tail component proteins.. 
PF05658 Hep_Hag;<br>Head domain of trimeric autotransporter adhesin. This seven residue repeat makes up the majority sequence of a family of bacterial haemagglutinins and invasins. The representative alignment contains four repeats.. 
PF05659 Arabidopsis broad-spectrum mildew resistance protein RPW8<br>Pfam-B_7373 (release 8.0). This family consists of several broad-spectrum mildew resistance proteins from Arabidopsis thaliana. Plant disease resistance (R) genes control the recognition of specific pathogens and activate subsequent defence responses. The Arabidopsis thaliana locus Resistance To Powdery Mildew 8 (RPW8) contains two naturally polymorphic, dominant R genes, RPW8.1 and RPW8.2, which individually control resistance to a broad range of powdery mildew pathogens. They induce localised, salicylic acid-dependent defences similar to those induced by R genes that control specific resistance. Apparently, broad-spectrum resistance mediated by RPW8 uses the same mechanisms as specific resistance [1,2].. 
PF05660 Coxiella burnetii protein of unknown function (DUF807)<br>Pfam-B_7114 (release 8.0). This family consists of several proteins of unknown function from Coxiella burnetii (the causative agent of a zoonotic disease called Q fever).. 
PF05661 Protein of unknown function (DUF808)<br>Pfam-B_7112 (release 8.0). This family consists of several bacterial proteins of unknown function.. 
PF05662 HIM;<br>Coiled stalk of trimeric autotransporter adhesin. This short motif is found in invasins and haemagglutinins, normally associated with (Pfam:PF05658).. 
PF05663 Protein of unknown function (DUF809)<br>Pfam-B_7264 (release 8.0). This family consists of several proteins of unknown function Raphanus sativus (Radish) and Brassica napus (Rape).. 
PF05664 Protein of unknown function (DUF810)<br>Pfam-B_5709 (release 8.0). This family consists of several plant proteins of unknown function.. 
PF05666 Fels-1 Prophage Protein-like<br>
PF05667 Protein of unknown function (DUF812)<br>Pfam-B_7417 (release 8.0). This family consists of several eukaryotic proteins of unknown function.. 
PF05669 SOH1; <br>Pfam-B_7443 (release 8.0). The family consists of Saccharomyces cerevisiae SOH1 homologues. SOH1 is responsible for the repression of temperature sensitive growth of the HPR1 mutant   and has been found to be a component of the RNA polymerase II transcription complex. SOH1 not only interacts with factors involved in DNA repair, but transcription as well. Thus, the SOH1 protein may serve to couple these two processes  . . 
PF05670 Domain of unknown function (DUF814)<br>Pfam-B_738 (Release 8.0). This domain occurs in proteins that have been annotated as Fibronectin/fibrinogen binding protein by similarity. This annotation comes from Swiss:O34693 where the N-terminal region is involved in this activity  .  Hence the activity of this C-terminal domain is unknown. This domain contains a conserved motif D/E-X-W/Y-X-H that may be functionally important.. 
PF05671 GETHR pentapeptide repeat (5 copies)<br>Pfam-B_8059 (release 8.0). 
PF05672 E-MAP-115; <br>MAP7 (E-MAP-115) family. Pfam-B_8157 (release 8.0). The organisation of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin  . The binding of this microtubule associated protein is nucleotide independent  .. 
PF05673 Protein of unknown function (DUF815)<br>Pfam-B_6403 (release 8.0). This family consists of several bacterial proteins of unknown function.. 
PF05674 Baculovirus protein of unknown function (DUF816)<br>Pfam-B_7178 (release 8.0). This family includes proteins that are about 200 amino acids in length.  The proteins are all from baculoviruses. This family includes ORF107 from Orgyia pseudotsugata multicapsid polyhedrosis virus (OpMNPV) and a variety of other numbered ORF proteins, such as ORF52 Swiss:Q91F03, ORF140 Swiss:Q9YMI8. The function of these proteins is unknown.. 
PF05675 Protein of unknown function (DUF817)<br>Pfam-B_7331 (release 8.0). This family consists of several bacterial proteins of unknown function.. 
PF05676 NDUFB7; <br>NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7). Pfam-B_7077 (release 8.0). This family consists of several NADH-ubiquinone oxidoreductase B18 subunit proteins from different eukaryotic organisms. Oxidative phosphorylation is the well-characterised process in which ATP, the principal carrier of chemical energy of individual cells, is produced due to a mitochondrial proton gradient formed by the transfer of electrons from NADH and FADH2 to molecular oxygen. The oxidative phosphorylation (OXPHOS) system is located in the mitochondrial inner membrane and consists of five multi-subunit enzyme complexes and two small electron carriers: coenzyme Q10 and cytochrome C. At least 70 structural proteins involved in the formation of the whole OXPHOS system are encoded by nuclear genes, whereas 13 structural proteins are encoded by the mitochondrial genome. Deficiency of NADH ubiquinone oxidoreductase, the first enzyme complex of the mitochondrial respiratory chain, is one of the most frequent causes of human mitochondrial encephalomyopathies  .. 
PF05677 Chlamydia CHLPS protein (DUF818)<br>Pfam-B_7510 (release 8.0). This family consists of several Chlamydia CHLPS proteins, the function of which are unknown.. 
PF05678 VQ motif<br>Pfam-B_7960 (release 8.0). 
PF05679 Chondroitin N-acetylgalactosaminyltransferase<br>Pfam-B_8249 (release 8.0). 
PF05680 ATP synthase E chain<br>Pfam-B_6116 (release 8.0). This family consists of several ATP synthase E chain sequences which are components of the CF(0) subunit  .. 
PF05681 Fumarate hydratase (Fumerase)<br>Pfam-B_2085 (release 8.0). This family consists of several bacterial fumarate hydratase proteins FumA and FumB. Fumarase, or fumarate hydratase (EC 4.2.1.2), is a component of the citric acid cycle. In facultative anaerobes such as Escherichia coli, fumarase also engages in the reductive pathway from oxaloacetate to succinate during anaerobic growth. Three fumarases, FumA, FumB, and FumC, have been reported in E. coli. fumA and fumB genes are homologous and encode products of identical sizes which form thermolabile dimers of Mr 120,000. FumA and FumB are class I enzymes and are members of the iron-dependent hydrolases, which include aconitase and malate hydratase. The active FumA contains a 4Fe-4S centre, and it can be inactivated upon oxidation to give a 3Fe-4S centre  .. 
PF05683 Fumarase C-terminus<br>Pfam-B_2085 (release 8.0). This family consists of the C terminal region of several bacterial fumarate hydratase proteins (FumA and FumB). Fumarase, or fumarate hydratase (EC 4.2.1.2), is a component of the citric acid cycle. In facultative anaerobes such as Escherichia coli, fumarase also engages in the reductive pathway from oxaloacetate to succinate during anaerobic growth  .. 
PF05684 Protein of unknown function (DUF819)<br>Pfam-B_9034 (release 8.0). This family contains proteins of unknown function from archaeal, bacterial and plant species.. 
PF05685 DUF820;<br>Putative restriction endonuclease. Pfam-B_7809 (release 8.0) & Pfam-B_8730 (release 14.0). This family consists of hypothetical proteins that are greatly expanded in cyanobacteria.  The proteins are found sporadically in other bacteria.  A small number of member proteins also contain Pfam:PF02861 domains that are involved in protein interactions. Solutions of several structures for members of this family show that it is likely to be acting as an endonuclease.. 
PF05686 DUF821;<br>Glycosyl transferase family 90. Pfam-B_6682 (Release 8.0) & Pfam-B_7101 (Release 8.0). This family of glycosyl transferases are specifically (mannosyl) glucuronoxylomannan/galactoxylomannan -beta 1,2-xylosyltransferases, EC:2.4.2.-.. 
PF05687 DUF822; Peptidase_M15_2; <br>Plant protein of unknown function (DUF822). Pfam-B_7149 (release 8.0). This family consists of the N terminal regions of several plant proteins of unknown function.. 
PF05688 Salmonella repeat of unknown function (DUF824)<br>Pfam-B_2973 (release 8.0). This family consists of several repeated sequences of around 45 residues.. 
PF05689 Salmonella repeat of unknown function (DUF823)<br>Pfam-B_2973 (release 8.0). This family consists of a series of repeated sequences (of around 180 residues) which are found in Salmonella typhimurium and Salmonella typhi. Sequences from this family are almost always found with Pfam:PF05688.. 
PF05690 Thiazole biosynthesis protein ThiG<br>Pfam-B_1138 (release 8.0). This family consists of several bacterial thiazole biosynthesis protein G sequences. ThiG , together with ThiF and ThiH, is proposed to be involved in the synthesis of 4-methyl-5-(b-hydroxyethyl)thiazole (THZ) which is an intermediate in the thiazole production pathway  .. 
PF05691 Raffinose synthase or seed imbibition protein Sip1<br>Moxon SJ, Eberhardt R. Pfam-B_3204 (release 8.0). This family consists of several raffinose synthase proteins, also known as seed imbibition (Sip1) proteins. Raffinose (O-alpha- D-galactopyranosyl- (1-->6)- O-alpha- D-glucopyranosyl-(1<-->2)- O-beta- D-fructofuranoside) is a widespread oligosaccharide in plant seeds and other tissues. Raffinose synthase (EC:2.4.1.82) is the key enzyme that channels sucrose into the raffinose oligosaccharide pathway  . Raffinose family oligosaccharides (RFOs) are ubiquitous in plant seeds and are thought to play critical roles in the acquisition of tolerance to desiccation and seed longevity. Raffinose synthases are alkaline alpha-galactosidases and are solely responsible for RFO breakdown in germinating maize seeds, whereas acidic galactosidases appear to have other functions  .\.    Glycoside hydrolase family 36 can be split into 11 families, GH36A to GH36K  . This family includes enzymes from GH36C.. 
PF05692 Mycoplasma haemagglutinin<br>Pfam-B_3547 (release 8.0). This family consists of several haemagglutinin sequences from Mycoplasma synoviae and Mycoplasma gallisepticum. The major plasma membrane proteins, pMGAs, of Mycoplasma gallisepticum are cell adhesin (hemagglutinin) molecules. It has been shown that the genetic determinants that code for the haemagglutinins are organised into a large family of genes and that only one of these genes is predominately expressed in any given strain [1,2,3].. 
PF05693 Glycogen synthase<br>Pfam-B_2874 (release 8.0). This family consists of the eukaryotic glycogen synthase proteins GYS1, GYS2 and GYS3 [1,2]. Glycogen synthase (GS) is the enzyme responsible for the synthesis of -1,4-linked glucose chains in glycogen. It is the rate limiting enzyme in the synthesis of the polysaccharide, and its activity is highly regulated through phosphorylation at multiple sites and also by allosteric effectors, mainly glucose 6-phosphate (G6P)  .. 
PF05694 56kDa selenium binding protein (SBP56)<br>Pfam-B_2816 (release 8.0). This family consists of several eukaryotic selenium binding proteins as well as three sequences from archaea. The exact function of this protein is unknown although it is thought that SBP56 participates in late stages of intra-Golgi protein transport  . The Lotus japonicus homologue of SBP56, LjSBP is thought to have more than one physiological role and can be implicated in controlling the oxidation/reduction status of target proteins, in vesicular Golgi transport  .. 
PF05695 Plant protein of unknown function (DUF825)<br>Pfam-B_8370 (release 8.0). This family consists of several plant proteins greater than 1000 residues in length. The function of this family is unknown.. 
PF05696 Protein of unknown function (DUF826)<br>Pfam-B_7303 (release 8.0). This family consists of several enterobacterial and siphoviral sequences of unknown function.. 
PF05697 Trigger;<br>Bacterial trigger factor protein (TF). Pfam-B_8447 (release 8.0). In the E. coli cytosol, a fraction of the newly synthesised proteins requires the activity of molecular chaperones for folding to the native state. The major chaperones implicated in this folding process are the ribosome-associated Trigger Factor (TF), and the DnaK and GroEL chaperones with their respective co-chaperones. Trigger Factor is an ATP-independent chaperone and displays chaperone and peptidyl-prolyl-cis-trans-isomerase (PPIase) activities in vitro. It is composed of at least three domains, an N-terminal domain which mediates association with the large ribosomal subunit, a central substrate binding and PPIase domain with homology to FKBP proteins, and a C-terminal domain of unknown function. The positioning of TF at the peptide exit channel, together with its ability to interact with nascent chains as short as 57 residues renders TF a prime candidate for being the first chaperone that binds to the nascent polypeptide chains  . This family represents the N-terminal region of the protein.. 
PF05698 Bacterial trigger factor protein (TF) C-terminus<br>Pfam-B_8447 (release 8.0). In the E. coli cytosol, a fraction of the newly synthesised proteins requires the activity of molecular chaperones for folding to the native state. The major chaperones implicated in this folding process are the ribosome-associated Trigger Factor (TF), and the DnaK and GroEL chaperones with their respective co-chaperones. Trigger Factor is an ATP-independent chaperone and displays chaperone and peptidyl-prolyl-cis-trans-isomerase (PPIase) activities in vitro. It is composed of at least three domains, an N-terminal domain which mediates association with the large ribosomal subunit, a central substrate binding and PPIase domain with homology to FKBP proteins, and a C-terminal domain of unknown function. The positioning of TF at the peptide exit channel, together with its ability to interact with nascent chains as short as 57 residues renders TF a prime candidate for being the first chaperone that binds to the nascent polypeptide chains  . This family represents the C-terminal region of the protein.. 
PF05699 hATC;<br>hAT family C-terminal dimerisation region. This dimerisation region is found at the C terminus of the  transposases of elements belonging to the Activator superfamily (hAT element superfamily). The isolated dimerisation region forms extremely stable dimers in vitro  .. 
PF05700 Breast carcinoma amplified sequence 2 (BCAS2)<br>Pfam-B_7922 (release 8.0). This family consists of several eukaryotic sequences of unknown function. The mammalian members of this family are annotated as breast carcinoma amplified sequence 2 (BCAS2) proteins  . BCAS2 is a putative spliceosome associated protein  .. 
PF05701 DUF827;<br>Weak chloroplast movement under blue light. Pfam-B_6516 (release 8.0). WEMBL consists of several plant proteins required for the chloroplast avoidance response under high intensity blue light. This avoidance response consists in the relocation of chloroplasts on the anticlinal side of exposed cells. Acts in association with PMI2 to maintain the velocity of chloroplast photo-relocation movement via the regulation of cp-actin filaments  .  Thus several member-sequences are described as "myosin heavy chain-like".. 
PF05702 Herpesvirus UL49.5 envelope/tegument protein<br>Pfam-B_7354 (release 8.0). UL49.5 protein consists of 98 amino acids with a calculated molecular mass of 10,155 Da. It contains putative signal peptide and transmembrane domains but lacks a consensus sequence for N glycosylation. UL49.5 protein is an O-glycosylated structural component of the viral envelope  .. 
PF05703 DUF828;<br>Moxon SJ, Eberhardt R. Pfam-B_7298 (release 8.0). This domain is frequently found at the N-terminus of proteins containing Pfam:PF08458 at the C-terminus. It is a component of the auto-regulatory loop which enables auxin canalisation by recruitment of the PIN1 auxin efflux protein to the cell membrane  .. 
PF05704 Capsular polysaccharide synthesis protein<br>Pfam-B_7575 (release 8.0). This family consists of several capsular polysaccharide proteins. Capsular polysaccharide (CPS) is a major virulence factor in Streptococcus pneumoniae  . . 
PF05705 Eukaryotic protein of unknown function (DUF829)<br>Pfam-B_7638 (release 8.0). This family consists of several uncharacterised eukaryotic proteins.. 
PF05706 Cyclin-dependent kinase inhibitor 3 (CDKN3)<br>Pfam-B_5217 (release 8.0). This family consists of cyclin-dependent kinase inhibitor 3 or kinase associated phosphatase proteins from several mammalian species. The cyclin-dependent kinase (Cdk)-associated protein phosphatase (KAP) is a human dual specificity protein phosphatase that dephosphorylates Cdk2 on threonine 160 in a cyclin-dependent manner [1,2].. 
PF05707 Zonular occludens toxin (Zot)<br>Pfam-B_3320 (release 8.0). This family consists  of bacterial and viral proteins which are very similar to the Zonular occludens toxin (Zot). Zot is elaborated by bacteriophages present in toxigenic strains of Vibrio cholerae. Zot is a single polypeptide chain of 44.8 kDa, with the ability to reversibly alter intestinal epithelial tight junctions, allowing the passage of macromolecules through mucosal barriers [1,2]. 
PF05708 Orthopoxvirus protein of unknown function (DUF830)<br>Pfam-B_5425 (release 8.0). This family consists of several Orthopoxvirus proteins of unknown function.. 
PF05709 Phage tail protein<br>Pfam-B_5084 (release 8.0) & Pfam-B_10063 (release 10.0). This family consists of several Siphovirus and other phage tail component proteins as well as some bacterial proteins of unknown function.. 
PF05710 Coiled coil<br>This region is found in a group of Dictyostelium discoideum proteins.  It is likely to form a coiled-coil. Some of the proteins are regulated by cyclic AMP and are expressed late in development ( ).. 
PF05711 Macrocin-O-methyltransferase (TylF)<br>Pfam-B_5055 (release 8.0). This family consists of bacterial macrocin O-methyltransferase (TylF) proteins. TylF is responsible for the methylation of macrocin to produce tylosin. Tylosin is a macrolide antibiotic used in veterinary medicine to treat infections caused by Gram-positive bacteria and as an animal growth promoter in the swine industry. It is produced by several Streptomyces species. As with other macrolides, the antibiotic activity of tylosin is due to the inhibition of protein biosynthesis by a mechanism that involves the binding of tylosin to the ribosome, preventing the formation of the mRNA-aminoacyl-tRNA-ribosome complex  . The structure of one representative sequence from this family, NovP, shows it to be an S-adenosyl-l-methionine-dependent O-methyltransferase that catalyses the penultimate step in the biosynthesis of the aminocoumarin antibiotic novobiocin. Specifically, it methylates at 4-OH of the noviose moiety, and the resultant methoxy group is important for the potency of the mature antibiotic. It is likely that the key structural features of NovP are common to the rest of the family and include: a helical 'lid' region that gates access to the co-substrate binding pocket and an active centre that contains a 3-Asp putative metal binding site. A further conserved Asp probably acts as the general base that initiates the reaction by de-protonating the 4-OH group of the noviose unit  .. 
PF05712 MRG<br>Moxon SJ, Mistry J, Wood V. Pfam-B_5530 (release 8.0). This family consists of three different eukaryotic proteins (mortality factor 4 (MORF4/MRG15), male-specific lethal 3(MSL-3) and ESA1-associated factor 3(EAF3)). It is thought that the MRG family is involved in transcriptional regulation via histone acetylation   .  It contains 2 chromo domains and a leucine zipper motif  .. 
PF05713 Bacterial mobilisation protein (MobC)<br>Pfam-B_2832 (release 8.0). This family consists of several bacterial MobC-like, mobilisation proteins. MobC proteins belong to the group of relaxases. Together with MobA and MobB they bind to a single cis-active site of a mobilising plasmid, the origin of transfer (oriT) region  . The absence of MobC has several different effects on oriT DNA. Site- and strand-specific nicking by MobA protein is severely reduced, accounting for the lower frequency of mobilisation. The localised DNA strand separation required for this nicking is less affected, but becomes more sensitive to the level of active DNA gyrase in the cell. In addition, strand separation is not efficiently extended through the region containing the nick site. These effects suggest a model in which MobC acts as a molecular wedge for the relaxosome-induced melting of oriT DNA. The effect of MobC on strand separation may be partially complemented by the helical distortion induced by supercoiling. However, MobC extends the melted region through the nick site, thus providing the single-stranded substrate required for cleavage by MobA  . . 
PF05714 Borrelia_lipo; <br>Borrelia burgdorferi virulent strain associated lipoprotein. Pfam-B_7866 (release 8.0). This family consists of several virulent strain associated lipoproteins from the Lyme disease spirochete Borrelia burgdorferi.. 
PF05715 Zf_piccolo; <br>This (predicted) Zinc finger is found in the  bassoon and piccolo proteins (e.g. Swiss:Q9JKS6). There are eight conserved cysteines, suggesting  that it coordinates two zinc ligands.. 
PF05716 A-kinase anchor protein 110 kDa (AKAP 110)<br>Pfam-B_5702 (release 8.0). This family consists of several mammalian protein kinase A anchoring protein 3 (PRKA3) or A-kinase anchor protein 110 kDa (AKAP 110) sequences. Agents that increase intracellular cAMP are potent stimulators of sperm motility. Anchoring inhibitor peptides, designed to disrupt the interaction of the cAMP-dependent protein kinase A (PKA) with A kinase-anchoring proteins (AKAPs), are potent inhibitors of sperm motility. PKA anchoring is a key biochemical mechanism controlling motility. AKAP110 shares compartments with both RI and RII isoforms of PKA and may function as a regulator of both motility- and head-associated functions such as capacitation and the acrosome reaction  .. 
PF05717 Transposase_34;<br>IS66 Orf2 like protein. Pfam-B_5707 (release 8.0). This protein is found in insertion sequences related to IS66.  The function of these proteins is uncertain, but they are probably essential for transposition  .. 
PF05718 Poxvirus intermediate transcription factor<br>Pfam-B_5843 (release 8.0). This family consists of several highly related Poxvirus sequences which are thought to be intermediate transcription factors.. 
PF05719 Golgi phosphoprotein 3 (GPP34)<br>Pfam-B_7957 (release 8.0). This family consists of several eukaryotic GPP34 like proteins. GPP34 localises to the Golgi complex and is conserved from yeast to humans. The cytosolic-ally exposed location of GPP34 predict a role for a novel coat protein in Golgi trafficking  .. 
PF05720 Cell-cell adhesion domain<br>This family is based on a group of Dictyostelium discoideum proteins that are essential in early development ( ). Swiss:P16642 and  Swiss:P16643 are located on the cell surface and mediate cell-cell adhesion.. 
PF05721 Phytanoyl-CoA dioxygenase (PhyH)<br>Pfam-B_5670 (release 8.0). This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalysing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterised by the accumulation of phytanic acid in plasma and tissues  .. 
PF05722 Ustilago B locus mating-type protein<br>Pfam-B_5804 (release 8.0). This family consists of several Ustilago mating-type proteins. The b locus of the phytopathogenic fungus Ustilago maydis encodes a multiallelic recognition function that controls the ability of the fungus to form a dikaryon and complete the sexual stage of the life cycle. The b locus has at least 25 alleles and any combination of two different alleles, brought together by mating between haploid cells, allows the fungus to cause disease and undergo sexual development within the plant  . . 
PF05724 Thiopurine S-methyltransferase (TPMT)<br>Pfam-B_5821 (release 8.0). This family consists of thiopurine S-methyltransferase proteins from both eukaryotes and prokaryotes. Thiopurine S-methyltransferase (TPMT) is a cytosolic enzyme that catalyses S-methylation of aromatic and heterocyclic sulfhydryl compounds, including anticancer and immunosuppressive thiopurines  . . 
PF05725 FNIP Repeat<br>This repeat is approximately 22 residues long and is only found in Dictyostelium discoideum. It appears to be related to Pfam:PF00560 (personal obs:C Yeats). The alignment consists of two tandem repeats. It is termed the FNIP repeat after the pattern of conserved residues.. 
PF05726 Pirin C-terminal cupin domain<br>This region is found the C-terminal half of the Pirin protein.. 
PF05727 Uncharacterised protein family (UPF0228)<br>
PF05728 Uncharacterised protein family (UPF0227)<br>Despite being classed as uncharacterised proteins, the members of this family are almost certainly enzymes that are distantly related to the Pfam:PF00561.. 
PF05729 NACHT domain<br>This NTPase domain is found in apoptosis proteins as well as those involved in MHC transcription activation  . This family is closely related to Pfam:PF00931.. 
PF05730 CFEM domain<br>This fungal specific cysteine rich domain is found in some proteins with proposed roles in fungal pathogenesis  .. 
PF05731 TROVE domain<br>This presumed domain is found in TEP1 and Ro60 proteins, that are RNA-binding components of Telomerase, Ro and Vault RNPs.  This domain has been named TROVE, (after Telomerase, Ro and Vault). This domain is probably RNA-binding. . 
PF05732 Firmicute plasmid replication protein (RepL)<br>Pfam-B_5929 (release 8.0). This family consists of Firmicute RepL proteins which are involved in plasmid replication.. 
PF05733 Tenuivirus_N;<br>Tenuivirus/Phlebovirus nucleocapsid protein. Pfam-B_5998 (release 8.0) & Pfam-B_19756 (release 10.0). This family consists of several Tenuivirus and Phlebovirus nucleocapsid proteins [1,2]. These are ssRNA viruses.. 
PF05734 Herpesvirus protein of unknown function (DUF832)<br>Pfam-B_7683 (release 8.0). This family consists of several herpesvirus proteins of unknown function.. 
PF05735 TSPC;<br>Thrombospondin C-terminal region. Pfam-B_1875 (release 8.0). This region is found at the C-terminus of thrombospondin  and related proteins.. 
PF05736 OprF_membrane; <br>OprF membrane domain. Pfam-B_4079 (release 8.0). This domain represents the presumed membrane spanning region of the OprF proteins. This region is involved in channel formation and is thought to form an 8-stranded beta-barrel  .. 
PF05737 Collagen binding domain<br>Pfam-B_5000 (release 8.0). The domain fold is a jelly-roll, composed of two antiparallel beta-sheets and two short alpha-helices  . A groove on beta-sheet I exhibited the best surface complementarity to the collagen. This site partially overlaps with the peptide sequence previously shown to be critical for collagen binding. Recombinant proteins containing single amino acid mutations designed to disrupt the surface of the putative binding site exhibited significantly lower affinities for collagen.. 
PF05738 Cna protein B-type domain<br>Pfam-B_366 (release 8.0). This domain is found in Staphylococcus aureus collagen-binding surface protein.  However, this region does not mediate collagen binding, the Pfam:PF05737 region carries out that function. The structure of the repetitive B-region has been solved   and forms a beta sandwich structure.  It is thought that this region forms a stalk in Staphylococcus aureus collagen-binding protein that presents the ligand binding domain away from the bacterial cell surface.. 
PF05739 SNARE domain<br>Pfam-B_6285 (release 8.0). Most if not all vesicular membrane fusion events in eukaryotic cells are believed to be mediated by a conserved fusion machinery, the SNARE [soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein (SNAP) receptors] machinery. The SNARE domain is thought to act as a protein-protein interaction module in the assembly of a SNARE protein complex  .. 
PF05741 Nanos; <br>Nanos RNA binding domain. Pfam-B_5908 (release 8.0). This family consists of several conserved novel zinc finger domains found in the eukaryotic proteins Nanos and Xcat-2. In Drosophila melanogaster, Nanos functions as a localised determinant of posterior pattern. Nanos RNA is localised to the posterior pole of the maturing egg cell and encodes a protein that emanates from this localised source. Nanos acts as a translational repressor and thereby establishes a gradient of the morphogen Hunchback  . Xcat-2 is found in the vegetal cortical region and is inherited by the vegetal blasomeres during development, and is degraded  very early in development. The localised and maternally restricted expression of Xcat-2 RNA suggests a role for its protein in setting up regional differences in gene expression that occur early in development  . . 
PF05742 DUF833;<br>Moxon SJ, Eberhardt R. Pfam-B_6481 (release 8.0). In eukaryotes this family is predicted to play a role in protein secretion and Golgi organisation  . In plants this family includes Swiss:A9X6Y0, which is involved in water permeability in the cuticles of fruit  . Swiss:P54797 has been found to be expressed during early embryogenesis in mice  . This protein contains a conserved NRDE motif.. 
PF05743 Tsg101; <br>Pfam-B_6022 (release 8.0). This family includes the eukaryotic tumour susceptibility gene 101 protein (TSG101). Altered transcripts of this gene have been detected in sporadic breast cancers and many other human malignancies. However, the involvement of this gene in neoplastic transformation and tumorigenesis is still elusive. TSG101 is required for normal cell function of embryonic and adult tissues but that this gene is not a tumour suppressor for sporadic forms of breast cancer  . This family is related to the ubiquitin conjugating enzymes.. 
PF05744 Benyvirus P25/P26 protein<br>Pfam-B_6153 (release 8.0). This family consists of P25 and P26 proteins from the beet necrotic yellow vein viruses.. 
PF05745 Chlamydia 15 kDa cysteine-rich outer membrane protein (CRPA)<br>Pfam-B_6389 (release 8.0). This family consists of several Chlamydia 15 kDa cysteine-rich outer membrane proteins which are associated with differentiation of reticulate bodies (RBs) into elementary bodies (EBs)  .. 
PF05746 tRNA-synt_1d_C; <br>DALR anticodon binding domain. Pfam-B_196 (release 8.0). This all alpha helical domain is the anticodon binding domain in Arginyl and glycyl tRNA synthetase. This domain is known as the DALR domain after characteristic  conserved amino acids  .. 
PF05748 Rubella membrane glycoprotein E1<br>Pfam-B_6726 (release 8.0). Rubella virus (RV), the sole member of the genus Rubivirus within the family Togaviridae, is a small enveloped, positive strand RNA virus.  The nucleocapsid consists of 40S genomic RNA and a single species of capsid protein which is enveloped within a host-derived lipid bilayer containing two viral glycoproteins, E1 (58 kDa) and E2 (42-46 kDa).  In virus infected cells, RV matures by budding either at the plasma membrane, or at the internal membranes depending on the cell type and enters adjacent uninfected cells by a membrane fusion process in the endosome, directed by E1-E2 heterodimers. The heterodimer formation is crucial for E1 transport out of the endoplasmic reticulum to the Golgi and plasma membrane. In RV E1, a cysteine at position 82 is crucial for the E1-E2 heterodimer formation and cell surface expression of the two proteins. The E1 has been shown to be a type 1 membrane protein, rich in cysteine residues with extensive intramolecular disulfide bonds  .. 
PF05749 Rubella membrane glycoprotein E2<br>Pfam-B_6726 (release 8.0). Rubella virus (RV), the sole member of the genus Rubivirus within the family Togaviridae, is a small enveloped, positive strand RNA virus.  The nucleocapsid consists of 40S genomic RNA and a single species of capsid protein which is enveloped within a host-derived lipid bilayer containing two viral glycoproteins, E1 (58 kDa) and E2 (42-46 kDa).  In virus infected cells, RV matures by budding either at the plasma membrane, or at the internal membranes depending on the cell type and enters adjacent uninfected cells by a membrane fusion process in the endosome, directed by E1-E2 heterodimers. The heterodimer formation is crucial for E1 transport out of the endoplasmic reticulum to the Golgi and plasma membrane. In RV E1, a cysteine at position 82 is crucial for the E1-E2 heterodimer formation and cell surface expression of the two proteins  .. 
PF05750 Rubella capsid protein<br>Pfam-B_6726 (release 8.0). Rubella virus is an enveloped positive-strand RNA virus of the family Togaviridae. Virions are composed of three structural proteins: a capsid and two membrane-spanning glycoproteins, E2 and E1. During virus assembly,  the capsid interacts with genomic RNA to form nucleocapsids. It has been discovered that capsid phosphorylation serves to negatively regulate binding of viral genomic RNA. This may delay the initiation of nucleocapsid assembly until sufficient amounts of virus glycoproteins accumulate at the budding site and/or prevent non-specific binding to cellular RNA when levels of genomic RNA are low. It follows that at a late stage in replication, the capsid may undergo dephosphorylation before nucleocapsid assembly occurs  .. 
PF05751 FixH<br>Pfam-B_6803 (release 8.0). This family consists of several Rhizobium FixH like proteins. It has been suggested that suggested that the four proteins FixG, FixH, FixI, and FixS may participate in a membrane-bound complex coupling the FixI cation pump with a redox process catalysed by FixG  .. 
PF05752 Calicivirus_MSP; <br>Calicivirus minor structural protein. Pfam-B_6811 (release 8.0). This family consists of minor structural proteins largely from human calicivirus isolates. Human calicivirus causes gastroenteritis  . The function of this family is unknown.. 
PF05753 Translocon-associated protein beta (TRAPB)<br>Pfam-B_6857 (release 8.0). This family consists of several eukaryotic translocon-associated protein beta (TRAPB) or signal sequence receptor beta subunit (SSR-beta) proteins. The normal translocation of nascent polypeptides into the lumen of the endoplasmic reticulum (ER) is thought to be aided in part by a translocon-associated protein (TRAP) complex consisting of 4 protein subunits. The association of mature proteins with the ER and Golgi, or other intracellular locales, such as lysosomes, depends on the initial targeting of the nascent polypeptide to the ER membrane. A similar scenario must also exist for proteins destined for secretion  .. 
PF05754 Domain of unknown function (DUF834)<br>Pfam-B_9258 (release 8.0). This short presumed domain is found in a large number of hypothetical plant proteins. The domain is quite rich in conserved glycine residues.\.  It occurs in some putative transposons but currently has no known function.. 
PF05755 Rubber elongation factor protein (REF)<br>Pfam-B_6903 (release 8.0). This family consists of the highly related rubber elongation factor (REF), small rubber particle protein (SRPP) and stress-related protein (SRP) sequences. REF and SRPP are released from the rubber particle membrane into the cytosol during osmotic lysis of the sedimentable organelles (lutoids). The exact function of this family is unknown  . . 
PF05756 S-antigen protein<br>Pfam-B_7194 (release 8.0). S-antigens are heat stable proteins that are found in the blood of individuals infected with malaria  .. 
PF05757 Oxygen evolving enhancer protein 3 (PsbQ)<br>Pfam-B_6905 (release 8.0). This family consists of the plant specific oxygen evolving enhancer protein 3 (PsbQ). Photosystem II (PSII)1 is a pigment-protein complex, which consists of at least 25 different protein subunits, at present denoted PsbA-Z according to the genes that encode them. PsbQ plays an important role in the lumenal oxygen-evolving activity of PSII from higher plants and green algae  . . 
PF05758 Ycf1<br>Pfam-B_6040 (release 8.0). The chloroplast genomes of most higher plants contain two giant open reading frames designated ycf1 and ycf2. Although the function of Ycf1 is unknown, it is known to be an essential gene  .. 
PF05760 Immediate early response protein (IER)<br>Pfam-B_6450 (release 8.0). This family consists of several eukaryotic immediate early response (IER) 2 and 5 proteins. The role of IER5 is unclear although it  play an important role in mediating the cellular response to mitogenic signals [1,2]. Again, little is known about the function of IER2 although it is thought to play a role in mediating the cellular responses to a variety of extracellular signals [3,4].. 
PF05761 5_nucleotidase; <br>5' nucleotidase family. Pfam-B_2948 (release 8.0). This family of eukaryotic proteins includes 5' nucleotidase enzymes, such as purine 5'-nucleotidase EC:3.1.3.5.. 
PF05762 vwa_CoxE; <br>VWA domain containing CoxE-like protein. Pfam-B_2956 (release 8.0). This family is annotated by SMART as containing a VWA (von Willebrand factor type A) domain.  The exact function of this family is unknown.  It is found as part of a CO oxidising (Cox) system operon is several bacteria  .. 
PF05763 Protein of unknown function (DUF835)<br>Pfam-B_3039 (release 8.0). The members of this archaebacterial protein family are around 250-300 amino acid residues in length. The function of these proteins is not known.. 
PF05764 YL1 nuclear protein<br>Pfam-B_3088 (release 8.0). The proteins in this family are designated YL1  . These proteins have been shown to be DNA-binding and may be a transcription factor  .. 
PF05766 Bacteriophage Lambda NinG protein<br>Pfam-B_7000 (release 8.0). NinG or Rap is involved in recombination. Rap (recombination adept with plasmid) increases lambda-by-plasmid recombination catalysed by Escherichia coli's RecBCD pathway  .. 
PF05767 Poxvirus virion envelope protein A14<br>Pfam-B_7009 (release 8.0). This family consists of several Poxvirus virion envelope protein A14 like sequences. A14 is a component of the virion membrane and has been found to be an H1 phosphatase substrate in vivo and in vitro. A14 is hyperphosphorylated on serine residues in the absence of H1 expression  .. 
PF05768 Glutaredoxin-like domain (DUF836)<br>Pfam-B_7010 (release 8.0) & Pfam-B_2829 (release 14.0). These proteins are related to the Pfam:PF00462 family.. 
PF05769 Protein of unknown function (DUF837)<br>Pfam-B_7035 (release 8.0). This family consists of several eukaryotic proteins of unknown function. One of the family members (Swiss:O02197) is a circulating cathodic antigen (CCA) found in Schistosoma mansoni (Blood fluke)  .. 
PF05770 Inositol 1, 3, 4-trisphosphate 5/6-kinase<br>Pfam-B_7042 (release 8.0). This family consists of several inositol 1, 3, 4-trisphosphate 5/6-kinase proteins. Inositol 1,3,4-trisphosphate is at a branch point in inositol phosphate metabolism. It is dephosphorylated by specific phosphatases to either inositol 3,4-bisphosphate or inositol 1,3-bisphosphate. Alternatively, it is phosphorylated to inositol 1,3,4,6-tetrakisphosphate or inositol 1,3,4,5-tetrakisphosphate by inositol trisphosphate 5/6-kinase  .. 
PF05771 Poxvirus A31 protein<br>Pfam-B_7044 (release 8.0). 
PF05772 NinB protein<br>Pfam-B_4884 (release 8.0). The ninR region of phage lambda contains two recombination genes, orf (ninB) and rap (ninG), that have roles when the RecF and RecBCD recombination pathways of E. coli, respectively, operate on phage lambda.. 
PF05773 RWD domain<br>Pfam-B_3991 (release 8.0). This domain was identified in WD40 repeat proteins and Ring finger domain proteins  . The function of this domain is unknown. GCN2 is the alpha-subunit of the only translation initiation factor (eIF2 alpha) kinase that appears in all eukaryotes. Its function requires an interaction with GCN1 via the domain at its N-terminus, which is termed the RWD domain   after three major RWD-containing proteins: RING finger-containing proteins, WD-repeat-containing proteins, and yeast DEAD (DEXD)-like helicases. The structure forms an alpha + beta sandwich fold consisting of two layers: a four-stranded antiparallel beta-sheet, and three side-by-side alpha-helices  .. 
PF05774 Herpesvirus helicase-primase complex component<br>Pfam-B_7045 (release 8.0). This family consists of several helicase-primase complex components from the Gammaherpesviruses.. 
PF05775 Enterobacteria AfaD invasin protein<br>Pfam-B_7107 (release 8.0). This family consists of several AfaD and related proteins from Escherichia coli and Salmonella bacteria. The afa gene clusters encode an afimbrial adhesive sheath produced by Escherichia coli. The adhesive sheath is composed of two proteins, AfaD and AfaE, which are independently exposed at the bacterial cell surface.  AfaE is required for bacterial adhesion to HeLa cells and AfaD for the uptake of adherent bacteria into these cells  . . 
PF05776 Papillomavirus E5A protein<br>Pfam-B_7244 (release 8.0). Human papillomaviruses (HPVs) are epitheliotropic viruses, and their life cycle is intimately linked to the stratification and differentiation state of the host epithelial tissues. The kinetics of E5a protein expression during the complete viral life cycle has been studied and the highest level was found to be coincidental with the onset of virion morphogenesis  . . 
PF05777 Drosophila accessory gland-specific peptide 26Ab (Acp26Ab)<br>Pfam-B_7275 (release 8.0). This family consists of accessory gland-specific 26Ab peptides or male accessory gland secretory protein 355B from different Drosophila species. Drosophila males, like males of most other insects, transfer a group of specific proteins (Acp26Ab and Acp26Aa in Drosophila) to the females during mating. These proteins are produced primarily in the accessory gland and are likely to influence the female's reproduction  . . 
PF05778 Apolipoprotein CIII (Apo-CIII)<br>Pfam-B_7283 (release 8.0). This family consists of several mammalian apolipoprotein CIII (Apo-CIII) sequences. Apolipoprotein C-III is a 79-residue glycoprotein. It is synthesised in the intestine and liver as part of the very low density lipoprotein (VLDL) and the high density lipoprotein (HDL) particles. Owing to its positive correlation with plasma triglyceride (Tg) levels, Apo-CIII is suggested to play a role in Tg metabolism and is therefore of interest regarding atherosclerosis. However, unlike other apolipoproteins such as Apo-AI, Apo E or CII for which many naturally occurring mutations are known, the structure-function relationships of apo C-III remains a subject of debate. One possibility is that apo C-III inhibits lipoprotein lipase (LPL) activity, as shown by in vitro experiments. Another suggestion, is that elevated levels of Apo-CIII displace other apolipoproteins at the lipoprotein surface, modifying their clearance from plasma  .. 
PF05781 MRVI1 protein<br>Pfam-B_7407 (release 8.0). This family consists of mammalian MRVI1 proteins which are related to the lymphoid-restricted membrane protein (JAW1) and the IP3 receptor associated cGMP kinase substrates A and B (IRAGA and IRAGB). The function of MRVI1 is unknown although mutations in the Mrvi1 gene induces myeloid leukaemia by altering the expression of a gene important for myeloid cell growth and/or differentiation so it has been speculated that Mrvi1 is a tumour suppressor gene  . IRAG is very similar in sequence to MRVI1 and is an essential NO/cGKI-dependent regulator of IP3-induced calcium release. Activation of cGKI decreases IP3-stimulated elevations in intracellular calcium, induces smooth muscle relaxation and contributes to the antiproliferative and pro-apoptotic effects of NO/cGMP  . Jaw1 is a member of a class of proteins with COOH-terminal hydrophobic membrane anchors and is structurally similar to proteins involved in vesicle targeting and fusion. This suggests that the function and/or the structure of the ER in lymphocytes may be modified by lymphoid-restricted resident ER proteins  .. 
PF05782 Extracellular matrix protein 1 (ECM1)<br>Pfam-B_7421 (release 8.0). This family consists of several eukaryotic extracellular matrix protein 1 (ECM1) sequences. ECM1 has been shown to regulate endochondral bone formation, stimulate the proliferation of endothelial cells and induce angiogenesis [1,2]. Mutations in the ECM1 gene can cause lipoid proteinosis, a disorder which causes generalised thickening of skin, mucosae and certain viscera. Classical features include beaded eyelid papules and laryngeal infiltration leading to hoarseness  .. 
PF05783 Dynein light intermediate chain (DLIC)<br>Pfam-B_7447 (release 8.0). This family consists of several eukaryotic dynein light intermediate chain proteins. The light intermediate chains (LICs) of cytoplasmic dynein consist of multiple isoforms, which undergo post-translational modification to produce a large number of species. DLIC1 is known to be involved in assembly, organisation, and function of centrosomes and mitotic spindles when bound to pericentrin [1,2]. DLIC2 is a subunit of cytoplasmic dynein 2 that may play a role in maintaining Golgi organisation by binding cytoplasmic dynein 2 to its Golgi-associated cargo  . . 
PF05784 Betaherpesvirus UL82/83 protein N terminus<br>Pfam-B_7466 (release 8.0). This family represents the N terminal region of the Betaherpesvirus UL82 and UL83 proteins. As viruses are reliant upon their host cell to serve as proper environments for their replication, many have evolved mechanisms to alter intracellular conditions to suit their own needs. Human cytomegalovirus induces quiescent cells to enter the cell cycle and then arrests them in late G(1), before they enter the S phase, a cell cycle compartment that is presumably favourable for viral replication. The protein product of the human cytomegalovirus UL82 gene, pp71, can accelerate the movement of cells through the G(1) phase of the cell cycle. This activity would help infected cells reach the late G(1) arrest point sooner and thus may stimulate the infectious cycle. pp71 also induces DNA synthesis in quiescent cells, but a pp71 mutant protein that is unable to induce quiescent cells to enter the cell cycle still retains the ability to accelerate the G(1) phase. Thus, the mechanism through which pp71 accelerates G(1) cell cycle progression appears to be distinct from the one that it employs to induce quiescent cells to exit G(0) and subsequently enter the S phase  . . 
PF05785 Rho-activating domain of cytotoxic necrotizing factor<br>Pfam-B_7489 (release 8.0). This family consists of several bacterial cytotoxic necrotizing factor proteins as well as related dermonecrotic toxin (DNT) from Bordetella species. Cytotoxic necrotizing factor 1 (CNF1) causes necrosis of rabbit skin and re-organisation of the actin cytoskeleton in cultured cells  . Bordetella dermonecrotic toxin (DNT) stimulates the assembly of actin stress fibres and focal adhesions by deamidating or polyaminating Gln63 of the small GTPase Rho. DNT is an A-B toxin which is composed of an N-terminal receptor-binding (B) domain and a C-terminal enzymatically active (A) domain  .. 
PF05786 Barren;<br>Condensin complex subunit 2. Pfam-B_7477 (release 8.0). This family consists of several Barren protein homologues from several eukaryotic organisms. In Drosophila Barren (barr) is required for sister-chromatid segregation in mitosis. barr encodes a novel protein that is present in proliferating cells and has homologues in yeast and human. Mitotic defects in barr embryos become apparent during cycle 16, resulting in a loss of PNS and CNS neurons.  Centromeres move apart at the metaphase-anaphase transition and Cyclin B is degraded, but sister chromatids remain connected, resulting in chromatin bridging. Barren protein localises to chromatin throughout mitosis. Colocalisation and biochemical experiments indicate that Barren associates with Topoisomerase II throughout mitosis and alters the activity of Topoisomerase II. It has been suggested that this association is required for proper chromosomal segregation by facilitating the decatenation of chromatids at anaphase  . This family forms one of the three non-structural maintenance of chromosomes (SMC) subunits of the mitotic condensation complex along with Cnd1 and Cnd3  .. 
PF05787 Bacterial protein of unknown function (DUF839)<br>Pfam-B_7480 (release 8.0). This family consists of several bacterial proteins of unknown function that contain a predicted beta-propeller repeats.. 
PF05788 Orbivirus_VP1; <br>Orbivirus RNA-dependent RNA polymerase (VP1). Pfam-B_7493 (release 8.0). This family consists of the RNA-dependent RNA polymerase protein VP1 from the Orbiviruses. VP1 may have both enzymatic and structural roles in the virus life cycle  .. 
PF05789 Baculovirus VP1054 protein<br>Pfam-B_7511 (release 8.0). This family consists of several VP1054 proteins from the Baculoviruses. VP1054 is a virus structural protein required for nucleocapsid assembly  . . 
PF05790 CD2;<br>Immunoglobulin C2-set domain. 
PF05791 Bacillus haemolytic enterotoxin (HBL)<br>Pfam-B_7539 (release 8.0). This family consists of several Bacillus haemolytic enterotoxins (HblC, HblD, HblA, NheA, and NheB) which can cause food poisoning in humans  .. 
PF05792 Candida agglutinin-like (ALS)<br>Pfam-B_7578 (release 8.0). This family consists of several agglutinin-like proteins from different Candida species. ALS genes of Candida albicans encode a family of cell-surface glycoproteins with a three-domain structure. Each Als protein has a relatively conserved N-terminal domain, a central domain consisting of a tandemly repeated motif of variable number, and a serine-threonine-rich C-terminal domain that is relatively variable across the family. The ALS family exhibits several types of variability that indicate the importance of considering strain and allelic differences when studying ALS genes and their encoded proteins  . Fungal adhesins, which include sexual agglutinins, virulence factors, and flocculins, are surface proteins that mediate cell-cell and cell-environment interactions. It is possible that both the serine/threonine-rich domain and the cysteine residues in the C-terminal and DIPSY Pfam:PF11763 participate in anchoring the terminal domains inside the wall, so that only the inner part of Map4p, including the repeat region, is sticking out as a fold-back loop then able to act in adhesing  .. 
PF05793 TFIIF-alpha; <br>Transcription initiation factor IIF, alpha subunit (TFIIF-alpha). Pfam-B_7586 (release 8.0). Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) or RNA polymerase II-associating protein 74 (RAP74) is the large subunit of transcription factor IIF (TFIIF), which is essential for accurate initiation and stimulates elongation by RNA polymerase II  .. 
PF05794 T-complex protein 11<br>Pfam-B_7604 (release 8.0). This family consists of several eukaryotic T-complex protein 11 (Tcp11) related sequences. Tcp11 is only expressed in fertile adult mammalian testes and is thought to be important in sperm function and fertility [1,2,3]. The family also contains the yeast Sok1 protein which is known to suppress cyclic AMP-dependent protein kinase mutants  .. 
PF05795 Plasmodium vivax Vir protein<br>Pfam-B_7631 (release 8.0). This family consists of several Vir proteins specific to Plasmodium vivax. The vir genes are present at about 600-1,000 copies per haploid genome and encode proteins that are immunovariant in natural infections, indicating that they may have a functional role in establishing chronic infection through antigenic variation  . . 
PF05796 Chordopoxvirus protein G2<br>Pfam-B_7672 (release 8.0). This family consists of several Chordopoxvirus isatin-beta-thiosemicarbazone dependent protein (protein G2) sequences. Inactivation of the gene coding for this protein renders the virus dependent upon isatin-beta-thiosemicarbazone (IBT) for growth  .. 
PF05797 Yeast_TAF; <br>Yeast trans-acting factor (REP1/REP2). Pfam-B_7680 (release 8.0). This family consists of the yeast trans-acting factor B and C (REP1 and 2) proteins. The yeast plasmid stability system consists of two plasmid-coded proteins, Rep1 and Rep2, and a cis-acting locus, STB. The Rep proteins show both self- and cross-interactions in vivo and in vitro, and bind to the STB DNA with assistance from host factor(s). Within the yeast nucleus, the Rep1 and Rep2 proteins tightly associate with STB-containing plasmids into well organised plasmid foci that form a cohesive unit in partitioning. It is generally accepted that the protein-protein and DNA-protein interactions engendered by the Rep-STB system are central to plasmid partitioning. Point mutations in Rep1 that knock out interaction with Rep2 or with STB simultaneously block the ability of these Rep1 variants to support plasmid stability  .. 
PF05798 Bacteriophage FRD3 protein<br>Pfam-B_7781 (release 8.0). This family consists of bacteriophage FRD3 proteins.. 
PF05800 Gas vesicle synthesis protein GvpO<br>Pfam-B_8221 (release 8.0). This family consists of archaeal GvpO proteins which are required for gas vesicle synthesis  . The family also contains two related sequences from Streptomyces coelicolor. . 
PF05801 Lagovirus protein of unknown function (DUF840)<br>Pfam-B_8265 (release 8.0). This family consists of several Lagovirus sequences of unknown function, largely from rabbit hemorrhagic disease virus.. 
PF05802 Enterobacterial EspB protein<br>Pfam-B_8424 (release 8.0). EspB is a type-III-secreted pore-forming protein of enteropathogenic Escherichia coli (EPEC) which is essential for EPEC pathogenesis  . EspB is also found in Citrobacter rodentium  .. 
PF05803 Chordopoxvirus L2 protein<br>Pfam-B_8620 (release 8.0). This family consists of several Chordopoxvirus L2 proteins.. 
PF05804 Kinesin-associated protein (KAP)<br>Pfam-B_8674 (release 8.0). This family consists of several eukaryotic kinesin-associated (KAP) proteins. Kinesins are intracellular multimeric transport motor proteins that move cellular cargo on microtubule tracks. It has been shown that the sea urchin KRP85/95 holoenzyme associates with a KAP115 non-motor protein, forming a heterotrimeric complex in vitro, called the Kinesin-II  .  . 
PF05805 L6 membrane protein<br>Pfam-B_7771 (release 8.0). This family consists of several eukaryotic L6 membrane proteins. L6, IL-TMP, and TM4SF5 are cell surface proteins predicted to have four transmembrane domains. Previous sequence analysis led to their assignment as members of the tetraspanin superfamily it has now been found that that they are not significantly related to genuine tetraspanins, but instead constitute their own L6 family  . Several members of this family have been implicated in human cancer [2,3].. 
PF05806 Noggin<br>Pfam-B_7925 (release 8.0). This family consists of the eukaryotic Noggin proteins. Noggin is a glycoprotein that binds bone morphogenetic proteins (BMPs) selectively and, when added to osteoblasts, it opposes the effects of BMPs. It has been found that noggin arrests the differentiation of stromal cells, preventing cellular maturation  .. 
PF05808 Podoplanin<br>Pfam-B_8548 (release 8.0). This family consists of several mammalian podoplanin like proteins which are thought to control specifically the unique shape of podocytes  .. 
PF05810 NinF protein<br>Pfam-B_8528 (release 8.0). This family consists of several bacteriophage NinF proteins as well as related sequences from E. coli.. 
PF05811 Eukaryotic protein of unknown function (DUF842)<br>Pfam-B_7096 (release 8.0). This family consists of a number of conserved eukaryotic proteins of unknown function. The sequences carry three sets of CxxxC motifs, which might suggest a type of zinc-finger formation.. 
PF05812 Herpesvirus BLRF2 protein<br>Pfam-B_7251 (release 8.0). This family consists of several Herpesvirus BLRF2 proteins.. 
PF05813 Orthopoxvirus F7 protein<br>Pfam-B_7318 (release 8.0). 
PF05814 Baculovirus protein of unknown function (DUF843)<br>Pfam-B_7353 (release 8.0). This family consists of several Baculovirus proteins of around 85 residues long with no known function.. 
PF05815 Baculovirus protein of unknown function (DUF844)<br>Pfam-B_7453 (release 8.0). This family consists of several Baculovirus sequences of between 350 and 380 residues long. The family has no known function.. 
PF05816 Toxic anion resistance protein (TelA)<br>Pfam-B_7534 (release 8.0). This family consists of several prokaryotic TelA like proteins. TelA and KlA are associated with tellurite resistance   and plasmid fertility inhibition  .. 
PF05817 Oligosaccharyltransferase subunit Ribophorin II<br>Pfam-B_7633 (release 8.0). This family contains eukaryotic Ribophorin II (RPN2) proteins. The mammalian oligosaccharyltransferase (OST) is a protein complex that effects the cotranslational N-glycosylation of newly synthesised polypeptides, and is composed of the following proteins: ribophorins I and II (RI and RII), OST48, and Dadl, N33/IAP, OST4, STT3. The family also includes the SWP1 protein from yeast. In yeast the oligosaccharyltransferase complex is composed 7 or 8 subunits, SWP1, being one of them   .. 
PF05818 Enterobacterial TraT complement resistance protein<br>Pfam-B_7686 (release 8.0). The traT gene is one of the F factor transfer genes and encodes an outer membrane protein which is involved in interactions between an Escherichia coli and its surroundings [1,2].. 
PF05819 NolX protein<br>Pfam-B_7801 (release 8.0). This family consists of Rhizobium NolX and Xanthomonas HrpF proteins. The interaction between the plant pathogen Xanthomonas campestris pv. vesicatoria and its host plants is controlled by hrp genes (hypersensitive reaction and pathogenicity), which encode a type III protein secretion system. Among type III-secreted proteins are avirulence proteins, effectors involved in the induction of plant defence reactions. HrpF is dispensable for protein secretion but required for AvrBs3 recognition in planta, is thought to function as a translocator of effector proteins into the host cell  . NolX, a soybean cultivar specificity protein, is secreted by a type III secretion system (TTSS) and shows homology to HrpF of the plant pathogen Xanthomonas campestris pv. vesicatoria. It is not known whether NolX functions at the bacterium-plant interface or acts inside the host cell. NolX is expressed in planta only during the early stages of nodule development  .. 
PF05820 Baculovirus protein of unknown function (DUF845)<br>Pfam-B_7739 (release 8.0). This family consists of several highly related Baculovirus proteins of unknown function.. 
PF05821 NDUFB8; <br>NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8). Pfam-B_7830 (release 8.0). This family consists of several eukaryotic NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI) proteins. NADH:ubiquinone oxidoreductase (complex I) is an extremely complicated multiprotein complex located in the inner mitochondrial membrane. Its main function is the transport of electrons from NADH to ubiquinone, which is accompanied by translocation of protons from the mitochondrial matrix to the intermembrane space. Human complex I appears to consist of 41 subunits  .. 
PF05822 Pyrimidine 5'-nucleotidase (UMPH-1)<br>Pfam-B_7840 (release 8.0). This family consists of several eukaryotic pyrimidine 5'-nucleotidase proteins. P5'N-1, also known as uridine monophosphate hydrolase-1 (UMPH-1), is a member of a large functional group of enzymes, characterised by the ability to dephosphorylate nucleic acids. P5'N-1 catalyses the dephosphorylation of pyrimidine nucleoside monophosphates to the corresponding nucleosides. Deficiencies in this proteins function can lead to several different disorders in humans  .. 
PF05823 Nematode fatty acid retinoid binding protein (Gp-FAR-1)<br>Pfam-B_7852 (release 8.0). Parasitic nematodes produce at least two structurally novel classes of small helix-rich retinol- and fatty-acid-binding proteins that have no counterparts in their plant or animal hosts and thus represent potential targets for new nematicides. Gp-FAR-1 is a member of the nematode-specific fatty-acid- and retinol-binding (FAR) family of proteins but localises to the surface of the organism, placing it in a strategic position for interaction with the host. Gp-FAR-1 functions as a broad-spectrum retinol- and fatty-acid-binding protein, and it is thought that it is involved in the evasion of primary host plant defence systems  .. 
PF05824 Pro-melanin-concentrating hormone (Pro-MCH)<br>Pfam-B_7863 (release 8.0). This family consists of several mammalian pro-melanin-concentrating hormone (Pro-MCH) 1 and 2 proteins. Melanin-concentrating hormone (MCH) is a 19 amino acid cyclic peptide that was first isolated from the pituitary of teleost fish. It is produced from pro-MCH that encodes, in addition to MCH, NEI, and a putative peptide, NGE. In lower vertebrates, MCH acts to regulate skin colour by antagonising the melanin-dispersing actions of small alpha, Greek-melanocyte stimulating hormone (small alpha, Greek-MSH). In mammals, MCH serves as a neuropeptide and is found in many regions of the brain and especially the hypothalamus. It affects many types of behaviours such as appetite, sexual receptivity, aggression, and anxiety. MCH also stimulates the release of luteinising hormone  .. 
PF05825 Beta-microseminoprotein (PSP-94)<br>Pfam-B_7865 (release 8.0). This family consists of the mammalian specific protein beta-microseminoprotein. Prostatic secretory protein of 94 amino acids (PSP94), also called beta-microseminoprotein, is a small, nonglycosylated protein, rich in cysteine residues. It was first isolated as a major protein from human seminal plasma  . The exact function of this protein is unknown.. 
PF05826 Phospholip_A2; <br>Pfam-B_7918 (release 8.0). This family consists of several phospholipase A2 like proteins mostly from insects  .. 
PF05827 Vacuolar ATP synthase subunit S1 (ATP6S1)<br>Pfam-B_8145 (release 8.0). This family consists of eukaryotic vacuolar ATP synthase subunit S1 proteins  . It also contains BIG1 ER integral membrane proteins which are involved in cell wall organisation and biogenesis  .. 
PF05829 Adenovirus_PX; <br>Adenovirus late L2 mu core protein (Protein X). Pfam-B_8179 (release 8.0). This family consists of several Adenovirus late L2 mu core protein or Protein X sequences.. 
PF05830 Nodulation protein Z (NodZ)<br>Pfam-B_8202 (release 8.0). The nodulation genes of Rhizobia are regulated by the nodD gene product in response to host-produced flavonoids and appear to encode enzymes involved in the production of a lipo-chitose signal molecule required for infection and nodule formation. NodZ is required for the addition of a 2-O-methylfucose residue to the terminal reducing N-acetylglucosamine of the nodulation signal. This substitution is essential for the biological activity of this molecule. Mutations in nodZ result in defective nodulation. nodZ represents a unique nodulation gene that is not under the control of NodD and yet is essential for the synthesis of an active nodulation signal  . . 
PF05831 GAGE protein<br>Pfam-B_8207 (release 8.0). This family consists of several GAGE and XAGE proteins which are found exclusively in humans. The function of this family is unknown although they have been implicated in human cancers  .. 
PF05832 Eukaryotic protein of unknown function (DUF846)<br>Pfam-B_8404 (release 8.0). This family consists of several of unknown function from a variety of eukaryotic organisms.. 
PF05833 Fibronectin-binding protein A N-terminus (FbpA)<br>Pfam-B_8577 (release 8.0). This family consists of the N-terminal region of the prokaryotic fibronectin-binding protein. Fibronectin binding is considered to be an important virulence factor in streptococcal infections. Fibronectin is a dimeric glycoprotein that is present in a soluble form in plasma and extracellular fluids; it is also present in a fibrillar form on cell surfaces. Both the soluble and cellular forms of fibronectin may be incorporated into the extracellular tissue matrix. While fibronectin has critical roles in eukaryotic cellular processes, such as adhesion, migration and differentiation, it is also a substrate for the attachment of bacteria. The binding of pathogenic Streptococcus pyogenes and Staphylococcus aureus to epithelial cells via fibronectin facilitates their internalisation and systemic spread within the host  . . 
PF05834 Lycopene cyclase protein<br>Pfam-B_8336 (release 8.0). This family consists of lycopene beta and epsilon cyclase proteins. Carotenoids with cyclic end groups are essential components of the photosynthetic membranes in all plants, algae, and cyanobacteria. These lipid-soluble compounds protect against photo-oxidation, harvest light for photosynthesis, and dissipate excess light energy absorbed by the antenna pigments. The cyclisation of lycopene (psi, psi-carotene) is a key branch point in the pathway of carotenoid biosynthesis. Two types of cyclic end groups are found in higher plant carotenoids: the beta and epsilon rings. Carotenoids with two beta rings are ubiquitous, and those with one beta and one epsilon ring are common; however, carotenoids with two epsilon rings are rare [1,2].  . 
PF05835 Synaphin protein<br>Pfam-B_8588 (release 8.0). This family consists of several eukaryotic synaphin 1 and 2 proteins. Synaphin/complexin is a cytosolic protein that preferentially binds to syntaxin within the SNARE complex. Synaphin promotes SNAREs to form precomplexes that oligomerise into higher order structures. A peptide from the central, syntaxin binding domain of synaphin competitively inhibits these two proteins from interacting and prevents SNARE complexes from oligomerising. It is thought that oligomerisation of SNARE complexes into a higher order structure creates a SNARE scaffold for efficient, regulated fusion of synaptic vesicles  . Synaphin promotes neuronal exocytosis by promoting interaction between the complementary syntaxin and synaptobrevin  transmembrane regions that reside in opposing membranes prior to fusion  .. 
PF05836 Chorion protein S16<br>Pfam-B_8659 (release 8.0). This family consists of several examples of the fruit fly specific chorion protein S16.  The chorion genes of Drosophila are amplified in response to developmental signals in the follicle cells of the ovary  . . 
PF05837 Centromere protein H (CENP-H)<br>Pfam-B_8705 (release 8.0). This family consists of several eukaryotic centromere protein H (CENP-H) sequences. Macromolecular centromere-kinetochore complex plays a critical role in sister chromatid separation, but its complete protein composition as well as its precise dynamic function during mitosis has not yet been clearly determined. CENP-H contains a coiled-coil structure and a nuclear localisation signal. CENP-H is specifically and constitutively localised in kinetochores throughout the cell cycle. CENP-H may play a role in kinetochore organisation and function throughout the cell cycle  . This the C-terminus of the region, which is conserved from fungi to humans.. 
PF05838 DUF847;<br>Glycosyl hydrolase 108. Pfam-B_8737 (release 8.0). This family acts as a lysozyme (N-acetylmuramidase), EC:3.2.1.17. It contains a conserved EGGY motif near the N-terminus, the glutamic acid within this motif is essential for catalytic activity  . In bacteria, it may activate the secretion of large proteins via the breaking and rearrangement of the peptidoglycan layer during secretion [2,3]. It is frequently found at the N-terminus of proteins containing a C-terminal Pfam:PF09374 domain.. 
PF05839 Apc13p protein<br>The anaphase-promoting complex (APC) is a conserved multi-subunit ubiquitin ligase required for the degradation of key cell cycle regulators Members of this family are components of the anaphase-promoting complex homologous to Apc13p  .. 
PF05840 Bacteriophage replication gene A protein (GPA)<br>Pfam-B_8738 (release 8.0). This family consists of a group of bacteriophage replication gene A protein (GPA) like sequences from both viruses and bacteria. The members of this family are likely to be endonucleases [1,2,3].. 
PF05841 Apc15p protein<br>The anaphase-promoting complex (APC) is a conserved multi-subunit ubiquitin ligase required for the degradation of key cell cycle regulators Members of this family are components of the anaphase-promoting complex homologous to Apc15p Swiss:O94688  .. 
PF05842 Euplotes octocarinatus mating pheromone protein<br>Pfam-B_8825 (release 8.0). This family consists of several mating pheromone proteins from Euplotes octocarinatus. Cells of the ten mating types of the ciliate Euplotes octocarinatus communicate by pheromones before they enter conjugation. The pheromones induce homotypic pairing when applied to mating types that do not secrete the same pheromone(s). Heterotypic pairs (i.e., those between cells of different mating types) are formed only when both mating types in a mixture secrete a pheromone that the other does not. The genetics of mating types is based on four codominant mating type alleles, each allele determining production of a different pheromone. The pheromones not only induce pair formation but also attract cells  .. 
PF05843 Suppressor of forked protein (Suf)<br>Pfam-B_8911 (release 8.0). This family consists of several eukaryotic suppressor of forked (Suf) like proteins. The Drosophila melanogaster Suppressor of forked [Su(f)] protein shares homology with the yeast RNA14 protein and the 77-kDa subunit of human cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilisation and an important role of the GU-rich sequence for this regulation to occur  .. 
PF05844 YopD protein<br>Pfam-B_8937 (release 8.0). This family consists of several bacterial YopD like proteins. Virulent Yersinia species harbour a common plasmid that encodes essential virulence determinants (Yersinia outer proteins [Yops]), which are regulated by the extracellular stimuli Ca2+ and temperature. YopD is thought to be a possible transmembrane protein and contains an amphipathic alpha-helix in its carboxy terminus  .  . 
PF05845 Bacterial phosphonate metabolism protein (PhnH)<br>Pfam-B_9057 (release 8.0). This family consists of several bacterial PhnH sequences which are known to be involved in phosphonate metabolism [1,2].. 
PF05846 Chordopoxvirus A15 protein<br>Pfam-B_9149 (release 8.0). This family consists of several Chordopoxvirus A15 like sequences.. 
PF05847 Nucleopolyhedrovirus late expression factor 3 (LEF-3)<br>Moxon SJ, Mistry J, Carstens EB. Pfam-B_9292 (release 8.0). This family consists of LEF-3 Nucleopolyhedrovirus late expression factor 3 (LEF-3) sequences which are known to be ssDNA-binding proteins  .  Alkaline nuclease (AN) and LEF-3 may participate in homologous recombination of the baculovirus genome in a manner similar to that of exonuclease (Redalpha) and DNA-binding protein (Redbeta) of the Red-mediated homologous recombination system of bacteriophage lambda  .\.       LEF-3 is essential for transporting the putative baculovirus helicase protein P143 into the nucleus where they function together during viral DNA replication  . LEF-3 and other proteins have been shown to bind to closely linked sites on viral chromatin in vivo, suggesting that they may form part of the baculovirus replisome  .. 
PF05848 Firmicute transcriptional repressor of class III stress genes (CtsR)<br>Pfam-B_9312 (release 8.0). This family consists of several Firmicute transcriptional repressor of class III stress genes (CtsR) proteins. CtsR of L. monocytogenes negatively regulates the clpC, clpP and clpE genes belonging to the CtsR regulon  .. 
PF05849 Fibroin light chain (L-fibroin)<br>Pfam-B_9321 (release 8.0). This family consists of several moth fibroin light chain (L-fibroin) proteins. Fibroin of the silkworm, Bombyx mori, is secreted into the lumen of posterior silk gland (PSG) from the surrounding PSG cells as a molecular complex consisting of a heavy (H)-chain of approximately 350 kDa, a light (L)-chain of 25 kDa and a P25 of about 27 kDa. The H- and L-chains are disulfide-linked but P25 is associated with the H-L complex by non-covalent force  .. 
PF05851 Lentivirus virion infectivity factor (VIF)<br>Pfam-B_9439 (release 8.0). This family consists of several feline specific Lentivirus virion infectivity factor (VIF) proteins. VIF is essential for productive FIV infection of host target cells in vitro  .. 
PF05852 Gammaherpesvirus protein of unknown function (DUF848)<br>Pfam-B_9475 (release 8.0). This family consists of several uncharacterised proteins from the Gammaherpesvirinae.. 
PF05853 Prokaryotic protein of unknown function (DUF849)<br>Pfam-B_9059 (release 8.0). This family consists of several hypothetical prokaryotic proteins with no known function.. 
PF05854 Non-histone chromosomal protein MC1<br>Pfam-B_9146 (release 8.0). This family consists of archaeal chromosomal protein MC1 sequences which protect DNA against thermal denaturation  . . 
PF05856 ARP2/3 complex 20 kDa subunit (ARPC4)<br>Pfam-B_9272 (release 8.0). This family consists of several eukaryotic ARP2/3 complex 20 kDa subunit (P20-ARC) proteins. The Arp2/3 protein complex has been implicated in the control of actin polymerisation in cells. The human complex consists of seven subunits which include the actin related proteins Arp2 and Arp3 it has been suggested that the complex promotes actin assembly in lamellipodia and may participate in lamellipodial protrusion  .. 
PF05857 TraX protein<br>Pfam-B_9375 (release 8.0). This family consists of several bacterial TraX proteins. TraX is responsible for the amino-terminal acetylation of F-pilin subunits [1,2].. 
PF05858 Bovine immunodeficiency virus surface protein (SU)<br>Pfam-B_9413 (release 8.0). The bovine lentivirus also known as the bovine immunodeficiency-like virus (BIV) has conserved and hypervariable regions in the surface envelope gene  . This family corresponds to the SU surface protein.. 
PF05859 Mis12 protein<br>Kinetochores are the chromosomal sites for spindle interaction and play a vital role in chromosome segregation. Fission yeast kinetochore protein Mis12, is required for correct spindle morphogenesis, determining metaphase spindle length  . Thirty-five to sixty percent extension of metaphase spindle length takes place in Mis12 mutants  . It has been shown that Mis12  genetically interacts with Mal2, another inner centromere core  complex protein in S. pombe  .. 
PF05860 haemagglutination activity domain<br>This domain is suggested to be a carbohydrate- dependent haemagglutination activity site ( ). It is found in a range of haemagglutinins and  haemolysins.. 
PF05861 Bacterial phosphonate metabolism protein (PhnI)<br>Pfam-B_9004 (release 8.0). This family consists of several Proteobacterial phosphonate metabolism protein (PhnI) sequences. Bacteria that use phosphonates as a phosphorus source must be able to break the stable carbon-phosphorus bond. In Escherichia coli phosphonates are broken down by a C-P lyase that has a broad substrate specificity. The genes for phosphonate uptake and degradation in E. coli are organised in an operon of 14 genes, named phnC to phnP. Three gene products (PhnC, PhnD and PhnE) comprise a binding protein-dependent phosphonate transporter, which also transports phosphate, phosphite, and certain phosphate esters such as phosphoserine; two gene products (PhnF and PhnO) may have a role in gene regulation; and nine gene products (PhnG, PhnH, PhnI, PhnJ, PhnK, PhnL, PhnM, PhnN, and PhnP) probably comprise a membrane-associated C-P lyase enzyme complex  .. 
PF05862 Helicobacter pylori IceA2 protein<br>Pfam-B_9436 (release 8.0). This family consists of several Helicobacter pylori specific IceA2 proteins. The function of this family is unknown.. 
PF05864 Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7)<br>Pfam-B_9596 (release 8.0). This family consists of several Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide sequences. DNA-dependent RNA polymerase catalyses the transcription of DNA into RNA.. 
PF05865 Cypovirus polyhedrin protein<br>Pfam-B_9652 (release 8.0). This family consists of several Cypovirus polyhedrin protein. Polyhedrin is known to form a crystalline matrix (polyhedra) in infected insect cells  .. 
PF05866 Endodeoxyribonuclease RusA<br>Pfam-B_8996 (release 8.0). This family consists of several bacterial and phage Holliday junction resolvase (RusA) like proteins. The RusA protein of Escherichia coli is an endonuclease that can resolve Holliday intermediates and correct the defects in genetic recombination and DNA repair associated with inactivation of RuvAB or RuvC [1,2].. 
PF05867 Protein of unknown function (DUF851)<br>Pfam-B_9669 (release 8.0), Jackhmmer:Q9N4S5. 
PF05868 Rotavirus major outer capsid protein VP7<br>Pfam-B_9690 (release 8.0). This family consists of several Rotavirus major outer capsid protein VP7 sequences. The rotavirus capsid is composed of three concentric protein layers. Proteins VP4 and VP7 comprise the outer layer. VP4 forms spikes and is the viral attachment protein. VP7 is a glycoprotein and the major constituent of the outer protein layer  .. 
PF05869 DNA N-6-adenine-methyltransferase (Dam)<br>Pfam-B_9691 (release 8.0). This family consists of several bacterial and phage DNA N-6-adenine-methyltransferase (Dam) like sequences  .. 
PF05870 Phenolic acid decarboxylase (PAD)<br>Pfam-B_9737 (release 8.0). This family consists of several bacterial phenolic acid decarboxylase proteins. Phenolic acids, also called substituted cinnamic acids, are important lignin-related aromatic acids and natural constituents of plant cell walls. These acids (particularly ferulic, p-coumaric, and caffeic acids) bind the complex lignin polymer to the hemicellulose and cellulose in plants. The Phenolic acid decarboxylase (PAD) gene (pad) is transcriptionally regulated by p-coumaric, ferulic, or caffeic acid; these three acids are the three substrates of PAD  .. 
PF05871 DUF852; <br>ESCRT-II complex subunit. Moxon SJ, Wood V, Mistry J. Pfam-B_9765 (release 8.0). This family of conserved eukaryotic proteins are subunits of the endosome associated complex ESCRT-II which recruits transport machinery for protein sorting at the multivesicular body (MVB)  .  This protein complex transiently associates with the endosomal membrane and thereby initiates the formation of ESCRT-III, a membrane-associated protein complex that functions immediately downstream of ESCRT-II during sorting of MVB cargo. ESCRT-II in turn functions downstream of ESCRT-I, a protein complex that binds to ubiquitinated endosomal cargo  .. 
PF05872 Bacterial protein of unknown function (DUF853)<br>Pfam-B_9798 (release 8.0). This family consists of several bacterial proteins of unknown function. Swiss:Q8YFZ2 is thought to be an ATPase.. 
PF05873 ATP synthase D chain, mitochondrial (ATP5H)<br>Pfam-B_9814 (release 8.0). This family consists of several ATP synthase D chain, mitochondrial (ATP5H) proteins. Subunit d has no extensive hydrophobic sequences, and is not apparently related to any subunit described in the simpler ATP synthases in bacteria and chloroplasts [1,2]. . 
PF05874 Pheromone biosynthesis activating neuropeptide (PBAN)<br>Pfam-B_9874 (release 8.0). This family consists of several moth pheromone biosynthesis activating neuropeptide (PBAN) sequences. Female moths produce and release species specific sex pheromones to attract males for mating. Pheromone biosynthesis is hormonally regulated by the Pheromone Biosynthesis Activating Neuropeptide (PBAN) which is biosynthesised in the subesophageal ganglion (SOG)  .  . 
PF05875 aPHC;<br>Pfam-B_9877 (release 8.0). This family consists of several ceramidases. Ceramidases are enzymes involved in regulating cellular levels of ceramides, sphingoid bases, and their phosphates, EC:3.5.1.23.. 
PF05876 Phage terminase large subunit (GpA)<br>Pfam-B_9892 (release 8.0). This family consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities  . . 
PF05878 Phytoreovirus nonstructural protein Pns9/Pns10<br>Pfam-B_9947 (release 8.0). This family consists of the Phytoreovirus nonstructural proteins Pns9 and Pns10. The function of this family is unknown.. 
PF05879 Root hair defective 3 GTP-binding protein (RHD3)<br>Pfam-B_9973 (release 8.0). This family consists of several eukaryotic root hair defective 3 like GTP-binding proteins. It has been speculated that the RHD3 protein is a member of a novel class of GTP-binding proteins that is widespread in eukaryotes and required for regulated cell enlargement  . The family also contains the homologous yeast synthetic enhancement of YOP1 (SEY1) protein which is involved in membrane trafficking  .. 
PF05880 Fijivirus 64 kDa capsid protein<br>Pfam-B_9976 (release 8.0). This family consists of several Fijivirus 64 kDa capsid proteins.. 
PF05881 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP or CNPase)<br>Moxon SJ, Mazumder R. Pfam-B_9997 (release 8.0). This family consists of the eukaryotic protein 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP). 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP) is one of the earliest myelin-related proteins expressed in differentiating oligodendrocytes and Schwann cells. CNP is abundant in the central nervous system and in oligodendrocytes. This protein is also found in mammalian photoreceptor cells, testis and lymphocytes. Although the biological function of CNP is unknown, it is thought to play a significant role in the formation of the myelin sheath, where it comprises 4% of total protein. CNP selectively cleaves 2',3'-cyclic nucleotides to produce 2'-nucleotides in vitro. Although physiologically relevant substrates with 2',3'-cyclic termini are still unknown, numerous cyclic phosphate containing RNAs occur transiently within eukaryotic cells. Other known protein families capable of hydrolysing 2',3'-cyclic nucleotides include tRNA ligases and plant cyclic phosphodiesterases. The catalytic domains from all these proteins contain two tetra-peptide motifs H-X-T/S-X, where X is usually a hydrophobic residue. Mutation of either histidine in CNP abolishes enzymatic activity  . CNPases belong to the 2H phosphoesterase superfamily. They share a common active site, characterised by two conserved histidines, with the bacterial tRNA-ligating enzyme LigT, vertebrate myelin-associated 2',3' phosphodiesterases, plant Arabidopsis thaliana CPDases and several several bacteria and virus proteins  .. 
PF05883 DUF855; <br>Baculovirus U-box/Ring-like domain. Pfam-B_9633 (release 8.0). This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.. 
PF05884 DUF856;<br>Interactor of ZYG-11. Pfam-B_9445 (release 8.0). This family of proteins represents the protein product of the gene W03D8.9 which has been identified as an interactor of ZYG-11.  ZYG-11 is the substrate-recognition subunit for a CUL-2 based complex that regulates cell division and embryonic development  .. 
PF05886 Orthopoxvirus F8 protein<br>Pfam-B_9539 (release 8.0). This family consists of several Orthopoxvirus F8 proteins. The function of this family is unknown.. 
PF05887 Trypano_PARP; <br>Procyclic acidic repetitive protein (PARP). Pfam-B_9554 (release 8.0). This family consists of several Trypanosoma brucei procyclic acidic repetitive protein (PARP) like sequences. The procyclic acidic repetitive protein (parp) genes of Trypanosoma brucei encode a small family of abundant surface proteins whose expression is restricted to the procyclic form of the parasite. They are found at two unlinked loci, parpA and parpB; transcription of both loci is developmentally regulated  .  . 
PF05889 Soluble liver antigen/liver pancreas antigen (SLA/LP autoantigen)<br>Pfam-B_9614 (release 8.0). This family consists of several eukaryotic and archaeal proteins which are related to the human soluble liver antigen/liver pancreas antigen (SLA/LP autoantigen). Autoantibodies are a hallmark of autoimmune hepatitis, but most are not disease specific. Autoantibodies to soluble liver antigen (SLA) and to liver and pancreas antigen (LP) have been described as disease specific, occurring in about 30% of all patients with autoimmune hepatitis  . The function of SLA/LP is unknown, however, it has been suggested that the protein may function as a serine hydroxymethyltransferase and may be an important enzyme in the thus far poorly understood selenocysteine pathway  . The archaeal sequences Swiss:Q8TXK0 and Swiss:Q8TYR3 are annotated as being pyridoxal phosphate-dependent enzymes.. 
PF05890 Eukaryotic rRNA processing protein EBP2<br>Moxon SJ, Mistry J, Wood V. Pfam-B_9615 (release 8.0). This family consists of several Eukaryotic rRNA processing protein EBP2 sequences.  Ebp2p is required for the maturation of 25S rRNA and 60S subunit assembly. Ebp2p may be one of the target proteins of Rrs1p for executing the signal to regulate ribosome biogenesis  .  This family also plays a role in chromosome segregation  .. 
PF05891 DUF858; Hydroxy-O-Methy;<br>AdoMet dependent proline di-methyltransferase. Pfam-B_9735 (release 8.0). This protein is expressed in the tail neuron PVT and in uterine cells in C. elegans [worm-base]. In Saccharomyces cerevisiae this is AdoMet dependent proline di-methyltransferase. This enzyme catalyses the di-methylation of ribosomal proteins Rpl12 and Rps25 at N-terminal proline residues. The methyltransferases described here specifically recognise the N-terminal X-Pro-Lys sequence motif, and they may account for nearly all previously described eukaryotic protein N-terminal methylation reactions. A number of other yeast and human proteins also share the recognition motif and may be similarly modified  . As with other methyltransferases, this family carries the characteristic GxGxG motif.. 
PF05892 Trichovirus coat protein<br>Pfam-B_9763 (release 8.0). This family consists of several coat proteins which are specific to the ssRNA positive-strand, no DNA stage viruses such as the Trichovirus and Vitivirus.. 
PF05893 Acyl-CoA reductase (LuxC)<br>Pfam-B_9766 (release 8.0). This family consists of several bacterial Acyl-CoA reductase (LuxC) proteins. The channelling of fatty acids into the fatty aldehyde substrate for the bacterial bioluminescence reaction is catalysed by a fatty acid reductase multienzyme complex, which channels fatty acids through the thioesterase (LuxD), synthetase (LuxE) and reductase (LuxC) components  .. 
PF05894 Podovirus DNA encapsidation protein (Gp16)<br>Pfam-B_9825 (release 8.0). This family consists of several DNA encapsidation protein (Gp16) sequences from the phi-29-like viruses. Gene product 16 catalyses the in vivo and in vitro genome-encapsidation reaction  . . 
PF05895 Siphovirus protein of unknown function (DUF859)<br>Pfam-B_9891 (release 8.0). This family consists of several uncharacterised proteins from the Siphoviruses as well as one bacterial sequence Swiss:Q8K6J6. Some of the members of this family are described as putative minor structural proteins.. 
PF05896 Na(+)-translocating NADH-quinone reductase subunit A (NQRA)<br>Pfam-B_3622 (release 8.0). This family consists of several bacterial Na(+)-translocating NADH-quinone reductase subunit A (NQRA) proteins. The Na(+)-translocating NADH: ubiquinone oxidoreductase (Na(+)-NQR) generates an electrochemical Na(+) potential driven by aerobic respiration  .. 
PF05899 DUF861; <br>Protein of unknown function (DUF861). Pfam-B_2000 (release 8.0). This family consists of several proteins which seem to be specific to plants and bacteria. The function of this family is unknown.. 
PF05901 Excalibur calcium-binding domain<br>Extracellular Ca2+-dependent nuclease YokF from Bacillus subtilis and several other surface-exposed proteins from diverse bacteria are encoded in the genomes in two paralogous forms that differ by a ~45 amino acid fragment, which comprises a novel conserved domain. Sequence analysis of this domain revealed a conserved DxDxDGxxCE motif, which is strikingly similar to the Ca2+-binding loop of the calmodulin-like EF-hand domains, suggesting an evolutionary relationship between them. Functions of many of the other proteins in which the novel domain, named Excalibur (extracellular calcium-binding region), is found, as well as a structural model of its conserved motif are consistent with the notion that the Excalibur domain binds calcium. This domain is but one more example of the diversity of structural contexts surrounding the EF-hand-like calcium-binding loop in bacteria. This loop is thus more widespread than hitherto recognised and the evolution of EF-hand-like domains is probably more complex than previously appreciated  .. 
PF05902 4.1 protein C-terminal domain (CTD)<br>At the C-terminus of all known 4.1 proteins is a sequence domain unique to these proteins, known as the C-terminal domain (CTD). Mammalian CTDs are associated with a growing number of protein-protein interactions, although  such activities have yet to be associated with invertebrate CTDs. Mammalian CTDs are generally defined by sequence alignment as encoded by exons 18-21. Comparison of known vertebrate 4.1 proteins with invertebrate 4.1 proteins indicates that mammalian 4.1 exon 19 represents a vertebrate adaptation that extends the sequence of the CTD with a Ser/Thr-rich sequence. The CTD was first described as a 22/24-kDa domain by chymotryptic digestion of erythrocyte 4.1 (4.1R). CTD is thought to represent an independent folding structure which has gained function since the divergence of vertebrates from invertebrates  . . 
PF05903 DUF862;<br>PPPDE putative peptidase domain. The PPPDE superfamily (after Permuted Papain fold Peptidases of DsRNA viruses and Eukaryotes), consists of predicted thiol peptidases with a circularly permuted papain-like fold. The inference of the likely DUB function of the PPPDE superfamily proteins is based on the fusions of the catalytic domain to Ub-binding PUG (PUB)/UBA domains and a novel alpha-helical Ub-associated domain (the PUL domain, after PLAP, Ufd3p and Lub1p)  .. 
PF05904 Plant protein of unknown function (DUF863)<br>Pfam-B_7732 (release 8.0). This family consists of a number of hypothetical proteins from Arabidopsis thaliana and Oryza sativa. The function of this family is unknown.. 
PF05906 Herpesvirus-7 repeat of unknown function (DUF865)<br>Pfam-B_9911 (release 8.0). This family consists of a series of 12 repeats of 35 amino acids in length which are found exclusively in Herpesvirus-7. The function of this family is unknown.. 
PF05907 Eukaryotic protein of unknown function (DUF866)<br>Pfam-B_8299 (release 8.0). This family consists of a number of hypothetical eukaryotic proteins of unknown function with an average length of around 165 residues.. 
PF05908 Protein of unknown function (DUF867)<br>Pfam-B_7778 (release 8.0). This family consists of a number of bacterial and phage proteins with no known function and is present in Bacillus species and the Lambda-like viruses.. 
PF05910 Plant protein of unknown function (DUF868)<br>Pfam-B_8013 (release 8.0). This family consists of several hypothetical proteins from Arabidopsis thaliana and Oryza sativa. The function of this family is unknown.. 
PF05911 Plant protein of unknown function (DUF869)<br>Pfam-B_8094 (release 8.0). This family consists of a number of sequences found in Arabidopsis thaliana, Oryza sativa and Lycopersicon esculentum (Tomato). The function of this family is unknown.  . 
PF05912 Caenorhabditis elegans protein of unknown function (DUF870)<br>Pfam-B_8400 (release 8.0). This family consists of a number of hypothetical proteins which seem to be specific to Caenorhabditis elegans. The function of this family is unknown.. 
PF05913 Bacterial protein of unknown function (DUF871)<br>Pfam-B_8510 (release 8.0). This family consists of several conserved hypothetical proteins from bacteria and archaea. The function of this family is unknown.. 
PF05914 RIB43A<br>Pfam-B_8571 (release 8.0). This family consists of several RIB43A-like eukaryotic proteins. Ciliary and flagellar microtubules contain a specialised set of protofilaments, termed ribbons, that are composed of tubulin and several associated proteins. RIB43A was first characterised in the unicellular biflagellate, Chlamydomonas reinhardtii although highly related sequences are present in several higher eukaryotes including humans. The function of this protein is unknown although the structure of RIB43A and its association with the specialised protofilament ribbons and with basal bodies is relevant to the proposed role of ribbons in forming and stabilising doublet and triplet microtubules and in organising their three-dimensional structure. Human RIB43A homologues could represent a structural requirement in centriole replication in dividing cells  .. 
PF05915 Eukaryotic protein of unknown function (DUF872)<br>Pfam-B_8741 (release 8.0). This family consists of several uncharacterised eukaryotic proteins. The function of this family is unknown.. 
PF05916 DUF873; <br>GINS complex protein. Pfam-B_8759 (release 8.0). The eukaryotic GINS complex is essential for the initiation and elongation phases of DNA replication [1-3].  It consists of four paralogous protein subunits (Sld5, Psf1, Psf2 and Psf3), all of which are included in this family.  The GINS complex is conserved from yeast to humans, and has been shown in human to bind directly to DNA primase  .. 
PF05917 Helicobacter pylori protein of unknown function (DUF874)<br>Pfam-B_8835 (release 8.0). This family consists of several hypothetical proteins specific to Helicobacter pylori. The function of this family is unknown.. 
PF05918 Apoptosis inhibitory protein 5 (API5)<br>Pfam-B_8916 (release 8.0). This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterised by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in human chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors [1,2].. 
PF05919 Mitovirus RNA-dependent RNA polymerase<br>Pfam-B_9906 (release 8.0). This family consists of several Mitovirus RNA-dependent RNA polymerase proteins. The family also contains fragment matches in the mitochondria of Arabidopsis thaliana.. 
PF05920 Coprinus_mating;<br>Pfam-B_4610 (release 8.0). This is a homeobox transcription factor KN domain conserved from fungi to human and plants.. 
PF05922 Subtilisin_N; <br>Peptidase inhibitor I9. Pfam-B_52 (release 8.0). This family includes the proteinase B inhibitor from Saccharomyces cerevisiae and the activation peptides from peptidases of the subtilisin family.  The subtilisin propeptides are known to function as molecular chaperones, assisting in the folding of the mature peptidase  , but have also been shown to act as 'temporary inhibitors'  .. 
PF05923 APC cysteine-rich region<br>This short region is found repeated in the mid region of the adenomatous polyposis  proteins (APCs). In the human protein many cancer-linked SNPs are found near the first three occurrences of the motif. These repeats bind beta-catenin  .. 
PF05924 SAMP Motif<br>This short region is found repeated in the mid region of the adenomatous polyposis proteins (APCs). This motif binds axin  .. 
PF05925 Enterobacterial virulence protein IpgD<br>Pfam-B_1987 (release 9.0). This family consists of several enterobacterial IpgD like virulence factor proteins. In the Gram-negative pathogen Shigella flexneri, the virulence factor IpgD is translocated directly into eukaryotic cells and acts as a potent inositol 4-phosphatase that specifically dephosphorylates phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P(2)] into phosphatidylinositol 5-monophosphate [PtdIns(5)P] that then accumulates. Transformation of PtdIns(4,5)P(2) into PtdIns(5)P by IpgD is responsible for dramatic morphological changes of the host cell, leading to a decrease in membrane tether force associated with membrane blebbing and actin filament remodelling  .. 
PF05926 Phage head completion protein (GPL)<br>Pfam-B_1860 (release 9.0). This family consists of several phage head completion protein (GPL) as well as related bacterial sequences. Members of this family allow the completion of filled heads by rendering newly packaged DNA in the heads resistant to DNase. The protein is thought to bind to DNA filled capsids  .. 
PF05927 Penaeidin<br>Pfam-B_2675 (release 9.0). This family consists of several isoforms of the penaeidin protein which is specific to shrimps. Penaeidins, a unique family of antimicrobial peptides (AMPs) with both proline and cysteine-rich domains, were initially identified in the hemolymph of the Pacific white shrimp, Litopenaeus vannamei  .  . 
PF05928 Zea mays MURB-like protein (MuDR)<br>Pfam-B_3145 (release 9.0). This family consists of several Zea mays specific MURB-like proteins. The transposition of Mu elements underlying Mutator activity in maize requires a transcriptionally active MuDR element. Despite variation in MuDR copy number and RNA levels in Mutator lines, transposition events are consistently late in plant development, and Mu excision frequencies are similar  .. 
PF05929 Phage capsid scaffolding protein (GPO) serine peptidase<br>Pfam-B_1730 (release 9.0). This family consists of several bacteriophage capsid scaffolding proteins (GPO) and some related bacterial sequences. GPO is thought to function in both the assembly of proheads and the cleavage of GPN  . The family is found to function as a serine peptidase, with a conserved Asp, His and Ser catalytic triad, as in subtilisin, and as represented in MEROPS:S73. The family includes SwissProt:P25478 from Enterobacteria phage P2 which cleaves itself and then becomes the scaffold protein upon which the bacteriophage prohead is built - a mechanism quite common amongst phages  .. 
PF05930 AlpA; <br>Prophage CP4-57 regulatory protein (AlpA). Pfam-B_2048 (release 9.0). This family consists of several short bacterial and phage proteins which are related to the E. coli protein AlpA. AlpA suppress two phenotypes of a delta lon protease mutant, overproduction of capsular polysaccharide and sensitivity to UV light  . Several of the sequences in this family are thought to be DNA-binding proteins.. 
PF05931 Staphylococcal AgrD protein<br>Pfam-B_2868 (release 9.0). This family consists of several AgrD proteins from many Staphylococcus species. The agr locus was initially described in Staphylococcus aureus as an element controlling the production of exoproteins implicated in virulence. Its pattern of action has been shown to be complex, upregulating certain extracellular toxins and enzymes expressed post-exponentially and repressing some exponential-phase surface components. AgrD encodes the precursor of the autoinducing peptide (AIP).The AIP derived from AgrD by the action of AgrB interacts with AgrC in the membrane to activate AgrA, which upregulates transcription both from promoter P2, amplifying the response, and from P3, initiating the production of a novel effector: RNAIII. In S. aureus, delta-hemolysin is the only translation product of RNA III and is not involved in the regulatory functions of the transcript, which is therefore the primary agent for modulating the expression of other operons controlled by agr  .. 
PF05932 Tir chaperone protein (CesT) family<br>Pfam-B_2921 (release 9.0). This family consists of a number of bacterial sequences which are highly similar to the Tir chaperone protein in E. Coli. In many Gram-negative bacteria, a key indicator of pathogenic potential is the possession of a specialised type III secretion system, which is utilised to deliver virulence effector proteins directly into the host cell cytosol. Many of the proteins secreted from such systems require small cytosolic chaperones to maintain the secreted substrates in a secretion-competent state. CesT serves a chaperone function for the enteropathogenic Escherichia coli (EPEC) translocated intimin receptor (Tir) protein, which confers upon EPEC the ability to alter host cell morphology following intimate bacterial attachment  .\.     This family also contains several DspF and related sequences from several plant pathogenic bacteria. The "disease-specific" (dsp) region next to the hrp gene cluster of Erwinia amylovora is required for pathogenicity but not for elicitation of the hypersensitive reaction. DspF and AvrF are small (16 kDa and 14 kDa) and acidic with predicted amphipathic alpha helices in their C termini; they resemble chaperones for virulence factors secreted by type III secretion systems of animal pathogens  .. 
PF05933 Fungal ATP synthase protein 8 (A6L)<br>Pfam-B_2993 (release 9.0). This family consists of fungus specific ATP synthase protein 8 (EC:3.6.3.14). The family may be related to the ATP synthase protein 8 found in other eukaryotes Pfam:PF00895.. 
PF05934 Mid-1-related chloride channel (MCLC)<br>Pfam-B_2711 (release 9.0). This family consists of several mid-1-related chloride channels. mid-1-related chloride channel (MCLC) proteins function as a chloride channel when incorporated in the planar lipid bilayer  .. 
PF05935 Arylsulfotransferase (ASST)<br>Pfam-B_3266 (release 9.0). This family consists of several bacterial Arylsulfotransferase proteins. Arylsulfotransferase (ASST) transfers a sulfate group from phenolic sulfate esters to a phenolic acceptor substrate  . . 
PF05936 Bacterial protein of unknown function (DUF876)<br>Pfam-B_3279 (release 9.0). This family consists of a series of hypothetical bacterial sequences of unknown function.. 
PF05937 EB-1 Binding Domain<br>This region at the C-terminus of the APC proteins binds the microtubule-associating protein EB-1  . At the C-terminus of the alignment is also a Pfam:PF00595 binding domain. A short motif in the middle of the region appears to be found in the APC2  proteins (e.g Swiss:O95996).. 
PF05938 Plant self-incompatibility protein S1<br>Pfam-B_3292 (release 9.0). This family consists of a series of plant proteins which are related to the Papaver rhoeas S1 self-incompatibility protein. Self incompatibility (SI) is the single most important outbreeding device found in angiosperms and is a mechanism that regulates the acceptance or rejection of pollen. S1 is known to exhibit specific pollen-inhibitory properties  .. 
PF05939 Phage minor tail protein<br>Pfam-B_3296 (release 9.0). This family consists of a series of phage minor tail proteins and related sequences from several bacterial species.. 
PF05940 NnrS protein<br>Pfam-B_3395 (release 9.0). This family consists of several bacterial NnrS like proteins. NnrS is a putative heme-Cu protein (NnrS) and a member of the short-chain dehydrogenase family  . Expression of nnrS is dependent on the transcriptional regulator NnrR, which also regulates expression of genes required for the reduction of nitrite to nitrous oxide, including nirK and nor. NnrS is a haem- and copper-containing membrane protein. Genes encoding putative orthologues of NnrS are sometimes but not always found in bacteria encoding nitrite and/or nitric oxide reductase  .. 
PF05941 Chordopoxvirus A20R protein<br>Pfam-B_3744 (release 9.0). This family consists of several Chordopoxvirus A20R proteins. The A20R protein is required for DNA replication, is associated with the processive form of the viral DNA polymerase, and directly interacts with the viral proteins encoded by the D4R, D5R, and H5R open reading frames. A20R may contribute to the assembly or stability of the multiprotein DNA replication complex  .. 
PF05942 Archaeal PaREP1/PaREP8 family<br>Pfam-B_2248 (release 9.0) & Pfam-B_9342 (release 9.0). This family consists of several archaeal PaREP1 and PaREP8 proteins the function of this family is unknown.. 
PF05943 Protein of unknown function (DUF877)<br>Pfam-B_2566 (release 9.0). This family consists of a number of uncharacterised bacterial proteins. The function of this family is unknown.. 
PF05944 Phage small terminase subunit<br>Pfam-B_2645 (release 9.0). This family consists of several phage small terminase subunit proteins as well as some related bacterial sequences  .. 
PF05946 Toxin-coregulated pilus subunit TcpA<br>Pfam-B_3639 (release 9.0). This family consists of toxin-coregulated pilus subunit (TcpA) proteins from Vibrio cholerae and related sequences. The major virulence factors of toxigenic Vibrio cholerae are cholera toxin (CT), which is encoded by a lysogenic bacteriophage (CTXPhi), and toxin-coregulated pilus (TCP), an essential colonisation factor which is also the receptor for CTXPhi. The genes for the biosynthesis of TCP are part of a larger genetic element known as the TCP pathogenicity island  .. 
PF05947 Bacterial protein of unknown function (DUF879)<br>Pfam-B_3751 (release 9.0). This family consists of several hypothetical bacterial proteins of unknown function.. 
PF05949 Bacterial protein of unknown function (DUF881)<br>Pfam-B_4053 (release 9.0). This family consists of a series of hypothetical bacterial proteins. One of the family members Swiss:Q45543 from Bacillus subtilis is thought to be involved in cell division and sporulation  .. 
PF05950 Orthopoxvirus A36R protein<br>Pfam-B_4070 (release 9.0). This family consists of several Orthopoxvirus A36R proteins. The A36R protein is predicted to be a type Ib membrane protein  .. 
PF05951 DUF882; <br>Bacterial protein of unknown function (DUF882). Pfam-B_4115 (release 9.0). This family consists of a series of hypothetical bacterial proteins of unknown function.. 
PF05952 Bacillus competence pheromone ComX<br>Pfam-B_4222 (release 9.0). Natural genetic competence in Bacillus subtilis is controlled by quorum-sensing (QS). The ComP- ComA two-component system detects the signalling molecule ComX, and this signal is transduced by a conserved phosphotransfer mechanism. ComX is synthesised as an inactive precursor and is then cleaved and modified by ComQ before export to the extracellular environment  .. 
PF05953 Allatostatin<br>Pfam-B_4313 (release 9.0). This family consists of allatostatins, bombystatins, helicostatins, cydiastatins and schistostatin from several insect species. Allatostatins (ASTs) of the Tyr/Phe-Xaa-Phe-Gly Leu/Ile-NH2 family are a group of insect neuropeptides that inhibit juvenile hormone biosynthesis by the corpora allata  .. 
PF05954 Phage late control gene D protein (GPD)<br>Pfam-B_4333 (release 9.0) & Pfam-B_12199 (release 10.0). This family includes a number of phage late control gene D proteins and related bacterial sequences.  This family also includes Bacteriophage Mu P proteins and related sequences.. 
PF05955 Eq_herpes_Gp2; <br>Equine herpesvirus glycoprotein gp2. Pfam-B_4360 (release 9.0). This family consists of a number of glycoprotein gp2 sequences from equine herpesviruses.. 
PF05956 APC basic domain<br>This region of the APC family of proteins is known as the basic domain. It contains a high proportion of positively charged  amino acids and interacts with microtubules  .. 
PF05957 Bacterial protein of unknown function (DUF883)<br>Pfam-B_4421 (release 9.0). This family consists of several hypothetical bacterial proteins of unknown function.. 
PF05958 tRNA (Uracil-5-)-methyltransferase<br>Pfam-B_4661 (release 9.0). This family consists of (Uracil-5-)-methyltransferases EC:2.1.1.35 from bacteria, archaea and eukaryotes. A 5-methyluridine (m(5)U) residue at position 54 is a conserved feature of bacterial and eukaryotic tRNAs. The methylation of U54 is catalysed by the tRNA(m5U54)methyltransferase, which in Saccharomyces cerevisiae is encoded by the nonessential TRM2 gene. It is thought that tRNA modification enzymes might have a role in tRNA maturation not necessarily linked to their known catalytic activity  .. 
PF05959 Nucleopolyhedrovirus protein of unknown function (DUF884)<br>Pfam-B_4679 (release 9.0). This family consists of several hypothetical Nucleopolyhedrovirus proteins of unknown function.. 
PF05960 Bacterial protein of unknown function (DUF885)<br>Pfam-B_4405 (release 9.0). This family consists of several hypothetical bacterial proteins several of which are putative membrane proteins.. 
PF05961 Chordopoxvirus A13L protein<br>Pfam-B_5061 (release 9.0). This family consists of A13L proteins from the Chordopoxviruses. A13L or p8 is one of the three most abundant membrane proteins of the intracellular mature Vaccinia virus  .. 
PF05962 DUF886;<br>Pfam-B_5160 (release 9.0). HutD from Pseudomonas fluorescens SBW25 is a component of the histidine uptake and utilisation operon. HutD is operonic with the well characterised repressor protein HutC. Genetic analysis using transcriptional fusions (lacZ) and deletion mutants shows that hutD is necessary to maintain fitness in environments replete with histidine. Evidence outlined by Zhang & Rainey (2007) suggests that HutD functions as a governor that sets an upper bound on the level of hut operon transcription  . The mechanistic basis is unknown, but in silico molecular docking studies based on the crystal structure of PA5104 (HutD from Pseudomonas aeruginosa) show that urocanate (the first breakdown product of histidine) docks with the active site of HutD.. 
PF05963 Cytomegalo_US3; <br>Cytomegalovirus US3 protein. Pfam-B_7187 (release 9.0). US3 of human cytomegalovirus is an endoplasmic reticulum resident transmembrane glycoprotein that binds to major histocompatibility complex class I molecules and prevents their departure. The endoplasmic reticulum retention signal of the US3 protein is contained in the luminal domain of the protein  .. 
PF05964 F/Y-rich N-terminus<br>Pfam-B_1170 (release 8.0). This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00541.. 
PF05965 F/Y rich C-terminus<br>Pfam-B_1170 (release 8.0). This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00542.. 
PF05966 Chordopoxvirus A33R protein<br>Pfam-B_4799 (release 9.0). This family consists of several Chordopoxvirus A33R proteins. A33R plays a role in promoting Ab-resistant cell-to-cell spread of virus   and interacts with A36R to incorporate the protein into the outer membrane of intracellular enveloped virions (IEV)  .. 
PF05968 Bacillus PapR protein<br>Pfam-B_4892 (release 9.0). This family consists of the Bacillus species specific PapR protein. The papR gene belongs to the PlcR regulon and is located 70 bp downstream from plcR. It encodes a 48-amino-acid peptide. Disruption of the papR gene abolishes expression of the PlcR regulon, resulting in a large decrease in haemolysis and virulence in insect larvae. A processed form of PapR activates the PlcR regulon by allowing PlcR to bind to its DNA target. This activating mechanism is strain specific  .. 
PF05969 DUF888;<br>Photosystem II complex subunit Ycf12. Pfam-B_4945 (release 9.0). Ycf12 has been identified as a core subunit in the photosystem II (PSII) complex [1-2].  PsbZ has been shown to be required for the association of PsbK and Ycf12 with PSII  .. 
PF05970 DUF889;<br>Pfam-B_4988 (release 9.0). This family includes homologues of the PIF1 helicase, which inhibits telomerase activity and is cell cycle regulated   . This family includes a large number of largely uncharacterised plant proteins.  This family includes a P-loop motif that is involved in nucleotide binding.. 
PF05971 DUF890; <br>Protein of unknown function (DUF890). Pfam-B_5064 (release 9.0). This family consists of several conserved hypothetical proteins from both eukaryotes and prokaryotes. The function of this family is unknown.. 
PF05972 APC 15 residue motif<br>This motif, known as the 15 aa repeat, is found in the APC protein family. They are involved in binding beta-catenin   along with the Pfam:PF05923 repeats. Many human cancer mutations map to the region around these motifs, and may be involved in disrupting their binding of beta-catenin.. 
PF05973 DUF891; <br>Phage derived protein Gp49-like (DUF891). Pfam-B_5075 (release 9.0) & Pfam-B_6067 (release 14.0). This family consists of hypothetical bacterial proteins of unknown function as well as phage Gp49 proteins.. 
PF05974 Domain of unknown function (DUF892)<br>Pfam-B_5115 (release 9.0). This family consists of several hypothetical bacterial proteins of unknown function.. 
PF05975 Bacterial ABC transporter protein EcsB<br>Pfam-B_4764 (release 9.0). This family consists of several bacterial ABC transporter proteins which are homologous to the EcsB protein of Bacillus subtilis. EcsB is thought to encode a hydrophobic protein with six membrane-spanning helices in a pattern found in other hydrophobic components of ABC transporters  .. 
PF05977 DUF894;<br>Transmembrane secretion effector. Moxon SJ, Eberhardt R. Pfam-B_4880 (release 9.0). This is a family of transport proteins. Members of this family include a protein responsible for the secretion of the ferric chelator, enterobactin  , and a protein involved in antibiotic resistance  .. 
PF05978 DUF895; UNC-93_Ce; <br>Ion channel regulatory protein UNC-93. Moxon SJ, Pollington J. Pfam-B_4965 (release 9.0). This family of proteins is a component of a multi-subunit protein complex which is involved in the coordination of muscle contraction. UNC-93 is most likely an ion channel regulatory protein  .. 
PF05979 Bacterial protein of unknown function (DUF896)<br>Pfam-B_5209 (release 9.0). In B. subtilis, one small SOS response operon under the control of LexA, the yneA operon, is comprised of three genes: yneA, yneB, and ynzC  . This family consists of several short, hypothetical bacterial proteins of unknown function. These proteins are mainly found in gram-positive firmicutes. Structures show that the N-terminus is composed of two alpha helices forming a helix-loop-helix motif. The structure of ynzC from B. subtilis forms a trimeric complex  . Structural modelling suggests this domain may bind nucleic acids  . This family is also known as UPF0291.. 
PF05980 toxin_7;<br>Pfam-B_5254 (release 9.0). This family consists of several short spider neurotoxin proteins including many from the Funnel-web spider.. 
PF05981 CreA protein<br>Pfam-B_5258 (release 9.0). This family consists of several bacterial CreA proteins, the function of which is unknown.. 
PF05982 Domain of unknown function (DUF897) <br>Pfam-B_8040 (release 9.0). Family of bacterial proteins with unknown function. 
PF05983 MED7; <br>Pfam-B_5278 (release 9.0). This family consists of several eukaryotic proteins which are homologues of the yeast MED7 protein. Activation of gene transcription in metazoans is a multi-step process that is triggered by factors that recognise transcriptional enhancer sites in DNA. These factors work with co-activators such as MED7 to direct transcriptional initiation by the RNA polymerase II apparatus  .. 
PF05984 Cytomegalovirus UL20A protein<br>Pfam-B_5345 (release 9.0). This family consists of several Cytomegalovirus UL20A proteins. UL20A is thought to be a glycoprotein  .. 
PF05985 Ethanolamine ammonia-lyase light chain (EutC)<br>Pfam-B_5363 (release 9.0). This family consists of several bacterial ethanolamine ammonia-lyase light chain (EutC) EC:4.3.1.7 sequences. Ethanolamine ammonia-lyase is a bacterial enzyme that catalyses the adenosylcobalamin-dependent conversion of certain vicinal amino alcohols to oxo compounds and ammonia  .  . 
PF05986 ADAM-TS Spacer 1<br>Pfam-B_1693 (release 8.0). This family represents the Spacer-1 region from the ADAM-TS family of metalloproteinases  .. 
PF05987 Bacterial protein of unknown function (DUF898)<br>Pfam-B_5347 (release 9.0). This family consists of several bacterial proteins of unknown function. Some of the family members are described as putative membrane proteins.. 
PF05988 Bacterial protein of unknown function (DUF899)<br>Pfam-B_5437 (release 9.0). This family consists of several uncharacterised bacterial proteins of unknown function.. 
PF05989 Chordopoxvirus A35R protein<br>Pfam-B_5472 (release 9.0). This family consists of several Chordopoxvirus sequences homologous to the Vaccinia virus A35R protein. The function of this family is unknown.. 
PF05990 Alpha/beta hydrolase of unknown function (DUF900)<br>Pfam-B_5475 (release 9.0). This family consists of several hypothetical proteins of unknown function mostly found in Rhizobium species. Members of this family have an alpha/beta hydrolase fold.. 
PF05991 DUF901;<br>YacP-like NYN domain. Pfam-B_5522 (release 9.0). This family consists of bacterial proteins related to YacP. This family is uncharacterised functionally, but it has been suggested that these proteins are nucleases due to them containing a NYN domain. NYN (for N4BP1, YacP-like Nuclease) domains were discovered by Anantharaman and Aravind  .  Based on gene neighborhoods it was suggested that the bacterial YacP proteins interact with the Ribonuclease III and TrmH methylase in a processome complex that catalyzes the maturation of rRNA and tRNA  .. 
PF05992 SbmA/BacA-like family<br>Pfam-B_8139 (release 9.0). The Rhizobium meliloti bacA gene encodes a function that is essential for  bacterial differentiation into bacteroids within plant cells in the symbiosis between R. meliloti and alfalfa. An Escherichia coli homolog of  BacA, SbmA, is implicated in the uptake of microcins and bleomycin.  This family is likely to be a subfamily of the ABC transporter family.. 
PF05993 Reovirus major virion structural protein Mu-1/Mu-1C (M2)<br>Pfam-B_5584 (release 9.0). This family consists of several Reovirus major virion structural protein Mu-1/Mu-1C (M2) sequences. This family is family is thought to play a role in host cell membrane penetration  .. 
PF05994 Cytoplasmic Fragile-X interacting family<br>Pfam-B_8072 (release 9.0). CYFIP1/2 (Cytoplasmic fragile X mental retardation interacting protein) like proteins for a  highly conserved protein family  .  The function of CYFIPs is unclear, but CYFIP interaction with fragile X mental  retardation interacting protein (FMRP) involves the domain of FMRP  which also mediating homo- and heteromerization  .. 
PF05995 Cysteine dioxygenase type I<br>Pfam-B_8006 (release 9.0). Cysteine dioxygenase type I (EC:1.13.11.20) converts cysteine to cysteinesulphinic acid and is the rate-limiting step in sulphate  production.. 
PF05996 Ferredoxin-dependent bilin reductase<br>Pfam-B_5667 (release 9.0). This family consists of several different but closely related proteins which include phycocyanobilin:ferredoxin oxidoreductase EC:1.3.7.5 (PcyA), 15,16-dihydrobiliverdin:ferredoxin oxidoreductase EC:1.3.7.2 (PebA) and phycoerythrobilin:ferredoxin oxidoreductase EC:1.3.7.3 (PebB). Phytobilins are linear tetrapyrrole precursors of the light-harvesting prosthetic groups of the phytochrome photoreceptors of plants and the phycobiliprotein photosynthetic antennae of cyanobacteria, red algae, and cryptomonads. It is known that that phytobilins are synthesised from heme via the intermediary of biliverdin IX alpha (BV), which is reduced subsequently by ferredoxin-dependent bilin reductases with different double-bond specificities  . . 
PF05997 Nucleolar protein,Nop52<br>Pfam-B_8003 (release 9.0). Nop52 believed to be involved in the generation of 28S rRNA  .. 
PF05999 Herpesvirus U5-like family<br>Pfam-B_8027 (release 9.0). This family of Herpesvirus includes U4, U5 and UL27.. 
PF06001 Domain of Unknown Function (DUF902)<br>Pfam-B_3539 (release 8.0). This domain of unknown function is found in several transcriptional co-activators including the CREB-binding protein, which is an acetyltransferase that acetylates histones, giving a specific tag for transcriptional activation. This short domain is found to the C-terminus of bromodomains. The 40 residue domain contains four conserved cysteines suggesting that it may be stabilised by a zinc ion. In CREB this domain is to the N-terminus of another zinc binding PHD domain.. 
PF06002 Alpha-2,3-sialyltransferase (CST-I)<br>Pfam-B_6887 (release 9.0). This family consists of several alpha-2,3-sialyltransferase (CST-I) proteins largely found in Campylobacter jejuni.. 
PF06003 Survival motor neuron protein (SMN)<br>Pfam-B_7026 (release 9.0). This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs  . . 
PF06004 Bacterial protein of unknown function (DUF903)<br>Pfam-B_7037 (release 9.0). This family consists of several small bacterial proteins several of which are classified as putative lipoproteins. The function of this family is unknown.. 
PF06005 Protein of unknown function (DUF904)<br>Pfam-B_7038 (release 9.0). This family consists of several bacterial and archaeal hypothetical proteins of unknown function.. 
PF06006 Bacterial protein of unknown function (DUF905)<br>Pfam-B_7072 (release 9.0). This family consists of several short hypothetical Enterobacteria proteins of unknown function. Structural analysis of the surface features of the protein YvyC has revealed a single cluster of highly conserved residues on the surface. Additionally, these residues fall into two groups which lie within the two largest of the three cavities identified over the surface. The conclusion from this is that these two cavities with, Leu 58, Glu 75, Ile 82, and Glu 83 and Pro 86, conserved, are likely to be important for the molecular function and reflect the cavities found on the surface of the FlaG proteins in Pfam:PF03646.. 
PF06007 Phosphonate metabolism protein PhnJ<br>Pfam-B_7179 (release 9.0). This family consists of several bacterial phosphonate metabolism (PhnJ) sequences. The exact role that PhnJ plays in phosphonate utilisation is unknown.. 
PF06008 Laminin Domain I<br>Pfam-B_1925 (release 8.0). coiled-coil structure. It has been suggested that the domains I and II from laminin A, B1 and B2 may come together to form a triple helical coiled-coil structure  .. 
PF06009 Laminin Domain II<br>Pfam-B_1925 (release 8.0). It has been suggested that the domains I and II from laminin A, B1 and B2 may come together to form a triple helical coiled-coil structure  .. 
PF06011 DUF907; <br>Transient receptor potential (TRP) ion channel. Moxon SJ, Mistry J, Wood V. Pfam-B_5564 (release 9.0). This family of proteins are transient receptor potential (TRP) ion channels.\. They are essential for cellular viability and are involved in cell growth and cell wall synthesis  .  The genes for these proteins are homologous to polycystic kidney disease related ion channel genes  .. 
PF06012 Domain of Unknown Function (DUF908)<br>Pfam-B_6534 (release 8.0). 
PF06013 DUF909; <br>Proteins of 100 residues with WXG. Pfam-B_7198 (release 9.0). ESAT-6 is a small protein appears to be of fundamental importance in virulence and protective immunity in Mycobacterium tuberculosis. Homologues have been detected in other Gram-positive bacterial species. It may represent a novel secretion system potentially driven by the Pfam:PF01580 domains in the YukA-like proteins  .. 
PF06014 Bacterial protein of unknown function (DUF910)<br>Pfam-B_7253 (release 9.0). This family consists of several short bacterial proteins of unknown function.. 
PF06015 Chordopoxvirus A30L protein<br>Pfam-B_7254 (release 9.0). This family consists of several short Chordopoxvirus proteins which are homologous to the A30L protein of Vaccinia virus. The vaccinia virus A30L protein is required for the association of electron-dense, granular, proteinaceous material with the concave surfaces of crescent membranes, an early step in viral morphogenesis. A30L is known to interact with the G7L protein and it has been shown that the stability of each is dependent on its association with the other  .. 
PF06016 Reovirus core-spike protein lambda-2 (L2)<br>Pfam-B_7350 (release 9.0). This family consists of several Reovirus core-spike protein lambda-2 (L2) sequences. The reovirus L2 genome segment encodes the core spike protein lambda-2, which mediates enzymatic reactions in 5' capping of the viral plus-strand transcripts  .. 
PF06017 M_tail; Myosin_tail_2; <br>Pfam-B_12631 (release 8.0). 
PF06018 CodY GAF-like domain<br>Pfam-B_7573 (release 9.0). This domain is a GAF-like domain found at the N-terminus of several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. Presumably this domain is involved in GTP binding. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions  . The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk  .. 
PF06019 Phage GP30.8 protein<br>Pfam-B_7692 (release 9.0). This family consists of several GP30.8 proteins from the T4-like phages. The function of this family is unknown.. 
PF06020 Drosophila roughex protein<br>Pfam-B_7712 (release 9.0). This family consists of several roughex (RUX) proteins specific to Drosophila species. Roughex can influence the intracellular distribution of cyclin A and is therefore defined as a distinct and specialised cell cycle  inhibitor for cyclin A-dependent kinase activity  . Rux is though to regulate the metaphase to anaphase transition during development  .. 
PF06021 Glycine_acyl_tr;<br>Aralkyl acyl-CoA:amino acid N-acyltransferase. Pfam-B_7828 (release 9.0). This family consists of several mammalian specific aralkyl acyl-CoA:amino acid N-acyltransferase (glycine N-acyltransferase) proteins EC:2.3.1.13.. 
PF06022 Plasmodium variant antigen protein Cir/Yir/Bir<br>Pfam-B_8754 (release 9.0). This family consists of several Cir, Yir and Bir proteins from the Plasmodium species P.chabaudi, P.yoelii and P.berghei.. 
PF06023 Archaeal protein of unknown function (DUF911)<br>Pfam-B_8782 (release 9.0). This family consists of several archaeal proteins of unknown function.. 
PF06024 Nucleopolyhedrovirus protein of unknown function (DUF912)<br>Pfam-B_8809 (release 9.0). This family consists of several Nucleopolyhedrovirus proteins of unknown function.. 
PF06025 Domain of Unknown Function (DUF913)<br>Pfam-B_6534 (release 8.0). Members of this family are found in various ubiquitin protein ligases.. 
PF06026 Ribose 5-phosphate isomerase A (phosphoriboisomerase A)<br>Pfam-B_5144 (release 9.0). This family consists of several ribose 5-phosphate isomerase A or phosphoriboisomerase A (EC:5.3.1.6) from bacteria, eukaryotes and archaea. . 
PF06027 Eukaryotic protein of unknown function (DUF914)<br>Pfam-B_7017 (release 9.0). This family consists of several hypothetical proteins of unknown function. Some of the sequences in this family are annotated as being putative membrane proteins.. 
PF06028 Alpha/beta hydrolase of unknown function (DUF915)<br>Pfam-B_7094 (release 9.0). This family consists of several bacterial proteins of unknown function. Members of this family have an alpha/beta hydrolase fold.. 
PF06029 AlkA N-terminal domain<br>Pfam-B_13157 (release 8.0). 
PF06030 Bacterial protein of unknown function (DUF916)<br>Pfam-B_7106 (release 9.0). This family consists of several hypothetical bacterial proteins of unknown function.. 
PF06031 SERTA motif<br>Pfam-B_7533 (Release 9.0). This family consists of a novel motif designated as SERTA (for SEI-1, RBT1, and TARA), corresponding to the largest conserved region among TRIP-Br proteins  . The function of this motif is uncertain, but the CDK4-interacting segment of p34SEI-1 (amino acid residues 44-161) includes most of the SERTA motif  .. 
PF06032 Protein of unknown function (DUF917)<br>Pfam-B_7195 (release 9.0). This family consists of hypothetical bacterial and archaeal proteins of unknown function.. 
PF06033 Nucleopolyhedrovirus protein of unknown function (DUF918)<br>Pfam-B_7213 (release 9.0). This family consists of several Nucleopolyhedrovirus proteins with no known function.. 
PF06034 Nucleopolyhedrovirus protein of unknown function (DUF919)<br>Pfam-B_7250 (release 9.0). This family consists of several short Nucleopolyhedrovirus proteins of unknown function.. 
PF06035 DUF920; BTLCP;<br>Bacterial transglutaminase-like cysteine proteinase BTLCP. Moxon SJ, Sammut SJ, Eberhardt R. Pfam-B_7277 (release 9.0). Members of this family are predicted to be bacterial transglutaminase-like cysteine proteinases. They contain a conserved Cys-His-Asp catalytic triad. Their structure is predicted to be similar to that of Salmonella typhimurium N-hydroxyarylamine O-acetyltransferase Swiss:Q00267, in Pfam:PF00797, however they lack the sub-domain which is important for arylamine recognition  .. 
PF06037 Bacterial protein of unknown function (DUF922)<br>Pfam-B_7397 (release 9.0). This family consists of several hypothetical bacterial proteins of unknown function.. 
PF06039 Malate:quinone oxidoreductase (Mqo)<br>Pfam-B_7465 (release 9.0). This family consists of several bacterial Malate:quinone oxidoreductase (Mqo) proteins (EC:1.1.99.16). Mqo takes part in the citric acid cycle. It oxidises L-malate to oxaloacetate and donates electrons to ubiquinone-1 and other artificial acceptors or, via the electron transfer chain, to oxygen. NAD is not an acceptor and the natural direct acceptor for the enzyme is most likely a quinone. The enzyme is therefore called malate:quinone oxidoreductase, abbreviated to Mqo. Mqo is a peripheral membrane protein and can be released from the membrane by addition of chelators  .  . 
PF06040 Adenovirus_E3; <br>Adenovirus E3 protein. Pfam-B_7475 (release 9.0). This family consists of several Adenovirus E3 proteins. The E3 protein does not seem to be essential for virus replication in cultured cells suggesting that the protein may function in virus-host interactions  . . 
PF06041 Bacterial protein of unknown function (DUF924)<br>Pfam-B_7600 (release 9.0). This family consists of several hypothetical bacterial proteins of unknown function.. 
PF06042 Bacterial protein of unknown function (DUF925)<br>Pfam-B_7663 (release 9.0). This family consists of several hypothetical bacterial proteins of unknown function. This family was recently identified as belonging to the nucleotidyltransferase superfamily  .. 
PF06043 Reovirus P9-like family<br>Pfam-B_8265 (release 9.0). 
PF06044 Dam-replacing family<br>Pfam-B_8314 (release 9.0). Dam-replacing protein (DRP) is an restriction endonuclease that is flanked by pseudo-transposable small repeat elements.  The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis  .. 
PF06045 Rhamnogalacturonate lyase family<br>Pfam-B_8355 (release 9.0). Rhamnogalacturonate lyase (EC:4.2.2.-) degrades the rhamnogalacturonan  I (RG-I) backbone of pectin  .  This family contains mainly members from plants, but also contains the plant pathogen Erwinia chrysanthemi.. 
PF06046 Exocyst complex component Sec6<br>Pfam-B_8361 (release 9.0). Sec6 is a component of the multiprotein exocyst complex.  Sec6 interacts with Sec8, Sec10 and Exo70.These exocyst proteins localise to regions of active exocytosis-at the growing ends of interphase cells and in the medial region of cells undergoing cytokinesis-in an F-actin-dependent and exocytosis- independent manner  .. 
PF06047 DUF926; <br>Ras-induced vulval development antagonist. Pfam-B_8083 (release 9.0). This family is from synthetic multi-vulval genes which encode chromatin-associated proteins involved in transcriptional repression. This protein has a role in antagonising Ras-induced vulval development  .. 
PF06048 Domain of unknown function (DUF927)<br>Pfam-B_8364 (release 9.0). Family of bacterial proteins of unknown function. The C-terminal half of this family contains a P-loop motif.. 
PF06049 Coagulation Factor V LSPD Repeat<br>These repeats are found in coagulation factor V (five). The name LSPD derives from the conserved residues in the middle of the repeat.They occur in the B domain, which is cleaved prior to activation of the protein. It has been suggested that domain B bring domains A and C together for activation ( ).. 
PF06050 2-hydroxyglutaryl-CoA dehydratase, D-component <br>Pfam-B_8369 (release 9.0). Degradation of glutamate via the hydroxyglutarate pathway involves the syn-elimination of water from 2-hydroxyglutaryl-CoA. This anaerobic process is catalysed by 2-hydroxyglutaryl-CoA dehydratase, an enzyme with two components (A and D) that reversibly associate during reaction cycles. This component contains one non-reducible [4Fe-4S]2+ cluster and a reduced riboflavin 5'-monophosphate  .. 
PF06051 Domain of Unknown Function (DUF928)<br>Pfam-B_8442 (release 9.0). Family of uncharacterised bacterial protein.. 
PF06052 3-hydroxyanthranilic acid dioxygenase<br>Pfam-B_8515 (release 9.0). In eukaryotes 3-hydroxyanthranilic acid dioxygenase (EC:1.13.11.6) is part of the kynurenine pathway for the degradation of tryptophan and the biosynthesis of nicotinic acid  .The prokaryotic homolog is involved in the 2-nitrobenzoate degradation pathway  .. 
PF06053 Domain of unknown function (DUF929)<br>Pfam-B_8458 (release 9.0). Family of proteins from the archaeon Sulfolobus, with undetermined  function.. 
PF06054 Competence protein CoiA-like family<br>Pfam-B_8535 (release 9.0). Many of the members of this family are described as transcription factors.  CoiA falls within a competence-specific operon in  Streptococcus.  CoiA is an uncharacterised protein.. 
PF06055 Exopolysaccharide synthesis, ExoD<br>Pfam-B_8604 (release 9.0). Among the bacterial genes required for nodule invasion are the exo genes. These genes are involved in the production of an extracellular polysaccharide.  Mutations in the exoD result in altered exopolysaccharide production and defects in nodule invasion  .. 
PF06056 Putative ATPase subunit of terminase (gpP-like)<br>Pfam-B_7152 (release 9.0). This family of proteins are annotated as ATPase subunits of phage terminase after  . Terminases are viral proteins that are involved in packaging viral DNA into the capsid.. 
PF06057 Bacterial virulence protein (VirJ)<br>Pfam-B_7524 (release 9.0). This family consists of several bacterial VirJ virulence proteins. VirJ is thought to be involved in the type IV secretion system. It is thought that the substrate proteins localised to the periplasm may associate with the pilus in a manner that is mediated by VirJ, and suggest a two-step process for type IV secretion in Agrobacterium  .. 
PF06058 Dcp1-like decapping family<br>Pfam-B_8271 (release 9.0). An essential step in mRNA turnover is decapping.  In yeast, two proteins have been identified that are essential for decapping, Dcp1 (this family) and Dcp2 (Pfam:PF05026).  The precise role of these proteins in the decapping reaction have not been established. Evidence suggests that the Dcp1 may enhance the function of Dcp2  .. 
PF06059 Domain of Unknown Function (DUF930)<br>Pfam-B_8283 (release 9.0). Family of bacterial proteins with undetermined function.  All bacteria in this family are from the Rhizobiales order. . 
PF06060 Pre-pro-megakaryocyte potentiating factor precursor (Mesothelin)<br>Pfam-B_8552 (release 9.0). This family consists of several mammalian pre-pro-megakaryocyte potentiating factor precursor (MPF) or mesothelin proteins. Mesothelin is a glycosylphosphatidylinositol-linked glycoprotein highly expressed in mesothelial cells, mesotheliomas, and ovarian cancer, but the biological function of the protein is not known [1,2].. 
PF06061 Baculoviridae ME53<br>Pfam-B_8086 (release 9.0). ME53 is one of the major early-transcribed genes. The ME53 protein is reported to contain a putative zinc finger motif  .. 
PF06062 Uncharacterised protein family (UPF0231)<br>Pfam-B_9027 (release 9.0). Family of uncharacterised Proteobacteria proteins.. 
PF06064 Host-nuclease inhibitor protein Gam<br>Pfam-B_9063 (release 9.0). The Gam protein inhibits RecBCD nuclease and is found in both bacteria and bacteriophage  .. 
PF06066 SepZ<br>Pfam-B_9064 (release 9.0). SepZ is a component of the type III secretion system use in bacteria. SepZ is a gene within the enterocyte effacement locus. SepZ mutants exhibit reduced invasion efficiency and lack of tyrosine phosphorylation  of Hp90  .. 
PF06067 Domain of unknown function (DUF932)<br>Pfam-B_9083 (release 9.0) & Pfam-B_002957 (release 23.0). Family of prokaryotic proteins with unknown function. Contains a number of highly conserved polar residues that could suggest an enzymatic activity.. 
PF06068 TIP49 C-terminus<br>Pfam-B_9170 (release 9.0). This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins. The N-terminal domain contains the Pfam:PF00004 domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway  . TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities.TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases  . . 
PF06069 PerC transcriptional activator<br>Pfam-B_9117 (release 9.0). PerC is a transcriptional activator of EaeA/BfpA expression in enteropathogenic bacteria  .. 
PF06070 Herpesvirus large structural phosphoprotein UL32<br>Pfam-B_9125 (release 9.0). The large phosphorylated protein (UL32-like) of herpes viruses  is the polypeptide most frequently reactive in immuno-blotting analyses with antisera when compared with other viral proteins  .. 
PF06071 DUF933; <br>Protein of unknown function (DUF933). Pfam-B_10000 (release 9.0). This domain is found at the C terminus of the YchF GTP-binding protein (Swiss:O13998) and is possibly related to the ubiquitin-like and MoaD/ThiS superfamilies. . 
PF06072 Alphaherpesvirus tegument protein US9<br>Pfam-B_7164 (release 9.0). This family consists of several US9 and related proteins from the Alphaherpesviruses. The function of the US9 protein is unknown although in Bovine herpesvirus 5 Us9 is essential for the anterograde spread of the virus from the olfactory mucosa to the bulb  .. 
PF06073 Bacterial protein of unknown function (DUF934)<br>Pfam-B_8947 (release 9.0). This family consists of several bacterial proteins of unknown function. One of the members of this family Swiss:Q8YEW3 is thought to be an oxidoreductase.. 
PF06074 Protein of unknown function (DUF935)<br>Pfam-B_10021 (release 9.0). This family consists of several bacterial proteins of unknown function as well as the Bacteriophage Mu gp29 protein Swiss:Q9T1W5.. 
PF06075 Plant protein of unknown function (DUF936)<br>Pfam-B_10047 (release 9.0). This family consists of several hypothetical proteins from Arabidopsis thaliana and Oryza sativa. The function of this family is unknown.. 
PF06076 Orthopoxvirus F14 protein<br>Pfam-B_10072 (release 9.0). This family consists of several short Orthopoxvirus F14 proteins. The function of this protein is unknown.. 
PF06078 Bacterial protein of unknown function (DUF937)<br>Pfam-B_7321 (release 9.0). This family consists of several hypothetical bacterial proteins of unknown function.. 
PF06079 SHAPY;<br>Pfam-B_7593 (release 9.0). This family consists of several eukaryotic apyrase proteins (EC:3.6.1.5). The salivary apyrases of blood-feeding arthropods are nucleotide hydrolysing enzymes implicated in the inhibition of host platelet aggregation through the hydrolysis of extracellular adenosine diphosphate.  . . 
PF06080 Protein of unknown function (DUF938)<br>Pfam-B_8833 (release 9.0). This family consists of several hypothetical proteins from both prokaryotes and eukaryotes. The function of this family is unknown.. 
PF06081 Bacterial protein of unknown function (DUF939)<br>Pfam-B_8873 (release 9.0). This family consists of several hypothetical bacterial proteins of unknown function.. 
PF06082 Bacterial putative lipoprotein (DUF940)<br>Pfam-B_9128 (release 9.0). This family consists of hypothetical bacterial proteins several of which are described as putative lipoproteins.. 
PF06083 Interleukin-17<br>Pfam-B_9152 (release 9.0). IL-17 is a potent proinflammatory cytokine produced by  activated memory T cells  . The IL-17 family is thought to represent a distinct signaling system that  appears to have been highly conserved across vertebrate evolution  .. 
PF06084 Cytomegalovirus TRL10 protein<br>Pfam-B_8875 (release 9.0). This family consists of several Cytomegalovirus TRL10 proteins. TRL10 represents a structural component of the virus particle and like the other HCMV envelope glycoproteins, is present in a disulfide-linked complex  . . 
PF06085 Lipoprotein Rz1 precursor<br>Pfam-B_8925 (release 9.0). This family consists of several bacteria and phage lipoprotein Rz1 precursors. Rz1 is a proline-rich lipoprotein from bacteriophage lambda which is known to have fusogenic properties. Rz1-induced liposome fusion is thought to be mediated primarily by the generation of local perturbation in the bilayer lipid membrane and to a lesser extent by electrostatic forces  . This family Rz1 and the Rz protein Rz (Pfam:PF03245) represent a unique example of two genes located in different reading frames in the same nucleotide sequence, which encode different proteins that are both required in the same physiological pathway  .. 
PF06086 Orthopoxvirus A26L/A30L protein<br>Pfam-B_8938 (release 9.0). This family consists of several Orthopoxvirus A26L and A30L proteins. The Vaccinia A30L gene is regulated by a late promoter and encodes a protein of approximately 9 kDa. It is thought that the A30L protein is needed for vaccinia virus morphogenesis, specifically the association of the dense viroplasm with viral membranes  .. 
PF06087 Tyrosyl-DNA phosphodiesterase<br>Pfam-B_8155 (release 9.0). Covalent intermediates between topoisomerase I and DNA  can become dead-end complexes that lead to cell death. Tyrosyl-DNA phosphodiesterase can hydrolyse the bond between  topoisomerase I and DNA  .. 
PF06088 Nucleopolyhedrovirus telokin-like protein-20 (TLP20)<br>Pfam-B_7657 (release 9.0). This family consists of several Nucleopolyhedrovirus telokin-like protein-20 (TLP20) sequences. The function of this family is unknown but TLP20 is known to shares some antigenic similarities to the smooth muscle protein telokin although the amino acid sequence shows no homologies to telokin  .. 
PF06089 L-asparaginase II<br>Pfam-B_7673 (release 9.0). This family consists of several bacterial L-asparaginase II proteins.  L-asparaginase (EC:3.5.1.1) catalyses the hydrolysis of L-asparagine to L-aspartate and ammonium. Rhizobium etli possesses two asparaginases: asparaginase I, which is thermostable and constitutive, and asparaginase II, which is thermolabile, induced by asparagine and repressed by the carbon source  .. 
PF06090 DUF941; <br>Inositol-pentakisphosphate 2-kinase. Pfam-B_9098 (release 9.0). This is a family of inositol-pentakisphosphate 2-kinases (EC 2.7.1.158) (also known as inositol 1,3,4,5,6-pentakisphosphate 2-kinase, Ins(1,3,4,5,6)P5 2-kinase) and InsP5 2-kinase).\.  This enzyme phosphorylates Ins(1,3,4,5,6)P5 to form Ins(1,2,3,4,5,6)P6 (also known as InsP6 or phytate). InsP6 is involved in many processes such as mRNA export, nonhomologous end-joining, endocytosis and ion channel regulation.. 
PF06092 Enterobacterial putative membrane protein (DUF943)<br>Pfam-B_7843 (release 9.0). This family consists of several hypothetical putative membrane proteins from Escherichia coli, Yersinia pestis and Salmonella typhi.. 
PF06093 Spt4/RpoE2 zinc finger<br>Pfam-B_7906 (release 9.0) & COG2093. This family consists of several eukaryotic transcription elongation Spt4 proteins as well as archaebacterial RpoE2  . Three transcription-elongation factors Spt4, Spt5, and Spt6 are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. Spt4 and Spt5 are tightly associated in a complex, while the physical association of the Spt4-Spt5 complex with Spt6 is considerably weaker. It has been demonstrated that Spt4, Spt5, and Spt6 play roles in transcription elongation in both yeast and humans including a role in activation by Tat. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles  .  RpoE2 is one of 13 subunits in the archaeal RNA polymerase. These proteins contain a C4-type zinc finger, and the structure has been solved in  . The structure reveals that Spt4-Spt5 binding is governed by an acid-dipole interaction between Spt5 and Spt4, and the complex binds to and travels along the elongating RNA polymerase. The Spt4-Spt5 complex is likely to be an ancient, core component of the transcription elongation machinery.. 
PF06094 AIG2-like family<br>Pfam-B_9771 (release 9.0). AIG2 is an Arabidopsis proteins that exhibit RPS2- and avrRpt2-dependent induction early after infection with Pseudomonas syringae pv maculicola strain ES4326 carrying avrRpt2  .. 
PF06096 Baculo_8Kda; <br>Baculoviridae 8.2 KDa protein. Pfam-B_8370 (release 9.0). Family of proteins from various Baculoviruses with undetermined function.. 
PF06097 Bacterial protein of unknown function (DUF945)<br>Pfam-B_9171 (release 9.0). This family consists of several hypothetical bacterial proteins of unknown function.. 
PF06098 Radial spoke protein 3<br>Pfam-B_9453 (release 9.0). This family consists of several radial spoke protein 3 (RSP3) sequences. Eukaryotic cilia and flagella present in diverse types of cells perform motile, sensory, and developmental functions in organisms from protists to humans. They are centred by precisely organised, microtubule-based structures, the axonemes. The axoneme consists of two central singlet microtubules, called the central pair, and nine outer doublet microtubules. These structures are well-conserved during evolution. The outer doublet microtubules, each composed of A and B sub-fibres, are connected to each other by nexin links, while the central pair is held at the centre of the axoneme by radial spokes. The radial spokes are T-shaped structures extending from the A-tubule of each outer doublet microtubule to the centre of the axoneme. Radial spoke protein 3 (RSP3), is present at the proximal end of the spoke stalk and helps in anchoring the radial spoke to the outer doublet. It is thought that radial spokes regulate the activity of inner arm dynein through protein phosphorylation and dephosphorylation  .. 
PF06099 Phenol hydroxylase subunit<br>Pfam-B_10062 (release 9.0). This family consists of several bacterial phenol hydroxylase subunit proteins which are part of a multicomponent phenol hydroxylase. Some bacteria can utilise phenol or some of its methylated derivatives as their sole source of carbon and energy. The first step in this process is the conversion of phenol into catechol. Catechol is then further metabolised via the meta-cleavage pathway into TCA cycle intermediates  . . 
PF06100 Streptococcal 67 kDa myosin-cross-reactive antigen like family <br>Pfam-B_9995 (release 9.0). Members of this family are thought to have structural features in  common with the beta chain of the class II antigens, as well as myosin,  and may play an important role in the pathogenesis .. 
PF06101 Plant protein of unknown function (DUF946)<br>Pfam-B_10066 (release 9.0). This family consists of several hypothetical proteins from Arabidopsis thaliana and Oryza sativa. The function of this family is unknown.. 
PF06102 Domain of unknown function (DUF947)<br>Pfam-B_9959 (release 9.0). Family of eukaryotic proteins with unknown function.. 
PF06103 Bacterial protein of unknown function (DUF948)<br>Pfam-B_10104 (release 9.0). This family consists of bacterial sequences several of which are thought to be general stress proteins.. 
PF06105 Aph-1 protein<br>Pfam-B_7927 (release 9.0). This family consists of several eukaryotic Aph-1 proteins.Gamma-secretase catalyses the intramembrane proteolysis of Notch, beta-amyloid precursor protein, and other substrates as part of a new signaling paradigm and as a key step in the pathogenesis of Alzheimer's disease. It is thought that the presenilin heterodimer comprises the catalytic site and that a highly glycosylated form of nicastrin associates with it. Aph-1 and Pen-2, two membrane proteins genetically linked to gamma-secretase, associate directly with presenilin and nicastrin in the active protease complex. Co-expression of all four proteins leads to marked increases in presenilin heterodimers, full glycosylation of nicastrin, and enhanced gamma-secretase activity  .. 
PF06106 Staphylococcus protein of unknown function (DUF950)<br>Pfam-B_8992 (release 9.0). This family consists of several hypothetical proteins from different Staphylococcus species. The function of this family is unknown.. 
PF06107 Bacterial protein of unknown function (DUF951)<br>Moxon SJ, Eberhardt R. Pfam-B_8994 (release 9.0). This family consists of several short hypothetical bacterial proteins of unknown function. Structural modelling suggests this domain may bind nucleic acids  .. 
PF06108 Protein of unknown function (DUF952)<br>Pfam-B_8995 (release 9.0). This family consists of several hypothetical bacterial and plant proteins of unknown function.. 
PF06109 Haemolysin E (HlyE)<br>Pfam-B_9001 (release 9.0). This family consists of several enterobacterial haemolysin (HlyE) proteins.Hemolysin E (HlyE) is a novel pore-forming toxin of Escherichia coli, Salmonella typhi, and Shigella flexneri. HlyE is unrelated to the well characterised pore-forming E. coli hemolysins of the RTX family, haemolysin A (HlyA), and the enterohaemolysin encoded by the plasmid borne ehxA gene of E. coli 0157. However, it is evident that expression of HlyE in the absence of the RTX toxins is sufficient to give a hemolytic phenotype in E. coli. HlyE is a protein of 34 kDa that is expressed during anaerobic growth of E. coli. Anaerobic expression is controlled by the transcription factor, FNR, such that, upon ingestion and entry into the anaerobic mammalian intestine, HlyE is produced and may then contribute to the colonisation of the host  .. 
PF06110 Eukaryotic protein of unknown function (DUF953)<br>Pfam-B_9087 (release 9.0). This family consists of several hypothetical eukaryotic proteins of unknown function.. 
PF06112 Gammaherpesvirus capsid protein<br>Pfam-B_9200 (release 9.0). This family consists of several Gammaherpesvirus capsid proteins. The exact function of this family is unknown.. 
PF06113 Brain and reproductive organ-expressed protein (BRE)<br>Pfam-B_9280 (release 9.0). This family consists of several eukaryotic brain and reproductive organ-expressed (BRE) proteins. BRE is a putative stress-modulating gene, found able to down-regulate TNF-alpha-induced-NF-kappaB activation upon over expression. A total of six isoforms are produced by alternative splicing predominantly at either end of the gene.Compared to normal cells, immortalised human cell lines uniformly express higher levels of BRE. Peripheral blood monocytes respond to LPS by down-regulating the expression of all the BRE isoforms.It is thought that the function of BRE and its isoforms is to regulate peroxisomal activities  .. 
PF06114 Domain of unknown function (DUF955)<br>Family of bacterial and viral proteins with undetermined function. A conserved H-E-X-X-H motif is suggestive of a catalytic active site and shows similarity to Pfam:PF01435.. 
PF06115 Domain of unknown function (DUF956)<br>Pfam-B_9146 (release 9.0). Family of bacterial sequences with undetermined function.. 
PF06116 Transcriptional activator RinB<br>Pfam-B_9294 (release 9.0). This family consists of several Staphylococcus aureus bacteriophage RinB proteins and related sequences from their host. The int gene of staphylococcal bacteriophage phi 11 is the only viral gene responsible for the integrative recombination of phi 11. rinA and rinB, are both required to activate expression of the int gene  .. 
PF06117 Enterobacterial protein of unknown function (DUF957)<br>Pfam-B_9300 (release 9.0). This family consists of several hypothetical proteins from Escherichia coli, Salmonella typhi, Shigella flexneri and Proteus vulgaris. The function of this family is unknown.. 
PF06119 DUF958; <br>Yeats C, Myerscough N. Pfam-B_1159 (release 8.0). This is a nidogen-like domain (NIDO) domain and is an extracellular domain found in nidogen and hypothetical proteins of unknown function  .. 
PF06120 Tail length tape measure protein<br>Pfam-B_10088 (release 9.0). This family consists of the tail length tape measure protein from bacteriophage HK97 and related sequences from Escherichia coli O157:H7.. 
PF06121 Domain of Unknown Function (DUF959) <br>Pfam-B_25471 (release 8.0). This N-terminal domain is not expressed in the 'Short' isoform of Collagen A  .. 
PF06122 Conjugative relaxosome accessory transposon protein<br>Pfam-B_10166 (release 9.0). The TraH protein is thought to be a relaxosome accessory component, also necessary for transfer but not for H-pilus synthesis within the conjugative transposon    .. 
PF06123 Inner membrane protein CreD<br>Pfam-B_10187 (release 9.0). This family consists of several bacterial CreD or Cet inner membrane proteins. Dominant mutations of the cet gene of Escherichia coli result in tolerance to colicin E2 and increased amounts of an inner membrane protein with an Mr of 42,000. The cet gene is shown to be in the same operon as the phoM gene, which is required in a phoR background for expression of the structural gene for alkaline phosphatase, phoA. Although the Cet protein is not required for phoA expression, it has been suggested that the Cet protein has an enhancing effect on the transcription of phoA  .. 
PF06124 Staphylococcal protein of unknown function (DUF960)<br>Pfam-B_10198 (release 9.0). This family consists of several hypothetical proteins from several species of Staphylococcus. The function of this family is unknown.. 
PF06125 Bacterial protein of unknown function (DUF961)<br>Pfam-B_10221 (release 9.0). This family consists of several hypothetical bacterial proteins of unknown function.. 
PF06126 Herpesvirus Latent membrane protein 2<br>Pfam-B_9147 (release 9.0). Family of Kaposi's sarcoma-associated herpesvirus (HHV8) latent membrane protein.. 
PF06127 Protein of unknown function (DUF962)<br>Pfam-B_10320 (release 9.0). This family consists of several eukaryotic and prokaryotic proteins of unknown function. The yeast protein Swiss:P25338 has been found to be non-essential for cell growth.. 
PF06128 Shigella flexneri OspC protein<br>Pfam-B_10333 (release 9.0). This family consists of the Shigella flexneri specific protein OspC. The function of this family is unknown but it is thought that Osp proteins may be involved in post invasion events related to virulence. Since bacterial pathogens adapt to multiple environments during the course of infecting a host, it has been proposed that Shigella evolved a mechanism to take advantage of a unique intracellular cue, which is mediated through MxiE, to express proteins when the organism reaches the eukaryotic cytosol  . . 
PF06129 Chordopoxvirus G3 protein<br>Pfam-B_10417 (release 9.0). This family consists of several Chordopoxvirus specific G3 proteins. The function of this family is unknown.. 
PF06130 Propanediol utilisation protein PduL<br>Pfam-B_10447 (release 9.0). 
PF06131 Schizosaccharomyces pombe repeat of unknown function (DUF963)<br>Pfam-B_10581 (release 9.0). This family consists of a series of repeated sequences from one hypothetical protein (Swiss:Q96WV6) found in Schizosaccharomyces pombe. The function of this family is unknown.. 
PF06133 Protein of unknown function (DUF964)<br>Pfam-B_10600 (release 9.0). This family consists of several relatively short bacterial and archaeal hypothetical sequences. The function of this family is unknown.. 
PF06134 L-rhamnose isomerase (RhaA)<br>Pfam-B_10641 (release 9.0). This family consists of several bacterial L-rhamnose isomerase proteins (EC:5.3.1.14).. 
PF06135 Bacterial protein of unknown function (DUF965)<br>Pfam-B_10661 (release 9.0). This family consists of several hypothetical bacterial proteins. The function of the family is unknown.. 
PF06136 Domain of unknown function (DUF966)<br>Pfam-B_8637 (release 9.0). Family of plant proteins with unknown function.. 
PF06138 Chordopoxvirus E11 protein<br>Pfam-B_10685 (release 9.0). This family consists of several Chordopoxvirus E11 proteins. The E11 gene of vaccinia virus encodes a 15-kDa polypeptide. Mutations in the E11 gene makes the virus temperature-sensitive due to either the fact that virus infectivity requires a threshold level of active E11 protein or that E11 function is conditionally essential  . . 
PF06139 BphX-like<br>Pfam-B_8664 (release 9.0). Family of bacterial proteins located in the phenyl dioxygenase  (bph) operon. The function of this family is unknown. . 
PF06140 Interferon-induced 6-16 family <br>Pfam-B_9299 (release 9.0). 
PF06141 Phage minor tail protein U<br>Pfam-B_9209 (release 9.0). Tail fibre component U of bacteriophage.. 
PF06143 Baculovirus 11 kDa family<br>Pfam-B_9424 (release 9.0). Family of uncharacterised Baculovirus proteins that are all about 11 kDa in size.. 
PF06144 DNA polymerase III, delta subunit<br>Pfam-B_9452 (release 9.0). DNA polymerase III, delta subunit (EC 2.7.7.7) is required for, along with delta' subunit, the assembly of the processivity factor beta(2) onto primed DNA in the DNA polymerase III holoenzyme-catalysed reaction  . The delta subunit is also known as HolA.. 
PF06145 Coronavirus nonstructural protein NS1<br>Pfam-B_9242 (release 9.0). Bovine coronavirus NS1 encodes a 4.9 kDa protein  .. 
PF06146 Phosphate-starvation-inducible E<br>Pfam-B_8639 (release 9.0). Phosphate-starvation-inducible E (PsiE) expression is under direct positive and negative control by PhoB and cAMP-CRP, respectively  .  The function of PsiE remains to be determined.. 
PF06147 Protein of unknown function (DUF968)<br>Pfam-B_9463 (release 9.0). Family of uncharacterised prophage proteins that  are also found in bacteria and eukaryotes.. 
PF06148 COG (conserved oligomeric Golgi) complex component, COG2<br>Pfam-B_9559 (release 9.0). The COG complex comprises eight proteins COG1-8. The COG complex plays critical roles in Golgi structure and function  . The proposed function of the complex is to mediate the initial physical contact between transport vesicles and their membrane targets. A comparable role in tethering vesicles has been suggested for at least six additional large multisubunit complexes, including the exocyst, a complex that mediates trafficking to the plasma membrane. COG2 structure reveals a six-helix bundle with few conserved surface features but a general resemblance to recently determined crystal structures of four different exocyst subunits. These bundles inCOG2 may act as platforms for interaction with other trafficing proteins including SNAREs (soluble N-ethylmaleimide factor attachment protein receptors) and Rabs  .. 
PF06149 Protein of unknown function (DUF969)<br>Pfam-B_9723 (release 9.0). Family of uncharacterised bacterial membrane proteins.. 
PF06150 ChaB<br>Pfam-B_7743 (release 9.0). This family of proteins contain a conserved 60 residue region.  This protein is known as ChaB in E. coli and is found next to ChaA which is a cation transporter protein.  ChaB may be regulate ChaA function in some way.. 
PF06151 Trehalose receptor<br>Pfam-B_9846 (release 9.0). In Drosophila, taste is perceived by gustatory neurons located in sensilla distributed on several different appendages throughout the  body of the animal.  This family represents the taste receptor sensitive to trehalose [1,2].. 
PF06152 Phage minor capsid protein 2<br>Pfam-B_9879 (release 9.0). Family of related phage minor capsid proteins.. 
PF06153 Protein of unknown function (DUF970)<br>Pfam-B_9915 (release 9.0). Family of uncharacterised bacterial proteins.. 
PF06154 YagB/YeeU/YfjZ family<br>Pfam-B_7771 (release 9.0). This family of proteins includes three proteins from E. coli YagB, YeeU and YfjZ.  The function of these proteins is unknown.  They are about 120 amino acids in length.. 
PF06155 Protein of unknown function (DUF971)<br>Pfam-B_10230 (release 9.0). This family consists of several short bacterial proteins and one sequence (Swiss:Q8RZ62) from Oryza sativa. The function of this family is unknown. . 
PF06156 Protein of unknown function (DUF972)<br>Pfam-B_10235 (release 9.0). This family consists of several hypothetical bacterial sequences. The function of this family is unknown.. 
PF06157 Protein of unknown function (DUF973)<br>Pfam-B_7947 (release 9.0). This family consists of several hypothetical archaeal proteins of unknown function.. 
PF06159 Protein of unknown function (DUF974)<br>Pfam-B_9042 (release 9.0). Family of uncharacterised eukaryotic proteins.. 
PF06160 Septation ring formation regulator, EzrA <br>Pfam-B_9703 (release 9.0). During the bacterial cell cycle, the tubulin-like cell-division protein  FtsZ polymerises into a ring structure that establishes the location of  the nascent division site.  EzrA modulates the frequency and position of  FtsZ ring formation  .. 
PF06161 Protein of unknown function (DUF975)<br>Pfam-B_8494 (release 9.0). Family of uncharacterised bacterial proteins.. 
PF06162 Caenorhabditis elegans protein of unknown function (DUF976)<br>Pfam-B_10032 (release 9.0). This family consists of several hypothetical Caenorhabditis elegans proteins of unknown function.. 
PF06163 Bacterial protein of unknown function (DUF977)<br>Pfam-B_10135 (release 9.0). This family consists of several hypothetical bacterial proteins from Escherichia coli and Salmonella typhi. The function of this family is unknown.. 
PF06165 Glycosyltransferase family 36<br>Pfam-B_9110 (release 9.0). The glycosyltransferase family 36 includes cellobiose phosphorylase  (EC:2.4.1.20), cellodextrin phosphorylase (EC:2.4.1.49), chitobiose  phosphorylase (EC:2.4.1.-).  Many members of this family contain two copies of this domain.. 
PF06166 Protein of unknown function (DUF979)<br>Pfam-B_10323 (release 9.0). This family consists of several putative bacterial membrane proteins. The function of this family is unclear.. 
PF06167 DUF980; MtfA;<br>Glucose-regulated metallo-peptidase M90. Pfam-B_8651 (release 9.0). MtfA (earlier known as YeeI) is a transcription factor A that binds Mlc (make large colonies), itself a repressor of glucose and hence a protein important in regulation of the phosphoenolpyruvate:glucose-phosphotransferase (ptsG) system, the major glucose transporter in E.coli. Mlc is a repressor of ptsG, and MtfA is found to bind and inactivate Mlc with high affinity  . The membrane-bound protein EIICBGlc encoded by the ptsG gene is the major glucose transporter in Escherichia coli. MtfA is found to be a glucose-regulated peptidase  , whose activity is regulated by binding to Mlc available in the cytoplasm, which in turn has been released from EIICBGlc during times when no glucose is taken up. A physiologically relevant target for this peptidase is not yet known.. 
PF06168 Protein of unknown function (DUF981)<br>Pfam-B_8691 (release 9.0). Family of uncharacterised proteins found in bacteria and archaea.. 
PF06169 Protein of unknown function (DUF982)<br>Moxon SJ, Eberhardt R. Pfam-B_10431 (release 9.0). This family consists of several hypothetical proteins from Rhizobium meliloti, Rhizobium loti and Agrobacterium tumefaciens. The function of this family is unknown. Structural modelling suggests this domain may bind nucleic acids  .. 
PF06170 Protein of unknown function (DUF983)<br>Pfam-B_10629 (release 9.0). This family consists of several bacterial proteins of unknown function.. 
PF06172 DUF985; <br>Cupin superfamily (DUF985). Pfam-B_9217 (release 9.0). Family of uncharacterised proteins found in bacteria and eukaryotes that belongs to the Cupin superfamily.. 
PF06173 Protein of unknown function (DUF986)<br>Pfam-B_10711 (release 9.0). This family consists of several bacterial putative membrane proteins of unknown function.. 
PF06174 Protein of unknown function (DUF987)<br>Pfam-B_9329 (release 9.0). Family of bacterial proteins that are related to the hypothetical  protein yeeT.. 
PF06175 tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE)<br>Pfam-B_10761 (release 9.0). This family consists of several bacterial tRNA-(MS IO A)-hydroxylase (MiaE) proteins. The modified nucleoside 2-methylthio-N-6-isopentenyl adenosine (ms2i6A) is present at position 37 (3' of the anticodon) of tRNAs that read codons beginning with U except tRNA(I,V Ser) in Escherichia coli. Salmonella typhimurium 2-methylthio-cis-ribozeatin (ms2io6A) is found in tRNA, probably in the corresponding species that have ms2i6A in E. coli.  The miaE gene is absent in E. coli, a finding consistent with the absence of the hydroxylated derivative of ms2i6A in this species  .. 
PF06176 Lipopolysaccharide core biosynthesis protein (WaaY)<br>Pfam-B_10767 (release 9.0). This family consists of several bacterial lipopolysaccharide core biosynthesis proteins (WaaY or RfaY). The waaY, waaQ, and waaP genes are located in the central operon of the waa (formerly rfa) locus on the chromosome of Escherichia coli. This locus contains genes whose products are involved in the assembly of the core region of the lipopolysaccharide molecule. WaaY is the enzyme that phosphorylates HepII in this system  .. 
PF06177 DUF988; <br>Pfam-B_10800 (release 9.0). This family includes the queT gene encoding a hypothetical integral membrane protein with 5 predicted transmembrane regions. The queT genes in Firmicutes are often preceded by the PreQ1 (7-aminomethyl-7-deazaguanine) riboswitches of two distinct classes [1-2], suggesting involvement of the QueT transporters in uptake of a queuosine biosynthetic intermediate.. 
PF06178 Oligogalacturonate-specific porin protein (KdgM)<br>Pfam-B_10852 (release 9.0). This family consists of several bacterial proteins which are homologous to the oligogalacturonate-specific porin protein KdgM (Swiss:Q934G3) from Erwinia chrysanthemi. The phytopathogenic Gram-negative bacteria Erwinia chrysanthemi secretes pectinases, which are able to degrade the pectic polymers of plant cell walls, and uses the degradation products as a carbon source for growth. KdgM is a major outer membrane protein, whose synthesis is strongly induced in the presence of pectic derivatives. KdgM behaves like a voltage-dependent porin that is slightly selective for anions and that exhibits fast block in the presence of trigalacturonate. In contrast to most porins, KdgM seems to be monomeric  .  . 
PF06179 SURF5; <br>Surfeit locus protein 5 subunit 22 of Mediator complex. Pfam-B_10889 (release 9.0). This family consists of several eukaryotic Surfeit locus protein 5 (SURF5) sequences. The human Surfeit locus has been mapped on chromosome 9q34.1.  The locus includes six tightly clustered housekeeping genes (Surf1-6), and the gene organisation is similar in human, mouse and chicken Surfeit locus.  The Med22 subunit of Mediator complex is part of the essential core head region    .. 
PF06180 Cobalt chelatase (CbiK)<br>Pfam-B_10975 (release 9.0). This family consists of several bacterial cobalt chelatase (CbiK) proteins (EC:4.99.1.-).. 
PF06181 Protein of unknown function (DUF989)<br>Pfam-B_11062 (release 9.0). This family consists of several hypothetical bacterial proteins of unknown function. The haem-binding domain towards the C-terminus has been merged into Cytochrome_C, Pfam:PF00034.. 
PF06182 DUF990;<br>ABC-2 family transporter protein. Moxon SJ, Eberhardt R. Pfam-B_11079 (release 9.0). This family acts as the transmembrane domain (TMD) of ABC transporters [1,2]. The family includes proteins responsible for the transport of herbicides  .. 
PF06183 DinI-like family<br>Pfam-B_3085 (release 9.0). This family of short proteins includes DNA-damage-inducible protein I (DinI) and related proteins. The SOS response, a set of cellular phenomena exhibited by eubacteria, is initiated by various causes that include DNA damage-induced replication arrest, and is positively regulated by the co- protease activity of RecA. Escherichia coli DinI, a LexA-regulated SOS gene product, shuts off the initiation of the SOS response when overexpressed in vivo. Biochemical and genetic studies indicated that DinI physically interacts with RecA to inhibit its co-protease activity  . The structure of DinI is known  .. 
PF06184 Potexvirus coat protein<br>Pfam-B_11093 (release 9.0). This family consists of several Potexvirus coat proteins.. 
PF06185 DUF991; <br>Pfam-B_11108 (release 9.0). This family consists of several bacterial YecM proteins of unknown function.. 
PF06186 Protein of unknown function (DUF992)<br>Pfam-B_11128 (release 9.0). This family consists of several hypothetical bacterial proteins of unknown function.. 
PF06187 Protein of unknown function (DUF993)<br>Pfam-B_11260 (release 9.0). This family consists of several hypothetical bacterial proteins of unknown function.. 
PF06188 HrpE/YscL/FliH and V-type ATPase subunit E<br>Pfam-B_11055 (release 9.0). This is a prokaryotic family that contains proteins of the FliH and HrpE/YscL family.\.   These proteins are involved in type III secretion, which is the process that drives flagellar biosynthesis and mediates bacterial-eukaryotic interactions [1-2].  This family also V-type ATPase subunit E.     This subunit appears to form a tight interaction with subunit G in the F0 complex  . Subunits E and G may act together as stators to prevent certain subunits from rotating with the central rotary element  .  Pfam:PF01991 also contains V-type ATPase subunit E proteins.. 
PF06189 5'-nucleotidase<br>Pfam-B_10008 (release 9.0). This family consists of both eukaryotic and prokaryotic 5'-nucleotidase sequences (EC:3.1.3.5).. 
PF06191 Protein of unknown function (DUF995)<br>Pfam-B_11307 (release 9.0). Family of uncharacterised Proteobacteria proteins.. 
PF06193 Orthopoxvirus A5L protein-like<br>Pfam-B_10342 (release 9.0). This family includes several Orthopoxvirus A5L proteins. The vaccinia virus WR A5L open reading frame (corresponding to open reading frame A4L in vaccinia virus Copenhagen) encodes an immunodominant late protein found in the core of the vaccinia virion. The A5 protein appears to be required for the immature virion to form the brick-shaped intracellular mature virion  .. 
PF06194 Phage Conserved Open Reading Frame 51<br>Pfam-B_11352 (release 9.0). Family of conserved bacteriophage open reading frames.. 
PF06195 Protein of unknown function (DUF996)<br>Pfam-B_11375 (release 9.0). Family of uncharacterised bacterial and archaeal proteins.. 
PF06196 Protein of unknown function (DUF997)<br>Pfam-B_11382 (release 9.0). Family of predicted bacterial membrane protein with unknown function.. 
PF06197 Protein of unknown function (DUF998)<br>Pfam-B_11425 (release 9.0). Family of conserved archaeal proteins.. 
PF06198 Protein of unknown function (DUF999)<br>Pfam-B_11426 (release 9.0). Family of conserved Schizosaccharomyces pombe proteins with  unknown function.. 
PF06199 Phage major tail protein 2<br>Pfam-B_11427 (release 9.0). Characterised members are major tail proteins from various phage, including lactococcal temperate bacteriophage TP901-1.. 
PF06200 Zim; <br>Pfam-B_3326 (release 9.0). This short possible domain is found in a variety of plant transcription factors that contain GATA domains as well as other motifs. Although previously known as the Zim domain this is now called the tify domain after its most conserved amino acids. TIFY proteins can be further classified into two groups depending on the presence (group I) or absence (group II) of a C2C2-GATA domain. Functional annotation of these proteins is still poor, but several screens revealed a link between TIFY proteins of group II and jasmonic acid-related stress response.. 
PF06201 DUF1000; Thioredox_dimer;<br>This family was formerly known as DUF1000. The full-length, Txnl1, protein which is a probable component of the 26S proteasome, uses its C-terminal, PITH, domain to associate specifically with the 26S proteasome. PITH derives from proteasome-interacting thioredoxin domain.. 
PF06202 Amylo-alpha-1,6-glucosidase <br>Pfam-B_3607 (release 9.0). This family includes human glycogen branching enzyme Swiss:P35573. This enzyme contains a number of distinct catalytic activities. It has been shown for the yeast homologue Swiss:O93808 that mutations in this region disrupt the enzymes Amylo-alpha-1,6-glucosidase (EC:3.2.1.33).. 
PF06203 CCT motif<br>Pfam-B_314 (release 9.0). This short motif is found in a number of plant proteins. It is rich in basic amino acids and has been called a CCT motif after Co, Col and Toc1  . The CCT motif is about 45 amino acids long and contains a putative nuclear localisation signal within the second half of the CCT motif  . Toc1 mutants have been identified in this region.. 
PF06204 Putative carbohydrate binding domain  <br>Pfam-B_9110 (release 9.0). 
PF06205 Glycosyltransferase 36 associated family  <br>Pfam-B_9110 (release 9.0). 
PF06206 DUF1001; <br>CpeT/CpcT family (DUF1001). Pfam-B_11004 (release 9.0). This family consists of proteins of proteins belonging to the CpeT/CpcT family. These proteins are around 200 amino acids in length.  The proteins contain a conserved motif PYR in the amino terminal half of the protein that may be functionally important. The species distribution of the family is interesting.  So far it is restricted to cyanobacteria, cryptomonads and plants. It has been shown that CpcT encodes a bilin lyase responsible for attachment of phycocyanobilin to the beta subunit of phycocyanin  .. 
PF06207 Protein of unknown function (DUF1002)<br>Pfam-B_10868 (release 9.0). This protein family has no known function. Its members are about 300 amino acids in length. It has so far been detected in Firmicute bacteria and some archaebacteria.. 
PF06208 Borna disease virus G protein<br>Pfam-B_10516 (release 9.0). This family consists of Borna disease virus G glycoprotein sequences. Borna disease virus (BDV) infection produces a variety of clinical diseases, from behavioural illnesses to classical fatal encephalitis  . G protein is important for viral entry into the host cell [2,3].. 
PF06209 Cofactor of BRCA1 (COBRA1)<br>Pfam-B_11228 (release 9.0). This family consists of several cofactor of BRCA1 (COBRA1) like proteins. It is thought that COBRA1 along with BRCA1 is involved in chromatin unfolding. COBRA1 is recruited to the chromosome site by the first BRCT repeat of BRCA1, and is itself sufficient to induce chromatin unfolding. BRCA1 mutations that enhance chromatin unfolding also increase its affinity for, and recruitment of, COBRA1. It is thought that that reorganisation of higher levels of chromatin structure is an important regulated step in BRCA1-mediated nuclear functions  .. 
PF06210 Protein of unknown function (DUF1003)<br>Pfam-B_10814 (release 9.0). This family consists of several hypothetical bacterial proteins of unknown function.. 
PF06211 BMP and activin membrane-bound inhibitor (BAMBI) N-terminal domain<br>Pfam-B_11792 (release 9.0). This family consists of several eukaryotic BMP and activin membrane-bound inhibitor (BAMBI) proteins. Members of the transforming growth factor-beta (TGF-beta) superfamily, including TGF-beta, bone morphogenetic proteins (BMPs), activins and nodals, are vital for regulating growth and differentiation. BAMBI is related to TGF-beta-family type I receptors but lacks an intracellular kinase domain. BAMBI is co-expressed with the ventralising morphogen BMP4 during Xenopus embryogenesis and requires BMP signalling for its expression. The protein stably associates with TGF-beta-family receptors and inhibits BMP and activin as well as TGF-beta signalling  .. 
PF06212 GRIM-19 protein<br>Pfam-B_10760 (release 9.0). This family consists of several eukaryotic gene associated with retinoic-interferon-induced mortality 19 (GRIM-19) proteins. GRIM-19, was reported to encode a small protein primarily distributed in the nucleus and was able to promote cell death induced by IFN-ß and RA. A bovine homologue of GRIM-19 was co-purified with mitochondrial NADH:ubiquinone oxidoreductase (complex I) in bovine heart. Therefore, its exact cellular localisation and function are unclear. It has now been discovered that GRIM-19 is a specific interacting protein which negatively regulates Stat3 activity  . . 
PF06213 Cobalamin biosynthesis protein CobT<br>Pfam-B_10956 (release 9.0). This family consists of several bacterial cobalamin biosynthesis (CobT) proteins. CobT is involved in the transformation of precorrin-3 into cobyrinic acid  . . 
PF06214 Signaling lymphocytic activation molecule (SLAM) protein<br>Pfam-B_11112 (release 9.0). This family consists of several mammalian signaling lymphocytic activation molecule (SLAM) proteins. Optimal T cell activation and expansion require engagement of the TCR plus co-stimulatory signals delivered through accessory molecules. SLAM, a 70-kDa co-stimulatory molecule belonging to the Ig superfamily, is defined as a human cell surface molecule that mediates CD28-independent proliferation of human T cells and IFN-gamma production by human Th1 and Th2 clones  . SLAM has also been recognised as a receptor for measles virus  .. 
PF06215 Infectious salmon anaemia virus haemagglutinin<br>Pfam-B_11275 (release 9.0). This family consists of several infectious salmon anaemia virus haemagglutinin proteins. Infectious salmon anaemia virus (ISAV), an orthomyxovirus-like virus, is an important fish pathogen in marine aquaculture  .  . 
PF06216 Rice tungro bacilliform virus P46 protein<br>Pfam-B_11281 (release 9.0). This family consists of several Rice tungro bacilliform virus P46 proteins. The function of this family is unknown.. 
PF06217 DUF1004; <br>GAGA binding protein-like family. Pfam-B_10604 (release 9.0). This family includes gbp a protein from Soybean that binds to GAGA element dinucleotide repeat DNA  . It seems likely that the this domain mediates DNA binding. This putative domain contains several conserved cysteines and a histidine suggesting this may be a zinc-binding DNA interaction domain.. 
PF06218 Nitrogen permease regulator 2<br>Pfam-B_11335 (release 9.0). This family of regulators are involved in post-translational control  of  nitrogen permease.. 
PF06219 Protein of unknown function (DUF1005)<br>Pfam-B_11366 (release 9.0). Family of plant proteins with undetermined function.. 
PF06220 zf-U1; U1_C; <br>Pfam-B_10606 (release 9.0). This family consists of several U1 small nuclear ribonucleoprotein C (U1-C) proteins. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site (ss) at early stages of spliceosome assembly.  Recruitment of U1 to a class of weak 5' ss is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' ss. Binding of TIA-1 in the vicinity of a 5' ss helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator  . This domain is probably a zinc-binding.  It is found in multiple copies in some members of the family.. 
PF06221 Zf-C2HC5; <br>Putative zinc finger motif, C2HC5-type. Pfam-B_11300 (release 9.0). This zinc finger appears to be common in activating signal  cointegrator 1/thyroid receptor interacting protein 4.. 
PF06222 Phage tail assembly chaperone<br>Pfam-B_11379 (release 9.0). 
PF06223 Minor tail protein T<br>Pfam-B_8084 (release 9.0). Minor tail protein T is located at the distal end and is involved in the assembly of the initiator complex for tail polymerisation  .. 
PF06224 DUF1006;<br>Winged helix DNA-binding domain. Pfam-B_8424 (release 9.0). This family contains two copies of a winged helix domain.. 
PF06226 Protein of unknown function (DUF1007)<br>Pfam-B_8585 (release 9.0). Family of conserved bacterial proteins with unknown function.. 
PF06227 Orthopox_N1;<br>Pfam-B_10619 (release 9.0). This is a family of dsDNA viruses, with no RNA stage, Poxvirus proteins.. 
PF06228 DUF1008;<br>Haem utilisation ChuX/HutX. Pfam-B_10620 (release 9.0). This family is found within haem utilisation operons. It has a similar structure to that of Pfam:PF05171. Pfam:PF05171 usually occurs as a duplicated domain, but this domain occurs as a single domain and forms a dimer. The organisation of the dimer is very similar to that of the duplicated Pfam:PF05171 domains [1,2]. It binds haem via conserved histidines  .. 
PF06229 FRG1-like family<br>Pfam-B_8590 (release 9.0). The human FRG1 gene maps to human chromosome 4q35 and has been identified   as a candidate for facioscapulohumeral muscular dystrophy.  Currently, the function of FRG1 is unknown  .. 
PF06230 Protein of unknown function (DUF1009)<br>Pfam-B_8705 (release 9.0). Family of uncharacterised bacterial proteins.. 
PF06231 Protein of unknown function (DUF1010)<br>Pfam-B_11467 (release 9.0). Family of plasmid encoded proteins with unknown function.. 
PF06232 Embryo-specific protein 3, (ATS3)<br>Pfam-B_11504 (release 9.0). Family of plant seed-specific proteins.. 
PF06233 Usg-like family<br>Pfam-B_11528 (release 9.0). Family of bacterial proteins, referred to as Usg. Usg is found in the same operon as trpF, trpB, and trpA and is expressed in a coupled transcription-translation system  .. 
PF06234 Toluene-4-monooxygenase system protein B (TmoB)<br>Moxon SJ, Iyer LM, Burroughs AM, Aravind L. Pfam-B_10626 (release 9.0). This family consists of several Toluene-4-monooxygenase system protein B (TmoB) sequences. Pseudomonas mendocina KR1 metabolises toluene as a carbon source. The initial step of the pathway is hydroxylation of toluene to form p-cresol by a multicomponent toluene-4-monooxygenase (T4MO) system  . TmoB adopts a ubiquitin fold  . Although TmoB is a component of the T4MO system, its  precise role remains unclear.. 
PF06235 NADH dehydrogenase subunit 4L (NAD4L)<br>Pfam-B_10667 (release 9.0). This family consists of NADH dehydrogenase subunit 4L (NAD4L) proteins from the mitochondria of several parasitic flatworms.. 
PF06236 Tyrosinase co-factor MelC1<br>Pfam-B_10673 (release 9.0). This family consists of several tyrosinase co-factor MELC1 proteins from a number of Streptomyces species. The melanin operon (melC) of Streptomyces antibioticus contains two genes, melC1 and melC2 (apotyrosinase). It is thought that MelC1 forms a transient binary complex with the downstream apotyrosinase MelC2 to facilitate the incorporation of copper ion and the secretion of tyrosinase indicating that MelC1 is a chaperone for the apotyrosinase MelC2  .. 
PF06237 Protein of unknown function (DUF1011)<br>Pfam-B_11463 (release 9.0). Family of uncharacterised eukaryotic proteins.. 
PF06238 Borrelia_lipopr; <br>Borrelia burgdorferi BBR25 lipoprotein. Pfam-B_15000 (release 9.0). This family consists of a number of lipoproteins from the Lyme disease spirochete Borrelia burgdorferi  .. 
PF06239 Evolutionarily conserved signalling intermediate in Toll pathway<br>Pfam-B_9306 (release 9.0). Activation of NF-kappaB as a consequence of signaling through the Toll and IL-1 receptors is a major element of innate immune responses. ECSIT plays an important role in signalling to NF-kappaB, functioning as the intermediate in the signaling pathways between TRAF-6 and MEKK-1  .. 
PF06240 CoxG; <br>Carbon monoxide dehydrogenase subunit G (CoxG). Pfam-B_9339 (release 9.0). The CO dehydrogenase structural genes coxMSL are flanked by nine accessory genes arranged as the cox gene cluster. The cox genes are specifically and coordinately transcribed under chemolithoautotrophic conditions in the presence of CO as carbon and energy source  .. 
PF06241 Protein of unknown function (DUF1012)<br>Pfam-B_9320 (release 9.0). Family of uncharacterised proteins found in both eukaryotes and bacteria.. 
PF06242 Protein of unknown function (DUF1013)<br>Pfam-B_9390 (release 9.0). Family of uncharacterised proteins found in Proteobacteria.. 
PF06243 Phenylacetic acid degradation B<br>Pfam-B_9426 (release 9.0). Phenylacetic acid degradation protein B (PaaB) is thought to be part of  a multicomponent oxygenase involved in  phenylacetyl-CoA hydroxylation  .. 
PF06244 Protein of unknown function (DUF1014)<br>Moxon SJ, Coggill PC. Pfam-B_11009 (release 9.0). This family consists of several hypothetical eukaryotic proteins of unknown function.. 
PF06245 Protein of unknown function (DUF1015)<br>Pfam-B_9451 (release 9.0). Family of proteins with unknown function found in archaea and bacteria.. 
PF06246 Isy1-like splicing family<br>Pfam-B_9462 (release 9.0). Isy1 protein is important in the optimisation of splicing  .. 
PF06247 Plasmodium ookinete surface protein Pvs28<br>Pfam-B_11346 (release 9.0). This family consists of several ookinete surface protein (Pvs28) from several species of Plasmodium. Pvs25 and Pvs28 are expressed on the surface of ookinetes. These proteins are potential candidates for vaccine and induce antibodies that block the infectivity of Plasmodium vivax in immunised animals  .. 
PF06248 Centromere/kinetochore Zw10<br>Pfam-B_9476 (release 9.0). Zw10 and rough deal proteins are both required for correct metaphase check-pointing during mitosis [1,2]. These proteins bind to the centromere/kinetochore  .. 
PF06249 Ethanolamine utilisation protein EutQ<br>Pfam-B_11530 (release 9.0). The eut operon of Salmonella typhimurium encodes proteins involved in the cobalamin-dependent degradation of ethanolamine. The role of EutQ in this process is unclear  .. 
PF06250 Protein of unknown function (DUF1016)<br>Pfam-B_9571 (release 9.0). Family of uncharacterised proteins found in viruses, archaea and bacteria.. 
PF06251 DUF1017;<br>Capsule biosynthesis GfcC. Pfam-B_9574 (release 9.0). Many bacteria are covered in a layer of surface-associated polysaccharide called the capsule. These capsules can be divided into four groups depending upon the organisation of genes responsible for capsule assembly, the assembly pathway and regulation  .  This family plays a role in group 4 capsule biosynthesis  .  These proteins have a beta-grasp fold  . Two beta-grasp domains, D2 and D3, are arranged in tandem. There is a C-terminal amphipathic helix which packs against D3. A helical hairpin insert in D2 binds to D3 and constrains its position, a conserved arginine residue at the end of this hairpin is essential for structural integrity  .. 
PF06252 Protein of unknown function (DUF1018)<br>Pfam-B_11125 (release 9.0). This family consists of several bacterial and phage proteins of unknown function.. 
PF06253 Trimethylamine methyltransferase (MTTB)<br>Pfam-B_11132 (release 9.0). This family consists of several trimethylamine methyltransferase (MTTB) (EC:2.1.1.-) proteins from numerous Rhizobium and Methanosarcina species.. 
PF06254 Protein of unknown function (DUF1019)<br>Pfam-B_9681 (release 9.0). Family of uncharacterised proteins found in Proteobacteria.. 
PF06255 Protein of unknown function (DUF1020)<br>Pfam-B_11136 (release 9.0). This family consists of several MafB proteins from Neisseria meningitidis and Neisseria gonorrhoeae. The function of this family is unknown.. 
PF06256 Nucleopolyhedrovirus LEF-12 protein<br>Pfam-B_11198 (release 9.0). This family consists of several Nucleopolyhedrovirus late expression factor-12 (LEF-12) proteins. The function of this family is unknown [1,2].. 
PF06257 Protein of unknown function (DUF1021)<br>Pfam-B_11556 (release 9.0). This family consists of several hypothetical bacterial proteins of unknown function.. 
PF06258 DUF1022;<br>Mitochondrial fission ELM1. Moxon SJ, Eberhardt R. Pfam-B_10595 (release 9.0). In plants, this family is involved in mitochondrial fission. It binds to dynamin-related proteins and plays a role in their relocation from the cytosol to mitochondrial fission sites  . Its function in bacteria is unknown.. 
PF06259 DUF1023;<br>Alpha/beta hydrolase. Pfam-B_9720 (release 9.0). Members of this family are predicted to have an alpha/beta hydrolase fold. They contain a predicted Ser-His-Asp catalytic triad, in which the serine is likely to act as a nucleophile  .. 
PF06260 Protein of unknown function (DUF1024)<br>Pfam-B_11584 (release 9.0). This family consists of several hypothetical Staphylococcus aureus and Staphylococcus aureus phage phi proteins. The function of this family is unknown.. 
PF06261 Actinobacillus actinomycetemcomitans leukotoxin activator LktC<br>Pfam-B_11552 (release 9.0). This family consists of several Actinobacillus actinomycetemcomitans leukotoxin activator (LktC) proteins. Actinobacillus actinomycetemcomitans is a Gram-negative bacterium that has been implicated in the etiology of several forms of periodontitis, especially localised juvenile periodontitis. LktC along with LktB and LktD are thought to be required for activation and localisation of the leukotoxin  .  . 
PF06262 Possibl zinc metallo-peptidase<br>Pfam-B_9726 (release 9.0). This is possibly a family of bacterial zinc metallo-peptidases. Although they carry the HExxHxxGxxD motif, they are missing a final methionine which would class them as Met-zincins.. 
PF06265 Protein of unknown function (DUF1027)<br>Pfam-B_11526 (release 9.0). This family consists of several hypothetical bacterial proteins of unknown function.. 
PF06266 HrpF protein<br>Pfam-B_11646 (release 9.0). The species Pseudomonas syringae encompasses plant pathogens with differing host specificities and corresponding pathovar designations. P. syringae requires the Hrp (type III protein secretion) system, encoded by a 25-kb cluster of hrp and hrc genes, in order to elicit the hypersensitive response (HR) in nonhosts or to be pathogenic in hosts. The exact function of HrpF is unknown but the protein is needed for pathogenicity  .. 
PF06267 Family of unknown function (DUF1028)<br>Pfam-B_9747 (release 9.0). Family of bacterial and archaeal proteins with unknown function. Some members are associated with a C-terminal peptidoglycan binding domain. So perhaps this could be an enzyme involved in peptidoglycan metabolism.. 
PF06268 Fascin domain<br>Pfam-B_11660 (release 9.0). This family consists of several eukaryotic fascin or singed proteins.  The fascins are a structurally unique and evolutionarily conserved group of actin cross-linking proteins. Fascins function in the organisation of two major forms of actin-based structures: dynamic, cortical cell protrusions and cytoplasmic microfilament bundles. The cortical structures, which include filopodia, spikes, lamellipodial ribs, oocyte microvilli and the dendrites of dendritic cells, have roles in cell-matrix adhesion, cell interactions and cell migration, whereas the cytoplasmic actin bundles appear to participate in cell architecture  .\.       Dictyostelium hisactophilin, another actin-binding protein, is a submembranous pH sensor that signals slight changes of the H+ concentration to actin by inducing actin polymerisation and binding to microfilaments only at pH values below seven  .  Members of this family are histidine rich, typically contain the repeated motif of HHXH  .. 
PF06269 Protein of unknown function (DUF1029)<br>Pfam-B_11672 (release 9.0). This family consists of several short Chordopoxvirus proteins of unknown function.. 
PF06270 Protein of unknown function (DUF1030)<br>Pfam-B_11673 (release 9.0). This family consists of several short Circovirus proteins of unknown function.. 
PF06271 RDD family<br>Pfam-B_1111 (release 9.0). 
PF06273 Plant_eIF4B; <br>Plant specific eukaryotic initiation factor 4B. Pfam-B_11679 (release 9.0). This family consists of several plant specific eukaryotic initiation factor 4B proteins.. 
PF06275 Protein of unknown function (DUF1031)<br>Pfam-B_11618 (release 9.0). This family consists of several Lactococcus lactis bacteriophage and Lactococcus lactis proteins of unknown function.. 
PF06276 Ferric iron reductase FhuF-like transporter<br>Pfam-B_11690 (release 9.0). This family consists of several bacterial ferric iron reductase protein (FhuF) sequences.\.      FhuF is involved in the reduction of ferric iron in cytoplasmic ferrioxamine B  .  This family also includes the IucA and IucC proteins.. 
PF06277 Ethanolamine utilisation protein EutA<br>Pfam-B_11716 (release 9.0). This family consists of several bacterial EutA ethanolamine utilisation proteins. The EutA protein is thought to protect the lyase (EutBC) from inhibition by CNB12  .. 
PF06278 Protein of unknown function (DUF1032)<br>Pfam-B_11729 (release 9.0). This family consists of several conserved eukaryotic proteins of unknown function.. 
PF06279 Protein of unknown function (DUF1033)<br>Pfam-B_11732 (release 9.0). This family consists of several hypothetical bacterial proteins. Many of the sequences in this family are annotated as putative DNA binding proteins but the function of this family is unknown.. 
PF06280 Fn3-like domain (DUF1034)<br>This family consists of several domains of unknown function which are present in several bacterial and plant peptidases. This domain is found in conjunction with Pfam:PF00082, Pfam:PF02225 and is often found with Pfam:PF00746. This domain has a structure similar to an Fn3 domain  .. 
PF06281 Protein of unknown function (DUF1035)<br>Pfam-B_11733 (release 9.0). This family consists of several Sulfolobus and Sulfolobus virus proteins of unknown function.. 
PF06282 Protein of unknown function (DUF1036)<br>Pfam-B_11760 (release 9.0). This family consists of several hypothetical bacterial proteins of unknown function.. 
PF06283 DUF1037; <br>Trehalose utilisation. Pfam-B_11803 (release 9.0). This family consists of several bacterial ThuA like proteins. ThuA appears to be involved in utilisation of trehalose  . The thuA and thuB genes form part of the trehalose/sucrose transport operon thuEFGKAB, which is located on the pSymB megaplasmid. The thuA and thuB genes are induced in vitro by trehalose but not by sucrose and the extent of its induction depends on the concentration of trehalose available in the medium  .. 
PF06284 Cytomegalo_UL84; <br>Cytomegalovirus UL84 protein. Pfam-B_11948 (release 9.0). This family consists of several Cytomegalovirus UL84 proteins. The open reading frame UL84 of human cytomegalovirus encodes a multifunctional regulatory protein which is required for viral DNA replication and binds with high affinity to the immediate-early transactivator IE2-p86  .. 
PF06286 Coleoptericin<br>Pfam-B_11996 (release 9.0). This family consists of several insect Coleoptericin, Acaloleptin, Holotricin and Rhinocerosin proteins which are all known to be antibacterial proteins  .. 
PF06287 Protein of unknown function (DUF1039)<br>Pfam-B_12079 (release 9.0). This family consists of several hypothetical bacterial proteins from Escherichia coli and Citrobacter rodentium. The function of this family is unknown.. 
PF06288 Protein of unknown function (DUF1040)<br>Pfam-B_12122 (release 9.0). This family consists of several bacterial YihD proteins of unknown function  .  . 
PF06289 Flagellar protein (FlbD)<br>Pfam-B_12586 (release 9.0). This family consists of several bacterial FlbD flagellar proteins. The exact function of this family is unknown  .. 
PF06290 Plasmid SOS inhibition protein (PsiB)<br>Pfam-B_12789 (release 9.0). This family consists of several plasmid SOS inhibition protein (PsiB) sequences  .. 
PF06291 Bor protein<br>Pfam-B_12850 (release 9.0). This family consists of several Bacteriophage lambda Bor and Escherichia coli Iss proteins. Expression of bor significantly increases the survival of the Escherichia coli host cell in animal serum. This property is a well known bacterial virulence determinant indeed, bor and its adjacent sequences are highly homologous to the iss serum resistance locus of the plasmid ColV2-K94, which confers virulence in animals. It has been suggested that lysogeny may generally have a role in bacterial survival in animal hosts, and perhaps in pathogenesis  .. 
PF06292 Domain of Unknown Function (DUF1041)<br>This family consists of several eukaryotic domains of unknown function. Members of this family are often found in tandem repeats and co-occur with Pfam:PF00168, Pfam:PF00130 and Pfam:PF00169 domains.. 
PF06293 Lipopolysaccharide kinase (Kdo/WaaP) family<br>Krupa A, Srinivasan N. These lipopolysaccharide kinases are related to protein kinases Pfam:PF00069. This family includes waaP (rfaP) gene product is required for the addition of phosphate to O-4 of the first heptose residue of the lipopolysaccharide (LPS) inner core region. It has previously been shown that WaaP is  necessary for resistance to hydrophobic and polycationic antimicrobials in E. coli and that it is required for virulence in invasive strains of S. enterica  .. 
PF06294 Domain of Unknown Function (DUF1042)<br>Spef is a region of sperm flagellar proteins. It probably exerts a role in spermatogenesis in that the protein is expressed predominantly in adult tissue. It is present in the tails of developing and epididymal sperm internal to the fibrous sheath and around the dense outer fibres of the sperm flagellum  . The amino-terminal domain (residues 1-110) shows a possible calponin homology (CH) domain; however Spef does not bind actin directly under in vitro conditions, so the function of the amino-terminal calponin-like domain is unclear  . Transcription aberrations leading to a truncated protein result in immotile sperm  .. 
PF06295 Protein of unknown function (DUF1043)<br>Pfam-B_12007 (release 9.0). This family consists of several hypothetical bacterial proteins of unknown function.. 
PF06296 Protein of unknown function (DUF1044)<br>Pfam-B_12045 (release 9.0). This family consists of several hypothetical bacterial proteins of unknown function.. 
PF06297 PET Domain<br>This domain is suggested to be involved in protein-protein interactions  . The family is found in conjunction with Pfam:PF00412.. 
PF06298 Photosystem II protein Y (PsbY)<br>Pfam-B_12212 (release 9.0). This family consists of several bacterial and plant photosystem II protein Y (PsbY) sequences. PsbY is a manganese-binding protein that has an L-arginine metabolising enzyme activity  .. 
PF06299 Protein of unknown function (DUF1045)<br>Pfam-B_12127 (release 9.0). This family consists of several hypothetical proteins from Agrobacterium, Rhizobium and Brucella species. The function of this family is unknown.. 
PF06300 Tsp45I type II restriction enzyme<br>Pfam-B_12151 (release 9.0). This family consists of several type II restriction enzymes.. 
PF06301 Bacteriophage lambda Kil protein<br>Pfam-B_12201 (release 9.0). This family consists of several Bacteriophage lambda Kil protein like sequences from both phages and bacteria. Induction of a lambda prophage causes the death of the host cell even in the absence of phage replication and lytic functions due to expression of the lambda kil gene  .. 
PF06303 DUF1047; <br>Organiser of macrodomain of Terminus of chromosome. Pfam-B_12243 (release 9.0). This family, many of whose members are YcbG, organises the macrodomain Ter of the chromosome of bacteria such as E coli. In these bacteria, insulated macrodomains influence the segregation of sister chromatids and the mobility of chromosomal DNA. Organisation of the Terminus region (Ter) into a macrodomain relies on the presence of a 13 bp motif called matS repeated 23 times in the 800-kb-long domain. MatS sites are the main targets in the E. coli chromosome of YcbG or MatP (macrodomain Ter protein). MatP accumulates in the cell as a discrete focus that co-localises with the Ter macrodomain. The effects of MatP inactivation reveal its role as the main organiser of the Ter macrodomain: in the absence of MatP, DNA is less compacted, the mobility of markers is increased, and segregation of the Ter macrodomain occurs early in the cell cycle. A specific organisational system is required in the Terminus region for bacterial chromosome management during the cell cycle.. 
PF06304 Protein of unknown function (DUF1048)<br>Pfam-B_12247 (release 9.0). This family consists of several hypothetical bacterial proteins of unknown function.. 
PF06305 Protein of unknown function (DUF1049)<br>Pfam-B_12262 (release 9.0). This family consists of several hypothetical bacterial proteins of unknown function.. 
PF06306 Beta-1,4-N-acetylgalactosaminyltransferase (CgtA)<br>Pfam-B_12320 (release 9.0). This family consists of several beta-1,4-N-acetylgalactosaminyltransferase proteins from Campylobacter jejuni  .. 
PF06307 Herpesvirus IR6 protein<br>Pfam-B_12322 (release 9.0). This family consists of several Herpesvirus IR6 proteins. The equine herpesvirus 1 (EHV-1) IR6 protein forms typical rod-like structures in infected cells, influences virus growth at elevated temperatures, and determines the virulence of EHV-1 Rac strains  .. 
PF06308 23S rRNA methylase leader peptide (ErmC)<br>Pfam-B_12332 (release 9.0). This family consists of several very short bacterial 23S rRNA methylase leader peptide (ErmC) sequences. ermC confers resistance to macrolide-lincosamide streptogramin B antibiotics by specifying a ribosomal RNA methylase, which results in decreased ribosomal affinity for these antibiotics. ermC expression is induced by exposure to erythromycin  .  . 
PF06311 NUMB domain<br>This presumed domain is found in the Numb family of proteins adjacent to the PTB domain... 
PF06312 Neurexophilin<br>Pfam-B_12369 (release 9.0). This family consists of mammalian neurexophilin proteins. Mammalian brains contain four different neurexophilin proteins. Neurexophilins form a family of related glycoproteins that are proteolytically processed after synthesis and bind to alpha-neurexins. The structure and characteristics of neurexophilins indicate that they function as neuropeptides that may signal via alpha-neurexins  . . 
PF06309 Torsin<br>Pfam-B_12047 (release 9.0). This family consists of several eukaryotic torsin proteins. Torsion dystonia is an autosomal dominant movement disorder characterised by involuntary, repetitive muscle contractions and twisted postures. The most severe early-onset form of dystonia has been linked to mutations in the human DYT1 (TOR1A) gene encoding a protein termed torsinA. While causative genetic alterations have been identified, the function of torsin proteins and the molecular mechanism underlying dystonia remain unknown. Phylogenetic analysis of the torsin protein family indicates these proteins share distant sequence similarity with the large and diverse family of (Pfam:PF00004) proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia  .. 
PF06313 Drosophila ACP53EA protein<br>Pfam-B_12718 (release 9.0). This family consists of several Drosophila ACP53EA accessory gland (seminal) proteins.. 
PF06314 Acetoacetate decarboxylase (ADC)<br>Pfam-B_12720 (release 9.0). This family consists of several acetoacetate decarboxylase (ADC) proteins (EC:4.1.1.4).. 
PF06315 Isocitrate dehydrogenase kinase/phosphatase (AceK)<br>Pfam-B_13100 (release 9.0). This family consists of several bacterial isocitrate dehydrogenase kinase/phosphatase (AceK) proteins (EC:2.7.1.116)  .. 
PF06316 Enterobacterial Ail/Lom protein<br>Pfam-B_12325 (release 9.0). This family consists of several bacterial and phage Ail/Lom-like proteins. The Yersinia enterocolitica Ail protein is a known virulence factor. Proteins in this family are predicted to consist of eight transmembrane beta-sheets and four cell surface-exposed loops. It is thought that Ail directly promotes invasion and loop 2 contains an active site, perhaps a receptor-binding domain  .  The phage protein Lom is expressed during lysogeny, and encode host-cell envelope proteins. Lom is found in the bacterial outer membrane, and is homologous to virulence proteins of two other enterobacterial genera. It has been suggested that lysogeny may generally have a role in bacterial survival in animal hosts, and perhaps in pathogenesis  .. 
PF06317 Arenavirus RNA polymerase<br>Pfam-B_12490 (release 9.0). This family consists of several Arenavirus RNA polymerase proteins (EC:2.7.7.48)  .. 
PF06319 Protein of unknown function (DUF1052)<br>Pfam-B_12539 (release 9.0). This family consists of several bacterial proteins of unknown function.. 
PF06320 GCN5-like protein 1 (GCN5L1)<br>Pfam-B_12526 (release 9.0). This family consists of several eukaryotic GCN5-like protein 1 (GCN5L1) sequences. The function of this family is unknown [1,2].. 
PF06321 Major fimbrial subunit protein (FimA)<br>Pfam-B_13339 (release 9.0). This family consists of several Porphyromonas gingivalis major fimbrial subunit protein (FimA) sequences. Fimbriae of Porphyromonas gingivalis, a periodontopathogen, play an important role in its adhesion to and invasion of host cells. The fimA genes encoding fimbrillin (FimA), a subunit protein of fimbriae, have been classified into five types, types I to V, based on nucleotide sequences. It has been found that type II FimA can bind to epithelial cells most efficiently through specific host receptors  . Human dental plaque is a multispecies microbial biofilm that is associated with two common oral diseases, dental caries and periodontal disease.  There is an inter-species contact-dependent communication system between P. gingivalis and S. cristatus that involces the Arc-A enzyme  .. 
PF06322 Phage NinH protein<br>Pfam-B_12973 (release 9.0). This family consists of several phage NinH proteins. The function of this family is unknown.. 
PF06323 Phage antitermination protein Q<br>Pfam-B_12730 (release 9.0). This family consists of several phage antitermination protein Q and related bacterial sequences. Phage 82 gene Q encodes a phage-specific positive regulator of late gene expression, thought, by analogy to the corresponding gene of phage lambda, to be a transcription antiterminator  .  . 
PF06324 Pigment-dispersing hormone (PDH)<br>Pfam-B_12230 (release 9.0). This family consists of several eukaryotic pigment-dispersing hormone (PDH) proteins. The pigment-dispersing hormone (PDH) is produced in the eyestalks of Crustacea where it induces light-adapting movements of pigment in the compound eye and regulates the pigment dispersion in the chromatophores  .. 
PF06325 Ribosomal protein L11 methyltransferase (PrmA)<br>Pfam-B_12272 (release 9.0). This family consists of several Ribosomal protein L11 methyltransferase (EC:2.1.1.-) sequences.. 
PF06326 Vesiculovirus matrix protein<br>Pfam-B_13088 (release 9.0). This family consists of several Vesiculovirus matrix proteins. The matrix (M) protein of vesicular stomatitis virus (VSV) expressed in the absence of other viral components causes many of the cytopathic effects of VSV, including an inhibition of host gene expression and the induction of cell rounding. It has been shown that M protein also induces apoptosis in the absence of other viral components. It is thought that the activation of apoptotic pathways causes the inhibition of host gene expression and cell rounding by M protein  .. 
PF06327 Domain of Unknown Function (DUF1053)<br>This domain is found in Adenylate cyclases.. 
PF06328 Ig-like C2-type domain<br>This domain is a ligand-binding immunoglobulin-like domain  . The two cysteine residues form a disulphide bridge.. 
PF06330 Trichodiene synthase (TRI5)<br>Pfam-B_13220 (release 9.0). This family consists of several fungal trichodiene synthase proteins (EC:4.2.3.6). TRI5 encodes the enzyme trichodiene synthase, which has been shown to catalyse the first step in the trichothecene pathways of Fusarium and Trichothecium species [1,2]. . 
PF06331 REX1; <br>Transcription factor TFIIH complex subunit Tfb5. This family is a component of the general transcription and DNA repair factor IIH.  TFB5 has been shown to be required for efficient recruitment of TFIIH to a promoter  .. 
PF06333 TRAP240; TRAP_240kDa; Med13; <br>Mediator complex subunit 13 C-terminal. Mediator is a large complex of up to 33 proteins that is conserved from plants through fungi to humans - the number and representation of individual subunits varying with species [1-2]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Med13 is part of the ancillary kinase module, together with Med12, CDK8 and CycC, which in yeast is implicated in transcriptional repression, though most of this activity is likely attributable to the CDK8 kinase. The large Med12 and Med13 proteins are required for specific developmental processes in Drosophila, zebrafish, and Caenorhabditis elegans but their biochemical functions are not understood  .. 
PF06334 Orthopoxvirus A47 protein<br>Pfam-B_13263 (release 9.0). This family consists of several Orthopoxvirus A47 proteins. The function of this family is unknown.. 
PF06335 Protein of unknown function (DUF1054)<br>Pfam-B_13269 (release 9.0). This family consists of several hypothetical bacterial proteins of unknown function.. 
PF06336 Coronavirus 5a protein<br>Pfam-B_13277 (release 9.0). This family consists of several Coronavirus 5a proteins. The function of this family is unknown  .. 
PF06337 DUF1055;<br>The DUSP (domain present in ubiquitin-specific protease) domain is found at the N-terminus of Ubiquitin-specific proteases. The structure of this domain has been solved  . Its tripod-like structure consists of a 3-fold alpha-helical bundle supporting a triple-stranded anti-parallel beta-sheet  .. 
PF06338 ComK protein<br>Pfam-B_13324 (release 9.0). This family consists of several bacterial ComK proteins. The ComK protein of Bacillus subtilis positively regulates the transcription of several late competence genes as well as comK itself. It has been found that ClpX plays an important role in the regulation of ComK at the post-transcriptional level  .. 
PF06339 Ectoine synthase<br>Pfam-B_14542 (release 9.0). This family consists of several bacterial ectoine synthase proteins. The ectABC genes encode the diaminobutyric acid acetyltransferase (EctA), the diaminobutyric acid aminotransferase (EctB), and the ectoine synthase (EctC). Together these proteins constitute the ectoine biosynthetic pathway  .. 
PF06340 Vibrio cholerae toxin co-regulated pilus biosynthesis protein F<br>Pfam-B_13058 (release 9.0). This family consists of several Vibrio cholerae toxin co-regulated pilus biosynthesis protein F (TcpF) sequences. TcpF is known to be a secreted virulence protein but its exact function is unknown  .. 
PF06341 Protein of unknown function (DUF1056)<br>Pfam-B_13260 (release 9.0). This family consists of several putative head-tail joining bacteriophage proteins.. 
PF06342 Alpha/beta hydrolase of unknown function (DUF1057)<br>Pfam-B_13294 (release 9.0). This family consists of several Caenorhabditis elegans specific proteins of unknown function. Members of this family have an alpha/beta hydrolase fold.. 
PF06344 VPG_P3B; <br>Parechovirus Genome-linked protein. This family is of the Parechovirus genome-linked protein Vpg type P3B.. 
PF06345 DRF Autoregulatory Domain<br>This motif is found in Diaphanous-related formins. It binds the N-terminal GTPase-binding domain; this link is broken when GTP-bound Rho binds to the GBD and activates the protein. The addition of DAD to mammalian cells induces actin filament formation, stabilises microtubules,  and activates serum-response mediated transcription ( ).. 
PF06346 Formin Homology Region 1<br>This region is found in some of the Diaphanous related formins (Drfs) ( ). It consists of low complexity repeats of around 12 residues.. 
PF06347 Bacterial SH3 domain<br>Pfam-B_13248 (release 9.0). This family consists of several hypothetical bacterial proteins of unknown function. These are composed of SH3-like domains.. 
PF06348 Protein of unknown function (DUF1059)<br>Pfam-B_13303 (release 9.0). This family consists of several short hypothetical archaeal proteins of unknown function.. 
PF06350 HSL; <br>Hormone-sensitive lipase (HSL) N-terminus. Pfam-B_13329 (release 9.0). This family consists of several mammalian hormone-sensitive lipase (HSL) proteins (EC:3.1.1.-). Hormone-sensitive lipase, a key enzyme in fatty acid mobilisation, overall energy homeostasis, and possibly steroidogenesis, is acutely controlled through reversible phosphorylation by catecholamines and insulin  .. 
PF06351 Allene oxide cyclase<br>Pfam-B_13374 (release 9.0). This family consists of several plant specific allene oxide cyclase proteins (EC:5.3.99.6). The allene oxide cyclase (AOC)-catalysed step in jasmonate (JA) biosynthesis is important in the wound response of tomato  .  . 
PF06353 Protein of unknown function (DUF1062)<br>Pfam-B_13377 (release 9.0). This family consists of several hypothetical bacterial proteins of unknown function.. 
PF06355 Aegerolysin<br>Pfam-B_13415 (release 9.0). This family consists of several bacterial and eukaryotic Aegerolysin-like proteins. It has been found that aegerolysin and ostreolysin are expressed during formation of primordia and fruiting bodies. It has been suggested that these haemolysins play an important role in initial phase of fungal fruiting. The bacterial members of this family are expressed during sporulation  .  Ostreolysin was found cytolytic to various erythrocytes and tumour cells  . It forms transmembrane pores 4 nm in diameter. The activity is inhibited by total membrane lipids, and modulated by lysophosphatides. The potential use of aegerolysins is reviewed   with special emphasis on their properties which would allow thier use in therapeutics.. 
PF06356 Protein of unknown function (DUF1064)<br>Pfam-B_13437 (release 9.0). This family consists of several phage and bacterial proteins of unknown function.. 
PF06357 Omega-atracotox;<br>Pfam-B_14633 (release 9.0). This family consists of several Hadronyche versuta (Blue mountains funnel-web spider) specific omega-atracotoxin proteins. Omega-Atracotoxin-Hv1a is an insect-specific neurotoxin whose phylogenetic specificity derives from its ability to antagonise insect, but not vertebrate, voltage-gated calcium channels. Two spatially proximal residues, Asn(27) and Arg(35), form a contiguous molecular surface that is essential for toxin activity. It has been proposed that this surface of the beta-hairpin is a key site for interaction of the toxin with insect calcium channels  . . 
PF06358 Protein of unknown function (DUF1065)<br>Pfam-B_14830 (release 9.0). This family consists of several Benyvirus proteins of unknown function.. 
PF06360 Euplotes raikovi mating pheromone<br>Pfam-B_14708 (release 9.0). This family consists of several Euplotes raikovi mating pheromone proteins. Diffusible polypeptide pheromones, which distinguish otherwise morphologically identical vegetative cell types from one another, are produced by some species of ciliates. In the marine sand-dwelling protozoan ciliate Euplotes raikovi, pheromone molecules promote the vegetative reproduction (mitogenic proliferation or growth) of the same cells from which they originate. As, understandably, such autocrine pheromone activity is primary to that of targeting and inducing a foreign cell to mate (paracrine functions), this finding provides an example of how the original function of a molecule can be obscured during evolution by the acquisition of a new one  .. 
PF06361 Rice tungro bacilliform virus P12 protein<br>Pfam-B_14960 (release 9.0). This family consists of several Rice tungro bacilliform virus P12 proteins. The function of this family is unknown  .. 
PF06362 Protein of unknown function (DUF1067)<br>Pfam-B_15074 (release 9.0). This family consists of several hypothetical Mycobacterium leprae specific proteins. The function of this family is unknown.. 
PF06363 Picornaviridae P3A protein<br>This family consists of the P3A protein of  picornaviridae. P3A has been identified as a genome-linked protein (VPg) and is involved in replication ( ).. 
PF06364 Protein of unknown function (DUF1068)<br>Pfam-B_14602 (release 9.0). This family consists of several hypothetical plant proteins from Arabidopsis thaliana and Oryza sativa. The function of this family is unknown.. 
PF06365 CD34/Podocalyxin family<br>Pfam-B_14609 (release 9.0) & Pfam-B_17463 (release 8.0). This family consists of several mammalian CD34 antigen proteins. The CD34 antigen is a human leukocyte membrane protein expressed specifically by lymphohematopoietic progenitor cells. CD34 is a phosphoprotein. Activation of protein kinase C (PKC) has been found to enhance CD34 phosphorylation  . This family contains several eukaryotic podocalyxin proteins. Podocalyxin is a major membrane protein of the glomerular epithelium and is thought to be involved in maintenance of the architecture of the foot processes and filtration slits characteristic of this unique epithelium by virtue of its high negative charge. Podocalyxin functions as an  anti-adhesin that maintains an open filtration pathway between neighbouring foot processes in the glomerular epithelium by charge repulsion  .. 
PF06366 Flagellar protein FlhE<br>Pfam-B_14631 (release 9.0). This family consists of several Enterobacterial FlhE flagellar proteins. The exact function of this family is unknown  .. 
PF06367 Diaphanous FH3 Domain<br>This region is found in the Formin-like and and diaphanous proteins [1,2].. 
PF06368 Methylaspartate mutase E chain (MutE)<br>Pfam-B_14693 (release 9.0). This family consists of several methylaspartate mutase E chain proteins (EC:5.4.99.1). Glutamate mutase catalyses the first step in the fermentation of glutamate by Clostridium tetanomorphum. This is an unusual isomerisation in which L-glutamate is converted to threo-beta-methyl L-aspartate  .. 
PF06369 Sea anemone cytotoxic protein<br>Pfam-B_14701 (release 9.0). Sea anemones are a rich source of cytotoxic proteins. Cytolysins comprise a group of more than 30 highly basic proteins with molecular masses of about 20 kDa. Cytolysins isolated from the sea anemone, Heteractis magnifica, include magnificalysin I (HMg I), magnificalysin II (HMg II) and Heteractis magnifica toxin (HMgtxn). These are highly homologous at their N-terminals. HMg I and II have molecular masses of approximately 19 kDa, and pI values of 9.4 and 10.0, respectively. Cytolysins isolated from other sea anemones Actinia tenebrosa (Tenebrosin-C, TN-C), Actinia equina (Equinatoxin, EqT) and Stichodactyla helianthus (ShC) exhibit pore-forming, haemolytic, cytotoxic, and heart stimulatory activities  .. 
PF06370 Protein of unknown function (DUF1069)<br>Pfam-B_14815 (release 9.0). This family consists of several Maize streak virus 21.7 kDa proteins. The function of this family is unknown.. 
PF06371 Diaphanous GTPase-binding Domain<br>This domain is bound to by GTP-attached Rho proteins, leading to activation of the Drf protein.. 
PF06372 Gemin6 protein<br>Pfam-B_14816 (release 9.0). This family consists of several mammalian Gemin6 proteins. The exact function of Gemin6 is unknown but it has been found to form part of the Pfam:PF06003 complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles  .. 
PF06373 Cocaine and amphetamine regulated transcript protein (CART)<br>Pfam-B_15325 (release 9.0). This family consists of several cocaine and amphetamine regulated transcript type I protein (CART) sequences. Cocaine and amphetamine regulated transcript (CART) peptide has been shown to be an anorectic peptide that inhibits both normal and starvation-induced feeding and completely blocks the feeding response induced by neuropeptide Y and regulated by leptin in the hypothalamus. The C-terminal part containing the three disulfide bridges is the biologically active part of the molecule affecting food intake. The solution structure of the active part of CART has a fold equivalent to other functionally distinct small proteins. CART consists mainly of turns and loops spanned by a compact framework composed by a few small stretches of antiparallel beta-sheet common to cystine knots  . . 
PF06374 NDUFC2; <br>NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2). Pfam-B_15334 (release 9.0). This family consists of several NADH-ubiquinone oxidoreductase subunit b14.5b proteins (EC:1.6.5.3).. 
PF06375 Bovine leukaemia virus receptor (BLVR)<br>Pfam-B_14559 (release 9.0). This family consists of several bovine specific leukaemia virus receptors which are thought to function as transmembrane proteins, although their exact function is unknown  .. 
PF06376 Protein of unknown function (DUF1070)<br>Pfam-B_14060 (release 9.0). This family consists of several short hypothetical plant proteins of unknown function.. 
PF06377 Adipokinetic hormone<br>Pfam-B_14600 (release 9.0). This family consists of several insect adipokinetic hormone as well as the related crustacean red pigment concentrating hormone. Flight activity of insects comprises one of the most intense biochemical processes known in nature, and therefore provides an attractive model system to study the hormonal regulation of metabolism during physical exercise. In long-distance flying insects, such as the migratory locust, both carbohydrate and lipid reserves are utilised as fuels for sustained flight activity. The mobilization of these energy stores in Locusta migratoria is mediated by three structurally related adipokinetic hormones (AKHs), which are all capable of stimulating the release of both carbohydrates and lipids from the fat body  .. 
PF06378 Protein of unknown function (DUF1071)<br>Pfam-B_14587 (release 9.0). This family consists of several hypothetical bacterial and phage proteins of unknown function.. 
PF06379 L-rhamnose-proton symport protein (RhaT)<br>Pfam-B_14617 (release 9.0). This family consists of several bacterial L-rhamnose-proton symport protein (RhaT) sequences [1,2].. 
PF06380 Protein of unknown function (DUF1072)<br>Pfam-B_14592 (release 9.0). This family consists of several Barley yellow dwarf virus proteins of unknown function.. 
PF06381 Protein of unknown function (DUF1073)<br>Pfam-B_14928 (release 9.0). This family consists of several hypothetical bacterial proteins. The function of this family is unknown.. 
PF06382 Protein of unknown function (DUF1074)<br>Pfam-B_14962 (release 9.0). This family consists of several proteins which appear to be specific to Drosophila melanogaster. The function of this family is unknown.. 
PF06384 Beta-catenin-interacting protein ICAT<br>Pfam-B_15027 (release 9.0). This family consists of several eukaryotic beta-catenin-interacting (ICAT) proteins. Beta-catenin is a multifunctional protein involved in both cell adhesion and transcriptional activation. Transcription mediated by the beta-catenin/Tcf complex is involved in embryological development and is upregulated in various cancers. ICAT selectively inhibits beta-catenin/Tcf binding in vivo, without disrupting beta-catenin/cadherin interactions  .. 
PF06385 Baculovirus LEF-11 protein<br>Pfam-B_15073 (release 9.0). This family consists of several Baculovirus LEF-11 proteins. The exact function of this family is unknown although it has been shown that LEF-11 is required for viral DNA replication during the infection cycle  .. 
PF06386 Gas vesicle synthesis protein GvpL/GvpF<br>Pfam-B_15376 (release 9.0). This family consists of several bacterial and archaeal gas vesicle synthesis protein (GvpL/GvpF) sequences. The exact function of this family is unknown.. 
PF06387 D1 dopamine receptor-interacting protein (calcyon)<br>Pfam-B_15400 (release 9.0). This family consists of several  D1 dopamine receptor-interacting (calcyon) proteins.  D1/D5 dopamine receptors in the basal ganglia, hippocampus, and cerebral cortex modulate motor, reward, and cognitive behaviour. D1-like dopamine receptors likely modulate neocortical and hippocampal neuronal excitability and synaptic function via Ca(2+) as well as cAMP-dependent signaling  . Defective calcyon proteins have been implicated in both attention-deficit/hyperactivity disorder (ADHD)   and schizophrenia  .. 
PF06388 Protein of unknown function (DUF1075)<br>Pfam-B_14186 (release 9.0). This family consists of several eukaryotic proteins of unknown function.. 
PF06389 Filovirus_VP24; <br>Filovirus membrane-associated protein VP24. Pfam-B_15734 (release 9.0). This family consists of several membrane-associated protein VP24 sequences from a variety of Ebola and Marburg viruses. The VP24 protein of Ebola virus is believed to be a secondary matrix protein and minor component of virions. VP24 possesses structural features commonly associated with viral matrix proteins and that VP24 may have a role in virus assembly and budding  .. 
PF06390 Neuroendocrine-specific golgi protein P55 (NESP55)<br>Pfam-B_16185 (release 9.0). This family consists of several mammalian neuroendocrine-specific golgi protein P55 (NESP55) sequences. NESP55 is a novel member of the chromogranin family and is a soluble, acidic, heat-stable secretory protein that is expressed exclusively in endocrine and nervous tissues, although less widely than chromogranins  .. 
PF06391 CDK-activating kinase assembly factor MAT1<br>Pfam-B_16773 (release 9.0). MAT1 is an assembly/targeting factor for cyclin-dependent kinase-activating kinase (CAK), which interacts with the transcription factor TFIIH  .  The domain found to the N-terminal side of this domain is a C3HC4 RING finger  .. 
PF06392 Acid shock protein repeat <br>Pfam-B_20230 (release 9.0). The Asr protein is synthesised as a precursor and the cleavage is essential for moderate to high acid tolerance  .. 
PF06393 BH3 interacting domain (BID)<br>Pfam-B_16321 (release 9.0). BID is a member of the BCL-2 superfamily of proteins are  key regulators of programmed cell death, hence this family is related to Pfam:PF00452 .  BID is a pro-apoptotic member of the Bcl-2 superfamily and as such posses the ability to target intracellular membranes and contains the BH3 death domain. The activity of BID is regulated by a Caspase 8-mediated cleavage event, exposing  the BH3 domain and significantly changing the surface  charge and hydrophobicity, which causes a change of  cellular localisation  .. 
PF06394 Pepsin inhibitor-3-like repeated domain<br>Pfam-B_13438 (release 9.0). Pepsin inhibitor-3 consisting of two domains, each comprising an antiparallel beta-sheet flanked by  an alpha-helix. In the enzyme-inhibitor complex, the  N-terminal beta-strand of PI-3 pairs with one strand  of the active site flap region of pepsin  . The two domains are tandem repeats of sequence, and has therefore been termed repeated domain.. 
PF06395 CDC24 Calponin<br>Pfam-B_32837 (release 8.0). Is a calponin homology domain.. 
PF06396 Angiotensin II, type I receptor-associated protein (AGTRAP)<br>Pfam-B_15509 (release 9.0). This family consists of several angiotensin II, type I receptor-associated protein (AGTRAP) sequences. AGTRAP is known to interact specifically with the carboxyl-terminal cytoplasmic region of the angiotensin II type 1 (AT(1)) receptor to regulate different aspects of AT(1) receptor physiology [1,2]. The function of this family is unclear.. 
PF06397 Desulfoferrodoxin, N-terminal domain<br>Pfam-B_11142 (release 9.0). Most members of this family are small (approximately 36 amino acids) proteins that from homodimeric complexes. Each subunit contains a high-spin iron atom tetrahedrally bound to four cysteinyl sulphur atoms This family has a similar fold to the rubredoxin metal binding domain  . It is also found as the N-terminal domain of desulfoferrodoxin, see (Pfam:PF01880).. 
PF06398 Integral peroxisomal membrane peroxin<br>Pfam-B_56111 (release 8.0). Peroxisomes play diverse roles in the cell, compartmentalising many activities related to lipid metabolism and functioning in the decomposition of toxic hydrogen peroxide. Sequence similarity was identified between two hypothetical proteins and the peroxin integral membrane protein Pex24p  .. 
PF06399 GTP cyclohydrolase I feedback regulatory protein (GFRP)<br>Pfam-B_63435 (release 9.0). Tetrahydrobiopterin, the cofactor required for hydroxylation  of aromatic amino acids regulates its own synthesis in via feedback inhibition of GTP cyclohydrolase I. This mechanism  is mediated by the regulatory subunit called GTP cyclohydrolase  I feedback regulatory protein (GFRP)  .. 
PF06400 Alpha-2-macroglobulin RAP, N-terminal domain<br>Pfam-B_44514 (release 9.0). The alpha-2-macroglobulin receptor-associated protein (RAP)  is a intracellular glycoprotein that binds to the 2-macroglobulin  receptor and other members of the low density lipoprotein receptor family. The protein inhibits binding of  all currently known ligands of these receptors  .  The N-terminal domain is predominately alpha helical  . Two different studies have provided conflicted domain boundaries [2,3].. 
PF06401 Alpha-2-macroglobulin RAP, C-terminal domain <br>Pfam-B_44514 (release 9.0). The alpha-2-macroglobulin receptor-associated protein (RAP)  is a intracellular glycoprotein that binds to the 2-macroglobulin  receptor and other members of the low density lipoprotein receptor family. The protein inhibits binding of  all currently known ligands of these receptors  .   Two different studies have provided conflicted domain boundaries [2,3].. 
PF06403 Lamprin<br>Pfam-B_15493 (release 9.0). This family consists of several lamprin proteins from the Sea lamprey Petromyzon marinus. Lamprin, an insoluble non-collagen, non-elastin protein, is the major connective tissue component of the fibrillar extracellular matrix of lamprey annular cartilage. Although not generally homologous to any other protein, soluble lamprins contain a tandemly repeated peptide sequence (GGLGY) which is present in both silkmoth chorion proteins and spider dragline silk. Strong homologies to this repeat sequence are also present in several mammalian and avian elastins. It is thought that these proteins share a structural motif which promotes self-aggregation and fibril formation in proteins through interdigitation of hydrophobic side chains in beta-sheet/beta-turn structures, a motif that has been preserved in recognisable form over several hundred million years of evolution  .. 
PF06404 Phytosulfokine precursor protein (PSK)<br>Pfam-B_16071 (release 9.0). This family consists of several plant specific phytosulfokine precursor proteins. Phytosulfokines, are active as either a pentapeptide or a C-terminally truncated tetrapeptide. These compounds were first isolated because of their ability to stimulate cell division in somatic embryo cultures of Asparagus officinalis  .. 
PF06405 Red chlorophyll catabolite reductase (RCC reductase)<br>Pfam-B_15577 (release 9.0). This family consists of several red chlorophyll catabolite reductase (RCC reductase) proteins. Red chlorophyll catabolite (RCC) reductase (RCCR) and pheophorbide (Pheide) a oxygenase (PaO) catalyse the key reaction of chlorophyll catabolism, porphyrin macrocycle cleavage of Pheide a to a primary fluorescent catabolite (pFCC)  . . 
PF06406 StbA protein<br>Pfam-B_12747 (release 9.0). This family consists of several bacterial StbA plasmid stability proteins  .. 
PF06407 Borna disease virus P40 protein<br>Pfam-B_15995 (release 9.0). This family consists of several Borna disease virus P40 proteins. Borna disease (BD) is a persistent viral infection of the central nervous system caused by the single-negative-strand, nonsegmented RNA Borna disease virus (BDV). P40 is known to be a nucleoprotein  .. 
PF06409 Nuclear pore complex interacting protein (NPIP)<br>Pfam-B_16418 (release 9.0). This family consists of a series of primate specific nuclear pore complex interacting protein (NPIP) sequences. The function of this family is unknown but is well conserved from African apes to humans  .. 
PF06411 HdeA/HdeB family<br>Pfam-B_63431 (release 9.0). HdeA (hns-dependent expression protein A) is a single domain alpha-helical protein localised in the periplasmic space. HdeA is involved in acid resistance essential for infectivity of enteric bacterial pathogens. Functional studies demonstrate that HdeA is activated by a dimer-to-monomer transition at acidic pH, leading to suppression of aggregation by acid-denatured proteins. The gene encoding HdeA was initially identified as part of an operon regulated by the nucleoid protein H-NS [1,2]. This family also contains HdeB  .. 
PF06412 Conjugal transfer protein TraD<br>Pfam-B_11863 (release 9.0). This family contains bacterial TraD conjugal transfer proteins  .  Mutations in the TraD gene result in loss of transfer  .. 
PF06413 Neugrin<br>Pfam-B_11274 (release 9.0). This family consists of several mouse and human neugrin proteins. Neugrin and m-neugrin are mainly expressed in neurons in the nervous system, and are thought to play an important role in the process of neuronal differentiation  .. 
PF06414 Zeta toxin<br>Pfam-B_12374 (release 9.0). This family consists of several bacterial zeta toxin proteins. Zeta toxin is thought to be part of a postregulational killing system in bacteria. It relies on antitoxin/toxin systems that secure stable inheritance of low and medium copy number plasmids during cell division and kill cells that have lost the plasmid  .. 
PF06415 BPG-independent PGAM N-terminus (iPGM_N)<br>Pfam-B_1338 (release 10.0). This family represents the N-terminal region of the 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (or phosphoglyceromutase or BPG-independent PGAM) protein (EC:5.4.2.1). The family is found in conjunction with Pfam:PF01676 (located in the C-terminal region of the protein).. 
PF06416 Protein of unknown function (DUF1076)<br>Pfam-B_2653 (release 9.0). This family consists of several hypothetical bacterial proteins exclusive to Escherichia coli and Salmonella typhi. The function of this family is unknown.. 
PF06417 Protein of unknown function (DUF1077)<br>Pfam-B_6645 (release 9.0). This family consists of several hypothetical eukaryotic proteins of unknown function.. 
PF06418 CTP synthase N-terminus<br>Pfam-B_226 (release 10.0). This family consists of the N-terminal region of the CTP synthase protein (EC:6.3.4.2). This family is found in conjunction with Pfam:PF00117 located in the C-terminal region of the protein. CTP synthase catalyses the synthesis of CTP from UTP by amination of the pyrimidine ring at the 4-position  .. 
PF06419 Conserved oligomeric complex COG6<br>Pfam-B_10345 (release 8.0). COG6 is a component of the conserved oligomeric golgi complex,  which is composed of eight different subunits and is required  for normal golgi morphology and localisation.. 
PF06420 Mitochondrial genome maintenance MGM101<br>Pfam-B_35151 (release 8.0). The mgm101 gene was identified as essential for maintenance of the mitochondrial genome in Saccharomyces cerevisiae  . Based on its DNA-binding activity, and experimental work with a temperature-sensitive mgm101 mutant, it has been proposed that the mgm101 gene product performs an essential function in the repair of oxidatively damaged mitochondrial DNA  .. 
PF06421 GTP-binding protein LepA C-terminus<br>Pfam-B_425 (release 10.0). This family consists of the C-terminal region of several pro- and eukaryotic GTP-binding LepA proteins  .. 
PF06422 CDR ABC transporter<br>Pfam-B_1005 (release 8.0). Corresponds to a region of the PDR/CDR subgroup of ABC transporters comprising extracellular loop 3, transmembrane segment 6 and linker region.. 
PF06423 GWT1<br>Pfam-B_15982 (release 8.0). Glycosylphosphatidylinositol (GPI) is a conserved post-translational modification to anchor cell surface proteins to plasma membrane in eukaryotes. GWT1 is involved in GPI anchor biosynthesis; it is required for inositol acylation in yeast [1-2].. 
PF06424 PRP1 splicing factor, N-terminal<br>Pfam-B_6467 (release 8.0). This domain is specific to the N-terminal part of the prp1 splicing factor, which is involved in mRNA splicing (and possibly also poly(A)+ RNA nuclear export and cell cycle progression). This domain is specific to the N terminus of the RNA splicing factor encoded by prp1  . It is involved in    mRNA splicing and possibly also poly(A)and RNA nuclear export and cell cycle progression.. 
PF06426 Serine acetyltransferase, N-terminal <br>Pfam-B_1192 (release 8.0). The N-terminal domain of serine acetyltransferase has a sequence that is conserved in plants   and bacteria  .. 
PF06427 UDP-glucose:Glycoprotein Glucosyltransferase<br>Pfam-B_4648 (release 8.0). The N-terminal region of this group of proteins is required for correct folding of the ER UDP-Glc: glucosyltransferase.. 
PF06428 GDP/GTP exchange factor Sec2p<br>Pfam-B_10665 (release 8.0). In Saccharomyces cerevisiae,  Sec2p is a GDP/GTP exchange factor for Sec4p, which is required for vesicular transport at the post-Golgi stage of yeast secretion  .. 
PF06429 DUF1078;<br>Flagellar basal body rod FlgEFG protein C-terminal. Pfam-B_807 (release 10.0). This family consists of a number of C-terminal domains of unknown function. This domain seems to be specific to flagellar basal-body rod and flagellar hook proteins in which Pfam:PF00460 is often present at the extreme N terminus.. 
PF06430 Lactococcus lactis RepB C-terminus<br>Pfam-B_717 (release 10.0). This family consists of the C-terminal region of RepB proteins from Lactococcus lactis (See Pfam:PF01051).. 
PF06431 Polyomavirus large T antigen C-terminus<br>Pfam-B_214 (release 10.0). 
PF06432 Phosphatidylinositol N-acetylglucosaminyltransferase<br>Pfam-B_33496 (release 8.0). Glycosylphosphatidylinositol (GPI) represents an important anchoring molecule for cell surface proteins. The first step in its synthesis is the transfer of N-acetylglucosamine (GlcNAc) from UDP-N-acetylglucosamine to phosphatidylinositol (PI). This  step involves products of three or four genes in both yeast (GPI1, GPI2 and GPI3) and mammals (GPI1, PIG A, PIG H and PIG C), respectively.. 
PF06433 Me-amine-deh_H;<br>Methylamine dehydrogenase heavy chain (MADH). Pfam-B_20644 (release 9.0). Methylamine dehydrogenase (EC:1.4.99.3) a periplasmic quinoprotein found in several methyltrophic bacteria. Induced when grown on methylamine as a carbon source MADH catalyses the oxidative deamination of amines to there corresponding aldehydes.  MADH is a hetero- tetramer, comprised of two heavy chains (H) and two light chains (L).  The H-chain forms a beta-propeller like structure  .. 
PF06434 Aconitate hydratase 2 N-terminus<br>Pfam-B_2605 (release 10.0). This family represents the N-terminal region of several bacterial Aconitate hydratase 2 proteins and is found in conjunction with Pfam:PF00330.. 
PF06435 Repeat of unknown function (DUF1079)<br>Pfam-B_1911 (release 10.0). This family consists of several repeats of 31 residues in length and seems to be exclusive to Moraxella catarrhalis UspA proteins. The UspA1 and UspA2 proteins of Moraxella catarrhalis are structurally related and are exposed on the bacterial cell surface where can function adhesins  . This family is commonly found with the Pfam:PF03895 family.. 
PF06436 Pneumovirus matrix protein 2 (M2)<br>Pfam-B_2318 (release 10.0). This family consists of several Pneumovirus matrix glycoprotein M2 sequences. This family functions as a transcription processivity factor that is essential for virus replication  .. 
PF06437 IMP-specific 5'-nucleotidase<br>Pfam-B_43910 (release 8.0). The Saccharomyces cerevisiae ISN1 (YOR155c) gene encodes an IMP-specific 5'-nucleotidase, which catalyses degradation of IMP to inosine as part of the purine salvage pathway.. 
PF06438 Heme-binding protein A (HasA)<br>Pfam-B_27216 (release 9.0). Free iron is limited in vertebrate hosts, thus an alternative to siderophores has been developed by pathogenic bacteria to access host iron bound in protein complexes.  HasA is a secreted hemophore that has the ability to obtain iron from hemoglobin. Once bound to HasA, the heme is shuttled to the receptor HasR, which releases the heme into the bacterium  .. 
PF06439 Domain of Unknown Function (DUF1080)<br>Yeats C, Eberhardt R. This family has structural similarity to an endo-1,3-1,4-beta glucanase belonging to glycoside hydrolase family 16. However, the structure surrounding the active site differs from that of the endo-1,3-1,4-beta glucanase.. 
PF06440 DNA polymerase III, theta subunit<br>Pfam-B_27631 (release 9.0). DNA polymerase III (EC 2.7.7.7) is comprised of three tightly associated subunits, alpha, epsilon and theta. This family contains the theta subunit.   The structure of the theta subunit shows that the N-terminal two thirds is comprised of three helices while the C-terminal third is disordered  .   The function of the theta subunit is poorly understood, but the interaction of the theta subunit with the epsilon subunit is thought to enhance the 3' to 5'  exonucleolytic proofreading activity of epsilon  .. 
PF06441 Epoxide hydrolase N terminus<br>This family represents the N-terminal region of the eukaryotic epoxide hydrolase protein. Epoxide hydrolases (EC:3.3.2.3) comprise a group of functionally related enzymes that catalyse the addition of water to oxirane compounds (epoxides), thereby usually generating vicinal trans-diols. EHs have been found in all types of living organisms, including mammals, invertebrates, plants, fungi and bacteria. In animals, the major interest in EH is directed towards their detoxification capacity for epoxides since they are important safeguards against the cytotoxic and genotoxic potential of oxirane derivatives that are often reactive electrophiles because of the high tension of the three-membered ring system and the strong polarization of the C--O bonds. This is of significant relevance because epoxides are frequent intermediary metabolites which arise during the biotransformation of foreign compounds  . This family is often found in conjunction with Pfam:PF00561.. 
PF06442 DHFR;<br>R67 dihydrofolate reductase. Pfam-B_27527 (release 9.0). R67 dihydrofolate reductase is a plasmid encoded enzyme that provides resistance to the antibacterial  drug trimethoprim.  The R67 dihydrofolate reductase does not share significant similarity to the chromosomal encoded dihydrofolate reductase  .. 
PF06443 SEF14-like adhesin <br>Pfam-B_36358 (release 9.0). Family of enterotoxigenic bacterial adhesins. . 
PF06444 NADH dehydrogenase subunit 2 C-terminus<br>Pfam-B_1662 (release 10.0). This family consists of the C-terminal region specific to the eukaryotic NADH dehydrogenase subunit 2 protein and is found in conjunction with Pfam:PF00361.. 
PF06445 AraC_E_bind;<br>GyrI-like small molecule binding domain. Pfam-B_36124 (release 9.0). This family contains the small molecule binding domain of a number of different bacterial transcription activators  .\. This family also contains DNA gyrase inhibitors. The GyrI superfamily contains a diad of the SHS2 module, adapted for small-molecule binding  .  The GyrI superfamily includes a family of secreted forms that is  found only in animals and the bacterial pathogen Leptospira  . . 
PF06446 Hepcidin<br>Pfam-B_41732 (release 9.0). Hepcidin is a antibacterial and antifungal protein expressed in the liver and is also a signaling molecule in iron metabolism. The hepcidin protein is cysteine-rich and forms a distorted beta-sheet with an unusual disulphide bond found at the turn of the hairpin  .. 
PF06448 Domain of Unknown Function (DUF1081)<br>This region is found in Apolipophorin proteins.. 
PF06449 Mitochondrial domain of unknown function (DUF1082)<br>Pfam-B_2173 (release 10.0). This family consists of the C-terminal region of several plant mitochondria specific proteins. The function of this family is unknown. This family is found in conjunction with Pfam:PF02326.. 
PF06450 Bacterial Na+/H+ antiporter B (NhaB)<br>Pfam-B_5993 (release 10.0). This family consists of several bacterial Na+/H+ antiporter B (NhaB) proteins. The exact function of this family is unknown [1,2].. 
PF06451 Moricin<br>Pfam-B_56760 (release 9.0). Moricin is a antibacterial peptide that is highly basic. The structure of moricin reveals that it is comprised of a long alpha-helix.  The N-terminus of the helix is amphipathic, and the C-terminus of the helix is predominately hydrophobic.  The amphipathic N-terminal segment of the alpha- helix is mainly responsible for the increase in permeability  of the bacterial membrane which kills the bacteria  .. 
PF06452 Domain of unknown function (DUF1083)<br>Pfam-B_2203 (release 10.0). This family consists of several domains of unknown function exclusively found in bacterial xylanase proteins (usually at the C-terminus) although it is tandemly repeated in a number of family members such as Swiss:P38535. This family is always found in conjunction with Pfam:PF00331 and usually with either Pfam:PF02018 or Pfam:PF00395. The function of this family is unknown.. 
PF06453 Type II heat-labile enterotoxin , B subunit (LT-IIB)<br>Pfam-B_61882 (release 9.0). Family of B subunits from the type II heat-labile enterotoxin. The B subunits form a pentameric ring, which interacts with one A subunit.  Thus, the structural arrangement of type I and type II heat-labile enterotoxins are very similar  . . 
PF06454 Protein of unknown function (DUF1084)<br>Pfam-B_12888 (release 10.0). This family consists of several hypothetical plant specific proteins of unknown function.. 
PF06455 NADH dehydrogenase subunit 5 C-terminus<br>Pfam-B_3060 (release 10.0). This family represents the C-terminal region of several NADH dehydrogenase subunit 5 proteins and is found in conjunction with Pfam:PF00361 and Pfam:PF00662.. 
PF06456 Arfaptin-like domain<br>Pfam-B_5314 (release 7.5). Arfaptin interacts with ARF1, a small GTPase involved  in vesicle budding at the Golgi complex and immature secretory granules.  The structure of arfaptin shows that upon binding to a small GTPase, arfaptin forms an elongated, crescent-shaped dimer of three-helix  coiled-coils  . The N-terminal region of ICA69 is similar to arfaptin  . . 
PF06457 Ectatomin<br>Pfam-B_63420 (release 9.0). Ectatomin is a toxic component from the Ectatomma tuberculatum  ant venom.  It is comprised of two subunits, A and B, which  are homologous.  The structure of ectatomin  reveals that each subunit is comprised of two helices and a connecting hinge region, the forms a hairpin structure that is stabilised by disulphide bridges.  The two hinges are connected by a disulphide bond  .. 
PF06458 DUF1085; <br>Pfam-B_4243 (release 10.0) & Galperin M. The MucBP (MUCin-Binding Protein) domain is found in a wide variety of bacterial proteins. The domain is found in bacterial peptidoglycan bound proteins and is often found in conjunction with Pfam:PF00746 and Pfam:PF00560.. 
PF06459 Ryanodine Receptor TM 4-6<br>This region covers TM regions 4-6 of the ryanodine receptor 1 family.. 
PF06460 Coronavirus NSP13<br>This family covers the NSP13 region of the coronavirus polyprotein. This protein has the predicted function of an mRNA cap-1 methyltransferase function ( ).. 
PF06461 Domain of Unknown Function (DUF1086)<br>This family consists of several eukaryotic domains of unknown function which are present in chromodomain helicase DNA binding proteins. This domain is often found in conjunction with Pfam:PF00176, Pfam:PF00271, Pfam:PF06465, Pfam:PF00385 and Pfam:PF00628.. 
PF06462 Propeller<br>Probable beta-propeller.. 
PF06463 Molybdenum Cofactor Synthesis C<br>This region contains two iron-sulphur (3Fe-4S) binding sites. Mutations in this region of  Swiss:O14940 cause MOCOD (Molybdenum Co-Factor Deficiency) type A.. 
PF06464 DMAP1-binding Domain<br>This domain binds DMAP1, a transcriptional co-repressor.. 
PF06465 Domain of Unknown Function (DUF1087)<br>Members of this family are found in various chromatin remodelling factors and transposases. Their exact function is, as yet, unknown.. 
PF06466 PCAF (P300/CBP-associated factor) N-terminal domain<br>This region is spliced out of Swiss:Q92830 isoform 2. It is predicted to be of a mixed alpha/beta fold -  though predominantly helical.. 
PF06467 zf_MYM; zf-MYM; <br>MYM-type Zinc finger with FCS sequence motif. MYM-type zinc fingers were identified in MYM family proteins  . Human protein Swiss:Q14202 is involved in a chromosomal translocation and may be responsible for X-linked retardation in XQ13.1  . Swiss:Q9UBW7 is also involved in disease. In myeloproliferative disorders it is fused to FGF receptor 1  ; in atypical myeloproliferative disorders it is rearranged  . Members of the family generally are involved in development. This Zn-finger domain functions as a transcriptional trans-activator of late vaccinia viral genes, and orthologues are also found in all nucleocytoplasmic large DNA viruses, NCLDV. This domain is also found fused to the C termini of recombinases from certain prokaryotic transposons  .. 
PF06468 Spondin_N<br>This conserved region is found at the in the N-terminal half of several Spondin proteins. Spondins are involved in patterning axonal growth trajectory through either inhibiting or promoting adhesion of embryonic nerve cells ( ). . 
PF06469 Domain of Unknown Function (DUF1088)<br>This family is found in the neurobeachins. The function of this region is not known.. 
PF06470 SMC proteins Flexible Hinge Domain<br>This family represents the hinge region of the SMC (Structural Maintenance of Chromosomes) family of proteins. The hinge region is responsible for formation of the DNA interacting dimer. It is also possible that the precise structure of it is an essential determinant of the specificity of the DNA-protein interaction ( ).  . 
PF06471 NSP11<br>This region of coronavirus polyproteins encodes the NSP11 protein.. 
PF06472 Ald_N; <br>ABC transporter transmembrane region 2. This domain covers the transmembrane of a small family of ABC transporters and shares sequence similarity with Pfam:PF00664. Mutations in this domain in Swiss:P28288 are believed responsible for Zellweger Syndrome-2  ; mutations in  Swiss:P33897 are responsible for recessive X-linked adrenoleukodystrophy  . A Saccharomyces cerevisiae homolog is involved in the import of long-chain fatty acids  .. 
PF06473 FGF binding protein 1 (FGF-BP1)<br>Pfam-B_14221 (release 10.0). This family consists of several mammalian FGF binding protein 1. Fibroblast growth factors (FGFs) play important roles during fetal and embryonic development  . Fibroblast growth factor-binding protein (FGF-BP) 1 is a secreted protein that can bind fibroblast growth factors (FGFs) 1 and 2  .. 
PF06474 MltD lipid attachment motif<br>This short motif is a lipid attachment site.. 
PF06475 DUF1089;<br>Putative glycolipid-binding. Pfam-B_14397 (release 10.0). This family has a novel fold known as a spiral beta-roll, consisting of a 15-stranded beta sheet wrapped around a single alpha helix. It forms dimers. It has some structural similarity to the E. coli lipoprotein localisation factors LolA, Swiss:P61316 and LolB, Swiss:P61320. Its structure suggests that it may have a role in glycolipid binding. Its genomic context supports a role in glycolipid metabolism  .. 
PF06476 Protein of unknown function (DUF1090)<br>Pfam-B_14862 (release 10.0). This family consists of several bacterial proteins of unknown function and is known as YqjC in E. coli.. 
PF06477 Protein of unknown function (DUF1091)<br>Pfam-B_14929 (release 10.0). This is a family of uncharacterised proteins. Based on its distant similarity to Pfam:PF02221 and conserved pattern of cysteine residues it is possible that these domains are also lipid binding.. 
PF06478 Coronavirus RPol N-terminus<br>This family covers the N-terminal region of the  coronavirus RNA-directed RNA Polymerase.. 
PF06479 Ribonuclease 2-5A<br>This domain is a endoribonuclease  . Specifically it cleaves  an intron from Hac1 mRNA in humans, which causes it to be much more efficiently translated.. 
PF06480 FtsH Extracellular<br>This domain is found in the FtsH family of proteins. FtsH is the only membrane-bound ATP-dependent protease universally conserved in prokaryotes ( ). It only efficiently degrades proteins that have a low thermodynamic stability - e.g. it lacks robust unfoldase activity. This feature may be key and implies that this could be a criterion for degrading a protein. In  Oenococcus oeni FtsH is involved in protection against  environmental stress ( ), and shows increased expression  under heat or osmotic stress. These two lines of evidence suggest that it is a fundamental prokaryotic self-protection mechanism that checks if proteins are correctly folded (personal obs: Yeats C). The precise function of this N-terminal region is unclear.. 
PF06481 COX Aromatic Rich Motif<br>COX2 (Cytochrome O ubiquinol OXidase 2) is a major component of the respiratory complex during vegetative growth. It  transfers electrons from a quinol to the binuclear centre  of the catalytic subunit 1. The function of this region is not known.. 
PF06482 Coll_NC10;<br>Collagenase NC10 and Endostatin. NC10 stands for Non-helical region 10 and is taken from Swiss:P39059. A mutation in this region in Swiss:P39060 is associated with an increased risk of prostrate cancer. This domain is cleaved from the precursor and forms endostatin. Endostatin is a key tumour suppressor and has been used highly successfully to treat cancer. It is a potent angiogenesis inhibitor ( ). Endostatin also binds a zinc ion near the N-terminus; this is likely to be of structural rather than functional importance according to ( ).. 
PF06483 Chitinase C<br>This ~170 aa region is found at the C-terminus of Pfam:PF00704.. 
PF06484 Teneurin Intracellular Region<br>This family is found in the intracellular N-terminal region of the Teneurin family of proteins. These proteins are 'pair-rule' genes and are involved in tissue patterning, specifically probably neural patterning. The intracellular domain is cleaved in response to homophilic interaction of the extracellular domain, and translocates to the nucleus. Here it probably carries out to some transcriptional  regulatory activity ( ). The length of this region and  the conservation suggests that there may be two structural domains here (personal obs:C Yeats).. 
PF06485 Protein of unknown function (DUF1092)<br>Pfam-B_14522 (release 10.0). This family consists of several hypothetical proteins of unknown function all from photosynthetic organisms including plants and cyanobacteria.. 
PF06486 Protein of unknown function (DUF1093)<br>Pfam-B_15034 (release 10.0). This family consists of several hypothetical bacterial proteins of unknown function.. 
PF06487 Sin3 associated polypeptide p18 (SAP18)<br>Pfam-B_15078 (release 10.0). This family consists of several eukaryotic Sin3 associated polypeptide p18 (SAP18) sequences. SAP18 is known to be a component of the Sin3-containing complex which is responsible for the repression of transcription via the modification of histone polypeptides  . SAP18 is also present in the ASAP complex  which is thought to be involved in the regulation of splicing during the execution of programmed cell death  .. 
PF06488 Lactococcus lactis bacteriophage major structural protein<br>Pfam-B_13945 (release 10.0). This family consists of several Lactococcus lactis bacteriophage major structural proteins.. 
PF06489 Orthopoxvirus A49R protein<br>Pfam-B_14072 (release 10.0). This family consists of several Orthopoxvirus A49R proteins. The function of this family is unknown.. 
PF06490 Flagellar regulatory protein FleQ<br>Pfam-B_13480 (release 9.0). This domain is found at the N terminus of a subset of sigma54-dependent transcriptional activators that are involved in regulation of flagellar motility e.g. FleQ in Pseudomonas aeruginosa.  It is clearly related to Pfam:PF00072, but lacks the conserved aspartate residue that undergoes phosphorylation in the classic two-component system response regulator (Pfam:PF00072).. 
PF06491 DUF1094;<br>Disulphide isomerase. Pfam-B_14101 (release 10.0). This family of proteins has disulphide isomerase activity, EC:5.3.4.1. It has a similar fold to thioredoxin, with an alpha-beta-alpha-beta-alpha-beta-beta-alpha topology. It has a conserved CGC motif in the loop immediately downstream of the first beta strand. This motif is essential for activity  .. 
PF06493 Protein of unknown function (DUF1096)<br>Pfam-B_15011 (release 10.0). This family represents the N-terminal region of several proteins found in C. elegans. The family is often found with Pfam:PF02363.. 
PF06495 Fruit fly transformer protein<br>Pfam-B_13780 (release 10.0). This family consists of transformer proteins from several Drosophila species and also from Ceratitis capitata (Mediterranean fruit fly). The transformer locus (tra) produces an RNA processing protein that alternatively splices the doublesex pre-mRNA in the sex determination hierarchy of Drosophila melanogaster  .. 
PF06496 Protein of unknown function (DUF1097)<br>Pfam-B_15055 (release 10.0). This family consists of several bacterial putative membrane proteins.. 
PF06497 Protein of unknown function (DUF1098)<br>Pfam-B_15446 (release 10.0). This family consists of several hypothetical Baculovirus proteins of unknown function.. 
PF06500 Alpha/beta hydrolase of unknown function (DUF1100)<br>Pfam-B_15719 (release 10.0). This family consists of several hypothetical bacterial proteins of unknown function. Members of this family have an alpha/beta hydrolase fold.. 
PF06501 Human herpesvirus U55 protein<br>Pfam-B_15779 (release 10.0). This family consists of several human herpesvirus U55 proteins. The function of this family is unknown.. 
PF06502 Equine infectious anaemia virus S2 protein<br>Pfam-B_15780 (release 10.0). This family consists of several equine infectious anaemia virus S2 proteins. The function of this family is unknown.. 
PF06503 Protein of unknown function (DUF1101)<br>Pfam-B_15836 (release 10.0). This family consists of several hypothetical Fijivirus proteins of unknown function.. 
PF06504 Replication protein C (RepC)<br>Pfam-B_15903 (release 10.0). This family consists of several bacterial replication protein C (RepC) sequences.. 
PF06505 Activator of aromatic catabolism<br>Pfam-B_2890 (release 9.0). This domain is found at the N terminus of a subset of sigma54-dependent transcriptional activators in several proteobacteria, including activators of phenol degradation such as XylR. It is found adjacent to Pfam:PF02830.. 
PF06506 Propionate catabolism activator<br>Pfam-B_10794 (release 9.0). This domain is found at the N terminus of several sigma54- dependent transcriptional activators including PrpR, which activates catabolism of propionate.. 
PF06507 Auxin response factor<br>Pfam-B_2015 (release 9.0). A conserved region of auxin-responsive transcription factors.. 
PF06508 ExsB;<br>Queuosine biosynthesis protein QueC. Pfam-B_715 (release 9.0). This family of proteins participate in the biosynthesis of 7-carboxy-7-deazaguanine. They catalyse the conversion of 7-deaza-7-carboxyguanine to preQ0 [1-3].. 
PF06510 Protein of unknown function (DUF1102)<br>Pfam-B_16043 (release 10.0). This family consists of several hypothetical archaeal proteins of unknown function.. 
PF06511 Invasion plasmid antigen IpaD<br>Pfam-B_16150 (release 10.0). This family consists of several invasion plasmid antigen IpaD proteins. Entry of Shigella flexneri into epithelial cells and lysis of the phagosome involve the IpaB, IpaC, and IpaD proteins, which are secreted by type III secretion machinery.. 
PF06512 Sodium ion transport-associated<br>Pfam-B_16808 (release 10.0). Members of this family contain a region found exclusively in eukaryotic sodium channels or their subunits, many of which are voltage-gated. Members very often also contain between one and four copies of Pfam:PF00520 and, less often, one copy of Pfam:PF00612.. 
PF06513 Repeat of unknown function (DUF1103)<br>Pfam-B_16075 (release 10.0). This family consists of several repeats of around 30 residues in length which are found specifically in mature-parasite-infected erythrocyte surface antigen proteins from Plasmodium falciparum. This family often found in conjunction with Pfam:PF00226.. 
PF06514 Photosystem II 12 kDa extrinsic protein (PsbU)<br>Pfam-B_13782 (release 10.0). This family consists of several photosystem II 12 kDa extrinsic protein (PsbU) proteins from cyanobacteria and algae. PsbU is an extrinsic protein of the photosystem II complex of cyanobacteria and red algae. PsbU is known to stabilise the oxygen-evolving machinery of the photosystem II complex against heat-induced inactivation  . This family appears to be related to the Helix-hairpin-helix domain.. 
PF06515 Borna disease virus P10 protein<br>Pfam-B_16237 (release 10.0). This family consists of several Borna disease virus P10 (or X) proteins. Borna disease virus (BDV) is unique among the non-segmented negative-strand RNA viruses of animals and man because it transcribes and replicates its genome in the nucleus of the infected cell. It has been suggested that the p10 protein plays a role in viral RNA synthesis or ribonucleoprotein transport  .. 
PF06516 Purine nucleoside permease (NUP)<br>Pfam-B_15961 (release 10.0). This family consists of several purine nucleoside permease from both bacteria and fungi  .. 
PF06517 Orthopoxvirus A43R protein<br>Pfam-B_16577 (release 10.0). This family consists of several Orthopoxvirus A43R proteins. The function of this family is unknown.. 
PF06518 Protein of unknown function (DUF1104)<br>Pfam-B_16082 (release 10.0). This family consists of several hypothetical proteins of unknown function which appear to be found largely in Helicobacter pylori.. 
PF06519 TolA C-terminal<br>Pfam-B_16081 (release 10.0). This family consists of several bacterial TolA proteins as well as two eukaryotic proteins of unknown function.  Tol proteins are involved in the translocation of group A colicins. Colicins are bacterial protein toxins, which are active against Escherichia coli and other related species (See Pfam:PF01024).  TolA is anchored to the cytoplasmic membrane by a single membrane spanning segment near the N-terminus, leaving most of the protein exposed to the periplasm  .. 
PF06521 PAR1 protein<br>Pfam-B_16232 (release 10.0). This family consists of several plant specific PAR1 proteins from Nicotiana tabacum and Arabidopsis thaliana. The function of this family is unknown.. 
PF06522 NADH-ubiquinone reductase complex 1 MLRQ subunit<br>Pfam-B_16238 (release 10.0). The MLRQ subunit of mitochondrial NADH-ubiquinone reductase complex I is nuclear   and is found in plants  , insects, fungi and higher metazoans  . It appears to act within the membrane and, in mammals, is highly expressed in muscle and neural tissue, indicative of a role in ATP generation  .. 
PF06523 Protein of unknown function (DUF1106)<br>Pfam-B_16281 (release 10.0). This family consists of several hypothetical bacterial proteins found in Escherichia coli and Citrobacter rodentium. The function of this family is unknown.. 
PF06524 NOA36 protein<br>Pfam-B_16330 (release 10.0). This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.. 
PF06525 Sulfocyanin (SoxE)<br>Pfam-B_16349 (release 10.0). This family consists of several archaeal sulfocyanin (or blue copper protein) sequences from a number of Sulfolobus species.. 
PF06526 Protein of unknown function (DUF1107)<br>Pfam-B_16434 (release 10.0). This family consists of several short, hypothetical bacterial proteins of unknown function.. 
PF06527 TniQ<br>Pfam-B_16755 (release 10.0). This family consists of several bacterial TniQ proteins. TniQ along with TniA and B is involved in the transposition of the mercury-resistance transposon Tn5053 which carries the mer operon. It has been suggested that the tni genes are involved in the dissemination of integrons  .. 
PF06528 Phage P2 GpE<br>Pfam-B_15359 (release 10.0). This family consists of several phage and bacterial proteins which are closely related to the GpE tail protein from Phage P2.. 
PF06529 Vertebrate interleukin-3 regulated transcription factor<br>Pfam-B_16154 (release 10.0). This family includes vertebrate transcription factors, some of which are regulated by IL-3/adenovirus E4 promoter binding protein  . Others were found to strongly repress transcription in a DNA-binding-site-dependent manner  .. 
PF06530 Phage antitermination protein Q<br>Pfam-B_3979 (release 10.0). This family consists of several phage antitermination protein Q and related bacterial sequences. Antiterminator proteins control gene expression by recognising control signals near the promoter and preventing transcriptional termination which would otherwise occur at sites that may be a long way downstream  .  . 
PF06531 Protein of unknown function (DUF1108)<br>Pfam-B_16830 (release 10.0). This family consists of several bacterial proteins from Staphylococcus aureus as well as a number of phage proteins. The function of this family is unknown.. 
PF06532 Protein of unknown function (DUF1109)<br>Pfam-B_17952 (release 10.0). This family consists of several hypothetical bacterial proteins of unknown function.. 
PF06533 Protein of unknown function (DUF1110)<br>Pfam-B_18243 (release 10.0). This family consists of hypothetical proteins specific to Oryza sativa. One sequence (Swiss:Q943P1) appears to be tandemly repeated.. 
PF06534 Repulsive guidance molecule (RGM) C-terminus<br>Pfam-B_18263 (release 10.0). This family consists of several mammalian and one bird sequence from Gallus gallus (Chicken). This family represents the C-terminal region of several sequences but in others it represents the full protein. All of the mammalian proteins are hypothetical and have no known function but Swiss:Q8JG54 from the chicken is annotated as being a repulsive guidance molecule (RGM). RGM is a GPI-linked axon guidance molecule of the retinotectal system. RGM is repulsive for a subset of axons, those from the temporal half of the retina. Temporal retinal axons invade the anterior optic tectum in a superficial layer, and encounter RGM expressed in a gradient with increasing concentration along the anterior-posterior axis. Temporal axons are able to receive posterior-dependent information by sensing gradients or concentrations of guidance cues. Thus, RGM is likely to provide positional information for temporal axons invading the optic tectum in the stratum opticum  .. 
PF06535 Repulsive guidance molecule (RGM) N-terminus<br>Pfam-B_18263 (release 10.0). This family consists of the N-terminal region of several mammalian and one bird sequence from Gallus gallus (Chicken). All of the mammalian proteins are hypothetical and have no known function but Swiss:Q8JG54 from the chicken is annotated as being a repulsive guidance molecule (RGM). RGM is a GPI-linked axon guidance molecule of the retinotectal system. RGM is repulsive for a subset of axons, those from the temporal half of the retina. Temporal retinal axons invade the anterior optic tectum in a superficial layer, and encounter RGM expressed in a gradient with increasing concentration along the anterior-posterior axis. Temporal axons are able to receive posterior-dependent information by sensing gradients or concentrations of guidance cues. Thus, RGM is likely to provide positional information for temporal axons invading the optic tectum in the stratum opticum  .. 
PF06536 Avian adenovirus fibre<br>Pfam-B_16053 (release 10.0). This family contains avian adenovirus fibre proteins, which have been linked to variations in virulence  . Avian adenoviruses possess penton capsomers that consist of a pentameric base associated with two fibres  .. 
PF06537 Protein of unknown function (DUF1111)<br>Pfam-B_16636 (release 10.0). This family consists of several hypothetical bacterial proteins of unknown function.. 
PF06540 Galanin message associated peptide (GMAP)<br>Pfam-B_16759 (release 10.0). This family consists of several galanin message associated peptides. In rat preprogalanin, galanin is C-terminally flanked by a 60 amino acid long peptide: galanin message-associated peptide (GMAP). GMAP sequences in different species show high degree of homology, but the biological function of this family is unknown  .. 
PF06541 Protein of unknown function (DUF1113)<br>Pfam-B_17933 (release 10.0). This family consists of several bacterial proteins of unknown function.. 
PF06542 DUF1114; <br>Regulator protein PHA-1. Vella Briffa B, Sammut SJ, Pollington J. Pfam-B_16084 (release 10.0). This family represents the protein product of the gene pha-1 which coordinates with lin-35 Rb during animal development. The protein is expressed during embryonic development and functions in the cytoplasm. PHA-1 acts in a parallel pathway with UBC-18 to regulate the activity of a common cellular target  .. 
PF06543 Lactococcus bacteriophage repressor<br>Pfam-B_16088 (release 10.0). This family represents the C-terminus of Lactococcus bacteriophage repressor proteins.. 
PF06544 Protein of unknown function (DUF1115)<br>Vella Briffa B, Sammut SJ. Pfam-B_16104 (release 10.0). This family represents the C-terminus of hypothetical eukaryotic proteins of unknown function.. 
PF06545 Protein of unknown function (DUF1116)<br>Pfam-B_16143 (release 10.0). This family contains hypothetical bacterial proteins of unknown function.. 
PF06546 Vertebrate heat shock transcription factor<br>Pfam-B_16244 (release 10.0). This family represents the C-terminal region of vertebrate heat shock transcription factors. Heat shock transcription factors regulate the expression of heat shock proteins - a set of proteins that protect the cell from damage caused by stress and aid the cell's recovery after the removal of stress  . This C-terminal region is found with the N-terminal Pfam:PF00447, and may contain a three-stranded coiled-coil trimerisation domain and a CE2 regulatory region, the latter of which is  involved in sustained heat shock response  .. 
PF06547 Protein of unknown function (DUF1117)<br>Pfam-B_16251 (release 10.0). This family represents the C-terminus of a number of hypothetical plant proteins.. 
PF06548 Kinesin-related<br>Pfam-B_16517 (release 10.0). This family represents a region within kinesin-related proteins from higher plants. Many family members also contain the Pfam:PF00225 domain. Kinesins are ATP-driven microtubule motor proteins that produce directed force  . Some family members are associated with the phragmoplast, a structure composed mainly of microtubules that executes cytokinesis in higher plants  .. 
PF06549 Protein of unknown function (DUF1118)<br>Pfam-B_17963 (release 10.0). This family consists of several hypothetical plant proteins of unknown function.. 
PF06550 Protein of unknown function (DUF1119)<br>Pfam-B_17985 (release 10.0). This family consists of several hypothetical archaeal proteins of unknown function.. 
PF06551 Protein of unknown function (DUF1120)<br>Pfam-B_17948 (release 10.0). This family consists of several hypothetical bacterial proteins of unknown function.. 
PF06552 Plant specific mitochondrial import receptor subunit TOM20<br>Pfam-B_17991 (release 10.0). This family consists of several plant specific mitochondrial import receptor subunit TOM20 (translocase of outer membrane 20 kDa subunit) proteins. Most mitochondrial proteins are encoded by the nuclear genome, and are synthesised in the cytosol. TOM20 is a general import receptor that binds to mitochondrial pre-sequences in the early step of protein import into the mitochondria  .  . 
PF06553 BNIP3<br>Pfam-B_18014 (release 10.0). This family consists of several mammalian specific BCL2/adenovirus E1B 19-kDa protein-interacting protein 3 or BNIP3 sequences. BNIP3 belongs to the Bcl-2 homology 3 (BH3)-only family, a Bcl-2-related family possessing an atypical Bcl-2 homology 3 (BH3) domain, which regulates PCD from mitochondrial sites by selective Bcl-2/Bcl-XL interactions. BNIP3 family members contain a C-terminal transmembrane domain that is required for their mitochondrial localisation, homodimerisation, as well as regulation of their pro-apoptotic activities. BNIP3-mediated apoptosis has been reported to be independent of caspase activation and cytochrome c release and is characterised by early plasma membrane and mitochondrial damage, prior to the appearance of chromatin condensation or DNA fragmentation  .. 
PF06554 Olfactory marker protein<br>Pfam-B_18049 (release 10.0). This family consists of several olfactory marker proteins. Expression of the olfactory marker protein (OMP) is highly restricted to mature olfactory receptor neurons in virtually all vertebrate species from fish to man.. 
PF06556 IAP-like protein p27 C-terminus<br>Pfam-B_18169 (release 10.0). This family represents the C-terminal region of the African swine fever virus IAP-like protein p27. This family is found in conjunction with Pfam:PF00653. It has been suggested that the family may be a host range gene involved in aspects of infection in the arthropod host, ticks of the genus Ornithodoros  .. 
PF06557 Protein of unknown function (DUF1122)<br>Pfam-B_18183 (release 10.0). This family consists of several hypothetical archaeal and bacterial proteins of unknown function.. 
PF06558 Secretion monitor precursor protein (SecM)<br>Pfam-B_18197 (release 10.0). This family consists of several bacterial Secretion monitor precursor (SecM) proteins. SecM is known to regulate SecA expression. The eubacterial protein secretion machinery consists of a number of soluble and membrane associated components. One critical element is SecA ATPase, which acts as a molecular motor to promote protein secretion at translocation sites that consist of SecYE, the SecA receptor, and SecG and SecDFyajC proteins, which regulate SecA membrane cycling  .. 
PF06559 2'-deoxycytidine 5'-triphosphate deaminase (DCD)<br>Pfam-B_18211 (release 10.0). This family consists of several bacterial 2'-deoxycytidine 5'-triphosphate deaminase proteins (EC:3.5.4.13).. 
PF06560 Glucose-6-phosphate isomerase (GPI)<br>Pfam-B_18250 (release 10.0). This family consists of several bacterial and archaeal glucose-6-phosphate isomerase (GPI) proteins (EC:5.3.1.9).. 
PF06563 Protein of unknown function (DUF1125)<br>Pfam-B_18065 (release 10.0). This family consists of several short Lactococcus lactis and bacteriophage proteins. The function of this family is unknown.. 
PF06564 YhjQ protein<br>Pfam-B_18260 (release 10.0). This family consists of several bacterial YhjQ proteins. The function of this family is unknown. However, the family does contain a P-loop sequence motif suggesting a nucleotide binding function.. 
PF06565 Repeat of unknown function (DUF1126)<br>Pfam-B_18695 (release 10.0). This family consists of several eukaryote specific repeats of around 35 residues in length. The function of this family is unknown.. 
PF06566 Chondroitin sulphate attachment domain<br>Pfam-B_16515 (release 10.0). This family represents the chondroitin sulphate attachment domain of vertebrate neural transmembrane proteoglycans that contain EGF modules. Evidence has been accumulated to support the idea that neural proteoglycans are involved in various cellular events including mitogenesis, differentiation, axonal outgrowth and synaptogenesis  . This domain contains several potential sites of chondroitin sulphate attachment, as well as potential sites of N-linked glycosylation  .. 
PF06567 Neural chondroitin sulphate proteoglycan cytoplasmic domain<br>Pfam-B_16515 (release 10.0). This family represents the C-terminal cytoplasmic domain of vertebrate neural chondroitin sulphate proteoglycans that contain EGF modules. Evidence has been accumulated to support the idea that neural proteoglycans are involved in various cellular events including mitogenesis, differentiation, axonal outgrowth and synaptogenesis  . This domain contains a number of potential sites of phosphorylation by protein kinase C  .. 
PF06568 Domain of unknown function (DUF1127)<br>Pfam-B_18606 (release 10.0). This family is found in several hypothetical bacterial proteins. In some cases it represents it represents the C-terminal region whereas in others it represents the whole sequence.. 
PF06569 Protein of unknown function (DUF1128)<br>Pfam-B_18651 (release 10.0). This family consists of several short, hypothetical bacterial proteins of unknown function.. 
PF06570 Protein of unknown function (DUF1129)<br>Pfam-B_18737 (release 10.0). This family consists of several hypothetical bacterial proteins of unknown function.. 
PF06572 Protein of unknown function (DUF1131)<br>Pfam-B_18811 (release 10.0). This family consists of several hypothetical bacterial proteins of unknown function.. 
PF06573 Churchill protein<br>Pfam-B_19061 (release 10.0). This family consists of several eukaryotic Churchill proteins. This protein contains a novel zinc binding region that mediates FGF signaling during neural development (unpublished obs Sheng G and Stern C).. 
PF06574 Flavokinase; <br>Moxon SJ, Mistry J, Eddy S. Pfam-B_18632 (release 10.0). This family corresponds to the N terminal domain of the bifunctional enzyme riboflavin kinase / FAD synthetase. These enzymes have both ATP:riboflavin 5'-phospho transferase and ATP:FMN-adenylyltransferase activity  .  They catalyse the 5'-phosphorylation of riboflavin to FMN and the adenylylation of FMN to FAD  .  This domain is thought to have the flavin mononucleotide (FMN) adenylyltransferase activity  .. 
PF06575 Protein of unknown function (DUF1132)<br>Pfam-B_19091 (release 10.0). This family consists of several hypothetical proteins from Neisseria meningitidis. The function of this family is unknown.. 
PF06576 Protein of unknown function (DUF1133)<br>Pfam-B_19184 (release 10.0). This family consists of a number of hypothetical proteins from Escherichia coli O157:H7 and Salmonella typhi. The function of this family is unknown.. 
PF06577 Protein of unknown function (DUF1134)<br>Pfam-B_19217 (release 10.0). This family consists of several hypothetical bacterial proteins of unknown function.. 
PF06578 YOP proteins translocation protein K (YscK)<br>Pfam-B_19248 (release 10.0). This family consists of several YscK proteins. The function of this protein is unknown but it belongs to an operon involved in the secretion of Yop proteins across bacterial membranes.. 
PF06579 Caenorhabditis elegans ly-6-related protein<br>Pfam-B_19267 (release 10.0). This family consists of several Caenorhabditis elegans specific ly-6-related HOT and ODR proteins. These proteins are involved in the olfactory system. Odr-2 mutants are known to be defective in the ability to chemotax to odorants that are recognised by the two AWC olfactory neurons. Odr-2 encodes a membrane-associated protein related to the Ly-6 superfamily of GPI-linked signaling proteins  .. 
PF06580 Histidine kinase<br>Pfam-B_794 (release 10.0). This family represents a region within bacterial histidine kinase enzymes. Two-component signal transduction systems such as those mediated by histidine kinase are integral parts of bacterial cellular regulatory processes, and are used to regulate the expression of genes involved in virulence  . Members of this family often contain Pfam:PF02518 and/or Pfam:PF00672.. 
PF06581 DUF1135;<br>Mad1 and Cdc20-bound-Mad2 binding. Pfam-B_19462 (release 10.0). This family is involved in the cell-cycle surveillance mechanism called the spindle checkpoint. This mechanism monitors the proper bipolar attachment of sister chromatids to spindle microtubules and ensures the fidelity of chromosome segregation during mitosis. A key player in mitosis is Mad2, and Mad2 exhibits an unusual two-state behaviour. A Mad1-Mad2 core complex recruits cytosolic Mad2 to kinetochores through Mad2 dimerisation and converts Mad2 to a conformer amenable to Cdc20 binding. p31comet inactivates the checkpoint by binding to Mad1- or Cdc20-bound Mad2 in such a way as to stop Mad2 activation and to promote the dissociation of the Mad2-Cdc20 complex  .. 
PF06582 Repeat of unknown function (DUF1136)<br>Pfam-B_19544 (release 10.0). This family consists of several eukaryote specific repeats of unknown function. This repeat seems to always be found with Pfam:PF00047.. 
PF06583 Neogenin_C-term; <br>Pfam-B_16188 (release 10.0). This family represents the C-terminus of eukaryotic neogenin precursor proteins, which contains several potential phosphorylation sites  . Neogenin is a member of the N-CAM family of cell adhesion molecules (and therefore contains multiple copies of Pfam:PF00047 and Pfam:PF00041) and is closely related to the DCC tumour suppressor gene product - these proteins may play an integral role in regulating differentiation programmes and/or cell migration events within many adult and embryonic tissues  .. 
PF06584 DIRP<br>Pfam-B_2017 (release 9.0). DIRP (Domain in Rb-related Pathway) is postulated to be involved in the Rb-related pathway, which is encoded by multiple eukaryotic genomes and is present in proteins including lin-9 of Caenorhabditis elegans, aly of fruit fly and mustard weed. Studies of lin-9  and  aly of fruit fly proteins containing DIRP suggest that this domain might be involved in development. Aly, lin-9, act in parallel to, or downstream of, activation of MAPK by the RTK-Ras signalling pathway.. 
PF06585 Haemolymph juvenile hormone binding protein (JHBP)<br>Pfam-B_19686 (release 10.0). This family consists of several insect-specific haemolymph juvenile hormone binding proteins (JHBP). Juvenile hormone regulates embryogenesis, maintains the status quo of larval development and stimulates reproductive maturation in the adult insect. JH is transported from the sites of its synthesis to target tissues by a haemolymph carrier called juvenile hormone-binding protein (JHBP). JHBP protects the JH molecules from hydrolysis by non-specific esterases present in the insect haemolymph  . The crystal structure of the JHBP from Galleria mellonella shows an unusual fold consisting of a long alpha-helix wrapped in a much curved antiparallel beta-sheet. The folding pattern for this structure closely resembles that found in some tandem-repeat mammalian lipid-binding and bactericidal permeability-increasing proteins, with a similar organisation of the major cavity and a disulfide bond linking the long helix and the beta-sheet. It would appear that JHBP forms two cavities, only one of which, the one near the N- and C-termini, binds the hormone; binding induces a conformational change, of unknown significance  . This family now includes DUF233, Pfam:PF03027.. 
PF06586 TraK protein<br>Pfam-B_19687 (release 10.0). This family consists of several TraK proteins from Escherichia coli, Salmonella typhi and Salmonella typhimurium. TraK is known to be essential for pilus assembly but its exact role in this process is unknown  .. 
PF06587 Protein of unknown function (DUF1137)<br>Pfam-B_20097 (release 10.0). This family consists of several hypothetical proteins specific to Chlamydia species. The function of this family is unknown.. 
PF06588 Muskelin N-terminus<br>Pfam-B_20299 (release 10.0). This family represents the N-terminal region of muskelin and is found in conjunction with several Pfam:PF01344 repeats. Muskelin is an intracellular, kelch repeat protein that is needed in cell-spreading responses to the matrix adhesion molecule, thrombospondin-1  .. 
PF06589 Circumsporozoite-related antigen (CRA)<br>Pfam-B_19386 (release 10.0). This family consists of several circumsporozoite-related antigen (CRA) or exported protein-1 (EXP1) sequences found specifically in Plasmodium species. The function of this family is unknown.. 
PF06590 PerB protein<br>Pfam-B_19494 (release 10.0). This family consists of several PerB or BfpV proteins found specifically in Escherichia coli. PerB is thought to play a role in regulating the expression of BfpA  .. 
PF06591 T4-like phage nuclear disruption protein (Ndd)<br>Pfam-B_19553 (release 10.0). This family consists of several nuclear disruption (Ndd) proteins from T4-like phages. Early in a bacteriophage T4 infection, the phage ndd gene causes the rapid destruction of the structure of the Escherichia coli nucleoid.  The targets of Ndd action may be the chromosomal sequences that determine the structure of the nucleoid  .. 
PF06592 Protein of unknown function (DUF1138)<br>Pfam-B_19518 (release 10.0). This family consists of several hypothetical short plant proteins from Arabidopsis thaliana and Oryza sativa. The function of this family is unknown.. 
PF06593 Raspberry bushy dwarf virus coat protein<br>Pfam-B_19630 (release 10.0). This family consists of several Raspberry bushy dwarf virus coat proteins.. 
PF06594 HCBP_repeat; <br>Haemolysin-type calcium binding protein related domain. Pfam-B_20041 (release 10.0). This family consists of a number of bacteria specific domains which are found in haemolysin-type calcium binding proteins. This family is found in conjunction with Pfam:PF00353 and is often found in multiple copies.. 
PF06595 Borna disease virus P24 protein<br>Pfam-B_20092 (release 10.0). This family consists of several Borna disease virus (BDV) P24 proteins. The function of this family is unknown.. 
PF06596 Photosystem II reaction centre X protein (PsbX)<br>Pfam-B_20149 (release 10.0). This family consists of several photosystem II reaction centre X protein (PsbX) sequences from both prokaryotes and eukaryotes.. 
PF06597 Clostridium P-47 protein<br>Pfam-B_20156 (release 10.0). This family consists of several P-47 proteins from various Clostridium species as well as two related sequences from Pseudomonas putida. The function of this family is unknown.. 
PF06598 Chlorovirus glycoprotein repeat<br>Pfam-B_19883 (release 10.0). This family consists of s number of repeats found in Chlorovirus glycoproteins. The function of this family is unknown.. 
PF06599 Protein of unknown function (DUF1139)<br>Pfam-B_20355 (release 10.0). This family consists of several hypothetical Fijivirus proteins of unknown function.. 
PF06600 Protein of unknown function (DUF1140)<br>Pfam-B_20379 (release 10.0). This family consists of several short, hypothetical phage and bacterial proteins. The function of this family is unknown.. 
PF06601 Orthopoxvirus F6 protein<br>Pfam-B_20433 (release 10.0). This family consists of several Orthopoxvirus F6L proteins the function of which are unknown.. 
PF06602 Myotubularin-like phosphatase domain<br>Pfam-B_795 (release 10.0). This family represents the phosphatase domain within eukaryotic myotubularin-related proteins. Myotubularin is a dual-specific lipid phosphatase that dephosphorylates phosphatidylinositol 3-phosphate and phosphatidylinositol (3,5)-bi-phosphate  . Mutations in gene encoding myotubularin-related proteins have been associated with disease  .. 
PF06603 DUF1141;<br>UpxZ family of transcription anti-terminator antagonists. Pfam-B_19606 (release 10.0). The UpxZ family of proteins acts to inhibit transcription of heterologous capsular polysaccharide loci in Bacteroides species by interfering with the action of the UpxY family of transcription anti-terminators. As antagonists of polysaccharide locus-specific UpxY transcription anti-terminators, the UpxZ proteins exert a hierarchical level of regulation, insuring that only one of the multiple phase-variable capsular polysaccharide loci per cell characteristic of this genus is transcribed at a time.. 
PF06605 DUF1142;<br>Prophage endopeptidase tail. Pfam-B_16284 (release 10.0). This family is of prophage tail proteins that are probably acting as endopeptidases.. 
PF06607 Prokineticin<br>Pfam-B_19802 (release 10.0). This family consists of several prokineticin proteins and related BM8 sequences. The suprachiasmatic nucleus (SCN) controls the circadian rhythm of physiological and behavioural processes in mammals. It has been shown that prokineticin 2 (PK2), a cysteine-rich secreted protein, functions as an output molecule from the SCN circadian clock. PK2 messenger RNA is rhythmically expressed in the SCN, and the phase of PK2 rhythm is responsive to light entrainment. Molecular and genetic studies have revealed that PK2 is a gene that is controlled by a circadian clock  .. 
PF06608 Protein of unknown function (DUF1143)<br>Pfam-B_19953 (release 10.0). This family consists of several hypothetical mammalian proteins (from mouse and human). The function of this family is unknown.. 
PF06609 Fungal trichothecene efflux pump (TRI12)<br>Pfam-B_19969 (release 10.0). This family consists of several fungal specific trichothecene efflux pump proteins. Many of the genes involved in trichothecene toxin biosynthesis in Fusarium sporotrichioides are present within a gene cluster.It has been suggested that TRI12 may play a role in F. sporotrichioides self-protection against trichothecenes  .. 
PF06610 Protein of unknown function (DUF1144)<br>Pfam-B_20026 (release 10.0). This family consists of several hypothetical bacterial proteins of unknown function.. 
PF06611 Protein of unknown function (DUF1145)<br>Pfam-B_20029 (release 10.0). This family consists of several hypothetical bacterial proteins of unknown function.. 
PF06612 Protein of unknown function (DUF1146)<br>Pfam-B_20141 (release 10.0). This family consists of several hypothetical bacterial proteins of unknown function.. 
PF06613 KorB C-terminal beta-barrel domain<br>Pfam-B_20369 (release 10.0). This family consists of several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon  . This beta-barrel domain is found at the C-terminus of KorB.. 
PF06614 Neuromodulin<br>Pfam-B_20438 (release 10.0). This family consists of several neuromodulin (Axonal membrane protein GAP-43) sequences and is found in conjunction with Pfam:PF00612. GAP-43 is a neuronal calmodulin-binding phosphoprotein that is concentrated in growth cones and pre-synaptic terminals  .. 
PF06615 Protein of unknown function (DUF1147)<br>Pfam-B_20563 (release 10.0). This family consists of several short Circovirus proteins of unknown function.. 
PF06616 BsuBI/PstI restriction endonuclease C-terminus<br>Pfam-B_16289 (release 10.0). This family represents the C-terminus of bacterial enzymes similar to type II restriction endonucleases BsuBI and PstI (EC:3.1.21.4). The enzymes of the BsuBI restriction/modification (R/M) system recognise the target sequence 5'CTGCAG and are functionally identical with those of the PstI R/M system  .. 
PF06617 M-phase inducer phosphatase<br>Pfam-B_16267 (release 10.0). This family represents a region within eukaryotic M-phase inducer phosphatases (EC:3.1.3.48), which also contain the Pfam:PF00581 domain. These proteins are involved in the control of mitosis  .. 
PF06618 Protein of unknown function (DUF1148)<br>Pfam-B_20595 (release 10.0). This family consists of several Maize streak virus proteins of unknown function.. 
PF06619 Protein of unknown function (DUF1149)<br>Pfam-B_20513 (release 10.0). This family consists of several hypothetical bacterial proteins of unknown function.. 
PF06620 Protein of unknown function (DUF1150)<br>Pfam-B_20612 (release 10.0). This family consists of several hypothetical bacterial proteins of unknown function.. 
PF06621 Single-minded protein C-terminus<br>Pfam-B_21144 (release 10.0). This family represents the C-terminal region of the eukaryotic single-minded (SIM) protein. Drosophila single-minded acts as a positive master gene regulator in central nervous system midline formation. There are two homologues in mammals: SIM1 and SIM2, which are members of the basic-helix-loop-helix PAS family of transcription factors. SIM1 and SIM2 are novel heterodimerisation partners for ARNT in vitro, and they may function both as positive and negative transcriptional regulators in vivo, during embryogenesis and in the adult organism  . SIM2 is thought to contribute to some specific Down syndrome phenotypes  . This family is found in conjunction with a Pfam:PF00989 domain and associated Pfam:PF00785 motif.. 
PF06622 SepQ protein<br>Pfam-B_21060 (release 10.0). This family consists of several enterobacterial SepQ proteins from Escherichia coli and Citrobacter rodentium. The function of this family is unclear.. 
PF06623 MHC_I C-terminus<br>Pfam-B_21327 (release 10.0). This family represents the C-terminal region of the MHC class I antigen. The family is found in conjunction with Pfam:PF00129 and Pfam:PF00047.. 
PF06624 Ribosome associated membrane protein RAMP4<br>Pfam-B_20959 (release 10.0). This family consists of several ribosome associated membrane protein RAMP4 (or SERP1) sequences. Stabilisation of membrane proteins in response to stress involves the concerted action of a rescue unit in the ER membrane comprised of SERP1/RAMP4, other components of the translocon, and molecular chaperones in the ER  .. 
PF06625 Protein of unknown function (DUF1151)<br>Pfam-B_21020 (release 10.0). This family consists of several hypothetical eukaryotic proteins of unknown function.. 
PF06626 Protein of unknown function (DUF1152)<br>Pfam-B_21029 (release 10.0). This family consists of several hypothetical archaeal proteins of unknown function.. 
PF06627 Protein of unknown function (DUF1153)<br>Pfam-B_21038 (release 10.0). This family consists of several short, hypothetical bacterial proteins of unknown function.. 
PF06628 Catalase-related immune-responsive<br>Vella Briffa B, Coggill P. Pfam-B_16304 (release 10.0). This family represents a small conserved region within catalase enzymes (EC:1.11.1.6). All members also contain the Catalase family, Pfam:PF00199 domain. Catalase decomposes hydrogen peroxide into water and oxygen, serving to protect cells from its toxic effects  . This domain carries the immune-responsive amphipathic octa-peptide that is recognised by T cells  .. 
PF06629 MltA-interacting protein MipA<br>Pfam-B_8359 (release 9.0). This family consists of several bacterial MltA-interacting protein (MipA) like sequences. As well as interacting with the membrane-bound lytic transglycosylase MltA, MipA is known to bind to PBP1B, a bifunctional murein transglycosylase/transpeptidase. MipA is considered to be a structural protein mediating the assembly of MltA to PBP1B into a complex  .. 
PF06630 Enterobacterial exodeoxyribonuclease VIII<br>Pfam-B_11449 (release 9.0). This family consists of several Enterobacterial exodeoxyribonuclease VIII proteins.. 
PF06631 Protein of unknown function (DUF1154)<br>Pfam-B_16329 (release 10.0). This family represents a small conserved region of unknown function within eukaryotic phospholipase C (EC:3.1.4.3). All members also contain Pfam:PF00387 and Pfam:PF00388.. 
PF06632 DNA double-strand break repair and V(D)J recombination protein XRCC4<br>Pfam-B_21077 (release 10.0). This family consists of several eukaryotic DNA double-strand break repair and V(D)J recombination protein XRCC4 sequences. In the non-homologous end joining pathway of DNA double-strand break repair, the ligation step is catalysed by a complex of XRCC4 and DNA ligase IV. It is thought that XRCC4 and ligase IV are essential for alignment-based gap filling, as well as for final ligation of the breaks  .. 
PF06633 Protein of unknown function (DUF1155)<br>Pfam-B_21101 (release 10.0). This family consists of several Cucumber mosaic virus ORF IIB proteins. The function of this family is unknown.. 
PF06634 Protein of unknown function (DUF1156)<br>Vella Briffa B, Eberhardt R. Pfam-B_16387 (release 10.0). This family represents a conserved region within hypothetical prokaryotic and archaeal proteins of unknown function. Structural modelling suggests this domain may bind nucleic acids  .. 
PF06635 Nodulation protein NolV<br>Pfam-B_21143 (release 10.0). This family consists of several nodulation protein NolV sequences from different Rhizobium species  . The function of this family is unclear.. 
PF06636 Protein of unknown function (DUF1157)<br>Pfam-B_21250 (release 10.0). This family consists of several uncharacterised proteins from Melanoplus sanguinipes entomopoxvirus (MsEPV). The function of this family is unknown.. 
PF06637 PV-1 protein (PLVAP)<br>Pfam-B_21397 (release 10.0). This family consists of several PV-1 (PLVAP) proteins which seem to be specific to mammals. PV-1 is a novel protein component of the endothelial fenestral and stomatal diaphragms  . The function of this family is unknown.. 
PF06638 Strabismus protein<br>Pfam-B_9849 (release 9.0). This family consists of several strabismus (STB) or Van Gogh-like (VANGL) proteins 1 and 2. The exact function of this family is unknown. It is thought, however that STB1 gene and STB2 may be potent tumour suppressor gene candidates  .. 
PF06639 Basal layer antifungal peptide (BAP)<br>Pfam-B_21444 (release 10.0). This family consists of several basal layer antifungal peptide (BAP) sequences specific to Zea mays. The BAP2 peptide exhibits potent broad-range activity against a range of filamentous fungi, including several plant pathogens  . . 
PF06640 P_prot_C-term; <br>P protein C-terminus. Pfam-B_16385 (release 10.0). This family represents the C-terminus of plant P proteins. The maize P gene is a transcriptional regulator of genes encoding enzymes for flavonoid biosynthesis in the pathway leading to the production of a red phlobaphene pigment  , and P proteins are homologous to the DNA-binding domain of myb-like transcription factors  . All members of this family contain the Pfam:PF00249 domain.. 
PF06643 Protein of unknown function (DUF1158)<br>Pfam-B_21508 (release 10.0). This family consists of several enterobacterial YbdJ proteins. The function of this family is unknown. 
PF06644 ATP11 protein<br>Moxon SJ, Hammonds G. Pfam-B_21093 (release 10.0). This family consists of several eukaryotic ATP11 proteins. In Saccharomyces cerevisiae, expression of functional F1-ATPase requires two proteins encoded by the ATP11 and ATP12 genes  . Atp11p is a molecular chaperone of the mitochondrial matrix that participates in the biogenesis pathway to form F1, the catalytic  unit of the ATP synthase  .. 
PF06645 Microsomal signal peptidase 12 kDa subunit (SPC12)<br>Pfam-B_21331 (release 10.0). This family consists of several microsomal signal peptidase 12 kDa subunit proteins. Translocation of polypeptide chains across the endoplasmic reticulum (ER) membrane is triggered by signal sequences. Subsequently, signal recognition particle interacts with its membrane receptor and the ribosome-bound nascent chain is targeted to the ER where it is transferred into a protein-conducting channel. At some point, a second signal sequence recognition event takes place in the membrane and translocation of the nascent chain through the membrane occurs. The signal sequence of most secretory and membrane proteins is cleaved off at this stage. Cleavage occurs by the signal peptidase complex (SPC) as soon as the lumenal domain of the translocating polypeptide is large enough to expose its cleavage site to the enzyme. The signal peptidase complex is possibly also involved in proteolytic events in the ER membrane other than the processing of the signal sequence, for example the further digestion of the cleaved signal peptide or the degradation of membrane proteins. Mammalian signal peptidase is as a complex of five different polypeptide chains. This family represents the 12 kDa subunit (SPC12).. 
PF06646 High affinity transport system protein p37<br>Pfam-B_21350 (release 10.0). This family consists of several high affinity transport system protein p37 sequences which are specific to Mycoplasma species. The p37 gene is part of an operon encoding two additional proteins which are highly similar to components of the periplasmic binding-protein-dependent transport systems of Gram-negative bacteria.It has been suggested that p37 is part of a homologous, high-affinity transport system in M. hyorhinis, a Gram-positive bacterium  .. 
PF06648 Protein of unknown function (DUF1160)<br>Pfam-B_21501 (release 10.0). This family consists of several hypothetical Baculovirus proteins of unknown function.. 
PF06649 Protein of unknown function (DUF1161)<br>Pfam-B_21545 (release 10.0). This family consists of several short, hypothetical bacterial proteins of unknown function.. 
PF06650 Protein of unknown function (DUF1162)<br>Pfam-B_16458 (release 10.0). This family represents a conserved region within several hypothetical eukaryotic proteins. Family members might be vacuolar protein sorting related-proteins. . 
PF06651 Protein of unknown function (DUF1163)<br>Pfam-B_16509 (release 10.0). This family represents the C-terminus of hypothetical Arabidopsis thaliana proteins of unknown function. . 
PF06652 Methuselah N-terminus<br>Pfam-B_3337 (release 10.0). This family represents the N-terminal region of the Drosophila specific Methuselah protein. Drosophila Methuselah (Mth) mutants have a 35% increase in average lifespan and increased resistance to several forms of stress, including heat, starvation, and oxidative damage. The protein affected by this mutation is related to G protein-coupled receptors of the secretin receptor family. Mth, like secretin receptor family members, has a large N-terminal ectodomain, which may constitute the ligand binding site  . This family is found in conjunction with Pfam:PF00002.. 
PF06653 DUF1164;<br>Tight junction protein, Claudin-like. Pfam-B_21553 (release 10.0). This is a family of probable membrane tight junction, Claudin-like, proteins.. 
PF06656 Tenuivirus PVC2 protein<br>Pfam-B_15006 (release 10.0). This family consists of several Tenuivirus PVC2 proteins from Rice grassy stunt virus, Maize stripe virus and Rice hoja blanca virus. The function of this family is unknown.. 
PF06657 DUF1167;<br>Centrosome microtubule-binding domain of Cep57. Pfam-B_9878 (release 9.0). This C-terminal region of Cep57 binds, nucleates and bundles microtubules. The N-terminal part, family Cep57_CLD, Pfam:PF14073, is the centrosome localisation domain Cep57  .. 
PF06658 Protein of unknown function (DUF1168)<br>Pfam-B_9807 (release 9.0). This family consists of several hypothetical eukaryotic proteins of unknown function. . 
PF06661 VirE3<br>Pfam-B_16550 (release 10.0). This family represents a conserved region within Agrobacterium tumefaciens VirE3. Agrobacterium tumefaciens (a plant pathogen) has a tumour-inducing (Ti) plasmid of which part, the transfer (T)-region, is transferred to plant cells during the infection process. Vir proteins mediate the processing of the T-region and the transfer of a single-stranded (ss) DNA copy of this region, the T-strand, into the recipient cells. VirE3 is a translocated effector protein, but its specific role has not been established  .. 
PF06662 C5-epim_C-term; <br>D-glucuronyl C5-epimerase C-terminus. Pfam-B_16571 (release 10.0). This family represents the C-terminus of D-glucuronyl C5-epimerase (EC:5.1.3.-). Glucuronyl C5-epimerases catalyse the conversion of D-glucuronic acid (GlcUA) to L-iduronic acid (IdceA) units during the biosynthesis of glycosaminoglycans  .. 
PF06663 Protein of unknown function (DUF1170)<br>Pfam-B_16582 (release 10.0). This family represents a conserved region of unknown function within MAGUIN, a neuronal membrane-associated guanylate kinase-interacting protein. This region is situated between the Pfam:PF00595 and Pfam:PF00169 domains  . All family members also contain an N-terminal Pfam:PF00536 domain.. 
PF06664 DUF1171; MIG-14_Ce; <br>Wnt-binding factor required for Wnt secretion. Vella Briffa B, Pollington JE. Pfam-B_16593 (release 10.0). MIG-14 is a Wnt-binding factor. Newly synthesised EGL-20/Wnt binds to MIG-14 in the Golgi, targetting the Wnt to the cell membrane for secretion. AP-2-mediated endocytosis and retromer retrieval at the sorting endosome would recycle MIG-14 to the Golgi, where it can bind to EGL-20/Wnt for next cycle of secretion  .. 
PF06666 Protein of unknown function (DUF1173)<br>Pfam-B_16904 (release 10.0). This family contains a group of hypothetical bacterial proteins that contain three conserved cysteine residues towards the N-terminal. The function of these proteins is unknown.. 
PF06667 Phage shock protein B<br>Pfam-B_21806 (release 10.0). This family consists of several bacterial phage shock protein B (PspB) sequences. The phage shock protein (psp) operon is induced in response to heat, ethanol, osmotic shock and infection by filamentous bacteriophages  . Expression of the operon requires the alternative sigma factor sigma54 and the transcriptional activator PspF. In addition, PspA plays a negative regulatory role, and the integral-membrane proteins PspB and PspC play a positive one  .. 
PF06668 ITI_HC_C-term; <br>Inter-alpha-trypsin inhibitor heavy chain C-terminus. Pfam-B_16674 (release 10.0). This family represents the C-terminal region of inter-alpha-trypsin inhibitor heavy chains. Inter-alpha-trypsin inhibitors are glycoproteins with a high inhibitory activity against trypsin, built up from different combinations of four polypeptides: bikunin and the three heavy chains that belong to this family (HC1, HC2, HC3). The heavy chains do not have any protease inhibitory properties but have the capacity to interact in vitro and in vivo with hyaluronic acid, which promotes the stability of the extra-cellular matrix  . All family members contain the Pfam:PF00092 domain.. 
PF06669 Xylella fastidiosa surface protein related<br>Pfam-B_21796 (release 10.0). This family consists of several Xylella fastidiosa surface protein specific repeats which are found in found in conjunction with Pfam:PF05662, Pfam:PF05658 and Pfam:PF03895.. 
PF06670 Microneme protein Etmic-2<br>Pfam-B_22009 (release 10.0). This family consists of several Microneme protein Etmic-2 sequences from Eimeria tenella. Etmic-2 is a 50 kDa acidic protein, which is found within the microneme organelles of Eimeria tenella sporozoites and merozoites  .. 
PF06671 Repeat of unknown function (DUF1174)<br>Pfam-B_22180 (release 10.0). This family consists of a number of Caenorhabditis elegans specific repeats of around 36 residues in length which are found in two hypothetical proteins. This family is found in conjunction with Pfam:PF00024.. 
PF06672 Protein of unknown function (DUF1175)<br>Pfam-B_21722 (release 10.0). This family consists of several hypothetical bacterial proteins of around 210 residues in length. The function of this family is unknown.. 
PF06673 Lactococcus lactis bacteriophage major capsid protein<br>Pfam-B_21754 (release 10.0). This family consists of several Lactococcus lactis bacteriophage major capsid proteins.. 
PF06674 Protein of unknown function (DUF1176)<br>Pfam-B_21791 (release 10.0). This family consists of several hypothetical bacterial proteins of around 340 residues in length. Members of this family contain six highly conserved cysteine residues. The function of this family is unknown.. 
PF06675 Protein of unknown function (DUF1177)<br>Pfam-B_21818 (release 10.0). This family consists of several hypothetical archaeal and and bacterial proteins of around 300 residues in length. The function of this family is unknown.. 
PF06676 Protein of unknown function (DUF1178)<br>Pfam-B_21872 (release 10.0). This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.. 
PF06677 Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)<br>Pfam-B_21881 (release 10.0). This family consists of several Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27) sequences. It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis  .. 
PF06678 Protein of unknown function (DUF1179)<br>Pfam-B_21899 (release 10.0). This family consists of several hypothetical Caenorhabditis elegans proteins of around 106 residues in length. The function of the family is unknown.. 
PF06679 Protein of unknown function (DUF1180)<br>Pfam-B_21907 (release 10.0). This family consists of several hypothetical mammalian proteins of around 190 residues in length. The function of this family is unknown.. 
PF06680 Protein of unknown function (DUF1181)<br>Pfam-B_21912 (release 10.0). This family consists of several hypothetical proteins of around 120 residues in length which are found specifically in Trypanosoma brucei. The function of this family is unknown.. 
PF06681 Protein of unknown function (DUF1182)<br>Pfam-B_21992 (release 10.0). This family consists of several hypothetical proteins of around 360 residues in length and seems to be specific to Caenorhabditis elegans. The function of this family is unknown.. 
PF06682 Protein of unknown function (DUF1183)<br>Pfam-B_22014 (release 10.0). This family consists of several eukaryotic proteins of around 360 residues in length. The function of this family is unknown.. 
PF06683 Protein of unknown function (DUF1184)<br>Pfam-B_16725 (release 10.0). This family contains a number of hypothetical proteins of unknown function from Arabidopsis thaliana.. 
PF06684 DUF1185;<br>Amino acid synthesis. Moxon SJ, Eberhardt R. Pfam-B_22398 (release 10.0). This family of proteins is structurally similar to proteins with the Bacillus chorismate mutase-like (BCM-like) fold. This structure, combined with its genomic context, suggest that it has a role in amino acid synthesis  .. 
PF06685 Protein of unknown function (DUF1186)<br>Pfam-B_22662 (release 10.0). This family consists of several hypothetical bacterial proteins of around 250 residues in length and is found in several Chlamydia and Anabaena species. The function of this family is unknown.. 
PF06686 Stage III sporulation protein AC/AD protein family<br>Pfam-B_22771 (release 10.0), TIGRFAMs. This family consists of several bacterial stage III sporulation protein AC (SpoIIIAC) and SpoIIIAD sequences. The exact function of this family is unknown.  SpoIIIAD is the an uncharacterised protein which is part of the spoIIIA operon that acts at sporulation stage III as part of a cascade of events leading to endospore formation. The operon is regulated by sigmaG  .. 
PF06687 SUR7/PalI family<br>Pfam-B_22775 (release 10.0). This family consists of several fungal-specific SUR7 proteins. Its activity regulates expression of RVS161, a homologue of human endophilin, suggesting a function for both in endocytosis [1,2]. The protein carries four transmembrane domains and is thus likely to act as an anchoring protein for the eisosome to the plasma membrane.  Eisosomes are the immobile protein complexes, that include the proteins Pil1 and Lsp1, which co-localise with sites of protein and lipid endocytosis at the plasma membrane. SUR7 protein may play a role in sporulation  . This family also includes PalI which is part of a pH signal transduction cascade.  Based on the similarity of PalI to the yeast Rim9 meiotic signal transduction component it has been suggested that PalI might be a membrane sensor for ambient pH  .. 
PF06688 Protein of unknown function (DUF1187)<br>Pfam-B_22781 (release 10.0). This family consists of several short, hypothetical bacterial proteins of around 62 residues in length. Members of this family are found in Escherichia coli and Salmonella typhi. The function of this family is unknown.. 
PF06689 ClpX C4-type zinc finger<br>Pfam-B_465 (release 10.0). The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type. This presumed zinc binding domain is found at the N-terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. The molecular function of this domain is now known.. 
PF06690 Protein of unknown function (DUF1188)<br>Pfam-B_22902 (release 10.0). This family consists of several hypothetical archaeal proteins of around 260 residues in length which seem to be specific to Methanobacterium, Methanococcus and Methanopyrus species. The function of this family is unknown.. 
PF06691 Protein of unknown function (DUF1189)<br>Pfam-B_22923 (release 10.0). This family consists of several hypothetical bacterial proteins of around 260 residues in length. The function of this family is unknown.. 
PF06692 Melon necrotic spot virus P7B protein<br>Pfam-B_22334 (release 10.0). This family consists of several Melon necrotic spot virus (MNSV) P7B proteins. The function of this family is unknown.. 
PF06693 Protein of unknown function (DUF1190)<br>Pfam-B_22972 (release 10.0). This family consists of several hypothetical Enterobacterial proteins of around 212 residues in length and is known as YjfM in Escherichia coli. The function of this family is unknown.. 
PF06694 Plant nuclear matrix protein 1 (NMP1)<br>Pfam-B_22388 (release 10.0). This family consists of several plant specific nuclear matrix protein 1 (NMP1) sequences. Nuclear Matrix Protein 1 is a ubiquitously expressed 36 kDa protein, which has no homologues in animals and fungi, but is highly conserved among flowering and non-flowering plants. NMP1 is located both in the cytoplasm and nucleus and that the nuclear fraction is associated with the nuclear matrix. NMP1 is a candidate for a plant-specific structural protein with a function both in the nucleus and cytoplasm  . . 
PF06695 sm_multidrug_ex; <br>Putative small multi-drug export protein. Pfam-B_16747 (release 10.0). This family contains a small number of putative small multi-drug export proteins.. 
PF06696 Streptococcal surface antigen repeat<br>Pfam-B_22674 (release 10.0). This family consists of a number of ~25 residue long repeats found commonly in Streptococcal surface antigens although one copy is present in the HPSR2-heavy chain potential motor protein of Giardia lamblia (Swiss:Q24984). This family is often found in conjunction with Pfam:PF00746.. 
PF06697 Protein of unknown function (DUF1191)<br>Pfam-B_16754 (release 10.0). This family contains hypothetical plant proteins of unknown function.. 
PF06698 Protein of unknown function (DUF1192)<br>Pfam-B_22780 (release 10.0). This family consists of several short, hypothetical, bacterial proteins of around 60 residues in length. The function of this family is unknown.. 
PF06699 GPI biosynthesis protein family Pig-F<br>Pfam-B_8602 (release 8.0). PIG-F is involved in glycosylphosphatidylinositol (GPI) anchor  biosynthesis [1-3].. 
PF06701 Mib_herc2<br>Pfam-B_6026 (release 8.0). Named "mib/herc2 domain" in  . Usually the protein also contains an E3 ligase domain (either Ring or Hect). . 
PF06702 Protein of unknown function (DUF1193)<br>Pfam-B_16766 (release 10.0). This family represents the C-terminus of several hypothetical eukaryotic proteins of unknown function. Family members contain two conserved motifs: DRHHYE and QCC, as well as a number of conserved cysteine residues.. 
PF06703 Microsomal signal peptidase 25 kDa subunit (SPC25)<br>Pfam-B_22374 (release 10.0). This family consists of several microsomal signal peptidase 25 kDa subunit proteins. Translocation of polypeptide chains across the endoplasmic reticulum (ER) membrane is triggered by signal sequences. Subsequently, signal recognition particle interacts with its membrane receptor and the ribosome-bound nascent chain is targeted to the ER where it is transferred into a protein-conducting channel. At some point, a second signal sequence recognition event takes place in the membrane and translocation of the nascent chain through the membrane occurs. The signal sequence of most secretory and membrane proteins is cleaved off at this stage. Cleavage occurs by the signal peptidase complex (SPC) as soon as the lumenal domain of the translocating polypeptide is large enough to expose its cleavage site to the enzyme. The signal peptidase complex is possibly also involved in proteolytic events in the ER membrane other than the processing of the signal sequence, for example the further digestion of the cleaved signal peptide or the degradation of membrane proteins. Mammalian signal peptidase is as a complex of five different polypeptide chains. This family represents the 25 kDa subunit (SPC25).. 
PF06705 SF-assemblin/beta giardin<br>Pfam-B_22934 (release 10.0). This family consists of several eukaryotic SF-assemblin and related beta giardin proteins. During mitosis the SF-assemblin-based cytoskeleton is reorganised; it divides in prophase and is reduced to two dot-like structures at each spindle pole in metaphase. During anaphase, the two dots present at each pole are connected again. In telophase there is an asymmetrical outgrowth of new fibres. It has been suggested that SF-assemblin is involved in re-establishing the microtubular root system characteristic of interphase cells after mitosis  . . 
PF06706 Citrus tristeza virus 6-kDa protein<br>Pfam-B_22973 (release 10.0). This family consists of several Citrus tristeza virus (CTV) 6-kDa, 51 residue long hydrophobic (P6) proteins. The function of this family is unknown.. 
PF06707 Protein of unknown function (DUF1194)<br>Pfam-B_22986 (release 10.0). This family consists of several hypothetical Rhizobiales specific proteins of around 270 residues in length. The function of this family is unknown.. 
PF06708 Protein of unknown function (DUF1195)<br>Pfam-B_22828 (release 10.0). This family consists of several plant specific hypothetical proteins of around 160 residues in length. The function of this family is unknown.. 
PF06709 Protein of unknown function (DUF1196)<br>Pfam-B_23162 (release 10.0). This family consists of several hypothetical bacterial proteins of around 51 residues in length which seem to be specific to Vibrio cholerae. The function of this family is unknown.. 
PF06711 Protein of unknown function (DUF1198)<br>Pfam-B_23016 (release 10.0). This family consists of several bacterial proteins of around 150 residues in length which are specific to Escherichia coli, Salmonella species and Yersinia pestis. The function of this family is unknown.. 
PF06712 Protein of unknown function (DUF1199)<br>Pfam-B_23160 (release 10.0). This family consists of several hypothetical Feline immunodeficiency virus (FIV) proteins. Members of this family are typically around 67 residues long and are often annotated as ORF3 proteins. The function of this family is unknown.. 
PF06713 DUF1200;<br>Pfam-B_23245 (release 10.0). This family consists of several hypothetical proteins specific to Oceanobacillus and Bacillus species. Members of this family are typically around 130 residues in length. The function of this family is unknown. Members of this family have a PH domain like structure  .. 
PF06714 Gp5 N-terminal OB domain<br>This domain is found at the N terminus of the Gp5 baseplate protein of bacteriophage T4.  This domain binds to the Gp27 protein  .  This domain has the common OB fold  .. 
PF06715 Gp5 C-terminal repeat (3 copies)<br>This repeat composes the C-terminal part of the bacteriophage T4 baseplate protein Gp5.  This region of the protein forms a needle like projection from the baseplate that is presumed to puncture the bacterial cell membrane. Structurally three copies of the repeated region trimerise to form a beta solenoid type structure  . This family also includes repeats from bacterial Vgr proteins.. 
PF06716 Protein of unknown function (DUF1201)<br>Pfam-B_23269 (release 10.0). This family consists of several Sugar beet yellow virus (SBYV) putative membrane-binding proteins of around 54 residues in length. The function of this family is unknown.. 
PF06717 Protein of unknown function (DUF1202)<br>Pfam-B_23300 (release 10.0). This family consists of several hypothetical bacterial proteins of around 335 residues in length. Members of this family are found exclusively in Escherichia coli and Salmonella species and are often referred to as YggM proteins. The function of this family is unknown.. 
PF06718 Protein of unknown function (DUF1203)<br>Pfam-B_23313 (release 10.0). This family consists of several hypothetical bacterial proteins of around 155 residues in length. Family members are present in Rhizobium, Agrobacterium and Streptomyces species.. 
PF06719 AraC_N-term; <br>AraC-type transcriptional regulator N-terminus. Pfam-B_16798 (release 10.0). This family represents the N-terminus of bacterial ARAC-type transcriptional regulators. In E. coli, these regulate the L-arabinose operon through sensing the presence of arabinose, and when the sugar is present, transmitting this information from the arabinose-binding domains to the protein's DNA-binding domains  . This family might represent the N-terminal arm of the protein, which binds to the C-terminal DNA binding domains to hold them in a state where the protein prefers to loop and remain non-activating  . All family members contain the Pfam:PF00165 domain.. 
PF06720 Bacteriophage phi-29 early protein GP16.7<br>Pfam-B_23362 (release 10.0). This family consists of several bacteriophage phi-29 early protein GP16.7 sequences of around 130 residues in length. The function of this family is unknown.. 
PF06721 Protein of unknown function (DUF1204)<br>Pfam-B_16832 (release 10.0). This family represents the C-terminus of a number of Arabidopsis thaliana hypothetical proteins of unknown function. Family members contain a conserved DFD motif.. 
PF06722 Protein of unknown function (DUF1205)<br>Pfam-B_16780 (release 10.0). This family represents a conserved region of unknown function within bacterial glycosyl transferases. Many family members contain Pfam:PF03033.. 
PF06723 MreB/Mbl protein<br>Pfam-B_471 (release 10.0). This family consists of bacterial MreB and Mbl proteins as well as two related archaeal sequences. MreB is known to be a rod shape-determining protein in bacteria and goes to make up the bacterial cytoskeleton. Genes coding for MreB/Mbl are only found in elongated bacteria, not in coccoid forms. It has been speculated that constituents of the eukaryotic cytoskeleton (tubulin, actin) may have evolved from prokaryotic precursor proteins closely related to today's bacterial proteins FtsZ and MreB/Mbl  .. 
PF06724 Domain of Unknown Function (DUF1206)<br>This region consists of two a pair of transmembrane helices and occurs three times in each of the family member proteins.. 
PF06725 3D domain<br>This short presumed domain contains three conserved aspartate residues, hence the name 3D. It has been shown to be part of the catalytic double psi beta barrel domain of MltA  .. 
PF06726 Bladder cancer-related protein BC10<br>Wood V, Moxon SJ, Coggill PC. This family consists of a series of short proteins of around 90 residues in length. The human protein Swiss:O60629 or BC10 has been implicated in bladder cancer where the transcription of the gene coding for this protein is nearly completely abolished in highly invasive transitional cell carcinomas (TCCs)  . The protein is a small globular protein containing two transmembrane helices, and it is a multiply edited transcript.  All the editing sites are found in either the 5'-UTR or the N-terminal section of the protein, which is predicted to be outside the membrane. The three coding edits are all non-synonymous and predicted to encode exposed residues  . The function of this family is unknown.. 
PF06727 Protein of unknown function (DUF1207)<br>Pfam-B_23454 (release 10.0). This family consists of a number of hypothetical bacterial proteins of around 410 residues in length which seem to be specific to Chlamydia species. The function of this family is unknown.. 
PF06728 GPI transamidase subunit PIG-U<br>Pfam-B_7677 (release 9.0). Many eukaryotic proteins are anchored to the cell surface via glycosylphosphatidylinositol (GPI), which is posttranslationally attached to the carboxyl-terminus by GPI transamidase. The mammalian GPI transamidase is a complex of at least four subunits, GPI8, GAA1, PIG-S, and PIG-T. PIG-U is thought to represent a fifth subunit in this complex and may be involved in the recognition of either the GPI attachment signal or the lipid portion of GPI  . . 
PF06729 NRIF3;<br>Kinetochore component, CENP-R. Pfam-B_23665 (release 10.0). This family consists of mammalian kinetochore sub-complex proteins CENP-R, also referred to as nuclear receptor co-activator NRIF3 proteins. NRIF3 exhibits a distinct receptor specificity in interacting with and potentiating the activity of only TRs and RXRs but not other examined nuclear receptors. NRIF3 as a co-regulator that possesses both transactivation and transrepression domains and/or functions. Collectively, the NRIF3 family of co-regulators may play dual roles in mediating both positive and negative regulatory effects on gene expression  . CENP-R is one of the 15 components that make up the constitutive centromere associated complex (CCAN) part of the kinetochore. A sub-complex of CCAN, consisting of CENP-P/O/R/Q/U self-assembles on kinetochores with varying stoichiometry and undergoes a pre-mitotic maturation step. Kinetochore assembly is a cell cycle regulated multi-step process. The initial step occurs during interphase and involves loading of the 15-subunit constitutive centromere associated complex (CCAN). Kinetochores are multi-protein megadalton assemblies that are required for attachment of microtubules to centromeres and, in turn, the segregation of chromosomes in mitosis [2,3].. 
PF06730 DUF1208;<br>Moxon SJ, Eberhardt R. Pfam-B_23546 (release 10.0). This family of proteins has a role in embryogenesis. During embryogenesis it is essential for ectoderm and axial mesoderm development  . It may regulate cell proliferation and apoptosis  .. 
PF06732 Pescadillo N-terminus<br>Pfam-B_77615 (release 9.0). This family represents the N-terminal region of Pescadillo. Pescadillo protein localises to distinct substructures of the interphase nucleus including nucleoli, the site of ribosome biogenesis. During mitosis pescadillo closely associates with the periphery of metaphase chromosomes and by late anaphase is associated with nucleolus-derived foci and prenucleolar bodies. Blastomeres in mouse embryos lacking pescadillo arrest at morula stages of development, the nucleoli fail to differentiate and accumulation of ribosomes is inhibited. It has been proposed that in mammalian cells pescadillo is essential for ribosome biogenesis and nucleologenesis and that disruption to its function results in cell cycle arrest  . This family is often found in conjunction with a Pfam:PF00533 domain.. 
PF06733 DEAD_2<br>Pfam-B_1713 (release 10.0). This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin. RAD3 is involved in nucleotide excision repair, and forms part of the transcription factor TFIIH in yeast  .. 
PF06734 UL97<br>Pfam-B_1747 (release 10.0). This family represents a conserved region within viral UL97 phosphotransferases. UL97 participates in the phosphorylation of the nucleoside analog ganciclovir (GCV) to produce GCV-monophosphate  .. 
PF06736 Protein of unknown function (DUF1211)<br>Pfam-B_2594 (release 10.0). This family represents a conserved region within a number of hypothetical proteins of unknown function found in eukaryotes, bacteria and archaea. These may possibly be integral membrane proteins.. 
PF06737 Transglycosylase-like domain<br>This family of proteins are very likely to act as transglycosylase enzymes related to Pfam:PF00062 and Pfam:PF01464. These other families are weakly matched by this family, and include the known active site residues.. 
PF06738 Protein of unknown function (DUF1212)<br>Pfam-B_1646 (release 10.0). This family represents a conserved region within a number of hypothetical membrane proteins of unknown function found in eukaryotes, bacteria and archaea.. 
PF06739 Beta-propeller repeat<br>This family is related to Pfam:PF00400 and is  likely to also form a beta-propeller. SBBP stands for Seven Bladed Beta Propeller.. 
PF06740 Protein of unknown function (DUF1213)<br>Pfam-B_2177 (release 10.0). This family represents a short conserved repeat within Drosophila melanogaster proteins of unknown function. Approximately 50 copies of this repeat are present in each protein.. 
PF06741 Ataxin-2-like; Ataxin-2_N; <br>Pfam-B_2543 (release 10.0). This domain is found associated with Lsm domain  .. 
PF06742 Protein of unknown function (DUF1214)<br>Pfam-B_2721 (release 10.0). This family represents the C-terminal region of several hypothetical proteins of unknown function. Family members are mostly bacterial, but a few are also found in eukaryotes and archaea.. 
PF06743 FAST_Leu-rich;<br>FAST kinase-like protein, subdomain 1. Vella Briffa B, Fenech M. Pfam-B_2858 (release 10.0). This family represents a conserved region of eukaryotic Fas-activated serine/threonine (FAST) kinases (EC:2.7.1.-) that contains several conserved leucine residues. FAST kinase is rapidly activated during Fas-mediated apoptosis, when it phosphorylates TIA-1, a nuclear RNA-binding protein that has been implicated as an effector of apoptosis  . Note that many family members are hypothetical proteins. This region is often found immediately N-terminal to the FAST kinase-like protein, subdomain 2.. 
PF06744 Protein of unknown function (DUF1215)<br>Pfam-B_2952 (release 10.0). This family represents a conserved region situated towards the C-terminal end of several hypothetical bacterial proteins of unknown function. A few members resemble the ImcF protein, which has been proposed   to be involved in Vibrio cholerae cell surface reorganisation that results in increased adherence to epithelial cells line and increased conjugation frequency.. 
PF06745 KaiC<br>Pfam-B_2234 (release 10.0). This family represents a conserved region within bacterial and archaeal proteins, most of which are hypothetical. More than one copy is sometimes found in each protein. This family includes KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria  .. 
PF06746 Protein of unknown function (DUF1216)<br>Pfam-B_3048 (release 10.0). This family represents a conserved region, within Arabidopsis thaliana proteins, of unknown function. Family members sometimes contain more than one copy.It has been reported that this domain will be found in other Brassicaceae.. 
PF06747 CHCH domain<br>Westerman BA, Poutsma A, Steegers E, Oudejans CBM. we have identified a conserved motif in the LOC118487 protein that we have called the CHCH motif. Alignment of this protein with related members showed the presence of three subgroups of proteins, which are called the S (Small), N (N-terminal extended) and C (C-terminal extended) subgroups. All three sub-groups of proteins have in common that they contain a predicted conserved [coiled coil 1]-[helix 1]-[coiled coil 2]-[helix 2] domain (CHCH domain). Within each helix of the CHCH domain, there are two cysteines present in a C-X9-C motif. The N-group contains an additional double helix domain, and each helix contains the C-X9-C motif. This family contains a number of characterised proteins: Cox19 protein - a nuclear gene of Saccharomyces cerevisiae, codes for an 11-kDa protein (Cox19p) required for expression of cytochrome oxidase. Because cox19 mutants are able to synthesise the mitochondrial and nuclear gene products of cytochrome oxidase, Cox19p probably functions post-translationally during assembly of the enzyme. Cox19p is present in the cytoplasm and mitochondria, where it exists as a soluble intermembrane protein. This dual location is similar to what was previously reported for Cox17p, a low molecular weight copper protein thought to be required for maturation of the CuA centre of subunit 2 of cytochrome oxidase. Cox19p have four conserved potential metal ligands, these are three cysteines and one histidine. Mrp10 - belongs to the class of yeast mitochondrial ribosomal proteins that are essential for translation  . Eukaryotic NADH-ubiquinone oxidoreductase 19 kDa (NDUFA8) subunit  . The CHCH domain was previously called DUF657  .. 
PF06748 Protein of unknown function (DUF1217)<br>Pfam-B_3199 (release 10.0). This family represents a conserved region that is found within bacterial proteins, most of which are hypothetical. Some members contain multiple copies.. 
PF06749 Protein of unknown function (DUF1218)<br>Pfam-B_3286 (release 10.0). This family contains hypothetical plant proteins of unknown function. Family members contain a number of conserved cysteine residues.. 
PF06750 Bacterial Peptidase A24 N-terminal domain<br>This family is found at the N-terminus of the pre-pilin peptidases (Pfam:PF01478). It's function has not been specifically determined; however some of the family have been characterised as bifunctional ( ), and this domain may contain the N-methylation activity (EC:2.1.1.-). It consists of an intracellular region between a pair of transmembrane. This region contains an invariant proline and two almost fully conserved disulphide bridges - hence the name DiS-P-DiS. The cysteines have been shown to be essential to the overall function of the enzyme in  , but their role was incorrectly ascribed. . 
PF06751 Ethanolamine ammonia lyase large subunit (EutB)<br>Pfam-B_6325 (release 10.0). This family consists of several bacterial ethanolamine ammonia lyase large subunit (EutB) proteins (EC:4.3.1.7). Ethanolamine ammonia-lyase is a bacterial enzyme that catalyses the adenosylcobalamin-dependent conversion of certain vicinal amino alcohols to oxo compounds and ammonia. The enzyme is a heterodimer composed of subunits of Mr approximately 55,000 (EutB) and 35,000 (EutC)  .  . 
PF06752 E_Pc_C-term; <br>Enhancer of Polycomb C-terminus. Pfam-B_16811 (release 10.0). This family represents the C-terminus of eukaryotic enhancer of polycomb  proteins, which have roles in heterochromatin formation  . This family contains several conserved motifs.. 
PF06753 Bradykinin<br>Pfam-B_7085 (release 10.0). This family consists of several bradykinin sequences. The skins of anuran amphibians, in addition to mucus glands, contain highly specialised poison glands, which, in reaction to stress or attack, exude a complex noxious cocktail of biologically active molecules. These secretions often contain a plethora of peptides among which bradykinin or structural variants have been identified  .. 
PF06754 Phosphonate metabolism protein PhnG<br>Pfam-B_6667 (release 10.0). This family consists of several bacterial phosphonate metabolism protein PhnG sequences. In Escherichia coli, the phn operon encodes proteins responsible for the uptake and breakdown of phosphonates. The exact function of PhnG is unknown, however it is thought likely that along with six other proteins PhnG makes up the the C-P (carbon-phosphorus) lyase  .. 
PF06755 Protein of unknown function (DUF1219)<br>Pfam-B_4928 (release 10.0). This family consists of several hypothetical proteins which seem to be specific to the Enterobacteria Escherichia coli and Shigella flexneri. Family members are often known as YeeV proteins and are around 125 residues in length. The function of this family is unknown.. 
PF06756 S19_C-term; <br>Chorion protein S19 C-terminal. Pfam-B_16839 (release 10.0). This family represents the C-terminal region of eukaryotic chorion protein S19. In Drosophilidae, the S19 gene is known to form part of an autosomal cluster that also contains s16, s15 and s18  . Note that members of this family contain a conserved PVA motif, and many contain Pfam:PF03964.. 
PF06757 Insect allergen related repeat, nitrile-specifier detoxification<br>Pfam-B_5947 (release 10.0). This family exemplifies a case of novel gene evolution. The case in point is the arms-race between plants and their infective insective herbivores in the area of the glucosinolate-myrosinase system. Brassicas have developed the glucosinolate-myrosinase system as chemical defence mechanism against the insects, and consequently the insects have adapted to produce a detoxifying molecule, nitrile-specifier protein (NSP). NSP is present in the small white butterfly Pieris rapae. NSP is structurally different from and has no amino acid homology to any known detoxifying enzymes, and it appears to have arisen by a process of domain and gene duplication of a sequence of unknown function that is widespread in insect species and referred to as insect-allergen-repeat protein. Thus this family is found either as a single domain or as a multiple repeat-domain  .. 
PF06758 Repeat of unknown function (DUF1220)<br>Pfam-B_6292 (release 10.0). 
PF06760 Protein of unknown function (DUF1221)<br>Pfam-B_16837 (release 10.0). This is a family of plant proteins, most of which are hypothetical and of unknown function. All members contain the Pfam:PF00069 domain, suggesting that they may possess kinase activity.. 
PF06761 ImcF-related; <br>Intracellular multiplication and human macrophage-killing. Pfam-B_3476 (release 10.0). This family represents a conserved region within several bacterial proteins that resemble IcmF, which has been proposed   to be involved in Vibrio cholerae cell surface reorganisation, resulting in increased adherence to epithelial cells and increased conjugation frequency. Note that many family members are hypothetical proteins.. 
PF06762 DUF1222;<br>Lipase maturation factor. Vella Briffa B, Eberhardt R. Pfam-B_3454 (release 10.0). This family of transmembrane proteins includes the lipase maturation factor, LMF1. Lipoprotein lipase and hepatic lipase require LMF1 to fold into their active states [1,2]. The precise role of LMF1 in lipase folding has yet to be determined  .. 
PF06763 Prophage minor tail protein Z (GPZ)<br>Pfam-B_6085 (release 10.0). This family consists of several prophage minor tail protein Z like sequences from Escherichia coli, Salmonella typhimurium and Lambda-like bacteriophages.. 
PF06764 Protein of unknown function (DUF1223)<br>Pfam-B_6655 (release 10.0). This family consists of several hypothetical proteins of around 250 residues in length which are found in both plants and bacteria. The function of this family is unknown.. 
PF06766 Fungal hydrophobin<br>Pfam-B_3587 (release 10.0). This is a family of fungal hydrophobins that seems to be restricted to ascomycetes. These are small, moderately hydrophobic extracellular proteins that have eight cysteine residues arranged in a strictly conserved motif. Hydrophobins are generally found on the outer surface of conidia and of the hyphal wall, and may be involved in mediating contact and communication between the fungus and its environment  . Note that some family members contain multiple copies.. 
PF06767 Sif protein<br>Pfam-B_7884 (release 10.0). This family consists of several SifA and SifB and SseJ proteins which seem to be specific to the Salmonella species. SifA, SifB and SseJ have been demonstrated to localise to the Salmonella-containing vacuole (SCV) and to Salmonella-induced filaments (Sifs). Trafficking of SseJ and SifB away from the SCV requires the SPI-2 effector SifA. SseJ trafficking away from the SCV along Sifs is unnecessary for its virulence function  .. 
PF06769 DUF1224; <br>Plasmid encoded toxin Txe. Pfam-B_7662 (release 10.0). The plasmid encoded Axe-Txe proteins in Enterococcus faecium act as an antitoxin-toxin pair.  When the plasmid is lost, the antitoxin (Axe) is degraded relatively quickly by host enzymes. This allows the toxin to interact with its intracellular target, thus killing the cell or impeding cell growth  . This family contains many hypothetical proteins. This domain forms complexes with Axe antitoxins containing Pfam:PF02604.. 
PF06770 Actin-rearrangement-inducing factor (Arif-1)<br>Pfam-B_6086 (release 10.0). This family consists of several Nucleopolyhedrovirus actin-rearrangement-inducing factor (Arif-1) proteins. In response to Autographa californica multicapsid nuclear polyhedrosis virus (AcMNPV) infection, a sequential rearrangement of the actin cytoskeleton occurs this is induced by Arif-1  . Arif-1 is tyrosine phosphorylated and is located at the plasma membrane as a component of the actin rearrangement-inducing complex  .. 
PF06771 1111; Desmo_N-term; <br>Viral Desmoplakin N-terminus. Pfam-B_3693 (release 10.0). This family represents the N-terminus of viral desmoplakin. Desmoplakin is a component of mature desmosomes, which are the main adhesive junctions in epithelia and cardiac muscle. Desmoplakin is also essential for the maturation of adherens junctions  . Note that many family members are hypothetical.. 
PF06772 Bacterial low temperature requirement A protein (LtrA)<br>Pfam-B_8368 (release 10.0). This family consists of several bacteria specific low temperature requirement A (LtrA) protein sequences which have been found to be essential for growth at low temperatures in Listeria monocytogenes  .. 
PF06773 Bim protein N-terminus<br>Pfam-B_8427 (release 10.0). This family represents the N-terminal region of several mammal specific Bim proteins. The Bim protein is one of the BH3-only proteins, members of the Bcl-2 family that have only one of the Bcl-2 homology regions, BH3. BH3-only proteins are essential initiators of apoptotic cell death  .. 
PF06775 DUF1226; <br>Putative adipose-regulatory protein (Seipin). Pfam-B_8703 (release 10.0). Seipin is a protein of approximately 400 residues, in humans, which is the product of a gene homologous to the murine guanine nucleotide-binding protein (G protein) gamma-3 linked gene.  This gene is implicated in the regulation of body fat distribution and insulin resistance and particularly in the auto-immune disease Berardinelli-Seip congenital lipodystrophy type 2. Seipin has no similarity with other known proteins or consensus motifs that might predict its function, but it is predicted to contain two transmembrane domains at residues 28-49 and 237-258, in human, and a third transmembrane domain might be present at residues 155-173. Seipin may also be implicated in Silver spastic paraplegia syndrome and distal hereditary motor neuropathy type V  .. 
PF06776 Invasion associated locus B (IalB) protein<br>Pfam-B_3703 (release 10.0). This family consists of several invasion associated locus B (IalB) proteins and related sequences. IalB is known to be a major virulence factor in Bartonella bacilliformis where it was shown to have a direct role in human erythrocyte parasitism. IalB is upregulated in response to environmental cues signaling vector-to-host transmission. Such environmental cues would include, but not be limited to, temperature, pH, oxidative stress, and haemin limitation. It is also thought that IalB would aide B. bacilliformis survival under stress-inducing environmental conditions  . The role of this protein in other bacterial species is unknown.. 
PF06777 Protein of unknown function (DUF1227)<br>Pfam-B_3660 (release 10.0). This family represents a conserved region within a number of eukaryotic DNA repair helicases (EC:3.6.1.-).. 
PF06778 Chlorite dismutase<br>Pfam-B_3770 (release 10.0). This family contains chlorite dismutase enzymes of bacterial and archaeal origin. This enzyme catalyses the disproportionation of chlorite into chloride and oxygen  . Note that many family members are hypothetical proteins.. 
PF06779 Protein of unknown function (DUF1228)<br>Pfam-B_5646 (release 10.0). This family represents the N-terminus of several putative bacterial membrane proteins, which may be sugar transporters. Note that many family members are hypothetical proteins.. 
PF06780 Erp_C-term; <br>Erp protein C-terminus. Pfam-B_4561 (release 10.0). This family represents the C-terminus of bacterial Erp proteins that seem to be specific to Borrelia burgdorferi (a causative agent of Lyme disease). Borrelia Erp proteins are particularly heterogeneous, which might enable them to interact with a wide variety of host components  .. 
PF06781 Uncharacterised protein family (UPF0233)<br>
PF06782 Uncharacterised protein family (UPF0236)<br>
PF06783 Uncharacterised protein family (UPF0239)<br>
PF06784 Uncharacterised protein family (UPF0240)<br>
PF06785 Uncharacterised protein family (UPF0242)<br>
PF06786 Uncharacterised protein family (UPF0253)<br>
PF06787 Uncharacterised protein family (UPF0254)<br>
PF06788 Uncharacterised protein family (UPF0257)<br>
PF06789 Uncharacterised protein family (UPF0258)<br>
PF06790 Uncharacterised protein family (UPF0259)<br>
PF06791 Prophage tail length tape measure protein<br>Pfam-B_3868 (release 10.0). This family represents a conserved region located towards the N-terminal end of prophage tail length tape measure protein (TMP). TMP is important for assembly of phage tails and involved in tail length determination. Mutated forms TMP cause tail fibres to be shortened  .. 
PF06792 Uncharacterised protein family (UPF0261)<br>
PF06793 Uncharacterised protein family (UPF0262)<br>
PF06794 Uncharacterised protein family (UPF0270)<br>
PF06795 Erythrovirus X protein<br>Pfam-B_9167 (release 10.0). This family consists of several Erythrovirus X proteins which seem to be found exclusively in human parvovirus and human erythrovirus. The function of this family is unknown.. 
PF06796 Periplasmic nitrate reductase protein NapE<br>Pfam-B_9066 (release 10.0). This family consists of several bacterial periplasmic nitrate reductase NapE proteins. Seven genes, napKEFDABC, encoding the periplasmic nitrate reductase system were cloned from the denitrifying phototrophic bacterium Rhodobacter sphaeroides f. sp. denitrificans IL106. NapE is thought to be a transmembrane protein  .. 
PF06797 Protein of unknown function (DUF1229)<br>Pfam-B_9402 (release 10.0). This family consists of several hypothetical proteins of around 415 residues in length which seem to be specific to the bacterium Leptospira interrogans.. 
PF06798 PrkA serine protein kinase C-terminal domain<br>Pfam-B_3917 (release 10.0). This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This family corresponds to the C-terminal domain  .. 
PF06799 Protein of unknown function (DUF1230)<br>Pfam-B_9232 (release 10.0). This family consists of several hypothetical plant and photosynthetic bacterial proteins of around 160 residues in length. The function of this family is unknown although looking at the species distribution the protein may play a part in photosynthesis.. 
PF06800 Sugar transport protein<br>Pfam-B_4126 (release 10.0). This is a family of bacterial sugar transporters approximately 300 residues long. Members include glucose uptake proteins  , ribose transport proteins, and several putative and hypothetical membrane proteins probably involved in sugar transport across bacterial membranes.. 
PF06802 Protein of unknown function (DUF1231)<br>Pfam-B_9856 (release 10.0). This family consists of several Orthopoxvirus specific proteins predominantly of around 340 residues in length. This family contains both B17 and B15 proteins, the function of which are unknown.. 
PF06803 Protein of unknown function (DUF1232)<br>Pfam-B_4265 (release 10.0). This family represents a conserved region of approximately 60 residues within a number of hypothetical bacterial and archaeal proteins of unknown function.. 
PF06804 NlpB/DapX lipoprotein<br>Pfam-B_10405 (release 10.0). This family consists of a number of bacterial lipoproteins often known as NlpB or DapX. This lipoprotein is detected in outer membrane vesicles in Escherichia coli and appears to be nonessential  .. 
PF06805 Bacteriophage lambda tail assembly protein I<br>Moxon SJ, Iyer LM, Burroughs AM, Aravind L. Pfam-B_7725 (release 10.0). This family consists of tail assembly proteins from lambdoid and T1 phages and related prophages, e.g. the tail assembly protein I  (TAPI). Members of this family contain a core ubiquitin fold domain   . The exact function of TAPI is not clear but  it is not incorporated into the mature tail. Gene neighborhoods  reveal that TAPI co-occurs with genes encoding the host-specificity  protein TapJ, and TapK, which contains a JAB metallopeptidase fused  to an NlpC/P60  peptidase. It is proposed that the TAPI protein is  processed by the  peptidase domains of TapK  .. 
PF06806 Putative excisionase (DUF1233)<br>Pfam-B_9240 (release 10.0). This family consists of several putative phage excisionase proteins of around 80 residues in length.. 
PF06807 Pre-mRNA cleavage complex II protein Clp1<br>Pfam-B_9787 (release 10.0). This family consists of several pre-mRNA cleavage complex II Clp1 (or HeaB) proteins. Six different protein factors are required in vitro for 3' end formation of mammalian pre-mRNAs by endonucleolytic cleavage and polyadenylation. Clp1 is a subunit of cleavage complex IIA, which is required for cleavage, but not for polyadenylation of pre-mRNA  .. 
PF06808 DctM-like transporters<br>Pfam-B_4075 (release 10.0). This family contains a diverse range of predicted transporter proteins. Including the DctM subunit of the bacterial and archaeal TRAP C4-dicarboxylate transport (Dct) system permease. In general, C4-dicarboxylate transport systems allow C4-dicarboxylates like succinate, fumarate, and malate to be taken up. TRAP C4-dicarboxylate carriers are secondary carriers that use an electrochemical H+ gradient as the driving force for transport. DctM is an integral membrane protein that is one of the constituents of TRAP carriers  . Note that many family members are hypothetical proteins.. 
PF06809 Neural proliferation differentiation control-1 protein (NPDC1)<br>Pfam-B_10407 (release 10.0). This family consists of several neural proliferation differentiation control-1 (NPDC1) proteins. NPDC1 plays a role in the control of neural cell proliferation and differentiation. It has been suggested that NPDC1 may be involved in the development of several secretion glands. This family also contains the C-terminal region of the C. elegans protein CAB-1 (Swiss:Q93249) which is known to interact with AEX-3  .. 
PF06810 Phage minor structural protein GP20<br>Pfam-B_8431 (release 10.0). This family consists of several phage minor structural protein GP20 sequences of around 180 residues in length. The function of this family is unknown.. 
PF06812 ImpA-rel_N-term; <br>ImpA-related N-terminal. Pfam-B_4308 (release 10.0). This family represents a conserved region located towards the N-terminal end of ImpA and related proteins. ImpA is an inner membrane protein, which has been suggested to be involved with proteins that are exported and associated with colony variations in Actinobacillus actinomycetemcomitans  . Note that many family members are hypothetical proteins.. 
PF06813 Nodulin-like<br>Pfam-B_4440 (release 10.0). This family represents a conserved region within plant nodulin-like proteins.. 
PF06814 Lung seven transmembrane receptor<br>Pfam-B_4367 (release 10.0). This family represents a conserved region with eukaryotic lung seven transmembrane receptors and related proteins.. 
PF06815 rvt_connect;<br>Reverse transcriptase connection domain. This domain is known as the connection domain. This domain lies between the thumb and palm domains  .. 
PF06816 NOD; NOD1; <br>NOTCH  signalling plays a fundamental role during a great number of developmental processes in multicellular animals [1-2]. NOD and NODP represent a region present in many NOTCH proteins and NOTCH homologs in multiple species such as NOTCH2 and NOTCH3, LIN12, SC1 and TAN1. Role of NOD domain remains to be  elucidated.. 
PF06817 rvt_thumb;<br>Reverse transcriptase thumb domain. This domain is known as the thumb domain. It is composed of a four helix bundle  .. 
PF06818 Fez1<br>Pfam-B_4593 (release 10.0). This family represents the eukaryotic Fez1 protein. Fez1 contains a leucine-zipper region with similarity to the DNA-binding domain of the cAMP-responsive activating-transcription factor 5  . There is evidence that Fez1 inhibits cancer cell growth through regulation of mitosis, and that its alterations result in abnormal cell growth  . Note that some family members contain more than one copy of this region.. 
PF06819 Archaeal Peptidase A24 C-terminal Domain<br>This region is of unknown function but is found in some archaeal Pfam:PF01478. It is predicted to be of mixed alpha/beta secondary structure by JPred.. 
PF06820 Tail_fib_C-term; <br>Putative prophage tail fibre C-terminus. Pfam-B_5030 (release 10.0). This family represents the C-terminus of a prophage tail fibre protein found mostly in E. coli. All family members contain a conserved RLGP motif.. 
PF06821 DUF1234;<br>Vella Briffa B, Eberhardt R. Pfam-B_4941 (release 10.0). Members of this family have serine hydrolase activity. They contain a conserved serine hydrolase motif, GXSXG/A, where the serine is a putative nucleophile  .\.       This family has an alpha-beta hydrolase fold [2,3]. Eukaryotic members of this family have a conserved LXCXE motif, which binds to retinoblastomas. This motif is absent from prokaryotic members of this family  .. 
PF06822 Protein of unknown function (DUF1235)<br>Pfam-B_4988 (release 10.0). This family contains a number of viral proteins of unknown function.. 
PF06823 Protein of unknown function (DUF1236)<br>Pfam-B_5056 (release 10.0). This family contains a number of hypothetical bacterial proteins of unknown function. Some family members contain more than one copy of the region represented by this family.. 
PF06824 Protein of unknown function (DUF1237)<br>Pfam-B_4981 (release 10.0). This family contains a number of hypothetical proteins of about 450 residues in length. Their function is unknown, and most are bacterial. However, structurally this family is part of the 6 hairpin glycosidase superfamily, suggesting a glycosyl hydrolase function.. 
PF06825 Heat shock factor binding protein 1<br>Pfam-B_20266 (release 10.0). Heat shock factor binding protein 1 (HSBP1) appears to be a negative regulator of the heat shock response  .. 
PF06826 Predicted Permease Membrane Region<br>This family represents five transmembrane helices that are normally found flanking (five either side) a pair of Pfam:PF02080 domains. This suggests that the paired regions form a ten helical structure, probably forming the pore, whereas the Pfam:PF02080) binds a ligand for export or regulation of the pore. Swiss:Q8L3K8 is described as a aspartate-alanine antiporter ( ). In  conjunction with Swiss:Q8L3K9 it forms a 'proton motive metabolic cycle catalysed by an aspartate-alanine exchange'. The general conservation of domain architecture in this family suggests that they are functional orthologues.. 
PF06827 Zinc finger found in FPG and IleRS<br>This zinc binding domain is found at the C-terminus of isoleucyl tRNA synthetase and the enzyme Formamidopyrimidine-DNA glycosylase EC:3.2.2.23.. 
PF06830 Root cap<br>Pfam-B_5867 (release 10.0). The cells at the periphery of the root cap are continuously sloughed off from the root into the mucilage, and are thought to be programmed to die  .This family represents a conserved region approximately 60 residues in length within plant root cap proteins, which may be involved in the process.. 
PF06831 Formamidopyrimidine-DNA glycosylase H2TH domain<br>Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidised purines from damaged DNA. This family is the central domain containing the DNA-binding helix-two turn-helix domain  .. 
PF06832 Penicillin-Binding Protein C-terminus Family<br>This conserved region of approximately 90 residues is found in a sub-group of bacterial Penicillin-Binding Proteins (PBPs). A variable length loop region separates this region from the transpeptidase unit (Pfam:PF00905). It is predicted by PROF to be an all beta fold.. 
PF06833 Malonate decarboxylase gamma subunit (MdcE)<br>Pfam-B_10907 (release 10.0). This family consists of several bacterial malonate decarboxylase gamma subunit proteins. Malonate decarboxylase of Klebsiella pneumoniae consists of four different subunits and catalyses the conversion of malonate plus H+ to acetate and CO2. The catalysis proceeds via acetyl and malonyl thioester residues with the phosphribosyl-dephospho-CoA prosthetic group of the acyl carrier protein (ACP) subunit. MdcD and E together probably function as malonyl-S-ACP decarboxylase  .  . 
PF06834 TraU protein<br>Pfam-B_10708 (release 10.0). This family consists of several bacterial TraU proteins. TraU appears to be more essential to conjugal DNA transfer than to assembly of pilus filaments  .. 
PF06835 DUF1239;<br>Lipopolysaccharide-assembly, LptC-related. Pfam-B_11065 (release 10.0). This family consists of several related groups of proteins one of which is the LptC family. LptC is involved in lipopolysaccharide-assembly on the outer membrane of Gram-negative organisms. The lipopolysaccharide component of the outer bacterial membrane is transported form its source of origin to the outer membrane by a set of proteins constituting a transport machinery that is made up of LptA, LptB, LptC, LptD, LptE. LptC is located on the inner membrane side of the intermembrane space.. 
PF06836 Protein of unknown function (DUF1240)<br>Pfam-B_11130 (release 10.0). This family consists of a number of hypothetical putative membrane proteins which seem to be specific to Yersinia pestis. The function of this family is unknown.. 
PF06837 Fijivirus P9-2 protein<br>Pfam-B_11357 (release 10.0). This family consists of several Fijivirus specific P9-2 proteins from Rice black streaked dwarf virus (RBSDV) and Fiji disease virus. The function of this family is unknown.. 
PF06838 Alum_res;<br>Methionine gamma-lyase . Vella Briffa B, Haft D. Pfam-B_5307 (release 10.0). This is a putative pyridoxal 5'-phosphate-dependent methionine gamma-lyase enzyme involved in methionine catabolism.. 
PF06839 GRF zinc finger<br>This presumed zinc binding domain is found in a variety of DNA-binding proteins.  It seems likely that this domain is involved in nucleic acid binding.  It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to Pfam:PF01396.. 
PF06840 Protein of unknown function (DUF1241)<br>Pfam-B_11380 (release 10.0). This family consists of several programmed cell death 10 protein (PDCD10 or TFAR15) sequences. The function of this family is unknown.. 
PF06841 T4_Gp19; <br>T4-like virus tail tube protein gp19. Pfam-B_11507 (release 10.0). This family consists of several tail tube protein gp19 sequences from the T4-like viruses [1,2].  This famiyl also contains bacterial members which suggest lateral transfer of genes.. 
PF06842 Protein of unknown function (DUF1242)<br>Pfam-B_11544 (release 10.0). This family consists of a number of eukaryotic proteins of around 72 residues in length. The function of this family is unknown.. 
PF06844 Protein of unknown function (DUF1244)<br>Pfam-B_11743 (release 10.0). This family consists of several short bacterial proteins of around 100 residues in length. The function of this family is unknown.. 
PF06847 Archaeal Peptidase A24 C-terminus Type II<br>This region is of unknown function but is found in some archaeal Pfam:PF01478. It is predicted to be of mixed alpha/beta secondary structure by Prof.. 
PF06848 Disaggregatase related repeat<br>Moxon SJ, Mistry J, Adindla S. Pfam-B_11958 (release 10.0). This family consists of several repeats which seem to be specific to the Methanosarcina archaea species and are often found in multiple copies in disaggregatase proteins. Members of this family are also found in single copies in several hypothetical proteins.  This repeat is also known as DNRLRE repeat and is predicted form a mainly beta-strand structure with two alpha-helices [Adindla et al. Comparative and Functional Genomics 2004; 5:2-16].  It is found in some cell surface proteins. . 
PF06849 Protein of unknown function (DUF1246)<br>Pfam-B_5448 (release 10.0). This family represents the N-terminus of a number of hypothetical archaeal proteins of unknown function.. 
PF06850 PHB_depo_C-term; <br>PHB de-polymerase C-terminus. Pfam-B_5697 (release 10.0). This family represents the C-terminus of bacterial poly(3-hydroxybutyrate) (PHB) de-polymerase. This degrades PHB granules to oligomers and monomers of 3-hydroxy-butyric acid.. 
PF06851 Protein of unknown function (DUF1247)<br>Pfam-B_5762 (release 10.0). This family contains a number of hypothetical viral proteins of unknown function approximately 200 residues long.. 
PF06852 Protein of unknown function (DUF1248)<br>Pfam-B_5811 (release 10.0). This family represents a conserved region within a number of proteins of unknown function that seem to be specific to C. elegans. Note that some family members contain more than one copy of this region.. 
PF06853 Protein of unknown function (DUF1249)<br>Pfam-B_11475 (release 10.0). This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.. 
PF06854 Bacteriophage Gp15 protein<br>Pfam-B_11759 (release 10.0). This family consists of bacteriophage Gp15 proteins and related bacterial sequences. The function of this family is unknown. 
PF06855 Protein of unknown function (DUF1250)<br>Pfam-B_11942 (release 10.0). This family consists of several short hypothetical bacterial proteins of around 70 residues in length. Members of this family seem to all belong to the order Bacillales or Lactobacillales. The function of this family is unknown.. 
PF06856 Protein of unknown function (DUF1251)<br>Pfam-B_12000 (release 10.0). This family consists of the N-terminal region of several hypothetical Nucleopolyhedrovirus proteins of unknown function.. 
PF06857 MdcD;<br>Malonate decarboxylase delta subunit (MdcD). Pfam-B_12010 (release 10.0). This family consists of several bacterial malonate decarboxylase delta subunit (MdcD) proteins.  Malonate decarboxylase of Klebsiella pneumoniae consists of four different subunits and catalyses the conversion of malonate plus H+ to acetate and CO2. The catalysis proceeds via acetyl and malonyl thioester residues with the phosphribosyl-dephospho-CoA prosthetic group of the acyl carrier protein (ACP) subunit. MdcC is the (apo) ACP subunit  . The family also contains the CitD family of citrate lyase acyl carrier proteins.. 
PF06858 Nucleolar GTP-binding protein 1 (NOG1)<br>Pfam-B_5853 (release 10.0). This family represents a conserved region of approximately 60 residues in length within nucleolar GTP-binding protein 1 (NOG1). In S. cerevisiae, the NOG1 gene has been shown to be essential for cell viability, suggesting that NOG1 may play an important role in nucleolar functions  . Family members include eukaryotic, bacterial and archaeal proteins.. 
PF06859 Bicoid-interacting protein 3 (Bin3)<br>Pfam-B_5564 (release 10.0). This family represents a conserved region of approximately 120 residues within eukaryotic Bicoid-interacting protein 3 (Bin3). Bin3, which shows similarity to a number of protein methyltransferases that modify RNA-binding proteins, interacts with Bicoid, which itself directs pattern formation in the early Drosophila embryo. The interaction might allow Bicoid to switch between its dual roles in transcription and translation  . Note that family members contain a conserved HLN motif.. 
PF06861 BALF1 protein<br>Pfam-B_12069 (release 10.0). This family consists of several BALF1 proteins which seem to be specific to the Lymphocryptoviruses. BALF1, inhibits the antiapoptotic activity of EBV BHRF1 and of KSBcl-2  .. 
PF06862 Protein of unknown function (DUF1253)<br>Pfam-B_6227 (release 10.0). This family represents the C-terminal portion (approximately 500 residues) of several hypothetical eukaryotic proteins of unknown function.. 
PF06863 Protein of unknown function (DUF1254)<br>Pfam-B_5911 (release 10.0). This family represents a conserved region about 130 residues long within hypothetical proteins of unknown function. Family members include eukaryotic, bacterial and archaeal proteins.. 
PF06864 Pilin accessory protein (PilO)<br>Pfam-B_12430 (release 10.0). This family consists of several enterobacterial PilO proteins. The function of PilO is unknown although it has been suggested that it is a cytoplasmic protein in the absence of other Pil proteins, but PilO protein is translocated to the outer membrane in the presence of other Pil proteins. Alternatively, PilO protein may form a complex with other Pil protein(s). PilO has been predicted to function as a component of the pilin transport apparatus and thin-pilus basal body  . This family does not seem to be related to Pfam:PF04350.. 
PF06865 Protein of unknown function (DUF1255)<br>Pfam-B_12498 (release 10.0). This family consists of several conserved hypothetical bacterial proteins of around 95 residues in length. The function of this family is unknown. 
PF06866 Protein of unknown function (DUF1256)<br>Pfam-B_12377 (release 10.0). This family consists of several uncharacterised bacterial proteins which seem to be specific to the orders Clostridia and Bacillales. Family members are typically around 180 residues in length. The function of this family is unknown. These proteins are related to peptidase family M63 and so may be peptidases.. 
PF06868 Protein of unknown function (DUF1257)<br>Pfam-B_5975 (release 10.0). This family contains hypothetical proteins of unknown function that are approximately 120 residues long. Family members include eukaryotic and bacterial proteins.. 
PF06869 Protein of unknown function (DUF1258)<br>Pfam-B_6065 (release 10.0). This family represents a conserved region approximately 260 residues long within a number of hypothetical proteins of unknown function that seem to be specific to C. elegans. Note that this family contains a number of conserved cysteine and histidine residues.. 
PF06870 A49-like RNA polymerase I associated factor <br>Pfam-B_20222 (release 10.0). Saccharomyces cerevisiae A49 is a specific subunit associated with RNA polymerase I (Pol I) in eukaryotes. Pol I maintains transcription activities in A49 deletion mutants. However, such mutants are deficient in transcription activity at low temperatures.  Deletion analysis of the fusion yeast  homolog indicate that only the C-terminal two thirds are required for function.  Transcript analysis has demonstrated that A49 is maximising transcription of ribosomal DNA  .. 
PF06871 DUF1259; <br>Pfam-B_13298 (release 10.0). This family consists of several TraH proteins which seem to be specific to Agrobacterium and Rhizobium species. This protein is thought to be involved in conjugal transfer but its function is unknown. This family does not appear to be related to Pfam:PF06122.. 
PF06872 EspG protein<br>Pfam-B_13549 (release 10.0). This family consists of several EspG like proteins from Citrobacter rodentium and Escherichia coli. EspG is secreted by the type III secretory system and is translocated into host epithelial cells. EspG is homologous with Shigella flexneri protein VirA and can rescue invasion in a Shigella virA mutant, indicating that these proteins are functionally equivalent in Shigella.  EspG plays an accessory but as yet undefined role in EPEC virulence that may involve intestinal colonisation  .. 
PF06873 Cell surface immobilisation antigen SerH<br>Pfam-B_13151 (release 10.0). This family consists of several cell surface immobilisation antigen SerH proteins which seem to be specific to Tetrahymena thermophila. The SerH locus of Tetrahymena thermophila is one of several paralogous loci with genes encoding variants of the major cell surface protein known as the immobilisation antigen (i-ag)  . . 
PF06874 Firmicut_FBPase; <br>Firmicute fructose-1,6-bisphosphatase. Pfam-B_13194 (release 10.0). This family consists of several bacterial fructose-1,6-bisphosphatase proteins (EC:3.1.3.11) which seem to be specific to phylum Firmicutes. Fructose-1,6-bisphosphatase (FBPase) is a well known enzyme involved in gluconeogenesis  . This family does not seem to be structurally related to Pfam:PF00316.. 
PF06875 Plethodontid receptivity factor PRF<br>Pfam-B_13241 (release 10.0). This family consists of several plethodontid receptivity factor (PRF) proteins which seem to be specific to Plethodon jordani (Jordan's salamander). PRF is a courtship pheromone produced by males increase female receptivity  .. 
PF06876 Plant self-incompatibility response (SCRL) protein<br>Pfam-B_13253 (release 10.0). This family consists of several Plant self-incompatibility response (SCRL) proteins. The male component of the self-incompatibility response in Brassica has been shown to be encoded by the S locus cysteine-rich gene (SCR). SCR is related, at the sequence level, to the pollen coat protein (PCP) gene family whose members encode small, cysteine-rich proteins located in the proteo-lipidic surface layer (tryphine) of Brassica pollen grains  .. 
PF06877 DUF1260;<br>Regulator of ribonuclease activity B. Pfam-B_13601 (release 10.0). This family of proteins regulate mRNA abundance by binding to RNaseE and inhibiting its endonucleolytic activity [1-2]. A subset of these proteins are predicted to function as immunity proteins  .. 
PF06878 Pkip-1 protein<br>Pfam-B_13784 (release 10.0). This family consists of several Pkip-1 proteins which seem to be specific to Nucleopolyhedroviruses. The function of this family is unknown although it has been found that Pkip-1 is not essential for virus replication in cell culture or by in vivo intrahaemocoelic injection  .  . 
PF06880 Protein of unknown function (DUF1262)<br>Pfam-B_6733 (release 10.0). This family represents a conserved region within a number of proteins of unknown function that seem to be specific to Arabidopsis thaliana. Note that some family members contain more than one copy of this region.. 
PF06881 RNA polymerase II transcription factor SIII (Elongin) subunit A<br>Pfam-B_6598 (release 10.0). This family represents a conserved region within RNA polymerase II transcription factor SIII (Elongin) subunit A. In mammals, the Elongin complex activates elongation by RNA polymerase II by suppressing transient pausing of the polymerase at many sites within transcription units. Elongin is a heterotrimer composed of A, B, and C subunits of 110, 18, and 15 kilodaltons, respectively. Subunit A has been shown to function as the transcriptionally active component of Elongin  .. 
PF06882 Protein of unknown function (DUF1263)<br>Pfam-B_6668 (release 10.0). This family represents a conserved region located towards the C-terminus of a number proteins of unknown function that seem to be specific to Oryza sativa.. 
PF06883 RNA polymerase I, Rpa2 specific domain <br>Pfam-B_4721 (release 10.0). This domain is found between domain 3 (Pfam:PF04565) and domain 5  (Pfam:PF04565), but shows no homology to domain 4 of Rpb2.  The external  domains in multisubunit RNA polymerase (those most distant from the  active site) are known to demonstrate more sequence variability  .. 
PF06884 Protein of unknown function (DUF1264)<br>Pfam-B_6839 (release 10.0). This family contains a number of bacterial and eukaryotic proteins of unknown function that are approximately 200 residues long. Some family members are annotated as putative lipoproteins.. 
PF06886 Targeting protein for Xklp2 (TPX2)<br>Pfam-B_6863 (release 10.0). This family represents a conserved region approximately 60 residues long within the eukaryotic targeting protein for Xklp2 (TPX2). Xklp2 is a kinesin-like protein localised on centrosomes throughout the cell cycle and on spindle pole microtubules during metaphase. In Xenopus, it has been shown that Xklp2 protein is required for centrosome separation and maintenance of spindle bi-polarity  . TPX2 is a microtubule-associated protein that mediates the binding of the C-terminal domain of Xklp2 to microtubules. It is phosphorylated during mitosis in a microtubule-dependent way  .. 
PF06887 Protein of unknown function (DUF1265)<br>Vella Briffa B, Pollington JE. Pfam-B_7101 (release 10.0). This family represents a conserved region approximately 50 residues long within a number of proteins of unknown function that seem to be restricted to C. elegans. The GO annotation for this protein indicate that its a protein involved in nematode larval development and has a positive regulation on growth rate.. 
PF06888 Putative Phosphatase<br>Pfam-B_7115 (release 10.0). This family contains a number of putative eukaryotic acid phosphatases. Some family members represent the products of the PSI14 phosphatase family in Lycopersicon esculentum (Tomato)  .. 
PF06889 Protein of unknown function (DUF1266)<br>Pfam-B_13878 (release 10.0). This family consists of several hypothetical bacterial proteins of around 235 residues in length. Members of this family seem to be found exclusively in the Enterobacteria Salmonella typhimurium and Escherichia coli. The function of this family is unknown.. 
PF06890 Bacteriophage Mu Gp45 protein<br>Pfam-B_10848 (release 10.0). This family consists of Bacteriophage Mu Gp45 related proteins from both phages and bacteria. The function of this family is unknown although it has been suggested that family members may be involved in baseplate assembly.. 
PF06891 P2 phage tail completion protein R (GpR)<br>Pfam-B_10918 (release 10.0). This family consists of P2 phage tail completion protein R (GpR) like sequences. GpR is thought to be a tail completion protein which is essential for stable head joining  .. 
PF06892 Phage regulatory protein CII (CP76)<br>Pfam-B_13444 (release 10.0). This family consists of several phage regulatory protein CII (CP76) sequences which are thought to be DNA binding proteins which are involved in the establishment of lysogeny  .. 
PF06894 Bacteriophage lambda minor tail protein (GpG)<br>Pfam-B_11957 (release 10.0). This family consists of Bacteriophage lambda minor tail protein G and related sequences. The role of GpG in tail assembly is not known  .. 
PF06896 Protein of unknown function (DUF1268)<br>Pfam-B_11819 (release 10.0). This family consists of several bacterial and phage proteins of around 115 residues in length. The function of this family is unknown.. 
PF06897 Protein of unknown function (DUF1269)<br>Pfam-B_14034 (release 10.0). This family consists of several bacterial and archaeal proteins of around 200 residues in length. The function of this family is unknown. The family carries a repeated glycine-zipper sequence- motif, GxxxGxxxG, where the x following the G is frequently found to be an alanine. As glycine-zippers occur in membrane proteins, this family is likely to be found spanning a membrane.. 
PF06898 Putative stage IV sporulation protein YqfD<br>Pfam-B_13823 (release 10.0). This family consists of several putative bacterial stage IV sporulation (SpoIV) proteins. YqfD of Bacillus subtilis (Swiss:P54469) is known to be essential for efficient sporulation although its exact function is unknown  .. 
PF06899 WzyE protein<br>Pfam-B_13849 (release 10.0). This family consists of several WzyE proteins which appear to be specific to Enterobacteria. Members of this family are described as putative ECA polymerases this has been found to be incorrect  . The function of this family is unknown.. 
PF06900 Protein of unknown function (DUF1270)<br>Pfam-B_13907 (release 10.0). This family consists of several hypothetical Staphylococcus aureus and phage proteins of 53 residues in length. The function of this family is unknown.. 
PF06901 RTX iron-regulated protein FrpC<br>Pfam-B_14005 (release 10.0). This family consists of several RTX iron-regulated FrpC proteins which appear to be found exclusively in Neisseria meningitidis. FrpC has been shown to be related to the RTX family of bacterial cytotoxins. FrpC is found in the meningococcal outer membrane. The function of this family is unknown although it is thought to be a virulence factor  .. 
PF06902 DUF1271;<br>Divergent 4Fe-4S mono-cluster. Pfam-B_13906 (release 10.0). Members of this family contain three highly conserved cysteine residues. This family includes proteins containing divergent domains which are most likely to bind to iron-sulfur clusters.. 
PF06903 VirK protein<br>Pfam-B_13955 (release 10.0). This family consists of several bacterial VirK proteins of around 145 residues in length. The function of this family is unknown  .. 
PF06904 Extensin-like protein C-terminus<br>Pfam-B_6925 (release 10.0). This family represents the C-terminus (approx. 120 residues) of a number of bacterial extensin-like proteins. Extensins are cell wall glycoproteins normally associated with plants, where they strengthen the cell wall in response to mechanical stress  . Note that many family members of this family are hypothetical.. 
PF06905 FAIM; <br>Fas apoptotic inhibitory molecule (FAIM1). Pfam-B_13985 (release 10.0). This family consists of several fas apoptotic inhibitory molecule (FAIM1) proteins. FAIM expression is upregulated in B cells by anti-Ig treatment that induces Fas-resistance, and overexpression of FAIM diminishes sensitivity to Fas-mediated apoptosis of B and non-B cell lines. FAIM1 is highly evolutionarily conserved and is widely expressed in murine tissues, suggesting that FAIM plays an important role in cellular physiology  .. 
PF06906 Protein of unknown function (DUF1272)<br>Pfam-B_14128 (release 10.0). This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.. 
PF06907 Latexin<br>Pfam-B_14203 (release 10.0). This family consists of several animal specific latexin proteins. Latexin is a carboxypeptidase A inhibitor and is expressed in a cell type-specific manner in both central and peripheral nervous systems in the rat  .. 
PF06908 Protein of unknown function (DUF1273)<br>Pfam-B_14270 (release 10.0). This family consists of several hypothetical bacterial proteins of around 180 residues in length. The function of this family is unknown.. 
PF06910 Male enhanced antigen 1 (MEA1)<br>Pfam-B_14358 (release 10.0). This family consists of several mammalian male enhanced antigen 1 (MEA1) proteins. The Mea-1 gene is found to be localised in primary and secondary spermatocytes and spermatids, but the protein products are detected only in spermatids. Intensive transcription of Mea-1 gene and specific localisation of the gene product suggest that Mea-1 may play a important role in the late stage of spermatogenesis  . . 
PF06911 Senescence-associated protein<br>Pfam-B_7525 (release 10.0). This family contains a number of plant senescence-associated proteins of approximately 450 residues in length. In Hemerocallis, petals have a genetically based program that leads to senescence and cell death approximately 24 hours after the flower opens, and it is believed that senescence proteins produced around that time have a role in this program  . This family extends to the higher vertebrates where the full-length protein is often a Spartin, associated with mitochondrial membranes and transportation along microtubules  .. 
PF06912 Protein of unknown function (DUF1275)<br>Pfam-B_13896 (release 10.0). This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown although a few members are thought to be membrane proteins.. 
PF06916 Protein of unknown function (DUF1279)<br>Pfam-B_7316 (release 10.0). This family represents the C-terminus (approx. 120 residues) of a number of eukaryotic proteins of unknown function.. 
PF06917 Periplasmic pectate lyase<br>Pfam-B_14500 (release 10.0). This family consists of several Enterobacterial periplasmic pectate lyase proteins (EC:4.2.2.2). A major virulence determinant of the plant-pathogenic enterobacterium Erwinia chrysanthemi is the production of pectate lyase enzymes that degrade plant cell walls  .. 
PF06918 Protein of unknown function (DUF1280)<br>Pfam-B_7457 (release 10.0). This family represents a conserved region approximately 200 residues long within a number of proteins of unknown function that seem to be specific to C. elegans.. 
PF06919 Phage Gp30.7 protein<br>Pfam-B_14625 (release 10.0). This family consists of several phage Gp30.7 proteins of 121 residues in length. Family members seem to be exclusively from the T4-like viruses. The function of this family is unknown.. 
PF06920 Dedicator of cytokinesis<br>Pfam-B_7154 (release 10.0). This family represents a conserved region approximately 200 residues long within a number of eukaryotic dedicator of cytokinesis proteins. These are potential guanine nucleotide exchange factors, which activate some small GTPases by exchanging bound GDP for free GTP.. 
PF06922 Citrus tristeza virus P13 protein<br>Pfam-B_14711 (release 10.0). This family consists of several Citrus tristeza virus (CTV) P13 13-kDa proteins. Citrus tristeza virus (CTV), a member of the closterovirus group, is one of the more complex single-stranded RNA viruses  . The function of this family is unknown.. 
PF06923 Glucitol operon activator protein (GutM)<br>Pfam-B_14714 (release 10.0). This family consists of several glucitol operon activator (GutM) proteins. Expression of the glucitol (gut) operon in Escherichia coli is regulated by an unusual, complex system which consists of an activator (encoded by the gutM gene) and a repressor (encoded by the gutR gene) in addition to the cAMP-CRP complex (CRP, cAMP receptor protein). Synthesis of the mRNA, which initiates at the promoter specific to the gutR gene, occurs within the gutM gene. Expressional control of the gut operon appears to occur as a consequence of the antagonistic action of the products of the autogenously regulated gutM and gutR genes  .. 
PF06924 Protein of unknown function (DUF1281)<br>Pfam-B_14730 (release 10.0). This family consists of several hypothetical enterobacterial proteins of around 170 residues in length. Members of this family are found in Escherichia coli, Salmonella typhimurium and Shigella species. The function of this family is unknown.. 
PF06925 Monogalactosyldiacylglycerol (MGDG) synthase<br>Pfam-B_8075 (release 10.0). This family represents a conserved region of approximately 180 residues within plant and bacterial monogalactosyldiacylglycerol (MGDG) synthase (EC:2.4.1.46). In Arabidopsis, there are two types of MGDG synthase which differ in their N-terminal portion: type A and type B  .. 
PF06926 Putative replisome organiser protein C-terminus<br>Pfam-B_6517 (release 10.0). This family represents the C-terminus (approximately 100 residues) of a putative replisome organiser protein in Lactococcus bacteriophages  .. 
PF06929 Rotavirus VP3 protein<br>Pfam-B_14798 (release 10.0). This family consists of several Rotavirus specific VP3 proteins. VP3 is known to be a viral guanylyltransferase and is thought to posses methyltransferase activity and therefore VP3 is a predicted multifunctional capping enzyme  . . 
PF06930 Protein of unknown function (DUF1282)<br>Pfam-B_14843 (release 10.0). This family consists of several hypothetical proteins of around 200 residues in length. The function of this family is unknown although a number of family members are thought to be putative membrane proteins.. 
PF06931 Mastadenovirus E4 ORF3 protein<br>Pfam-B_14868 (release 10.0). This family consists of several Mastadenovirus E4 ORF3 proteins. Early proteins E4 ORF3 and E4 ORF6 have complementary functions during viral infection. Both proteins facilitate efficient viral DNA replication, late protein expression, and prevention of concatenation of viral genomes. A unique function of E4 ORF3 is the reorganisation of nuclear structures known as PML oncogenic domains (PODs). The function of these domains is unclear, but PODs have been implicated in a number of important cellular processes, including transcriptional regulation, apoptosis, transformation, and response to interferon  .. 
PF06932 Protein of unknown function (DUF1283)<br>Pfam-B_15035 (release 10.0). This family consists of several hypothetical proteins of around 115 residues in length which seem to be specific to Enterobacteria. The function of the family is unknown.. 
PF06933 Special lobe-specific silk protein SSP160<br>Pfam-B_14947 (release 10.0). This family consists of several special lobe-specific silk protein SSP160 sequences which appear to be specific to Chironomus (Midge) species [1,2].. 
PF06934 Fatty acid cis/trans isomerase (CTI)<br>Pfam-B_14967 (release 10.0). This family consists of several fatty acid cis/trans isomerase proteins which appear to be found exclusively in bacteria of the orders Vibrionales and Pseudomonadales. Cis/trans isomerase (CTI) catalyses the cis-trans isomerisation of esterified fatty acids in phospholipids, mainly cis-oleic acid (C(16:1,9)) and cis-vaccenic acid (C(18:1,11)), in response to solvents. The CTI protein has been shown to be involved in solvent resistance in Pseudomonas putida  .. 
PF06935 Protein of unknown function (DUF1284)<br>Pfam-B_14822 (release 10.0). This family consists of several hypothetical bacterial and archaeal proteins of around 130 residues in length. The function of this family is unknown, although it is thought that they may be iron-sulphur binding proteins.. 
PF06936 Selenoprotein S (SelS)<br>Pfam-B_15061 (release 10.0). This family consists of several mammalian selenoprotein S (SelS) sequences. SelS is a plasma membrane protein and is present in a variety of tissues and cell types  . The function of this family is unknown.. 
PF06937 EURL protein<br>Pfam-B_14914 (release 10.0). This family consists of several animal EURL proteins. EURL is preferentially expressed in chick retinal precursor cells as well as in the anterior epithelial cells of the lens at early stages of development. EURL transcripts are found primarily in the peripheral dorsal retina, i.e., the most undifferentiated part of the dorsal retina. EURL transcripts are also detected in the lens at stage 18 and remain abundant in the proliferating epithelial cells of the lens until at least day 11. The distribution pattern of EURL in the developing retina and lens suggest a role before the events leading to cell determination and differentiation  .  . 
PF06938 Protein of unknown function (DUF1285)<br>Pfam-B_15060 (release 10.0). This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown. The structures revealed a conserved core with domain duplication and a superficial similarity for the C-terminal domain to pleckstrin homology-like folds. The conservation of the domain- interface indicates a potential binding site that is likely to involve a nucleotide-based ligand, with genome-context and gene-fusion analyses additionally supporting a role for this family in signal transduction, possibly during oxidative stress.. 
PF06939 Protein of unknown function (DUF1286)<br>Pfam-B_15105 (release 10.0). This family consists of several hypothetical archaeal proteins of around 120 residues in length. All members of this family seem to be Sulfolobus species specific. The function of this family is unknown.. 
PF06940 Domain of unknown function (DUF1287)<br>Pfam-B_15116 (release 10.0). This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown. This family is related to Pfam:PF00877.. 
PF06941 5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C)<br>Pfam-B_14848 (release 10.0). This family consists of several 5' nucleotidase, deoxy (Pyrimidine), cytosolic type C (NT5C) proteins. 5'(3')-Deoxyribonucleotidase is a ubiquitous enzyme in mammalian cells whose physiological function is not known  . . 
PF06942 GlpM protein<br>Pfam-B_15323 (release 10.0). This family consists of several bacterial GlpM membrane proteins. GlpM is a hydrophobic protein containing 109 amino acids. It is thought that GlpM may play a role in alginate biosynthesis in Pseudomonas aeruginosa  .. 
PF06943 LSD1 zinc finger<br>Pfam-B_15249 (release 10.0). This family consists of several plant specific LSD1 zinc finger domains. Arabidopsis lsd1 mutants are hyper-responsive to cell death initiators and fail to limit the extent of cell death. Superoxide is a necessary and sufficient signal for cell death propagation. LSD1 monitors a superoxide-dependent signal and negatively regulates a plant cell death pathway. LSD1 protein contains three zinc finger domains, defined by CxxCxRxxLMYxxGASxVxCxxC. It has been suggested that LSD1 defines a zinc finger protein subclass and that LSD1 regulates transcription, via either repression of a pro-death pathway or activation of an anti-death pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death  . . 
PF06945 Protein of unknown function (DUF1289)<br>Moxon SJ, Eberhardt R. Pfam-B_15170 (release 10.0). This family consists of a number of hypothetical bacterial proteins.  The aligned region spans around 56 residues and contains 4 highly conserved cysteine residues towards the N-terminus. The function of this family is unknown. Structural modelling suggests this domain may bind nucleic acids  .. 
PF06946 Phage holin<br>Pfam-B_15309 (release 10.0). This family consists of several Listeria bacteriophage holin proteins and  related bacterial sequences. Holins are a diverse family of proteins that cause bacterial membrane lysis during late-protein synthesis. It is thought that the temporal precision of holin-mediated lysis may occur through the build up of a holin oligomer which causes the lysis  .. 
PF06947 Protein of unknown function (DUF1290)<br>Pfam-B_15248 (release 10.0). This family consists of several bacterial small basic proteins of around 100 residues in length. The function of this family is unknown.. 
PF06949 Protein of unknown function (DUF1292)<br>Pfam-B_15310 (release 10.0). This family consists of several hypothetical bacterial proteins of around 90 residues in length. The function of this family is unknown.. 
PF06950 Protein of unknown function (DUF1293)<br>Pfam-B_15399 (release 10.0). This family consists of several bacterial and phage proteins of around 115 residues in length. The function of this family is unknown.. 
PF06951 Group XII secretory phospholipase A2 precursor (PLA2G12)<br>Pfam-B_15422 (release 10.0). This family consists of several group XII secretory phospholipase A2 precursor (PLA2G12) (EC:3.1.1.4) proteins. Group XII and group V PLA(2)s are thought to participate in helper T cell immune response through release of immediate second signals and generation of downstream eicosanoids  . . 
PF06952 PsiA protein<br>Pfam-B_15432 (release 10.0). This family consists of several Enterobacterial PsiA proteins. The function of PsiA is unknown although it is thought that it may affect the generation of an SOS signal in Escherichia coli  .. 
PF06953 Arsenical resistance operon trans-acting repressor ArsD<br>Pfam-B_15383 (release 10.0). This family consists of several bacterial arsenical resistance operon trans-acting repressor ArsD proteins. ArsD is a trans-acting repressor of the arsRDABC operon that confers resistance to arsenicals and antimonials in Escherichia coli. It possesses two-pairs of vicinal cysteine residues, Cys(12)-Cys(13) and Cys(112)-Cys(113), that potentially form separate binding sites for the metalloids that trigger dissociation of ArsD from the operon. However, as a homodimer it has four vicinal cysteine pairs  .. 
PF06954 Resistin<br>Pfam-B_15476 (release 10.0). This family consists of several mammalian resistin proteins. Resistin is a 12.5-kDa cysteine-rich secreted polypeptide first reported from rodent adipocytes. It belongs to a multigene family termed RELMs or FIZZ proteins. Plasma resistin levels are significantly increased in both genetically susceptible and high-fat-diet-induced obese mice. Immunoneutralisation of resistin improves hyperglycemia and insulin resistance in high-fat-diet-induced obese mice, while administration of recombinant resistin impairs glucose tolerance and insulin action in normal mice. It has been demonstrated that increases in circulating resistin levels markedly stimulate glucose production in the presence of fixed physiological insulin levels, whereas insulin suppressed resistin expression. It has been suggested that resistin could be a link between obesity and type 2 diabetes  .. 
PF06955 Xyloglucan endo-transglycosylase (XET) C-terminus<br>Pfam-B_20045 (release 10.0). This family represents the C-terminus (approximately 60 residues) of plant xyloglucan endo-transglycosylase (XET). Xyloglucan is the predominant hemicellulose in the cell walls of most dicotyledons. With cellulose, it forms a network that strengthens the cell wall. XET catalyses the splitting of xyloglucan chains and the linking of the newly generated reducing end to the non-reducing end of another xyloglucan chain, thereby loosening the cell wall  . Note that all family members contain the Pfam:PF00722 domain.. 
PF06956 Regulator of RNA terminal phosphate cyclase<br>Pfam-B_17814 (release 10.0). RtcR is a sigma54-dependent enhancer binding protein   that activates transcription of the rtcBA operon. The product of the rtcA gene is an RNA 3'-terminal phosphate cyclase  . This domain is found at the N terminus of the RtcR sequence. RtcR, and other sigma54-dependent activators, contain Pfam:PF00158 in the central region of the protein sequence.. 
PF06957 Coatomer (COPI) alpha subunit C-terminus<br>Pfam-B_20121 (release 10.0). This family represents the C-terminus (approximately 500 residues) of the eukaryotic coatomer alpha subunit. Coatomer (COPI) is a large cytosolic protein complex which forms a coat around vesicles budding from the Golgi apparatus. Such coatomer-coated vesicles have been proposed to play a role in many distinct steps of intracellular transport  . Note that many family members also contain the Pfam:PF04053 domain.. 
PF06958 S-type Pyocin<br>Pfam-B_20020 (release 10.0). This family represents a conserved region approximately 180 residues long within bacterial S-type pyocins. Pyocins are polypeptide toxins produced by, and active against, bacteria. S-type pyocins cause cell death by DNA breakdown due to endonuclease activity  .. 
PF06959 RecQ helicase protein-like 5 (RecQ5)<br>Pfam-B_20083 (release 10.0). This family represents a conserved region approximately 200 residues long within eukaryotic RecQ helicase protein-like 5 (RecQ5). The RecQ helicases have been implicated in DNA repair and recombination, and RecQ5 may have an important role in DNA metabolism  .. 
PF06961 Protein of unknown function (DUF1294)<br>Pfam-B_3405 (release 10.0). This family includes a number of hypothetical bacterial and archaeal proteins of unknown function.. 
PF06962 Putative rRNA methylase<br>Pfam-B_3461 (release 10.0). This family contains a number of putative rRNA methylases. Note that many family members are hypothetical proteins.. 
PF06963 Ferroportin1 (FPN1)<br>Pfam-B_3588 (release 10.0). This family represents a conserved region approximately 100 residues long within eukaryotic Ferroportin1 (FPN1), a protein that may play a role in iron export from the cell  . This family may represent a number of transmembrane regions in Ferroportin1.. 
PF06964 Alpha-L-arabinofuranosidase C-terminus<br>Pfam-B_3625 (release 10.0). This family represents the C-terminus (approximately 200 residues) of bacterial and eukaryotic alpha-L-arabinofuranosidase (EC:3.2.1.55). This catalyses the hydrolysis of nonreducing terminal alpha-L-arabinofuranosidic linkages in L-arabinose-containing polysaccharides  .. 
PF06965 Na+/H+ antiporter 1<br>Pfam-B_1828 (release 10.0). This family contains a number of bacterial Na+/H+ antiporter 1 proteins. These are integral membrane proteins that catalyse the exchange of H+ for Na+ in a manner that is highly dependent on the pH  .. 
PF06966 Protein of unknown function (DUF1295)<br>Pfam-B_3514 (release 10.0). This family contains a number of bacterial and eukaryotic proteins of unknown function that are approximately 300 residues long.. 
PF06967 Mo-dependent nitrogenase C-terminus<br>Pfam-B_6998 (release 10.0). This family represents the C-terminus (approximately 80 residues) of a number of bacterial Mo-dependent nitrogenases. These are involved in nitrogen fixation in cyanobacteria  . Note that many family members are hypothetical proteins.. 
PF06968 Biotin and Thiamin Synthesis associated domain<br>Pfam-B_5417 (release 10.0). 
PF06969 HemN C-terminal domain<br>Pfam-B_833 (release 10.0). Members of this family are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX  , one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain (Pfam:PF04055) suggest it may be a substrate binding domain.. 
PF06970 Replication initiator protein A (RepA) N-terminus<br>Pfam-B_1808 (release 10.0). This of family of predicted proteins represents the N-terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids  . Most proteins in this family are bacterial, but archaeal and eukaryotic members are also included  .. 
PF06971 Put_DNA-bind_C; <br>Putative DNA-binding protein N-terminus. Pfam-B_3389 (release 10.0). This family represents the N-terminus (approximately 50 residues) of a number of putative bacterial DNA-binding proteins.. 
PF06972 Protein of unknown function (DUF1296)<br>Vella Briffa B, Eberhardt R. Pfam-B_4035 (release 10.0). This family represents a conserved region approximately 60 residues long within a number of plant proteins of unknown function. Structural modelling suggests this domain may bind nucleic acids  .. 
PF06973 Domain of unknown function (DUF1297)<br>Pfam-B_3819 (release 10.0). This family represents the C-terminus (approximately 200 residues) of a number of archaeal proteins of unknown function. One member is annotated as being a possible carboligase enzyme.. 
PF06974 Protein of unknown function (DUF1298)<br>Pfam-B_4362 (release 10.0). This family represents the C-terminus (approximately 170 residues) of a number of hypothetical plant proteins of unknown function.. 
PF06975 Protein of unknown function (DUF1299)<br>Pfam-B_3488 (release 10.0). This family represents a conserved region approximately 50 residues long within a number of proteins of unknown function that seem to be specific to Arabidopsis thaliana. Note that many family members contain multiple copies of this region.. 
PF06977 SdiA-regulated<br>Pfam-B_2520 (release 10.0). This family represents a conserved region approximately within a number of hypothetical bacterial proteins that may be regulated by SdiA, a member of the LuxR family of transcriptional regulators  . Some family members contain the Pfam:PF01436 repeat.. 
PF06978 Ribonucleases P/MRP protein subunit POP1<br>Pfam-B_7848 (release 10.0). This family represents a conserved region approximately 150 residues long located towards the N-terminus of the POP1 subunit that is common to both the RNase MRP and RNase P ribonucleoproteins (EC:3.1.26.5)  . These RNA-containing enzymes generate mature tRNA molecules by cleaving their 5' ends.. 
PF06979 Protein of unknown function (DUF1301)<br>Pfam-B_8295 (release 10.0). This family contains a number of eukaryotic proteins of unknown function that are approximately 160 residues long.. 
PF06980 Protein of unknown function (DUF1302)<br>Pfam-B_7023 (release 10.0). This family contains a number of hypothetical bacterial proteins of unknown function that are approximately 600 residues long. Most family members seem to be from Pseudomonas.. 
PF06983 3-demethylubiquinone-9 3-methyltransferase<br>Pfam-B_6583 (release 10.0). This family represents a conserved region approximately 100 residues long within a number of bacterial and archaeal 3-demethylubiquinone-9 3-methyltransferases (EC:2.1.1.64). Note that some family members contain more than one copy of this region, and that many members are hypothetical proteins.. 
PF06984 Mitochondrial 39-S ribosomal protein L47 (MRP-L47)<br>Pfam-B_6890 (release 10.0). This family represents the N-terminal region (approximately 8 residues) of the eukaryotic mitochondrial 39-S ribosomal protein L47 (MRP-L47). Mitochondrial ribosomal proteins (MRPs) are the counterparts of the cytoplasmic ribosomal proteins, in that they fulfil similar functions in protein biosynthesis. However, they are distinct in number, features and primary structure  .. 
PF06985 Heterokaryon incompatibility protein (HET)<br>Pfam-B_8200 (release 10.0). This family represents a conserved region approximately 150 residues long within various heterokaryon incompatibility proteins that seem to be restricted to ascomycete fungi. Genetic differences in specific het genes prevent a viable heterokaryotic fungal cell from being formed by the fusion of filaments from two different wild-type strains  . Many family members also contain the Pfam:PF00400 repeat and the  Pfam:PF05729 domain.. 
PF06986 Type-1V conjugative transfer system mating pair stabilisation<br>Pfam-B_8400 (release 10.0). TraN is a large cysteine-rich outer membrane protein involved in the mating-pair stabilisation (adhesin) component of the F-type conjugative plasmid transfer system. TraN is believed to interact with the core type IV secretion system apparatus through the TraV protein    .. 
PF06988 NifT/FixU protein<br>Pfam-B_5696 (release 10.0). This family consists of several NifT and FixU bacterial proteins. The function of NifT is unknown although it is thought that the protein may be involved in biosynthesis of the FeMo cofactor of nitrogenase although perturbation of nifT expression in K. pneumoniae has only a limited effect on nitrogen fixation  .. 
PF06989 BAALC N-terminus<br>Pfam-B_5793 (release 10.0). This family represents the N-terminal region of the mammalian BAALC proteins.\.  BAALC (brain and acute leukaemia, cytoplasmic), that is highly conserved among mammals but evidently absent from lower organisms. Two isoforms are specifically expressed in neuroectoderm-derived tissues, but not in tumours or cancer cell lines of non-neural tissue origin. It has been shown that blasts from a subset of patients with acute leukaemia greatly overexpress eight different BAALC transcripts, resulting in five protein isoforms.  Among patients with acute myeloid leukaemia, those overexpressing BAALC show distinctly poor prognosis, pointing to a key role of the BAALC products in leukaemia. It has been suggested that BAALC is a gene implicated in both neuroectodermal and hematopoietic cell functions  .. 
PF06990 Galactose-3-O-sulfotransferase <br>Pfam-B_6301 (release 10.0). This family consists of several mammalian galactose-3-O-sulfotransferase proteins. Gal-3-O-sulfotransferase is thought to play a critical role in 3'-sulfation of N-acetyllactosamine in both O- and N-glycans  .. 
PF06991 MFAP1_C;<br>Splicing factor, Prp19-binding domain. Pfam-B_8343 (release 10.0). This family represents the C-terminus (approximately 300 residues) of proteins that are involved as binding partners for Prp19 as part of the nuclear pore complex.\.    The family in Drosophila is necessary for pre-mRNA splicing, and the human protein has been found in purifications of the spliceosome. In the past this family was thought, erroneously, to be associated with microfibrillin.. 
PF06992 Replication protein P<br>Pfam-B_6611 (release 10.0). This family consists of several Bacteriophage lambda replication protein P like proteins. The bacteriophage lambda P protein promoters replication of the phage chromosome by recruiting a key component of the cellular replication machinery to the viral origin. Specifically, P protein delivers one or more molecules of Escherichia coli DnaB helicase to a nucleoprotein structure formed by the lambda O initiator at the lambda replication origin  . . 
PF06993 Protein of unknown function (DUF1304)<br>Pfam-B_7246 (release 10.0). This family consists of several hypothetical bacterial proteins of around 120 residues in length. The function of this family is unknown.. 
PF06994 Involucrin<br>Pfam-B_8443 (release 10.0). This family represents a conserved region approximately 60 residues long, multiple copies of which are found within eukaryotic involucrin, and which is rich in glutamine and glutamic acid residues. Involucrin forms part of the insoluble cornified cell envelope (a specialised protective barrier) of stratified squamous epithelia  . Members of this family seem to be restricted to mammals.. 
PF06995 Phage P2 GpU<br>Pfam-B_7670 (release 10.0). This family consists of several bacterial and phage proteins of around 130 residues in length which seem to be related to the bacteriophage P2 GpU protein (Swiss:O64315) which is thought to be involved in tail assembly  .. 
PF06996 Protein of unknown function (DUF1305)<br>Pfam-B_9388 (release 10.0). This family consists of several hypothetical bacterial proteins of around 300 residues in length. The function of this family is unknown although one member (Swiss:Q93IT4) from Salmonella enterica is thought to be involved in virulence  .. 
PF06998 Protein of unknown function (DUF1307)<br>Pfam-B_10058 (release 10.0). This family consists of several hypothetical bacterial proteins of around 150 residues in length. Some family members are described as putative lipoproteins but the function of the family is unknown.. 
PF06999 Sucrase/ferredoxin-like<br>Pfam-B_8856 (release 10.0). This family contains a number of bacterial and eukaryotic proteins approximately 400 residues long that resemble ferredoxin and appear to have sucrolytic activity  .. 
PF07000 Protein of unknown function (DUF1308)<br>Pfam-B_13288 (release 10.0). This family consists of several hypothetical eukaryotic sequences of around 400 residues in length. The function of this family is unknown.. 
PF07001 BAT2 N-terminus<br>Pfam-B_9101 (release 10.0). This family represents the N-terminus (approximately 200 residues) of the proline-rich protein BAT2. BAT2 is similar to other proteins with large proline-rich domains, such as some nuclear proteins, collagens, elastin, and synapsin  .. 
PF07002 Copine<br>Pfam-B_9705 (release 10.0). This family represents a conserved region approximately 180 residues long within eukaryotic copines. Copines are Ca(2+)-dependent phospholipid-binding proteins that are thought to be involved in membrane-trafficking, and may also be involved in cell division and growth  .. 
PF07004 DUF1309;<br>Sperm-tail PG-rich repeat. Pfam-B_8734 (release 10.0). This family represents a short conserved region carrying a PGP motif that is repeated in eukaryotic proteins of sperm-tails. Shippo orthologues from some species may include up to 40 Pro-Gly-Pro repeats.. 
PF07005 Hop; PF07005; <br>Protein of unknown function, DUF1537. Pfam-B_8609 (release 10.0). This conserved region is found in proteins of unknown function in a range of Proteobacteria as well as the  Gram-positive Oceanobacillus iheyensis.. 
PF07006 Protein of unknown function (DUF1310)<br>Pfam-B_10153 (release 10.0). This family consists of several hypothetical proteins of around 125 residues in length. Members of this family seem to be specific to Listeria and Streptococcus species. The function of this family is unknown.. 
PF07007 Protein of unknown function (DUF1311)<br>Pfam-B_10506 (release 10.0). This family consists of several bacterial proteins of around 120 residues in length. Members of this family contain four highly conserved cysteine residues. The function of this family is unknown.. 
PF07009 Protein of unknown function (DUF1312)<br>Pfam-B_10829 (release 10.0). This family consists of several bacterial proteins of around 120 residues in length. The function of this family is unknown.. 
PF07010 Endomucin<br>Pfam-B_10834 (release 10.0). This family consists of several mammalian endomucin proteins. Endomucin is an early endothelial-specific antigen that is also expressed on putative hematopoietic progenitor cells. . 
PF07011 Protein of unknown function (DUF1313)<br>Pfam-B_10989 (release 10.0). This family consists of several hypothetical plant proteins of around 100 residues in length. The function of this family is unknown.. 
PF07012 Curlin associated repeat<br>Pfam-B_10299 (release 10.0). This family consists of several bacterial repeats of around 30 residues in length. These repeats are often found in multiple copies in the curlin proteins CsgA and CsgB. Curli fibres are thin aggregative surface fibres, connected with adhesion, which bind laminin, fibronectin, plasminogen, human contact phase proteins, and major histocompatibility complex (MHC) class I molecules. Curli fibres are coded for by the csg gene cluster, which is comprised of two divergently transcribed operons. One operon encodes the csgB, csgA, and csgC genes, while the other encodes csgD, csgE, csgF, and csgG. The assembly of the fibres is unique and involves extracellular self-assembly of the curlin subunit (CsgA), dependent on a specific nucleator protein (CsgB). CsgD is a transcriptional activator essential for expression of the two curli fibre operons, and CsgG is an outer membrane lipoprotein involved in extracellular stabilisation of CsgA and CsgB  . . 
PF07013 Protein of unknown function (DUF1314)<br>Pfam-B_10999 (release 10.0). This family consists of several Alphaherpesvirus proteins of around 200 residues in length. The function of this family is unknown.. 
PF07014 Hs1pro-1; <br>Hs1pro-1 protein C-terminus. Moxon SJ, Vella Briffa B. Pfam-B_11205 (release 10.0). This family represents the C-terminus (approximately 270 residues) of a number of plant Hs1pro-1 proteins, which are believed to confer nematode resistance  .. 
PF07015 VirC1 protein<br>Pfam-B_11309 (release 10.0). This family consists of several bacterial VirC1 proteins. In Agrobacterium tumefaciens, a cis-active 24-base-pair sequence adjacent to the right border of the T-DNA, called overdrive, stimulates tumour formation by increasing the level of T-DNA processing. It is thought that the virC operon which enhances T-DNA processing probably does so because the VirC1 protein interacts with overdrive. It has now been shown that the virC1 gene product binds to overdrive but not to the right border of T-DNA  . . 
PF07016 Cysteine-rich acidic integral membrane protein precursor<br>Pfam-B_11042 (release 10.0). This family consists of several 24 residue repeats from the Trypanosoma brucei cysteine-rich, acidic integral membrane protein precursor (CRAM). CRAM is concentrated in the flagellar pocket, an invagination of the cell surface of the trypanosome where endocytosis has been documented  .. 
PF07017 Antimicrobial peptide resistance and lipid A acylation protein PagP<br>Pfam-B_11014 (release 10.0). This family consists of several bacterial antimicrobial peptide resistance and lipid A acylation (PagP) proteins. The bacterial outer membrane enzyme PagP transfers a palmitate chain from a phospholipid to lipid A. In a number of pathogenic Gram-negative bacteria, PagP confers resistance to certain cationic antimicrobial peptides produced during the host innate immune response. . 
PF07019 Rab5-interacting protein (Rab5ip)<br>Pfam-B_11031 (release 10.0). This family consists of several Rab5-interacting protein (RIP5 or Rab5ip ) sequences. The ras-related GTPase rab5 is rate-limiting for homotypic early endosome fusion. Rab5ip represents a novel rab5 interacting protein that may function on endocytic vesicles as a receptor for rab5-GDP and participate in the activation of rab5  .. 
PF07020 Orthopoxvirus C10L protein<br>Pfam-B_12732 (release 10.0). This family consists of several Orthopoxvirus C10L proteins. C10L viral protein can play an important role in vaccinia virus evasion of the host immune system. It may consist in the blockade of IL-1 receptors by the C10L protein, a homologue of the IL-1 Ra  . . 
PF07021 Methionine biosynthesis protein MetW<br>Pfam-B_11086 (release 10.0). This family consists of several bacterial and one archaeal methionine biosynthesis MetW proteins. Biosynthesis of methionine from homoserine in Pseudomonas putida takes place in three steps. The first step is the acylation of homoserine to yield an acyl-L-homoserine. This reaction is catalysed by the products of the metXW genes and is equivalent to the first step in enterobacteria, gram-positive bacteria and fungi, except that in these microorganisms the reaction is catalysed by a single polypeptide (the product of the metA gene in Escherichia coli and the met5 gene product in Neurospora crassa). In Pseudomonas putida, as in gram-positive bacteria and certain fungi, the second and third steps are a direct sulfhydrylation that converts the O-acyl-L-homoserine into homocysteine and further methylation to yield methionine. The latter reaction can be mediated by either of the two methionine synthetases present in the cells  . . 
PF07022 Bacteriophage CI repressor helix-turn-helix domain<br>Pfam-B_11145 (release 10.0). This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic  .. 
PF07023 Protein of unknown function (DUF1315)<br>Pfam-B_11170 (release 10.0). This family consists of several bacterial proteins of around 90 residues in length. The function of this family is unknown.. 
PF07024 ImpE protein<br>Pfam-B_11208 (release 10.0). This family consists of several bacterial proteins including ImpE (Swiss:Q93EC9) from Rhizobium leguminosarum. It has been suggested that the imp locus is involved in the secretion to the environment of proteins, including periplasmic RbsB protein, that cause blocking of infection specifically in pea plants  . The exact function of this family is unknown.. 
PF07026 Protein of unknown function (DUF1317)<br>Pfam-B_12646 (release 10.0). This family consists of several hypothetical bacterial and phage proteins of around 60 residues in length. The function of this family is unknown.. 
PF07027 Protein of unknown function (DUF1318)<br>Pfam-B_11321 (release 10.0). This family consists of several bacterial proteins of around 100 residues in length and is often known as YdbL. The function of this family is unknown.. 
PF07028 Protein of unknown function (DUF1319)<br>Pfam-B_10434 (release 10.0). This family contains a number of viral proteins of unknown function approximately 200 residues long. Family members seem to be restricted to badnaviruses.. 
PF07029 CryBP1 protein<br>Pfam-B_11415 (release 10.0). This family consists of several CryBP1 like proteins from Bacillus thuringiensis and Paenibacillus popilliae. Members of this family are thought to be involved in the overall toxicity of the bacteria to their hosts [1,2].. 
PF07030 Protein of unknown function (DUF1320)<br>Pfam-B_13638 (release 10.0). This family consists of both hypothetical bacterial and phage proteins of around 145 residues in length. The function of this family is unknown.. 
PF07032 Protein of unknown function (DUF1322)<br>Pfam-B_13233 (release 10.0). This family consists of several hypothetical 9.4 kDa Borrelia burgdorferi (Lyme disease spirochete) proteins of around 78 residues in length. The function of this family is unknown.. 
PF07033 Orthopoxvirus B11R protein<br>Pfam-B_13245 (release 10.0). This family consists of several Orthopoxvirus B11R proteins of around 70 residues in length. The function of this family is unknown.. 
PF07034 Origin recognition complex (ORC) subunit 3 N-terminus<br>Pfam-B_10452 (release 10.0). This family represents the N-terminus (approximately 300 residues) of subunit 3 of the eukaryotic origin recognition complex (ORC). Origin recognition complex (ORC) is composed of six subunits that are essential for cell viability. They collectively bind to the autonomously replicating sequence (ARS) in a sequence-specific manner and lead to the chromatin loading of other replication factors that are essential for initiation of DNA replication  .. 
PF07035 Colon cancer-associated protein Mic1-like<br>Pfam-B_10041 (release 10.0). This family represents the C-terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1.. 
PF07037 Putative transcription regulator (DUF1323)<br>Pfam-B_12705 (release 10.0). This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. This family appears to have an HTH domain and is therefore likely to act as a transcriptional regulator.. 
PF07038 Protein of unknown function (DUF1324)<br>Pfam-B_12735 (release 10.0). This family consists of several Circovirus proteins of around 60 residues in length. The function of this family is unknown.. 
PF07039 SGF29 tudor-like domain<br>Pfam-B_13304 (release 10.0). This domain is found in the yeast protein SAGA-associated factor 29. This domain is related to members of the Tudor domain superfamily such as Pfam:PF05641. The SAGA complex is involved in RNA polymerase II-dependent transcriptional regulation. The membership of the tudor domain superfamily suggests this domain may bind to RNA.. 
PF07040 Protein of unknown function (DUF1326)<br>Pfam-B_11597 (release 10.0). This family consists of several hypothetical bacterial proteins which seem to be found exclusively in Rhizobium and Ralstonia species. Members of this family are typically around 210 residues in length and contain 5 highly conserved cysteine residues at their N-terminus. The function of this family is unknown.. 
PF07041 Protein of unknown function (DUF1327)<br>Pfam-B_11630 (release 10.0). This family consists of several hypothetical bacterial proteins of around 115 residues in length which seem to be specific to Escherichia coli. The function of this family is unknown.. 
PF07042 TrfA protein<br>Pfam-B_12321 (release 10.0). This family consists of several bacterial TrfA proteins. The trfA operon of broad-host-range IncP plasmids is essential to activate the origin of vegetative replication in diverse species. The trfA operon encodes two ORFs. The first ORF is highly conserved and encodes a putative single-stranded DNA binding protein (Ssb). The second, trfA, contains two translational starts as in the IncP alpha plasmids, generating related polypeptides of 406 (TrfA1) and 282 (TrfA2) amino acids. TrfA2 is very similar to the IncP alpha product, whereas the N-terminal region of TrfA1 shows very little similarity to the equivalent region of IncP alpha TrfA1. This region has been implicated in the ability of IncP alpha plasmids to replicate efficiently in Pseudomonas aeruginosa  .. 
PF07043 Protein of unknown function (DUF1328)<br>Pfam-B_12535 (release 10.0). This family consists of several hypothetical bacterial proteins of around 50 residues in length. The function of this family is unknown.. 
PF07044 Protein of unknown function (DUF1329)<br>Pfam-B_12608 (release 10.0). This family consists of several hypothetical bacterial proteins of around 475 residues in length. The majority of family members are from Pseudomonas species but the family also contains sequences from Shewanella oneidensis and Thauera aromatica.. 
PF07045 Protein of unknown function (DUF1330)<br>Pfam-B_12466 (release 10.0). This family consists of several hypothetical bacterial proteins of around 90 residues in length. The function of this family is unknown.. 
PF07046 Cytoplasmic repetitive antigen (CRA) like repeat<br>Pfam-B_12798 (release 10.0). This family consists of several repeats of around 42 residues in length. These repeated sequences are found in multiple copies in Trypanosoma cruzi antigens, Swiss:Q26907 contains 23 copies of this repeat.. 
PF07047 Optic atrophy 3 protein (OPA3)<br>Pfam-B_12863 (release 10.0). This family consists of several optic atrophy 3 (OPA3) proteins. OPA3 deficiency causes type III 3-methylglutaconic aciduria (MGA) in humans. This disease manifests with early bilateral optic atrophy, spasticity, extrapyramidal dysfunction, ataxia, and cognitive deficits, but normal longevity  . . 
PF07048 Protein of unknown function (DUF1331)<br>Pfam-B_12865 (release 10.0). This family consists of several Circovirus proteins of around 35 residues in length. Members of this family are described as ORF-10 proteins and their function is unknown.. 
PF07051 Ovarian carcinoma immunoreactive antigen (OCIA)<br>Pfam-B_13720 (release 10.0). This family consists of several ovarian carcinoma immunoreactive antigen  (OCIA) and related eukaryotic sequences. The function of this family is unknown [1,2].. 
PF07052 Hepatocellular carcinoma-associated antigen 59<br>Pfam-B_10544 (release 10.0). This family represents a conserved region approximately 100 residues long within mammalian hepatocellular carcinoma-associated antigen 59 and similar proteins. Family members are found in a variety of eukaryotes, mainly as hypothetical proteins.. 
PF07054 Pericardin like repeat<br>Pfam-B_13724 (release 10.0). This family consists of several repeated sequences of around 34 residues in length. This repeat is found in multiple copies in the Drosophila pericardin and other extracellular matrix proteins.. 
PF07055 scADH;<br>Enoyl reductase FAD binding domain. Vella Briffa B, Coggill P. Pfam-B_10602 (release 10.0). This family carries the region of the enzyme trans-2-enoyl-CoA reductase, at the very C-terminus, that binds to FAD. The activity was characterised in Euglena where an unusual fatty acid synthesis path-way in mitochondria performs a malonyl-CoA independent synthesis of fatty acids leading to accumulation of wax esters, which serve as the sink for electrons stemming from glycolytic ATP synthesis and pyruvate oxidation. The full enzyme catalyses the reduction of enoyl-CoA to acyl-CoA. The conserved region is seen as the motif FGFxxxxxDY  .. 
PF07056 Protein of unknown function (DUF1335)<br>Pfam-B_10636 (release 10.0). This family represents a conserved region approximately 130 residues long within a number of proteins of unknown function that seem to be specific to the white spot syndrome virus (WSSV).. 
PF07057 DNA helicase TraI<br>Pfam-B_10638 (release 10.0). This family represents a conserved region approximately 130 residues long within the bacterial DNA helicase TraI (EC:3.6.1.-). TraI is a bifunctional protein that catalyses the unwinding of duplex DNA as well as acts as a sequence-specific DNA trans-esterase, providing the site- and strand-specific nick required to initiate DNA transfer  .. 
PF07058 Myosin II heavy chain-like<br>Pfam-B_10658 (release 10.0). This family represents a conserved region within a number of myosin II heavy chain-like proteins that seem to be specific to Arabidopsis thaliana.. 
PF07059 Protein of unknown function (DUF1336)<br>Pfam-B_10173 (release 10.0). This family represents the C-terminus (approximately 250 residues) of a number of hypothetical plant proteins of unknown function.. 
PF07061 DUF1337; <br>Swi5 is involved in meiotic DNA repair synthesis and meiotic joint molecule formation    .  It is known to interact with Swi2, Rhp51 and Swi6  .. 
PF07062 Clc-like<br>Pfam-B_11218 (release 10.0). This family contains a number of Clc-like proteins that are approximately 250 residues long.. 
PF07063 Domain of unknown function (DUF1338)<br>Pfam-B_10864 (release 10.0). This domain is found in a variety of bacterial and fungal hypothetical proteins of unknown function. The structure of this domain has been solved by structural genomics. The structure implies a zinc-binding function, so it is a putative metal hydrolase (information derived from TOPSAN for PDB:3iuz).. 
PF07064 DUF1339; <br>Vella Briffa B, Wood V. Pfam-B_11581 (release 10.0). RIC1 has been identified in yeast as a Golgi protein involved in retrograde transport to the cis-Golgi network.  It forms a heterodimer with Rgp1 and functions as a guanyl-nucleotide exchange factor  .. 
PF07065 D123<br>Pfam-B_10915 (release 10.0). This family contains a number of eukaryotic D123 proteins approximately 330 residues long. It has been shown that mutated variants of D123 exhibit temperature-dependent differences in their degradation rate  . D123 proteins are regulators of eIF2, the central regulator of  translational initiation  .. 
PF07066 Phage_Lacto_M3;<br>Lactococcus phage M3 protein. Pfam-B_13997 (release 10.0). This family consists of several Lactococcus phage middle-3 (M3) proteins of around 160 residues in length. The function of this family is unknown.. 
PF07067 Protein of unknown function (DUF1340)<br>Pfam-B_14083 (release 10.0). This family consists of several hypothetical Streptococcus thermophilus bacteriophage proteins of around 235 residues in length. The function of this family is unknown.. 
PF07068 Major capsid protein Gp23<br>Pfam-B_12245 (release 10.0). This family contains a number of major capsid Gp23 proteins approximately 500 residues long, from T4-like bacteriophages.. 
PF07069 Porcine reproductive and respiratory syndrome virus 2b <br>Pfam-B_13261 (release 10.0). This family consists of several Porcine reproductive and respiratory syndrome virus (PRRSV) ORF2b proteins. The function of this family is unknown however it is known that large amounts of 2b protein are present in the virion and it is thought that this protein may be an integral component of the virion  .. 
PF07070 SpoOM protein<br>Pfam-B_13263 (release 10.0). This family consists of several bacterial SpoOM proteins which are thought to control sporulation in Bacillus subtilis.Spo0M exerts certain negative effects on sporulation and its gene expression is controlled by sigmaH  .. 
PF07071 Protein of unknown function (DUF1341)<br>Pfam-B_14024 (release 10.0). This family consists of several hypothetical bacterial proteins of around 220 residues in length. The function of this family is unknown.. 
PF07072 Protein of unknown function (DUF1342)<br>Pfam-B_14075 (release 10.0). This family consists of several hypothetical bacterial proteins of around 250 residues in length. Members of this family are often known as YacF after the Escherichia coli protein Swiss:P36680. The function of this family is unknown.. 
PF07073 Modulator of Rho-dependent transcription termination (ROF)<br>Pfam-B_13280 (release 10.0). This family consists of several bacterial modulator of Rho-dependent transcription termination (ROF) proteins. ROF binds transcription termination factor Rho and inhibits Rho-dependent termination in vivo  . . 
PF07074 Translocon-associated protein, gamma subunit (TRAP-gamma)<br>Pfam-B_13437 (release 10.0). This family consists of several eukaryotic translocon-associated protein, gamma subunit (TRAP-gamma) sequences. The translocation site (translocon), at which nascent polypeptides pass through the endoplasmic reticulum membrane, contains a component previously called 'signal sequence receptor' that is now renamed as 'translocon-associated protein' (TRAP). The TRAP complex is comprised of four membrane proteins alpha, beta, gamma and delta which are present in a stoichiometric relation, and are genuine neighbours in intact microsomes.  The gamma subunit is predicted to span the membrane four times  . . 
PF07075 Protein of unknown function (DUF1343)<br>Pfam-B_13635 (release 10.0). This family consists of several hypothetical bacterial proteins of around 400 residues in length. The function of this family is unknown.. 
PF07076 Protein of unknown function (DUF1344)<br>Pfam-B_13761 (release 10.0). This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.. 
PF07077 Protein of unknown function (DUF1345)<br>Pfam-B_13768 (release 10.0). This family consists of several hypothetical bacterial proteins of around 230 residues in length. The function of this family is unknown.. 
PF07078 DUF1346; <br>Forty-two-three protein. Pfam-B_13991 (release 10.0). This family consists of several mammalian proteins of around 320 residues in length called 40-2-3 proteins. The function of this family is unknown.. 
PF07079 Protein of unknown function (DUF1347)<br>Pfam-B_14317 (release 10.0). This family consists of several hypothetical bacterial proteins of around 610 residues in length. Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.. 
PF07080 Protein of unknown function (DUF1348)<br>Pfam-B_14137 (release 10.0). This family consists of several highly conserved hypothetical proteins of around 150 residues in length. The function of this family is unknown.. 
PF07081 Protein of unknown function (DUF1349)<br>Pfam-B_14150 (release 10.0). This family consists of several hypothetical bacterial proteins but contains one sequence (Swiss:P40893) from Saccharomyces cerevisiae. Members of this family are typically around 200 residues in length. The function of this family is unknown.. 
PF07082 Protein of unknown function (DUF1350)<br>Pfam-B_14167 (release 10.0). This family consists of several hypothetical proteins from both cyanobacteria and plants. Members of this family are typically around 250 residues in length. The function of this family is unknown but the species distribution indicates that the family may be involved in photosynthesis.. 
PF07083 Protein of unknown function (DUF1351)<br>Pfam-B_14178 (release 10.0). This family consists of several bacterial and phage proteins of around 230 residues in length. The function of this family is unknown.. 
PF07084 Thyroid hormone-inducible hepatic protein Spot 14<br>Pfam-B_14186 (release 10.0). This family consists of several thyroid hormone-inducible hepatic protein (Spot 14 or S14) sequences. Mainly expressed in tissues that synthesise triglycerides, the mRNA coding for Spot 14 has been shown to be increased in rat liver by insulin, dietary carbohydrates, glucose in hepatocyte culture medium, as well as thyroid hormone. In contrast, dietary fats and polyunsaturated fatty acids, have been shown to decrease the amount of Spot 14 mRNA, while an elevated level of cAMP acts as a dominant negative factor. In addition, liver-specific factors or chromatin organisation of the gene have been shown to contribute to the regulation of its expression  . Spot 14 protein is thought to be required for induction of hepatic lipogenesis  .. 
PF07085 DRTGG domain<br>
PF07086 Protein of unknown function (DUF1352)<br>Pfam-B_14369 (release 10.0). This family consists of several hypothetical eukaryotic proteins of around 190 residues in length. The function of this family is unknown.. 
PF07087 Protein of unknown function (DUF1353)<br>Pfam-B_14433 (release 10.0). This family consists of several hypothetical bacterial proteins of around 100 residues in length. The function of this family is unknown.. 
PF07088 GvpD gas vesicle protein<br>Pfam-B_14302 (release 10.0). This family consists of several archaeal GvpD gas vesicle proteins. GvpD is thought to be involved in the regulation of gas vesicle formation [1,2].. 
PF07090 Protein of unknown function (DUF1355)<br>Pfam-B_14563 (release 10.0). This family consists of several hypothetical bacterial proteins of around 250 residues in length. The function of this family is unknown. THe structure of this domain was solved by the Midwest Center for Structural Genomics (MCSG). The structure has been classified as part of the Class-I Glutamine amidotransferase superfamily.. 
PF07091 Ribosomal RNA methyltransferase (FmrO)<br>Pfam-B_14605 (release 10.0). This family consists of several bacterial ribosomal RNA methyltransferase (aminoglycoside-resistance methyltransferase) proteins [1,2].. 
PF07092 Protein of unknown function (DUF1356)<br>Pfam-B_14617 (release 10.0). This family consists of several hypothetical mammalian proteins of around 250 residues in length. The function of this family is unknown.. 
PF07093 SGT1 protein<br>Pfam-B_14698 (release 10.0). This family consists of several eukaryotic SGT1 proteins. Human SGT1 or hSGT1 is known to suppress GCR2 and is highly expressed in the muscle and heart. The function of this family is unknown although it has been speculated that SGT1 may be functionally analogous to the Gcr2p protein of Saccharomyces cerevisiae which is known to be a regulatory factor of glycolytic gene expression  .. 
PF07094 Protein of unknown function (DUF1357)<br>Pfam-B_14833 (release 10.0). This family consists of several hypothetical bacterial proteins of around 225 residues in length. Members of this family appear to be specific Borrelia burgdorferi (Lyme disease spirochete). The function of this family is unknown.. 
PF07095 Intracellular growth attenuator protein IgaA<br>Pfam-B_14923 (release 10.0). This family consists of several bacterial intracellular growth attenuator  (IgaA) proteins. IgaA is involved in negative control of bacterial proliferation within fibroblasts. IgaA is homologous to the E. coli YrfF and P. mirabilis UmoB proteins. Whereas the biological function of YrfF is currently unknown, UmoB has been shown elsewhere to act as a positive regulator of FlhDC, the master regulator of flagella and swarming. FlhDC has been shown to repress cell division during P. mirabilis swarming, suggesting that UmoB could repress cell division via FlhDC. This biological function, if maintained in S. enterica, could sustain a putative negative control of cell division and growth exerted by IgaA in intracellular bacteria  . . 
PF07096 Protein of unknown function (DUF1358)<br>Pfam-B_14731 (release 10.0). This family consists of several hypothetical eukaryotic proteins of around 125 residues in length. The function of this family is unknown.. 
PF07097 Protein of unknown function (DUF1359)<br>Pfam-B_14784 (release 10.0). This family consists of several hypothetical bacterial and phage proteins of around 100 residues in length. Members of this family seem to be found exclusively in Lactococcus lactis and the bacteriophages that infect this species. The function of this family is unknown.. 
PF07098 Protein of unknown function (DUF1360)<br>Pfam-B_14863 (release 10.0). This family consists of several bacterial proteins of around 115 residues in length. Members of this family are found in Bacillus species and Streptomyces coelicolor, the function of the family is unknown.. 
PF07099 Protein of unknown function (DUF1361)<br>Pfam-B_14870 (release 10.0). This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown although some members are annotated as being putative integral membrane proteins.. 
PF07100 DUF1362;<br>Anabaena sensory rhodopsin transducer. Pfam-B_14972 (release 10.0). The family of bacterial Anabaena sensory rhodopsin transducers are likely to bind sugars or related metabolites. The entire protein is comprised of a single globular domain with an eight-stranded beta-sandwich fold. There are a few characteristics which define this beta-sandwich fold as being distinct from other so-named folds, and these are: 1) a well conserved tryptophan, usually following a polar residue, present at the start of the first strand; this tryptophan appears to be central to a hydrophobic interaction required to hold the two beta-sheets of the sandwich together, and 2) a nearly absolutely conserved asparagine located at the end of the second beta-strand, that hydrogen bonds with the backbone carbonyls of the residues 2 and 4 positions downstream from it, thereby stabilising the characteristic tight turn between strands 2 and 3 of the structure.. 
PF07101 Protein of unknown function (DUF1363)<br>Pfam-B_14992 (release 10.0). This family consists of several Trypanosoma brucei putative variant specific antigen proteins of around 80 residues in length.. 
PF07102 Protein of unknown function (DUF1364)<br>Pfam-B_14821 (release 10.0). This family consists of several bacterial and phage proteins of around 95 residues in length. The function of this family is unknown. . 
PF07103 Protein of unknown function (DUF1365)<br>Pfam-B_14846 (release 10.0). This family consists of several bacterial and plant proteins of around 250 residues in length. The function of this family is unknown.. 
PF07104 Protein of unknown function (DUF1366)<br>Pfam-B_14849 (release 10.0). This family consists of several hypothetical Streptococcus thermophilus bacteriophage proteins of around 130 residues in length. One of the sequences in this family, from phage Sfi11 (Swiss:O80186) is known as Gp149. The function of this family is unknown. . 
PF07105 Protein of unknown function (DUF1367)<br>Pfam-B_14892 (release 10.0). This family consists of several highly conserved, hypothetical phage proteins of around 200 residues in length. The function of this family is unknown. Some proteins are annotated as IrsA (intracellular response to stress).. 
PF07106 Tat binding protein 1(TBP-1)-interacting protein (TBPIP)<br>Pfam-B_14830 (release 10.0). This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation  .. 
PF07107 Wound-induced protein WI12<br>Pfam-B_15477 (release 10.0). This family consists of several plant wound-induced protein sequences related to WI12 from Mesembryanthemum crystallinum (Swiss:Q9XES3). Wounding, methyl jasmonate, and pathogen infection is known to induce local WI12 expression. WI12 expression is also thought to be developmentally controlled in the placenta and developing seeds. WI12 preferentially accumulates in the cell wall and it has been suggested that it plays a role in the reinforcement of cell wall composition after wounding and during plant development  . This family seems partly related to the NTF2-like superfamily.. 
PF07108 PipA protein<br>Pfam-B_15507 (release 10.0). This family consists of several Salmonella PipA (pathogenicity island-encoded protein A) and related phage sequences. PipA is thought to contribute to enteric but not to systemic salmonellosis  . The family carries a highly conserved HEXXH sequence motif along with several highly conserved glutamic acid residues which might be indicative of the family being a metallo-peptidase.. 
PF07109 Magnesium-protoporphyrin IX methyltransferase C-terminus<br>Pfam-B_12015 (release 10.0). This family represents the C-terminus (approximately 100 residues) of bacterial and eukaryotic Magnesium-protoporphyrin IX methyltransferase (EC:2.1.1.11). This converts magnesium-protoporphyrin IX to magnesium-protoporphyrin IX methylester using S-adenosyl-L-methionine as a cofactor  .. 
PF07110 EthD domain<br>Pfam-B_15539 (release 10.0). This family consists of several bacterial sequences which are related to the EthD protein of Rhodococcus ruber (Swiss:Q93EX2). In Rhodococcus ruber, EthD is thought to be involved in the degradation of ethyl tert-butyl ether (ETBE). EthD synthesis is induced by ETBE but it's exact function is unknown, it is however thought to be essential to the ETBE degradation system.. 
PF07111 Alpha helical coiled-coil rod protein (HCR)<br>Pfam-B_15548 (release 10.0). This family consists of several mammalian alpha helical coiled-coil rod HCR proteins. The function of HCR is unknown but it has been implicated in psoriasis in humans and is thought to affect keratinocyte proliferation  .. 
PF07112 Protein of unknown function (DUF1368)<br>Pfam-B_14994 (release 10.0). This family consists of several proteins with seem to be specific to red algae plasmids. Members of this family are typically around 415 residues in length. The function of this family is unknown.. 
PF07114 Protein of unknown function (DUF1370)<br>Pfam-B_15274 (release 10.0). This family consists of several hypothetical eukaryotic proteins of around 200 residues in length. Members of this family seem to be specific to mammals and their function is unknown.. 
PF07115 Protein of unknown function (DUF1371)<br>Pfam-B_15275 (release 10.0). This family consists of several hypothetical bacterial proteins of around 110 residues in length. The function of this family is unknown but members seem to be specific to Borrelia burgdorferi (Lyme disease spirochete).. 
PF07116 Protein of unknown function (DUF1372)<br>Pfam-B_15278 (release 10.0). This family consists of several Streptococcus bacteriophage sequences and related proteins from Streptococcus species. Members of this family are typically around 100 residues in length and their function is unknown.. 
PF07117 Protein of unknown function (DUF1373)<br>Pfam-B_15084 (release 10.0). This family consists of several hypothetical proteins which seem to be specific to Oryzias latipes (Japanese ricefish). Members of this family are typically around 200 residues in length. The function of this family is unknown.. 
PF07118 Protein of unknown function (DUF1374)<br>Pfam-B_15191 (release 10.0). This family consists of several hypothetical Sulfolobus virus proteins of around 100 residues in length. The function of this family is unknown.. 
PF07119 Protein of unknown function (DUF1375)<br>Pfam-B_15247 (release 10.0). This family consists of several hypothetical, putative lipoproteins of around 80 residues in length. Members of this family seem to be specific to the Class Gammaproteobacteria. The function of this family is unknown.. 
PF07120 Protein of unknown function (DUF1376)<br>Pfam-B_15380 (release 10.0). This family consists of several hypothetical bacterial proteins of around 95 residues in length. The function of this family is unknown.. 
PF07122 Variable length PCR target protein (VLPT)<br>Pfam-B_15500 (release 10.0). This family consists of a number of 29 residue repeats which seem to be specific to the Ehrlichia chaffeensis variable length PCR target (VLPT) protein. Ehrlichia chaffeensis is a tick-transmitted rickettsial agent and is responsible for human monocytic ehrlichiosis (HME). The function of this family is unknown  . . 
PF07123 PsbW_2; <br>Photosystem II reaction centre W protein (PsbW). Pfam-B_15117 (release 10.0). This family consists of several plant specific photosystem II reaction centre W (PsbW) proteins. PsbW is a nuclear-encoded protein located in the thylakoid membrane of the chloroplast. PsbW is a core component of photosystem II but not photosystem I  . This family does not appear to be related to Pfam:PF03912.. 
PF07124 Phytoreovirus outer capsid protein P8<br>Pfam-B_15606 (release 10.0). This family consists of several Phytoreovirus outer capsid protein P8 sequences  .. 
PF07125 Protein of unknown function (DUF1378)<br>Pfam-B_15650 (release 10.0). This family consists of hypothetical bacterial and phage proteins of around 59 residues in length. Bacterial members of this family seem to be specific to Enterobacteria. The function of this family is unknown. Structural modelling suggests this domain may bind nucleic acids  .. 
PF07126 Protein of unknown function (DUF1379)<br>Pfam-B_15837 (release 10.0). This family consists of several hypothetical bacterial proteins of around 180 residues in length. The function of this family is unknown.. 
PF07127 Late nodulin protein<br>Pfam-B_15657 (release 10.0). This family consists of several plant specific late nodulin sequences which are homologous to the Pisum sativum (Garden pea) ENOD3 protein.  ENOD3 is expressed in the late stages of root nodule formation and contains two pairs of cysteine residues towards the C-terminus which may be involved in metal-binding  .. 
PF07128 Protein of unknown function (DUF1380)<br>Pfam-B_15699 (release 10.0). This family consists of several hypothetical bacterial proteins of around 140 residues in length. Members of this family seem to be specific to Enterobacteria. The function of this family is unknown.. 
PF07129 Protein of unknown function (DUF1381)<br>Pfam-B_15743 (release 10.0). This family consists of several hypothetical Staphylococcus aureus and Staphylococcus aureus bacteriophage proteins of around 65 residues in length. The function of this family is unknown.. 
PF07130 YebG protein<br>Pfam-B_15760 (release 10.0). This family consists of several bacterial YebG proteins of around 75 residues in length. The exact function of this protein is unknown but it is thought to be involved in the SOS response. The induction of the yebG gene occurs as cell enter into the stationary growth phase and is dependent on  is dependent on cyclic AMP and H-NS  . . 
PF07131 Protein of unknown function (DUF1382)<br>Moxon SJ, Eberhardt R. Pfam-B_15770 (release 10.0). This family consists of several hypothetical Escherichia coli and bacteriophage lambda-like proteins of around 60 residues in length.  The function of this family is unknown. Structural modelling suggests this domain may bind nucleic acids  .. 
PF07133 Merozoite surface protein (SPAM)<br>Pfam-B_15860 (release 10.0). This family consists of several Plasmodium falciparum SPAM (secreted polymorphic antigen associated with merozoites) proteins. Variation among SPAM alleles is the result of deletions and amino acid substitutions in non-repetitive sequences within and flanking the alanine heptad-repeat domain. Heptad repeats in which the a and d position contain hydrophobic residues generate amphipathic alpha-helices which give rise to helical bundles or coiled-coil structures in proteins. SPAM is an example of a P. falciparum antigen in which a repetitive sequence has features characteristic of a well-defined structural element [1,2]. . 
PF07134 Protein of unknown function (DUF1383)<br>Pfam-B_15868 (release 10.0). This family consists of several hypothetical Nucleopolyhedrovirus proteins of around 375 residues in length. The function of this family is unknown.. 
PF07136 Protein of unknown function (DUF1385)<br>Pfam-B_12671 (release 10.0). This family contains a number of hypothetical bacterial proteins of unknown function approximately 300 residues in length. Some family members are predicted to be metal-dependent.. 
PF07137 Violaxanthin de-epoxidase (VDE)<br>Pfam-B_12679 (release 10.0). This family represents a conserved region approximately 150 residues long within plant violaxanthin de-epoxidase (VDE). In higher plants, violaxanthin de-epoxidase forms part of a conserved system that dissipates excess energy as heat in the light-harvesting complexes of photosystem II (PSII), thus protecting them from photo-inhibitory damage  .. 
PF07138 Protein of unknown function (DUF1386)<br>Pfam-B_16196 (release 10.0). This family consists of several hypothetical Nucleopolyhedrovirus proteins of around 350 residues in length. The function of this family is unknown.. 
PF07139 Protein of unknown function (DUF1387)<br>Pfam-B_10471 (release 10.0). This family represents a conserved region approximately 300 residues long within a number of hypothetical proteins of unknown function that seem to be restricted to mammals.. 
PF07140 Interferon gamma receptor (IFNGR1)<br>Pfam-B_15930 (release 10.0). This family consists of several eukaryotic and viral interferon gamma receptor proteins. Molecular interactions among cytokines and cytokine receptors in eukaryotes form the basis of many cell-signaling pathways relevant to immune function. Human interferon-gamma (IFN-gamma) signals through a multimeric receptor complex consisting of two different but structurally related transmembrane chains: the high-affinity receptor-binding subunit (IFN-gammaRalpha) and a species specific accessory factor (AF-1 or IFN-gammaRbeta).  The vaccinia viral interferon gamma receptor has been shown to be secreted from infected cells during early infection  . The structure has been halved such that the N-terminus of this family is now represented by Tissue_fac Pfam:PF01108.. 
PF07141 Putative bacteriophage terminase small subunit<br>Pfam-B_15957 (release 10.0). This family consists of several putative Lactococcus bacteriophage terminase small subunit proteins. The exact function of this family is unknown.. 
PF07142 Repeat of unknown function (DUF1388)<br>Pfam-B_16000 (release 10.0). This family consists of several repeats of around 29 residues in length. Members of this family are found in the variable surface lipoproteins in Mycoplasma bovis and in mammalian neurofilament triplet H (NefH or NF-H) proteins. This repeat contains several Lys-Ser-Pro (KSP) motifs and in NefH these are thought to function as the main target for neurofilament directed protein kinases in vivo  .. 
PF07143 Hydroxyneurosporene synthase (CrtC)<br>Pfam-B_16004 (release 10.0). This family consists of several purple photosynthetic bacterial hydroxyneurosporene synthase (CrtC) proteins. The enzyme catalyses the conversion of various acyclic carotenes including 1-hydroxy derivatives. This broad substrate specificity reflects the participation of CrtC in 1'-HO-spheroidene and in spirilloxanthin biosynthesis  .\.      This family also contains the members of the old Pfam family DUF2006.  Structural characterisation of DUF2006 family member Swiss:Q82US3 has revealed a lipocalin-like fold with domain duplication.. 
PF07145 Ataxin-2; Ataxin-2_C;<br>Ataxin-2 C-terminal region. The PABP-interacting motif PAM2 has been identified in various eukaryotic proteins as an important binding site for Pfam:PF00658. It has been found in a wide range of eukaryotic proteins  . Strikingly, this motif appears to occur solely outside of globular domains  .. 
PF07146 Protein of unknown function (DUF1389)<br>Pfam-B_16027 (release 10.0). This family consists of several hypothetical bacterial proteins which seem to be specific to Chlamydia pneumoniae. Members of this family are typically around 400 residues in length. The function of this family is unknown.. 
PF07147 Mitochondrial 28S ribosomal protein S30 (PDCD9)<br>Pfam-B_16045 (release 10.0). This family consists of several eukaryotic mitochondrial 28S ribosomal protein S30 (or programmed cell death protein 9 PDCD9) sequences. The exact function of this family is unknown although it is known to be a component of the mitochondrial ribosome and a component in cellular apoptotic signaling pathways  .. 
PF07148 Maltose operon periplasmic protein precursor (MalM)<br>Pfam-B_16111 (release 10.0). This family consists of several maltose operon periplasmic protein precursor (MalM) sequences. The function of this family is unknown  .. 
PF07149 Pes-10<br>Pfam-B_16134 (release 10.0). This family consists of several Caenorhabditis elegans pes-10 and related proteins. Members of this family are typically around 400 residues in length. The function of this family is unknown.. 
PF07150 Protein of unknown function (DUF1390)<br>Pfam-B_16182 (release 10.0). This family consists of several Paramecium bursaria chlorella virus 1 (PBCV-1) proteins of around 250 residues in length. The function of this family is unknown.. 
PF07151 Protein of unknown function (DUF1391)<br>Pfam-B_16216 (release 10.0). This family consists of several Enterobacterial proteins of around 50 residues in length. Members of this family are found in Escherichia coli and Salmonella typhi where they are often known as YdfA. The function of this family is unknown.. 
PF07152 YaeQ protein<br>Pfam-B_16245 (release 10.0). This family consists of several hypothetical bacterial proteins of around 180 residues in length which are often known as YaeQ. YaeQ is homologous to RfaH, a specialised transcription elongation protein. YaeQ is known to compensate for loss of RfaH function  .. 
PF07153 Marek's disease-like virus SORF3 protein<br>Pfam-B_16263 (release 10.0). This family consists of several SORF3 proteins from the Marek's disease-like viruses. Members of this family are around 350 residues in length. The function of this family is unknown.. 
PF07154 Protein of unknown function (DUF1392)<br>Pfam-B_16270 (release 10.0). This family consists of several hypothetical cyanobacterial proteins of around 150 residues in length which seem to be specific to Anabaena species. The function of this family is unknown.. 
PF07155 DUF1393;<br>ECF-type riboflavin transporter, S component. Moxon SJ, Eberhardt R. Pfam-B_16301 (release 10.0). This family is the substrate-binding component (S component) of the energy coupling-factor (ECF)-type riboflavin transporter. It is a transmembrane protein which binds riboflavin, and is responsible for riboflavin-uptake by cells [1,2].. 
PF07156 Prenylcysteine lyase<br>Pfam-B_12448 (release 10.0). This family contains prenylcysteine lyases (EC:1.8.3.5) that are approximately 500 residues long. Prenylcysteine lyase is a FAD-dependent thioether oxidase that degrades a variety of prenylcysteines, producing free cysteine, an isoprenoid aldehyde and hydrogen peroxide as products of the reaction  . It has been noted that this enzyme has considerable homology with ClP55, a 55 kDa protein that is associated with chloride ion pumps  .. 
PF07157 DNA circularisation protein N-terminus<br>Pfam-B_12343 (release 10.0). This family represents the N-terminus (approximately 100 residues) of a number of phage DNA circularisation proteins.. 
PF07158 Dicarboxylate carrier protein MatC N-terminus<br>Pfam-B_16346 (release 10.0). This family represents the N-terminal region of the bacterial dicarboxylate carrier protein MatC. The MatC protein is an integral membrane protein that could function as a malonate carrier  .. 
PF07159 Protein of unknown function (DUF1394)<br>Pfam-B_16260 (release 10.0). This family consists of several hypothetical eukaryotic proteins of around 320 residues in length. The function of this family is unknown.. 
PF07160 Protein of unknown function (DUF1395)<br>Pfam-B_16376 (release 10.0). This family consists of several hypothetical eukaryotic proteins of around 250 residues in length. The function of this family is unknown.. 
PF07161 Protein of unknown function (DUF1396)<br>Pfam-B_16343 (release 10.0). This family consists of several putative lipoproteins from Mycobacterium species. The function of this family is unknown.. 
PF07162 B9;<br>Ciliary basal body-associated, B9 protein. Vella Briffa B, Coggill P. Pfam-B_12595 (release 10.0). The B9-C2 domain is found in proteins associated with the ciliary basal body. B9 domains were identified as a specific family of C2 domains  .  There are three sub-families represented by this family, notably, Mks1-Xbx7, Stumpy-Tza1 and Tza2 groups of proteins. Mutations in human Mks1 result in the developmental disorder Mechler-Gruber syndrome  ; mutations in mouse Stumpy lead to perinatal hydrocephalus and severe polycystic kidney disease  . All the three distinct types of B9-C2 proteins cooperatively localise to the basal body or centrosome of cilia.    . 
PF07163 Pex26 protein<br>Pfam-B_16379 (release 10.0). This family consists of Pex26 and related mammalian proteins. Pex26 is a type II peroxisomal membrane protein which recruits Pex6-Pex1 complexes to peroxisomes  . Mutations in Pex26 can lead to human disorders  .. 
PF07165 Protein of unknown function (DUF1397)<br>Pfam-B_16395 (release 10.0). This family consists of several insect specific proteins. Swiss:Q25513 is annotated as being a haemolymph glycoprotein precursor. The function of this family is unknown  .. 
PF07166 Protein of unknown function (DUF1398)<br>Pfam-B_16404 (release 10.0). This family consists of several hypothetical Enterobacterial proteins of around 130 residues in length. Members of this family seem to be found exclusively in Escherichia coli and Salmonella species. The function of this family is unknown.. 
PF07167 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus<br>Pfam-B_16456 (release 10.0). This family represents the N-terminal region of the bacterial poly-beta-hydroxybutyrate polymerase (PhaC). Polyhydroxyalkanoic acids (PHAs) are carbon and energy reserve polymers produced in some bacteria when carbon sources are plentiful and another nutrient, such as nitrogen, phosphate, oxygen, or sulfur, becomes limiting. PHAs composed of monomeric units ranging from 3 to 14 carbons exist in nature. When the carbon source is exhausted, PHA is utilised by the bacterium. PhaC links D-(-)-3-hydroxybutyrl-CoA to an existing PHA molecule by the formation of an ester bond  .  This family appears to be a partial segment of an alpha/beta hydrolase domain.. 
PF07168 FAE_3-kCoA_syn1; Ureide_perm;<br>Pfam-B_11634 (release 10.0). Heterocyclic nitrogen compounds may serve as nitrogen sources or nitrogen transport compounds in plants that are not able to fix nitrogen. This family represents ureide permease, a transporter of a wide spectrum of oxo derivatives of heterocyclic nitrogen compounds, including allantoin, uric acid and xanthine; it has 10 putative transmembrane domains with a large cytosolic central domain containing a 'Walker A' motif. Ureide permease is likely to transport other purine degradation products when nitrogen sources are low. Transport is dependent on glucose and a proton gradient  .  The family is found in bacteria, plants and yeast.. 
PF07171 MlrC C-terminus<br>Pfam-B_6316 (release 10.0). This family represents the C-terminus (approximately 200 residues) of the product of a bacterial gene cluster that is involved in the degradation of the cyanobacterial toxin microcystin LR. Many members of this family are hypothetical proteins.. 
PF07172 Glycine rich protein family<br>Pfam-B_15819 (release 10.0). This family of proteins includes several glycine rich proteins as well as two nodulins 16 and 24.  The family also contains proteins that are induced in response to various stresses.. 
PF07173 Protein of unknown function (DUF1399)<br>Pfam-B_13062 (release 10.0). This family represents a conserved region approximately 150 residues long within a number of hypothetical plant proteins of unknown function.. 
PF07174 Fibronectin-attachment protein (FAP)<br>Pfam-B_16585 (release 10.0). This family contains bacterial fibronectin-attachment proteins (FAP). Family members are rich in alanine and proline, are approximately 300 long, and seem to be restricted to mycobacteria. These proteins contain a fibronectin-binding motif that allows mycobacteria to bind to fibronectin in the extracellular matrix  .. 
PF07175 Osteoregulin<br>Pfam-B_16589 (release 10.0). This family represents a conserved region approximately 180 residues long within osteoregulin, a bone-remodelling protein expressed highly in osteocytes within trabecular and cortical bone. A conserved RGD motif is found towards the C-terminal end of this region, and this is potentially involved in integrin recognition  .. 
PF07176 Alpha/beta hydrolase of unknown function (DUF1400)<br>Pfam-B_16606 (release 10.0). This family contains a number of hypothetical proteins of unknown function that seem to be specific to cyanobacteria. Members of this family have an alpha/beta hydrolase fold.. 
PF07177 Neuralized<br>Pfam-B_16611 (release 10.0). This family contains a conserved region approximately 60 residues long within eukaryotic neuralized and neuralized-like proteins. Neuralized belongs to a group of ubiquitin ligases and is required in a subset of Notch pathway-mediated cell fate decisions during development of the Drosophila nervous system  . Some family members contain multiple copies of this region.. 
PF07178 TraL protein<br>Pfam-B_16378 (release 10.0). This family consists of several bacterial TraL proteins. TraL is a predicted peripheral membrane protein which is thought to be involved in bacterial sex pilus assembly  . The exact function of this family is unclear.. 
PF07179 SseB protein N-terminal domain<br>Pfam-B_16678 (release 10.0). This family consists of several SseB proteins which appear to be found exclusively in Enterobacteria. SseB is known to enhance serine-sensitivity in Escherichia coli   and is part of the Salmonella pathogenicity island 2 (SPI-2) translocon  . This entry contains the presumed N-terminal domain of SseB.. 
PF07180 Protein of unknown function (DUF1401)<br>Pfam-B_16789 (release 10.0). This family consists of several hypothetical bacterial proteins of around 135 residues in length. Members of this family appear to be found exclusively in the Enterobacteria Escherichia coli, Citrobacter rodentium and Salmonella typhi. The function of this family is unknown.. 
PF07181 VirC2 protein<br>Pfam-B_16860 (release 10.0). This family consists of several VirC2 proteins which seem to be found exclusively in Agrobacterium species and Rhizobium etli. VirC2 is known to be involved in virulence in Agrobacterium species but its exact function is unclear [1,2].. 
PF07182 Protein of unknown function (DUF1402)<br>Pfam-B_16561 (release 10.0). This family consists of several hypothetical bacterial proteins of around 310 residues in length. Members of this family seem to be found exclusively in Agrobacterium, Rhizobium and Brucella species. The function of this family is unknown.. 
PF07183 Protein of unknown function (DUF1403)<br>Pfam-B_16581 (release 10.0). This family consists of several hypothetical bacterial proteins of around 320 residues in length. Members of this family are mainly found in Rhizobium and Agrobacterium species. The function of this family is unknown.. 
PF07184 Citrus tristeza virus P33 protein<br>Pfam-B_16614 (release 10.0). This family consists of several Citrus tristeza virus (CTV) P33 proteins. The function of P33 is unclear although it is known that the protein is not needed for virion formation  .. 
PF07185 Protein of unknown function (DUF1404)<br>Pfam-B_16616 (release 10.0). This family consists of several archaeal proteins of around 180 residues in length. Members of this family seem to be found exclusively in Sulfolobus tokodaii and Sulfolobus solfataricus. The function of this family is unknown.. 
PF07187 Protein of unknown function (DUF1405)<br>Pfam-B_16845 (release 10.0). This family consists of several bacterial and related archaeal protein of around 180 residues in length. The function of this family is unknown.. 
PF07188 Kaposi's sarcoma-associated herpesvirus (KSHV) K8 protein<br>Pfam-B_16868 (release 10.0). This family consists of Kaposi's sarcoma-associated herpesvirus (KSHV) K8 proteins. KSHV is a human Gammaherpesvirus related to Epstein-Barr virus (EBV) and herpesvirus saimiri. KSHV open reading frame K8 encodes a basic region-leucine zipper protein of 237 aa that homodimerises. K8 interacts and co-localises with human Pfam:PF04855, a cellular chromatin-remodelling factor, both in vivo and in vitro. K8 is thought to function as a transcriptional activator under specific conditions and its transactivation activity requires its interaction with the cellular chromatin remodelling factor hSNF5  . . 
PF07189 Splicing factor 3B subunit 10 (SF3b10)<br>Pfam-B_16870 (release 10.0). This family consists of several eukaryotic splicing factor 3B subunit 10 (SF3b10) proteins. SF3b10 is a 10 kDa subunit of the splicing factor SF3b. SF3b associates with the splicing factor SF3a and a 12S RNA unit to form the  U2 small nuclear ribonucleoproteins complex. SF3b10 and SF3b14b are also thought to facilitate the interaction of U2 with the branch site  .. 
PF07190 Protein of unknown function (DUF1406)<br>Pfam-B_16883 (release 10.0). This family consists of several Orthopoxvirus proteins of around 185 resides in length. Members of this family seem to be exclusive to Vaccinia, Camelpox and Cowpox viruses. Some family members are annotated as being C8 proteins but their function is unknown.. 
PF07191 DUF1407;<br>Pfam-B_16889 (release 10.0). This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family have 8 highly conserved cysteine residues, which form two zinc ribbon domains.. 
PF07192 SNURF/RPN4 protein<br>Pfam-B_16890 (release 10.0). This family consists of several mammalian SNRPN upstream reading frame (SNURF) proteins. SNURF or RPF4 is a RING-finger protein and a coregulator of androgen receptor-dependent transcription. It has been suggested that  SNURF is involved in the regulation of processes required for late steps of spermatid maturation [1,2].. 
PF07193 Protein of unknown function (DUF1408)<br>Pfam-B_16879 (release 10.0). This family consists of several hypothetical Lactococcus lactis and related phage proteins of around 75 residues in length. The function of this family is unknown.. 
PF07194 P2 response regulator binding domain<br>Pfam-B_7970 (release 10.0). The response regulators for CheA bind to the P2 domain, which is found between Pfam:PF01627 and Pfam:PF02895 as either one or two copies.  Highly flexible linkers connect P2 to the  rest of CheA and impart remarkable mobility to the P2 domain. This feature is thought to enhance the inter CheA dimer phosphotransfer  reactions within the signalling complex, thereby amplifying the phosphorylation signal  .. 
PF07195 Flagellar hook-associated protein 2 C-terminus<br>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  . This alignment covers the C-terminal region of this family of proteins.. 
PF07196 Flagellin hook IN motif<br>The function of this region is not clear, but it is found in many flagellar hook proteins, including FliD homologues ( ). It is normally repeated, but is also apparently seen as a singleton. A conserved IN is seen at the centre of the motif. The diversity of these motifs makes it likely that some members of the family are not identified.. 
PF07197 Protein of unknown function (DUF1409)<br>Pfam-B_16557 (release 10.0). This family represents a short conserved region (approximately 50 residues long), sometimes repeated, within a number of hypothetical Oryza sativa proteins of unknown function.. 
PF07198 Protein of unknown function (DUF1410)<br>Pfam-B_13132 (release 10.0). This family represents a conserved domain approximately 100 residues long, multiple copies of which are found within hypothetical Ureaplasma parvum proteins of unknown function, as well as related species.. 
PF07199 Protein of unknown function (DUF1411)<br>Pfam-B_16764 (release 10.0). This family represents a conserved region approximately 150 residues long that is sometimes repeated within some Babesia bovis proteins of unknown function.. 
PF07200 Modifier of rudimentary (Mod(r)) protein<br>Vella Briffa B, Wood V, Mistry J. Pfam-B_16631 (release 10.0). This family represents a conserved region approximately 150 residues long within a number of eukaryotic proteins that show homology with Drosophila melanogaster Modifier of rudimentary (Mod(r)) proteins. The N-terminal half of Mod(r) proteins is acidic, whereas the C-terminal half is basic  , and both of these regions are represented in this family.  Members of this family include the Vps37 subunit of the endosomal sorting complex ESCRT-I, a complex involved in recruiting transport machinery for protein sorting at the multivesicular body (MVB).  The yeast ESCRT-I complex consists of three proteins (Vps23, Vps28 and Vps37).  The mammalian homologue of Vps37 interacts with Tsg101 (Pfam: PF05743) through its mod(r) domain and its function is essential for lysosomal sorting of EGF receptors  .. 
PF07201 HrpJ-like domain<br>Pfam-B_16649 & Pfam-B_11026(release 10.0) & Pfam-B_1285(release 5.4). This family represents a conserved region approximately 200 residues long within a number of bacterial hypersensitivity response secretion protein HrpJ and similar proteins. HrpJ forms part of a type III secretion system through which, in phytopathogenic bacterial species, virulence factors are thought to be delivered to plant cells  .  This family also includes the InvE invasion protein from Salmonella.  This protein is involved in host parasite interactions and mutations in the InvE gene render Salmonella typhimurium non-invasive  .  InvE S. typhimurium mutants fail to elicit a rapid Ca2+ increase in cultured cells, an important event in the infection procedure and internalisation of S. typhimurium into epithelial cells  . This family includes bacterial SepL and SsaL proteins. SepL plays an essential role in the infection process of enterohemorrhagic Escherichia coli and is thought to be responsible for the secretion of EspA, EspD, and EspB  . SsaL of Salmonella typhimurium is thought to be a component of the type III secretion system  .. 
PF07202 T-complex protein 10 C-terminus<br>Pfam-B_13039 (release 10.0). This family represents the C-terminus (approximately 180 residues) of eukaryotic T-complex protein 10. The T-complex is involved in spermatogenesis in mice  .. 
PF07203 Protein of unknown function (DUF1412)<br>Pfam-B_16907 (release 10.0). This family consists of several Caenorhabditis elegans proteins of around 70-75 residues in length. The function of this family is unknown.. 
PF07204 Orthoreovirus membrane fusion protein p10<br>Pfam-B_16940 (release 10.0). This family consists of several Orthoreovirus membrane fusion protein p10 sequences.  p10 is thought to be a multifunctional protein that plays a key role in virus-host interaction  . . 
PF07205 Domain of unknown function (DUF1413)<br>Pfam-B_16942 (release 10.0). This family consists of several hypothetical bacterial proteins which seem to be specific to firmicute species. Members of this family are typically around 100 residues in length. The function of this family is unknown.. 
PF07206 Baculovirus late expression factor 10 (LEF-10)<br>Pfam-B_16893 (release 10.0). This family consists of several Baculovirus specific late expression factor 10 (LEF-10) sequences. LEF-10 is thought to be a late expressed structural protein although its exact function is unknown  .. 
PF07207 Light regulated protein Lir1<br>Pfam-B_16937 (release 10.0). This family consists of several plant specific light regulated Lir1 proteins.\.  Lir1 mRNA accumulates in the light, reaching maximum and minimum steady-state levels at the end of the light and dark period, respectively. Plants germinated in the dark have very low levels of lir1 mRNA, whereas plants germinated in continuous light express lir1 at an intermediate but constant level. It is thought that lir1 expression is controlled by light and a circadian clock.  The exact function of this family is unclear  .. 
PF07208 Protein of unknown function (DUF1414)<br>Pfam-B_16906 (release 10.0). This family consists of several hypothetical bacterial proteins of around 70 residues in length. Members of this family are often referred to as YejL. The function of this family is unknown.. 
PF07209 Protein of unknown function (DUF1415)<br>Pfam-B_16932 (release 10.0). This family consists of several hypothetical bacterial proteins of around 180 residues in length. The function of this family is unknown.. 
PF07210 Protein of unknown function (DUF1416)<br>Pfam-B_16939 (release 10.0). This family consists of several hypothetical bacterial proteins of around 100 residues in length. Members of this family appear to be Actinomycete specific. The function of this family is unknown.. 
PF07212 Hyaluronidase; <br>Hyaluronidase protein (HylP). Pfam-B_16578 (release 10.0). This family consists of several phage associated hyaluronidase proteins (EC:3.2.1.35) which seem to be specific to Streptococcus pyogenes and Streptococcus pyogenes bacteriophages. The substrate of hyaluronidase is hyaluronic acid, a sugar polymer composed of alternating N-acetylglucosamine and glucuronic acid residues. Hyaluronic acid is found in the ground substance of human connective tissue and the vitreous of the eye and also is the sole component of the capsule of group A streptococci. The capsule has been shown to be an important virulence factor of this organism by virtue of its ability to resist phagocytosis. Production by S. pyogenes of both a hyaluronic acid capsule and hyaluronidase enzymatic activity capable of destroying the capsule is an interesting, yet-unexplained, phenomenon  .. 
PF07213 DAP10 membrane protein<br>Pfam-B_16910 (release 10.0). This family consists of several mammalian DAP10 membrane proteins. In activated mouse natural killer (NK) cells, the NKG2D receptor associates with two intracellular adaptors, DAP10 and DAP12, which trigger phosphatidyl inositol 3 kinase (PI3K) and Syk family protein tyrosine kinases, respectively. It has been suggested that the DAP10-PI3K pathway is sufficient to initiate NKG2D-mediated killing of target cells  .. 
PF07214 Protein of unknown function (DUF1418)<br>Pfam-B_16971 (release 10.0). This family consists of several hypothetical Enterobacterial proteins of around 100 residues in length. Members of this family are often described as YbjC. In E. coli the ybjC gene is located downstream of nfsA (which encodes the major oxygen-insensitive nitroreductase). It is thought that nfsA and ybjC form an operon an its promoter is  a class I SoxS-dependent promoter  . The function of this family is unknown.. 
PF07215 Protein of unknown function (DUF1419)<br>Pfam-B_16972 (release 10.0). This family consists of several bacterial proteins of around 110 residues in length. Members of this family seem to be specific to Agrobacterium species and to Rhizobium loti. The function of this family is unknown.. 
PF07216 LcrG protein<br>Pfam-B_16974 (release 10.0). This family consists of several bacterial LcrG proteins. Yersiniae are equipped with the Yop virulon, an apparatus that allows extracellular bacteria to deliver toxic Yop proteins inside the host cell cytosol in order to sabotage the communication networks of the host cell or even to cause cell death. LcrG is a component of the Yop virulon involved in the regulation of secretion of the Yops  .  . 
PF07217 Heterokaryon incompatibility protein Het-C<br>Pfam-B_16951 (release 10.0). In filamentous fungi, het loci (for heterokaryon incompatibility) are believed to regulate self/nonself-recognition during vegetative growth. As filamentous fungi grow, hyphal fusion occurs within an individual colony to form a network. Hyphal fusion can occur also between different individuals to form a heterokaryon, in which genetically distinct nuclei occupy a common cytoplasm. However, heterokaryotic cells are viable only if the individuals involved have identical alleles at all het loci  .  . 
PF07218 Rhoptry-associated protein 1 (RAP-1)<br>Pfam-B_16981 (release 10.0). This family consists of several rhoptry-associated protein 1 (RAP-1) sequences which appear to be specific to Plasmodium falciparum  .. 
PF07219 HemY protein N-terminus<br>Pfam-B_16745 (release 10.0). This family represents the N-terminus (approximately 150 residues) of bacterial HemY porphyrin biosynthesis proteins. This is a membrane protein involved in a late step of protoheme IX synthesis  .. 
PF07220 Protein of unknown function (DUF1420)<br>Pfam-B_17056 (release 10.0). This family consists of several hypothetical putative lipoproteins which seem to be found specifically in the bacterium Leptospira interrogans. Members of this family are typically around 670 resides in length and their function is unknown.. 
PF07221 N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase)<br>Pfam-B_17012 (release 10.0). This family contains a number of eukaryotic and bacterial N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) enzymes (EC:5.3.1.8) approximately 500 residues long. This converts N-acyl-D-glucosamine to N-acyl-D-mannosamine.. 
PF07222 Proacrosin binding protein sp32<br>Pfam-B_17278 (release 10.0). This family consists of several mammalian specific proacrosin binding protein sp32 sequences. sp32 is a sperm specific protein which is known to bind with with 55- and 53-kDa proacrosins and the 49-kDa acrosin intermediate. The exact function of sp32 is unclear, it is thought however that the binding of sp32 to proacrosin may be involved in packaging the acrosin zymogen into the acrosomal matrix  . . 
PF07223 Protein of unknown function (DUF1421)<br>Pfam-B_17006 (release 10.0). This family represents a conserved region approximately 350 residues long within a number of plant proteins of unknown function.. 
PF07224 Chlorophyllase<br>Pfam-B_17130 (release 10.0). This family consists of several plant specific Chlorophyllase proteins (EC:3.1.1.14). Chlorophyllase (Chlase) is the first enzyme involved in chlorophyll (Chl) degradation and catalyses the hydrolysis of ester bond to yield chlorophyllide and phytol  .. 
PF07225 NDUFB4; <br>NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4). Pfam-B_17132 (release 10.0). This family consists of several NADH-ubiquinone oxidoreductase B15 subunit proteins (EC:1.6.5.3). . 
PF07226 Protein of unknown function (DUF1422)<br>Pfam-B_17087 (release 10.0). This family consists of several hypothetical bacterial proteins of around 120 residues in length. The function of this family is unknown.. 
PF07227 Protein of unknown function (DUF1423)<br>Pfam-B_17028 (release 10.0). This family represents a conserved region approximately 500 residues long within a number of Arabidopsis thaliana proteins of unknown function.. 
PF07228 Stage II sporulation protein E (SpoIIE)<br>Pfam-B_17063 (release 10.0). This family contains a number of bacterial stage II sporulation E proteins (EC:3.1.3.16). These are required for formation of a normal polar septum during sporulation. The N-terminal region is hydrophobic and is expected to contain up to 12 membrane-spanning segments  .. 
PF07229 VirE2<br>Pfam-B_17380 (release 10.0). This family consists of several VirE2 proteins which seem to be specific to Agrobacterium tumefaciens and Rhizobium etli. VirE2 is known to interact, via its C terminus, with VirD4. Agrobacterium tumefaciens transfers oncogenic DNA and effector proteins to plant cells during the course of infection. Substrate translocation across the bacterial cell envelope is mediated by a type IV secretion (TFS) system composed of the VirB proteins, as well as VirD4, a member of a large family of inner membrane proteins implicated in the coupling of DNA transfer intermediates to the secretion machine. VirE2 is therefore thought to be a protein substrate of a type IV secretion system which is recruited to a member of the coupling protein superfamily  . . 
PF07230 Phage_T4_Gp20;<br>Bacteriophage T4-like capsid assembly protein (Gp20). Pfam-B_17388 (release 10.0). This family consists of several bacteriophage T4-like capsid assembly (or portal) proteins. The exact mechanism by which the double-stranded (ds) DNA bacteriophages incorporate the portal protein at a unique vertex of the icosahedral capsid is unknown. In phage T4, there is evidence that this vertex, constituted by 12 subunits of gp20, acts as an initiator for the assembly of the major capsid protein and the scaffolding proteins into a prolate icosahedron of precise dimensions. The regulation of portal protein gene expression is an important regulator of prohead assembly in bacteriophage T4  . This family represents the protease responsible for the proteolysis of head proteins, a critical step in the morphogenesis of many tailed phages, Cleavage facilitates the conversion of the prohead to the mature capsid. All these cleavages are carried out by action at consensus S/A/G-X-E recognition sequences at 39 cleavage sites. Evidence of multiple processing sites in nine phiKZ proteins appears to represent a built-in mechanism by which the phage ensures that the majority of the propeptide regions are removed, and emphasizes the essential nature of processing in phiKZ-head morphogenesis  . The family is classified by MEROPS as a serine peptidase.. 
PF07231 Nematode_res_N; <br>Pfam-B_17124 (release 10.0). This family represents the N-terminus (approximately 180 residues) of plant Hs1pro-1, which is believed to confer resistance to nematodes  .. 
PF07232 Putative rep protein (DUF1424)<br>Pfam-B_17284 (release 10.0). This family consists of several archaeal proteins of around 320 residues in length. Members of this family seem to be found exclusively in Halobacterium and Haloferax species. The function of this family is unknown. This protein is probably a rep protein due to conservation of functional motifs.. 
PF07233 Protein of unknown function (DUF1425)<br>Pfam-B_17314 (release 10.0). This family consists of several hypothetical bacterial proteins of around 125 residues in length. Several members of this family are described as putative lipoproteins and are often known as YcfL. The function of this family is unknown.. 
PF07234 Protein of unknown function (DUF1426)<br>Pfam-B_17431 (release 10.0). This family consists of several Banana bunchy top virus proteins of around 120 residues in length. Swiss:Q9IGU4 is annotated a movement protein whereas most other family members are hypothetical. The function of this family is unknown.. 
PF07235 Protein of unknown function (DUF1427)<br>Pfam-B_17474 (release 10.0). This family consists of several bacterial proteins of around 100 residues in length. The function of this family is unknown.. 
PF07236 Phytoreovirus S7 protein<br>Pfam-B_17475 (release 10.0). This family consists of several Phytoreovirus S7 proteins which are thought to be viral core proteins  .. 
PF07237 Protein of unknown function (DUF1428)<br>Pfam-B_17402 (release 10.0). This family consists of several hypothetical bacterial and one archaeal sequence of around 120 residues in length. The function of this family is unknown.. 
PF07238 PilZ domain<br>Pfam-B_17421 (release 10.0). PilZ is a c-di-GMP binding domain   which is found C terminal to Pfam:PF07317.  Proteins which contain PilZ are known to interact with the flagellar switch-complex proteins FliG and FliM.  This interaction results in a reduction of torque generation and induces CCW motor bias  .  This domain forms a beta barrel structure.. 
PF07239 Outer membrane protein OpcA<br>Pfam-B_17433 (release 10.0). This family consists of several Neisseria species specific OpcA outer membrane proteins. Opc (formerly called 5C) is one of the major outer membrane proteins and has been shown to play an important role in meningococcal adhesion and invasion of both epithelial and endothelial cells  .. 
PF07240 Stress-inducible humoral factor Turandot<br>Pfam-B_17438 (release 10.0). This family consists of several Drosophila species specific Turandot proteins. The Turandot A (TotA) gene encodes a humoral factor, which is secreted from the fat body and accumulates in the body fluids. TotA is strongly induced upon bacterial challenge, as well as by other types of stress such as high temperature, mechanical pressure, dehydration, UV irradiation, and oxidative agents. It is also up-regulated during metamorphosis and at high age. Flies that over-express TotA show prolonged survival and retain normal activity at otherwise lethal temperatures. Although TotA is only induced by severe stress, it responds to a much wider range of stimuli than heat shock genes such as hsp70 or immune genes such as Cecropin A1  .. 
PF07242 Protein of unknown function (DUF1430)<br>Pfam-B_17033 (release 10.0). This family represents the C-terminus (approximately 120 residues) of a number of hypothetical bacterial proteins of unknown function. These are possibly membrane proteins involved in immunity.. 
PF07243 Phlebovirus glycoprotein G1<br>Pfam-B_17508 (release 10.0). This family consists of several Phlebovirus glycoprotein G1 sequences. Members of the Bunyaviridae family acquire an envelope by budding through the lipid bilayer of the Golgi complex. The budding compartment is thought to be determined by the accumulation of the two heterodimeric membrane glycoproteins G1 and G2 in the Golgi  .. 
PF07244 Surface antigen variable number repeat<br>This family is found primarily in bacterial surface antigens, normally as variable number repeats at the N-terminus. The C-terminus of these proteins is normally represented by Pfam:PF01103. The alignment centres on a -GY- or -GF- motif. Some members of this family are found in the mitochondria. It is predicted to have a mixed alpha/beta secondary structure.. 
PF07245 Phlebovirus glycoprotein G2<br>Pfam-B_17508 (release 10.0). This family consists of several Phlebovirus glycoprotein G2 sequences. Members of the Bunyaviridae family acquire an envelope by budding through the lipid bilayer of the Golgi complex. The budding compartment is thought to be determined by the accumulation of the two heterodimeric membrane glycoproteins G1 and G2 in the Golgi  .. 
PF07246 Phlebovirus nonstructural protein NS-M<br>Pfam-B_17508 (release 10.0). This family consists of several Phlebovirus nonstructural NS-M proteins which represent the N-terminal region of the M polyprotein precursor. The function of this family is unknown.. 
PF07247 Alcohol acetyltransferase<br>Pfam-B_17349 (release 10.0). This family contains a number of alcohol acetyltransferase (EC:2.3.1.84) enzymes approximately 500 residues long found in both bacteria and metazoa. These catalyse the esterification of isoamyl alcohol by acetyl coenzyme A  .. 
PF07248 Protein of unknown function (DUF1431)<br>Pfam-B_17470 (release 10.0). This family contains a number of Drosophila melanogaster proteins of unknown function. These contain several conserved cysteine residues.. 
PF07249 Cerato-platanin<br>Pfam-B_17594 (release 10.0). This family contains a number of fungal cerato-platanin phytotoxic proteins approximately 150 residues long. Cerato-platanin contains four cysteine residues that form two disulphide bonds  .. 
PF07250 Glyoxal oxidase N-terminus<br>Pfam-B_17519 (release 10.0). This family represents the N-terminus (approximately 300 residues) of a number of plant and fungal glyoxal oxidase enzymes. Glyoxal oxidase catalyses the oxidation of aldehydes to carboxylic acids, coupled with reduction of dioxygen to hydrogen peroxide. It is an essential component of the extracellular lignin degradation pathways of the wood-rot fungus Phanerochaete chrysosporium  .. 
PF07252 Protein of unknown function (DUF1433)<br>Pfam-B_17690 (release 10.0). This family contains a number of hypothetical bacterial proteins of unknown function approximately 100 residues in length.. 
PF07253 Gypsy protein<br>Pfam-B_17444 (release 10.0). This family consists of several Gypsy/Env proteins from Drosophila and Ceratitis fruit fly species. Gypsy is an endogenous retrovirus of Drosophila melanogaster. Phylogenetic studies suggest that occasional horizontal transfer events of gypsy occur between Drosophila species.  Gypsy possesses infective properties associated with the products of the envelope gene that might be at the origin of these interspecies transfers  . This family contains many members with full-length matches; however, it also includes a number of very short sequences and short matches of sequences with other unrelated domains on them, which cannot be excluded. These matches may represent remnants of once-functional genes.. 
PF07254 Protein of unknown function (DUF1434)<br>Pfam-B_17586 (release 10.0). This family consists of several hypothetical bacterial proteins of around 135 residues in length. Members of this family all appear to be Enterobacterial proteins. The function of this family is unknown.. 
PF07255 Benyvirus 14KDa protein<br>Pfam-B_17595 (release 10.0). This family consists of several Benyvirus specific 14KDa proteins of around 125 residues in length. Members of this family contain 9 conserved cysteine residues. The function of this family is unknown.. 
PF07256 Protein of unknown function (DUF1435)<br>Pfam-B_17631 (release 10.0). This family consists of several hypothetical Enterobacterial proteins of around 80 residues in length. The function of this family is unknown.. 
PF07258 HCaRG protein<br>Pfam-B_17801 (release 10.0). This family consists of several mammalian HCaRG(hypertension-related, calcium-regulated gene) proteins. HCaRG is negatively regulated by extracellular calcium concentration, and its basal mRNA levels are higher in hypertensive animals. HCaRG is a nuclear protein potentially involved in the control of cell proliferation  . . 
PF07259 ProSAAS precursor<br>Pfam-B_17813 (release 10.0). This family consists of several mammalian proSAAS precursor proteins. ProSAAS mRNA is expressed primarily in brain and other neuroendocrine tissues (pituitary, adrenal, pancreas); within brain, the mRNA is broadly distributed among neurons. ProSAAS is thought to be an endogenous inhibitor of prohormone convertase 1   may function as a neuropeptide  . N-terminal fragments of proSAAS in intracellular Pick Bodies (PBs) may cause a functional disturbance of neurons in Pick's disease  .. 
PF07260 Progressive ankylosis protein (ANKH)<br>Pfam-B_17517 (release 10.0). This family consists of several progressive ankylosis protein (ANK or ANKH) sequences. The ANK protein spans the outer cell membrane and shuttles inorganic pyrophosphate (PPi), a major inhibitor of physiologic and pathologic calcification, bone mineralisation and bone resorption  . Mutations in ANK are thought to give rise to Craniometaphyseal dysplasia (CMD) which is a rare skeletal disorder characterised by progressive thickening and increased mineral density of craniofacial bones and abnormally developed metaphyses in long bones  .. 
PF07261 Replication initiation and membrane attachment<br>Pfam-B_17543 (release 10.0). This family consists of several bacterial replication initiation and membrane attachment (DnaB) proteins, as well as DnaD which is a component of the PriA primosome.  The PriA primosome functions to recruit the replication fork helicase onto the DNA  . The DnaB protein is essential for both replication initiation and membrane attachment of the origin region of the chromosome and plasmid pUB110 in Bacillus subtilis. It is known that there are two different classes (DnaBI and DnaBII) in the DnaB mutants; DnaBI is essential for both chromosome and pUB110 replication, whereas DnaBII is necessary only for chromosome replication  . DnaD has been merged into this family. This family also includes Ftn6, a cyanobacterial-specific divisome component possibly playing a role at the interface between DNA replication and cell division  . Ftn6 possesses a conserved domain localised within the N-terminus of the proteins. This domain, named FND, exhibits sequence and structure similarities with the DnaD-like domains Pfam:PF04271 now merged into Pfam:PF07261.. 
PF07262 Protein of unknown function (DUF1436)<br>Pfam-B_17809 (release 10.0). This family consists of several hypothetical bacterial proteins of around 160 residues in length. The function of this family is unknown.. 
PF07263 Dentin matrix protein 1 (DMP1)<br>Pfam-B_17812 (release 10.0). This family consists of several mammalian dentin matrix protein 1 (DMP1) sequences. The dentin matrix acidic phosphoprotein 1 (DMP1) gene has been mapped to human chromosome 4q21  . DMP1 is a bone and teeth specific protein initially identified from mineralised dentin.  DMP1 is primarily localised in the nuclear compartment of undifferentiated osteoblasts. In the nucleus, DMP1 acts as a transcriptional component for activation of osteoblast-specific genes like osteocalcin. During the early phase of osteoblast maturation, Ca(2+) surges into the nucleus from the cytoplasm, triggering the phosphorylation of DMP1 by a nuclear isoform of casein kinase II. This phosphorylated DMP1 is then exported out into the extracellular matrix, where it regulates nucleation of hydroxyapatite. DMP1 is a unique molecule that initiates osteoblast differentiation by transcription in the nucleus and orchestrates mineralised matrix formation extracellularly, at later stages of osteoblast maturation  . The DMP1 gene has been found to be ectopically expressed in lung cancer although the reason for this is unknown  .. 
PF07264 Etoposide-induced protein 2.4 (EI24)<br>Pfam-B_17540 (release 10.0). This family contains a number of eukaryotic etoposide-induced 2.4 (EI24) proteins approximately 350 residues long as well as bacterial CysZ proteins (formerly known as DUF540). In cells treated with the cytotoxic drug etoposide, EI24 is induced by p53  . It has been suggested to play an important role in negative cell growth control  .. 
PF07265 Tapetum specific protein TAP35/TAP44<br>Pfam-B_17587 (release 10.0). This family consists of several plant tapetum specific proteins. Members of this family are found in Arabidopsis thaliana, Brassica napus and Sinapis alba. Members of this family may be involved in sporopollenin formation and/or deposition  .. 
PF07267 Nucleopolyhedrovirus capsid protein P87<br>Pfam-B_17842 (release 10.0). This family consists of several Nucleopolyhedrovirus capsid protein P87 sequences. P87 is expressed late in infection and concentrated in infected cell nuclei  .. 
PF07268 Exported protein precursor (EppA/BapA)<br>Pfam-B_17945 (release 10.0). This family consists of a number of exported protein precursor (EppA and BapA) sequences which seem to be specific to Borrelia burgdorferi (Lyme disease spirochete). bapA gene sequences are quite stable but the encoded proteins do not provoke a strong immune response in most individuals. Conversely, EppA proteins are much more antigenic but are more variable in sequence. It is thought that BapA and EppA play important roles during the Borrelia burgdorferi infectious cycle  .. 
PF07270 Protein of unknown function (DUF1438)<br>Pfam-B_18024 (release 10.0). This family consists of several hypothetical proteins of around 170 residues in length which appear to be mouse specific. The function of this family is unknown.. 
PF07271 Cytadhesin P30/P32<br>Pfam-B_18052 (release 10.0). This family consists of several Mycoplasma species specific Cytadhesin P32 and P30 proteins. P30 has been found to be membrane associated and localised on the tip organelle. It is thought that it is important in cytadherence and virulence  .. 
PF07272 Orthoreovirus P17 protein<br>Pfam-B_18125 (release 10.0). This family consists of several Orthoreovirus P17 proteins. P17 is specified be ORF2 of the S1 gene and represents a nonstructural protein which associate with cell membranes  .. 
PF07273 Protein of unknown function (DUF1439)<br>Pfam-B_18280 (release 10.0). This family consists of several hypothetical bacterial proteins of around 190 residues in length. Several members of this family are annotated as being putative lipoproteins and are often known as YceB. The function of this family is unknown.. 
PF07274 Protein of unknown function (DUF1440)<br>Pfam-B_17831 (release 10.0). This family contains a number of bacterial proteins of unknown function approximately 180 residues long. These are possibly integral membrane proteins.. 
PF07275 Antirestriction protein (ArdA)<br>Pfam-B_17857 (release 10.0). This family consists of several bacterial antirestriction (ArdA) proteins.\.       ArdA functions in bacterial conjugation to allow an unmodified plasmid to evade restriction in the recipient bacterium and yet acquire cognate modification  .. 
PF07276 Apopolysialoglycoprotein (PSGP)<br>Pfam-B_17916 (release 10.0). This family represents a series of 13 reside repeats found in the apopolysialoglycoprotein of Oncorhynchus mykiss (Rainbow trout) and Oncorhynchus masou (Cherry salmon). Polysialoglycoprotein (PSGP) of unfertilised eggs of rainbow trout consists of tandem repeats of a glycotridecapeptide, Asp-Asp-Ala-Thr*-Ser*-Glu-Ala-Ala-Thr*-Gly-Pro-Ser- Gly (* denotes the attachment site of a polysialoglycan chain). In response to egg activation, PSGP is discharged by exocytosis into the space between the vitelline envelope and the plasma membrane, i.e. the perivitelline space, where the 200-kDa PSGP molecules undergo rapid and dramatic depolymerisation by proteolysis into glycotridecapeptides  .. 
PF07277 SapC<br>Pfam-B_17881 (release 10.0). This family contains a number of bacterial SapC proteins approximately 250 residues long. In Campylobacter fetus, SapC forms part of a paracrystalline surface layer (S-layer) that confers serum resistance  .. 
PF07278 Protein of unknown function (DUF1441)<br>Pfam-B_17966 (release 10.0). This family consists of several hypothetical Enterobacterial proteins of around 160 residues in length. The function of this family is unknown. However, it appears to be distantly related to other HTH families so may act as a transcriptional regulator.. 
PF07279 Protein of unknown function (DUF1442)<br>Pfam-B_18012 (release 10.0). This family consists of several hypothetical Arabidopsis thaliana proteins of around 225 residues in length. The function of this family is unknown.. 
PF07280 Protein of unknown function (DUF1443)<br>Pfam-B_18027 (release 10.0). This family consists of several Baculovirus proteins of around 55 residues in length. The function of this family is unknown.. 
PF07281 Insulin-induced protein (INSIG)<br>Pfam-B_17905 (release 10.0). This family contains a number of eukaryotic Insulin-induced proteins (INSIG-1 and INSIG-2) approximately 200 residues long. INSIG-1 and INSIG-2 are found in the endoplasmic reticulum and bind the sterol-sensing domain of SREBP cleavage-activating protein (SCAP), preventing it from escorting SREBPs to the Golgi. Their combined action permits feedback regulation of cholesterol synthesis over a wide range of sterol concentrations [1,2].. 
PF07282 Transposase_35;<br>Putative transposase DNA-binding domain. Pfam-B_4755 (release 10.0). This putative domain is found at the C-terminus of a large number of transposase proteins.  This domain contains four conserved cysteines suggestive of a zinc binding domain.  Given the need for transposases to bind DNA as well as the large number of DNA-binding zinc fingers we hypothesise this domain is DNA-binding.. 
PF07283 Conjugal transfer protein TrbH<br>Pfam-B_17942 (release 10.0). This family contains TrbH, a bacterial conjugal transfer protein approximately 150 residues long. This contains a putative membrane lipoprotein lipid attachment site  .. 
PF07284 2-vinyl bacteriochlorophyllide hydratase (BCHF)<br>Pfam-B_17961 (release 10.0). This family contains the bacterial enzyme 2-vinyl bacteriochlorophyllide hydratase (EC:4.2.1.-) (approximately 150 residues long). This is involved in the light-independent bacteriochlorophyll biosynthesis pathway by adding water across the 2-vinyl group  .. 
PF07285 Protein of unknown function (DUF1444)<br>Pfam-B_18053 (release 10.0). This family contains several hypothetical bacterial proteins of unknown function that are approximately 250 residues long.. 
PF07286 Protein of unknown function (DUF1445)<br>Pfam-B_18180 (release 10.0). This family represents a conserved region approximately 150 residues long within a number of hypothetical bacterial and eukaryotic proteins of unknown function.. 
PF07287 Protein of unknown function (DUF1446)<br>Pfam-B_17949 (release 10.0). This family consists of several bacterial and plant proteins of around 400 residues in length. The function of this family is unknown.. 
PF07288 Protein of unknown function (DUF1447)<br>Pfam-B_18163 (release 10.0). This family consists of several bacterial proteins of around 70 residues in length. The function of this family is unknown.. 
PF07289 Protein of unknown function (DUF1448)<br>Pfam-B_18223 (release 10.0). This family consists of several eukaryotic proteins of around 375 residues in length. The function of this family is unknown. It appears that this family includes a divergent GRAM domain.. 
PF07290 Protein of unknown function (DUF1449)<br>Pfam-B_18269 (release 10.0). This family consists of several bacterial proteins of around 210 residues in length. The function of this family is unknown.. 
PF07291 Methylamine utilisation protein MauE<br>Pfam-B_18306 (release 10.0). This family consists of several bacterial methylamine utilisation MauE proteins. Synthesis of enzymes involved in methylamine oxidation via methylamine dehydrogenase (MADH) is encoded by genes present in the mau cluster. MauE and MauD are specifically involved in the processing, transport, and/or maturation of the beta-subunit and that the absence of each of these proteins leads to production of a non-functional beta-subunit which becomes rapidly degraded  .. 
PF07292 Nmi/IFP 35 domain (NID)<br>Pfam-B_17864 (release 10.0). This family represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi). This domain mediates Nmi-Nmi protein interactions and subcellular localisation  .. 
PF07293 Protein of unknown function (DUF1450)<br>Pfam-B_18439 (release 10.0). This family consists of several hypothetical bacterial proteins of around 80 residues in length. Members of this family contain four highly conserved cysteine residues. The function of this family is unknown.. 
PF07294 Fibroin P25<br>Pfam-B_18451 (release 10.0). This family consists of several insect fibroin P25 proteins. Silk fibroin produced by the silkworm Bombyx mori consists of a heavy chain, a light chain, and a glycoprotein, P25. The heavy and light chains are linked by a disulfide bond, and P25 associates with disulfide-linked heavy and light chains by non-covalent interactions. P25 is plays an important role in maintaining integrity of the complex  .. 
PF07295 Protein of unknown function (DUF1451)<br>Pfam-B_18524 (release 10.0). This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.. 
PF07296 TraP protein<br>Pfam-B_18635 (release 10.0). This family consists of several bacterial conjugative transfer TraP proteins from Escherichia coli and Salmonella typhimurium. TraP appears to play a minor role in conjugation and may interact with TraB, which varies in sequence along with TraP, in order to stabilise the proposed transmembrane complex formed by the tra operon products  .. 
PF07297 Dolichol phosphate-mannose biosynthesis regulatory protein (DPM2)<br>Pfam-B_18649 (release 10.0). This family consists of several eukaryotic dolichol phosphate-mannose biosynthesis regulatory (DPM2) proteins. Biosynthesis of glycosylphosphatidylinositol and N-glycan precursor is dependent upon a mannosyl donor, dolichol phosphate-mannose (DPM). DPM2, an 84 amino acid membrane protein expressed in the endoplasmic reticulum (ER), makes a complex with DPM1 that is essential for the ER localisation and stable expression of DPM1. Moreover, DPM2 enhances binding of dolichol phosphate, a substrate of DPM synthase. Biosynthesis of DPM in mammalian cells is regulated by DPM2  .. 
PF07298 NnrU protein<br>Pfam-B_18406 (release 10.0). This family consists of several plant and bacterial NnrU proteins. NnrU is thought to be involved in the reduction of nitric oxide. The exact function of NnrU is unclear. It is thought however that  NnrU and perhaps NnrT are required for expression of both nirK and nor  .. 
PF07299 Fibronectin-binding protein (FBP)<br>Pfam-B_18450 (release 10.0). This family consists of several bacterial fibronectin-binding proteins which are thought to be involved in virulence in Listeria species [1,2].. 
PF07301 Protein of unknown function (DUF1453)<br>Pfam-B_18607 (release 10.0). This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown. Members of this family seem to be found exclusively in the Order Bacillales.. 
PF07302 AroM protein<br>Pfam-B_18608 (release 10.0). This family consists of several bacterial and archaeal AroM proteins. In Escherichia coli the aroM gene is cotranscribed with aroL  . The function of this family is unknown.. 
PF07303 Occludin homology domain<br>Pfam-B_18556 (release 10.0). This domain represents a conserved region approximately 100 residues long within eukaryotic occludin proteins and the RNA polymerase II elongation factor ELL. Occludin is an integral membrane protein that localises to tight junctions  , while ELL is an elongation factor that can increase the catalytic rate of RNA polymerase II transcription by suppressing transient pausing by polymerase at multiple sites along the DNA  . This shared domain is thought to mediate protein interactions  .. 
PF07304 Steroid receptor RNA activator (SRA1)<br>Pfam-B_18506 (release 10.0). This family consists of several hypothetical mammalian steroid receptor RNA activator proteins. SRA-RNAs likely to encode stable proteins are widely expressed in breast cancer cell lines. SRA-RNA is a steroid receptor co-activator which acts as a functional RNA and is classified as belonging to the growing family of functional non-coding RNAs. . 
PF07305 Protein of unknown function (DUF1454)<br>Pfam-B_18833 (release 10.0). This family consists of several Enterobacterial sequences of around 200 residues in length which are often known as YiiQ proteins. The function of this family is unknown.. 
PF07306 Protein of unknown function (DUF1455)<br>Pfam-B_19038 (release 10.0). This family consists of several hypothetical putative outer membrane proteins which appear to be specific to Anaplasma marginale and Anaplasma ovis.. 
PF07307 Heptaprenyl diphosphate synthase (HEPPP synthase) subunit 1<br>Pfam-B_18592 (release 10.0). This family contains subunit 1 of bacterial heptaprenyl diphosphate synthase (HEPPP synthase) (EC:2.5.1.30) (approximately 230 residues long). The enzyme consists of two subunits, both of which are required for catalysis of heptaprenyl diphosphate synthesis  .. 
PF07308 Protein of unknown function (DUF1456)<br>This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.. 
PF07309 Flagellar protein FlaF<br>Pfam-B_19331 (release 10.0). This family consists of several bacterial FlaF flagellar proteins. FlaF and FlaG are trans-acting, regulatory factors that modulate flagellin synthesis during flagellum biogenesis  .. 
PF07310 DUF1457; <br>Pfam-B_18761 (release 10.0). This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long. This region is is distantly similar to other PAS domains.. 
PF07311 DUF1458;<br>Moxon SJ, Anantharaman V. Pfam-B_18876 (release 10.0). Dodecin is a flavin-binding protein  ,found in several bacteria and  few archaea and represents a stand-alone version of the SHS2  domain  . It most closely resembles the SHS2 domains of FtsA and  Rpb7p, and represents a single domain small-molecule binding form .. 
PF07312 Protein of unknown function (DUF1459)<br>Pfam-B_18877 (release 10.0). This family consists of several hypothetical Caenorhabditis elegans proteins of around 85 residues in length. The function of this family is unknown.. 
PF07313 Protein of unknown function (DUF1460)<br>Pfam-B_18925 (release 10.0). This family consists of several hypothetical bacterial proteins of around 260 residues in length. The function of this family is unknown.. 
PF07314 Protein of unknown function (DUF1461)<br>Pfam-B_18854 (release 10.0). This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long. These are possibly integral membrane proteins.. 
PF07315 Protein of unknown function (DUF1462)<br>Pfam-B_19094 (release 10.0). This family consists of several hypothetical bacterial proteins of around 100 residues in length. The function of this family is unknown.. 
PF07316 Protein of unknown function (DUF1463)<br>Pfam-B_19113 (release 10.0). This family consists of several hypothetical bacterial proteins of around 140 residues in length. Members of this family seem to be found exclusively in Borrelia burgdorferi (Lyme disease spirochete). The function of this family is unknown.. 
PF07317 Flagellar regulator YcgR<br>Pfam-B_19142 (release 10.0). This domain is found N terminal to Pfam:PF07238.  Proteins which contain YcgR domains are known to interact with the flagellar switch-complex proteins FliG and FliM.  This interaction results in a reduction of torque generation and induces CCW motor bias  .. 
PF07318 Protein of unknown function (DUF1464)<br>Pfam-B_19143 (release 10.0). This family consists of several hypothetical archaeal proteins of around 350 residues in length. The function of this family is unknown.. 
PF07319 Primosomal protein DnaI N-terminus<br>Pfam-B_18931 (release 10.0). This family represents the N-terminus (approximately 120 residues) of bacterial primosomal DnaI proteins, although one family member appears to be of viral origin. DnaI is one of the components of the Bacillus subtilis replication restart primosome, and is required for the DnaB75-dependent loading of the DnaC helicase  .. 
PF07321 Type III secretion protein YscO<br>Pfam-B_19036 (release 10.0). This family contains the bacterial type III secretion protein YscO, which is approximately 150 residues long. YscO has been shown to be required for high-level expression and secretion of the anti-host proteins V antigen and Yops in Yersinia pestis  .. 
PF07322 Seadornavirus Vp10<br>Pfam-B_18930 (release 10.0). This family consists of several Seadornavirus Vp10 proteins found in the Banna and Kadipiro viruses. Members of this family are typically around 240 residues in length. The function of this family is unknown.. 
PF07323 Protein of unknown function (DUF1465)<br>Pfam-B_19346 (release 10.0). This family consists of several hypothetical bacterial proteins of around 180 residues in length. The function of this family is unknown.. 
PF07324 DiGeorge syndrome critical region 6 (DGCR6) protein<br>Pfam-B_19101 (release 10.0). This family contains DiGeorge syndrome critical region 6 (DGCR6) proteins (approximately 200 residues long) of a number of vertebrates. DGCR6 is a candidate for involvement in the DiGeorge syndrome pathology by playing a role in neural crest cell migration into the third and fourth pharyngeal pouches, the structures from which derive the organs affected in DiGeorge syndrome  . Also found in this family is the Drosophila melanogaster gonadal protein gdl.. 
PF07325 Curtovirus V2 protein<br>Pfam-B_19350 (release 10.0). This family consists of several Curtovirus V2 proteins. The exact function of V2 is unclear but it is known that the protein is required for a successful host infection process  .. 
PF07326 Protein of unknown function (DUF1466)<br>Pfam-B_19433 (release 10.0). This family consists of several hypothetical mammalian proteins of around 240 residues in length.. 
PF07327 Neuroparsin<br>Pfam-B_19487 (release 10.0). This family consists of several locust specific neuroparsin proteins. Neuroparsins are produced by the A1 type of protocerebral median neurosecretory cells of the PI-CC system and display pleiotropic activities: inhibition of the effect of juvenile hormone, stimulation of fluid reabsorption of isolated recta, induction of an increase in hemolymph lipid and trehalose levels, and neurotrophic effects  .. 
PF07328 T-DNA border endonuclease VirD1<br>Pfam-B_19558 (release 10.0). This family consists of several T-DNA border endonuclease VirD1 proteins which appear to be found exclusively in Agrobacterium species. Agrobacterium, a plant pathogen, is capable to stably transform the plant cell with a segment of its own DNA called T-DNA (transferred DNA). This process depends, among others, on the specialised bacterial virulence proteins VirD1 and VirD2 that excise the T-DNA from its adjacent sequences. VirD1 is thought to interact with VirD2 in this process  .. 
PF07330 Protein of unknown function (DUF1467)<br>Pfam-B_19588 (release 10.0). This family consists of several bacterial proteins of around 90 residues in length. The function of this family is unknown.. 
PF07331 DUF1468;<br>Tripartite tricarboxylate transporter TctB family. Pfam-B_19347 (release 10.0). This family consists of several hypothetical bacterial proteins of around 150 residues in length. This family was formerly known as DUF1468.. 
PF07332 Protein of unknown function (DUF1469)<br>Pfam-B_19352 (release 10.0) & COG5393. This family consists of several hypothetical bacterial proteins of around 140 residues in length. The function of this family is unknown.. 
PF07333 S locus-related glycoprotein 1 binding pollen coat protein (SLR1-BP)<br>Pfam-B_19392 (release 10.0). This family consists of a number of cysteine rich SLR1 binding pollen coat like proteins. Adhesion of pollen grains to the stigmatic surface is a critical step during sexual reproduction in plants. In Brassica, S locus-related glycoprotein 1 (SLR1), a stigma-specific protein belonging to the S gene family of proteins, has been shown to be involved in this step. SLR1-BP specifically binds SLR1 with high affinity. The SLR1-BP gene is specifically expressed in pollen at late stages of development and is a member of the class A pollen coat protein (PCP) family, which includes PCP-A1, an SLG (S locus glycoprotein)-binding protein  .. 
PF07334 Interferon-induced 35 kDa protein (IFP 35) N-terminus<br>Pfam-B_17864 (release 10.0). This family represents the N-terminus of interferon-induced 35 kDa protein (IFP 35) (approximately 80 residues long), which contains a leucine zipper motif in an alpha helical configuration  . This family also includes N-myc-interactor (Nmi), a homologous interferon-induced protein.. 
PF07335 Chitosanase;<br>Fungal chitosanase of glycosyl hydrolase group 75. Pfam-B_19431 (release 10.0). This family consists of several fungal chitosanase proteins. Chitin, xylan, 6-O-sulphated chitosan and O-carboxymethyl chitin are indigestible by chitosanase  . EC:3.2.1.132. The mechanism is likely to be inverting, and the probable catalytic neutrophile base is Asp, with the probable catalytic proton donor being Glu. (see the Chitosanase web-page from CAZY).. 
PF07336 Protein of unknown function (DUF1470)<br>Pfam-B_19432 (release 10.0). This family consists of several hypothetical bacterial proteins of around 180 residues in length. Members of this family are found in Streptomyces, Rhizobium, Ralstonia, Agrobacterium and Bradyrhizobium species. The function of this family is unknown.. 
PF07337 DC-EC Repeat<br>This repeat is found in the CagY proteins - part of the CAG pathogenicity island - and involved in delivery of the protein CagA into host cells ( ). It forms part of a surface needle structure, and this repeat may form an alpha-helical rod structure ( ). A conserved -DC- and -EC- can be seen in regularly spaced in the alignment.. 
PF07338 Protein of unknown function (DUF1471)<br>Pfam-B_19452 (release 10.0). This family consists of several hypothetical Enterobacterial proteins of around 90 residues in length. Some members of this family are annotated as ydgH precursors and contain two copies of this region, one at the N-terminus and the other at the C-terminus. The function of this family is unknown.. 
PF07339 Protein of unknown function (DUF1472)<br>Pfam-B_19493 (release 10.0). This family consists of several Enterobacterial proteins of around 125 residues in length and contains 6 highly conserved cysteine residues. The function of this family is unknown.. 
PF07340 Cytomegalovirus IE1 protein<br>Pfam-B_22587 (release 10.0). Expression from a human cytomegalovirus early promoter (E1.7) has been shown to be activated in trans by the IE2 gene product. Although the IE1 gene product alone had no effect on this early viral promoter, maximal early promoter activity was detected when both IE1 and IE2 gene products were present  .  The IE1 protein from cytomegalovirus is also known as UL123.. 
PF07341 Protein of unknown function (DUF1473)<br>Pfam-B_19856 (release 10.0). This family consists of several hypothetical bacterial proteins of around 150 residues in length. Members of this family seem to be found exclusively in Borrelia burgdorferi (Lyme disease spirochete). The function of this family is unknown.. 
PF07342 Protein of unknown function (DUF1474)<br>Pfam-B_19882 (release 10.0). This family consists of several bacterial proteins of around 100 residues in length. Members of this family seem to be found exclusively in Staphylococcus aureus. The function of this family is unknown.. 
PF07343 Protein of unknown function (DUF1475)<br>Pfam-B_19887 (release 10.0). This family consists of several hypothetical plant proteins of around 250 residues in length. Members of this family seem to be found exclusively in Arabidopsis thaliana. The function of this family is unknown.. 
PF07344 Amastin surface glycoprotein<br>Pfam-B_19245 (release 10.0). This family contains the eukaryotic surface glycoprotein amastin (approximately 180 residues long).In Trypanosoma cruzi, amastin is particularly abundant during the amastigote stage.. 
PF07345 Domain of unknown function (DUF1476)<br>Pfam-B_19680 (release 10.0). This family consists of several hypothetical bacterial proteins of around 100 residues in length. Members of this family are found in Bradyrhizobium, Rhizobium, Brucella and Caulobacter species. The function of this family is unknown.. 
PF07346 Protein of unknown function (DUF1477)<br>Pfam-B_19762 (release 10.0). This family consists of several hypothetical Nucleopolyhedrovirus proteins of around 100 resides in length. The function of this family is unknown.. 
PF07347 NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a)<br>Pfam-B_19436 (release 10.0). This family contains the eukaryotic NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) (EC:1.6.5.3). This is approximately 100 residues long, and forms part of a multiprotein complex that resides on the inner mitochondrial membrane. The main function of the complex is the transport of electrons from NADH to ubiquinone, accompanied by translocation of protons from the mitochondrial matrix to the intermembrane space  .. 
PF07348 Syd protein (SUKH-2)<br>Vella Briffa B, Zhang D, Aravind L. Pfam-B_19909 (release 10.0). This family contains a number of bacterial Syd proteins approximately 180 residues long. It has been suggested that Syd is loosely associated with the cytoplasmic surface of the cytoplasmic membrane, and that interaction with SecY may be involved in this membrane association  . Operon analysis showed that Syd protein may function as immunity protein in bacterial toxin systems  .. 
PF07349 Protein of unknown function (DUF1478)<br>Pfam-B_20105 (release 10.0). This family consists of several hypothetical Sapovirus proteins of around 165 residues in length. The function of this family is unknown.. 
PF07350 Protein of unknown function (DUF1479)<br>Pfam-B_20226 (release 10.0). This family consists of several hypothetical Enterobacterial proteins, of around 420 residues in length. Members of this family are often known as YbiU. The function of this family is unknown.. 
PF07351 Protein of unknown function (DUF1480)<br>Pfam-B_20253 (release 10.0). This family consists of several hypothetical Enterobacterial proteins of around 80 residues in length. The function of this family is unknown.. 
PF07352 Bacteriophage Mu Gam like protein<br>Pfam-B_19455 (release 10.0). This family consists of bacterial and phage Gam proteins. The gam gene of bacteriophage Mu encodes a protein which protects linear double stranded DNA from exonuclease degradation in vitro and in vivo  .. 
PF07353 Uroplakin II<br>Pfam-B_19993 (release 10.0). This family contains uroplakin II, which is approximately 180 residues long and seems to be restricted to mammals. Uroplakin II is an integral membrane protein, and is one of the components of the apical plaques of mammalian urothelium formed by the asymmetric unit membrane - this is believed to play a role in strengthening the urothelial apical surface to prevent the cells from rupturing during bladder distension  .. 
PF07354 Zona-pellucida-binding protein (Sp38)<br>Pfam-B_19996 (release 10.0). This family contains a number of zona-pellucida-binding proteins that seem to be restricted to mammals. These are sperm proteins that bind to the 90-kDa family of zona pellucida glycoproteins in a calcium-dependent manner  . These represent some of the specific molecules that mediate the first steps of gamete interaction, allowing fertilisation to occur  .. 
PF07355 Glycine/sarcosine/betaine reductase selenoprotein B (GRDB)<br>Pfam-B_19711 (release 10.0). This family represents a conserved region approximately 350 residues long within the selenoprotein B component of the bacterial glycine, sarcosine and betaine reductase complexes.. 
PF07356 Protein of unknown function (DUF1481)<br>Pfam-B_20042 (release 10.0). This family consists of several hypothetical bacterial proteins of around 230 residues in length. Members of this family are often referred to as YjaH and are found in the Orders Vibrionales and Enterobacteriales. The function of this family is unknown.. 
PF07357 Dinitrogenase reductase ADP-ribosyltransferase (DRAT)<br>Pfam-B_20108 (release 10.0). This family consists of several bacterial dinitrogenase reductase ADP-ribosyltransferase (DRAT) proteins. Members of this family seem to be specific to Rhodospirillum, Rhodobacter and Azospirillum species. Dinitrogenase reductase ADP-ribosyl transferase (DRAT) carries out the transfer of the ADP-ribose from NAD to the Arg-101 residue of one subunit of the dinitrogenase reductase homodimer, resulting in inactivation of that enzyme. Dinitrogenase reductase-activating glycohydrolase (DRAG) removes the ADP-ribose group attached to dinitrogenase reductase, thus restoring nitrogenase activity. The DRAT-DRAG system negatively regulates nitrogenase activity in response to exogenous NH4+ or energy limitation in the form of a shift to darkness or to anaerobic conditions  .. 
PF07358 Protein of unknown function (DUF1482)<br>Pfam-B_20128 (release 10.0). This family consists of several Enterobacterial proteins of around 60 residues in length. The function of this family is unknown.. 
PF07359 Liver-expressed antimicrobial peptide 2 precursor (LEAP-2)<br>Pfam-B_20235 (release 10.0). This family consists of several mammalian liver-expressed antimicrobial peptide 2 (LEAP-2) sequences. LEAP-2 is a cysteine-rich, and cationic protein. LEAP-2 contains a core structure with two disulfide bonds formed by cysteine residues in relative 1-3 and 2-4 positions. LEAP-2 is synthesised as a 77-residue precursor, which is predominantly expressed in the liver and highly conserved among mammals. The largest native LEAP-2 form of 40 amino acid residues is generated from the precursor at a putative cleavage site for a furin-like endoprotease. In contrast to smaller LEAP-2 variants, this peptide exhibits dose-dependent antimicrobial activity against selected microbial model organisms  . The exact function of this family is unclear.. 
PF07361 Cytochrome_b562;<br>Pfam-B_18074 (release 10.0). This family contains the bacterial cytochrome b562. This forms a four-helix bundle that non-covalently binds a single heme prosthetic group.  .. 
PF07362 Post-segregation antitoxin CcdA<br>Pfam-B_20349 (release 10.0). This family consists of several Enterobacterial post-segregation antitoxin CcdA proteins. The F plasmid-carried bacterial toxin, the CcdB protein, is known to act on DNA gyrase in two different ways. CcdB poisons the gyrase-DNA complex, blocking the passage of polymerases and leading to double-strand breakage of the DNA. Alternatively, in cells that overexpress CcdB, the A subunit of DNA gyrase (GyrA) has been found as an inactive complex with CcdB. Both poisoning and inactivation can be prevented and reversed in the presence of the F plasmid-encoded antidote, the CcdA protein  .. 
PF07363 Protein of unknown function (DUF1484)<br>Pfam-B_20389 (release 10.0). This family consists of several hypothetical bacterial proteins of around 110 residues in length. Members of this family appear to be found exclusively in Ralstonia solanacearum. The function of this family is unknown.. 
PF07364 Protein of unknown function (DUF1485)<br>Pfam-B_20495 (release 10.0). This family consists of several hypothetical bacterial proteins of around 300 residues in length. Members of this family all appear to be in the Phylum Proteobacteria. The function of this family is unknown.. 
PF07365 Alpha conotoxin precursor<br>Pfam-B_20562 (release 10.0). This family consists of several alpha conotoxin precursor proteins from a number of Conus species. The alpha-conotoxins are small peptide neurotoxins from the venom of fish-hunting cone snails which block nicotinic acetylcholine receptors (nAChRs)  . . 
PF07366 DUF1486; <br>SnoaL-like polyketide cyclase. Pfam-B_20348 (release 10.0), Pfam-B_4335 (release 18.0). This family includes SnoaL   a polyketide cyclase involved in nogalamycin biosynthesis. This family was formerly known as DUF1486.  The proteins in this family adopt a distorted alpha-beta barrel fold  .  Structural data together with site-directed mutagenesis experiments have shown that SnoaL has a different mechanism to that of the classical aldolase for catalysing intramolecular aldol condensation  .. 
PF07367 Fungal fruit body lectin<br>Pfam-B_20370 (release 10.0). This family consists of several fungal fruit body lectin proteins. Fruit body lectins are thought to have insecticidal activity [1,2] and may also function in capturing nematodes  . . 
PF07368 Protein of unknown function (DUF1487)<br>Pfam-B_20425 (release 10.0). This family consists of several uncharacterised proteins from Drosophila melanogaster. The function of this family is unknown.. 
PF07369 Protein of unknown function (DUF1488)<br>Pfam-B_20604 (release 10.0). This family consists of several hypothetical bacterial proteins of around 85 residues in length. The function of this family is unknown.. 
PF07370 Protein of unknown function (DUF1489)<br>Pfam-B_20654 (release 10.0). This family consists of several hypothetical bacterial proteins of around 150 residues in length. Members of this family seem to be founds exclusively in the Class Alphaproteobacteria. The function of this family is unknown.. 
PF07371 Protein of unknown function (DUF1490)<br>Pfam-B_20678 (release 10.0). This family consists of several hypothetical bacterial proteins of around 90 residues in length. Members of the family seem to be found exclusively in Mycobacterium species. The function of this family is unknown.. 
PF07372 Protein of unknown function (DUF1491)<br>Pfam-B_20742 (release 10.0). This family consists of several bacterial proteins of around 115 residues in length. Members of this family seem to be found exclusively in the Class Alphaproteobacteria. The function of this family is unknown.. 
PF07373 CAMP factor (Cfa)<br>Pfam-B_20762 (release 10.0). This family consists of several bacterial CAMP factor (Cfa) proteins which seem to be specific to Streptococcus species. The CAMP reaction is a synergistic lysis of erythrocytes by the interaction of an extracellular protein (CAMP factor) produced by some streptococcal species with the Staphylococcus aureus sphingomyelinase C (beta-toxin)  . . 
PF07374 Protein of unknown function (DUF1492)<br>Pfam-B_20776 (release 10.0). This family consists of several hypothetical, highly conserved Streptococcal and related phage proteins of around 100 residues in length.  The function of this family is unknown. It appears to be distantly related to Pfam:PF08281.. 
PF07376 Prosystemin<br>Pfam-B_20835 (release 10.0). This family consists of several plant specific prosystemin proteins. Prosystemin is the precursor protein of the 18 amino acid wound signal systemin which activates systemic defence in plant leaves against insect herbivores  .. 
PF07377 Protein of unknown function (DUF1493)<br>Pfam-B_20460 (release 10.0). This family consists of several bacterial proteins of around 115 residues in length. Members of this family seem to be found exclusively in Salmonella and Yersinia species and several have been described as being putative cytoplasmic proteins. The function of this family is unknown.. 
PF07378 Flagellar protein FlbT<br>Pfam-B_20574 (release 10.0). This family consists of several FlbT proteins. FlbT is a post-transcriptional regulator of flagellin. FlbT is associated with the 5' untranslated region (UTR) of fljK (25 kDa flagellin) mRNA and that this association requires a predicted loop structure in the transcript. Mutations within this loop abolish FlbT association and result in increased mRNA stability. It is therefore thought that FlbT promotes the degradation of flagellin mRNA by associating with the 5' UTR  .. 
PF07379 Protein of unknown function (DUF1494)<br>Pfam-B_20601 (release 10.0). This family consists of several bacterial proteins of around 175 residues in length. Members of this family seem to be found exclusively in Chlamydia species. The function of this family is unknown.. 
PF07380 Pneumovirus M2 protein<br>Pfam-B_20478 (release 10.0). This family consists of several Pneumovirus M2 proteins. The M2-1 protein of respiratory syncytial virus (RSV) is a transcription processivity factor that is essential for virus replication  .. 
PF07381 Winged helix DNA-binding domain (DUF1495)<br>Pfam-B_20509 (release 10.0). This family consists of several hypothetical archaeal proteins of around 110 residues in length. The structure of this domain possesses a winged helix DNA-binding domain suggesting these proteins are bacterial transcription factors.. 
PF07382 Histone H1-like nucleoprotein HC2<br>Pfam-B_20179 (release 10.0). This family contains the bacterial histone H1-like nucleoprotein HC2 (approximately 200 residues long), which seems to be found mostly in Chlamydia. HC2 functions in DNA condensation, although it has been suggested that it also has other roles  .. 
PF07383 Protein of unknown function (DUF1496)<br>Pfam-B_20554 (release 10.0). This family consists of several bacterial proteins of around 90 residues in length. Members of this family seem to be found exclusively in the Orders Vibrionales and Enterobacteriales. The function of this family is unknown.. 
PF07384 Protein of unknown function (DUF1497)<br>Pfam-B_20585 (release 10.0). This family consists of several phage and bacterial proteins of around 59 residues in length. Members of this family seem to be found exclusively in Lactococcus lactis and the bacteriophages that infect this organism. The function of this family is unknown.. 
PF07385 Protein of unknown function (DUF1498)<br>Pfam-B_20610 (release 10.0). This family consists of several hypothetical bacterial proteins of around 225 residues in length. The function of this family is unknown.. 
PF07386 Protein of unknown function (DUF1499)<br>Pfam-B_20643 (release 10.0). This family consists of several hypothetical bacterial and plant proteins of around 125 residues in length. The function of this family is unknown.. 
PF07387 Seadornavirus VP7<br>Pfam-B_20657 (release 10.0). This family consists of several Seadornavirus specific VP7 proteins of around 305 residues in length. The function of this family is unknown. However, it appears to be distantly related to protein kinases.. 
PF07388 Alpha-2,8-polysialyltransferase (POLYST)<br>Pfam-B_20294 (release 10.0). This family contains the bacterial enzyme alpha-2,8-polysialyltransferase (EC:2.4.99.-) (approximately 500 residues long). This catalyses the polycondensation of alpha-2,8-linked sialic acid required for the synthesis of polysialic acid (PSA)  .. 
PF07389 Protein of unknown function (DUF1500)<br>Pfam-B_20659 (release 10.0). This family consists of several Orthopoxvirus specific proteins of around 100 residues in length. The function of this family is unknown.. 
PF07390 Mycoplasma P30 protein<br>Pfam-B_20617 (release 10.0). This family consists of several P30 proteins which seem to be specific to Mycoplasma agalactiae. P30 is a 30-kDa immunodominant antigen and is known to be a transmembrane protein  .. 
PF07391 NPR nonapeptide repeat (2 copies)<br>This nine residue repeat which I have called NPR after NonaPeptide Repeat.  It is found in two malarial proteins and has the consensus EEhhEEhhP where h stands for a hydrophobic amino acid.. 
PF07392 Cyclin-dependent kinase inhibitor 2a p19Arf N-terminus<br>Pfam-B_20449 (release 10.0). This family represents the N-terminus (approximately 50 residues) of  cyclin-dependent kinase inhibitor 2a p19Arf, which seems to be restricted to mammals. This is a tumour-suppressor protein that has been shown to inhibit the growth of human tumour cells lacking functional p53 by inducing a transient G2 arrest and subsequently apoptosis  .. 
PF07393 Exocyst complex component Sec10<br>Pfam-B_20545 (release 10.0). This family contains the Sec10 component (approximately 650 residues long) of the eukaryotic exocyst complex, which specifically affects the synthesis and delivery of secretory and basolateral plasma membrane proteins  .. 
PF07394 Protein of unknown function (DUF1501)<br>Pfam-B_20578 (release 10.0). This family contains a number of hypothetical bacterial proteins of unknown function approximately 400 residues long.. 
PF07395 Mig-14<br>Pfam-B_20642 (release 10.0). This family contains a number of bacterial mig-14 proteins (approximately 270 residues long). In Salmonella, mig-14 contributes to resistance to antimicrobial peptides, although the mechanism is not fully understood  .. 
PF07396 Phosphate-selective porin O and P<br>Pfam-B_20808 (release 10.0). This family represents a conserved region approximately 400 residues long within the bacterial phosphate-selective porins O and P. These are anion-specific porins, the binding site of which has a higher affinity for phosphate than chloride ions. Porin O has a higher affinity for polyphosphates, while porin P has a higher affinity for orthophosphate  . In P. aeruginosa, porin O was found to be expressed only under phosphate-starvation conditions during the stationary growth phase  .. 
PF07397 Repeat of unknown function (DUF1502)<br>Pfam-B_20836 (release 10.0). This family consists of a number of repeats of around 34 residues in length. Members of this family seem to be found exclusively in three hypothetical Murid herpesvirus 4 proteins. The function of this family is unknown.. 
PF07398 MDMPI C-terminal domain<br>Pfam-B_20685 (release 10.0). This domain is found at the C-terminus of the mycothiol maleylpyruvate isomerase enzyme (MDMPI). The structure of this protein has been solved  . This domain appears weakly similar to Pfam:PF08608.. 
PF07399 Protein of unknown function (DUF1504)<br>Pfam-B_20945 (release 10.0). This family consists of several hypothetical bacterial proteins of around 440 residues in length. The function of this family is unknown.. 
PF07400 Interleukin 11<br>Pfam-B_20854 (release 10.0). This family contains interleukin 11 (approximately 200 residues long). This is a secreted protein that stimulates megakaryocytopoiesis, resulting in increased production of platelets, as well as activating osteoclasts, inhibiting epithelial cell proliferation and apoptosis, and inhibiting macrophage mediator production. These functions may be particularly important in mediating the hematopoietic, osseous and mucosal protective effects of interleukin 11  . Family members seem to be restricted to mammals.. 
PF07401 Bovine Lentivirus VIF protein<br>Pfam-B_21067 (release 10.0). This family consists of several Lentivirus viral infectivity factor (VIF) proteins. VIF is known to be essential for ability of cell-free virus preparation to infect cells  . Members of this family are specific to  Bovine immunodeficiency virus (BIV) and Jembrana disease virus which also infects cattle.. 
PF07402 Human herpesvirus U26 protein<br>Pfam-B_21150 (release 10.0). This family consists of several Human herpesvirus U26 proteins of around 300 residues in length. The function of this family is unknown.. 
PF07403 Protein of unknown function (DUF1505)<br>Pfam-B_21179 (release 10.0). This family consists of several uncharacterised Caenorhabditis elegans proteins of around 115 resides in length. Members of this family contain 6 highly conserved cysteine residues. The function of this family is unknown.. 
PF07404 Telomere-binding protein beta subunit (TEBP beta)<br>Pfam-B_20928 (release 10.0). This family consists of several telomere-binding protein beta subunits which appear to be specific to the family Oxytrichidae. Telomeres are specialised protein-DNA complexes that compose the ends of eukaryotic chromosomes. Telomeres protect chromosome termini from degradation and recombination and act together with telomerase to ensure complete genome replication. TEBP beta forms a complex with TEBP alpha and this complex is able to recognise and bind ssDNA to form a sequence-specific, telomeric nucleoprotein complex that caps the very 3' ends of chromosomes  . . 
PF07405 Protein of unknown function (DUF1506)<br>Pfam-B_20962 (release 10.0). This family consists of several bacterial proteins of around 130 residues in length. Members of this family seem to be specific to Borrelia burgdorferi (Lyme disease spirochete). The function of this family is unknown.. 
PF07406 NICE-3 protein<br>Pfam-B_21003 (release 10.0). This family consists of several eukaryotic NICE-3 and related proteins. The gene coding for NICE-3 is part of the epidermal differentiation complex (EDC) which comprises a large number of genes that are of crucial importance for the maturation of the human epidermis  . The function of NICE-3 is unknown.. 
PF07407 Seadornavirus VP6 protein<br>Pfam-B_21021 (release 10.0). This family consists of several VP6 proteins from the Banna virus as well as a related protein VP5 from the Kadipiro virus. Members of this family are typically of around 420 residues in length. The function of this family is unknown.. 
PF07408 Protein of unknown function (DUF1507)<br>Pfam-B_21047 (release 10.0). This family consists of several hypothetical bacterial proteins of around 90 residues in length. The function of this family is unknown.. 
PF07409 Phage protein GP46<br>Pfam-B_20855 (release 10.0). This family contains GP46 phage proteins (approximately 120 residues long).. 
PF07410 Streptococcus thermophilus bacteriophage Gp111 protein<br>Pfam-B_20904 (release 10.0). This family consists of several Streptococcus thermophilus bacteriophage Gp111 proteins of around 110 residues in length. The function of this family is unknown.. 
PF07411 Domain of unknown function (DUF1508)<br>Pfam-B_20853 (release 10.0). This family represents a series of bacterial domains of unknown function of around 50 residues in length. Members of this family are often found as tandem repeats and in some cases represent the whole protein. All member proteins are described as being hypothetical.. 
PF07412 Geminin<br>Pfam-B_20861 (release 10.0). This family contains the eukaryotic protein geminin (approximately 200 residues long). Geminin inhibits DNA replication by preventing the incorporation of MCM complex into prereplication complex, and is degraded during the mitotic phase of the cell cycle. It has been proposed that geminin inhibits DNA replication during S, G2, and M phases and that geminin destruction at the metaphase-anaphase transition permits replication in the succeeding cell cycle  .. 
PF07413 Herpes_UL37; <br>Betaherpesvirus immediate-early glycoprotein UL37. Pfam-B_21151 (release 10.0). This family consists of several Betaherpesvirus immediate-early glycoprotein UL37 sequences. The human cytomegalovirus (HCMV) UL37 immediate-early regulatory protein is a type I integral membrane N-glycoprotein which traffics through the ER and the Golgi network  .. 
PF07415 Gammaherpesvirus latent membrane protein (LMP2) protein<br>Pfam-B_21212 (release 10.0). This family consists of several Gammaherpesvirus latent membrane protein (LMP2) proteins. Epstein-Barr virus is a human Gammaherpesvirus that infects and establishes latency in B lymphocytes in vivo. The latent membrane protein 2 (LMP2) gene is expressed in latently infected B cells and encodes two protein isoforms, LMP2A and LMP2B, that are identical except for an additional N-terminal 119 aa cytoplasmic domain which is present in the LMP2A isoform. LMP2A is thought to play a key role in either the establishment or the maintenance of latency and/or the reactivation of productive infection from the latent state. The significance of LMP2B and its role in pathogenesis remain unclear  .. 
PF07416 Crinivirus P26 protein<br>Pfam-B_21324 (release 10.0). This family consists of several Crinivirus P26 proteins which seem to be found exclusively in the Lettuce infectious yellows virus. The function of this family is unknown.. 
PF07417 Transcriptional regulator Crl<br>Pfam-B_20900 (release 10.0). This family contains the bacterial transcriptional regulator Crl (approximately 130 residues long). This is a transcriptional regulator of the csgA curlin subunit gene for curli fibres that are found on the surface of certain bacteria  .. 
PF07418 Acidic phosphoprotein precursor PCEMA1<br>Pfam-B_20971 (release 10.0). This family consists of several acidic phosphoprotein precursor PCEMA1 sequences which appear to be found exclusively in Plasmodium chabaudi. PCEMA1 is an antigen that is associated with the membrane of the infected erythrocyte throughout the entire intraerythrocytic cycle  . The exact function of this family is unclear. . 
PF07419 PilM<br>Pfam-B_20906 (release 10.0). This family contains the bacterial protein PilM (approximately 150 residues long). PilM is an inner membrane protein that has been predicted to function as a component of the pilin transport apparatus and thin-pilus basal body  .. 
PF07420 Protein of unknown function (DUF1509)<br>Pfam-B_21379 (release 10.0). This family consists of several uncharacterised viral proteins from the Marek's disease-like viruses. Members of this family are typically around 400 residues in length. The function of this family is unknown.. 
PF07421 Neurotensin/neuromedin N precursor<br>Pfam-B_20947 (release 10.0). This family contains the precursor of bacterial neurotensin/neuromedin N (approximately 170 residues long). This the common precursor of two biologically active related peptides, neurotensin and neuromedin N. It undergoes tissue-specific processing leading to the formation in some tissues and cancer cell lines of large peptides ending with the neurotensin or neuromedin N sequence  .. 
PF07422 Sexual stage antigen s48/45 domain<br>Pfam-B_21037 (release 10.0) and Pfam-B_4621 (release 14.0). This family contains sexual stage s48/45 antigens from Plasmodium (approximately 450 residues long). These are surface proteins expressed by Plasmodium male and female gametes that have been shown to play a conserved and important role in fertilisation  . This domain contains 6 conserved cysteines suggesting 3 disulphide bridges.. 
PF07423 Protein of unknown function (DUF1510)<br>Pfam-B_21355 (release 10.0). This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.. 
PF07424 TrbM<br>Pfam-B_21098 (release 10.0). This family contains the bacterial protein TrbM (approximately 180 residues long). In Comamonas testosteroni T-2, TrbM is derived from the IncP1beta plasmid pTSA, which encodes the widespread genes for p-toluenesulfonate (TSA) degradation  .. 
PF07425 Pardaxin<br>Pfam-B_21422 (release 10.0). This family consists of several Pardaxin proteins. Pardaxin, a 33-amino-acid pore-forming polypeptide toxin isolated from the Red Sea Moses sole Pardachirus marmoratus, has a helix-hinge-helix structure. This is a common structural motif found both in antibacterial peptides that can act selectively on bacterial membranes (e.g., cecropin), and in cytotoxic peptides that can lyse both mammalian and bacterial cells (e.g., melittin). Pardaxin possesses a high antibacterial activity with a significantly reduced haemolytic activity towards human red blood cells compared with melittin  . Pardaxin has also been found to have a shark repellent action  .. 
PF07426 Dynactin subunit p22<br>Pfam-B_21336 (release 10.0). This family contains p22, the smallest subunit of dynactin, a complex that binds to cytoplasmic dynein and is a required activator for cytoplasmic dynein-mediated vesicular transport. Dynactin localises to the cleavage furrow and to the midbodies of dividing cells, suggesting that it may function in cytokinesis  . Family members are approximately 170 residues long.. 
PF07428 15-O-acetyltransferase Tri3<br>Pfam-B_21449 (release 10.0). This family represents a conserved region approximately 400 residues long within 15-O-acetyltransferase (Tri3), which seems to be restricted to ascomycete fungi. In Fusarium sporotrichioides, this is required for acetylation of the C-15 hydroxyl group of trichothecenes in the biosynthesis of T-2 toxin  .. 
PF07429 Fuc4NAc_transf;<br>4-alpha-L-fucosyltransferase glycosyl transferase group 56. Pfam-B_21451 (release 10.0). This family contains the bacterial enzyme 4-alpha-L-fucosyltransferase (Fuc4NAc transferase) (EC 2.4.1.-) (approximately 360 residues long). This catalyses the synthesis of Fuc4NAc-ManNAcA-GlcNAc-PP-Und (lipid III) as part of the biosynthetic pathway of enterobacterial common antigen (ECA), a polysaccharide comprised of the trisaccharide repeat unit Fuc4NAc-ManNAcA-GlcNAc  .. 
PF07430 Phloem filament protein PP1<br>Pfam-B_20843 (release 10.0). This family represents a conserved region approximately 200 residues long, four copies of which are found within the plant phloem filament protein PP1. This is one of the constituents of the proteinaceous filaments found in the sieve elements of Cucurbita phloem  .. 
PF07431 Protein of unknown function (DUF1512)<br>Pfam-B_21354 (release 10.0). This family consists of several archaeal proteins of around 370 residues in length. The function of this family is unknown.. 
PF07432 Histone H1-like protein Hc1<br>Pfam-B_21362 (release 10.0). This family consists of several bacterial histone H1-like Hc1 proteins. In Chlamydia, Hc1 is expressed in the late stages of the life cycle, concomitant with the reorganisation of chlamydial reticulate bodies into elementary bodies. This suggests that Hc1 protein plays a role in the condensation of chromatin during intracellular differentiation  .. 
PF07433 Protein of unknown function (DUF1513)<br>Pfam-B_21436 (release 10.0). This family consists of several bacterial proteins of around 360 residues in length. The function of this family is unknown.. 
PF07434 CblD like pilus biogenesis initiator<br>Pfam-B_21452 (release 10.0). This family consists of several minor pilin proteins including CblD from Burkholderia cepacia which is known to CblD be the initiator of pilus biogenesis  . The family also contains a variety of Enterobacterial minor pilin proteins.. 
PF07435 YycH protein<br>Vella Briffa B, Szurmant H, Mistry J. Pfam-B_21457 (release 10.0). This family contains the bacterial protein YycH which is approximately 450 residues long. YycH plays a role in signal transduction and is found immediately downstream of the essential histidine kinase YycG.  YycG forms a two component system together with its cognate response regulator YycF. PhoA fusion studies have shown that YycH is transported across the cytoplasmic protein. It is postulated that YycH functions as an antagonist to YycG  . The molecule is made up of three domains, and has a novel three-dimensional structure. The N-terminal domain features a calcium binding site and the central domain contains two conserved loop regions  .. 
PF07436 Curtovirus V3 protein<br>Pfam-B_21777 (release 10.0). This family consists of several Curtovirus V3 proteins of around 90 residues in length. The function of this family is unknown.. 
PF07437 YfaZ_precursor; <br>Pfam-B_21552 (release 10.0). This family contains the precursor of the bacterial protein YfaZ  (approximately 180 residues long). Many members of this family are hypothetical proteins.. 
PF07438 Protein of unknown function (DUF1514)<br>Moxon SJ, Eberhardt R. Pfam-B_21857 (release 10.0). This family consists of several Staphylococcus aureus and related bacteriophage proteins of around 65 residues in length. The function of this family is unknown. Structural modelling suggests this domain may bind nucleic acids  .. 
PF07439 Protein of unknown function (DUF1515)<br>Pfam-B_21875 (release 10.0). This family consists of several hypothetical bacterial proteins of around 130 residues in length. Members of this family seem to be found exclusively in Rhizobium species. The function of this family is unknown.. 
PF07440 Caerin 1 protein<br>Pfam-B_22039 (release 10.0). This family consists of several caerin 1 proteins from Litoria species. The caerin 1 peptides are among the most powerful of the broad-spectrum antibiotic amphibian peptides  .. 
PF07441 SigmaK-factor processing regulatory protein BofA<br>Pfam-B_21773 (release 10.0). This family contains the sigmaK-factor processing regulatory protein BofA (Bypass-of-forespore protein A) (approximately 80 residues long). During sporulation in Bacillus subtilis, transcription is controlled in the developing sporangium by a cascade of sporulation-specific transcription factors (sigma factors). Following engulfment, processing of sigmaK is inhibited by BofA. It has been suggested that this effect is exerted by alteration of the level of the SpoIVFA protein  .. 
PF07442 Ponericin<br>Pfam-B_21790 (release 10.0). This family contains a number of ponericin peptides (approximately 30 residues long) from the venom of the predatory ant Pachycondyla goeldii. These peptides exhibit antibacterial and insecticidal properties, and may adopt an amphipathic alpha-helical structure in polar environments such as cell membranes  .. 
PF07444 Ycf66 protein N-terminus<br>Pfam-B_21840 (release 10.0). This family represents the N-terminus (approximately 80 residues) of Ycf66, a protein that seems to be restricted to eukaryotes that contain chloroplasts and to cyanobacteria.. 
PF07445 Primosomal replication protein priB and priC<br>Pfam-B_22037 (release 10.0). This family contains the bacterial primosomal replication proteins priB and priC (approximately 180 residues long). In Escherichia coli, these function in the assembly of the primosome  .. 
PF07447 Matrix protein VP40<br>Pfam-B_22295 (release 10.0). This family contains viral VP40 matrix proteins that seem to be restricted to the Filoviridae. These play an important role in the assembly process of virus particles by interacting with cellular factors, cellular membranes, and the ribonuclearprotein particle complex. It has been shown that the N-terminal region of VP40 folds into a mixture of hexameric and octameric states - these may have distinct roles  .. 
PF07448 Secreted phosphoprotein 24 (Spp-24)<br>Pfam-B_22318 (release 10.0). This family represents a conserved region approximately 140 residues long within secreted phosphoprotein 24 (Spp-24), which seems to be restricted to vertebrates. This is a non-collagenous protein found in bone that is related in sequence to the cystatin family of thiol protease inhibitors. This suggests that Spp-24 could function to modulate the thiol protease activities known to be involved in bone turnover. It is also possible that the intact form of Spp-24 found in bone could be a precursor to a biologically active peptide that coordinates an aspect of bone turnover  .. 
PF07449 Hydrogenase-1 expression protein HyaE<br>Pfam-B_21851 (release 10.0). This family contains bacterial hydrogenase-1 expression proteins approximately 120 residues long. This includes the E. coli protein HyaE, and the homologous proteins HoxO of R. eutropha and HupG of R. leguminosarum. Deletion of the hoxO gene in R. eutropha led to complete loss of the uptake [NiFe] hydrogenase activity, suggesting that it has a critical role in hydrogenase assembly  .. 
PF07450 Formate hydrogenlyase maturation protein HycH<br>Pfam-B_22086 (release 10.0). This family contains the bacterial formate hydrogenlyase maturation protein HycH, which is approximately 140 residues long. This may be required for the conversion of a precursor form of the large subunit of hydrogenlyase 3 into a mature form  .. 
PF07451 Stage V sporulation protein AD (SpoVAD)<br>Pfam-B_22130 (release 10.0). This family contains the bacterial stage V sporulation protein AD (SpoVAD), which is approximately 340 residues long. This is one of six proteins encoded by the spoVA operon, which is transcribed exclusively in the forespore at about the time of dipicolinic acid (DPA) synthesis in the mother cell. The functions of the proteins encoded by the spoVA operon are unknown, but it has been suggested they are involved in DPA transport during sporulation  .. 
PF07452 CHRD domain<br>CHRD (after SWISS-PROT abbreviation for chordin) is a novel domain identified in chordin, an inhibitor of bone morphogenetic proteins.  This family includes bacterial homologues. It is anticipated to have an immunoglobulin-like beta-barrel structure based on limited similarity to superoxide dismutases but, as yet, no clear functional prediction can be made. Its most conserved feature is a GE[I/L]RCG[V/I/L] motif towards its C-terminal end Most bacterial proteins in this family have only one CHRD domain, whereas it is found repeated in many eukaryotic proteins such as human chordin (Swiss:Q9H2X0) and Drosophila SOG (Swiss:Q24025).  .. 
PF07453 NUMOD1 domain<br>
PF07454 Stage II sporulation protein P (SpoIIP)<br>Pfam-B_21650 (release 10.0). This family contains the bacterial stage II sporulation protein P (SpoIIP) (approximately 350 residues long). It has been shown that a block in polar cytokinesis in Bacillus subtilis is mediated partly by transcription of spoIID, spoIIM and spoIIP. This inhibition of polar division is involved in the locking in of asymmetry after the formation of a polar septum during sporulation  . Engulfment in Bacillus subtilis is mediated by two complementary systems: the first includes the proteins SpoIID, SpoIIM and SpoIIP (DMP) which carry out the engulfment, and the second includes the SpoIIQ-SpoIIIAGH (Q-AH) zipper, that recruits other proteins to the septum in a second-phase of the engulfment. The course of events follows as the incorporation firstly of SpoIIB into the septum during division to serve directly or indirectly as a landmark for localising SpoIIM and then SpoIIP and SpoIID to the septum. SpoIIP and SpoIID interact together to form part of the DMP complex  . SpoIIP itself has been identified as an autolysin with peptidoglycan hydrolase activity  .. 
PF07455 Phage polarity suppression protein (Psu)<br>Pfam-B_21666 (release 10.0). This family contains a number of phage polarity suppression proteins (Psu) (approximately 190 residues long). The Psu protein of bacteriophage P4 causes suppression of transcriptional polarity in Escherichia coli by overcoming Rho termination factor activity  .. 
PF07456 Heptaprenyl diphosphate synthase component I<br>Pfam-B_22032 (release 10.0). This family contains component I of bacterial heptaprenyl diphosphate synthase (EC:2.5.1.30) (approximately 170 residues long). This is one of the two dissociable subunits that form the enzyme, both of which are required for the catalysis of the biosynthesis of the side chain of menaquinone-7  .. 
PF07457 Protein of unknown function (DUF1516)<br>Pfam-B_22136 (release 10.0). This family contains a number of hypothetical bacterial proteins of unknown function approximately 120 residues long.. 
PF07458 Sperm protein associated with nucleus, mapped to X chromosome<br>Pfam-B_22197 (release 10.0). This family contains human sperm proteins associated with the nucleus and mapped to the X chromosome (SPAN-X) (approximately 100 residues long). SPAN-X proteins are cancer-testis antigens (CTAs), and thus represent potential targets for cancer immunotherapy because they are widely distributed in tumours but not in normal tissues, except testes. They are highly insoluble, acidic, and polymorphic  .. 
PF07459 CTX phage RstB protein<br>Pfam-B_22203 (release 10.0). This family contains a number of RstB proteins approximately 120 residues long, including RstB1 and RstB2, from the Vibrio cholerae phage CTX. Functional analyses indicate that rstB2 is required for integration of the CTXphi phage into the V. cholerae chromosome  .. 
PF07460 NUMOD3 motif (2 copies)<br>NUMOD3 is a DNA-binding motif found in homing endonucleases and related proteins. It occurs on its own or in tandem repeats in GIY-YIG (Pfam:PF01541) and HTH proteins. It constitutes a beta-turn-loop-helix subregion of the the DNA-binding domain of I-TevI homing endonuclease (Swiss:P13299)  .. 
PF07461 Nicotine adenine dinucleotide glycohydrolase (NADase)<br>Pfam-B_21586 (release 10.0). This family consists of several bacterial nicotine adenine dinucleotide glycohydrolase (NGA) proteins which appear to be specific to Streptococcus pyogenes. NAD glycohydrolase (NADase) is a potential virulence factor. Streptococcal NADase may contribute to virulence by its ability to cleave beta-NAD at the ribose-nicotinamide bond, depleting intracellular NAD pools and producing the potent vasoactive compound nicotinamide  .. 
PF07462 Merozoite surface protein 1 (MSP1) C-terminus<br>Pfam-B_21542 (release 10.0). This family represents the C-terminal region of merozoite surface protein 1 (MSP1) which are found in a number of Plasmodium species. MSP-1 is a 200-kDa protein expressed on the surface of the P. vivax merozoite. MSP-1 of Plasmodium species is synthesised as a high-molecular-weight precursor and then processed into several fragments. At the time of red cell invasion by the merozoite, only the 19-kDa C-terminal fragment (MSP-119), which contains two epidermal growth factor-like domains, remains on the surface. Antibodies against MSP-119 inhibit merozoite entry into red cells, and immunisation with MSP-119 protects monkeys from challenging infections. Hence, MSP-119 is considered a promising vaccine candidate  .. 
PF07463 NUMOD4 motif<br>NUMOD4 is a putative DNA-binding motif found in homing endonucleases and related proteins  .. 
PF07464 Apolipophorin-III precursor (apoLp-III)<br>Pfam-B_31170 (release 10.0). This family consists of several insect apolipoprotein-III sequences. Exchangeable apolipoproteins constitute a functionally important family of proteins that play critical roles in lipid transport and lipoprotein metabolism. Apolipophorin III (apoLp-III) is a prototypical exchangeable apolipoprotein found in many insect species that functions in transport of diacylglycerol (DAG) from the fat body lipid storage depot to flight muscles in the adult life stage  .. 
PF07465 Photosystem I protein M (PsaM)<br>Pfam-B_21548 (release 10.0). This family consists of several plant and cyanobacterial photosystem I protein M (PsaM) sequences. PsaM forms part of the photosystem I complex and its binding is stabilised by PsaI  .. 
PF07466 Protein of unknown function (DUF1517)<br>Pfam-B_22018 (release 10.0). This family consists of several hypothetical glycine rich plant and bacterial proteins of around 300 residues in length. The function of this family is unknown.. 
PF07467 Beta-lactamase inhibitor (BLIP)<br>Pfam-B_41444 (release 10.0). The structure of BLIP reveals two structural domains, which form a polar, concave surface that docks onto a predominantly polar, convex protrusion on beta-lactamase. The ability of BLIP to adapt to a variety of class A beta-lactamases is thought to be due to flexibility between these two domains  .. 
PF07468 Agglutinin<br>Pfam-B_57133 (release 10.0). 
PF07469 Domain of unknown function (DUF1518) <br>Pfam-B_1525 (release 10.0). This domain, which is usually found tandemly repeated, is found various receptor co-activating proteins.. 
PF07470 Glycosyl Hydrolase Family 88<br>Pfam-B_10896 (release 10.0). Unsaturated glucuronyl hydrolase catalyses the hydrolytic release of  unsaturated glucuronic acids from oligosaccharides (EC:3.2.1.-) produced by the reactions of polysaccharide lyases  . . 
PF07471 Phage DNA packaging protein Nu1<br>Pfam-B_11430 (release 10.0). Terminase, the DNA packaging enzyme of bacteriophage lambda, is a  heteromultimer composed of subunits Nu1 and A.  The smaller  Nu1 terminase subunit has  a low-affinity ATPase stimulated by non-specific DNA  . . 
PF07472 Fucose-binding lectin II (PA-IIL)<br>Pfam-B_17609 (release 10.0). In Pseudomonas aeruginosa the fucose-binding lectin II (PA-IIL) contributes to the pathogenic virulence of the bacterium. PA-IIL functions as a tetramer when binding fucose. Each monomer is comprised of a nine-stranded, antiparallel beta-sandwich arrangement and contains two calcium cations that mediate the binding of fucose in a recognition mode unique among carbohydrate-protein interactions  .. 
PF07473 Spasmodic peptide gm9a<br>Pfam-B_90829 (release 10.0). This family consists of several spasmodic peptide gm9a sequences. Conotoxin gm9a is a putative 27-residue polypeptide encoded by Conus gloriamaris and is known to be a homologue of the "spasmodic peptide", tx9a, isolated from the venom of the mollusk-hunting cone shell Conus textile  . Upon injection of this venom component, normal mice are converted into behavioural phenocopies of a well-known mutant, the spasmodic mouse  .. 
PF07474 G2F domain<br>Nidogen, an invariant component of basement membranes, is a multifunctional protein that interacts with most other major basement membrane proteins. The G2 fragment or (G2F domain) contains binding sites for collagen IV and perlecan. The structure is composed of an 11-stranded beta-barrel with a central helix. This domain is structurally related to that of green fluorescent protein Pfam:PF01353. A large surface patch on the beta-barrel is conserved in all metazoan nidogens.. 
PF07475 HPr Serine kinase C-terminal domain<br>This family represents the C terminal kinase domain of Hpr Serine/threonine kinase PtsK.  This kinase is  the sensor in a multicomponent phosphorelay system in control of carbon  catabolic repression in bacteria  .  This kinase in unusual in that it  recognises the tertiary structure of its target and is a member of a novel family unrelated to any previously described protein phosphorylating  enzymes  . X-ray analysis of the full-length crystalline enzyme from Staphylococcus xylosus at a resolution of 1.95 A shows the enzyme to consist of two clearly separated domains that are assembled in a hexameric structure resembling a three-bladed propeller  .. 
PF07476 Methylaspartate ammonia-lyase C-terminus<br>Methylaspartate ammonia-lyase EC:4.3.1.2 catalyses the second step of fermentation of glutamate. It is a homodimer. This family represents the C-terminal region of Methylaspartate ammonia-lyase and contains a TIM barrel fold similar to the Pfam:PF01188. This family represents the catalytic domain and contains a metal binding site  .. 
PF07477 Glycosyl hydrolase family 67 C-terminus<br>Alpha-glucuronidases, components of an ensemble of enzymes central to the recycling of photosynthetic biomass, remove the alpha-1,2 linked 4-O-methyl glucuronic acid from xylans. This family represents the C terminal region of alpha-glucuronidase which is mainly alpha-helical. It wraps around the catalytic domain (Pfam:PF07488), making additional interactions both with the N-terminal domain (Pfam:PF03648) of its parent monomer and also forming the majority of the dimer-surface with the equivalent C-terminal domain of the other monomer of the dimer  .. 
PF07478 D-ala D-ala ligase C-terminus<br>This family represents the C-terminal, catalytic domain of the D-alanine--D-alanine ligase enzyme EC:6.3.2.4. D-Alanine is one of the central molecules of the cross-linking step of peptidoglycan assembly. There are three enzymes involved in the D-alanine branch of peptidoglycan biosynthesis: the pyridoxal phosphate-dependent D-alanine racemase (Alr), the ATP-dependent D-alanine:D-alanine ligase (Ddl), and the ATP-dependent D-alanine:D-alanine-adding enzyme (MurF)  .. 
PF07479 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus<br>NAD-dependent glycerol-3-phosphate dehydrogenase (GPDH) catalyses the interconversion of dihydroxyacetone phosphate and L-glycerol-3-phosphate. This family represents the C-terminal substrate-binding domain  .. 
PF07481 Domain of Unknown Function (DUF1521)<br>This family of unknown function is found in a limited  set of Bradyrhizobium proteins. There appears to be a periodic -DG- motif in it.. 
PF07482 Domain of Unknown Function (DUF1522)<br>
PF07483 Tryptophan-rich Synechocystis species C-terminal domain<br>This domain is found at the C-terminus, normally between 2-3 copies, of a range of Synechocystis membrane proteins. This domain is fairly tryptophan rich as well. . 
PF07484 Phage Tail Collar Domain<br>This region is occasionally found in conjunction with Pfam:PF03335. Most of the family appear to be phage tail proteins; however some appear to be involved in other processes. For instance Swiss:Q03314 from Rhizobium leguminosarum may be involved in plant-microbe interactions ( ). A related protein Swiss:Q9L3N1 is involved in the pathogenicity of Microcystis aeruginosa. The finding of this family in a structural component of the phage tail fibre baseplate (Swiss:P10930) suggests that its function is structural rather than enzymatic. Structural studies show this region consists of a helix and a loop ( ) and three beta-strands. This alignment does not catch the third strand as it is separated from the rest of the structure by around 100 residues. This strand is conserved in homologues but the intervening sequence is not. Much of the function of Swiss:P10930 appears to reside in this intervening region. In the tertiary structure of the phage baseplate this domain forms part of the 'collar'. The domain may bind SO4, however the residues accredited with this vary between the PDB file and the Swiss-Prot entry. The long unconserved region maybe due to domain swapping in and out of a loop or reflective of rapid evolution. . 
PF07485 DUF1259; <br>Domain of Unknown Function (DUF1259). This family is the lppY/lpqO homologue family.. 
PF07486 Cell Wall Hydrolase<br>These enzymes have been implicated in cell wall hydrolysis, most extensively in Bacillus subtilis. For instance Swiss:P50739 is expressed during sporulation as an inactive form and then deposited on the cell outer cortex. During germination the the enzyme is activated and hydrolyses the cortex( ). A similar role is carried out by the partially redundant Swiss:P42249 ( ). It is not clear  whether these enzymes are amidases or peptidases.. 
PF07487 SopE GEF domain<br>Pfam-B_18665 (release 7.8). This family represents the C-terminal guanine nucleotide exchange factor (GEF) domain of SopE. Salmonella typhimurium employs a type III secretion system to inject bacterial toxins into the host cell cytosol. These toxins transiently activate Rho family GTP-binding protein-dependent signaling cascades to induce cytoskeletal rearrangements. SopE, can activate Cdc42, an essential component of the host cellular signaling cascade, in a Dbl-like fashion despite its lack of sequence similarity to Dbl-like proteins, the Rho-specific eukaryotic guanine nucleotide exchange factors  .. 
PF07488 Glycosyl hydrolase family 67 middle domain<br>Alpha-glucuronidases, components of an ensemble of enzymes central to the recycling of photosynthetic biomass, remove the alpha-1,2 linked 4-O-methyl glucuronic acid from xylans.  This family represents the central catalytic domain of alpha-glucuronidase  .. 
PF07489 Translocated intimin receptor (Tir) C-terminus<br>Intimin and its translocated intimin receptor (Tir) are bacterial proteins that mediate adhesion between mammalian cells and attaching and effacing (A/E) pathogens. A unique and essential feature of A/E bacterial pathogens is the formation of actin-rich pedestals beneath the intimately adherent bacteria and localised destruction of the intestinal brush border. The bacterial outer membrane adhesin, intimin, is necessary for the production of the A/E lesion and diarrhoea. The A/E bacteria translocate their own receptor for intimin, Tir, into the membrane of mammalian cells using the type III secretion system. The translocated Tir triggers additional host signalling events and actin nucleation, which are essential for lesion formation  . This family represents the Tir C-terminal domain  which has been reported to bind uninfected host cells and beta-1 integrins although the role of intimin binding to integrins is unclear. This intimin C-terminal domain has also been shown to be sufficient for Tir recognition  .. 
PF07490 Translocated intimin receptor (Tir) N-terminus<br>Griffiths-Jones SR, Moxon SJ. Intimin and its translocated intimin receptor (Tir) are bacterial proteins that mediate adhesion between mammalian cells and attaching and effacing (A/E) pathogens. A unique and essential feature of A/E bacterial pathogens is the formation of actin-rich pedestals beneath the intimately adherent bacteria and localised destruction of the intestinal brush border. The bacterial outer membrane adhesin, intimin, is necessary for the production of the A/E lesion and diarrhoea. The A/E bacteria translocate their own receptor for intimin, Tir, into the membrane of mammalian cells using the type III secretion system. The translocated Tir triggers additional host signalling events and actin nucleation, which are essential for lesion formation  . This family represents the Tir N-terminal domain  which is involved in Tir stability and Tir secretion  .. 
PF07491 Protein phosphatase inhibitor  <br>Pfam-B_11090 (release 10.0). These proteins include Ypi1,  (Swiss:P43587), a novel Saccharomyces cerevisiae type 1 protein phosphatase inhibitor   and ppp1r11/hcgv (Swiss:O60927), annotated as having protein phosphatase inhibitor activity [2-3].. 
PF07492 Neutral trehalase Ca2+ binding domain<br>Neutral trehalases mobilise trehalose accumulated by fungal cells as a protective and storage carbohydrate. This family represents a calcium-binding domain similar to EF hand. Residues 97 and 108 in Swiss:O42893 have been implicated in this interaction. It is thought that this domain may provide a general mechanism for regulating neutral trehalase activity in yeasts and filamentous fungi  .. 
PF07494 Two component regulator propeller<br>A large group of two component regulator proteins appear to have the same N-terminal structure of  14 tandem repeats. These repeats show homology to Pfam:PF01011 and Pfam:PF00400 indicating that they are likely to form a beta-propeller. This family has been built with artificially high cut-offs in order to avoid overlaps with other beta-propeller  families. The fourteen repeats are likely to form two propellers; it is not clear if these structures are likely to recruit other proteins or interact with DNA.. 
PF07495 Y_Y_Y domain<br>This domain is mostly found at the end of the beta propellers (Pfam:PF07494) in a family of two component regulators. However they are also found tandemly repeated in Swiss:Q891H4 without other signal conduction domains being present. It's named after the conserved tyrosines found in the alignment. The exact function is not known.. 
PF07496 CW-type Zinc Finger<br>This domain appears to be a zinc finger. The alignment shows four conserved cysteine residues and a conserved tryptophan. It was first identified by  , and is predicted to be a "highly specialised mononuclear four-cysteine zinc finger...that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including ...chromatin methylation status and early embryonic development." Weak homology to Pfam:PF00628 further evidences these predictions (personal obs: C Yeats). Twelve different CW-domain-containing protein subfamilies are described, with different subfamilies being characteristic of vertebrates, higher plants and other animals in which these domain is found  .. 
PF07497 Rho termination factor, RNA-binding domain<br>Pfam-B_1610 (release 11.0). The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts.  It it thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers  .. 
PF07498 Rho termination factor, N-terminal domain<br>Pfam-B_1610 (release 11.0). The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts.  It it thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers  . This domain is found to the N-terminus of the RNA binding domain (Pfam:PF07497).. 
PF07499 RuvA, C-terminal domain<br>Pfam-B_1373 (release 11.0). Homologous recombination is a crucial process  in all living organisms.  In bacteria, this process the RuvA, RuvB, and RuvC proteins are involved. More specifically the proteins process the Holliday junction DNA. RuvA is comprised of three distinct domains. The domain represents the C-terminal domain and plays a significant role in the ATP-dependent branch migration of the hetero-duplex  through direct contact with RuvB  . Within the Holliday junction, the C-terminal domain  makes no interaction with DNA  .. 
PF07500 Transcription factor S-II (TFIIS), central domain<br>Pfam-B_1373 (release 11.0). Transcription elongation by RNA polymerase II is regulated by  the general elongation factor TFIIS. This factor stimulates  RNA polymerase II to transcribe through regions of DNA that  promote the formation of stalled ternary complexes. TFIIS is composed of three structural domains, termed I, II, and III.  The two C-terminal  domains (II and III), this domain and Pfam:PF01096  are required for transcription activity  .. 
PF07501 G5 domain<br>This domain is found in a wide range of extracellular proteins. It is found tandemly repeated in up to 8 copies.  It is found in the N-terminus of peptidases belonging to the M26 family which cleave human IgA.  The domain is also found in proteins involved in metabolism of bacterial cell walls suggesting this domain may have an adhesive function.. 
PF07502 MANSC; <br>This region of similarity, comprising 8 conserved cysteines, is found in the N-terminal region of several membrane-associated and extracellular proteins  .  Although formerly called MANSC (for motif at N terminus with seven cysteines) it has now been renamed by MANEC (motif at N terminus with eight cysteines) by Richard Mitter and Stephen Fitzgerald after the discovery of an eighth conserved cysteine. It is postulated that this domain may play a role in the formation of protein complexes involving various protease activators and inhibitors  .. 
PF07503 HypF finger<br>The HypF family of proteins are involved in the maturation and  regulation of hydrogenase ( ). In the N-terminus they appear to have two Zinc finger domains, as modelled by this family.. 
PF07504 Fungalysin/Thermolysin Propeptide Motif<br>This motif is found in both the bacterial M4 peptidase propeptide and the fungal M36 propeptide. Its exact function is not clear, but it is likely to either  inhibit the peptidase, so as to prevent its premature activation, or has a chaperone activity. Both of these roles have been ascribed to the M4 and M36 propeptides ( ,  ).. 
PF07505 Phage protein Gp37/Gp68<br>Homologues of phage proteins Gp37 and Gp68 are found in several bacteria.. 
PF07506 ParB; <br>RepB plasmid partitioning protein. This family includes proteins with sequence similarity to the RepB partitioning protein of the large Ti (tumour-inducing) plasmids of Agrobacterium tumefaciens[1-2].. 
PF07507 WavE lipopolysaccharide synthesis<br>These proteins are encoded by putative wav gene  clusters, which are responsible for the synthesis of the core oligosaccharide (OS) region of  Vibrio cholerae lipopolysaccharide  . . 
PF07508 Recombinase<br>This domain is usually found associated with Pfam:PF00239 in putative integrases/recombinases of mobile genetic elements of diverse bacteria and phages.. 
PF07509 Protein of unknown function (DUF1523)<br>
PF07510 Protein of unknown function (DUF1524)<br>COGs (COG3472) & PSI2 target BIG_246. This family of uncharacterised proteins contain a conserved HXXP motif. A similar motif is seen in protein families in the His-Me finger endonuclease superfamily which suggests this family of proteins may also act as endonucleases.. 
PF07511 Protein of unknown function (DUF1525)<br>
PF07514 Putative helicase<br>Some members of this family have been annotated as helicases.. 
PF07515 Protein of unknown function (DUF1528)<br>
PF07516 SecA Wing and Scaffold domain<br>SecA protein binds to the plasma membrane where it interacts with proOmpA to support translocation of proOmpA through the membrane.  SecA protein achieves this translocation, in association with SecY protein, in an ATP  dependent manner.  This family is composed of two C-terminal alpha helical subdomains: the wing and scaffold subdomains  .. 
PF07517 SecA DEAD-like domain<br>SecA protein binds to the plasma membrane where it interacts with proOmpA to support translocation of proOmpA through the membrane. SecA protein achieves this translocation, in association with SecY protein, in an ATP dependent manner [1,2].  This domain represents the N-terminal ATP-dependent helicase domain, which is related to the Pfam:PF00270  .. 
PF07519 Tannase and feruloyl esterase<br>This family includes fungal tannase   and feruloyl esterase [2-3]. It also includes several bacterial homologues of unknown function.. 
PF07520 Virulence factor SrfB<br>This family includes homologues of  SsrAB is a two-component regulatory system encoded within the Salmonella pathogenicity island SPI-2.  Among the products of genes activated by SsrAB within epithelial and macrophage cells is Swiss:Q9KIJ9  . Homologues are found in several other proteobacteria.. 
PF07521 RNA-metabolising metallo-beta-lactamase<br>Pfam-B_760 (release 11.0). The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in Pfam:PF00753 and are common to all metallo-beta-lactamases.  The fifth motif appears to be specific to function.\.     This entry represents the fifth motif from metallo-beta-lactamases involved in RNA metabolism  .. 
PF07522 DNA repair metallo-beta-lactamase<br>The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in Pfam:PF00753 and are common to all metallo-beta-lactamases.  The fifth motif appears to be specific to function.\.     This entry represents the fifth motif from metallo-beta-lactamases involved in DNA repair  .. 
PF07523 Bacterial Ig-like domain (group 3)<br>This family consists of bacterial domains with an Ig-like fold. Members of this family are found in a variety of bacterial surface proteins.. 
PF07524 Bromodomain associated<br>This domain is predicted to bind DNA   and is often found associated with Pfam:PF00439 and in transcription factors. It has a histone-like fold.. 
PF07525 Clip; SOCS_Clip; <br>The SOCS box acts as a bridge between specific substrate- binding domains and more generic proteins that comprise a large family of E3 ubiquitin protein ligases.. 
PF07526 Associated with HOX<br>The function of this domain is unknown  . It is often found in plant proteins associated with Pfam:PF00046.. 
PF07527 Hairy Orange<br>The Orange domain is found in the Drosophila proteins Hesr-1, Hairy, and Enhancer of Split [1,2].  The Orange domain is proposed to mediate specific protein-protein interaction between Hairy and Scute .. 
PF07528 DZF domain<br>The function of this domain is unknown  . It is often found associated with Pfam:PF00098 or Pfam:PF00035. This domain has been predicted to belong to the nucleotidyltransferase superfamily  .. 
PF07529 HSA<br>This domain is predicted to bind DNA   and is often found associated with helicases.. 
PF07530 Associated with zinc fingers<br>This function of this domain is unknown   and is often found associated with Pfam:PF00096.. 
PF07531 NHR1 homology to TAF<br>This corresponds to the region NHR1 that is  conserved between the product of the nervy gene in Drosophila and the human mtg8b protein  , which is hypothesised to be a transcription factor.  . 
PF07532 Bacterial Ig-like domain (group 4)<br>This family consists of bacterial domains with an Ig-like fold. Members of this family are found in a variety of bacterial surface proteins.. 
PF07533 TCH; <br>The function of this domain is unknown  . It is often found associated with helicases and transcription factors.. 
PF07534 TLD<br>This domain is predicted to be an enzyme   and is often found associated with Pfam:PF01476. It's structure consists of a beta-sandwich surrounded by two helices and two one-turn helices  .. 
PF07535 DBF zinc finger<br>This domain is predicted to bind metal ions   and is often found associated with Pfam:PF00533 and Pfam:PF02178. It was first identified in the Drosophila chiffon gene product  , and is associated with initiation of DNA replication.. 
PF07536 HWE histidine kinase<br>Two-component systems, consisting of a histidine kinase and a cognate response regulator protein, represent the best-known apparatus for transducing external cues into a physiological response in bacteria.  The HWE domain is found in a subset of two-component system kinases, belonging to the same superfamily as Pfam:PF00512  .  The family was defined by   the presence of a highly conserved H residue in the kinase domain and a WxE motif in a C-terminal ATPase domain that is related to Pfam:PF02518. These proteins are found in a variety of alpha- and gamma-proteobacteria, with significant enrichment in the rhizobia.. 
PF07537 CamS sex pheromone cAM373 precursor<br>Pfam-B_18913 (release 11.0). This family includes CamS (Swiss:Q8L313), from which Staphylococcus aureus sex pheromone staph-cAM373 is processed.. 
PF07538 Clostridial hydrophobic W<br>A novel extracellular macromolecular system has been proposed based on the proteins containing ChW repeats  . ChW stands for Clostridial hydrophobic with conserved W (tryptophan). This repeat was originally described in Clostridium acetobutylicum but is also found in other Gram-positive bacteria including Enterococcus faecalis, Streptococcus agalactiae and Streptomyces coelicolor.. 
PF07539 Down-regulated in metastasis<br>Pfam-B_10642 (release 11.0). These eukaryotic proteins include DRIM  (Down-Regulated In Metastasis) (Swiss:O75691), which is differentially expressed in metastatic and non-metastatic human breast carcinoma cells  .  It is believed to be involved in processing of non-coding RNA  .. 
PF07540 Nucleolar complex-associated protein<br>Pfam-B_8562 (release 11.0). Nucleolar complex-associated protein (Noc3p, Swiss:Q07896) is conserved in eukaryotes and has essential roles in replication and rRNA processing in Saccharomyces cerevisiae  .. 
PF07541 Eukaryotic translation initiation factor 2 alpha subunit<br>Pfam-B_5125 (release 11.0). These proteins share a region of similarity that falls towards the C terminus from Pfam:PF00575.. 
PF07542 ATP12 chaperone protein<br>Pfam-B_6737 (release 11.0). Mitochondrial F1-ATPase is an oligomeric enzyme composed of five distinct subunit polypeptides. The alpha and beta subunits make up the bulk of protein mass of F1. In Saccharomyces cerevisiae both subunits are synthesised as precursors with amino-terminal targeting signals that are removed upon translocation of the proteins to the matrix compartment  .  These proteins include examples from eukaryotes and bacteria and may have chaperone activity, being involved in F1 ATPase complex assembly.. 
PF07543 DUF1531; <br>Protein trafficking PGA2. Pfam-B_46790 (release 11.0). A Saccharomyces cerevisiae member of this family (PGA2) is an ER protein which has been implicated in protein trafficking  .. 
PF07544 CSE2; <br>RNA polymerase II transcription mediator complex subunit 9. Pfam-B_45625 (release 11.0). This family of Med9 proteins is conserved in yeasts. It forms part of the middle region of Mediator  . Med9 has two functional domains. The species-specific amino-terminal half (aa 1-63) plays a regulatory role in transcriptional regulation, whereas this well-conserved carboxy-terminal half (aa 64-149) has a more fundamental function involved in direct binding to the amino-terminal portions of Med4 and Med7 and the assembly of Med9 into the Middle module. Also, some unidentified factor(s) in med9 extracts may impact the binding of TFIID to the promoter  .. 
PF07545 Vestigial/Tondu family<br>The mammalian TEF and the Drosophila scalloped genes belong to a conserved family of transcriptional factors that possesses a TEA/ATTS DNA-binding domain. Transcriptional activation by these proteins likely requires interactions with specific coactivators. In Drosophila, Scalloped (Sd) interacts with Vestigial (Vg) to form a complex, which binds DNA through the Sd TEA/ATTS domain. The Sd-Vg heterodimer is a key regulator of wing development, which directly controls several target genes and is able to induce wing outgrowth when ectopically expressed. This short conserved region is needed for interaction with Sd  .. 
PF07546 EMI domain<br>The Pfam alignment is truncated at the C-terminus and does not include the final cysteine defined in Callebaut et al  . This is to stop the family overlapping with other domains.. 
PF07547 RSD-2 N-terminal domain<br>This domain is found in three copies in the N-terminus of the C. elegans RSD-2 protein. RSD-2 (RNAi spreading defective) is involved in systemic RNAi  .  Mutations in the rsd-2 gene do not effect somatic genes but only germline expressed genes  .. 
PF07548 Chlamydia polymorphic membrane protein middle domain<br>This family contains several Chlamydia polymorphic membrane proteins.  Chlamydia pneumoniae is an obligate intracellular bacterium and a common human pathogen causing infection of the upper and lower respiratory tract.  This domain is found between the beta-helical repeats (Pfam:PF02415) and the C-terminal Pfam:PF03797. This domain is excised subsequent to secretion  .. 
PF07549 SecD/SecF GG Motif<br>This family consists of various prokaryotic SecD and SecF protein export membrane proteins.\.    This SecD and SecF proteins are part of the multimeric protein export complex comprising SecA, D, E, F, G, Y, and YajC  . SecD and SecF are required to maintain a proton motive force  . This alignment encompasses a -GG- motif typically found in N-terminal half of the SecD/SecF proteins .. 
PF07550 Protein of unknown function (DUF1533)<br>This family consists of several hypothetical bacterial proteins and is around 60 residues in length. It's function is not known.. 
PF07551 Protein of unknown function (DUF1534)<br>This family is found in a group of small bacterial proteins. Its function is not known.. 
PF07552 Spore Coat Protein X and V domain<br>This family is found in the Bacilliales coat protein X as a tandem repeat and also in coat protein V. The proteins are found in the insoluble fraction  .. 
PF07553 DUF1535; <br>Host cell surface-exposed lipoprotein. This is a family of lipoproteins that is involved in superinfection exclusion.  Proteins in this family have been shown to act at the stage of DNA release from the phage head into the cell  .. 
PF07554 Uncharacterised Sugar-binding Domain<br>This domain is found in a wide variety of contexts, but mostly occurring in cell wall associated proteins. A lack of conserved catalytic residues suggests that it is a binding domain. From context, possible substrates are hyaluronate or fibronectin (personal obs: C Yeats). This is further evidenced by  . Possibly the exact substrate is N-acetyl glucosamine. Finding it in the same protein as Pfam:PF05089 further supports this proposal. It is found in the  C-terminal part of Swiss:O82833, which is removed during maturation  ( ). Some of the proteins it is found in (e.g. Swiss:Q9RL69) are  involved in methicillin resistance ( ). The name FIVAR derives from Found In Various Architectures. . 
PF07555 Hyaluronidase_2; <br>beta-N-acetylglucosaminidase . Pfam-B_4394 (release 12.0). This family has previously been described as a hyaluronidase [1,2]. However, more recently it has been shown that this family has beta-N-acetylglucosaminidase activity  .. 
PF07556 Protein of unknown function (DUF1538)<br>This family contains several conserved glycines and phenylalanines.. 
PF07557 Shugoshin C terminus<br>Shugoshin-like proteins contain this conserved sequence at the C terminus, which is rich in basic amino-acids. Shugoshin (Sgo1) protects Rec8 at centromeres during anaphase I (during meiosis) so that sister chromatids remain tethered  . Sgo2 is a paralogue of Sgo1 and is involved in correctly orienting sister-centromeres  .. 
PF07558 Shugoshin N-terminal coiled-coil region<br>The Shugoshin protein is found to have this conserved N-terminal coiled-coil region and a highly conserved C-terminal basic region, family Shugoshin_C Pfam:PF07557. Shugoshin is a crucial target of Bub1 kinase function at kinetochores, necessary for both meiotic and mitotic localisation of shugoshin to the kinetochore  . Human shugoshin is diffusible and mediates kinetochore-driven formation of kinetochore-microtubules during bipolar spindle assembly  . Further, the primary role of shugoshin is to ensure bipolar attachment of kinetochores, and its role in protecting cohesion has co-developed to facilitate this process  .. 
PF07559 Flagellar basal body protein FlaE<br>This family consists of several bacterial FlaE flagellar proteins. These  proteins are part of the flageller basal body rod complex.. 
PF07560 Domain of Unknown Function (DUF1539)<br>
PF07561 Domain of Unknown Function (DUF1540)<br>This family has four conserved cysteines, which is suggestive of a metal binding function.. 
PF07562 ANF_assoc; <br>Nine Cysteines Domain of family 3 GPCR. This conserved sequence contains several highly-conserved Cys residues that are predicted to form disulphide bridges. It is predicted to lie outside the cell membrane, tethered to the Pfam:PF00003 in several receptor proteins.. 
PF07563 Protein of unknown function (DUF1541)<br>This family consists of several hypothetical bacterial and occurs as a tandem repeat.. 
PF07564 Domain of Unknown Function (DUF1542)<br>This domain is found in several cell surface proteins. Some are involved in antibiotic resistance (e.g Swiss:Q9RL69 and Swiss:Q9LCJ9)   and/or cellular adhesion (e.g. Swiss:Q931R6)  .. 
PF07565 Band 3 cytoplasmic domain<br>Pfam-B_1004 (release 3.0). This family contains the cytoplasmic domain of the Band 3 anion exchange proteins that exchange Cl-/HCO3-. Band 3 constitutes the most abundant polypeptide in the red blood cell membrane, comprising 25% of the total membrane protein. The cytoplasmic domain of band 3 functions primarily as an anchoring site for other membrane-associated proteins. Included among the protein ligands of cdb3 are ankyrin, protein 4.2, protein 4.1, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), phosphofructokinase, aldolase, hemoglobin, hemichromes, and the protein tyrosine kinase (p72syk).  . 
PF07566 Domain of Unknown Function (DUF1543)<br>This domain is found as 1-2 copies in a small family of proteins of unknown function.. 
PF07568 Histidine kinase<br>This is the dimerisation and phosphoacceptor domain of a sub-family of histidine kinases. It shares sequence similarity with Pfam:PF00512 and Pfam:PF07536. It is usually found adjacent to a C-terminal ATPase domain (Pfam:PF02518). This domain is found in a wide range of Bacteria and also several Archaea.. 
PF07569 TUP1-like enhancer of split<br>Pfam-B_7106 (release 12.0). The Hira proteins are found in a range of eukaryotes and are implicated in the assembly of repressive chromatin. These proteins also contain Pfam:PF00400.. 
PF07571 Protein of unknown function (DUF1546)<br>Pfam-B_3691 (release 12.0). Associated with Pfam:PF02969 in  Transcription initiation factor TFIID subunit 6 (TAF6).. 
PF07572 Bucentaur or craniofacial development<br>Pfam-B_10149 (release 12.0). Bucentaur or craniofacial development protein 1 (BCNT) in ruminents has a different domain architecture to that in mouse and human. For this reason it has been used as a model for molecular  evolution [1-3]. Both bovine and human BCNTs are phosphorylated by casein kinase II in vitro  .. 
PF07573 Nitrogen regulatory protein AreA N terminus<br>Pfam-B_11486 (release 11.0). The AreA nitrogen regulatory protein proteins (which are  GATA type transcription factors) share a highly conserved N terminus and Pfam:PF00320 at the C terminus.. 
PF07574 Nse1 non-SMC component of SMC5-6 complex<br>Pfam-B_24547 (release 11.0). S. cerevisiae Nse1 (Swiss:Q07913) forms part of a complex with SMC5-SMC6 This non-structural maintenance of chromosomes (SMC) complex plays an essential role in genomic stability, being involved in DNA repair and DNA metabolism [1,2].  It is conserved in eukaryotes from yeast to human.. 
PF07575 Nuceloporin_Nup85; Nucelopor_Nup85; <br>Pfam-B_55990 (release 11.0). A family of nucleoporins conserved from yeast to human. THe nuclear pore complex is a large assembly composed of two essential complexes: the heptameric Nup84 complex and the heteromeric Nic96-containing complex.  The Nup84 complex is composed of one copy each of Nup84, Nup85, Nup120, Nup133, Nup145C, Sec13, and Seh1. The structure of a complex of Nup85 and Seh1 was solved  . The N-terminus of Nup85 is inserted and forms a three-stranded blade that completes the Seh1 6-bladed beta-propeller in trans. Following its N-terminal insertion blade, Nup85 forms a compact cuboid structure composed of 20 helices, with two distinct modules, referred to as crown and trunk  .. 
PF07576 BRCA1-associated protein 2<br>Pfam-B_5419 (release 11.0). These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening  . These proteins share a region of sequence similarity at their N terminus.  They also have Pfam:PF02148 at the C terminus.. 
PF07577 Domain of Unknown Function (DUF1547)<br>This family appears to be found only in a small family of Chlamydia species.. 
PF07578 Lipid A Biosynthesis N-terminal domain<br>This family is found at the N-terminus of a group of Chlamydial Lipid A biosynthesis proteins. It is also found by itself in a family of proteins of unknown function.. 
PF07579 Domain of Unknown Function (DUF1548)<br>This family appears to be found only in a small family of Chlamydia proteins.. 
PF07580 M26 IgA1-specific Metallo-endopeptidase C-terminal region<br>These peptidases, which cleave mammalian IgA, are found in Gram-positive bacteria. Often found associated  with Pfam:PF00746, they may be attached to the cell wall.. 
PF07581 The GLUG motif<br>This family is found in the IgA1 (M26) peptidases, which attached to the cell wall peptidoglycan by an amide bond ( ). IgA1 protease selectively cleaves human IgA1 and  is likely to be a pathogenicity factor in some pathogens ( ). This family is also found in various other contexts, including with Pfam:PF05860. It is named GLUG after the mostly conserved G-L-any-G motif.. 
PF07582 AP endonuclease family 2 C terminus<br>This highly-conserved sequence is found at the C terminus of several apurinic/apyrimidinic (AP) endonucleases. in a range of Gram-positive and Gram-negative bacteria. See also Pfam:PF01261.. 
PF07583 DUF1549; PSC2; <br>Protein of unknown function (DUF1549). Blast single linkage clustering. A family of paralogues in the planctomyces.. 
PF07584 DUF1550; <br>Aerotolerance regulator N-terminal. Blast clustering of Pirellula proteome. These proteins share a highly-conserved sequence at their N-terminus.  They include several proteins from Rhodopirellula baltica and also several from proteobacteria. The proteins are produced by the Batl operon which appears to be important in pathogenicity and aerotolerance. This family is the conserved N-terminus, but the full length proteins carry multiple membrane-spanning domains  . BatA ensures bacterial survival in the early stages of the infection process, when the infected sites are aerobic, and is produced under conditions of oxidative stress  .. 
PF07585 Protein of unknown function (DUF1551)<br>Blast clustering of Pirellula proteome. A family of proteins identified in Rhodopirellula baltica.. 
PF07586 DUF1552; <br>Protein of unknown function (DUF1552). Blast clustering of Pirellula proteome. A family of proteins identified in Rhodopirellula baltica.. 
PF07587 DUF1553; <br>Protein of unknown function (DUF1553). Blast clustering of Pirellula genome. A family of proteins found in Rhodopirellula baltica.. 
PF07588 Protein of unknown function (DUF1554)<br>Blast clustering of Leptospira proteome. A family of proteins identified in Leptospira interrogans. . 
PF07589 DUF1555;<br>Blast clustering of Pirellula genome. This motif has been identified in a wide range of bacteria at their C-terminus.  It has been suggested that this is a protein sorting signal. Based on phylogenetic profiling it has been suggested that the EpsH family of proteins mediate this function  .. 
PF07590 Protein of unknown function (DUF1556)<br>Blast clustering of Pirellula proteome. 
PF07591 DUF1557;<br>Pretoxin HINT domain. Blast clustering of Leptospira proteome.. A member of the HINT superfamily of proteases that is usually found N-terminal to the toxin module in polymorphic toxin systems. The  domain is predicted to function in releasing the toxin domain by  autoproteolysis  .. 
PF07592 Transposase_36;<br>Rhodopirellula transposase DDE domain. Blast clustering of Pirellula proteome. These transposases are found in the planctomycete Rhodopirellula baltica, the cyanobacterium Nostoc, and the Gram-positive bacterium Streptomyces.. 
PF07593 ASPIC and UnbV<br>Blast clustering of Pirellula proteome. This conserved sequence is found associated with Pfam:PF00515 in several paralogous proteins in Rhodopirellula baltica.  It is also found associated with Pfam:PF01839 in several eukaryotic integrin-like proteins (e.g. human ASPIC Swiss:Q9NQ78) and in several other bacterial proteins (e.g. Swiss:Q84HN1  ).. 
PF07595 Planctomycete extracellular<br>Blast clustering of Pirellula proteome. This motif is conserved as the N terminus of several Rhodopirellula baltica proteins predicted to be extracellular.. 
PF07596 DUF1559; <br>Protein of unknown function (DUF1559). Blast clustering of Pirellula proteome. A large family of paralogous proteins apparently unique to planctomycetes.. 
PF07597 Protein of unknown function (DUF1560)<br>Blast clustering of Pirellula genome. Small family of short hypothetical proteins in Rhodopirellula baltica.. 
PF07598 Protein of unknown function (DUF1561)<br>Blast clustering of Leptospira proteome. A family of paralogous proteins in Leptospira interrogans.. 
PF07599 Protein of unknown function (DUF1563)<br>Blast clustering of Leptospira proteome. A small family of short hypothetical proteins in Leptospira interrogans.. 
PF07600 Protein of unknown function (DUF1564)<br>Blast clustering of Leptospira proteome. A family of paralogous proteins in Leptospira interrogans. Several (e.g. Swiss:Q8F4V2) have been annotated as possible CopG-like transcriptional regulators (see Pfam:PF01402).. 
PF07602 Protein of unknown function (DUF1565)<br>Blast clustering of Leptospira proteome. These proteins share a region of homology in their N termini, and are found in several phylogenetically diverse bacteria and in the archaeon Methanosarcina acetivorans. Some of these proteins also contain characterised domains such as Pfam:PF00395 (e.g. Swiss:Q8YWJ6) and Pfam:PF03422 (e.g. Swiss:Q9FBS2).. 
PF07603 Protein of unknown function (DUF1566)<br>Blast clustering of the Leptospira proteome. These proteins of unknown function are found in Leptospira interrogans and in several gamma proteobacteria.. 
PF07606 Protein of unknown function (DUF1569)<br>Blast clustering of Pirellula proteome. A family of hypothetical proteins identified in Rhodopirellula baltica.. 
PF07607 Protein of unknown function (DUF1570)<br>Blast clustering of Pirellula proteome. A family of hypothetical proteins in Rhodopirellula baltica. This family carries a highly conserved HExxH sequence motif characteristic of members of the Peptidase clan MA.. 
PF07608 Protein of unknown function (DUF1571)<br>Blast clustering of Pirellula proteome. A family of paralogous proteins in Rhodopirellula baltica.. 
PF07609 Protein of unknown function (DUF1572)<br>Blast search with Q7UW06. These proteins, from several diverse bacteria, share a short conserved sequence towards their N termini.. 
PF07610 Protein of unknown function (DUF1573)<br>Blast clustering of Pirellula proteome. These hypothetical proteins, from bacteria such as Rhodopirellula baltica, Bacteroides thetaiotaomicron, and Porphyromonas gingivalis, share a region of conserved sequence towards their N-termini.. 
PF07611 Protein of unknown function (DUF1574)<br>A family of hypothetical proteins in Leptospira interrogans.. 
PF07613 Protein of unknown function (DUF1576)<br>This small family is found in several undescribed proteins. The alignment is distinguished by the frequent occurrence of conserved glycine and aromatic residues.. 
PF07614 Protein of unknown function (DUF1577)<br>Blast clustering of Leptospira proteome. A family of hypothetical proteins in Leptospira interrogans.. 
PF07615 YKOF-related Family<br>
PF07617 Protein of unknown function (DUF1579)<br>Blast clustering of Pirellula proteome. A family of paralogous hypothetical proteins identified in Rhodopirellula baltica that also has members in Gloeobacter violaceus, Sinorhizobium meliloti and Agrobacterium tumefaciens.. 
PF07618 Protein of unknown function (DUF1580)<br>Blast clustering of Pirelllula proteome. A family of short hypothetical proteins found in Rhodopirellula baltica.. 
PF07619 Protein of unknown function (DUF1581)<br>Blast clustering of Pirellula proteome. Several Rhodopirellula baltica proteins share this probable domain. Most of these proteins are predicted to be secreted or membrane-associated.. 
PF07620 SLEI<br>Blast clustering of Leptospira proteome. This highly conserved sequence motif is found at the C terminus of several short hypothetical proteins in Leptospira spp and related organisms.. 
PF07621 Protein of unknown function (DUF1582)<br>Blast clustering of Pirellula proteome. A family of hypothetical proteins in Rhodopirellula baltica.. 
PF07622 Protein of unknown function (DUF1583)<br>Blast clustering of Pirellula proteome. Most of these Rhodopirellula baltica hypothetical proteins also match Pfam:PF07619.. 
PF07623 DUF1584; <br>Protein of unknown function (DUF1584). Blast clustering of Pirellula proteome. This sequence motif is highly conserved in several short hypothetical proteins in Rhodopirellula baltica. It also is associated with Pfam:PF07621 in Swiss:Q7UJJ9.. 
PF07624 DUF1585; <br>Protein of unknown function (DUF1585). Blast clustering of Pirellula proteome . A conserved sequence region at the C terminus of several cytochrome-like proteins in Rhodopirellula baltica.. 
PF07625 Protein of unknown function (DUF1586)<br>Blast clustering of Pirellula proteome. A family of short hypothetical proteins in Rhodopirellula baltica.. 
PF07626 DUF1587; <br>Protein of unknown function (DUF1587). Blast clustering of Pirellula proteome. A region of similarity shared by several Rhodopirellula baltica cytochrome-like proteins that are predicted to be secreted. These proteins also match Pfam:PF07624.. 
PF07627 DUF1588; PSC1; <br>Protein of unknown function (DUF1588). Blast clustering of Pirellula proteome. A region of similarity shared by several Rhodopirellula baltica cytochrome-like proteins that are predicted to be secreted. These proteins also match Pfam:PF07626 and Pfam:PF07624.. 
PF07628 Protein of unknown function (DUF1589)<br>Blast clustering of Pirellula proteome. A family of short hypothetical proteins in Rhodopirellula baltica.. 
PF07629 Protein of unknown function (DUF1590)<br>Blast clustering of Pirellula proteome. These hypothetical proteins in Rhodopirellula baltica have a conserved C terminal region.. 
PF07631 DUF1592; <br>Protein of unknown function (DUF1592). Blast clustering of Pirellula proteome. A region of similarity shared by several Rhodopirellula baltica cytochrome-like proteins that are predicted to be secreted. These proteins also match Pfam:PF07627, Pfam:PF07626, and Pfam:PF07624.. 
PF07632 Protein of unknown function (DUF1593)<br>Blast clustering of Pirellula proteome. A family of proteins in Rhodopirellula baltica that are predicted to be secreted. Also, a member has been identified in Caulobacter crescentus (Swiss:Q9AAT9). These proteins mat be related to Pfam:PF01156.. 
PF07634 RtxA repeat<br>This short repeat is found in the RtxA toxin family  .. 
PF07635 Cytochrom_C_p; PSC3; <br>Planctomycete cytochrome C. Blast clustering of Pirellula proteome. These proteins share a region of homology at their N-terminus that contains the C-{CPWHF}-{CPWR}-C-H-{CFYW} motif typical of cytochromes C, or CxxCH.. 
PF07636 PSRT<br>Blast clustering of Pirellula proteome. This motif is found at the N terminus of several short hypothetical proteins in Rhodopirellula baltica and the predicted Arylsulfatase B (EC:3.1.6.12) Swiss:Q7UX97.. 
PF07637 DUF1595; <br>Protein of unknown function (DUF1595). Blast clustering of Pirellula proteome . A family of proteins in Rhodopirellula baltica, associated with Pfam:PF07635, Pfam:PF07626, Pfam:PF07631, Pfam:PF07627, and Pfam:PF07624.. 
PF07638 ECF sigma factor<br>Blast clustering of Pirellula proteome. These proteins are probably RNA polymerase sigma factors belonging to the extra-cytoplasmic function (ECF) subfamily   and show sequence similarity to Pfam:PF04542 and Pfam:PF04545.. 
PF07639 YTV<br>Blast clustering of Pirellula proteome. These hypothetical proteins in Rhodopirellula baltica contain several repeats of a sequence whose core is the residues YTV.. 
PF07640 QPP<br>Blast clustering of Pirellula proteome. These Rhodopirellula baltica proteins share a highly conserved sequence, centred around an invariant QPP motif, at their N termini.  This motif may represent an export signal.. 
PF07642 Outer membrane protein family (DUF1597)<br>Blast clustering of Pirellula proteome. This family of proteins are likely to be outer membrane beta barrel proteins. Possibly acting as porins.. 
PF07643 Protein of unknown function (DUF1598)<br>Blast clustering of Pirellula proteome. A family of Rhodopirellula baltica hypothetical proteins of about 500 amino acids in length.. 
PF07644 Planctomycete PGAMP<br>Blast clustering of Pirellula proteome. This conserved sequence is centred around an invariant motif of PGAMP in several short hypothetical proteins from  the planctomycete Rhodopirellula baltica. The motif also occurs twice in Swiss Q7UVK9.. 
PF07645 Calcium-binding EGF domain<br>Pfam-B_330 (release 10.0) . 
PF07646 Kelch motif<br>The kelch motif was initially discovered in Kelch (Swiss:Q04652). In this protein there are six copies of the motif.  It has been shown that Swiss:Q04652 is related to Galactose Oxidase   for which a structure has been solved  . The kelch motif forms a beta sheet.  Several of these sheets associate to form a beta propeller structure as found in Pfam:PF00064, Pfam:PF00400 and Pfam:PF00415.. 
PF07647 SAM domain (Sterile alpha motif)<br>
PF07648 Kazal-type serine protease inhibitor domain<br>Usually indicative of serine protease inhibitors. However, kazal-like domains are also seen in the extracellular part of agrins, which are not known to be protease inhibitors. Kazal domains often occur in tandem arrays. Small alpha+beta fold containing three disulphides.. 
PF07649 C1-like domain<br>This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in Pfam:PF00130.. 
PF07650 KH domain<br>
PF07652 Flavivirus DEAD domain <br>Pfam-B_199 (release 3.0). 
PF07651 ANTH domain<br>AP180 is an endocytotic accessory proteins that has been implicated in the formation of clathrin-coated pits.\.    The domain is involved in phosphatidylinositol 4,5-bisphosphate binding and is a universal adaptor for nucleation of clathrin coats [1,2].. 
PF07653 Variant SH3 domain<br>SH3 (Src homology 3) domains are often indicative of a protein involved in  signal transduction related to cytoskeletal organisation. First described in the Src cytoplasmic tyrosine kinase Swiss:P12931. The structure is a partly opened beta barrel.. 
PF07654 Immunoglobulin C1-set domain<br>
PF00008 EGF-like domain<br>Swissprot_feature_table. There is no clear separation between noise and signal. Pfam:PF00053 is very similar, but has 8 instead of 6 conserved cysteines. Includes some cytokine receptors. The EGF domain misses the N-terminus regions of the Ca2+ binding EGF domains (this is the main reason of discrepancy between swiss-prot domain start/end and Pfam).  The family is hard to model due to many similar but  different sub-types of EGF domains. Pfam certainly misses a number of EGF domains. . 
PF07655 Secretin N-terminal domain<br>This is a short domain found in bacterial type II/III secretory system proteins. The architecture of these proteins suggest that this family may be functionally analogous to Pfam:PF03958.. 
PF07443 HepA-related protein (HARP)<br>Pfam-B_21761 (release 10.0). This family represents a conserved region approximately 60 residues long within eukaryotic HepA-related protein (HARP). This exhibits single-stranded DNA-dependent ATPase activity, and is ubiquitously expressed in human and mouse tissues  . Family members may contain more than one copy of this region.. 
PF07657 N terminus of Notch ligand<br>This entry represents a region of conserved sequence at the N terminus of several Notch ligand proteins.. 
PF07659 Domain of Unknown Function (DUF1599)<br>
PF07660 Secretin and TonB N terminus short domain<br>This is a short domain found at the N-terminus of the Secretins of the bacterial type II/III secretory system as well as the TonB-dependent receptor proteins. These proteins are involved in TonB-dependent active uptake of selective substrates.. 
PF07661 MORN repeat variant<br>This family represents an apparent variant of the Pfam:PF02493 repeat (personal obs:C Yeats).. 
PF07662 Na+ dependent nucleoside transporter C-terminus<br>This family consists of nucleoside transport proteins. Swiss:Q62773 is a purine-specific Na+-nucleoside cotransporter localised to the bile canalicular membrane  . Swiss:Q62674 is a a Na+-dependent nucleoside transporter selective for pyrimidine nucleosides and adenosine it also transports the anti-viral nucleoside analogues AZT and ddC  . This alignment covers the C-terminus of this family of transporters.. 
PF07663 Sorbitol phosphotransferase enzyme II C-terminus<br>TIGRFAMs, Griffiths-Jones SR, Yeats C. 
PF07664 Ferrous iron transport protein B C terminus<br>Escherichia coli has an iron(II) transport system (feo) which may make an important contribution to the iron supply of the cell under anaerobic conditions  . FeoB has been identified as part of this transport system. FeoB is a large 700-800 amino acid integral membrane protein. The N-terminus has been previously erroneously described as being ATP-binding  . Recent work shows that it is similar to eukaryotic G-proteins and that it is a GTPase  . . 
PF07666 M penetrans paralogue family 26<br>These proteins include those ascribed to M penetrans paralogue family 26 in  .. 
PF07667 Protein of unknown function (DUF1600)<br>BLAST clustering of M. penetrans proteome. These proteins appear to be specific to Mycoplasma species.. 
PF07668 M penetrans paralogue family 1<br>This family of paralogous proteins identified in Mycoplasma penetrans includes homologues of p35  . . 
PF07669 Eco57I restriction-modification methylase<br>Homologues of the Escherichia coli Eco57I restriction-modification methylase are found in several phylogenetically diverse bacteria. The structure of TaqI has been solved  .. 
PF07670 Nucleoside recognition<br>This region in the nucleoside transporter proteins are responsible for determining nucleoside specificity in the human CNT1 and CNT2 proteins (e.g Swiss:O00337)  . In the FeoB proteins (e.g.  Swiss:O25396), which are believed to be Fe2+ transporters, it includes the membrane pore region, so the function of this region is likely to be more general than just nucleoside specificity  . This family may represent the pore and gate, with a wide potential range of specificity. Hence its name 'Gate'.. 
PF07671 Protein of unknown function (DUF1601)<br>This repeat is found in a small number of proteins and is apparently limited to Coxiella and related species.. 
PF07672 MFS_Mycoplamsa; <br>Mycoplasma MFS transporter. BLAST clustering of Mycoplasma proteome. These proteins share some similarity with members of the Major Facilitator Superfamily  (MFS).. 
PF07673 Protein of unknown function (DUF1602)<br>Clustering of A. pernix proteome. 
PF07675 Cleaved Adhesin Domain<br>This is a family of bacterial protein modules thought to function in various roles including cell adhesion, cell lysis and carbohydrate binding  .  The beta-sandwich jelly-roll topology of these modules is known as the galactose-binding domain-like superfamily, clan CL0202. A tandem repeat of these modules (either two or three repeats) constitute the haemagglutinin/adhesin (HA) regions of the gingipains, RgpA, Swiss:Q51816 and Kgp, Swiss:P72194 and Swiss:P72197   expressed by Porphyromonas gingivalis (Bacteroides gingivalis)  .  They form components of the major extracellular virulence complex RgpA-Kgp - a mixture of proteinases and adhesin domains  . The adhesin domains in this complex are found in proteinase-cleaved forms when isolated from the cell surface  .  Haemagglutinin genes of P. gingivalis   (hagA1 HAGA1_PORGI - Swiss:P59915 - and hagA2 HAGA2_PORGI - Swiss:Q51845) suggest that such proteins are composed of eight to ten tandem repeats of these adhesin modules  . Genomic data predicts that homologous protein modules are also expressed by a number of other bacteria and form part of putative multi-domain proteins, eg. Swiss:Q26BR9 and Swiss:B0VGL6. These domains may be acting in concert with other adhesion modules thought to be part of these multi-domain proteins such as fibronectin type III, Pfam:PF00041, and Meprin, A5, mu (MAM), Pfam:PF00629, domains.. 
PF07676 WD40-like Beta Propeller Repeat<br>Yeats C, Mistry J, Adindla S. This family appears to be related to the Pfam:PF00400 repeat This This repeat corresponds to the RIVW repeat identified in cell surface proteins [Adindla et al. Comparative and Functional Genomics 2004; 5:2-16].. 
PF07677 A2M2; <br>A-macroglobulin receptor. This family includes the receptor domain region of the alpha-2-macroglobulin family.. 
PF07678 A2M3; <br>A-macroglobulin complement component. This family includes the complement components region of the alpha-2-macroglobulin family.. 
PF07679 Immunoglobulin I-set domain<br>
PF07680 TQO small subunit DoxA<br>Thiosulphate:quinone oxidoreductase (TQO) is one of the early steps in elemental sulphur oxidation.  A novel TQO enzyme was purified from the thermo-acidophilic archaeon Acidianus ambivalens and shown to consist of a large subunit (DoxD) and a smaller subunit (DoxA). The DoxD- and DoxA-like two subunits are fused together in a single polypeptide in Swiss:Q8AAF0.. 
PF07681 DoxX<br>These proteins appear to have some sequence similarity with Pfam:PF04173 but their function is unknown  .. 
PF07682 Sulphur oxygenase reductase<br>The sulphur oxygenase/reductase (SOR) of the thermo-acidophilic archaeon Acidianus ambivalens is an unusual enzyme consisting of 24 identical subunits arranged in a perfectly symmetrical hollow sphere and containing a mononuclear non-heme iron centre (personal communication: A. Kletzin). At 85 degrees C in vitro, elemental sulphur is oxidised to sulphite, thiosulphate and hydrogen sulphide with no external cofactors needed. The proposed equation is:  4S + O2 + 4 H2O ---> 2 HSO3- + 2 H2S + 2 H+.. 
PF07683 Cobalamin synthesis protein cobW C-terminal domain<br>Pfam-B_1247 (release 5.4). This is a large and diverse family of putative metal chaperones that can be separated into up to 15 subgroups. In addition to known roles in cobalamin biosynthesis   and the activation of the Fe-type nitrile hydratase, this family is also known to be involved in the response to zinc limitation. The CobW subgroup involved in cobalamin synthesis represents only a small sub-fraction of the family  .. 
PF07684 NOD; NOD1; <br>NOTCH  signalling plays a fundamental role during a great number of developmental processes in multicellular animals [1-2]. NOD and NODP represent a region present in many NOTCH proteins and NOTCH homologs in multiple species such as NOTCH2 and NOTCH3, LIN12, SC1 and TAN1. The role of the NOD and NODP domains remains to be  elucidated.. 
PF07685 CobB/CobQ-like glutamine amidotransferase domain<br>
PF07686 Immunoglobulin V-set domain<br>This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.. 
PF07688 KaiA domain<br>The cyanobacterial clock proteins KaiA and KaiB are proposed as regulators of the circadian rhythm in cyanobacteria. The overall fold of the KaiA monomer is that of a four-helix bundle, which forms a dimer in the known structure  .. 
PF07689 KaiB domain<br>The cyanobacterial clock proteins KaiA and KaiB are proposed as regulators of the circadian rhythm in cyanobacteria. Mutations in both proteins have been reported to alter or abolish circadian rhythmicity. KaiB adopts an alpha-beta meander motif and is found to be a dimer  .. 
PF07690 Major Facilitator Superfamily<br>Pfam-B_5 (Release 13.0). 
PF07691 PA14 domain<br>Rigden DJ, Mello LV, Galperin MY. This domain forms an insert in bacterial beta-glucosidases and is found in other glycosidases, glycosyltransferases, proteases, amidases, yeast adhesins, and bacterial toxins, including anthrax protective antigen (PA). The domain also occurs in a Dictyostelium prespore-cell-inducing factor Psi and in fibrocystin, the mammalian protein whose mutation leads to polycystic kidney and hepatic disease. The crystal structure of PA shows that this domain (named PA14 after its location in the PA20 pro-peptide) has a beta-barrel structure. The PA14 domain sequence suggests a binding function, rather than a catalytic role. The PA14 domain distribution is compatible with carbohydrate binding.. 
PF07687 Peptidase_M20; <br>Peptidase dimerisation domain. Pfam-B_253 (release 4.0). This domain consists of 4 beta strands and two alpha helices which make up the dimerisation surface of members of the M20 family of peptidases  . 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.. 
PF07692 HCR1;<br>Low iron-inducible periplasmic protein. Pfam-B_60541 (release 13.0). In Chlamydomonas reinhardtii, the gene encoding Swiss:Q9LD42 is induced by iron deficiency  .  In green algae, this protein is periplasmic. The two paralogues FEA1 and FEA2 are the major proteins secreted by iron-deficient Chlamydomonas reinhardtii, and both are up-regulated in response to iron deficiency. FEA1 but not FEA2 is up-regulated by high CO2 concentration. Both FEA1 and FEA2 are secreted into the periplasmic space and genetic evidence confirms that their association with the cell is required for growth in low iron  .. 
PF07693 KAP family P-loop domain<br>The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals. Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side  .. 
PF07694 5TMR of 5TMR-LYT<br>This entry represents the transmembrane region of the 5TM-LYT (5TM Receptors of the LytS-YhcK type)  .. 
PF07695 7TM diverse intracellular signalling<br>This entry represents the transmembrane region of the 7TM-DISM (7TM Receptors with Diverse Intracellular Signalling Modules)  .. 
PF07696 7TMR-DISM extracellular 2<br>This entry represents one of two distinct types of extracellular domain found in the 7TM-DISM (7TM Receptors with Diverse Intracellular Signalling Modules) bacterial transmembrane proteins  . It is possible that this domain adopts a jelly roll fold and acts as a receptor for carbohydrates and their derivatives  .. 
PF07697 7TM-HD extracellular<br>This entry represents the extracellular domain of the 7TM-HD (7TM Receptors with HD hydrolase)  .. 
PF07698 7TM receptor with intracellular HD hydrolase<br>These bacterial 7TM receptor proteins have an intracellular Pfam:PF01966.  This entry corresponds to the 7 helix transmembrane domain.  These proteins also contain an N-terminal extracellular domain.. 
PF07699 GCC2 and GCC3<br>
PF07700 Heme NO binding<br>The HNOB (Heme NO Binding) domain, is a predominantly alpha-helical domain and binds heme via a covalent linkage to  histidine. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce  diverse downstream signals, in both bacteria and animals.. 
PF07701 Heme NO binding associated<br>The HNOBA domain is found associated with the HNOB domain and Pfam:PF00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce  diverse downstream signals, in both bacteria and animals.. 
PF07702 UTRA domain<br>The UbiC transcription regulator-associated (UTRA) domain is a conserved ligand-binding domain that has a similar fold to Pfam:PF04345  . It is believed to modulate activity of bacterial transcription factors in response to binding small molecules  .. 
PF07703 Alpha-2-macroglobulin family N-terminal region<br>This family includes a region of the alpha-2-macroglobulin family.. 
PF07704 Rv0623-like transcription factor<br>This entry represents the Rv0623-like (Swiss:P96913) family of transcription factors associated with the PSK operon  .. 
PF07705 DUF1604; APHP; <br>Cell adhesion related domain found in bacteria.. 
PF07706 Aminotransferase ubiquitination site<br>Pfam-B_15367 (release 13.0). This segment contains a probable site of ubiquitination that ensures rapid  degradation of tyrosine aminotransferase in rats.  The half life of the enzyme  in vivo is about  2-4 hours. In addition, unpublished information identifies at least 2 phosphorylation  sites including CAPK at Ser29 and, at the other end of the protein, a casein kinase II site at  S*QEECDK. This region of TAT is probably primarily related to regulatory events.   Most other transaminases are much more stable and are not phosphorylated.. 
PF07707 BTB And C-terminal Kelch<br>
PF07708 Tash protein PEST motif<br>This motif is found in the Tash AT-hook proteins of Theileria annulata. These proteins are transported to the hosts nucleus and are likely to be involved in pathogenesis  . It is also often found in conjunction with Pfam:PF04385. It is suggested that they may be 'part of PEST motifs' (a signal for rapid proteolytic degradation) in  ,  though this is not definite. This motif is also found in other T. annulata proteins, which have no other known domains in (unpublished data: C Yeats).. 
PF07709 Seven Residue Repeat<br>Associated with Pfam:PF02969 in  This repeat is found in some Plasmodium and Theileria proteins.. 
PF07710 P53 tetramerisation motif<br>Pfam-B_782 (release 3.0). 
PF07711 Rab geranylgeranyl transferase alpha-subunit, insert domain <br>Pfam-B_20675 (release 13.0) . Rab geranylgeranyl transferase (RabGGT) catalyses the addition of two geranylgeranyl groups to the C-terminal cysteine residues of Rab proteins, which is crucial for membrane association and function of these proteins in intracellular vesicular trafficking  .  This domain is inserted between Pfam:PF01239 repeats.  This domain adopts an Ig-like fold and is thought to be involved in protein-protein interactions and might be involved in the recognition and binding of REP  .. 
PF07712 Stress up-regulated Nod 19<br>Pfam-B032880 release 13.0. 
PF07713 Protein of unknown function (DUF1604)<br>This family is found at the N-terminus of several eukaryotic RNA processing proteins (e.g Swiss:Q8N3B7).. 
PF07714 Protein tyrosine kinase<br>
PF07715 TonB-dependent Receptor Plug Domain<br>The Plug domain has been shown to be an independently folding subunit of the TonB-dependent receptors ( ). It acts as the channel gate, blocking the pore until the channel is bound by ligand. At this point it under goes conformational changes opens the channel.. 
PF07716 Basic region leucine zipper<br>PfamB-200; Release 14.0;. 
PF07717 DUF1605;<br>Oligonucleotide/oligosaccharide-binding (OB)-fold. This family is found towards the C-terminus of the DEAD-box helicases (Pfam:PF00270). In these helicases it is apparently always found in association with Pfam:PF04408. There do seem to be a couple of instances where it occurs by itself - e.g. Swiss:Q84VZ2. The structure PDB:3i4u adopts an OB-fold. helicases (Pfam:PF00270). In these helicases it is apparently always found in association with Pfam:PF04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins  .. 
PF07718 DUF1606; <br>Coatomer beta C-terminal region. This family is found at the C-terminus of the coatamer beta subunit proteins (Beta-coat proteins). This C-terminal domain probably adapts the function of the N-terminal Pfam:PF01602 domain. . 
PF07719 Tetratricopeptide repeat<br>Context matches from Pfam 14.0. This Pfam entry includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by Pfam:PF00515.. 
PF07720 Tetratricopeptide repeat<br>This Pfam entry includes tetratricopeptide-like repeats found in the LcrH/SycD-like chaperones  .. 
PF07721 Tetratricopeptide repeat<br>This Pfam entry includes tetratricopeptide-like repeats not detected by the Pfam:PF00515, Pfam:PF07719 and Pfam:PF07720 models.. 
PF07722 Peptidase C26<br>These peptidases have gamma-glutamyl hydrolase activity; that is they catalyse the cleavage of the gamma-glutamyl bond in poly-gamma-glutamyl substrates. They are structurally related to Pfam:PF00117, but contain extensions in four loops and at the C terminus  .. 
PF07723 Leucine Rich Repeat<br>PfamB-152 (release 14.0). This Pfam entry includes some LRRs that fail to be detected with the Pfam:PF00560 model.. 
PF07724 AAA domain (Cdc48 subfamily)<br>PfamB-40 (Release 14.0). This Pfam entry includes some of the AAA proteins not detected by the Pfam:PF00004 model.. 
PF07726 ATPase family associated with various cellular activities (AAA)<br>PfamB-40 (Release 14.0). This Pfam entry includes some of the AAA proteins not detected by the Pfam:PF00004 model.. 
PF07727 Reverse transcriptase (RNA-dependent DNA polymerase)<br>PfamB-40 (Release 14.0). A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. This Pfam entry includes reverse transcriptases not recognised by the Pfam:PF00078 model.. 
PF07728 AAA domain (dynein-related subfamily)<br>PfamB-136 (Release 14.0). This Pfam entry includes some of the AAA proteins not detected by the Pfam:PF00004 model.. 
PF07729 FCD domain<br>Pfam-B_117 (release 14.0). This domain is the C-terminal ligand binding domain of many members of the GntR family. This domain probably binds to a range of effector molecules that regulate the transcription of genes through the action of the N-terminal DNA-binding domain Pfam:PF00392. This domain is found in Swiss:P45427 and Swiss:P31460 that are regulators of sugar biosynthesis operons. It is also in the known structure of FadR where it binds to acyl-coA, the domain is alpha helical  . This family has been named as FCD for (FadR C-terminal Domain).. 
PF07730 Histidine kinase<br>This is the dimerisation and phosphoacceptor domain of a sub-family of histidine kinases. It shares sequence similarity with Pfam:PF00512 and Pfam:PF07536.. 
PF07731 Multicopper oxidase<br>PfamB-49 (Release 14.0). This entry contains many divergent copper oxidase-like domains that are not recognised by the Pfam:PF00394 model.. 
PF07732 Multicopper oxidase<br>PfamB-43 (Release 14.0). This entry contains many divergent copper oxidase-like domains that are not recognised by the Pfam:PF00394 model.. 
PF07733 Bacterial DNA polymerase III alpha subunit<br>Pfam-B111 (Release 14.0). 
PF07734 DUF1607; <br>Pfam-B128 (Release 14.0). Most of these proteins contain Pfam:PF00646 at the N terminus, suggesting that they are effectors linked with ubiquitination.. 
PF07735 F-box associated<br>Pfam-B128 (Release 14.0). Most of these proteins contain Pfam:PF00646 at the N terminus, suggesting that they are effectors linked with ubiquitination.. 
PF07736 Chorismate mutase type I<br>Chorismate mutase EC:5.4.99.5 catalyses the conversion of chorismate to prephenate in the pathway of tyrosine and phenylalanine biosynthesis. This enzyme is negatively regulated by tyrosine, tryptophan and phenylalanine [2,3].. 
PF07737 Anthrax toxin lethal factor, N- and C-terminal domain<br>Pfam-B_23800 (release 14.0). The C-terminal domain is the catalytically active domain whereas the N-terminal domain is likely to be inactive.. 
PF07738 Sad1 / UNC-like C-terminal <br>Pfam-B_5052 (release 14.0). The C. elegans UNC-84 protein is a nuclear envelope protein that is involved in nuclear anchoring and migration during development.  The S. pombe Sad1 protein localises at the spindle pole body. UNC-84 and and Sad1 share a common C-terminal region, that is often termed the SUN (Sad1 and UNC) domain [1-2]. In mammals, the SUN domain is present in two proteins, Sun1 and Sun2  .  The SUN domain of Sun2 has been demonstrated to be in the periplasm  .. 
PF07725 Leucine Rich Repeat<br>PfamB-184 (release 14.0). This Pfam entry includes some LRRs that fail to be detected by the Pfam:PF00560 model.. 
PF07739 TipAS antibiotic-recognition domain<br>Pfam-B_8785 (release 14.0). This domain is found at the C-terminus of some MerR family transcription factors. The domain has an alpha-helical  globin-like fold  . The family includes Mta a central regulator of multidrug resistance in Bacillus subtilis.. 
PF07740 Ion channel inhibitory toxin<br>Pfam-B_20319 (release 14.0). This is a family of potent toxins that function as ion-channel inhibitors for several different ions. Omega-Grammotoxin SIA is a VSCC antagonist that inhibits neuronal N- and P-type VSCC responses  . Huwentoxin-IV, from the Chinese bird spider, is a highly potent neurotoxin that specifically inhibits the neuronal tetrodotoxin-sensitive voltage-gated sodium channel in rat dorsal root ganglion neurons  . Hainantoxin-4, from the venom of spider Selenocosmia hainana, adopts an inhibitor cystine knot structural motif like huwentoin-IV, and is a potent antagonist that acts at site 1 on tetrodotoxin-sensitive (TTX-S) sodium channels  . Study of the molecular nature of toxin-receptor interactions has helped elucidate the functioning of many ion-channels  .. 
PF07741 Brf1-like TBP-binding domain<br>Pfam-B_18050 (release 14.0). This region covers both the Brf homology II and III regions  . This region is involved in binding TATA binding protein  .. 
PF07742 BTG family<br>Pfam-B_9208 (release 14.0). 
PF07743 HSCB C-terminal oligomerisation domain<br>Pfam-B_6234 (release 14.0). This domain is the HSCB C-terminal oligomerisation domain and is found on co-chaperone proteins.. 
PF07744 SPOC domain<br>The SPOC (Spen paralogue and orthologue C-terminal) domain is involved in developmental signalling  .. 
PF07745 Glycosyl hydrolase family 53<br>Pfam-B_5764 (release 14.0). This domain belongs to family 53 of the glycosyl hydrolase classification  .  These enzymes are enzymes are endo-1,4- beta-galactanases (EC:3.2.1.89). The structure of this domain is known   and has a TIM barrel fold.. 
PF07746 Aromatic-ring-opening dioxygenase LigAB, LigA subunit<br>Pfam-B_18522 (release 14.0). This is a family of aromatic ring opening dioxygenases which catalyse the ring-opening reaction of protocatechuate and related compounds  .. 
PF07747 MTH865-like family<br>Pfam-B_25445 (release 14.0). This domain has an EF-hand like fold.. 
PF07748 Glycosyl hydrolases family 38 C-terminal domain<br>Pfam-B_731 (release 3.0). Glycosyl hydrolases are key enzymes of carbohydrate metabolism.. 
PF07749 Endoplasmic reticulum protein ERp29, C-terminal domain<br>Pfam-B_5062 (release 14.0). ERp29 is a ubiquitously expressed endoplasmic reticulum protein found in mammals.  ERp29 is comprised of two domains. This domain, the C-terminal domain, has an all helical fold  . ERp29 is thought to form part of the thyroglobulin folding complex  .. 
PF07750 GcrA cell cycle regulator<br>Pfam-B_23428 (release 14.0). GcrA is a master cell cycle regulator that, together with CtrA (see Pfam:PF00072 and Pfam:PF00486), is involved in controlling cell cycle progression and asymmetric polar morphogenesis  . During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA.  The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes  .  More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery  .. 
PF07751 Abi-like protein<br>Pfam-B_8740 (release 14.0). This family, found in various bacterial species, contains sequences that are similar to the Abi group of proteins,  which are involved in bacteriophage resistance mediated by  abortive infection in Lactococcus species [1,2]. The  proteins are thought to have helix-turn-helix motifs, found in many DNA-binding proteins, allowing them to perform their function  .. 
PF07752 DUF1608;<br>Fenech M, Eberhardt RY. Pfam-B_2293 (release 14.0). Archaeal S-layer proteins consist of two copies of this domain [1-2].. 
PF07753 Protein of unknown function (DUF1609)<br>Pfam-B_2149 (release 14.0). This region is found in a number of hypothetical proteins thought to be expressed by the eukaryote Encephalitozoon cuniculi, an obligate intracellular  microsporidial parasite. It is approximately 200  residues long.. 
PF07754 Domain of unknown function (DUF1610)<br>Pfam-B_8731 (release 14.0). This zinc ribbon domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.. 
PF07755 Protein of unknown function (DUF1611)<br>Pfam-B_8752 (release 14.0). This region is found in a number of hypothetical bacterial and archaeal proteins. The region is  approximately 350 residues long. A member of this family (Swiss:Q6M063) is thought to associate with another subunit to form an H+-transporting ATPase, but no evidence has been found to support this.. 
PF07756 Protein of unknown function (DUF1612)<br>Pfam-B_8688 (release 14.0). This family includes sequences of largely unknown function but which share a number of features in common. They are expressed by bacterial species,  and in many cases these bacteria are known to  associate symbiotically with plants. Moreover, the majority are coded for by plasmids, which in many cases are known to confer on the organism the ability to interact symbiotically with  leguminous plants. An example of such a plasmid is NGR234, which encodes Y4CF, a protein of unknown function that is a member of this family  . Other  members of this family are expressed by organisms with a documented genomic similarity to plant symbionts  .. 
PF07757 DUF1613; <br>Predicted AdoMet-dependent methyltransferase. Pfam-B_8934 (release 14.0). Proteins in this family have been predicted to function as AdoMet-dependent methyltransferases  .. 
PF07758 Protein of unknown function (DUF1614)<br>Pfam-B_8844 (release 14.0). This is a family of sequences coming from hypothetical proteins found in both bacterial and archaeal species.. 
PF07759 Protein of unknown function (DUF1615)<br>Pfam-B_8943 (release 14.0). This is a family of proteins of unknown function expressed by various bacterial species. Some members of this family (e.g. Swiss:Q8Z8Z7, Swiss:Q8ZRF4) are thought to be lipoproteins. Another member of this family (Swiss:Q93SV8) is thought to be involved in photosynthesis  .. 
PF07760 Protein of unknown function (DUF1616)<br>Pfam-B_8886 (release 14.0). This is a family of sequences from hypothetical archaeal proteins.  The region in question is approximately 330 amino acid residues long.. 
PF07761 Protein of unknown function (DUF1617)<br>Pfam-B_8981 (release 14.0). This is a family of sequences from hypothetical bacterial and bacteriophage proteins. The region in question is approximately 150 residues long and is highly conserved throughout the family.. 
PF07762 Protein of unknown function (DUF1618)<br>Pfam-B_8857 (release 14.0). The members of this family are mainly hypothetical proteins expressed by Oryza sativa.. 
PF07763 FEZ-like protein<br>Pfam-B_8854 (release 14.0). This is a family of eukaryotic proteins thought to be involved in axonal outgrowth and fasciculation  . The N-terminal regions of these sequences are less conserved than the C-terminal regions, and are highly acidic  .  The C. elegans homolog, UNC-76 (Swiss:Q7JNU9), may play structural and signalling roles in the control of axonal extension and adhesion (particularly in the presence of adjacent neuronal cells  ) and these roles have also been postulated for other FEZ family proteins  . Certain homologs have been definitively found to interact with the N-terminal variable region (V1) of PKC-zeta, and this interaction causes cytoplasmic translocation of the FEZ family protein in mammalian neuronal cells  . The C-terminal region probably participates in the association with the regulatory domain of PKC-zeta  . The members of this family are predicted to form coiled-coil structures [2,3], which may interact with members of the RhoA family of signalling proteins  , but are not thought to contain other characteristic protein motifs  . Certain members of this family are expressed almost exclusively in the brain, whereas others (such as FEZ2, Swiss:Q76LN0) are expressed in other tissues, and are thought to perform similar but unknown functions in these tissues  .. 
PF07764 Omega Transcriptional Repressor<br>Pfam-B_63922 (release 14.0). The omega transcriptional repressor regulates expression of involved in copy number control and stable maintenance of plasmids. The omega protein belongs to the structural superfamily of MetJ/Arc repressors featuring a ribbon-helix-helix DNA-binding motif with the beta-ribbon located in and recognising the major groove of operator DNA  .. 
PF07765 KIP1-like protein<br>Pfam-B_2332 (release 14.0). This is a family of sequences found exclusively  in plants. They are similar to kinase interacting protein 1 (KIP1), which has been found to interact with the kinase domain of PRK1, a receptor-like  kinase  . This particular region contains two  coiled-coils, which are described as motifs involved in protein-protein interactions  . It has also been suggested that the protein's coiled- coils allow it to dimerise in vivo  .. 
PF07766 LETM1-like protein<br>Fenech M, Wood V, Mistry J. Pfam-B_2202 (release 14.0). Members of this family are inner mitochondrial membrane proteins which play a role in potassium and hydrogen  ion exchange  . Deletion of LETM1 is thought to be involved in the development of Wolf-Hirschhorn syndrome in humans  .. 
PF07767 P60;<br>Nop53 (60S ribosomal biogenesis). Fenech M, Wood V, Mistry J. Pfam-B_8778 (release 14.0). This nucleolar family of proteins are involved in 60S ribosomal biogenesis.  They are specifically involved in the processing beyond the 27S stage of 25S rRNA maturation  . This family contains sequences that bear similarity to the glioma tumour suppressor candidate region gene 2 protein (p60)  . This protein has been found to interact with herpes simplex type 1 regulatory proteins  .. 
PF07768 PVL ORF-50-like family<br>Pfam-B_8834 (release 14.0). This is a family of sequences found in both bacteria and bacteriophages. This region is approximately 130 residues long and in some cases is found as part of the PVL (Panton-Valentine leukocidin) group of genes, which encode a member of the leukocidin group of bacterial toxins that kill leukocytes by creation of pores in the cell membrane  . PVL appears to be a virulence factor associated with a number of human diseases  .. 
PF07769 psiF repeat<br>Pfam-B_8872 (release 14.0). This region is approximately 35 residues long. It is found repeated in a number of putative phosphate starvation- inducible proteins expressed by various bacterial species. psiF (Swiss:Q7AH28) is known to be an example of such phosphate starvation-inducible proteins  .. 
PF07771 Tick salivary peptide group 1<br>Pfam-B_2333 (release 14.0). This contains a group of peptides derived from a salivary gland cDNA library of the tick Ixodes scapularis  . Also present are peptides from a related tick species, Ixodes  ricinus. They are characterised by a putative signal peptide indicative of secretion and conserved cysteine residues.. 
PF07773 Protein of unknown function (DUF1619)<br>Pfam-B_8790 (release 14.0). This is a family of sequences derived from hypothetical eukaryotic proteins. The region in question is approximately 330 residues long and has a cysteine rich amino-terminus.. 
PF07774 Protein of unknown function (DUF1620)<br>Pfam-B_8944 (release 14.0). These sequences are mainly derived from predicted eukaryotic proteins. The region in question lies towards the C-terminus of these large proteins and is approximately 300 amino acid residues long.. 
PF07775 PaRep2b protein<br>Pfam-B_4098 (release 14.0). This is a family of proteins, expressed in the crenarchaeon Pyrobaculum aerophilum, whose members are variable in  length and level of conservation. The presence of numerous frameshifts and internal stop codons in multiple alignments are thought to indicate that most family members are no longer  functional  . . 
PF07776 Zinc-finger associated domain (zf-AD)  <br>Pfam-B_14442 (release 14.0). The zf-AD domain, also known as ZAD, forms an atypical treble-cleft-like zinc co-ordinating fold.  The zf-AD domain is thought to be involved in mediating dimer formation, but does not bind to DNA  .. 
PF07777 G-box binding protein MFMR<br>Pfam-B_5000 (release 14.0). This region is found to the N-terminus of the Pfam:PF00170 transcription factor domain.  It is between 150 and 200 amino acids in length. The N-terminal half is rather rich in proline residues and has been termed the PRD (proline rich domain)  , whereas the C-terminal half is more polar and has been called the MFMR (multifunctional mosaic region). It has been suggested that this family is composed of three sub-families called A, B and C  , classified according to  motif composition. It has been suggested that some of these motifs may be involved in mediating protein-protein interactions  . The MFMR region contains a nuclear localisation signal in bZIP opaque and GBF-2  . The MFMR also contains a transregulatory activity in TAF-1. The MFMR in CPRF-2 contains cytoplasmic retention signals  .. 
PF07778 Mis6;<br>Pfam-B_17323 (release 13.0). Mis6 is an essential centromere connector protein acting during G1-S phase of the cell cycle. Mis6 is thought to be required for recruiting CENP-A, the centromere- specific histone H3 variant, an important event for centromere function and chromosome segregation during mitosis [1,2].. 
PF07779 10 TM Acyl Transferase domain found in Cas1p<br>Cas1p protein of Cryptococcus neoformans is required for the  synthesis of O-acetylated glucuronoxylomannans, a consitutent of the capsule, and is critical for its virulence  . The multi TM domain of the Cas1p was unified with the 10 TM Sugar Acyltransferase  superfamily  . This superfamily is comprised of members from the  OatA, MdoC, OpgC, NolL and GumG families in addition to the Cas1p family  . The Cas1p protein has a N terminal PC-Esterase domain with the opposing Acyl esterase activity  .. 
PF07780 Spb1 C-terminal domain<br>Pfam-B_5001 (release 14.0). This presumed domain is found at the C-terminus of a family of FtsJ-like methyltransferases. Members of this family are involved in 60S ribosomal biogenesis, for example Swiss:P25582  .. 
PF07781 Reovirus minor core protein Mu-2<br>Pfam-B_9308 (release 14.0). This family represents the Reovirus core protein Mu-2. Mu-2 is a microtubule associated protein and is thought to play a key role in the formation and structural organisation of reovirus inclusion bodies  . . 
PF07782 DC-STAMP-like protein<br>Pfam-B_9122 (release 14.0). This is a family of sequences which are similar to a region of the dendritic cell-specific transmembrane protein (DC-STAMP, Swiss:Q9H295). This is thought to be a novel receptor protein that shares no identity with other multimembrane-spanning proteins  . It is thought to have seven putative transmembrane regions  , two of which are found in the region featured in this family. DC-STAMP is also described as having potential N-linked glycosylation sites and a potential phosphorylation site for PKC  , but these are not conserved throughout the family.. 
PF07784 Protein of unknown function (DUF1622)<br>Pfam-B_9062 (release 14.0). This is a family of 14 highly conserved sequences, from hypothetical proteins expressed by both bacterial and archaeal species.. 
PF07785 Protein of unknown function (DUF1623)<br>Pfam-B_9100 (release 14.0). The members of this family are all derived from  relatively short hypothetical proteins thought to  be expressed by various Nucleopolyhedroviruses.. 
PF07786 Protein of unknown function (DUF1624)<br>Pfam-B_9180 (release 14.0). These sequences are found in hypothetical proteins of unknown function expressed by bacterial and  archaeal species. The region in question is approximately 230 residues long.. 
PF07787 Protein of unknown function (DUF1625)<br>Pfam-B_8907 (release 14.0). Sequences making up this family are derived from  hypothetical proteins expressed by both prokaryotic and eukaryotic species. The region in question is  approximately 250 residues long.. 
PF07788 Protein of unknown function (DUF1626)<br>Pfam-B_9705 (release 14.0). This is a family consisting of sequences from hypothetical proteins of unknown function expressed by certain species of archaebacteria. One member (Swiss:Q9YCN7) is thought to be similar to tropomyosin  .. 
PF07789 Protein of unknown function (DUF1627)<br>Pfam-B_9837 (release 14.0). This is a group of sequences found in hypothetical proteins predicted to be expressed in a number of  bacterial species. The region in question is  approximately 150 amino acid residues long.. 
PF07790 Protein of unknown function (DUF1628)<br>Pfam-B_5107 (release 14.0). The sequences making up this family are derived from hypothetical proteins of unknown function  expressed by various archaeal species. The region  in question is approximately 160 residues long.. 
PF07791 Protein of unknown function (DUF1629)<br>Pfam-B_9012 (release 14.0). This family consists of sequences from hypothetical proteins thought to be expressed by two members of the Xanthomonas genus. The region in question is 125 amino acid residues long.. 
PF07792 DUF1630;<br>Docking domain of Afi1 for Arf3 in vesicle trafficking. Pfam-B_9160 (release 14.0). This domain occurs at the N-terminal of Afi1, an Arf3p-interacting protein, is a protein necessary for vesicle trafficking in yeast. This domain is the interacting region of the protein which binds to Arf3, the highly conserved small GTPases (ADP-ribosylation factors). Afi1 is distributed asymmetrically at the plasma membrane and is required for polarized distribution of Arf3 but not of an Arf3 guanine nucleotide-exchange factor, Yel1p. However, Afi1 is not required for targeting of Arf3 or Yel1p to the plasma membrane. Afi1 functions as an Arf3 polarization-specific adapter and participates in development of polarity. Although Arf3 is the homologue of human Arf6 it does not function in the same way, not being necessary for endocytosis or for mating factor receptor internalization. In the S phase, however, it is concentrated at the plasma membrane of the emerging bud. Because of its polarized localisation and its critical function in the normal budding pattern of yeast, Arf3 is probably a regulator of vesicle trafficking, which is important for polarized growth.. 
PF07793 Protein of unknown function (DUF1631)<br>Pfam-B_9170 (release 14.0). The members of this family are sequences derived from a group of hypothetical proteins expressed by certain bacterial species. The region concerned  is approximately 440 amino acid residues in length.. 
PF07794 Protein of unknown function (DUF1633)<br>Pfam-B_9750 (release 14.0). This family contains sequences derived from a group of hypothetical proteins expressed  by Arabidopsis thaliana. These sequences are  highly similar and the region concerned is  about 100 residues long.. 
PF07795 Protein of unknown function (DUF1635)<br>Pfam-B_9707 (release 14.0). The members of this family include sequences that are parts of hypothetical proteins expressed by plant species. The region in question is about 170 amino acids long.. 
PF07796 Protein of unknown function (DUF1638)<br>Pfam-B_6091 (release 14.0) & Pfam-B_3149 (release 23.0). This family contains sequences covering an approximately 270 amino acid stretch of a group of hypothetical proteins.\.   These proteins are expressed by archaeal species of the Methanosarcina genus.. 
PF07797 Protein of unknown function (DUF1639)<br>Pfam-B_6036 (release 14.0). This approximately 50 residue region is found in a  number of sequences derived from hypothetical plant proteins. This region features a highly basic 5 amino-acid stretch towards its centre.. 
PF07798 Protein of unknown function (DUF1640)<br>Pfam-B_6194 (release 14.0). This family consists of sequences derived from  hypothetical eukaryotic proteins. A region approximately 100 residues in length is featured. . 
PF07799 Protein of unknown function (DUF1643)<br>Pfam-B_9851 (release 14.0). The members of this family are all sequences found within hypothetical proteins expressed  by various bacterial species. The region  concerned is approximately 150 residues long.. 
PF07800 Protein of unknown function (DUF1644)<br>Pfam-B_5078 (release 14.0). This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, and is probably a zinc-binding domain.. 
PF07801 Protein of unknown function (DUF1647)<br>Fenech M, Pollington J. Pfam-B_5249 (release 14.0). The sequences making up this family are all derived from hypothetical proteins expressed by C. elegans. The region in question is approximately 160 amino acids long. The GO annotation for this protein indicates the protein to be involved in nematode larval development and to have a positive regulation on growth rate.. 
PF07802 GCK domain<br>Pfam-B_8992 (release 14.0). This domain is found in proteins carrying other domains known to be involved in intracellular signalling pathways (such as Pfam:PF00071) indicating that it might also be involved in these pathways. It has 4 highly conserved cysteine residues, suggesting that it can bind zinc ions. Moreover, it is found repeated in some members of this family (such as Swiss:Q9LMF3); this may indicate that these domains are able to interact with one another, raising the possibility that this domain mediates heterodimerisation.. 
PF07803 GSG1-like protein<br>Pfam-B_9727 (release 14.0). This family contains sequences bearing similarity to a region of GSG1 (Swiss:Q9Z1H7), a protein specifically expressed in testicular germ cells  . It is possible that overexpression of the human  homolog may be involved in tumourigenesis of human testicular germ cell tumours  . The region in question  has four highly-conserved cysteine residues.. 
PF07804 HipA-like C-terminal domain<br>Pfam-B_8632 (release 14.0). The members of this family are similar to a region close to the C-terminus of the HipA protein expressed by various bacterial species (for example Swiss:P23874). This protein is known to be involved in high-frequency persistence to the lethal effects of inhibition of either DNA or peptidoglycan synthesis  . When expressed alone, it is toxic to bacterial  cells  , but it is usually tightly associated with  HipB  , and the HipA-HipB complex may be involved in autoregulation of the hip operon. The hip proteins may be involved in cell division control and may interact with  cell division genes or their products  .. 
PF07805 HipA-like N-terminal domain<br>Pfam-B_8632 (release 14.0). The members of this family are similar to a region close to the N-terminus of the HipA protein expressed by various bacterial species (for example Swiss:P23874). This protein is known to be involved in high-frequency persistence to the lethal effects of inhibition of either DNA or peptidoglycan synthesis  . When expressed alone, it is toxic to bacterial  cells  , but it is usually tightly associated with  HipB  , and the HipA-HipB complex may be involved in autoregulation of the hip operon. The hip proteins may be involved in cell division control and may interact with  cell division genes or their products  .. 
PF07806 Nodule-specific GRP repeat<br>Pfam-B_8942 (release 14.0). The region featured in this family is found repeated in a number of plant proteins, some of which are expressed specifically in nodules formed during symbiotic interactions with certain bacterial species  . Some of these proteins are also termed glycine-rich proteins (GRPs), due to the presence of a glycine-rich C-terminal region in their structures  . Bacterial infection is required for the induction of nodule-specific GRP genes, and it is thought that nodule-specific GRPs may play non-redundant roles required at specific stages of nodule development  . Members of this group of proteins may be cytosolic, whereas others are thought to be membrane-associated  .. 
PF07807 RED-like protein C-terminal region<br>Pfam-B_9789 (release 14.0). This family contains sequences that are similar to the  C-terminal region of Red protein (Swiss:Q13123). This and  related proteins are thought to be localised to the nucleus,  and contain a RED repeat which consists of a number of RE and  RD sequence elements  . The region in question has several  conserved NLS sequences  . The function of Red protein is unknown,  but efficient sequestration to nuclear bodies suggests that its  expression may be tightly regulated or that the protein self-aggregates extremely efficiently  .. 
PF07808 RED-like protein N-terminal region<br>Pfam-B_9780 (release 14.0). This family contains sequences that are similar to the N-terminal region of Red protein (Swiss:Q13123). This and related proteins contain a RED repeat which consists of a number of RE and RD sequence elements  . The region in question has several conserved NLS sequences and a putative trimeric coiled-coil region  , suggesting that these proteins are expressed in the nucleus  . The function of Red protein is unknown, but efficient sequestration to nuclear bodies suggests that its expression may be tightly regulated of that the protein self-aggregates extremely efficiently  .. 
PF07809 RTP801 C-terminal region<br>Pfam-B_5179 (release 14.0). The members of this family are sequences similar to the C-terminal region of RTP801, the protein product of a hypoxia-inducible factor 1 (HIF-1)- responsive gene  . Two members of this family expressed by Drosophila melanogaster, Scylla (Swiss:Q9NHN4) and Charybde (Swiss:Q9NHN5), are designated by the GenBank as Hox targets  .  RTP801 is thought to be involved in various cellular processes  .  Its overexpression caused the apoptosis- resistant phenotype in cycling cells, and apoptosis sensitivity in growth arrested cells  . Moreover, the protein product of the mouse homolog of RTP801 (dig2 (Swiss:Q9D3F7)) is thought to be induced by diverse apoptotic signals, and also by dexamethasone treatment  .. 
PF07810 TMC domain<br>Pfam-B_5063 (release 14.0). These sequences are similar to a region conserved amongst various protein products of the transmembrane channel-like (TMC) gene family, such as Transmembrane channel-like protein 3 (Swiss:Q7TN63) and EVIN2 (Swiss:Q8IU68) - this region is termed the TMC domain  .  Mutations in these genes are implicated in a number of human conditions, such as deafness and epidermodysplasia verruciformis  . TMC proteins are thought to have important cellular roles, and may be modifiers of ion channels or transporters  .. 
PF07811 TadE-like protein<br>Pfam-B_9054 (release 14.0). The members of this family are similar to a region of  the protein product of the bacterial tadE locus (Swiss:Q9S4A6). In various bacterial species, the tad locus is closely  linked to flp-like genes, which encode proteins required  for the production of pili involved in adherence to  surfaces  . It is thought that the tad loci encode  proteins that act to assemble or export an Flp pilus in  various bacteria  . All tad loci but TadA have putative transmembrane regions  , and in fact the region in  question is this family has a high proportion of hydrophobic  amino acid residues.. 
PF07812 TfuA-like protein<br>Pfam-B_9826 (release 14.0). This family consists of a group of sequences that are similar to a region of TfuA protein (Swiss:Q52872). This protein is involved in the production of trifolitoxin (TFX), an gene-encoded, post-translationally modified peptide antibiotic  . The role of TfuA in TFX synthesis is unknown, and it may be involved in other cellular processes  .. 
PF07813 LTXXQ motif family protein<br>Pfam-B_6101 (release 14.0). This protein family includes two copies of a five residue motif is found in a number of bacterial proteins bearing similarity to the protein CpxP (Swiss:P32158). This is a periplasmic protein that aids in combating extracytoplasmic protein-mediated toxicity, and may also be involved in the response to alkaline pH  . Another member of this family, Spy (Swiss:P77754) is also a periplasmic protein that may be involved in the response to stress  . The homology between CpxP and Spy may indicate that these two proteins are functionally related  .. 
PF07814 Wings apart-like protein regulation of heterochromatin<br>Pfam-B_9039 (release 14.0). This family contains sequences expressed in eukaryotic organisms bearing high similarity to the WAPL conserved region of D. melanogaster wings apart-like protein. This protein is involved in the regulation of heterochromatin structure  . hWAPL (Swiss:Q7Z5K2), the human homologue, is found to play a role in the development of cervical carcinogenesis, and is thought to have similar functions to Drosophila wapl protein  . Malfunction of the hWAPL pathway is thought to activate an apoptotic pathway that consequently leads to cell death  .. 
PF07815 Abl-interactor HHR<br>Pfam-B_9732 (release 14.0). The region featured in this family is found towards the N-terminus of a number of adaptor proteins that interact  with Abl-family tyrosine kinases  . More specifically,  it is termed the homeo-domain homologous region (HHR), as it  is similar to the DNA-binding region of homeo-domain  proteins  . Other homeo-domain proteins have been  implicated in specifying positional information during embryonic development, and in the regulation of the expression of  cell-type specific genes  . The Abl-interactor proteins are thought to coordinate the cytoplasmic and nuclear functions of the Abl-family kinases, and seem to be involved  in cytoskeletal reorganisation, but their precise role remains  unclear  .. 
PF07816 Protein of unknown function (DUF1645)<br>Pfam-B_8798 (release 14.0). These sequences are derived from a number of hypothetical plant proteins. The region in question is approximately 270 amino acids long. Some members of this family are annotated as yeast pheromone receptor proteins AR781 but no literature was found to support this.. 
PF07817 GLE1-like protein<br>Pfam-B_9182 (release 14.0). The members of this family are sequences that are similar to the human protein GLE1 (Swiss:O75458). This protein is localised at the nuclear pore complexes and functions in poly(A)+ RNA export to the cytoplasm [1,2].. 
PF07818 HCNGP-like protein<br>Pfam-B_9462 (release 14.0). This family comprises sequences bearing significant  similarity to the mouse transcriptional regulator  protein HCNGP (Swiss:Q02614). This protein is localised to the nucleus and is thought to be involved in the  regulation of beta-2-microglobulin genes.. 
PF07819 PGAP1-like protein<br>Pfam-B_9244 (release 14.0). The sequences found in this family are similar to PGAP1 (Swiss:Q765A7). This is an endoplasmic reticulum membrane protein with a catalytic serine containing motif that is  conserved in a number of lipases. PGAP1 functions as a  GPI inositol-deacylase; this deacylation is important for the efficient transport of GPI-anchored proteins from the endoplasmic reticulum to the Golgi body  .. 
PF07820 TraC-like protein<br>Pfam-B_9690 (release 14.0). The members of this family are sequences that are similar to TraC (Swiss:Q84HT8). The gene encoding this protein is one of a group of genes found on plasmid p42a of Rhizobium etli CFN42 that are thought to be involved in the process of plasmid self-transmission. Mobilisation of plasmid p42a is of importance as it is required for transfer of plasmid p42a, which is also known as plasmid pSym as it carries most of the genes required for nodulation and nitrogen fixation by the symbiotic bacterium. The predicted protein products of p42a are similar to known transfer proteins of Agrobacterium tumefaciens plasmid pTiC58  .. 
PF07821 Alpha-amylase C-terminal beta-sheet domain<br>Pfam-B_1278 (release 14.0). This domain is organised as a five-stranded  anti-parallel beta-sheet [1,2]. It is the  probable result of a decay of the common-fold.. 
PF07822 Neurotoxin B-IV-like protein<br>Pfam-B_66513 (release 14.0). The members of this family resemble neurotoxin B-IV (Swiss:P01525), which is a crustacean-selective neurotoxin produced by the marine worm Cerebratulus lacteus. This highly cationic peptide is approximately 55 residues and is arranged to form two antiparallel helices connected by a well-defined loop in a hairpin structure. The branches of the hairpin are linked by four disulphide bonds. Three residues identified as being important for activity, namely Arg-17, -25 and -34, are found on the same face of the molecule, while another residue important for activity, Trp30, is on the opposite side. The protein's mode of action is not entirely understood, but it may act on voltage-gated sodium channels, possibly by binding to an as yet uncharacterised site on these proteins. Its site of interaction may also be less specific, for example it may interact with negatively charged membrane lipids  .. 
PF07823 Cyclic phosphodiesterase-like protein<br>Pfam-B_73368 (release 14.0). Cyclic phosphodiesterase (CPDase, Swiss:O04147) is involved in the tRNA splicing pathway. This protein exhibits a bilobal arrangement of two alpha-beta modules. Two antiparallel helices are found on the outer side of each lobe and frame an antiparallel beta-sheet that is wrapped around an accessible cleft.  Moreover, the beta-strands of each lobe interact with the other lobe. The central water-filled cavity houses the enzyme's active site  .. 
PF07824 Type III secretion chaperone domain<br>Pfam-B_32938 (release 14.0). Type III secretion chaperones are involved in delivering virulence effector proteins from  bacterial pathogens directly into eukaryotic cells. The chaperones may prevent aggregation and degradation of their substrates, may target the effector to the  secretion apparatus, and may ensure a secretion-component unfolded confirmation of their specific substrate. One member of this family, SigE (Swiss:O30917) forms  homodimers in crystal. The monomers have a novel fold  with an alpha-beta(3)-alpha-beta(2)-alpha topology  .. 
PF07825 Excisionase-like protein<br>Pfam-B_46296 (release 14.0). The phage-encoded excisionase protein (Xis, Swiss:P03699) is involved in excisive recombination by regulating the assembly of the excisive intasome and by inhibiting viral integration. It adopts an unusual 'winged'-helix structure in which two alpha helices are packed against two extended strands.  Also present in the structure is a two-stranded anti-parallel beta-sheet, whose strands are connected by a four-residue 'wing'.  During interaction with DNA, helix alpha2 is thought to insert into the major groove, while the wing contacts the adjacent minor groove or phosphodiester backbone. The C-terminal region of Xis is involved in interaction with phage-encoded integrase (Int), and a putative C-terminal alpha helix may fold upon interaction with Int and/or DNA  .. 
PF07826 IMP cyclohydrolase-like protein<br>Pfam-B_50235 (release 14.0). This enzyme (Swiss:O27099) is may catalyse the cyclization of 5-formylamidoimidazole-4-carboxamide ribonucleotide to inosine monophosphate (IMP), a reaction which is important in de novo purine biosynthesis in archaeal species. This single domain protein is arranged to form an overall fold that consists of a four-layered alpha-beta-beta-alpha core structure. The two antiparallel beta-sheets pack against each other and are covered by alpha-helices on one face of the molecule. The protein is structurally similar to members of the N-terminal nucleophile (NTN) hydrolase superfamily.  A deep pocket was in fact found on the surface of IMP cyclohydrolase in a position equivalent to that of active sites of NTN-hydrolases, but an N-terminal nucleophile could not be found. Therefore, it is thought that this enzyme is structurally but not functionally similar to members of the NTN-hydrolase family  .. 
PF07827 KNTase C-terminal domain<br>Pfam-B_29524 (release 14.0). Kanamycin nucleotidyltransferase (KNTase) is involved  in conferring resistance to aminoglycoside antibiotics  and catalyses the transfer of a nucleoside monophosphate  group from a nucleotide to kanamycin. This enzyme is dimeric with each subunit being composed of two domains.  The C-terminal domain contains five alpha helices, four of which are organised into an up-and-down alpha helical  bundle. Residues found in this domain may contribute to this enzyme's active site  .. 
PF07828 PA-IL-like protein<br>Pfam-B_99281 (release 14.0). The members of this family are similar to the galactophilic  lectin-1 expressed by P. aeruginosa ((PA-IL, Swiss:Q05097).  Lectins recognising specific carbohydrates found on the  surface of host cells are known to be involved in the  initiation of infections by this organism. The protein is thought to be organised into an extensive network of beta-sheets, as is the case with many other lectins  .. 
PF07829 Alpha-A conotoxin PIVA-like protein<br>Pfam-B_46690 (release 14.0). Alpha-A conotoxin PIVA (Swiss:P55963) is the major paralytic  toxin found in the venom produced by the piscivorous snail  Conus purpurascens. This peptide acts by blocking the  acetylcholine binding site of the nicotinic acetylcholine receptor at the neuromuscular junction  . The overall shape of the peptide is described as an "iron" with a highly charged  hydrophilic loop of 15S-19R forming the "handle" domain that  is exposed to the exterior of the protein. The stability of  the conotoxin is primarily governed by three disulphide bonds. A triangular structural motif formed by residues 19R, 12H and  6Y is thought to constitute a "binding core" that is important in binding to the acetylcholine receptor  .. 
PF07830 Protein serine/threonine phosphatase 2C, C-terminal domain<br>Pfam-B_5253 (release 14.0). Protein phosphatase 2C (PP2C) is involved in regulating  cellular responses to stress in various eukaryotes. It  consists of two domains: an N-terminal catalytic domain  and a C-terminal domain characteristic of mammalian PP2Cs. This domain consists of three antiparallel alpha helices,  one of which packs against two corresponding alpha-helices of the N-terminal domain. The C-terminal domain does not  seem to play a role in catalysis, but it may provide protein substrate specificity due to the cleft that is created between it and the catalytic domain  .. 
PF07831 Pyrimidine nucleoside phosphorylase C-terminal domain<br>Pfam-B_1661 (release 14.0). This domain is found at the C-terminal end of the large alpha/beta domain making up various pyrimidine nucleoside phosphorylases [1,2]. It has slightly different conformations in different members of this family. For example, in pyrimidine nucleoside phosphorylase (PYNP, Swiss:P77826) there is an added three-stranded anti-parallel beta sheet as compared to other members of the family, such as E. coli thymidine phosphorylase (TP, Swiss:P07650)  . The domain contains an alpha/ beta hammerhead fold and residues in this domain seem to be important in formation of the homodimer  .. 
PF07832 Cfr10I/Bse634I restriction endonuclease<br>Pfam-B_46671 (release 14.0). Cfr10I (Swiss:P56200) and Bse634I (Swiss:Q8RT53) are two Type II restriction endonucleases. They exhibit a conserved  tetrameric architecture that is of functional importance, wherein two dimers are arranged 'back-to-back' with their  putative DNA-binding clefts facing opposite directions.  These clefts are formed between two monomers that interact, mainly via hydrophobic interactions supported by a few hydrogen bonds, to form a U-shaped dimer. Each monomer is folded to form a compact alpha-beta structure, whose core is made up of a five-stranded mixed beta-sheet.The monomer may be split into  separate N-terminal and C-terminal subdomains at a hinge located in helix alpha3  .. 
PF07833 Copper amine oxidase N-terminal domain<br>Pfam-B_46519 (release 14.0). Copper amine oxidases catalyse the oxidative deamination  of primary amines to the corresponding aldehydes, while reducing molecular oxygen to hydrogen peroxide. These  enzymes are dimers of identical subunits, each comprising four domains. The N-terminal domain, which is absent in  some amine oxidases, consists of a five-stranded antiparallel beta sheet twisted around an alpha helix. The D1 domains from the two subunits comprise the 'stalk' of the mushroom-shaped dimer, and interact with each other but do not pack tightly against each other [1,2].. 
PF07834 RanGAP1 C-terminal domain<br>Pfam-B_23411 (release 14.0). Ran-GTPase activating protein 1 (RanGAP1, Swiss:P46061) is a GTPase activator for the nuclear Ras-related regulatory protein Ran, converting it to the putatively inactive GDP-bound state. Its C-terminal domain is required for RanGAP1 localisation at the vertebrate nuclear pore complex, and is sumoylated by the small ubiquitin-related modifier protein (SUMO-1, Swiss:Q93068). This domain is composed almost entirely of helical substructures that are organised into an alpha-alpha superhelix fold, with the exception of the peptide containing the lysine residue required for SUMO-1 conjugation  .. 
PF07835 Bacterial aa3 type cytochrome c oxidase subunit IV<br>Pfam-B_86185 (release 14.0). Bacterial cytochrome c oxidase is found bound to the  to the cell membrane, where it is involved in the  generation of the transmembrane proton electrochemical gradient. It is composed of four subunits. Subunit IV consists of one transmembrane helix that does not interact  directly with the other subunits, but maintains its position by indirect contacts via phospholipid molecules found in the structure. The function of subunit IV is as yet unknown  .. 
PF07836 DmpG-like communication domain<br>Pfam-B_1675 (release 14.0). This domain is found towards the C-terminal region  of various aldolase enzymes. It consists of five  alpha-helices, four of which form an antiparallel helical bundle that plugs the C-terminus of the N-terminal TIM barrel domain  . The communication domain is thought to play an important role in the  heterodimerisation of the enzyme  .. 
PF07837 Formiminotransferase domain, N-terminal subdomain<br>Pfam-B_4434 (release 14.0). The formiminotransferase (FT) domain of formiminotransferase- cyclodeaminase (FTCD) forms a homodimer, and each protomer comprises two subdomains. The N-terminal subdomain is made up of a six-stranded mixed beta-pleated sheet and five alpha helices, which are arranged on the external surface of the beta sheet. This,  in turn, faces the beta-sheet of the C-terminal subdomain to form a double beta-sheet layer. The two subdomains are separated by a  short linker sequence, which is not thought to be any more flexible than the remainder of the molecule. The substrate is predicted to  form a number of contacts with residues found in both the N-terminal and C-terminal subdomains  .. 
PF07839 Plant calmodulin-binding domain<br>Pfam-B_9279 (release 14.0). The sequences featured in this family are found repeated  in a number of plant calmodulin-binding proteins (such as Swiss:Q8W235, Swiss:Q84ZT8 and Swiss:Q8H6X1), and are  thought to constitute the calmodulin-binding domains [1,2]. Binding of the proteins to calmodulin depends on the presence of calcium ions [1,2]. These proteins are thought to be  involved in various processes, such as plant defence responses   and stolonisation or tuberization  .. 
PF07840 FadR C-terminal domain<br>Pfam-B_11411 (release 14.0). This family contains sequences that are similar to the fatty acid metabolism regulator protein (FadR, Swiss:P09371). This functions as a dimer, with each monomer being composed of an N-terminal DNA-binding domain and a regulatory C-terminal domain. A linker comprising two short alpha helices joins the two domains. In the C-terminal domain, an antiparallel array of six alpha helices forms a barrel-like structure, while a seventh alpha helix forms a 'lid' at the end closest to the N-terminal domain. This structure was found to be similar to that of the C-terminal domain of the Tet repressor. Long-chain acyl-CoA thioesters interact directly and reversibly with the C-terminal domain, and this interaction affects the structure and therefore the DNA binding properties of the N-terminal domain  .. 
PF07841 DM4/DM12 family<br>Pfam-B_5243 (release 14.0). This family contains sequences derived from hypothetical proteins expressed by two insect species, D. melanogaster and A. gambiae. The region in question is approximately 115 amino acid residues long and contains four highly- conserved cysteine residues.. 
PF07842 GC-rich sequence DNA-binding factor-like protein<br>Fenech M, Mistry J, Wood V. Pfam-B_9357 (release 14.0) & Pfam-B_9894 (release 19.0). Sequences found in this family are similar to a region of a human GC-rich sequence DNA-binding factor homolog (Swiss:Q9Y5B6). This is thought to be a protein involved in transcriptional regulation due to partial homologies  to a transcription repressor and histone-interacting protein   . This family also contains tuftelin interacting protein 11 which has been identified as both a nuclear and cytoplasmic protein, and has been implicated in the secretory pathway.  Sip1, a septin interacting protein   is also a member of this family.. 
PF07843 Protein of unknown function (DUF1634)<br>Pfam-B_9594 (release 14.0). This family contains many hypothetical bacterial and archaeal proteins. A few members of this family are annotated as being putative transmembrane proteins, and the region in question in fact contains many  hydrophobic residues.. 
PF07845 Protein of unknown function (DUF1636)<br>Pfam-B_9608 (release 14.0). The sequences featured in this family are derived from a number of hypothetical prokaryotic proteins. The region in question is approximately 130 amino acids long.. 
PF07846 Metallothio_7;<br>Metallothionein family. Pfam-B_9622 (release 14.0). The sequences making up Metallothio_Cad are found repeated in metallothionein proteins expressed by several different Tetrahymena species. Metallothioneins are low molecular mass, cysteine-rich metal-binding proteins that are thought to be involved in the regulation of levels of trace metals, and detoxification of these metals when present in excess  . Some of the metallothioneins found in this family (for example, Swiss:Q8T6B3) are known to be induced by cadmium and are thought to be involved in the cellular sequestration of toxic metal ions. The high proportion of cysteine residues allows the metal ions to be bound by the formation of clusters of metal-thiolate complexes  . Tetrahymena spp. metallothioneins differ from other eukaryotic metallothioneins mainly in the length of their sequences and in the cysteine-containing motifs they exhibit.. 
PF07847 Protein of unknown function (DUF1637)<br>Pfam-B_6051 (release 14.0). This family contains many eukaryotic hypothetical proteins. The region featured in this family is approximately 120 residues long. According to InterPro annotation, some members of this family may belong to the cupin superfamily.. 
PF07848 PaaX-like protein<br>Pfam-B_9563 (release 14.0). This family contains proteins that are similar to the product  of the paaX gene of Escherichia coli (Swiss:P76086). This protein  is involved in the regulation of expression of a group of proteins  known to participate in the metabolism of phenylacetic acid  .  In fact, some members of this family are annotated by InterPro as  containing a winged helix DNA-binding domain (Interpro:IPR009058).. 
PF07849 Protein of unknown function (DUF1641)<br>Pfam-B_9217 (release 14.0). Archaeal and bacterial hypothetical proteins are found in this family, with the region in question  being approximately 40 residues long.. 
PF07850 Renin receptor-like protein<br>Pfam-B_9266 (release 14.0). The sequences featured in this family are similar to a region of the human renin receptor (Swiss:Q8NG15) that bears a putative transmembrane spanning segment  .  The renin receptor is involved in intracellular signal  transduction by the activation of the ERK1/ERK2 pathway,  and it also serves to increase the efficiency of angiotensinogen  cleavage by receptor-bound renin, therefore facilitating  angiotensin II generation and action on a cell surface  .. 
PF07851 TMPIT-like protein<br>Pfam-B_9674 (release 14.0). A number of members of this family are annotated as being transmembrane proteins induced by tumour necrosis factor alpha, but no literature was found to support this.. 
PF07852 Protein of unknown function (DUF1642)<br>Pfam-B_9838 (release 14.0). The sequences making up this family are derived from various hypothetical phage and prophage proteins. The region in question is approximately 140 amino acids long.. 
PF07853 Protein of unknown function (DUF1648)<br>Pfam-B_9801 (release 14.0). Members of this family are hypothetical proteins  expressed by either bacterial or archaeal species. Some of these are annotated as being transmembrane  proteins, and in fact many of these sequences contain a high proportion of hydrophobic residues.. 
PF07854 Protein of unknown function (DUF1646)<br>Pfam-B_9337 (release 14.0). Some of the members of this family are hypothetical bacterial and archaeal proteins, but others are annotated as being cation transporters expressed by the archaebacterium Methanosarcina mazei (Swiss:Q8PXG5, Swiss:Q8PXG7 and Swiss:Q8PXG8).. 
PF07855 Protein of unknown function (DUF1649)<br>Pfam-B_9402 (release 14.0). This family is made up of sequences derived from hypothetical eukaryotic proteins of unknown function. . 
PF07856 DUF1650; Orai-1_Ce; <br>Mediator of CRAC channel activity. Fenech M, Pollington JE. Pfam-B_9685 (release 14.0). ORAI-1 is a protein homologue of Drosophila Orai and human Orai1, Orai2 and Orai3. ORAI-1 GFP reporters are co- expressed with STIM-1 (ER CA(2+) sensors) in the gonad and intestine. The protein has four predicted transmembrane domains with a highly conserved region between TM2 ad TM3. This conserved domain is thought to function in channel regulation. ORAI1- related proteins are required for the production of the calcium channel, CRAC, along with STIM1-related proteins  .. 
PF07857 CEO family (DUF1632)<br>Pfam-B_9654 (release 14.0). These sequences are found in hypothetical eukaryotic proteins of unknown function. The region concerned is approximately 280 residues long. This family has been termed the CEO family for C. elegans ORF  .. 
PF07858 Limonene-1,2-epoxide hydrolase catalytic domain<br>Pfam-B_15033 (release 14.0). Epoxide hydrolases catalyse the hydrolysis of epoxides to corresponding diols, which is important in detoxification, synthesis of signal molecules, or metabolism. Limonene-1,2- epoxide hydrolase (LEH) differs from many other epoxide hydrolases in its structure and its novel one-step catalytic mechanism. Its main fold consists of a six-stranded mixed beta-sheet, with three N-terminal alpha helices packed to one side to create a pocket that extends into the protein core. A fourth helix lies in such a way that it acts as a rim to this pocket. Although mainly lined by hydrophobic residues, this pocket features a cluster of polar groups that lie at its deepest point and constitute the enzyme's active site  .. 
PF07859 alpha/beta hydrolase fold<br>Pfam-B_100 (release 15.0). This catalytic domain is found in a very wide range of enzymes.. 
PF07860 WisP family C-Terminal Region<br>This family is found at the C-terminus of the Tropheryma whipplei WisP family proteins ( ).. 
PF07861 WisP family N-Terminal Region<br>This family is found at the N-terminus of the Tropheryma whipplei WisP family proteins ( ).. 
PF07862 Nitrogen fixation protein of unknown function<br>This domain is found in the Cyanobacteria, and may be involved in nitrogen fixation, but no role has been assigned ( ).. 
PF07863 Homologues of TraJ from Bacteroides conjugative transposon<br>Members of this family have been implicated in as being involved in an unusual form of DNA transfer (conjugation) in Bacteroides ( ). The family has been named CtnDOT_TraJ to avoid confusion with other conjugative transfer systems.. 
PF07864 Protein of unknown function (DUF1651)<br>This is a family containing bacterial proteins of unknown function.. 
PF07865 Protein of unknown function (DUF1652)<br>This is a family containing hypothetical bacterial proteins.. 
PF07866 Protein of unknown function (DUF1653)<br>This is a family of hypothetical bacterial proteins of unknown function.. 
PF07867 Protein of unknown function (DUF1654)<br>This family consists of proteins from the Pseudomonadaceae.. 
PF07868 Protein of unknown function (DUF1655)<br>This protein is found in some prophages found in Lactobacillales lactis ( ).. 
PF07869 Protein of unknown function (DUF1656)<br>This family contains bacterial proteins, many of which are hypothetical.  Some proteins in this family are putative membrane proteins.. 
PF07870 Protein of unknown function (DUF1657)<br>This domain appears to be restricted to the Bacillales.. 
PF07871 Protein of unknown function (DUF1658)<br>This family of small proteins seems to be found in several places in the Coxiella genome.. 
PF07872 Protein of unknown function (DUF1659)<br>This family consists of hypothetical bacterial proteins of unknown function.. 
PF07873 YabP family<br>This family of proteins is involved in spore coat assembly during the process of sporulation  .. 
PF07874 Prophage protein (DUF1660)<br>This protein is found in Lactobacillae prophages.. 
PF07875 Coat F domain<br>The Coat F proteins, which contribute to the Bacillales spore coat.  It occurs multiple times in the genomes it is found in.. 
PF07876 Stress responsive A/B Barrel Domain<br>The function of this family is unknown, but it is upregulated in response to salt stress in Populus balsamifera ( ). It is also found at the C-terminus of an fructose 1,6-bisphosphate aldolase from Hydrogenophilus thermoluteolus (Swiss:Q9ZA13;  ). Swiss:Q93NG5 is found in the pA01 plasmid, which encodes genes for molybdopterin uptake and degradation of plant alkaloid nicotine. The structure of one has been solved (Swiss:Q9LUV2) and the domain forms an a/b barrel dimer ( ). Although there is a clear duplication within the domain it is not obviously detectable in the sequence.. 
PF07877 Protein of unknown function (DUF1661)<br>This is a family containing bacterial proteins of unknown function.  Many of the proteins in this family are hypothetical.. 
PF07878 Protein of unknown function (DUF1662)<br>This family contains bacterial proteins of unknown function. This domain belongs to the Ribbon-helix-helix superfamily suggesting these may be DNA-binding proteins.. 
PF07879 PHB/PHA accumulation regulator DNA-binding domain<br>This domain is found at the N-terminus of the Polyhydroxyalkanoate (PHA) synthesis regulators. These regulators have been shown to directly bind DNA and PHA ( ). The invariant nature of this domain compared to the C-terminal Pfam:PF05233 domain(s) suggests that it contains the DNA-binding function.. 
PF07880 Bacteriophage T4 gp9/10-like protein<br>Pfam-B_73396 (release 14.0). The members of this family are similar to gene products 9 (gp9) and 10 (gp10) of bacteriophage T4. Both proteins are components of the viral baseplate  . Gp9 (Swiss:P10927) connects the long tail fibres of the virus to the baseplate and triggers tail contraction after viral attachment to a host cell. The protein is active as a trimer, with each monomer being composed of three domains.  The N-terminal domain consists of an extended polypeptide chain and two alpha helices. The alpha1 helix from each of the three monomers in the trimer interacts with its counterparts to form a coiled-coil structure. The middle domain is a seven-stranded beta-sandwich that is thought to be a novel protein fold. The C-terminal domain is thought to be essential for gp9 trimerisation and is organised into an eight- stranded antiparallel beta-barrel, which was found to resemble the 'jelly roll' fold found in many viral capsid proteins. The long flexible region between the N-terminal and middle domains may be required for the function of gp9 to transmit signals from the long tail fibres  . Together with gp11, gp10 (Swiss:P10928) initiates the assembly of wedges that then go on to associate with a hub to form the viral baseplate  .. 
PF07881 L-fucose isomerase, first N-terminal domain<br>Pfam-B_11456 (release 14.0). The members of this family are similar to L-fucose isomerase expressed by E. coli (Swiss:P11552, EC:5.3.1.3). This enzyme corresponds to glucose-6-phosphate isomerase in glycolysis,  and converts an aldo-hexose to a ketose to prepare it for aldol cleavage. The enzyme is a hexamer, with each subunit being wedge-shaped and composed of three domains. Both domains 1 and 2 contain central parallel beta-sheets with surrounding  alpha helices. Domain 1 demonstrates the beta-alpha-beta-alpha- beta Rossman fold. The active centre is shared between pairs of subunits related along the molecular three-fold axis, with domains 2 and 3 from one subunit providing most of the substrate-contacting  residues, and domain 1 from the adjacent subunit contributing some other residues  .. 
PF07882 L-fucose isomerase, second N-terminal domain<br>Pfam-B_11456 (release 14.0). The members of this family are similar to L-fucose isomerase expressed by E. coli (Swiss:P11552, EC:5.3.1.3). This enzyme corresponds to glucose-6-phosphate isomerase in glycolysis, and converts an aldo-hexose to a ketose to prepare it for aldol cleavage.  The enzyme is a hexamer, with each subunit being wedge-shaped and composed of three domains. Both domains 1 and 2 contain central parallel beta- sheets with surrounding alpha helices. The active centre is shared between pairs of subunits related along the molecular three-fold axis, with domains 2 and 3 from one subunit providing most of the substrate-contacting residues  .. 
PF07883 Cupin domain<br>Pfam-B_81 (release 15.0). This family represents the conserved barrel domain of the 'cupin' superfamily   ('cupa' is the Latin term for a small barrel).. 
PF07884 Vitamin K epoxide reductase family<br>Vitamin K epoxide reductase (VKOR) recycles reduced vitamin K, which is used subsequently as a co-factor in the gamma-carboxylation of glutamic acid residues in blood coagulation enzymes. VKORC1 is a member of a large family of predicted enzymes that are present in vertebrates, Drosophila, plants, bacteria and archaea  . Four cysteine residues and one residue, which is either serine or threonine, are identified as likely active-site residues  . In some plant and bacterial homologues the VKORC1 homologous domain is fused with domains of the thioredoxin family of oxidoreductases  .. 
PF07885 Ion channel<br>Pfam-B_55 (release 15.0). This family includes the two membrane helix type ion channels found in bacteria.. 
PF07886 BA14K-like protein<br>Pfam-B_4068 (release 14.0). The sequences found in this family are similar to the BA14K proteins expressed by Brucella abortus (Swiss:Q44701) and by Brucella suis (Swiss:Q8FVU0).  BA14K was found to be strongly immunoreactive; it induces both humoral and cellular responses in hosts throughout the infective process  .. 
PF07887 Calmodulin binding protein-like<br>Pfam-B_4579 (release 14.0). The members of this family are putative or actual calmodulin binding proteins expressed by various plant  species. Some members (for example, Swiss:Q8H6T7), are known to be involved in the induction of plant defence responses  . However, their precise function in this regards is as yet unknown.. 
PF07888 CoCoA; <br>Calcium binding and coiled-coil domain (CALCOCO1) like. Pfam-B_4504 (release 14.0). Proteins found in this family are similar to the coiled-coil transcriptional coactivator protein coexpressed by Mus musculus (CoCoA/CALCOCO1, Swiss:Q8CGU1). This protein binds to a highly conserved N-terminal domain of p160 coactivators, such as GRIP1 (Swiss:Q61026), and thus enhances transcriptional activation by a number of nuclear receptors. CALCOCO1 has a central coiled-coil region with three leucine zipper motifs, which is required for its interaction with GRIP1 and may regulate the autonomous transcriptional activation activity of the C-terminal region  .. 
PF07889 Protein of unknown function (DUF1664)<br>Pfam-B_4797 (release 14.0). The members of this family are hypothetical plant proteins of unknown function. The region  featured in this family is approximately 100  amino acids long.. 
PF07890 DUF1665; <br>Fenech M, Mistry J, Wood V. Pfam-B_9434 (release 14.0). Rrp15p is required for the formation of 60S ribosomal subunits  .. 
PF07891 Protein of unknown function (DUF1666)<br>Pfam-B_9387 (release 14.0). These sequences are derived from hypothetical plant proteins of unknown function. The region in question  is approximately 250 residues long.. 
PF07892 Protein of unknown function (DUF1667)<br>Pfam-B_9631 (release 14.0). Hypothetical archaeal and bacterial proteins make up this family. A few proteins are annotated as being potential metal-binding proteins, and in fact the members of this family have four highly conserved cysteine residues, but no further literature evidence was found in this regard.. 
PF07893 Protein of unknown function (DUF1668)<br>Pfam-B_5066 (release 14.0). The hypothetical proteins found in this family are  expressed by Oryza sativa and are of unknown function.. 
PF07894 Protein of unknown function (DUF1669)<br>Pfam-B_9335 (release 14.0). This family is composed of sequences derived from hypothetical eukaryotic proteins of unknown function. Some members of this family are annotated as being potential phospholipases but no literature was found to support this.. 
PF07895 Protein of unknown function (DUF1673)<br>Pfam-B_4746 (release 14.0). This family contains hypothetical proteins of unknown function expressed by two archaeal species.. 
PF07896 Protein of unknown function (DUF1674)<br>Pfam-B_4326 (release 14.0). The members of this family are sequences derived from hypothetical eukaryotic and bacterial proteins. The  region in question is approximately 60 residues long.. 
PF07897 Protein of unknown function (DUF1675)<br>Pfam-B_4280 (release 14.0). The members of this family are sequences derived from hypothetical plant proteins of unknown function. One member of this family (Swiss:Q9SFV5) is annotated as  a putative RNA-binding protein, but no evidence was found to support this.. 
PF07898 Protein of unknown function (DUF1676)<br>Pfam-B_4779 (release 14.0). This family contains sequences derived from proteins of unknown function expressed by Drosophila melanogaster and Anopheles gambiae.. 
PF07899 Frigida-like protein<br>Pfam-B_4728 (release 14.0). This family is composed of plant proteins that are similar to FRIGIDA protein expressed by Arabidopsis thaliana (Swiss:Q9FDW0). This protein is probably nuclear and is required for the regulation of flowering time in the late-flowering phenotype. It is known to increase RNA levels of flowering locus C. Allelic variation at the FRIGIDA locus is a major determinant of natural variation in flowering time  .. 
PF07900 Protein of unknown function (DUF1670)<br>Pfam-B_9559 (release 14.0). The hypothetical eukaryotic proteins found in this family are of unknown function.. 
PF07901 Protein of unknown function (DUF1672)<br>Pfam-B_9698 (release 14.0). This family is composed of hypothetical bacterial proteins of unknown function.. 
PF07902 gp58-like protein<br>Pfam-B_4289 (release 14.0). Sequences found in this family are derived from a number of bacteriophage and prophage proteins. They are similar to gp58 (Swiss:Q38355), a minor structural protein of Lactococcus delbrueckii bacteriophage LL-H  .. 
PF07903 PaRep2a protein<br>Pfam-B_4102 (release 14.0). This is a family of proteins expressed by the  crenarchaeon Pyrobaculum aerophilum. The members  are highly variable in length and level of conservation.  The presence of numerous frameshifts and internal stop  codons in multiple alignments are thought to indicate  that most family members are no longer functional  .. 
PF07904 CT20;<br>Chromatin modification-related protein EAF7. The S. cerevisiae member of this family Swiss:P53911 is part of NuA4, the only essential histone acetyltransferase complex in Saccharomyces cerevisiae involved in global histone acetylation  .. 
PF07905 Purine catabolism regulatory protein-like family<br>Pfam-B_4388 (release 14.0). The bacterial proteins found in this family are similar to the purine catabolism regulatory protein expressed by Bacillus subtilis (PucR, Swiss:O32138). PucR is thought to be a transcriptional activator involved in the induction of the purine degradation pathway, and may contain a LysR-like DNA-binding domain.  It is similar to LysR-type regulators in that it represses its own expression  . The other members of this family are also annotated as being putative regulatory proteins.. 
PF07906 ShET2 enterotoxin, N-terminal region<br>Pfam-B_4512 (release 14.0). The members of this family are are sequences that are similar to the N-terminal half of the ShET2 enterotoxin produced by Shigella flexneri (Swiss:Q47635) and Escherichia coli (Swiss:Q47634). This protein was found to confer toxigenicity in the Ussing chamber, and the N-terminal region was found to be important for the protein's enterotoxic effect. It is thought to be a hydrophobic protein that forms inclusion bodies within the bacterial cell, and may be secreted by the Mxi system  . Most members of this family are annotated as putative enterotoxins, but one member (Swiss:Q8X606) is a regulator of acetyl CoA synthetase, and another two members (Swiss:P76205 and Swiss:P23325) are annotated as ankyrin-like regulatory proteins and contain Ank repeats (Pfam:PF00023).. 
PF07907 YibE/F-like protein<br>Pfam-B_4781 (release 14.0). The sequences featured in this family are similar to two proteins expressed by Lactococcus lactis, YibE (Swiss:Q9CHC5) and YibF (Swiss:Q9CHC4). Most of the members of this family are annotated as being putative  membrane proteins, and in fact the sequences contain  a high proportion of hydrophobic residues.. 
PF07908 D-aminoacylase, C-terminal region<br>Pfam-B_13711 (release 14.0). D-aminoacylase (Swiss:Q9AGH8, EC:3.5.1.81) hydrolyses a wide variety  of N-acyl derivatives of neutral D-amino acids, in a zinc-dependent  manner. The enzyme is composed of a small beta-barrel domain and a  larger catalytic alpha/beta-barrel. The C-terminal region featured  in this family forms part of the beta-barrel domain, together with  a short N-terminal segment. The beta-strands of both barrels were  found to superimpose well. The small beta-barrel domain does not  seem to contribute to the substrate-binding site or to be involved  in the catalytic process  .. 
PF07909 Protein of unknown function (DUF1663)<br>Pfam-B_4106 (release 14.0). The members of this family are hypothetical proteins expressed by Trypanosoma cruzi, a  eukaryotic parasite that causes Chagas' disease in humans. This region is found as multiple copies per protein.. 
PF07910 DUF1671; <br>Peptidase family C78. Pfam-B_9699 (release 14.0). This family formerly known as DUF1671 has been shown to be a cysteine peptidase called (Ufm1)-specific protease  .. 
PF07911 Protein of unknown function (DUF1677)<br>Pfam-B_4922 (release 14.0). The sequences found in this family are all derived from hypothetical plant proteins of unknown function. The region features a number of highly conserved cysteine residues.. 
PF07912 ERp29, N-terminal domain<br>Pfam-B_28781 (release 14.0). ERp29 (Swiss:P52555) is a ubiquitously expressed endoplasmic reticulum protein, and is involved in  the processes of protein maturation and protein  secretion in this organelle [1,2]. The protein exists as a homodimer, with each monomer being  composed of two domains. The N-terminal domain  featured in this family is organised into a  thioredoxin-like fold that resembles the a domain  of human protein disulphide isomerase (PDI)  .  However, this domain lacks the C-X-X-C motif  required for the redox function of PDI; it is  therefore thought that ERp29's function is similar  to the chaperone function of PDI  . The N-terminal domain is exclusively responsible for the homodimerisation of the protein, without covalent linkages or additional contacts with other domains  .. 
PF07913 Protein of unknown function (DUF1678)<br>Pfam-B_4886 (release 14.0). This family is composed of uncharacterized proteins expressed by Methanopyrus kandleri, a hyperthermophilic archaebacterium. . 
PF07914 Protein of unknown function (DUF1679)<br>Pfam-B_4694 (release 14.0). The region featured in this family is found in a number of  C. elegans proteins, in one case (Swiss:Q19034) as a repeat. In many of the family members, this region is associated with the CHK region described by SMART as being found in ZnF_C4 and HLH domain-containing kinases. In fact, one member of this family (Swiss:Q9GUC1) is annotated as being a member of the nuclear hormone receptor family, and contains regions typical of such proteins  (Interpro:IPR000536, Interpro:IPR008946, and Interpro:IPR001628).. 
PF07915 Glucosidase II beta subunit-like protein<br>Pfam-B_9407 (release 14.0). The sequences found in this family are similar to a region found in the beta-subunit of glucosidase II (Swiss:P14314), which is also known as protein kinase C substrate 80K-H (PRKCSH). The enzyme catalyses the sequential removal of two alpha-1,3-linked glucose residues in the second step of N-linked oligosaccharide processing  . The beta subunit is required for the solubility and stability of the heterodimeric enzyme, and is involved in retaining the enzyme within the endoplasmic reticulum  . Mutations in the gene coding for PRKCSH have been found to be involved in the development of autosomal dominant polycystic liver disease (ADPLD), but the precise role the protein has in the pathogenesis of this disease is unknown  .  This family also includes an ER sensor for misfolded glycoproteins and is therefore likely to be a generic sugar binding domain.. 
PF07916 TraG-like protein, N-terminal region<br>Fenech M, Mistry J, Coggill P. Pfam-B_4841 (release 14.0) & Pfam-B_689 (release 23.0). The bacterial sequences found in this family are similar to the N-terminal region of the TraG protein (Swiss:P33790).  This is a membrane-spanning protein, with three predicted transmembrane segments and two periplasmic regions  . TraG protein is known to be essential for DNA transfer in the process of conjugation, with the N-terminal portion being required for F pilus assembly [1,2]. The protein is thought to interact with the periplasmic domain of TraN (Swiss:P24082) to stabilise mating-cell interactions  .. 
PF07918 CAP160 repeat<br>Pfam-B_9359 (release 14.0). This region featured in this family is repeated in spinach cold acclimation protein CAP160 (Swiss:O50054) CAP160 is induced during periods of drought stress; its precise function is unknown but it has been implicated in the stabilisation of membranes, cytoskeletal elements, and ribosomes. By acting as a compatible solute, it may reduce the toxic effects of cellular solutes that accumulate at high concentration during dehydration; it may also function as an enzyme that produces such a solute  . Other members of this family are also induced by water stress, abscisic acid, and/or low temperature, such as desiccation-responsive protein 29B (Swiss:Q04980) and CDet11-24 protein (Swiss:O23764).. 
PF07919 DUF1683;<br>Gryzun, putative trafficking through Golgi. Fenech M, Pollington J. Pfam-B_9179 (release 14.0). The proteins featured in this family are all eukaryotic, and many of them are annotated as being Gryzun. Gryzun is distantly related to, but distinct from, the Trs130 subunit of the TRAPP complex but is absent from S. cerevisiae. RNAi of human Gryzun (Swiss:Q7Z392) blocks Golgi exit. Thus the family is likely to be involved with trafficking of proteins through membranes, perhaps as part of the TRAPP complex.. 
PF07920 Protein of unknown function (DUF1684)<br>Pfam-B_9328 (release 14.0). The sequences featured in this family are found in hypothetical archaeal and bacterial proteins  of unknown function. The region in question is approximately 200 amino acids long.. 
PF07921 Fibritin C-terminal region<br>Pfam-B_31175 (release 14.0). This family features sequences bearing similarity to the C-terminal portion of the bacteriophage T4 protein fibritin (Swiss:P10104). This protein is responsible for attachment of long tail fibres to virus particle, and forms the 'whiskers' or fibres on the neck of the virion. The region seen in this family contains an N-terminal coiled-coil portion and the C-terminal globular foldon domain (residues 457-486), which is essential for fibritin trimerisation and folding  . This domain consists of a beta-hairpin; three such hairpins come together in a beta-propeller-like arrangement in the trimer, which is stabilised by hydrogen bonds, salt bridges and hydrophobic interactions  .. 
PF07922 Glycosyltransferase family 52<br>Pfam-B_2778 (release 14.0). This family features glycosyltransferases belonging to  glycosyltransferase family 52  , which have alpha-2,3- sialyltransferase (EC:4.2.99.4) and alpha-glucosyltransferase  (EC 2.4.1.-) activity. For example, beta-galactoside alpha-2,3- sialyltransferase expressed by Neisseria meningitidis (Swiss:P72097) is a member of this family and is involved in a step of lipooligosaccharide  biosynthesis requiring sialic acid transfer; these lipooligosaccharides  are thought to be important in the process of pathogenesis  . This family includes several bacterial lipooligosaccharide sialyltransferases similar to the Haemophilus ducreyi LST protein. Haemophilus ducreyi is the cause of the sexually transmitted disease chancroid and produces a lipooligosaccharide (LOS) containing a terminal sialyl N-acetyllactosamine trisaccharide  .  . 
PF07923 N1221-like protein<br>Pfam-B_9309 (release 14.0). The sequences featured in this family are similar to a hypothetical protein product of ORF N1221 in the CPT1-SPC98 intergenic region of the yeast genome (Swiss:P53917). This encodes an acidic polypeptide with several possible transmembrane regions  .. 
PF07924 Nuclease A inhibitor-like protein<br>Pfam-B_43172 (release 14.0). This family consists of protein sequences that are similar to the nuclease A inhibitor expressed by bacteria of the genus Anabaena ((NuiA, Swiss:Q44296). This sequence is organised to form an alpha-beta-alpha sandwich fold, which is similar to the PR-1-like fold.  NuiA interacts with nuclease A by means of residues located at one end of the molecule, including residues making up the loop between helices III and IV and the loop between strands C and D.  The mechanism of inhibition of nuclease A by NuiA is as yet incompletely understood  .. 
PF07925 Reovirus RNA-dependent RNA polymerase lambda 3<br>Pfam-B_9372 (release 14.0). The sequences in this family are similar to the reoviral minor core protein lambda 3 (Swiss:P17378), which functions as a RNA-dependent RNA polymerase within the protein capsid.\.      It is organised into 3 domains. N- and C-terminal domains create a 'cage' that encloses a conserved central catalytic domain within a hollow centre; this catalytic domain is arranged to form 'fingers', 'palm' and 'thumb' subdomains.  Unlike other RNA polymerases, like HIV reverse transcriptase and T7 RNA polymerase, lambda 3 protein binds template and substrate with only localised rearrangements, and catalytic activity can occur with little structural change. However, the structure of the catalytic complex is similar to that of other polymerase catalytic complexes with known structure  .. 
PF07926 TPR/MLP1/MLP2-like protein<br>Pfam-B_9285 (release 14.0). The sequences featured in this family are similar to a region of human TPR protein (Swiss:P12270) and to yeast myosin-like proteins 1 (MLP1, Swiss:Q02455) and 2 (MLP2, Swiss:P40457). These proteins share a number of features; for example, they all have coiled-coil regions and all three are associated with nuclear pores [1,2,3]. TPR is thought to be a component of nuclear pore complex- attached intra-nuclear filaments  , and is implicated in nuclear protein import  . Moreover, its N-terminal region is involved in the activation of oncogenic kinases, possibly by mediating the dimerisation of kinase domains or by targeting these kinases to the nuclear pore complex  . MLP1 and MLP2 are involved in the process of telomere length regulation, where they are thought to interact with proteins such as Tel1p and modulate their activity  .. 
PF07927 YcfA-like protein<br>Pfam-B_2914 (release 14.0). The viral, archaeal and bacterial proteins making up this family are similar to the YcfA protein expressed by E.  coli (Swiss:Q9F561). Most of these proteins are hypothetical proteins of unknown function.. 
PF07928 Vps54-like protein<br>Pfam-B_9294 (release 14.0). This family contains various proteins that are homologs of the yeast Vps54 protein, such as the rat homolog  (Swiss:Q9JMK8), the human homolog (Swiss:Q86YF7), and  the mouse homolog (Swiss:Q8R3X1). In yeast, Vps54 associates with Vps52 and Vps53 proteins to form a trimolecular complex  that is involved in protein transport between Golgi, endosomal, and vacuolar compartments  . All Vps54 homologs contain a coiled coil region (not found in the region featured in this family) and multiple dileucine motifs  .. 
PF07929 Plasmid pRiA4b ORF-3-like protein<br>Pfam-B_4929 (release 14.0). Members of this family are similar to the protein product of ORF-3 (Swiss:Q44206) found on plasmid  pRiA4 in the bacterium Agrobacterium rhizogenes.  This plasmid is responsible for tumourigenesis at  wound sites of plants infected by this bacterium, but the ORF-3 product does not seem to be involved in the pathogenetic process  . Other proteins found in this family are annotated as being putative TnpR resolvases (Swiss:Q9LCU7, Swiss:Q50439), but no  further evidence was found to back this. Moreover,  another member of this family is described as a probable  lexA repressor (Swiss:Q7UEI4) and in fact carries a LexA  DNA binding domain (Pfam:PF01726), but no references were  found to expand on this.. 
PF07930 D-aminopeptidase, domain B<br>Pfam-B_29283 (release 14.0). D-aminopeptidase (Swiss:Q9ZBA9) is a dimeric enzyme with each monomer being composed of three domains. Domain B is organised to form a beta barrel made up of eight antiparallel beta strands. It is connected  to domain A, the catalytic domain, by an eight-residue sequence, and also interacts with both domains A and C  via non-covalent bonds. Domain B probably functions in maintaining domain C in a good position to interact with domain A  .. 
PF07931 Chloramphenicol phosphotransferase-like protein<br>Pfam-B_29509 (release 14.0). The members of this family are all similar to chloramphenicol  3-O phosphotransferase (CPT, Swiss:Q56148) expressed by Streptomyces venezuelae. Chloramphenicol (Cm) is a metabolite produced by this bacterium that can inhibit ribosomal peptidyl transferase activity and therefore protein production. By transferring a phosphate group  to the C-3 hydroxyl group of Cm, CPT inactivates this potentially  lethal metabolite  .. 
PF07932 D-aminopeptidase, domain C<br>Pfam-B_29283 (release 14.0). D-aminopeptidase (Swiss:Q9ZBA9) is a dimeric enzyme with each monomer being composed of three domains. Domain C is organised to form a beta barrel made up of eight antiparallel beta strands. It is connected to domain B by a short linker sequence, and interacts extensively with the domain A, the catalytic domain. The gamma loop of domain C forms part of the wall of the catalytic pocket; domain C is in fact thought to confer substrate and inhibitor specificity to the enzyme  .. 
PF07933 Protein of unknown function (DUF1681)<br>Pfam-B_4989 (release 14.0). This family is composed of sequences derived from a  number of hypothetical eukaryotic proteins of unknown  function.. 
PF07934 8-oxoguanine DNA glycosylase, N-terminal domain<br>Pfam-B_29151 (release 14.0). The presence of 8-oxoguanine residues in DNA can give rise  to G-C to T-A transversion mutations. This enzyme is found  in archaeal, bacterial and eukaryotic species, and is  specifically responsible for the process which leads to the  removal of 8-oxoguanine residues. It has DNA glycosylase  activity (EC:3.2.2.23) and DNA lyase activity (EC:4.2.99.18)   . The region featured in this family is the N-terminal  domain, which is organised into a single copy of a TBP-like  fold. The domain contributes residues to the 8-oxoguanine binding pocket  .. 
PF07935 ORF D-335-like protein<br>Pfam-B_4933 (release 14.0). The sequences featured in this family are similar to  a probable integrase (Swiss:P20214) expressed by the SSV1 virus of the archaebacterium Sulfolobus shibatae. This protein may be necessary for the integration of the virus into the host genome by a process of site-specific  recombination  .. 
PF07936 BDS_I_II;<br>Potassium-channel blocking toxin. Pfam-B_56105 (release 14.0). This family features the antihypertensive and antiviral proteins BDS-I (Swiss:P11494) and BDS-II (Swiss:P59084) expressed by Anemonia sulcata. BDS-I is organised into a triple-stranded antiparallel beta-sheet, with an additional small antiparallel beta-sheet at the N-terminus  . Both peptides are known to specifically block the Kv3.4 potassium channel, and thus bring about a decrease in blood pressure  . Moreover, they inhibit the cytopathic effects of mouse hepatitis virus strain MHV-A59 on mouse liver cells, by an unknown mechanism  .. 
PF07937 Protein of unknown function (DUF1686)<br>Pfam-B_5313 (release 14.0). The members of this family are all hypothetical proteins of unknown function expressed by the eukaryotic parasite Encephalitozoon cuniculi GB-M1. The region in question is approximately 250 amino acids long.. 
PF07938 Fungal fucose-specific lectin<br>Pfam-B_48600 (release 14.0). Lectins are involved in many recognition events at the molecular or cellular level. These fungal lectins, such as Aleuria aurantia lectin (AAL,  Swiss:P18891), specifically recognise fucosylated  glycans. AAL is a dimeric protein, with each monomer  being organised into a six-bladed beta-propeller fold and a small antiparallel two-stranded beta-sheet. The beta-propeller fold is important in fucose recognition; five binding pockets are found between the propeller blades. The small beta-sheet, on the other hand, is involved in the dimerisation process  . . 
PF07939 Protein of unknown function (DUF1685)<br>Pfam-B_5502 (release 14.0). The members of this family are hypothetical eukaryotic proteins of unknown function. The region in question is approximately 100 amino acid residues long.. 
PF07940 Heparinase II/III-like protein<br>Pfam-B_5577 (release 14.0). This family features sequences that are similar to  a region of the Flavobacterium heparinum proteins heparinase II (Swiss:Q46080) and heparinase III (Swiss:Q59289). The former is known to degrade heparin and heparan sulphate, whereas the latter predominantly degrades heparan sulphate. Both are secreted into the periplasmic space upon induction with heparin  .. 
PF07941 Potassium channel Kv1.4 tandem inactivation domain<br>Pfam-B_7603 (release 14.0). This family features the tandem inactivation domain found at the N-terminus of the Kv1.4 potassium channel. It is composed of two subdomains. Inactivation domain 1 (ID1, residues 1-38) consists of a flexible N-terminus anchored at a 5-turn helix, and is thought to work by occluding the ion pathway, as is the case with a classical ball domain. Inactivation domain 2 (ID2, residues 40-50) is a 2.5 turn helix with a high proportion of hydrophobic residues that probably serves to attach ID1 to the cytoplasmic face of the channel. In this way, it can promote rapid access of ID1 to the receptor site in the open channel. ID1 and ID2 function together to being about fast inactivation of the Kv1.4 channel, which is important for the channel's role in short-term plasticity  .. 
PF07942 N2227-like protein<br>Pfam-B_5433 (release 14.0). This family features sequences that are similar to a region of hypothetical yeast gene product N2227 (Swiss:P53934). This is thought to be expressed during meiosis and may be involved in the defence response to stressful conditions  .. 
PF07943 Penicillin-binding protein 5, C-terminal domain<br>Pfam-B_1086 (release 14.0). Penicillin-binding protein 5 expressed by E. coli (Swiss:P04287) functions as a D-alanyl-D-alanine carboxypeptidase. It is composed of two domains that are oriented at approximately right angles to each other. The N-terminal domain (Pfam:PF00768) is the catalytic domain.  The C-terminal domain featured in this family is organised into a sandwich of two anti-parallel beta-sheets, and has a relatively hydrophobic surface as compared to the N-terminal domain. Its precise function is unknown; it may mediate interactions with other cell wall-synthesising enzymes, thus allowing the protein to be recruited to areas of active cell wall synthesis. It may also function as a linker domain that positions the active site in the catalytic domain closer to the peptidoglycan layer, to allow it to interact with cell wall peptides  .. 
PF07944 Putative glycosyl hydrolase of unknown function (DUF1680)<br>Pfam-B_4918 (release 14.0). The members of this family are sequences derived from hypothetical bacterial and eukaryotic proteins of unknown function. One members of this family is annotated as a possible arabinosidase, but no references were found to back this. These proteins are related to a large family of glycosyl hydrolases.. 
PF07945 Janus-atracotoxin<br>Pfam-B_50381 (release 14.0). This family includes three peptides secreted by the  spider Hadronyche versuta (Swiss:P82226, Swiss:P82227, Swiss:P82228). These are insect-selective, excitatory neurotoxins that may function by antagonising muscle  acetylcholine receptors, or acetylcholine receptor  subtypes present in other invertebrate neurons  . Janus atracotoxin-Hv1c (J-ACTX-Hv1c, Swiss:P82228) is organised into a disulphide-rich globular core (residues 3-19) and a beta-hairpin (residues 20-34). There are  4 disulphide bridges, one of which is a vicinal disulphide bridge; this is known to be unimportant in the maintenance  of structure but critical for insecticidal activity  .. 
PF07946 Protein of unknown function (DUF1682)<br>Pfam-B_4955 (release 14.0). The members of this family are all hypothetical eukaryotic proteins of unknown function. One  member (Swiss:Q920S6) is described as being an adipocyte-specific protein, but no evidence of this was found.. 
PF07947 YhhN-like protein<br>Pfam-B_5325 (release 14.0). The members of this family are similar to the hypothetical protein yhhN expressed by E. coli (Swiss:P37616). Many of the members  of this family are annotated as being possible transmembrane proteins, and in fact they all have a high proportion of hydrophobic residues.. 
PF07948 Nairovirus M polyprotein-like<br>Pfam-B_5426 (release 14.0). The sequences in this family are similar to the Dugbe virus M polyprotein precursor (Swiss:Q02004), which includes glycoproteins G1 and G2. Both are  thought to be inserted in the membrane of the Golgi complex of the infected host cell, and G1 is known to have a role in infection of vertebrate hosts  .. 
PF07949 YbbR-like protein<br>Pfam-B_4990 (release 14.0). The members of this family are are all hypothetical bacterial proteins of unknown function, and are  similar to the YbbR protein expressed by Bacillus  subtilis (Swiss:O34659, Swiss:O87088). One member (Swiss:Q97EN2) is annotated as an uncharacterized secreted protein, whereas another member (Swiss:P43521) is described as a hypothetical protein in the 5'region  of the def gene of Thermus thermophilus, which encodes  a deformylase  , but no further information was found  in either case. This region is found repeated up to four times in many members of this family.. 
PF07950 Protein of unknown function (DUF1691)<br>This family of fungal proteins is uncharacterised. Each protein contains two copies of this region.. 
PF07951 Clostridium neurotoxin, C-terminal receptor binding<br>Pfam-B_3087 (release 15.0). The Clostridium neurotoxin family is composed of tetanus neurotoxins and seven serotypes of botulinum neurotoxin. The structure of the botulinum neurotoxin reveals a four domain protein.  The N-terminal catalytic domain (Pfam:PF01742), the central translocation domains and two receptor binding domains  .  This domains is the C-terminal receptor binding domain, which adopts a modified beta-trefoil fold with a six stranded beta-barrel and a beta-hairpin triplet capping the domain  . The first step in the intoxication process is a binding event between this domains and the pre-synaptic nerve ending  .. 
PF07952 Clostridium neurotoxin, Translocation domain<br>Pfam-B_4943 (release 15.0). The Clostridium neurotoxin family is composed of tetanus neurotoxin and seven serotypes of botulinum neurotoxin. The structure of the botulinum neurotoxin reveals a four domain protein.  The N-terminal catalytic domain (Pfam:PF01742), the central translocation domains and two receptor binding domains  . Subsequent to cell surface binding and receptor mediated endocytosis of the neurotoxin, an acid induced conformational change in the neurotoxin translocation domain is believed to allow the domain to penetrate the endosome and from a  pore, thereby facilitating the passage of the catalytic domain across the membrane into the cytosol  . The structure of the translocation reveals a pair of helices that are 105 Angstroms long and is structurally distinct from  other pore forming toxins  .. 
PF07953 Clostridium neurotoxin, N-terminal receptor binding<br>Pfam-B_1058 (release 15.0). The Clostridium neurotoxin family is composed of tetanus neurotoxin and seven serotypes of botulinum neurotoxin. The structure of the botulinum neurotoxin reveals a four domain protein.  The N-terminal catalytic domain (Pfam:PF01742), the central translocation domains and two receptor binding domains  . This domains is the N-terminal receptor binding domain,which is  comprised of two seven-stranded beta-sheets sandwiched together to form a jelly role motif  . The role of this domain in receptor binding appears to be indirect.. 
PF07954 Protein of unknown function (DUF1689) <br>Family of fungal proteins with unknown function. A member of this family has been found to localise in the  mitochondria  .. 
PF07955 Protein of unknown function (DUF1687) <br>This is a putative redox protein which is predicted to have a thioredoxin fold containing a single active cysteine  .. 
PF07956 Protein of Unknown function (DUF1690) <br>Family of uncharacterised fungal proteins.. 
PF07957 Ribosomal_MRP8; <br>Protein of unknown function (DUF3294). This family was annotated as mitochondrial Ribosomal protein MRP8, based on the presumed similarity of the S.cerevisiae protein to an E.coli mitochondrial ribosomal protein; however, this similarity is spurious, and the function is not known [Wood, V].. 
PF07958 Protein of unknown function (DUF1688)<br>A family of uncharacterised proteins.. 
PF07959 L-fucokinase<br>Pfam-B_121298 (release 15.0). In the salvage pathway of GDP-L-fucose, free cytosolic fucose is phosphorylated by L-fucokinase to form L-fucose-L-phosphate, which is then further converted to GDP-L-fucose in the reaction catalysed by GDP-L-fucose pyrophosphorylase  .. 
PF07960 CBP4<br>The CBP4 in S. cerevisiae is essential for the expression and activity  of ubiquinol-cytochrome c reductase [1,2].  This family appears to be  fungal specific.. 
PF07961 MBA1-like protein<br>Mba1 is an inner membrane protein that is part of the mitochondrial protein export machinery   .  It binds to the large subunit of mitochondrial ribosomes and cooperates with the C-terminal ribosome-binding domain of Oxa1, which is a central component of the insertion machinery of the inner membrane. In the absence of both Mba1 and the C-terminus of Oxa1, mitochondrial translation products fail to be properly inserted into the inner membrane and serve as substrates of the matrix chaperone Hsp70  .  It is proposed that Mba1 functions as a ribosome receptor that cooperates with Oxa1 in the positioning of the ribosome exit site to the insertion machinery of the inner membrane  .. 
PF07962 Replication Fork Protection Component Swi3<br>Pfam-B_9217 (release 15.0). Replication fork pausing is required to initiate a recombination events.  More specifically, Swi1 is required for recombination near the mat1 locus.  Swi3 has been found to co-purify with Swi1 Swi3, together with Swi1, define a fork protection complex that coordinates leading- and lagging-strand synthesis and stabilises stalled replication forks  . The Swi1-Swi3 complex is required for accurate replication, fork protection and replication checkpoint signalling [1,2]. 
PF07963 Prokaryotic N-terminal methylation motif<br>Pfam-B_6484 (release 14.0). This short motif directs methylation of the conserved phenylalanine residue.  It is most often found at the N-terminus of pilins and other proteins involved in secretion, see Pfam:PF00114, Pfam:PF05946, Pfam:PF02501 and Pfam:PF07596.. 
PF07964 Rec10 / Red1<br>Rec10 / Red1 is involved in meiotic recombination and chromosome  segregation during homologous chromosome formation.  This protein  localises to the synaptonemal complex in S. cerevisiae and the analogous structures (linear elements) in S. pombe  . This family is currently only found in fungi.. 
PF07965 Integrin beta tail domain<br>Pfam-B_1876 (release 14.0). This is the beta tail domain of the Integrin protein.  Integrins are receptors which are involved in cell-cell and cell-extracellular matrix interactions.. 
PF07966 A1 Propeptide <br>Pfam-B_386 (release 15.0). Most eukaryotic endopeptidases (Merops Family A1) are synthesised with signal and propeptides.  The animal pepsin-like endopeptidase propeptides form a distinct family of propeptides, which contain a conserved motif approximately 30 residues long. In pepsinogen A, the first 11 residues of the mature pepsin sequence are displaced by residues of the propeptide.  The propeptide contains two helices that block the active site cleft, in particular the conserved Asp11 residue, in pepsin, hydrogen bonds to a conserved Arg residues in the propeptide.  This hydrogen bond stabilises the propeptide conformation and is probably responsible for triggering the conversion of pepsinogen to pepsin under acidic conditions [1,2].. 
PF07967 C3HC zinc finger-like <br>This zinc-finger like domain is distributed throughout the eukaryotic kingdom in NIPA (Nuclear interacting partner of ALK) proteins. NIPA is implicate to perform some sort of antiapoptotic role in  nucleophosmin-anaplastic lymphoma kinase (ALK) mediated signaling  events  . The domain is often repeated, with the second domain usually containing  a large insert (approximately 90 residues) after the first three  cysteine residues. The Schizosaccharomyces pombe the protein containing this domain  (Swiss:O94506) is involved in mRNA export from the nucleus  .. 
PF07968 Leukocidin/Hemolysin toxin family<br>
PF07969 Amidohydrolase family<br>Pfam-B_751 (release 15.0). 
PF07970 DUF1692; Erv41; Erv46; <br>Endoplasmic reticulum vesicle transporter . Pfam-B_2028 (release 16.0). This family is conserved from plants and fungi to humans. Erv46 works in close conjunction with Erv41 and together they form a complex which cycles between the endoplasmic reticulum and Golgi complex. Erv46-41 interacts strongly with the endoplasmic reticulum glucosidase II. Mammalian glucosidase II comprises a catalytic alpha-subunit and a 58 kDa beta subunit, which is required for ER localisation. All proteins identified biochemically as Erv41p-Erv46p interactors are localised to the early secretory pathway and are involved in protein maturation and processing in the ER and/or sorting into COPII vesicles for transport to the Golgi  .. 
PF07971 Glycosyl hydrolase family 92<br>Pfam-B_1199 (release 16.0). Members of this family are alpha-1,2-mannosidases, enzymes which remove alpha-1,2-linked mannose residues from Man(9)(GlcNAc)(2) by hydrolysis. They are critical for the maturation of N-linked oligosaccharides and ER-associated degradation  .. 
PF07972 NrdI Flavodoxin like <br>Pfam-B_1603 (release 16.0). 
PF07973 Threonyl and Alanyl tRNA synthetase second additional domain<br>Pfam-B_270 (release 16.0). The catalytically active from of threonyl/alanyl tRNA synthetase is a dimer. Within the tRNA synthetase class II dimer, the bound tRNA interacts with both monomers making specific interactions with the catalytic domain, the C-terminal domain, and this domain (the second additional domain).  The second additional domain is comprised of a pair of perpendicularly orientated antiparallel beta sheets, of four and three strands, respectively, that surround a central alpha helix that forms the core of the domain  .. 
PF07974 EGF-like domain<br>Pfam-B_80 (Release 16.0). This family contains EGF domains found in a variety of extracellular proteins.. 
PF07975 TFIIH C1-like domain<br>Pfam-B_10678 (release 16.0). The carboxyl-terminal region of TFIIH is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif.  The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C (Pfam:PF00130)  .. 
PF07976 Phenol hydroxylase, C-terminal dimerisation domain <br>Pfam-B_19435 (release 16.0). Phenol hydroxylase acts a homodimer, to hydroxylates phenol to catechol or similar product.  The enzyme is comprised of three domains.  The first two domains from the active site.  The third domain, this domain, is involved in forming the dimerisation interface.  The domain adopts a thioredoxin-like fold  . . 
PF07977 FabA-like domain<br>This enzyme domain has a HotDog fold.. 
PF07978 NIPSNAP <br>Pfam-B_3436 (release 16.0). Members of this family include many hypothetical proteins.  It also  includes members of the NIPSNAP family which have putative roles in  vesicular transport  .  This domain is often found in duplicate.  . 
PF07979 Intimin C-type lectin domain<br>Pfam-B_1879 (Release 16.0). This domain is found at the C-terminus of intimin. Its structure has been solved and shown to have a C-lectin type of structure  . Intimin is a bacterial adhesion molecule involved in intimate attachment of enteropathogenic and enterohemorrhagic Escherichia coli to mammalian host cells. Intimin targets the translocated intimin receptor (Tir), which is exported by the bacteria and integrated into the host cell plasma membrane.. 
PF07980 SusD_RagB;<br>Pfam-B_1855 (release 16.0). This family includes several hypothetical proteins.  It also contains RagB, Swiss:Q9ZA59, a protein involved in signalling   and SusD, Swiss:Q8A1G2, an outer membrane protein involved in nutrient binding  .. 
PF07981 Plasmodium repeat_MYXSPDY<br>Pfam-B_3138 (release 16.0). This repeat is found in two hypothetical Plasmodium proteins.. 
PF07982 Herpes UL74 glycoproteins <br>Pfam-B_3076 (release 16.0). Members of this family are viral glycoproteins that form part of an  envelope complex  .. 
PF07983 X8 domain<br>Pfam-B_374 (Release 16.0). The X8 domain   domain contains at least 6 conserved cysteine residues that presumably form three disulphide bridges. The domain is found in an Olive pollen allergen   as well as at the C-terminus of several families of glycosyl hydrolases  . This domain may be involved in carbohydrate binding. This domain is characteristic of GPI-anchored domains [4,5].. 
PF07984 Domain of unknown function (DUF1693) <br>Pfam-B_3630 (release 16.0). This family contains many hypothetical proteins.  It also includes four nematode prion-like proteins. This domain has been identified as part of the nucleotidyltransferase superfamily  .. 
PF07985 SRR1<br>Pfam-B_29119 (release 16.0). SRR1 proteins are signalling proteins involved in regulating the  circadian clock in Arabidopsis .. 
PF07986 Tubulin binding cofactor C<br>Pfam-B_4111 (release 16.0). Members of this family are involved in the folding pathway of tubulins and form a beta helix structure  .. 
PF07987 Bacterial_GLE1; <br>Domain of unkown function (DUF1775). Pfam-B_12641 (release 16.0). Domain found in bacteria with undetermined function. Its structure has been determined and is an immunoglobulin-like fold.. 
PF07988 Wos2;<br>Pfam-B_4851 (release 16.0). This region of Myb proteins has previously been described as the transcriptional activation domain present in the vertebrate c-Myb and A-Myb, but neither vertebrate B-Myb proteins nor Myb proteins of invertebrates. Because vertebrate B-Myb (but neither A-Myb nor c-Myb) can partially complement Drosophila Myb null mutants, this region appears to have been a relatively recent insertion.. 
PF07989 Spindle_assoc; <br>Microtubule associated. Pfam-B_45034 (release 16.0). This presumed domain has been identified in two microtubule associated proteins in Schizosaccharomyces pombe, Mto1 and Pcp1. Mto1 has been identified in association with spindle pole body and non-spindle pole body microtubules  . The pericentrin homolog Pcp1 is also associated with the fungal centrosome or spindle pole body (SPB)  .. 
PF07990 Nucleic acid binding protein NABP<br>Pfam-B_10222 (release 16.0). Many members of this family are putative nucleic acid binding proteins. One member of this family has been partially characterised   and  contains two putative phosphorylation sites and a possible dimerisation  / leucine zipper domain.. 
PF07991 Acetohydroxy acid isomeroreductase, catalytic domain<br>Prodom_2380 (release 99.1). Acetohydroxy acid isomeroreductase catalyses the conversion of acetohydroxy acids into dihydroxy valerates. This reaction is the second in the synthetic pathway of the essential branched side chain amino acids valine and isoleucine.. 
PF07992 Pyridine nucleotide-disulphide oxidoreductase<br>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.. 
PF07993 Male sterility protein<br>Pfam-B_1115 (release 6.4). 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.. 
PF07994 Myo-inositol-1-phosphate synthase<br>Pfam-B_959 (release 4.1). This is a family of myo-inositol-1-phosphate synthases. Inositol-1-phosphate catalyses the conversion of glucose-6- phosphate to inositol-1-phosphate, which is then dephosphorylated  to inositol  . Inositol phosphates play an important role in  signal transduction.. 
PF07995 Glucose / Sorbosone dehydrogenase<br>Pfam-B_1863 (release 16.0). Members of this family are glucose/sorbosone dehydrogenases that possess a beta-propeller fold.. 
PF07996 Type IV secretion system proteins<br>Pfam-B_4497 (release 16.0). Members of this family  are components of the type IV  secretion system.  They mediate intracellular transfer of macromolecules via a mechanism ancestrally related to that of bacterial conjugation  machineries   .. 
PF07997 Protein of unknown function (DUF1694)<br>Pfam-B_4517 (release 16.0). This family contains many hypothetical proteins.. 
PF07998 DUF1695; <br>Peptidase family M54. Pfam-B_4509 (release 16.0). This is a family of metallopeptidases.  Two human proteins have been reported to degrade synthetic substrates and peptides  .. 
PF07999 Retrotransposon hot spot protein<br>Pfam-B_4567 (release 16.0). Members of this family are retrotransposon hot spot proteins.  They  are associated with polymorphic subtelomeric regions in Trypanosoma. These proteins contain a P-loop motif.. 
PF08000 DUF1696;<br>Pfam-B_4657 (release 16.0). This family contains many bacterial hypothetical proteins. The structures of Swiss:A1SD03, PDB:3hsa, and Swiss:A3QB43, PDB:3dcx, show similarities to the PH or pleckstrin homology domain. First evidence of PH-like domains in bacteria suggests role in  cell envelope stress response  .. 
PF08001 CMV US<br>Pfam-B_4698 (release 16.0). This is a family of unique short (US) cytoplasmic glycoproteins which are expressed in cytomegalovirus  .. 
PF08002 Protein of unknown function (DUF1697)<br>Pfam-B_4800 (release 16.0). This family contains many hypothetical bacterial proteins.. 
PF08003 DUF1698; <br>Protein of unknown function (DUF1698). Pfam-B_4787 (release 16.0). This family contains many hypothetical proteins.  It also includes two  putative methyltransferase proteins, Swiss:Q8EEE6 and Swiss:Q88MX8.. 
PF08004 Protein of unknown function (DUF1699)<br>Pfam-B_4896 (release 16.0). This family contains many archaeal proteins which have very conserved sequences.  . 
PF08005 PHR domain <br>This domain is called PHR as it was original found in the proteins PAM (Swiss:O75592), highwire (Swiss:Q9NB71) and RPM (Swiss:Q17551)  .  This domain can be duplicated in the highwire, PFAM and PRM sequence.\.      The C-terminal region of the protein BTBD1 includes the PHR domain and is known to interact with Topoisomerase I, an enzyme which relaxes DNA supercoils  .. 
PF08006 Protein of unknown function (DUF1700)<br>Pfam-B_5023 (release 16.0). This family contains many hypothetical bacterial proteins and two putative membrane proteins (Swiss:Q6GFD0 and Swiss:Q6G806). . 
PF08007 DUF1701; <br>Cupin superfamily protein. Pfam-B_5011 (release 16.0). This family contains many hypothetical proteins that belong to the cupin superfamily.. 
PF08008 Viral cysteine rich<br>Pfam-B_4965 (release 16.0). Members of this family are polydna viral proteins that contain a cysteine rich motif  .  Some members of this family have  multiple copies of this domain.. 
PF08009 TOM13; <br>CDP-alcohol phosphatidyltransferase 2. Pfam-B_51131 (release 16.0). This domain is found on CDP-alcohol phosphatidyltransferases. These enzymes 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.. 
PF08010 Bacteriophage protein GP30.3<br>Pfam-B_5273 (release 16.0). Proteins in this family are bacteriophage GP30.3 proteins.  Their  function is poorly characterised   .. 
PF08011 Protein of unknown function (DUF1703)<br>Pfam-B_5377 (release 16.0). This family contains many hypothetical bacterial proteins.  It has been identified as a member of the PD-(D/E)XK nuclease superfamily through transitive meta profile searches  . DUF1703 has the predicted secondary structure pattern of the restriction endonuclease-like fold core and contains an additional beta-strand at the C-terminus  .. 
PF08012 Protein of unknown function (DUF1702)<br>Pfam-B_5312 (release 16.0). This family of proteins contains many bacterial proteins that are encoded by the UnbL gene.\.    The function of these proteins is unknown.. 
PF08013 Tagatose 6 phosphate kinase<br>Pfam-B_5149 (release 16.0). Proteins in this family are tagatose 6 phosphate kinases. . 
PF08014 Domain of unknown function (DUF1704)<br>Pfam-B_5490 (release 16.0). This family contains many hypothetical proteins.. 
PF08015 Fungal mating-type pheromone<br>This family corresponds to mating-type pheromone proteins. The homobasidiomycetes, or mushroom fungi, have arguably the most complex mating system of all known organisms. Many species possess a mating system known as bifactorial incompatibility, where two unlinked loci control the mating -type of an individual incompatibility loci (the A and  B mating-type loci). Each A mating-type sublocus encodes a pair of divergently transcribed homeodomain transcription  factors while the genes responsible for B mating-type  activity encode lipopeptide pheromones and G-protein -coupled pheromone receptors  .. 
PF08016 Polycystin cation channel<br>This family contains the cation channel region of PKD1 and PKD2 proteins.. 
PF08017 Fibrinogen binding protein <br>Pfam-B_4323 (release 16.0). Proteins in this family bind to fibrinogen.  Members of this family includes the fibrinogen receptor, FbsA, (Swiss:Q8GIU3) which  mediates platelet aggregation  .. 
PF08018 Frog antimicrobial peptide <br>This family includes antimicrobial peptides secreted from skins of frogs. The secretion of antimicrobial peptides from the skins of frogs plays an important role in the self defense of these frogs. Structural characterization of these peptides showed that they belonged to four known families: the brevinin-1 family, the esculentin-2 family, the ranatuerin-2 family and the temporin family  .. 
PF08019 Domain of unknown function (DUF1705)<br>Pfam-B_1101 (release 16.0). Some members of this family are putative bacterial membrane proteins. This domain is found immediately N terminal to the sulfatase domain in many sulfatases.. 
PF08020 Protein of unknown function (DUF1706)   <br>Pfam-B_5540 (release 16.0). This family contains many hypothetical proteins from bacteria  and yeast.. 
PF08021 Siderophore-interacting FAD-binding domain<br>
PF08022 FAD-binding domain<br>Pfam-B_728 (release 4.2). 
PF08023 Frog antimicrobial peptide <br>This family consists of the major classes of antimicrobial peptides secreted from the skin of frogs that  protect the frogs against invading microbes. They are typically between 10-50 amino acids long and are derived from proteolytic cleavage of larger precursors. Major classes of peptides such  esculentin, gaegurin, brevinin, rugosin and ranatuerin are included in this family  .. 
PF08024 Ant antimicrobial peptide<br>Short protein clustering. This family consists of the ponericin family of antimicrobial peptides isolated from predatory ant Pachycondyla goeldii. The ponericin peptides may adopt amphipathic alpha-helical structure in polar environments. In the ant colony, these peptides exhibit a defensive role against microbial pathogens  arising from prey introduction and/or ingestion  .. 
PF08025 Spider antimicrobial peptide<br>Short protein clustering. This family includes antimicrobial peptides isolated from the crude venom of the wolf spider Oxyopes kitabensis. These peptides, known as oxyopinins, are the largest linear cationic amphipathic peptides chemically characterised and exhibit disrupting activities towards biological membranes  .. 
PF08026 Bee antimicrobial peptide<br>Short protein clustering. This family consists of antimicrobial peptides produced by bees. These peptides have strong antimicrobial and some anti-fungal activity and has homology to abaecin which is the largest proline-rich antimicrobial peptide isolated from European bumblebee Bombus pascuorum  .. 
PF08027 Albumin I<br>Pfam-B_100627 (release 16.0). The albumin I protein, a hormone-like peptide, stimulates kinase activity upon binding a membrane bound 43 kDa receptor. The structure of this domain reveals a knottin like fold, comprise of three beta strands  .. 
PF08028 Acyl-CoA dehydrogenase, C-terminal domain<br>Pfam-B_8101 (release 16.0). 
PF08029 HisG, C-terminal domain<br>Pfam-B_1550 (release 16.0). 
PF08030 Ferric reductase NAD binding domain<br>
PF08031 Berberine and berberine like <br>Pfam-B_649 (release 16.0). This domain is found in the berberine bridge and berberine bridge- like enzymes which are involved in the biosynthesis of numerous isoquinoline alkaloids.  They catalyse the transformation of the N-methyl group of (S)-reticuline into the C-8 berberine bridge carbon of (S)-scoulerine   .. 
PF01238 Phosphomannose isomerase type I<br>This is a family of Phosphomannose isomerase type I enzymes (EC 5.3.1.8).. 
PF08032 RNA 2'-O ribose methyltransferase substrate binding<br>Pfam-B_742 (release 16.0). This domain is a RNA 2'-O ribose methyltransferase substrate binding domain.. 
PF08033 Sec23/Sec24 beta-sandwich domain<br>
PF08034 Trematode eggshell synthesis protein<br>This domain has been identified in a number of distantly related species  of trematodes. This protein domain is crucial for eggshell synthesis in trematodes (Ebersberger I).. 
PF08035 Opioids neuropeptide<br>This family corresponds to the conserved YGG motif that is found in a wide variety of opioid neuropeptides such as enkephalin.. 
PF08036 Diapausin family of antimicrobial peptide<br>Short protein clustering. This family consists of diapausin-related antimicrobial peptides. Diapause during periods of environmental adversity is an essential part of the life cycle of many organisms with the molecular basis being different among animals.  Diapause-specific peptides provide anti-fungal activity and act as N-type voltage-gated calcium channel blocker  .. 
PF08037 Attractin family<br>Short protein clustering. This family consists of the attractin family of water-borne pheromone. Mate attraction in Aplysia  involves a long-distance water-borne signal in  the form of the attractin peptide, that is released  during egg laying. These peptides contain 6 conserved  cysteines and are folded into 2 antiparallel helices.  The second helix contains the IEECKTS sequence conserved in Aplysia attractins  .. 
PF08038 TOM7 family<br>Short protein clustering. This family consists of TOM7 family of mitochondrial import receptors. TOM7 forms part of the translocase of the outer mitochondrial membrane (TOM) complex and it appears to function as a modulator of the dynamics of the mitochondrial protein transport machinery by promoting the dissociation of subunits of the outer membrane translocase  .. 
PF08039 Mit_preoteolip; <br>Mitochondrial proteolipid. Short protein clustering. This family consists of proteins with similarity to the mitochondrial proteolipids. Mitochondrial proteolipid consists of about 60 amino acids residues and is about 6.8 kDa in size  .. 
PF08040 MNLL subunit<br>Short protein clustering. This family consists of the MNLL subunits of NADH-ubiquinone  oxidoreductase complex. NADH-ubiquinone oxidoreductase is involved in the transfer of electrons from NADH to the electron  transport chain. This oxidation of NADH is coupled to proton  transfer across the membrane, generating a proton motive force  that is utilised for the synthesis of ATP  . MNLL subunit is   one of the many subunits found in the complex and it contains  a mitochondrial import sequence. However, the role of MNLL  subunit is unclear  .. 
PF08041 PetM family of cytochrome b6f complex subunit 7<br>Short protein clustering. This family consists of the PetM family of cytochrome b6f complex subunit IV. The cytochrome b6f complex consists of 7 subunits and contains 2 beta hemes and 1 chlorophyll alpha per cytochrome f. It is highly active in transferring electrons from decylplastoquinol to oxidised plastocyanin  .. 
PF08042 PqqA family<br>Short protein clustering. This family consists of proteins belonging to the coenzyme Pyrroloquinoline quinone A (pqqA) family. PQQ is the non-covalently bounded prosthetic group  of many quinoproteins catalysing reactions in the periplasm of Gram-negative bacteria. PQQ is formed by the fusion of glutamate and tyrosine and synthesis of PQQ require the proteins encoded by the pqqABCDEF operon but details of the biosynthetic pathway are  unclear  .. 
PF08043 Actin_bind_SAA; <br>The repeat has the consensus sequence GDV(K/Q/R)(T/S/G)X(R/K/T) WLFETXPLD.  This repeat motif is typically found in the N-terminus of the proteins, with a copy number between 2 and 28 repeats.  Direct evidence for binding to and stabilising F-actin has been found   in the human protein Swiss:Q702N9. The homologues in mouse and chicken localise in the adherens junction complex of the intercalated disc in cardiac muscle and in the myotendon junction of skeletal muscle. mXin may co-localise with Vinculin which is known to attach the actin to the cytoplasmic membrane  . It has been shown that the amino-terminus of human xin (CMYA1) binds the EVH1 domain of Mena/VASP/EVL, and the carboxy-terminus binds the, for the filamin family unique, domain 20 of filaminC  . This confirms the proposed role of xin repeat containing proteins as F-actin-binding adapter proteins.. 
PF08044 Domain of unknown function (DUF1707)<br>This domain is found in a variety of Actinomycetales proteins.  All of  the proteins containing this domain are hypothetical and probably membrane bound or associated. Currently, it is unclear to the function  of this domain.. 
PF08045 Cell division control protein 14, SIN component<br>Cdc14 is a component of the septation initiation network (SIN) and is required for the localisation and activity of Sid1.  Sid1 is a protein kinase that localises asymmetrically to one spindle pole body (SPB) in anaphase disappears prior to cell separation    .. 
PF08046 IlvGEDA operon leader peptide<br>Short protein clustering. This family consists of the leader peptides of ilvGEDA  operon. The expression of the ilvGEDA operon of E coli  K-12 is multivalently controlled by the three branched -chain amino acids. Regulation is thought to occur by  attenuation of transcription in response to the changing  levels of the cognate tRNAs. Transcription of this operon  is usually terminated at the end of the leader (regulatory)  region  .. 
PF08047 Histidine operon leader peptide<br>Short protein clustering. This family consists of the leader peptide of  the histidine (his) operon. The his operon contains  all the genes necessary for histidine biosynthesis.  The region corresponding to the untranslated 5' end  of the transcript, named the his leader region, displays  the typical features of the T box transcriptional  attenuation mechanism which is involved in the regulation  of many amino acid biosynthetic operons  .. 
PF08048 Tap RepA1 leader peptide<br>Short protein clustering. This family consists of the RepA1 leader peptides.  The frequency of replication of IncFII plasmid NR1 during the cell division cycle is regulated by the control of the synthesis of the plasmid-specific replication initiation protein (RepA1). When RepA1 is synthesised, it binds to the plasmid replication origin (ori) and effects the assembly of a replication complex composed of host proteins that mediate the replication of the plasmid  . The tap gene encodes a 24-amino acids protein. The translation of tap is required for translation of repA.. 
PF08049 IlvB leader peptide<br>Short protein clustering. This family consists of the leader peptides of the ilvB operon. This region encodes a potential leader polypeptide containing 32 amino acids, 12 of which are the regulatory amino acids valine and leucine. A model for the multivalent regulation of this operon by valyl- and leucyl-tRNA is proposed on the basis of the mutually exclusive formation of five strong stem-and-loop structures in the leader mRNA  .. 
PF08050 Tetracycline resistance leader peptide<br>Short protein clustering. This family consists of the tetracycline resistance leader peptide. The presence of 3 inverted repeats  which can form 2 different conformations of mRNA  suggests that the tetracycline resistance (TcR) region is regulated by a translational attenuation mechanism. A Rho-independent transcriptional terminator structure is present immediately after the translational stop codon  of the TET protein  .. 
PF08051 Erythromycin resistance leader peptide<br>Short protein clustering. This family consists of erythromycin resistance gene leader peptides.  These leader peptides are involved in the translational attenuation of erythromycin resistance genes. Interestingly, the consensus sequence of peptides conferring erythromycin resistance is similar to that of the leader peptides, thus indicating that a similar type of interaction between the nascent peptide and antibiotics can occur in both cases  . This family also includes a small number of regions from within larger proteins from actinomycetes.. 
PF08052 PyrBI operon leader peptide<br>Short protein clustering. This family consists of the pyrBI operon leader peptides. The expression of the pyrBI operon, which encodes the subunits of the pyrimidine biosynthetic enzyme aspartate transcarbamylase.  is regulated primarily through a UTP-sensitive transcriptional attenuation control mechanism.  In this mechanism, the concentration of UTP determines the extent of coupling between transcription and translation within the pyrBI leader region, hence determining the level of rho-independent transcriptional termination at an attenuator preceding the pyrB gene  .. 
PF08053 Tryptophanese operon leader peptide<br>Short protein clustering. This family consists of the tryptophanese (tna) operon leader peptide. Tna catalyses the degradation of L-tryptophan to indole, pyruvate and ammonia, enabling the bacteria to utilise tryptophan as a source of carbon, nitrogen and energy.  The tna operon of E. coli contains two major structural genes, tnaA and tnaB. Preceding tnaA in the tna operon is a 319 -nucleotide transcribed regulatory region that contains the coding region for a 24-residue leader peptide, TnaC. The RNA sequence in the vicinity of the tnaC stop codon is rich in Cytidylate residues which is required for efficient Rho -dependent termination in the leader region of the tna operon  .. 
PF08054 Leucine operon leader peptide<br>Short protein clustering. This family consists of the leucine operon leader peptide. The leucine operon is involved in the control of the biosynthesis of leucine. Four adjacent leucine codons within the leucine leader RNA are critically important in transcription attenuation-mediated control of leucine operon expression in bacteria. The leader RNA contains translational start and stop signals, a cluster of four leucine codons and overlapping regions of dyad symmetry that are capable of forming stem-and-loop structures  .. 
PF08055 Tryptophan leader peptide<br>Short protein clustering. This family consists of the tryptophan (trp) leader peptides. Tryptophan accumulation is the principal event resulting in downregulation of transcription of the structural genes of the trp operon. The leader peptide of the trp operon forms mutually exclusive secondary structures that would either result in the termination of transcription of the trp operon when tryptophan is in plentiful supply or vice versa  .. 
PF08056 Tryptophan operon leader peptide<br>Short protein clustering. This family consists of the tryptophan operon  leader peptides. The tryptophan operon is regulated  by transcription attenuation in response to changes  in the level of tryptophan. The transcript of the  leader peptide can adopt alternative mutually-exclusive  secondary structures that would either result in  termination of transcription of the tryptophan structural  genes or in transcription of the entire operon  .. 
PF08057 Erythromycin resistance leader peptide<br>Short protein clustering. This family consists of erythromycin resistance gene leader peptides.  These leader peptides are involved in the transcriptional attenuation control of the synthesis of the macrolide-lincosamide -streptogramin B resistance protein. It acts as a transcriptional attenuator, in contrast to other inducible erm genes. The mRNA leader sequence can fold in either of two mutually exclusive conformations, one of which is postulated to form in the absence of induction, and to contain two rho factor-independent terminators.  .. 
PF08058 Nuclear pore complex component<br>Wood V, Mistry J, Novatchkova M. Proteins containing this domain are components of the  nuclear pore complex  .  One member of this family  is Nucleoporin POM34 (Swiss: Q12445) which is thought to have a role in  anchoring peripheral Nups into the pore and mediating pore formation  .. 
PF08059 SEP domain<br>Pfam-B_1894 (release 16.0). The SEP domain is named after Saccharomyces cerevisiae Shp1, Drosophila melanogaster eyes closed gene (eyc), and vertebrate p47.  In p47, the SEP domain has been shown to bind to and inhibit the cysteine protease cathepsin L  .  Most SEP domains are succeeded closely by a UBX domain  .. 
PF08060 NOSIC (NUC001) domain<br>This is the central domain in Nop56/SIK1-like proteins  .. 
PF08061 P68HR (NUC004) repeat<br>This short region is found in two copies in p68-like RNA helicases  .. 
PF08062 P120R (NUC006) repeat<br>This characteristic repeat of proliferating cell nuclear antigen P120 is found in three copies  .. 
PF08063 PADR1 (NUC008) domain<br>This domain is found in poly(ADP-ribose)-synthetases  . The function of this domain is unknown.. 
PF08064 UME (NUC010) domain<br>This domain is characteristic of UVSB PI-3 kinase, MEI-41 and ESR1  .. 
PF08065 K167R (NUC007) repeat<br>This family represents the K167/Chmadrin repeat  . The function of this repeat is unknown.. 
PF08066 PMC2NT (NUC016) domain<br>This domain is found at the N-terminus of 3'-5' exonucleases with HRDC domains, and also in putative exosome components  .. 
PF08067 ROKNT (NUC014) domain<br>This presumed domain is found at the N-terminus of RNP K-like proteins that also contains KH domains Pfam:PF00013  .. 
PF08068 DKCLD (NUC011) domain<br>This is a TruB_N/PUA domain associated N-terminal domain of Dyskerin-like proteins  .. 
PF08069 Ribosomal S13/S15 N-terminal domain<br>This domain is found at the N-terminus of ribosomal S13 and S15 proteins.\.      This domain is also identified as NUC021  .. 
PF08070 DTHCT (NUC029) region<br>The DTCHT region is the C-terminal part of DNA gyrases B / topoisomerase IV / HATPase proteins  . This region is composed of quite low complexity sequence.. 
PF08071 RS4NT (NUC023) domain<br>This is the N-terminal domain of Ribosomal S4 / S4e proteins. This domain is associated with S4 and KOW domains  .. 
PF08072 BDHCT (NUC031) domain<br>This is a C-terminal domain in Bloom's syndrome DEAD helicase subfamily  .. 
PF08073 CHDNT (NUC034) domain<br>The CHDNT domain is found in PHD/RING finger and chromo domain-associated helicases  .. 
PF08074 CHDCT2 (NUC038) domain<br>The CHDCT2 C-terminal domain is found in PHD/RING finger and chromo domain-associated CHD-like helicases  .. 
PF08075 NOPS (NUC059) domain<br>This domain is found at the C-terminus of NONA and PSP1 proteins  adjacent to 1 or 2 Pfam:PF00076 domains  .. 
PF08076 Tetracycline resistance determinant leader peptide<br>Short protein clustering. This family consists of the tetracycline resistance  determinant tet(M) leader peptides. A short open  reading frame corresponding to a 28 amino acid peptide  which contain a number of inverted repeat sequences was  found immediately upstream of the tet(M). Transcriptional  analyses has found that expression of tet(M) resulted from an  extension of a small transcript representing the upstream  leader region into the resistance determinant. Thus this  leader sequence is responsible for transcriptional attenuation  and thus regulation of the transcription of tet(M)  .. 
PF08077 Chloramphenicol resistance gene leader peptide<br>Short protein clustering. This family consists of chloramphenicol (Cm) resistance  gene leader peptides. Inducible resistance to Cm in both  Gram positive and Gram negative bacteria is controlled  by translation attenuation. In translation attenuation,  the ribosome-binding-site (RBS) for the resistance  determinant is sequestered in a secondary structure domain  within the mRNA. Preceding the secondary structure is a  short, translated ORF termed the leader. Ribosome stalling  in the leader causes the destabilization of the downstream  secondary structure, allowing initiation of translation  of the Cm resistance gene  .. 
PF08078 PsaX family<br>Short protein clustering. This family consists of the PsaX family of photosystem I (PSI) protein subunits.\.       PSI is a large multi-subunit pigment protein complex embedded in the thylakoid membranes of green plants and cyanobacteria. PsaX is one of the 12 protein subunits found in PSI and these subunits are arranged as monomers or trimers within the membrane as shown by the structure of the trimeric complex from Synechococcus elongatus  .. 
PF08079 Ribosomal L30 N-terminal domain<br>This presumed domain is found at the N-terminus of Ribosomal L30 proteins and has been termed RL30NT or NUC018  .. 
PF08080 RNPHF zinc finger<br>This domain is a putative zinc-binding domain (CHHC motif) in RNP H and F.  The domain is often associated with Pfam:PF00076.. 
PF08081 RBM1CTR (NUC064) family<br>This C-terminal region is found in RBM1-like RNA binding hnRNPs  .. 
PF08082 PRO8NT (NUC069), PrP8 N-terminal domain<br>The PRO8NT domain is found at the N-terminus of pre-mRNA splicing factors of PRO8 family  . The NLS or nuclear localisation signal for these spliceosome proteins begins at the start and runs for 60 residues. N-terminal to this domain is a highly variable proline-rich region  .. 
PF08083 PROCN (NUC071) domain<br>The PROCN domain is the central domain in pre-mRNA splicing factors of PRO8 family  .. 
PF08084 PROCT (NUC072) domain<br>The PROCT domain is the C-terminal domain in pre-mRNA splicing factors of PRO8 family  .. 
PF08085 Entericidin EcnA/B family<br>Short protein clustering. This family consists of the entericidin antidote/toxin peptides. The entericidin locus is activated in stationary phase under high osmolarity conditions by rho-S and simultaneously repressed by the osmoregulatory EnvZ/OmpR signal transduction pathway. The entericidin locus encodes tandem paralogous genes (ecnAB) and directs the synthesis of two small cell-envelope lipoproteins which can maintain plasmids in bacterial population by means of post-segregational killing  .. 
PF08086 Ergtoxin family<br>Short protein clustering. This family consists of ergtoxin peptides which are toxins secreted by the scorpions.\.  The ergtoxins are capable of blocking the function of K+ channels. More than 100 ergtoxins have been found from scorpion venoms and they have been classified into three subfamilies according to their primary structures  .. 
PF08087 Conotoxin O-superfamily<br>Short protein clustering. This family consists of members of the conotoxin  O-superfamily. The O-superfamily of conotoxins  consists of 3 groups of Conus peptides that belong  to the same structural group. These 3 groups differ  in their pharmacological properties: the w-conotoxins  which inhibit calcium channels, the delta-conotoxins  which slow down the inactivation rate of voltage -sensitive sodium channels and the muO-conotoxins block  the voltage sensitive sodium currents  .. 
PF08088 Conotoxin I-superfamily<br>Short protein clustering. This family consists of the I-superfamily of  conotoxins. This is a new class of peptides in  the venom of some Conus species. These toxins  are characterised by four disulfide bridges and  inhibit of modify ion channels of nerve cells.  The I-superfamily conotoxins is found in five or  six major clades of cone snails and could possible  be found in many more species  .. 
PF08089 Huwentoxin-II family<br>Short protein clustering. This family consists of the huwentoxin-II (HWTX-II)  family of toxins secreted by spiders. These toxins are found in venom that secreted from the bird spider  Selenocosmia huwena Wang. The HWTX-II adopts a novel  scaffold different from the ICK motif that is found in  other huwentoxins. HWTX-II consists of 37 amino acids  residues including six cysteines involved in three  disulfide bridges  .. 
PF08090 Enterotoxin_ST; <br>Heat stable E.coli enterotoxin 1. Short protein clustering. Heat-stable toxin 1 of entero-aggregative E.coli (EAST1) is a small toxin. It is not, however, solely associated with entero-aggregative E.coli but also with many other diarrhoaeic E. coli families. Some studies have established the role of EAST1 in some human outbreaks of diarrhoea. Isolates from farm animals have been shown to carry the astA gene coding for EAST1. However, the relation between the presence of EAST1 and disease is not conclusive  .. 
PF08091 Spider insecticidal peptide<br>Short protein clustering. This family consists of insecticidal peptides isolated  from venom of spiders of Aptostichus schlingeri and  Calisoga sp. Nine insecticidal peptides were isolated  from the venom of the Aptostichus schlingeri spider and  seven of these toxins cause flaccid paralysis to insect  larvae within 10 min of injection. However, all nine  peptides were lethal within 24 hours  .. 
PF08092 Magi peptide toxin family <br>Short protein clustering. This family consists of Magi peptide toxins (Magi 1, 2 and 5) isolated from the venom of Hexathelidae spider. These insecticidal peptide toxins bind to sodium channels and induce flaccid paralysis when injected into lepidopteran larvae. However, these peptides are not toxic to mice when injected intracranially at 20 pmol/g  .. 
PF08093 Magi 5 toxic peptide family<br>Short protein clustering. This family consists of toxic peptides (Magi 5) found in the venom of the Hexathelidae spider. Magi 5 is the first spider toxin with binding affinity to site 4 of a mammalian sodium channel and the toxin has an insecticidal effect on larvae, causing paralysis when injected into the larvae  .. 
PF08094 Conotoxin TVIIA/GS family<br>Short protein clustering. This family consists of conotoxins isolated from the venom  of cone snail Conus tulipa and Conus geographus. Conotoxin  TVIIA, isolated from Conus tulipa displays little sequence  homology with other well-characterised pharmacological  classes of peptides, but displays similarity with conotoxin GS, a peptide from Conus geographus. Both these peptides  block skeletal muscle sodium channels and also share  several biochemical features and represent a distinct subgroup  of the four-loop conotoxins  .. 
PF08095 Hefutoxin family<br>Short protein clustering. This family consists of the hefutoxins that are found  in the venom of the scorpion Heterometrus fulvipes.  These toxins, kappa-hefutoxin1 and kappa-hefutoxin2,  exhibit no homology to any known toxins. The hefutoxins  are potassium channel toxins  .. 
PF08096 Bombolitin family<br>Short protein clustering. This family consists of the bombolitin peptides that  are found in the venom of the bumblebee Megabombus  pennsylvanicus. Bombolitins are structurally and  functionally very similar. They lyse erythrocytes and  liposomes, release histamine from rat peritoneal mast  cells, and stimulate phospholipase A2 from different  sources  .. 
PF08097 Conotoxin T-superfamily<br>Short protein clustering. This family consists of the T-superfamily of conotoxins.  Eight different T-superfamily peptides from five Conus species were identified. These peptides share a consensus signal sequence, and a conserved arrangement of cysteine residues. T-superfamily peptides were found expressed in venom ducts of all major feeding types of Conus, suggesting that the T-superfamily is a large and diverse group of peptides, widely distributed in the 500 different Conus species  .. 
PF08098 Anemonia sulcata toxin III family<br>Short protein clustering. This family consists of the Anemonia sulcata toxin III  (ATX III) neurotoxin family. ATX III is a neurotoxin  that is produced by sea anemone; it adopts a compact  structure containing four reverse turns and two other  chain reversals, but no regular alpha-helix or beta-sheet.  A hydrophobic patch found on the surface of the peptide may  constitute part of the sodium channel binding surface  .. 
PF08099 Scorpion calcine family<br>Short protein clustering. This family consists of the calcine family of scorpion  toxins. The calcine family consists of Maurocalcine and  Imperatoxin. These toxins have been shown to be potent  effector of ryanodyne-sensitive calcium channel from  skeletal muscles. These toxins are thus useful for  dihydropyridine receptor/ryanodyne receptor interaction  studies [1,2].. 
PF08100 Dimerisation domain<br>Pfam-B_455 (Release 16.0). This domain is found at the N-terminus of a variety of plant O-methyltransferases. It has been shown to mediate dimerisation of these proteins  .. 
PF08101 Domain of unknown function (DUF1708)<br>Mistry J, Wood V, Novatchkova M. This is a yeast domain of unknown function.. 
PF08102 Scorpion antimicrobial peptide <br>Short protein clustering. This family consists of antimicrobial peptides secreted by scorpions. Novel antimicrobial peptides have been isolated from scorpions, namely the opistoporin   and the pandinin  . These peptides form essentially helical structures and demonstrate high antimicrobial activity against Gram-negative and Gram-positive bacteria respectively.. 
PF08103 Uperin family<br>Short protein clustering. This family consists of the uperin family of antimicrobial peptides.  Uperin is a wide-spectrum antibiotic peptide isolated from the Australian toadlet, Uperoleia mjobergii. Being only 17 amino acid residues long, it is smaller than most other wide-spectrum antibiotic peptides isolated from amphibians. Uperin adopts a well-defined amphipathic alpha-helix with distinct hydrophilic and hydrophobic faces  .. 
PF08104 Ponericin L family<br>Short protein clustering. This family consists of the ponericin L family of antimicrobial peptides that are isolated from the venom of the predatory ant Pachycondyla goeldii. Ponericin L family shares similarities with dermaseptins. Ponericin L may adopt an amphipathic alpha-helical structure in polar environments and these peptides exhibit a defensive role against microbial pathogens arising from prey introduction and/or ingestion  .. 
PF08105 Metchnikowin family<br>Short protein clustering. This family consists of the metchnikowin family of antimicrobial peptides from Drosophila.\.       metchnikowin is a proline-rich peptide whose expression is immune-inducible. Induction of the metchnikowin gene expression can be mediated either by the TOLL pathway or by the imd gene product. The metchnikowin peptide is unique among the Drosophila antimicrobial peptides in that it is active against both bacteria and fungi  .. 
PF08106 Formaecin family<br>Short protein clustering. This family consists of the formaecin family of  antimicrobial peptides isolated from the bulldog  ant Myrmecia gulosa in response to bacterial  infection. Formaecins are inducible peptide  antibiotics and are active against growing  Escherichia coli but were inactive against other  Gram-negative and Gram-positive bacteria. Formaecin peptides are 16 amino acids long, are rich in proline  and have N-acetylgalactosamine O-linked to a conserved  threonine  .. 
PF08107 Pleurocidin family<br>Short protein clustering. This family consists of the pleurocidin family of antimicrobial peptides. Pleurocidins are found in the skin mucous secretions of the winter flounder (Pleuronectes americanus) and these peptides exhibit antimicrobial activity against Escherichia coli. Pleurocidin is predicted to assume an amphipathic alpha-helical conformation similar to other linear antimicrobial peptides and may play a role in innate host defense  .. 
PF08108 Halocidin family<br>Short protein clustering. This family consists of the halocidin family of antimicrobial peptides. Halocidins are isolated from the haemocytes of the tunicate, Halocynthia aurantium. They are dimeric in structures which are found via a disulfide linkage between cysteines of two different- sized monomers. Halocidins have been shown to have strong antimicrobial activities against a wide variety of pathogenic bacteria and could be ideal candidates as peptide antibiotics against multidrug-resistant bacteria  .. 
PF08109 Lactocin 705 family<br>Short protein clustering. This family consists of lactocin 705 which is a bacteriocin  produced by Lactobacillus casei CRL 705. Lactocin 705 is a class IIb bacteriocin, whose activity depends upon the  complementation of two peptides (705-alpha and 705-beta) of  33 amino acid residues each. Lactocin 705 is active against  several Gram-positive bacteria, including food-borne pathogens  and is a good candidate to be used for biopreservation of  fermented meats  .. 
PF08110 Ocellatin family<br>Short protein clustering. This family consists of the ocellatin family of antimicrobial peptides. Ocellatins are produced from the electrical-stimulated skin secretions of the South American frog, Leptodactylus ocellatus.  The family consists of three structurally related peptides, ocellatin 1, ocellatin 2 and ocellatin 3.  These peptides present hemolytic activity against human erythrocytes and are also active against Escherichia coli  .. 
PF08111 Pea-VEAacid family<br>Short protein clustering. This family consists of the PEA-VEAacid neuropeptides  family. These neuropeptides are isolated from the  abdominal perisympathetic organs of the American cockroach.  These peptides are found together with Pea-YLS-amide and Pea-SKNacid, giving a unique neuropeptide pattern in abdominal  perisympathetic organs. The functions of these neuropeptides  are unknown  .. 
PF08112 ATP synthase epsilon subunit<br>Short protein clustering. This family consists of epsilon subunits of the ATP  synthase. The ATP synthase complex is composed of an  oligomeric transmembrane sector (CF0), and a catalytic  core (CF1). CF1 is composed of 5 subunits, of which  the epsilon subunit functions as a potent inhibitor of  ATPase activity in both soluble and bound CF1. Only  when the epsilon inhibition is disabled is high  ATPase activity detected in ATPase  . 
PF08113 Cytochrome c oxidase subunit IIa family<br>Short protein clustering. This family consists of the cytochrome c oxidase subunit IIa family.  The bax-type cytochrome c oxidase from Thermus thermophilus is known as a two subunit enzyme. From its crystal structure, it was discovered that an additional transmembrane helix 'subunit IIa' spans the membrane.  This subunit consists of 34 residues forming one helix across the membrane. The presence of this subunit seems to be important for the function of cytochrome c oxidases  .. 
PF08114 ATPase proteolipid family<br>Short protein clustering. This family consists of small proteolipids associated with the plasma membrane H+ ATPase. Two proteolipids (PMP1 and PMP2) are associated with the ATPase and both genes are similarly expressed in the wild-type strain of yeast with no modification of the level of transcription of one PMP gene is detected in a strain deleted of the other. Though both proteolipids show similarity with other small proteolipids associated with other cation -transporting ATPases, their functions remain unclear  .. 
PF08115 SFI toxin family<br>Short protein clustering. This family consists of the SFI family of spider toxins. This family of toxins might share structural, evolutionary and functional relationships with other small, highly structurally constrained spider neurotoxins. These toxins are highly selective agonists/antagonists of different voltage-dependent calcium channels and are extremely valuable reagents in the analysis of neuromuscular function  .. 
PF08116 PhTx neurotoxin family<br>Short protein clustering. This family consists of PhTx insecticidal neurotoxins that are found in the venom of Brazilian, Phoneutria nigriventer. The venom of the Phoneutria nigrivente contains numerous neurotoxic polypeptides of 30-140 amino acids which exert a range of biological effects.  While some of these neurotoxins are lethal to mice after intracerebroventricular injections, others are extremely toxic to insects of the orders Diptera and Dictyoptera but had much weaker toxic effects on mice  .. 
PF08117 Ptu family<br>Short protein clustering. This family consists of toxic peptides that are  isolated from the saliva of assassin bugs. The  saliva contains a complex mixture of proteins  that are used by the bug either to immobilise  the prey or to digest it. One of the proteins (Ptu1)  has been purified and shown to block reversibly the  N-type calcium channels and to be less specific for  the L- and P/Q- type calcium channels expressed in  BHK cells  .. 
PF08118 Yeast mitochondrial distribution and morphology (MDM) proteins <br>Pfam-B_37122 (release 16.0). Proteins in this family are yeast mitochondrial inner membrane proteins MDM31 and MDM32.\.       These proteins are required for the maintenance of mitochondrial morphology, and the stability of mitochondrial DNA  .. 
PF08119 Scorpion acidic alpha-KTx toxin family<br>Short protein clustering. This family consists of acidic alpha-KTx short chain scorpion toxins. These toxins named parabutoxins, block voltage-gated K channels and have extremely low pI values. Furthermore, they lack the crucial pore-plugging lysine. In addition, the second important residue of the dyad, the hydrophobic residue (Phe or Tyr) is also missing  .. 
PF08120 Tamulustoxin family<br>Short protein clustering. This family consists of the tamulustoxins which are  found in the venom of the Indian red scorpion (Mesobuthus  tamulus). Tamulustoxin shares no similarity with other  scorpion venom toxins, although the positions of its six  cysteine residues suggest that it shares the same  structural scaffold. Tamulustoxin acts as a potassium channel  blocker  .. 
PF08121 Waglerin family<br>Short protein clustering. This family consists of the lethal peptides (waglerins)  that are found in the venom of Trimeresurus wagleri.  Waglerins are 22-24 residue lethal peptides and are  competitive antagonist of the muscle nicotinic receptor  (nAChR). Waglerin-1 possesses a distinctive selectivity  for the alpha-epsilon interface binding site of the mouse  nAChR  .. 
PF08122 NADH-ubiquinone oxidoreductase B12 subunit family<br>Short protein clustering. This family consists of the NADH-ubiquinone  oxidoreductase B12 subunit proteins. NADH is the  central source of electrons in the mitochondrial  and bacterial respiration. NADH-ubiquinone  oxidoreductase is involved in the transfer of  electrons from NADH to the electron transport  chain. This oxidation of NADH is coupled to  proton transfer across the membrane, generating  a proton motive force that is utilised for the  synthesis of ATP. The function of this subunit is unclear  .. 
PF08123 Histone methylation protein DOT1 <br>Pfam-B_12064 (release 16.0). The DOT1 domain regulates gene expression by methylating histone H3  . H3 methylation by DOT1 has been shown to be required for the DNA damage checkpoint in yeast  .. 
PF08124 Polysaccharide lyase family 8, N terminal alpha-helical domain<br>Pfam-B_2438 (release 16.0). This family consists of a group of secreted bacterial lyase enzymes EC:4.2.2.1 capable of acting on hyaluronan and chondroitin in the extracellular matrix of host tissues, contributing to the invasive capacity of the pathogen.. 
PF08125 Mannitol dehydrogenase C-terminal domain<br>
PF08126 Propeptide_C25<br>This is found at the N terminal end of some of the members of the C25 peptidase family (PF01364).  Little is known about the function of this motif.. 
PF08127 Peptidase family C1 propeptide<br>This motif is found at the N terminal of some members of the Peptidase_C1 family (Pfam:PF00112) and is involved in activation of this peptidase  .. 
PF08129 Alpha/beta enterocin family<br>Short protein clustering. This family consists of the alpha and beta enterocins and  lactococcin G peptides. These peptides have some antimicrobial  properties; they inhibit the growth of Enterococcus spp. and a  few other gram-positive bacteria. These peptides act as pore- forming toxins that create cell membrane channels through a  barrel-stave mechanism and thus produce an ionic imbalance in  the cell. These family of antimicrobial peptides belong to the  class II group of bacteriocin  .. 
PF08130 Type A lantibiotic family<br>Short protein clustering. This family consists of the type A lantibiotic peptides. Both Pep5  and epicidin-280 are ribosomally-synthesised antimicrobial peptides  produced by Gram-positive bacteria that are characterised by the  presence of lanthionine and/or methyllanthionine residues. The  lantibiotics family has a highly specific activity against multi- drug resistant bacteria and has potential to be utilised in a wide range of medical applications [1,2].. 
PF08131 Defensin-like peptide family<br>Short protein clustering. This family consists of the defensin-like peptides (DLPs) isolated from platypus venom. These DLPs show similar three-dimensional fold to that of beta-defensin-12 and sodium-channel neurotoxin Shl. However the side chains known to be functionally important to beta-defensin-12 and Shl are not conserved in DLPs. This suggests a different biological function. Consistent with this contention, DLPs have been shown to possess no anti-microbial properties and have no observable activity on rat dorsal-root-ganglion sodium-channel currents  .. 
PF08132 S-adenosyl-l-methionine decarboxylase leader peptide<br>Short protein clustering. This family consists of the S-adenosyl-l-methionine decarboxylase (AdoMetDC) leader peptides. AdoMetDC is a key regulatory enzymes in the biosynthesis of polyamines. All expressed plant AdoMetDC mRNA 5' leader sequences contain a highly conserved pair of overlapping upstream ORFs (uORFs) that overlap by one base. Sequences of the small uORFs are highly conserved between monocot, dicot and gymnosperm AdoMetDC mRNA species, suggesting a translational regulatory mechanism  .. 
PF08133 Anticodon nuclease activator family<br>Short protein clustering. This family consists of the anticodon nuclease activator proteins.  Pre-existing host tRNAs are reprocessed during bacteriophage T4 infection of certain Escherichia coli strains. In this pathway, tRNA(Lys) is cleaved 5' by the anticodon nuclease to the wobble base and is later restored in polynucleotide kinase and RNA ligase reactions  .. 
PF08134 cIII protein family<br>Short protein clustering. This family consists of the cIII family of  regulatory proteins. The lambda CIII protein  has 54 amino acids and it forms an amphipathic  helix within its amino acid sequence. Lambda  cIII stabilises the lambda cII protein and the  host sigma factor 32, responsible for transcribing  genes of the heat shock regulon  . . 
PF08135 Major transforming protein E5 family<br>Short protein clustering. This family consists of the major transforming proteins (E5)  of the bovine papilloma virus (BPV). The equine sarcoid is  one of the most common dermatological lesion in equids. It is  a benign, locally invasive dermal fibroblastic lesion and  studies have shown an association of the lesions with BPV. E5  is a short hydrophobic membrane protein localising to the Golgi  apparatus and other intracellular membranes. It binds to and  constitutively activates the platelet-derived growth factor-beta  in transformed cells. This stimulation activates a receptor  signaling cascade which results in an intracellular growth  stimulatory signal  .. 
PF08136 30S ribosomal protein subunit S22 family<br>Short protein clustering. This family consists of the 30S ribosomal proteins subunit  S22 polypeptides. This polypeptide is 47 amino acids in length  and has a molecular weight of about 5 kDa. The S22 subunit is a  component of the stationary-phase-specific ribosomal protein and  is assembled in the ribosomal particles in the stationary phase.  This subunit along with other stationary-phase-specific ribosomal  proteins result in compositional changes of ribosomes during the  stationary phase. The significance of this change is not clear as  yet  .. 
PF08137 DVL family<br>Short protein clustering. This family consists of the DVL family of proteins.  In a gain-of-function genetic screen for genes that influence fruit development in Arabidopsis, DEVIL (DVL) gene was identified. DVL is a small protein and overexpression of the protein results in pleiotropic phenotypes featured by shortened stature, rounder rosette leaves, clustered inflorescences, shortened pedicles, and siliques with pronged tips. DVL family is a novel class of small polypeptides and the overexpression phenotypes suggest that these polypeptides may have a role in plant development  .. 
PF08138 Sex peptide (SP) family<br>Short protein clustering. This family consists of Sex Peptides (SP) that are found in Drosophila. On mating, Drosophila females decreases her remating rate and increases her egg-laying rate due, in part, to the transfer of SP from the male to the female. SP are found in seminal fluids transferred from the male to the female during mating. The male seminal fluid proteins are referred to as accessory gland proteins (Acps). The SP is one of the most interesting Acps and plays an important role in reproduction  .. 
PF08139 VirB;<br>Prokaryotic membrane lipoprotein lipid attachment site. Short protein clustering. In prokaryotes, membrane lipoproteins are synthesized with a precursor signal peptide, which is cleaved by a specific lipoprotein signal peptidase (signal peptidase II). The peptidase recognizes a conserved sequence and cuts upstream of a cysteine residue to which a glyceride-fatty acid lipid is attached  .. 
PF08140 Crustacean cuticle protein repeat<br>Short protein clustering. This family consists of the cuticle proteins from the Cancer  pagurus and the Homarus americanus. These proteins are isolated  from the calcified regions of the crustacean and they contain two  copies of an 18 residue sequence motif, which thus far has been  found only in crustacean calcified exoskeletons  .. 
PF08141 Small acid-soluble spore protein H family<br>Short protein clustering. This family consists of the small acid-soluble spore proteins  (SASP) of the H type (sspH). SspH are unique to spores of Bacillus  subtilis and are expressed only in the forespore compartment  during sporulation of this organism. The sspH genes are  monocistronic and are recognised by the forespore-specific  sigma factor for RNA polymerase - sigma-G. The specific role  of this protein is unclear but is thought to play a role in  sporulation under conditions different from that of the common laboratory tests of spore properties  .. 
PF08142 AARP2CN (NUC121) domain<br>This domain is the central domain of AARP2.  It is weakly similar to  the GTP-binding domain of elongation factor TU  .. 
PF08143 CBFNT (NUC161) domain<br>This N terminal domain is found in proteins of CARG-binding factor A-like proteins  .. 
PF08144 CPL (NUC119) domain<br>This C terminal domain is fund in Penguin-like proteins associated  with Pumilio like repeats  .. 
PF08145 BOP1NT (NUC169) domain<br>This N terminal domain is found in BOP1-like WD40 proteins  .. 
PF08146 BP28CT (NUC211) domain<br>This C terminal domain is found in BAP28-like nucleolar proteins  .. 
PF08147 DBP10CT (NUC160) domain<br>This C terminal domain is found in the Dbp10p subfamily of  hypothetical RNA helicases  . . 
PF08148 DSHCT (NUC185) domain<br>This C terminal domain is found in DOB1/SK12/helY-like DEAD box helicases  .. 
PF08149 BING4CT (NUC141) domain<br>This C terminal domain is found in the BING4 family of nucleolar  WD40 repeat proteins  .. 
PF08150 FerB (NUC096) domain<br>This is central domain B in proteins of the Ferlin family  .. 
PF08151 FerI (NUC094) domain<br>This domain is present in proteins of the Ferlin family.  It is often located between two C2 domains  .. 
PF08152 GUCT (NUC152) domain<br>This is the C terminal domain found in the RNA helicase II / Gu  protein family  .. 
PF08153 NGP1NT (NUC091) domain<br>This N terminal domain is found in a subfamily of hypothetical nucleolar GTP-binding proteins similar to human NGP1  .. 
PF08154 NLE (NUC135) domain<br>This domain is located N terminal to WD40 repeats.  It is found in  the microtubule-associated protein Swiss:Q12024  . . 
PF08155 NOGCT (NUC087) domain<br>This C terminal domain is found in the NOG subfamily of nucleolar GTP-binding proteins  .. 
PF08156 NOP5NT (NUC127) domain<br>This N terminal domain is found in RNA-binding proteins of the  NOP5 family  .. 
PF08157 NUC129 domain<br>This C terminal domain is found in a novel family of hypothetical nucleolar proteins  .. 
PF08158 NUC130/3NT domain<br>This N terminal domain is found in a novel nucleolar protein family  .. 
PF08159 NUC153 domain<br>This small domain is found in a a novel nucleolar family  . . 
PF08161 NUC173 domain<br>This is the central domain of of novel family of hypothetical  nucleolar proteins  .. 
PF08163 NUC194 domain<br>This is domain B in the catalytic subunit of DNA-dependent protein kinases.. 
PF08164 Apoptosis-antagonizing transcription factor, C-terminal<br>This C terminal domain is found in traube proteins  . This is the domain of the AATF proteins that interacts with BLOS2 or Ceap, that functions as an adaptor in processes such as protein and vesicle processing and transport, and perhaps transcription.. 
PF08165 FerA (NUC095) domain<br>This is central domain A in proteins of the Ferlin family  .. 
PF08166 NUC202 domain<br>This domain is found in a novel family of nucleolar proteins  .. 
PF08167 NUC201;<br>rRNA processing/ribosome biogenesis. Rix1 is a nucleoplasmic particle involved in rRNA processing/ribosome assembly [1,2]. It associates with two other proteins, Ipi1 and Ipi3, to form the RIX1 complex that allows Rea1 - the AAA ATPase - to associate with the 60S ribosomal subunit. More than 170 assembly factors are involved in the construction and maturation of yeast ribosomes, and after these factors have completed their function they need to be released from the pre-ribosomes. Rea1 induces the release of the assembly protein complex in a mechanical fashion  . This family is usually associated with NUC202, Pfam:PF08166.. 
PF08168 NUC205 domain<br>This domain is found in a novel family of nucleolar proteins  .. 
PF08169 RBB1NT (NUC162) domain<br>This domain is found N terminal to the ARID/BRIGHT domain in   DNA-binding proteins of the Retinoblastoma-binding protein 1 family  .. 
PF08170 POPLD (NUC188) domain<br>This domain is found in POP1-like nucleolar proteins  .. 
PF08171 Mad3_like; <br>Mad3/BUB1 homology region 2. Pfam-B_113144 (release 16.0). This domain is found in checkpoint proteins which are involved in cell division.  This region has been shown to be necessary and sufficient for the binding of MAD3 to BUB3 in Saccharomyces cerevisiae. This domain is present in BUB1 which also binds BUB3  .. 
PF08172 CASP C terminal<br>Pfam-B_7701 (release 16.0). This domain is the C-terminal region of the CASP family of proteins.  It is a Golgi membrane protein which is thought to have a role in vesicle transport  .. 
PF08173 Membrane bound YbgT-like protein<br>Short protein clustering. This family contains a set of membrane proteins, typically 33 amino acids long.  The family has no known function, but the protein is found  in the operon CydAB in E. coli. Members have a consensus motif (MWYFXW)  which is rich in aromatic residues.  The protein forms a single membrane-spanning helix.  This family seems to be restricted to Proteobacteria  .. 
PF08174 DUF1709;<br>Cell division protein anillin. Pfam-B_55293 (release 16.0). Anillin is a protein involved in septin organisation during cell division.\.     It is an actin binding protein that is localised to the cleavage furrow, and it maintains the localisation of active myosin, which ensures the spatial control of concerted contraction during cytokinesis  .. 
PF08175 Small acid-soluble spore protein O family<br>Short protein clustering. This family consists of the small acid-soluble spore proteins  (SASP) O type (sspO). SspO (originally cotK) are unique to  the spores of Bacillus subtilis and are expressed only in the  forespore compartment of sporulating cells of this organism.  The sspO is the first gene in a likely operon with sspP and  transcription of this gene is primarily by RNA polymerase with  the forespore-specific sigma factor, sigma-G. Mutation deleting sspO causes the loss of the SspO from the forespore but had no  discernible effect on sporulation, spore properties or spore  germination  .. 
PF08176 Small acid-soluble spore protein K family<br>Short protein clustering. This family consists of the small acid-soluble spore proteins (SASP) belonging to the K type (sspK). The sspK are unique to the spores of Bacillus subtilis and are expressed only in the forespore compartment of sporulating cells of this organism.  The sspK gene is monocistronic and transcription is primarily by the RNA polymerase with the forespore-specific sigma factor, sigma-G. Mutation deleting sspK results in loss of SspK from the spore but had no discernible effect on sporulation, spore properties or spore germination  .. 
PF08177 Small acid-soluble spore protein N family<br>Short protein clustering. This family consists of the small acid-soluble spore protein  (SASP) N type (sspN). SspN is a 48 residues protein that is  expressed only in the forespore compartment of sporulating  Bacillus subtilis. The sspN gene is recognised equally by both  sigma-G and sigma-F. The role of SspN is still not well-defined  .. 
PF08178 GnsA/GnsB family<br>Short protein clustering. This family consists of the GnsA/GnsB family. GnsA and GnsB  are multicopy suppressors of the secG null mutation. These  proteins participate in the synthesis of phospholipids,  suggesting the functional relationship between SecG and  membrane phospholipids. Overexpression of gnsA and gnsB causes  a remarkable increase in the unsaturated fatty acid content.  However, the gnsA-gnsB double null mutant exhibits no effect.  Both proteins are predicted to possess a helix-turn-helix  structure  .. 
PF08179 Small acid-soluble spore protein P family<br>Short protein clustering. This family consists of the small acid-soluble spore proteins (SASP) P type (sspP). sspP is expressed only in the forespore compartment of the sporulating cell. sspP is also expressed under sigma-G control from the same promoter as sspO. Mutations deleting sspP causes no discernible effect on sporulation, spore properties or spore germination  .. 
PF08180 B melanoma antigen family<br>Short protein clustering. This family consists of the B melanoma antigen (BAGE) peptides.  The BAGE gene encodes a human tumour antigen that is recognised  by a cytolytic T lymphocyte. BAGE genes are expressed in melanomas,  bladder and lung carcinomas and in a few tumours of other histological  types  .. 
PF08181 DegQ (SacQ) family<br>Short protein clustering. This family consists of the DegQ (formerly sacQ) regulatory peptides. The DegQ family of peptides control the rates of synthesis of a class of both secreted and intracellular degradative enzymes in Bacillus subtilis. DegQ is 46 amino acids long and activates the synthesis of degradative enzymes.  The expression of this peptide was shown to be subjected both to catabolite repression and DegS-DegU-mediated control. Thus allowing an increase in the rate of synthesis of degQ under conditions of nitrogen starvation  .. 
PF08182 Pedibin/Hym-346 family<br>Short protein clustering. This family consists of the pedibin and Hym-346 signaling peptides.  These two peptides have been isolated from Hydra vulgaris and Hydra magnipapillata. Experiments have indicated that both cause a reduction in the positional value gradient, the principle patterning process governing the maintenance of form in the adult hydra. The peptides cause an increase in the rate of foot regeneration following bisection of the body column. Thus both play important signaling roles in patterning processes in cnidaria and maybe in more complex metazoans  .. 
PF08183 Stage V sporulation protein family<br>Short protein clustering. This family consists of the stage V sporulation (SpoV) proteins  of Bacillus subtilis which includes SpoVM. SpoVM is an small,  26 residue-long protein that is produced in the mother cell chamber  of the sporangium during the process of sporulation in B. subtilis.  SpoVM forms an amphipathic alpha-helix and is recruited to the polar  septum shortly after the sporangium undergoes asymmetric division.  The function of SpoVM depends on proper subcellular localisation  .. 
PF08184 Cuticle protein 7 isoform family<br>Short protein clustering. This family consists of cuticle protein 7 isoforms that are  isolated from the carapace cuticle of a juvenile horseshoe crab, Limulus polyphemus. There are 3 isoforms of cuticle  protein 7. The 3 isoforms are N-terminally blocked but could  be deblocked by treatment with pyroglutaminase, showing that  the N-terminal residue is a pyroglutamine residue  . . 
PF08186 Wound-inducible basic protein family<br>Short protein clustering. This family consists of the wound-inducible basic proteins  from plants. The metabolic activities of plants are  dramatically altered upon mechanical injury or pathogen  attack. A large number of proteins accumulates at wound or  infection sites, such as the wound-inducible basic proteins.  These proteins are small, 47 amino acids in length, has no  signal peptides and are hydrophilic and basic  .. 
PF08187 Myoactive tetradecapeptides family<br>Short protein clustering. This family consists of myoactive tetradecapeptides that are  isolated from the gut of earthworms, Eisenia foetida and  Pheretima vitata. These peptides were termed ETP and PTP  respectively. Both peptides showed a potent excitatory action  on spontaneous contractions of the anterior gut. These peptides  show similarity to Molluscan tetradecapeptides and arthropodan  tridecapeptides  .. 
PF08188 Spermatozal protamine family<br>Short protein clustering. This family consists of the spermatozal protamines.  Spermatozal protamines play an important role in remodelling of the sperm chromatin during mammalian spermiogenesis. Nuclear elongation and chromatin condensation are concomitant with modifications in the basic protein complement associated with DNA.  Somatic histones are initially replaced by testis -specific histone variants, then by transitional proteins, and ultimately by protamines  .. 
PF08189 Meleagrin/Cygnin family<br>Short protein clustering. This family consists of meleagrin and cygnin basic peptides that are isolated from turkey and black swan respectively. Both peptides are low in molecular weight and contains three disulphide bonds with high concentrations of aromatic residues. These peptides show similarity to transferrins and probably play some vital role in avian eggs but the exact function is still unknown  .. 
PF08190 Nop17p; <br>pre-RNA processing PIH1/Nop17. Pfam-B_10462 (release 16.0). This domain is involved in pre-rRNA processing  .  It has has been shown to be required either for nucleolar retention or correct assembly of the box C/D snoRNP in Saccharomyces cerevisiae  . The C-terminal region of this family has similarity to the CS domain Pfam:PF04969.. 
PF08191 LRR adjacent<br>Mistry J, Schubert WD. Pfam-B_1177 (release 16.0). These are small, all beta strand domains, structurally described for the protein Internalin (InlA) and related proteins InlB, InlE, InlH from the pathogenic bacterium Listeria monocytogenes. Their function appears to be mainly structural: They are fused to the C-terminal end of leucine-rich repeats (LRR), significantly stabilising the LRR, and forming a common rigid entity with the LRR.  They are themselves not involved in protein-protein-interactions but help to present the adjacent LRR-domain for this purpose.  These domains belong to the family of Ig-like domains in that they consist of two sandwiched beta sheets that follow the classical connectivity of Ig-domains. The beta strands in one of the sheets is, however, much smaller than in most standard Ig-like domains, making it somewhat of an outlier      .. 
PF08192 Peptidase family S64<br>Mistry J, Rawlings N. This family of fungal proteins is involved in the processing of membrane bound transcription factor Stp1  .  The processing causes the signalling domain of Stp1 to be passed to the nucleus where several permease genes are induced.  The permeases are important for uptake of amino acids, and processing of tp1 only occurs in an amino acid-rich environment.  This family is predicted to be distantly related to the trypsin family (MEROPS:S1) and to have a typical trypsin-like catalytic triad  .. 
PF08193 DUF1711; <br>INO80 complex subunit Ies4. The INO80 ATPase is a member of the SNF2 family of ATPases and functions as an integral component of a multisubunit ATP-dependent chromatin remodelling complex.  This family of proteins corresponds to the fungal Ies4 subunit of INO80.. 
PF08194 DIM protein<br>Short protein clustering. Drosophila immune-induced molecules (DIMs) are short proteins induced during the immune response of Drosophila. This family includes DIMs 1 to 4 that have masses below 5 kDa  .. 
PF08195 TRI9 protein<br>Short protein clustering. Putative gene of 129 bp in the Trichothecene gene cluster of Fusarium sporotrichioides and F. graminearum. Encoding a predicted protein of 43 amino acids which function is unknown [1,2].. 
PF08196 UL2 protein<br>Short protein clustering. Orf UL2 of Human cytomegalovirus (HCMV) which is a short protein of unknown function  . 
PF08197 pORF2a truncated protein<br>Short protein clustering. Most isolated ORF2 of TT virus (TTV) encode a 49 amino acids protein  (pORF2a) because of an in-frame stop codon. ORF2s isolated from G1 TTV  encode 202 amino acids protein (pORF2ab)  .  . 
PF08198 Thymopoietin protein<br>Short protein clustering. Short protein of 49 amino acid isolated from bovine spleen cells  . Thymopoietins (TMPOs) are a group of ubiquitously expressed nuclear proteins. They are suggested to play an important role in nuclear envelope organisation and cell cycle control  .. 
PF08199 Bacteriophage E2-like protein<br>Short protein clustering. Short conseved protein described in Lactococcus Bacteriophage c2  of 37 amino acids  .. 
PF08200 Bacteriophage 1.1 Protein <br>Short protein clustering. Gene 1.1 in Bacteriophage T7 encodes a 42 amino acid protein, rich in basic amino acids suggesting its interaction with nucleic acids  .  Many homologs are present in different T7 and T3-like bacteriophage.. 
PF08201 BssC/TutF protein<br>Short protein clustering. BssC short protein (57 amino acids) has been described as the  gamma-subunit of benzylsuccinate synthase from Thauera aromatica  strain K172  .  TutF has been identified and described as highly similar to BssC in  T.aromatica strain T1  . . 
PF08202 Mis12_component;<br>Mis12-Mtw1 protein family. Pfam-B_127825  (release 16.0). Mis12-Mtw1 is a eukaryotic conserved kinetochore protein that is involved in chromosome segregation  .. 
PF08203 Yeast RNA polymerase I subunit RPA14<br>This is a family of yeast proteins.  A14 is one of the final two subunits of Saccharomyces cerevisiae RNA polymerase I and is proposed to play a role in the recruitment of pol I to the promoter  .. 
PF08204 CD47 immunoglobulin-like domain<br>Pfam-B_2739 (release 7.5). This family represents the CD47 leukocyte antigen V-set like Ig domain [1,2].. 
PF08205 CD80-like C2-set immunoglobulin domain <br>Pfam-B_280 (release 17.0). These domains belong to the immunoglobulin superfamily.. 
PF08206 Ribonuclease B OB domain<br>Pfam-B_484 (release 17.0). This family includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.. 
PF08207 Elongation factor P (EF-P) KOW-like domain<br>
PF08208 RNA_polI_final; <br>DNA-directed RNA polymerase I subunit RPA34.5. This is a family of proteins conserved from yeasts to human. Subunit A34.5 of RNA polymerase I is a non-essential subunit which is thought to help Pol I overcome topological constraints imposed on ribosomal DNA during the process of transcription  .. 
PF08209 Sgf11 (transcriptional regulation protein)<br>The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae.  The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation  .. 
PF08210 APOBEC-like N-terminal domain<br>A mechanism of generating protein diversity is mRNA editing. Members of this family are C-to-U editing enzymes.  The N-terminal domain of APOBEC-1 like proteins is the catalytic domain, while the C-terminal domain is a pseudocatalyitc domain. More specifically, the catalytic domain is a zinc dependent deaminases domain and is essential for cytidine deamination.APOBEC-3 like members contain two copies of this domain.  RNA editing by APOBEC-1 requires homodimerisation and this  complex interacts with RNA binding proteins to from the editosome    (and references therein). This family also includes the functionally  homologous activation induced deaminase (AID), which is essential for the development of antibody diversity in B lymphocytes, and the sea  lamprey PmCDA1 and PmCDA2, which are predicted to play an AID-like  role in the adaptive immune response of jawless vertebrates  .  Divergent members of this family are present in various eukaryotes such as Nematostella, C. elegans, Micromonas and Emiliania, and  prokaryotes such as Wolbachia and Pseudomonas brassicacearum  .. 
PF08211 Cytidine and deoxycytidylate deaminase zinc-binding region <br>Pfam-B_8221 (release 16.0). 
PF08212 Lipocalin-like domain<br>Pfam-B_2479 (Release 17.0). Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The structure is an eight-stranded beta barrel.. 
PF08213 Mitochondrial domain of unknown function (DUF1713)<br>This domain is found at the C terminal end of mitochondrial proteins of unknown function.. 
PF08214 DUF1714; RTT109; <br>Histone acetylation protein. Histone acetylation is required in many cellular processes including transcription, DNA repair, and chromatin assembly. This family contains the fungal KAT11 protein (previously known as RTT109) which is required for H3K56 acetylation.  Loss of KAT11 results in the loss of H3K56 acetylation, both on bulk histone and on chromatin  . KAT11 and H3K56 acetylation appear to correlate with actively transcribed genes and associate with the elongating form of Pol II in yeast  .  This family also incorporates the p300/CBP histone acetyltransferase domain which has different catalytic properties and cofactor regulation to KAT11  .. 
PF08216 DUF1716;<br>Catenin-beta-like, Arm-motif containing nuclear. Pfam-B_13045 (release 16.0). CTNNBL is a family of eukaryotic nuclear proteins of the catenin-beta-like 1 type that contain an armadillo motif. A human nuclear protein with this domain (Swiss:Q8WYA6) is thought to have a role in apoptosis  . The interaction of CTNNBL1 with its known partners (the Prp19-CDC5L complex and AID) is mediated by recognition of NLS (nuclear localisation signal) motifs. The RNA-splicing factor Prp31 is also an interactor, with recognition also occurring through the NLS. CTNNBL1 uses its central armadillo (ARM) domain to bind NLS-containing partners [2,3].. 
PF08217 Fungal domain of unknown function (DUF1712)<br>The function of this family of proteins is unknown.. 
PF08218 Citrate lyase ligase C-terminal domain<br>Pfam-B_3588 (release 16.0). This family is composed of the C-terminal domain of citrate lyase ligase EC:6.2.1.22.. 
PF08219 Outer membrane protein TOM13<br>The TOM13 family of proteins are mitochondrial outer membrane proteins that mediate the assembly of beta-barrel proteins  .. 
PF08220 DeoR-like helix-turn-helix domain<br>
PF08221 RNA polymerase III subunit RPC82 helix-turn-helix domain<br>Pfam-B_9884 (release 8.0). This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In Saccharomyces cerevisiae, the enzyme is composed of 15 subunits, ranging from 160 to about 10 kDa  . This region is a probably DNA-binding helix-turn-helix.. 
PF08222 CodY helix-turn-helix domain<br>Pfam-B_7573 (release 9.0). This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions  . The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk  .. 
PF08223 PaaX-like protein C-terminal domain<br>Pfam-B_9563 (release 14.0). This family contains proteins that are similar to the product  of the paaX gene of Escherichia coli (Swiss:P76086). This protein  is involved in the regulation of expression of a group of proteins  known to participate in the metabolism of phenylacetic acid  . . 
PF08224 Domain of unknown function (DUF1719)<br>Mistry J, Myung-il K. Pfam-B_27966 (release 16.0). This is a domain of unknown function.  It may have a role in ATPase activation.. 
PF08225 Pseudin antimicrobial peptide<br>Short protein clustering. Pseudins are a subfamily of the FSAP family (Frog Secreted Active Peptides) extracted from the skin of the paradoxical frog Pseudis paradoxa (Pseudidae).  The pseudins belong to the class of cationic, amphipathic-helical antimicrobial peptides  .. 
PF08226 Domain of unknown function (DUF1720)<br>Pfam-B_19709 (release 16.0). This domain is found in different combinations with cortical patch components EF hand, SH3 and ENTH and is therefore likely to be involved in cytoskeletal processes.  This family contains many hypothetical proteins.. 
PF08227 DUF1721; <br>DASH complex subunit Hsk3 like. The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis  . In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro [2,3].  This family also includes several higher eukaryotic proteins. However, other DASH subunits do not appear to be conserved in higher eukaryotes.. 
PF08228 RNase P subunit Pop3<br>This family of fungal proteins form a subunit of RNase P, the ribonucleoprotein enzyme that cleaves the leader sequence of precursor tRNAs to generate mature tRNAs.\.   The structure of Pop3 has been assigned the L7Ae/L30e fold  .\. This RNA-binding fold is also present in human RNase P subunit Rpp38, raising the possibility that Pop3p and Rpp38 are functional homologs.. 
PF08229 ER membrane protein SH3 <br>This family of proteins are membrane localised chaperones that are required for correct plasma membrane localisation of amino acid permeases (AAPs)  .  SH3 prevents AAPs proteins from aggregating and assists in their correct folding. In the absence of SH3, AAPs are retained in the ER.. 
PF08230 Cpl-7 lysozyme C-terminal domain<br>This domain was originally found in the C-terminal moiety of the Cpl-7 lysozyme encoded by the Streptococcus pneumoniae bacteriophage Cp-7 (Swiss:P19385). It is assumed that these repeats represent cell wall binding motifs although no direct evidence has been obtained so far.. 
PF08231 SYF2 splicing factor<br>Pfam-B_11988 (release 17.0). Proteins in this family are involved in cell cycle progression and pre-mRNA splicing    .. 
PF08232 Striatin family<br>Pfam-B_7946 (release 17.0). Striatin is an intracellular protein which has a caveolin-binding motif, a coiled-coil structure, a calmodulin-binding site, and a WD (Pfam:PF00400) repeat domain  . It acts as a scaffold protein   and is involved in signalling pathways    .. 
PF08234 Chromosome segregation protein Spc25<br>Pfam-B_14484 (release 16.0). This is a family of chromosome segregation proteins.  It contains Spc25, which is a conserved eukaryotic kinetochore protein involved in cell division. In fungi the Spc25 protein is a subunit of the Nuf2-Ndc80 complex  , and in vertebrates it forms part of the Ndc80 complex  .. 
PF08235 LNS2 (Lipin/Ned1/Smp2)<br>Pfam-B_2646 (release 16.0). This domain is found in Saccharomyces cerevisiae protein SMP2, proteins with an N-terminal lipin domain (Pfam: PF04571) and phosphatidylinositol transfer proteins  .  SMP2 (also known as PAH1) is involved in plasmid maintenance and respiration  , and has been identified as a Mg2+-dependent phosphatidate phosphatase (EC:3.1.3.4) that contains a haloacid dehalogenase (HAD)-like domain  .  Lipin proteins are involved in adipose tissue development and insulin resistance  .. 
PF08236 SRI (Set2 Rpb1 interacting) domain<br>Pfam-B_106465 (release 17.0) & pdb_2a7o. The SRI (Set2 Rpb1 interacting) domain mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation  .  This domain is conserved from yeast to humans. Members of this family form a compact, closed three-helix bundle, with an up-down-up topology. The first and second helices are antiparallel to each other and are of similar length; the third helix, which is packed across helices alpha1 and alpha2 is slightly shorter, consisting of only 15 amino acids. Most conserved hydrophobic residues are largely buried in the interior of the structure and form an extensive and contiguous hydrophobic core that stabilises the packing of the three-helix bundle. This domain mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation  .. 
PF08237 PE-PPE domain<br>This domain is found C terminal to the PE (Pfam:PF00934) and PPE (Pfam:PF00823) domains.  The secondary structure of this domain is predicted to be a mixture of alpha helices and beta strands  .. 
PF08238 Sel1 repeat<br>Pfam-B_49 (Release 17.0). This short repeat is found in the Sel1 protein  .  It is related to TPR repeats.. 
PF08239 Bacterial SH3 domain<br>Pfam-B_178 (Release 17.0). 
PF08240 Alcohol dehydrogenase GroES-like domain<br>Pfam-B_7 (Release17.0). This is the catalytic domain of alcohol dehydrogenases.  Many of them contain an inserted zinc binding domain. This domain  has a GroES-like structure [1-2].. 
PF08241 Methyltransferase domain<br>Pfam-B_21 (release 17.0). Members of this family are SAM dependent methyltransferases.. 
PF08242 Methyltransferase domain<br>Pfam-B_46 (release 17.0). Members of this family are SAM dependent methyltransferases.. 
PF08243 SPT2 chromatin protein<br>This family includes the Saccharomyces cerevisiae protein SPT2 which is a chromatin protein involved in transcriptional regulation  .. 
PF08244 glycosyl_hydro2; Glyco_hydro_32; <br>Glycosyl hydrolases family 32 C terminal. This domain corresponds to the C terminal domain of glycosyl hydrolase family 32.  It forms a beta sandwich module  .. 
PF08245 Mur ligase middle domain<br>Pfam-B_26 (release 17.0). 
PF08246 Cathepsin propeptide inhibitor domain (I29)<br>Pfam-B_14 (release 17.0) . This domain is found at the N-terminus of some C1 peptidases such as Cathepsin L where it acts as a propeptide.  There are also a number of proteins that are composed solely of multiple copies of this domain such as the peptidase inhibitor salarin Swiss:Q70SU8. This family is classified as I29 by MEROPS.. 
PF08247 ENOD40 protein<br>Short protein clustering. Rohrig et al. reported the in vitro translation of two peptides of 12 and 24 amino acids from the short, overlapping ORFs of soybean ENOD40 mRNA  . The putative role of the enod40 genes has been in favour of organogenesis, such as induction of the cortical cell divisions that lead to initiation of nodule primordia, in developing lateral roots and embryonic tissues. This supports the hypothesis for a role of enod40 in lateral organ development  .. 
PF08248 Tryptophyllin-3 skin active peptide<br>Short protein clustering. PdT-3 or Tryptophyllin-3 peptide is a subfamily of the family Tryptophyllin and of the superfamily FSAP (Frog Skin Active Peptide).  Originally identified in skin extracts of Neotropical leaf frogs, Phyllomedusa sp. This subfamily has an average length of 13 amino acids. The pharmacological activity of the tryptophyllins remains to be established   but it seems that these peptides possess an action on liver protein synthesis and body weight  .. 
PF08249 Mastoparan protein<br>Short protein clustering. Mastoparans are a family of tetradecapeptides from wasp venom, that have been shown to directly activate GTP-binding regulatory proteins.  These peptides show selectivity among G proteins: they strongly activate Go and Gi but not Gs or Gt.  The peptide of this family are composed by 14 amino acids but they can assume different structures  .. 
PF08250 Sperm-activating peptides<br>Short protein clustering. The sperm-activating peptides (SAPs) are isolated in egg-conditioned media (egg jelly) of sea urchins. SAPs have several effects on sea urchin spermatozoa: stimulate sperm respiration and motility through intracellular alkalinization, transient elevation of cAMP, cGMP and Ca++levels in sperm cells [1,2].. 
PF08251 Mastoparan peptide<br>Short protein clustering. Mastoparan (MP) peptides I II and III are extracted from the venom  gland of the Neotropical social wasp Protopolybia exigua(Saussure) They are tetradecapeptides presenting from seven to ten  hydrophobic amino acid residues and from two to four lysine  residues in their primary sequences. These peptide cause the degranulation of mast cells. Protopolybia-MP-I also act causing hemolysis in erythrocytes.. 
PF08252 arg-2/CPA1 leader peptide <br>Short protein clustering. In this family there are Leaders Peptides involved in the regulation the glutaminase subunit (small subunit) of arginine-specific carbamoyl phosphate synthetase.  In Neurospora crassa it is a small upstream ORF of 24 codon above the arg-2 locus  . In yeast it is the leader peptide of the CPA1 gene. The 5' region of CPA1 mRNA contains a 25 codon upstream open reading frame. The leader peptide, the product of the upstream open reading frame, plays an essential, negative role in the specific repression of CPA1 by arginine  .. 
PF08253 Erm Leader peptide <br>Short protein clustering. These short proteins are Leader peptides (15-19 amino acids) of  erm genes that code for resistance determinants in Staphylococcus  aureus  .. 
PF08254 Threonine leader peptide<br>Short protein clustering. Threonine leader peptide of the Threonine operon thrA1A2BC.  It as been sequenced in different bacteria: E. coli, Serratia marcescens, Salmonella typhi [1,2].. 
PF08255 Trp-operon Leader Peptide<br>Short protein clustering. The tryptophan operon regulatory region of C. freundii's (leader transcript) encodes a 14-residue peptide containing characteristic tandem tryptophan residues. It is about 10 nucleotides shorter than those of E. coli and S. typhimurium  .. 
PF08256 Aurein-like antibiotic peptide<br>Short protein clustering. This family of antibacterial peptides are secreted from the granular dorsal glands of the Green and Golden Bell Frog Litoria aurea, Southern Bell Frog L. raniformis, Blue Mountains tree-frog Litoria citropa (genus Litoria) and frogs from genus Uperoleia. They are a part of the FSAP peptide family.  Amongst the more active of these are aurein 1.2, aurein 2.2 and aurein 3.1; caerin 1.1, maculatin 1.1, uperin 3.6  ; citropin 1.1, citropin 1.2, citropin 1.3 and a minor peptide are wide-spectrum antibacterial peptides  .. 
PF08257 Sulfakinin family<br>Short protein clustering. The sulfakinin (SK) family of neuropeptides have only been identified in crustaceans and insects.  For most species there is the potential for producing two sulfakinin peptides one have a short sulfakinin sequence The function of the sulfakinins is difficult to assess.  For the American cockroach, various forms of the endogenous sulfakinins have been shown to be active on the hindgut, and also on the heart.  In C. vomitoria the peptides act as neurotransmitters or neuromodulators, linking the brain with all thoracic and abdominal ganglia.  In adults of P. monodon they appear to be restricted to a few neurones in the brain with a neural pathway extending along to the ventral thoracic and abdominal ganglia  .. 
PF08258 WWamide peptide<br>Short protein clustering. This family contain neuropeptides, isolated from ganglia of the African giant snail, Achatina fulica.  Each peptide has a Trp residue at both the N- and C-termini.  Purified WWamide-1, -2 and -3 showed an inhibitory effect on the phasic contractions of the anterior byssus retractor muscle (ABRM)  .. 
PF08259 Periviscerokinin family<br>Short protein clustering. Abdominal Perisympathetic organs of insects contain  Periviscerokinins neuropeptides of about 11 amino acids. . 
PF08260 Insect kinin peptide<br>Short protein clustering. These neuropeptides are the first members of the insect kinin-family isolated from the American cockroach. Their occurrence in the retrocerebral complex suggests a physiological role as a neurohormone. The C-terminal sequence Phe-X-Ser-Trp-Gly-NH2 characterised the peptides as members of the insect kinin family.  Data suggest a possible involvement of insect kinins in water-balance by regulating the osmoregulation. These peptides have length from 6 to 14 amino acids  .. 
PF08261 Carcinustatin peptide<br>Short protein clustering. A total of 20 peptides of the superfamily allostatin were isolated from the shore crab Carcinus maenas. They are named carcinustatin 1 to 20 and their length ranges from 5 to 27 amino acids. This family includes carcinustatin 8,9,15 and 16.. 
PF08262 Leucophaea maderae tachykinin-related peptide <br>Short protein clustering. These peptides are designated Leucophaea maderae tachykinin-related peptides (Lem TRPs). Some were isolated from the midgut of L. maderae, whereas others appear to be brain specific.  The Lem TRPs of the brain are myotropic and induce increases in the amplitude and frequency of spontaneous contractions and tonus of hindgut muscle in L. maderae  .  They were also isolated from brain-corpora, cardiaca-corpora, allata-suboesophageal ganglion extracts of the Locusta migratoria.  They stimulate visceral muscle contractions of the oviduct and the foregut of Locusta migratoria  .. 
PF08263 Leucine rich repeat N-terminal domain<br>Pfam-B_35 (release 17.0). Leucine Rich Repeats Pfam:PF00560 are short sequence motifs present in a number of proteins with diverse functions and cellular locations. Leucine Rich Repeats are often flanked by cysteine rich domains. This domain is often found at the N-terminus of tandem leucine rich repeats.. 
PF08264 Anticodon-binding domain of tRNA<br>Pfam-B_23 (Release 17.0). This domain is found mainly hydrophobic tRNA synthetases. The domain binds to the anticodon of the tRNA.. 
PF08265 YL1 nuclear protein C-terminal domain<br>Pfam-B_3088 (release 8.0). This domain is found in proteins of the YL1 family  . These proteins have been shown to be DNA-binding and may be a transcription factor  . This domain is found in proteins that are not YL1 proteins.. 
PF08266 Cadherin-like<br>Pfam-B_179 (release 17.0). This cadherin domain is usually the most N-terminal copy of the domain.   . 
PF08267 Cobalamin-independent synthase, N-terminal domain<br>Pfam-B_553 (release 17.0). The N-terminal domain and C-terminal domains of cobalamin-independent synthases together define a catalytic cleft in the enzyme.  The N-terminal domain is thought to bind the substrate, in particular, the negatively charged polyglutamate chain.  The N-terminal domain is also thought to stabilise a loop from the C-terminal domain  .. 
PF08268 F-box associated domain<br>Pfam-B_322 (release 17.0). 
PF08269 Cache domain<br>Pfam-B_865 (release 17.0). 
PF08270 M protein trans-acting positive regulator (MGA) PRD domain<br>Pfam-B_5126 (release 7.7). Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions  . This corresponds to the PRD like region.. 
PF08271 TFIIB_Zn_Ribbon;<br>Pfam-B_1298 (release 17.0). The transcription factor TFIIB contains a zinc-binding motif near the N-terminus.  This domain is involved in the interaction with RNA pol II and TFIIF and plays a crucial role in selecting the transcription initiation site.  The domain adopts a zinc ribbon like structure  .. 
PF08272 Topoisomerase I zinc-ribbon-like <br>Pfam-B_5615 (release 17.0). Some Proteobacteria topoisomerase I contain two zinc-ribbon-like domains at the C-terminus that structurally homologous to Pfam:PF01396. However, this domain no longer bind zinc.  Indeed, only one of the four cysteine residues remains  .. 
PF08273 Zinc-binding domain of primase-helicase<br>Pfam-B_18441 (release 17.0). 
PF08274 PhnA Zinc-Ribbon <br>
PF08275 DNA primase catalytic core, N-terminal domain<br>Pfam-B_313 (release 17.0). 
PF08276 PAN-like domain<br>Pfam-B_291 (release 17.0). 
PF08277 PAN-like domain<br>Pfam-B_1455 (release 17.0). 
PF08278 DNA primase DnaG DnaB-binding <br>Pfam-B_3213 (release 17.0). Eubacterial DnaG primases interact with several factors to from the replisome.  One of these factors in DnaB, a helicase.  This domain has been demonstrated to be responsible for the interaction between DnaG and DnaB .. 
PF08279 HTH domain<br>Pfam-B_125 (Release 17.0). This family includes helix-turn-helix domains in a wide variety of proteins.. 
PF08280 M protein trans-acting positive regulator (MGA) HTH domain<br>Pfam-B_5126 (release 7.7). Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions  .. 
PF08281 Sigma-70, region 4<br>Pfam-B_125 (Release 17.0). Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif  .. 
PF08282 haloacid dehalogenase-like hydrolase<br>Pfam-B_66 (Release 17.0). This family contains haloacid dehalogenase-like hydrolase enzymes.. 
PF08283 Geminivirus rep protein central domain<br>Pfam-B_286 (release 2.1). This is the cetral domain of the geminivirus rep proteins  .. 
PF08284 Retroviral aspartyl protease<br>Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases. 
PF08285 Dolichol-phosphate mannosyltransferase subunit 3 (DPM3)<br>This family corresponds to subunit 3 of dolichol-phosphate mannosyltransferase, an enzyme which generates mannosyl donors for glycosylphosphatidylinositols, N-glycan and protein O- and C-mannosylation.  DPM3 is an integral membrane protein and plays a role in stabilising the dolichol-phosphate mannosyl transferase complex  .. 
PF08286 Spc24 subunit of Ndc80<br>Spc24 is a component of the evolutionarily conserved kinetochore-associated Ndc80 complex and is involved in chromosome segregation  . 
PF08287 Spc19; <br>Spc19 is a component of the DASH complex.\.      The DASH complex associates with the spindle pole body and is important for spindle and kinetochore integrity during cell division   .. 
PF08288 PIGA (GPI anchor biosynthesis)<br>Pfam-B_6971 (release 17.0). This domain is found on phosphatidylinositol n-acetylglucosaminyltransferase proteins. These proteins are involved in GPI anchor biosynthesis and are associated with disease the paroxysmal nocturnal haemoglobinuria  .. 
PF08289 Influenza Matrix protein (M1) C-terminal domain<br>Pfam-B_30 (Release 17.0). This region is thought to be a second domain of the M1 matrix protein.. 
PF08290 Hepatitis core protein, putative zinc finger<br>This short region is found at the N-terminus of some hepatitis core proteins.\.  Its conservation of four cys and his suggests a zinc binding domain.. 
PF08291 Peptidase M15 <br>
PF08292 RNA polymerase III subunit Rpc25<br>Pfam-B_9841 (release 17.0). Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III  .. 
PF08293 Mit_rib_S27; <br>Mitochondrial ribosomal subunit S27. Pfam-B_31036 (release 17.0). This family of proteins corresponds to mitochondrial ribosomal subunit S27 in prokaryotes   and to subunit S33 in humans  . It is a small 106 residue protein.The evolutionary history of the mitoribosomal proteome that is encoded by a diverse subset of eukaryotic genomes, reveals an ancestral ribosome of alpha-proteobacterial descent that more than doubled its protein content in most eukaryotic lineages. Several new MRPs have originated via duplication of existing MRPs as well as by recruitment from outside of the mitoribosomal proteome  .. 
PF08294 TIM21<br>TIM21 interacts with the outer mitochondrial TOM complex and promotes the insertion of proteins into the inner mitochondrial membrane  .. 
PF08295 HDAC_interact;<br>Sin3 family co-repressor. Pfam-B_2731 (release 17.0). This domain is found on transcriptional regulators.  It forms interactions with histone deacetylases  .. 
PF08297 U3_snoRNA; <br>U3 snoRNA associated. This family of proteins is associated with U3 snoRNA  . U3 snoRNA is required for nucleolar processing of pre-18S ribosomal RNA.. 
PF08298 PrkA AAA domain<br>Pfam-B_3917 (release 10.0). This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain  .. 
PF08299 Bacterial dnaA protein helix-turn-helix<br>
PF08300 Hepatitis C virus non-structural 5a zinc finger domain<br>The molecular function of the non-structural 5a protein is uncertain.  The NS5a protein is phosphorylated when expressed in mammalian cells.  It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR, Swiss:P19525 [1,2]. This domain corresponds to the N-terminal zinc binding domain  .. 
PF08301 Hepatitis C virus non-structural 5a domain 1b<br>The molecular function of the non-structural 5a protein is uncertain.  The NS5a protein is phosphorylated when expressed in mammalian cells.  It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR, Swiss:P19525 [1,2]. This region corresponds to the 1b domain  .. 
PF08302 Fungal tRNA ligase phosphodiesterase domain<br>Pfam-B_49998 (release 17.0). This domain is found in fungal tRNA ligases and has cyclic phosphodiesterase activity  .  tRNA ligases are enzymes required for the splicing of precursor tRNA molecules containing introns.. 
PF08303 tRNA ligase kinase domain<br>Pfam-B_49998 (release 17.0). This domain is found in fungal tRNA ligases and has kinase activity  .  tRNA ligases are enzymes required for the splicing of precursor tRNA molecules containing introns. This family contains a P-loop motif.. 
PF08305 NPCBM/NEW2 domain<br>This novel putative carbohydrate binding module (NPCBM) domain is found at the N-terminus of glycosyl hydrolase family 98 proteins. This domain has also been called the NEW2 domain (Naumoff DG. Phylogenetic analysis of alpha-galactosidases of the GH27 family. Molecular Biology (Engl Transl). (2004)38:388-399.). 
PF08306 Glycosyl hydrolase family 98<br>This domain is the putative catalytic domain of glycosyl hydrolase family 98 proteins.. 
PF08307 Glycosyl hydrolase family 98 C-terminal domain<br>This putative domain is found at the C-terminus of glycosyl hydrolase family 98 proteins. This domain is not expected to form part of the catalytic activity.. 
PF08308 PEGA domain<br>This domain is found in both archaea and bacteria and has similarity to S-layer (surface layer) proteins.  It is named after the characteristic PEGA sequence motif found in this domain. The secondary structure of this domain is predicted to be beta-strands [Adindla et al. Comparative and Functional Genomics 2004; 5:2-16].. 
PF08309 LVIVD repeat<br>This repeat is found in bacterial and archaeal cell surface proteins, many of which are hypothetical.  The secondary structure corresponding to this repeat is predicted to comprise 4 beta-strands which may associate to form a beta-propeller [Adindla et al. Comparative and Functional Genomics 2004; 5:2-16].  The repeat copy number varies from 2-14.  This repeat is sometimes found with the PKD domain Pfam:PF00801.. 
PF08310 LGFP repeat<br>This 54 amino acid repeat is found in many hypothetical proteins. Several hypothetical proteins from C.glutamicum and C.efficiens along with PS1 protein contain this repeat region. The N-terminus region of PS1 contains an esterase domain which transfers corynomycolic acid. The C-terminus region consists of 4 tandem LGFP repeats. It is hypothesised that the PS1 proteins in Corynebacterium, when associated with the cell wall, may be anchored via the LGFP tandem repeats that may be important for maintaining cell wall integrity [Adindla et al. Comparative and Functional Genomics 2004; 5:2-16].  Deletion of Swiss:Q01377 protein results in a 10-fold increase in the cell volume of the organism and infers the corresponding proteins involvement in the cell shape formation  . The secondary structure of each repeat is predicted to comprise two beta-strands and one alpha-helix [Adindla et al. 2004].. 
PF08311 Mad3/BUB1 homology region 1<br>Pfam-B_3330 (release 17.0). Proteins containing this domain are checkpoint proteins involved in cell division.  This region has been shown to be essential for the binding of the binding of BUB1 and MAD3 to CDC20p  .. 
PF08312 cwf21 domain<br>Pfam-B_14400 (release 17.0). The cwf21 family is involved in mRNA splicing.  It has been isolated as a subcomplex of the splicosome in Schizosaccharomyces pombe  . The function of the cwf21 domain is to bind directly to the spliceosomal protein Prp8. Mutations in the cwf21 domain prevent Prp8 from binding  . The structure of this domain has recently been solved which shows this domain to be composed of two alpha helices.. 
PF08313 SCA7, zinc-binding domain<br>Pfam-B_21229 (release 17.0). This domain is found in the protein Sgf73/Sca7 which is a component of the multihistone acetyltransferase complexes SAGA and SILK  .  This domain is also found in Ataxin-7, a human protein which in its polyglutamine expanded pathological form, is responsible for the neurodegenerative disease spinocerebellar ataxia 7 (SCA7)  .  Ataxin-7 is an integral component of the mammalian SAGA-like complexes, the TATA-binding protein-free TAF-containing complex (TFTC) and the SPT3/TAF9/GCN5 acetyltransferase complex (STAGA). This domain is a minimal domain in ataxin-7-like proteins that is required for interaction with TFTC/STAGA subunits and is conserved highly through evolution. The domain contains a conserved Cys(3)His motif that binds zinc, thus indicating this to be a new zinc-binding domain  .. 
PF08314 Secretory pathway protein Sec39<br>Mistry J, Wood V, Schmitt HD. Mnaimneh et al   identified Sec39p as a protein involved in ER-Golgi transport in a large scale promoter shut down analysis of essential yeast genes.  Kraynack et al. (2005)   showed that Sec39p (Dsl3p) is required for Golgi-ER retrograde transport and is part of a very stable protein complex that also includes Dsl1p (in mammals ZW10), Tip20p (Rint-1) and the ER localized Q-SNARE proteins Ufe1p (syntaxin-18), Sec20p and Use1p. This was confirmed in a genome-wide analysis of protein complexes by Gavin et al (2006)  .. 
PF08315 cwf18 pre-mRNA splicing factor <br>Pfam-B_19718 (release 17.0). The cwf18 family is involved in mRNA splicing.  It has been isolated as a subcomplex of the splicosome in Schizosaccharomyces pombe  .. 
PF08316 Pal1 cell morphology protein<br>Pal1 is a membrane associated protein that is involved in the maintenance of cylindrical cellular morphology.  It localises to sites of active growth.  Pal1 physically interacts and displays overlapping localisation with the Huntingtin-interacting-protein (Hip1)-related protein Sla2p/End4p  .. 
PF08317 Spc7 kinetochore protein<br>This domain is found in cell division proteins which are required for kinetochore-spindle association  .. 
PF08318 Sec38; <br>COG4 transport protein. This region is found in yeast oligomeric golgi complex component 4 which is involved in ER to Golgi an intra Golgi transport  .. 
PF08320 PIG-X / PBN1<br>Mammalian PIG-X and yeast PBN1 are essential components of glycosylphosphatidylinositol-mannosyltransferase I  .  These enzymes are involved in the transfer of sugar molecules.. 
PF08321 PPT1; <br>PPP5 TPR repeat region. Pfam-B_6912 (release 17.0). This region is specific to the PPP5 subfamily of serine/threonine phosphatases and contains TPR repeats.. 
PF08323 Starch synthase catalytic domain<br>Pfam-B_148 (Release 17.0). 
PF08324 PUL domain<br>The PUL (PLAP, Ufd3p and Lub1p) domain is a novel alpha-helical Ub-associated domain.  It directly binds to Cdc48, a chaperone-like AAA ATPase that collects ubiquitylated substrates   .. 
PF08325 WLM domain<br>This is a predicted metallopeptidase domain called WLM (Wss1p-like metalloproteases).  These are linked to the Ub-system by virtue of fusions with the UB-binding PUG (PUB), Ub-like, and Little Finger domains. More specifically, genetic evidence implicates the WLM family in de-SUMOylation  .. 
PF08326 Acetyl-CoA carboxylase, central region<br>Pfam-B_2008 (release 18.0). The region featured in this family is found in various eukaryotic acetyl-CoA carboxylases, N-terminal to the catalytic domain (Pfam:PF01039). This enzyme (EC:6.4.1.2) is involved in the synthesis of long-chain fatty acids, as it catalyses the rate-limiting step in this process.. 
PF08327 Activator of Hsp90 ATPase homolog 1-like protein<br>Pfam-B_4145 (release 18.0). This family includes eukaryotic, prokaryotic and archaeal proteins that bear similarity to a C-terminal region of human activator of 90 kDa heat shock protein ATPase homolog 1 (AHSA1/p38, Swiss:O95433). This protein is known to interact with the middle domain of Hsp90, and stimulate its ATPase activity  . It is probably a general upregulator of Hsp90 function, particularly contributing to its efficiency in conditions of increased stress  . p38 is also known to interact with the cytoplasmic domain of the VSV G protein, and may thus be involved in protein transport  . It has also been reported as being underexpressed in Down's syndrome. This region is found repeated in two members of this family (Swiss:Q8XY04 and Swiss:Q6MH87).. 
PF08328 Adenylosuccinate lyase C-terminal<br>Pfam-B_1176 (release 18.0). This domain is found at the C-terminus of adenylosuccinate lyase(ASL; PurB in E. coli). It has been identified in bacteria, eukaryotes and archaea and is found together with the lyase domain Pfam:PF00206.  ASL catalyses the cleavage of succinylaminoimidazole carboxamide ribotide to aminoimidazole carboxamide ribotide and fumarate and the cleavage of adenylosuccinate to adenylate and fumarate  .. 
PF08329 Chitinase A, N-terminal domain<br>Pfam-B_1049 (release 18.0). This domain is found in a number of bacterial chitinases and similar viral proteins. It is organised into a fibronectin III module domain-like fold, comprising only beta strands. Its function is not known, but it may be involved in interaction with the enzyme substrate, chitin [1,2]. It is separated by a hinge region from the catalytic domain (Pfam:PF00704); this hinge region is probably mobile, allowing the N-terminal domain to have different relative positions in solution  .. 
PF08331 Domain of unknown function (DUF1730)<br>Pfam-B_1023 (release 18.0). This domain of unknown function occurs in Iron-sulfur cluster-binding proteins together with the 4Fe-4S binding domain (Pfam:PF00037).. 
PF08332 Calcium/calmodulin dependent protein kinase II Association<br>Pfam-B_1025 (release 18.0). This domain is found at the C-terminus of the Calcium/calmodulin dependent protein kinases II (CaMKII).  These proteins also have a Ser/Thr protein kinase domain (Pfam:PF00069) at their N-terminus  .  The function of the CaMKII association domain is the assembly of the single proteins into large (8 to 14 subunits) multimers  .. 
PF08333 Protein of unknown function (DUF1725)<br>Pfam-B_2110 (release 18.0). This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members.. 
PF08334 GSPII_G;<br>Type II secretion system (T2SS), protein G. Pfam-B_1144 (release 18.0). The Type II secretion system, also called Secretion-dependent pathway (SDP), is responsible for the transport of proteins across the outer membrane first exported to the periplasm by the Sec or Tat translocon in Gram-negative (diderm) bacteria [1,2]. The T2SG family includes proteins such as EpsG (P45773) in Vibrio cholera, XcpT also called PddA (Q00514) in Pseudomonas aeruginosa or PulG (P15746)in Klebsiella pneumoniae. The PulG is thought to be anchored in the inner membrane with its C-terminus directed towards the periplasme  . Together with other members of the Type II secretion machinery, it is thought to assemble into a pilus-like structure that may function as a dynamic mechanism to push secreted proteins out of the cell. The polypeptide is organized into a long N-terminal alpha-helix followed by a loop region that separates it from a C-terminal anti-parallel beta-sheet  .. 
PF08335 GlnD PII-uridylyltransferase<br>Pfam-B_2147 (release 18.0). This is a family of bifunctional uridylyl-removing enzymes/uridylyltransferases (UR/UTases, GlnD) that are responsible for the modification (EC:2.7.7.59) of the regulatory protein P-II, or GlnB (e.g. Swiss:P05826, Pfam:PF00543). In response to nitrogen limitation, these transferases (e.g. Swiss:P27249) catalyse the uridylylation of the PII protein, which in turn stimulates deadenylylation of glutamine synthetase (GlnA). Deadenylylated glutamine synthetase is the more active form of the enzyme  . Moreover, uridylylated PII can act together with NtrB and NtrC to increase transcription of genes in the sigma54 regulon, which include glnA and other nitrogen-level controlled genes  . It has also been suggested that the product of the glnD gene is involved in other physiological functions such as control of iron metabolism in certain species  . The region described in this family is found in many of its members to be C-terminal to a nucleotidyltransferase domain (Pfam:PF01909), and N-terminal to an HD domain (Pfam:PF01966) and two ACT domains (Pfam:PF01842)  .. 
PF08336 Prolyl 4-Hydroxylase alpha-subunit, N-terminal region<br>Pfam-B_2013 (release 18.0). The members of this family are eukaryotic proteins, and include all three isoforms of the prolyl 4-hydroxylase alpha subunit. This enzyme (EC:1.14.11.2) is important in the post-translational modification of collagen, as it catalyses the formation of 4-hydroxyproline. In vertebrates, the complete enzyme is an alpha2-beta2 tetramer; the beta-subunit is identical to protein disulphide isomerase [1-4]. The function of the N-terminal region featured in this family does not seem to be known.. 
PF08337 Plexin cytoplasmic RasGAP domain<br>Pfam-B_3123 (release 18.0). This family features the C-terminal regions of various plexins (e.g. Swiss:P51805). Plexins are receptors for semaphorins, and plexin signalling is important in path finding and patterning of both neurons and developing blood vessels [1,2]. The cytoplasmic region, which has been called a SEX domain in some members of this family  , is involved in downstream signalling pathways, by interaction with proteins such as Rac1, RhoD, Rnd1 and other plexins  . This domain acts as a RasGAP domain  .. 
PF08338 Domain of unknown function (DUF1731)<br>Pfam-B_1045 (release 18.0). This domain of unknown function appears towards the C-terminus of proteins of the NAD dependent epimerase/dehydratase family (Pfam:PF01370) in bacteria, eukaryotes and archaea.  Many of the proteins in which it is found are involved in cell-division inhibition.. 
PF08339 RTX C-terminal domain<br>Pfam-B_2178 (release 18.0). This family describes the C-terminal region of various bacterial haemolysins and leukotoxins, which belong to the RTX family of toxins. These are produced by various Gram negative bacteria, such as E. coli (Swiss:P09983) and Actinobacillus pleuropneumoniae (Swiss:P15377). RTX toxins may interact with lipopolysaccharide (LPS) to functionally impair and eventually kill leukocytes  . This region is found in association with the RTX N-terminal domain (Pfam:PF02382) and multiple hemolysin-type calcium-binding repeats (Pfam:PF00353).. 
PF08340 Domain of unknown function (DUF1732)<br>Wuster A, Eberhardt R. Pfam-B_1065 (release 18.0). This domain of unknown function is often found at the C-terminus of bacterial proteins, many of which are hypothetical, including proteins of the YicC family which have Pfam:PF03755 at the N-terminus. These include a protein important in the stationary phase of growth, and required for growth at high temperature  . Structural modelling suggests this domain may bind nucleic acids  .. 
PF08341 Fibronectin-binding protein signal sequence<br>Pfam-B_4004 (release 18.0). This domain is found near the N-terminus of fibronectin-binding proteins in Streptococcus where it functions as a signal sequence  .. 
PF08343 Ribonucleotide reductase N-terminal<br>Pfam-B_1066 (release 18.0). This domain is found at the N-terminus of bacterial ribonucleoside-diphosphate reductases (ribonucleotide reductases, RNRs) which catalyse the formation of deoxyribonucleotides  . It occurs together with the RNR all-alpha domain (Pfam:PF00317) and the RNR barrel domain (Pfam:PF02867).. 
PF08344 Transient receptor ion channel II<br>Pfam-B_1032 (release 18.0). This domain is found in the transient receptor ion channel (Trp) family of proteins.  There is strong evidence that Trp proteins are structural elements of calcium-ion entry channels activated by G protein-coupled receptors  .  This domain does not tend to appear with the TRP domain (Pfam:PF06011) but is often found to the C-terminus of Ankyrin repeats (Pfam:PF00023).. 
PF08345 Flagellar M-ring protein C-terminal<br>Pfam-B_1149 (release 18.0). This domain is found in bacterial flagellar M-ring (FliF) proteins together with the YscJ/FliF domain (Pfam:PF01514).. 
PF08346 AntA/AntB antirepressor<br>Pfam-B_2097 (release 18.0). In E. coli the two proteins AntA and AntB have 62% amino acid identities near their N termini. AntA appears to be encoded by a truncated and divergent copy of AntB.  The two proteins are homologous to putative antirepressors found in numerous bacteriophages, such as the hypothetical antirepressor protein encoded by the gene LO142 of the bacteriophage 933W  .. 
PF08347 N-terminal CTNNB1 binding<br>Pfam-B_2064 (release 18.0). This region tends to appear at the N-terminus of proteins also containing DNA-binding HMG (high mobility group) boxes (Pfam:PF00505) and appears to bind the armadillo repeat of CTNNB1 (beta-catenin), forming a stable complex. Signaling by Wnt through TCF/LCF is involved in developmental patterning, induction of neural tissues, cell fate decisions and stem cell differentiation  .  Isoforms of HMG T-cell factors lacking the N-terminal CTNNB1-binding domain cannot fulfill their role as transcriptional activators in T-cell differentiation [1,2].. 
PF08348 YheO; <br>YheO-like PAS domain. Pfam-B_2023 (release 18.0). This family contains various hypothetical bacterial proteins that are similar to the E. coli protein YheO (Swiss:P64624). Their function is unknown, but are likely to be involved in signalling based on the presence of this PAS domain.. 
PF08349 Protein of unknown function (DUF1722)<br>Pfam-B_4169 (release 18.0). This domain of unknown function is found in bacteria and archaea and is homologous to the hypothetical protein ybgA from E. coli.. 
PF08350 Domain of unknown function (DUF1724)<br>Pfam-B_1158 (release 18.0). This domain of unknown function has so far only been found at the C-terminus of archaean proteins, including several transcriptional regulators of the ArsR family (see Pfam:PF01022).. 
PF08351 Domain of unknown function (DUF1726)<br>Wuster A, Eberhardt R. Pfam-B_3131 (release 18.0). This domain of unknown function is often found at the N-terminus of proteins containing Pfam:PF05127. Its fold resembles that of Pfam:PF05127, but it does not appear to bind ATP  .. 
PF08352 Oligopeptide/dipeptide transporter, C-terminal region<br>Pfam-B_3025 (release 18.0). This family features a region found towards the C-terminus of oligopeptide ABC transporter ATP binding proteins, immediately following the ATP-binding domain (Pfam:PF00005). All characterised members appear able to be involved in the transport of oligopeptides or dipeptides. Some are important for sporulation or antibiotic resistance. Some dipeptide transporters also act on the heme precursor delta-aminolevulinic acid.. 
PF08353 Domain of unknown function (DUF1727)<br>Pfam-B_2131 (release 18.0). This domain of unknown function is found at the C-terminus of bacterial proteins which include UDP-N-acetylmuramyl tripeptide synthase and the related Mur ligase.. 
PF08354 Domain of unknown function (DUF1729)<br>Pfam-B_3179 (release 18.0). This domain of unknown function is found in fatty acid synthase beta subunits together with the MaoC-like domain (Pfam:PF01575) and the Acyltransferase domain (Pfam:PF00698)  .  The domain has been identified in fungi and bacteria.. 
PF08355 EF hand associated<br>Pfam-B_4111 (release 18.0). This region typically appears on the C-terminus of EF hands in GTP-binding proteins such as Arht/Rhot (may be involved in mitochondrial homeostasis and apoptosis ).  The EF hand associated region is found in yeast, vertebrates and plants.. 
PF08356 EF hand associated<br>Pfam-B_3018 (release 18.0). This region predominantly appears near EF-hands (Pfam:PF00036) in GTP-binding proteins. It is found in all three eukaryotic kingdoms.. 
PF08357 SEFIR domain<br>Pfam-B_33671 (release 17.0). This family comprises IL17 receptors (IL17Rs, e.g. Swiss:Q60943) and SEF proteins (e.g. Swiss:Q8QHJ9). The latter are feedback inhibitors of FGF signalling and are also thought to be receptors. Due to its similarity to the TIR domain (Pfam:PF01582), the SEFIR region is thought to be involved in homotypic interactions with other SEFIR/TIR-domain-containing proteins. Thus, SEFs and IL17Rs may be involved in TOLL/IL1R-like signalling pathways  .. 
PF08358 Carlavirus coat<br>Pfam-B_2014 (release 18.0). This domain is found together with the viral coat protein domain (Pfam:PF00286) in coat/capsid proteins of Carlaviruses infecting plants.. 
PF08359 YsiA-like protein, C-terminal region<br>Pfam-B_20730 (release 17.0). The members of this family are thought to be TetR-type transcriptional regulators that bear particular similarity to YsiA (Swiss:P94548), a hypothetical protein expressed by B. subtilis.. 
PF08360 QacR-like protein, C-terminal region<br>Pfam-B_96140 (release 17.0). This family features the C-terminal region of a number of proteins that bear similarity to the QacR protein (Swiss:P23217), a transcriptional regulator of the TetR family. QacR is able to bind various environmental agents, which include a number of cationic lipophilic compounds, and thus regulate the transcription of QacA (Swiss:P23215), a multidrug efflux pump  . The C-terminal region contains the multifaceted, expansive drug-binding pocket, which is composed of several separate, but linked, binding sites  .. 
PF08361 MAATS-type transcriptional repressor, C-terminal region<br>Pfam-B_3020 (release 18.0). This family is named after the various transcriptional regulatory proteins that it contains, including MtrR (Swiss:Q6RV06), AcrR (Swiss:P34000), ArpR (Swiss:Q9KJC4), TtgR (Swiss:Q9AIU0) and SmeT (Swiss:Q8KLP4). These are members of the TetR family of transcriptional repressors, that are involved in the control of expression of multidrug resistance proteins [1,2,3].. 
PF08362 YcdC-like protein, C-terminal region<br>Pfam-B_4012 (release 17.0). This family comprises proteins that belong to the TetR family of transcriptional regulators. They bear particular similarity to YcdC (Swiss:P75899), a putative HTH-containing protein. This family features the C-terminal region of these sequences, which does not include the helix-turn-helix.. 
PF08363 Glucan-binding protein C<br>Pfam-B_3074 (release 18.0). This domain is found in the Streptococcus Glucan-binding protein C (GbpC) and also in surface protein antigen (Spa)-family proteins which show sequence similarity to GbpC  .. 
PF08364 Bacterial translation initiation factor IF-2 associated region<br>Pfam-B_3037 (release 18.0). Most of the sequences in this alignment come from bacterial translation initiation factors (IF-2, also Pfam:PF04760), but the domain is also found in the eukaryotic translation initiation factor 4 gamma in yeast and in a hypothetical Euglenozoa protein of unknown function.. 
PF08365 Insulin-like growth factor II E-peptide<br>Pfam-B_4175 (release 18.0). This domain is found at the C-terminal domain of the insulin-like growth factor II (IGF-2, also see Pfam:PF00049) in vertebrates and seems to represent the E-peptide [1,2].. 
PF08366 LLGL2<br>Pfam-B_4088 (release 18.0). This domain is found in lethal giant larvae homolog 2 (LLGL2) proteins and syntaxin-binding proteins like tomosyn  .  It has been identified in eukaryotes and tends to be found together with WD repeats (Pfam:PF00400).. 
PF08367 Peptidase M16C associated<br>Pfam-B_3062 (release 18.0). This domain appears in eukaryotes as well as bacteria and tends to be found near the C-terminus of the metalloprotease M16C (Pfam:PF05193).. 
PF08368 FAST kinase-like protein, subdomain 2<br>Vella Briffa B, Fenech M. Pfam-B_2858 (release 10.0). This family represents a conserved region of eukaryotic Fas-activated serine/threonine (FAST) kinases (EC:2.7.1.-) that contains several conserved leucine residues. FAST kinase is rapidly activated during Fas-mediated apoptosis, when it phosphorylates TIA-1, a nuclear RNA-binding protein that has been implicated as an effector of apoptosis  . Note that many family members are hypothetical proteins. This subdomain is often found associated with the FAST kinase-like protein, subdomain 2.. 
PF08369 Proto-chlorophyllide reductase 57 kD subunit<br>Pfam-B_2047 (release 18.0). This domain is found in bacteria and plant chloroplast proteins. It often appears at the C-terminal of Nitrogenase component 1 type Oxidoreductases (Pfam:PF00148) and sometimes independently in bacterial proteins such as the Proto-chlorophyllide reductase 57 kD subunit of the Cyanobacterium Synechocystis.. 
PF08370 Plant PDR ABC transporter associated<br>Pfam-B_2126 (release 18.0). This domain is found on the C-terminus of ABC-2 type transporter domains (Pfam:PF01061).  It seems to be associated with the plant pleiotropic drug resistance (PDR) protein family of ABC transporters.  Like in yeast, plant PDR ABC transporters may also play a role in the transport of antifungal agents [1, also Pfam:PF06422].  The PDR family is characterised by a configuration in which the ABC domain is nearer the N-terminus of the protein than the transmembrane domain  .. 
PF08372 Plant phosphoribosyltransferase C-terminal<br>Pfam-B_3195 (release 18.0). This domain is found at the C-terminus of phosphoribosyltransferases and phosphoribosyltransferase-like proteins.  It contains putative transmembrane regions.  It often appears together with calcium-ion dependent C2 domains (Pfam:PF00168).. 
PF08373 RAP domain<br>Pfam-B_5583 (release 17.0). This domain is found in various eukaryotic species, where it is found in proteins that are important in various parasite-host cell interactions. It is thought to be an RNA-binding domain  . The domain is involved in plant defence in response to bacterial infection [2,3].. 
PF08374 Protocadherin<br>Pfam-B_4100 (release 18.0). The structure of protocadherins is similar to that of classic cadherins (Pfam:PF00028), but particularly on the cytoplasmic domains they also have some unique features.  They are expressed in a variety of organisms and are found in high concentrations in the brain where they seem to be localised mainly at cell-cell contact sites.  Their expression seems to be developmentally regulated  .. 
PF08375 Proteasome regulatory subunit C-terminal<br>Pfam-B_4098 (release 18.0). This eukaryotic domain is found at the C-terminus of 26S proteasome regulatory subunits such as the non-ATPase Rpn3 subunit which is essential for proteasomal function  .  It occurs together with the PCI/PINT domain (Pfam:PF01399).. 
PF08376 Nitrate and nitrite sensing<br>Pfam-B_37103 (release 17.0). The nitrate- and nitrite sensing domain (NIT) is found in receptor components of signal transducing pathways in bacteria which control gene expression, cellular motility and enzyme activity in response to nitrate and nitrite concentrations.  The NIT domain is predicted to be all alpha-helical in structure  .. 
PF08377 MAP2/Tau projection domain<br>Pfam-B_26981 (release 17.0). This domain is found in the MAP2/Tau family of proteins which includes MAP2, MAP4, Tau, and their homologs.  All isoforms contain a conserved C-terminal domain containing tubulin-binding repeats (Pfam:PF00418), and a N-terminal projection domain of varying size.  This domain has a net negative charge and exerts a long-range repulsive force.  This provides a mechanism that can regulate microtubule spacing which might facilitate efficient organelle transport [1,2].. 
PF08378 Nuclease-related domain<br>Pfam-B_9750 (release 17.0). The nuclease-related domain (NERD) is found in a range of bacterial as well as archaeal and plant proteins.  It has distant similarity to endonucleases (hence its name) and its predicted secondary structure is helix - sheet - sheet - sheet - sheet - weak sheet/long loop - helix - sheet - sheet. The majority of NERD-containing proteins are single-domain, but in several cases proteins containing NERD have additional domains which in 75% of cases are involved in DNA processing  .. 
PF08379 Bacterial transglutaminase-like N-terminal region<br>Pfam-B_2190 (release 18.0). This region is found towards the N-terminus of various archaeal and bacterial hypothetical proteins. Some of these are annotated as being transglutaminase-like proteins, and in fact contain a transglutaminase-like superfamily domain (Pfam:PF01841).. 
PF08381 DZC;<br>Transcription factor regulating root and shoot growth via Pin3. Pfam-B_2116 (release 18.0). The BREVIS RADIX (BRX) domain was characterised as being a transcription factor in plants regulating the extent of cell proliferation and elongation in the growth zone of the root [1,2]. BRX is rate limiting for auxin-responsive gene-expression by mediating cross-talk with the brassino-steroid pathway.  BRX has a ubiquitous, although quantitatively variable role in modulating the growth rate in both the root and the shoot  . The family features a short region of alpha-helix, approximately 60 residues in length, which is found repeated up to three times  . BRX is expressed in the vasculature and is rate-limiting for transcriptional auxin action  .. 
PF08383 Maf N-terminal region<br>Pfam-B_3103 (release 18.0). This region is found in various leucine zipper transcription factors of the Maf family. These are implicated in the regulation of insulin gene expression  , in erythroid differentiation  , and in differentiation of the neuroretina  .. 
PF08384 Pro-opiomelanocortin, N-terminal region<br>Pfam-B_1053 (release 18.0). This family features the N-terminal peptide of pro-opiomelanocortin (NPP). It is thought to represent an important pituitary peptide, given its high yield from pituitary glands, and exhibits a potent in vitro aldosterone-stimulating activity  .. 
PF08385 Dynein heavy chain, N-terminal region 1<br>Pfam-B_3094 (release 18.0). Dynein heavy chains interact with other heavy chains to form dimers, and with intermediate chain-light chain complexes to form a basal cargo binding unit  . The region featured in this family includes the sequences implicated in mediating these interactions  . It is thought to be flexible and not to adopt a rigid conformation  .. 
PF08386 TAP-like protein<br>Pfam-B_3096 (release 18.0). This is a family of putative bacterial peptidases and hydrolases that bear similarity to a tripeptidyl aminopeptidase isolated from Streptomyces lividans (Swiss:Q54410). A member of this family (Swiss:Q6E3K7) is thought to be involved in the C-terminal processing of propionicin F, a bacteriocidin characterised from Propionibacterium freudenreichii  .. 
PF08387 FBD<br>Pfam-B_1153 (release 18.0). This region is found in F-box (Pfam:PF00646) and other domain containing plant proteins; it is repeated in two family members. Its precise function is unknown, but it is thought to be associated with nuclear processes  . In fact, several family members are annotated as being similar to transcription factors.. 
PF08388 Group II intron, maturase-specific domain<br>Pfam-B_4063 (release 18.0). This region is found mainly in various bacterial and archaeal species, but a few members of this family are expressed by fungal and chlamydomonal species. It has been implicated in the binding of intron RNA during reverse transcription and splicing  .. 
PF08389 Exportin 1-like protein<br>Pfam-B_4058 (release 18.0). The sequences featured in this family are similar to a region close to the N-terminus of yeast exportin 1 (Xpo1, Crm1, Swiss:P14068). This region is found just C-terminal to an importin-beta N-terminal domain (Pfam:PF03810) in many members of this family. Exportin 1 is a nuclear export receptor that interacts with leucine-rich nuclear export signal (NES) sequences, and Ran-GTP, and is involved in translocation of proteins out of the nucleus [1,2].. 
PF08390 TRAM1-like protein<br>Pfam-B_3108 (release 18.0). This family comprises sequences that are similar to human TRAM1 (Swiss:Q15629). This is a transmembrane protein of the endoplasmic reticulum, thought to be involved in the membrane transfer of secretory proteins  . The region featured in this family is found N-terminal to the longevity-assurance protein region (Pfam:PF03798).. 
PF08391 Ly49-like protein, N-terminal region<br>Pfam-B_1187 (release 18.0). The sequences making up this family are annotated as, or are similar to, Ly49 receptors (e.g. Swiss:P20937). These are type II transmembrane receptors expressed by mouse natural killer (NK) cells. They are classified as being activating (e.g.Ly49D and H) or inhibitory (e.g. Ly49A and G), depending on their effect on NK cell function  . They are members of the C-type lectin receptor superfamily  , and in fact in many family members this region is found immediately N-terminal to a lectin C-type domain (Pfam:PF00059).. 
PF08392 FAE1/Type III polyketide synthase-like protein<br>Pfam-B_1177 (release 18.0). The members of this family are described as 3-ketoacyl-CoA synthases, type III polyketide synthases, fatty acid elongases and fatty acid condensing enzymes, and are found in both prokaryotic and eukaryotic (mainly plant) species. The region featured in this family contains the active site residues, as well as motifs involved in substrate binding  .. 
PF08393 Dynein heavy chain, N-terminal region 2<br>Pfam-B_3094 (release 18.0). Dyneins are described as motor proteins of eukaryotic cells, as they can convert energy derived from the hydrolysis of ATP to force and movement along cytoskeletal polymers, such as microtubules. This region is found C-terminal to the dynein heavy chain N-terminal region 1 (Pfam:PF08385) in many members of this family. No functions seem to have been attributed specifically to this region.. 
PF08394 Archaeal TRASH domain<br>Pfam-B_18882 (release 17.0). This region is found in the C-terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module  .. 
PF08395 7tm Chemosensory receptor<br>This family includes a number of gustatory and odorant receptors mainly from insect species such as A. gambiae and D. melanogaster. They are classified as G-protein-coupled receptors (GPCRs), or seven-transmembrane receptors. They show high sequence divergence, consistent with an ancient origin for the family [1,2].. 
PF08396 Spider toxin omega agatoxin/Tx1 family<br>Mondal S, Ramakumar S. The Tx1 family lethal spider neurotoxin induces excitatory  symptoms in mice  .. 
PF08397 IRSp53/MIM homology domain<br>Pfam-B_4120 (release 18.0). The N-terminal predicted helical stretch of the insulin receptor tyrosine kinase substrate p53 (IRSp53) is an evolutionary conserved F-actin bundling domain involved in filopodium formation. The domain has been named IMD after the IRSp53 and missing in metastasis (MIM) proteins in which it occurs. Filopodium-inducing IMD activity is regulated by Cdc42 and Rac1 and is SH3-independent  .. 
PF08398 Parvovirus coat protein VP1<br>Pfam-B_2198 (release 18.0). This is the N-terminal region of the Parvovirus VP1 coat protein. Also see Parvovirus coat protein VP2 (Pfam:PF00740).. 
PF08399 VWA N-terminal<br>Pfam-B_2075 (release 18.0). This domain is found at the N-terminus of proteins containing von Willebrand factor type A (VWA, Pfam:PF00092) and Cache (Pfam:PF02743) domains.  It has been found in vertebrates, Drosophila and C. elegans but has not yet been identified in other eukaryotes. It is probably involved in the function of some voltage-dependent calcium channel subunits  .. 
PF08400 Prophage tail fibre N-terminal<br>Pfam-B_3101 (release 18.0). This domain is found at the N-terminus of prophage tail fibre proteins.. 
PF08401 Domain of unknown function (DUF1738)<br>Pfam-B_3014 (release 18.0). This region is found in a number of bacterial hypothetical proteins. Some members are annotated as being similar to replication primases, and in fact this region is often found together with the Toprim domain (Pfam:PF01751).. 
PF08402 TOBE domain<br>Pfam-B_4178 (release 18.0). The TOBE domain   (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. Probably involved in the recognition of small ligands such as molybdenum (eg Swiss:P46930) and sulphate (Swiss:P16676). Found in ABC transporters immediately after the ATPase domain. In this family a strong RPE motif is found at the presumed N-terminus of the domain.. 
PF08403 Amino acid permease N-terminal<br>Pfam-B_3112 (release 18.0). This domain is found to the N-terminus of the amino acid permease domain (Pfam:PF00324) in metazoan Na-K-Cl cotransporters.. 
PF08404 Baculoviridae P74 N-terminal<br>Pfam-B_3059 (release 18.0). This domain is found at the N-terminus of P74 occlusion-derived virus (ODV) envelope proteins which are required for oral infectivity.  The envelope proteins are found in baculoviruses which are insect pathogens.  The C-terminus of P74 is anchored to the membrane whereas the N-terminus is exposed to the virion surface.  Furthermore P74 is unusual for a virus envelope protein as it lacks an N-terminal localisation signal sequence  .\.   Also see Pfam:PF04583.. 
PF08405 Viral polyprotein N-terminal<br>Pfam-B_4167 (release 18.0). This domain is found at the N-terminus of non-structural viral polyproteins of the Caliciviridae subfamily.. 
PF08406 CbbQ/NirQ/NorQ C-terminal <br>Pfam-B_3065 (release 18.0). This domain is found at the C-terminus of proteins of the CbbQ/NirQ/NorQ family of proteins which play a role in the post-translational activation of Rubisco  .  It is also found in the Thauera aromatica TutH protein which is similar to the CbbQ/NirQ/NorQ family  , as well as in putative chaperones.  The ATPase family associated with various cellular activities (AAA) Pfam:PF07728 is found in the same bacterial and archaeal proteins as the domain described here.. 
PF08407 Chitin synthase N-terminal<br>Pfam-B_1105 (release 18.0). This is the N-terminal domain of Chitin synthase (Pfam:PF01644).. 
PF08408 DNA polymerase family B viral insert<br>Pfam-B_3028 (release 18.0). This viral domain is found between the exonuclease domain of the DNA polymerase family B (Pfam:PF03104) and the Pfam:PF00136 domain, connecting the two.. 
PF08409 Domain of unknown function (DUF1736)<br>Pfam-B_4104 (release 18.0). This domain of unknown function is found in various hypothetical metazoan proteins.. 
PF08410 Domain of unknown function (DUF1737)<br>Pfam-B_2030 (release 18.0). This domain of unknown function is found at the N-terminus of bacterial and viral hypothetical proteins.. 
PF08411 Exonuclease C-terminal<br>Pfam-B_3061 (release 18.0). This bacterial domain is found at the C-terminus of Exodeoxyribonuclease I/Exonuclease I (Pfam:PF00929), which is a single-strand specific DNA nuclease affecting recombination and expression pathways.  The exonuclease I protein in E. coli is associated with DNA deoxyribophosphodiesterase (dRPase)  .. 
PF08412 Ion transport protein N-terminal<br>Pfam-B_4115 (release 18.0). This metazoan domain is found to the N-terminus of Pfam:PF00520 in voltage- and cyclic nucleotide-gated K/Na ion channels.. 
PF08414 Respiratory burst NADPH oxidase<br>Pfam-B_2127 (release 18.0). This domain is found in plant proteins such as respiratory burst NADPH oxidase proteins which produce reactive oxygen species as a defence mechanism.  It tends to occur to the N-terminus of an EF-hand (Pfam:PF00036), which suggests a direct regulatory effect of Ca2+ on the activity of the NADPH oxidase in plants  .. 
PF08415 Nonribosomal peptide synthase<br>Pfam-B_1156 (release 18.0). This domain is found in bacterial nonribosomal peptide synthetases (NRPS).  NRPS are megaenzymes organised as iterative modules, one for each amino acid to be built into the peptide product  . NRPS modules are involved in epothilone biosynthesis (EpoB), myxothiazol biosynthesis (MtaC and MtaD), and other functions  .  The NRPS domain tends to be found together with the condensation domain (Pfam:PF00668) and the phosphopantetheine binding domain (Pfam:PF00550).. 
PF08416 Phosphotyrosine-binding domain<br>Pfam-B_3174 (release 18.0). The phosphotyrosine-binding domain (PTB, also phosphotyrosine-interaction or PI domain) in the protein tensin tends to be found at the C-terminus.  Tensin is a multi-domain protein that binds to actin filaments and functions as a focal-adhesion molecule (focal adhesions are regions of plasma membrane through which cells attach to the extracellular matrix).  Human tensin has actin-binding sites, an SH2 (Pfam:PF00017) domain and a region similar to the tumour suppressor PTEN  .  The PTB domain interacts with the cytoplasmic tails of beta integrin by binding to an NPXY motif  .. 
PF08417 Pheophorbide a oxygenase<br>Pfam-B_3102 (release 18.0). This domain is found in bacterial and plant proteins to the C-terminus of a Rieske 2Fe-2S domain (Pfam:PF00355).  One of the proteins the domain is found in is Pheophorbide a oxygenase (PaO) which seems to be a key regulator of chlorophyll catabolism. Arabidopsis PaO (AtPaO) is a Rieske-type 2Fe-2S enzyme that is identical to Arabidopsis accelerated cell death 1 and homologous to lethal leaf spot 1 (LLS1) of maize  , in which the domain described here is also found.. 
PF08418 DNA polymerase alpha subunit B N-terminal<br>Pfam-B_4046 (release 18.0). This is the eukaryotic DNA polymerase alpha subunit B N-terminal domain which is involved in complex formation  .  Also see Pfam:PF04058.. 
PF08421 Putative zinc binding domain<br>Pfam-B_2038 (release 18.0). This domain is found at the N-terminus of bacterial methyltransferases and contains four conserved cysteines suggesting a potential zinc binding domain.. 
PF08423 Rad51<br>Pfam-B_684 (release 17.0). Rad51 is a DNA repair and recombination protein and is a homologue of the bacterial ATPase RecA protein.. 
PF08424 DUF1740;<br>NRDE-2, necessary for RNA interference. Pfam-B_21376 (release 17.0). This is a family of eukaryotic proteins.  Eukaryotic cells express a wide variety of endogenous small regulatory RNAs that regulate heterochromatin formation, developmental timing, defence against parasitic nucleic acids, and genome rearrangement. Many small regulatory RNAs are thought to function in nuclei, and in plants and fungi small interfering (si)RNAs associate with nascent transcripts and direct chromatin and/or DNA modifications. This family protein, NRDE-2, is required for small interfering (si)RNA-mediated silencing in nuclei. NRDE-2 associates with the Argonaute protein NRDE-3 within nuclei and is recruited by NRDE-3/siRNA complexes to nascent transcripts that have been targeted by RNA interference, RNAi, the process whereby double-stranded RNA (dsRNA) directs the sequence-specific degradation of mRNA  .. 
PF08426 ICE2<br>ICE2 is a fungal ER protein which has been shown to play an important role in forming/maintaining the cortical ER  .  It has also bee identified as a protein which is necessary for nuclear inner membrane targeting  .. 
PF08427 Domain of unknown function (DUF1741)<br>Pfam-B_35314 (release 17.0). This is a eukaryotic domain of unknown function.. 
PF08428 Rib/alpha-like repeat<br>Pfam-B_3139 (release 18.0). The region featured in this family is found repeated in a number of bacterial surface proteins, such as Rib (Swiss:P72362) and alpha (Swiss:Q02192). These are expressed by group B streptococci, and Rib is thought to confer protective immunity.. 
PF08429 PLU-1-like protein<br>Pfam-B_4023 (release 18.0). Sequences in this family bear similarity to the central region of PLU-1 (Swiss:Q9Y3Q5). This is a nuclear protein that may have a role in DNA-binding and transcription, and is closely associated with the malignant phenotype of breast cancer  . This region is found in various other Jumonji/ARID domain-containing proteins (see Pfam:PF02373, Pfam:PF01388).. 
PF08430 Forkhead N-terminal region<br>Pfam-B_3191 (release 18.0). The region described in this family is found towards the N-terminus of various eukaryotic fork head/HNF-3-related transcription factors (which contain the Pfam:PF00250 domain). These proteins play key roles in embryogenesis, maintenance of differentiated cell states, and tumorigenesis  .. 
PF08432 DUF1742;<br>AAA-ATPase Vps4-associated protein 1. Vps Four-Associated 1, Vfa1, in yeast, is an endosomal protein that interacts with the AAA-ATPase Vps4. It would seem to be involved in regulating the trafficking of other proteins to the endocytic vacuole  .  There is a CCCH zinc finger at the N-terminus.. 
PF08433 Chromatin associated protein KTI12 <br>Pfam-B_11625 (release 17.0). This is a family of chromatin associated proteins which interact with the Elongator complex, a component of the elongating form of RNA polymerase II  .  The Elongator complex has histone acetyltransferase activity.. 
PF08434 Calcium-activated chloride channel<br>Pfam-B_3091 (release 18.0). The CLCA family of calcium-activated chloride channels has been identified in many epithelial and endothelial cell types as well as in smooth muscle cells   and has four or five putative transmembrane regions.  Additionally to their role as chloride channels some CLCA proteins function as adhesion molecules and may also have roles as tumour suppressors  .  The domain described here is found at the N-terminus of CLCAs.. 
PF08435 Calici_coat_N; <br>Calicivirus coat protein C-terminal. Pfam-B_108 (release 18.0). This is the calicivirus coat protein (Pfam:PF00915) C-terminal region.. 
PF08436 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal<br>Pfam-B_445 (release 18.0). This domain is found to the C-terminus of Pfam:PF02670 domains in bacterial and plant 1-deoxy-D-xylulose 5-phosphate reductoisomerases which catalyse the formation of 2-C-methyl-D-erythritol 4-phosphate from 1-deoxy-D-xylulose-5-phosphate in the presence of NADPH  .. 
PF08437 Glyco_transf_8N;<br>Glycosyl transferase family 8 C-terminal. Pfam-B_3038 (release 18.0). This domain is found at the C-terminus of the Pfam: PF01501 domain in bacterial glucosyltransferase and galactosyltransferase proteins.. 
PF08438 GTPase of unknown function C-terminal<br>Pfam-B_4095 (release 18.0). This domain is found at the C-terminus of Pfam:PF01926 in archaeal and eukaryotic GTP-binding proteins. The C-terminal domain of the GTP-binding proteins is necessary for the complete activity of the protein of interacting with the 50S ribosome and binding of both adenine and guanine nucleotides, with a preference for guanine nucleotides.. 
PF08439 Oligopeptidase F<br>Pfam-B_679 (release 18.0). This domain is found to the N-terminus of the Pfam:PF01432 domain in bacterial and archaeal proteins including Oligoendopeptidase F.  An example of this protein is Lactococcus lactis PepF  .. 
PF08440 Potyviridae polyprotein<br>Pfam-B_237 (release 18.0). This domain is found in polyproteins of the viral Potyviridae taxon.. 
PF08441 Integrin alpha<br>Pfam-B_609 (release 18.0). This domain is found in integrin alpha and integrin alpha precursors to the C terminus of a number of Pfam:PF01839 repeats and to the N-terminus of the Pfam:PF00357 cytoplasmic region. This region is composed of three immunoglobulin-like domains.. 
PF08442 ATP-grasp domain<br>
PF08443 RimK-like ATP-grasp domain<br>This ATP-grasp domain is found in the ribosomal S6 modification enzyme RimK  .. 
PF08444 Aralkyl acyl-CoA:amino acid N-acyltransferase, C-terminal region<br>Pfam-B_7828 (release 9.0). This family features the C-terminal region of several mammalian specific aralkyl acyl-CoA:amino acid N-acyltransferase (glycine N-acyltransferase) proteins EC:2.3.1.13.. 
PF08445 FR47-like protein<br>Pfam-B_71946 (release 17.0). The members of this family are similar to the C-terminal region of the D. melanogaster hypothetical protein FR47 (Swiss:Q9VR51). This protein has been found to consist of two N-acyltransferase-like domains swapped with the C-terminal strands.. 
PF08446 PAS fold<br>Pfam-B_437 (Release 18.0). The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs  . The PAS fold appears in archaea, eubacteria and eukarya.. 
PF08447 PAS fold<br>Pfam-B_64 (Release 18.0). The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs  . The PAS fold appears in archaea, eubacteria and eukarya.. 
PF08448 PAS fold<br>Pfam-B_493 (Release 18.0). The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs  . The PAS fold appears in archaea, eubacteria and eukarya.. 
PF08449 UAA transporter family<br>Pfam-B_606 (release 18.0). This family includes transporters with a specificity for UDP-N-acetylglucosamine  .. 
PF08450 SMP-30/Gluconolaconase/LRE-like region<br>Pfam-B_3630 (release 7.0). This family describes a region that is found in proteins expressed by a variety of eukaryotic and prokaryotic species. These proteins include various enzymes, such as senescence marker protein 30 (SMP-30, Swiss:Q15493), gluconolactonase (Swiss:Q01578) and luciferin-regenerating enzyme (LRE, Swiss:Q86DU5). SMP-30 is known to hydrolyse diisopropyl phosphorofluoridate in the liver, and has been noted as having sequence similarity, in the region described in this family, with PON1 (Swiss:P52430) and LRE  .. 
PF08451 Adenosine/AMP deaminase N-terminal<br>Pfam-B_3145 (release 18.0). This domain is found to the N-terminus of the Adenosine/AMP deaminase domain (Pfam:PF00962) in metazoan proteins such as the Cat eye syndrome critical region protein 1 and its homologues.. 
PF08452 DNA polymerase family B exonuclease domain, N-terminal<br>Pfam-B_3196 (release 18.0). This domain is found in viral DNA polymerases to the N-terminus of DNA polymerase family B exonuclease domains (Pfam:PF03104).. 
PF08453 Peptidase family M9 N-terminal<br>Pfam-B_4156 (release 18.0). This domain is found in microbial collagenase metalloproteases to the N-terminus of Pfam:PF01752.  . 
PF08454 RyR and IP3R Homology associated<br>Pfam-B_4135 (release 18.0). This eukaryotic domain is found in ryanodine receptors (RyR) and inositol 1,4,5-trisphosphate receptors (IP3R) which together form a superfamily of homotetrameric ligand-gated intracellular Ca2+ channels  .  There seems to be no known function for this domain  . Also see the IP3-binding domain Pfam:PF01365 and Pfam:PF02815.. 
PF08455 Bacterial SNF2 helicase associated<br>Pfam-B_3199 (release 18.0). This domain is found in bacterial proteins of the SWF/SNF/SWI helicase family to the N-terminus of the SNF2 family N-terminal domain (Pfam:PF00176) and together with the Helicase conserved C-terminal domain (Pfam:PF00271). The function of the domain is not clear  .. 
PF08456 Viral methyltransferase C-terminal<br>Pfam-B_2153 (release 18.0). This domain is found to the C-terminus of the viral methyltransferase domain (Pfam:PF01660) in single-stranded-RNA positive-strand viruses with no DNA stage in the Virgaviridae family.. 
PF08457 Sfi1 spindle body protein<br>Pfam-B_54813 (release 17.0). This is a family of fungal spindle pole body proteins that play a role in spindle body duplication. They contain binding sites for calmodulin-like proteins called centrins   which are present in microtubule-organising centres.. 
PF08458 Plant pleckstrin homology-like region<br>Pfam-B_7298 (release 8.0). This family describes a pleckstrin homology (PH)-like region found in several plant proteins of unknown function.. 
PF08459 UvrC Helix-hairpin-helix N-terminal<br>Pfam-B_288 (release 18.0). This domain is found in the C subunits of the bacterial and archaeal UvrABC system which catalyses nucleotide excision repair in a multi-step process.  UvrC catalyses the first incision on the fourth or fifth phosphodiester bond 3' and on the eighth phosphodiester bond 5' from the damage that is to be excised  . The domain described here is found to the N-terminus of a helix hairpin helix (Pfam:PF00633) motif and also co-occurs with the Pfam:PF01541 catalytic domain which is found at the N-terminus of the same proteins.. 
PF08460 Bacterial SH3 domain<br>Pfam-B_1108 (Release 18.0). 
PF08462 Carmovirus coat protein<br>Pfam-B_4180 (release 18.0). This domain is found to the C-terminus of the Pfam:PF00729 domain in Carmoviruses.. 
PF08463 EcoEI R protein C-terminal<br>Pfam-B_4136 (release 18.0). The restriction enzyme EcoEI recognises 5'-GAGN(7)ATGC-3' and is composed of the three proteins R, M, and S. The domain described here is found at the C-terminus of the R protein (HsdR) which is required for both nuclease and ATPase activity [1,2].. 
PF08464 Geminivirus AC4/5 conserved region<br>Pfam-B_4177 (release 18.0). This domain is found in replication initiator (Rep) associated proteins such as AC5 in the Geminivirus/Begomovirus.. 
PF08465 Thymidine kinase from Herpesvirus C-terminal<br>Pfam-B_4030 (release 18.0). This domain is found towards the C terminus in Herpesvirus Thymidine kinases.. 
PF08466 Inward rectifier potassium channel N-terminal<br>Pfam-B_4080 (release 18.0). This metazoan domain is found to the N-terminus of the Pfam:PF01007 domain in Inward rectifier potassium channels (KIR2 or IRK2).. 
PF08467 Luteovirus RNA polymerase P1-P2/replicase<br>Pfam-B_4011 (release 18.0). This domain is found in RNA-dependent RNA polymerase P1-P2 fusion/replicase proteins in plant Luteoviruses.. 
PF08468 Methyltransferase small domain N-terminal<br>Pfam-B_4172 (release 18.0). This domain is found to the N-terminus of the methyltransferase small domain (Pfam:PF05175) in bacterial proteins  .. 
PF08469 Nucleoside triphosphatase I C-terminal<br>Pfam-B_4183 (release 18.0). This viral domain is found to the C-terminus of Poxvirus nucleoside triphosphatase phosphohydrolase I (NPH I,  ) together with the helicase conserved C-terminal domain (Pfam:PF00271).. 
PF08470 Nontoxic nonhaemagglutinin C-terminal<br>Pfam-B_4024 (release 18.0). Bacteria of the Clostridium genus produce protein neurotoxins, which are complexes consisting of neurotoxin (NT), haemagglutinin (HA), nontoxic nonhaemagglutinin (NTNH), and RNA [1, 2].  The domain described here is found at the C-terminus of the NTNH component.. 
PF08471 Class II vitamin B12-dependent ribonucleotide reductase<br>Pfam-B_4121 (release 18.0). This domain is found to the N-terminus of the ribonucleotide reductase barrel domain (Pfam:PF02867).  It occurs in bacterial class II ribonucleotide reductase proteins which depend upon coenzyme B12 (deoxyadenosylcobalamine)  .. 
PF08472 Sucrose-6-phosphate phosphohydrolase C-terminal<br>Pfam-B_4159 (release 18.0). This is the Sucrose-6-phosphate phosphohydrolase (S6PP or SPP) C-terminal domain   as found in in plant sucrose phosphatases. These enzymes irreversibly catalyse the last step in sucrose synthesis following the formation of Sucrose-6-Phosphate via sucrose-phosphate synthase (SPS).. 
PF08473 Neuronal voltage-dependent calcium channel alpha 2acd<br>Pfam-B_4072 (release 18.0). This eukaryotic domain has been found in the neuronal voltage-dependent calcium channel (VGCC) alpha 2a, 2c, and 2d subunits.\.  It is also found in other calcium channel alpha-2 delta subunits to the N-terminus of a Cache domain (Pfam:PF02743).. 
PF08474 Myelin transcription factor 1<br>Pfam-B_4029 (release 18.0). This domain is found in the myelin transcription factor 1 (MYT1) of chordates.  MYT1 contains C2HC zinc finger domains (Pfam:PF01530) and is expressed in developing neurons of the central nervous system   where it is involved in the selection of neuronal precursor cells  .. 
PF08461 Ribonuclease R winged-helix domain<br>N-terminus of DUF128 family. This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaebacteria.. 
PF08475 Viral capsid protein 91 N-terminal<br>Pfam-B_4034 (release 18.0). This domain is found in Baculoviridae including the nucleopolyhedrovirus at the N-terminus of the viral capsid protein 91 (VP91)  .. 
PF08476 Viral D10 N-terminal<br>Pfam-B_4155 (release 18.0). This domain is found on the N-terminus of the viral protein D10 (VD10) and the related MutT motif proteins  .  The VD10 protein is probably essential for virus replication   and is often found to the N-terminus of a Pfam:PF00293 domain.. 
PF08477 Miro-like protein<br>Pfam-B_1154 (release 17.0). Mitochondrial Rho proteins (Miro-1, Swiss:Q8IXI2, and Miro-2, Swiss:Q8IXI1), are atypical Rho GTPases. They have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (Pfam:PF00036), that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis   .. 
PF08478 POTRA domain, FtsQ-type<br>Pfam-B_1605 (release 7.0). FtsQ/DivIB bacterial division proteins (Pfam:PF03799) contain an N-terminal POTRA domain (for polypeptide-transport-associated domain). This is found in different types of proteins, usually associated with a transmembrane beta-barrel. FtsQ/DivIB may have chaperone-like roles, which has also been postulated for the POTRA domain in other contexts  .. 
PF08479 POTRA domain, ShlB-type<br>The POTRA domain (for polypeptide-transport-associated domain) is found towards the N-terminus of ShlB family proteins (Pfam:PF03865). ShlB is important in the secretion and activation of the haemolysin ShlA. It has been postulated that the POTRA domain has a chaperone-like function over ShlA; it may fold back into the C-terminal beta-barrel channel  .. 
PF08480 Disaggregatase related<br>Pfam-B_4000 (release 18.0). This domain is found in disaggregatases and several hypothetical proteins of the archaeal genus Methanosarcina. Disaggregatases cause aggregates to separate into single cells   and contain parallel beta-helix repeats.  Also see Pfam:PF06848.. 
PF08481 GBS Bsp-like repeat<br>Pfam-B_2122 (release 18.0). This domain is found as a repeat in a number of Streptococcus proteins including some hypothetical proteins and Bsp.  Bsp is a protein of group B Streptococcus (GBS) which might control cell morphology  .. 
PF08482 ATP-dependent helicase C-terminal<br>Pfam-B_2170 (release 18.0). This domain is found near the C-terminus of bacterial ATP-dependent helicases such as HrpB.. 
PF08483 IstB_N;<br>IstB-like ATP binding N-terminal. Pfam-B_3188 (release 18.0). This bacterial domain is found to the N-terminus of the Pfam:PF01695 like ATP binding domain in proteins which are putative transposase subunits  .. 
PF08484 C-methyltransferase C-terminal domain<br>Pfam-B_2106 (release 18.0). This domain is found in bacterial C-methyltransferase proteins. This domain is found C-terminal to methyltransferase domains such as Pfam:PF08241 or Pfam:PF08242. But this domain is not a methyltransferase.. 
PF08485 Polysaccharide biosynthesis protein C-terminal<br>Pfam-B_4073 (release 18.0). This domain is found to the C-terminus of the Pfam:PF02719 domain in bacterial polysaccharide biosynthesis enzymes including the capsule protein CapD   and several putative epimerases/dehydratases.. 
PF08486 Stage II sporulation protein<br>Pfam-B_1108 (release 18.0). This domain is found in the stage II sporulation protein SpoIID. SpoIID is necessary for membrane migration as well as for some of the earlier steps in engulfment during bacterial endospore formation  .  The domain is also found in amidase enhancer proteins.  Amidases, like SpoIID, are cell wall hydrolases  .. 
PF08487 Vault protein inter-alpha-trypsin domain<br>Pfam-B_2015 (release 18.0). Inter-alpha-trypsin inhibitors (ITIs) consist of one light chain and a variable set of heavy chains.  ITIs play a role in extracellular matrix (ECM) stabilisation and tumour metastasis as well as in plasma protease inhibition  .  The vault protein inter-alpha-trypsin (VIT) domain described here is found to the N-terminus of a von Willebrand factor type A domain (Pfam:PF00092) in ITI heavy chains (ITIHs) and their precursors.. 
PF08488 Wall-associated kinase<br>Pfam-B_4138 (release 18.0). This domain is found together with the eukaryotic protein kinase domain Pfam:PF00069 in plant wall-associated kinases (WAKs) and related proteins.\.     WAKs are serine-threonine kinases which might be involved in signalling to the cytoplasm and are required for cell expansion  .. 
PF08489 Domain of unknown function (DUF1743)<br>Pfam-B_4001 (release 18.0). This domain of unknown function is found in many hypothetical proteins and predicted DNA-binding proteins such as transcription-associated proteins.  It is found in bacteria and archaea.. 
PF08490 Domain of unknown function (DUF1744)<br>Pfam-B_5917 (release 18.0). This domain is found on the epsilon catalytic subunit of DNA polymerase.  It is found C terminal to Pfam:PF03104 and Pfam:PF00136.. 
PF08491 Squalene epoxidase<br>Pfam-B_3107 (release 18.0). This domain is found in squalene epoxidase (SE) and related proteins which are found in taxonomically diverse groups of eukaryotes and also in bacteria.\.       SE was first cloned from Saccharomyces cerevisiae where it was named ERG1.  It contains a putative FAD binding site and is a key enzyme in the sterol biosynthetic pathway  .  Putative transmembrane regions are found to the protein's C-terminus.. 
PF08492 SRP72 RNA-binding domain<br>Pfam-B_7529 (Release 18.0). This region has been identified as the binding site of the SRP72 protein to SRP RNA  .. 
PF08493 Aflatoxin regulatory protein<br>Pfam-B_2081 (release 18.0). This domain is found in the aflatoxin regulatory protein (AflR) which is involved in the regulation of the biosynthesis of aflatoxin in the fungal genus Aspergillus  .  It occurs together with the fungal Zn(2)-Cys(6) binuclear cluster domain (Pfam:PF00172).. 
PF08494 DEAD/H associated<br>Pfam-B_4150 (release 18.0). This domain is found in ATP-dependent helicases as well as a number of hypothetical proteins together with the helicase conserved C-terminal domain (Pfam:PF00270) and the Pfam:PF00271 domain.. 
PF08495 DUF1745; <br>The FIST N domain is a novel sensory domain, which is present in signal transduction proteins from Bacteria, Archaea and Eukarya. Chromosomal proximity of FIST-encoding genes to those coding for proteins involved in amino acid metabolism and transport suggest that FIST domains bind small ligands, such as amino acids  .. 
PF08496 Peptidase family S49 N-terminal<br>Pfam-B_4027 (release 18.0). This domain is found to the N-terminus of bacterial signal peptidases of the S49 family (Pfam:PF01343) [1,2].. 
PF08497 Radical SAM N-terminal<br>Pfam-B_2018 (release 18.0). This domain tends to occur to the N-terminus of the Pfam:PF04055 domain in hypothetical bacterial proteins.. 
PF08498 Sterol methyltransferase C-terminal<br>Pfam-B_3143 (release 18.0). This domain is found to the C-terminus of a methyltransferase domain (Pfam:PF08241) in fungal and plant sterol methyltransferases  .. 
PF08499 3'5'-cyclic nucleotide phosphodiesterase N-terminal<br>Pfam-B_3045 (release 18.0). This domain is found to the N-terminus of the calcium/calmodulin-dependent 3'5'-cyclic nucleotide phosphodiesterase domain (Pfam:PF00233).. 
PF08500 Tombusvirus p33 <br>Pfam-B_2139 (release 18.0). Tombusviruses, which replicate in a wide range of plant hosts, replicate with the help of viral replicase protein including the overlapping p33 and p92 proteins which contain the domain described here  .. 
PF08501 Shikimate dehydrogenase substrate binding domain<br>Pfam-B_99 (release 18.0). This domain is the substrate binding domain of shikimate dehydrogenase  .. 
PF08502 LeuA allosteric (dimerisation) domain<br>Pfam-B_223 (release 18.0). This is the C-terminal regulatory (R) domain of alpha-isopropylmalate synthase, which catalyses the first committed step in the leucine biosynthetic pathway  .\.      This domain, is an internally duplicated structure with a novel fold  . It comprises two similar units that are arranged such that the two -helices pack together in the centre, crossing at an angle of 34 degrees, sandwiched between the two three-stranded, antiparallel beta-sheets. The overall domain is thus constructed as a beta-alpha-beta three-layer sandwich  .. 
PF08503 DapD_N;<br>Tetrahydrodipicolinate succinyltransferase N-terminal. Pfam-B_4065 (release 18.0). This domain is found at the N-terminus of tetrahydrodipicolinate N-succinyltransferase (DapH) which catalyses the acylation of L-2-amino-6-oxopimelate to 2-N-succinyl-6-oxopimelate in the meso-diaminopimelate/lysine biosynthetic pathway of bacteria, blue-green algae, and plants  . The N-terminal domain as defined here contains three alpha-helices and two twisted hairpin loops  .. 
PF08504 Runx inhibition domain<br>Pfam-B_4085 (release 18.0). This domain lies to the C-terminus of Runx-related transcription factors and homologous proteins (AML, CBF-alpha, PEBP2).  Its function might be to interact with functional cofactors  .. 
PF08505 DSL1;<br>Mitochondrial Myo2 receptor-related protein. Myo2p, a class V myosin, is essential for mitochondrial distribution, class V being vital for organelle distribution in S. cerevisiae. It is the myosin essential for mitochondrial distribution. The established mechanism for distribution of cellular components by class V myosins is that they interact with the cargo at the C-terminal tail domain and transport it along the actin cytoskeleton using the N-terminal motor domain. Cargo-specific myosin receptors act as the link between the myosin tail and cargo. Myo2 binds with MMR1 (mitochondrial Myo2p receptor-related 1), the receptor on cargo, via the C-terminal domain.. 
PF08506 Cse1<br>Pfam-B_9217 (release 17.0). This domain is present in Cse1 nuclear export receptor proteins. Cse1 mediates the nuclear export of importin alpha.  This domain contains HEAT repeats  .. 
PF08507 COPI associated protein<br>Proteins in this family colocalise with COPI vesicle coat proteins  .. 
PF08508 Fungal domain of unknown function (DUF1746)<br>This is a fungal domain of unknown function.. 
PF08509 Adenylate cyclase G-alpha binding domain<br>This fungal domain is found in adenylate cyclase and interacts with the alpha subunit of heterotrimeric G proteins  .. 
PF08510 PIG-P<br>PIG-P (phosphatidylinositol N-acetylglucosaminyltransferase subunit P) is an enzyme involved in GPI anchor biosynthesis  .. 
PF08511 COQ9<br>COQ9 is an enzyme that is required for the biosynthesis of coenzyme Q  .  It may either catalyse a reaction in the coenzyme Q biosynthetic pathway or have a regulatory role.. 
PF08512 DUF1747; <br>Histone chaperone Rttp106-like. This family includes Rttp106, a histone chaperone involved in heterochromatin-mediated silencing  . This domain belongs to the Pleckstrin homology domain superfamily.. 
PF08513 LisH<br>Pfam-B_8344 (release 17.0). The LisH (lis homology) domain mediates protein dimerisation and tetramerisation.  The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes.  It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex  .. 
PF08514 STAG domain  <br>Pfam-B_4766 (release 17.0). STAG domain proteins are subunits of cohesin complex - a protein complex required for sister chromatid cohesion in eukaryotes. The STAG domain is present in Schizosaccharomyces pombe mitotic cohesin Psc3, and the meiosis specific cohesin Rec11. Many organisms express a meiosis-specific STAG protein, for example, mice and humans have a meiosis specific variant called STAG3, although budding yeast does not have a meiosis specific version  .. 
PF08515 Transforming growth factor beta type I GS-motif<br>Pfam-B_630 (release 18.0). This motif is found in the transforming growth factor beta (TGF-beta) type I which regulates cell growth and differentiation.  The name of the GS motif comes from its highly conserved GSGSGLP signature in the cytoplasmic juxtamembrane region immediately preceding the protein's kinase domain.  Point mutations in the GS motif modify the signaling ability of the type I receptor  .. 
PF08516 ADAM cysteine-rich<br>Pfam-B_197 (release 18.0). ADAMs are membrane-anchored proteases that proteolytically modify cell surface and extracellular matrix (ECM) in order to alter cell behaviour.  It has been shown that the cysteine-rich domain of ADAM13 regulates the protein's metalloprotease activity  .. 
PF08517 Ataxin-1 and HBP1 module (AXH)<br>Pfam-B_5484 (release 18.0). AXH is a protein-protein and RNA binding motif found in Ataxin-1 (ATX1).  ATX1 is responsible for the autosomal-dominant neurodegenerative disorder Spinocerebellar ataxia type-1 (SCA1) in humans.  The AXH module has also been identified in the apparently unrelated transcription factor HBP1 which is thought to be involved in the architectural regulation of chromatin and in specific gene expression  .. 
PF08518 Spa2 homology domain (SHD) of GIT<br>Pfam-B_13873 (release 18.0). GIT proteins are signaling integrators with GTPase-activating function which may be involved in the organisation of the cytoskeletal matrix assembled at active zones (CAZ).  The function of the CAZ might be to define sites of neurotransmitter release.  Mutations in the Spa2 homology domain (SHD) domain of GIT1 described here interfere with the association of GIT1 with Piccolo, beta-PIX, and focal adhesion kinase  .. 
PF08519 Replication factor RFC1 C terminal domain<br>Pfam-B_5399 (release 17.0). This is the C terminal domain of replication factor C, RFC1.  RFC complexes hydrolyse ATP and load sliding clamps such as PCNA (proliferating cell nuclear antigen) onto double-stranded DNA. RFC1 is essential for RFC function in vivo   .. 
PF08520 Fungal protein of unknown function (DUF1748)<br>This is a family of fungal proteins of unknown function.. 
PF08521 Two-component sensor kinase N-terminal<br>Pfam-B_4164 (release 18.0). This domain is found in bacterial two-component sensor kinases towards the N-terminus.. 
PF08522 Domain of unknown function (DUF1735)<br>Pfam-B_2199 (release 18.0). This domain of unknown function is found in a number of bacterial proteins including acylhydrolases.. 
PF08523 Multiprotein bridging factor 1<br>Pfam-B_4141 (release 18.0). This domain is found in the multiprotein bridging factor 1 (MBF1) which forms a heterodimer with MBF2.  It has been shown to make direct contact with the TATA-box binding protein (TBP) and interacts with Ftz-F1, stabilising the Ftz-F1-DNA complex  . It is also found in the endothelial differentiation-related factor (EDF-1). Human EDF-1 is involved in the repression of endothelial differentiation, interacts with CaM and is phosphorylated by PKC  .  The domain is found in a wide range of eukaryotic proteins including metazoans, fungi and plants.\.      A helix-turn-helix motif (Pfam:PF01381) is found to its C-terminus.. 
PF08524 rRNA processing<br>This is a family of proteins that are involved in rRNA processing  .  In a localisation study they were found to localise to the nucleus and nucleolus  . The family also includes other metazoa members from plants to mammals where the protein has been named BR22 and is associated with TTF-1, thyroid transcription factor 1  . In the lungs, the family binds TTF-1 to form a complex which influences the expression of the key lung surfactant protein-B (SP-B) and -C (SP-C), the small hydrophobic surfactant proteins that maintain surface tension in alveoli  .. 
PF08525 Opacity-associated protein A N-terminal motif<br>This family includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonisation, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [1,2]. This motif occurs at the N-terminus of these proteins. It contains a conserved histidine followed by a run of hydrophobic residues.. 
PF08526 Protein-arginine deiminase (PAD) N-terminal domain<br>Pfam-B_2195 (release 6.4). This family represents the N-terminal non-catalytic domain of protein-arginine deiminase. This domain has a cupredoxin-like fold.. 
PF08527 Protein-arginine deiminase (PAD) middle domain<br>Pfam-B_2195 (release 6.4). This family represents the central non-catalytic domain of protein-arginine deiminase. This domain has an immunoglobulin-like fold.. 
PF08528 Nrm1; <br>In metazoans, cyclin-dependent kinase(CDK) dependent phosphorylation of the retinoblastoma Tudor suppressor protein (Rb) alleviates repression of E2F and thereby activates G1/S transcription. The cell size regulator Whi5 appears to be an analogous target of CDK activity during G1 phase  .. 
PF08529 NusA N-terminal domain<br>Pfam-B_407 (Release 18.0). This domain represents the RNA polymerase binding domain of NusA.. 
PF08530 X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain<br>This domain contains a beta sandwich domain.. 
PF08531 Alpha-L-rhamnosidase N-terminal domain<br>Pfam-B_8527 (release 8.0). This family consists of bacterial rhamnosidase A and B enzymes. This domain is probably involved in substrate recognition.. 
PF08532 Beta-galactosidase trimerisation domain<br>Pfam-B_2131 (release 5.4). This is non catalytic domain B of beta-galactosidase enzymes belong to the glycosyl hydrolase 42 family. This domain is related to glutamine amidotransferase enzymes, but the catalytic residues are replaced by non functional amino acids. This domain is involved in trimerisation  .. 
PF08533 Beta-galactosidase C-terminal domain<br>Pfam-B_2131 (release 5.4). This domain is found at the C-terminus of beta-galactosidase enzymes that belong to the glycosyl hydrolase 42 family  .. 
PF08535 KorB domain<br>Pfam-B_20369 (release 10.0). This family consists of several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon  . This domain includes the DNA-binding HTH motif  .. 
PF08536 Plant_TF; <br>Whirly transcription factor. Mistry J, Pachon DMR. This family contains the plant whirly transcription factors.. 
PF08537 Fungal Nap binding protein NBP1<br>NBP1 is a nuclear protein which has been shown in Saccharomyces cerevisiae to be essential for the G2/M transition of the cell cycle.. 
PF08538 Protein of unknown function (DUF1749)<br>This is a plant and fungal family of unknown function.  This family contains many hypothetical proteins.. 
PF08539 HbrB-like<br>HbrB is involved hyphal growth and polarity  .. 
PF08540 Hydroxymethylglutaryl-coenzyme A synthase C terminal<br>
PF08541 ACP_C; <br>3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal  . Pfam-B_67 (release 18.0). This domain is found on 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III EC:2.3.1.41, the enzyme responsible for initiating the chain of reactions of the fatty acid synthase in plants and bacteria.. 
PF08542 Replication factor C C-terminal domain<br>Pfam-B_930 (release 18.0). This is the C-terminal domain of RFC (replication factor-C) protein of the clamp loader complex which binds to the DNA sliding clamp (proliferating cell nuclear antigen, PCNA).  The five modules of RFC assemble into a right-handed spiral, which results in only three of the five RFC subunits (RFC-A, RFC-B and RFC-C) making contact with PCNA, leaving a wedge-shaped gap between RFC-E and the PCNA clamp-loader complex. The C-terminal is vital for the correct orientation of RFC-E with respect to RFC-A  .. 
PF08543 Phosphomethylpyrimidine kinase<br>Pfam-B_787 (release 18.0). This enzyme EC:2.7.4.7 is part of the Thiamine pyrophosphate (TPP) synthesis pathway, TPP is an essential cofactor for many enzymes  .. 
PF08544 GHMP kinases C terminal <br>This family includes homoserine kinases, galactokinases and mevalonate kinases.. 
PF08545 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III<br>Pfam-B_135 (release 18.0). This domain is found on 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III EC:2.3.1.180, the enzyme responsible for initiating the chain of reactions of the fatty acid synthase in plants and bacteria.. 
PF08546 Ketopantoate reductase PanE/ApbA C terminal<br>Pfam-B_396 (release 18.0). This is a family of 2-dehydropantoate 2-reductases also known as ketopantoate reductases, EC:1.1.1.169.  The reaction catalysed by this enzyme is: (R)-pantoate + NADP(+) <=> 2-dehydropantoate + NADPH.  AbpA catalyses the NADPH reduction of ketopantoic acid to pantoic acid in the alternative pyrimidine biosynthetic (APB) pathway  .  ApbA and PanE are allelic  .  ApbA, the ketopantoate reductase enzyme is required for the synthesis of thiamine via the APB biosynthetic pathway  .. 
PF08547 Complex I intermediate-associated protein 30 (CIA30)<br>This protein is associated with mitochondrial Complex I intermediate-associated protein 30 (CIA30) in human and mouse. The family is also present in Schizosaccharomyces pombe which does not contain the NADH dehydrogenase component of complex I, or many of the other essential subunits.\.  This means it is possible that this family of protein may not be directly involved in oxidative phosphorylation   .. 
PF08548 Peptidase M10 serralysin C terminal<br>Mistry J, Rawlings ND. Serralysins are peptidases related to mammalian matrix metallopeptidases (MMPs).\. The peptidase unit is found at the N terminal while this domain at the C terminal forms a corkscrew and is thought to be important for secretion of the protein through the bacterial cell wall. This domain contains the calcium ion binding domain Pfam:PF00353.. 
PF08549 DUF1750; SWI-SNF_ssr4; <br>Fungal domain of unknown function (DUF1750). This is a fungal domain of unknown function.. 
PF08550 Fungal protein of unknown function (DUF1752)<br>This is a family of fungal proteins of unknown function. This short section domain is bounded by two highly conserved tryptophans. The family contains Swiss:P34072 that is thought to be a negative regulator of RAS-cAMP pathway in S.cerevisiae. the Sch.pombe member is a GAF1 transcription factor Swiss:Q10280 that is also associated with the zinc finger family GATA Pfam:PF00320.. 
PF08551 Eukaryotic integral membrane protein (DUF1751)<br>Pfam-B_13217 (release 18.0). This domain is found in eukaryotic integral membrane proteins. Swiss:Q12239, a Saccharomyces cerervisiae protein, has been shown to localise COP II vesicles  .. 
PF08552 DUF1753;<br>Inositolphosphorylceramide synthase subunit Kei1. Kei1 is a subunit of Saccharomyces cerevisiae inositol phosphorylceramide (IPC) synthase  . It is localised to the Golgi and is cleaved by the late Golgi processing endopeptidase Kex2  .  Kei1 is essential for both the activity and the Golgi localization of IPC synthase  .. 
PF08553 VID27 cytoplasmic protein<br>This is a family of fungal and plant proteins and contains many hypothetical proteins.  VID27 is a cytoplasmic protein that plays a potential role in vacuolar protein degradation.. 
PF08555 Eukaryotic family of unknown function (DUF1754)<br>Daub J, Mistry J, Wood V. Pfam-B_10536 (release 18.0). This is a eukaryotic protein family of unknown function.. 
PF08557 Sphingolipid Delta4-desaturase (DES)<br>Daub J, Mistry J, Wood V. Pfam-B_9504 (release 18.0). Sphingolipids are important membrane signalling molecules involved in many different cellular functions in eukaryotes. Sphingolipid delta 4-desaturase catalyses the formation of (E)-sphing-4-enine  .  Some proteins in this family have bifunctional delta 4-desaturase/C-4-hydroxylase activity.  Delta 4-desaturated sphingolipids may play a role in early signalling required for entry into meiotic and spermatid differentiation pathways during Drosophila spermatogenesis  .  This small domain associates with FA_desaturase Pfam:PF00487 and appears to be specific to sphingolipid delta 4-desaturase.. 
PF08558 Telomere repeat binding factor (TRF)<br>Pfam-B_8956 (release 18.0) . Telomere repeat binding factor (TRF) family proteins are important for the regulation of telomere stability. The two related human TRF proteins hTRF1 and hTRF2 form homodimers and bind directly to telomeric TTAGGG repeats via the myb DNA binding domain Pfam:PF00249 at the carboxy terminus  . TRF1 is implicated in telomere length regulation and TRF2 in telomere protection  . Other telomere complex associated proteins are recruited through their interaction with either TRF1 or TRF2. The fission yeast protein Taz1p (telomere-associated in Schizosaccharomyces pombe) has similarity to both hTRF1 and hTRF2 and may perform the dual functions of TRF1 and TRF2 at fission yeast telomeres  . This domain is composed of multiple alpha helices   arranged in a solenoid conformation similar to TPR repeats. The fungal members have now also been found to carry two double strand telomeric repeat binding factors  .. 
PF08559 Cut8;<br>Cut8 six-helix bundle. Daub J, Wood V, Eberhardt R. In Schizosaccharomyces pombe, Cut8 is a nuclear envelope protein that physically interacts with and tethers 26S proteasome in the nucleus resulting in the nuclear accumulation of proteasome  . Cut8 comprises three functional domains. An N-terminal lysine-rich segment (Pfam:PF14482) which binds to the proteasome when ubiquitinated, a central dimerisation domain (Pfam:PF14483) and a C-terminal six-helix bundle (this entry), which shows structural similarity to 14-3-3 phosphoprotein-binding domains. The six-helix bundle is necessary for liposome and cholesterol binding  . Cut8 is a proteasome substrate and the N-terminal segment is polyubiquitinated and functions as a degron tag. Ubiquitination of the amino N-terminal segment is essential to the function of Cut8  . Lysine residues in the N-terminal segment of Cut8 are required for physical interaction with proteasome  . In fission yeast the function of Cut8 has been demonstrated to be regulated by ubiquitin-conjugating Rhp6/Ubc2/Rad6 and ligating enzymes Ubr1  . Cut8 homologues have been identified in Drosophila melanogaster, Anopheles gambiae and Dictyostelium discoideum  .. 
PF08560 Protein of unknown function (DUF1757)<br>This family of proteins are about 150 amino acids in length and have no known function.. 
PF08561 Mitochondrial ribosomal protein L37<br>This family includes yeast MRPL37 a mitochondrial ribosomal protein  .. 
PF08562 Crisp<br>This domain is found on Crisp proteins which contain Pfam:PF00188 and has been termed the Crisp domain. It is found in the mammalian reproductive tract and the venom of reptiles, and has been shown to regulate ryanodine receptor Ca2+ signalling  . It contains 10 conserved cysteines which are all involved in disulphide bonds and is structurally related to the ion channel inhibitor toxins BgK and ShK  .. 
PF08563 P53 transactivation motif<br>Pfam-B_3515 (release 19.0). The binding of the p53 transactivation domain by regulatory proteins regulates p53 transcription activation.  This motif is comprised of a single amphipathic alpha helix and contains a highly conserved sequence [1-2].. 
PF08564 Cdc37;<br>Cdc37 C terminal domain. Pfam-B_3345 (release 6.5). Cdc37 is a protein required for the activity of numerous eukaryotic protein kinases.  This domains corresponds to the C terminal domain whose function is unclear.  It is found C terminal to the Hsp90 chaperone (Heat shocked protein 90) binding domain Pfam:PF08565 and the N terminal kinase binding domain of Cdc37 Pfam:PF03234  .. 
PF08565 Cdc37;<br>Cdc37 Hsp90 binding domain. Pfam-B_3345 (release 6.5). Cdc37 is a molecular chaperone required for the activity of numerous eukaryotic protein kinases.  This domains corresponds to the Hsp90 chaperone (Heat shocked protein 90) binding domain of Cdc37  .  It is found between the N terminal Cdc37 domain Pfam:PF03234, which is predominantly involved in kinase binding, and the C terminal domain of Cdc37 Pfam:PF08564 whose function is unclear.. 
PF08566 Mitochondrial import protein Pam17<br>The presequence translocase-associated motor (PAM) drives the completion of preprotein translocation into the mitochondrial matrix.  The Pam17 subunit is required for formation of a stable complex between cochaperones Pam16 and Pam18 and promotes the association of Pam16-Pam18 with the presequence translocase  . Mitochondria lacking Pam17 are selectively impaired in the import of matrix proteins  .. 
PF08567 TFIIH p62 subunit, N-terminal domain<br>Pfam-B_31040 (release 19.0). The N-terminal domain of the TFIIH basal transcription factor complex p62 subunit (BTF2-p62) forms an interaction with the 3' endonuclease XPG, which is essential for activity.  The 3' endonuclease XPG is a major component of the nucleotide excision repair machinery. The structure of the N-terminal domain reveals that it adopts a pleckstrin homology (PH) fold [1,2].. 
PF08568 DUF1760; <br>Uncharacterised protein family, YAP/Alf4/glomulin. Mistry J, Wood V, Lonsdale D. This entry contains a number of protein families with apparently unrelated functions. These include the YAP binding proteins of yeasts. These are stress response and redox homeostasis proteins, induced by hydrogen peroxide or induced in response to alkylating agent methyl methanesulphonate (MMS) [1,2]. The family includes Aberrant root formation protein 4 (Alf4) of Arabidopsis thaliana (Mouse-ear cress), which is required for the initiation of lateral roots independent from auxin signalling. It may also function in maintaining the pericycle in the mitotically competent state needed for lateral root formation    . The family includes glomulin (FAP68), which is essential for normal development of the vasculature and may represent a naturally occurring ligand of the immunophilins FKBP59 and FKBP12 [4,5].. 
PF08569 Mo25-like<br>Pfam-B_5502 (release 18.0). Mo25-like proteins are involved in both polarised growth and cytokinesis.  In fission yeast Mo25 is localised alternately to the spindle pole body and to the site cell division in a cell cycle dependent manner [1,2].. 
PF08570 Protein of unknown function (DUF1761)<br>Pfam-B_85869 (release 19.0). Family of conserved fungal and bacterial membrane proteins with unknown function.. 
PF08571 Yos1-like<br>Pfam-B_23321 (release 19.0). In yeast, Yos1 is a subunit of the Yip1p-Yif1p complex and is required for transport between the endoplasmic reticulum and the Golgi complex. Yos1 appears to be conserved in eukaryotes .. 
PF08572 pre-mRNA processing factor 3 (PRP3)<br>Pfam-B_7232 (release 18.0). Pre-mRNA processing factor 3 (PRP3) is a U4/U6-associated splicing factor.  The human PRP3 has been implicated in autosomal retinitis pigmentosa  .. 
PF08573 DNA repair protein endonuclease SAE2/CtIP C-terminus<br>SAE2 is a protein involved in repairing meiotic and mitotic double-strand breaks in DNA.  It has been shown to negatively regulate DNA damage checkpoint signalling   . SAE2 is homologous to the CtIP proteins in mammals and an homologous protein in plants. Crucial sequence motifs that are highly conserved are the CxxC and the RHR motifs in this C-terminal part of the protein  . It is now known to be an endonuclease. In budding yeast, genetic evidence suggests that the SAE2 protein is essential for the processing of hairpin DNA intermediates and meiotic double-strand breaks by Mre11/Rad50 complexes. SAE2 binds DNA and exhibits endonuclease activity on single-stranded DNA independently of Mre11/Rad50 complexes, but hairpin DNA structures are cleaved cooperatively in the presence of Mre11/Rad50 or Mre11/Rad50/Xrs2.  Hairpin structures are not processed at the tip by SAE2 but rather at single-stranded DNA regions adjacent to the hairpin. The catalytic activities of SAE2 are important for its biological functions  .. 
PF08574 Protein of unknown function (DUF1762)<br>This is a family of proteins of unknown function.\.     Swiss:Q07532 is known to interact with RNA polymerase II and deletion of this protein results in hypersensitivity to the K1 killer toxin  .. 
PF08576 Eukaryotic protein of unknown function (DUF1764)<br>This is a family of eukaryotic proteins of unknown function. This family contains many hypothetical proteins.. 
PF08577 PI31_Prot_Reg;<br>PI31 proteasome regulator . PI31 is a cellular regulator of proteasome formation and of proteasome-mediated antigen processing  .. 
PF08578 Protein of unknown function (DUF1765)<br>This region represents a conserved region found in hypothetical proteins from fungi, mycetozoa and entamoebidae.. 
PF08579 Mitochondrial ribonuclease P subunit (RPM2)<br>Ribonuclease P (RNase P) generates mature tRNA molecules by cleaving their 5' ends.  RPM2 is a protein subunit of the yeast mitochondrial RNase P.  It has the ability to act as transcriptional activator in the nucleus where it plays a role in defining the steady-state levels of mRNAs for some nucleus-encoded mitochondrial components  .. 
PF08580 Yeast cortical protein KAR9<br>The KAR9 protein in Saccharomyces cerevisiae is a cytoskeletal protein required for karyogamy, correct positioning of the mitotic spindle and for orientation of cytoplasmic microtubules  . KAR9 localises at the shmoo tip in mating cells and at the tip of the growing bud in anaphase  .. 
PF08581 Tup N-terminal<br>Pfam-B_9595 (release 19.0). The N-terminal domain of the Tup protein has been shown to interact with the Ssn6 transcriptional co-repressor  .. 
PF08583 UPF0287; <br>Cytochrome c oxidase biogenesis protein Cmc1 like. Cmc1 is a metallo-chaperone like protein which is known to localise to the inner mitochondrial membrane in Saccharomyces cerevisiae.  It is essential for full expression of cytochrome c oxidase and respiration  .  Cmc1 contains two Cx9C motifs and is able to bind copper(I).  Cmc1 is thought to play a role in mitochondrial copper trafficking and transfer to cytochrome c oxidase  .. 
PF08584 Ribonuclease P 40kDa (Rpp40) subunit<br>The tRNA processing enzyme ribonuclease P (RNase P) consists of an RNA molecule and at least eight protein subunits. Subunits hpop1, Rpp21, Rpp29, Rpp30, Rpp38, and Rpp40 (this entry) are involved in extensive, but weak, protein-protein interactions in the holoenzyme complex  .. 
PF08585 Domain of unknown function (DUF1767)<br>Eukaryotic domain of unknown function.  This domain is found to the N-terminus of the nucleic acid binding domain.. 
PF08586 RSC complex, Rsc14/Ldb7 subunit<br>RSC is an ATP-dependent chromatin remodelling complex found in yeast. The RSC components Rsc7/Npl6 and Rsc14/Ldb7 interact physically and/or functionally with Rsc3, Rsc30, and Htl1 to form a module important for a broad range of RSC functions  .. 
PF08587 Ubiquitin associated domain (UBA) <br>Pfam-B_10238 (Release 18.0). This is a UBA (ubiquitin associated) domain  .  Ubiquitin is involved in intracellular proteolysis.. 
PF08588 Protein of unknown function (DUF1769)<br>Family of fungal protein with unknown function.. 
PF08589 Fungal protein of unknown function (DUF1770)<br>The function of this family is unknown. These proteins are rather dissimilar except for a single strongly conserved motif (PDLRFEQ).. 
PF08590 Domain of unknown function (DUF1771)<br>Pfam-B_10757 (release 18.0). This domain is always found adjacent to Pfam:PF01713.. 
PF08591 Ribonucleotide reductase inhibitor<br>This family includes S. pombe Spd1. Spd1p inhibits fission yeast RNR activity by interacting with the Cdc22p  .. 
PF08592 Domain of unknown function (DUF1772)<br>This domain is of unknown function.. 
PF08593 DUF1773; <br>Meiotically up-regulated glycoproteins C-terminal. Pfam-B_26890 (release 18.0). This is the C-terminal part of some meiotically up-regulated gene products from fission yeast. The actual function is not yet known but the proteins are likely to be cell-surface glycoproteins.. 
PF08594 Uncharacterised protein family (UPF0300)<br>Pfam-B_20198 (release 18.0). This family of proteins appear to be specific to S. pombe.. 
PF08595 RXT2-like, N-terminal<br>The family represents the N-terminal region of RXT2-like proteins.  In S. cerevisiae, RXT2 has been demonstrated to be involved in conjugation with cellular fusion (mating) and invasive growth  .  A high throughput localisation study has localised RXT2 to the nucleus  .. 
PF08596 Lethal giant larvae(Lgl) like, C-terminal<br>The Lethal giant larvae (Lgl) tumour suppressor family is conserved from yeast to mammals.  The Lgl family functions in cell polarity, at least in part, by regulating SNARE-mediated membrane delivery events at the cell surface  .  The N-terminal half of Lgl members contains WD40 repeats (see Pfam:PF00400), while the C-terminal half appears specific to the family  .. 
PF08597 Translation initiation factor eIF3 subunit<br>This is a family of proteins which are subunits of the eukaryotic translation initiation factor 3 (eIF3).  In yeast it is called Hcr1.  The Saccharomyces cerevisiae protein Swiss:Q05775 has been shown to be required for processing of 20S pre-rRNA and binds to 18S rRNA and eIF3 subunits Rpg1p and Prt1p   .. 
PF08598 Sds3-like<br>Repression of gene transcription is mediated by histone deacetylases containing repressor-co-repressor complexes, which are recruited to promoters of target genes via interactions with sequence-specific transcription factors. The co-repressor complex contains a core of at least seven proteins  .\.     This family represents the conserved region found in Sds3, Dep1 and BRMS1-homologue p40 proteins.. 
PF08599 Nbs1_N; <br>DNA damage repair protein Nbs1. This C terminal region of the DNA damage repair protein Nbs1 has been identified to be necessary for the binding of Mre11 and Tel1   .. 
PF08600 Rsm1-like<br>Rsm1 is a protein involved in mRNA export from the nucleus  . 
PF08601 Transcription factor PAP1<br>Pfam-B_20528 (release 18.0). The transcription factor Pap1 regulates antioxidant-gene transcription in response to H2O2  .  This region is cysteine rich.  Alkylation of cysteine residues following treatment with a cysteine alkylating agent can mask the accessibility of the nuclear exporter Crm1, triggering nuclear accumulation and Pap1 dependent transcriptional expression  .. 
PF08602 Mgr1-like, i-AAA protease complex subunit<br>The S. cerevisiae Mgr1 protein has been shown to be required for mitochondrial viability in yeast lacking mitochondrial DNA. It is a mitochondrial inner membrane protein, which interacts with Yme1 and is a new subunit of the i-AAA protease complex  .. 
PF08603 CAP;<br>Adenylate cyclase associated (CAP) C terminal. 
PF08604 Nucleoporin Nup153-like<br>Pfam-B_56527 (release 19.0). This family contains both the nucleoporin Nup153 from human and Nup153 from fission yeast.  These have been demonstrated to be functionally equivalent  .. 
PF08605 Fungal Rad9-like Rad53-binding<br>In Saccharomyces cerevisiae the Rad9 a key adaptor protein in DNA damage checkpoint pathways.  DNA damage induces Rad9 phosphorylation, and Rad53 specifically associates with this region of Rad9, when phosphorylated, via Rad53 Pfam:PF00498 domains  . This region is structurally composed of a pair of TUDOR domains  .. 
PF08606 Prp19/Pso4-like<br>Pfam-B_6384 (release 18.0). This regions is found specifically in PRP19-like protein.\.       The region represented by this family covers the sequence implicated in self-interaction and a coiled-coiled motif  .  PRP19-like proteins form an oligomer that is necessary for spliceosome assembly  .. 
PF08534 Redoxin<br>This family of redoxins includes peroxiredoxin, thioredoxin and glutaredoxin proteins.. 
PF08608 Wyosine base formation<br>Some proteins in this family appear to be important in wyosine base formation in a subset of phenylalanine specific tRNAs.  It has been proposed that they participates in converting tRNA(Phe)-m(1)G(37) to tRNA(Phe)-yW  .. 
PF08609 Nucleotide exchange factor Fes1<br>Pfam-B_36022 (release 18.0). Fes1 is a cytosolic homologue of Sls1, an ER protein which has nucleotide exchange factor activity.  Fes1 in yeast has been shown to bind to the molecular chaperone Hsp70 and has adenyl-nucleotide exchange factor activity  .. 
PF08610 Peroxisomal membrane protein (Pex16)<br>Pex16 is a peripheral protein located at the matrix face of the peroxisomal membrane  .. 
PF08611 Fungal protein of unknown function (DUF1774)<br>This is a fungal family of unknown function.. 
PF08612 TATA_RF; <br>TATA-binding related factor (TRF) of subunit 20 of Mediator complex. This family of proteins is related to TATA-binding protein (TBP). TBP is a highly conserved RNA polymerase II general transcription factor that binds to the core promoter and initiates assembly of the preinitiation complex.  Human TRF has been shown to associate with an RNA polymerase II-SRB complex  . This Med20 subunit of Mediator is found in the non-essential part of the head  .. 
PF08613 Cyclin<br>Pfam-B_6792 (release 18.0). This family includes many different cyclin proteins.  Members include the G1/S-specific cyclin pas1  , and the phosphate system cyclin PHO80/PHO85  .. 
PF08614 Autophagy protein 16 (ATG16)<br>Autophagy is a ubiquitous intracellular degradation system for eukaryotic cells.\.       During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. ATG16 (also known as Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate in the yeast autophagy pathway  .. 
PF08615 RNase_H1_sml;<br>Ribonuclease H2 non-catalytic subunit (Ylr154p-like). Pfam-B_36578 (release 18.0). This entry represents the non-catalytic subunit of RNase H2, which in S. cerevisiae is Ylr154p/Rnh203p Swiss:Q12338 (. Whereas bacterial and archaeal RNases H2 are active as single polypeptides, the Saccharomyces cerevisiae homologue, Rnh2Ap, when expressed in Escherichia coli, fails to produce an active RNase H2. For RNase H2 activity three proteins are required [Rnh2Ap (Rnh201p), Ydr279p (Rnh202p) and Ylr154p (Rnh203p)]. Deletion of any one of the proteins or mutations in the catalytic site in Rnh2A leads to loss of RNase H2 activity  . RNase H2 ia an endonuclease that specifically degrades the RNA of RNA:DNA hybrids. It participates in DNA replication, possibly by mediating the removal of lagging-strand Okazaki fragment RNA primers during DNA replication.. 
PF08616 SPB_interacting;<br>Stabilization of polarity axis. Swiss:Q99222 has been shown to interact with the outer plaque of the spindle pole body  . In Aspergillus nidulans the protein member is necessary for stabilization of the polarity axes during septation  . and in S. cerevisiae it functions as a polarisation-specific docking factor  .. 
PF08617 Kinase binding protein CGI-121<br>CGI-121 has been shown to bind to the p53-related protein kinase (PRPK)  .  PRPK is a novel protein kinase which binds to and induces phosphorylation of the tumour suppressor protein p53. CGI-121 is part of a conserved protein complex, KEOPS. The KEOPS complex is involved in telomere uncapping and telomere elongation  .  Interestingly this family also include archaeal homologues, formerly in the DUF509 family. A structure for these proteins has been solved by structural genomics.. 
PF08618 Transcription factor Opi1<br>Opi1 is a leucine zipper containing yeast transcription factor that negatively regulates phospholipid biosynthesis  .  It represses the expression of several UAS(INO) cis acting element containing genes and its activity is mediated by phosphorylations catalysed by protein kinase A, protein kinase C and casein kinase II  .. 
PF08619 Alkali metal cation/H+ antiporter Nha1 C terminus<br>The C terminus of the plasma membrane Nha1 antiporter plays an important role in the immediate cell response to hypo-osmotic shock which prevents an execessive loss of ions and water  .  This  domain is found with Pfam:PF00999.. 
PF08620 RPAP1-like, C-terminal<br>Inhibition of RPAP1 synthesis in Saccharomyces cerevisiae results in changes in global gene expression that are similar to those caused by the loss of the RNAPII subunit Rpb11  .\.   This entry represents the C-terminal region that contains the motif GLHHH. This region is conserved from yeast to humans.. 
PF08621 RPAP1-like, N-terminal<br>Inhibition of RPAP1 synthesis in Saccharomyces cerevisiae results in changes in global gene expression that are similar to those caused by the loss of the RNAPII subunit Rpb11  .\.     This entry represents the N-terminal region of RPAP-1 that is conserved from yeast to humans.. 
PF08622 Svf1-like<br>Family of proteins that are involved in survival during oxidative stress .. 
PF08623 TATA-binding protein interacting (TIP20)<br>TIP120 (also known as cullin-associated and neddylation-dissociated protein 1) is a TATA binding protein interacting protein that enhances transcription  .. 
PF08624 Chromatin remodelling complex Rsc7/Swp82 subunit<br>Pfam-B_56720 (release 18.0). This family has been identified as a subunit of chromatin remodelling complexes.  Saccharomyces cerevisiae Swiss:P32832 and its paralogue Swiss:P43554 have been identified as subunits of the RSC chromatin remodelling complex, and SWI/SNF chromatin remodelling complex respectively  .. 
PF08625 Utp13 specific WD40 associated domain<br>Pfam-B_8625 (release 19.0). Utp13 is a component of the five protein Pwp2 complex that forms part of a stable particle subunit independent of the U3 small nucleolar ribonucleoprotein that is essential for the initial assembly steps of the 90S pre-ribosome  . Pwp2 is capable of interacting directly with the 35 S pre-rRNA 5' end  .. 
PF08626 Trs120;<br>Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit. Pfam-B_15686 (release 19.0). This region is found at the N terminal of Saccharomyces cerevisiae Trs120 protein (Swiss:Q04183).  Trs120 is a subunit of the multiprotein complex TRAPP (transport particle protein) which functions in ER to Golgi traffic  . Trs120 is specific to the larger TRAPP complex, TRAPP II, along with Trs65p and Trs130p(TRAPPC10). It is suggested that Trs120p is required for the stability of the Trs130p subunit, suggesting that these two proteins might interact in some way  . It is likely that there is a complex function for TRAPP II in multiple pathways  .. 
PF08627 CRT-like<br>Pfam-B_67420 (release 18.0). This region is found in proteins related to Plasmodium falciparum chloroquine resistance transporter (CRT).. 
PF08628 Sorting nexin C terminal<br>Pfam-B_5897 (release 19.0). This region is found a the C terminal of proteins belonging to the sorting nexin family.  It is found on proteins which also contain Pfam:PF00787.. 
PF08629 PDE8 phosphodiesterase<br>Pfam-B_72889 (release 17.0). This region is found in members of the PDE8 phosphodiesterase family  .  It is found with Pfam:PF00233.. 
PF08630 Dfp1/Him1, central region<br>Pfam-B_28140 (release 19.0). This is the middle regions described by Ogino et al  .  This region, together with the C-terminal zinc finger (Pfam:PF07535) is essential for the mitotic and kinase activation functions of Dfp1/Him1  .. 
PF08631 Meiosis protein SPO22/ZIP4 like<br>SPO22/ZIP4 in yeast is a meiosis specific protein involved in sporulation  .  It has been shown to regulate crossover distribution by promoting synaptonemal complex formation  .. 
PF08632 Zds1_C; <br>Activator of mitotic machinery Cdc14 phosphatase activation C-term. Pfam-B_44907 (release 19.0). This region of the Zds1 protein is critical for sporulation and has also been shown to suppress the calcium sensitivity of Zds1 deletions  . The C-terminal motif is common to both Zds1 and Zds2 proteins, both of which are putative interactors of Cdc55 and are required for the completion of mitotic exit and cytokinesis. They both contribute to timely Cdc14 activation during mitotic exit and are required downstream of separase to facilitate nucleolar Cdc14 release .. 
PF08633 Rox3 mediator complex subunit<br>The mediator complex is part of the RNA polymerase II holoenzyme. Rox3 is a subunit of the mediator complex.. 
PF08634 Mitochondrial protein Pet127<br>Pet127 has been implicated in mitochondrial RNA stability and/or processing and is localised to the mitochondrial membrane  . The Pet127 family is part of the PD-(D/E)XK nuclease superfamily   including a full set of active site residues.. 
PF08635 Putative oxidoreductase C terminal<br>This is the C terminal of a family of putative oxidoreductases.. 
PF08636 ER protein Pkr1<br>Pkr1 has been identified as an ER protein of unknown function.. 
PF08637 ATP synthase regulation protein NCA2<br>Pfam-B_15813 (release 19.0). NCA2 has been shown to be required for the regulation of ATP synthase subunits Atp6p and Atp8p in Saccharomyces cerevisiae  .. 
PF08638 MED14; <br>Mediator complex subunit MED14. Pfam-B_13303 (release 19.0). Saccharomyces cerevisiae RGR1 mediator complex subunit affects chromatin structure, transcriptional regulation of diverse genes and sporulation, required for glucose repression, HO repression, RME1 repression and sporulation   .  This subunit is also found in higher eukaryotes and Med14 is the agreed unified nomenclature for this subunit. Med14 is found in the tail region of Mediator  .. 
PF08639 DNA replication regulator SLD3<br>The SLD3 DNA replication regulator is required for loading and maintenance of Cdc45 on chromatin during DNA replication  .. 
PF08640 U3 small nucleolar RNA-associated protein 6<br>Pfam-B_8720 (release 19.0). This is a family of U3 nucleolar RNA-associated proteins which are involved in nucleolar processing of pre-18S ribosomal RNA  .. 
PF08641 Kinetochore protein Mis14 like<br>Mis14 is a kinetochore protein which is known to be recruited to kinetochores independently of CENP-A  .. 
PF08642 Histone deacetylation protein Rxt3<br>Rxt3 has been shown in yeast to be required for histone deacetylation  .. 
PF08643 Fungal family of unknown function (DUF1776)<br>Mistry J, Groocock L. This is a fungal family of unknown function.  One of the proteins in this family Swiss:P32792 has been localised to the mitochondria  .. 
PF08644 FACT complex subunit (SPT16/CDC68)<br>Pfam-B_4478 (release 19.0). Proteins in this family are subunits the FACT complex.  The FACT complex plays a role in transcription initiation and promotes binding of TATA-binding protein (TBP) to a TATA box in chromatin  .. 
PF08645 Polynucleotide kinase 3 phosphatase<br>Pfam-B_6220 (release 19.0). Polynucleotide kinase 3 phosphatases play a role in the repair of single breaks in DNA induced by DNA-damaging agents such as gamma radiation and camptothecin  . . 
PF08646 Replication factor-A C terminal domain<br>Pfam-B_3457 (release 19.0). This domain is found at the C terminal of replication factor A. Replication factor A (RPA) binds single-stranded DNA and is involved in replication, repair, and recombination of DNA  .. 
PF08647 BRE1 E3 ubiquitin ligase<br>Pfam-B_35727 (release 19.0). BRE1 is an E3 ubiquitin ligase that has been shown to act as a transcriptional activator through direct activator interactions  .. 
PF08648 Protein of unknown function (DUF1777)<br>This is a family of eukaryotic proteins of unknown function. Some of the proteins in this family are putative nucleic acid binding proteins.. 
PF08649 DASH complex subunit Dad1<br>The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis  . In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro [2,3].  Components of the DASH complex, including Dam1, Duo1, Spc34, Dad1 and Ask1, are essential and connect the centromere to the plus end of spindle microtubules  . Throughout the cell cycle Dad1 remains bound to kinetochores throughout the cell cycle and its association is dependent on the Mis6 and Mal2  .. 
PF08650 DASH complex subunit Dad4<br>The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis  . In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro [2,3].. 
PF08651 DASH complex subunit Duo1<br>The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis  . In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro [2,3].. 
PF08652 RAI1 like PD-(D/E)XK nuclease<br>Pfam-B_13095 (release 19.0). 
PF08653 DASH complex subunit Dam1<br>The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis  . In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro [2,3].  Components of the DASH complex, including Dam1, Duo1, Spc34, Dad1 and Ask1, are essential and connect the centromere to the plus end of spindle microtubules  . . 
PF08654 DASH complex subunit Dad2<br>The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis  . In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro [2,3].. 
PF08655 DASH complex subunit Ask1<br>The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis  . In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro [2,3].  Components of the DASH complex, including Dam1, Duo1, Spc34, Dad1 and Ask1, are essential and connect the centromere to the plus end of spindle microtubules  . . 
PF08656 DASH complex subunit Dad3<br>The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis  . In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro [2,3].. 
PF08657 DASH complex subunit Spc34 <br>The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis  . In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro [2,3].  Components of the DASH complex, including Dam1, Duo1, Spc34, Dad1 and Ask1, are essential and connect the centromere to the plus end of spindle microtubules  .. 
PF08658 Rad54 N terminal<br>Pfam-B_26946 (release 19.0). This is the N terminal of the DNA repair protein Rad54  .. 
PF08659 KR domain<br>This enzymatic domain is part of bacterial polyketide synthases and catalyses the first step in the reductive modification of the beta-carbonyl centres in the growing polyketide chain. It uses NADPH to reduce the keto group to a hydroxy group  .. 
PF08660 Oligosaccharide biosynthesis protein Alg14 like<br>Pfam-B_12992 (release 19.0). Alg14 is involved dolichol-linked oligosaccharide biosynthesis and anchors the catalytic subunit Alg13 to the ER membrane  .. 
PF08661 Replication factor A protein 3<br>Replication factor A is involved in eukaryotic DNA replication, recombination and repair.. 
PF08662 Eukaryotic translation initiation factor eIF2A<br>Pfam-B_7957 (release 19.0). This is a family of eukaryotic translation initiation factors.. 
PF08663 HalX domain<br>HalX is a domain of unknown function, previously (mis)annotated as HoxA-like transcriptional regulator.. 
PF08664 YcbB domain<br>YcbB is a DNA-binding domain  .. 
PF08665 PglZ domain<br>This family is a member of the Alkaline phosphatase clan.. 
PF08666 SAF domain<br>This domain family includes a range of different proteins. Such as antifreeze proteins and flagellar FlgA proteins, and CpaB pilus proteins.. 
PF08667 BetR domain<br>This family includes an N-terminal helix-turn-helix domain.. 
PF08668 HDOD domain<br>
PF08669 Glycine cleavage T-protein C-terminal barrel domain<br>Pfam-B_933 (release 4.0). This is a family of glycine cleavage T-proteins, part of the glycine  cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl transferase. . 
PF08670 MEKHLA domain<br>The MEKHLA domain shares similarity with the PAS domain and is found in the 3' end of plant HD-ZIP III homeobox genes, and bacterial proteins.. 
PF08671 Anti-repressor SinI<br>SinR is a pleiotropic regulator of several late growth processes. It is a tetrameric DNA binding protein whose activity is down-regulated thorough the formation of a SinI:SinR protein complex.  When complexed with SinI, the SinR tetramer is disrupted such that is no longer able to bind DNA.. 
PF08672 Anaphase promoting complex (APC) subunit 2<br>The anaphase promoting complex or cyclosome (APC2) is an E3 ubiquitin ligase which is part of the SCF family of ubiquitin ligases.  Ubiquitin ligases catalyse the transfer of ubiquitin from the ubiquitin conjugating enzyme (E2), to the substrate protein.. 
PF08673 Phosphoserine phosphatase RsbU, N-terminal domain<br>RsbU is a phosphoserine phosphatase which acts as a positive regulator of the general stress-response factor of gram positive organisms, sigma-B.  The phosphatase activity of RsbU is stimulated by association with the RsbT kinase.  Deletions in the N terminal domain are deleterious to the activity of RsbU  .. 
PF08674 Acetylcholinesterase tetramerisation domain<br>The acetylcholinesterase tetramerisation domain is found at the C terminus and forms a left handed superhelix.. 
PF08675 RNA binding domain<br>This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN).. 
PF08676 MutL C terminal dimerisation domain<br>MutL and MutS are key components of the DNA repair machinery that corrects replication errors  .  MutS recognises mispaired or unpaired bases in a DNA duplex and in the presence of ATP, recruits MutL to form a DNA signaling complex for repair. The N terminal region of MutL contains the ATPase domain and the C terminal is involved in dimerisation  .. 
PF08677 GP11 baseplate wedge protein<br>GP11 is a viral structural protein that connects short tail fibres to the baseplate.  The tail region is responsible for attachment to the host bacteria during infection.. 
PF08678 Rsbr N terminal<br>Rsbr is a regulator of the RNA polymerase sigma factor subunit sigma(B).\.     The structure of the N terminal domain belongs to the globin fold superfamily  .. 
PF08679 Dissimilatory sulfite reductase D (DsrD)<br>The structure of the DsrD protein has shown it to contain a winged-helix motif similar to those found in DNA binding proteins  .  The structure suggests a possible role for DsrD in transcription of translation of genes which catalyse dissimilatory sulfite reduction.. 
PF08680 Protein of unknown function (DUF1779)<br>This is a family of uncharacterised proteins.  The structure of the ywmB protein from Bacillus subtilis has shown it to adopt an alpha/beta fold.. 
PF08681 Protein of unknown function (DUF1778)<br>This is a family of uncharacterised proteins.  The structure of one of the hypothetical proteins in this family has been solved and it forms a helix structure which may form interactions with DNA.. 
PF08682 Protein of unknown function (DUF1780)<br>This is a family of uncharacterised proteins.  The structure of a hypothetical protein from Pseudomonas aeruginosa has shown it to adopt an alpha/beta fold.. 
PF08683 DUF1781; CKK;<br>Microtubule-binding calmodulin-regulated spectrin-associated. This is the C-terminal domain of a family of eumetazoan proteins collectively defined as calmodulin-regulated spectrin-associated, or CAMSAP, proteins. CAMSAP proteins carry an N-terminal region that includes the CH domain, a central region including a predicted coiled-coil and this C-terminal, or CKK, domain - defined as being present in CAMSAP, KIAA1078 and KIAA1543, The C-terminal domain is the part of the CAMSAP proteins that binds to microtubules. The domain appears to act by producing inhibition of neurite extension, probably by blocking microtubule function. CKK represents a domain that has evolved with the metazoa. The structure of a murine hypothetical protein from RIKEN cDNA has shown the domain to adopt a mainly beta barrel structure with an associated alpha-helical hairpin.. 
PF08684 DNA mimic ocr<br>The structure of an ocr protein from bacteriophage T7 has shown that this protein mimics the size and shape of a bent DNA molecule  . ocr has also been shown to be an inhibitor of the complex type I DNA restriction enzymes  .. 
PF08685 GON domain<br>Mistry J, Rawlings ND. The GON domain is found in the ADAMTS (a disintegrin and metalloproteinase domain with thrombospondin type-1 modules) family of proteins.  It contains several conserved cysteine residues.. 
PF08686 PLAC (protease and lacunin) domain<br>Mistry J, Rawlings ND. The PLAC (protease and lacunin) domain is a short six-cysteine region that is usually found at the C terminal of proteins.  It is found in a range of proteins including PACE4 (paired basic amino acid cleaving enzyme 4) and the extracellular matrix protein lacunin  .. 
PF08687 Apx/Shroom domain ASD2<br>Mistry J, Hildebrand JD. This region is found in the actin binding protein Shroom which mediates apical contriction in epithelial cells and is required for neural tube closure.. 
PF08688 Apx/Shroom domain ASD1<br>Mistry J, Hildebrand JD. This region is found in the actin binding protein Shroom which mediates apical contriction in epithelial cells and is required for neural tube closure.  ASD1 has been implicated directly in F-actin binding.. 
PF08689 Mediator complex subunit Med5<br>The mediator complex is required for the expression of nearly all RNA pol II dependent genes in Saccharomyces cerevisiae.  Deletion of the MED5 gene leads to increased transcription of nuclear genes encoding components of the oxidative phosphorylation machinery, and decreased transcription of mitochondrial genes encoding components of the same machinery  . There is no orthologue from pombe, and this subunit appears to be fungal specific  .. 
PF08690 GET complex subunit GET2<br>This family corresponds to the GET complex subunit GET2.  The GET complex is involved in the retrieval of ER resident proteins from the Golgi  .. 
PF08691 DNA repair proteins Nse5 and Nse6<br>Nse5 and Nse6 are non essential nuclear proteins that are critical for chromosome segregation in fission yeast  .  Nse5 forms a dimer with Nse6 and facilitates DNA repair as part of the Smc5-Smc6 holocomplex.. 
PF08692 Mitochondrial protein Pet20<br>Pet20 is a mitochondrial protein which is thought to play a role in the correct assembly/maintenance of mitochondrial components  .. 
PF08693 Transmembrane alpha-helix domain<br>SKG6/Axl2 are membrane proteins that show polarised intracellular localisation  . SKG6_Tmem is the highly conserved transmembrane alpha-helical domain of SKG6 and Axl2 proteins  ,  . The full-length fungal protein has a negative regulatory function in cytokinesis  .. 
PF08694 DUF1782; <br>Ubiquitin-fold modifier-conjugating enzyme 1. Ubiquitin-like (UBL) post-translational modifiers are covalently linked to most, if not all, target protein(s) through an enzymatic cascade analogous to ubiquitylation, consisting of E1 (activating), E2 (conjugating), and E3 (ligating) enzymes. Ubiquitin-fold modifier 1 (Ufm1) a ubiquitin-like protein is activated by a novel E1-like enzyme, Uba5, by forming a high-energy thioester bond. Activated Ufm1 is then transferred to its cognate E2-like enzyme, Ufc1, in a similar thioester linkage. This family represents the E2-like enzyme.. 
PF08695 DUF1783;<br>Cytochrome oxidase complex assembly protein 1. Coa1 is an inner mitochondrial membrane protein that associates with Shy1 and is required for cytochrome oxidase complex IV assembly. It contains a conserved hydrophobic segment (amino acids 74-92) with the potential to form a membrane-spanning helix. The N-terminus of Coa1 is rich in positively charged amino acids and could form an amphipathic alpha helix, characteristic of a mitochondrial presequence. A cleavage site for the mitochondrial processing peptidase is predicted adjacent to the presequence. Upon in vitro import into mitochondria, Coa1 is processed to a mature form, indicating that it possesses a cleavable presequence  . The eukaryotic cytochrome oxidase complex consists of 12-13 subunits, with three mitochondrial encoded subunits, Cox1-Cox3, forming the core enzyme. Translation of the Cox1 transcript requires the two promoters, Pet309 and Mss51, and the latter has an additional role in translational elongation. Coa1 is necessary for linking the activity of Mss51 to Cox1 insertion into the assembly complex  .. 
PF08696 DNA replication factor Dna2<br>Pfam-B_8878 (release 19.0). Dna2 is a DNA replication factor with single-stranded DNA-dependent ATPase, ATP-dependent nuclease, ( 5'-flap endonuclease) and helicase activities.  It is required for Okazaki fragment processing and is involved in DNA repair pathways  .. 
PF08698 DUF1784; <br>Fcf2 pre-rRNA processing. Pfam-B_13623 (release 19.0). This is a family of eukaryotic nucleolar proteins that are involved in pre-rRNA processing  .. 
PF08699 Domain of unknown function (DUF1785)<br>Pfam-B_1585 (release 19.0). This region is found in argonaute   proteins and often co-occurs with Pfam:PF02179 and Pfam:PF02171.. 
PF08700 Vps51/Vps67<br>This family includes a presumed domain found in a number of components of vesicular transport.  The VFT tethering complex (also known as GARP complex, Golgi associated retrograde protein complex, Vps53 tethering complex) is a conserved eukaryotic docking complex which is involved recycling of proteins from endosomes to the late Golgi .  Vps51 (also known as Vps67) is a subunit of VFT and interacts with the SNARE Tlg1  .  Cog1_N is the N-terminus of the Cog1 subunit of the eight-unit Conserved Oligomeric Golgi (COG) complex that participates in retrograde vesicular transport and is required to maintain normal Golgi structure and function. The subunits are located in two lobes and Cog1 serves to bind the two lobes together probably via the highly conserved N-terminal domain of approximately 85 residues  .. 
PF08701 GNL3L/Grn1 putative GTPase<br>Pfam-B_22650 (release 19.0). Grn1 (yeast) and GNL3L (human) are putative GTPases which are required for growth and play a role in processing of nucleolar pre-rRNA  .  This family contains a potential nuclear localisation signal.. 
PF08702 Fibrinogen alpha/beta chain family<br>Fibrinogen is a protein involved in platelet aggregation and is essential for the coagulation of blood.  This domain forms part of the central coiled coiled region of the protein which is formed from two sets of three non-identical chains (alpha, beta and gamma).. 
PF08703 PLC-beta C terminal<br>This domain corresponds to the alpha helical C terminal domain of phospholipase C beta.. 
PF08704 tRNA methyltransferase complex GCD14 subunit<br>Pfam-B_5615 (release 19.0). GCD14 is a subunit of the tRNA methyltransferase complex and is required for 1-methyladenosine modification and maturation of initiator methionyl-tRNA  .. 
PF08705 Gag protein p6<br>HIV protein p6 contains two late-budding domains (L domains) which are short sequence motifs essential for viral particle release.  p6 interacts with the endosomal sorting complex and represents a docking site for several cellular and binding factors  .  The PTAP motif interacts with the cellular budding factor TSG101  .  This domain is also found in some chimpanzee immunodeficiency virus (SIV-cpz) proteins.. 
PF08706 D5 N terminal like<br>This domain is found in D5 proteins of DNA viruses and bacteriophage P4 DNA primases phages.. 
PF08707 Primase C terminal 2 (PriCT-2)   <br>This alpha helical domain is found at the C terminal of primases.. 
PF08708 Primase C terminal 1 (PriCT-1)<br>This alpha helical domain is found at the C terminal of primases.. 
PF08709 Inositol 1,4,5-trisphosphate/ryanodine receptor<br>This domain corresponds to the ligand binding region on inositol 1,4,5-trisphosphate receptor, and the N terminal region of the ryanodine receptor.  Both receptors are involved in Ca2+ release. They can couple to the activation of neurotransmitter-gated receptors and voltage-gated Ca2+ channels on the plasma membrane, thus allowing the endoplasmic reticulum discriminate between different types of neuronal activity  .. 
PF08710 nsp9 replicase<br>nsp9 is a single-stranded RNA-binding viral protein likely to be involved in RNA synthesis  .  Its structure comprises of a single beta barrel  .. 
PF08711 TFIIS;<br>TFIIS helical bundle-like domain. pdb_1wjt & Pfam-B_7936 (release 8.0). Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species {1-2]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function  . Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. Notably, the 'small' and 'large' Mediator complexes differ in their subunit composition: the Med26 subunit preferentially associates with the small, active complex, whereas cdk8, cyclin C, Med12 and Med13 associate with the large Mediator complex  . This family includesthe C terminal region of a number of eukaryotic hypothetical proteins which are homologous to the Saccharomyces cerevisiae protein IWS1. IWS1 is known to be an Pol II transcription elongation factor and interacts with Spt6 and Spt5 [5,6].. 
PF08712 Scaffold protein Nfu/NifU N terminal<br>This domain is found at the N terminus of NifU and NifU related proteins, and in the human Nfu protein.  Both of these proteins are thought to be involved in the the assembly of iron-sulphur clusters   .. 
PF08713 DNA alkylation repair enzyme<br>Proteins in this family are predicted to be DNA alkylation repair enzymes.  The structure of a hypothetical protein in this family shows it to adopt a supercoiled alpha helical structure.. 
PF08714 Formaldehyde-activating enzyme (Fae)<br>Formaldehyde-activating enzyme is an enzyme required for energy metabolism and formaldehyde detoxification.  It catalyses the condensation of formaldehyde and tetrahydromethanopterin to methylene tetrahydromethanopterin  .. 
PF08715 Papain like viral protease<br>This family of viral proteases are similar to the papain protease and are required for proteolytic processing of the replicase polyprotein.  The structure of this protein has shown it adopts a fold similar that of de-ubiquitinating enzymes  .. 
PF08716 nsp7 replicase<br>nsp7 (non structural protein 7) has been implicated in viral RNA replication and is predominantly alpha helical in structure  . It forms a hexadecameric supercomplex with nsp7 that adopts a hollow cylinder-like structure  .  The dimensions of the central channel and positive electrostatic properties of the cylinder imply that it confers processivity on RNA-dependent RNA polymerase  .. 
PF08717 nsp8 replicase<br>Viral nsp8 (non structural protein 8) forms a hexadecameric supercomplex with nsp7 that adopts a hollow cylinder-like structure  .  The dimensions of the central channel and positive electrostatic properties of the cylinder imply that it confers processivity on RNA-dependent RNA polymerase  .. 
PF08718 Glycolipid transfer protein (GLTP)<br>GLTP is a cytosolic protein that catalyses the intermembrane transfer of glycolipids   .. 
PF08719 Domain of unknown function (DUF1768)<br>This is a domain of unknown function.  It is alpha helical in structure. The GO annotation for this protein suggests it is involved in nematode larval development and has a positive regulation on growth rate.. 
PF08720 FluC_stalk; <br>Influenza C hemagglutinin stalk. This domain corresponds to the stalk segment of hemagglutinin in influenza C virus.  It forms a coiled coil structure  .. 
PF08721 TnsA_C;<br>TnsA endonuclease C terminal. The Tn7 transposase is composed of proteins TnsA and TnsB.  DNA breakage at the 5' end of the transposon is carried out by TnsA, and breakage and joining at the 3' end is carried out by TnsB. The C terminal domain of TnsA binds DNA.. 
PF08722 TnsA_N;<br>TnsA endonuclease N terminal. The Tn7 transposase is composed of proteins TnsA and TnsB.  DNA breakage at the 5' end of the transposon is carried out by TnsA, and breakage and joining at the 3' end is carried out by TnsB. The N terminal domain of TnsA is catalytic.. 
PF08723 Gag protein p15<br>Gag p15 is a viral membrane-binding matrix protein which is alpha helical in structure.. 
PF08724 Rep protein catalytic domain like<br>Adeno-associated virus (AAV) Replication (Rep) protein is essential for viral replication and integration.  The catalytic domain has DNA binding and endonuclease activity.. 
PF08725 Integrin beta cytoplasmic domain<br>Integrins are a group of transmembrane proteins which function as extracellular matrix receptors and in cell adhesion.  Integrins are ubiquitously expressed and are heterodimeric, each composed of an alpha and beta subunit.  Several variations of the the alpha and beta subunits exist, and association of different alpha and beta subunits can have different a different binding specificity.  This domain corresponds to the cytoplasmic domain of the beta subunit.. 
PF08726 efhand_Ca_insen;<br>Ca2+ insensitive EF hand. EF hands are helix-loop-helix binding motifs involved in the regulation of many cellular processes.  EF hands usually bind to Ca2+ ions which causes a major conformational change that allows the protein to interact with its designated targets.  This domain corresponds to an EF hand which has partially or entirely lost its calcium-binding properties.  The calcium insensitive EF hand is still able to mediate protein-protein recognition  .. 
PF08727 Poliovirus 3A protein like<br>This domain is found in positive-strand RNA viruses.  The 3A protein is a critical component of the poliovirus replication complex, and is also an inhibitor of host cell ER to Golgi transport.. 
PF08728 CRT10<br>CRT10 is a transcriptional regulator of ribonucleotide reductase (RNR) genes  .  RNR catalyses the rate limiting step in dNTP synthesis.  Mutations in CRT10 have been shown to enhance hydroxyurea resistance  .. 
PF08729 HPC2; HRD;<br>HPC2 and ubinuclein domain. Mistry J, Wood V, Balaji S, Iyer LM, Aravind L. HPC2 (Histone promoter control 2) is required for cell-cycle regulation of histone transcription  .  It regulates transcription of the histone genes during the S-phase of the cell cycle by repressing transcription at other cell cycle stages. HPC2 mutants display synthetic interactions with FACT complex which allows RNA Pol II to elongate through nucleosomes  . Hpc2 is one of the proteins  of one of the multi-subunit complexes that mediate replication- independent nucleosome assembly, along with histone chaperone  proteins. the Hip4 sequence from SCH. pombe is an integral component  of this complex that is required for transcriptional silencing at  multiple loci  . HPC2, ubinuclein/yemanuclein, and the cell cycle  regulator FLJ25778 share a conserved domain that is predicted to  bind histone tails  . This domain is also referred to as the  HRD or Hpc2-related domain.. 
PF08730 Rad33<br>Rad33 is involved in nucleotide excision repair (NER).  NER is the main pathway for repairing DNA lesions induced by UV. Cells deleted for RAD33 display intermediate UV sensitivity that is epistatic with NER  .. 
PF08731 Transcription factor AFT<br>AFT (activator of iron transcription) is an iron regulated transcriptional activator that regulates the expression of genes involved in iron homeostasis .  This family includes the paralogous pair of transcription factors AFT1 and AFT2.. 
PF08732 HIM1<br>HIM1 (high induction of mutagenesis protein 1) plays a role in the control of spontaneous and induced mutagenesis  .  It is thought to participate in the control of processing of mutational intermediates appearing during error-prone bypass of DNA damage.. 
PF08733 PalH/RIM21<br>PalH (also known as RIM21) is a transmembrane protein required for proteolytic cleavage of Rim101/PacC transcription factors which are activated by C terminal proteolytic processing. Rim101/PacC family proteins play a key role in pH-dependent responses and PalH has been implicated as a pH sensor  .. 
PF08734 GYD domain<br>This protein is found in a range of bacteria.  It is usually less than 100 amino acids in length. The function of the protein is unknown.  It may belong to the dimeric alpha/beta barrel superfamily.. 
PF08735 Putative pyruvate format-lyase activating enzyme (DUF1786)<br>This family is annotated as pyruvate formate-lyase activating enzyme (EC:1.97.1.4) in UniProt. It is not clear where this annotation comes from.. 
PF08736 FERM adjacent (FA)<br>This region is found adjacent to Band 4.1 / FERM domains (Pfam:PF00373) in a subset of FERM containing protein.  The region has been hypothesised to play a role in regulatory adaptation, based on similarity to other protein kinase substrates .. 
PF08737 Rgp1<br>Rgp1 forms heterodimer with Ric1 (Pfam:PF07064) which associates with Golgi membranes and functions as a guanyl-nucleotide exchange factor  .. 
PF08738 Gon7 family<br>In S. cerevisiae Gon7 is a member of the KEOPS protein complex. A protein complex proposed to be involved in transcription and promoting telomere uncapping and telomere elongation  .. 
PF08740 BCS1 N terminal<br>Pfam-B_10126 (release 19.0). This domain is found at the N terminal of the mitochondrial ATPase BSC1.  It encodes the import and intramitochondrial sorting for the protein  .. 
PF08741 YwhD family<br>PSI2 target PSI-blast from BH3813. This family of proteins are currently uncharacterised.  They are around 170 amino acids in length.. 
PF08742 DUF1787; <br>This domain contains 8 conserved cysteine residues, but this family only contains 7 of them to overlaps with other domains. It is found in disease-related proteins including von Willebrand factor, Alpha tectorin, Zonadhesin and Mucin.  It is often found on proteins containing Pfam:PF00094 and Pfam:PF01826.. 
PF08743 SUMO_ligase; Nse4;<br>Nse4 is a component of the Smc5/6 DNA repair complex.  It forms interactions with Smc5 and Nse1  . The exact function of this highly conserved C-terminal domain is not known.. 
PF08744 Plant transcription factor NOZZLE<br>Pfam-B_86265 (release 19.0). NOZZLE is a transcription factor that plays a role in patterning the proximal-distal and adaxial-abaxial axes   .. 
PF08745 UPF0278 family<br>Members of this family are uncharacterised proteins about 200 amino acids in length.. 
PF08746 RING-like domain<br>This is a zinc finger domain that is related to the C3HC4 RING finger domain (Pfam:PF00097).. 
PF08747 Domain of unknown function (DUF1788)<br>PSI2 target Npun02004481. Putative uncharacterised domain in proteins of length around 200 amino acids.. 
PF08748 Domain of unknown function (DUF1789)<br>PSI2 target CAE43632.1. Putative uncharacterised domain found in phage-related conserved hypothetical protein from Bordetella.. 
PF08750 CNP1-like family<br>PSI2 target CAB84161.1. This family of proteins are likely to be lipoproteins. CNP1 (cryptic neisserial protein) has been expressed in E. coli and shown to be localised periplasmicly  .. 
PF08751 TrwC relaxase<br>Relaxases are DNA strand transferases which function during the conjugative cell to cell DNA transfer.  TrwC binds to the origin of transfer (oriT) and melts the double helix.. 
PF08752 Gamma-COP;<br>Coatomer gamma subunit appendage platform subdomain. COPI-coated vesicles function in retrograde transport from the Golgi to the ER, and in intra-Golgi transport.  This is the platform subdomain of the coatomer gamma subunit appendage domain.\.       It carries a protein-protein interaction site at UniProt:P53620, residue W776, which in yeast binds to the ARFGAP Glo3p, and in mammalian gamma-COP binds to a Glo3p orthologue, ARFGAP2  .. 
PF08753 NikR C terminal nickel binding domain<br>NikR is a transcription factor that regulates nickel uptake. It consists of two dimeric DNA binding domains separated by a tetrameric regulatory domain that binds nickel.  This domain corresponds to the C terminal regulatory domain which contains four nickel binding sites at the tetramer interface  .. 
PF08755 Hemimethylated DNA-binding protein YccV like<br>YccV is a hemimethylated DNA binding protein which has been shown to regulate dnaA gene expression  .  The structure of one of the hypothetical proteins in this family has been solved and it forms a beta sheet structure with a terminating alpha helix.. 
PF08756 YfkB-like domain<br>PSI2 structural target yfkB. This protein is adjacent to YfkA in B. subtilis.  In other bacterial species it is fused to this protein. As YfkA contains a Radical SAM domain it suggests this domain is interacts with them.. 
PF08757 CotH protein<br>PSI2 structural target cotH. Members of this family include the spore coat protein H (cotH).. 
PF08758 Cadherin prodomain like<br>Cadherins are a family of proteins that mediate calcium dependent cell-cell adhesion.  They are activated through cleavage of a prosequence in the late Golgi.  This domain corresponds to the folded region of the prosequence, and is termed the prodomain. The prodomain shows structural resemblance to the cadherin domain, but lacks all the features known to be important for cadherin-cadherin interactions  .. 
PF08759 Domain of unknown function (DUF1792)<br>PSI2 structural target AAO75156.1. This putative domain is probably missannotated as a glycosyl transferase 8 family member. This domain is found at the C-terminus of protein such as Swiss:Q97P75 that also contain the glycosyl transferase domain at the N-terminus.. 
PF08760 Domain of unknown function (DUF1793)<br>PSI2 structural target AAO78587.1. This presumed domain is found at the C-terminus of a glutaminase protein from fungi  . This domain is also found as a single domain protein in Bacteroides thetaiotaomicron.. 
PF08761 dUTPase<br>2-Deoxyuridine 5-triphosphate nucleotidohydrolase (dUTPase) catalyses the hydrolysis of dUTP to dUMP and pyrophosphate (EC:3.6.1.23).  Members of this family have a novel all-alpha fold and are unrelated to the all-beta fold found in dUTPases of the majority of organisms  .  This family contains both dUTPase homologues of dUTPase including dCTPase of phage T4.. 
PF08762 CRPV capsid protein like<br>This is a family of capsid proteins found in positive stranded ssRNA viruses such as cricket paralysis virus (CRPV).  It forms an all beta sheet structure  .. 
PF08763 Voltage gated calcium channel IQ domain<br>Voltage gated calcium channels control cellular calcium entry in response to changes in membrane potential.  The isoleucine-glutamine (IQ) motif in the voltage gated calcium channel IQ domain interacts with hydrophobic pockets of Ca2+/calmodulin  .  The interaction regulates two self-regulatory calcium dependent feedback mechanism, calcium dependent inactivation (CDI), and calcium-dependent facilitation (CDF).. 
PF08764 Staphylococcus aureus coagulase<br>Staphylococcus aureus secretes a cofactor called coagulase. Coagulase is an extracellular protein that forms a complex with human prothrombin, and activates it without the usual proteolytic cleavages.  The resulting complex directly initiates blood clotting.. 
PF08765 Mor transcription activator family<br>Mor (Middle operon regulator) is a sequence specific DNA binding protein.  It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase.  The N terminal region of Mor is the dimerisation region, and the C terminal contains a helix-turn-helix motif which binds DNA.. 
PF08766 DEK C terminal domain<br>DEK is a chromatin associated protein that is linked with cancers and autoimmune disease.  This domain is found at the C terminal of DEK and is of clinical importance since it can reverse the characteristic abnormal DNA-mutagen sensitivity in fibroblasts from ataxia-telangiectasia (A-T) patients  .\.     The structure of this domain shows it to be homologous to the E2F/DP transcription factor family  .  This domain is also found in chitin synthase proteins like Swiss:Q8TF96, and in protein phosphastases such as Swiss:Q6NN85.. 
PF08767 CRM1 C terminal<br>CRM1 (also known as Exportin1) mediates the nuclear export of proteins bearing a leucine-rich nuclear export signal (NES). CRM1 forms a complex with the NES containing protein and the small GTPase Ran.  This region forms an alpha helical structure formed by six helical hairpin motifs that are structurally similar to the HEAT repeat, but share little sequence similarity to the HEAT repeat  .. 
PF08768 Domain of unknown function (DUF1794)<br>Mistry J, Pollington JE. This domain forms a beta barrel structure but the function is unknown. The GO annotation for this protein indicates that the protein has a function in nematode larval development and has a positive regulation on growth rate.. 
PF08769 Sporulation initiation factor Spo0A C terminal<br>The response regulator Spo0A is comprised of a phophoacceptor domain and a transcription activation domain.  This domain corresponds to the transcription activation domain and forms an alpha helical structure comprising of 6 alpha helices.  The structure contains a helix-turn-helix and binds DNA   .. 
PF08770 Sulphur oxidation protein SoxZ<br>SoxZ forms an anti parallel beta structure and forms a complex with SoxY.  Sulphur oxidation occurs at the thiol of a conserved cysteine residue of the SoxY subunit  .. 
PF08771 Rapamycin binding domain<br>This domain forms an alpha helical structure and binds to rapamycin  .. 
PF08772 Nin one binding (NOB1) Zn-ribbon like<br>This domain corresponds to a zinc ribbon and is found on the RNA binding protein NOB1 (Nin one binding).. 
PF08773 Cathepsin C exclusion domain<br>Cathepsin C (dipeptidyl peptidase I) is the physiological activator of a group of serine proteases.  This domain corresponds to the exclusion domain whose structure excludes the approach of a polypeptide apart from its termini.  It forms an enclosed beta barrel structure composed from 8 anti-parallel beta strands  . Based on a structural comparison and interaction data, it is suggested that the exclusion domain originates from a metallo-protease inhibitor  .. 
PF08774 VRR-NUC domain<br>
PF08775 ParB family<br>ParB is a component of the par system which mediates accurate DNA partition during cell division.  It recognises A-box and B-box DNA motifs.  ParB forms an asymmetric dimer with 2 extended helix-turn-helix (HTH) motifs that bind to A-boxes.  The HTH motifs emanate from a beta sheet coiled coil DNA binding module  . Both DNA binding elements are free to rotate around a flexible linker, this enables them to bind to complex arrays of A- and B-box elements on adjacent DNA arms of the looped partition site  .. 
PF08776 VASP tetramerisation domain<br>Vasodilator-stimulated phosphoprotein (VASP) is an actin cytoskeletal regulatory protein.  This region corresponds to the tetramerisation domain which forms a right handed alpha helical coiled coil structure  .. 
PF08777 RNA binding motif<br>This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif  .. 
PF08778 HIF-1 alpha C terminal transactivation domain<br>Hypoxia inducible factor-1 alpha (HIF-1 alpha) is the regulatory subunit of the heterodimeric transcription factor HIF-1.  It plays a key role in cellular response to low oxygen tension. This region corresponds to the C terminal transactivation domain.. 
PF08779 SARS coronavirus X4 like<br>The structure of the coronavirus X4 protein (also known as 7a and U122) shows similarities to the immunoglobulin like fold and suggests a binding activity to integrin I domains  .  In SARS-CoV- infected cells, the X4 protein is expressed and retained intra-cellularly within the Golgi network  .  X4 has been implicated to function during the replication cycle of SARS-CoV  .. 
PF08780 Nucleotidyltransferase substrate binding protein like<br>Nucleotidyltransferases (EC 2.7.7) comprise a large enzyme family with diverse roles in polynucleotide synthesis and modification. This domain is structurally related to kanamycin nucleotidyltransferase (KNTase) and forms a complex with HI0073, a sequence homolog of the nucleotide-binding domain of this nucleotidyltransferase superfamily  .. 
PF08781 Transcription factor DP<br>DP forms a heterodimer with E2F and regulates genes involved in cell cycle progression.  The transcriptional activity of E2F is inhibited by the retinoblastoma protein which binds to the E2F-DP heterodimer   and negatively regulates the G1-S transition.. 
PF08782 c-SKI Smad4 binding domain<br>c-SKI is an oncoprotein that inhibits TGF-beta signaling through interaction with Smad proteins  .  This domain binds to Smad4  . 
PF08783 DWNN domain<br>DWNN is a ubiquitin like domain found at the N terminus of the RBBP6 family of splicing-associated proteins  .  The DWNN domain is independently expressed in higher vertebrates so it may function as a novel ubiquitin-like modifier of other proteins  .. 
PF08784 Replication protein A C terminal<br>This domain corresponds to the C terminal of the single stranded DNA binding protein RPA (replication protein A).  RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints.. 
PF08785 Ku C terminal domain like<br>The non-homologous end joining (NHEJ) pathway is one method by which double stranded breaks in chromosomal DNA are repaired.  Ku is a component of a multi-protein complex that is involved in the NHEJ.  Ku has affinity for DNA ends and recruits the DNA-dependent protein kinase catalytic subunit (DNA-PKcs).  This domain is found at the C terminal of Ku which binds to DNA-PKcs  .. 
PF08786 Domain of unknown function (DUF1795)<br>This is a bacterial domain of unknown function.  It forms an antiparallel beta sheet structure and contains some alpha helical regions.. 
PF08787 Alginate lyase<br>Alginate lyases are enzymes that degrade the linear polysaccharide alignate.\. They cleave the glycosidic linkage of alignate through a beta-elimination reaction.  This family forms an all beta fold and is different to all alpha fold of Pfam:PF05426.. 
PF08788 NHR2 domain like<br>The NHR2 (Nervy homology 2) domain is found in the ETO protein where it mediates oligomerisation and protein-protein interactions.  It forms an alpha-helical tetramer  .. 
PF08789 PBCV-specific basic adaptor domain<br>The small PBCV-specific basic adaptor domain is found fused to S/T protein kinases and the 2-Cysteine domain  .. 
PF08790 LYAR-type C2HC zinc finger <br>This C2HC zinc finger is found in LYAR proteins such as Swiss:Q08288 which are involved in cell growth regulation.. 
PF08792 A2L zinc ribbon domain<br>This zinc ribbon domain is found associated with some viral A2L transcription factors  .. 
PF08793 2-cysteine adaptor domain<br>The virus-specific 2-cysteine adaptor domain is found fused to OTU/A20-like peptidases and S/T protein kinases.  The domain associations of these proteins indicate that they might function as viral adaptors connecting the kinases and OTU/A20 peptidases to specific targets  .. 
PF08794 Lipoprotein GNA1870 C terminal like<br>GNA1870 is a surface exposed lipoprotein in Neisseria meningitidis that and is a potent antigen of Meningococcus.  The structure of the C terminal domain consists of an anti-parallel beta barrel overlaid by a short alpha helical region  .. 
PF08795 Putative papain-like cysteine peptidase (DUF1796)<br>
PF08796 Protein of unknown function (DUF1797)<br>This is a domain of unknown function.  It forms a central anti-parallel beta sheet with flanking alpha helical regions.. 
PF08797 HIRAN domain<br>The HIRAN domain (HIP116, Rad5p N-terminal) is found in the N-terminal regions of the SWI2/SNF2 proteins typified by HIP116 and Rad5p. The HIRAN domain is found as a standalone protein in several bacteria and prophages, or fused to other catalytic domains, such as a nuclease of the restriction endonuclease fold and TDP1-like DNA phosphoesterases, in the eukaryotes  . It has been predicted that this domain functions as a DNA-binding domain that probably recognises features associated with damaged DNA or stalled replication forks  . 
PF08798 CRISPR associated protein<br>This domain forms an anti-parallel beta strand structure with flanking alpha helical regions.. 
PF08799 pre-mRNA processing factor 4 (PRP4) like<br>This small domain is found on PRP4 ribonuleoproteins.  PRP4 is a U4/U6 small nuclear ribonucleoprotein that is involved in pre-mRNA processing.. 
PF08800 VirE N-terminal domain<br>PSI2 target AAO76744.1. This presumed domain is found at the N-terminus of VirE proteins.. 
PF08801 Nup133_N;<br>Nup133 N terminal like. Nup133 is a nucleoporin that is crucial for nuclear pore complex (NPC) biogenesis. The N terminal forms a seven-bladed beta propeller structure  . This family now contains other sized nucleoporins, including Nup155, Nup8, Nuo132, Nup15 and Nup170.. 
PF08802 Cytochrome B6-F complex Fe-S subunit <br>The cytochrome B6-F complex mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions.  This domain corresponds to the alpha helical transmembrane domain of the cytochrome B6-F complex iron-sulphur subunit.. 
PF08803 Putative mono-oxygenase ydhR<br>ydhR is a homodimeric protein that comprises of a central four-stranded beta sheet and four surrounding alpha helices  .  It shows structural homology to the ActVA-Orf6 and YgiN proteins which indicates it could be a mono-oxygenase.. 
PF08804 gp32 DNA binding protein like<br>gp32 is a single stranded (ss) DNA binding protein in bacteriophage T4 that is essential for DNA replication, recombination and repair. The ssDNA binding cleft of gp32 comprises regions from three structural subdomains  .. 
PF08805 PilS N terminal<br>Type IV pili are bacterial virulence-associated adhesins that promote bacterial attachment to host cells.  In Salmonella typhi, the structural pilin protein PilS interacts with the cystic fibrosis transmembrane conductance regulator  .  Mutagenesis studies suggest that residues on an alpha-beta loop and the C terminal disulphide-bonded region of PilS might be involved in binding specificity of the pilus  .. 
PF08806 Sep15/SelM redox domain<br>Sep15 and SelM are eukaryotic selenoproteins that have a thioredoxin-like domain and a surface accessible active site redox motif  .  This suggests that they function as thiol-disulphide isomerases involved in disulphide bond formation in the endoplasmic reticulum  .. 
PF08807 Bacterial domain of unknown function (DUF1798)<br>This domain is found in many hypothetical proteins.  The structure of one of the proteins in this family has been solved and it adopts an all alpha helical fold.. 
PF08808 RES domain<br>PSI2 target CAE41587.1. This presumed domain contains 3 highly conserved polar groups that could form an active site. These are an arginine, glutamate and serine, hence the RES domain. The domain is found widely distributed in bacteria. The domain is about 150 residues in length.. 
PF08809 Phage related hypothetical protein (DUF1799)<br>PSI2 target CAE43631.1. Members of this family are about 100 amino acids in length and are uncharacterised.. 
PF08810 Kinase associated protein B<br>This bacterial protein forms an anti-parallel beta sheet with an extending alpha helical region.. 
PF08811 Protein of unknown function (DUF1800)<br>PSI2 target AAK23953.1. This is a family of large bacterial proteins of unknown function.. 
PF08812 YtxC-like family<br>PSI2 target YtxC B.subtilis. This family includes proteins similar to B. subtilis YtxC an uncharacterised protein.. 
PF08813 Phage tail protein<br>PSI2 target CAE43633.1. This family of proteins include phage tail proteins.  They probably include bacterial Ig-like domains related to Pfam:PF02368. Which also includes a number of phage tail invasin proteins.. 
PF08814 XisH protein<br>PSI2 target ZP_00111899.1. The fdxN element, along with two other DNA elements, is excised from the chromosome during heterocyst differentiation in cyanobacteria. The xisH as well as the xisF and xisI genes are required  .. 
PF08815 Nuclear receptor coactivator<br>This region is found on eukaryotic nuclear receptor coactivators and forms an alpha helical structure.. 
PF08816 Inhibitor of vertebrate lysozyme (Ivy)<br>This bacterial family is a strong inhibitor of vertebrate lysozyme.. 
PF08817 WXG100 protein secretion system (Wss), protein YukD<br>Mistry J, Desvaux M, Burroughs AM, Iyer LM, Aravind L. The YukD protein family members participate in the formation of a translocon required for the secretion of WXG100 proteins (Pfam:PF06013) in monoderm bacteria, with the WXG100 protein secretion system (Wss). Like the cytoplasmic protein EsaC in Staphylococcus aureus, YukD was hypothesized to play a role of a chaperone. YukD adopts a ubiquitin-like fold  . Usually, ubiquitin covalently binds to protein and flags them for protein degradation, however conjugation assays have indicated that the classical YukD lacks the capacity for covalent bond formation with other proteins  . In contrast to the situation in firmicutes, YukD-like proteins in actinobacteria are often fused to a transporter involved in the ESAT-6/ESX/Wss secretion pathway [6,7]. Members of the YukD family are also associated in gene neighborhoods with other enzymatic members of the ubiquitin signaling and degradation pathway such as the E1, E2 and E3 trienzyme complex that catalyze ubiquitin transfer to substrates, and the JAB family metallopeptidases that are involved in its release  . This suggests that a subset of the YukD family in bacteria are conjugated and released from proteins as in the eukaryotic ubiquitin-mediated signaling and degradation pathway  .. 
PF08818 Domain of unknown function (DU1801)<br>PSI2 target AAO81511.1. This large family of bacterial proteins is uncharacterised.  They contain a presumed domain about 110 amino acids in length.. 
PF08819 Domain of unknown function (DUF1802)<br>The function of this family is unknown.  This region is found associated with a Pfam:PF04471 suggesting they could be part of a restriction modification system... 
PF08820 Domain of unknown function (DUF1803)<br>PSI2 target AAO81393.1. This small domain is found in one or two copies in proteins from bacteria. The function of this domain is unknown.. 
PF08821 CGGC domain<br>PSI2 target AAB98576.1. This putative domain contains a quite highly conserved sequence of CGGC in its central region.  The domain has many conserved cysteines and histidines suggestive of a zinc binding function.. 
PF08822 Protein of unknown function (DUF1804)<br>PSI2 target CAB84459.1. This family of bacterial protein is uncharacterised.. 
PF08823 Putative peptidoglycan binding domain<br>This family may be a peptidoglycan binding domain.. 
PF08824 Serine rich protein interaction domain<br>This is a serine rich domain that is found in the docking protein p130(cas) (Crk-associated substrate).  This domain folds into a four helix bundle which is associated with protein-protein interactions  .. 
PF08825 E2 binding domain<br>E1 and E2 enzymes play a central role in ubiquitin and ubiquitin-like protein transfer cascades.  This is an E2 binding domain that is found on NEDD8 activating E1 enzyme.  The domain resembles ubiquitin, and recruits the catalytic core of the E2 enzyme Ubc12 in a similar manner to that in which ubiquitin interacts with ubiquitin binding domains  .. 
PF08826 DMPK coiled coil domain like<br>This domain is found in the myotonic dystrophy protein kinase (DMPK) and adopts a coiled coil structure.  It plays a role in dimerisation  .. 
PF08827 Domain of unknown function (DUF1805)<br>This domain is found in bacteria and archaea and has an N terminal tetramerisation region that is composed of beta sheets.. 
PF08828 Doublesex dimerisation domain<br>Doublesex (DSX) is a transcription factor that regulates somatic sexual differences in Drosophila.\.     The structure of this domain has revealed a novel dimeric arrangement of ubiquitin-associated folds that has not previously been identified in a transcription factor  .. 
PF08829 Alpha C protein N terminal<br>The alpha C protein (ACP) is found in Streptococcus and acts as an invasin which plays a role in the internalisation and translocation of the organism across human epithelial surfaces. Group B Streptococcus is the leading cause of diseases including bacterial pneumonia, sepsis and meningitis.\.  The N terminal of ACP is associated with virulence and forms a beta sandwich and a three helix bundle [1-3].. 
PF08830 Protein of unknown function (DUF1806)<br>This is a bacterial family of uncharacterised proteins.  The structure of one of the proteins in this family has been solved and it adopts a beta barrel-like structure.. 
PF08831 Class II MHC-associated invariant chain trimerisation domain<br>The class II associated invariant chain peptide is required for folding and localisation of MHC class II heterodimers.  This domain is involved in trimerisation of the ectoderm and interferes with DM/class II binding.  The trimeric protein forms a cylindrical shape which is thought to be important for interactions between the invariant chain and class II molecules  .. 
PF08832 Steroid receptor coactivator<br>This domain is found in steroid/nuclear receptor coactivators and contains two LXXLL motifs that are involved in receptor binding  .  The family includes SRC-1/NcoA-1, NcoA-2/TIF2, pCIP/ACTR/GRIP-1/AIB1.. 
PF08833 Axin beta-catenin binding domain<br>This domain is found on the scaffolding protein Axin which is a component of the beta-catenin destruction complex.  It competes with the tumour suppressor adenomatous polyposis coli protein (APC) for binding to beta-catenin  .. 
PF08837 Protein of unknown function (DUF1810)<br>This is a family of uncharacterised proteins.  The structure of one of the members in this family has been solved and it adopts a mainly alpha helical structure.. 
PF08838 Protein of unknown function (DUF1811)<br>This is a bacterial family of uncharacterised proteins.  Some of the proteins are annotated as being transcriptional regulators (see Swiss:Q4MQL7, Swiss:Q65MA2).  The structure of one of the proteins in this family has revealed a beta-barrel like structure with helix-turn-helix like motif.. 
PF08839 DNA replication factor CDT1 like<br>CDT1 is a component of the replication licensing system and promotes the loading of the mini-chromosome maintenance complex onto chromatin.  Geminin is an inhibitor of CDT1 and prevents inappropriate re-initiation of replication on an already fired origin.  This region of CDT1 binds to Geminin  .. 
PF08840 BAAT / Acyl-CoA thioester hydrolase C terminal<br>Pfam-B_4571 (release 20.0). This catalytic domain is found at the C terminal of acyl-CoA thioester hydrolases and bile acid-CoA:amino acid N-acetyltransferases (BAAT).. 
PF08841 Diol dehydratase reactivase ATPase-like domain<br>Diol dehydratase (DDH, EC:4.2.1.28) and its isofunctional homologue glycerol dehydratase (GDH, EC.4.2.1.30) are enzymes which catalyse the conversion of glycerol 1,2-propanediol, and 1,2-ethanediol to aldehydes  .  These reactions require coenzyme B12.  Cleavage of the Co-C bond of coenzyme B12 by substrates or coenzyme analogues results in inactivation during which coenzyme B12 remains tightly bound to the apoenzyme.  This family comprises of the large subunit of the diol dehydratase and glycerol dehydratase reactivating factors whose function is to reactivate the holoenzyme by exchange of a damaged cofactor for intact coenzyme.. 
PF08842 DUF1812; Mfa;<br>Fimbrillin-A associated anchor proteins Mfa1 and Mfa2. PSI2 target AAO79331.1. This family of proteins may be lipoproteins principally from bacilli.  They are between 300 and 400 residues. Many Bacteroides-like bacterial species, including Porphyromonas gingivalis, the causal agent of periodontal infection, carry at least two types of fimbriae, namely FimA and Mfa1 fimbriae, following the names of their major subunit proteins  . Normally, FimA fimbriae are long filaments that are easily detached from cells, whereas Mfa1 fimbriae are short filaments that are tightly bound to cells; however, in the absence of Mfa2 protein, the Mfa1 fimbriae are also very long and are not attached. Mfa2 and Mfa1 are associated with each other in whole P. gingivalis cells to the extent that Mfa2 is located on the cell surface and probably associated with Mfa1 fimbriae in such a way that it anchors the Mfa1 fimbriae to the cell surface and regulates Mfa1 filament length  .. 
PF08843 Nucleotidyl transferase of unknown function (DUF1814)<br>PSI2 target CAD86002.1. This large family of proteins are largely uncharacterised.  Some are annotated as abortive infective proteins but support for this annotation could not be found. This family was recently identified as belonging to the nucleotidyltransferase superfamily  .. 
PF08844 Domain of unknown function (DUF1815)<br>PSI2 target ZP_00111304.2 (BIG_33). This presumed domain is about 100 amino acids in length and is functionally uncharacterised.. 
PF08845 DUF1813;<br>Toxin SymE, type I toxin-antitoxin system. PSI2 target AAC77303.1. SymE (SOS-induced yjiW gene with similarity to MazE ) is an SOS-induced toxin. It inhibits cell growth, decreases protein synthesis and increases RNA degradation. It may play a role in the recycling of RNAs damaged under SOS response-inducing conditions. It is predicted to have an AbrB fold, similar to that of the antitoxin MazE. Its translation is repressed by the antisense RNA SymR, which acts as an antitoxin [1,2].. 
PF08846 Domain of unknown function (DUF1816)<br>PSI2 target ZP_00109395.2 BIG_34. Swiss:Q4C9H3 is associated with the Pfam:PF01383 domain suggesting this presumed domain could have a role in phycobilisomes.. 
PF08847 Domain of unknown function (DUF1817)<br>PSI2 target ZP_00111140.1 BIG_36. Members of this family are functionally uncharacterised.. 
PF08848 Domain of unknown function (DUF1818)<br>PSI2 target ZP_00110314.1 BIG_37. This presumed domain is found in a small family of cyanobacterial protein. These proteins are functionally uncharacterised.. 
PF08849 Putative inner membrane protein (DUF1819)<br>PSI2 target ZP_00108899.1 BIG_41. These proteins are functionally uncharacterised.  Several are annotated as putative inner membrane proteins.. 
PF08850 Domain of unknown function (DUF1820)<br>PSI2 target AAG07366.1 BIG_46. This family includes small functionally uncharacterised proteins around 100 amino acids in length.. 
PF08852 Protein of unknown function (DUF1822)<br>PSI2 target ZP_00109005.1 BIG_39. This family of proteins are functionally uncharacterised.. 
PF08853 Domain of unknown function (DUF1823)<br>PSI2 target ZP_00108651.1 BIG_42. This presumed domain is functionally uncharacterised.. 
PF08854 Domain of unknown function (DUF1824)<br>This uncharacterised family of proteins are principally found in cyanobacteria.. 
PF08855 Domain of unknown function (DUF1825)<br>This uncharacterised family of proteins are principally found in cyanobacteria.. 
PF08856 Protein of unknown function (DUF1826)<br>These proteins are functionally uncharacterised.. 
PF08857 Putative ParB-like nuclease<br>PSI2 target AAG07772.1 BIG_47. This domain is probably distantly related to Pfam:PF02195. Suggesting these uncharacterised proteins have a nuclease function.. 
PF08858 IDEAL domain<br>This short domain is found at the C-terminus of proteins in the UPF0302 family.  The domain is named after the sequence of the most conserved region in some members.\.  The function of this domain is unknown.. 
PF08859 DGC domain<br>This domain appears to be a zinc binding domain from the conservation of four potential chelating cysteines. The domain is named after a conserved central motif. The function of this domain is unknown.. 
PF08860 Domain of unknown function (DUF1827)<br>This presumed domain has no known function.. 
PF08861 Domain of unknown function DUF1828<br>This presumed domain is functionally uncharacterised.. 
PF08862 Domain of unknown function DUF1829<br>This short domain is usually associated with Pfam:PF08861.. 
PF08863 YolD-like protein<br>Members of this family are functionally uncharacterised. However it has been predicted that thes proteins are functionally equivalent to the UmuD subunit of polymerase V from gram-negative bacteria  .. 
PF08864 UPF0302 domain<br>This family is known as UPF0302. It is currently uncharacterised.. 
PF08865 Domain of unknown function (DUF1830)<br>This family of short proteins is functionally uncharacterised.. 
PF08866 Putative amino acid metabolism<br>Solution of the structure of the Lactobacillus plantarum protein from this family has indicated a potential new fold with remote similarities to TBP-like (TATA-binding protein) structures. This similarity, in combination with genomic context analysis, leads us to propose an involvement in amino-acid metabolism. The potentially novel fold is an alpha + beta fold comprising two beta sheets packed against a single helix. The enzyme is present in the cytosol.. 
PF08867 FRG domain<br>This presumed domain contains a conserved N-terminal (F/Y)RG motif. It is functionally uncharacterised.. 
PF08868 YugN-like family<br>This family of proteins related to B. subtilis YugN are functionally uncharacterised.. 
PF08869 XisI protein<br>The fdxN element, along with two other DNA elements, is excised from the chromosome during heterocyst differentiation in cyanobacteria. The xisH as well as the xisF and xisI genes are required  .. 
PF08870 Domain of unknown function (DUF1832)<br>This family of proteins are functionally uncharacterised.. 
PF08872 KGK domain<br>This presumed domain is found in one or two copies in cyanobacterial proteins. It is named after a short sequence motif.. 
PF08873 Domain of unknown function (DUF1834)<br>This family of proteins are functionally uncharacterised. One member is the Gp37 protein from the FluMu prophage.. 
PF08874 Domain of unknown function (DUF1835)<br>This family of proteins are functionally uncharacterised.. 
PF08875 Domain of unknown function (DUF1833)<br>This family of proteins are functionally uncharacterised and are  predicted to adopt an all-beta fold  . They are often found in gene neighborhoods containing genes for an NlpC peptidase and a  Ubiquitin domain predicted to be involved in tail assembly  . . 
PF08876 Domain of unknown function (DUF1836)<br>This family of proteins are functionally uncharacterised.. 
PF08877 MepB protein<br>MepB is a functionally uncharacterised protein in the mepRAB gene cluster of Staphylococcus aureus.. 
PF08878 Domain of unknown function (DUF1837)<br>This family of proteins are functionally uncharacterised.. 
PF08879 WRC<br>The WRC domain, named after the conserved Trp-Arg-Cys motif,  contains two distinctive features: a putative nuclear localisation  signal and a zinc-finger motif (C3H). It is suggested that  the WRC domain functions in DNA binding  .. 
PF08880 QLQ<br>The QLQ domain is named after the conserved Gln, Leu, Gln motif.  The QLQ domain is found at the N-terminus of SWI2/SNF2 protein,  which has been shown to be involved in protein-protein interactions.   This domain has thus been postulated to be involved in mediating  protein interactions  .. 
PF08881 CNVH; <br>CyanoVirin-N Homology domains are found in the sugar-binding antiviral protein cyanovirin-N (CVN) as well as filamentous ascomycetes and in the fern Ceratopteris richardii.. 
PF08882 Acetone carboxylase gamma subunit<br>Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO(2) to form acetoacetate.. 
PF08883 Dopa 4,5-dioxygenase family<br>This family of proteins are related to Swiss:P87064 a DOPA 4,5-dioxygenase that is involved in synthesis of betalain. DOPA-dioxygenase is the key enzyme involved in betalain biosynthesis. It converts 3,4-dihydroxyphenylalanine to betalamic acid, a yellow chromophore.. 
PF08884 Flagellin D3 domain<br>This domain is found in the central portion bacterial flagellin FliC.  The domain contains a structural motif called a beta-folium fold  .  Although no specific function is assigned to this domain its deletion leads to a reduction in filament stability  .. 
PF08885 GSCFA family<br>This family of proteins are functionally uncharacterised. They have been named GSCFA after a highly conserved N-terminal motif in the alignment. Distant similarity to the Pfam:PF00657 lipases suggests these proteins are likely to be enzymes.. 
PF08886 Glutamate-cysteine ligase<br>This is a rare family of glutamate--cysteine ligases, EC:6.3.2.2, demonstrated first in Thiobacillus ferrooxidans and present in a few other Proteobacteria  . It is the first of two enzymes for glutathione biosynthesis. It is also called gamma-glutamylcysteine synthetase.  The structure of this family has been solved, and is similar to that of human glutathione synthetase and very different to gamma-glutamylcysteine synthetase from Escherichia coli.. 
PF08887 GAD-like domain<br>This domain is functionally uncharacterised, but it appears to be distantly related to the GAD domain Pfam:PF02938.. 
PF08888 HopJ type III effector protein<br>Pathovars of Pseudomonas syringae interact with their plant hosts via the action of Hrp outer protein (Hop) effector proteins, injected into plant cells by the type III secretion system. The proteins in this family are called HopJ after the original member HopPmaJ  .. 
PF08889 WbqC-like protein family<br>This family of proteins are functionally uncharacterised. However it is found in an O-antigen gene cluster in E. coli   and other bacteria   suggesting a role in O-antigen production. Feng et al. suggest that wbnG may code for a glycine transferase  .. 
PF08890 Phage XkdN-like protein<br>This family of proteins are functionally uncharacterised. They are found in prophage sequence in various bacteria.. 
PF08891 YfcL protein<br>This family of proteins are functionally uncharacterised. THey are related to the short YfcL protein from E. coli.. 
PF08892 YqcI/YcgG family<br>This family of proteins are functionally uncharacterised. The family include YqcI and YcgG from B. subtilis. The alignment contains a conserved FPC motif at the N-terminus and CPF at the C-terminus.. 
PF08893 Domain of unknown function (DUF1839)<br>This family of proteins are functionally uncharacterised.. 
PF08894 Protein of unknown function (DUF1838)<br>This family of proteins are functionally uncharacterised.. 
PF08895 Domain of unknown function (DUF1840)<br>This family of proteins are functionally uncharacterised.. 
PF08896 Domain of unknown function (DUF1842)<br>This domain is found at the N-terminus of proteins that are functionally uncharacterised.. 
PF08897 Domain of unknown function (DUF1841)<br>This family of proteins are functionally uncharacterised.. 
PF08898 Domain of unknown function (DUF1843)<br>This domain is found at the C-terminus of a family of proteins that are functionally uncharacterised. The presumed domain is about 60 amino acid residues in length and is found independently in some proteins.. 
PF08899 Domain of unknown function (DUF1844)<br>This family of proteins are functionally uncharacterised.. 
PF08900 Domain of unknown function (DUF1845)<br>This family of proteins are functionally uncharacterised.. 
PF08901 Protein of unknown function (DUF1847)<br>This family of proteins are functionally uncharacterised. THey contain 4 N-terminal cysteines that may form a zinc binding domain.. 
PF08902 Domain of unknown function (DUF1848)<br>This family of proteins are functionally uncharacterised. The C-terminus contains a cluster of cysteines that are similar to the iron-sulfur cluster found at the N-terminus of Pfam:PF04055.. 
PF08903 Domain of unknown function (DUF1846)<br>This family of proteins are functionally uncharacterised. Some members of the family are annotated as ATP-dependent peptidases. However, we can find no support for this annotation.. 
PF08904 Domain of unknown function (DUF1849)<br>This family of proteins are functionally uncharacterised.. 
PF08905 Domain of unknown function (DUF1850)<br>This family of proteins are functionally uncharacterised. Some members of this family appear to be misannotated as RocC an amino acid transporter from B. subtilis.. 
PF08906 Domain of unknown function (DUF1851)<br>This domain is found at the C-terminus of a variety of proteins that are functionally uncharacterised.. 
PF08907 Domain of unknown function (DUF1853)<br>This family of proteins are functionally uncharacterised.. 
PF08908 Domain of unknown function (DUF1852)<br>This family of proteins are functionally uncharacterised.. 
PF08909 Domain of unknown function (DUF1854)<br>This potential domain is functionally uncharacterised. It is found at the C-terminus of a number of ATP transporter proteins suggesting this domain may be involved in ligand binding.. 
PF08910 DUF1855; Aida_N; Aida-C2;<br>Mistry J, Sammut SJ, Coggill P, Zhang D, Eberhardt R. This is the N-terminal domain of the axin interactor, dorsalization-associated protein family  .. 
PF08911 NUP50 (Nucleoporin 50 kDa)<br>Nucleoporin 50 kDa (NUP50) acts as a cofactor for the importin-alpha:importin-beta heterodimer, which in turn allows for transportation of many nuclear-targeted proteins through nuclear pore complexes. The C terminus of NUP50 binds importin-beta through RAN-GTP, the N terminus binds the C terminus of importin-alpha, while a central domain binds importin-beta. NUP50:importin-alpha:importin-beta then binds cargo and can stimulate nuclear import. The N-terminal domain of NUP50 is also able to actively displace nuclear localisation signals from importin-alpha  .. 
PF08912 Rho Binding<br>Rho Binding Domain is responsible for the recognition and binding of Rho binding domain-containing proteins (such as ROCK) to Rho, resulting in activation of the GTPase which in turn modulates the phosphorylation of various signalling proteins. This domain is within an amphipathic alpha-helical coiled-coil and interacts with Rho through predominantly hydrophobic interactions  .. 
PF08913 Vinculin Binding Site<br>Vinculin binding sites are predominantly found in talin and talin-like molecules, enabling binding of vinculin to talin, stabilising integrin-mediated cell-matrix junctions. Talin, in turn, links integrins to the actin cytoskeleton. The consensus sequence for Vinculin binding sites is LxxAAxxVAxxVxxLIxxA, with a secondary structure prediction of four amphipathic helices. The hydrophobic residues that define the VBS are themselves 'masked' and are buried in the core of a series of helical bundles that make up the talin rod  .. 
PF08914 Rap1 Myb domain<br>
PF08915 Archaea-specific editing domain of threonyl-tRNA synthetase<br>Archaea-specific editing domain of threonyl-tRNA synthetase, with marked structural similarity to D-amino acids deacylases found in eubacteria and eukaryotes. This domain can bind D-amino acids, and ensures high fidelity during translation. It is especially responsible for removing incorrectly attached serine from tRNA-Thr. The domain forms a fold that can be be defined as two layers of beta-sheets (a three-stranded sheet and a five-stranded sheet), with two alpha-helices located adjacent to the five-stranded sheet  .. 
PF08916 Phenylalanine zipper<br>The phenylalanine zipper consists of aromatic side chains from ten phenylalanine residues that are stacked within a hydrophobic core. This zipper mediates dimerisation of various proteins, such as APS, SH2-B and Lnk  .. 
PF08917 Transforming growth factor beta receptor 2 ectodomain<br>The Transforming growth factor beta receptor 2 ectodomain is a compact fold consisting of nine beta-strands and a single helix stabilised by a network of six intra strand disulphide bonds. The folding topology includes a central five-stranded antiparallel beta-sheet, eight-residues long at its centre, covered by a second layer consisting of two segments of two-stranded antiparallel beta-sheets (beta1-beta4, beta3-beta9)  .. 
PF08918 PhoQ Sensor<br>The PhoQ Sensor is required for the virulence of various Gram-negative bacteria by allowing interaction of PhoPQ with the intracellular membrane, resulting in remodelling of the bacterial cell surface and subsequent bacterial resistance to host antimicrobial peptides. The domain contains a major flat acidic surface, which binds to at least 3 calcium ions, neutralising the domain's negative charge and allowing interaction with the negatively charged membrane  .. 
PF08919 F-actin binding<br>The F-actin binding domain forms a compact bundle of four antiparallel alpha-helices, which are arranged in a left-handed topology. Binding of F-actin to the F-actin binding domain may result in cytoplasmic retention and subcellular distribution of the protein, as well as possible inhibition of protein function  .. 
PF08920 Splicing factor 3B subunit 1<br>This family consists of several eukaryotic splicing factor 3B subunit 1 proteins, which associate with p14 through a C-terminus beta-strand that interacts with beta-3 of the p14 RNA recognition motif (RRM) beta-sheet, which is in turn connected to an alpha-helix by a loop that makes extensive contacts with both the shorter C-terminal helix and RRM of p14. This subunit is required for 'A' splicing complex assembly (formed by the stable binding of U2 snRNP to the branchpoint sequence in pre-mRNA) and 'E' splicing complex assembly  .. 
PF08921 Domain of unknown function (DUF1904)<br>This domain is found in a set of hypothetical bacterial proteins.. 
PF08922 Domain of unknown function (DUF1905)<br>This domain is found in a set of hypothetical bacterial proteins.. 
PF08923 Mitogen-activated protein kinase kinase 1 interacting<br>Mitogen-activated protein kinase kinase 1 interacting protein is a small subcellular adaptor protein required for MAPK signaling and ERK1/2 activation. The overall topology of this domain has a central five-stranded beta-sheet sandwiched between a two alpha-helix and a one alpha-helix layer  .. 
PF08924 Domain of unknown function (DUF1906)<br>This domain is found in a set of uncharacterised hypothetical bacterial proteins.. 
PF08925 Domain of Unknown Function (DUF1907)<br>The structure of this domain displays an alpha-beta-beta-alpha four layer topology, with an HxHxxxxxxxxxH motif that coordinates a zinc ion, and an acetate anion at a site that likely supports the enzymatic activity of an ester hydrolase  .. 
PF08926 Domain of unknown function (DUF1908)<br>This domain is found in a set of hypothetical/structural eukaryotic proteins.. 
PF08928 Domain of unknown function (DUF1910)<br>This domain is found in a set of hypothetical bacterial proteins.. 
PF08929 Domain of unknown function (DUF1911)<br>This domain is found in a set of hypothetical bacterial proteins.. 
PF08930 Domain of unknown function (DUF1912)<br>This domain has no known function. It is found in various Streptococcal proteins.. 
PF08931 Domain of unknown function (DUF1913)<br>This domain has no known function. It is found in a various putative receptor proteins from Lactococcus bacteriophages.. 
PF08932 Domain of unknown function (DUF1914)<br>This domain has no known function. It is found in a various putative receptor proteins from Lactococcus bacteriophages.. 
PF08933 Domain of unknown function (DUF1864)<br>This domain has no known function. It is found in various hypothetical and conserved domain proteins.. 
PF08934 Rb C-terminal domain<br>The Rb C-terminal domain is required for high-affinity binding to E2F-DP complexes and for maximal repression of E2F-responsive promoters, thereby acting as a growth suppressor by blocking the G1-S transition of the cell cycle. This domain has a strand-loop-helix structure, which directly interacts with both E2F1 and DP1, followed by a tail segment that lacks regular secondary structure  .. 
PF08935 DUF1865;<br>Viral protein VP4 subunit. This domain is predominantly found in viral proteins from the family Picornaviridae. It is VP4 of the viral polyprotein which, in poliovirus, is part of the capsid that consists of 60 copies each of four proteins VP1, VP2, VP3, and VP4 arranged on an icosahedral lattice  . VP4 is on the inside and differs from the others in being small, myristoylated and having an extended structure. Productive infection involves the externalisation of the VP4, which is cleaved from the rest, along with the N-terminus of VP1. There thus seem to be three stages of the virus, ie a multi-step process for cell entry involving RNA translocation through a membrane channel formed by the externalised N termini of VP1  .. 
PF08936 Carboxysome Shell Carbonic Anhydrase<br>Carboxysome Shell Carbonic Anhydrase is a bacterial carbonic anhydrase localised in the carboxysome, where it converts bicarbonate ions to carbon dioxide for use in carbon fixation. It contains three domains, these being: (1) an N-terminal domain composed primarily of four alpha-helices; (2) a catalytic domain containing a tightly bound zinc ion and (3) a C-terminal domain with weak structural similarity to the catalytic domain  .. 
PF08937 MTH538 TIR-like domain (DUF1863)<br>This domain adopts the flavodoxin fold, that is, five parallel beta-strands and four helical segments. The structure is a three-layer sandwich with alpha-1 and alpha-4 on one side of the beta-sheet, and alpha-2 and alpha-3 on the other side. Probable role in signal transduction as a phosphorylation-independent conformational switch protein  . This domain is similar to  the TIR domain.. 
PF08938 DUF1916;<br>Mistry J, Sammut SJ, Eberhardt R. This domain is found at the N-terminus of HBS1 proteins. It interacts with the ribosomal protein rpS3 at the mRNA entry site  .. 
PF08939 Domain of unknown function (DUF1917)<br>This domain is found in various hypothetical and basophilic leukaemia proteins. It has no known function.. 
PF08940 Domain of unknown function (DUF1918)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF08941 USP8 interacting<br>This domain interacts with the UBP deubiquitinating enzyme USP8.. 
PF08942 Domain of unknown function (DUF1919)<br>This domain has no known function. It is found in various hypothetical and putative bacterial proteins.. 
PF08943 CsiD<br>This family consists of various bacterial proteins pertaining to the non-haem Fe(II)-dependent oxygenase family. Exact function is unknown, but a putative role includes involvement in the control of utilisation of gamma-aminobutyric acid  .. 
PF08944 NADPH oxidase subunit p47Phox, C terminal domain<br>The C terminal domain of the phagocyte NADPH oxidase subunit p47Phox contains conserved PxxP motifs that allow binding to SH3 domains, with subsequent activation of the NADPH oxidase, and generation of superoxide, which plays a crucial role in host defense against microbial infection  .. 
PF08945 Bcl-x interacting, BH3 domain<br>This domain is a long alpha helix, required for interaction with Bcl-x. It is found in BAM, Bim and Bcl2-like protein 11  . This domain is also known as the BH3 domain between residues 146 and 161.. 
PF08946 Osmosensory transporter coiled coil<br>The osmosensory transporter coiled coil is a C-terminal domain found in various bacterial osmoprotective transporters, such as ProP, Proline/betaine transporter, Proline permease 2 and the citrate proton symporters. It adopts an antiparallel coiled-coil structure, and is essential for osmosensory and osmoprotectant transporter function  .. 
PF08947 BPS (Between PH and SH2) <br>The BPS (Between PH and SH2) domain, comprised of 2 beta strands and a C-terminal helix, is an approximately 45 residue region found in the adaptor proteins Grb7/10/14 that mediates inhibition of the tyrosine kinase domain of the insulin receptor by binding of the N-terminal portion of the BPS domain to the substrate peptide groove of the kinase, acting as a pseudosubstrate inhibitor  .. 
PF08948 Domain of unknown function (DUF1859)<br>This domain has no known function. It is predominantly found in the N-terminus of bacteriophage spike proteins  .. 
PF08949 Domain of unknown function (DUF1860)<br>This domain has no known function. It is predominantly found in the C-terminus of bacteriophage spike proteins  .. 
PF08950 Protein of unknown function (DUF1861)<br>This hypothetical protein, found in bacteria and in the eukaryote Leishmania, has no known function.. 
PF08951 Enterocin A Immunity<br>Mistry J, Sammut SJ, Coggill P. Gram-positive lactobacilli produce bacteriocins to kill closely-related competitor species  . To protect themselves from the bacteriocidal activity of this molecule they co-express an immunity protein (for discussion of this operon see Bacteriocin_IIc Pfam:PF10439). The immunity protein structure is a soluble, cytoplasmic, antiparallel four alpha-helical globular bundle with a fifth, more flexible and more divergent C-terminal helical hair-pin  . The C-terminal hair-pin recognises the C-terminus of the producer bacteriocin and this interaction is sufficient to dis-orient the bacteriocin within the membrane and close up the permeabilising pore that on its own the bacteriocin creates  . These immunity proteins interact in the same way with other bacteriocins, family Bacteriocin_II, Pfam:PF01721. Since many enterococci can produce more than one bacteriocin it seems likely that the whole operon can be carried on transferable plasmids  .. 
PF08952 Domain of unknown function (DUF1866) <br>This domain, found in Synaptojanin, has no known function.. 
PF08953 Domain of unknown function (DUF1899)<br>This set of domains is found in various eukaryotic proteins. Function is unknown.. 
PF08954 Domain of unknown function (DUF1900)<br>This domain is predominantly found in the structural protein coronin, and is duplicated in some sequences. It has no known function  .. 
PF08955 DUF1901;<br>BofC C-terminal domain. The C-terminal domain of the bacterial protein 'bypass of forespore C' contains a three-stranded beta-sheet and three alpha-helices. Its exact function is, as yet, unknown  .. 
PF08956 Domain of unknown function (DUF1869)<br>This domain is found in a set of hypothetical bacterial proteins.. 
PF08958 Domain of unknown function (DUF1871)<br>This set of hypothetical proteins is produced by prokaryotes pertaining to the Bacillus genus.. 
PF08960 Domain of unknown function (DUF1874)<br>This domain is found in a set of hypothetical viral and bacterial proteins.. 
PF08961 Domain of unknown function (DUF1875)<br>The MIT domain, found in Nuclear receptor-binding factor 2, has no known function.. 
PF08962 Domain of unknown function (DUF1876)<br>This domain is found in a set of hypothetical bacterial proteins.. 
PF08963 Protein of unknown function (DUF1878)<br>This domain is found in a set of hypothetical bacterial proteins.. 
PF08964 DUF1881;<br>Beta/Gamma crystallin. Mistry J, Sammut SJ, Eberhardt R. This family of beta/gamma crystallins includes the N-terminal domain of Dictyostelium discoideum Calcium-dependent cell adhesion molecule 1 (Swiss:P54657), which mediates cell-cell adhesion through homophilic interactions  .. 
PF08965 Domain of unknown function (DUF1870)<br>This domain is found in a set of hypothetical bacterial proteins. It contains a helix-turn-helix domain so may be a DNA-binding protein.. 
PF08966 Domain of unknown function (DUF1882)<br>This domain is found in a set of hypothetical bacterial proteins.. 
PF08967 Domain of unknown function (DUF1884)<br>This domain is found in a set of hypothetical bacterial proteins. It shows similarity to the N-terminus of ATP-synthase.. 
PF08968 Domain of unknown function (DUF1885)<br>This domain is found in a set of hypothetical proteins produced by bacteria of the Bacillus genus.. 
PF08969 DUF1873;<br>USP8 dimerisation domain. This domain is predominantly found in the amino terminal region of Ubiquitin carboxyl-terminal hydrolase 8 (USP8). It forms a five helical bundle that dimerises  .. 
PF08970 Sporulation inhibitor A<br>Members of this protein family contain two antiparallel alpha helices that are linked by a highly structured inter-helix loop to form a helical hairpin; the structure is stabilised by numerous hydrophobic and electrostatic interactions. These sporulation inhibitors are antikinases that bind to the histidine kinase KinA phosphotransfer domain and act as a molecular barricade that inhibit productive interaction between the ATP binding site and the phosphorylatable KinA His residue. This results in the inhibition of sporulation (by preventing phosphorylation of spo0A)  .. 
PF08971 Glycogen synthesis protein<br>Members of this family are involved in glycogen synthesis in Enterobacteria. The structure of the polypeptide chain comprises a bundle of two parallel amphipathic helices, alpha-1 and alpha-3, and a short hydrophobic helix alpha-2 sandwiched between them  .. 
PF08972 Domain of unknown function (DUF1902)<br>Members of this family of prokaryotic proteins adopt a fold consisting of one alpha-helix and four beta-strands. Their function has not, as yet, been elucidated  .. 
PF08973 DUF1893;<br>Domain of unknown function (DUF1893). Mistry J, Sammut SJ, Iyer, LM. A member of the deaminase fold that binds an unknown ligand in  the crystal structure. The protein is ADP-ribosylated at a conserved aspartate  . Contextual analysis suggests that the domain  is likely to bind NAD or ADP ribose either to sense redox states or to function as a regulatory ADP ribosyltransferase  .. 
PF08974 Domain of unknown function (DUF1877)<br>This domain is found in a set of hypothetical bacterial proteins.. 
PF08975 DUF1868; <br>Domain of unknown function (DUF1868). This group of 2H-phosphodiesterases comprises a single family typified by the protein mlr3352 from M.loti. Members are also present in various alpha-proteobacteria, Synechocystis, Streptococcus and Chilo iridescent virus. The presence of a member of this predominantly bacterial group in a large eukaryotic DNA virus represents a potential case of horizontal transfer from a bacterial source into a virus. Several proteins of bacterial origin have been noticed in the insect viruses (L.M.Iyer, E.V.Koonin and L.Aravind, unpublished observations and these appear to have been acquired from endo-symbiotic or parasitic bacteria that share the same host cells with the viruses. Presence of 2H proteins in the proteomes of large DNA viruses (e.g. T4 57B protein and the Fowl-pox virus FPV025) may point to some role for these proteins in regulating the viral tRNA metabolism. Each member of this family contains an internal duplication, each of which contains an HXTX motif that defines the family.. 
PF08976 Domain of unknown function (DUF1880)<br>This domain is found predominantly in DJ binding protein. It has no known function.. 
PF08977 Bypass of Forespore C, N terminal<br>The N-terminal domain of 'bypass of forespore C' is composed of a four-stranded beta-sheet covered by an alpha-helix. The beta-sheet has a beta2-beta1-beta4-beta3 topology, where strands beta1 and beta2 and strands beta3 and beta4 are connected by beta-turns, whereas strands beta2 and beta3 are joined by an alpha-helix that runs across one face of the beta-sheet. This domain is similar to the third immunoglobulin G-binding domain of protein G from Streptococcus, the latter belonging to a large and diverse group of cell surface-associated proteins that bind to immunoglobulins. It has been hypothesised that this domain may be a mediator of protein-protein interactions involved in proteolytic events at the cell surface  .. 
PF08978 Reoviridae VP9<br>This domain is found in various VP9 viral outer-coat proteins. It has no known function.. 
PF08979 Domain of unknown function (DUF1894)<br>Members of this family have an important role in methanogenesis. They assume an alpha-beta globular structure consisting of six beta-strands and three alpha-helices forming the secondary structural topological arrangement of alpha1-beta1-alpha2-beta2-beta3-beta4-beta5-beta6-alpha3  .. 
PF08980 Domain of unknown function (DUF1883)<br>This domain is found in a set of hypothetical bacterial proteins.. 
PF08982 Domain of unknown function (DUF1857)<br>This domain has no known function. It is found in various hypothetical bacterial and fungal proteins.. 
PF08983 Domain of unknown function (DUF1856)<br>This domain has no known function. It is found in the C-terminal segment of various vasopressin receptors.. 
PF08984 Domain of unknown function (DUF1858)<br>This domain has no known function. It is found in various hypothetical bacterial proteins.. 
PF08985 Domain of unknown function (DUF1888)<br>This domain is found in a set of hypothetical bacterial proteins.. 
PF08986 Domain of unknown function (DUF1889)<br>This domain is found in a set of hypothetical bacterial proteins.. 
PF08987 Protein of unknown function (DUF1892)<br>Members of this family, that are synthesised by Saccharomycetes, adopt a structure consisting of a four-stranded beta-sheet, with strand order beta2-beta1-beta4-beta3, and two alpha-helices, with an overall topology of beta-beta-alpha-beta-beta-alpha. They have no known function  .. 
PF08988 Protein of unknown function (DUF1895)<br>The YscE protein, produced by the pathogen Yersinia, assumes a secondary structure composed of two anti-parallel alpha-helices separated by a flexible loop. The function of this protein is, as yet, unknown  .. 
PF08989 Domain of unknown function (DUF1896)<br>This domain is found in a set of hypothetical bacterial proteins.. 
PF08990 Erythronolide synthase docking<br>The N terminal docking domain found in modular polyketide synthase assumes an alpha-helical structure, wherein two alpha-helices are connected by a short loop. Two such N-terminal domains dimerise to form amphipathic parallel alpha-helical coiled coils: dimerisation is essential for protein function  .. 
PF08991 Domain of unknown function (DUF1903)<br>Members of this family adopt a coiled coil structure, with two antiparallel alpha-helices that are tightly strapped together by two disulfide bridges at each end. The protein sequence shows a cysteine motif, required for the stabilisation of the coiled-coil-like structure. Additional inter-helix hydrophobic contacts impart stability to this scaffold. The precise function of this eukaryotic domain is, as yet, unknown  .. 
PF08992 Quinohemoprotein amine dehydrogenase, gamma subunit<br>Members of this family contain a cross-linked, proteinous quinone cofactor, cysteine tryptophylquinone, which is required for catalysis of the oxidative deamination of a wide range of aliphatic and aromatic amines. The domain assumes a globular secondary structure, with two short alpha-helices having many turns and bends  .. 
PF08993 T4-helicase_N;<br>T4 gene Gp59 loader of gp41 DNA helicase. Bacteriophage T4 gene-59 helicase assembly protein is required for recombination-dependent DNA replication, which is the predominant mode of DNA replication in the late stage of T4 infection. T4 gene-59 helicase assembly protein accelerates the loading of the T4 gene-41 helicase during DNA synthesis by the T4 replication system in vitro. T4 gene-59 helicase assembly protein binds to both T4 gene-41 helicase and T4 gene-32 single-stranded DNA binding protein, and to single and double-stranded DNA. The structure of T4 gene-59 helicase assembly protein reveals a novel alpha-helical bundle fold with two domains of similar size, this being the N-terminal domain that consists of six alpha-helices linked by loop segments and short turns. The surface of the domain contains large regions of exposed hydrophobic residues and clusters of acidic and basic residues. This domain has structural similarity to members of the high-mobility-group (HMG) family of DNA minor groove binding proteins including rat HMG1A and lymphoid enhancer-binding factor, and is required for binding of the helicase to the DNA minor groove  .. 
PF08994 T4-helicase_C;<br>T4 gene Gp59 loader of gp41 DNA helicase C-term. Bacteriophage T4 gene-59 helicase assembly protein is required for recombination-dependent DNA replication, which is the predominant mode of DNA replication in the late stage of T4 infection. T4 gene-59 helicase assembly protein accelerates the loading of the T4 gene-41 helicase during DNA synthesis by the T4 replication system in vitro.  T4 gene-59 helicase assembly protein binds to both T4 gene-41 helicase and T4 gene-32 single-stranded DNA binding protein, and to single and double-stranded DNA. The structure of T4 gene-59 helicase assembly protein reveals a novel alpha-helical bundle fold with two domains of similar size, this being the C-terminal domain that consists of seven alpha-helices with short intervening loops and turns. The surface of the domain contains large regions of exposed hydrophobic residues and clusters of acidic and basic residues. The hydrophobic region on the 'bottom' surface of the domain near the C-terminal helix binds the leading strand DNA, whilst the hydrophobic region on the 'top' surface of the domain lies between the two arms of the fork DNA, allowing for T4 gene 41 helicase binding and assembly into a hexameric complex around the lagging strand  .. 
PF08995 Necrosis inducing protein-1<br>Necrosis inducing protein-1, a fungal avirulence protein produced by plants, consists of two parts containing beta-sheets of two and three anti-parallel strands, respectively. Five intramolecular disulfide bonds, stabilise these parts and their position with respect to each other, providing a high level of stability  .. 
PF08996 DNA Polymerase alpha zinc finger<br>The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. Function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain  .. 
PF08997 Ubiquinol-cytochrome C reductase complex, 6.4kD protein<br>The ubiquinol-cytochrome C reductase complex (cytochrome bc1 complex) is an essential component of the mitochondrial cellular respiratory chain. This family represents the 6.4kD protein, which may be closely linked to the iron-sulphur protein in the complex and function as an iron-sulphur protein binding factor  .. 
PF08998 Bacterial epsilon antitoxin<br>The epsilon antitoxin, produced by various prokaryotes, forms part of a postsegregational killing system which is involved in the initiation of programmed cell death of plasmid-free cells. The protein is folded into a three-helix bundle that directly interacts with the zeta toxin, inactivating it  .. 
PF08999 Surfactant protein C, N terminal propeptide<br>The N-terminal propeptide of surfactant protein C adopts an alpha-helical structure, with turn and extended regions. It's main function is the stabilisation of metastable surfactant protein C (SP-C), since the latter can irreversibly transform from its native alpha-helical structure to beta-sheet aggregates and form amyloid-like fibrils. The correct intracellular trafficking of proSP-C has also been reported to depend on the propeptide  .. 
PF09000 Cytotoxic<br>The cytotoxic domain confers cytotoxic activity to proteins, enabling the formation of nucleolytic breaks in 16S ribosomal RNA. The structure of the domain reveals a highly twisted central beta-sheet elaborated with a short N-terminal alpha-helix  .. 
PF09001 Domain of unknown function (DUF1890)<br>This domain is found in a set of hypothetical archaeal proteins.. 
PF09002 Domain of unknown function (DUF1887)<br>This domain is found in a set of hypothetical bacterial proteins.. 
PF09003 Bacteriophage lambda integrase, N-terminal domain <br>The amino terminal domain of bacteriophage lambda integrase folds into a three-stranded, antiparallel beta-sheet that packs against a C-terminal alpha-helix, adopting a fold that is structurally related to the three-stranded beta-sheet family of DNA-binding domains (which includes the GCC-box DNA-binding domain and the N-terminal domain of Tn916 integrase). This domain is responsible for high-affinity binding to each of the five DNA arm-type sites and is also a context-sensitive modulator of DNA cleavage  .. 
PF09004 Domain of unknown function (DUF1891)<br>This domain is found in a set of hypothetical eukaryotic proteins.. 
PF09005 Domain of unknown function (DUF1897)<br>This domain is found in Psi proteins produced by Drosophila, and in various eukaryotic hypothetical proteins. It has no known function.. 
PF09006 Lung surfactant protein D coiled-coil trimerisation<br>This domain, predominantly found in lung surfactant protein D, forms a triple-helical parallel coiled coil, and mediates trimerisation of the protein  .. 
PF09007 EBP50, C-terminal<br>This C terminal domain allows interaction of EBP50 with FERM (four-point one ERM) domains, resulting in the activation of Ezrin-radixin-moesin (ERM), with subsequent cytoskeletal modulation and cellular growth control  .. 
PF09008 Head binding<br>The head binding domain found in the Phage P22 tailspike protein contains two regular beta-sheets, A and B, oriented nearly perpendicular to each other and composed of five and three strands respectively. The topology of the strands is exclusively antiparallel. The tailspike protein trimerises through this domain, and the direction of the strands with respect to the molecular triad is almost parallel for beta-sheet A, whereas beta-sheet B is perpendicular to the triad, forming a dome-like structure. This domain is dispensable for thermostability and SDS resistance of the intact protein, and its deletion has only minor effects on tailspike folding kinetics  .. 
PF09009 Exotoxin A catalytic<br>Members of this family, which are found in prokaryotic exotoxin A, catalyse the transfer of ADP ribose from nicotinamide adenine dinucleotide (NAD) to elongation factor-2 in eukaryotic cells, with subsequent inhibition of protein synthesis  .. 
PF09010 Anti-Sigma Factor A<br>Anti-sigma factor A is a transcriptional inhibitor that inhibits sigma 70-directed transcription by weakening its interaction with the core of the host's RNA polymerase. It is an all-helical protein, composed of six helical segments and intervening loops and turns, as well as a helix-turn-helix DNA binding motif, although neither free anti-sigma factor nor anti-sigma factor bound to sigma-70 has been shown to interact directly with DNA. In solution, the protein forms a symmetric dimer of small (10.59 kDa) protomers, which are composed of helix and coil regions and are devoid of beta-strand/sheet secondary structural elements  .. 
PF09011 DUF1898;<br>Mistry J, Sammut SJ, Coggill P. This short 71 residue domain is an HMG-box domain. HMG-box domains mediate re-modelling of chromatin-structure. Mammalian HMG-box proteins are of two types: those that are non-sequence-specific DNA-binding proteins with two HMG-box domains and a long highly acidic C-tail; and a diverse group of sequence-specific transcription factor-proteins with either a single HMG-box or up to six copies, and no acidic C-tail  .. 
PF09012 DUF1920; <br>FeoC like transcriptional regulator. This family contains several transcriptional regulators, including FeoC, which contain a HTH motif.  FeoC acts as a [Fe-S] dependant transcriptional repressor  .. 
PF09013 YopH, N-terminal<br>The N-terminal domain of YopH is a compact structure composed of four alpha-helices and two beta-hairpins. Helices alpha-1 and alpha-3 are parallel to each other and antiparallel to helices alpha-2 and alpha-4. This domain targets YopH for secretion from the bacterium and translocation into eukaryotic cells, and has phosphotyrosyl peptide-binding activity, allowing for recognition of p130Cas and paxillin  .. 
PF09014 Beta-2-glycoprotein-1 fifth domain<br>The fifth domain of beta-2-glycoprotein-1 (b2GP-1) is composed of four well-defined anti-parallel beta-strands and two short alpha-helices, as well as a long highly flexible loop. It plays an important role in the binding of b2GP-1 to negatively charged compounds and subsequent capture for binding of anti-b2GP-1 antibodies  .. 
PF09015 NgoMIV restriction enzyme<br>Members of this family are prokaryotic DNA restriction enzymes, exhibiting an alpha/beta structure, with a central region comprising a mixed six-stranded beta-sheet with alpha-helices on each side. A long 'arm' protrudes out of the core of the domain between strands beta2 and beta3 and is mainly involved in the tetramerisation interface of the protein. These restriction enzymes recognise the double-stranded sequence GCCGGC and cleave after G-1  .. 
PF09016 Pas factor saposin fold<br>Members of this family adopt a compact structure comprising five alpha helices. Charged and polar residues are exposed mostly on the surface, while most of the hydrophobic residues are buried inside the hydrophobic core of the helical bundle. The precise function of this domain is unknown, but it is has been shown to induce secretion of periplasmic proteins, especially collagenase  .. 
PF09017 Microbial transglutaminase<br>Microbial transglutaminase (MTG) catalyses an acyl transfer reaction by means of a Cys-Asp diad mechanism, in which the gamma-carboxyamide groups of peptide-bound glutamine residues act as the acyl donors. The MTG molecule forms a single, compact domain belonging to the alpha+beta folding class, containing 11 alpha-helices and 8 beta-strands. The alpha-helices and the beta-strands are concentrated mainly at the amino and carboxyl ends of the polypeptide, respectively. These secondary structures are arranged so that a beta-sheet is surrounded by alpha-helices, which are clustered into three regions  .. 
PF09018 P3 major capsid protein<br>The P3 major capsid protein adopts a 'double-barrel' structure comprising two eight-stranded viral beta-barrels or jelly rolls, each of which contains a 12-residue alpha-helix. This protein then trimerises through a 'trimerisation loop' sequence, and is incorporated within the viral capsid  .. 
PF09019 EcoRII C terminal<br>The C-terminal catalytic domain of the Restriction Endonuclease EcoRII has a restriction endonuclease-like fold with a central five-stranded mixed beta-sheet surrounded on both sides by alpha-helices. It cleaves DNA specifically at single 5' CCWGG sites  .. 
PF09020 YopE, N terminal<br>The N terminal YopE domain targets YopE for secretion from the bacterium and translocation into eukaryotic cells  .. 
PF09021 HutP<br>The HutP protein family regulates the expression of Bacillus 'hut' structural genes by an anti-termination complex, which recognises three UAG triplet units, separated by four non-conserved nucleotides on the RNA terminator region. L-histidine and Mg2+ ions are also required. These proteins exhibit the structural elements of alpha/beta proteins, arranged in the order: alpha-alpha-beta-alpha-alpha-beta-beta-beta in the primary structure, and the four antiparallel beta-strands form a beta-sheet in the order beta1-beta2-beta3-beta4, with two alpha-helices each on the front (alpha1 and alpha2) and at the back (alpha3 and alpha4) of the beta-sheet  .. 
PF09022 Staphostatin A<br>The staphostatin A polypeptide chain folds into a slightly deformed, eight-stranded beta-barrel, with strands beta-4 through beta-8 forming an antiparallel sheet while the N-terminus forms a a psi-loop motif. Members of this family constitute a class of cysteine protease inhibitors distinct in the fold and the mechanism of action from any known inhibitors of these enzymes  .. 
PF09023 Staphostatin B<br>
PF09025 YopR Core<br>The YopR core domain, predominantly found in the Yersinia pestis virulence factor YopR, is composed of five alpha-helices, four of which are arranged in an antiparallel bundle. Little is known about this domain, though it may contribute to the virulence of the protein YopR  .. 
PF09026 Cenp-B_dimeris;<br>Centromere protein B dimerisation domain. The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation  .. 
PF09027 GTPase binding<br>The GTPase binding domain binds to the G protein Cdc42, inhibiting both its intrinsic and stimulated GTPase activity. The domain is largely unstructured in the absence of Cdc42  .. 
PF09028 Mac 1<br>The bacterial protein Mac 1 adopts an alpha/beta fold, with 14 beta strands and 9 alpha helices. The N-terminal domain is made up predominantly of alpha helices, whereas the C-terminal domain consists predominantly of beta sheets. Mac 1 blocks polymorphonuclear opsonophagocytosis, inhibits the production of reactive oxygen species and contains IgG endopeptidase activity  .. 
PF09029 5-aminolevulinate synthase presequence<br>The N terminal presequence domain found in 5-aminolevulinate synthase exists as an amphipathic helix, with a positively charged surface provided by lysine residues and no stable helix at the N-terminus. The domain is essential for the import process by which ALAS is transported into the mitochondria: translocase of the outer membrane (Tom) and translocase of the inner membrane protein complexes appear responsible for recognition and import through the mitochondrial membrane. The protein Tom20 is anchored to the mitochondrial outer membrane, and its interaction with presequences is thought to be the recognition step which allows subsequent import  .. 
PF09030 Creb binding<br>The Creb binding domain assumes a structure comprising of three alpha-helices which pack in a bundle, exposing a hydrophobic groove between alpha-1 and alpha-3 within which complimentary domains found in the protein 'activator for thyroid hormone and retinoid receptors' (ACTR) can dock. Docking of these domains is required for the recruitment of RNA polymerase II and the basal transcription machinery  .. 
PF09032 Siah interacting protein, N terminal <br>The N terminal domain of Siah interacting protein (SIP) adopts a helical hairpin structure with a hydrophobic core stabilised by a classic knobs-and-holes arrangement of side chains contributed by the two amphipathic helices. Little is known about this domain's function, except that it is crucial for interactions with Siah. It has also been hypothesised that SIP can dimerise through this N terminal domain  .. 
PF09033 DNA Fragmentation factor 45kDa, C terminal domain<br>The C terminal domain of DNA Fragmentation factor 45kDa (DFF-C) consists of four alpha-helices, which are folded in a helix-packing arrangement, with alpha-2 and alpha-3 packing against a long C-terminal helix (alpha-4). The main function of this domain is the inhibition of DFF40 by binding to its C-terminal catalytic domain through ionic interactions, thereby inhibiting the fragmentation of DNA in the apoptotic process. In addition to blocking the DNase activity of DFF40, the C-terminal region of DFF45 is also important for the DFF40-specific folding chaperone activity, as demonstrated by the ability of DFF45 to refold DFF40  .. 
PF09034 TRADD, N-terminal domain<br>The N terminal domain of 'Tumour necrosis factor receptor type 1 associated death domain protein' (TRADD) folds into an alpha-beta sandwich with a four-stranded beta sheet and six alpha helices, each forming one layer of the structure. The domain allows docking of TRADD onto 'tumour necrosis factor receptor-associated factor' (TRAF): the binding is at the beta-sandwich domain, away from the coiled-coil domain. Binding ensures the recruitment of cIAPs to the signaling complex, which may be important for direct caspase-8 inhibition and the immediate suppression of apoptosis at the apical point of the cascade  .. 
PF09035 Excisionase from transposon Tn916<br>The phage-encoded excisionase protein Tn916-Xis adopts a winged-helix structure that consists of a three-stranded anti-parallel beta-sheet that packs against a helix-turn-helix (HTH) motif and a third C-terminal alpha-helix. It is encoded for by Tn916, which also codes for the integrase Tn916-Int. The protein interacts with DNA by the insertion of helix alpha-2 into the major groove and the contact of the hairpin that connects strands beta-2 and beta-3 with the adjacent phosphodiester backbone and/or minor groove. Tn916-Xis stimulates phage excision and inhibits viral integration by stabilising distorted DNA structures  .. 
PF09036 Bcr-Abl oncoprotein oligomerisation domain<br>The Bcr-Abl oncoprotein oligomerisation domain consists of a short N-terminal helix (alpha-1), a flexible loop and a long C-terminal helix (alpha-2). Together these form an N-shaped structure, with the loop allowing the two helices to assume a parallel orientation. The monomeric domains associate into a dimer through the formation of an antiparallel coiled coil between the alpha-2 helices and domain swapping of two alpha-1 helices, where one alpha-1 helix swings back and packs against the alpha-2 helix from the second monomer. Two dimers then associate into a tetramer. The oligomerisation domain is essential for the oncogenicity of the Bcr-Abl protein  .. 
PF09037 Stf0 sulphotransferase<br>Members of this family are essential for the biosynthesis of sulpholipid-1 in prokaryotes. They adopt a structure that belongs to the sulphotransferase superfamily, consisting of a single domain with a core four-stranded parallel beta-sheet flanked by alpha-helices  .. 
PF09038 Tumour suppressor p53-binding protein-1 Tudor<br>Members of this family consist of ten beta-strands and a carboxy-terminal alpha-helix. The amino-terminal five beta-strands and the C-terminal five beta-strands adopt folds that are identical to each other. This domain is essential for the recruitment of proteins to double stranded breaks in DNA, which is mediated by interaction with methylated Lys 79 of histone H3  .. 
PF09039 Mu_I-gamma;<br>Mu DNA binding, I gamma subdomain. Members of this family are responsible for binding the DNA attachment sites at each end of the Mu genome. They adopt a secondary structure comprising a four helix bundle tightly packed around a hydrophobic core consisting of aliphatic and aromatic amino acid residues. Helices 1 and 2 are oriented antiparallel to each other. Helix 3 crosses helices 1 and 2 at angles of 60 and 120 degrees, respectively. Excluding the C-terminal helix 4, the fold of the I-gamma subdomain is remarkably similar to that of the homeodomain family of helix-turn-helix DNA-binding proteins, although their amino acid sequences are completely unrelated  .. 
PF09040 Gastric H+/K+-ATPase, N terminal domain<br>Members of this family adopt an alpha-helical conformation under hydrophobic conditions. The domain contains tyrosine residues, phosphorylation of which regulates the function of the ATPase. Additionally, the domain also interacts with various structural proteins, including the spectrin-binding domain of ankyrin III  .. 
PF09041 Aurora-A binding <br>The Aurora-A binding domain binds to two distinct sites on the Aurora kinase: the upstream residues bind at the N-terminal lobe, whilst the downstream residues bind in an alpha-helical conformation between the N- and C-terminal lobes. The two Aurora-A binding motifs are connected by a flexible linker that is variable in length and sequence across species. Binding of the domain results strong activation of Aurora-A and protection from deactivating dephosphorylation by phosphatase PP1  .. 
PF09042 Titin Z<br>The titin Z domain, that recognises and binds to the C-terminal calmodulin-like domain of alpha-actinin-2 (Act-EF34), adopts a helical structure, and binds in a groove formed by the two planes between the helix pairs of Act-EF34. This interaction is essential for sarcomere assembly  .. 
PF09043 D-Lysine 5,6-aminomutase alpha subunit<br>Members of his family are involved in the 1,2 rearrangement of the terminal amino group of DL-lysine and of L-beta-lysine, using adenosylcobalamin (AdoCbl) and pyridoxal-5'-phosphate as cofactors. The structure is predominantly a PLP-binding TIM barrel domain, with several additional alpha-helices and beta-strands at the N and C termini. These helices and strands form an intertwined accessory clamp structure that wraps around the sides of the TIM barrel and extends up toward the Ado ligand of the Cbl cofactor, providing most of the interactions observed between the protein and the Ado ligand of the Cbl, suggesting that its role is mainly in stabilising AdoCbl in the precatalytic resting state  .. 
PF09044 Kp4<br>Members of this fungal family of toxins specifically inhibit voltage-gated calcium channels in mammalian cells. They adopt an alpha/beta-sandwich structure, comprising a five-stranded antiparallel beta-sheet with two antiparallel alpha-helices lying at approximately 45 degrees to these strands  .. 
PF09045 L27_2<br>The L27_2 domain is a protein-protein interaction domain capable of organising scaffold proteins into supramolecular assemblies by formation of heteromeric L27_2 domain complexes. L27_2 domain-mediated protein assemblies have been shown to play essential roles in cellular processes including asymmetric cell division, establishment and maintenance of cell polarity, and clustering of receptors and ion channels. Members of this family form specific heterotetrameric complexes, in which each domain contains three alpha-helices. The two N-terminal helices of each L27_2 domain pack together to form a tight, four-helix bundle in the heterodimer, whilst the third helix of each L27_2 domain forms another four-helix bundle that assembles the two units of the heterodimer into a tetramer  .. 
PF09046 AvrPtoB E3 ubiquitin ligase<br>The E3 ubiquitin ligase domain found in the bacterial protein AvrPtoB inhibits immunity-associated programmed cell death (PCD) when translocated into plant cells, probably by recruiting E2 enzymes and transferring ubiquitin molecules to cellular proteins involved in regulation of PCD and targeting them for degradation. The structure of this domain reveals a globular fold centred on a four-stranded beta-sheet that packs against two helices on one face and has three very extended loops connecting the elements of secondary structure, with remarkable homology to the RING-finger and U-box families of proteins involved in ubiquitin ligase complexes in eukaryotes  .. 
PF09047 MEF2 binding<br>The myocyte enhancer factor-2 (MEF2) binding domain, predominantly found in the calcineurin-binding protein CABIN 1, adopts an amphipathic alpha-helical structure, which allows it to bind a hydrophobic groove on the MEF2S domain, forming a triple-helical interaction. Interaction of this domain with MEF2 causes repression of transcription  .. 
PF09048 Cro<br>Members of this family are involved in the repression of transcription by binding as a homodimer to palindromic DNA operator sites in phage lambda: they repress genes expressed in early phage development and are necessary for the late stage of lytic growth. These proteins have a secondary structure consisting of three alpha-helices and three beta-sheets, and dimerise through interactions between the two antiparallel beta-strands  .. 
PF09049 Stannin transmembrane<br>Members of this family consist of a single highly hydrophobic transmembrane helix that transverses the lipid bilayer at a 20 degree angle with respect to the membrane normal. They contain a conserved cysteine residue (Cys32) that, together with Cys34 found in the stannin unstructured linker domain, constitutes the putative trimethyltin-binding site that resides at the end of the transmembrane domain close to the lipid/solvent interface  .. 
PF09050 Stannin unstructured linker<br>Members of this family are unstructured, acting as connectors of the stannin helical domains. They contain a conserved CXC metal-binding motif and a putative 14-3-3-zeta binding domain. Upon coordinating dimethytin, considerable structural or dynamic changes in the flexible loop region of SNN may take place, recruiting other binding partners such as 14-3-3-zeta, and thereby initiating the apoptotic cascade  .. 
PF09051 Stannin cytoplasmic<br>Members of this family consist of a distorted cytoplasmic helix that is partially absorbed into the plane of the lipid bilayer with a tilt angle of approximately 80 degrees from the membrane normal. They interact with the surface of the lipid bilayer, and contribute to the initiation of the apoptotic cascade on binding of the unstructured linker domain to dimethyltin  .. 
PF09052 Salmonella invasion protein A<br>Salmonella invasion protein A is an actin-binding protein that contributes to host cytoskeletal rearrangements by stimulating actin polymerisation and counteracting F-actin destabilising proteins. Members of this family possess an all-helical fold consisting of eight alpha-helices arranged so that six long, amphipathic helices form a compact fold that surrounds a final, predominantly hydrophobic helix in the middle of the molecule  .. 
PF09053 CagZ<br>CagZ is a 23 kDa protein consisting of a single compact L-shaped domain, composed of seven alpha-helices that run antiparallel to each other. 70% of the residues are in alpha-helix conformation and no beta-sheet is present. CagZ is essential for the translocation of the pathogenic protein CagA into host cells  .. 
PF09055 Nickel-containing superoxide dismutase<br>Nickel containing superoxide dismutase (NiSOD) is a metalloenzyme containing a hexameric assembly of right-handed 4-helix bundles of up-down-up-down topology with an N-terminal His-Cys-X-X-Pro-Cys-Gly-X-Tyr motif that chelates the active site Ni ions. NiSOD catalyses the disproportionation of superoxide to peroxide and molecular oxygen through alternate oxidation and reduction of Ni, protecting cells from the toxic products of aerobic metabolism  .. 
PF09056 Prokaryotic phospholipase A2<br>The prokaryotic phospholipase A2 domain is predominantly found in bacterial and fungal phospholipases, as well as various hypothetical and putative proteins. It enables the liberation of fatty acids and lysophospholipid by hydrolysing the 2-ester bond of 1,2-diacyl-3-sn-phosphoglycerides. The domain adopts an alpha-helical secondary structure, consisting of five alpha-helices and two helical segments  .. 
PF09057 Second Mitochondria-derived Activator of Caspases<br>Second Mitochondria-derived Activator of Caspases promotes apoptosis by activating caspases in the cytochrome c/Apaf-1/caspase-9 pathway, and by opposing the inhibitory activity of inhibitor of apoptosis proteins (XIAP-BIR3). The protein assumes an elongated three-helix bundle structure, and forms a dimer in solution  .. 
PF09058 L27_1<br>The L27 domain is a protein interaction module that exists in a large family of scaffold proteins, functioning as an organisation centre of large protein assemblies required for the establishment and maintenance of cell polarity. L27 domains form specific heterotetrameric complexes, in which each domain contains three alpha-helices  .. 
PF09059 TyeA<br>Members of this family are composed of two pairs of parallel alpha-helices, and interact with the bacterial protein YopN via hydrophobic residues located on the helices. Association of TyeA with the C terminus of YopN is accompanied by conformational changes in both polypeptides that create order out of disorder: the resulting structure then serves as an impediment to type III secretion of YopN  .. 
PF09060 L27_N<br>The L27_N domain plays a role in the biogenesis of tight junctions and in the establishment of cell polarity in epithelial cells. Each L27_N domain consists of three alpha-helices, the first two of which form an antiparallel coiled-coil. Two L27 domains come together to form a four-helical bundle with the antiparallel coiled-coils formed by the first two helices. The third helix of each domain forms another coiled-coil packing at one end of the four-helix bundle, creating a large hydrophobic interface: the hydrophobic interactions are the major force that drives heterodimer formation  .. 
PF09062 PI-PfuI Endonuclease subdomain<br>The endonuclease subdomain, found in the prokaryotic protein ribonucleotide reductase, assumes an alpha-beta-beta-alpha-beta-beta-alpha-alpha topology. The four stranded beta-sheet forms a saddle-shaped surface and assembles together through an interface made of alpha-helices. The presence of 14 basic residues on the surface of the beta-sheets suggests that this large groove may be involved in DNA binding  .. 
PF09063 Phage PP7 coat protein<br>Members of this family form the capsid of P. aeruginosa phage PP7. They adopt a secondary structure consisting of a six stranded beta sheet and an alpha helix  .. 
PF09064 Thrombomodulin like fifth domain, EGF-like<br>Members of this family adopt a fold similar to other EGF domains, with a flat major and a twisted minor beta sheet. Disulphide pairing, however, is not of the usual 1-3, 2-4, 5-6 type; rather 1-2, 3-4, 5-6 pairing is found. Its extended major sheet (strands beta-2 and beta-3 and the connecting loop) projects into thrombin's active site groove. This domain is required for interaction of thrombomodulin with  thrombin, and subsequent activation of protein-C  .. 
PF09065 Haemadin<br>Members of this family adopt a secondary structure consisting of five short beta-strands (beta1-beta5), which are arranged in two antiparallel distorted sheets formed by strands beta1-beta4-beta5 and beta2-beta3 facing each other. This beta-sandwich is stabilised by six enclosed cysteines arranged in a [1-2, 3-5, 4-6] disulphide pairing resulting in a disulphide-rich hydrophobic core that is largely inaccessible to bulk solvent. The close proximity of disulfide bonds [3-5] and [4-6] organises haemadin into four distinct loops. The N-terminal segment of this domain binds to the active site of thrombin, inhibiting it  .. 
PF09066 Beta2-adaptin appendage, C-terminal sub-domain<br>Members of this family adopt a structure consisting of a 5 stranded beta-sheet, flanked by one alpha helix on the outer side, and by two alpha helices on the inner side. This domain is required for binding to clathrin, and its subsequent polymerisation. Furthermore, a hydrophobic patch present in the domain also binds to a subset of D-phi-F/W motif-containing proteins that are bound by the alpha-adaptin appendage domain (epsin, AP180, eps15)  .. 
PF09067 Erythropoietin receptor, ligand binding<br>Members of this family interact with erythropoietin (EPO), with subsequent initiation of the downstream chain of events associated with binding of EPO to the receptor, including EPO-induced erythroblast proliferation and differentiation through induction of the JAK2/STAT5 signaling cascade. The domain adopts a secondary structure composed of a short amino-terminal helix, followed by two beta-sandwich regions  .. 
PF09068 efhand_1; EF_hand_2;<br>
PF09069 efhand_2;<br>
PF09070 PFU (PLAA family ubiquitin binding)<br>Pfam-B_5813 (release 20.0). This domain is found N terminal to Pfam:PF08324 and binds to ubiquitin  .. 
PF09071 Alpha-amylase, C terminal<br>Members of this family, which are found in the prokaryotic protein glycosyltrehalose trehalohydrolase, assume a gamma-crystallin-type fold with a five-stranded anti-parallel beta-sheet that packs against the C-terminal side of a beta-alpha barrel. This domain is common to family 13 glycosidases and typically contains a five to ten strand beta-sheet, however its precise fold varies  .. 
PF09072 Translation machinery associated TMA7<br>TMA7 plays a role in protein translation. Deletions of the TMA7 gene results in altered protein synthesis rates  .. 
PF09073 BUD22<br>BUD22 has been shown in yeast to be a nuclear protein involved in bud-site selection.  It plays a role in positioning the proximal bud pole signal  . More recently it has been shown to be involved in ribosome biogenesis [2,3].. 
PF09074 Mer2<br>Mer2 (Rec107) forms part of a complex  that is required for meiotic double strand DNA break formation.  Mer2 increases in abundance and is phosphorylated during the prophase phase of cell division  . Blocking double strand break formation results in delayed dephosphorylation and dissociation of Mer2 from the chromosome  .. 
PF09075 Heat-stable enterotoxin B, secretory<br>Members of this family assume a helical secondary structure, with two alpha helices forming a disulphide crosslinked alpha-helical hairpin. The disulphide bonds are crucial for the toxic activity of the protein, and are required for maintenance of the tertiary structure, and subsequent interaction with the particulate form of guanylate cyclase, increasing cyclic GMP levels within the host intestinal epithelial cells  .. 
PF09076 Sklp_toxin;<br>Beta/Gamma crystallin. Sammut SJ, Eberhardt R. Members of this family assume a beta-gamma-crystallin fold [1,2], wherein nine beta-strands are connected by loop, and are separated into two sheets, each sheet forming the Greek key motif. The two Greek key motifs face each other in the global topology. The three-dimensional structure of the molecule is a 'sandwich'-shaped beta-barrel structure: hydrophobic side-chains are packed in the large interface area of the beta-sheets. In Streptomyces killer toxin-like protein domain confers a cytocidal effect to the toxin, causing cell death in both budding and fission yeasts, and morphological changes in yeasts and filamentous fungi  .  This family also includes chitin-biding antifungal proteins [2-3].. 
PF09077 Mu B transposition protein, C terminal <br>The C terminal domain of the B transposition protein from Bacteriophage Mu comprises four alpha-helices arranged in a loosely packed bundle, where helix alpha1 runs parallel to alpha3, and anti-parallel to helices alpha2 and alpha4. The domain allows for non-specific binding of Mu to double-stranded DNA, allowing for integration into the bacterial genome, and mediates dimerisation of the protein  .. 
PF09078 CheY binding<br>Members of this family adopt a secondary structure consisting of an open-face beta/alpha sandwich, with four antiparallel beta-strands and two alpha-helices. They bind to a corresponding domain on CheY, with subsequent phosphorylation of the CheY Asp57 residue, and activation of CheY, which then affects flagellar rotation  .. 
PF09079 CDC6, C terminal <br>The C terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity  .. 
PF09080 K cyclin, C terminal<br>Members of this family adopt a secondary structure consisting of a five alpha-helix cyclin fold. Interaction with cyclin dependent kinases (CDKs) at a PSTAIRE sequence motif within the catalytic cleft of CDK results in the regulation of CDK activity  .. 
PF09081 Domain of unknown function (DUF1921)<br>This domain, which is found in a set of prokaryotic amylases, has no known function  .. 
PF09082 Domain of unknown function (DUF1922)<br>Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C-terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown  .. 
PF09083 Domain of unknown function (DUF1923)<br>Members of this family are found in maltosyltransferases, and adopt a secondary structure consisting of eight antiparallel beta-strands, which form an open-sided 'jelly roll' Greek key beta-barrel. Their exact function is, as yet, unknown  .. 
PF09084 NMT1/THI5 like<br>Pfam-B_2797 (release 20.0). This family contains the NMT1 and THI5 proteins.  These proteins are proposed to be required for the biosynthesis of the pyrimidine moiety of thiamine    .  They are regulated by thiamine  .. 
PF09085 Adhesion molecule, immunoglobulin-like<br>Members of this family are found in a set of mucosal cellular adhesion proteins and adopt an immunoglobulin-like beta-sandwich structure, with seven strands arranged in two beta-sheets in a Greek-key topology. They are essential for recruitment of lymphocytes to specific tissues  .. 
PF09086 Domain of unknown function (DUF1924)<br>This domain is found in a set of bacterial proteins, including Cytochrome c-type protein. It is functionally uncharacterised.. 
PF09087 Cyclomaltodextrinase, N-terminal<br>Members of this family assume a beta-sandwich structure composed of the eight antiparallel beta-strands. A ten residue linker is also present at the C-terminal end, which connects the N terminal domain to a distal domain in the protein. This domain participates in oligomerisation of the protein, wherein the N-terminal domain of one subunit contacts the active centre of the other subunit, and is also required for binding of cyclodextrin to substrate  .. 
PF09088 MIF4G like<br>Members of this family are involved in mediating U snRNA export from the nucleus. They adopt a highly helical structure, wherein the polypeptide chain forms a right-handed solenoid. At the tertiary level, the domain is composed of a superhelical arrangement of successive antiparallel pairs of helices  .. 
PF09089 Phage short tail fibre protein gp12, middle domain<br>Members of this family adopt a right-handed triple-stranded beta-helix fold, and are found in the middle of the phage short tail fibre protein gp12  .. 
PF09090 MIF4G like<br>Members of this family are involved in mediating U snRNA export from the nucleus. They adopt a highly helical structure, wherein the polypeptide chain forms a right-handed solenoid. At the tertiary level, the domain is composed of a superhelical arrangement of successive antiparallel pairs of helices  .. 
PF09092 Lyase, N terminal<br>Members of this family are predominantly found in chondroitin ABC lyase I, and adopt a jelly-roll fold topology consisting of a two-layered bent beta-sheet sandwich with one short alpha-helix. The convex beta sheet is composed of five antiparallel strands, whilst the concave beta-sheet contains five antiparallel beta-strands with a loop between two consecutive strands folding back onto the concave surface. This domain is required for binding of the protein to long glycosaminoglycan chains  .. 
PF09093 Lyase, catalytic<br>Members of this family are predominantly found in chondroitin ABC lyase I, and adopt a helical structure, with fifteen alpha-helices which are at least two turns long and several short helical turns. The bulk of the domain is formed by ten alpha-helices forming five hairpin-like pairs and arranged into an incomplete toroid, the (alpha/alpha)5 fold. Additionally, two long and two short alpha-helices at the N terminus of the domain wrap around the toroid. At the C-terminal end of the toroid there is one additional short alpha-helix. This domain is required for degradation of polysaccharides containing 1,4-beta-D-hexosaminyl and 1,3-beta-D-glucoronosyl or 1,3-alpha-L-iduronosyl linkages to disaccharides containing 4-deoxy-beta-D-gluc-4-enuronosyl groups  .. 
PF09094 Domain of unknown function (DUF1925)<br>Members of this family, which are found in a set of prokaryotic transferases, adopt an immunoglobulin/albumin-binding domain-like fold, with a bundle of three alpha-helices. Their function is, as yet, unknown  .. 
PF09095 Domain of unknown function (DUF1926)<br>Members of this family, which are found in a set of prokaryotic transferases, adopt a beta-sandwich fold, in which two layers of anti-parallel beta-sheets are arranged in a nearly parallel fashion. The exact function of this family is, as yet, unknown, however it has been proposed that they may play a role in transglycosylation reactions  .. 
PF09096 Baseplate structural protein, domain 2<br>Members of this family adopt a beta barrel structure with a Greek key topology, which is topologically similar to the FMN-binding split barrel. They are structural component of the viral baseplate, predominantly found in the structural protein gp27  .. 
PF09097 Baseplate structural protein, domain 1<br>Members of this family adopt a beta barrel structure with a Greek key topology, which is topologically similar to the FMN-binding split barrel. They are structural component of the viral baseplate, predominantly found in the structural protein gp27  .. 
PF09098 Quinohemoprotein amine dehydrogenase A, alpha subunit, haem binding<br>Sammut SJ, Eberhardt R. Members of this family are predominantly found in the prokaryotic protein quinohemoprotein amine dehydrogenase. They have a predominantly alpha-helical structure and can be divided into two subdomains, each binding a haem C group via a conserved CXXCH motif [1,2].. 
PF09099 DUF1927;<br>Quinohemoprotein amine dehydrogenase, alpha subunit domain III. Sammut SJ, Eberhardt R. Members of this family, which are predominantly found in the prokaryotic protein quinohemoprotein amine dehydrogenase, adopt an immunoglobulin-like beta-sandwich fold, with seven strands arranged into two beta sheets; the fold is possibly related to the immunoglobulin and/or fibronectin type III superfamilies. The precise function of this domain has not, as yet, been defined [1,2].. 
PF09100 DUF1928;<br>Quinohemoprotein amine dehydrogenase, alpha subunit domain IV. Sammut SJ, Eberhardt R. Members of this family, which are predominantly found in the prokaryotic protein quinohemoprotein amine dehydrogenase, adopt an immunoglobulin-like beta-sandwich fold, with seven strands arranged into two beta sheets; the fold is possibly related to the immunoglobulin and/or fibronectin type III superfamilies. The precise function of this domain has not, as yet, been defined [1,2].. 
PF09101 Exotoxin A binding<br>Members of this family are found in Pseudomonas aeruginosa exotoxin A, and are responsible for binding of the toxin to the alpha-2-macroglobulin receptor, with subsequent internalisation into endosomes. The domain adopts a thirteen-strand antiparallel beta jelly roll topology, which belongs to the Concanavalin A-like lectins/glucanases fold superfamily  .. 
PF09102 Exotoxin A, targeting<br>Members of this family are found in Pseudomonas aeruginosa exotoxin A, and are responsible for transmembrane targeting of the toxin, as well as transmembrane translocation of the catalytic domain into the cytoplasmic compartment. A furin cleavage site is present within the domain: cleavage generates a 37 kDa carboxy-terminal fragment, which includes the enzymatic domain, which is then is translocated into the cytoplasm. The domain adopts a helical structure, with six alpha-helices forming a bundle  .. 
PF09103 BRCA2, oligonucleotide/oligosaccharide-binding, domain 1<br>Members of this family assume an OB fold, which consists of a highly curved five-stranded beta-sheet that closes on itself to form a beta-barrel. OB1 has a shallow groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for weak single strand DNA binding. The domain also binds the 70-amino acid DSS1 (deleted in split-hand/split foot syndrome) protein, which was originally identified as one of three genes that map to a 1.5-Mb locus deleted in an inherited developmental malformation syndrome  .. 
PF09104 BRCA2, oligonucleotide/oligosaccharide-binding, domain 3<br>Members of this family assume an OB fold, which consists of a highly curved five-stranded beta-sheet that closes on itself to form a beta-barrel. OB3 has a pronounced groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for strong ssDNA binding  .. 
PF09105 Elongation factor SelB, winged helix <br>Members of this family adopt a winged-helix fold, with an alpha/beta structure consisting of three alpha-helices and a twisted three-stranded antiparallel beta-sheet, with an alpha-beta-alpha-alpha-beta-beta connectivity. They are involved in both DNA and RNA binding  .. 
PF09106 Elongation factor SelB, winged helix <br>Members of this family adopt a winged-helix fold, with an alpha/beta structure consisting of three alpha-helices and a twisted three-stranded antiparallel beta-sheet, with an alpha-beta-alpha-alpha-beta-beta connectivity. They are involved in both DNA and RNA binding  .. 
PF09107 Elongation factor SelB, winged helix <br>Members of this family adopt a winged-helix fold, with an alpha/beta structure consisting of three alpha-helices and a twisted three-stranded antiparallel beta-sheet, with an alpha-beta-alpha-alpha-beta-beta connectivity. They are involved in both DNA and RNA binding  .. 
PF09108 Switch protein XOL-1, N-terminal<br>Members of this family, which are required for the formation of the active site of the sex-determining protein Xol-1, adopt a secondary structure consisting of five alpha helices and six antiparallel beta sheets, in a beta-alpha-beta-beta-beta-alpha-beta-alpha-alpha-alpha-beta arrangement. The fold of this family is similar to that found in ribosomal protein S5 domain 2-like  .. 
PF09109 Switch protein XOL-1, GHMP-like<br>Members of this family, which are required for the formation of the active site of the sex-determining protein Xol-1, adopt a secondary structure consisting of five alpha helices and seven antiparallel beta sheets, in a beta-alpha-beta-alpha-alpha-alpha-beta-beta-alpha-beta-beta-beta arrangement. The fold of this family is structurally similar to that found in the C-terminal domain of GHMP Kinase  .. 
PF09110 HAND<br>The HAND domain adopts a secondary structure consisting of four alpha helices, three of which (H2, H3, H4) form an L-like configuration. Helix H2 runs antiparallel to helices H3 and H4, packing closely against helix H4, whilst helix H1 reposes in the concave surface formed by these three helices and runs perpendicular to them. The domain confers DNA and nucleosome binding properties to the protein  .. 
PF09111 SLIDE<br>The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (Pfam:PF00249) repeats or homeodomains  .. 
PF09112 PngaseF_N;<br>Peptide-N-glycosidase F, N terminal. Members of this family adopt an eight-stranded antiparallel beta jelly roll configuration, with the beta strands arranged into two sheets. They are similar in topology to many viral capsid proteins, as well as lectins and several glucanases. The domain allows the protein to bind sugars and catalyses the complete removal of N-linked oligosaccharide chains from glycoproteins  .. 
PF09113 PngaseF_C;<br>Peptide-N-glycosidase F, C terminal. Members of this family adopt an eight-stranded antiparallel beta jelly roll configuration, with the beta strands arranged into two sheets. They are similar in topology to many viral capsid proteins, as well as lectins and several glucanases. The domain allows the protein to bind sugars and catalyses the complete removal of N-linked oligosaccharide chains from glycoproteins  .. 
PF09114 Transcription factor MotA, activation domain<br>Members of this family of viral protein domains are implicated in transcriptional activation. They are almost completely alpha-helical, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2  .. 
PF09115 DNA polymerase III, delta subunit, C terminal<br>Members of this family, which are predominantly found in prokaryotic DNA polymerase III, assume an alpha helical structure, with a core of five alpha helices, and an additional small helix. They are essential for the formation of the polymerase clamp loader  .. 
PF09116 gp45 sliding clamp, C terminal<br>Members of this family are essential for the interaction of the gp45 sliding clamp with the corresponding polymerase. They adopt a DNA clamp fold, consisting of two alpha helices and two beta sheets - the fold is duplicated and has internal pseudo two-fold symmetry  .. 
PF09117 MiAMP1<br>MiAMP1 is a highly basic protein from the nut kernel of Macadamia integrifolia which inhibits the growth of several microbial plant pathogens in vitro while having no effect on mammalian or plant cells. It consists of eight beta-strands which are arranged in two Greek key motifs. These Greek key motifs then associate to form a Greek key beta-barrel  .. 
PF09118 Domain of unknown function (DUF1929)<br>Members of this family adopt a secondary structure consisting of a bundle of seven, mostly antiparallel, beta-strands surrounding a hydrophobic core. The 7 strands are arranged in 2 sheets, in a Greek-key topology. Their precise function, has not, as yet, been defined, though they are mostly found in sugar-utilising enzymes, such as galactose oxidase  .. 
PF09119 SicP binding<br>Members of this family bind the chaperone SicP, which is required both to maintain the stability of SptP, as well as to ensure the eventual secretion of the protein. The domain is found in the Salmonella effector protein SptP, which interacts with SicP chaperone dimers mainly through four regions of its chaperone-binding domain. The structure of the SptP-SicP complex contains four molecules of SicP, aligned in a linear fashion and arranged in two sets of tightly bound homodimers that bind two SptP molecules. The SicP homodimers do not interact with each other, but are held together by a molecular interface formed between two SptP molecules. Each SptP molecule is wrapped around by three SicP chaperones (two chaperones from one homodimer and a third one from the opposite homodimer pair)  .. 
PF09121 Tower<br>Members of this family adopt a secondary structure consisting of a pair of long, antiparallel alpha-helices (the stem) that support a three-helix bundle (3HB) at their end. The 3HB contains a helix-turn-helix motif and is similar to the DNA binding domains of the bacterial site-specific recombinases, and of eukaryotic Myb and homeodomain transcription factors. The Tower domain has an important role in the tumour suppressor function of BRCA2, and is essential for appropriate binding of BRCA2 to DNA  .. 
PF09122 Domain of unknown function (DUF1930)<br>Members of this family are found in 3-mercaptopyruvate sulfurtransferase, and have no known function. They adopt a structure consisting of a four-stranded antiparallel beta-sheet and an alpha-helix, arranged in a beta(2)-alpha-beta(2) fashion, and bearing a remarkable structural similarity to the FK506-binding protein class of peptidylprolyl cis/trans-isomerase  .. 
PF09123 Domain of unknown function (DUF1931)<br>Members of this family, which are found in a set of hypothetical bacterial proteins, contain a core of six alpha-helices, where one central helix is surrounded by the other five. The exact function of this family has not, as yet, been determined  .. 
PF09124 T4 recombination endonuclease VII, dimerisation<br>Members of this family, which are predominantly found in Bacteriophage T4 recombination endonuclease VII, adopt a helical secondary structure, with three alpha helices oriented parallel to each other. They mediate dimerisation of the protein, as well as binding to the DNA major groove  .. 
PF09125 Cytochrome C oxidase subunit II, transmembrane<br>Members of this family adopt a tertiary structure consisting of two antiparallel transmembrane helices, in a transmembrane helix hairpin fold  .. 
PF09126 Restriction endonuclease NaeI <br>Members of this family adopt a secondary structure consisting of nine alpha-helices, six 3-10 helices and 13 beta-strands. They bind two GCC-CGG recognition sequences to cleave DNA into blunt-ended products  .. 
PF09127 Leukotriene A4 hydrolase, C-terminal<br>Members of this family adopt a structure consisting of two layers of parallel alpha-helices, five in the inner layer and four in the outer, arranged in an antiparallel manner, with perpendicular loops containing short helical segments on top. They are required for the formation of a deep cleft harbouring the catalytic Zn2+ site in Leukotriene A4 hydrolase  .. 
PF09128 Regulator of G protein signalling-like domain<br>Members of this family adopt a structure consisting of twelve helices that fold into a compact domain that contains the overall structural scaffold observed in other RGS proteins and three additional helical elements that pack closely to it. Helices 1-9 comprise the RGS (Pfam:PF00615) fold, in which helices 4-7 form a classic antiparallel bundle adjacent to the other helices. Like other RGS structures, helices 7 and 8 span the length of the folded domain and form essentially one continuous helix with a kink in the middle. Helices 10-12 form an apparently stable C-terminal extension of the structural domain, and although other RGS proteins lack this structure, these elements are intimately associated with the rest of the structural framework by hydrophobic interactions. Members of the family bind to active G-alpha proteins, promoting GTP hydrolysis by the alpha subunit of heterotrimeric G proteins, thereby inactivating the G protein and rapidly switching off G protein-coupled receptor signalling pathways  .. 
PF09129 Cholesterol oxidase, substrate-binding<br>The substrate-binding domain found in Cholesterol oxidase is composed of an eight-stranded mixed beta-pleated sheet and six alpha-helices. This domain is positioned over the isoalloxazine ring system of the FAD cofactor bound by FAD_binding_4 (PF:PF01565) and forms the roof of the active site cavity, allowing for catalysis of oxidation and isomerisation of cholesterol to cholest-4-en-3-one  .. 
PF09130 Domain of unknown function (DUF1932)<br>This domain is found in a set of hypothetical prokaryotic proteins. Its exact function has not, as yet, been described.. 
PF09131 Bacillus thuringiensis delta-Endotoxin, middle domain<br>Members of this family adopt a structure consisting of three four-stranded beta-sheets, each with a Greek key fold, with internal pseudo threefold symmetry. Thus they act as a receptor binding beta-prism, binding to insect-specific receptors of gut epithelial cells  .. 
PF09132 BmKX<br>Members of this family assume a structure adopted by most short-chain scorpion toxins, consisting of a cysteine-stabilised alpha/beta scaffold consisting of a short 3-10-helix and a two-stranded antiparallel beta-sheet. They are predominantly found in short-chain scorpion toxins, and their biological method of action has not, as yet, been defined  .. 
PF09133 SANTA (SANT Associated)<br>The SANTA domain (SANT Associated domain) is approximately 90 amino acids in length and is conserved in Eukaryota.  It is sometimes found in association with the SANT domain (Pfam:PF00249, also known as Myb-like DNA-binding domain) implying a putative function in regulating chromatin remodelling  .  Sequence analysis has showed that the SANTA domain is likely to form four central beta-sheets with three flanking alpha- helixes  .  Many conserved hydrophobic residues are present which implying a possible role in protein-protein interactions  .. 
PF09134 Invasin, domain 3<br>Members of this family adopt a structure consisting of an immunoglobulin-like beta-sandwich, with seven strands in two beta-sheets, arranged in a Greek-key topology. It forms part of the extracellular region of the protein, which can be expressed as a soluble protein (Inv497) that binds integrins and promotes subsequent uptake by cells when attached to bacteria  .. 
PF09135 Alb1<br>Alb1 is a nuclear shuttling factor involved in ribosome biogenesis  .. 
PF09136 Glucodextranase, domain B<br>Members of this family adopt a structure consisting of seven/eight-strand antiparallel beta-sheets, in a Greek-key topology, similar to the immunoglobulin beta-sandwich fold. They act as cell wall anchors, where they interact with the S-layer present in the cell wall of Gram-positive bacteria by hydrophobic interactions. In glucodextranase, Domain B is buried in the S-layer, and a flexible linker located between domain B and the catalytic unit confers motion to the catalytic unit, which is capable of efficient hydrolysis of the substrates located close to the cell surface  .. 
PF09137 Glucodextranase, domain N<br>Members of this family, which are uniquely found in bacterial and archaeal glucoamylases and glucodextranases, adopt a structure consisting of 17 antiparallel beta-strands. These beta-strands are divided into two beta-sheets, and one of the beta-sheets is wrapped by an extended polypeptide, which appears to stabilise the domain. Members of this family are mainly concerned with catalytic activity, hydrolysing alpha-1,6-glucosidic linkages of dextran to release beta-D-glucose from the non-reducing end via an inverting reaction mechanism  .. 
PF09138 Urm1 (Ubiquitin related modifier)<br>Pfam-B_16507 (release 20.0). Urm1 is a ubiquitin related protein that modifies proteins in the yeast ubiquitin-like pathway urmylation  . Structural comparisons and phylogenetic analysis of the ubiquitin superfamily has indicated that Urm1 has the most conserved structural and sequence features of the common ancestor of the entire superfamily  .. 
PF09139 Mitochondrial matrix Mmp37<br>Pfam-B_15301 (release 20.0). MMp37 is a mitochondrial matrix protein that functions in the translocation of proteins across the mitochondrial inner membrane  . It has been shown that MMP37 proteins possess the NTase fold but they have only one active site carboxylate and thus probably are not able to carry out enzymatic reaction. These potentially non-active members of NTase fold superfamily may bind ATP, hydrolysis of which is necessary for the translocation of proteins through the membrane  .. 
PF09140 ATPase MipZ<br>Mistry J, Thanbichler M. Pfam-B_23525 (release 20.0). MipZ is an ATPase that forms a complex with the chromosome partitioning protein ParB near the chromosomal origin of replication  .  It is responsible for the temporal and spatial regulation of FtsZ ring formation  .. 
PF09141 Talin, middle domain<br>Members of this family adopt a structure consisting of five alpha helices that fold into a bundle. They contain a Vinculin binding site (VBS) composed of a hydrophobic surface spanning five turns of helix four. Activation of the VBS causes subsequent recruitment of Vinculin, which enables maturation of small integrin/talin complexes into more stable adhesions. Formation of the complex between VBS and Vinculin requires prior unfolding of this middle domain: once released from the talin hydrophobic core, the VBS helix is then available to induce the 'bundle conversion' conformational change within the vinculin head domain thereby displacing the intramolecular interaction with the vinculin tail, allowing vinculin to bind actin  .. 
PF09142 tRNA Pseudouridine synthase II, C terminal<br>The C terminal domain of tRNA Pseudouridine synthase II adopts a PUA (Pfam:PF01472) fold, with a four-stranded mixed beta-sheet flanked by one alpha-helix on each side. It allows for binding of the enzyme to RNA, as well as stabilisation of the RNA molecule  .. 
PF09143 AvrPphF-ORF-2<br>Members of this family of plant pathogenic proteins adopt an elongated structure somewhat reminiscent of a mushroom that can be divided into 'stalk' and 'head' subdomains. The stalk subdomain is composed of the N-terminal helix (alpha1) and beta strands beta3-beta4. An antiparallel beta sheet (beta5, beta7-beta8) forms the base of the head subdomain that interacts with the stalk. A pair of twisted antiparallel beta sheets (beta1 and beta6; beta2 and beta9/9') supported by alpha2 form the dome of the head. The head subdomain possesses weak structural similarity with the catalytic portion of a number of ADP-ribosyltransferase toxins  .. 
PF09144 Yersinia pseudotuberculosis mitogen<br>Members of this family of Yersinia pseudotuberculosis mitogens adopt a sandwich structure consisting of nine strands in two beta sheets, in a jelly-roll topology. As with other superantigens, they are able to excessively activate T cells by binding to the T cell receptor  .. 
PF09145 Ubiquitin-associated<br>Ubiquitin associated domains contain approximately 40 residues and bind ubiquitin noncovalently. They adopt a secondary structure consisting of three alpha-helices, and have been identified in various modular proteins involved in protein trafficking, clathrin assembly/disassembly, DNA repair, proteasomal degradation, and cell cycle regulation  .. 
PF09147 Domain of unknown function (DUF1933)<br>Members of this family are predominantly found in carbapenam synthetase, and are composed of two antiparallel six-stranded beta-sheets that form a sandwich, flanked on each side by two alpha-helices. Their exact function has not, as yet, been determined  .. 
PF09148 Domain of unknown function (DUF1934)<br>Members of this family are found in a set of hypothetical bacterial proteins. Their precise function has not, as yet, been defined.. 
PF09149 Domain of unknown function (DUF1935)<br>Members of this family are found in various bacterial and eukaryotic hypothetical proteins, as well as in the cysteine protease calpain. Their exact function has not, as yet, been defined.. 
PF09150 Orange carotenoid protein, N-terminal <br>Members of this family adopt an alpha-helical structure consisting of two four-helix bundles. They are predominantly found in prokaryotic orange carotenoid protein, and carotenoid binding proteins  .. 
PF09151 Domain of unknown function (DUF1936)<br>This domain is found in a set of hypothetical Archaeal proteins. Its exact function has not, as yet, been defined. It possesses a zinc ribbon fold.. 
PF09152 Domain of unknown function (DUF1937)<br>This domain is found in a set of hypothetical bacterial proteins. Their exact function has not, as yet, been described.. 
PF09153 Domain of unknown function (DUF1938)<br>Members of this family, which are predominantly found in the archaeal protein O6-alkylguanine-DNA alkyltransferase, adopt a secondary structure consisting of a three stranded antiparallel beta-sheet and three alpha helices. Their exact function has not, as yet, been defined, though it has been postulated that they confer thermostability to the archaeal protein  .. 
PF09154 Domain of unknown function (DUF1939)<br>Members of this family, which are predominantly found in Archaeal amylase, adopt a secondary structure consisting of an eight-stranded antiparallel beta-sheet containing a Greek key motif. Their exact function has not, as yet, been determined  .. 
PF09155 Domain of unknown function (DUF1940)<br>Members of this family adopt a secondary structure consisting of six alpha helices, with four long helices (alpha1, alpha2, alpha5, alpha6) form a left-handed, antiparallel alpha helical bundle. The function of this family of Archaeal hypothetical proteins has not, as yet, been defined  .. 
PF09156 Anthrax toxin lethal factor, middle domain<br>Members of this family, which are predominantly found in anthrax toxin lethal factor, adopt a structure consisting of a core of antiparallel beta sheets and alpha helices. They form a long deep groove within the protein that anchors the 16-residue N-terminal tail of MAPKK-2 before cleavage. It has been noted that this domain resembles the ADP-ribosylating toxin from Bacillus cereus, but the active site has been modified to augment substrate recognition  .. 
PF09157 Pseudouridine synthase II TruB, C-terminal<br>Members of this family adopt a secondary structure consisting of a four-stranded beta sheet and one alpha helix. They are predominantly RNA-binding domains, mostly found in Pseudouridine synthase II TruB  .. 
PF09158 Bacteriophage T4 MotA, C-terminal<br>Members of this family adopt a compact alpha/beta structure comprising three alpha-helices and six beta-strands in the order: alpha1-beta1-beta2-beta3-beta4-alpha2-beta5-beta6-alpha3. The beta-strands form a single anti-parallel beta-sheet and the three alpha-helices pack side-by-side onto one surface of the beta-sheet. In this architecture, the domain's hydrophobic core is at the sheet-helix interface, and the second surface of the beta-sheet is completely exposed. The domain is a DNA-binding motif, with a consensus sequence containing nine base pairs (5'-TTTGCTTTA-3'), that appears to bind to various mot boxes, allowing access to the minor groove towards the 5'-end of this sequence and the major groove towards the 3'-end  .. 
PF09159 Mitochondrial resolvase Ydc2 / RNA splicing MRS1<br>Members of this family adopt a secondary structure consisting of two beta sheets and one alpha helix, arranged as a beta-alpha-beta motif.  Each beta sheet has five strands, arranged in a 32145 order, with the second strand being antiparallel to the rest. Mitochondrial resolvase Ydc2 is capable of resolving Holliday junctions and cleaves DNA after 5'-CT-3' and 5'-TT-3' sequences  .  This family also contains the mitochondrial RNA-splicing protein MRS1 which is involved in the excision of group I introns [2-3].. 
PF09160 FimH, mannose binding<br>Members of this family adopt a secondary structure consisting of a beta sandwich, with nine strands arranged in two sheets in a Greek key topology. They are predominantly found in bacterial mannose-specific adhesins, since they are capable of binding to D-mannose  .. 
PF09162 Tap, RNA-binding<br>Members of this family adopt a structure consisting of an alpha+beta sandwich with an antiparallel beta-sheet, arranged in a 2(beta-alpha-beta) motif. They are mainly found in mRNA export factors, and mediate the sequence nonspecific nuclear export of cellular mRNAs as well as the sequence-specific export of retroviral mRNAs bearing the constitutive transport element  .. 
PF09163 Formate dehydrogenase N, transmembrane<br>Members of this family are predominantly found in the beta subunit of formate dehydrogenase, and consist of a single transmembrane helix. They act as a transmembrane anchor, and allow for conduction of electrons within the protein  .. 
PF09164 Vitamin D binding protein, domain III<br>Members of this family are predominantly found in Vitamin D binding protein, and adopt a multihelical structure. They are required for formation of an actin 'clamp', allowing the protein to bind to actin  .. 
PF09165 Ubiquinol-cytochrome c reductase 8 kDa, N-terminal<br>Members of this family adopt a structure consisting of many antiparallel beta sheets, with few alpha helices, in a non-globular arrangement. They are required for proper functioning of the respiratory chain  .. 
PF09166 Biliverdin reductase, catalytic<br>Members of this family adopt a structure consisting of four alpha helices and six beta sheets, in an alpha-beta-alpha-alpha-alpha-beta-beta-beta-beta-beta arrangement. They contain a catalytic active site, capable of reducing the gamma-methene bridge of the open tetrapyrrole, biliverdin IX alpha, to bilirubin with the concomitant oxidation of a NADH or NADPH cofactor  .. 
PF09167 Domain of unknown function (DUF1942)<br>Members of this family of bacterial proteins assume a beta-sandwich structure consisting of two antiparallel beta-sheets similar to an immunoglobulin-like fold, with an additional small, antiparallel beta-sheet. The longer-stranded beta-sheet is made up of four antiparallel beta-strands. The shorter-stranded beta-sheet consists of five beta-strands, four of these beta-strands form an antiparallel beta-sheet. The exact function of this family of proteins is unkown, though a putative role includes involvement in host-bacterial interactions involved in endocytosis or phagocytosis, possibly during bacterial internalisation  .. 
PF09168 X-Prolyl dipeptidyl aminopeptidase PepX, N-terminal<br>Members of this family adopt a secondary structure consisting of a helical bundle of eight alpha helices and three beta strands, the last alpha helix connecting to the first strand of the catalytic domain. The first strand of the N-terminus also forms a small parallel beta sheet with strand 5' of catalytic domain. The domain mediates dimerisation of the protein, with two proline residues present in the domain being critical for interaction  .. 
PF09169 BRCA2, helical<br>Members of this family adopt a helical structure, consisting of a four-helix cluster core (alpha 1, alpha 8, alpha 9, alpha 10) and two successive beta-hairpins (beta 1 to beta 4). An approx. 50-amino acid segment that contains four short helices (alpha 2 to alpha 4), meanders around the surface of the core structure. In BRCA2, the alpha 9 and alpha 10 helices pack with BRCA-2_OB1 (Pfam:PF09103) through van der Waals contacts involving hydrophobic and aromatic residues, and also through side-chain and backbone hydrogen bonds. The domain binds the 70-amino acid DSS1 (deleted in split-hand/split foot syndrome) protein, which was originally identified as one of three genes that map to a 1.5-Mb locus deleted in an inherited developmental malformation syndrome  .. 
PF09170 DUF1879;<br>CST, Suppressor of cdc thirteen homolog, complex subunit STN1. STN1 is a component of the CST complex, a complex that binds to single-stranded DNA and is required for protecting telomeres from DNA degradation. The CST complex binds single-stranded DNA with high affinity in a sequence-independent manner, while isolated subunits bind DNA with low affinity on their own. In addition to telomere protection, the CST complex probably has a more general role in DNA metabolism at non-telomeric sites.. 
PF09171 Domain of unknown function (DUF1886)<br>This domain is predominantly found in the Archaeal protein N-glycosylase/DNA lyase.. 
PF09172 Domain of unknown function (DUF1943)<br>Members of this family adopt a structure consisting of several large open beta-sheets. Their exact function has not, as yet, been determined  .. 
PF09173 Initiation factor eIF2 gamma, C terminal<br>Members of this family, which are found in the initiation factors eIF2 and EF-Tu, adopt a structure consisting of a beta barrel with Greek key topology. They are required for formation of the ternary complex with GTP and initiator tRNA  .. 
PF09174 Maf1 regulator<br>Maf1 is a negative regulator of RNA polymerase III   .  It targets the initiation factor TFIIIB  .. 
PF09175 Domain of unknown function (DUF1944)<br>Members of this family adopt a structure consisting of several large open beta-sheets. Their exact function has not, as yet, been determined  .. 
PF09176 Methylene-tetrahydromethanopterin dehydrogenase, N-terminal<br>Members of this family adopt a alpha-beta structure, with a core comprising three alpha/beta/alpha layers, in which each sheet contains four strands. They are predominantly found in prokaryotic methylene-tetrahydromethanopterin dehydrogenase, which catalyses the dehydrogenation of methylene-tetrahydromethanopterin and the reversible dehydrogenation of methylene-H(4)F  .. 
PF09177 Syntaxin 6, N-terminal<br>Members of this family, which are found in the amino terminus of various SNARE proteins, adopt a structure consisting of an antiparallel three-helix bundle. Their exact function has not been determined, though it is known that they regulate the SNARE motif, as well as mediate various protein-protein interactions involved in membrane-transport  .. 
PF09178 Domain of unknown function (DUF1945)<br>Members of this family, which are predominantly found in prokaryotic 4-alpha-glucanotransferase, adopt a structure composed of six antiparallel beta-strands, four of which form a beta-sheet and another two form a type I' beta-hairpin. The role of this family of domains, has not, as yet, been defined  .. 
PF09179 DUF1946; <br>TilS substrate binding domain. This domain is found in the tRNA(Ile) lysidine synthetase (TilS) protein.. 
PF09180 Prolyl-tRNA synthetase, C-terminal<br>Members of this family are predominantly found in prokaryotic prolyl-tRNA synthetase. They contain a zinc binding site, and adopt a structure consisting of alpha helices and antiparallel beta sheets arranged in 2 layers, in a beta-alpha-beta-alpha-beta motif  .. 
PF09181 Prolyl-tRNA synthetase, C-terminal<br>Members of this family are predominantly found in prokaryotic prolyl-tRNA synthetase. They contain a zinc binding site, and adopt a structure consisting of alpha helices and antiparallel beta sheets arranged in 2 layers, in a beta-alpha-beta-alpha-beta motif  .. 
PF09182 Bacterial purine repressor, N-terminal<br>
PF09183 Domain of unknown function (DUF1947)<br>Members of this family are found in a set of hypothetical Archaeal proteins. Their exact function has not, as yet, been defined.. 
PF09184 PPP4R2<br>PPP4R2 (protein phosphatase 4 core regulatory subunit R2) is the regulatory subunit of the histone H2A phosphatase complex.  It has been shown to confer resistance to the anticancer drug cisplatin in yeast  , and may confer resistance in higher eukaryotes.. 
PF09185 Domain of unknown function (DUF1948)<br>Members of this family of Mycoplasma hypothetical proteins adopt a helical structure, with one central alpha-helix surrounded by five others, in a NusB-like fold. Their function has not, as yet, been determined  .. 
PF09186 Domain of unknown function (DUF1949)<br>Members of this family pertain to a set of functionally uncharacterised hypothetical bacterial proteins. They adopt a ferredoxin-like fold, with a beta-alpha-beta-beta-alpha-beta arrangement  .. 
PF09187 Domain of unknown function(DUF1950)<br>Members of this family pertain to a set of functionally uncharacterised hypothetical eukaryotic proteins  .. 
PF09188 Domain of unknown function (DUF1951)<br>Members of this family of Mycoplasma hypothetical proteins adopt a helical structure, with a buried central helix. Their function has not, as yet, been determined.. 
PF09189 Domain of unknown function (DUF1952)<br>Members of this family are found in various Thermus thermophilus proteins. Their exact function has not, as yet, been determined.. 
PF09190 DALR domain<br>This DALR domain is found in cysteinyl-tRNA-synthetases  .. 
PF09191 CD4, extracellular<br>Members of this family adopt an immunoglobulin-like beta-sandwich, with seven strands in 2 beta sheets, in a Greek key topology. They are predominantly found in the extracellular portion of CD4 proteins, where they enable interaction with major histocompatibility complex class II antigens  .. 
PF09192 Actin-fragmin kinase, catalytic<br>Members of this family assume a secondary structure consisting of eight beta strands and 11 alpha-helices, organised in two lobes. They are predominantly found in actin-fragmin kinase, where they act as a catalytic domain that mediates the phosphorylation of actin  .. 
PF09193 Cholecystokinin A receptor, N-terminal<br>Members of this family are found in the extracellular region of the cholecystokinin A receptor, where they adopt a tertiary structure consisting of a few helical turns and a disulphide-crosslinked loop. They are required for interaction of the cholecystokinin A receptor with it's corresponding hormonal ligand  .. 
PF09194 Restriction endonuclease BsobI<br>Members of this family of prokaryotic restriction endonucleases recognise the double-stranded sequence CYCGRG (where Y = T/C, and R = A/G) and cleave after C-1. They catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates  .. 
PF09195 Restriction endonuclease BglII<br>Members of this family are predominantly found in prokaryotic restriction endonuclease BglII, and adopt a structure consisting of an alpha/beta core containing a six-stranded beta-sheet surrounded by five alpha-helices, two of which are involved in homodimerisation of the endonuclease. They recognise the double-stranded DNA sequence AGATCT and cleave after A-1, resulting in specific double-stranded fragments with terminal 5'-phosphates  .. 
PF09196 Domain of unknown function (DUF1953)<br>This domain is found in the Archaeal protein maltooligosyl trehalose synthase produced by Sulfolobus spp. Its function has not, as yet, been defined.. 
PF09197 Rap1, DNA-binding<br>Members of this family, which are predominantly found in the yeast protein rap1, assume a secondary structure consisting of a three-helix bundle and an N-terminal arm. They contain an Arg-Asp-Arg-Lys sequence that interacts with an ACACC region in the 3' region of the DNA-binding site  .. 
PF09198 Bacteriophage T4 beta-glucosyltransferase<br>Members of this family are DNA-modifying enzymes encoded by bacteriophage T4 that transfer glucose from uridine diphosphoglucose to 5-hydroxymethyl cytosine bases of phage T4 DNA  .. 
PF09199 Domain of unknown function (DUF1954)<br>Members of this family are found in various staphylococcal toxins, and adopt an OB fold, wherein the domain folds into a five-stranded beta-barrel. The exact manner in which they confer pathogenic properties to the protein has not, as yet, been determined  .. 
PF09200 Monellin<br>Monellin, a protein produced by the West African plant Dioscoreophyllum cumminsii, is approximately 70,000 times sweeter than sucrose on a molar basis. The protein adopts an alpha-beta structure, with a cystatin-like fold, where each helix packs against a coiled antiparallel beta-sheet  .. 
PF09201 SRX<br>Members of this family, which are predominantly found in eukaryotic signal recognition particle receptor alpha, consist of a central six-stranded anti-parallel beta-sheet sandwiched by helix alpha1 on one side and helices alpha2-alpha4 on the other. They interact with the small GTPase SR-beta, forming a complex that matches a class of small G protein-effector complexes, including Rap-Raf, Ras-PI3K(gamma), Ras-RalGDS, and Arl2-PDE(delta)  .. 
PF09202 Rio2, N-terminal<br>Members of this family are found in Rio2, and are structurally homologous to the winged helix (wHTH) domain. They adopt a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains  .. 
PF09203 MspA<br>MspA is a membrane porin produced by Mycobacteria, allowing hydrophilic nutrients to enter the bacterium. The protein forms a tightly interconnected octamer with eightfold rotation symmetry that resembles a goblet and contains a central channel. Each subunit fold contains a beta-sandwich of Ig-like topology and a beta-ribbon arm that forms an oligomeric transmembrane barrel  .. 
PF09204 ColicinD;<br>Bacterial self-protective colicin-like immunity. Colicin D, which is synthesised by various prokaryotes, adopts an antiparallel four helical bundle fold: the helices are tightly packed, forming a compact cylindrical molecule. The protein specifically cleaves the anticodon loop of all four tRNA-Arg isoacceptors, thereby inactivating prokaryotic protein synthesis and leading to cell death  . This family also contains immunity proteins to klebicins and microcins. Many bacteria produce proteins that destroy their competitors. Colicin D is one such. The immunity proteins are expressed on the same operon as their cognate bacteriocins and protect the expressing bacterium from the effects of its own bacteriocin  .. 
PF09205 Domain of unknown function (DUF1955)<br>Members of this family are found in hypothetical proteins synthesised by the Archaeal organism Sulfolobus. Their exact function has not, as yet, been determined.. 
PF09206 Alpha-L-arabinofuranosidase B, catalytic<br>Members of this family, which are present in fungal alpha-L-arabinofuranosidase B, adopt a beta-sandwich fold similar to that of Concanavalin A-like lectins/glucanase. The beta-sandwich fold consists of two anti-parallel beta-sheets with seven and and six strands, respectively. In addition, there are four helices outside of the beta-strands. The beta-sandwich strands are closely packed and curved with a jelly roll topology, creating a small catalytic pocket. The domain catalyses the hydrolysis of alpha-1,2-, alpha-1,3- and alpha-1,5-L-arabinofuranosidic bonds in L-arabinose-containing hemicelluloses such as arabinoxylan and L-arabinan  .. 
PF09207 Yeast killer toxin<br>Members of this family, which are produced by Williopsis fungi, adopt a secondary structure consisting of eight strands in two beta sheets, in a Greek-key topology  .. 
PF09208 Restriction endonuclease MspI <br>Members of this family of prokaryotic restriction endonucleases recognise the palindromic tetranucleotide sequence 5'-CCGG and cleave between the first and second nucleotides, leaving 2 base 5' overhangs. They fold into an alpha/beta architecture, with a five-stranded mixed beta-sheet sandwiched on both sides by alpha-helices  .. 
PF09209 Domain of unknown function (DUF1956)<br>Members of this family are found in various prokaryotic transcriptional regulator proteins. Their exact function has not, as yet, been identified.. 
PF09210 Domain of unknown function (DUF1957)<br>This domain is found in a set of hypothetical bacterial proteins. Its exact function has not, as yet, been defined.. 
PF09211 Domain of unknown function (DUF1958)<br>Members of this functionally uncharacterised family are found in prokaryotic penicillin-binding protein 4.. 
PF09212 Carbohydrate binding module 27<br>Members of this family are carbohydrate binding modules that bind to beta-1, 4-mannooligosaccharides, carob galactomannan, and konjac glucomannan, but not to cellulose (insoluble and soluble) or soluble birchwood xylan. They adopt a beta sandwich structure comprising 13 beta strands with a single, small alpha-helix and a single metal atom  .. 
PF09213 M3<br>Members of this family of viral chemokine binding proteins adopt a structure consisting of two different beta-sandwich domains of partial topological similarity to immunoglobulin-like folds. They bind with the CC-chemokine MCP-1, acting as cytokine decoy receptors  .. 
PF09214 Bacteriophage Prd1, adsorption protein P2<br>Members of this family form a set of bacteriophage adsorption proteins, composed mainly of beta-strands whose complicated topology forms an elongated seahorse-shaped molecule with a distinct head, containing a pseudo-beta propeller structure with approximate 6-fold symmetry, and tail. They are required for the attachment of the phage to the host conjugative DNA transfer complex. This is a poorly understood large transmembrane complex of unknown architecture, with at least 11 different proteins  .. 
PF09215 Bacteriophage T4, Gp8<br>Members of this family of viral baseplate structural proteins adopt a structure consisting of a three-layer beta-sandwich with two finger-like loops containing an alpha-helix at the opposite sides of the sandwich. The two peripheral, five-stranded, antiparallel beta-sheets are stacked against the middle, four-stranded, antiparallel beta-sheet. Attachment of this family of proteins to the baseplate during assembly creates a binding site for subsequent attachment of Gp6  .. 
PF09216 Pfg27<br>Members of this family are essential for gametocytogenesis in Plasmodium falciparum. They contain a fold composed of two pseudo dyad-related repeats of the helix-turn-helix motif, serving as a platform for RNA and Src homology-3 (SH3) binding  .. 
PF09217 Restriction endonuclease EcoRII, N-terminal<br>The N-terminal effector-binding domain of the Restriction Endonuclease EcoRII has a DNA recognition fold, allowing for binding to 5'-CCWGG sequences. It assumes a structure composed of an eight-stranded beta-sheet with the strands in the order of b2, b5, b4, b3, b7, b6, b1 and b8. They are mostly antiparallel to each other except that b3 is parallel to b7. Alternatively, it may also be viewed as consisting of two mini beta-sheets of four antiparallel beta-strands, sheet I from beta-strands b2, b5, b4, b3 and sheet II from strands b7, b6, b1, b8, folded into an open mixed beta-barrel with a novel topology. Sheet I has a simple Greek key motif while sheet II does not  .. 
PF09218 Domain of unknown function (DUF1959)<br>This domain is found in a set of uncharacterised Archaeal hypothetical proteins. Its function has not, as yet, been described.. 
PF09220 L-A virus, major coat protein<br>Members of this family form the major coat protein of the Saccharomyces cerevisiae L-A virus  .. 
PF09221 Bacterioc_AS-48;<br>Bacteriocin class IId cyclical uberolysin-like. Sammut SJ, Coggill P, Eberhardt R. Members of this family are membrane-interacting peptides, produced by Firmicutes that display a broad anti-microbial spectrum against Gram-positive and Gram-negative bacteria. They adopt a helical structure, with four or five alpha helices forming a Saposin-like fold [2,5].  The structure has been found to be cyclical [1, 3, 5]. It should be pointed out that one reference   implies that both circularin A and gassericin A are class V or IIc-type bacteriocins; however we find that these two proteins fall into different Pfam families families, this one and BacteriocIIc_cy, Pfam:PF12173.. 
PF09222 Fimbrial adhesin F17-AG, lectin domain<br>Members of this family are carbohydrate-specific lectin domains found in bacterial fimbrial adhesins. They adopt a compact, elongated structure consisting of a beta-sandwich with two major sheets: one consisting of five long strands in mixed orientations, and a front sheet with four antiparallel strands, forming an immunoglobin-like fold  .. 
PF09223 YodA lipocalin-like domain<br>Members of this family of prokaryotic domains have been identified as part of the response of bacteria to a challenge with the toxic heavy metal cadmium. They are able to bind to cadmium, and ensure its subsequent elimination  .. 
PF09224 Domain of unknown function (DUF1961)<br>Members of this family are found in a set of hypothetical bacterial proteins. Their exact function has not, as yet, been determined.. 
PF09225 Restriction endonuclease PvuII<br>Members of this family are predominantly found in prokaryotic restriction endonuclease PvuII. They recognise the double-stranded DNA sequence 5'-CAGCTG-3' and cleave after G-3, resulting in specific double-stranded fragments with terminal 5'-phosphates  .. 
PF09226 Restriction endonuclease HincII<br>Members of this family of prokaryotic restriction endonucleases recognise the double-stranded sequence 5'-GTYRAC-3' and cleave after Y-3. They catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates  .. 
PF09227 Domain of unknown function (DUF1962)<br>Members of this family of fungal domains are functionally uncharacterised  .. 
PF09228 Prokaryotic Transcriptional repressor TraM<br>Members of this family of transcriptional repressors adopt a T-shaped structure, with a core composed of two antiparallel alpha-helices. These proteins can be divided into two parts, a 'globular head' and an 'elongated tail', and they negatively regulate conjugation and the expression of tra genes by antagonising traR/AAI-dependent activation  .. 
PF09229 Activator of Hsp90 ATPase, N-terminal<br>Members of this family, which are predominantly found in the protein 'Activator of Hsp90 ATPase' adopt a secondary structure consisting of an N-terminal alpha-helix leading into a four-stranded meandering antiparallel beta-sheet, followed by a C-terminal alpha-helix. The two helices are packed together, with the beta-sheet curving around them. They bind to the molecular chaperone HSP82 and stimulate its ATPase activity  .. 
PF09230 DNA fragmentation factor 40 kDa<br>Members of this family of eukaryotic apoptotic proteins induce DNA fragmentation and chromatin condensation during apoptosis  .. 
PF09231 Rice dwarf virus p3<br>Members of this family are core structural proteins found in the double-stranded RNA virus Phytoreovirus. They are large proteins without apparent domain division, with a number of all-alpha regions and one all beta domain near the C-terminal end  .. 
PF09232 Caenorhabditis elegans Her-1<br>Her-1 adopts an all-helical structure with two subdomains: residues 19-80 comprise a left-handed three-helix bundle with an overhand connection between the second and third helices, whilst residues 81-164 comprise a left-handed anti-parallel four-helix bundle in which the first helix consists of four consecutive turns of 3-10-helix. Fourteen Cys are conserved in all known HER-1 sequences and form seven disulfide bonds. The protein dictates male development in Caenorhabditis elegans, probably by playing a direct role in cell signaling during C. elegans sex determination. It also inhibits the function of tra-2a  .. 
PF09233 Restriction endonuclease EcoRV<br>Members of this family of prokaryotic restriction endonucleases recognise the double-stranded sequence 5'-GATATC-3' and cleave after T-3. They catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates  .. 
PF09234 Domain of unknown function (DUF1963)<br>This domain is found in a set of hypothetical bacterial proteins. Its exact function has not, as yet, been described.. 
PF09235 Ste50p, sterile alpha motif<br>The fungal Ste50p SAM domain consists of five helices, which form a compact, globular fold. It is required for mediation of homodimerisation and heterodimerisation (and in some cases oligomerisation) of the protein  .. 
PF09236 Alpha-haemoglobin stabilising protein<br>Alpha-haemoglobin stabilising protein (AHSP) acts a molecular chaperone for free alpha-haemoglobin, preventing the harmful aggregation of alpha-haemoglobin during normal erythroid cell development: it specifically protects free alpha-haemoglobin from precipitation. AHSP adopts a helical secondary structure consisting of an elongated antiparallel three alpha-helix bundle  .. 
PF09237 GAGA factor<br>Members of this family bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence  .. 
PF09238 Interleukin-4 receptor alpha chain, N-terminal<br>Members of this family are related in overall topology to fibronectin type III modules and fold into a sandwich comprising seven antiparallel beta sheets arranged in a three-strand and a four-strand beta-pleated sheet. They are required for binding of interleukin-4 to the receptor alpha chain, which is a crucial event for the generation of a Th2-dominated early immune response  .. 
PF09239 Topoisomerase VI B subunit, transducer<br>Members of this family adopt a structure consisting of a four-stranded beta-sheet backed by three alpha-helices, the last of which is over 50 amino acids long and extends from the body of the protein by several turns. This domain has been proposed to mediate intersubunit communication by structurally transducing signals from the ATP binding and hydrolysis domains to the DNA binding and cleavage domains of the gyrase holoenzyme  .. 
PF09240 Interleukin-6 receptor alpha chain, binding<br>Members of this family adopt a structure consisting of an immunoglobulin-like beta-sandwich, with seven strands in two beta-sheets, in a Greek-key topology. They are required for binding to the cytokine Interleukin-6  .. 
PF09241 Herpesviridae viral cyclin<br>Members of this family of viral cyclins adopt a helical structure consisting of five alpha-helices, with one helix surrounded by the others. They specifically activate CDK6 of host cells to a very high degree  .. 
PF09242 Flavocytochrome c sulphide dehydrogenase, flavin-binding<br>Members of this family adopt a structure consisting of a beta(3,4)-alpha(3) core, and an alpha+beta sandwich. They are required for binding to flavin, and subsequent electron transfer  .. 
PF09243 Mitochondrial small ribosomal subunit Rsm22<br>Pfam-B_8789 (release 20.0). Rsm22 has been identified as a mitochondrial small ribosomal subunit   and is a methyltransferase.  In Schizosaccharomyces pombe, Rsm22 is tandemly fused to Cox11 (a factor required for copper insertion into cytochrome oxidase) and the two proteins are proteolytically cleaved after import into the mitochondria  .. 
PF09244 Domain of unknown function (DUF1964)<br>Members of this family of bacterial domains adopt a beta-sandwich fold, with Greek-key topology. They are C-terminal to the catalytic sucrose phosphorylase beta/alpha barrel domain, and are functionally uncharacterised  .. 
PF09245 Mycoplasma arthritidis-derived mitogen<br>Mycoplasma arthritidis-derived mitogen (MA-Mit) adopts a completely alpha-helical structure consisting of ten alpha helices. It is a superantigen that can activate large fractions of T cells bearing particular TCR V-beta elements. Two MA-Mit molecules form an asymmetric dimer and cross-link two MHC antigens to form a dimerised MA-Mit-MHC complex  .. 
PF09246 PHAT<br>The PHAT (pseudo-HEAT analogous topology) domain assumes a structure consisting of a layer of three parallel helices packed against a layer of two antiparallel helices, into a cylindrical shaped five-helix bundle. It is found in the RNA-binding protein Smaug, where it is essential for high-affinity RNA binding  .. 
PF09247 TATA box-binding protein binding<br>Members of this family adopt a structure consisting of three alpha helices and a beta-hairpin. They bind to TATA box-binding protein (TBP), inhibiting TBP interaction with the TATA element, thereby resulting in shutting down of gene transcription  .. 
PF09248 Domain of unknown function (DUF1965)<br>Members of this family of fungal domains adopt a structure that consists of an alpha/beta motif. Their exact function has not, as yet, been determined  .. 
PF09249 tRNA nucleotidyltransferase, second domain<br>Members of this family adopt a structure consisting of a five helical bundle core. They are predominantly found in Archaeal tRNA nucleotidyltransferase, following the catalytic nucleotidyltransferase domain  .. 
PF09250 Bifunctional DNA primase/polymerase, N-terminal<br>Members of this family adopt a structure consisting of a core of antiparallel beta sheets. They are found in various bacterial hypothetical proteins, and have been shown to harbour both primase and polymerase activities  .. 
PF09251 Salmonella phage P22 tail-spike<br>Members of this family of viral domains adopt a structure consisting of a single-stranded right-handed beta-helix, which in turn is made of parallel beta-strands and short turns. They are required for recognition of the 0-antigenic repeating units of the cell surface, and for subsequent infection of the bacterial cell  .. 
PF09252 Allergen Fel d I-B chain<br>Members of this family of cat allergens adopt a helical structure consisting of eight alpha helices, in a Uteroglobin-like fold. They are one of the most important causes of allergic asthma worldwide  .. 
PF09253 Pollen allergen ole e 6<br>Members of this family consist of two nearly antiparallel alpha-helices, that are connected by a short loop and followed by a long, unstructured C-terminal tail. They are highly allergenic, primarily mediating olive allergy  .. 
PF09254 Restriction endonuclease FokI, C terminal<br>Members of this family are predominantly found in prokaryotic restriction endonuclease FokI, and adopt a structure consisting of an alpha/beta/alpha core containing a five-stranded beta-sheet. They recognise the double-stranded DNA sequence 5'-GGATG-3' and cleave DNA phosphodiester groups 9 base pairs away on this strand and 13 base pairs away on the complementary strand  .. 
PF09255 Caf1 Capsule antigen<br>Members of this family are predominantly found in the F1 capsule antigen Caf1 synthesised by Yersinia bacteria. They adopt a structure consisting of a seven strands arranged in two beta-sheets, in a Greek-key topology, and mediate targeting of the bacterium to sites of infection  .. 
PF09256 BAFF-R, TALL-1 binding<br>Members of this family, which are predominantly found in the tumour necrosis factor receptor superfamily member 13c, BAFF-R, are required for binding to tumour necrosis factor ligand TALL-1  .. 
PF09257 BCMA, TALL-1 binding<br>Members of this family, which are predominantly found in the tumour necrosis factor receptor superfamily member 17, BCMA, are required for binding to tumour necrosis factor ligand TALL-1  .. 
PF09258 EXTL2; <br>Glycosyl transferase family 64 domain. Members of this family catalyse the transfer reaction of N-acetylglucosamine and N-acetylgalactosamine from the respective UDP-sugars to the non-reducing end of [glucuronic acid]beta 1-3[galactose]beta 1-O-naphthalenemethanol, an acceptor substrate analog of the natural common linker of various glycosylaminoglycans. They are also required for the biosynthesis of heparan-sulphate  .. 
PF09259 Fungal immunomodulatory protein Fve<br>Fve is a major fruiting body protein from Flammulina velutipes, a mushroom possessing immunomodulatory activity. It stimulates lymphocyte mitogenesis, suppresses systemic anaphylaxis reactions and oedema, enhances transcription of IL-2, IFN-gamma and TNF-alpha, and haemagglutinates red blood cells. It appears to be a lectin with specificity for complex cell-surface carbohydrates. Fve adopts a tertiary structure consisting of an immunoglobulin-like beta-sandwich, with seven strands arranged in two beta sheets, in a Greek-key topology. It forms a non-covalently linked homodimer containing no Cys, His or Met residues; dimerisation occurs by 3-D domain swapping of the N-terminal helices and is stabilised predominantly by hydrophobic interactions  .. 
PF09260 Domain of unknown function (DUF1966)<br>This domain is found in various fungal alpha-amylase proteins. Its exact function has not, as yet, been defined  .. 
PF09261 Alpha mannosidase, middle domain<br>Members of this family adopt a structure consisting of three alpha helices, in an immunoglobulin/albumin-binding domain-like fold. They are predominantly found in the enzyme alpha-mannosidase  .. 
PF09262 Peroxisome biogenesis factor 1, N-terminal <br>Members of this family adopt a double psi beta-barrel fold, similar in structure to the Cdc48 N-terminal domain. It has been suggested that this domain may be involved in interactions with ubiquitin, ubiquitin-like protein modifiers, or ubiquitin-like domains, such as Ubx. Furthermore, the domain may possess a putative adaptor or substrate binding site, allowing for peroxisomal biogenesis, membrane fusion and protein translocation  .. 
PF09263 Peroxisome biogenesis factor 1, N-terminal <br>Members of this family adopt a Cdc48 domain 2-like fold, with a beta-alpha-beta(3) arrangement. It has been suggested that this domain may be involved in interactions with ubiquitin, ubiquitin-like protein modifiers, or ubiquitin-like domains, such as Ubx. Furthermore, the domain may possess a putative adaptor or substrate binding site, allowing for peroxisomal biogenesis, membrane fusion and protein translocation  .. 
PF09264 Vibrio cholerae sialidase, lectin insertion<br>Members of this family are predominantly found in Vibrio cholerae sialidase, and adopt a beta sandwich structure consisting of 12-14 strands arranged in two beta-sheets. They bind to lectins with high affinity helping to target the protein to sialic acid-rich environments, thereby enhancing the catalytic efficiency of the enzyme  .. 
PF09265 Cytokinin dehydrogenase 1, FAD and cytokinin binding<br>Members of this family adopt an alpha+beta sandwich structure with an antiparallel beta-sheet, in a ferredoxin-like fold. They are predominantly found in plant cytokinin dehydrogenase 1, where they are capable of binding both FAD and cytokinin substrates. The substrate displays a 'plug-into-socket' binding mode that seals the catalytic site and precisely positions the carbon atom undergoing oxidation in close contact with the reactive locus of the flavin  .. 
PF09266 Viral DNA topoisomerase I, N-terminal<br>Members of this family are predominantly found in viral DNA topoisomerase, and assume a beta(2)-alpha-beta-alpha-beta(2) fold, with a left-handed crossover between strands beta2 and beta3  .. 
PF09267 Dictyostelium STAT, coiled coil<br>Members of this family are found in Dictyostelium STAT proteins and adopt a structure consisting of four long alpha-helices, folded into a coiled coil. They are responsible for nuclear export of the protein  .. 
PF09268 Clathrin, heavy-chain linker<br>Members of this family adopt a structure consisting of alpha-alpha superhelix. They are predominantly found in clathrin, where they act as a heavy-chain linker domain  .. 
PF09269 Domain of unknown function (DUF1967)<br>Members of this family contain a four-stranded beta sheet and three alpha helices flanked by an additional beta strand. They are predominantly found in the bacterial GTP-binding protein Obg, and are still functionally uncharacterised  .. 
PF09270 Beta-trefoil;<br>Beta-trefoil DNA-binding domain. Members of this family of DNA binding domains adopt a beta-trefoil fold, that is, a capped beta-barrel with internal pseudo threefold symmetry. In the DNA-binding protein LAG-1, it also is the site of mutually exclusive interactions with NotchIC (and the viral protein EBNA2) and co-repressors (SMRT/N-Cor and CIR)  .. 
PF09271 LAG1, DNA binding<br>Members of this family are found in various eukaryotic hypothetical proteins and in the DNA-binding protein LAG-1. They adopt a beta sandwich structure, with nine strands in two beta-sheets, in a Greek-key topology, and allow for DNA binding  .  This domain is also known as RHR-N (Rel-homology region) as it related to Rel domain proteins.. 
PF09272 Hepsin, SRCR<br>Members of this family form an extracellular domain of the serine protease hepsin. They are formed primarily by three elements of regular secondary structure: a 12-residue alpha helix, a twisted five-stranded antiparallel beta sheet, and a second, two-stranded, antiparallel sheet. The two beta-sheets lie at roughly right angles to each other, with the helix nestled between the two, adopting an SRCR fold. The exact function of this domain has not been identified, though it probably may serve to orient the protease domain or place it in the vicinity of its substrate  .. 
PF09273 Rubisco LSMT substrate-binding<br>Members of this family adopt a multihelical structure, with an irregular array of long and short alpha-helices. They allow binding of the protein to substrate, such as the N-terminal tails of histones H3 and H4 and the large subunit of the Rubisco holoenzyme complex  .. 
PF09274 ParG<br>Members of this family of plasmid partition proteins adopt a ribbon-helix-helix fold, with a core of four alpha-helices. They are an essential component of the DNA partition complex of the multidrug resistance plasmid TP228  .. 
PF09275 Pertussis toxin S4 subunit<br>Members of this family of Bordetella pertussis toxins adopt a structure consisting of an OB fold, with a closed or partly opened beta-barrel in a Greek-key topology  .. 
PF09276 Pertussis toxin S5 subunit <br>Members of this family of Bordetella pertussis toxins adopt a structure consisting of an OB fold, with a closed or partly opened beta-barrel in a Greek-key topology  .. 
PF09277 Erythronolide synthase, docking<br>Members of this family of docking domains are found in prokaryotic erythronolide synthase. They adopt a structure consisting of a bundle of four alpha-helices, and mediate homodimerisation of the protein, stabilising the resulting complex  .. 
PF09278 MerR, DNA binding<br>Members of this family of DNA-binding domains are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold  .. 
PF09279 efhand_like;<br>Phosphoinositide-specific phospholipase C, efhand-like. Members of this family are predominantly found in phosphoinositide-specific phospholipase C. They adopt a structure consisting of a core of four alpha helices, in an EF like fold, and are required for functioning of the enzyme  .. 
PF09280 XPC-binding domain<br>Members of this family adopt a structure consisting of four alpha helices, arranged in an array. They bind specifically and directly to the xeroderma pigmentosum group C protein (XPC) to initiate nucleotide excision repair  .. 
PF09281 Taq polymerase, exonuclease<br>Members of this family are found in prokaryotic Taq DNA polymerase, where they assume a ribonuclease H-like motif. The domain confers 5'-3' exonuclease activity to the polymerase  .. 
PF09282 Mago binding<br>Members of this family adopt a structure consisting of a small globular all-beta-domain, with a three-stranded beta-sheet and a contiguous beta-hairpin. They bind to Mago alpha-helices via extensive electrostatic interactions and at a beta2-beta3 loop via hydrophobic interactions  .. 
PF09284 Rhamnogalacturonase B, N-terminal<br>Members of this family are found in prokaryotic Rhamnogalacturonase B, and adopt a structure consisting of a beta supersandwich, with eighteen strands in two beta-sheets. The exact function of the domain is unknown, but a putative role includes carbohydrate-binding  .. 
PF09285 Elongation factor P, C-terminal<br>Members of this family of nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology  .. 
PF09286 Pro-kumamolisin, activation domain <br>Members of this family are found in various subtilase propeptides, and adopt a ferredoxin-like fold, with an alpha+beta sandwich. Cleavage of the domain results in activation of the peptide  .. 
PF09287 CEP-1, DNA binding<br>Members of this family of DNA-binding domains are found the transcription factor CEP-1. They adopt a beta sandwich structure, with nine strands in two beta-sheets, in a Greek-key topology  .. 
PF09288 Fungal ubiquitin-associated domain <br>Members of this family of ubiquitin binding domains adopt a structure consisting of a three alpha-helix bundle. They are predominantly found in fungal ubiquitin-protein ligases  .. 
PF09289 Follistatin/Osteonectin-like EGF domain<br>Members of this family are predominantly found in osteonectin and follistatin and adopt an EGF-like fold [1,2].. 
PF09290 Prokaryotic acetaldehyde dehydrogenase, dimerisation<br>Members of this family are found in prokaryotic acetaldehyde dehydrogenase (acylating), and adopt a structure consisting of an alpha-beta-alpha-beta(3) core. They mediate dimerisation of the protein  .. 
PF09291 Domain of unknown function (DUF1968)<br>Members of this family are found in mammalian T-cell antigen receptor, and adopt an immunoglobulin-like beta-sandwich fold, with seven strands in two beta-sheets in a Greek-key topology. Their exact function has not, as yet, been determined.. 
PF09292 Endonuclease VIII-like 1, DNA bind<br>Members of this family are predominantly found in Endonuclease VIII-like 1 and adopt a glucocorticoid receptor-like fold. They allow for DNA binding  .. 
PF09293 T4 RNase H, C terminal<br>Members of this family are found in T4 RNaseH ribonuclease, and adopt a SAM domain-like fold, consisting of a bundle of four/five helices. These residues may have a role in providing a docking site for other proteins or enzymes in the replication fork  .. 
PF09294 Interferon-alpha/beta receptor, fibronectin type III<br>Members of this family adopt a secondary structure consisting of seven beta-strands arranged in an immunoglobulin-like beta-sandwich, in a Greek-key topology. They are required for binding to interferon-alpha  .. 
PF09295 ChAPs (Chs5p-Arf1p-binding proteins)<br>Pfam-B_11349 (release 19.0). ChAPs (Chs5p-Arf1p-binding proteins) are required for the export of specialised cargo from the Golgi.\.  They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they form also interactions with each other  .. 
PF09296 NADH pyrophosphatase-like rudimentary NUDIX domain<br>The N-terminal domain in NADH pyrophosphatase, which has a rudiment Nudix fold according to SCOP.. 
PF09297 NADH pyrophosphatase zinc ribbon domain<br>This domain is found in between two duplicated NUDIX domains. It has a zinc ribbon structure.. 
PF09298 DUF1969;<br>Fumarylacetoacetase N-terminal. Sammut SJ, Eberhardt R. The N-terminal domain of fumarylacetoacetate hydrolase is functionally uncharacterised, and adopts a structure consisting of an SH3-like barrel  .. 
PF09299 Mu transposase, C-terminal<br>Members of this family are found in various prokaryotic integrases and transposases. They adopt a beta-barrel structure with Greek-key topology  .. 
PF09300 Tectiviridae, minor capsid<br>Members of this family form the minor capsid protein of various Tectiviridae  .. 
PF09301 Domain of unknown function (DUF1970)<br>Members of this family consist of various uncharacterised viral hypothetical proteins.. 
PF09302 XLF (XRCC4-like factor)<br>Mistry J, Wood V, Hentges P, Doherty A. XLF (also called Cernunnos) interacts with the XRCC4-DNA ligase IV complex to promote DNA non-homologous end-joining.  It directly interacts with the XRCC4-Ligase IV complex and siRNA-mediated downregulation of XLF in human cell lines leads to radio-sensitivity and impaired DNA non-homologous end-joining  .  This family contains Nej1 (non-homologous end-joining factor)  , and Lif1  .. 
PF09303 KCNMB2, ball and chain domain<br>Members of this family are found in the cytoplasmic N-terminus of KCNMB2, the beta-2 subunit of large conductance calcium and voltage-activated potassium channels. They are responsible for the fast inactivation of these channels  .. 
PF09304 Cortexillin I, coiled coil<br>Members of this family are predominantly found in the actin-bundling protein Cortexillin I from Dictyostelium discoideum. They adopt a structure consisting of an 18-heptad-repeat alpha-helical coiled-coil, and are a prerequisite for the assembly of Cortexillin I  .. 
PF09305 TACI, cysteine-rich domain<br>Members of this family are predominantly found in tumour necrosis factor receptor superfamily, member 13b (TACI), and are required for binding to the ligands APRIL and BAFF  .. 
PF09306 Bacteriophage, scaffolding protein<br>Members of this family of scaffolding proteins are produced by various bacteriophages  .. 
PF09307 CLIP, MHC2 interacting<br>Members of this family are found in class II invariant chain-associated peptide (CLIP), and are required for association with class II major histocompatibility complex (MHC) in the MHC class II processing pathway  .. 
PF09308 LuxQ, periplasmic<br>Members of this family constitute the periplasmic sensor domain of the prokaryotic protein LuxQ, and assume a structure consisting of two tandem Per/ARNT/Simple-minded (PAS) folds  .. 
PF09309 FCP1, C-terminal<br>The C-terminal domain of FCP-1 is required for interaction with the carboxy terminal domain of RAP74. Interaction relies extensively on van der Waals contacts between hydrophobic residues situated within alpha-helices in both domains  .. 
PF09310 POU domain, class 2, associating factor 1<br>Members of this family are transcriptional coactivators that specifically associate with either OCT1 or OCT2, through recognition of their POU domains. They are essential for the response of B-cells to antigens and required for the formation of germinal centres  .. 
PF09311 Rabaptin-like protein<br>Members of this family are predominantly found in Rabaptin and allow for binding to the GTPase Rab5. This interaction is necessary and sufficient for Rab5-dependent recruitment of Rabaptin5 to early endosomal membranes  .. 
PF09312 SurA N-terminal domain<br>This domain is found at the N-terminus of the chaperone SurA. It is a helical domain of unknown function. The C-terminus of the SurA protein folds back and forms part of this domain also but is not included in the current alignment.. 
PF09313 Domain of unknown function (DUF1971)<br>Pfam-B_3000 (release 20.0). Members of this family of functionally uncharacterised domains are predominantly found in bacterial Tellurite resistance protein.. 
PF09314 Domain of unknown function (DUF1972)<br>Pfam-B_3020 (release 20.0). Members of this family of functionally uncharacterised domains are found in bacterial glycosyltransferases and rhamnosyltransferases.. 
PF09315 Domain of unknown function (DUF1973)<br>Pfam-B_3022 (release 20.0). Members of his family of functionally uncharacterised domains are found in various eukaryotic calcium-dependent chloride channels.. 
PF09316 C-myb, C-terminal<br>Pfam-B_3027 (release 20.0). Members of this family are predominantly found in the proto-oncogene c-myb and the viral transforming protein myb. Truncation of the domain results in 'activation' of c-myb and subsequent tumourigenesis  .. 
PF09317 Domain of unknown function (DUF1974)<br>Pfam-B_3029 (release 20.0). Members of this family of functionally uncharacterised domains are predominantly found in various prokaryotic acyl-coenzyme a dehydrogenases. . 
PF09318 Domain of unknown function (DUF1975)<br>Pfam-B_3057 (release 20.0). Members of this family of functionally uncharacterised domains are predominantly found in the N-terminal region of various prokaryotic alpha-glucosyltransferases.. 
PF09320 Domain of unknown function (DUF1977)<br>Pfam-B_3043 (release 20.0). Members of this family of functionally uncharacterised domains are predominantly found in dnaj-like proteins.. 
PF09321 Domain of unknown function (DUF1978)<br>Pfam-B_3044 (release 20.0). Members of this family are found in various hypothetical proteins produced by the bacterium Chlamydia pneumoniae. Their exact function has not, as yet, been identified.. 
PF09322 Domain of unknown function (DUF1979)<br>Pfam-B_3053 (release 20.0). Members of this family of functionally uncharacterised domains are found in various Oryza sativa mutator-like transposases.. 
PF09323 Domain of unknown function (DUF1980)<br>Pfam-B_3062 (release 20.0). Members of this family are found in a set of prokaryotic hypothetical proteins. Their exact function, has not, as yet, been defined.. 
PF09324 Domain of unknown function (DUF1981)<br>Pfam-B_3041 (release 20.0). Members of this family of functionally uncharacterised domains are found in various plant and yeast protein transport proteins.. 
PF09325 Vps5 C terminal like<br>Pfam-B_6206 (release 20.0). Vps5 is a sorting nexin that functions in membrane trafficking. This is the C terminal dimerisation domain  .. 
PF09326 Domain of unknown function (DUF1982)<br>Pfam-B_3077 (release 20.0). Members of this family of functionally uncharacterised domains are found in the C-terminal region of various prokaryotic NADH dehydrogenases.. 
PF09327 Domain of unknown function (DUF1983)<br>Pfam-B_3073 (release 20.0). Members of this family of functionally uncharacterised domains are found in various bacteriophage host specificity proteins.. 
PF09328 DUF1984; <br>Domain of unknown function (DUF1984). Pfam-B_3070 (release 20.0). Members of this family of functionally uncharacterised domains are found at the C-terminus of plant phytochelatin synthases.. 
PF09329 Primase zinc finger<br>Pfam-B_9710 (release 20.0). This zinc finger is found in yeast Mcm10 proteins and DnaG-type primases  .. 
PF09330 D-lactate dehydrogenase, membrane binding<br>Members of this family are predominantly found in prokaryotic D-lactate dehydrogenase, forming the cap-membrane-binding domain, which consists of a large seven-stranded antiparallel beta-sheet flanked on both sides by alpha-helices. They allow for membrane association  .. 
PF09331 Domain of unknown function (DUF1985)<br>Pfam-B_3094 (release 20.0). Members of this family of functionally uncharacterised domains are found in a set of Arabidopsis thaliana hypothetical proteins.. 
PF09332 Mcm10 replication factor<br>Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha  .. 
PF09333 ATG C terminal domain<br>Pfam-B_61662 (release 20.0). ATG2 (also known as Apg2) is a peripheral membrane protein.  It functions in both cytoplasm to vacuole targeting and autophagy  .. 
PF09334 tRNA synthetases class I (M)<br>Pfam-B_107 (release 20.0). This family includes methionyl tRNA synthetases.. 
PF09335 SNARE associated Golgi protein<br>This is a family of SNARE associated Golgi proteins.  The yeast member of this family (Swiss:P36164) localises with the t-SNARE Tlg2  .. 
PF09336 Vps4 C terminal oligomerisation domain<br>Pfam-B_8681 (release 20.0). This domain is found at the C terminal of ATPase proteins involved in vacuolar sorting. It forms an alpha helix structure and is required for oligomerisation  .. 
PF09337 His(2)-Cys(2) zinc finger<br>This domain binds to histone upstream activating sequence (UAS) elements that are found in histone gene promoters  .. 
PF09338 Glycine/sarcosine/betaine reductase component B subunits<br>Pfam-B_25756 (release 20.0). This is a family of glycine reductase, sarcosine reductase and betaine reductases.  These enzymes catalyse the following reactions.  sarcosine reductase: Acetyl phosphate + methylamine + thioredoxin disulphide = N-methylglycine + phosphate + thioredoxin Acetyl phosphate + NH(3) + thioredoxin disulphide = glycine + phosphate + thioredoxin. betaine reductase: Acetyl phosphate + trimethylamine + thioredoxin disulphide = N,N,N-trimethylglycine + phosphate + thioredoxin  .. 
PF09339 IclR helix-turn-helix domain<br>Pfam-B_70 (release 18.0). 
PF09340 Histone acetyltransferase subunit NuA4<br>Pfam-B_29415 (release 20.0). The NuA4 histone acetyltransferase (HAT) multisubunit complex is responsible for acetylation of histone H4 and H2A N-terminal tails in yeast  .  NuA4 complexes are highly conserved in eukaryotes and play primary roles in transcription, cellular response to DNA damage, and cell cycle control  .. 
PF09341 Transcription factor Pcc1<br>Pcc1 is a transcription factor that functions in regulating genes involved in cell cycle progression and polarised growth  .. 
PF09342 Domain of unknown function (DUF1986)<br>Mistry J, Rawlings ND. Pfam-B_99782 (release 20.0). This domain is found in serine proteases and is predicted to contain disulphide bonds (see Swiss:P98159).. 
PF09343 CHP2217;<br>Conserved hypothetical protein 2217 (DUF2460). This model represents a family of conserved hypothetical proteins. It is usually (but not always) found in apparent phage-derived regions of bacterial chromosomes.. 
PF09344 CT1975-like protein<br>CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This family is represented by CT1975 of Chlorobium tepidum.. 
PF09345 Domain of unknown function (DUF1987)<br>This family of proteins are functionally uncharacterised.. 
PF09346 DUF1988; <br>SMI1 / KNR4 family (SUKH-1). Proteins in this family are involved in the regulation of 1,3-beta-glucan synthase activity and cell-wall formation   . Genome contextual information showed that SMI1 are primary immunity proteins in bacterial toxin systems  . . 
PF09347 Domain of unknown function (DUF1989)<br>This family of proteins are functionally uncharacterised.. 
PF09348 Domain of unknown function (DUF1990)<br>This family of proteins are functionally uncharacterised.. 
PF09349 DUF1991; <br>The proteins in this family are OHCU decarboxylase - enzymes of the purine catabolism that catalyse the conversion of OHCU into S(+)-allantoin  . This is the third step of the conversion of uric acid (a purine derivative) to allantoin. Step one is catalysed by urate oxidase (Pfam:PF01014) and step two is catalysed by HIUases (Pfam:PF00576).. 
PF09350 Domain of unknown function (DUF1992)<br>This family of proteins are functionally uncharacterised.. 
PF09351 Domain of unknown function (DUF1993)<br>This family of proteins are functionally uncharacterised.. 
PF09353 Domain of unknown function (DUF1995)<br>This family of proteins are functionally uncharacterised.. 
PF09354 HNF3 C-terminal domain<br>This presumed domain is found in the C-terminal region of Hepatocyte Nuclear Factor 3 alpha and beta chains. Its specific function is uncertain. The N-terminal region of this presumed domain contains an EH1 (engrailed homology 1) motif, that is characterised by the FxIxxIL sequence  .. 
PF09355 Phage protein Gp19/Gp15/Gp42<br>This family of proteins are functionally uncharacterised. They are found in a variety of bacteriophage.. 
PF09356 Phage conserved hypothetical protein BR0599<br>This entry describes a family of proteins found almost exclusively in phage or in prophage regions of bacterial genomes, including the phage-like Rhodobacter capsulatus gene transfer agent, which packages DNA. An apparent exception is Wolbachia pipientis wMel, a bacterial endosymbiont of the fruit fly, which has several candidate phage-related genes physically separate from obvious prophage regions.. 
PF09357 RteC protein<br>Human colonic Bacteroides species harbor a family of large conjugative transposons, called tetracycline resistance (Tcr) elements. Activities of these elements are enhanced by pregrowth of bacteria in medium containing tetracycline, indicating that at least some Tcr element genes are regulated by tetracycline. An insertional disruption in the rteC gene abolished self-transfer of the Tcr element to Bacteroides recipients, indicating that the gene was essential for self-transfer  .. 
PF09358 Ubiquitin-activating enzyme e1 C-terminal domain<br>This presumed domain found at the C-terminus of Ubiquitin-activating enzyme e1 proteins is functionally uncharacterised.. 
PF09359 VTC domain<br>This presumed domain is found in the yeast vacuolar transport chaperone proteins VTC2, VTC3 and VTC4. This domain is also found in a variety of bacterial proteins.. 
PF09360 Iron-binding zinc finger CDGSH type<br>The CDGSH-type zinc finger domain binds iron rather than zinc as a redox-active pH-labile 2Fe-2S cluster. The conserved sequence C-X-C-X2-(S/T)-X3-P-X-C-D-G-(S/A/T)-H is a defining feature of this family  . The domain is oriented towards the cytoplasm and is tethered to the mitochondrial membrane by a more N-terminal domain found in higher vertebrates, MitoNEET_N, Pfam:PF10660  . The domain forms a uniquely folded homo-dimer and spans the outer mitochondrial membrane, orienting the iron-binding residues towards the cytoplasm  .. 
PF09361 Phasin protein<br>This entry describes a group of small proteins found associated with inclusions in bacterial cells. Most associate with polyhydroxyalkanoate (PHA) inclusions, the most common of which consist of polyhydroxybutyrate (PHB). These are designated granule-associate proteins or phasins.. 
PF09362 Domain of unknown function (DUF1996)<br>This family of proteins are functionally uncharacterised.. 
PF09363 XFP C-terminal domain<br>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:4.1.2.22  .. 
PF09364 XFP N-terminal domain<br>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:4.1.2.22  . This family is distantly related to transketolases e.g. Pfam:PF02779.. 
PF09365 CHP02453; <br>Conserved hypothetical protein (DUF2461). Members of this family are widely (though sparsely) distributed bacterial proteins, about 230 residues in length. All members have a motif RxxRDxRFxxx[DN]KxxY. The function of this protein family is unknown.. 
PF09366 Protein of unknown function (DUF1997)<br>This family of proteins are functionally uncharacterised.. 
PF09367 CpeS-like protein<br>This family, that includes CpeS proteins, is functionally uncharacterised.. 
PF09368 Sas10_Utp3_C;<br>Sas10 C-terminal domain. Sas10 is an Essential subunit of U3-containing Small Subunit (SSU) processome complex involved in the production of the 18S rRNA and assembly of the small ribosomal subunit.. 
PF09369 Domain of unknown function (DUF1998)<br>This family of proteins are functionally uncharacterised. They are mainly found in helicase proteins so could be RNA binding. This family includes a probable zinc binding motif at its C-terminus.. 
PF09370 TIM-barrel signal transduction protein<br>This domain is likely to have a TIM barrel fold related to IGPS. Although this family of proteins are functionally uncharacterised this domain is found as an N-terminal domain of sigma 54 -dependent transcriptional activators (enhancer-binding proteins) suggesting a potential role in signal recognition/receiving and signal transduction.. 
PF09371 Tex-like protein N-terminal domain<br>This presumed domain is found at the N-terminus of Swiss:Q45388. This protein defines a novel family of prokaryotic transcriptional accessory factors  .. 
PF09372 PRANC domain<br>This presumed domain is found at the C-terminus of a variety of Pox virus proteins. The PRANC (Pox proteins Repeats of ANkyrin - C terminal) domain is also found on its own in some proteins. The function of this domain is unknown, but it appears to be related to the F-box domain and may play a similar role.. 
PF09373 Pseudomurein-binding repeat<br>Pfam-B_12784 (Release 21.0). Methanothermobacter thermautotrophicus is a methanogenic Gram-positive microorganism with a cell wall consisting of pseudomurein. This repeat specifically binds to pseudomurein. This repeat is found at the N terminus of PeiW and PeiP which are pseudomurein binding phage proteins.. 
PF09374 Predicted Peptidoglycan domain<br>Pfam-B_8737 (release 8.0). This family contains a potential peptidoglycan binding domain.. 
PF09375 Imelysin<br>The imelysin peptidase was first identified in Pseudomonas aeruginosa. The active site residues have not been identified. However, His201 and Glu204 are completely conserved in the family and occur in an HXXE motif that is also found in family M14.. 
PF09376 NurA domain<br>This family includes NurA a nuclease exhibiting both single-stranded endonuclease activity and 5'-3' exonuclease activity on single-stranded and double-stranded DNA from the hyperthermophilic archaeon Sulfolobus acidocaldarius  .. 
PF09377 SBDS protein C-terminal domain<br>This family is highly conserved in species ranging from archaea to vertebrates and plants. The family contains several Shwachman-Bodian-Diamond syndrome (SBDS) proteins from both mouse and humans. Shwachman-Diamond syndrome is an autosomal recessive disorder with clinical features that include pancreatic exocrine insufficiency, haematological dysfunction and skeletal abnormalities.  Members of this family play a role in RNA metabolism    .. 
PF09378 HAS barrel domain<br>The HAS barrel is named after HerA-ATP Synthase. In ATP synthases, this domain is implicated in the assembly of the catalytic toroid and docking of accessory subunits, such as the subunit of the ATP synthase complex. Similar roles in docking of the functional partner, the NurA nuclease, and assembly of the HerA toroid complex appear likely for the HAS-barrel of the HerA family  .. 
PF09379 FERM N-terminal domain <br>This domain is the N-terminal ubiquitin-like structural domain of the FERM domain.. 
PF09380 FERM C-terminal PH-like domain<br>Pfam-B_851 (release 2.1). 
PF09381 Outer membrane protein G (OmpG)<br>Porins are channel proteins in the outer membrane of gram negative bacteria which mediate the uptake of molecules required for growth and survival.  Escherichia coli OmpG forms a 14 stranded beta-barrel and in contrast to most porins, appears to function as a monomer  .  The central pore of OmpG is wider than other E. coli porins and it is speculated that it may form a non-specific channel for the transport of larger oligosaccharides  .. 
PF09382 RQC domain<br>Pfam-B_571 (release 21.0). This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure.  The RQC domain, found only in RecQ family enzymes, is a high affinity G4 DNA binding domain  .. 
PF09383 NIL domain<br>Pfam-B_524 (release 21.0). This domain is found at the C-terminus of ABC transporter proteins involved in D-methionine transport as well as a number of ferredoxin-like proteins. This domain is likely to act as a substrate binding domain. The domain has been named after a conserved sequence in some members of the family.. 
PF09384 U3_snoRNA_C;<br>Pfam-B_7112 (release 21.0). U3 snoRNA is ubiquitous in eukaryotes and is required for nucleolar processing of pre-18S ribosomal RNA  . It is a component of the ribosomal small subunit (SSU) processome. UTP15 is needed for optimal pre-ribosomal RNA transcription by RNA polymerase I, together with a subset of U3 proteins required for transcription (t-UTPs)  . This entry represents the C terminal of UTP15, and is found adjacent to WD40 repeats (Pfam:PF00400).. 
PF09385 Histidine kinase N terminal<br>This domain is found at the N terminal of sensor histidine kinase proteins.. 
PF09386 Antitoxin ParD<br>ParD is a plasmid anti-toxin than forms a ribbon-helix-helix DNA binding structure  .  It stabilises plasmids by inhibiting ParE toxicity in cells that express ParD and ParE.  ParD forms a dimer and also regulates its own promoter (parDE).. 
PF09387 Mitochondrial RNA binding protein MRP<br>MRP1 and MRP2 are mitochondrial RNA binding proteins that form a heteromeric complex.  The MRP1/MRP2 heterotetrameric complex binds to guide RNAs and stabilises them in an unfolded conformation suitable for RNA-RNA hybridisation.  Each MRP subunit adopts a 'whirly' transcription factor fold  .. 
PF09388 Spo0E like sporulation regulatory protein<br>Spore formation is an extreme response to starvation and can also be a component of disease transmission.  Sporulation is controlled by an expanded two-component system where starvation signals result in sensor kinase activation and phosphorylation of the master sporulation response regulator Spo0A.  Phosphatases such as Spo0E dephosphorylate Spo0A thereby inhibiting sporulation.  This is a family of Spo0E-like phosphatases.  The structure of a Bacillus anthracis member of this family has revealed an anti-parallel alpha-helical structure  .. 
PF09390 Protein of unknown function (DUF1999)<br>This family contains a putative Fe-S binding reductase (Swiss:Q72J89) whose structure adopts an alpha and beta fold.. 
PF09391 Protein of unknown function (DUF2000)<br>This is a family of proteins of unknown function. The structure of one of the proteins in this family has been shown to adopt an alpha beta fold.. 
PF09392 Type III secretion needle MxiH like<br>Type III secretion systems are essential virulence determinants for many gram-negative bacterial pathogens.  MxiH is an extracellular alpha helical needle that is required for translocation of effector proteins into host cells  .  Once inside, the effector proteins subvert normal cell function to aid infection.. 
PF09393 Protein of unknown function (DUF2001)<br>This family includes phage-like element PBSX protein (Swiss:P54332) whose structure adopts a beta barrel flanked with alpha helical regions.. 
PF09394 Chagasin_I42;<br>Chagasin family peptidase inhibitor I42. Chagasin is a cysteine peptidase inhibitor   which forms a beta barrel structure  .. 
PF09396 Thrombin light chain<br>Thrombin is an enzyme that cleaves bonds after Arg and Lys, converts fibrinogen to fibrin and activates factors V, VII, VIII. Prothrombin is activated on the surface of a phospholipid membrane where factor Xa removes the activation peptide and cleaves the remaining part into light and heavy chains. This domain corresponds to the light chain of thrombin.. 
PF09397 Ftsk gamma domain<br>This domain directs oriented DNA translocation and forms a winged helix structure  .  Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding  .. 
PF09398 FOP N terminal dimerisation domain<br>Fibroblast growth factor receptor 1 (FGFR1) oncogene partner (FOP) is a centrosomal protein that is involved in anchoring microtubules to subcellular structures.  This domain includes a Lis-homology motif.  It forms an alpha helical bundle and is involved in dimerisation  .. 
PF09399 SARS lipid binding protein<br>This is a family of proteins found in SARS coronavirus.  The protein has a novel fold which forms a dimeric tent-like beta structure with an amphipathic surface, and a central hydrophobic cavity that binds lipid molecules  . This cavity is likely to be involved in membrane attachment  .. 
PF09400 Protein of unknown function (DUF2002)<br>This is a family of putative cytoplasmic proteins.  The structure of these proteins form an antiparallel beta and sheet and contain some alpha helical regions.. 
PF09401 RNA synthesis protein NSP10<br>Non-structural protein 10 (NSP10) is involved in RNA synthesis. it is synthesised as a polyprotein whose cleavage generates many non-structural proteins.  NSP10 contains two zinc binding motifs and forms two anti-parallel helices which are stacked against an irregular beta sheet  .\.   A cluster of basic residues on the protein surface suggests a nucleic acid-binding function.. 
PF09402 MAN1_C;<br>Man1-Src1p-C-terminal domain. MAN1 is an integral protein of the inner nuclear membrane which binds to chromatin associated proteins and plays a role in nuclear organisation.  The C terminal nucleoplasmic region forms a DNA binding winged helix and binds to Smad  . This C-terminal tail is also found in S. cerevisiae and is thought to consist of three conserved helices followed by two downstream strands  .. 
PF09403 Adhesion protein FadA<br>FadA (Fusobacterium adhesin A) is an adhesin which forms two alpha helices.. 
PF09404 Eukaryotic protein of unknown function (DUF2003)<br>This is a family of proteins of unknown function which adopt an alpha helical and beta sheet structure.. 
PF09405 CASC3/Barentsz eIF4AIII binding<br>This domain is found on CASC3 (cancer susceptibility candidate gene 3 protein) which is also known as Barentsz (Btz).  CASC3 is a component of the EJC (exon junction complex) which is a complex that is involved in post-transcriptional regulation of mRNA in metazoa.  The complex is formed by the association of four proteins (eIF4AIII, Barentsz, Mago, and Y14), mRNA, and ATP. This domain wraps around eIF4AIII and stacks against the 5' nucleotide   .. 
PF09406 Protein of unknown function (DUF2004)<br>This is a family of proteins with unknown function.  The structure of one of the proteins in this family has revealed a novel alpha-beta fold  .. 
PF09407 Protein of unknown function (DUF2005)<br>This is a family of proteins with unknown function.. 
PF09408 Spike receptor binding domain<br>Spike is an envelope glycoprotein which aids viral entry into the host cell.  This domain corresponds is the immunogenic receptor binding domain of the protein which binds to angiotensin-converting enzyme 2 (ACE2)  .. 
PF09409 PUB domain<br>The PUB (also known as PUG) domain is found in peptide N-glycanase where it functions as a AAA ATPase binding domain  . This domain is also found on other proteins linked to the ubiquitin-proteasome system.. 
PF09411 Lipid A 3-O-deacylase (PagL)<br>PagL is an outer membrane protein with lipid A 3-O-deacylase activity. It forms an 8 stranded beta barrel structure  .. 
PF09412 Endoribonuclease XendoU<br>This is a family of endoribonucleases involved in RNA biosynthesis which has been named XendoU in Xenopus laevis. XendoU is a U-specific metal dependent enzyme that produces products with a 2'-3' cyclic phosphate termini.. 
PF09413 Domain of unknown function (DUF2007)<br>This is a family of proteins with unknown function.. 
PF09414 RNA ligase<br>This is a family of RNA ligases. The enzyme repairs RNA strand breaks in nicked DNA:RNA and RNA:RNA but not in DNA:DNA duplexes.. 
PF09415 DUF2008;<br>CENP-S associating Centromere protein X. The centromere, essential for faithful chromosome segregation during mitosis, has a network of constitutive centromere-associated (CCAN) proteins associating with it during mitosis. So far in vertebrates at least 15 centromere proteins have been identified, which are divided into several subclasses based on functional and biochemical analyses. These provide a platform for the formation of a functional kinetochore during mitosis. CENP-S is one that does not associate with the CENP-H-containing complex but rather interacts with CENP-X to form a stable assembly of outer kinetochore proteins that functions downstream of other components of the CCAN. This complex may directly allow efficient and stable formation of the outer kinetochore on the CCAN platform.. 
PF09416 RNA helicase (UPF2 interacting domain)<br>UPF1 is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation.  This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD)  .. 
PF09418 Protein of unknown function (DUF2009)<br>Pfam-B_18128 (release 21.0). This is a eukaryotic family of proteins with unknown function.. 
PF09419 DUF2010;<br>Mitochondrial PGP phosphatase. Pfam-B_22310 (release 21.0). This is a family of proteins that acts as a mitochondrial phosphatase in cardiolipin biosynthesis. Cardiolipin is a unique dimeric phosphoglycerolipid predominantly present in mitochondrial membranes. The inverted phosphatase motif includes the highly conserved DKD triad  .. 
PF09420 Ribosome biogenesis protein Nop16<br>Pfam-B_6406 (release 21.0). Nop16 is a protein involved in ribosome biogenesis.. 
PF09421 Frequency clock protein<br>The frequency clock protein, is the central component of the frq-based circadian negative feedback loop, regulates various aspects of the circadian clock in Neurospora crassa  . This protein has been shown to interact with itself via a coiled-coil  .. 
PF09422 WTX protein<br>The WTX protein is found to be inactivated in one third of Wilms tumours  . The WTX protein is functionally uncharacterised.. 
PF09423 PhoD-like phosphatase<br>
PF09424 Yqey-like protein<br>The function of this domain found in the YqeY protein is uncertain.. 
PF09425 Divergent CCT motif<br>This short motif is found in a number of plant proteins. It appears to be related to the N-terminal half of the CCT motif. The CCT motif is about 45 amino acids long and contains a putative nuclear localisation signal within the second half of the CCT motif  .. 
PF09426 Vacuolar R-SNARE Nyv1 N terminal<br>Pfam-B_50964 (release 21.0). This domain corresponds to the N terminal domain of vacuolar R-SNARE Nyv1 which adopts a longin fold  .  In yeast it has been shown that this domain is sufficient to direct the transport of Nyv1 to limiting membrane of the vacuole  .. 
PF09427 SREBP_C; <br>Domain of unknown function (DUF2014) . Pfam-B_71890 (release 21.0). This domain is found at the C terminal of a family of ER membrane bound transcription factors called sterol regulatory element binding proteins (SREBP).. 
PF09428 Fungal protein of unknown function (DUF2011)<br>This is a family of fungal proteins whose function is unknown.. 
PF09429 WW domain binding protein 11<br>Pfam-B_13108 (release 21.0). The WW domain is a small protein module with a triple-stranded beta-sheet fold.  This is a family of WW domain binding proteins.. 
PF09430 Protein of unknown function (DUF2012)<br>Pfam-B_49614 (release 21.0). This is a eukaryotic family of uncharacterised proteins.. 
PF09431 Protein of unknown function (DUF2013)<br>Pfam-B_11317 (release 21.0). This region is found at the C terminal of a group of cytoskeletal proteins.. 
PF09432 Tho complex subunit THP2<br>The THO complex plays a role in coupling transcription elongation to mRNA export.  It is composed of subunits THP2, HPR1, THO2 and MFT1  .. 
PF09435 Fungal protein of unknown function (DUF2015)<br>This is a fungal family of uncharacterised proteins.. 
PF09436 Domain of unknown function (DUF2016)<br>A predicted alpha+beta domain that is usually fused N-terminal to the JAB metallopeptidase. This protein in turn is found in conserved gene neighborhoods that include genes encoding the bacterial homologs of the ubiquitin modification system such as the E1, E2 and Ub proteins  . The domain is also known as the JAB-N domain.. 
PF09437 Pombe specific 5TM protein<br>
PF09438 Domain of unknown function (DUF2017)<br>Mistry J, Iyer LM, Burroughs AM, Aravind L. This is an alpha-helical domain found in gene neighborhoods that contain genes encoding ubiquitin, cysteine synthases and JAB  peptidases  .. 
PF09439 Signal recognition particle receptor beta subunit<br>Pfam-B_7840 (release 21.0). The beta subunit of the signal recognition particle receptor (SRP) is a transmembrane GTPase which anchors the alpha subunit to the endoplasmic reticulum membrane  .. 
PF09440 eIF3 subunit 6 N terminal domain<br>Pfam-B_4886 (release 21.0). This is the N terminal domain of subunit 6 translation initiation factor eIF3.. 
PF09441 ARS binding protein 2<br>This DNA-binding protein binds to the autonomously replicating sequence (ARS) binding element. It may play a role in regulating the cell cycle response to stress signals  .. 
PF09442 Domain of unknown function (DUF2018)<br>Acid-adaptive protein possibly of physiological significance when H.pylori colonises the human stomach, which adopts a unique four alpha-helical triangular conformations. The biologically active form is thought to be a tetramer. The protein is expressed along with six other proteins, some of which are related to iron storage and haem biosynthesis  .. 
PF09443 Cripto_Frl-1_Cryptic (CFC)<br>CFC domain is one half of the membrane protein Cripto, a protein overexpressed in many tumours [1,2] and structurally similar to the C-terminal extracellular portions of Jagged 1 and Jagged 2  .  CFC is approx 40-residues long, compacted by three internal disulphide bridges, and binds Alk4 via a hydrophobic patch. CFC is structurally homologous to the VWFC-like domain  .. 
PF09444 MRC1-like domain<br>This putative domain is found to be the most conserved region in mediator of replication checkpoint protein 1.. 
PF09445 RNA cap guanine-N2 methyltransferase<br>Pfam-B_9480 (Release 21.0). RNA cap guanine-N2 methyltransferases such as Schizosaccharomyces pombe Tgs1 and Giardia lamblia Tgs2 catalyse methylation of the exocyclic N2 amine of 7-methylguanosine  .. 
PF09446 VMA21-like domain<br>This presumed short domain appears to contain two potential transmembrane helices. VMA21 is localised in the ER where it is needed as an accessory factor for assembly of the V0 component of the vacuolar ATPase  .. 
PF09447 Cnl2/NKP2 family protein<br>This family includes the Cnl2 kinetochore protein  .. 
PF09448 Methylmuconolactone methyl-isomerase <br>MmlI is a short, approx 115 residue, protein of two alpha helices and four beta strands. It is involved in the catabolism of methyl-substituted aromatics via a modified oxo-adipate pathway in bacteria. The enzyme appears to be monomeric in some species   and tetrameric in others  . The known structure shows two copies of the protein form a dimeric alpha beta barrel.. 
PF09449 Domain of unknown function (DUF2020)<br>Protein of unknown function found in bacteria.. 
PF09450 Domain of unknown function (DUF2019)<br>Protein of unknown function found in bacteria.. 
PF09451 Autophagy-related protein 27<br>
PF09452 ESCRT-I subunit Mvb12<br>The endosomal sorting complex required for transport (ESCRT) complexes play a critical role in receptor down-regulation and retroviral budding. A new component of the ESCRT-I complex was identified  , multivesicular body sorting factor of 12 kD (Mvb12), which binds to the coiled-coil domain of the ESCRT-I subunit vacuolar protein sorting 23 (Vps23)  .. 
PF09453 HIRA B motif<br>The HirA B (Histone regulatory homologue A binding) motif is the essential binding interface between HIRA Pfam:PF07569 and ASF1a, of approx. 40 residues. It forms an antiparallel beta-hairpin that binds perpendicular to the strands of the beta-sandwich of ASF1a N-terminal core domain, via beta-sheet, salt bridge and van der Waals interactions  . The two histone chaperone proteins, HIRA and ASF1a, form a heterodimer with histones H3 and H4. HIRA is the human orthologue of Hir proteins known to silence histone gene expression and create transcriptionally silent heterochromatin in yeast, flies, plants and humans. The yeast CAF1B proteins which bind H3 also carry this motif at their very C-terminus. . 
PF09454 Vps23 core domain<br>ESCRT complexes form the main machinery driving protein sorting from endosomes to lysosomes. The core domain of the Vps23 subunit of the heterotrimeric ESCRT-I complex is a helical hairpin sandwiched in a fan-like formation between two other helical hairpins from Vps28 (Pfam:PF03997) and Vps37. Vps23 gives ESCRT-I complex its stability  .. 
PF09455 CRISPR-associated (Cas) DxTHG family<br>CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins.  The family describes Cas proteins of about 400 residues that include the motif [VIL]-D-x-[ST]-H-[GS]. The CRISPR and associated proteins are thought to be involved in the evolution of host resistance. The exact molecular function of this family is currently unknown.. 
PF09456 RcsC Alpha-Beta-Loop (ABL)<br>This domain is found in the C-terminus of the phospho-relay kinase RcsC between Pfam:PF00512 and Pfam:PF00072, and forms a discrete alpha/beta/loop structure  .. 
PF09457 FIP domain <br>The FIP domain is the Rab11-binding domain (RBD) at the C-terminus of a family of Rab11-interacting proteins (FIPs). The Rab proteins constitute the largest family of small GTPases (>60 members in mammals). Among them Rab11 is a well characterised regulator of endocytic and recycling pathways. Rab11 associates with a broad range of post-Golgi organelles, including recycling endosomes  .. 
PF09458 H-type lectin domain<br>The H-type lectin domain is a unit of six beta chains, combined into a homo-hexamer. It is involved in self/non-self recognition of cells, through binding with carbohydrates  . It is sometimes found in association with the F5_F8_type_C domain Pfam:PF00754.. 
PF09459 Ethylbenzene dehydrogenase<br>Eythylbenzene dehydrogenase is a heterotrimer of three subunits that catalyses the anaerobic degradation of hydrocarbons. The alpha subunit contains the catalytic centre as a Molybdenum cofactor-complex. This removes an electron-pair from the hydrocarbon and passes it along an electron transport system involving iron-sulphur complexes held in the beta subunit and a Haem b molecule contained in the gamma subunit. The electron-pair is then subsequently passed to an as yet unknown receiver  . The enzyme is found in a variety of different bacteria.. 
PF09460 Saf-pilin pilus formation protein<br>This domain consists of the adjacent Saf-Nte and Saf-pilin chains of the pilus-forming complex. Pilus assembly in Gram-negative bacteria involves a Donor-strand exchange mechanism between the C- and the N-termini of this domain. The C-terminal subunit forms an incomplete Ig-fold which is then complemented by the 10-18 residue N-terminus of another, incoming, pilus subunit which is not involved in the Ig-fold. The N-terminus sequences contain a motif of alternating hydrophobic residues that occupy the P2 to P5 binding pockets in the groove of the first pilus subunit  .. 
PF09461 Phytotoxin PcF protein<br>PcF is a 52 residue protein factor of two alpha helices, containing a 4-hydroxyproline and three cysteine bridges. The presence of the hydroxyproline is unique in relation to other fungal phytotoxic proteins. The protein has a high content of acidic side-chains implying a lack of binding with lipid-rich components of membranes and appears to be an extracellular phytotoxin that causes leaf necrosis in strawberries.. 
PF09462 Mus7/MMS22 family<br>This family includes a conserved region from the Mus7 protein  . Mus7 is involved in the repair of replication-associated DNA damage in the fission yeast Schizosaccharomyces pombe. Mus7 functions in the same pathway as Mus81, a subunit of the Mus81-Eme1 structure-specific endonuclease, which has been implicated in the repair of the replication-associated DNA damage  . The MMS22 proteins are involved in repairing double-stranded DNA breaks created by the cleavage reaction of topoisomerase II  .. 
PF09463 Opy2 protein<br>Opy2p acts as a membrane anchor in the HOG signalling pathway  .. 
PF09465 Lamin-B receptor of TUDOR domain<br>The Lamin-B receptor, found on the TUDOR domain Pfam:PF00567, is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner Nuclear Envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with Importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the NE  .. 
PF09466 Hypothetical protein Yqai<br>This hypothetical protein is expressed in bacteria, particularly Bacillus subtilis. It forms a homo-dimer, with each monomer containing an alpha helix and four beta strands.. 
PF09467 Hypothetical protein Yopt<br>This hypothetical protein is expressed in bacteria, particularly Bacillus subtilis. It forms homo-dimers, with each monomer consisting of one alpha helix and three beta strands.. 
PF09468 Ydr279p protein family (RNase H2 complex component)<br>RNases H are enzymes that specifically hydrolyse RNA when annealed to a complementary DNA and are present in all living organisms. In yeast RNase H2 is composed of a complex of three proteins (Rnh2Ap, Ydr279p and Ylr154p), this family represents the homologues of Ydr279p  . It is not known whether non yeast proteins in this family fulfil the same function.. 
PF09469 Cordon-bleu ubiquitin-like domain<br>The Cordon-bleu protein domain is highly conserved among vertebrates. The sequence contains three repeated lysine, arginine, and proline-rich regions, the KKRAP motif. The exact function of the protein is unknown but it is thought to be involved in mid-brain neural tube closure. It is expressed specifically in the node  . This domain has a ubiquitin-like fold.. 
PF09470 Telethonin protein<br>Telethonin is a 167-residue protein which complexes with the large muscle protein, titin. The very N-terminus of titin, composed of two immunoglobulin-like (Ig) domains, referred to as Z1 and Z2, interacts with the N-terminal region (residues 1-53) of telethonin, mediating the antiparallel assembly of two Z1Z2 domains. The C-terminus of the telethonin appears to induce dimerisation of this 2:1 titin/telethonin structure which thus forms a complex necessary for myofibril assembly and maintenance of the intact Z-disk of skeletal and cardiac muscles  .. 
PF09471 IgA Peptidase M64<br>This is a family of highly selective metallo-endopeptidases.  The primary structure of the Clostridium ramosum IgA proteinase shows no significant overall similarity to any other known metallo-endopeptidase  .. 
PF09472 Tetrahydromethanopterin S-methyltransferase, F subunit (MtrF)<br>Many archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This domain is mostly found in MtrF, where it covers the entire length of the protein. This polypeptide is one of eight subunits of the N5-methyltetrahydromethanopterin: coenzyme M methyltransferase complex found in methanogenic archaea. This is a membrane-associated enzyme complex that uses methyl-transfer reactions to drive a sodium-ion pump. MtrF itself is involved in the transfer of the methyl group from N5-methyltetrahydromethanopterin to coenzyme M. Subsequently, methane is produced by two-electron reduction of the methyl moiety in methyl-coenzyme M by another enzyme, methyl-coenzyme M reductase. In some organisms this domain is found at the C terminal region of what appears to be a fusion of the MtrA and MtrF proteins. The function of these proteins is unknown, though it is likely that they are involved in C1 metabolism.. 
PF09474 type_III_YscX; <br>Type III secretion system YscX (type_III_YscX). Members of this family are encoded within bacterial type III secretion gene clusters. Among all species with type III secretion, those with this protein are found among those that target animal rather than plant cells. The member of this family in Yersinia was shown by mutation to be required for type III secretion of Yops effector proteins and therefore is believed to be part of the secretion machinery.. 
PF09475 dot_icm_IcmQ; <br>Dot/Icm secretion system protein (dot_icm_IcmQ). Proteins in this entry are the IcmQ component of Dot/Icm secretion systems, as found in the obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the literature now seems to favour calling this the Dot/Icm system. This protein was shown to be essential for translocation.. 
PF09476 pilus_cpaD; Pilus_cpaD; <br>Pilus biogenesis CpaD protein (pilus_cpaD). Proteins in this entry consist of a pilus biogenesis protein, CpaD, from Caulobacter, and homologues in other bacteria, including three in the root nodule bacterium Bradyrhizobium japonicum. The molecular function of the homologues is not known.. 
PF09477 type_III_yscG; Type_III_yscG; <br>Bacterial type II secretion system chaperone protein (type_III_yscG). YscG is a molecular chaperone for YscE, where both are part of the type III secretion system that in Yersinia is designated Ysc (Yersinia secretion). The secretion system delivers effector proteins, designated Yops (Yersinia outer proteins), in Yersinia. This entry consists of YscG from Yersinia and functionally equivalent type III secretion proteins in other species: e.g. AscG in Aeromonas and LscG in Photorhabdus luminescens.. 
PF09478 Carbohydrate binding domain CBM49<br>Mistry J, Urbanowicz B. Pfam-B_6310 (release 21.0). This domain is found at the C terminal of cellulases and in vitro binding studies have shown it to binds to crystalline cellulose  .. 
PF09479 flg_new; <br>Listeria-Bacteroides repeat domain (List_Bact_rpt). This model describes a conserved core region of about 43 residues, which occurs in at least two families of tandem repeats. These include 78-residue repeats which occur from 2 to 15 times in some proteins of Bacteroides forsythus ATCC 43037, and 70-residue repeats found in families of internalins of Listeria species. Single copies are found in proteins of Fibrobacter succinogenes, Geobacter sulfurreducens, and a few other bacteria.. 
PF09480 Type III secretion system protein PrgH-EprH (PrgH)<br>In Salmonella, the gene encoding this protein is part of a four-gene operon PrgHIJK, while in other organisms it is found in type III secretion operons. PrgH has been shown to be required for type III secretion and is a structural component of the needle complex, which is the core component of type III secretion systems.. 
PF09481 CRISPR_cse1; <br>CRISPR-associated protein Cse1 (CRISPR_cse1). Clusters of short DNA repeats with non-homologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognisable features. This family is known as CRISPR (short for Clustered, Regularly Interspaced Short Palindromic Repeats). A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This entry, represented by CT1972 from Chlorobaculum tepidum, is found in the CRISPR/Cas subtype Ecoli regions of many bacteria (most of which are mesophiles), and not in Archaea. It is designated Cse1.. 
PF09482 Bacterial type III secretion apparatus protein (OrgA_MxiK)<br>This protein is encoded by genes which are found in type III secretion operons, and has been shown to be essential for the invasion phenotype in Salmonella and a component of the secretion apparatus. The protein is known as OrgA in Salmonella due to its oxygen-dependent expression pattern in which low-oxygen levels up-regulate the gene. In Shigella the gene is called MxiK and has been shown to be essential for the proper assembly of the needle complex, which is the core component of type III secretion systems.. 
PF09483 Type III secretion protein (HpaP)<br>This entry represents proteins encoded by genes which are always found in type III secretion operons, although their function in the processes of secretion and virulence is unclear. Hpa stands for Hrp-associated gene, where Hrp stands for hypersensitivity response and virulence. see also PMID:18584024. 
PF09484 cas_TM1802; <br>CRISPR-associated protein TM1802 (cas_TM1802). Clusters of short DNA repeats with non-homologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognisable features. This family is known as CRISPR (short for Clustered, Regularly Interspaced Short Palindromic Repeats). A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This minor cas protein is found in at least five prokaryotic genomes: Methanosarcina mazei, Sulfurihydrogenibium azorense, Thermotoga maritima, Carboxydothermus hydrogenoformans, and Dictyoglomus thermophilum, the first of which is archaeal while the rest are bacterial.. 
PF09485 CRISPR_cse2; <br>CRISPR-associated protein Cse2 (CRISPR_cse2). Clusters of short DNA repeats with non-homologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognisable features. This family is known as CRISPR (short for Clustered, Regularly Interspaced Short Palindromic Repeats). A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This family of proteins, represented by CT1973 from Chlorobaculum tepidum, is encoded by genes found in the CRISPR/Cas subtype Ecoli regions of many bacteria (most of which are mesophiles), and not in Archaea. It is designated Cse2.. 
PF09486 Bacterial type III secretion protein (HrpB7)<br>This entry represents proteins encoded by genes which are found in type III secretion operons in a narrow range of species including Xanthomonas, Burkholderia and Ralstonia.. 
PF09487 Bacterial type III secretion protein (HrpB2)<br>This entry represents proteins encoded by genes which are found in type III secretion operons in a narrow group of species including Xanthomonas, Burkholderia and Ralstonia.. 
PF09488 osmo_MPGsynth; <br>Mannosyl-3-phosphoglycerate synthase (osmo_MPGsynth). This family consists of examples of mannosyl-3-phosphoglycerate synthase (MPGS), which together with mannosyl-3-phosphoglycerate phosphatase (MPGP) EC:2.4.1.217, comprises a two-step pathway for mannosylglycerate biosynthesis. Mannosylglycerate is a compatible solute that tends to be restricted to extreme thermophiles of archaea and bacteria. Note that in Rhodothermus marinus, this pathway is one of two; the other is condensation of GDP-mannose with D-glycerate by mannosylglycerate synthase.. 
PF09489 Probable cobalt transporter subunit (CbtB)<br>This entry represents a family of proteins which have been proposed to act as cobalt transporters acting in concert with vitamin B12 biosynthesis systems. Evidence for this assignment includes 1) prediction of a single transmembrane segment and a C-terminal histidine-rich motif likely to be a metal-binding site, 2) positional gene linkage with known B12 biosynthesis genes, 3) upstream proximity of B12 transcriptional regulatory sites, 4) the absence of other known cobalt import systems and 5) the obligate co-localisation with a protein (CbtA) predicted to have five additional transmembrane segments.. 
PF09490 Probable cobalt transporter subunit (CbtA)<br>This entry represents a family of proteins which have been proposed to act as cobalt transporters acting in concert with vitamin B12 biosynthesis systems. Evidence for this assignment includes 1) prediction of five transmembrane segments, 2) positional gene linkage with known B12 biosynthesis genes, 3) upstream proximity of B12 transcriptional regulatory sites, 4) the absence of other known cobalt import systems and 5) the obligate co-localisation with a small protein (CbtB) having a single additional transmembrane segment and a C-terminal histidine-rich motif likely to be a metal-binding site.. 
PF09491 AlwI restriction endonuclease<br>This family includes the AlwI (recognises GGATC), Bsp6I (recognises GC^NGC) , BstNBI (recognises GASTC), PleI(recognises GAGTC) and MlyI (recognises GAGTC) restriction endonucleases.. 
PF09492 pec_lyase; <br>Members of this family are isozymes of pectate lyase (EC:4.2.2.2), also called polygalacturonic transeliminase and alpha-1,4-D-endopolygalacturonic acid lyase.. 
PF09493 CHP02450_Tryp; <br>Tryptophan-rich protein (DUF2389). Members of this family are small hypothetical proteins of 60 to 100 residues from Cyanobacteria and some Proteobacteria. Prochlorococcus marinus strains have two members, other species one only. Interestingly, of the eight most conserved residues, four are aromatic and three are invariant tryptophans. It appears all species that encode this protein can synthesise tryptophan de novo.. 
PF09494 Slx4 endonuclease<br>The Slx4 protein is a heteromeric structure-specific endonuclease found from fungi to mammals.  Slx4 with Slx1 acts as a nuclease on branched DNA substrates, particularly simple-Y, 5'-flap, or replication fork structures by cleaving the strand bearing the 5' non-homologous arm at the branch junction and thus generating ligatable nicked products from 5'-flap or replication fork substrates  .. 
PF09495 UPF0390;<br>Protein of unknown function (DUF2462). This protein is highly conserved, but its function is unknown. It can be isolated from HeLa cell nucleoli and is found to be homologous with Leydig cell tumour protein whose function is unknown [1, supplementary Table I].. 
PF09496 Cenp-O;<br>Cenp-O kinetochore centromere component. This eukaryotic protein is a component of the inner kinetochore subcomplex of the centromere.  It has been shown to be involved in chromosome segregation via regulation of the spindle in both yeast and human   .. 
PF09497 Transcription mediator complex subunit Med12<br>Med12 is a negative regulator of the Gli3-dependent sonic hedgehog signalling pathway via its interaction with Gli3 within the RNA polymerase II transcriptional Mediator. A complex is formed between Med12, Med13, CDK8 and CycC which is responsible for suppression of transcription. This subunit forms part of the Kinase section of Mediator  .. 
PF09498 CHP02448; <br>Protein of unknown function (DUF2388). This family consists of small hypothetical proteins, about 100 amino acids in length. The family includes five members (three in tandem) in Pseudomonas aeruginosa PAO1 and in Pseudomonas putida (strain KT2440), four in Pseudomonas syringae DC3000, and single members in several other Proteobacteria. The function is unknown.. 
PF09499 ApaLI-like restriction endonuclease<br>This family includes R.ApaLI and R.XbaI restriction endonucleases. ApaLI recognises and cleaves the sequence GTGCAC.. 
PF09500 yiiD_Cterm; <br>Putative thioesterase (yiiD_Cterm). This entry consists of a broadly distributed uncharacterised domain often found as a standalone protein. The member from Shewanella oneidensis is described from crystallography work as a putative thioesterase because it belongs to the HotDog clan of enzymes. About half of the members of this family are fused to an Acetyltransf_1 domain Pfam:PF00583.. 
PF09501 Bac_small_yrzI; <br>Probable sporulation protein (Bac_small_yrzI). Members of this family are very small proteins, about 47 residues each, in the genus Bacillus. Single members are found in Bacillus subtilis and Bacillus halodurans, while arrays of six members in tandem are found in Bacillus cereus and Bacillus anthracis. An EIxxE motif present in most members of this family resembles cleavage sites by the germination protease GPR in a number of small acid-soluble spore proteins (SASP). A role in sporulation is possible.. 
PF09502 Bacterial type III secretion protein (HrpB4)<br>This entry represents proteins encoded by genes which are found in type III secretion operons in a narrow range of species including Xanthomonas, Burkholderia and Ralstonia.. 
PF09504 Bsp6I restriction endonuclease<br>This family includes the Bsp6I (recognises and cleaves GC^NGC) restriction endonucleases.. 
PF09505 Dimethylamine methyltransferase (Dimeth_PyL)<br>This family consists of dimethylamine methyltransferases from the genus Methanosarcina. It is found in three nearly identical copies in each of Methanosarcina acetivorans, Methanosarcina barkeri, and Methanosarcina mazei. It is one of a suite of three non-homologous enzymes with a critical UAG-encoded pyrrolysine residue in these species (along with trimethylamine methyltransferase and monomethylamine methyltransferase). It demethylates dimethylamine, leaving monomethylamine, and methylates the prosthetic group of the small corrinoid protein MtbC. The methyl group is then transferred by methylcorrinoid:coenzyme M methyltransferase to coenzyme M. Note that the pyrrolysine residue is variously translated as K or X, or as a stop codon that truncates the sequence.. 
PF09506 Glucosylglycerol-phosphate phosphatase (Salt_tol_Pase)<br>Proteins in this family are glucosylglycerol-phosphate phosphatases, with the gene symbol stpA (Salt Tolerance Protein A). A motif characteristic of acid phosphatases is found, but otherwise this family shows little sequence similarity to other phosphatases. This enzyme acts on the glucosylglycerol phosphate, product of glucosylglycerol phosphate synthase and immediate precursor of the osmoprotectant glucosylglycerol.. 
PF09508 CHP02336; <br>Lacto-N-biose phosphorylase. The gene which codes for this protein in gut-bacteria is located in a novel putative operon for galactose metabolism. The protein appears to be a carbohydrate-processing phosphorolytic enzyme (EC:2.4.1.211), unlike either glycoside hydrolases or glycoside lyase. Intestinal colonisation by bifidobacteria is important for human health, especially in pediatrics, because colonisation seems to prevent infection by some pathogenic bacteria that cause diarrhoea or other illnesses. The operon seems to be involved in intestinal colonisation by bifidobacteria mediated by metabolism of mucin sugars. In addition, it may also resolve the question of the nature of the bifidus factor in human milk as the lacto-N-biose structure found in milk oligosaccharides.. 
PF09507 DNA polymerase subunit Cdc27<br>This protein forms the C subunit of DNA polymerase delta. It carries the essential residues for binding to the Pol1 subunit of polymerase alpha, from residues 293-332, which are characterised by the motif D--G--VT, referred to as the DPIM motif. The first 160 residues of the protein form the minimal domain for binding to the B subunit, Cdc1, of polymerase delta, the final 10 C-terminal residues, 362-372, being the DNA sliding clamp, PCNA, binding motif.. 
PF09509 Hypoth_ymh; <br>Protein of unknown function (Hypoth_ymh). This entry consists of a relatively rare prokaryotic protein family (about 8 occurrences per 200 genomes). Genes for members of this family appear to be associated variously with phage and plasmid regions, restriction system loci, transposons, and housekeeping genes. Their function is unknown.. 
PF09510 Rtt102p-like transcription regulator protein<br>This protein is found in fungi. The family includes Rtt102p, a transcription regulator protein which appears to be integrally associated with both the Swi-Snf and the RSC chromatin remodelling complexes,  .. 
PF09511 RNA ligase<br>TIGRFAMs, Coggill P, Mistry J, Wood V. TIGRFAMs & Pfam-B_49998 (release 17.0). Members of this family include T4 phage proteins with ATP-dependent RNA ligase activity. Host defence to phage may include cleavage and inactivation of specific tRNA molecules; members of this family act to reverse this RNA damage. The enzyme is adenylated, transiently, on a Lys residue in a motif KXDGSL. This family also includes fungal tRNA ligases that have adenylyltransferase activity  .  tRNA ligases are enzymes required for the splicing of precursor tRNA molecules containing introns.. 
PF09512 Thiamine-precursor transporter protein (ThiW)<br>Levels of thiamine pyrophosphate (TPP) or thiamine regulate transcription or translation of a number of thiamine biosynthesis, salvage, or transport genes in a wide range of prokaryotes. The mechanism involves direct binding, with no protein involved, to a structural element called THI found in the untranslated upstream region of thiamine metabolism gene operons. This element is called a riboswitch and is seen also for other metabolites such as FMN and glycine. This protein family consists of proteins identified in operons controlled by the THI riboswitch and designated ThiW. The hydrophobic nature of this protein and reconstructed metabolic background suggests that this protein acts in transport of a thiazole precursor of thiamine.. 
PF09514 SSXRD motif<br>Pfam-B_23332 (Release 21.0). SSX1 can repress transcription, and this has been attributed to a putative Kruppel associated box (KRAB) repression domain at the N-terminus. However, from the analysis of these deletion constructs further repression activity was found at the C-terminus of SSX1. Which has been called the SSXRD (SSX Repression Domain). The potent repression exerted by full-length SSX1 appears to localise to this region  .. 
PF09515 Thiamine transporter protein (Thia_YuaJ)<br>Members of this protein family have been assigned as thiamine transporters by a phylogenetic analysis of families of genes regulated by the THI element, a broadly conserved RNA secondary structure element through which thiamine pyrophosphate (TPP) levels can regulate transcription of many genes related to thiamine transport, salvage, and de novo biosynthesis. Species with this protein always lack the ThiBPQ ABC transporter. In some species (e.g. Streptococcus mutans and Streptococcus pyogenes), yuaJ is the only THI-regulated gene. Evidence from Bacillus cereus indicates thiamine uptake is coupled to proton translocation.. 
PF09516 CfrBI restriction endonuclease<br>This family includes the CfrBI (recognises and cleaves C^CWWGG) restriction endonuclease.. 
PF09517 Eco29kI restriction endonuclease<br>This family includes the Eco29kI (recognises and cleaves CCGC^GG ) restriction endonuclease.. 
PF09518 HindIII restriction endonuclease<br>This family includes the HindIII (recognises and cleaves A^AGCTT) restriction endonuclease.. 
PF09519 HindVP restriction endonuclease<br>This family includes the HindVP (recognises GRCGYC bu the cleavage site is unknown) restriction endonucleases.. 
PF09520 RE_MjaII;<br>Type II restriction endonuclease, TdeIII. This family includes many TdeIII restriction endonucleases that recognise and cleave at GGNCC sites. TdeIII cleave unmethylated double-stranded DNA  .. 
PF09521 NgoPII restriction endonuclease<br>This family includes the NgoPII (recognises and cleaves GG^CC) restriction endonuclease.. 
PF09522 R.Pab1 restriction endonuclease<br>
PF09523 CHP02444; <br>Protein of unknown function (DUF2390). Members of this family are bacterial hypothetical proteins, about 160 amino acids in length, found in various proteobacteria, including members of the genera Pseudomonas and Vibrio. The C-terminal region is poorly conserved and is not included in the model.. 
PF09524 Conserved phage C-terminus (Phg_2220_C)<br>This entry represents the conserved C-terminal domain of a family of proteins found exclusively in bacteriophage and in bacterial prophage regions. The functions of this domain and the proteins containing it are unknown.. 
PF09526 CHP02443; <br>Probable metal-binding protein (DUF2387). Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.. 
PF09527 Putative F0F1-ATPase subunit (ATPase_gene1)<br>This model represents a protein found encoded in F1F0-ATPase operons in several genomes, including Methanosarcina barkeri (archaeal) and Chlorobium tepidum (bacterial). It is a small protein (about 100 amino acids) with long hydrophobic stretches and is presumed to be a subunit of the enzyme.. 
PF09528 Ehrlichia tandem repeat (Ehrlichia_rpt)<br>This entry represents 77 residues of an 80 amino acid (240 nucleotide) tandem repeat, found in a variable number of copies in an immunodominant outer membrane protein of Ehrlichia chaffeensis, a tick-borne obligate intracellular pathogen.. 
PF09529 intg_mem_TP0381; <br>Integral membrane protein (intg_mem_TP0381). This entry represents a family of hydrophobic proteins with seven predicted transmembrane alpha helices. Members are found in Bacillus subtilis (ywaF), TP0381 from Treponema pallidum (TP0381), Streptococcus pyogenes, Rhodococcus erythropolis, etc.. 
PF09531 Nucleoporin protein Ndc1-Nup<br>Ndc1 is a nucleoporin protein that is a component of the Nuclear Pore Complex, and, in fungi, also of the Spindle Pole Body. It consists of six transmembrane segments, three lumenal loops, both concentrated at the N-terminus and cytoplasmic domains largely at the C-terminus, all of which are well conserved.. 
PF09532 DFDF;<br>The FDF domain, so called because of the conserved FDF at its  N termini, is an entirely alpha-helical domain with multiple exposed hydrophilic loops  . It is found at the C terminus of Scd6p-like SM domains   . It is also found with other divergent Sm domains and in proteins such as Dcp3p and FLJ21128, where it is found N terminal to the YjeF-N domain, a novel Rossmann fold domain  .. 
PF09533 CHP02269_MYXXA; <br>Predicted lipoprotein of unknown function (DUF2380). This family consists of at least 9 paralogs in Myxococcus xanthus, a member of the Deltaproteobacteria. One appears truncated toward the N-terminus; the others are predicted lipoproteins. The function is unknown.. 
PF09534 Tryptophan-associated transmembrane protein (Trp_oprn_chp)<br>Members of this family are predicted transmembrane proteins with four membrane-spanning helices. Members are found in the Actinobacteria (Mycobacterium, Corynebacterium, Streptomyces), always associated with genes for tryptophan biosynthesis.. 
PF09535 Protein of unknown function (Gmx_para_CXXCG)<br>This entry consists of at least 10 paralogous proteins from Myxococcus xanthus and that lack detectable sequence similarity to any other protein family. An imperfectly conserved CXXCG motif, a probable binding site, appears twice in the multiple sequence alignment.. 
PF09536 Mxa_TIGR02265; <br>Protein of unknown function (DUF2378). This family consists of a set of at least 17 paralogous proteins in Myxococcus xanthus DK 1622 and and 12 in Stigmatella aurantiaca DW4/3-1. Members are about 200 amino acids in length. The function is unknown.. 
PF09537 CHP2284; <br>Domain of unknown function (DUF2383). Members of this protein family are found mostly in the Proteobacteria, although one member is found in the the marine planctomycete Pirellula sp. strain 1. The function is unknown.. 
PF09538 Protein of unknown function (FYDLN_acid)<br>Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.. 
PF09539 CHP02301; <br>Protein of unknown function (DUF2385). Members of this uncharacterised protein family are found in a number of alphaproteobacteria, including root nodule bacteria, Brucella suis, Caulobacter crescentus, and Rhodopseudomonas palustris. Conserved residues include two well-separated cysteines, suggesting a disulfide bond. The function is unknown.. 
PF09543 CHP02267_MYXXA; <br>Protein of unknown function (DUF2379). This family consists of at least 7 paralogs in Myxococcus xanthus and 6 in Stigmatella aurantiaca, both members of the Deltaproteobacteria. The function is unknown.. 
PF09544 Mxa_TIGR02268; <br>Protein of unknown function (DUF2381). This family consists of at least 8 paralogs in Myxococcus xanthus, a member of the Deltaproteobacteria. The function is unknown.. 
PF09545 AccI restriction endonuclease<br>This family includes the AccI (recognises and cleaves GT^MKAC) restriction endonuclease.. 
PF09546 spore_III_AE; <br>Stage III sporulation protein AE (spore_III_AE). This represents the stage III sporulation protein AE, which is encoded in a spore formation operon spoIIIAABCDEFGH under the control of sigma G. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species.. 
PF09547 spore_IV_A; <br>Stage IV sporulation protein A (spore_IV_A). SpoIVA is designated stage IV sporulation protein A. It acts in the mother cell compartment and plays a role in spore coat morphogenesis. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species.. 
PF09548 spore_III_AB; <br>Stage III sporulation protein AB (spore_III_AB). SpoIIIAB represents the stage III sporulation protein AB, which is encoded in a spore formation operon: spoIIIAABCDEFGH that is under sigma G regulation  . A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species.. 
PF09549 Bpu10I restriction endonuclease<br>This family includes the Bpu10I (recognises and cleaves CCTNAGC (-5/-2)) restriction endonucleases.. 
PF09550 CHP2216_phage; <br>Conserved hypothetical phage protein (DUF2376). This entry describes a family of proteins found exclusively in phage or in prophage regions of bacterial genomes, including the phage-like Rhodobacter capsulatus gene transfer agent, which packages DNA.. 
PF09551 spore_II_R; <br>Stage II sporulation protein R (spore_II_R). SpoIIR is designated stage II sporulation protein R. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species. SpoIIR is a signalling protein that links the activation of sigma E to the transcriptional activity of sigma F during sporulation.. 
PF09552 BstXI restriction endonuclease<br>This family includes the BstXI (recognises and cleaves CCANNNNN^NTGG) restriction endonuclease.. 
PF09553 Eco47II restriction endonuclease<br>This family includes the Eco47II (which recognises GGNCC, but the cleavage site unknown) restriction endonuclease.. 
PF09554 HaeII restriction endonuclease<br>This family includes the HaeII (recognises and cleaves RGCGC^Y) restriction endonuclease.. 
PF09556 HaeIII restriction endonuclease<br>This family includes the HaeIII (recognises and cleaves GG^CC) restriction endonuclease.. 
PF09557 CHP2271_C; <br>Domain of unknown function (DUF2382). This entry describes an uncharacterized domain, sometimes found in association with a PRC-barrel domain Pfam:PF05239 which is also found in rRNA processing protein RimM and in a photosynthetic reaction centre complex protein). This domain is found in proteins from Bacillus subtilis, Deinococcus radiodurans, Nostoc sp. PCC 7120, Myxococcus xanthus, and several other species. The function is not known.. 
PF09558 CHP02922; <br>Protein of unknown function (DUF2375). TIGRFAMs, Coggilll P. Two members of this family are found in Colwellia psychrerythraea (strain 34H / ATCC BAA-681) and one each in various other species of Colwellia and Shewanella. One member from C. psychrerythraea is of special interest because it is preceded by the same cis-regulatory site as a number of genes that have the PEP-CTERM domain described by PEP_anchor (IPR013424).. 
PF09559 Cas6 Crispr<br>The Cas6 Crispr family of proteins averaging 140 residues are characterised by having a GhGxxxxxGhG motif, where h indicates a hydrophobic residue, at the C-terminus  . The CRISPR-Cas system is possibly a mechanism of defence against invading pathogens and plasmids that functions analogously to the RNA interference (RNAi) systems in eukaryotes  .. 
PF09560 Spo_YunB; Spo_yunB; <br>Sporulation protein YunB (Spo_YunB). Spo_YunB is the sporulation protein YunB. In Bacillus subtilis its expression is controlled by sigmaE.The gene YunB seems to code for a protein involved, at least indirectly, in the pathway leading to the activation of sigmaK. Inactivation of YunB delays sigmaK activation and results in reduced sporulation efficiency.. 
PF09561 HpaII restriction endonuclease<br>This family includes the HpaII (recognises and cleaves C^CGG) restriction endonuclease.. 
PF09562 LlaMI restriction endonuclease<br>This family includes the LlaMI (recognises and cleaves CC^NGG) restriction endonuclease.. 
PF09563 LlaJI restriction endonuclease<br>This family includes the LlaJI (recognises GACGC) restriction endonucleases.. 
PF09564 NgoBV restriction endonuclease<br>This family includes the NgoBV (recognises GGNNCC but cleavage site is unknown) restriction endonuclease.. 
PF09565 NgoFVII restriction endonuclease<br>This family includes the NgoFVII (recognises GCSGC but cleavage site unknown) restriction endonuclease.. 
PF09566 SacI restriction endonuclease<br>This family includes the SacI (recognises and cleaves GAGCT^C) restriction endonuclease.. 
PF09567 MamI restriction endonuclease<br>This family includes the MamI (recognises and cleaves GATNN^NNATC) restriction endonuclease.. 
PF09568 MjaI restriction endonuclease<br>This family includes the MjaI (recognises CTAG but cleavage site unknown) restriction endonuclease.. 
PF09569 ScaI restriction endonuclease<br>This family includes the ScaI (recognises and cleaves AGT^ACT) restriction endonuclease.. 
PF09570 SinI restriction endonuclease<br>This family includes the SinI (recognises and cleaves G^GWCC) restriction endonuclease.. 
PF09571 XcyI restriction endonuclease<br>This family includes the XcyI (recognises and cleaves C^CCGGG) restriction endonucleases.. 
PF09572 XamI restriction endonuclease<br>This family includes the XamI (recognises GTCGAC but cleavage site unknown) restriction endonuclease.. 
PF09573 TaqI restriction endonuclease<br>This family includes the TaqI (recognises and cleaves T^CGA) restriction endonuclease.. 
PF09574 Short_TIGR02808; <br>Protein  of unknown function (Duf2374). This very small protein (about 46 amino acids) consists largely of a single predicted membrane-spanning region. It is found in Photobacterium profundum SS9 and in three species of Vibrio, always near periplasmic nitrate reductase genes, but far from the periplasmic nitrate reductase genes in Aeromonas hydrophila ATCC 7966.. 
PF09575 Spore_SspJ; <br>Small spore protein J (Spore_SspJ). Spore_SspJ represents a group of small acid-soluble proteins (SASP) from Bacillus sp., which are present in spores but not in growing cells. The sspJ gene is transcribed in the forespore compartment by RNA polymerase with the forespore-specific sigmaG. Loss of SspJ causes a slight decrease in the rate of spore outgrowth in an otherwise wild-type background.. 
PF09577 Sporulation protein YpjB (SpoYpjB)<br>These proteins are found in the endospore-forming bacteria which include Bacillus species. In Bacillus subtilis, ypjB was found to be part of the sigma-E regulon. Sigma-E is a sporulation sigma factor that regulates expression in the mother cell compartment. Null mutants of ypjB show a sporulation defect, but this gene is not, however, a part of the endospore formation minimal gene set.. 
PF09578 Spore cortex protein YabQ (Spore_YabQ)<br>This protein is predicted to span the membrane several times. It is only found in genomes of species that perform sporulation, such as Bacillus subtilis, Clostridium tetani, and other members of the Firmicutes (low-GC Gram-positive bacteria). Mutation of this sigmaE-dependent gene blocks development of the spore cortex. The length of the C-terminal region, which includes some hydrophobic regions, is variable.. 
PF09579 Sporulation protein YtfJ (Spore_YtfJ)<br>Proteins in this family are encoded by bacterial genomes if, and only if, the species is capable of endospore formation. YtfJ was confirmed in spores of B. subtilis; it appears to be expressed in the forespore under control of SigF.. 
PF09580 Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ)<br>This entry contains YhcN and YlaJ, which are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic, 40-residue C-terminal domain.. 
PF09581 Stage III sporulation protein AF (Spore_III_AF)<br>This family represents the stage III sporulation protein AF (Spore_III_AF) of the bacterial endospore formation program, which exists in some but not all members of the Firmicutes (formerly called low-GC Gram-positives). The C-terminal region of these proteins is poorly conserved.. 
PF09582 Iron only nitrogenase protein AnfO (AnfO_nitrog)<br>Proteins in this entry include Anf1 from Rhodobacter capsulatus (Rhodopseudomonas capsulata) and AnfO from Azotobacter vinelandii. They are found exclusively in species which contain the iron-only nitrogenase, and are encoded immediately downstream of the structural genes for the nitrogenase enzyme in these species.. 
PF09583 Phage shock protein G (Phageshock_PspG)<br>This protein was previously designated as YjbO in Escherichia coli. It is found only in genomes that have the phage shock operon (psp), but it is only rarely encoded near other psp genes. The psp regulon is upregulated in response to a number of stress conditions, including ethanol, expression of the filamentous phage secretin protein IV and other secretins and heat shock.. 
PF09584 Phage shock protein PspD (Phageshock_PspD)<br>Members of this family are phage shock protein PspD, found in a minority of bacteria that carry the defining genes of the phage shock regulon (pspA, pspB, pspC, and pspF). It is found in Escherichia coli, Yersinia pestis, and closely related species, where it is part of the phage shock operon. It is known to be expressed but its function is unknown.. 
PF09585 Conserved hypothetical protein (Lin0512_fam)<br>This family consists of few members, broadly distributed. It occurs so far in several Firmicutes (twice in Oceanobacillus), one Cyanobacterium, one alpha Proteobacterium, and (with a long prefix) in plants. The function is unknown. The alignment includes a well conserved motif GxGxDxHG near the N-terminus.. 
PF09586 Bacterial membrane protein YfhO<br>Pfam-B_2727 (release 21.0). This protein is a conserved membrane protein  . The yfhO gene is transcribed in Difco sporulation medium and the transcription is affected by the YvrGHb two-component system. Some members of this family have been annotated as glycosyl transferases of the PMT family.. 
PF09587 Bacterial capsule synthesis protein PGA_cap<br>Pfam-B_1441 (release 21.0). This protein is a putative poly-gamma-glutamate capsule biosynthesis protein found in bacteria. Poly-gamma-glutamate is a natural polymer that may be involved in virulence and may help bacteria survive in high salt concentrations. It is a surface-associated protein  .. 
PF09588 YqaJ-like viral recombinase domain<br>Pfam-B_3587 (release 21.0). This protein family is found in many different bacterial species but is of viral origin. The protein forms an oligomer and functions as a processive alkaline exonuclease that digests linear double-stranded DNA in a Mg(2+)-dependent reaction, It has a preference for 5'-phosphorylated DNA ends. It thus forms part of the two-component SynExo viral recombinase functional unit  .. 
PF09589 HrpA pilus formation protein<br>Pfam-B_3574 (release 21.0). HrpA is an essential component of the type III secretion system (TTSS) which pathogens use to inject virulence factors directly into their host cells, and to cause disease. The TTSS has an Hrp pilus appendage for channelling effector proteins through the plant cell wall and this pilus elongates by the addition of HrpA pilin subunits at the distal end  .. 
PF09590 Lentivirus surface glycoprotein<br>Pfam-B_3269 (release 21.0). This protein is found in feline immunodeficiency retrovirus. It represents the surface glycoprotein which is found in the polyprotein C-terminal to the Env protein.. 
PF09591 UPF0328; <br>Protein of unknown function (DUF2463). Pfam-B_3132 (release 21.0). This protein is found in eukaryotic, parasitic microsporidia. Its function is unknown.. 
PF09592 Protein of unknown function (DUF2031)<br>Pfam-B_2630 (release 21.0). This protein is expressed in Plasmodium; its function is unknown. It may be the product of gene family pyst-b  .. 
PF09593 Phage_C1; <br>Beta-satellite pathogenicity beta C1 protein. Pfam-B_991 (release 21.0). Cotton leaf-curl disease - CLCuD - is of major economic importance in cotton-growing areas of the far-east. The infectious agent appears to be a single-stranded DNA molecule of approx 1350 nucleotides in length, which, when inoculated with the Begomovirus into cotton, induces symptoms typical of CLCuD. This molecule requires the Begomovirus for replication and encapsidation  . DNA beta encodes a single protein, betaC1. The intracellular distribution of betaC1 is consistent with the hypothesis that it has a role in transporting the DNA A of Begomovirus from the nuclear site of replication to the plasmodesmatal exit sites of the infected cell. The DNA beta-encoded protein, betaC1, is the determinant of both pathogenicity and suppression of gene silencing  .. 
PF09594 Protein of unknown function (DUF2029)<br>Pfam-B_1780 (release 21.0). This is a putative transmembrane protein from bacteria. It is likely to be conserved between Mycobacterium species  .. 
PF09595 Metaviral_G glycoprotein<br>Pfam-B_922 (release 21.0). This is a viral attachment glycoprotein from region G of metaviruses. It is high in serine and threonine suggesting it is highly glycosylated  .. 
PF09596 MamL-1 domain<br>The MamL-1 domain is a polypeptide of up to 70 residues, numbers 15-67 of which adopt an elongated kinked helix that wraps around ANK and CSL forming one of the complexes in the build-up of the Notch transcriptional complex for recruiting general transcription factors.. 
PF09597 IGR protein motif<br>This domain is found in fungal proteins and contains a conserved IGR motif. Its function is unknown.. 
PF09598 Stm1<br>Pfam-B_39435 (release 21.0). This region is found at the N terminal of the Stm1 protein.  Stm1 is a G4 quadraplex and purine motif triplex nucleic acid-binding protein.  It has been implicated in many biological processes including apoptosis and telomere biosynthesis. Stm1 is known to interact with CDC13  , and is known to associate with ribosomes and nuclear telomere cap complexes  .. 
PF09599 Salmonella-Shigella invasin protein C (IpaC_SipC)<br>This entry represents a family of proteins associated with bacterial type III secretion systems, which are injection machines for virulence factors into host cell cytoplasm. Characterized members of this protein family are known to be secreted and are described as invasins, including IpaC from Shigella flexneri and SipC from Salmonella typhimurium. Members may be referred to as invasins, pathogenicity island effectors, and cell invasion proteins.. 
PF09600 Cyd operon protein YbgE (Cyd_oper_YbgE)<br>This entry describes a small protein of unknown function, about 100 amino acids in length, essentially always found in an operon with CydAB, subunits of the cytochrome d terminal oxidase. It appears to be an integral membrane protein. It is found so far only in the Proteobacteria.. 
PF09601 Chp_urease_rgn;<br>Protein of unknown function (DUF2459). This conserved hypothetical protein of unknown function is found in several Proteobacteria. Its function is unknown and its genome context is not well-conserved. It is found amid urease genes in at least one species.. 
PF09602 Polyhydroxyalkanoic acid inclusion protein (PhaP_Bmeg)<br>This entry describes a protein found in polyhydroxyalkanoic acid (PHA) gene regions and incorporated into PHA inclusions in Bacillus cereus and Bacillus megaterium. The role of the protein may include amino acid storage.. 
PF09603 Fibrobacter succinogenes major domain (Fib_succ_major)<br>This domain of about 175 to 200 amino acids is found, in from one to five copies, in over 50 proteins in Fibrobacter succinogenes S85, an obligate anaerobe of the rumen. Many members of this family have an apparent lipoprotein signal sequence. Conserved cysteine residues, suggestive of disulfide bond formation, are also consistent with an extracytoplasmic location for this domain. This domain can also be found in small numbers of proteins in Chlorobium tepidum and Bacteroides thetaiotaomicron.. 
PF09604 F subunit of K+-transporting ATPase (Potass_KdpF)<br>This entry describes a very small integral membrane peptide KdpF, a subunit of the K(+)-translocating Kdp complex. It is found upstream of the KdpA subunit (IPR004623). Because of its very small size and highly hydrophobic character, it is sometimes missed in genome annotation.. 
PF09605 Hypothetical bacterial integral membrane protein (Trep_Strep)<br>This family consists of strongly hydrophobic proteins about 190 amino acids in length with a strongly basic motif near the C-terminus. It is found in rather few species, but in paralogous families of 12 members in the oral pathogenic spirochaete Treponema denticola and 2 in Streptococcus pneumoniae R6.. 
PF09606 ARC105; ARC105_Med_act; <br>ARC105 or Med15 subunit of Mediator complex non-fungal. The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development  .. 
PF09607 Brinker DNA-binding domain<br>This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway  .. 
PF09608 Putative transmembrane protein (Alph_Pro_TM)<br>This family consists of predicted transmembrane proteins of about 270 amino acids. Members are found, so far, only among the Alphaproteobacteria and only once in each genome.. 
PF09609 CRISPR-associated protein, GSU0054 family (Cas_GSU0054)<br>This entry represents a rare CRISPR-associated protein. So far, members are found in Geobacter sulfurreducens and in two unpublished genomes: Gemmata obscuriglobus and Actinomyces naeslundii. CRISPR-associated proteins typically are found near CRISPR repeats and other CRISPR-associated proteins, have low levels of sequence identify, have sequence relationships that suggest lateral transfer, and show some sequence similarity to DNA-active proteins such as helicases and repair proteins.. 
PF09610 Mycoplasma virulence signal region (Myco_arth_vir_N)<br>This entry represents the N-terminal region of a family of large, virulence-associated proteins in Mycoplasma arthritidis and smaller proteins in Mycoplasma capricolum. It includes a probable signal sequence or signal anchor, which, in most instances, has four consecutive Lys residues before the hydrophobic stretch.. 
PF09611 CRISPR-associated protein (Cas_Csy1)<br>CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This entry, typified by YPO2465 of Yersinia pestis, is a CRISPR-associated (Cas) entry strictly associated with the Ypest subtype of CRISPR/Cas locus. It is designated Csy1, for CRISPR/Cas Subtype Ypest protein 1.. 
PF09612 Bacterial protein of unknown function (HtrL_YibB)<br>The protein from this rare, uncharacterized protein family is designated HtrL or YibB in E. coli, where its gene is found in a region of LPS core biosynthesis genes  . Homologues are found in Shigella flexneri, Campylobacter jejuni, and Caenorhabditis elegans only. The htrL gene may represent an insertion to the LPS core biosynthesis region, rather than an LPS biosynthetic protein.. 
PF09613 Bacterial type III secretion protein (HrpB1_HrpK)<br>This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.. 
PF09614 CRISPR-associated protein (Cas_Csy2)<br>CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This entry, typified by YPO2464 of Yersinia pestis, is a CRISPR-associated (Cas) entry strictly associated with the Ypest subtype of CRISPR/Cas locus. It is designated Csy2, for CRISPR/Cas Subtype Ypest protein 2.. 
PF09615 CRISPR-associated protein (Cas_Csy3)<br>CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This entry, typified by YPO2463 of Yersinia pestis, is a CRISPR-associated (Cas) entry strictly associated with the Ypest subtype of CRISPR/Cas locus. It is designated Csy3, for CRISPR/Cas Subtype Ypest protein 3.. 
PF09617 CRISPR-associated protein GSU0053 (Cas_GSU0053)<br>This entry is found in CRISPR-associated (cas) proteins in the genomes of Geobacter sulfurreducens PCA and Desulfotalea psychrophila LSv54 (both Desulfobacterales from the Deltaproteobacteria), Gemmata obscuriglobus (a Planctomycete), and Actinomyces naeslundii MG1 (Actinobacteria).. 
PF09618 CRISPR-associated protein (Cas_Csy4)<br>CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This protein family, typified by YPO2462 of Yersinia pestis, is a CRISPR-associated (Cas) family strictly associated with the Ypest subtype of CRISPR/Cas locus. It is designated Csy4, for CRISPR/Cas Subtype Ypest protein 4.. 
PF09619 Type III secretion system lipoprotein chaperone (YscW)<br>This entry is encoded within type III secretion operons. The protein has been characterised as a chaperone for the outer membrane pore component YscC. YscW is a lipoprotein which is itself localized to the outer membrane and, it is believed, facilitates the oligomerisation and localisation of YscC.. 
PF09620 CRISPR-associated protein (Cas_csx3)<br>This entry is encoded in CRISPR-associated (cas) gene clusters, near CRISPR repeats, in the genomes of several different thermophiles: Archaeoglobus fulgidus (archaeal), Aquifex aeolicus (Aquificae), Dictyoglomus thermophilum (Dictyoglomi), and a thermophilic Synechococcus (Cyanobacteria). It is not yet assigned to a specific CRISPR/cas subtype (hence the x designation csx3).. 
PF09621 Type III secretion system regulator (LcrR)<br>This family of proteins are encoded within type III secretion operons and have been characterised in Yersinia as a regulator of the Low-Calcium Response (LCR).. 
PF09622 CHP02587; <br>Putative integral membrane protein (DUF2391). This entry is found in Nostoc sp. PCC 7120, Agrobacterium tumefaciens, Rhizobium meliloti, and Gloeobacter violaceus in a conserved two-gene neighbourhood. Proteins containing this entry appear to span the membrane seven times.. 
PF09623 CRISPR-associated protein NE0113 (Cas_NE0113)<br>Members of this minor CRISPR-associated (Cas) protein family are encoded in cas gene clusters in Vibrio vulnificus YJ016, Nitrosomonas europaea ATCC 19718, Mannheimia succiniciproducens MBEL55E, and Verrucomicrobium spinosum.. 
PF09624 CHP02588; <br>Protein of unknown function (DUF2393). The function of this protein is unknown. It is always found as part of a two-gene operon with IPR013416, a protein that appears to span the membrane seven times. It has so far been found in the bacteria Nostoc sp. PCC 7120, Agrobacterium tumefaciens, Rhizobium meliloti, and Gloeobacter violaceus.. 
PF09625 VP9 protein<br>VP9 is a protein containing a ferredoxin fold. Two dimers come together to form one asymmetric unit which possesses a DNA recognition fold and specific metal binding sites possibly for zinc. It is postulated that being a non-structural protein VP9 is involved in the transcriptional regulation of the White spot syndrome virus, WSSV, from which it comes. WSSV is the major viral pathogen in shrimp aquaculture  . VP9 is found N-terminal to the Pfam:PF07056 domain.. 
PF09626 Dihaem cytochrome c<br>Dihaem cytochrome c (DHC) is a soluble c-type cytochrome that folds into two distinct domains, each binding a single haem group and connected by a small linker region. Despite little sequence similarity, the N-terminal domain (residues 12-75) is a class I type cytochrome c, that binds one of the haems, but the domain surrounding the other haem is structurally unique. DHC binds electrostatically to an oxygen-binding protein, sphaeroides haem protein (SHP), as a component of a conserved electron transfer pathway.  DHC acts as the physiological electron donor for SHP during phototrophic growth  . In certain species DHC is found upstream of Pfam:PF01292.. 
PF09627 PrgU-like protein<br>This hypothetical protein of 125 residues is expressed in bacteria but is thought to be plasmid in origin. It forms a six beta-strand barrel with three accompanying alpha helices and is probably a homo-dimer in the cell. It may be involved in pheromone-inducible conjugation  .. 
PF09628 Yvfg; <br>Yvfg is a hypothetical protein of 71 residues expressed in some bacteria. The monomer consists of two parallel alpha helices, and the protein crystallises as a homo-dimer.. 
PF09629 YorP protein<br>YorP is a 71 residue protein found in bacteria. As it is also found in a bacteriophage it might be of viral origin. The structure is of an alpha helix between two of five beta strands. The function is unknown.. 
PF09630 Domain of unknown function (DUF2024)<br>This protein of 86 residues is expressed in bacteria.  It consists of four alpha helices and two beta strands. Its function is unknown. One UniProt entry gives the gene name as Traf5.. 
PF09631 Sen15 protein<br>The Sen15 subunit of the tRNA intron-splicing endonuclease is one of the two structural subunits of this hetero-tetrameric enzyme. Residues 36-157 of this subunit possess a novel homodimeric fold.  Each monomer consists of three alpha-helices and a mixed antiparallel/parallel beta-sheet. Two monomers of Sen15 fold with two monomers of Sen34, one of the two catalytic subunits, to form an alpha2-beta2 tetramer as part of the functional endonuclease assembly.. 
PF09632 Rac1-binding domain<br>The Rac1-binding domain is the C-terminal portion of YpkA from Yersinia. It is an all-helical molecule consisting of two distinct subdomains connected by a linker. the N-terminal end, residues 434-615, consists of six helices organised into two three-helix bundles packed against each other. This region is involved with binding to GTPases. The C-terminal end, residues 705-732. is a novel and elongated fold consisting of four helices clustered into two pairs, and this fold carries the helix implicated in actin activation. Rac1-binding domain mimics host guanidine nucleotide dissociation inhibitors (GDIs) of the Rho GTPases, thereby inhibiting nucleotide exchange in Rac1 and causing cytoskeletal disruption in the host  . It is usually found downstream of Pfam:PF00069.. 
PF09633 Protein of unknown function (DUF2023)<br>This protein of approx.120 residues consists of three beta strands and five alpha helices, thought to fold into a homo-dimer. It is expressed in bacteria.. 
PF09634 Protein of unknown function (DUF2025)<br>This protein is produced from gene PA1123 in Pseudomonas. It contains three alpha helices and six beta strands and is thought to be monomeric.  It appears to be present in the biofilm layer and may be a lipoprotein.. 
PF09635 MetRS-N binding domain<br>The MetRS-N domain binds an Arc1-P domain in a tetrameric complex resembling a classical GST homo-dimer. Domain-swapping between symmetrically related MetRS-N and Arc1p-N domains generates a 2:2 tetramer held together by van der Waals forces. This domain is necessary for formation of the aminoacyl-tRNA synthetase complex necessary for tRNA nuclear export and shuttling as part of the translational apparatus. The domain is associated with Pfam:PF09334.. 
PF09636 XkdW protein<br>This protein of approx. 100 residues contains two alpha helices and two beta strands and is probably monomeric. It is expressed in bacteria but is probably viral in origin. Its function is unknown.. 
PF09637 Med18 protein<br>Med18 is one subunit of Mediator, a head-module multiprotein complex, that stimulates basal RNA polymerase II (Pol II) transcription. Med18 consists of an eight-stranded beta-barrel with a central pore and three flanking helices. It complexes with Med8 and Med20 proteins by forming a heterodimer of two-fold symmetry with Med20 and binding the C-terminal alpha-helix region of Med8 across the top of its barrel. This complex creates a multipartite TBP-binding site that can be modulated by transcriptional activators  .. 
PF09638 Ph1570 protein<br>This is a hypothetical protein from Pyroccous horikoshii of unknown function.\.    It contains six alpha helices and eight beta strands and is thought to be monomeric.. 
PF09639 YjcQ protein<br>YjcQ is a protein of approx. 100 residues containing four alpha helices and three beta strands. It is expressed in bacteria and also in viruses. It appears to be under the regulation of SigD RNA polymerase which is responsible for the expression of many genes encoding cell-surface proteins related to flagellar assembly, motility, chemotaxis and autolysis in the late exponential growth phase. The exact function of YjcQ is unknown  . However, it is thought to be a prophage head protein in viruses  .. 
PF09640 Domain of unknown function (DUF2027)<br>This protein domain is of unknown function. though putatively involved in DNA mismatch repair. It is associated with Pfam:PF01713.. 
PF09641 Protein of unknown function (DUF2026)<br>This protein of approx. 100 residues is found in bacteria. It contains up to five alpha helices and up to seven beta strands and is probably monomeric. Its function is unknown. It is cited as a major prophage head protein  , so might generally be of viral origin.. 
PF09642 YonK protein<br>YonK protein is expressed by the bacterial prophage SPbetaC  . It is a 63 residue protein that associates into a homo-octamer in the form of a beta-stranded barrel with four outer helical features at points of the compass.  Its function is unknown.. 
PF09643 YopX protein<br>YopX is a protein that is largely helical, with three identical chains probably complexing into a twelve-chain structure.. 
PF09644 Mg296 protein<br>This protein of 129 residues is expressed in bacteria. It consists of three identical chains of five alpha helices.  Two copies of each chain associate into a complex of six units of possible biological significance but of unknown function.. 
PF09645 F-112 protein<br>F-112 protein is of 70-110 residues and is found in viruses. Its winged-helix structure suggests a DNA-binding function.. 
PF09646 Gp37 protein<br>This protein of 154 residues consists of a unit of helices and beta sheets that crystallises into a beautiful asymmetrical dodecameric barrel-structure, of two six-membered rings one on top of the other. It is expressed in bacteria but is of viral origin as it is found in phage BcepMu and is probably a pathogenesis factor  .. 
PF09648 YycH protein<br>Pfam-B_6483 (Release 21.0). This domain is exclusively found in YycI proteins in the low GC content Gram positive species.  These two domains share the same structural fold with domains two and three of YycH   Pfam:PF07435. Both, YycH and YycI are always found in pair on the chromosome, downstream of the essential histidine kinase YycG. Additionally, both proteins share a function in regulating the YycG kinase with which they appear to form a ternary complex. Lastly, the two proteins always contain an N-terminal transmembrane helix and are localized to the periplasmic space as shown by PhoA fusion studies.. 
PF09649 Histone chaperone domain CHZ<br>This domain is highly conserved from yeasts to humans and is part of the chaperone protein HIRIP3 in vertebrates which interacts with the H3.3 chaperone HIRA, implicated in histone replacement during transcription. N- and C- termini of Chz family members are relatively divergent but do contain similar acidic stretches rich in Glu/Asp residues, characteristic of all histone chaperones  .. 
PF09650 Putative polyhydroxyalkanoic acid system protein (PHA_gran_rgn)<br>Proteins in this entry are encoded by genes involved in either polyhydroxyalkanoic acid (PHA) biosynthesis or utilisation, including proteins found at the surface of PHA granules. These proteins have so far been found in the Pseudomonadales, Xanthomonadales, and Vibrionales, all of which belong to the Gammaproteobacteria.. 
PF09651 CRISPR-associated protein (Cas_APE2256)<br>This entry represents a conserved region of about 150 amino acids found in at least five archaeal and three bacterial species. These species all contain CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats). In six of eight species, the protein is encoded the vicinity of a CRISPR/Cas locus.. 
PF09652 Putative CRISPR-associated protein (Cas_VVA1548)<br>This entry represents a conserved region of about 95 amino acids found exclusively in species with CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats). In all bacterial species that contain this entry, the genes encoding the proteins are in the midst of a cluster of cas (CRISPR-associated) genes.. 
PF09654 CHP02652; <br>Protein of unknown function (DUF2396). These conserved hypothetical proteins have so far been found only in the Cyanobacteria. They are about 170 amino acids long and contain a CxxCx(14)CxxH motif near the N-terminus.. 
PF09655 Conserved nitrate reductase-associated protein (Nitr_red_assoc)<br>Proteins in this entry are found in the Cyanobacteria, and are mostly encoded near nitrate reductase and molybdopterin biosynthesis genes. Molybdopterin guanine dinucleotide is a cofactor for nitrate reductase. These proteins are sometimes annotated as nitrate reductase-associated proteins, though their function is unknown.. 
PF09656 CHP02611; <br>Putative transmembrane protein (PGPGW). Proteins in this entry are putative Actinobacterial proteins of about 150 amino acids in length, with three predicted transmembrane helices and an unusual motif with consensus sequence PGPGW.. 
PF09657 CRISPR-associated protein Csx8 (Cas_Csx8)<br>Clusters of short DNA repeats with nonhomologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognisable features. This family is known as CRISPR (short for Clustered, Regularly Interspaced Short Palindromic Repeats). A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This entry describes proteins of unknown function which are encoded in the midst of a cas gene operon.. 
PF09658 CRISPR-associated protein (Cas_Csx9)<br>Clusters of short DNA repeats with nonhomologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognisable features. This family is known as CRISPR (short for Clustered, Regularly Interspaced Short Palindromic Repeats). A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This entry describes archaeal proteins encoded in cas gene regions.. 
PF09659 CRISPR-associated protein (Cas_Csm6)<br>Clusters of short DNA repeats with nonhomologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognisable features. This family is known as CRISPR (short for Clustered, Regularly Interspaced Short Palindromic Repeats). A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins.. 
PF09660 CHP02677; <br>Protein of unknown function (DUF2397). Proteins in this entry are encoded within a conserved gene four-gene neighbourhood found sporadically in a phylogenetically broad range of bacteria including: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria).. 
PF09661 CHP02678; <br>Protein of unknown function (DUF2398). Proteins in this entry are encoded within a conserved gene four-gene neighbourhood found sporadically in a phylogenetically broad range of bacteria including: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria).. 
PF09662 Phenylphosphate carboxylase gamma subunit (Phenyl_P_gamma)<br>Members of this protein family are the gamma subunit of phenylphosphate carboxylase. Phenol (methyl-benzene) is converted to phenylphosphate, then para-carboxylated by this four-subunit enzyme, with the release of phosphate, to 4-hydroxybenzoate. The enzyme contains neither biotin nor thiamin pyrophosphate. The gamma subunit has no known homologues.. 
PF09663 Amidohydrolase ring-opening protein (Amido_AtzD_TrzD)<br>Members of this family are ring-opening amidohydrolases, including cyanuric acid amidohydrolase (EC:3.5.2.15) (AtzD and TrzD) and barbiturase. Note that barbiturase does not act as defined for EC:3.5.2.1 (barbiturate + water = malonate + urea) but rather catalyses the ring opening of barbiturase acid to ureidomalonic acid.. 
PF09664 CHP02679; <br>Protein of unknown function C-terminus (DUF2399). Proteins in this entry are encoded within a conserved gene four-gene neighbourhood found sporadically in a phylogenetically broad range of bacteria including: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Beta-proteobacteria). Just the C-terminal region is ioncluded here.. 
PF09665 Type II restriction endonuclease (RE_Alw26IDE)<br>Members of this entry are type II restriction endonucleases of the Alw26I/Eco31I/Esp3I family. Characterised specificities of the three members are GGTCTC, CGTCTC and the shared subsequence GTCTC.. 
PF09666 Sororin protein<br>Sororin is an essential, cell cycle-dependent mediator of sister chromatid cohesion  . The protein is nuclear in interphase cells, dispersed from the chromatin in mitosis, and interacts with the cohesin complex  .. 
PF09667 Domain of unknown function (DUF2028)<br>This region of similarity is found in the vertebrate homologues of the drosophila Bobby Sox.. 
PF09668 Aspartyl protease<br>Pfam-B_9589 (release 20.0). This family of eukaryotic aspartyl proteases have a fold similar to retroviral proteases which implies they function proteolytically during regulated protein turnover  .. 
PF09669 Phage regulatory protein Rha (Phage_pRha)<br>Members of this protein family are found in temperate phage and bacterial prophage regions. Members include the product of the rha gene of the lambdoid phage phi-80, a late operon gene. The presence of this gene interferes with infection of bacterial strains that lack integration host factor (IHF), which regulates the rha gene. It is suggested that Rha is a phage regulatory protein.. 
PF09670 CRISPR-associated protein (Cas_Cas02710)<br>Members of this family are found, exclusively in the vicinity of CRISPR repeats and other CRISPR-associated (cas) genes, in Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum), Thermus thermophilus (Deinococcus-Thermus), Chloroflexus aurantiacus (Chloroflexi), and Thermomicrobium roseum (Thermomicrobia).. 
PF09671 Spore coat protein (Spore_GerQ)<br>Members of this protein family are the spore coat protein GerQ of endospore-forming Firmicutes (low GC Gram-positive bacteria). This protein is cross-linked by a spore coat-associated transglutaminase.. 
PF09673 Type-F conjugative transfer system pilin assembly protein<br>This entry represents TrbC, a protein that is an essential component of the F-type conjugative pilus assembly system for the transfer of plasmid DNA. The N-terminal portion of these proteins is heterogeneous.. 
PF09674 CHP02757; <br>Protein of unknown function (DUF2400). Members of this uncharacterised protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides. The function is unknown and its gene neighbourhoods show little conservation.. 
PF09675 Chlamydia-phage Chp2 scaffold (Chlamy_scaf)<br>Members of this entry are encoded by genes in chlamydia-phage such as Chp2. These viruses have around eight genes and obligately infect intracellular bacterial pathogens of the genus Chlamydia. This protein is annotated as VP3 or structural protein (as if a protein of mature viral particles), however, it is displaced from procapsids as DNA is packaged, and therefore is more correctly described as a scaffolding protein.. 
PF09676 Type IV conjugative transfer system lipoprotein (TraV)<br>This entry includes TraV, which is a component of conjugative type IV secretion system. TraV is an outer membrane lipoprotein that is believed to interact with the secretin TraK. The alignment contains three conserved cysteines in the N-terminal half.. 
PF09677 Type-F conjugative transfer system protein (TrbI_Ftype)<br>This entry represents TrbI, an essential component of the F-type conjugative transfer system for plasmid DNA transfer that has been shown to be localized to the periplasm.. 
PF09678 Cytochrome c oxidase caa3 assembly factor (Caa3_CtaG)<br>Members of this family are the CtaG protein required for assembly of active cytochrome c oxidase of the caa3 type, as found in Bacillus subtilis.. 
PF09679 Type-F conjugative transfer system pilin chaperone (TraQ)<br>This entry represents TraQ, a protein that makes a specific interaction with pilin (TraA) to aid its transfer through the inner membrane during the process of F-type conjugative pilus assembly.. 
PF09680 Protein of unknown function (Tiny_TM_bacill)<br>This entry represents a family of hypothetical proteins, half of which are 40 residues or less in length. Members are found only in spore-forming species. A Gly-rich variable region is followed by a strongly conserved, highly hydrophobic region, predicted to form a transmembrane helix, ending with an invariant Gly. The consensus for this stretch is FALLVVFILLIIV.. 
PF09681 N-terminal phage replisome organiser (Phage_rep_org_N)<br>This entry represents the N-terminal domain of a small family of phage proteins. The protein contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The region is N-terminal to the low-complexity region.. 
PF09682 Phage holin protein (Holin_LLH)<br>This entry identifies a family of putative phage holin from a number of phage and prophage regions of Gram-positive bacteria. Like other holins, it is small (about 100 amino acids) with stretches of hydrophobic sequence and is encoded adjacent to lytic enzymes.. 
PF09683 Bacteriocin (Lactococcin_972)<br>These sequences represent bacteriocins related to lactococcin. Members tend to be found in association with a seven transmembrane putative immunity protein.. 
PF09684 Phage tail protein (Tail_P2_I)<br>These sequences represent the family of phage P2 protein I and related tail proteins from a number of temperate phage of Gram-negative bacteria.. 
PF09685 Tic20-like protein<br>TIGRFAMs & Jackhmmer:D3PVW8. Chloroplast function requires the import of nuclear encoded proteins from the cytoplasm across the chloroplast double membrane. This is accomplished by two protein complexes, the Toc complex located at the outer membrane and the Tic complex located at the inner membrane. The Toc complex recognises specific proteins by a cleavable N-terminal sequence and is primarily responsible for translocation through the outer membrane, while the Tic complex translocates the protein through the inner membrane. This entry represents Tic20, a core member of the Tic complex. This protein is deeply embedded in the inner envelope membrane and is thought to function as a protein- conducting component of the Tic complex. This family also includes many proteins of unknown function from non-synthetic organisms.. 
PF09686 Plasmid protein of unknown function (Plasmid_RAQPRD)<br>This entry identifies a family of proteins, which are about 100 amino acids in length, including a predicted signal sequence and a perfectly conserved motif RAQPRD towards the C terminus. Members are found in the Pseudomonas putida TOL plasmid pWW0 and in cryptic plasmid regions of Salmonella enterica subsp. enterica serovar Typhi and Pseudomonas syringae DC3000. The function of these proteins are unknown.. 
PF09687 P_fal_TIGR01639; PHIST_a_b; PHIST_a_c; PRESAC; DUF3837; PRESAC;<br>Plasmodium RESA N-terminal. The short, four-helical domain first identified in the Plasmodium export proteins PHISTa and PHISTc   has been extended to become this six-helical PRESAN domain identified in the P. falciparum-specific RESA-type (Ring-infected erythrocyte surface antigen) proteins in association with the DnaJ domain. Overall, at least 67 proteins have been detected in P. falciparum with complete copies of the PRESAN domain. No versions of this domain were detected in other apicomplexan genera, suggesting that the domain was 'invented' after the divergence of the lineage leading to the genus Plasmodium undergoing a dramatic proliferation only in P. falciparum. A secondary structure-prediction derived from the multiple alignment of the PRESAN family reveals that it is composed of an all-helical fold with six conserved helical segments. There is some evidence it might localise to membranes  .. 
PF09688 CHP1606_PLAF3D7; <br>Protein of unknown function (Wx5_PLAF3D7). This set of protein sequences represent a family of at least four proteins in Plasmodium falciparum (isolate 3D7). An interesting feature is five perfectly conserved Trp residues.. 
PF09689 Plasmodium yoelii repeat (PY_rept_46)<br>This repeat is found in the products of only 2 genes in Plasmodium yoelii, in each of these proteins it is repeated 9 times. It is found in no other organism.. 
PF09690 Plasmodium yoelii subtelomeric region (PYST-C1)<br>This group of sequences are defined by the N-terminal domain of a paralogous family of Plasmodium yoelii genes preferentially located in the subtelomeric regions of the chromosomes. There are no obvious homologues to these genes in any other organism. The C-terminal portions of the genes that contain this domain are divergent and some contain other yoelii-specific paralogous domains such as PYST-C2 (IPR006491).. 
PF09691 Bacterial chaperone lipoprotein (PulS_OutS)<br>This family comprises lipoproteins from four gamma proteobacterial species: PulS protein of Klebsiella pneumoniae (P20440), the OutS protein of Erwinia chrysanthemi (Q01567) and Pectobacterium chrysanthemi, and the functionally uncharacterized E. coli protein EtpO. PulS and OutS have been shown to interact with and facilitate insertion of secretins into the outer membrane, suggesting a chaperone-like, or piloting function for members of this family.. 
PF09692 Argonaute siRNA chaperone (ARC) complex subunit Arb1<br>Arb1 is required for histone H3 Lys9 (H3-K9) methylation, heterochromatin, assembly and siRNA generation in fission yeast  .. 
PF09693 Phage uncharacterised protein (Phage_XkdX)<br>This entry identifies a family of small (about 50 amino acid) phage proteins, found in at least 12 different phage and prophage regions of Gram-positive bacteria. In a number of these phage, the gene for this protein is found near the holin and endolysin genes.. 
PF09694 Bacterial protein of unknown function (Gcw_chp)<br>This entry represents a conserved hypothetical protein about 240 residues in length found so far in Proteobacteria including Shewanella oneidensis and Ralstonia solanacearum, usually as part of a paralogous family. The function is unknown.. 
PF09695 Bacterial protein of unknown function (YtfJ_HI0045)<br>These are sequences from gamma proteobacteria that are related to the E. coli protein, YtfJ.. 
PF09696 Ctf8<br>Pfam-B_46199 (release 21.0). Ctf8 (chromosome transmissions fidelity 8) is a component of the Ctf18 RFC-like complex which is a DNA clamp loader involved in sister chromatid cohesion.. 
PF09697 Protein of unknown function (Porph_ging)<br>This family of proteins of unknown function is found in Porphyromonas gingivalis (Bacteroides gingivalis).. 
PF09698 Geobacter CxxxxCH...CXXCH motif (GSu_C4xC__C2xCH)<br>This motif occurs from three to eight times in eight different proteins of Geobacter sulfurreducens. The final CXXCH motif matches the cytochrome c family haem-binding site signature, suggesting that the sequence may be involved in haem-binding.. 
PF09699 Doubled CXXCH motif (Paired_CXXCH_1)<br>This entry represents a domain of about 41 amino acids that contains, among other motifs, two copies of the motif CXXCH associated with haem binding. This domain is predicted to be a high molecular weight c-type cytochrome and is often found in multiple copies. Members are found mostly in species of Shewanella, Geobacter, and Vibrio.. 
PF09700 CRISPR-associated protein (Cas_Cmr3)<br>CRISPR is a term for Clustered Regularly Interspaced Short Palindromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. This highly divergent family, found in at least ten different archaeal and bacterial species, is represented by TM1793 from Thermotoga maritima.. 
PF09701 CRISPR-associated protein (Cas_Cmr5)<br>CRISPR is a term for Clustered, Regularly Interspaced Short Palindromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This family, represented by TM1791.1 of Thermotoga maritima, is found in both archaeal and bacterial species.. 
PF09702 CRISPR-associated protein (Cas_Csa5)<br>CRISPR is a term for Clustered, Regularly Interspaced Short Palindromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This entry represents a minor family of Cas proteins found in various species of Sulfolobus and Pyrococcus (all archaeal). It is found with two different CRISPR loci in Sulfolobus solfataricus.. 
PF09703 CRISPR-associated protein (Cas_Csa4)<br>CRISPR loci appear to be mobile elements with a wide host range. This entry represents a protein that tends to be found near CRISPR repeats. The species range for this species, so far, is exclusively archaeal. It is found so far in only four different species, and includes two tandem genes in Pyrococcus furiosus DSM 3638. CRISPR is a term for Clustered, Regularly Interspaced Short Palindromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins.. 
PF09704 CRISPR-associated protein (Cas_Cas5)<br>CRISPR is a term for Clustered, Regularly Interspaced Short Palindromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This small Cas family is represented by CT1134 of Chlorobium tepidum.. 
PF09706 CRISPR-associated protein (Cas_CXXC_CXXC)<br>CRISPR is a term for Clustered, Regularly Interspaced Short Palindromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This entry describes a conserved region of about 65 amino acids from an otherwise highly divergent protein found in a minority of CRISPR-associated protein regions. This region features two motifs of CXXC.. 
PF09707 CRISPR-associated protein (Cas_Cas2CT1978)<br>This entry represents a minor branch of the Cas2 family of CRISPR-associated protein which are found in IPR003799. Cas proteins are found adjacent to a characteristic short, palindromic repeat cluster termed CRISPR, a probable mobile DNA element.. 
PF09709 CRISPR-associated protein (Cas_Csd1)<br>CRISPR loci appear to be mobile elements with a wide host range. This entry represents proteins that tend to be found near CRISPR repeats. The species range, so far, is exclusively bacterial and mesophilic, although CRISPR loci are particularly common among the archaea and thermophilic bacteria. Clusters of short DNA repeats with nonhomologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognisable features. This family is known as CRISPR (short for Clustered, Regularly Interspaced Short Palindromic Repeats). A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins.. 
PF09710 Treponema clustered lipoprotein (Trep_dent_lipo)<br>This entry represents a family of six predicted lipoproteins from a region of about 20 tandemly arranged genes in the Treponema denticola genome. Two other neighbouring genes share the lipoprotein signal peptide region but do not show more extensive homology. The function of this locus is unknown.. 
PF09711 CRISPR-associated protein (Cas_Csn2)<br>CRISPR loci appear to be mobile elements with a wide host range. This entry represents proteins found only in CRISPR-containing species, near other CRISPR-associated proteins (cas). The species range so far for these proteins is pathogenic bacteria only. Clusters of short DNA repeats with nonhomologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognisable features. This family is known as CRISPR (short for Clustered, Regularly Interspaced Short Palindromic Repeats).. 
PF09712 Poly(R)-hydroxyalkanoic acid synthase subunit (PHA_synth_III_E)<br>This entry represents the PhaE subunit of the heterodimeric class (class III) of polymerase for poly(R)-hydroxyalkanoic acids (PHAs), carbon and energy storage polymers of many bacteria. The most common PHA is polyhydroxybutyrate but about 150 different constituent hydroxyalkanoic acids (HAs) have been identified in various species.. 
PF09713 Plant protein 1589 of unknown function (A_thal_3526)<br>This plant-specific family of proteins is defined by an uncharacterised region 57 residues in length. It is found toward the N terminus of most proteins that contain it. Examples include at least several proteins from Arabidopsis thaliana and Oryza sativa. The function of the proteins are unknown.. 
PF09715 Plasmodium protein of unknown function (Plasmod_dom_1)<br>These sequences represent an uncharacterised family consisting of a small number of hypothetical proteins of the malaria parasite Plasmodium falciparum (isolate 3D7).. 
PF09716 Malarial early transcribed membrane protein (ETRAMP)<br>These sequences represent a family of proteins from the malaria parasite Plasmodium falciparum, several of which have been shown to be expressed specifically in the ring stage as well as the rodent parasite Plasmodium yoelii. A homologue from Plasmodium chabaudi was localized to the parasitophorous vacuole membrane. Members have an initial hydrophobic, Phe/Tyr-rich, stretch long enough to span the membrane, a highly charged region rich in Lys, a second putative transmembrane region and a second highly charged, low complexity sequence region. Some members have up to 100 residues of additional C-terminal sequence. These genes have been shown to be found in the sub-telomeric regions of both Plasmodium falciparum and P. yoelii chromosomes.. 
PF09717 Plasmodium falciparum domain of unknown function (CPW_WPC)<br>This group of sequences is defined by a domain of about 61 residues in length with six well-conserved cysteine residues and six well-conserved aromatic sites. The domain can be found in tandem repeats, and is known so far only in Plasmodium falciparum. It is named for motifs of CPxxW and (less well conserved) WPC. Its function is unknown.. 
PF09718 Lambda phage tail tape-measure protein (Tape_meas_lam_C)<br>This represents a relatively well-conserved region near the C terminus of the tape measure protein of a lambda and related phage. The protein, which controls phage tail length, is typically about 1000 residues in length. Both low-complexity sequence and insertion/deletion events appear common in this family. Mutational studies suggest a ruler or template role in the determination of phage tail length. Similar behaviour is attributed to proteins from distantly related or unrelated families in other phage.. 
PF09719 Putative redox-active protein (C_GCAxxG_C_C)<br>This entry represents a putative redox-active protein of about 140 residues, with four perfectly conserved Cys residues. It includes a CGAXXG motif. Most members are found within one or two loci of transporter or oxidoreductase genes. A member from Geobacter sulfurreducens, located in a molybdenum transporter operon, has a TAT (twin-arginine translocation) signal sequence for Sec-independent transport across the plasma membrane, a hallmark of bound prosthetic groups such as FeS clusters.. 
PF09720 Stabl_TIGR02574; <br>Putative addiction module component. This entry defines several short bacterial proteins, typically about 75 amino acids long, which are always found as part of a pair (at least) of small genes. The other protein in the pair always belongs to a family of plasmid stabilisation proteins (IPR007712). It is likely that this protein and its partner comprise some form of addiction module - a pair of genes consisting of a stable toxin and an unstable antitoxin which mediate programmed cell death - although these gene-pairs are usually found on the bacterial main chromosome.. 
PF09721 Transmembrane exosortase (Exosortase_EpsH)<br>Members of this family are designated exosortase, analogous to sortase in cell wall sorting mediated by LPXTG domains in Gram-positive bacteria. The phylogenetic distribution of the proteins in this entry is nearly perfectly correlated with the distribution of the proteins having the PEP-CTERM anchor motif, IPR013424. Members of this entry are integral membrane proteins with eight predicted transmembrane helices in common. Some members of this family have long trailing sequences past the region described by this model. This model does not include the region of the first predicted transmembrane region. The best characterised member is EpsH of Methylobacillus sp. 12S, where it is part of a locus associated with biosynthesis of the exopolysaccharide methanol-an.. 
PF09722 CHP2293; <br>Protein of unknown function (DUF2384). Proteins in this family are found almost exclusively in the Proteobacteria, but also in Gloeobacter violaceus PCC 7421, a cyanobacterium. The function is unknown.. 
PF09723 CxxC_CxxC_SSSS;<br>This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.. 
PF09724 Uncharacterized conserved protein (DUF2036)<br>This family of proteins includes members ranging in size from approximately 300 to 460 residues. There are a number of well-conserved domains along the length.. 
PF09725 Folate-sensitive fragile site protein Fra10Ac1<br>This entry represents the full-length proteins in which, in higher eukaryotes, the nested domain EDSLL lies. Fra10Ac1 is a highly conserved protein, of unknown function that is nuclear and highly expressed in brain  .. 
PF09726 Transmembrane protein<br>This entry is a highly conserved protein present in eukaryotes.. 
PF09727 Cortactin-binding protein-2<br>This entry is the first approximately 250 residues of cortactin-binding protein 2. In addition to being a positional candidate for autism this protein is expressed at highest levels in the brain in humans.  The human protein has six associated ankyrin repeat domains Pfam:PF00023 towards the C-terminus which act as protein-protein interaction domains  .. 
PF09728 Myosin-like coiled-coil protein<br>Taxilin contains an extraordinarily long coiled-coil domain in its C-terminal half and is ubiquitously expressed. It is a novel binding partner of several syntaxin family members and is possibly involved in Ca2+-dependent exocytosis in neuroendocrine cells  . Gamma-taxilin, described as leucine zipper protein Factor Inhibiting ATF4-mediated Transcription (FIAT), localises to the nucleus in osteoblasts and dimerises with ATF4 to form inactive dimers, thus inhibiting ATF4-mediated transcription  .. 
PF09729 Gti1/Pac2 family<br>In S. pombe the gti1 protein promotes the onset of gluconate uptake upon glucose starvation  . In S. pombe the Pac2 protein controls the onset of sexual development, by inhibiting the expression of ste11, in a pathway that is independent of the cAMP cascade  .. 
PF09730 Microtubule-associated protein Bicaudal-D<br>BicD proteins consist of three coiled-coiled domains and are involved in dynein-mediated minus end-directed transport from the Golgi apparatus to the endoplasmic reticulum (ER). For full functioning they bind with GSK-3beta Pfam:PF05350 to maintain the anchoring of microtubules to the centromere. It appears that amino-acid residues 437-617 of BicD and the kinase activity of GSK-3 are necessary for the formation of a complex between BicD and GSK-3beta in intact cells  .. 
PF09731 Mitochondrial inner membrane protein<br>Mitofilin controls mitochondrial cristae morphology. Mitofilin is enriched in the narrow space between the inner boundary and the outer membranes, where it forms a homotypic interaction and assembles into a large multimeric protein complex  . The first 78 amino acids contain a typical amino-terminal-cleavable mitochondrial presequence rich in positive-charged and hydroxylated residues and a membrane anchor domain.  In addition, it has three centrally located coiled coil domains  .. 
PF09732 Cactin; <br>Cactus-binding C-terminus of cactin protein. CactinC_cactus is the C-terminal 200 residues of the cactin protein which are necessary for the association of cactin with IkappaB-cactus as one of the intracellular members of the Rel complex. The Rel (NF-kappaB) pathway is conserved in invertebrates and vertebrates. In mammals, it controls the activities of the immune and inflammatory response genes as well as viral genes, and is critical for cell growth and survival. In Drosophila, the Rel pathway functions in the innate cellular and humoral immune response, in muscle development, and in the establishment of dorsal-ventral polarity in the early embryo  . Most members of the family also have a Cactin_mid domain Pfam:PF10312 further upstream.. 
PF09733 VEFS-Box of polycomb protein<br>The VEFS-Box (VRN2-EMF2-FIS2-Su(z)12) box is the C-terminal region of these proteins, characterised by an acidic cluster and a tryptophan/methionine-rich sequence, the acidic-W/M domain  . Some of these sequences are associated with a zinc-finger domain about 100 residues towards the N-terminus. This protein is one of the polycomb cluster of proteins which control HOX gene transcription as it functions in heterochromatin-mediated repression  .. 
PF09734 RNA polymerase III transcription factor (TF)IIIC subunit<br>TFIIIC1 is a multisubunit DNA binding factor that serves as a dynamic platform for assembly of pre-initiation complexes on class III genes. This entry represents the tau 95 subunit which holds a key position in TFIIIC, exerting both upstream and downstream influence on the TFIIIC-DNA complex by rendering the complex more stable. Once bound to tDNA-intragenic promoter elements, TFIIIC directs the assembly of TFIIIB on the DNA, which in turn recruits the RNA polymerase III (pol III) and activates multiple rounds of transcription.. 
PF09735 Membrane-associated apoptosis protein<br>Expression of this protein was found to be markedly reduced in patients with Alzheimer's disease  . It is involved in the regulation of actin polymerisation in the brain as part of a WAVE2 signalling complex  .. 
PF09736 DUF2050; <br>Pre-mRNA-splicing factor of RES complex. This entry is characterised by proteins with alternating conserved and low-complexity regions. Bud13 together with Snu17p and a newly identified factor, Pml1p/Ylr016c, form a novel trimeric complex. called The RES complex, pre-mRNA retention and splicing complex. Subunits of this complex are not essential for viability of yeasts but they are required for efficient splicing in vitro and in vivo. Furthermore, inactivation of this complex causes pre-mRNA leakage from the nucleus. Bud13 contains a unique, phylogenetically conserved C-terminal region of unknown function  .. 
PF09737 De-etiolated protein 1 Det1<br>
PF09738 Double stranded RNA binding protein (DUF2051)<br>This is a novel protein identified as interacting with the leucine-rich repeat domain of human flightless-I, FliI protein.. 
PF09739 DUF2044;<br>Mini-chromosome maintenance replisome factor. This entry is of proteins of approximately 600 residues in length containing alternating regions of conservation and low complexity.  The Arabidopsis protein is a replisome factor found to bind with the mini-chromosome maintenance, MCM-binding, complex and is crucial for efficient DNA replication.. 
PF09740 Uncharacterized conserved protein (DUF2043)<br>This is a 100 residue conserved region of a family of proteins found from fungi to humans.  This region contains three conserved Cysteines and a motif of {CP}{y/l}{HG}.. 
PF09741 Uncharacterized conserved protein (DUF2045)<br>This entry is the conserved 250 residues of proteins of approximately 450 amino acids. It contains several highly conserved motifs including a CVxLxxxD motif.The function is unknown.. 
PF09742 Dyggve-Melchior-Clausen syndrome protein<br>Dymeclin (Dyggve-Melchior-Clausen syndrome protein) contains a large number of leucine and isoleucine residues and a total of 17 repeated dileucine motifs. It is characteristically about 700 residues long and present in plants and animals.  Mutations in the gene coding for this protein in humans give rise to the disorder Dyggve-Melchior-Clausen syndrome (DMC, MIM 223800) which is an autosomal-recessive disorder characterised by the association of a spondylo-epi-metaphyseal dysplasia and mental retardation  . DYM transcripts are widely expressed throughout human development and Dymeclin is not an integral membrane protein of the ER, but rather a peripheral membrane protein dynamically associated with the Golgi apparatus  . . 
PF09743 Uncharacterized conserved protein (DUF2042)<br>This entry is the conserved N-terminal 300 residues of a group of proteins found from protozoa to Humans.  The function is unknown.. 
PF09744 JNK_SAPK-associated protein-1<br>This is the N-terminal 200 residues of a set of proteins conserved from yeasts to humans. Most of the proteins in this entry have an RhoGEF Pfam:PF00621 domain at their C-terminal end.. 
PF09745 Coiled-coil domain-containing protein 55 (DUF2040)<br>This entry is a conserved domain of approximately 130 residues of proteins conserved from fungi to humans. The proteins do contain a coiled-coil domain, but the function is unknown.. 
PF09746 Tumour-associated protein<br>Membralin is evolutionarily highly conserved; though it seems to represent a unique protein family. The protein appears to contain several transmembrane regions. In humans it is expressed in certain cancers, particularly ovarian cancers  . Membralin-like gene homologues have been identified in plants including grape, cotton and tomato  .. 
PF09747 Coiled-coil domain containing protein (DUF2052)<br>This entry is of sequences of two conserved domains separated by a region of low complexity, spanning some 200 residues. The function is unknown.. 
PF09748 Transcription factor subunit Med10 of Mediator complex<br>Med10 is one of the protein subunits of the Mediator complex, tethered to Rgr1 protein. The Mediator complex is required for the transcription of most RNA polymerase II (Pol II)-transcribed genes. Med10 specifically mediates basal-level HIS4 transcription via Gcn4, and, additionally, there is a putative requirement for Med10 in Bas2-mediated transcription  . Med10 is part of the middle region of Mediator  .. 
PF09749 Uncharacterised conserved protein<br>This entry is of proteins of approximately 300 residues conserved from plants to humans.  It contains two conserved motifs, HxSL and FHVSL. The function is unknown.. 
PF09750 DRY; <br>Alternative splicing regulator  . This entry represents the conserved N-terminal region of SWAP (suppressor-of-white-apricot protein) proteins.  This region contains two highly conserved motifs, viz: DRY and EERY, which appear to be the sites for alternative splicing of exons 2 and 3 of the SWAP mRNA  . These proteins are thus thought to be involved in auto-regulation of pre-mRNA splicing. Most family members are associated with two Surp domains Pfam:PF01805 and an Arginine- serine-rich binding region towards the C-terminus.. 
PF09751 Nuclear protein Es2<br>This entry is of a family of proteins of approximately 500 residues with alternating regions of low complexity and conservation where the domain similarities are strong.  Apart from a predicted coiled-coil domain, no other known functional domains have been characterised. The protein appears to be expressed in the nucleus and particularly highly in the pons sub-region of the brain. The protein is clearly necessary for normal development of the nervous system  .. 
PF09752 Uncharacterized conserved protein (DUF2048)<br>The proteins in this family are conserved from plants to vertebrates. The function is unknown.. 
PF09753 Membrane fusion protein Use1<br>This entry is of a family of proteins all approximately 300 residues in length. The proteins have a single C-terminal trans-membrane domain and a SNARE [soluble NSF (N-ethylmaleimide-sensitive fusion protein) attachment protein receptor] domain of approximately 60 residues. The SNARE domains are essential for membrane fusion and are conserved from yeasts to humans. Use1 is one of the three protein subunits that make up the SNARE complex and it is specifically required for Golgi-endoplasmic reticulum retrograde transport.. 
PF09754 HCCA3;<br>This PAC2 (Proteasome assembly chaperone) family of proteins is found in bacteria, archaea and eukaryotes.  Proteins in this family are typically between 247 and 307 amino acids in length. These proteins function as a chaperone for the 26S proteasome. The 26S proteasome mediates ubiquitin-dependent proteolysis in eukaryotic cells. A number of studies including very recent ones have revealed that assembly of its 20S catalytic core particle is an ordered process that involves several conserved proteasome assembly chaperones (PACs). Two heterodimeric chaperones, PAC1-PAC2 and PAC3-PAC4, promote the assembly of rings composed of seven alpha subunits  .. 
PF09755 Uncharacterized conserved protein H4 (DUF2046)<br>This is the conserved N-terminal 350 residues of a family of proteins of unknown function possibly containing a coiled-coil domain.. 
PF09756 DDRGK domain<br>This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif.. 
PF09757 Arb2 domain<br>A second fission yeast Argonaute complex (Argonaute siRNA chaperone, ARC) that contains two previously uncharacterized proteins, Arb1 and Arb2, both of which are required for histone H3 Lys9 (H3-K9) methylation, heterochromatin assembly and siRNA generation  . This family includes a region found in Arb2 and the Hda1 protein.. 
PF09758 Uncharacterised conserved protein<br>This entry represents an N-terminal region of approximately 150 residues of a family of proteins of unknown function. It contains a highly conserved FPL motif.. 
PF09759 Spinocerebellar ataxia type 10 protein domain<br>This is the conserved C-terminal 100 residues of Ataxin-10. Ataxin-10 belongs to the family of armadillo repeat proteins and in solution it tends to form homotrimeric complexes, which associate via a tip-to-tip association in a horseshoe-shaped contact with the concave sides of the molecules facing each other. This domain may represent the homo-association site since that is located near the C-terminus of Ataxin-10. The protein does not contain a signal sequence for secretion or any subcellular compartment confirming its cytoplasmic localisation, specifically to the olivocerebellar region  .. 
PF09762 Coiled-coil domain-containing protein (DUF2037)<br>This entry represents the conserved N-terminal 200 residues of a family of proteins conserved from plants to vertebrates. In Drosophila it comes from the Fidipidine gene, and is of unknown function.. 
PF09763 Sec3;<br>Exocyst complex component Sec3. This entry is the conserved middle and C-terminus of the Sec3 protein. Sec3 binds to the C-terminal cytoplasmic domain of GLYT1 (glycine transporter protein 1). Sec3 is the exocyst component that is closest to the plasma membrane docking site and it serves as a spatial landmark in the plasma membrane for incoming secretory vesicles. Sec3 is recruited to the sites of polarised membrane growth through its interaction with Rho1p, a small GTP-binding protein.. 
PF09764 WDYHV;<br>N-terminal glutamine amidase. This protein is conserved from plants to humans. It represents a family of N terminal glutamine amidases. The enzyme removes the NH2 group from a Gln, at the N-terminal, rendering it a Glu.. 
PF09765 WD-repeat region<br>This entry is of a region of approximately 100 residues containing three WD repeats and six cysteine residues possibly as three cystine-bridges. These regions are contained within the Fancl protein in humans which is the putative E3 ubiquitin ligase subunit of the FA complex (Fanconi anaemia). Eight subunits of the Fanconi anaemia gene products form a multisubunit nuclear complex which is required for mono-ubiquitination of a downstream FA protein, FANCD2. The WD repeats are required for interaction with other subunits of the FA complex.. 
PF09766 Fms-interacting protein<br>This entry carries part of the crucial 144 N-terminal residues of the FmiP protein, which is essential for the binding of the protein to the cytoplasmic domain of activated Fms-molecules in M-CSF induced haematopoietic differentiation of macrophages. The C-terminus contains a putative nuclear localisation sequence and a leucine zipper which suggest further, as yet unknown, nuclear functions. The level of FMIP expression might form a threshold that determines whether cells differentiate into macrophages or into granulocytes.. 
PF09767 Predicted membrane protein (DUF2053)<br>This entry is of the conserved N-terminal 150 residues of proteins conserved from plants to humans. The function is unknown although some annotation suggests it to be a transmembrane protein.. 
PF09768 Ku70-bp; <br>Peptidase M76 family. This is a family of metalloproteases.  Proteins in this family are also annotated as Ku70-binding proteins.. 
PF09769 Apolipoprotein O<br>Members of this family promote cholesterol efflux from macrophage cells. They are present in various lipoprotein complexes, including HDL, LDL and VLDL. The apoprotein is secreted by a microsomal triglyceride transfer protein (MTTP)-dependent mechanism, probably as a VLDL-associated protein that is subsequently transferred to HDL  .. 
PF09770 Topoisomerase II-associated protein PAT1<br>Members of this family are necessary for accurate chromosome transmission during cell division  . . 
PF09771 Transmemb_18; Tmem18A; <br>Transmembrane protein 188. The function of this family of transmembrane proteins has not, as yet, been determined.. 
PF09772 Transmemb_26; <br>Transmembrane protein 26. The function of this family of transmembrane proteins has not, as yet, been determined.. 
PF09773 Meckelin (Transmembrane protein 67)<br>Members of this family are thought to be related to the ciliary basal body.  Defects result in Meckel syndrome type 3, [MIM:607361], an autosomal recessive disorder characterised by a combination of renal cysts and variably associated features including developmental anomalies of the central nervous system (typically encephalocele), hepatic ductal dysplasia and cysts, and polydactyly. Joubert syndrome type 6 [MIM:610688] is also a manifestation of certain mutations; it is an autosomal recessive congenital malformation of the cerebellar vermis and brainstem with abnormalities of axonal decussation (crossing in the brain) affecting the corticospinal tract and superior cerebellar peduncles. Individuals with Joubert syndrome have motor and behavioral abnormalities, including an inability to walk due to severe clumsiness and 'mirror' movements, and cognitive and behavioural disturbances   .. 
PF09774 Caffeine-induced death protein 2<br>Members of this family of proteins mediate the disruption of the DNA replication checkpoint (S-M checkpoint) mechanism caused by caffeine.. 
PF09775 Keratinocyte-associated protein 2<br>Members of this family comprise various keratinocyte-associated proteins. Their exact function has not, as yet, been determined.. 
PF09776 Mitochondrial ribosomal protein L55<br>Members of this family are involved in mitochondrial biogenesis and G2/M phase cell cycle progression. They form a component of the mitochondrial ribosome large subunit (39S) which comprises a 16S rRNA and about 50 distinct proteins.. 
PF09777 Osteopetrosis-associated transmembrane protein 1 precursor<br>Members of this family of proteins are required for osteoclast and melanocyte maturation and function. Mutations give rise to autosomal recessive osteopetrosis [MIM:259700]; also called autosomal recessive Albers-Schonberg disease.. 
PF09778 Guanylylate cyclase<br>Members of this family of proteins catalyse the conversion of guanosine triphosphate (GTP) to 3',5'-cyclic guanosine monophosphate (cGMP) and pyrophosphate.. 
PF09779 DUF2349;<br>Ima1 N-terminal domain. This domain occurs at the N-terminus of the Schizosaccharomyces pombe inner nuclear membrane protein, Ima1. Ima1 interacts with other inner nuclear membrane proteins [1-2].. 
PF09781 NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit<br>Members of this family mediate the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone, the reaction that occurs being: NADH + ubiquinone = NAD(+) + ubiquinol   .. 
PF09782 NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit<br>Members of this family mediate the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone, the reaction that occurs being: NADH + ubiquinone = NAD(+) + ubiquinol  .. 
PF09783 Vacuolar import and degradation protein<br>Members of this family are involved in the negative regulation of gluconeogenesis. They are required for both proteosome-dependent and vacuolar catabolite degradation of fructose-1,6-bisphosphatase (FBPase), where they probably regulate FBPase targeting from the FBPase-containing vesicles to the vacuole   .. 
PF09784 Mitochondrial ribosomal protein L31<br>Pfam-B_24102 (release 21.0). This is a family of mitochondrial ribosomal proteins.  L31 is essential for mitochondrial function in yeast  .. 
PF09785 Prp31 C terminal domain<br>Pfam-B_7665 (release 21.0). This is the C terminal domain of the pre-mRNA processing factor Prp31.  Prp31 is required for U4/U6.U5 tri-snRNP formation  . In humans this protein has been linked to autosomal dominant retinitis pigmentosa   .. 
PF09786 Cytochrome B561, N terminal<br>Members of this family are found in the N terminal region of cytochrome B561, as well as in various other putative uncharacterised proteins.. 
PF09787 Golgin subfamily A member 5<br>Members of this family of proteins are involved in maintaining Golgi structure. They stimulate the formation of Golgi stacks and ribbons, and are involved in intra-Golgi retrograde transport. Two main interactions have been characterised: one with RAB1A that has been activated by GTP-binding and another with isoform CASP of CUTL1  .. 
PF09788 Transmemb_55A; Tmem55A; <br>Transmembrane protein 55A. Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.. 
PF09789 Uncharacterized coiled-coil protein (DUF2353)<br>Members of this family of uncharacterised proteins have no known function.. 
PF09790 Hyccin<br>Members of this family of proteins may have a role in the beta-catenin-Tcf/Lef signaling pathway, as well as in the process of myelination of the central and peripheral nervous system. Defects in Hyccin are the cause of hypomyelination with congenital cataracts [MIM:610532]. This disorder is characterised by congenital cataracts, progressive neurologic impairment, and diffuse myelin deficiency. Affected individuals experience progressive pyramidal and cerebellar dysfunction, muscle weakness and wasting prevailing in the lower limbs   .. 
PF09791 Oxidoreductase-like protein, N-terminal<br>Members of this family are found in the N terminal region of various oxidoreductase like proteins. Their exact function is, as yet, unknown.. 
PF09792 DUF2295; <br>Ubiquitin 3 binding protein But2 C-terminal domain. Pfam-B_45554 (release 21.0). This family is of proteins conserved in yeasts. It binds to Uba3 and is involved in the NEDD8 signalling pathway  . This family represents a presumed C-terminal domain.. 
PF09793 Anticodon-binding domain<br>This domain of approximately 100 residues is conserved from plants to humans. It is frequently found in association with Lsm domain-containing proteins. It is an anticodon-binding domain of a prolyl-tRNA synthetase, whose PDB structure is available under the identifier 1h4q.. 
PF09794 Transport protein Avl9<br>Pfam-B_12001 (release 21.0). Avl9 is a protein involved in exocytic transport from the Golgi. It has been speculated that Avl9 could play a role in deforming membranes for vesicle fission and/or in recruiting cargo  .. 
PF09795 Autophagy-related protein 31<br>Pfam-B_60001 (release 21.0). Autophagy is an intracellular degradation system that responds to nutrient starvation.  Cis1/Atg31 has been shown to be required for autophagosome formation in Saccharomyces cerevisiae  .  It interacts with Atg17  .. 
PF09796 Ubiquinol-cytochrome-c reductase complex subunit (QCR10)<br>The QCR10 family of proteins are a component of the ubiquinol-cytochrome c reductase complex (also known as complex III or cytochrome b-c1 complex).  This complex is located on the inner mitochondrial membrane and it couples electron transfer from ubiquinol to cytochrome.  This subunit (QCR10) is required for stable association of the iron-sulfur protein with the complex  .. 
PF09797 N-acetyltransferase B complex (NatB) non catalytic subunit<br>Pfam-B_12009 (release 21.0). This is the non-catalytic subunit of the N-terminal acetyltransferase B complex (NatB). The NatB complex catalyses the acetylation of the amino-terminal methionine residue of all proteins beginning with Met-Asp or Met-Glu and of some proteins beginning with Met-Asn or Met-Met.  In Saccharomyces cerevisiae this subunit is called MDM20 and in Schizosaccharomyces pombe it is called Arm1.  NatB acetylates the Tpm1 protein and regulates and tropomyocin-actin interactions.  This subunit is required by the NatB complex for the N-terminal acetylation of Tpm1  .. 
PF09798 DNA damage checkpoint protein<br>Pfam-B_41058 (release 21.0). This is a family of proteins which regulate checkpoint kinases. In Schizosaccharomyces pombe this protein is called Rad26 and in Saccharomyces cerevisiae it is called LCD1  .. 
PF09799 Transmemb_17; Tmem17; <br>Predicted membrane protein. KOGs (KOG4694), (KOG4502). This is a 100 amino acid region of a family of proteins conserved from nematodes to humans. It is predicted to be a transmembrane region but its function is not known.. 
PF09801 Integral membrane protein S linking to the trans Golgi network<br>Members of this family are integral membrane proteins involved in protein trafficking between the late Golgi and endosome. They may also serve as a receptor for ADP-ribosylation factor-related protein 1 (ARFRP1)  . Sys1p is a small integral membrane protein with four predicted transmembrane domains that localises to the Trans Golgi network TGN in yeast and human cells  .. 
PF09802 Preprotein translocase subunit Sec66<br>Members of this family of proteins are a component of the heterotetrameric Sec62/63 complex composed of SEC62, SEC63, SEC66 and SEC72. The Sec62/63 complex associates with the Sec61 complex to form the Sec complex. Sec 66 is involved in SRP-independent post-translational translocation across the endoplasmic reticulum and functions together with the Sec61 complex and KAR2 in a channel-forming translocon complex. Furthermore, Sec66 is also required for growth at elevated temperatures     .. 
PF09803 Uncharacterized conserved protein (DUF2346)<br>Members of this family of proteins have no known function.. 
PF09804 Uncharacterized conserved protein (DUF2347)<br>Members of this family of hypothetical proteins have no known function.. 
PF09805 Nucleolar protein 12 (25kDa)<br>Members of this family of proteins are part of the yeast nuclear pore complex-associated pre-60S ribosomal subunit  . The family functions as a highly conserved exonuclease that is required for the 5'-end maturation of 5.8S and 25S rRNAs, demonstrating that 5'-end processing also has a redundant pathway. Nop25 binds late pre-60S ribosomes, accompanying them from the nucleolus to the nuclear periphery; and there is evidence for both physical and functional links between late 60S subunit processing and export  .. 
PF09806 Cyclin-dependent kinase 2-associated protein<br>Members of this family of proteins are cell-growth suppressors, associating with and influencing the biological activities of important cell cycle regulators in the S phase including monomeric non-phosphorylated cyclin-dependent kinase 2 (CDK2) and DNA polymerase alpha/primase. An association between mutations in the gene coding for this protein and oral cancer has been described.. 
PF09807 Uncharacterized conserved protein (DUF2348)<br>Members of this family of putative uncharacterized proteins have no known function.. 
PF09808 Small nuclear RNA activating complex (SNAPc), subunit SNAP43<br>Members of this family are part of the SNAPc complex required for the transcription of both RNA polymerase II and III small-nuclear RNA genes. They bind to the proximal sequence element (PSE), a non-TATA-box basal promoter element common to these 2 types of genes. Furthermore, they also recruit TBP and BRF2 to the U6 snRNA TATA box.. 
PF09809 MRP_L27; <br>Mitochondrial ribosomal protein L27. Members of this family of proteins are components of the mitochondrial ribosome large subunit. They are also involved in apoptosis and cell cycle regulation.. 
PF09810 Morph_protein1;<br>Exonuclease V - a 5' deoxyribonuclease. Exonuclease V is a monomeric 5' deoxyribonuclease that is localised in the nucleus. It degrades single-stranded, but not double-stranded, DNA from the 5'-end, and the products are dinucleotides, except the 3'-terminal tri- and tetranucleotides, which are not degraded. The initial hydrolytic cut of exonuclease V on the dephosphorylated substrate produces a mixture of dinucleoside monophosphates and trinucleoside diphosphates. The enzyme is processive in action  . Exo5 is specific for single-stranded DNA and does not hydrolyze RNA. However, Exo5 has the capacity to slide across 5' double-stranded DNA or 5' RNA sequences and resume cutting two nucleotides downstream of the double-stranded-to-single-stranded junction or RNA-to-DNA junction, respectively  .. 
PF09811 Essential protein Yae1, N terminal<br>Members of this family are found in the N terminal region of the essential protein Yae1. Their exact function has not, as yet, been determined. The family DUF1715, Pfam:PF08215 has now been merged into this family.. 
PF09812 MRP_L28; <br>Mitochondrial ribosomal protein L28. Members of this family are components of the mitochondrial large ribosomal subunit.  Mature mitochondrial ribosomes consist of a small (37S) and a large (54S) subunit. The 37S subunit contains at least 33 different proteins and 1 molecule of RNA (15S). The 54S subunit contains at least 45 different proteins and 1 molecule of RNA (21S)   .. 
PF09813 Coiled-coil domain-containing protein 56<br>Members of this family of proteins have no known function.. 
PF09814 DUF2351;<br>HECT-like Ubiquitin-conjugating enzyme (E2)-binding. HECT_2 is a family of UbcH10-binding proteins.. 
PF09815 XK-related protein<br>Members of this family comprise various XK-related proteins, that are involved in sodium-dependent transport of neutral amino acids or oligopeptides. These proteins are responsible for the Kx blood group system - defects results in McLeod syndrome [MIM:314850], an X-linked multi-system disorder characterised by late onset abnormalities in the neuromuscular and hematopoietic systems   .. 
PF09816 RNA polymerase II transcription elongation factor<br>Members of this family act as transcriptional transactivators of ELL and ELL2 elongation activities     . Eaf proteins form a stable heterodimer complex with ELL proteins to facilitate the binding of RNA polymerase II to activate transcription elongation. The N-terminus of approx 120 residues is globular and highly conserved  .. 
PF09817 Uncharacterized conserved protein (DUF2352)<br>Members of this family of uncharacterised proteins have no known function.. 
PF09818 Predicted ATPase of the ABC class<br>Members of this family include various bacterial predicted ABC class ATPases.. 
PF09819 ABC-type cobalt transport system, permease component<br>Members of this family of prokaryotic proteins include various hypothetical proteins as well as ABC-type cobalt transport systems.. 
PF09820 Predicted AAA-ATPase<br>Pfam-B_5377 (release 16.0). This family contains many hypothetical bacterial proteins.  This family was previously the N-terminal part of the Pfam DUF1703 (Pfam:PF08011) family before it was split into two.  This region is predicted to be an AAA-ATPase domain  .. 
PF09821 ABC_transp; AAA_36;<br>C-terminal AAA-associated domain. This had been thought to be an ATPase domain of ABC-transporter proteins. However, only one member has any trans-membrane regions. It is associated with an upstream ATP-binding cassette family, Pfam:PF00005.. 
PF09822 ABC-type uncharacterized transport system<br>This domain is found in various eukaryotic and prokaryotic intra-flagellar transport proteins involved in gliding motility, as well as in several hypothetical proteins.. 
PF09823 Domain of unknown function (DUF2357)<br>This entry was previously the N terminal portion of DUF524 (Pfam:PF04411) before it was split into two.  This domain has no known function.  It is predicted to adopt an all beta secondary structure pattern followed by mainly alpha-helical structures  .. 
PF09824 ArsR transcriptional regulator<br>Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family.. 
PF09825 Biotin-protein ligase, N terminal<br>The function of this structural domain is unknown. It is found to the N terminus of the biotin protein ligase catalytic domain.. 
PF09826 Beta propeller domain<br>Members of this family comprise secreted bacterial proteins containing C-terminal beta-propeller domain distantly related to WD-40 repeats.. 
PF09827 CRISPR associated protein Cas2<br>Members of this family of bacterial proteins comprise various hypothetical proteins, as well as CRISPR (clustered regularly interspaced short palindromic repeats) associated proteins, conferring resistance to infection by certain bacteriophages.. 
PF09828 Chromate resistance exported protein<br>Members of this family of bacterial proteins, are involved in the reduction of chromate accumulation and are essential for chromate resistance.. 
PF09829 Uncharacterized protein conserved in bacteria (DUF2057)<br>This domain, found in various prokaryotic proteins, has no known function.. 
PF09830 ATP adenylyltransferase<br>Members of this family of proteins catabolise Ap4N nucleotides (where N is A,C,G or U). Additionally they catalise the conversion of adenosine-5-phosphosulfate (AMPs) plus Pi to ADP plus sulphate, the exchange of NDP and phosphate and the synthesis of Ap4A from AMPs plus ATP  .. 
PF09831 Uncharacterized protein conserved in bacteria (DUF2058)<br>This domain, found in various prokaryotic proteins, has no known function.. 
PF09832 Uncharacterized protein conserved in bacteria (DUF2059)<br>This domain, found in various prokaryotic proteins, has no known function.. 
PF09834 Predicted membrane protein (DUF2061)<br>This domain, found in various prokaryotic proteins, has no known function.. 
PF09835 Uncharacterized protein conserved in bacteria (DUF2062)<br>This domain, found in various prokaryotic proteins, has no known function.. 
PF09836 Uncharacterized protein conserved in bacteria (DUF2063)<br>This domain, found in various prokaryotic proteins, has no known function.. 
PF09837 Uncharacterized protein conserved in bacteria (DUF2064)<br>This family has structural similarity to proteins in the nucleotide-diphospho-sugar transferases superfamily. The similarity suggests that it is an enzyme with a sugar substrate.. 
PF09838 Uncharacterized protein conserved in bacteria (DUF2065)<br>This domain, found in various prokaryotic proteins, has no known function.. 
PF09839 Uncharacterized protein conserved in bacteria (DUF2066)<br>This domain, found in various prokaryotic proteins, has no known function.. 
PF09840 Uncharacterized protein conserved in archaea (DUF2067)<br>This domain, found in various archaeal proteins, has no known function.. 
PF09842 Predicted membrane protein (DUF2069)<br>This domain, found in various prokaryotes, has no known function.. 
PF09843 Predicted membrane protein (DUF2070)<br>This domain of unknown function is found in various bacterial hypothetical proteins, as well as in prokaryotic polyketide synthase.. 
PF09844 Uncharacterized conserved protein (COG2071)<br>This conserved protein (similar to YgjF), found in various prokaryotes, has no known function.. 
PF09845 Zn-ribbon containing protein (DUF2072)<br>This archaeal protein has no known function.. 
PF09846 Uncharacterized protein conserved in archaea (DUF2073)<br>This archaeal protein has no known function.. 
PF09847 Predicted permease (DUF2074)<br>This domain, found in various archaeal hypothetical proteins, has no known function.. 
PF09848 Uncharacterized conserved protein (DUF2075)<br>This domain, found in various prokaryotic proteins (including putative ATP/GTP binding proteins), has no known function.. 
PF09849 Uncharacterized protein conserved in bacteria (DUF2076)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function. The domain, however, is found in various periplasmic ligand-binding sensor proteins.. 
PF09850 Uncharacterized protein conserved in bacteria (DUF2077)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function.. 
PF09851 DUF2078;<br>Short C-terminal domain. 
PF09852 Predicted membrane protein (DUF2079)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function.. 
PF09853 Putative transposon-encoded protein (DUF2080)<br>This domain, found in various hypothetical archaeal proteins, has no known function.. 
PF09855 Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082)<br>This domain, found in various hypothetical prokaryotic proteins, as well as some Zn-ribbon nucleic-acid-binding proteins has no known function.. 
PF09856 Predicted transcriptional regulator (DUF2083)<br>This domain is found in various prokaryotic transcriptional regulatory proteins belonging to the XRE family. Its exact function is, as yet, unknown.. 
PF09857 Uncharacterized protein conserved in bacteria (DUF2084)<br>This domain, found in various hypothetical prokaryotic proteins,as well as proteins belonging to the UPF0386 family, has no known function.. 
PF09858 Predicted membrane protein (DUF2085)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function.. 
PF09859 DUF2086;<br>Oxygenase, catalysing oxidative methylation of damaged DNA. This family of bacterial sequences is predicted to catalyse oxidative de-methylation of damaged bases in DNA.. 
PF09860 Uncharacterized protein conserved in bacteria (DUF2087)<br>This domain, found in various hypothetical prokaryotic proteins and transcriptional activators, has no known function. Structural modelling suggests this domain may bind nucleic acids  .. 
PF09861 Domain of unknown function (DUF2088)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function.. 
PF09862 Protein of unknown function (DUF2089)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function. This domain is a zinc-ribbon.. 
PF09863 Uncharacterized protein conserved in bacteria (DUF2090)<br>This domain, found in various prokaryotic carbohydrate kinases, has no known function.. 
PF09864 DUF2091;<br>Membrane-bound lysozyme-inhibitor of c-type lysozyme. Lysozymes are ancient and important components of the innate immune system of animals that hydrolyse peptidoglycan, the major bacterial cell wall polymer. Various mechanisms have evolved by which bacteria can evade this bactericidal enzyme, one being the production of lysozyme inhibitors. MliC (membrane bound lysozyme inhibitor of c-type lysozyme) of E. coli and Pseudomonas aeruginosa, possess lysozyme inhibitory activity and confer increased lysozyme tolerance upon expression in E. coli  . Structural analyses show that the invariant loop of MliC plays a crucial role in the inhibition of the lysozyme by its insertion into the active site cleft of the lysozyme, where the loop forms hydrogen and ionic bonds with the catalytic residues  .. 
PF09865 Predicted periplasmic protein (DUF2092)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function.. 
PF09866 Uncharacterized protein conserved in bacteria (DUF2093)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function.. 
PF09867 Uncharacterized protein conserved in bacteria (DUF2094)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function.. 
PF09868 Uncharacterized protein conserved in archaea (DUF2095)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function.. 
PF09869 Uncharacterized protein conserved in archaea (DUF2096)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function.. 
PF09870 Uncharacterized protein conserved in archaea (DUF2097)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function.. 
PF09871 Uncharacterized protein conserved in archaea (DUF2098)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function.. 
PF09872 Uncharacterized protein conserved in archaea (DUF2099)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function.. 
PF09873 Uncharacterized protein conserved in archaea (DUF2100)<br>This domain, found in various hypothetical archaeal proteins, has no known function.. 
PF09874 Predicted membrane protein (DUF2101)<br>This domain, found in various archaeal and bacterial proteins, has no known function.. 
PF09875 Uncharacterized protein conserved in archaea (DUF2102)<br>This domain, found in various hypothetical archaeal proteins, has no known function.. 
PF09876 Predicted metal-binding protein (DUF2103)<br>This domain, found in various putative metal binding prokaryotic proteins, has no known function.. 
PF09877 Predicted membrane protein (DUF2104)<br>This domain, found in various hypothetical archaeal proteins, has no known function.. 
PF09878 Predicted membrane protein (DUF2105)<br>This domain, found in various hypothetical archaeal proteins, has no known function.. 
PF09879 Predicted membrane protein (DUF2106)<br>This domain, found in various hypothetical archaeal proteins, has no known function.. 
PF09880 Predicted membrane protein (DUF2107)<br>This domain, found in various hypothetical archaeal proteins, has no known function.. 
PF09881 Predicted membrane protein (DUF2108)<br>This domain, found in various hypothetical archaeal proteins, has no known function.. 
PF09882 Predicted membrane protein (DUF2109)<br>This domain, found in various hypothetical archaeal proteins, has no known function.. 
PF09883 Uncharacterized protein conserved in archaea (DUF2110)<br>This domain, found in various hypothetical archaeal proteins, has no known function.. 
PF09884 Uncharacterized protein conserved in archaea (DUF2111)<br>This domain, found in various hypothetical archaeal proteins, has no known function.. 
PF09885 Uncharacterized protein conserved in archaea (DUF2112)<br>This domain, found in various hypothetical archaeal proteins, has no known function.. 
PF09886 Uncharacterized protein conserved in archaea (DUF2113)<br>This domain, found in various hypothetical archaeal proteins, has no known function.. 
PF09887 Uncharacterized protein conserved in archaea (DUF2114)<br>This domain, found in various hypothetical archaeal proteins, has no known function.. 
PF09888 Uncharacterized protein conserved in archaea (DUF2115)<br>This domain, found in various hypothetical archaeal proteins, has no known function.. 
PF09889 Uncharacterized protein containing a Zn-ribbon (DUF2116)<br>This domain, found in various hypothetical archaeal proteins, has no known function.  Structural modelling suggests this domain may bind nucleic acids  .. 
PF09890 Uncharacterized protein conserved in archaea (DUF2117)<br>This domain, found in various hypothetical archaeal proteins, has no known function.. 
PF09891 Uncharacterized protein conserved in archaea (DUF2118)<br>This domain, found in various hypothetical archaeal proteins, has no known function.. 
PF09892 Uncharacterized protein conserved in archaea (DUF2119)<br>This domain, found in various hypothetical archaeal proteins, has no known function.. 
PF09893 Uncharacterized protein conserved in archaea (DUF2120)<br>This domain, found in various hypothetical archaeal proteins, has no known function.. 
PF09894 Uncharacterized protein conserved in archaea (DUF2121)<br>This domain, found in various hypothetical archaeal proteins, has no known function.. 
PF09895 RecB-family nuclease (DUF2122)<br>This domain, found in various hypothetical archaeal proteins, has no known function.. 
PF09897 Uncharacterized protein conserved in archaea (DUF2124)<br>This domain, found in various hypothetical archaeal proteins, has no known function.. 
PF09898 Uncharacterized protein conserved in bacteria (DUF2125)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function.. 
PF09899 Putative amidoligase enzyme (DUF2126)<br>Members of this family of bacterial domains are predominantly found in transglutaminase and transglutaminase-like proteins. Their exact function is, as yet, unknown, but they are likely to act as amidoligase enzymes   Protein in this family are found in conserved gene neighborhoods encoding a glutamine amidotransferase-like thiol peptidase (in proteobacteria) or an Aig2 family cyclotransferase protein (in firmicutes)  .. 
PF09900 Predicted membrane protein (DUF2127)<br>COGs (COG4331&COG3305)). This domain, found in various hypothetical prokaryotic and archaeal proteins, has no known function.. 
PF09902 Uncharacterized protein conserved in bacteria (DUF2129)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function. Structural modelling suggests this domain may bind nucleic acids  .. 
PF09903 Uncharacterized protein conserved in bacteria (DUF2130)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function.. 
PF09904 DUF2131;<br>Winged helix-turn helix. This family, found in various hypothetical prokaryotic proteins, is a probable winged helix DNA-binding domain.. 
PF09905 Uncharacterized conserved protein (DUF2132)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function.. 
PF09906 Uncharacterized protein conserved in bacteria (DUF2135)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function.. 
PF09907 Uncharacterized protein conserved in bacteria (DUF2136)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function.. 
PF09909 Uncharacterized protein conserved in bacteria (DUF2138)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function.. 
PF09910 Uncharacterized protein conserved in archaea (DUF2139)<br>This domain, found in various hypothetical archaeal proteins, has no known function.. 
PF09911 Uncharacterized protein conserved in bacteria (DUF2140)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function.. 
PF09912 Uncharacterized protein conserved in bacteria (DUF2141)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function.. 
PF09913 Predicted membrane protein (DUF2142)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function.. 
PF09916 Uncharacterized protein conserved in bacteria (DUF2145)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function.. 
PF09917 Uncharacterized protein conserved in bacteria (DUF2147)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function.. 
PF09918 Uncharacterized protein containing a ferredoxin domain (DUF2148)<br>This domain, found in various hypothetical bacterial proteins containing a ferredoxin domain, has no known function.. 
PF09919 Uncharacterized conserved protein (DUF2149)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function.. 
PF09920 Uncharacterized protein conserved in archaea (DUF2150)<br>This domain, found in various hypothetical archaeal proteins, has no known function.. 
PF09921 Uncharacterized protein conserved in archaea (DUF2153)<br>This domain, found in various hypothetical archaeal proteins, has no known function.. 
PF09922 Cell wall-active antibiotics response protein (DUF2154)<br>
PF09923 Uncharacterized protein conserved in bacteria (DUF2155)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function.. 
PF09924 Uncharacterized conserved protein (DUF2156)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function.. 
PF09925 Predicted membrane protein (DUF2157)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function.. 
PF09926 Uncharacterized small protein (DUF2158)<br>Members of this family of prokaryotic proteins have no known function.. 
PF09928 Predicted small integral membrane protein (DUF2160)<br>The members of this family of hypothetical prokaryotic proteins have no known function. It is thought that they are transmembrane proteins, but their function has not been inferred yet.. 
PF09929 Uncharacterized conserved protein (DUF2161)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function.. 
PF09930 Predicted transporter (DUF2162)<br>Members of this family of bacterial proteins are thought to be membrane transporters, but their exact function has not, as yet, been elucidated.. 
PF09931 Uncharacterized conserved protein (DUF2163)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function.. 
PF09932 Uncharacterized conserved protein (DUF2164)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function.. 
PF09933 Predicted small integral membrane protein (DUF2165)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function.. 
PF09935 Protein of unknown function (DUF2167)<br>This domain, found in various hypothetical membrane-anchored prokaryotic proteins, has no known function.. 
PF09936 DUF2168;<br>SAM-dependent RNA methyltransferase. This family has a Rossmanoid fold, with a deep trefoil knot in its C-terminal region. It has structural similarity to RNA methyltransferases, and is likely to function as an S-adenosyl-L-methionine (SAM)-dependent RNA 2'-O methyltransferase  .. 
PF09937 Uncharacterized protein conserved in bacteria (DUF2169)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function.. 
PF09938 Uncharacterized protein conserved in bacteria (DUF2170)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function.. 
PF09939 Uncharacterized protein conserved in bacteria (DUF2171)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function.. 
PF09940 Domain of unknown function (DUF2172)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function. An aminopeptidase domain is conserved within the family, but its relevance has not been established yet.. 
PF09941 Uncharacterized conserved protein (DUF2173)<br>This domain, found in various hypothetical prokaryotic proteins, has no known function.. 
PF09943 Uncharacterized protein conserved in archaea (DUF2175)<br>This domain, found in various hypothetical archaeal proteins, has no known function.. 
PF09945 Predicted membrane protein (DUF2177)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF09946 Predicted membrane protein (DUF2178)<br>This domain, found in various hypothetical archaeal proteins, has no known function.. 
PF09947 Uncharacterized protein conserved in archaea (DUF2180)<br>This domain, found in various hypothetical archaeal proteins, has no known function. A few of the family members contain a zinc finger domain.. 
PF09948 Predicted metal-binding integral membrane protein (DUF2182)<br>This domain, found in various hypothetical bacterial membrane proteins having predicted metal-binding properties, has no known function.. 
PF09949 Uncharacterized conserved protein (DUF2183)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF09950 Uncharacterized protein conserved in bacteria (DUF2184)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF09951 Protein of unknown function (DUF2185)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF09952 Uncharacterized protein conserved in bacteria (DUF2186)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF09953 Uncharacterized protein conserved in bacteria (DUF2187)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF09954 Uncharacterized protein conserved in bacteria (DUF2188)<br>COGs (COG4876) & Jackhmmer:B5ZC26. This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF09955 Predicted integral membrane protein (DUF2189)<br>Members of this family are found in various hypothetical prokaryotic proteins, as well as putative cytochrome c oxidases. Their exact function has not, as yet, been established.. 
PF09956 Uncharacterized conserved protein (DUF2190)<br>This domain, found in various hypothetical prokaryotic proteins, as well as in some putative RecA/RadA recombinases, has no known function.. 
PF09957 Uncharacterized protein conserved in bacteria (DUF2191)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF09958 Uncharacterized protein conserved in archaea (DUF2192)<br>This domain, found in various hypothetical archaeal proteins, has no known function.. 
PF09959 Uncharacterized protein conserved in archaea (DUF2193)<br>This domain, found in various hypothetical archaeal proteins, has no known function.. 
PF09960 Uncharacterized protein conserved in bacteria (DUF2194)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF09961 Uncharacterized protein conserved in bacteria (DUF2195)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF09962 Uncharacterized conserved protein (DUF2196)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF09963 Uncharacterized protein conserved in bacteria (DUF2197)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF09964 Uncharacterized protein conserved in bacteria (DUF2198)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF09965 Uncharacterized protein conserved in bacteria (DUF2199)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF09966 Uncharacterized protein conserved in bacteria (DUF2200)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF09967 VWA-like domain (DUF2201)<br>This domain, found in various hypothetical bacterial proteins, has no known function. However, it is clearly related to the VWA domain.. 
PF09968 Uncharacterized protein domain (DUF2202)<br>This domain, found in various hypothetical archaeal proteins, has no known function.. 
PF09969 Uncharacterized conserved protein (DUF2203)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF09970 Nucleotidyl transferase of unknown function (DUF2204)<br>This domain, found in various hypothetical archaeal proteins, has no known function. However, this family was identified as belonging to the nucleotidyltransferase superfamily  .. 
PF09971 Predicted membrane protein (DUF2206)<br>This domain, found in various hypothetical archaeal proteins, has no known function.. 
PF09972 Predicted membrane protein (DUF2207)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF09973 Predicted membrane protein (DUF2208)<br>This domain, found in various hypothetical archaeal proteins, has no known function.. 
PF09974 Uncharacterized protein conserved in archaea (DUF2209)<br>This domain, found in various hypothetical archaeal proteins, has no known function.. 
PF09976 DUF2133;<br>Tetratricopeptide repeat. 
PF09977 DUF2134;<br>Putative Tad-like Flp pilus-assembly. This domain, found in various hypothetical prokaryotic proteins, is likely to be involved in Flp lius biogenesis.. 
PF09979 Uncharacterized protein conserved in bacteria (DUF2213)<br>Members of this family of bacterial proteins comprise various hypothetical and phage-related proteins. The exact function of these proteins has not, as yet, been determined.. 
PF09980 Predicted membrane protein (DUF2214)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF09981 Uncharacterized protein conserved in bacteria (DUF2218)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF09982 Uncharacterized protein conserved in bacteria (DUF2219)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF09983 Uncharacterized protein conserved in bacteria C-term(DUF2220)<br>This domain, found in various hypothetical bacterial proteins, has no known function. The family represents just the C-terminus.. 
PF09984 Uncharacterized signal transduction histidine kinase domain (DUF2222)<br>Members of this family of domains are found in various BarA-like signal transduction histidine kinases, which are involved in the regulation of carbon metabolism via the csrA/csrB regulatory system. The role of this domain has not, as yet, been established.. 
PF09985 Domain of unknown function (DUF2223)<br>Members of this family are found in various prokaryotic membrane-anchored proteins predicted to be involved in the regulation of amylopullulanase.. 
PF09986 Uncharacterized protein conserved in bacteria (DUF2225)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF09987 Uncharacterized protein conserved in archaea (DUF2226)<br>This domain, found in various hypothetical archaeal proteins, has no known function.. 
PF09988 Uncharacterized metal-binding protein (DUF2227)<br>Members of this family of hypothetical bacterial proteins possess metal binding properties; however, their exact function has not, as yet, been determined.. 
PF09989 CoA enzyme activase uncharacterised domain (DUF2229)<br>Members of this family include various bacterial hypothetical proteins, as well as CoA enzyme activases. The exact function of this domain has not, as yet, been defined.. 
PF09990 Predicted membrane protein (DUF2231)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF09991 Predicted membrane protein (DUF2232)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF09992 Predicted periplasmic protein (DUF2233)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF09994 Uncharacterized alpha/beta hydrolase domain (DUF2235)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF09995 Uncharacterized protein conserved in bacteria (DUF2236)<br>This domain, found in various hypothetical bacterial proteins, has no known function. This family contains a highly conserved arginine and histidine that may be active site residues for an as yet unknown catalytic activity.. 
PF09996 Uncharacterized protein conserved in bacteria (DUF2237)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF09997 Predicted membrane protein (DUF2238)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF09998 Uncharacterized protein conserved in bacteria (DUF2239)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF09999 Uncharacterized protein conserved in archaea (DUF2240)<br>This domain, found in various hypothetical archaeal proteins, has no known function.. 
PF10000 DUF2241;<br>This domain, found in various hypothetical bacterial proteins, has no known function. However, its structure is similar to the ACT domain which suggests that it binds to amino acids and regulates other protein activity. This family was formerly known as DUF2241.. 
PF10001 Uncharacterized protein conserved in bacteria (DUF2242)<br>This domain is found in various hypothetical bacterial proteins, and has no known function.. 
PF10002 Predicted membrane protein (DUF2243)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF10003 Integral membrane protein (DUF2244)<br>This domain, found in various bacterial hypothetical and putative membrane proteins, has no known function.. 
PF10004 Uncharacterized protein conserved in bacteria (DUF2247)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF10005 Uncharacterized protein conserved in bacteria (DUF2248)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10006 Uncharacterized conserved protein (DUF2249)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10007 Uncharacterized protein conserved in archaea (DUF2250)<br>Members of this family of hypothetical archaeal proteins have no known function.. 
PF10008 Uncharacterized protein conserved in bacteria (DUF2251)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10009 Uncharacterized protein conserved in bacteria (DUF2252)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF10011 Predicted membrane protein (DUF2254)<br>Members of this family of bacterial proteins comprises various hypothetical and putative membrane proteins. Their exact function, has not, as yet, been defined.. 
PF10012 Uncharacterized protein conserved in bacteria (DUF2255)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10013 Uncharacterized protein conserved in bacteria (DUF2256)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10014 DUF2257; BsmA;<br>This family contains 2-oxoglutarate (2OG) and Fe-dependent dioxygenases. It includes L-isoleucine dioxygenase (IDO)  .. 
PF10015 Uncharacterized protein conserved in archaea (DUF2258)<br>Members of this family of hypothetical bacterial archaeal have no known function.  Structural modelling suggests this domain may bind nucleic acids  .. 
PF10016 Predicted secreted protein (DUF2259)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10017 DUF2260;<br>Histidine-specific methyltransferase, SAM-dependent. The mycobacterial members of this family are expressed from part of the ergothioneine biosynthetic gene cluster. EGTD is the histidine methyltransferase that transfers three methyl groups to the alpha-amino moiety of histidine, in the first stage of the production of this histidine betaine derivative that carries a thiol group attached to the C2 atom of an imidazole ring  .. 
PF10018 VDRIP; <br>Vitamin-D-receptor interacting Mediator subunit 4. Members of this family function as part of the Mediator (Med) complex, which links DNA-bound transcriptional regulators and the general transcription machinery, particularly the RNA polymerase II enzyme. They play a role in basal transcription by mediating activation or repression according to the specific complement of transcriptional regulators bound to the promoter   .. 
PF10020 Uncharacterized protein conserved in bacteria (DUF2262)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF10021 Uncharacterized protein conserved in bacteria (DUF2263)<br>This domain, found in various hypothetical bacterial and eukaryotic proteins, has no known function.. 
PF10022 Uncharacterized protein conserved in bacteria (DUF2264)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10023 Predicted aminopeptidase (DUF2265)<br>Members of this family of bacterial proteins comprise various hypothetical proteins and putative aminopeptidases. Their exact function, has not, as yet, been defined.. 
PF10025 Uncharacterized conserved protein (DUF2267)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF10026 Predicted Zn-dependent protease (DUF2268)<br>This domain, found in various hypothetical bacterial proteins, as well as predicted zinc dependent proteases, has no known function.. 
PF10027 Predicted integral membrane protein (DUF2269)<br>Members of this family of bacterial hypothetical integral membrane proteins have no known function.. 
PF10028 Predicted integral membrane protein (DUF2270)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF10029 Predicted periplasmic protein (DUF2271)<br>This domain, found in various hypothetical bacterial proteins and misannotated lysozyme proteins, it has no known function.. 
PF10030 Uncharacterized protein conserved in bacteria (DUF2272)<br>Members of this family of hypothetical bacterial proteins have no known function. However, given its similarity to the CHAP domain it seems likely that this is an enzyme involved in cleaving peptidoglycan.. 
PF10031 Small integral membrane protein (DUF2273)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10032 Phosphate transport (Pho88)<br>Members of this family of proteins are involved in regulating inorganic phosphate transport, as well as telomere length regulation and maintenance     .. 
PF10033 Autophagy-related protein 13<br>Members of this family of phosphoproteins are involved in cytoplasm to vacuole transport (Cvt), and more specifically in Cvt vesicle formation. They are probably involved in the switching machinery regulating the conversion between the Cvt pathway and autophagy. Finally, ATG13 is also required for glycogen storage    .. 
PF10034 DUF2211;<br>Q-cell neuroblast polarisation. Dyp-19, formerly known as DUF2211, is a transmembrane domain family that is required to orient the neuroblast cells, QR and QL accurately on the anterior-posterior axis: QL and QR are born in the same anterior-posterior position, but polarise and migrate left-right asymmetrically, QL migrating towards the posterior and QR migrating towards the anterior. It is also required, with unc-40, to express mab-5 correctly in the Q cell descendants  . The Dpy-19 protein derives from the C. elegans DUMPY mutant, Swiss:P34413.. 
PF10035 Uncharacterized protein conserved in bacteria (DUF2179)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF10036 Putative carnitine deficiency-associated protein<br>This family of proteins conserved from nematodes to humans is of approximately 250 amino acids. It is purported to be carnitine deficiency-associated protein but this could not be confirmed. It carries a characteristic RLL sequence-motif. The function is unknown.. 
PF10037 MRP_S27; <br>Mitochondrial 28S ribosomal protein S27. Members of this family of small ribosomal proteins possess one of three conserved blocks of sequence found in proteins that stimulate the dissociation of guanine nucleotides from G-proteins, leaving open the possibility that MRP-S27 might be a functional partner of GTP-binding ribosomal proteins  .. 
PF10038 Protein of unknown function (DUF2274)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10039 Predicted integral membrane protein (DUF2275)<br>This domain, found in various hypothetical bacterial proteins and in the RNA polymerase sigma factor, has no known function.. 
PF10040 Uncharacterized conserved protein (DUF2276)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF10041 Uncharacterized conserved protein (DUF2277)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10042 Uncharacterized conserved protein (DUF2278)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10043 Predicted periplasmic lipoprotein (DUF2279)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF10044 Retinal tissue protein<br>Rtp is a family of proteins of approximately 112 amino acids in length which is conserved from nematodes to humans. The proposed tertiary structure is of almost entirely alpha helix interrupted only by loops located at proline residues. Three sites in the protein sequence reveal two types of possible post-translation modification. A serine residue, at position 41, is a candidate for protein kinase C phosphorylation. Glycine residues at position 69 and 91 are probable sites for acetylation by covalent amide linkage of myristate via N-myristoyl transferase. Rtp is differentially expressed in the trout retina between parr and smolt developmental stages (smoltification). It is likely to be a house-keeping protein  .. 
PF10045 Uncharacterized conserved protein (DUF2280)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10046 Biogenesis of lysosome-related organelles complex-1 subunit 2 <br>Members of this family of proteins play a role in cellular proliferation, as well as in the biogenesis of specialized organelles of the endosomal-lysosomal system.. 
PF10047 Protein of unknown function (DUF2281)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10048 Predicted integral membrane protein (DUF2282)<br>Members of this family of hypothetical bacterial proteins and putative signal peptide proteins have no known function.. 
PF10049 Protein of unknown function (DUF2283)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10050 Predicted metal-binding protein (DUF2284)<br>Members of this family of metal-binding hypothetical bacterial proteins have no known function.. 
PF10051 Uncharacterized protein conserved in archaea (DUF2286)<br>Members of this family of hypothetical archaeal proteins have no known function.. 
PF10052 Protein of unknown function (DUF2288)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10053 Uncharacterized conserved protein (DUF2290)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10054 Predicted periplasmic lipoprotein (DUF2291)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10055 Uncharacterized small protein (DUF2292)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10056 Uncharacterized conserved protein (DUF2293)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF10057 Uncharacterized conserved protein (DUF2294)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10058 Predicted integral membrane metal-binding protein (DUF2296)<br>This domain, found in various hypothetical bacterial and eukaryotic metal-binding proteins, has no known function.. 
PF10060 Uncharacterized membrane protein (DUF2298)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF10061 Uncharacterized conserved protein (DUF2299)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10062 Predicted secreted protein (DUF2300)<br>This domain, found in various bacterial hypothetical and putative signal peptide proteins, has no known function.. 
PF10063 Uncharacterized integral membrane protein (DUF2301)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF10065 Uncharacterized conserved protein (DUF2303)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10066 Uncharacterized conserved protein (DUF2304)<br>Members of this family of hypothetical archaeal proteins have no known function.. 
PF10067 Predicted membrane protein (DUF2306)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10069 DUF2308;<br>Sensory domain found in DIguanylate Cyclases & Two-component systems. DICT is a sensory domain found associated with GGDEF, EAL, HD-GYP STAS, and two component systems  . It assumes an alpha+beta fold  with a 4-stranded beta-sheet and might have a role in light response  .. 
PF10070 Uncharacterized protein conserved in bacteria (DUF2309)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10071 Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310)<br>Members of this family of proteobacterial zinc ribbon proteins are thought to bind to nucleic acids, however their exact function has not as yet been defined.. 
PF10073 Uncharacterized protein conserved in bacteria (DUF2312)<br>Members of this family of hypothetical bacterial proteins have no known function. Structural modelling suggests this domain may bind nucleic acids  .. 
PF10074 Uncharacterized conserved protein (DUF2285)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF10075 COP9 signalosome, subunit CSN8<br>This PCI_Csn8 domain is conserved from plants to humans. It is a signature protein motif found in components of CSN (COP9 signalosome).  It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development  .. 
PF10076 Uncharacterized protein conserved in bacteria (DUF2313)<br>Members of this family of proteins comprise various hypothetical and putative bacteriophage tail proteins.. 
PF10077 Uncharacterized protein conserved in bacteria (DUF2314)<br>This domain is found in various bacterial hypothetical proteins, as well as putative ankyrin repeat proteins. The exact function of the domains comprising this family has not, as yet, been determined.. 
PF10078 Uncharacterized protein conserved in bacteria (DUF2316)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10079 Uncharacterized protein conserved in bacteria (DUF2317)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10080 Predicted membrane protein (DUF2318)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10081 DUF2319;<br>Alpha/beta-hydrolase family. This is a family of alpha/beta hydrolases which may function as lipases. This domain is the catalytic domain and includes the catalytic triad and the GXSXG sequence motif which is a characteristic of these enzymes  .. 
PF10082 Uncharacterized protein conserved in bacteria (DUF2320)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF10083 Uncharacterized protein conserved in bacteria (DUF2321)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10084 Uncharacterized protein conserved in bacteria (DUF2322)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10086 Putative membrane peptidase family (DUF2324)<br>This domain, found in various hypothetical bacterial proteins, has no known function. This family appears to be related to the prenyl protease 2 family Pfam:PF02517, suggesting this family may be peptidases.. 
PF10087 Uncharacterized protein conserved in bacteria (DUF2325)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10088 Uncharacterized protein conserved in bacteria (DUF2326)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF10090 Uncharacterized protein conserved in bacteria (DUF2328)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10091 DUF2329;<br>Putative glucoamylase. The structure of UniProt:Q5LIB7 has an alpha/alpha toroid fold and is similar structurally to a number of glucoamylases. Most of these structural homologues are glucoamylases, involved in breaking down complex sugars (e.g. starch). The biologically relevant state is likely to be monomeric. The putative active site is located at the centre of the toroid with a well defined large cavity.. 
PF10092 Uncharacterized protein conserved in bacteria (DUF2330)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10093 Uncharacterized protein conserved in bacteria (DUF2331)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10094 Uncharacterized protein conserved in bacteria (DUF2332)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10095 Uncharacterized protein conserved in bacteria (DUF2333)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10096 Uncharacterized protein conserved in bacteria (DUF2334)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF10097 Predicted membrane protein (DUF2335)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10098 Uncharacterized protein conserved in bacteria (DUF2336)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10099 DUF2337;<br>Anti-sigma-K factor rskA. This domain, formerly known as DUF2337, is the anti-sigma-K factor, RskA. In Mycobacterium tuberculosis the protein positively regulates expression of the antigenic proteins MPB70 and MPB83  .. 
PF10100 Uncharacterized protein conserved in bacteria (DUF2338)<br>Members of this family of hypothetical bacterial proteins have no known function.. 
PF10101 Predicted membrane protein (DUF2339)<br>This domain, found in various hypothetical bacterial proteins, has no known function.. 
PF10102 Domain of unknown function (DUF2341)<br>Members of this family are found in various bacterial proteins, including MotA/TolQ/ExbB proton channels and other transport proteins. The exact function of this set of domains has not, as yet, been determined.. 
PF10103 Uncharacterised conserved protein (DUF2342)<br>Members of this family of bacterial hypothetical and uncharacterised proteins have no known function.. 
PF10104 DUF2343; <br>Di-sulfide bridge nucleocytoplasmic transport domain. COGs (COG5085), KOGs (KOG4503). Brr6_like_C_C is the highly conserved C-terminal region of a group of proteins found in fungi. It carries four highly conserved cysteine residues. It is suggested that members of the family interact with each other via di-sulfide bridges to form a complex which is involved in nucleocytoplasmic transport  . Brr6 in yeast is an essential integral membrane protein of the NE-ER, wit two predicted transmembrane domains, and is a dosage suppressor of Apq12, Pfam:PF12716  .. 
PF10105 Uncharacterized protein conserved in bacteria (DUF2344)<br>This domain, found in various hypothetical bacterial proteins and Radical Sam domain proteins, has no known function.. 
PF10106 Uncharacterized protein conserved in bacteria (DUF2345)<br>Members of this family are found in various bacterial hypothetical proteins, as well as Rhs element Vgr proteins.. 
PF10107 Endonuclease related to archaeal Holliday junction resolvase<br>This domain is found in various predicted bacterial endonucleases which are distantly related to archaeal Holliday junction resolvases.. 
PF10108 Exon_PolB;<br>Predicted 3'-5' exonuclease related to the exonuclease domain of PolB. This domain is found in various prokaryotic 3'-5' exonucleases and hypothetical proteins.. 
PF10109 Mu-like prophage FluMu protein gp41<br>Jackhmmer:Q1GH51.1(1-98). Members of this family of prokaryotic proteins include various gp41 proteins and related sequences  .. 
PF10110 Membrane domain of glycerophosphoryl diester phosphodiesterase<br>Members of this family comprise the membrane domain of the prokaryotic enzyme glycerophosphoryl diester phosphodiesterase.. 
PF10111 GlycosTransf;<br>Glycosyltransferase like family 2. Members of this family of prokaryotic proteins include putative glucosyltransferase, which are involved in bacterial capsule biosynthesis   .. 
PF10112 5-bromo-4-chloroindolyl phosphate hydrolysis protein<br>Members of this family of prokaryotic proteins mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.. 
PF10113 Fibrillarin-like archaeal protein<br>Members of this family of proteins include archaeal fibrillarin homologs.. 
PF10114 Hist_Kin_Sens;<br>Sensory domain found in PocR. PocR, a ligand binding domain, has a novel variant of the PAS-like Fold   . Evidence suggests that it binds small hydrocarbon  derivatives such as 1,3-propanediol  . . 
PF10115 Transcriptional activator HlyU<br>This domain, found in various hypothetical prokaryotic proteins, has no known function. One of the sequences in this family corresponds to the transcriptional activator HlyU, indicating a possible similar role in other members.. 
PF10116 Protein required for attachment to host cells<br>Members of this family of bacterial proteins are required for the attachment of the bacterium to host cells   .. 
PF10117 McrBC 5-methylcytosine restriction system component<br>Members of this family of bacterial proteins modify the specificity of mcrB restriction by expanding the range of modified sequences restricted   .. 
PF10118 Predicted metal-dependent hydrolase<br>Members of this family of proteins comprise various bacterial transition metal-dependent hydrolases.. 
PF10119 Predicted methyltransferase regulatory domain<br>Members of this family of domains are found in various prokaryotic methyltransferases, where they regulate the activity of the methyltransferase domain.. 
PF10120 MethylPyrKinase;<br>Members of this family of archaeal and bacterial proteins are likely to be aldolases.. 
PF10122 Mu-like prophage protein Com<br>Members of this family of proteins comprise the translational regulator of mom   .. 
PF10123 Mu-like prophage I protein<br>Members of this family of proteins comprise various viral Mu-like prophage I proteins.. 
PF10124 Mu-like prophage major head subunit gpT<br>Members of this family of proteins comprise various caudoviral prophage proteins, including the Mu-like prophage major head subunit gpT.. 
PF10125 NADH dehydrogenase I, subunit N related protein<br>This family comprises a set of NADH dehydrogenase I, subunit N related proteins found in archaea. Their exact function, has not, as yet, been determined.. 
PF10126 Uncharacterized protein, homolog of nitrogen regulatory protein PII<br>This domain, found in various hypothetical archaeal proteins, has no known function. It is distantly similar to the nitrogen regulatory protein PII.. 
PF10127 Predicted nucleotidyltransferase<br>Members of this family of bacterial proteins catalyze the transfer of nucleotide residues from nucleoside diphosphates or triphosphates into dimer or polymer forms.. 
PF10128 Glucose-6-phosphate dehydrogenase subunit<br>Members of this family are found in various prokaryotic OpcA and glucose-6-phosphate dehydrogenase proteins. The exact function of the domain is, as yet, unknown.. 
PF10129 OpgC protein<br>This domain, found in various hypothetical and OpgC prokaryotic proteins. It is likely to act as an acyltransferase enzyme.. 
PF10130 PIN domain<br>Members of this family of bacterial domains are predicted to be RNases (from similarities to 5'-exonucleases).. 
PF10131 6-pyruvoyl-tetrahydropterin synthase related domain; membrane protein<br>This domain is found in various bacterial hypothetical membrane proteins, as well as in tetratricopeptide TPR_2 repeat protein. The exact function of the domain has not, as yet, been established.. 
PF10133 Predicted RNA-binding protein<br>Members of this family of bacterial proteins are thought to have RNA-binding properties, however, their exact function has not, as yet, been defined.. 
PF10134 Replication initiator protein A<br>Members of this family of bacterial proteins are single-stranded DNA binding proteins that are involved in DNA replication, repair and recombination.. 
PF10135 Rod binding protein<br>Members of this family are involved in the assembly of the prokaryotic flagellar rod.. 
PF10136 Site-specific recombinase<br>Members of this family of bacterial proteins are found in various putative site-specific recombinase transmembrane proteins.. 
PF10137 Predicted nucleotide-binding protein containing TIR-like domain<br>Members of this family of bacterial nucleotide-binding proteins contain a TIR-like domain. Their exact function has not, as yet, been defined.. 
PF10138 Tellurium_res;<br>vWA found in TerF C terminus . vWA domain fused to TerD domain typified by the  TerF protein  . Some times found as solos. . 
PF10139 Putative bacterial virulence factor<br>Members of this family of prokaryotic proteins include various putative virulence factor effector proteins. Their exact function is, as yet, unknown.. 
PF10140 essB;<br>WXG100 protein secretion system (Wss), protein YukC. Members of this family of proteins include predicted membrane proteins homologous to YukC in B. subtilis. The YukC protein family would participate to the formation of a translocon required for the secretion of WXG100 proteins (Pfam:PF06013) in monoderm bacteria, the WXG100 protein secretion system (Wss). This family includes EssB in Staphylococcus aureus.. 
PF10141 Single-strand DNA-specific exonuclease, C terminal domain<br>Members of this set of prokaryotic domains are found in a set of single-strand DNA-specific exonucleases, including RecJ. Their exact function has not, as yet, been determined.. 
PF10142 PhoPQ-activated pathogenicity-related protein<br>Members of this family of bacterial proteins are involved in the virulence of some pathogenic proteobacteria  .. 
PF10143 2,3-bisphosphoglycerate-independent phosphoglycerate mutase<br>Members of this family are found in various bacterial 2,3-bisphosphoglycerate-independent phosphoglycerate mutase enzymes, which catalyse the interconversion of 2-phosphoglycerate and 3-phosphoglycerate in the reaction: [2-phospho-D-glycerate + 2,3-diphosphoglycerate = 3-phospho-D-glycerate + 2,3-diphosphoglycerate].. 
PF10144 Bacterial virulence factor haemolysin<br>Members of this family of bacterial proteins are membrane proteins that effect the expression of haemolysin under anaerobic conditions  .. 
PF10145 Phage-related minor tail protein<br>Members of this family are found in putative phage tail tape measure proteins. . 
PF10146 Zinc finger-containing protein <br>This is a family of proteins which appears to have a highly conserved zinc finger domain at the C terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members are annotated as being tumour-associated antigen HCA127 in humans but this could not confirmed.. 
PF10147 Growth arrest and DNA-damage-inducible proteins-interacting protein 1<br>Members of this family of proteins act as negative regulators of G1 to S cell cycle phase progression by inhibiting cyclin-dependent kinases. Inhibitory effects are additive with GADD45 proteins but occur also in the absence of GADD45 proteins. Furthermore, they act as a repressor of the orphan nuclear receptor NR4A1 by inhibiting AB domain-mediated transcriptional activity  .. 
PF10148 Schwannomin-interacting protein 1<br>Members of this family are coiled coil protein involved in linking membrane proteins to the cytoskeleton.. 
PF10149 NAcGluc_Transf;<br>Transmembrane protein 231. This is a family of transmembrane proteins, given the number 231, of unknown function. It is conserved in eukaryotes.. 
PF10150 Ribonuclease E/G family<br>Pfam-B_234 (Release 21.0). Ribonuclease E and Ribonuclease G are related enzymes that cleave a wide variety of RNAs  .. 
PF10151 Uncharacterised conserved protein (DUF2359)<br>This is a 450 amino acid region of a family of proteins conserved from insects to humans. The mouse protein, Q8BM55, is annotated as being a putative Vitamin K-dependent carboxylation gamma-carboxyglutamic (GLA) domain containing protein, but this could not be confirmed. The function is not known.. 
PF10152 Predicted coiled-coil domain-containing protein (DUF2360)<br>This is the conserved 140 amino acid region of a family of proteins conserved from nematodes to humans. One C. elegans member is annotated as a Daf-16-dependent longevity protein 1 but this could not be confirmed. The function is unknown.. 
PF10153 Uncharacterised conserved protein (DUF2361)<br>This is a region of 120 amino acids that is conserved in a family of proteins found from plants to fungi. The function is not known.. 
PF10154 Uncharacterized conserved protein (DUF2362)<br>This is a family of proteins conserved from nematodes to humans. The function is not known.. 
PF10155 Uncharacterized conserved protein (DUF2363)<br>This is a region of 120 amino acids of a family of proteins conserved from plants to humans.  The function is not known.. 
PF10156 DUF2364; <br>Subunit 17 of Mediator complex. This Mediator complex subunit was formerly known as Srb4 in yeasts or Trap80 in Drosophila and human. The Med17 subunit is located within the head domain and is essential for cell viability to the extent that a mutant strain of cerevisiae lacking it shows all RNA polymerase II-dependent transcription ceasing at non-permissive temperatures.. 
PF10157 Uncharacterized conserved protein (DUF2365)<br>This is a family of conserved proteins found from nematodes to humans. The function is unknown.. 
PF10158 Tumour suppressor protein<br>This is a region of 130 amino acids that is the most conserved region of hypothetical proteins involved in loss of heterozygosity and thus tumour suppression  . The exact function is not known.. 
PF10159 Kinase phosphorylation protein<br>This is a glycine-rich domain that is the most highly conserved region of a family of proteins that in vertebrates are associated with tumours in multiple myelomas. The region may contain phosphorylation sites for several protein kinases, as well as N-myristoylation sites and nuclear localisation signals, so it might act as a signal molecule in the nucleus  .. 
PF10160 Tmem40; <br>Predicted membrane protein. This is a region of 280 amino acids from a group of proteins conserved from plants to humans. It is predicted to be a membrane protein but its function is otherwise unknown.. 
PF10161 Putative mitochondrial precursor protein<br>This is a family of small conserved proteins found from nematodes to humans. The C-terminal region is rich in asparagine. Members are putatively assigned to be mitochondrial precursor proteins but this could not be confirmed.. 
PF10162 G8 domain<br>This domain is found in disease proteins PKHD1 and KIAA1199 and is named G8 after its 8 conserved glycines. It is predicted to contain 10 beta strands and an alpha helix.. 
PF10163 Transcription factor e(y)2<br>EnY2 is a small transcription factor which is combined in a complex with the TAFII40 protein  . The protein is conserved from paramecium to humans.. 
PF10164 Uncharacterized conserved protein (DUF2367)<br>This is a highly conserved family of proteins which contains three pairs of cysteine residues within a length of 42 amino acids and is rich in proline residues towards the N-terminus. The function is unknown. Several members are putatively assigned as brain protein i3 but this was not validated.. 
PF10165 Guanine nucleotide exchange factor synembryn<br>Ric8 is involved in the EGL-30 neurotransmitter signalling pathway  . It is a guanine nucleotide exchange factor   that regulates neurotransmitter secretion.. 
PF10166 Uncharacterised conserved protein (DUF2368)<br>This family is conserved from nematodes to humans. The function is not known.. 
PF10167 Uncharacterised conserved protein<br>This is the N-terminal 80 residues of a family of proteins conserved from plants to humans. It contains a characteristic NEP sequence motif. The function is not known.. 
PF10168 Nuclear pore component<br>Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain  . Nup88 is overexpressed in tumour cells  .. 
PF10169 Learning-associated protein<br>This is a family of 121-amino acid secretory proteins. Laps functions in the regulation of neuronal cell adhesion and/or movement and synapse attachment  . Laps binds to the ApC/EBP (Aplysia CCAAT/enhancer binding protein) promoter and activates the transcription of ApC/EBP mRNA  .. 
PF10170 Cysteine-rich domain<br>This is the N-terminal approximately 100 amino acids of a family of proteins found from nematodes to humans. It contains between six and eight highly conserved cysteine residues and a characteristic DPF sequence motif. One member is putatively named as receptor for egg jelly protein but this could not confirmed.. 
PF10171 Uncharacterised conserved protein (DUF2366)<br>This is a family of proteins conserved from nematodes to humans. The function is not known.. 
PF10172 Det1 complexing ubiquitin ligase<br>DDA1 (De-etiolated 1, Damaged DNA binding protein 1 associated 1) protein binds strongly with DDB1 and Det1 forming a DDD complex which is part of the ubiquitin conjugation system  .. 
PF10173 DUF2343;<br>Mitochondrial K+-H+ exchange-related. The members of this family function as mitochondrial potassium-hydrogen exchange transporters. The family is part of a large mitochondrial KHE protein complex.. 
PF10174 RIM-binding protein of the cytomatrix active zone<br>This is a family of proteins that form part of the CAZ (cytomatrix at the active zone) complex which is involved in determining the site of synaptic vesicle fusion  . The C-terminus is a PDZ-binding motif that binds directly to RIM (a small G protein Rab-3A effector). The family also contains four coiled-coil domains  .. 
PF10175 M-phase phosphoprotein 6<br>This is a family of M-phase phosphoprotein 6s which is necessary for generation of the 3' end of the 5.8S rRNA precursor. It preferentially binds to poly(C) and poly(U).. 
PF10176 Protein of unknown function (DUF2370)<br>This family is conserved from fungi to humans. The human member is annotated as a Golgi-associated protein-Nedd4 WW domain-binding protein but this could not be confirmed.. 
PF10177 Uncharacterised conserved protein (DUF2371)<br>This is a family of proteins conserved from nematodes to humans. The function is not known.. 
PF10178 Uncharacterised conserved protein (DUF2372)<br>This family consists of proteins found from plants to humans. The function is not known.. 
PF10179 Uncharacterised conserved protein (DUF2369)<br>This is a proline-rich region of a group of proteins found from plants to fungi. The function is not known.. 
PF10180 Uncharacterised conserved protein (DUF2373)<br>This is the C-terminal conserved region of a family of proteins found from fungi to humans. The function is not known.. 
PF10181 GPI-GlcNAc transferase complex, PIG-H component<br>PIG-H is a family of conserved proteins that complexes with three other proteins to form the GPI-GnT (glycosylphosphatidylinositol anchor biosynthesis transferase) complex. It appears to be a peripheral membrane protein facing the cytoplasm involved in the first step in GPI anchor formation.. 
PF10182 Flo11 domain<br>Pfam-B_18862 (Release 22.0). This presumed domain is found at the N-terminus of the S. cerevisiae Flo11 protein. Flo11 is required for diploid pseudohyphal formation and haploid invasive growth. It belongs to a family of proteins involved in invasive growth, cell-cell adhesion, and mating, many of which can substitute for each other under abnormal conditions  .. 
PF10183 ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) <br>This subunit is part of the mitochondrial NADH:ubiquinone oxidoreductase (complex I). It carries mitochondrial import sequences  .. 
PF10184 Uncharacterized conserved protein (DUF2358)<br>DUF2358 is a family of conserved proteins found from plants to humans. The function is unknown.. 
PF10185 Chaperone for wingless signalling and trafficking of LDL receptor<br>Mesd is a family of highly conserved proteins found from nematodes to humans. The final C-terminal residues, KEDL, are the endoplasmic reticulum retention sequence as it is an ER protein specifically required for the intracellular trafficking of members of the low-density lipoprotein family of receptors (LDLRs)  . The N- and C-terminal sequences are predicted to adopt a random coil conformation, with the exception of an isolated predicted helix within the N-terminal region, The central folded domain flanked by natively unstructured regions is the necessary structure for facilitating maturation of LRP6 (Low-Density Lipoprotein Receptor-Related Protein 6 Maturation)  .. 
PF10186 DUF2355;<br>UV radiation resistance protein and autophagy-related subunit 14. KOGs (KOG4398), Wood V. The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway  . There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localisation of this complex at the PAS is controlled by Atg14  . Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex  .. 
PF10187 N-terminal domain of NEFA-interacting nuclear protein NIP30<br>This is a the N-terminal 100 amino acids of a family of proteins conserved from plants to humans. The full-length protein has putatively been called NEFA-interacting nuclear protein NIP30, however no reference could be found to confirm this.. 
PF10188 Organic solute transport protein 1<br>Oscp1 is a family of proteins conserved from plants to humans. It is called organic solute transport protein or oxido-red- nitro domain-containing protein 1, however no reference could be find to confirm the function of the protein.. 
PF10189 Conserved protein (DUF2356)<br>This is a 200 amino acid region of a family of proteins conserved from plants to humans. Some members have been putatively annotated as being integrator complex subunit 3 but this could not be confirmed. The function is unknown.. 
PF10190 Tmem170; <br>Putative transmembrane protein 170. Tmem170 is a family of putative transmembrane proteins conserved from nematodes to humans. The protein is only of approximately 130 amino acids in length. The function is unknown.. 
PF10191 DUF2354; <br>Golgi complex component 7 (COG7). COG7 is a component of the conserved oligomeric Golgi complex which is required for normal Golgi morphology and localisation. Mutation in COG7 causes a congenital disorder of glycosylation  .. 
PF10192 Rhodopsin-like GPCR transmembrane domain<br>This region of 270 amino acids is the seven transmembrane alpha-helical domains included within five GPCRRHODOPSN4 motifs of a G-protein-coupled-receptor (GPCR) protein, conserved from nematodes to humans. GPCRs are integral membrane receptors whose intracellular actions are mediated by signalling pathways involving G proteins and downstream secondary messengers  .. 
PF10193 Telomere length regulation protein<br>This family is the central conserved 110 amino acid region of a group of proteins called telomere-length regulation or clock abnormal protein-2 which are conserved from plants to humans. The full-length protein regulates telomere length and contributes to silencing of sub-telomeric regions. In vitro the protein binds to telomeric DNA repeats.. 
PF10195 DNA-binding nuclear phosphoprotein p8<br>P8 is a short 80-82 amino acid protein that is conserved from nematodes to humans. It carries at least one protein kinase C domain suggesting a possible role in signal transduction and it is thought to be a phosphoprotein, but the sites of phosphorylation and the kinases involved remain to be determined  .. 
PF10197 N-terminal domain of CBF1 interacting co-repressor CIR<br>This is a 45 residue conserved region at the N-terminal end of a family of proteins referred to as CIRs (CBF1-interacting co-repressors). CBF1 (centromere-binding factor 1) acts as a transcription factor that causes repression by binding specifically to GTGGGAA motifs in responsive promoters, and it requires CIR as a co-repressor. CIR binds to histone deacetylase and to SAP30 and serves as a linker between CBF1 and the histone deacetylase complex  .. 
PF10198 Histone acetyltransferases subunit 3<br>Ada3 is a family of proteins conserved from yeasts to humans  . It is an essential component of the Ada transcriptional coactivator (alteration/deficiency in activation) complex. Ada3 plays a key role in linking histone acetyltransferase-containing complexes to p53 (tumour suppressor protein) thereby regulating p53 acetylation, stability and transcriptional activation following DNA damage  .. 
PF10199 KYY; <br>Alpha and gamma adaptin binding protein p34. p34 is a protein involved in membrane trafficking.  It is known to interact with both alpha and gamma adaptin  .  It has been speculated that p34 may play a chaperone role such as preventing the soluble adaptors from co-assembling with soluble clathrin, or helping to remove the adaptors from the coated vesicle. Another possible function is in aiding the recruitment of soluble adaptors onto the membrane  .. 
PF10200 NADH:ubiquinone oxidoreductase, NDUFS5-15kDa<br>This is a family of short, approximately 105 amino acid residue, proteins which form part of NADH:ubiquinone oxidoreductase complex I. Complex I is the first multisubunit inner membrane protein complex of the mitochondrial electron transport chain and it transfers two electrons from NADH to ubiquinone. The protein carries four highly conserved cysteine residues but these do not appear to be in a configuration which would favour metal binding so the exact function of the protein is uncertain  .. 
PF10203 Cytochrome c oxidase assembly protein PET191<br>Pet191_N is the conserved N-terminal of a family of conserved proteins found from nematodes to humans. It carries six highly conserved cysteine residues. Pet191 is required for the assembly of active cytochrome c oxidase but does not form part of the final assembled complex  .. 
PF10204 Dual oxidase maturation factor<br>DuoxA (Dual oxidase maturation factor) is the essential protein necessary for the final release of DUOX2 (an NADPH:O2 oxidoreductase flavoprotein) from the endoplasmic reticulum. Dual oxidases (DUOX1 and DUOX2) constitute the catalytic core of the hydrogen peroxide generator, which generates H2O2 at the apical membrane of thyroid follicular cells, essential for iodination of thyroglobulin by thyroid peroxidases.  DuoxA carries five membrane-integral regions including a reverse signal-anchor with external N-terminus (type III) and two N-glycosylation sites  . It is conserved from nematodes to humans.. 
PF10205 Predicted coiled-coil domain-containing protein<br>This is the N-terminal 100 amino acid domain of a family of proteins conserved from nematodes to humans. It carries a characteristic KLRAQ sequence-motif. The function is not known.. 
PF10206 Mitochondrial F1F0-ATP synthase, subunit f<br>This is a family of small proteins of approximately 110 amino acids, which are highly conserved from nematodes to humans. Some members of the family have been annotated in Swiss-Prot as being the f subunit of mitochondrial F1F0-ATP synthase but this could not be confirmed. The sequence has a well-conserved WRW motif. The exact function of the protein is not known.. 
PF10208 Degradation arginine-rich protein for mis-folding<br>This is a family of small proteins of approximately 170 residues which contain four di-sulfide bridges that are highly conserved from nematodes to humans. Armet is a soluble protein resident in the endoplasmic reticulum and induced by ER stress. It appears to be involved with dealing with mis-folded proteins in the ER, thus in quality control of ER stress  .. 
PF10209 Uncharacterized conserved protein (DUF2340)<br>This is a family of small proteins of approximately 150 amino acids of unknown function.. 
PF10210 Mitochondrial 28S ribosomal protein S32<br>This entry is of a family of short, approximately 100 amino acid residues, proteins which are mitochondrial 28S ribosomal proteins named as MRP-S32.\.   Their exact function could not be confirmed.. 
PF10211 Axonemal dynein light chain<br>Axonemal dynein light chain proteins play a dynamic role in flagellar and cilia motility. Eukaryotic cilia and flagella are complex organelles consisting of a core structure, the axoneme, which is composed of nine microtubule doublets forming a cylinder that surrounds a pair of central singlet microtubules. This ultra-structural arrangement seems to be one of the most stable micro-tubular assemblies known and is responsible for the flagellar and ciliary movement of a large number of organisms ranging from protozoan to mammals. This light chain interacts directly with the N-terminal half of the heavy chains  .. 
PF10212 Predicted coiled-coil domain-containing protein<br>This is the C-terminal 500 amino acids of a family of proteins with a predicted coiled-coil domain conserved from nematodes to humans. It carries a characteristic TTKRSYEDQ sequence-motif. The function is not known.. 
PF10213 Mitochondrial ribosomal subunit protein <br>This is a conserved region of approx. 125 residues of one of the proteins that makes up the small subunit of the mitochondrial ribosome. In Saccharomyces cerevisiae the protein is MRP-S24 whereas in humans it is MRP-S28. The human mitochondrial ribosome has 29 distinct proteins in the small subunit and these have homologues in, for example, Drosophila melanogaster, Caenorhabditis elegans, and in the genomes of several fungi  .. 
PF10214 RNA polymerase I-specific transcription-initiation factor<br>RNA polymerase I-specific transcription-initiation factor Rrn6 and Rrn7 represent components of a multisubunit transcription factor essential for the initiation of rDNA transcription by Pol I  . These proteins are found in fungi.. 
PF10215 Oligosaccaryltransferase  <br>Ost4 is a very short, approximately 30 residues, enzyme found from fungi to vertebrates. It is a member of the ER oligosaccaryltansferase complex, EC 2.4.1.119, that catalyses the asparagine-linked glycosylation of proteins. It appears to be an integral membrane protein that mediates the en bloc transfer of a preassembled high-mannose oligosaccharide onto asparagine residues of nascent polypeptides as they enter the lumen of the rough endoplasmic reticulum (RER).. 
PF10216 CO2 hydration protein (ChpXY)<br>This small family of proteins includes paralogues ChpX and ChpY in Synechococcus sp. PCC7942 and other cyanobacteria, associated with distinct NAD(P)H dehydrogenase complexes. These proteins collectively enable light-dependent CO2 hydration and CO2 uptake; loss of both blocks growth at low CO2 concentrations.. 
PF10217 Uncharacterized conserved protein (DUF2039)<br>This entry is a region of approximately 100 residues containing three pairs of cysteine residues. The region is conserved from plants to humans but its function is unknown.. 
PF10218 Uncharacterized conserved protein (DUF2054)<br>This entry contains 14 conserved cysteines, three of which are CC-dimers. The region is of approximately 200 residues in length but its function is unknown.. 
PF10220 Uncharacterized conserved protein (DUF2146)<br>This is a family of proteins conserved from plants to humans. In Dictyostelium it is annotated as Mss11p but this could not be confirmed. Mss11p is required for the activation of pseudo-hyphal and invasive growth by Ste12p in yeast.. 
PF10221 Cell cycle and development regulator<br>This is a set of proteins conserved from worms to humans. The proteins are a PAN GU kinase substrate, Mat89Bb, essential for S-M cycles of early Drosophila embryogenesis, Xenopus embryonic cell cycles and morphogenesis, and cell division in cultured mammalian cells.. 
PF10222 Uncharacterized conserved protein (DUF2152)<br>This is a family of proteins conserved from worms to humans. Its function is unknown.. 
PF10223 Uncharacterized conserved protein (DUF2181)<br>This is region of approximately 250 residues conserved from worms to humans. Its function is unknown.. 
PF10224 Predicted coiled-coil protein (DUF2205)<br>This entry represent a highly conserved 100 residue region which is likely to be a coiled-coil structure. The exact function is unknown.. 
PF10225 Uncharacterized conserved protein (DUF2215)<br>This entry is the central 200 residues of a family of proteins conserved from worms to humans. The function is unknown.. 
PF10226 Uncharacterized conserved proteins (DUF2216)<br>This is the conserved N-terminal half of a proteins which are found from worms to humans. some annotation suggests it might be PKR, the Hepatitis delta antigen-interacting protein A, but this could not be confirmed.. 
PF10228 Uncharacterised conserved protein (DUF2228)<br>This is a family of conserved proteins of approximately 700 residues found from worms to humans.. 
PF10229 Uncharacterized conserved protein (DUF2246)<br>This is a family of proteins conserved from worms to humans of approximately 300 residues. The function is unknown.. 
PF10230 Uncharacterised conserved protein (DUF2305)<br>This family of proteins is conserved from plants to humans. The function is unknown.. 
PF10231 Uncharacterised conserved protein (DUF2315)<br>This is a family of small conserved proteins found from worms to humans. The function is not known.. 
PF10232 Arc32; <br>Mediator of RNA polymerase II transcription complex subunit 8. Arc32, or Med8, is one of the subunits of the Mediator complex of RNA polymerase II. The region conserved contains two alpha helices putatively necessary for binding to other subunits within the core of the Mediator complex  . The N-terminus of Med8 binds to the essential core Head part of Mediator and the C-terminus hinges to Med18 on the non-essential part of the Head that also includes Med20  .. 
PF10233 Uncharacterized conserved protein CG6151-P<br>This is a family of small, less than 200 residue long, proteins which are named as CG6151-P proteins that are conserved from fungi to humans. The function is unknown.  The fungal members have a characteristic ICP sequence motif. Some members are annotated as putative clathrin-coated vesicle protein but this could not be defined.. 
PF10234 Clusterin-associated protein-1<br>This protein is conserved from worms to humans. The protein of 413 amino acids contains a central coiled-coil domain, possibly the region that binds to clusterin. Cluap1 expression is highest in the nucleus and gradually increases during late S to G2/M phases of the cell cycle and returns to the basal level in the G0/G1 phases. In addition, it is upregulated in colon cancer tissues compared to corresponding non-cancerous mucosa. It thus plays a crucial role in the life of the cell  .. 
PF10235 Microtubule-associated protein CRIPT<br>The CRIPT protein is a cytoskeletal protein involved in microtubule production. The C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners.  SAP90 is concentrated in the post synaptic density of glutamatergic neurons  .. 
PF10236 Mitochondrial ribosomal death-associated protein 3<br>This is a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis  . DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix   and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29).. 
PF10237 DPPF;<br>Probable N6-adenine methyltransferase. This is a protein of approximately 200 residues which is conserved from plants to humans  .  It contains a highly conserved QFW motif close to the N-terminus and a DPPF motif in the centre. The DPPF motif is characteristic of N-6 adenine-specific DNA methylases, and this family is found in eukaryotes  .. 
PF10238 E2F-associated phosphoprotein<br>This entry represents the conserved C-terminal portion of an E2F binding protein. E2F transcription factors play an essential role in cell proliferation and apoptosis and their activity is frequently deregulated in human cancers. E2F activity is regulated by a variety of mechanisms, frequently mediated by proteins binding to individual members or a subgroup of the family. EAPP interacts with a subset of E2F factors and influences E2F-dependent promoter activity. EAPP is present throughout the cell cycle but disappears during mitosis  .. 
PF10239 FAM98AB; <br>Protein of unknown function (DUF2465). FAM98A and B proteins are found from worms to humans but their function is unknown. This entry is of a family of proteins that is rich in glycines.. 
PF10240 Fam125A; <br>Protein of unknown function (DUF2464). This is a family of proteins conserved from worms to humans. Members have been annotated as FAM125A proteins, but their function is unknown.. 
PF10241 Uncharacterized conserved protein<br>This is a family of short proteins which are conserved over a region of 80 residues.  There is a characteristic KxDL motif towards the C-terminus.  The function is unknown.. 
PF10242 Lipoma HMGIC fusion partner-like protein<br>This is a group of proteins expressed from a series of genes referred to as Lipoma HGMIC fusion partner-like. The proteins carry four highly conserved transmembrane domains in this entry. In certain instances, eg in LHFPL5, mutations cause deafness in humans   and hypospadias  , and LHFPL1 is transcribed in six liver tumour cell lines  .. 
PF10243 Microtubule-binding protein MIP-T3<br>This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3.  The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved  .. 
PF10244 Mitochondrial ribosomal subunit<br>MRP-L51 is a family of small proteins from the intact 55 S mitochondrial ribosome  . It has otherwise been referred to as bMRP-64  . The exact function of this family is not known.. 
PF10245 Mitochondrial 28S ribosomal protein S22<br>This is the conserved N-terminus and central portion of the mitochondrial small subunit 28S ribosomal protein S22.  Mammalian mitochondria carry out the synthesis of 13 polypeptides that are essential for oxidative phosphorylation and, hence, for the synthesis of the majority of the ATP used by eukaryotic organisms. The number of proteins produced by prokaryotes is smaller, reflected in the lower number of ribosomal proteins present in them  .. 
PF10246 Mitochondrial ribosomal protein MRP-S35<br>This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. that are highly conserved from worms to humans. The structure has previously been referred to as MRP-S18 but the current numbering fits the preferred nomenclature from these authors.. 
PF10247 Mit_gmP; <br>Reactive mitochondrial oxygen species modulator 1. This is a family of small, approximately 100 amino acid, proteins found from yeasts to humans. The majority of endogenous reactive oxygen species (ROS) in cells are produced by the mitochondrial respiratory chain. An increase or imbalance in ROS alters the intracellular redox homeostasis, triggers DNA damage, and may contribute to cancer development and progression  . Members of this family are mitochondrial reactive oxygen species modulator 1 (Romo1) proteins that are responsible for increasing the level of ROS in cells. Increased Romo1 expression can have a number of other effects including: inducing premature senescence of cultured human fibroblasts [2,3] and increased resistance to 5-fluorouracil  .. 
PF10248 Myelodysplasia-myeloid leukemia factor 1-interacting protein<br>This entry is the conserved central region of a group of proteins that are putative transcriptional repressors  . The structure contains a putative 14-3-3 binding motif involved in the subcellular localisation of various regulatory molecules, and it may be that interaction with the transcription factor DREF could be regulated through this motif. DREF regulates proliferation-related genes in Drosophila  . Mlf1IP is expressed in both the nuclei and the cytoplasm and thus may have multi-functions  .. 
PF10249 NADH-ubiquinone oxidoreductase subunit 10<br>NDUFB10 is a family of conserved proteins of up to 180 residues. It is one of the 41 protein subunits within the hydrophobic fraction of the NADH:ubiquinone oxidoreductase (complex I), a multiprotein complex located in the inner mitochondrial membrane whose main function is the transport of electrons from NADH to ubiquinone, which is accompanied by translocation of protons from the mitochondrial matrix to the intermembrane space. NDUFB10 is encoded in the nucleus.. 
PF10250 GDP-fucose protein O-fucosyltransferase<br>This is a family of conserved proteins representing the enzyme responsible for adding O-fucose to EGF (epidermal growth factor-like) repeats. Six highly conserved cysteines are present in O-FucT-1 as well as a DXD-like motif (ERD), conserved in mammals, Drosophila, and C. elegans. Both features are characteristic of several glycosyltransferase families. The enzyme is a membrane-bound protein released by proteolysis and, as for most glycosyltransferases, is strongly activated by manganese  .. 
PF10251 Presenilin enhancer-2 subunit of gamma secretase<br>This entry is a short 101 peptide protein which is the smallest subunit of the gamma-secretase aspartyl protease complex that catalyses the intramembrane cleavage of a subset of type I transmembrane proteins. The other active constituents of the complex are presenilin (PS) nicastrin and anterior pharynx defective-1 (APH-1) protein. PEN-2 adopts a hairpin orientation in the membrane with its N- and C-terminal domains facing the luminal/extracellular space, and the C-terminal domain maintains PS stability within the complex  .. 
PF10252 Casein kinase substrate phosphoprotein PP28<br>This domain is a region of 70 residues conserved in proteins from plants to humans and contains a serine/arginine rich motif. In rats the full protein is a casein kinase substrate, and this region contains phosphorylation sites for both cAMP-dependent protein kinase and casein kinase II  .. 
PF10253 PRCC_Cterm;<br>Mitotic checkpoint regulator, MAD2B-interacting. This family constitutes the major, conserved, portion of PRCC proteins. In humans this family interacts with MAD2B, the mitotic checkpoint protein [1,2].\.      In Schizosaccharomyces pombe this protein is part of the Cwf-complex that is known to be involved in pre-mRNA splicing  .. 
PF10254 PACS-1 cytosolic sorting protein<br>PACS-1 is a cytosolic sorting protein that directs the localisation of membrane proteins in the trans-Golgi network (TGN)/endosomal system. PACS-1 connects the clathrin adaptor AP-1 to acidic cluster sorting motifs contained in the cytoplasmic domain of cargo proteins such as furin, the cation-independent mannose-6-phosphate receptor and in viral proteins such as human immunodeficiency virus type 1 Nef  .. 
PF10255 RNA polymerase I-associated factor PAF67<br>RNA polymerase I is a multisubunit enzyme and its transcription competence is dependent on the presence of PAF67  . This family of proteins is conserved from worms to humans.. 
PF10256 QRDY; <br>Golgin subfamily A member 7/ERF4 family. KOGs (KOG4069 & KOG4101). This family of proteins includes Golgin subfamily A member 7 proteins as well as Ras modification protein ERF4.. 
PF10257 Retinoic acid induced 16-like protein<br>This is the conserved N-terminal 450 residues of a family of proteins described as retinoic acid-induced protein 16-like proteins. The exact function is not known. The proteins are found from worms to humans.. 
PF10258 PHAX RNA-binding domain<br>RNA_GG_bind is the highly conserved U3 snoRNA-binding domain of PHAX (phosphorylated adaptor for RNA export) whose function is to transport U3 snoRNA from the nucleus after transcription  . It is characterised by having two pairs of adjacent glycines, as GGx12GG.. 
PF10259 Rogdi leucine zipper containing protein<br>This is a family of conserved proteins which have been suggested as containing leucine-zipper domains. A leucine zipper domain is a region of 30 amino acids with leucines repeating every seven or eight residues; these proteins do have many such leucines. The protein in Drosophila comes from the gene ROGDI.. 
PF10260 Uncharacterized conserved domain (SAYSvFN)<br>This domain of approximately 75 residues contains a highly conserved SATSv/iFN motif. The function is unknown but the domain is conserved from plants to humans.. 
PF10261 Inositol phospholipid synthesis and fat-storage-inducing TM<br>This is a family of transmembrane proteins which are variously annotated as possibly being inositol phospholipid synthesis protein   and fat-storage-inducing. The members are conserved from yeasts to humans and are localised to the endoplasmic reticulum where they are involved in triglyceride lipid droplet formation  .. 
PF10262 SelT; <br>KOGs (KOG3286) & COG3526. This entry is an approximately 100 residue region of selenoprotein-T, conserved from plants to humans. The protein binds to UDP-glucose:glycoprotein glucosyltransferase (UGTR), the endoplasmic reticulum (ER)-resident protein, which is known to be involved in the quality control of protein folding  . Selenium (Se) plays an essential role in cell survival and most of the effects of Se are probably mediated by selenoproteins, including selenoprotein T. However, despite its binding to UGTR and that its mRNA is up-regulated in extended asphyxia, the function of the protein and hence of this region of it is unknown  . Selenoprotein W contains selenium as selenocysteine  in the primary protein structure and levels of this  selenoprotein are affected by selenium  .. 
PF10263 SprT-like family<br>This family represents a domain found in eukaryotes and prokaryotes.  The domain contains a characteristic motif of the zinc metallopeptidases. This family includes the bacterial SprT protein.. 
PF10264 Winged helix Storkhead-box1 domain<br>This is the conserved N-terminal winged helix domain of Storkhead-box1 protein which is likely to be a DNA binding domain. In humans the full-length protein controls polyploidization of extravillus trophoblast and is implicated in pre-eclampsia.. 
PF10265 Uncharacterized conserved protein (DUF2217)<br>This is a family of conserved proteins of from 500 - 600 residues found from worms to humans. Its function is not known.. 
PF10266 Hereditary spastic paraplegia protein strumpellin<br>This is a family of proteins conserved from plants to humans, in which two closely situated point mutations in the human protein lead to the condition of hereditary spastic paraplegia. Strumpellin contains one known domain called a spectrin repeat that consists of three alpha-helices of a characteristic length wrapped in a left-handed coiled coil. The spectrin proteins have multiple copies of this repeat, which can then form multimers in the cell. Spectrin associates with the cell membrane via spectrin repeats in the ankyrin protein. The spectrin repeat is a structural platform for cytoskeletal protein assemblies.. 
PF10267 Tmcc1; Transmemb_cc2; Tmemcc2; <br>Predicted transmembrane and coiled-coil 2 protein. This family of transmembrane coiled-coil containing proteins is conserved from worms to humans. Its function is unknown.. 
PF10268 Tmem161AB; Transmemb_161AB; Tmem161AB; <br>Predicted transmembrane protein 161AB. Transmemb_161AB is a family of conserved proteins found from worms to humans. Members are putative transmembrane proteins but otherwise the function is not known.. 
PF10269 Tmem185A; <br>Transmembrane Fragile-X-F protein . This is a family of conserved transmembrane proteins that appear in humans to be expressed from a region upstream of the FragileXF site and to be intimately linked with the Fragile-X syndrome. Absence of TMEM185A does not necessarily lead to developmental delay, but might in combination with other, yet unknown, factors. Otherwise, the lack of the TMEM185A protein is either disposable (redundant) or its function can be complemented by the highly similar chromosome 2 retro-pseudogene product, TMEM185B  .. 
PF10270 Tmem32; Tmemb_32;<br>Membrane magnesium transporter. This entry represents a novel family of membrane magnesium transporters (MMgT)  . The proteins, MMgT1 and MMgT2, are localised to the Golgi complex and post-Golgi vesicles, including the early endosomes, suggesting that they may provide regulated pathways for Mg(2+) transport in the Golgi and post-Golgi organelles of epithelium-derived cells  .. 
PF10271 Putative transmembrane protein<br>This is a family of conserved proteins found from worms to humans. They are putative transmembrane proteins but the function is unknown.. 
PF10272 Putative transmembrane protein precursor<br>This is a family of proteins conserved from worms to humans. The proteins are purported to be transmembrane protein-precursors but the function is unknown.. 
PF10273 Pre-rRNA-processing protein TSR2<br>This entry represents the central conserved section of a family of proteins described as pre-rRNA-processing protein TSR2. The region has a distinctive WGG motif but the function is unknown.. 
PF10274 Parkin co-regulated protein<br>This family of proteins is transcribed anti-sense along the DNA to the Parkin gene product and the two appear to be transcribed under the same promoter. The protein has predicted alpha-helical and beta-sheet domains which suggest its function is in the ubiquitin/proteasome system  .  Mutations in parkin are the genetic cause of early-onset and autosomal recessive juvenile parkinsonism.. 
PF10275 Otubain; <br>Peptidase C65 Otubain. This family of proteins conserved from plants to humans is a highly specific ubiquitin iso-peptidase that removes ubiquitin from proteins. The modification of cellular proteins by ubiquitin (Ub) is an important event that underlies protein stability and function in eukaryote being a dynamic and reversible process. Otubain carries several key conserved domains: (i) the OTU (ovarian tumour domain) in which there is an active cysteine protease triad (ii) a nuclear localisation signal, (iii) a Ub interaction motif (UIM)-like motif phi-xx-A-xxxs-xx-Ac (where phi indicates an aromatic amino acid, x indicates any amino acid and Ac indicates an acidic amino acid), (iv) a Ub-associated (UBA)-like domain and (v) the LxxLL motif.. 
PF10276 Zinc-finger domain<br>This is a short zinc-finger domain conserved from fungi to humans. It is Cx8Hx14Cx2C.. 
PF10277 Frag1/DRAM/Sfk1 family<br>KOGs (KOG3979) & KOGs (KOG4320) & Pfam-B_15139 (release 21.0). This family includes Frag1, DRAM and Sfk1 proteins.  Frag1 (FGF receptor activating protein 1) is a protein that is conserved from fungi to humans.  There are four potential iso-prenylation sites throughout the peptide, viz CILW, CIIW and CIGL. Frag1 is a membrane-spanning protein that is ubiquitously expressed in adult tissues suggesting an important cellular function  .  Dram is a family of proteins conserved from nematodes to humans with six hydrophobic transmembrane regions and an Endoplasmic Reticulum signal peptide. It is a lysosomal protein that induces macro-autophagy as an effector of p53-mediated death, where p53 is the tumour-suppressor gene that is frequently mutated in cancer. Expression of Dram is stress-induced  .  This region is also part of a family of small plasma membrane proteins, referred to as Sfk1, that may act together with or upstream of Stt4p to generate normal levels of the essential phospholipid PI4P, thus allowing proper localisation of Stt4p to the actin cytoskeleton [3-4].. 
PF10278 Mediator of RNA pol II transcription subunit 19 <br>Med19 represents a family of conserved proteins which are members of the multi-protein co-activator Mediator complex. Mediator is required for activation of RNA polymerase II transcription by DNA binding transactivators  .. 
PF10279 Latarcin precursor<br>This family represents the precursor proteins for a number of short antimicrobial peptides called Latarcins. Latarcins were discovered in the venom of the spider Lachesana tarabaevi  . Latarcins are likely to adopt amphipathic alpha-helical structure in the plasma membrane.. 
PF10280 HSPC296_Med11; <br>Mediator complex protein . Mediator is a large, modular protein complex that is conserved from yeast to human and conveys regulatory signals from DNA-binding transcription factors to RNA polymerase II. Not only are the polypeptides conserved but the structural organisation is also largely conserved. One or two subunits are either fungal or vertebral specific but Med11 is one of the subunits that is conserved from fungi to humans  . Med11 appears to be necessary for the full and successful assembly of the core head sub-region  .. 
PF10281 Putative stress-responsive nuclear envelope protein<br>Pfam-B_11056 (release 21.0). This family of proteins found in fungi is a putative stress-responsive nuclear envelope protein Ish1  .. 
PF10282 DUF2394; Muc_lac_enz;<br>Lactonase, 7-bladed beta-propeller. Pfam-B_1372 (release 21.0). This entry contains bacterial 6-phosphogluconolactonases (6PGL)YbhE-type (EC:3.1.1.31) which hydrolyse 6-phosphogluconolactone to 6-phosphogluconate. The entry also contains the fungal muconate lactonising enzyme carboxy-cis,cis-muconate cyclase (EC:5.5.1.5) and muconate cycloisomerase (EC:5.5.1.1), which convert cis,cis-muconates to muconolactones and vice versa as part of the microbial beta-ketoadipate pathway.\.     Structures of proteins in this family have revealed a 7-bladed beta-propeller fold  .. 
PF10283 Zinc-finger (CX5CX6HX5H) motif<br>Pfam-B_93850 (release 21.0). This domain is a zinc-finger motif that in humans is part of the APLF, aprataxin- and PNK-like forkead association domain-containing protein. The ZnF is highly conserved both in primary sequence and in the spacing between the putative zinc coordinating residues and is configured CX5CX6HX5H. Many of the proteins containing the APLF-like ZnF are involved in DNA strand break repair and/or contain domains implicated in DNA metabolism.. 
PF10284 Luciferase helical bundle domain<br>This domain is found associated with the the catalytic domain of dinoflagellate luciferase . Luciferase is involved in catalysing the light emitting reaction in bioluminescence. The structure of this domain has been solved  . This domain has a three helix bundle structure that holds four important histidines that are thought to play a role in the pH regulation of the enzyme.. 
PF10285 Luciferase catalytic domain<br>This domain is the catalytic domain of dinoflagellate luciferase . Luciferase is involved in catalysing the light emitting reaction in bioluminescence. The structure of this domain has been solved  . The core part of the domain is a 10 stranded beta barrel that is structurally similar to lipocalins and FABP  .. 
PF10287 Putative TOS1-like glycosyl hydrolase (DUF2401)<br>Pfam-B_11571 (release 21.0). This family of proteins is conserved in fungi. One member is annotated putatively as OPEL, a house-keeping protein, but this could not be confirmed. It contains 5 highly conserved cysteines two of which form a characteristic CGC sequence motif. It has recently been shown that this family is related to known glycosyl hydrolases  .. 
PF10288 Protein of unknown function (DUF2392)<br>Pfam-B_10085 (release 21.0). This is a family of proteins conserved from plants to humans. The function is not known.  It carries a characteristic GRG sequence motif.. 
PF10290 Glycine-rich protein domain (DUF2403)<br>Pfam-B_11570 (release 21.0). This domain is found in the N-terminal region of members of DUF2401 Pfam:PF10287. The function of this glycine-rich region is unknown.. 
PF10291 SAFF;<br>Muniscin C-terminal mu homology domain. Yang H, Pfam-B_7632 (release 21.0). The muniscins are a family of endocytic adaptors that is conserved from yeast to humans.This C-terminal domain is structurally similar to mu homology domains, and is the region of the muniscin proteins involved in the interactions with the endocytic adaptor-scaffold proteins Ede1-eps15. This interaction influences muniscin localisation. The muniscins provide a combined adaptor-membrane-tubulation activity that is important for regulating endocytosis.. 
PF10292 Srab; <br>Serpentine type 7TM GPCR receptor class ab chemoreceptor. Thomas JH, Robertson H. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type  . Srab is part of the Sra superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'  . The expression pattern of the srab genes is biologically intriguing. Of the six promoters successfully expressed in transgenic organisms, one was exclusively expressed in the tail phasmid neurons, two were exclusively expressed in a head amphid neuron, and two were expressed both in the head and tail neurons as well as a limited number of other cells  .. 
PF10293 Domain of unknown function (DUF2405)<br>Pfam-B_12420 (release 21.0). This is a conserved region of a family of proteins conserved in fungi. The function is unknown.. 
PF10294 Putative methyltransferase<br>Pfam-B_19672 (Release 21.0). 
PF10295 Uncharacterised protein (DUF2406)<br>Pfam-B_13850 (release 21.0). This is a family of small proteins conserved in fungi. The function is not known.. 
PF10296 Putative integral membrane protein conserved region (DUF2404)<br>Pfam-B_12178 (release 21.0). This domain is conserved from plants to humans. The function is not known.. 
PF10297 Minimal binding motif of Hap4 for binding to Hap2/3/5   <br>In Saccharomyces cerevisiae, the haem-activated protein complex Hap2/3/4/5 plays a major role in the transcription of genes involved in respiration  . Hap4_Hap_bind is the essential domain of Hap4 which allows it to associate with Hap2, Hap3 and Hap5 to form the Hap complex  .. 
PF10298 WhiA N-terminal LAGLIDADG-like domain<br>This domain is found at the N terminal of sporulation factor WhiA. This domain is related to the LAGLIDADG Homing endonuclease domain while the C terminal domain of WhiA is predicted to be a DNA binding helix-turn-helix domain  .. 
PF10300 Deme6; IML2;<br>Protein of unknown function (DUF3808). Pfam-B_15386 (release 21.0). This is a family of proteins conserved from fungi to humans. Members of this family also carry a TPR_2 domain Pfam:PF07719 at their C-terminus.. 
PF10302 DUF2407 ubiquitin-like domain<br>Pfam-B_17915 (release 21.0). This is a family of proteins found in fungi. The function is not known. This domain is related to the ubiquitin domain.. 
PF10303 Protein of unknown function (DUF2408)<br>Pfam-B_16841 (release 21.0). This is a family of proteins conserved in fungi. The function is unknown.. 
PF10304 Domain of unknown function (DUF2411)<br>Pfam-B_15078 (release 21.0). This is a 38 residue domain that is found in proteins at the extreme C-terminal end of some HEAT repeats Pfam: PF02985. the function of this domain is not known.. 
PF10305 RNA pol II promoter Fmp27 protein domain<br>Pfam-B_15444 (release 21.0). Fmp27_SW is a conserved domain of a family of proteins involved in RNA polymerase II transcription initiation  . It contains characteristic SW and GKG sequence motifs.. 
PF10306 Hypothetical protein FLILHELTA<br>Pfam-B_18082 (release 21.0). This is a family of conserved proteins found in fungi. It contains a characteristic FL(I)LHE(L)TA sequence motif, where the bracketed residues are I, L or V. The function is not known.. 
PF10307 Hypothetical protein (DUF2410)<br>Pfam-B_19378 (release 21.0). This is a family of proteins conserved in fungi. The function is not known.There are two characteristic sequence motifs, GGWW and TGR.. 
PF10309 Protein of unknown function (DUF2414)<br>Pfam-B_22455 (release 21.0). This is a family of proteins conserved from fungi to mammals. One mouse member is referred to as ELG protein but this is not a homologue of human ELG protein.  The function is not known.. 
PF10310 Protein of unknown function (DUF2413)<br>Pfam-B_20450 (release 21.0). This is a family of proteins conserved in fungi.  The function is not known.. 
PF10311 Increased loss of mitochondrial DNA protein 1<br>Pfam-B_22448 (release 21.0). This is a family of proteins of approximately 200 residues that are conserved in fungi. Ilm1 is part of the peroxisome, a complex that is the sole site of beta-oxidation in Saccharomyces cerevisiae and known to be required for optimal growth in the presence of fatty acid. Ilm1 may participate in the control of the C16/C18 ratio since it interacts strongly with Mga2p, a transcription factor that controls expression of Ole1, the sole fatty acyl desaturase in S. cerevisiae responsible for conversion of the saturated fatty acids stearate (C18) and palmitate (C16) to oleate and palmitoleate, respectively  .. 
PF10312 Conserved mid region of cactin<br>Pfam-B_20647 (release 21.0). This is the conserved middle region of a family of proteins referred to as cactins. The region contains two of three predicted coiled-coil domains. Most members of this family have a CactinC_cactus Pfam:PF09732 domain at the C-terminal end. Upstream of Mid_cactin in Drosophila members are a serine-rich region, some non-typical RD motifs and three predicted bipartite nuclear localisation signals, none of which are well-conserved. Cactin associates with IkappaB-cactus as one of the intracellular members of the Rel (NF-kappaB) pathway which is conserved in invertebrates and vertebrates. In mammals, this pathway controls the activities of the immune and inflammatory response genes as well as viral genes, and is critical for cell growth and survival. In Drosophila, the Rel pathway functions in the innate cellular and humoral immune response, in muscle development, and in the establishment of dorsal-ventral polarity in the early embryo  .. 
PF10313 Uncharacterised protein domain (DUF2415)<br>Pfam-B_25751 (release 21.0). This is a short, 30 residue domain, from a family of proteins conserved in fungi. The function is unknown. There is a characteristic DLL sequence motif.. 
PF10315 Protein of unknown function (DUF2416)<br>Pfam-B_28778 (release 21.0). This is a family of conserved proteins found in fungi. The function is not known.. 
PF10316 Srbc; <br>Serpentine type 7TM GPCR chemoreceptor Srbc . Thomas JH, Robertson H. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type  . Srbc is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'  .. 
PF10317 Srd; <br>Serpentine type 7TM GPCR chemoreceptor Srd. Thomas JH, Robertson H. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type  . Srd is part of the larger Str superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'  .. 
PF10318 Srh; <br>Serpentine type 7TM GPCR chemoreceptor Srh. Thomas JH, Robertson H. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type  . Srh is part of the Str superfamily of chemoreceptors  . Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'  .. 
PF10319 Srj; <br>Serpentine type 7TM GPCR chemoreceptor Srj. Thomas JH, Robertson H. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type  . Srj is part of the Str superfamily of chemoreceptors. The srj family is designated as the out-group based on its location in preliminary phylogenetic analyses of the entire superfamily  . Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'  .. 
PF10320 Srsx; <br>Serpentine type 7TM GPCR chemoreceptor Srsx. Thomas JH, Robertson H. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type  . Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'  .. 
PF10321 Srt; <br>Serpentine type 7TM GPCR chemoreceptor Srt. Thomas JH, Robertson H. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type  . Srt is a member of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'  .. 
PF10322 Sru; <br>Serpentine type 7TM GPCR chemoreceptor Sru. Thomas JH, Robertson H. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type  . Sru is a member of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'  .. 
PF10323 Srv; <br>Serpentine type 7TM GPCR chemoreceptor Srv. Thomas JH, Robertson H. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type  . Srv is a member of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'  .. 
PF10324 Srw; <br>Serpentine type 7TM GPCR chemoreceptor Srw. Thomas JH, Robertson H. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type  . Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'  . The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz  .. 
PF10325 Srz; <br>Serpentine type 7TM GPCR chemoreceptor Srz. Thomas JH, Robertson H. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type  . Srz is a solo families amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'  . The genes encoding Srz appear to be under strong adaptive evolutionary pressure  .. 
PF10326 Str; <br>Serpentine type 7TM GPCR chemoreceptor Str. Thomas JH, Robertson H. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type  . Str is a member of the Str superfamily of chemoreceptors. Almost a quarter (22.5%) of str and srj family genes and pseudogenes in C. elegans appear to have been newly formed by gene duplications since the species split  .  Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'  .. 
PF10327 Serpentine_Sri; <br>Serpentine type 7TM GPCR chemoreceptor Sri. Thomas JH, Robertson H. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type  . Sri is part of the Str superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'  .. 
PF10328 Serpentine_Srx; <br>Serpentine type 7TM GPCR chemoreceptor Srx. Thomas JH, Robertson H. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type  . Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'  .. 
PF10329 Region of unknown function (DUF2417)<br>Pfam-B_22799 (release 21.0). This is a region of a family of proteins conserved in fungi some of whose members also have the Abhydrolase_1, Pfam:PF00561, domain in their sequence. The function of this region is not known.. 
PF10330 Putative Sin3 binding protein<br>Pfam-B_24989 (release 21.0). This is a family of the conserved N-terminal end of a group of proteins conserved in fungi. It is likely to be a Sin3 binding protein. Sin3p does not bind DNA directly even though the yeast SIN3 gene functions as a transcriptional repressor. Sin3p is part of a large multiprotein complex  . Stb3 appears to bind directly to ribosomal RNA Processing Elements (RRPE) although there are no obvious domains which would accord with this, implying that Stb3 may be a novel RNA-binding protein  .. 
PF10332 Protein of unknown function (DUF2418)<br>Pfam-B_29723 (release 21.0). This is a conserved 100 residue central region of a family of proteins found in fungi. It carries a characteristic EYD sequence motif. The function is not known.. 
PF10333 GPI-Mannosyltransferase II co-activator<br>Pfam-B_50403 (release 21.0). Pga1 is found only in yeasts and not in mammals. It localises in the ER as a glycosylated integral membrane protein. It binds to the GPI-mannosyltransferase II subunit of the GPI and it is responsible for the second mannose addition to GPI precursors. The GPI-anchoring complex is a glycolipid that functions as a membrane anchor for many cell-surface proteins  .. 
PF10334 Protein of unknown function (DUF2421)<br>Pfam-B_39020 (release 21.0). This is a family of proteins conserved in fungi. The function is not known.. 
PF10335 Putative nucleotidyltransferase substrate binding domain<br>This domain is found associated with presumed nucleotidyltransferase domains and seems to be distantly related to other helical substrate binding domains.. 
PF10336 Protein of unknown function (DUF2420)<br>Pfam-B_32350 (release 21.0). This is a family of proteins conserved in fungi.  The function is not known.. 
PF10337 Protein of unknown function (DUF2422)<br>Pfam-B_42729 (release 21.0). This is a family of proteins conserved in fungi. The function is not known. This family is the C-terminal half of some member proteins which contain the DUF2421 Pfam:PF10334 domain at their N-terminus.. 
PF10338 Protein of unknown function (DUF2423)<br>Pfam-B_46946 (release 21.0). This is a family of proteins conserved in fungi. The function is not known.. 
PF10339 Yeast-specific zinc responsive<br>Pfam-B_50673 (release 21.0). This is a small family of proteins from Saccharomyces and related species. The function is not known but member proteins are highly induced in zinc-depleted conditions [1,2] and have increased expression in NAP1-deletion mutants  . The S. cerevisiae genes are named VEL by association with Velum formation in the wine making process http://www.ajevonline.org/content/48/1/55.abstract. 
PF10340 Protein of unknown function (DUF2424)<br>Pfam-B_51256 (release 21.0). This is a family of proteins conserved in yeasts. The function is not known.. 
PF10341 Est3;<br>Shelterin complex subunit, TPP1/ACD. TPP1 is a component of the telomerase holoenzyme, involved in telomere replication.  It has been demonstrated that TPP1 dimerises and binds to DNA and RNA. Furthermore, TPP1 stimulates the dissociation of RNA/DNA hetero-duplexes [1,2]. Yeast telomerase protein TPP1 (Est3 in yeast) is a novel type of GTPase  . The key residues in Swiss:Q03096 are an Asp at residue 86 and the Arg at residue 110.  The Asp is totally conserved in the family, whereas the Arg is not so well conserved. The N-terminal of TPP1 is likely to be the binding surface for TINF2, whereas the C-terminus probably binds to POT1, thereby tethering POT1 to the shelterin complex  .  The complex bound to telomeric DNA increases the activity and processivity of the human telomerase core enzyme, thus helping to maintain the length of the telomeres [5,6]. This domain is conserved from fungi to mammals, hence family Telomere_Pot1 has been merged into the family  . The human shelterin complex includes six proteins: telomere repeat binding factor 1 (TRF1), TRF2, repressor/activator protein 1 (RAP1), TRF1-interacting nuclear protein 2 (TIN2), TIN2-interacting protein 1 (TPP1) and protection of telomeres 1 (POT1)  .. 
PF10342 Drmip_Hesp; Drmip_MAPK;<br>Ser-Thr-rich glycosyl-phosphatidyl-inositol-anchored membrane family. Pfam-B_42324 (release 21.0). Some members of this family appear to be serine- threonine-rich membrane-anchored proteins, anchored by glycosyl-phosphatidylinositol. In A. fumigatus these proteins play a role in fungal cell wall organisation. In Lentinula edodes this family is involved in fruiting body formation, and may have a more general role in signalling in other organisms as it interacts with MAPK. The family is also found in archaea and bacteria.. 
PF10343 Protein of unknown function (DUF2419)<br>Pfam-B_35257 (release 21.0). This is a family of conserved proteins found from plants to humans. The function is not known. A few members are annotated as being cobyrinic acid a,c-diamide synthetase but this could not be confirmed.. 
PF10344 DUF2425; <br>Mitochondrial protein from FMP27. Pfam-B_54917 (release 21.0). This family contains mitochondrial FMP27 proteins which in yeasts together with SEN1 are long genes that exist in a looped conformation, effectively bringing together their promoter and terminator regions. Pol-II is located at both ends of FMP27 when this gene is transcribed from a GAL1 promoter under induced and non-induced conditions  . The exact function of the Fmp27 protein is not certain.. 
PF10345 Cohesin loading factor<br>Cohesin_load is a common cohesin loading factor protein that is conserved in fungi. It is associated with the cohesin complex and is required in G1 for cohesin binding to chromosomes but dispensable in G2 when cohesion has been established. It is referred to as both Ssl3, in pombe, and Scc4, in S.cerevisiae. It complexes with Mis4  .. 
PF10346 Conidiation protein 6<br>Pfam-B_35316 (release 21.0). Con-6 is the conserved N-terminal region of a family of small proteins found in fungi  . It is expressed at approximately 6 hours after the induction of development and is induced just prior to major constriction-chain growth  .. 
PF10347 RNA pol II promoter Fmp27 protein domain<br>Pfam-B_5282 (release 21.0). Fmp27_GFWDK is a conserved domain of a family of proteins involved in RNA polymerase II transcription initiation  . It contains characteristic GFWDK sequence motifs. Some members are associated with domain Fmp27_SW (Pfam:PF10305) towards the N terminus.. 
PF10348 Domain of unknown function (DUF2427)<br>Pfam-B_52268 (release 21.0). This is the N-terminal region of a family of proteins conserved in fungi.  Several members are annotated as being Ftp1 but this could not be confirmed. The function is not known.. 
PF10349 WW-domain ligand protein<br>Pfam-B_5077 (release 21.0). The WWbp domain is characterised by several short PY and PT-like motifs of the PPPPY form. These appear to bind directly to the WW domains of WWP1 and WWP2 and other such diverse proteins as dystrophin and YAP (Yes-associated protein). This is the WW-domain binding protein WWbp via PY and PY_like motifs. The presence of a phosphotyrosine residue in the pWBP-1 peptide abolishes WW domain binding which suggests a potential regulatory role for tyrosine phosphorylation in modulating WW domain-ligand interactions.  Given the likelihood that WWP1 and WWP2 function as E3 ubiquitin-protein ligases, it is possible that initial substrate-specific recognition occurs via WW domain-substrate protein interaction followed by ubiquitin transfer and subsequent proteolysis  . This domain lies just downstream of the GRAM (Pfam:PF02893) in many members.. 
PF10350 Putative death-receptor fusion protein (DUF2428)<br>Pfam-B_6748 (release 21.0). This is a family of proteins conserved from plants to humans. The function is not known. Several members have been annotated as being HEAT repeat-containing proteins while others are designated as death-receptor interacting proteins, but neither of these could be confirmed.. 
PF10351 Golgi-body localisation protein domain<br>Pfam-B_6317 (release 21.0). This is the C-terminus of a family of proteins conserved from plants to humans.  The plant members are localised to the Golgi proteins and appear to regulate membrane trafficking, as they are required for rapid vesicle accumulation at the tip of the pollen tube  . The C-terminus probably contains the Golgi localisation signal and it is well-conserved.. 
PF10353 Protein of unknown function (DUF2430)<br>Pfam-B_67886 (release 21.0). This is a family of short, 111 residue, proteins found in S. pombe.  The function is not known.. 
PF10354 Domain of unknown function (DUF2431)<br>Pfam-B_6967 (release 21.0). This is the N-terminal domain of a family of proteins found from plants to humans. The function is not known.. 
PF10355 Protein of unknown function (Ytp1)<br>Pfam-B_7247 (release 21.0). This is a family of proteins found in fungi. The region appears to contain regions similar to mitochondrial electron transport proteins.  The C-terminal domain is hydrophobic and negatively charged. There are consensus sites for both N-linked glycosylation and cAMP-dependent protein kinase phosphorylation  .. 
PF10356 Protein of unknown function (DUF2034)<br>This protein is expressed in fungi but its function is unknown.. 
PF10357 Domain of Kin17 curved DNA-binding protein<br>Pfam-B_7469 (release 21.0). Kin17_mid is the conserved central 169 residue region of a family of Kin17 proteins. Towards the N-terminal end there is a zinc-finger domain, and in human and mouse members there is a RecA-like domain further downstream. The Kin17 protein in humans forms intra-nuclear foci during cell proliferation and is re-distributed in the nucleoplasm during the cell cycle  .. 
PF10358 Eeig1;<br>N-terminal C2 in EEIG1 and EHBP1 proteins. Wood V, Coggill PC, Zhang D, Aravind L. Pfam-B_7857 (release 21.0). This version of the C2 domain was initally identified in the  vertebrate estrogen early-induced gene 1 (EEIG1)  , and its Drosophila ortholog required for uptake of dsRNA via  the endocytotic machinery to induce RNAi silencing  .  It is also in C.elegans ortholog Sym-3  (SYnthetic lethal with Mec-3) and the mammalian protein EHBP1  (EH domain Binding Protein-1) that regulates endocytotic recycling  and two plant proteins, RPG that regulates Rhizobium-directed polar  growth and PMI1 (Plastid Movement Impaired 1) that is essential for  intracellular movement of chloroplasts in response to blue light  . . 
PF10359 RNA pol II promoter Fmp27 protein domain<br>Pfam-B_8838 (release 21.0). Fmp27_WPPW is a conserved domain of a family of proteins involved in RNA polymerase II transcription initiation  . It contains characteristic HQR and WPPW sequence motifs. and is towards the C-terminal in members which contain Fmp27_SW Pfam:PF10305.. 
PF10360 Protein of unknown function (DUF2433)<br>Pfam-B_83000 (release 21.0). This is a conserved 120 residue region of a family of proteins found in fungi. The function is not known.. 
PF10361 Protein of unknown function (DUF2434)<br>Pfam-B_84994 (release 21.0). This is a family of proteins conserved in fungi.  The function is not known.. 
PF10363 DUF2435; Pmp3;<br>Protein of unknown function (DUF2435). Pfam-B_7476 (release 21.0). This is a conserved region of approximately 400 residues which is found only in eukaryotes. It is associated with HEAT domains Pfam:PF02985 in all members. The function is not known.. 
PF10364 Putative capsular polysaccharide synthesis protein<br>Pfam-B_99492 (release 21.0). Found only in Vibrio species, pombe and one other fungi, this is a the N-terminal 150 residues of a family of proteins of unknown function.\.    There is a characteristic NKWYS sequence motif.. 
PF10365 Domain of unknown function (DUF2436)<br>Pfam-B_5683 (Release 22.0). This domain is found on peptidase C25 proteins and has no known function.. 
PF10366 Vacuolar sorting protein 39 domain 1<br>This domain is found on the vacuolar sorting protein Vps39 which is a component of the C-Vps complex  .  Vps39 is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole  .  In Saccharomyces cerevisiae, Vps39 has been shown to stimulate nucleotide exchange  .  The precise function of this domain has not been characterised.. 
PF10367 Vacuolar sorting protein 39 domain 2<br>This domain is found on the vacuolar sorting protein Vps39 which is a component of the C-Vps complex  .  Vps39 is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole  .  In Saccharomyces cerevisiae, Vps39 has been shown to stimulate nucleotide exchange  .  This domain is involved in localisation and in mediating the interactions of Vps39 with Vps11  .. 
PF10368 Putative cell-wall binding lipoprotein<br>YkyA is a family of proteins containing a lipoprotein signal and a hydrolase domain. It is similar to cell wall binding proteins and might also be recognisable by a host immune defence system. It is thus likely to belong to pathways important for pathogenicity  .. 
PF10369 Small subunit of acetolactate synthase<br>ALS_ss_C is the C-terminal half of a family of proteins which are the small subunits of acetolactate synthase.  Acetolactate synthase is a tetrameric enzyme, containing probably two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides  .. 
PF10370 Domain of unknown function (DUF2437)<br>This is the N-terminal 50 amino acids of a group of bacterial proteins annotated as fumarylacetoacetate hydrolase-containing enzymes. In most cases members are associated with FAA_hydrolase Pfam:PF01557 further towards the C-terminus.. 
PF10371 Domain of unknown function<br>EKR is a short, 33 residue, domain found in bacterial and some lower eukaryotic species which lies between a POR (pyruvate ferredoxin/flavodoxin oxidoreductase) Pfam:PF01558 and the 4Fe-4S binding domain Fer4 Pfam:PF00037. It contains a characteristic EKR sequence motif. The exact function of this domain is not known.. 
PF10372 Bacterial membrane-spanning protein N-terminus<br>YojJ is the N-terminus of a family of bacterial proteins some of which are associated with DUF147 Pfam:PF02457 towards the C-terminus. It is a putative membrane-spanning protein.. 
PF10373 Est1 DNA/RNA binding domain<br>Pfam-B_24280 (release 22.0). Est1 is a protein which recruits or activates telomerase at the site of polymerisation   . This is the DNA/RNA binding domain of EST1   .. 
PF10374 Telomerase activating protein Est1<br>Pfam-B_39673 (release 22.0). Est1 is a protein which recruits or activates telomerase at the site of polymerisation   .. 
PF10375 GRIP-related Arf-binding domain <br>The GRAB (GRIP-related Arf-binding) domain is towards the C-terminus of Rud3 type proteins. This domain is related to the GRIP domain, but the conserved tyrosine residue found at position 4 in all GRIP domains is replaced by a leucine residue. The Arf small GTPase is localised to the cis-Golgi where it recruits proteins via their GRAB domain, as part of the transport of cargo from the endoplasmic reticulum to the plasma membrane  .. 
PF10376 Double-strand recombination repair protein  <br>Mei5 is one of a pair of meiosis-specific proteins which facilitate the loading of Dmc1 on to Rad51 on DNA at double-strand breaks during recombination. Recombination is carried out by a large protein complex based around the two RecA homologues, Rad51 and Dmc1. This complex may play both a catalytic and a structural role in the interaction between homologous chromosomes during meiosis. Mei5 is seen to contain a coiled-coli region.. 
PF10377 Autophagy-related protein 11<br>Pfam-B_21462 (release 21.0). The function of this family is conflicting. In the fission yeast, Schizosaccharomyces pombe, this protein has been shown to interact with the telomere cap complex [1,2]. However, in budding yeast, Saccharomyces cerevisiae, this protein is called ATG11 and is shown to be involved in autophagy  .. 
PF10378 RMM; <br>Putative RRM domain  . Griffiths-Jones S, Coggill PC. This is a putative RRM, RNA-binding, domain found only in fungi. It occurs in proteins annotated as Nrd1 yeast proteins, which are known to carry RRM domains.  It is not homologous with any of the other RRM domains, eg RRM_1 Pfam:PF00076.. 
PF10379 Virulence protein nec1<br>Mistry J, Morningstar A. Pfam-B_11405 (release 21.0). This is a family of virulence proteins that are found in pathogenic Streptomyces species.. 
PF10380 Transcription factor CRF1<br>Pfam-B_25525 (release 21.0). CRF1 is a transcription factor that co-represses ribosomal genes with FHL1 via the TOR signalling pathway and protein kinase A  .. 
PF10381 Autophagocytosis associated protein C-terminal<br>Pfam-B_10019 (release 7.3). Autophagocytosis is a starvation-induced process responsible for transport of cytoplasmic proteins to the vacuole. The small C-terminal domain is likely to be a distinct binding region for the stability of the autophagosome complex  . It carries a highly characteristic conserved FLKF sequence motif.. 
PF10382 Protein of unknown function (DUF2439)<br>Pfam-B_19050 (release 22.0). Proteins in this family have been implicated in telomere maintenance in Saccharomyces cerevisiae   and in meiotic chromosome segregation in Schizosaccharomyces pombe  . 
PF10383 Transcription-silencing protein Clr2   <br>Clr2 is a chromatin silencing protein, one of a quartet of proteins forming the core of SHREC, a multienzyme effector complex that mediates hetero-chromatic transcriptional gene silencing in fission yeast. Clr2 does not have any obvious well-conserved domains but, along with the other core proteins, binds to the histone deacetylase Clr3, and on its own might also have a role in chromatin organisation at the cnt domain, the site of kinetochore assembly.. 
PF10384 Centromere protein Scm3<br>Pfam-B_19394 (release 21.0). Scm3 is a centromere protein that has been shown in Saccharomyces cerevisiae to be required for G2/M progression and Cse4 localisation  .  The C terminal region of Scm3 proteins is variable in size and sometimes consists of DNA binding motifs  .. 
PF10385 RNA polymerase beta subunit external 1 domain<br>RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between domains 4 and 5 of the yeast protein. It is also known as the external 1 region of the polymerase and is bound in association with the external 2 region  .. 
PF10386 Protein of unknown function (DUF2441)<br>This is a family of highly conserved, predicted, proteins from Bacillus species. The structure forms a homo-dimer. The function is unknown.. 
PF10387 Protein of unknown function (DUF2442)<br>Gene3D, pdb_2auw & Pfam-B_2245 (release 23.0). This family of bacterial and fungal proteins has several members annotated as being putative molybdopterin-guanine dinucleotide biosynthesis protein A; however this could not be verified. Hence the function is not known.  This family also includes the DUF3532 that was found to be related and was merged into this family. Members of this family also fall into the NE0471 N-terminal domain-like superfamily, a family of proteins with a unique fold in SCOP:143880.. 
PF10388 EAL-domain associated signalling protein domain<br>In Bacillus species this highly conserved region of the YkuI protein lies immediately downstream of the EAL (diguanylate cyclase/phosphodiesterase domain 2) Pfam:PF00563 domain so that together they form a monomer which dimerises for its enzymatic action. The region contains three alpha helices and five beta strands and is the C-terminal half of the structure.. 
PF10389 Bacteriophage coat protein B <br>CoatB is a single filamentous bacteriophage alpha helix of approximately 44 residues. It is likely to assemble into a complex of 35 monomers in a Catherine-wheel like formation  . It is the major coat protein of the virion.. 
PF10390 RNA polymerase II elongation factor ELL  <br>ELL is a family of RNA polymerase II elongation factors. It is bound stably to elongation-associated factors 1 and 2, EAFs, and together these act as a strong regulator of transcription activity. by direct interaction with Pol II. ELL binds to pol II on its own but the affinity is greatly increased by the cooperation of EAF  . Some members carry an Occludin domain Pfam:PF07303 just downstream. There is no S. cerevisiae member.. 
PF10391 Fingers domain of DNA polymerase lambda<br>DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. DNA_pol_lambd_f is the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone  .. 
PF10392 Golgi transport complex subunit 5<br>Pfam-B_24958 (release 21.0). The COG complex, the peripheral membrane oligomeric protein complex involved in intra-Golgi protein trafficking, consists of eight subunits arranged in two lobes bridged by Cog1. Cog5 is in the smaller, B lobe, bound in with Cog6-8, and is itself bound to Cog1 as well as, strongly, to Cog7.. 
PF10393 Trimeric coiled-coil oligomerisation domain of matrilin<br>This short domain is a coiled coil structure and has a single cysteine residue at the start which is likely to form a di-sulfide bridge with a corresponding cysteine in an upstream EGF (Pfam:PF00008) domain thereby spanning a VWA (Pfam:PF00092) domain. All three domains can be associated together as in the cartilage matrix protein matrilin, where this domain is likely to be responsible for oligomerisation  .. 
PF10394 Histone acetyl transferase HAT1 N-terminus<br>This domain is the N-terminal half of the structure of histone acetyl transferase HAT1. It is often found in association with the C-terminal part of the GNAT Acetyltransf_1 (Pfam:PF00583) domain. It seems to be motifs C and D of the structure. Histone acetyltransferases (HATs) catalyse the transfer of an acetyl group from acetyl-CoA to the lysine E-amino groups on the N-terminal tails of histones. HATs are involved in transcription since histones tend to be hyper-acetylated in actively transcribed regions of chromatin, whereas in transcriptionally silent regions histones are hypo-acetylated  .. 
PF10395 Utp8 family<br>Pfam-B_24590 (release 22.0). Utp8 is an essential component of the nuclear tRNA export machinery in Saccharomyces cerevisiae.  It is a tRNA binding protein that acts at a step between tRNA maturation /aminoacylation, and translocation of the tRNA across the nuclear pore complex  .. 
PF10396 GTP-binding protein TrmE N-terminus<br>This family represents the shorter, B, chain of the homo-dimeric structure which is a guanine nucleotide-binding protein that binds and hydrolyses GTP.  TrmE is homologous to the tetrahydrofolate-binding domain of N,N-dimethylglycine oxidase and indeed binds formyl-tetrahydrofolate. TrmE actively participates in the formylation reaction of uridine and regulates the ensuing hydrogenation reaction of a Schiff's base intermediate.  This B chain is the N-terminal portion of the protein consisting of five beta-strands and three alpha helices and is necessary for mediating dimer formation within the protein  .. 
PF10397 Adenylosuccinate lyase C-terminus<br>This is the C-terminal seven alpha helices of the structure whose full length represents the enzyme adenylosuccinate lyase. This sequence lies C-terminal to the conserved motif necessary for beta-elimination reactions  , Adenylosuccinate lyase catalyses two steps in the synthesis of purine nucleotides: the conversion of succinylaminoimidazole-carboxamide ribotide into aminoimidazole-carboxamide ribotide, the eighth step of the de novo pathway, and the formation of adenosine monophosphate (AMP) from adenylosuccinate, the second step in the conversion of inosine monophosphate into AMP  .. 
PF10398 Protein of unknown function (DUF2443)<br>This is a small family of highly conserved proteins from bacteria, in particular Helicobacter species, The structure is a bundle of alpha helices. The function is not known.. 
PF10399 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal<br>This is the N-terminal region of the E or R chain, Ubiquitinol-cytochrome C reductase Fe-S subunit, of the hetero-hexameric cytochrome bc1 complex. This region is a TAT-signal region. The cytochrome bc1 complex is an oligomeric membrane protein complex that is a component of respiratory and photosynthetic electron transfer chains.\.   The enzyme couples the transfer of electrons from ubiquinol to cytochrome c with the the generation of a protein gradient across the membrane  . The motif is also associated with Rieske (Pfam:PF00355), UCR_TM (Pfam:PF02921) and Ubiq-Cytc-red_N (Pfam:PF09165).. 
PF10400 Virulence activator alpha C-term<br>This structure is homo-dimeric, and the domain here is the C-terminal half of the structure, often associated with PadR upstream, (Pfam:PF03551), which is a transcriptional regulator.. 
PF10401 Interferon-regulatory factor 3<br>This is the interferon-regulatory factor 3 chain of the hetero-dimeric structure which also contains the shorter chain CREB-binding protein.  These two subunits make up the DRAF1 (double-stranded RNA-activated factor 1).\.   Viral dsRNA produced during viral transcription or replication leads to the activation of DRAF1. The DNA-binding specificity of DRAF1 correlates with transcriptional induction of ISG (interferon-alpha,beta-stimulated gene). IRF-3 preexists in the cytoplasm of uninfected cells and translocates to the nucleus following viral infection. Translocation of IRF-3 is accompanied by an increase in serine and threonine phosphorylation, and association with the CREB coactivator occurs only after infection.. 
PF10403 Rad4 beta-hairpin domain 1<br>This short domain is found in the Rad4 protein. This domain binds to DNA  .. 
PF10404 Rad4 beta-hairpin domain 2<br>This short domain is found in the Rad4 protein. This domain binds to DNA  .. 
PF10405 Rad4 beta-hairpin domain 3<br>This short domain is found in the Rad4 protein. This domain binds to DNA  .. 
PF10406 Transcription factor TFIID complex subunit 8 C-term <br>This is the C-terminal, Delta, part of the TAF8 protein  . The N-terminal is generally the histone fold domain, Bromo_TP (Pfam:PF07524). TAF8 is one of the key subunits of the transcription factor for pol II, TFIID. TAF8 is one of the several general cofactors which are typically involved in gene activation to bring about the communication between gene-specific transcription factors and components of the general transcription machinery  .. 
PF10407 Cdc14 phosphatase binding protein N-terminus   <br>Wood V, Pfam-B_23062 (release 22.0). Cytokinesis in yeasts involves a family of proteins whose essential function is to bind Cdc14-family phosphatase and prevent this from being sequestered and inhibited in the nucleolus. This is the highly conserved N-terminus of a family of proteins which act as cytokinesis checkpoint controls by allowing cells to cope with cytokinesis defects. These proteins are required for rDNA silencing and mini-chromosome maintenance  .. 
PF10408 Ubiquitin elongating factor core<br>Wood V, Pfam-B_4085 (release 22.0). This is the most conserved part of the core region of Ufd2P ubiquitin elongating factor or E4, running from helix alpha-11 to alpha-38. It consists of 31 helices of variable length connected by loops of variable size forming a compact unit; the helical packing pattern of the compact unit consists of five structural repeats that resemble tandem Armadillo (ARM) repeats. This domain is involved in ubiquitination as it binds Cdc48p and escorts ubiquitinated proteins from Cdc48p to the proteasome for degradation. The core is structurally similar to the nuclear transporter protein importin-alpha. The core is associated with the U-box at the C-terminus, Pfam:PF04564, which has ligase activity.. 
PF10409 C2 domain of PTEN tumour-suppressor protein<br>This is the C2 domain-like domain, in greek key form, of the PTEN protein, phosphatidyl-inositol triphosphate phosphatase, and it is the C-terminus. This domain may well include a CBR3 loop which means it plays a central role in membrane binding.  This domain associates across an extensive interface with the N-terminal phosphatase domain DSPc (Pfam:PF00782) suggesting that the C2 domain productively positions the catalytic part of the protein onto the membrane  .. 
PF10410 DnaB-helicase binding domain of primase<br>This domain is the C-terminal region three-helical domain of primase  . Primases synthesise short RNA strands on single-stranded DNA templates, thereby generating the hybrid duplexes required for the initiation of synthesis by DNA polymerases.  Primases are recruited to single-stranded DNA by helicases, and this domain is the region of the primase which binds DnaB-helicase  . It is associated with the Toprim domain (Pfam:PF01751) which is the central catalytic core.. 
PF10411 Disulfide bond isomerase protein N-terminus<br>This is the N-terminal domain of the disulfide bond isomerase DsbC. The whole molecule is V-shaped, where each arm is a DsbC monomer of two domains linked by a hinge; and the N-termini of each monomer join to form the dimer interface at the base of the V, so are vital for dimerisation  . DsbC is required for disulfide bond formation and functions as a disulfide bond isomerase during oxidative protein-folding in bacterial periplasm. It also has chaperone activity  .. 
PF10412 Type IV secretion-system coupling protein DNA-binding domain<br>The plasmid conjugative coupling protein TrwB forms hexamers from six structurally very similar protomers  . This hexamer contains a central channel running from the cytosolic pole (made up by the AADs) to the membrane pole ending at the transmembrane pore shaped by 12 transmembrane helices, rendering an overall mushroom-like structure. The TrwB_AAD (all-alpha domain) domain appears to be the DNA-binding domain of the structure. TrwB, a basic integral inner-membrane nucleoside-triphosphate-binding protein, is the structural prototype for the type IV secretion system coupling proteins, a family of proteins essential for macromolecular transport between cells and export  .. 
PF10413 Amino terminal of the G-protein receptor rhodopsin<br>Rhodopsin is the archetypal G-protein-coupled receptor. Such receptors participate in virtually all physiological processes, as signalling molecules. They utilise heterotrimeric guanosine triphosphate (GTP)-binding proteins to transduce extracellular signals to intracellular events.  Rhodopsin is important because of the pivotal role it plays in visual signal transduction. Rhodopsin is a dimeric transmembrane protein and its intradiskal surface consists of this amino terminal domain and three loops connecting six of the seven transmembrane helices. The N-terminus is a compact domain of alpha-helical regions with breaks and bends at proline residues outside the membrane  . The transmembrane part of rhodopsin is represented by 7tm_1 (Pfam:PF00001). The N-terminal domain is extracellular is and is necessary for successful dimerisation and molecular stability  .. 
PF10414 Sirohaem synthase dimerisation region<br>Bacterial sulfur metabolism depends on the iron-containing porphinoid sirohaem. CysG, S-adenosyl-L-methionine (SAM)-dependent bis-methyltransferase, dehydrogenase and ferrochelatase, synthesises sirohaem from uroporphyrinogen III via reactions which encompass two branchpoint intermediates in tetrapyrrole biosynthesis, diverting flux first from protoporphyrin IX biosynthesis and then from cobalamin (vitamin B12) biosynthesis. CysG is a dimer of two structurally similar protomers held together asymmetrically through a number of salt-bridges across complementary residues in the CysG_dimeriser region to produce a series of active sites, accounting for CysG's multifunctionality, catalysing four diverse reactions: two SAM-dependent methylations, NAD+-dependent tetrapyrrole dehydrogenation and metal chelation. The CysG_dimeriser region holding the two protomers together is of 74 residues  .. 
PF10415 Fumarase C C-terminus<br>Fumarase C catalyses the stereo-specific interconversion of fumarate to L-malate as part of the Kreb's cycle. The full-length protein forms a tetramer with visible globular shape. FumaraseC_C is the C-terminal 65 residues referred to as domain 3. The core of the molecule consists of a bundle of 20 alpha-helices from the five-helix bundle of domain 2. The projections from the core of the tetramer are generated from domains 1 and 3 of each subunit  . FumaraseC_C does not appear to be part of either the active site or the activation site but is helical in structure forming a little bundle.. 
PF10416 Transcription-initiator DNA-binding domain IBD<br>In Trichomonas vaginalis, thought to be the earliest extant eukaryote, the sole initiator element for control of the start of transcription is Inr, and this is recognised by the initiator binding protein IBP39. IBP39 contains an N-terminal Inr binding domain, IBD, connected via a flexible, proteolytically sensitive, linker (residues 127-145) to a C-terminal domain. The IBD structure reveals a winged-helix-wing conformation with each element binding to DNA, the central helix-turn-helix contributing the majority of the specificity-determining contacts with the Inr core motif TCAPy(T/A). The binding of IBP39 to the Inr directly recruits RNA polymerase II and in this way initiates transcription  .. 
PF10417 C-terminal domain of 1-Cys peroxiredoxin<br>This is the C-terminal domain of 1-Cys peroxiredoxin (1-cysPrx), a member of the peroxiredoxin superfamily which protect cells against membrane oxidation through glutathione (GSH)-dependent reduction of phospholipid hydroperoxides to corresponding alcohols  . The C-terminal domain is crucial for providing the extra cysteine necessary for dimerisation of the whole molecule. Loss of the enzyme's peroxidase activity is associated with oxidation of the catalytic cysteine, upstream of this domain; and glutathionylation, presumably through its disruption of protein structure, facilitates access for GSH, resulting in spontaneous reduction of the mixed disulfide to the sulfhydryl and consequent activation of the enzyme  .  The domain is associated with family AhpC-TSA, Pfam:PF00578, which carries the catalytic cysteine.. 
PF10418 Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B<br>Lactococcus lactis is one of the few organisms with two dihydroorotate dehydrogenases, DHODs, A and B  . The B enzyme is a prototype for DHODs in Gram-positive bacteria that use NAD+ as the second substrate. DHODB is a hetero-tetramer composed of a central homodimer of PyrDB subunits resembling the DHODA structure and two PyrK subunits along with three different cofactors: FMN, FAD, and a [2Fe-2S] cluster. The [2Fe-2S] iron-sulfur cluster binds to this C-terminal domain of the PyrK subunit, which is at the interface between the flavin and NAD binding domains and contains three beta-strands. The four cysteine residues at the N-terminal part of this domain are the ones that bind, in pairs, to the iron-sulfur cluster. The conformation of the whole molecule means that the iron-sulfur cluster is localised in a well-ordered part of this domain close to the FAD binding site  . The FAD and and NAD binding domains are FAD_binding_6, Pfam:PF00970 and NAD_binding_1, Pfam:PF00175.. 
PF10419 TFIIIC_subunit;<br>Pfam-B_14433 (release 21.0). This is a family of proteins subunits of TFIIIC  .  TFIIIC in yeast and humans is required for transcription of tRNA and 5 S RNA genes by RNA polymerase III.  Yeast members of this family are fused to phosphoglycerate mutase domain.. 
PF10420 Cytokine interleukin-12p40 C-terminus<br>IL12p40_C is the largely beta stranded C-terminal, D3, domain of interleukin-12p40 or interleukin-12B. This interleukin is produced on stimulation by macrophage-engulfed micro-organisms and other stimuli, when it dimerises with interleukin-12p35 to form a heterodimer which then binds to receptors on natural killer cells to activate them to destroy the micro-organisms  . This domain contains two disulfide bridges, one of which serves to bind p40 to p35 and the other to hold the beta strands within the domain together. The cupped shape of the p35 binding interface matches the elbow-like bend between D2 and D3 in p40  . The domain is often associated with family fn3, Pfam:PF00041.. 
PF10421 2'-5'-oligoadenylate synthetase 1, domain 2, C-terminus <br>This is the largely alpha-helical, C-terminal half of 2'-5'-oligoadenylate synthetase 1, being described as domain 2 of the enzyme and homologous to a tandem ubiquitin repeat. It carries the region of enzymic activity between 320 and 344 at the extreme C-terminal end  . Oligoadenylate synthetases are antiviral enzymes that counteract vial attack by degrading viral RNA. The enzyme uses ATP in 2'-specific nucleotidyl transfer reactions to synthesise 2'.5'-oligoadenylates, which activate latent ribonuclease, resulting in degradation of viral RNA and inhibition of virus replication  . This domain is often associated with NTP_transf_2 Pfam:PF01909.. 
PF10422 Monopolin complex subunit LRS4<br>Pfam-B_63451 (release 22.0). Monopolin is a protein complex, originally identified in Saccharomyces cerevisiae, that is required for the segregation of homologous centromeres to opposite poles of a dividing cell during meiosis I   . The orthologous complex in Schizosaccharomyces pombe is not required for meiosis I chromosome segregation, but is proposed to play a similar physiological role in clamping microtubule binding sites  .  In S .cerevisiae this subunit is called LRS4, and in S. pombe it is known as Mde4.. 
PF10423 Bacterial AMP nucleoside phosphorylase N-terminus <br>This is the N-terminal domain of bacterial AMP nucleoside phosphorylase (AMNp). The N- and C-termini form distinct domains which intertwine with each other to form a stable monomer which associates with five other monomers to yield the active hexamer. The N-terminus consists of a long helix and a four-stranded sheet with a novel topology. The C-terminus binds the nucleoside whereas the N-terminus acts as the enzymatic regulatory domain. AMNp (EC:3.2.2.4) catalyses the hydrolysis of AMP to form adenine and ribose 5-phosphate. thereby regulating intracellular AMP levels  .. 
PF10425 C-terminus of bacterial fibrinogen-binding adhesin<br>This is the C-terminal half of a bacterial fibrinogen-binding adhesin SdrG. SdrG is a Gram-positive cell-wall-anchored adhesin that allows attachment of the bacterium to host tissues via specific binding to the beta-chain of human fibrinogen (Fg). SdrG binds to its ligand with a dynamic "dock, lock, and latch" mechanism which represents a general mode of ligand-binding for structurally related cell wall-anchored proteins in most Gram-positive bacteria. The C-terminal part of SdrG(276-596) is integral to the folding of the immunoglobulin-like whole to create the docking grooves necessary for Fg binding. The domain is associated with families of Cna_B, Pfam:PF05738  .. 
PF10426 Recombination-activating protein 1 zinc-finger domain<br>This is a C2-H2 zinc-finger domain closely resembling the classical TFIIIA-type zinc-finger, CX3FX5LX2-3H, despite having a valine and a tyrosine at the core instead of a phenylalanine and a leucine, hence CX3VX1LX2YX2H.  The structure, nevertheless, contains the characteristic two-stranded beta-sheet and alpha-helix of a classical zinc-finger. The domain binds one zinc and, in complex with the zinc-RING-finger domain, helps to stabilise the whole of the dimerisation region of recombination activating protein 1 (RAG1)  . The function of the whole is to bind double-stranded DNA.. 
PF10427 Argonaute hook<br>This region has been called the argonaute hook  . It has been shown to bind to the Piwi domain Pfam:PF02171 of Argnonaute proteins.. 
PF10428 RAM signalling pathway protein<br>Pfam-B_35594 (release 22.0). SOG2 proteins in Saccharomyces cerevisiae are involved in cell separation and cytokinesis  .. 
PF10429 Nuclear pore RNA shuttling protein Mtr2<br>Mtr2 is a monomeric, dual-action, RNA-shuttle protein found in yeasts. Transport across the nuclear-cytoplasmic membrane is via the macro-molecular membrane-spanning nuclear pore complex, NPC. The pore is lined by a subset of NPC members called nucleoporins that present FG (Phe-Gly) receptors, characteristically GLFG and FXFG motifs, for shuttling RNAs and proteins. RNA cargo is bound to soluble transport proteins (nuclear export factors) such as Mex67 in yeasts, and TAP in metazoa, which pass along the pore by binding to successive FG receptors. Mtr2 when bound to Mex67 maximises this FG-binding. Mtr2 also acts independently of Mex67 in transporting the large ribosomal RNA subunit through the pore  .. 
PF10430 Tie-2 Ig-like domain 1<br>
PF10431 C-terminal, D2-small domain, of ClpB protein <br>This is the C-terminal domain of ClpB protein, referred to as the D2-small domain, and is a mixed alpha-beta structure. Compared with the D1-small domain (included in AAA, Pfam:PF00004) it lacks the long coiled-coil insertion, and instead of helix C4 contains a beta-strand (e3) that is part of a three stranded beta-pleated sheet. In Thermophilus the whole protein forms a hexamer with the D1-small and D2-small domains located on the outside of the hexamer, with the long coiled-coil being exposed on the surface. The D2-small domain is essential for oligomerisation, forming a tight interface with the D2-large domain of a neighbouring subunit and thereby providing enough binding energy to stabilise the functional assembly  . The domain is associated with two Clp_N, Pfam:PF02861, at the N-terminus as well as AAA, Pfam:PF00004 and AAA_2, Pfam:PF07724.. 
PF10432 Bacterial phospho-glucose isomerase C-terminal region<br>This is the C-terminal half of a bacterial phospho-glucose isomerase EC:5.3.1.9 protein which is similar to eukaryote homologues to the extent that the sequence includes the cluster of threonines and serines that forms the sugar phosphate-binding site in conventional PGI. This domain contributes a good proportion of the active catalytic site residues. This PGI uses the same catalytic mechanisms for both glucose ring-opening and isomerisation for the interconversion of glucose 6-phosphate to fructose 6-phosphate  . It is associated with family SIS, Pfam:PF01380.. 
PF10433 MMS1;<br>Mono-functional DNA-alkylating methyl methanesulfonate N-term. Pfam-B_64607 (release 22.0). MMS1 is a protein that protects against replication-dependent DNA damage in Saccharomyces cerevisiae  . MMS1 belongs to the DDB1 family of cullin 4 adaptors and the two proteins are homologous. MMS1 bridges the interaction of MMS22 and Crt10 with Cul8/Rtt101  .  Cul8/Rtt101 is a cullin protein involved in the regulation of DNA replication subsequent to DNA damage.  The N-terminal region of MMS1 and the C-terminal of MMS22 are required for the the MMS1-MMS22 interaction  . The human HIV-1 virion-associated protein Vpr assembles with DDB1 through interaction with DCAF1 (chromatin assembly factor) to form an E3 ubiquitin ligase that targets cellular substrates for proteasome-mediated degradation and subsequent G2 arrest  .. 
PF10434 Monopolin complex protein MAM1<br>Pfam-B_58835 (release 22.0). Monopolin is a protein complex, originally identified in Saccharomyces cerevisiae, that is required for the segregation of homologous centromeres to opposite poles of a dividing cell during meiosis I   . MAM1 is required in S. cerevisiae for monopolar attachment  .. 
PF10435 Beta-galactosidase, domain 2<br>This is the second domain of the five-domain beta-galactosidase enzyme that altogether catalyses the hydrolysis of beta(1-3) and beta(1-4) galactosyl bonds in oligosaccharides as well as the inverse reaction of enzymatic condensation and trans-glycosylation. This domain is made up of 16 antiparallel beta-strands and an alpha-helix at its C terminus. The fold of this domain appears to be unique.  In addition, the last seven strands of the domain form a subdomain with an immunoglobulin-like (I-type Ig) fold in which the first strand is divided between the two beta-sheets. In penicillin spp this strand is interrupted by a 12-residue insertion which forms an additional edge-strand to the second beta-sheet of the sub-domain. The remainder of the second domain forms a series of beta-hairpins at its N terminus, four strands of which are contiguous with part of the Ig-like sub-domain, forming in total a seven-stranded antiparallel beta-sheet. This domain is associated with family Glyco_hydro_35, Pfam:PF01301, which is N-terminal to it, but itself has no metazoan members.. 
PF10436 Mitochondrial branched-chain alpha-ketoacid dehydrogenase kinase<br>Catabolism and synthesis of leucine, isoleucine and valine are finely balanced, allowing the body to make the most of dietary input but removing excesses to prevent toxic build-up of their corresponding keto-acids. This is the butyryl-CoA dehydrogenase, subunit A domain 3, a largely alpha-helical bundle of the enzyme BCDHK. This enzyme is the regulator of the dehydrogenase complex that breaks branched-chain amino-acids down, by phosphorylating and thereby inactivating it when synthesis is required. The domain is associated with family HATPase_c Pfam:PF02518 which is towards the C-terminal.. 
PF10437 Bacterial lipoate protein ligase C-terminus<br>This is the C-terminal domain of a bacterial lipoate protein ligase.  There is no conservation between this C-terminus and that of vertebrate lipoate protein ligase C-termini, but both are associated with the domain BPL_LipA_LipB Pfam:PF03099, further upstream.  This domain is required for adenylation of lipoic acid by lipoate protein ligases. The domain is not required for transfer of lipoic acid from the adenylate to the lipoyl domain. Upon adenylation, this domain rotates 180 degrees away from the active site cleft. Therefore, the domain does not interact with the lipoyl domain during transfer.. 
PF10438 Cyclo-malto-dextrinase C-terminal domain<br>This domain is at the very C-terminus of cyclo-malto-dextrinase proteins and consists of 8 beta strands, is largely globular and appears to help stabilise the acitve sites created by upstream domains, Cyc-maltodext_N Pfam:PF09087, and Alpha-amylase Pfam:PF00128.  Cyclo-malto-dextrinases hydrolyse cyclodextrans to maltose and glucose and catalyse trans-glycosylation of oligosaccharides to the C3-, C4- or C6-hydroxyl groups of various acceptor sugar molecules.. 
PF10439 Bacteriocin class II with double-glycine leader peptide<br>This is a family of bacteriocidal bacteriocins secreted by Streptococcal species in order to kill off closely-related competitor Gram-positives. The sequence includes the peptide precursor, this being cleaved off proteolytically at the double-glycine. The family does not carry the YGNGVXC motif characteristic of pediocin-like Bacteriocins, Bacteriocin_II Pfam:PF01721. The producer bacteria are protected from the effects of their own bacteriocins by production of a specific immunity protein which is co-transcribed with the genes encoding the bacteriocins, eg family EntA_Immun Pfam:PF08951. The bacteriocins are structurally more specific than their immunity-protein counterparts. Typically, production of the bacteriocin gene is from within an operon carrying up to 6 genes including a typical two-component regulatory system (R and H), a small peptide pheromone (C), and a dedicated ABC transporter (A and -B) as well as an immunity protein  . The ABC transporter is thought to recognise the N termini of both the pheromone and the bacteriocins and to transport these peptides across the cytoplasmic membrane, concurrent with cleavage at the conserved double-glycine motif. Cleaved extracellular C can then bind to the sensor kinase, H, resulting in activation of R and up-regulation of the entire gene cluster via binding to consensus sequences within each promoter  . It seems likely that this whole regulon is carried on a transmissible plasmid which is passed between closely related Firmicute species since many clinical isolates from different Firmicutes can produce at least two bacteriocins. and the same bacteriocins can be produced by different species.. 
PF10440 Ubiquitin-binding WIYLD domain<br>This presumed domain has been predicted to contain three alpha helices. The domain was named the WIYLD domain based on the pattern of most conserved residues  . It binds ubiquitin. In the Arabidopsis thaliana histone-lysine N-methyltransferase SUVR4, Swiss:Q8W595, binding of ubiquitin to this domain stimulates enzymatic activity and converts its activity from a strict dimethylase to a di/trimethylase  .. 
PF10441 Urb2/Npa2 family<br>Pfam-B_28626 (Release 22.0). This family includes the Urb2 protein from yeast that are involved in ribosome biogenesis  .. 
PF10442 FIST C domain<br>The FIST C domain is a novel sensory domain, which is present in signal transduction proteins from Bacteria, Archaea and Eukarya. Chromosomal proximity of FIST-encoding genes to those coding for proteins involved in amino acid metabolism and transport suggest that FIST domains bind small ligands, such as amino acids  .. 
PF10443 RNA12 protein<br>Pfam-B_18000 (Release 22.0). This family includes RNA12 from S. cerevisiae.  That protein contains an RRM domain.  This region is C-terminal to that and includes a P-loop motif suggesting this region binds to NTP. The RNA12 proteins is involved in pre-rRNA maturation  .. 
PF10444 DUF2455;<br>Nbl1 / Borealin N terminal. Mistry J, Hartsuiker E, Wood V. Nbl1 is a subunit of the conserved CPC, the chromosomal passenger complex, which regulates mitotic chromosome segregation.  In Fungi and Animalia, this complex consists of the kinase Aurora B/AIR-2/Ipl1p, INCENP/ICP-1/Sli15p, and Survivin/BIR-1/Bir1p.  In Animalia, a fourth subunit (Borealin/Dasra/CSC-1) is required for targeting CPC to centromeres and central spindles.  Nbl1 has been shown in budding yeast to be essential for viability, and for CPC localisation, stability, integrity, and function  .  The N terminus of Borealin is homologous to Nbl1  .  This family contains both Nbl1, and the N terminal region of Borealin.. 
PF10445 Protein of unknown function (DUF2456)<br>Hartsuiker E, Wood V, Mistry J. Pfam-B_97171 (release 22.0). This is a family of uncharacterised proteins.. 
PF10446 Protein of unknown function (DUF2457)<br>Hartsuiker E, Wood V, Mistry J. This is a family of uncharacterised proteins.. 
PF10447 Exosome component EXOSC1/CSL4<br>Pfam-B_6887 (release 22.0). This family of proteins are components of the exosome 3'->5' exoribonuclease complex.  The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions  .. 
PF10448 POC1; <br>20S proteasome chaperone. Pfam-B_75798 (release 22.0). This family contains chaperones of the 20S proteasome which function in early 20S proteasome assembly. The structures of two of the proteins in this family (DMP1 and DMP2) have been solved, and they closely resemble that of the mammalian proteasome assembling chaperone PAC3, although there is little sequence similarity between them  .. 
PF10450 POC4; <br>In yeast, POC1 is a chaperone of the 20S proteasome which functions in early 20S proteasome assembly.. 
PF10451 Telomere regulation protein Stn1<br>Pfam-B_51291 (release 21.0). The budding yeast protein Stn1 is a DNA-binding protein which has specificity for telomeric DNA.  Structural profiling has predicted an OB-fold  . This domain is the N-terminal part of the molecule, which adopts the OB fold. Protection of telomeres by multiple proteins with OB-fold domains is conserved in eukaryotic evolution  .. 
PF10452 TORC1 subunit TCO89<br>Pfam-B_61649 (release 22.0). TC089 is a component of the TORC1 complex.  TORC1 is responsible for a wide range of rapamycin-sensitive cellular activities.. 
PF10453 Nuclear fragile X mental retardation-interacting protein 1 (NUFIP1)<br>Proteins in this family have been implicated in the assembly of the large subunit of the ribosome   and in telomere maintenance  .  Some proteins in this family contain a CCCH zinc finger. This family contains a protein called human fragile X mental retardation-interacting protein 1, which is known to bind RNA   and is phosphorylated upon DNA damage  .. 
PF10454 Protein of unknown function (DUF2458)<br>Hartsuiker H, Wood V, Mistry J. This a is family of uncharacterised proteins.. 
PF10455 Bin/amphiphysin/Rvs domain for vesicular trafficking<br>Pfam-B_12557 (release 22.0). This Pfam entry includes proteins that are not matched by Pfam:PF03114.. 
PF10456 WASP-binding domain of Sorting nexin protein<br>Pfam-B_43522 (release 20.0). The C-terminal region of the Sorting nexin group of proteins appears to carry a BAR-like (Bin/amphiphysin/Rvs) domain. This domain is very diverse and the similarities with other BAR domains are few. In the Sorting nexins it is associated with family PX, Pfam:PF00787.13, and in combination with PX appears to be necessary to bind WASP along with p85 to form a multimeric signalling complex  .. 
PF10457 Cholesterol-capturing domain<br>Pfam-B_16187 (release 22.0). Human meta-static lymph node (MLN) 64 is a late endosomal membrane protein, and carries this MENTAL (MLN64N-terminal) domain at its N-terminus. The domain is composed of four trans-membrane helices with three short intervening loops  . The function of the domain is to capture cholesterol and pass it to the associated START domain Pfam:PF01852 for transfer to a cytosolic acceptor protein or membrane. In mammals, the MENTAL domain is involved in the localisation of MLN64 and MENTHO in late endosomes, and also in homo-and of hetero-interactions of these two proteins  .. 
PF10458 Valyl tRNA synthetase tRNA binding arm<br>This domain is found at the C-terminus of Valyl tRNA synthetases.. 
PF10459 Peptidase S46<br>Rawlings N, Mistry J. Dipeptidyl-peptidase 7 (DPP-7) is the best characterised member of this family.  It is a serine peptidase that is located on the cell surface and is predicted to have two N-terminal transmembrane domains.. 
PF10460 Peptidase M30<br>Rawlings N, Mistry J. This family contains the metallopeptidase hyicolysin.  Hyicolysin has a zinc ion which is liganded by two histidine and one glutamate residue.. 
PF10461 Peptidase S68<br>Rawlings N, Mistry J. This family of serine peptidases contains PIDD proteins.  PIDD forms a complex with RAIDD and procaspase-2 that is known as the 'PIDDosome'.  The PIDDosome forms when DNA damage occurs and either activates NF-kappaB, leading to cell survival, or caspase-2, which leads to apoptosis.. 
PF10462 Peptidase M66<br>Rawlings N, Mistry J. This family of metallopeptidases contains StcE, a virulence factor found in Shiga toxigenic Escherichia coli organisms.  StcE peptidase cleaves C1 esterase inhibitor  .. 
PF10463 Peptidase U49<br>Rawlings N, Mistry J. This family contains Lit peptidase from Escherichia coli. Lit protease functions in bacterial cell death in response to infection by bacteriophage T4. Following binding of Gol peptide to domains II and III of elongation factor Tu, the Lit peptidase cleaves domain I of the elongation factor. This prevents binding of guanine nucleotides, shuts down translation and leads to cell death.. 
PF10464 Peptidase U40<br>Rawlings N, Mistry J. This family contains P5 murein endopeptidase from bacteriophage phi-6.  P5 murein endopeptidase has lytic activity against several gram-negative bacteria.  It is thought that the enzyme cleaves the cell wall peptide bridge formed by meso-2,6-diaminopimelic acid and D-Ala. 
PF10465 Peptidase_I24; <br>PinA peptidase inhibitor . Rawlings N, Mistry J. PinA inhibits the endopeptidase La.  It binds to the La homotetramer but does not interfere with the ATP binding site or the active site of La.. 
PF10466 Saccharopepsin inhibitor I34<br>The saccharopepsin inhibitor is highly specific for the aspartic peptidase saccharopepsin.\.     It is largely unstructured in the absence of saccharopepsin  , but in the presence, the inhibitor undergoes a conformation change forming an almost perfect alpha-helix from Asn2 to Met32 in the active site cleft of the peptidase.. 
PF10467 Peptidase inhibitor clitocypin<br>Rawlings N, Mistry J. Clitocypin binds and inhibits cysteine proteinases.  It has no similarity to any other known cysteine proteinase inhibitors but bears some similarity to a lectin-like family of proteins from mushrooms  .. 
PF10468 Carboxypeptidase inhibitor I68<br>Rawlings N, Mistry J. This is a family of tick carboxypetidase inhibitors.. 
PF10469 AKAP7 2'5' RNA ligase-like domain<br>AKAP7_NLS is the N-terminal domain of the cyclic AMP-dependent protein kinase A, PKA, anchor protein AKAP7. This protein anchors PKA for its role in regulating PKA-mediated gene transcription in both somatic cells and oocytes  . AKAP7_NLS carries the nuclear localisation signal (NLS) KKRKK, that indicates the cellular destiny of this anchor protein  . Binding to the regulatory subunits RI and RII of PKA is mediated via the family AKAP7_RIRII_bdg. at the C-terminus. This family represents a region that contains two 2'5' RNA ligase like domains Pfam:PF02834. Presumably this domain carried out some as yet unknown enzymatic function.. 
PF10470 PKA-RI-RII subunit binding domain of A-kinase anchor protein<br>AKAP7_RIRII_bdg is the C-terminal domain of the cyclic AMP-dependent protein kinase A, PKA, anchor protein AKAP7. This protein anchors PKA, for its role in regulating PKA-mediated gene transcription in both somatic cells and oocytes, by binding to its regulatory subunits, RI and RII, hence being known as a dual-specific AKAP  . The 25 crucial amino acids of RII-binding domains in general form structurally conserved amphipathic helices with unrelated sequences; hydrophobic amino acid residues form the backbone of the interaction and hydrogen bond- and salt-bridge-forming amino acid residues increase the affinity of the interaction  . The N-terminus, of family AKAP7_NLS, carries the nuclear localisation signal.. 
PF10471 Anaphase-promoting complex APC subunit 1<br>The anaphase-promoting complex (APC) or cyclosome is a cell cycle-regulated ubiquitin-protein ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins thereby targeting them for proteolysis by the 26S proteasome. CDC26 is one of the nine or so subunits identified within APC but its exact function is not known  . The APC/C becomes active at the metaphase/anaphase transition and remains active during G1 phase. One mechanism linked to activation of the APC/C is phosphorylation.  The yeast APC/C is composed of at least 13 subunits, but the function of many of the subunits is unknown. Hcn1 is the smallest subunit of the S. pombe APC/C, and is found to be essential for cell viability, APC/C integrity, and proper APC/C regulation. In addition, Hcn1 phosphorylation indicates a specific role for the phosphorylation of this subunit late in the cell cycle  .. 
PF10472 eIF2-alpha phosphatase phosphorylation constitutive repressor<br>This is the conserved N-terminal domain of CReP, constitutive repressor of eIF2-alpha phosphorylation/protein phosphatase 1, catalytic subunit. It functions in the dephosphorylation of eIF2-alpha under basal conditions in the absence of stress. In response to translation inhibition, there is reduced synthesis of the labile CReP that contributes to elevated levels of eIF2-alpha phosphorylation  . The C-terminus, family PP1c, is shared with the apoptosis-associated protein Gadd34 and herpes simplex virus  .. 
PF10473 Cenp-F_leu_zip;<br>Leucine-rich repeats of kinetochore protein Cenp-F/LEK1. Cenp-F, a centromeric kinetochore, microtubule-binding protein consisting of two 1,600-amino acid-long coils, is essential for the full functioning of the mitotic checkpoint pathway [1,2]. There are several leucine-rich repeats along the sequence of LEK1 that are considered to be zippers, though they do not appear to be binding DNA directly in this instance  .. 
PF10474 Protein of unknown function C-terminus (DUF2451)<br>This protein is found in eukaryotes but its function is not known. The C-terminal part of some members is DUF2450.. 
PF10475 Protein of unknown function N-terminal domain (DUF2450)  <br>This protein is found in eukaryotes but its function is not known. The C-terminal part of some members is DUF2451.. 
PF10476 Protein of unknown function C-terminus (DUF2448) <br>The family DUF2349 is the N-terminal part of this family. This protein is found in eukaryotes but its function is not known.. 
PF10477 Nucleocytoplasmic shuttling protein for mRNA cap-binding EIF4E<br>EIF4E-T is the transporter protein for shuttling the mRNA cap-binding protein EIF4E protein, targeting it for nuclear import. EIF4E-T contains several key binding domains including two functional leucine-rich NESs (nuclear export signals) between residues 438-447 and 613-638 in the human protein. The other two binding domains are an EIF4E-binding site, between residues 27-42 in Q9EST3, and a bipartite NLS (nuclear localisation signals) between 194-211, and these lie in family EIF4E-T_N. EIF4E is the eukaryotic translation initiation factor 4E that is the rate-limiting factor for cap-dependent translation initiation  .. 
PF10479 Fragile site-associated protein C-terminus<br>This is the conserved C-terminal half of the protein KIAA1109 which is the fragile site-associated protein FSA  . Genome-wide-association studies showed this protein to linked to the susceptibility to coeliac disease  . The protein may also be associated with polycystic kidney disease  .. 
PF10480 Beta-1 integrin binding protein<br>ICAP-1 is a serine/threonine-rich protein that binds to the cytoplasmic domains of beta-1 integrins in a highly specific manner, binding to a NPXY sequence motif on the beta-1 integrin. The cytoplasmic domains of integrins are essential for cell adhesion, and the fact that phosphorylation of ICAP-1 by interaction with the cell-matrix implies an important role of ICAP-1 during integrin-dependent cell adhesion  . Overexpression of ICAP-1 strongly reduces the integrin-mediated cell spreading on extracellular matrix and inhibits both Cdc42 and Rac1. In addition, ICAP-1 induces release of Cdc42 from cellular membranes and prevents the dissociation of GDP from this GTPase  . An additional function of ICAP-1 is to promote differentiation of osteoprogenitors by supporting their condensation through modulating the integrin high affinity state  ,. 
PF10481 Cenp-F_N;<br>Cenp-F N-terminal domain. Mitosin or centromere-associated protein-F (Cenp-F) is found bound across the centromere as one of the proteins of the outer layer of the kinetochore  . Most of the kinetochore/centromere functions appear to depend upon binding of the C-terminal par to f the molecule, whereas the N-terminal part, here, may be a cytoplasmic player in controlling the function of microtubules and dynein  .. 
PF10482 Tumour-suppressor protein CtIP N-terminal domain<br>CtIP is predominantly a nuclear protein that complexes with both BRCA1 and the BRCA1-associated RING domain protein (BARD1). At the protein level, CtIP expression varies with cell cycle progression in a pattern identical to that of BRCA1. Thus, the steady-state levels of CtIP polypeptides, which remain low in resting cells and G1 cycling cells, increase dramatically as Dividing cells traverse the G1/S boundary. CtIP can potentially modulate the functions ascribed to BRCA1 in transcriptional regulation, DNA repair, and/or cell cycle checkpoint control  . This N-terminal domain carries a coiled-coil region and is essential for homodimerisation of the protein  . The C-terminal domain is family Pfam:PF08573.. 
PF10483 Hap2_elong;<br>Elongator subunit Iki1. Coggill P, Eberhardt R. Pfam-B_26773 (release 22.0). This family is a component of the RNA polymerase II elongator complex [1,2]. This complex is involved in elongation of RNA polymerase II transcription and in modification of wobble nucleosides in tRNA [3,4].. 
PF10484 Mitochondrial ribosomal protein S23<br>MRP-S23 is one of the proteins that makes up the 55S ribosome in eukaryotes from nematodes to humans. It does not appear to carry any common motifs, either RNA binding or ribosomal protein motifs  . All of the mammalian MRPs are encoded in nuclear genes that are evolving more rapidly than those encoding cytoplasmic ribosomal proteins. The MRPs are imported into mitochondria where they assemble coordinately with mitochondrially transcribed rRNAs into ribosomes that are responsible for translating the 13 mRNAs for essential proteins of the oxidative phosphorylation system  . MRP-S23 is significantly up-regulated in uterine cancer cells  .. 
PF10486 DUF2447; <br>Phosphoinositide 3-kinase gamma adapter protein p101 subunit. Class I PI3Ks are dual-specific lipid and protein kinases involved in numerous intracellular signaling pathways. Class IB PI3K, p110gamma, is mainly activated by seven-transmembrane G-protein-coupled receptors (GPCRs), through its regulatory subunit p101 and G-protein beta-gamma subunits  .. 
PF10487 Nucleoporin subcomplex protein binding to Pom34<br>This is one of the many peptides that make up the nucleoporin complex (NPC), and is found across eukaryotes  . The Nup188 subcomplex (Nic96p-Nup188p-Nup192p-Pom152p) is one of at least six that make up the NPC, and as such is symmetrically localised on both faces of the NPC at the nuclear end, being integrally bound to the C-terminus of Pom34p  .. 
PF10488 Phosphatase-1 catalytic subunit binding region<br>This conserved C-terminus appears to be a protein phosphatase-1 catalytic subunit (PP1C) binding region, which may in some circumstances also be retroviral in origin since it is found in both herpes simplex virus and in mouse and man. This domain is found in Gadd-34 apoptosis-associated proteins as well as the constitutive repressor of eIF2-alpha phosphorylation/protein phosphatase 1, regulatory (inhibitor) subunit 15b, otherwise known as CReP. Diverse stressful conditions are associated with phosphorylation of the {alpha} subunit of eukaryotic translation initiation factor 2 (eIF2{alpha}) on serine 51. This signaling event, which is conserved from yeast to mammals, negatively regulates the guanine nucleotide exchange factor, eIF2-B and inhibits the recycling of eIF2 to its active GTP bound form. In mammalian cells eIF2{alpha} phosphorylation emerges as an important event in stress signaling that impacts on gene expression at both the translational and transcriptional levels  .. 
PF10489 Ret finger protein-like 3 antisense<br>This short transcript is purported to be the antisense protein of exon 2 of RFPL3 gene, however this was not confirmed. Since the RFPL3 (ret-finger protein-like 3) gene is expressed in testis the suggestion is that this may have a role in the antisense regulation of the RFPL genes. RFPL transcripts encode proteins with tripartite structure of RING finger, coiled-coil, and B30-2 domains, which are characteristic of the RING-B30 family. Each of these domains is thought to mediate protein-protein interactions by promoting homo- or heterodimerisation  .. 
PF10490 Rb-bdg_C_Cenp-F;<br>Rb-binding domain of kinetochore protein Cenp-F/LEK1. Cenp-F, a centromeric kinetochore, microtubule-binding protein consisting of two 1,600-amino acid-long coils, is essential for the full functioning of the mitotic checkpoint pathway [1,2]. This domain is at the very C-terminus of the C-terminal coiled-coil, and is one of the key Rb-binding domains  .. 
PF10491 NLS-binding and DNA-binding and dimerisation domains of Nrf1<br>In Drosophila, the erect wing (ewg) protein is required for proper development of the central nervous system and the indirect flight muscles. The fly ewg gene encodes a novel DNA-binding domain that is also found in four genes previously identified in sea urchin, chicken, zebrafish, and human  . Nuclear respiratory factor-1 is a transcriptional activator that has been implicated in the nuclear control of respiratory chain expression in vertebrates. The first 26 amino acids of nuclear respiratory factor-1 are required for the binding of dynein light chain. The interaction with dynein light chain is observed for both ewg and Nrf-1, transcription factors that are structurally and functionally similar between humans and Drosophila  . The highest level of expression of both ewg and Nrf-1 was found in the central nervous system, somites, first branchial arch, optic vesicle, and otic vesicle. In the mouse Nrf-1 protein, Swiss-Prot:Q8C4C0, there is also an NLS domain at 88-116, and a DNA binding and dimerisation domain at 127-282. Ewg is a site-specific transcriptional activator, and evolutionarily conserved regions of ewg contribute both positively and negatively to transcriptional activity  .. 
PF10492 Nrf1 activator activation site binding domain<br>In Drosophila, the erect wing (ewg) protein is required for proper development of the central nervous system and the indirect flight muscles. The fly ewg gene encodes a novel DNA-binding domain that is also found in four genes previously identified in sea urchin, chicken, zebrafish, and human  . Nuclear respiratory factor-1 is a transcriptional activator that has been implicated in the nuclear control of respiratory chain expression in vertebrates. The first 26 amino acids of nuclear respiratory factor-1 are required for the binding of dynein light chain. The interaction with dynein light chain is observed for both ewg and Nrf-1, transcription factors that are structurally and functionally similar between humans and Drosophila  . The highest level of expression of both ewg and Nrf-1 was found in the central nervous system, somites, first branchial arch, optic vesicle, and otic vesicle. In the mouse Nrf-1 protein, Swiss:Q8C4C0, there is an activation domain at 303-469, the most conserved part of which is this domain 446-469.  Ewg is a site-specific transcriptional activator, and evolutionarily conserved regions of ewg contribute both positively and negatively to transcriptional activity  . The family Nrf1_DNA-bind is associated with this domain towards the N-terminal, as is the N terminal of the activation domain.. 
PF10493 Rough deal protein C-terminal region<br>Buljan M,, Coggill P. Rod, the Rough deal protein, displays a dynamic intracellular staining pattern, localising first to kinetochores in pro-metaphase, but moving to kinetochore microtubules at metaphase. Early in anaphase the protein is once again restricted to the kinetochores, where it persists until the end of telophase. This behaviour is in all respects similar to that described for ZW10  , and indeed the two proteins function together, localisation of each depending upon the other  . These two proteins are found at the kinetochore in complex with a third, Zwilch, in both flies and humans. The C-terminus is the most conserved part of the protein. During pro-metaphase, the ZW10-Rod complex, dynein/dynactin, and Mad2 all accumulate on unattached kinetochores; microtubule capture leads to Mad2 depletion as it is carried off by dynein/dynactin; ZW10-Rod complex accumulation continues, replenishing kinetochore dynein. The continuing recruitment of the ZW10-Rod complex during metaphase may serve to maintain adequate dynein/dynactin complex on kinetochores for assisting chromatid movement during anaphase . The ZW10-Rod complex acts as a bridge whose association with Zwint-1 links Mad1 and Mad2, components that are directly responsible for generating the diffusible 'wait anaphase' signal, to a structural, inner kinetochore complex containing Mis12 and KNL-1AF15q14, the last of which has been proved to be essential for kinetochore assembly in C. elegans. Removal of ZW10 or Rod inactivates the mitotic checkpoint  .. 
PF10494 Serine-threonine protein kinase 19<br>This serine-threonine protein kinase number 19 is expressed from the MHC and predominantly in the nucleus. Protein kinases are involved in signal transduction pathways and play fundamental roles in the regulation of cell functions. This is a novel Ser/Thr protein kinase, that has Mn2+-dependent protein kinase activity that phosphorylates alpha -casein at Ser/Thr residues and histone at Ser residues. It can be covalently modified by the reactive ATP analogue 5'-p-fluorosulfonylbenzoyladenosine in the absence of ATP, and this modification is prevented in the presence of 1 mM ATP, indicating that the kinase domain of is capable of binding ATP  .. 
PF10495 Pericentrin-AKAP-450 domain of centrosomal targeting protein<br>This domain is a coiled-coil region close to the C-terminus of centrosomal proteins that is directly responsible for recruiting AKAP-450 and pericentrin to the centrosome. Hence the suggested name for this region is a PACT domain (pericentrin-AKAP-450 centrosomal targeting). This domain is also present at the C-terminus of coiled-coil proteins from Drosophila and S. pombe, and that from the Drosophila protein is sufficient for targeting to the centrosome in mammalian cells. The function of these proteins is unknown but they seem good candidates for having a centrosomal or spindle pole body location. The final 22 residues of this domain in AKAP-450 appear specifically to be a calmodulin-binding domain indicating that this member at least is likely to contribute to centrosome assembly  .. 
PF10496 SNARE-complex protein Syntaxin-18 N-terminus <br>This is the conserved N-terminal of Syntaxin-18. Syntaxin-18 is found in the SNARE complex of the endoplasmic reticulum and functions in the trafficking between the ER intermediate compartment and the cis-Golgi vesicle. In particular, the N-terminal region is important for the formation of ER aggregates  . More specifically, syntaxin-18 is involved in endoplasmic reticulum-mediated phagocytosis, presumably by regulating the specific and direct fusion of the ER with the plasma or phagosomal membranes  .. 
PF10497 Zinc-finger domain of monoamine-oxidase A repressor R1<br>R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type  .. 
PF10498 Intra-flagellar transport protein 57  <br>Eukaryotic cilia and flagella are specialised organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated  . This protein is known as Huntington-interacting protein-1 in humans.. 
PF10500 Nuclear RNA-splicing-associated protein<br>SR-25, otherwise known as ADP-ribosylation factor-like factor 6-interacting protein 4, is expressed in virtually all tissues. At the N-terminus there is a repeat of serine-arginine (SR repeat), and towards the middle of the protein there are clusters of both serines and of basic amino acids. The presence of many nuclear localisation signals strongly implies that this is a nuclear protein that may contribute to RNA splicing  . SR-25 is also implicated, along with heat-shock-protein-27, as a mediator in the Rac1 (GTPase ras-related C3 botulinum toxin substrate 1) signalling pathway  .. 
PF10501 Ribosomal_S39; <br>Ribosomal subunit 39S. The 39S ribosomal protein appears to be a subunit of one of the larger mitochondrial 66S or 70S units  . Under conditions of ethanol-stress in rats the larger subunit is largely dissociated into its smaller components  . In E. coli, in the absence of the enzyme pseudouridine synthase (RluD) synthase, there is an accumulation of 50S and 30S subunits and the appearance of abnormal particles (62S and 39S), with concomitant loss of 70S ribosomes  .. 
PF10502 Signal peptidase, peptidase S26 <br>Mistry J. Rawlings N. This is a family of membrane signal serine endopeptidases which function in the processing of newly-synthesised secreted proteins.  Peptidase S26 removes the hydrophobic, N-terminal, signal peptides as proteins are translocated across membranes. The active site residues take the form of a catalytic dyad that is Ser, Lys in subfamily S26A; the Ser is the nucleophile in catalysis, and the Lys is the general base.. 
PF10503 Esterase PHB depolymerase<br>Mistry J, Fushinobu S. This family of proteins include acetyl xylan esterases (AXE), feruloyl esterases (FAE), and poly(3-hydroxybutyrate) (PHB) depolymerases.. 
PF10504 Protein of unknown function (DUF2452)<br>This protein is found in eukaryotes but its function is unknown.. 
PF10505 NMDA receptor-regulated gene protein 2 C-terminus<br>Buljan M, Coggill P, Berhardt R. The transition of neuronal cells from pre-cursor to mature state is regulated by the N-methyl-d-aspartate (NMDA) receptor, a glutamate-gated ion channel that is permeable to Ca2+. NMDA receptors probably mediate this activity by permitting expression of NARG2.  NARG2 is transiently expressed, being a regulatory protein that is present in the nucleus of dividing cells and then down-regulated as progenitors exit the cell cycle and begin to differentiate. NARG2 contains repeats of (S/T)PXX, (11 in mouse , six in human), a putative DNA-binding motif that is found in many gene-regulatory proteins including Kruppel, Hunchback and Antennapedi  . This C-terminal domain belongs to the PD-(D/E)XK nuclease superfamily  .. 
PF10506 PDZ domain of MCC-2 bdg protein for Usher syndrome<br>The protein has a high homology to the tumour suppressor MCC (mutated in colon cancer; or MCC1 hereafter) and was named MCC2. MCC2 protein binds the first PDZ domain of AIE-75 with its C-terminal amino acids -DTFL. A possible role of MCC2 as a tumor suppressor has been put forward. The carboxyl terminus of the predicted protein was DTFL which matched the consensus motif X-S/T-X-phi (phi: hydrophobic amino acid residue) for binding to the PDZ domain of AIE-75.. 
PF10507 Protein of unknown function (DUF2453)<br>Some members of this family are purported to contain GAF domains but this could not be confirmed. The function is not known. It is likely to be a transmembrane protein.. 
PF10508 Proteasom_PSMB5; <br>Proteasome non-ATPase 26S subunit. The 26S proteasome, a eukaryotic ATP-dependent, dumb-bell shaped, protease complex with a molecular mass of approx 20kDa consists of a central 20S proteasome,functioning as a catalytic machine, and two large V-shaped terminal modules, having possible regulatory roles,composed of multiple subunits of 25- 110 kDa attached to the central portion in opposite orientations. It is responsible for degradation of abnormal intracellular proteins, including oxidatively damaged proteins, and may play a role as a component of a cellular anti-oxidative system. Expression of catalytic core subunits including PSMB5 and peptidase activities of the proteasome were elevated following incubation with 3-methylcholanthrene. The 20S proteasome comprises a cylindrical stack of four rings, two outer rings formed by seven alpha-subunits (alpha1-alpha7) and two inner rings of seven beta-subunits (beta1-beta7). Two outer rings of alpha subunits maintain structure, while the central beta rings contain the proteolytic active core subunits beta1 (PSMB6), beta2 (PSMB7), and beta5 (PSMB5). Expression of PSMB5 can be altered by chemical reactants, such as 3-methylcholanthrene  .. 
PF10509 Galactokinase galactose-binding signature<br>PROSITE_PS00106, Pfam-B_2277 (release 22.0). This is the highly conserved galactokinase signature sequence which appears to be present in all galactokinases irrespective of how many other ATP binding sites, etc that they carry  . The function of this domain appears to be to bind galactose  , and the domain is normally at the N-terminus of the enzymes, EC:2.7.1.6  . This domain is associated with the families GHMP_kinases_C, Pfam:PF08544 and GHMP_kinases_N, Pfam:PF00288.. 
PF10510 Phosphatidylinositol-glycan biosynthesis class S protein<br>PIG-S is one of several key, core, components of the glycosylphosphatidylinositol (GPI) trans-amidase complex that mediates GPI anchoring in the endoplasmic reticulum. Anchoring occurs when a protein's C-terminal GPI attachment signal peptide is replaced with a pre-assembled GPI  . Mammalian GPITransamidase consists of at least five components: Gaa1, Gpi8, PIG-S, PIG-T, and PIG-U, all five of which are required for function. It is possible that Gaa1, Gpi8, PIG-S, and PIG-T form a tightly associated core that is only weakly associated with PIG-U.  The exact function of PIG-S is unclear  .. 
PF10511 Trappin protein transglutaminase binding domain<br>Trappin-2, itself a protease inhibitor, has this unique N-terminal domain that enables it to become cross-linked to extracellular matrix proteins by transglutaminase  . This domain contains several repeated motifs with the the consensus sequence Gly-Gln-Asp-Pro-Val-Lys, and these together can anchor the whole molecule to extracellular matrix proteins, such as laminin, fibronectin, beta-crystallin, collagen IV, fibrinogen, and elastin, by transglutaminase-catalysed cross-links. The whole domain is rich in glutamine and lysine, thus allowing and transglutaminase(s) to catalyse the formation of an intermolecular epsilon-(gamma-glutamyl)lysine isopeptide bond  . Cementoin is associated with the WAP family, Pfam:PF00095, at the C-terminus.. 
PF10512 Cell division cycle-associated protein 8 <br>The chromosomal passenger complex of Aurora B kinase, INCENP, and Survivin has essential regulatory roles at centromeres and the central spindle in mitosis. Borealin is also a member of the complex. Approximately half of Aurora B in mitotic cells is complexed with INCENP, Borealin, and Survivin. Depletion of Borealin by RNA interference delays mitotic progression and results in kinetochore-spindle mis-attachments and an increase in bipolar spindles associated with ectopic asters  .. 
PF10513 Enhancer of polycomb-like<br>Pfam-B_3033 (release 22.0). This is a family of EPL1 (Enhancer of polycomb-like) proteins. The EPL1 protein is a member of a histone acetyltransferase complex which is involved in transcriptional activation of selected genes  .. 
PF10514 Pro-apoptotic Bcl-2 protein, BAD<br>BAD is a Bcl-2 homology domain 3 (BH3)-only pro-apoptotic member of the Bcl-2 protein family that is regulated by phosphorylation in response to survival factors  . Binding of BAD to mitochondria is thought to be exclusively mediated by its BH3 domain. Membrane localisation of BAD mediates membrane translocation of Bcl-XL. The C-terminal part of BAD is sufficient for membrane binding. There are two segments with differing lipid-binding preferences, LBD1 and LBD2, that are responsible for this binding: (i) LBD1 located in the proximity of the BH3 domain (amino acids 122-131) and (ii) LBD2, the putative C-terminal alpha-helix-5  . Phosphorylation-regulated 14-3-3 protein binding may expose the cholesterol-preferring LBD1 and bury the LBD2, thereby mediating translocation of BAD to raft-like micro-domains  .. 
PF10515 beta-amyloid precursor protein C-terminus<br>PROSITE_PS00320, Pfam-B_2082 (release 22.0). This is the amyloid, C-terminal, protein of the beta-Amyloid precursor protein (APP) which is a conserved and ubiquitous transmembrane glycoprotein strongly implicated in the pathogenesis of Alzheimer's disease but whose normal biological function is unknown. The C-terminal 100 residues are released and aggregate into amyloid deposits which are strongly implicated in the pathology of Alzheimer's disease plaque-formation. The domain is associated with family A4_EXTRA, Pfam:PF02177, further towards the N-terminus.. 
PF10516 SHNi-TPR<br>Pfam-B_14727 (release 22.0). SHNi-TPR family members contain a reiterated sequence motif that is an interrupted form of TPR repeat  .. 
PF10517 Electron transfer DM13<br>The DM13 domain is a component of a novel electron-transfer system potentially involved in oxidative modification of animal cell-surface proteins  .  It contains a nearly absolutely conserved cysteine, which could be involved in a redox reaction, either as a naked thiol group or through binding a prosthetic group like heme  .. 
PF10518 TAT (twin-arginine translocation) pathway signal sequence<br>
PF10520 Kua-ubiquitin conjugating enzyme hybrid localisation domain<br>
PF10521 Protein of unknown function (DUF2454)<br>Pfam-B_82729 (release 22.0). A Schizosaccharomyces pombe member of this family is known to interact with Tel2.  Tel2 is a component of the TOR complexes  .. 
PF10522 RII binding domain<br>Vijayaraghavan et al. Mol Endocrinology 13(5):705-717 (1999). This domain is found is a wide variety of AKAPs (A kinase anchoring proteins)  .. 
PF10523 BEN domain<br>The BEN domain is found in diverse animal proteins such as BANP/SMAR1, NAC1 and the Drosophila mod(mdg4) isoform C, in the chordopoxvirus virosomal protein E5R and in several proteins of polydnaviruses. Computational analysis suggests that the BEN domain mediates protein-DNA and protein-protein interactions during chromatin organisation and transcription  .. 
PF10524 Nuclear factor I protein pre-N-terminus<br>The Nuclear factor I (NFI) family of site-specific DNA-binding proteins (also known as CTF or CAAT box transcription factor) functions both in viral DNA replication and in the regulation of gene expression in higher organisms. The N-terminal 200 residues contains the DNA-binding and dimerisation domain, but also has an 8-47 residue highly conserved region 5' of this, whose function is not known. Deletion of the N-terminal 200 amino acids removes the DNA-binding activity, dimerisation-ability and the stimulation of adenovirus DNA replication  .. 
PF10525 Engrailed homeobox C-terminal signature domain<br>PROSITE_PS00033, Pfam-B_11539 (release 22.0). Engrailed homeobox proteins are characterised by the presence of a conserved region of some 20 amino-acid residues located at the C-terminal of the 'homeobox' domain. This domain of approximately 20 residues forms a kind of a signature pattern for this subfamily of proteins  .. 
PF10528 GLEYA domain<br>This presumed domain is found in fungal adhesins and is related to the PA14 domain.. 
PF10529 Histidine-rich Calcium-binding repeat region<br>This is a histidine-rich calcium binding repeat which appears in proteins called histidine-rich-calcium binding proteins (HRC). HRC is a high capacity, low affinity Ca2+-binding protein, residing in the lumen of the sarcoplasmic reticulum. HRC binds directly to triadin. This binding interaction occurs between the histidine-rich region of HRC and multiple clusters of charged amino acids, named as the KEKE motifs, in the lumenal domain of triadin. The region in which this repeat is found in many copies is long and variable but is the acidic region of the protein. There is also a cysteine-rich region further towards the C-terminus  . HRC may regulate sarcoplasmic reticular calcium transport and play a critical role in maintaining calcium homeostasis and function in the heart. HRC as a candidate regulator of sarcoplasmic reticular calcium uptake  .. 
PF10530 Toxin with inhibitor cystine knot ICK or Knottin scaffold<br>Spider toxins of the CSTX family are ion channel toxins containing an inhibitor cystine knot (ICK) structural motif or Knottin scaffold. The four disulfide bonds present in the CSTX spider toxin family are arranged in the following pattern: 1-4, 2-5, 3-8 and 6-7. CSTX-1 is the most important component of C. salei venom in terms of relative abundance and toxicity and therefore is likely to contribute significantly to the overall toxicity of the whole venom. CSTX-1 blocked rat neuronal L-type, but no other types of HVA Cav channels  . Interestingly, the omega-toxins from Phoneutria nigriventer venom (another South American species also belonging to the Ctenidae family) are included as they carry the same disulfide bond arrangement. suggested that CSTX-1 may interact with Cav channels. Calcium ion voltage channel heteromultimer containing an L-type pore-forming alpha1-subunit is the most probable candidate for the molecular target of CSTX-1 these toxins  .. 
PF10531 SLBB domain<br>
PF10532 Plant specific N-all beta domain<br>This domain was identified by Babu and colleagues  . It is found associated with the WRKY domain Pfam:PF03106.. 
PF10533 Plant zinc cluster domain<br>This zinc binding domain was identified by Babu and colleagues and found associated with the WRKY domain Pfam:PF03106  .. 
PF10534 Connector enhancer of kinase suppressor of ras<br>The CRIC - Connector enhancer of kinase suppressor of ras - domain functions as a scaffold in several signal cascades and acts on proliferation, differentiation and apoptosis.. 
PF10536 Plant mobile domain<br>This domain was identified by Babu and colleagues in a variety of transposases  .. 
PF10537 ATP-utilising chromatin assembly and remodelling N-terminal<br>ACF (for ATP-utilising chromatin assembly and remodelling factor) is a chromatin-remodelling complex that catalyses the ATP-dependent assembly of periodic nucleosome arrays. The WAC (WSTF/Acf1/cbp146) domain is an approximately 110-residue module present at the N-termini of Acf1-related proteins in a variety of organisms. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA.. 
PF10538 Immunoreceptor tyrosine-based activation motif<br>Signal transduction by T and B cell antigen receptors and certain receptors for Ig Fc regions involves a conserved sequence motif, termed an immunoreceptor tyrosine-based activation motif (ITAM). It is also found in the cytoplasmic domain of apoptosis receptor.. 
PF10539 Development and cell death domain<br>The DCD domain is found in plant proteins involved in development and cell death. The DCD domain is an approximately 130 amino acid long stretch that contains several mostly invariable motifs. These include a FGLP and a LFL motif at the N-terminus and a PAQV and a PLxE motif towards the C-terminus of the domain. The DCD domain is present in proteins with different architectures. Some of these proteins contain additional recognisable motifs, like the KELCH repeats or the ParB domain.. 
PF10540 Munc13 (mammalian uncoordinated) homology domain<br>Munc13 proteins constitute a family of three highly homologous molecules (Munc13-1, Munc13-2 and Munc13-3) with homology to Caenorhabditis elegans unc-13p. Munc13 proteins contain a phorbol ester-binding C1 domain and two C2 domains, which are Ca2+/phospholipid binding domains. Sequence analyses have uncovered two regions called Munc13 homology domains 1 (MHD1) and 2 (MHD2) that are arranged between two flanking C2 domains. MHD1 and MHD2 domains are present in a wide variety of proteins from Arabidopsis thaliana, C. elegans, Drosophila melanogaster, mouse, rat and human, some of which may function in a Munc13-like manner to regulate membrane trafficking. The MHD1 and MHD2 domains are predicted to be alpha-helical.. 
PF10541 Nuclear envelope localisation domain<br>The KASH (for Klarsicht/ANC-1/Syne-1 homology) or KLS domain is a highly hydrophobic nuclear envelope localisation domain of approximately 60 amino acids comprising a 20-amino-acid transmembrane region and a 30-35-residue C-terminal region that lies between the inner and the outer nuclear membranes  . During meiotic prophase, telomeres cluster to form a bouquet arrangement of chromosomes. SUN and KASH domain proteins form complexes that span both membranes of the nuclear envelope. The KASH domain links the dynein motor complex of the microtubules, through the outer nuclear membrane to the Sad1 domain in the inner nuclear membrane which then interacts with the bouquet proteins Bqt1 and Bqt2 that are complexed with Bqt4, Rap1 and Taz1 and attached to the telomere  .  SUN domain-containing proteins are essential for recruiting KASH domain proteins at the outer nuclear membrane, and KASH domains provide a generic NE tethering device for functionally distinct proteins whose cytoplasmic domains mediate nuclear positioning, maintain physical connections with other cellular organelles, and possibly even influence chromosome dynamics  .. 
PF10542 Vitelline membrane cysteine-rich region<br>In Drosophila melanogaster the vitelline membrane (VM) is the first layer of the eggshell produced by the follicular epithelium. It is composed of at least four different proteins. VM proteins are similarly organised with a central highly conserved 38-amino acid domain which is flanked by unrelated regions. The domain contains three highly conserved cysteines.. 
PF10543 ORF6N domain<br>This domain was identified by Iyer and colleagues  .. 
PF10544 T5orf172 domain<br>This domain was identified by Iyer and colleagues  .. 
PF10545 Alcohol dehydrogenase transcription factor Myb/SANT-like<br>The myb/SANT-like domain in Adf-1 (MADF) is an approximately 80-amino-acid module that directs sequence specific DNA binding to a site consisting of multiple tri-nucleotide repeats. The MADF domain is found in one or more copies in eukaryotic and viral proteins and is often associated with the BESS domain. It is likely that the MADF domain is more closely related to the myb/SANT domain than it is to other HTH domains.. 
PF10546 P63C domain<br>This domain was identified by Iyer and colleagues  .. 
PF10547 P22_AR N-terminal domain<br>This domain was identified by Iyer and colleagues  .. 
PF10548 P22AR C-terminal domain<br>This domain was identified by Iyer and colleagues  . It is found associated with Pfam:PF10547.. 
PF10549 ORF11CD3 domain<br>This domain was identified by Iyer and colleagues  .. 
PF10550 Conantokin-G mollusc-toxin<br>The conantokins are a family of neuroactive peptides found in the venoms of fish-hunting cone snails. They possess a high content of gamma-carboxyglutamic acid (Gla) (4-5 residues), a non-standard amino-acid made by the post-translational modification of glutamate (Glu) residue. Conantokins are the only natural biochemically characterised peptides known to be N-methyl-D-aspartate (NMDA) receptor antagonists.. 
PF10551 MULE transposase domain<br>This domain was identified by Babu and colleagues  .. 
PF10552 ORF6C domain<br>This domain was identified by Iyer and colleagues  .. 
PF10553 MSV199 domain<br>This domain was identified by Iyer and colleagues  .. 
PF10554 Ash protein family<br>This family was identified by Iyer and colleagues  . It includes the Ash protein from bacteriophage P4.. 
PF10555 Phospho-N-acetylmuramoyl-pentapeptide-transferase signature 1 <br>Phospho-N-acetylmuramoyl-pentapeptide-transferase (EC 2.7.8.13) (mraY) is a bacterial enzyme responsible for the formation of the first lipid intermediate of the cell wall peptidoglycan synthesis. It catalyses the formation of undecaprenyl-pyrophosphoryl-N-acetylmuramoyl-pentapeptide from UDP-MurNAc-pentapeptide and undecaprenyl-phosphate. It is an integral membrane protein with probably ten transmembrane domains. This domain is located at the end of the first cytoplasmic loop and the beginning of the second transmembrane domain.. 
PF10557 Cullin protein neddylation domain<br>This is the neddylation site of cullin proteins which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae, and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue  .. 
PF10558 Mitochondrial 18 KDa protein (MTP18)  <br>This family of proteins are mitochondrial 18KDa proteins that are often misannotated as carbonic anhydrases. It was shown that knockdown of MTP18 protein results in a cytochrome c release from mitochondria and consequently leads to apoptosis  . Overexpression studies suggest that MTP18 is required for mitochondrial fission  .. 
PF10559 Plug_Sec61p; <br>Plug domain of Sec61p. The Sec61/SecY translocon mediates translocation of proteins across the membrane and integration of membrane proteins into the lipid bilayer. The structure of the translocon revealed a plug domain blocking the pore on the lumenal side.The plug is unlikely to be important for sealing the translocation pore in yeast but it plays a role in stabilising Sec61p during translocon formation. The domain runs from residues 52-74  .. 
PF10561 Uncharacterised protein family UPF0565<br>This family of proteins has no known function.. 
PF10562 Calmodulin-binding domain C0 of NMDA receptor NR1 subunit<br>Pfam-B_7118 (release 22.0). This is a very short highly conserved domain that is C-terminal to the cytosolic transmembrane region IV of the NMDA-receptor 1. It has been shown to bind Calmodulin-Calcium with high affinity. The ionotropic N-methyl-D-aspartate receptor (NMDAR) is a major source of calcium flux into neurons in the brain and plays a critical role in learning, memory, neural development, and synaptic plasticity. Calmodulin (CaM) regulates NMDARs by binding tightly to the C0 and C1 regions of their NR1 subunit. The conserved tryptophan is considered to be the anchor residue  .. 
PF10563 Cadmium carbonic anhydrase repeat<br>This domain is the cadmium carbonic anhydrase repeat unit of the beta-carbonic anhydrase of a marine diatom  , that uses both zinc and cadmium for catalysis of the reversible hydration of carbon dioxide for use in inorganic carbon acquisition for photosynthesis (thus being a cambialistic enzyme). Compared with alpha- and gamma-carbonic anhydrases that use three histidines to coordinate the zinc-atom, this beta-carbonic anhydrase has two cysteines and one histidine, and rapidly binds cadmium  .. 
PF10564 Sialic-acid binding micronemal adhesive repeat<br>This domain is a novel carbohydrate-binding domain found on micronemal proteins. Micronemal proteins (MICs) are released onto the parasite surface just before invasion of host cells and play important roles in host cell recognition, attachment and penetration. Toxoplasma gondii can infect and replicate within all nucleated cells  . This domain interacts with sialylated oligosaccharides; the protein in Toxoplasma gondii is a monomer but several MAR domains are carried on the protein. Each MAR domain contains one central sialic acid-binding pocket  .. 
PF10565 N-methyl D-aspartate receptor 2B3 C-terminus<br>Pfam-B_53396 (release 22.0). This domain is found at the C-terminus of many NMDA-receptor proteins, many of which also carry the Ligated ion-channel family Pfam:PF00060 further upstream as well as the ANF_receptor family Pfam:PF01094. This region is predicted to be a large extra-cellular domain of the NMDA receptor proteins, being highly hydrophilic, and is thought to be integrally involved in the function of the receptor. The region also carries a number of potential N-glycosylation sites  .. 
PF10566 Glycoside hydrolase 97  <br>This domain is the catalytic region of the bacterial glycosyl-hydrolase family 97. This central part of the GH97 family protein sequences represents a typical and complete (beta/alpha)8-barrel or catalytic TIM-barrel type domain. The N- and C-terminal parts of the sequences, mainly consisting of beta-strands, form two additional non-catalytic domains  .  In all known glycosidases with the (beta-alpha)8-barrel fold, the amino acid residues at the active site are located on the C-termini of the beta-strands [2,3].. 
PF10567 RNA-recognition motif<br>Griffiths-Jones S, Coggill P. Pfam-B_57293 (release 21.0). This conserved domain is found in fungal proteins and appears to be involved in RNA-processing. It binds to poly-adenylated RNA, interacts genetically with mRNA 3'-end processing factors, copurifies with the nuclear cap-binding protein Cbp20p, and is found in complexes containing other translation factors, such as EIF4G as in Swiss:P39935 and Swiss:P39936.. 
PF10568 Outer mitochondrial membrane transport complex protein<br>Pfam-B_30563 (release 22.0). The TOM37 protein is one of the outer membrane proteins that make up the TOM complex for guiding cytosolic mitochondrial beta-barrel proteins from the cytosol across the outer mitochondrial membrane into the intramembrane space. In conjunction with TOM70 it guides peptides without an MTS into TOM40, the protein that forms the passage through the outer membrane  . It has homology with Metaxin-1, also part of the outer mitochondrial membrane beta-barrel protein transport complex  .. 
PF10569 Alpha-macro-globulin thiol-ester bond-forming region<br>This short highly conserved region of proteinase-binding alpha-macro-globulins contains the cysteine and a glutamine of a thiol-ester bond that is cleaved at the moment of proteinase binding, and mediates the covalent binding of the alpha-macro-globulin to the proteinase. The GCGEQ motif is highly conserved.. 
PF10570 Myelin-PO_N;<br>Myelin-PO cytoplasmic C-term p65 binding region. Pfam-B_1437 (release 22.0), PROSITE_PS00568. Myelin protein zero is the major myelin protein in the peripheral central nervous system and is essential for normal myelination. The family is a single-pass transmembrane molecule containing one Ig-like loop in the extracellular domain and this highly basic 69 residue C-terminal cytoplasmic domain which is the region that interacts with protein p65  .. 
PF10571 Uncharacterised protein family UPF0547<br>This domain contains a zinc-ribbon motif.. 
PF10572 Uncharacterised protein family UPF0556<br>This family of proteins has no known function.. 
PF10573 Uncharacterised protein family UPF0561<br>This family of proteins has no known function.. 
PF10574 Uncharacterised protein family UPF0552<br>This family of proteins has no known function.. 
PF10576 Iron-sulfur binding domain of endonuclease III<br>Escherichia coli endonuclease III (EC 4.2.99.18)   is a DNA repair enzyme that acts both as a DNA N-glycosylase, removing oxidised pyrimidines from DNA, and as an apurinic/apyrimidinic (AP) endonuclease, introducing a single-strand nick at the site from which the damaged base was removed. Endonuclease III is an iron-sulfur protein that binds a single 4Fe-4S cluster. The 4Fe-4S cluster does not seem to be important for catalytic activity, but is probably involved in the proper positioning of the enzyme along the DNA strand  . The 4Fe-4S cluster is bound by four cysteines which are all located in a 17 amino acid region at the C-terminal end of endonuclease III. A similar region is also present in the central section of mutY and in the C-terminus of ORF-10 and of the Micro-coccus UV endonuclease  .. 
PF10577 Uncharacterised protein family UPF0560<br>This family of proteins has no known function.. 
PF10578 Seminal vesicle protein repeat<br>
PF10579 Rapsyn N-terminal myristoylation and linker region<br>Neuromuscular junction formation relies upon the clustering of acetylcholine receptors and other proteins in the muscle membrane. Rapsyn is a peripheral membrane protein that is selectively concentrated at the neuromuscular junction and is essential for the formation of synaptic acetylcholine receptor aggregates. Acetylcholine receptors fail to aggregate beneath nerve terminals in mice where rapsyn has been knocked out. The N-terminal six amino acids of rapsyn are its myristoylation site, and myristoylation is necessary for the targeting of the protein to the membrane  .. 
PF10580 Gap junction protein N-terminal region<br>
PF10581 Synapsin N-terminal<br>This highly conserved domain of synapsin proteins has a serine at position 9 or 10 which is a phosphorylation site. The domain appears to be the part of the molecule that binds to calmodulin  .. 
PF10582 Gap junction channel protein cysteine-rich domain<br>Pfam-B_1437 (release 22.0), PROSITE_PS00408. 
PF10583 Involucrin of squamous epithelia N-terminus<br>Pfam-B_7423 (release 22.0), PROSITE_PS00795. This is the N-terminal three beta strands of involucrin, a protein present in keratinocytes of epidermis and other stratified squamous epithelia. Involucrin first appears in the cell cytosol, but ultimately becomes cross-linked to membrane proteins by transglutaminase thus helping in the formation of an insoluble envelope beneath the plasma membrane  .\.   Apigenin is a plant-derived flavanoid that has significant promise as a skin cancer chemopreventive agent. It has been found that apigenin regulates normal human keratinocyte differentiation by suppressing it and this is associated with reduced cell proliferation without apoptosis  . The downstream part of the protein is represented by the family Involucrin, Pfam:PF00904.. 
PF10584 Proteasome subunit A N-terminal signature<br>This domain is conserved in the A subunits of the proteasome complex proteins.. 
PF10585 Ubiquitin-activating enzyme active site <br>Ubiquitin-activating enzyme (E1 enzyme) activates ubiquitin by first adenylating with ATP its C-terminal glycine residue and thereafter linking this residue to the side chain of a cysteine residue in E1, yielding an ubiquitin-E1 thiolester and free AMP. Later the ubiquitin moiety is transferred to a cysteine residue on one of the many forms of ubiquitin-conjugating enzymes (E2)  . This domain carries the last of five conserved cysteines that is part of the active site of the enzyme, responsible for ubiquitin thiolester complex formation, the active site being represented by the sequence motif PICTLKNFP  .. 
PF10587 Eukaryotic elongation factor 1 beta central acidic region<br>Pfam-B_9497 (release 22.0), PROSITE_PS00824. 
PF10588 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region<br>Pfam-B_202 (release 22.0), PROSITE_PS00642. 
PF10589 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region<br>Pfam-B_339 (release 22.0), PROSITE_PS00645. 
PF10590 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region<br>Pfam-B_685 (release 22.0), PROSITE_PS01064. Pyridoxine 5'-phosphate oxidase (PNPOx) catalyses the terminal step in the biosynthesis of pyridoxal 5'-phosphate (PLP), a cofactor used by many enzymes involved in amino acid metabolism. The enzyme oxidises either the 4'-hydroxyl group of pyridoxine 5'-phosphate (PNP) or the 4'-primary amine of pyridoxamine 5'-phosphate (PMP) to an aldehyde. PNPOx is a homodimeric enzyme with one flavin mononucleotide (FMN) molecule non-covalently bound to each subunit. This domain represents one of the two dimerisation regions of the protein, located at the edge of the dimer interface, at the C-terminus, being the last three beta strands, S6, S7, and S8 along with the last three residues to the end. In Swiss:P21159, S6 runs from residues 178-192, S7 from 200-206 and S8 from 211-215. the extended loop, of residues 167-177 may well be involved in the pocket formed between the two dimers that positions the FMN molecule  .. 
PF10591 Secreted protein acidic and rich in cysteine Ca binding region<br>Pfam-B_3882 (release 22.0), PROSITE_PS00613. The SPARC_Ca_bdg domain of Secreted Protein Acidic and Rich in Cysteine is responsible for the anti-spreading activity of human urothelial cells. It is rich in alpha-helices. This extracellular calcium-binding domain contains two EF-hands that each coordinates one Ca2+ ion, forming a helix-loop-helix structure that not only drives the conformation of the protein but is also necessary for biological activity. The anti-spreading activity was dependent on the coordination of Ca2+ by a Glu residue at the Z position of EF-hand 2  .. 
PF10592 AIPR protein<br>This family of proteins was identified in   as an abortive infection phage resistance protein often found in restriction modification system operons.. 
PF10593 Z1 domain<br>This uncharacterised domain was identified by Iyer and colleagues  . It is found associated with a helicase domain of superfamily type II.. 
PF10595 Uncharacterised protein family UPF0564<br>This family of proteins has no known function. However, one of the members, Swiss:Q22CP8, is annotated as an EF-hand family protein.. 
PF10596 U6-snRNA interacting domain of PrP8<br>This domain incorporates the interacting site for the U6-snRNA as part of the U4/U6.U5 tri-snRNPs complex of the spliceosome, and is the prime candidate for the role of cofactor for the spliceosome's RNA core. The essential spliceosomal protein Prp8 interacts with U5 and U6 snRNAs and with specific pre-mRNA sequences that participate in catalysis. This close association with crucial RNA sequences, together with extensive genetic evidence, suggests that Prp8 could directly affect the function of the catalytic core, perhaps acting as a splicing cofactor  .. 
PF10597 U5-snRNA binding site 2 of PrP8<br>The essential spliceosomal protein Prp8 interacts with U5 and U6 snRNAs and with specific pre-mRNA sequences that participate in catalysis  . This close association with crucial RNA sequences, together with extensive genetic evidence, suggests that Prp8 could directly affect the function of the catalytic core, perhaps acting as a splicing cofactor  .. 
PF10598 RNA recognition motif of the spliceosomal PrP8<br>The large RNA-protein complex of the spliceosome catalyses pre-mRNA splicing. One of the most conserved core proteins is PrP8 which occupies a central position in the catalytic core of the spliceosome, and has been implicated in several crucial molecular rearrangements that occur there, and has recently come under the spotlight for its role in the inherited human disease, Retinitis Pigmentosa  . The RNA-recognition motif of PrP8 is highly conserved and provides a possible RNA binding centre for the 5-prime SS, BP, or 3-prime SS of pre-mRNA which are known to contact with Prp8. The most conserved regions of an RRM are defined as the RNP1 and RNP2 sequences. Recognition of RNA targets can also be modulated by a number of other factors, most notably the two loops beta1-alpha1, beta2-beta3 and the amino acid residues C-terminal to the RNP2 domain  .. 
PF10599 Retro-transposon transporting motif  <br>This is the highly conserved C-terminal motif GRKIxxxxxRRKx of nucleoporins that plays a critical and unique role in the nuclear import of retro-transposons in both yeasts and higher organisms. It would appear that the arginine residues at positions 2 and 9-10 constitute a bipartite nuclear localisation signal, with two basic peptide motifs separated by an interchangeable spacer sequence, that is crucial for the retro-transposon activity  .. 
PF10600 PDZ-associated domain of NMDA receptors<br>Pfam-B_10923 (release 22.0). This domain is found in higher eukaryotes between the second and third PDZ domains, Pfam:PF00595, of glutamate receptor like proteins. Its exact function is not known.. 
PF10601 LITAF-like zinc ribbon domain<br>Clustering of trematode sequences. Members of this family display a conserved zinc ribbon structure   with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS) . The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure  .. 
PF10602 26S proteasome subunit RPN7<br>Pfam-B_4112 (release 22.0). RPN7 (known as the non ATPase regulatory subunit 6 in higher eukaryotes) is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae to be required for structural integrity  .  The 26S proteasome is is involved in the ATP-dependent degradation of ubiquitinated proteins.. 
PF10604 Polyketide cyclase / dehydrase and lipid transport<br>Lakshminarayan L, Mistry J. This family contains polyketide cylcases/dehydrases which are enzymes involved in polyketide synthesis. It also includes other proteins of the START superfamily  .. 
PF10605 3HB-oligomer hydrolase (3HBOH) <br>FIG094011 (Release 2.0). D-(-)-3-hydroxybutyrate oligomer hydrolase (also known as 3HB-oligomer hydrolase) functions in the degradation of poly-3-hydroxybutyrate (PHB).  It catalyses the hydrolysis of D(-)-3-hydroxybutyrate oligomers (3HB-oligomers) into 3HB-monomers.. 
PF10606 Homer-binding domain of metabotropic glutamate receptor <br>Pfam-B_17370 (release 22.0). This is the proline-rich region of metabotropic glutamate receptor proteins that binds Homer-related synaptic proteins. The Homer proteins form a physical tether linking mGluRs with the inositol trisphosphate receptors (IP3R) that appears to be due to the proline-rich "Homer ligand" (PPXXFr). Activation of PI turnover triggers intracellular calcium release  . MGluR function is altered in the mouse model of human Fragile X syndrome mental retardation, a disorder caused by loss of function mutations in the Fragile X mental retardation gene Fmr1. Homer 3 (and to a lesser extent Homer 1b/c) has been shown to form a multimeric complex with mGlu1a and the IP3 receptor, indicating that Homers may play a role in the localisation of receptors to their signalling partners  .. 
PF10607 RanBPM_CRA;<br>CTLH/CRA C-terminal to LisH motif domain. Pfam-B_3765 (release 22.0), UPF0559. RanBPM is a scaffolding protein and is important in regulating cellular function in both the immune system and the nervous system.  This domain is at the C-terminus of the proteins and is the binding domain for the CRA motif (for CT11-RanBPM), which is comprised of approximately 100 amino acids at the C terminal of RanBPM. It was found to be important for the interaction of RanBPM with fragile X mental retardation protein (FMRP), but its functional significance has yet to be determined  . This region contains CTLH and CRA domains annotated by SMART; however, these may be a single domain, and it is refereed to as a C-terminal to LisH motif  .. 
PF10608 Polyubiquitination (PEST) N-terminal domain of MAGUK<br>Pfam-B_18049 (release 22.0). The residues upstream of this domain are the probable palmitoylation sites, particularly two cysteines. The domain has a putative PEST site at the very start that seems to be responsible for poly-ubiquitination  . PEST domains are polypeptide sequences enriched in proline (P), glutamic acid (E), serine (S) and threonine (T) that target proteins for rapid destruction. The whole domain, in conjunction with a C-terminal domain of the longer protein, is necessary for dimerisation of the whole protein  .. 
PF10609 ParA/MinD ATPase like<br>Pfam-B_177 (release 21.0). This family contains ATPases involved in plasmid partitioning  .  It also contains the cytosolic Fe-S cluster assembling factor NBP35 which is required for biogenesis and export of both ribosomal subunits  .. 
PF10610 Thin aggregative fimbriae synthesis protein<br>FIGFAMs, Mistry J, Coggill P. FIG009025 (Release 2.0). Fimbriae are cell-surface protein polymers, of eg. E coli and Salmonella spp, that mediate interactions important for host and environmental persistence, development of biofilms, motility, colonisation and invasion of cells, and conjugation. Four general assembly pathways for different fimbriae have been proposed, one of which is extracellular nucleation-precipitation (ENP), that differs from the others in that fibre-growth occurs extracellularly. Thin aggregative fimbriae (Tafi) are the only fimbriae dependent on the ENP pathway. Tafi were first identified in Salmonella spp and the controlling operon termed agf; however subsequent isolation of the homologous operon in E coli led to its being called csg. Tafi are known as curli because, in the absence of extracellular polysaccharides, their morphology appears curled; however, when expressed with such polysaccharides their morphology appears as a tangled amorphous matrix. The gene agfC is found to be transcribed at low levels, localised to the periplasm in a mature form, and in combination with AgfE is important for AgfA extracellular assembly, which facilitates the synthesis of Tafi. The genes involved in Tafi production are organised into two adjacent divergently transcribed operons, agfBAC and agfDEFG, both of which are required for biosynthesis and assembly  .. 
PF10611 Protein of unknown function (DUF2469)<br>FIG004032 (Release 2.0). Member proteins often found in Actinomycetes clustered with signal peptidase and/or RNAse-HII.. 
PF10612 Spore coat protein Z<br>FIGFAMs, Mistry J, Coggill P. FIG014057 (Release 2.0). This family has members annotated as Spore coat protein Z, otherwise known as CotZ, It is a cysteine-rich spore coat family, and along with CotY is necessary for assembly of intact exosporium.. 
PF10613 Ligated ion channel L-glutamate- and glycine-binding site<br>Pfam-B_203 (release 22.0). This region, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and it binds L-glutamate and glycine  . It is found in association with Lig_chan, Pfam:PF00060.. 
PF10614 Tafi-CsgF;<br>Type VIII secretion system (T8SS), CsgF protein. FIGFAMs, Mistry J, Coggill P, Desvaux M. FIG077109 (Release 2.0). The extracellular nucleation-precipitation (ENP) pathway or Type VIII secretion system (T8SS) in Gram-negative (diderm) bacteria is responsible for the secretion and assembly of prepilins for fimbiae biogenesis, the prototypical curli. Besides the T2SS that can be involved in the assembly of prototypical Type 4 pilus, the T4SS that can be involved in the biogenesis of the prototypical pilus T, the T3SS involved in the assembly of the injectisome and the T7SS involved in the formation of the prototypical Type 1 pilus, the T8SS differs in that fibre-growth occurs extracellularly. The curli, also called thin aggregative fimbriae (Tafi), are the only fimbriae dependent on the T8SS. Tafi were first identified in Salmonella spp and the controlling operon termed agf; however subsequent isolation of the homologous operon in E coli led to its being called csg. In the absence of extracellular polysaccharides Tafi appear curled, although when expressed with such polysaccharides their morphology appears as a tangled amorphous matrix  . CsgF is one of three putative curli assembly factors appearing to act as a nucleator protein. Unlike eukaryotic amyloid formation, curli biogenesis is a productive pathway requiring a specific assembly machinery  .. 
PF10615 Protein of unknown function (DUF2470)<br>FIGFAMs, Mistry J, Coggill P. FIG076093 (Release 2.0). This family is a putative haem-iron utilisation family, as many members are annotated as being pyridoxamine 5'-phosphate oxidase-related, FMN-binding; however this could not be confirmed.. 
PF10616 Protein of unknown function (DUF2471) <br>FIGFAMs, Mistry J, Coggill P. FIG076041 (Release 2.0). The function of this family is unknown. Members all come from Burkholderia spp. Swiss:A2WH83 is annotated as Serine/threonine-protein kinase, but this could not be confirmed.. 
PF10617 Protein of unknown function (DUF2474)<br>FIGfam, Mistry J, Coggill P. FIG073099 (Release 2.0). This family of short proteins has no known function.. 
PF10618 DUF2473; <br>Phage tail tube protein. FIG030252 (Release 2.0). This bacterial family of proteins contains phage tail tube proteins related to the Mu phage protein Swiss:P79679  . Bacteriophage Mu has an eicosahedral head and contractile tail. The tail is composed of an outer sheath and an inner tube.. 
PF10620 Phosphoribosyl-dephospho-CoA transferase MdcG<br>FIG003211 (Release 2.0). MdcG is a phosphoribosyl-dephospho-CoA transferase that is involved in the biosynthesis of the prosthetic group of malonate decarboxylase  .  Malonate decarboxylase from Klebsiella pneumoniae contains an acyl carrier protein (MdcC) to which a 2'-(5' '-phosphoribosyl)-3'-dephospho-CoA prosthetic group is attached via phosphodiester linkage. MdcG catalyses the following reaction: 2'-(5''-triphosphoribosyl)-3'-dephospho-CoA + apo-[acyl-carrier-protein] = holo-[acyl-carrier-protein] + diphosphate.. 
PF10621 zf-Fe2-S2-FpoO; <br>F420H2 dehydrogenase subunit FpoO . FIGfam, Mistry J, Coggill P. FIG062058 (Release 2.0). This is the FpoO subunit of F420H2 dehydrogenase, an enzyme which oxidises reduced coenzyme F420.  Reduced coenzyme F420 is a universal electron carrier in methanogens.. 
PF10622 Energy-converting hydrogenase B subunit P (EhbP)<br>FIG124174 (Release 2.0). Ehb (energy-converting hydrogenase B) is an methanogenic archaeal enzyme that functions in one of the metabolic pathways involved in methanol reduction to methane.  This family contains subunit P of Ehb.. 
PF10623 Plasmid conjugative transfer protein PilI<br>FIG136100 (Release 2.0). The thin pilus of plasmid R64 belongs to the type IV family and is required for liquid matings.  pilI is one of 14 genes that have been identified as being involved in biogenesis of the R64 thin pilus  .. 
PF10624 Plasmid conjugative transfer entry exclusion protein TraS<br>FIG105028 (Release 2.0). Entry exclusion (Eex) is a process which prevents redundant transfer of DNA between donor cells.  TraS is a protein involved in Eex.  It blocks redundant conjugative DNA synthesis and transport between donor cells, and it is suggested that TraS interferes with a signalling pathway that is required to trigger DNA transfer  .  TraS on the recipient cell is known to form an interaction with TraG on the donor cell  .. 
PF10625 Universal stress protein B (UspB)<br>FIG002192 (Release 2.0). UspB in Escherichia coli is a 14kDa protein which is predicted to be an integral membrane protein.  Overexpression of UspB results in cell death in stationary phase, and mutants of uspB are sensitive to ethanol exposure during stationary phase  .. 
PF10626 Conjugative transposon protein TraO<br>FIG055244 (Release 2.0). This is a family of conjugative transposon proteins.. 
PF10627 Curli assembly protein CsgE<br>FIG091002 (Release 2.0). Curli are a class highly aggregated surface fibres that are part of a complex extracellular matrix.  They promote biofilm formation in addition to other activities.  CsgE is a non-structural protein involved in curli biogenesis  .\.       CsgE forms an outer membrane complex with the curli assembly proteins CsgG and CsgF  .. 
PF10628 Outer spore coat protein E (CotE)<br>FIG006437 (Release 2.0). CotE is a morphogenic protein that is required for the assembly of the outer coat of the endospore   and spore resistance to lysozyme  . CotE also regulates the expression of cotA, cotB, cotC and other genes encoding spore outer coat proteins  .  The timing of cotE expression has been shown in Bacillus subtilis to affect spore coat morphology but not lysozyme resistance  .. 
PF10629 Protein of unknown function (DUF2475)<br>This family of proteins has no known function.. 
PF10630 Protein of unknown function (DUF2476)<br>This is a family of proteins of unknown function.\.     The family is rich in proline residues.. 
PF10631 Protein of unknown function (DUF2477)<br>This is a family of proteins with no known function. The family is rich in proline residues.. 
PF10632 He_PIG associated, NEW1 domain of bacterial glycohydrolase<br>Naumoff D, Coggill P. Pfam-B_97991 (release 22.0). The English-language version of the first reference can be found on pages 388-399 of the above. This domain has been named NEW1 but its actual function is not known. It is found on proteins which are bacterial galactosidases  . The domain is associated with the He_PIG family, Pfam:PF05345, a putative Ig-containing domain.. 
PF10633 NPCBM-assoc; <br>NPCBM-associated, NEW3 domain of alpha-galactosidase. Naumoff D, Coggill P. Pfam-B_97993 (release 22.0). The English-language version of the first reference can be found on pages 388-399 of the above. This domain has been named NEW3 but its actual function is not known. It is found on proteins which are bacterial galactosidases  . The domain is associated with the NPCBM family, Pfam:PF08305, a novel putative carbohydrate binding module found at the N-terminus of glycosyl hydrolases.. 
PF10634 Fe2+ transport protein<br>FIG005173 (Release 2.0). This is a bacterial family of periplasmic proteins that are thought to function in high-affinity Fe2+ transport.. 
PF10635 DisA bacterial checkpoint controller linker region <br>The DisA protein is a bacterial checkpoint protein that dimerises into an octameric complex. The protein consists of three distinct domains. the first, N-terminal region, from 1-145 is globular and is represented by family DisA_N, Pfam:PF02457; the next 146-289 residues is this domain that consists of an elongated bundle of three alpha helices (alpha-6, alpha-10, and alpha-11), one side of which carries an additional three helices (alpha7-9), thus forming a spine like-linker between domains 1 and 3. The C-terminal residues of domain 3 are family HHH, Pfam:PF00633, the specific DNA-binding domain. The octameric complex thus has structurally linked nucleotide-binding and DNA-binding HhH domains and the nucleotide-binding domains are bound to a cyclic di-adenosine phosphate such that DisA is a specific di-adenylate cyclase. The di-adenylate cyclase activity is strongly suppressed by binding to branched DNA, but not to duplex or single-stranded DNA, suggesting a role for DisA as a monitor of the presence of stalled replication forks or recombination intermediates via DNA structure-modulated c-di-AMP synthesis  .. 
PF10636 Hemin uptake protein hemP<br>FIG024330 (Release 2.0). This is a bacterial family of proteins that are involved in the uptake of the iron source hemin  .. 
PF10637 Oxoglutarate and iron-dependent oxygenase degradation C-term<br>Pfam-B_18095 (release 22.0). Ofd1 is a prolyl 4-hydroxylase-like 2-oxoglutarate-Fe(II) dioxygenase that accelerates the degradation of Sre1N in the presence of oxygen.  The domain is conserved from yeasts to humans. Yeast Sre1 is the orthologue of mammalian sterol regulatory element binding protein (SREBP), and it responds to changes in oxygen-dependent sterol synthesis as an indirect measure of oxygen availability. However, unlike the prolyl 4-hydroxylases that regulate mammalian hypoxia-inducible factor, Ofd1 uses multiple domains to regulate Sre1N degradation by oxygen; the Ofd1 N-terminal dioxygenase domain is required for oxygen sensing and this Ofd1 C-terminal domain accelerates Sre1N degradation in yeasts  .. 
PF10638 Spindle body associated protein C-terminus  <br>This C-terminal domain of spindle-body-associated protein Sfi1 has an important role to play in the bridge-splitting during bi-polar spindle assembly, and this separation event possibly requires interaction with integral components of the nuclear envelope, such as the Mps2-Bbp1 complex  . Centrally to this domain is a region carrying centrin-binding repeats with repeating units containing tryptophan, family Sfi1_central, Pfam:PF08457.. 
PF10639 Uncharacterised protein family UPF0546<br>This family of proteins has no known function.  Many members are annotated as potential transmembrane proteins.. 
PF10640 mRNA capping enzyme N-terminal, ATPase and guanylyltransferase<br>This domain is the N-terminus of the large subunit viral mRNA capping enzyme, and carries both the ATPase and the guanylyltransferase activities of the enzyme. The guanylyltransferase enzymatic region runs from residues 242 (leucine)-273(arginine)  , the core of the acitve site being the lysine residue at 260  . The ATPase activity is at the very N-terminal part of the domain  .. 
PF10642 Mitochondrial import receptor subunit or translocase<br>Pfam-B_89651 (release 22.0). This protein family is very short and is only found in yeasts. Tom5 is one of three very small translocases of the mitochondrial outer membrane. Tom5 links mitochondrial preprotein receptors to the general import pore  . Although Tom5 has allegedly been identified in vertebrates this could not be confirmed.. 
PF10643 Photosystem P840 reaction-centre cytochrome c-551<br>FIGFam, Mistry J, Coggill P. FIG055090 (Release 2.0). A photosynthetic reaction-centre complex is found in certain green sulphur bacteria such as Chlorobium vibrioforme which are anaerobic photo-auto-trophic organisms. The primary electron donor is P840, a probable B-Chl a dimer, and the primary electron acceptor is a B-Chl monomer. Also on the donor side c-type cytochromes are known to function as electron donors to photo-oxidised P840. This family is thus the secondary endogenous donor of the photosynthetic reaction-centre complex and is a membrane-bound cytochrome containing a single haem group.. 
PF10644 Misat_Myo_SegII;<br>Misato Segment II tubulin-like domain. Pfam-B_7826 (release 21.0). The misato protein contains three distinct, conserved domains, segments I, II and III. Segments I and III are common to Tubulins Pfam:PF00091, but segment II aligns with myosin heavy chain sequences from D. melanogaster (PIR C35815), rabbit (SP P04460), and human (PIR S12458). Segment II of misato is a major contributor to its greater length compared with the various tubulins. The most significant sequence similarities to this 54-amino acid region are from a motif found in the heavy chains of myosins from different organisms. A comparison of segment II with the vertebrate myosin heavy chains reveals that it is homologous to a myosin peptide in the hinge region linking the S2 and LMM domains. Segment II also contains heptad repeats which are characteristic of the myosin tail alpha-helical coiled-coils  . This myosin-like homology may be due only to the fact that both myosin and Misato carry coiled-coils, which appear similar but are not necessarily homologous (Wood V, personal communication).. 
PF10645 Carbohydrate binding<br>Pfam-B_63360 (release 22.0). This is a carbohydrate binding domain which has been shown in Schizosaccharomyces pombe to be required for septum localisation  .. 
PF10646 GerMN;<br>Sporulation and spore germination. The GerMN domain is a region of approximately 100 residues that is found, duplicated, in the Bacillus GerM protein and is implicated in both sporulation and spore germination. The domain is found in a number of different bacterial species both alone and in association with other domains such as Amidase_3 Pfam:PF01520, Gmad1 and Gmad2.  It is predicted to have a novel alpha-beta fold.. 
PF10647 Lipoprotein LpqB beta-propeller domain<br>The Gmad1 domain is found associated with the GerMN family, Pfam:PF10646, in bacterial spore formation. It is predicted to have a beta-propeller fold and to have a passive binding role rather than a catalytic function owing to the low number of conserved hydrophilic residues.. 
PF10648 Immunoglobulin-like domain of bacterial spore germination<br>This domain is found linked to the GerMN domain Pfam:PF10646 in some bacterial proteins. It is predicted to contain an immunoglobulin-like all-beta fold.. 
PF10649 Protein of unknown function (DUF2478)<br>FIGfam, Mistry J, Coggill P. FIG046046 (Release 2.0) . This is a family of hypothetical bacterial proteins found in the vicinity of Molybdenum ABC transporter ATP-binding gene-products MobA MobB and MobC. However the function could not be confirmed. This family appears to belong to the P-loop superfamily by alignment to Pfam:PF03266. However, the characteristic P-loop sequence motif appears to have diverged beyond recognition in this family.. 
PF10650 Putative zinc-finger domain<br>This domain is conserved in fungi and might be a zinc-finger domain as it contains three conserved Cs and an H in the C-x8-C-x5-C-x3-H conformation typical of a zinc-finger.. 
PF10651 Domain of unknown function (DUF2479)<br>FIGfam, Mistry J, Coggill P. FIG015005 (Release 2.0). This domain is found in phage from a number of different bacteria.  It is purported to be a putative long tail fibre (Bacteriophage A118) protein, but this could not be confirmed.. 
PF10652 Protein of unknown function (DUF2480)<br>FIGfam, Mistry J, Coggill P. FIG020045 (Release 2.0) . All the members of this family are uncharacterised proteins, but the environment in which they are found on the bacterial genome suggests a function as a glucose-6-phosphate isomerase (EC 5.3.1.9).  This could not, however, be confirmed.. 
PF10653 Protein gp45 of Bacteriophage A118<br>FIGfam, Mistry J, Coggill P. FIG0160151 (Release 2.0). This domain is found in bacteriophage and is thought to have a gp45 function within the phage tail-fibre system.. 
PF10654 DUF2482; <br>Protein of unknown function (DUF2481) . FIGfam, Mistry J, Coggill P. FIG020094 (Release 2.0). This is a hypothetical protein family homologous to Lmo2305 in Bacteriophage A118 systems.. 
PF10655 Hypothetical protein of unknown function (DUF2482)<br>FIGfam, Mistry J, Coggill P. FIG030041 (Release 2.0). All the members of this very small, very short family are derived from bacteriophages, of the SA bacteriophages 11, Mu50B, system, and from the Staphylococcal_phi-Mu50B-like_prophages subsystem. All members are hypothetical proteins.. 
PF10656 Hypothetical protein of unknown function (DUF2483)<br>FIGfam, Mistry J, Coggill P. FIG032091 (Release 2.0). This is a family of proteins found in bacteriophage particularly of the SA bacteriophages 11, Mu50B, family, homologous to phi-ETA orf16.. 
PF10657 Photosystem P840 reaction centre protein PscD<br>FIGfam, Mistry J, Coggill P. FIG031038 (Release 2.0). The photosynthetic reaction centres (RCs) of aerotolerant organisms contain a heterodimeric core, built up of two strongly homologous polypeptides each of which contributes five transmembrane peptide helices to hold a pseudo-symmetric double set of redox components. Two molecules of PscD are housed within a subunit. PscD may be involved in stabilising the PscB component since it is found to co-precipitate with FMO (Fenna-Mathews-Olson BChl a-protein) and PscB. It may also be involved in the interaction with ferredoxin  .. 
PF10658 Protein of unknown function (DUF2484)<br>FIGfam, Mistry J, Coggill P. FIG030013 (Release 2.0). A role of this family in UDP-N-acetylenolpyruvoylglucosamine reductase, as MurB, could not be confirmed.. 
PF10659 Trypanosome variant surface glycoprotein C-terminal domain<br>Pfam-B_1351 (release 3.0). The trypanosome parasite expresses these proteins to evade the immune response.. 
PF10660 Iron-containing outer mitochondrial membrane protein N-terminus  <br>MitoNEET_N is the N-terminal region of the MitoNEET and Miner-type proteins that carry a zf-CDGSH, Pfam:PF09360, redox-active 2Fe-2S cluster.  The whole protein regulates oxidative capacity. The domain is an anchor sequence that tethers the protein to the outer membrane.. 
PF10661 WXG100 protein secretion system (Wss), protein EssA<br>FIGfam, Mistry J, Coggill P, Desvaux M. FIG043089 (Release 2.0). The WXG100 protein secretion system (Wss) is responsible for the secretion of WXG100 proteins (Pfam:PF06013) such as ESAT-6 and CFP-10 in Mycobacterium tuberculosis or EsxA and EsxB in Staphylococcus aureus. In S. aureus, the Wss seems to be encoded by a locus of eight CDS, called ess (eSAT-6 secretion system). This locus encodes, amongst several other proteins, EssA, a protein predicted to possess one transmembrane domain. Due to its predicted membrane location and its absolute requirement for WXG100 protein secretion, it has been speculated that EssA could form a secretion apparatus in conjunction with the polytopic membrane protein EsaA, YukC (Pfam:PF10140) and YukAB, which is a membrane-bound ATPase containing Ftsk/SpoIIIE domains (Pfam:PF01580) called EssC in S. aureus and Snm1/Snm2 in Mycobacterium tuberculosis. Proteins homologous to EssA, YukC, EsaA and YukD seem absent from mycobacteria  .. 
PF10662 Ethanolamine utilisation - propanediol utilisation<br>FIGfam, Mistry J, Coggill P. FIG047026 (Release 2.0). Members of this family function in ethanolamine and propanediol degradation pathways, however the exact roles of these proteins is poorly understood [1-3].. 
PF10664 DUF2485; NADHqo1-M; NADHdh-M;<br>Cyanobacterial and plastid NDH-1 subunit M. FIGfam, Mistry J, Coggill P. FIG006356 (Release 2.0). The proton-pumping NADH:ubiquinone oxidoreductase catalyses the electron transfer from NADH to ubiquinone linked with proton translocation across the membrane. It is the largest, most complex and least understood of the respiratory chain enzymes and is referred to as Complex I. The subunit composition of the enzyme varies between groups of organisms. Complex I originating from mammalian mitochondria contains 45 different proteins, whereas in bacteria, the corresponding complex NDH-1 consists of 14 different polypeptides.  Homologues of these 14 proteins are found among subunits of the mitochondrial complex I, and therefore bacterial NDH-1 might be considered a model proton-pumping NADH dehydrogenase with a minimal set of subunits. Escherichia coli NDH-1 readily disintegrates into 3 sub-complexes: a water-soluble NADH dehydrogenase fragment (NuoE, -F, and -G),the connecting fragment (NuoB, -C, -D, and -I), and the membrane fragment (NuoA, -H, -J, -K, -L, -M, -N). In cyanobacteria and their descendants, the chloroplasts of green plants, the subunit composition of NDH-1 remains obscure. The genes for eleven subunits NdhA-NdhK, homologous to the NuoA-NuoD and NuoH-NuoN of the E. coli complex, have been found in the genome of Synechocystis sp. PCC 6803 which has a family of 6 ndhD genes and a family of 3 ndhF genes. Two reported multisubunit complexes, NDH-1L and NDH-1M, represent distinct NDH-1 complexes in the thylakoid membrane of Synechocystis 6803 -cyanobacterium. NDH-1L was shown to be essential for photoheterotrophic cell growth, whereas expression of NDH-1M was a prerequisite for CO2 uptake and played an important role in growth of cells at low CO2. Here we report the subunit composition of these two complexes. Fifteen proteins were discovered in NDH-1L including NdhL, a new component of the membrane fragment, and Ssl1690 (designated as NdhO), a novel peripheral subunit  . The cyanobacterial NDH-1 complex contains additional subunits, NdhM and NdhN, compared with the minimal set of the bacterial enzyme and these seem to be specific for thylakoid-located NDH-1 of photosynthetic organisms  . The three subunits of NDH-1, NdhM, NdhN and NdhO are essential for effecting cyclic electron flow around photosystem I, by supplying extra-ATP for photosynthesis in both plastids and cyanobacteria [3, 4].. 
PF10665 Phage_Gp9;<br>Minor capsid protein. FIGfam, Mistry J, Coggill P. FIG016324 (Release 2.0). This is a putative tail-knob or minor capsid protein from bacteriophages.. 
PF10666 Phage protein Gp14<br>FIGfam, Mistry J, Coggill P. This phage protein family is of unknown function but is expressed from within a cluster of tail- and base plate-producing genes  .. 
PF10667 Protein of unknown function (DUF2486)<br>FIGfam, Mistry J, Coggill P. FIG008383 (Release 2.0). This family is made up of members from various Burkholderia spp. The function is unknown.. 
PF10668 Phage terminase small subunit<br>FIGfams, Mistry J, Coggill P. FIG022212 (Release 2.0). This family of small highly conserved proteins come from a subset of Firmicute species. Its putative function is as a phage terminase small subunit.. 
PF10669 Protein gp23 (Bacteriophage A118)<br>FIGfam, Mistry J, Coggill P. FIG018382 (Release 2.0). This is the highly conserved family of the major tail subunit protein.. 
PF10670 NikM;<br>Domain of unknown function (DUF4198). Pfam-B_42996 (release 22.0). This family was previously missannotated in Pfam as NikM.. 
PF10671 Toxin co-regulated pilus biosynthesis protein Q<br>FIGfam, Mistry J, Coggill P. FIG032035 (Release 2.0). The toxin-coregulated pilus (TCP) of Vibrio cholerae and the soluble TcpF protein that is secreted via the TCP biogenesis apparatus are essential for intestinal colonisation in the disease of cholera. TcpQ is part of an outer membrane complex of the TCP biogenesis apparatus, comprised of TcpC and TcpQ, and the TcpQ is required for proper localisation of TcpC to the outer membrane. The domain is found in other Proteobacterial species apart from Vibrio.. 
PF10672 S-adenosylmethionine-dependent methyltransferase<br>Members of this family are S-adenosylmethionine-dependent methyltransferases from gamma-proteobacterial species. The diversity in the roles of methylation is matched by the almost bewildering number of methyltransferase enzymes that catalyse the methylation reaction. Although several classes of methyltransferase enzymes are known, the great majority of methylation reactions are catalysed by the S-adenosylmethionine-dependent methyltransferases.. 
PF10673 Protein of unknown function (DUF2487)<br>This is a bacterial family of uncharacterised proteins.. 
PF10674 DUF2488;<br>Protein of unknown function (DUF2488). This protein is conserved in the green lineage and located in the chloroplast.. 
PF10675 Protein of unknown function (DUF2489)<br>This is a bacterial family of uncharacterised proteins.. 
PF10676 Spore germination protein gerPA/gerPF<br>This is a bacterial family of proteins that are required for the formation of functionally normal spores.  Proteins in this family may be involved in establishing normal coat structure and/or permeability which could control the access of germinants to their receptor.. 
PF10677 Protein of unknown function (DUF2490)<br>This is a bacterial family of uncharacterised proteins. They appear to belong to the outer membrane beta barrel superfamily.. 
PF10678 Protein of unknown function (DUF2492)<br>This is a bacterial family of uncharacterised proteins.. 
PF10679 Protein of unknown function (DUF2491)<br>This is a bacterial family of uncharacterised proteins.. 
PF10680 RNA polymerase I specific transcription initiation factor<br>Pfam-B_44021 (release 22.0). Initiation of transcription of ribosomal DNA (rDNA) in yeast involves an interaction of upstream activation factor (UAF) with the upstream element of the promoter, to form a stable UAF-template complex. UAF, together with the TATA-binding transcription initiation factor protein TBP, then recruits an essential core factor to the promoter, to form a stable preinitiation complex  . This Rrn9 domain, which seems to be constrained to fungi, is the two highly conserved regions of proteins which form one of the subunits of UAF and appears to be the region responsible for the interaction with TBP. The family includes the S.pombe Arc1 protein, Swiss:Q10204, which is found to be essential for the accumulation of condensin at kinetochores  .. 
PF10681 Chaperone for protein-folding within the ER, fungal<br>Pfam-B_27706 (release 22.0). This conserved fungal family is an essential molecular chaperone in the endoplasmic reticulum. Molecular chaperones transiently interact with unfolded proteins to inhibit their self-aggregation and to support their folding and/or assembly. Rot1 is a general chaperone with some substrate specificity, its substrates being the structurally unrelated Kre5 Kre6 Big1 Atg22, which are type I, type II, and polytopic membrane proteins. The dependencies of each for Rot1 do not share similarities. However, their folding does require BiP, and one of these proteins was simultaneously associated with both Rot1 and BiP. In addition, Rot1 may cooperate with BiP/Kar2 in the folding of Kre6  .. 
PF10682 Glycoprotein of human cytomegalovirus HHV-5<br>This is glycoprotein UL40 from human cytomegalovirus or herpesvirus 5. The signal sequence of the UL40 polypeptide contains an HLA-E ligand identical with HLA-Cw*0304. The first 37 residues of UL40, including this ligand, are predicted to encode a signal peptide.  The virus thus prevents the lysis by NK (natural killer) cells of the cell it has invaded [1-2].. 
PF10683 Hermes_DBD;<br>Hermes transposase DNA-binding domain  . This domain confers specific DNA-binding on Hermes transposase  .. 
PF10684 Putative biofilm-dependent modulation protein<br>This is a family of tightly conserved proteins from Enterobacteriaceae which are annotated as being biofilm-dependent modulation protein homologues.. 
PF10685 Stress-induced bacterial acidophilic repeat motif<br>This repeat is found in proteins which are expressed under conditions of stress in bacteria. The repeat contains a highly conserved, characteristic sequence motif,KGG, that is also recognised by plants and lower eukaryotes and repeated in their LEA (late embryogenesis abundant) family of proteins, thereby rendering those proteins bacteriostatic. An example of such an LEA family is LEA_5, Pfam:PF00477. Further downstream from this motif is a Walker A, nucleotide binding, motif GXXXXGK(S,T), that in YciG of E coli, eg Swiss:Q8X7B4, is QSGGNKSGKS [URL]. YciG is expressed as part of a three-gene operon, yciGFE, and this operon is induced by stress and is regulated by RpoS, which controls the general stress-response in E coli. YciG was shown to be important for stationary-phase resistance to thermal stress and in particular to acid stress.. 
PF10686 Protein of unknown function (DUF2493)<br>Members of this family are all Proteobacteria. The function is not known.. 
PF10688 Bacterial inner membrane protein<br>This is a family of inner membrane proteins. Many of the members are YgjV protein.. 
PF10689 Protein of unknown function (DUF2496)<br>This family consists of proteins from Gammaproteobacteria spp. Many members are annotated as being like the E coli protein YbaM.. 
PF10690 Myticin pre-proprotein from the mussel<br>Myticin is a cysteine-rich peptide produced in three isoforms, A, B and C, by Mytilus galloprovincialis, the Mediterranean mussel. Some isoforms show antibacterial activity against gram-positive bacteria, while others are additionally active against the fungus Fusarium oxysporum and a gram-negative bacterium, Escherichia coli D31.  Myticin-prepro is the precursor peptide. The mature molecule, named myticin, consists of 40 residues, with four intramolecular disulfide bridges and a cysteine array in the primary structure different from that of previously characterised cysteine-rich antimicrobial peptides. The first 20 amino acids are a putative signal peptide, and the antimicrobial peptide sequence is a 36-residue C-terminal extension. Such a structure suggests that myticins are synthesised as prepro-proteins that are then processed by various proteolytic events before storage in the haemocytes as the active peptide. Myticin precursors are expressed mainly in the haemocytes. The family Mytilin has been merged into this family.. 
PF10691 Protein of unknown function (DUF2497) <br>Members of this family belong to the Alphaproteobacteria. The function of the family is not known.. 
PF10692 Protein of unknown function (DUF2498)<br>Members of this family are Gammaproteobacteria. Many are annotated as like E coli protein YciN. The function is not known.. 
PF10693 Protein of unknown function (DUF2499)<br>Members of this family are found in plants, lower eukaryotes, and bacteria and the chloroplast where it is annotated as Ycf49 or Ycf49-like.  The function is not known though several members are annotated as putative membrane proteins.. 
PF10694 Protein of unknown function (DUF2500)<br>The members of this family are largely confined to the Gammaproteobacteria. The function is not known.. 
PF10696 Protein of unknown function (DUF2501)<br>Members of this family are all Proteobacteria. Several are annotated as being YjjA or YjjA-like, but this protein is uncharacterised.. 
PF10697 Protein of unknown function (DUF2502)<br>Members of this family are all Gammaproteobacteria. The function is not known.. 
PF10698 Protein of unknown function (DUF2505)<br>Members of this family are all Actinobacteria. The function is not known.. 
PF10699 Male gamete fusion factor<br>The gene encoding Arabidopsis HAP2 is allelic with GCS1 (Generative cell-specific protein 1). HAP2 is expressed only in the haploid sperm and is required for efficient guidance of the pollen tube to the ovules. In Arabidopsis the protein is a predicted membrane protein with an N-terminal secretion signal, a single transmembrane domain and a C-terminal histidine-rich domain  . HAP2-GCS1 is found from plants to lower eukaryotes and is necessary for the fusion of the gametes in fertilisation. It is involved in a novel mechanism for gamete fusion where a first species-specific protein binds male and female gamete membranes together after which a second, broadly conserved protein, either directly or indirectly, causes fusion of the two membranes together. The broadly conserved protein is represented by this HAP2-GCS1 domain, conserved from plants to lower eukaryotes  . In Plasmodium berghei the protein is expressed only in male gametocytes and gametes, having a male-specific function during the interaction with female gametes, and being indispensable for parasite fertilisation. The gene in plants and eukaryotes might well have originated from acquisition of plastids from red algae  .. 
PF10702 Protein of unknown function (DUF2507)<br>This family is conserved in Firmicutes. The function is not known.. 
PF10703 Molybdenum cofactor biosynthesis protein F<br>MoaF protein is essential for the production of the monoamine-inducible 30kDa protein in Klebsiella  . It is necessary for reconstituting organoautotrophic growth in Ralstonia eutropha  . It is conserved in Proteobacteria and some lower eukaryotes. The operon regulating the Moa genes is responsible for molybdenum cofactor biosynthesis.. 
PF10704 Protein of unknown function (DUF2508)<br>This family is conserved in Firmicutes. Several members are annotated as being the protein YaaL. The function is not known.. 
PF10705 Chloroplast protein precursor Ycf15 putative<br>In some species of plants the ycf15 gene is probably not a protein-coding gene because the protein in these species has premature stop codons. Most of the members of the family are hypothetical or uncharacterised  .. 
PF10706 Aminoglycoside-2''-adenylyltransferase<br>This family is conserved in Bacteria. It confers resistance to kanamycin, gentamicin, and tobramycin  . The protein is also produced by plasmids in various bacterial species and confers resistance to essentially all clinically available aminoglycosides except streptomycin, and it eliminates the synergism between aminoglycosides and cell-wall active agents  .. 
PF10707 PhoP regulatory network protein YrbL<br>This is a family of proteins that are activated by PhoP. PhoP protein controls the expression of a large number of genes that mediate adaptation to low Mg2+ environments and/or virulence in several bacterial species. YbrL is proposed to be acting in a loop activity with PhoP and PrmA analogous to the multicomponent loop in Salmonella where the PhoP-dependent PmrD protein activates the regulatory protein PmrA, and the activated PmrA then represses transcription from the PmrD promoter which harbours binding sites for both the PhoP and PmrA proteins. Expression of YrbL is induced in low Mg2+ in a PhoP-dependent fashion and repressed by Fe3+ in a PmrA-dependent manner  .. 
PF10708 Protein of unknown function (DUF2510)<br>This is family of proteins conserved in Actinobacteria. Many members are annotated as putative membrane proteins but this could not be confirmed.. 
PF10709 Protein of unknown function (DUF2511)<br>This family is conserved in bacteria. The function is not known.. 
PF10710 Protein of unknown function (DUF2512)<br>Proteins in this family are predicted to be integral membrane proteins, and many of them are annotated as being YndM protein. They are all found in Firmicutes. The true function is not known.. 
PF10711 Hypothetical protein (DUF2513)<br>This family is found in bacteria. The function is not known.. 
PF10712 NAD-specific glutamate dehydrogenase<br>The members of this are annotated as being NAD-specific glutamate dehydrogenase encoded in antisense gene pair with DnaK-J  .. 
PF10713 Protein of unknown function (DUF2509) <br>This family is conserved in Proteobacteria. The function is not known but many of the members are annotated as protein YgdB.. 
PF10714 Late embryogenesis abundant protein 18<br>This is a family of late embryogenesis-abundant proteins There is high accumulation of this protein in dry seeds, and in the roots of full-grown plants in response to dehydration and ABA (abscisic acid application) treatments  . This LEA protein disappears after germination. It accumulates in growing regions of well irrigated hypocotyls and meristems suggesting a role in seedling growth resumption on rehydration  . As a group the LEA proteins are highly hydrophilic, contain a high percentage of glycine residues, lack Cys and Trp residues and do not coagulate upon exposure to high temperature, and for these reasons are considered to be members of a group of proteins called hydrophilins  . Expression of the protein is negatively regulated during etiolating growth, particularly in roots, in contrast to its expression patterns during normal growth  .. 
PF10715 Endoribonuclease RegB T4-bacteriophage encoded<br>The RegB endoribonuclease encoded by bacteriophage T4 is a unique sequence-specific nuclease that cleaves in the middle of GGAG or, in a few cases, GGAU tetranucleotides, preferentially those found in the Shine-Dalgarno regions of early phage mRNAs. Phage RB49 in addition to gpRegB utilises Escherichia coli endoribonuclease E for the degradation of its transcripts for gene regB. The deduced primary structure of RegB proteins of 32 phages studied is almost identical to that of T4, while the sequences of RegB encoded by phages RB69, TuIa and RB49 show substantial divergence from their T4 counterpart.. 
PF10716 NADH dehydrogenase transmembrane subunit<br>The NdhL family is a component of the NDH-1L complex that is one of the proton-pumping NADH:ubiquinone oxidoreductases that catalyse the electron transfer from NADH to ubiquinone linked with proton translocation across the membrane. NDH-1L is essential for photoheterotrophic cell growth. NdhL appears to contain two transmembrane helices and it is necessary for the functioning of though not the correct assembly of the NDH-1 complex in Synechocystis 6803. The conservation between cyanobacteria and green plants suggests that chloroplast NDH-1 complexes contain related subunits  .. 
PF10717 Occlusion-derived virus envelope protein ODV-E18<br>This family of occlusion-derived viral envelope proteins are detected in viral-induced intranuclear microvesicles and are not detected in the plasma membrane, cytoplasmic membranes, or the nuclear envelope. The ODV-E18 protein is encoded by baculovirus late genes with transcription initiating from a TAAG motif. It exists as a dimer in the ODV envelope and contains a hydrophobic domain which is putatively acting as a target or retention signal for intranuclear microvesicles  .. 
PF10718 Hypothetical chloroplast protein Ycf34<br>This family is of proteins annotated as hypothetical chloroplast protein YCF34.  The function is not known.. 
PF10719 Late competence development protein ComFB<br>This family is conserved in bacteria. Some members, with three conserved cysteines, are annotated as late competence development protein ComFB.. 
PF10720 Protein of unknown function (DUF2515)<br>This family is conserved in Firmicutes. Several members are annotated as YppC. The function is not known.. 
PF10721 Protein of unknown function (DUF2514)<br>This family is conserved in bacteria and some viruses. The function is not known.. 
PF10722 Putative bacterial sensory transduction regulator<br>YbjN is a putative sensory transduction regulator protein found in Proteobacteria. As it is a multi-copy suppressor of the coenzyme A-associated temperature sensitivity in temperature-sensitive mutant strains of Escherichia coli the suggestion is that it both helps CoA-A1 and possibly works as a general stabiliser for some other unstable proteins  . This family was expanded to subsume other related families: DUF1790, DUF1821 and DUF2596.. 
PF10723 Replication regulatory protein RepB<br>This is a family of proteins which regulate replication of rolling circle replication (RCR) plasmids that have a double-strand replication origin (dso). Regulation of replication of RCR plasmids occurs mainly at initiation of leading strand synthesis at the dso, such that Rep protein concentration controls plasmid replication  .. 
PF10724 Protein of unknown function (DUF2516)<br>This family is conserved in Actinobacteria. The function is not known.. 
PF10725 Protein of unknown function (DUF2517)<br>This family is conserved in Proteobacteria. Several members are annotated as being protein YbfA. The function is not known.. 
PF10726 Protein of function (DUF2518)<br>This family is conserved in Cyanobacteria. Several members are annotated as the protein Ycf51.  The function is not known.. 
PF10727 Rossmann-like domain<br>This family of proteins contain a Rossmann-like domain.. 
PF10728 Domain of unknown function (DUF2520)<br>This presumed domain is found C-terminal to a Rossmann-like domain suggesting that these proteins are oxidoreductases.. 
PF10729 Cell division activator CedA<br>CedA is made up of four antiparallel beta-strands and an alpha-helix. It activates cell division by inhibiting chromosome over-replication. This is mediated by binding to dsDNA via the beta-sheet. [1,2].. 
PF10730 Protein of unknown function (DUF2521)<br>Family of unknown function specific to Bacillus.. 
PF10731 Thrombin inhibitor from mosquito<br>Members of this family are all inhibitors of thrombin, the peptidase that is at the end of the blood coagulation cascade and which creates the clot by cleaving fibrinogen.  The interaction between thrombin and fibrinogen involves two different areas of contact - via the thrombin active site and via a second substrate-binding site known as an exosite.  The inhibitor acts by blocking the exosite, rather than by interacting with the active site.  The inhibitors are from mosquitoes that feed on human blood and which, by inhibiting thrombin, prevent the blood from clotting and keep it flowing.. 
PF10732 Protein of unknown function (DUF2524)<br>This family of proteins with unknown function appears to be restricted to Bacillaceae bacteria. . 
PF10733 Protein of unknown function (DUF2525)<br>This family of proteins with unknown function appears to be restricted to Enterobacteriaceae. The family has a highly conserved sequence.. 
PF10734 Protein of unknown function (DUF2523)<br>This is a family of phage related proteins whose function is uncharacterised.. 
PF10735 Protein of unknown function (DUF2526)   <br>This family of proteins with unknown function is restricted to Enterobacteriaceae. The family has a highly conserved sequence.. 
PF10736 Protein of unknown function (DUF2627) <br>This family of proteins with unknown function appears to be restricted to a family of Enterobacterial proteins. It has a highly conserved sequence.. 
PF10737 Spore germination protein GerPC<br>GerPC is required for the formation of functionally normal spores. The gerP locus encodes a number of proteins which are thought to be involved in the establishment of normal spore coat structure and/or permeability, which allows the access of germinants to their receptor  .. 
PF10738 Probable lipoprotein LpqN<br>This family is conserved in Mycobacteriaceae and is likely to be a lipoprotein  .. 
PF10739 Protein of unknown function (DUF2550)<br>This family is conserved in Corynebacterineae. The function is not known though most members are annotated as either secreted, or membrane, proteins.. 
PF10740 Protein of unknown function (DUF2529)<br>This family is conserved in the Bacillales. The function is not known. Several members are annotated as being YWJG, a protein expressed downstream of pyrG, a gene encoding for cytidine triphosphate synthetase.. 
PF10741 GspM_II;<br>Type II secretion system (T2SS), protein M subtype b. Mistry J, Coggill P, Desvaux M. The T2SMb family is conserved in Proteobacteria and Actinobacteria, and differs from the T2SM proteins in Vibrio spp. (Pfam:PF04612).. 
PF10742 Protein of unknown function (DUF2555)<br>This family is conserved in Cyanobacteria. The function is not known.. 
PF10743 Regulatory phage protein cox<br>This family of phage Cox proteins is expressed by Enterobacteria phages. The Cox protein is a 79-residue basic protein with a predicted strong helix-turn-helix DNA-binding motif. It inhibits integrative recombination and it activates site-specific excision of the HP1 genome from the Haemophilus influenzae chromosome, Hp1. Cox appears to function as a tetramer. Cox binding sites consist of two direct repeats of the consensus motif 5'-GGTMAWWWWA, one Cox tetramer binding to each motif. Cox binding interferes with the interaction of HP1 integrase with one of its binding sites, IBS5. This competition is central to directional control. Both Cox binding sites are needed for full inhibition of integration and for activating excision, because it plays a positive role in assembling the nucleoprotein complexes that produce excisive recombination, by inducing the formation of a critical conformation in those complexes  .. 
PF10744 Med1-Trap220; <br>Mediator of RNA polymerase II transcription subunit 1. Pfam-B_51442 (release 22.0). Mediator complexes are basic necessities for linking transcriptional regulators to RNA polymerase II.  This domain, Med1, is conserved from plants to fungi to humans and forms part of the Med9 submodule of the Srb/Med complex. it is one of three subunits essential for viability of the whole organism via its role in environmentally-directed cell-fate decisions  . Med1 is part of the tail region of the Mediator complex  .. 
PF10745 Protein of unknown function (DUF2530)<br>This family of proteins with unknown function appears to be restricted to mycobacteria.. 
PF10746 Phage holin family 6<br>Holins are a diverse family of proteins that cause bacterial membrane lysis during late-protein synthesis.. 
PF10747 Protein of unknown function (DUF2522)<br>This family of proteins with unknown function appears to be restricted to Bacillus.. 
PF10748 Protein of unknown function (DUF2531)<br>This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.. 
PF10749 Protein of unknown function (DUF2534)<br>This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.. 
PF10750 Protein of unknown function (DUF2536)<br>This family of proteins with unknown function appears to be restricted to Bacillus spp. Structural modelling suggests this domain may bind nucleic acids  .. 
PF10751 Protein of unknown function (DUF2535)<br>This family of proteins with unknown function appears to be restricted to Bacillus spp.. 
PF10752 Protein of unknown function (DUF2533) <br>This family of proteins with unknown function appears to be restricted to Bacillus spp.. 
PF10753 Protein of unknown function (DUF2566)<br>This family is conserved in Enterobacteriaceae. The function is not known.. 
PF10754 Protein of unknown function (DUF2569)<br>This family is conserved in bacteria. The function is not known, but several members are annotated as being YdgK or a homologue thereof.. 
PF10756 DUF2581;<br>This domain has a bacterial type PH domain structure. This domain was previously known as DUF2581. This family is conserved in the Actinomycetales.  Although several members are annotated as RbiX homologues, RbiX being a putative regulator of riboflavin biosynthesis, the function could not be confirmed.. 
PF10755 Protein of unknown function (DUF2585)<br>This family is conserved in Proteobacteria. The function is not known.. 
PF10757 Biofilm formation regulator YbaJ<br>YbaJ regulates biofilm formation. It also has an important role in the regulation of motility in the biofilm. YbaJ functions in increasing conjugation, aggregation and decreasing the motility, resulting in an increase of biofilm  . 
PF10758 Protein of unknown function (DUF2586)<br>This bacterial family of proteins has no known function.. 
PF10759 Protein of unknown function (DUF2587)<br>This is a bacterial family of proteins with no known function.. 
PF10761 Protein of unknown function (DUF2590)<br>This family of proteins has no known function.. 
PF10762 Protein of unknown function (DUF2583)   <br>Some members in this family of proteins are annotated as YchH however currently no function is known.. 
PF10763 Protein of unknown function (DUF2584)<br>This bacterial family of proteins have no known function.. 
PF10764 Inhibitor of sigma-G Gin<br>Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB  .. 
PF10765 Protein of unknown function (DUF2591)<br>This bacterial family of proteins has no known function.. 
PF10766 Protein of unknown function (DUF2592)<br>This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.. 
PF10767 Protein of unknown function (DUF2593)<br>This family of proteins appear to be restricted to Enterobacteriaceae. Some members in the family are annotated as YbjO however currently there is no known function.. 
PF10768 Class II flagellar assembly regulator<br>The FliX protein is possibly a transient component of the flagellum that is required for the assembly process. FliX may contribute to the targeting or assembly of the P- and L-ring protein monomers at the cell pole. The family carries a potential N-terminal signal sequence and at least one transmembrane domain indicating that it might function either in or in association with the cell membrane  .. 
PF10769 Protein of unknown function (DUF2594)<br>This family of proteins with unknown function appear to be restricted to Enterobacteriaceae.. 
PF10771 Protein of unknown function (DUF2582)<br>This family is conserved in bacteria and archaea. The function is not known.. 
PF10772 Protein of unknown function (DUF2597)<br>This family of proteins has no known function.. 
PF10774 BssS;<br>Domain of unknown function (DUF4226). This family of mycobacterial proteins are uncharacterised.. 
PF10775 ATP synthase complex subunit h<br>Subunit h is a component of the yeast mitochondrial F1-F0 ATP synthase. It is essential for the correct assembly and functioning of this enzyme. Subunit h occupies a central place in the peripheral stalk between the F1 sector and the membrane  .. 
PF10776 Protein of unknown function (DUF2600)<br>This is a bacterial family of proteins. Some members in the family are annotated as YtpB however currently no function is known.. 
PF10777 Inner membrane protein YlaC<br>Members of this family include proteins annotated as inner membrane protein YlaC in E. coli and Salmonella. The function of this family is unknown.. 
PF10778 Halocarboxylic acid dehydrogenase DehI<br>Haloacid dehalogenases catalyse the removal of halides from organic haloacids. DehI can process both L- and D-substrates.  A crucial aspartate residue is predicted to activate a water molecule for nucleophilic attack of the substrate chiral centre resulting in an inversion of the configuration of either L- or D-substrates in contrast to D-only enzymes  .. 
PF10779 Haemolysin XhlA<br>XhlA is a cell-surface associated haemolysin that lyses the two most prevalent types of insect immune cells (granulocytes and plasmatocytes) as well as rabbit and horse erythrocytes  . This family has had DUF1267, Pfam:PF06895, merged into it.. 
PF10780 39S ribosomal protein L53/MRP-L53<br>MRP-L53 is also known as Mrp144. It is part of the 39S ribosome  .. 
PF10781 Dextransucrase DSRB<br>DSRB is a novel dextransucrase which produces a dextran different from the typical dextran, as it contains (1-6) and (1-2) linkages, when this strain is grown in the presence of sucrose  .. 
PF10782 Protein of unknown function (DUF2602)<br>This bacterial family of proteins has no known function.. 
PF10783 Protein of unknown function (DUF2599)<br>This family is conserved in Actinobacteria. The function is not known.. 
PF10784 Plasmid stability protein<br>This family is conserved in the Enterobacteriales. It is a putative plasmid stability protein in that it is expressed from the operon involved in stability, but its actual function has not yet been characterised.. 
PF10785 NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit<br>This family is the N-terminal domain of NADH-ubiquinone oxidoreductase 21 kDa subunits from fungi, lower metazoa and plants.. 
PF10786 Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49)<br>This family is conserved in Firmicutes and Proteobacteria. Several members are annotated as being glucose-6-phosphate 1-dehydrogenase (EC:1.1.1.49) but this could not be confirmed.. 
PF10787 Uncharacterised protein from bacillus cereus group<br>This family is conserved in the Bacillus cereus group. Several members are called YfmQ but the function is not known.. 
PF10788 Protein of unknown function (DUF2603)<br>This family is conserved in Epsilon-proteobacteria. The function is not known.. 
PF10789 Phage RNA polymerase binding, RpbA<br>Upon infection the RpbA encode phage protein binds to the ADP-ribosylated core RNA polymerase and modulates function to preferentially bind T4 promoters.\.      This is a non-essential protein to the phage life cycle.. 
PF10790 Protein of Unknown function (DUF2604)<br>Family of bacterial proteins with undetermined function.. 
PF10791 Mitochondrial F1-F0 ATP synthase subunit F of fungi<br>The membrane bound F1-FO-type H+ ATP synthase of mitochondria catalyses the terminal step in oxidative respiration converting the generation of the electrochemical gradient into ATP for cellular biosynthesis. The general structure and the core subunits of the enzyme are highly conserved in both prokaryotic and eukaryotic organisms.. 
PF10792 Protein of unknown function (DUF2605)<br>This family is conserved in Cyanobacteria. The function is not known.. 
PF10793 Gloverin-like protein <br>This family of proteins are Gloverin-like. Gloverin is a 13.8kDa inducible antibacterial insect protein which inhibits the synthesis of vital outer membrane proteins leading to a permeable outer membrane. Gloverin contains a large number of glycine residues  .. 
PF10794 Protein of unknown function (DUF2606)<br>Family of bacterial proteins with unknown function. These proteins have been classified as membrane proteins. 
PF10795 Protein of unknown function (DUF2607)<br>This family is conserved in Gammaproteobacteria. The function is not known.. 
PF10796 Sigma-S stabilisation anti-adaptor protein <br>This family is conserved in Enterobacteriaceae. It is one of a series of proteins, expressed by these bacteria in response to stress, that help to regulate Sigma-S, the stationary phase sigma factor of Escherichia coli and Salmonella. IraP is essential for Sigma-S stabilisation in some but not all starvation conditions  .. 
PF10797 Protein of unknown function<br>This family is conserved in Firmicutes and Proteobacteria. The function is not known but several members are annotated as being homologues of E coli YhfT, a protein thought to be involved in fatty acid oxidation.. 
PF10798 Biofilm development protein YmgB/AriR<br>YmgB is part of the three gene cluster ymgABC which has a role in biofilm development and stability. YmgB represses biofilm formation in rich medium containing glucose, decreases cellular motility and also protects the cell from acid which indicates that YmgB has an important function in acid-resistance  . YmgB binds as a dimer to genes which are important for biofilm formation via a ligand. Due to its important function in acid resistance it is also known as AriR (regulator of acid resistance influenced by indole)  .. 
PF10799 Biofilm formation protein (YliH/bssR)<br>YliH is induced in biofilms and is involved in repression of motility in the biofilms  . YliH is also known as bssR (regulator of biofilm through signal secreton).. 
PF10800 Protein of unknown function (DUF2528) <br>This family of proteins has no known function. Some of the sequences are annotated as ea10 however the function of this protein is unknown.. 
PF10801 Protein of unknown function (DUF2537)<br>This bacterial family of proteins has no known function.. 
PF10802 Protein of unknown function (DUF2540)<br>This family of proteins with unknown function appears to be restricted to Methanococcus.. 
PF10803 DUF2539;<br>Spore germination GerPB. Members of this family are required for formation of functionally normal spores. They may be involved in the establishment of spore coat structure or permeability  .. 
PF10804 Protein of unknown function (DUF2538) <br>This family of proteins has no known function.. 
PF10805 Protein of unknown function (DUF2730)<br>This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.. 
PF10806 Protein of unknown function (DUF2731)<br>This eukaryotic family of proteins has no known function.. 
PF10807 Protein of unknown function (DUF2541)<br>This family of proteins with unknown function appears to be restricted to Enterobacteriaceae. All proteins are annotated as YaaI precursor however currently no function is known.. 
PF10808 Protein of unknown function (DUF2542) <br>This family of proteins with unknown function appears to be restricted to Enterobacteriaceae. The family has a highly conserved sequence.. 
PF10809 Protein of unknown function (DUF2732)<br>This family of proteins has no known function.. 
PF10810 Protein of unknown function (DUF2545)   <br>This family of proteins with unknown function is restricted to Enterobacteriaceae. The sequence is highly conserved.. 
PF10811 Protein of unknown function (DUF2532)<br>This bacterial family of proteins has no known function.. 
PF10812 Protein of unknown function (DUF2561)<br>This family of proteins with unknown function appears to be restricted to Mycobacterium spp.. 
PF10813 Protein of unknown function (DUF2733)<br>This viral family of proteins has no known function.. 
PF10814 Protein of unknown function (DUF2562)<br>This protein of unknown function appears to be restricted to Mycobacterium spp.. 
PF10815 ComZ<br>ComZ is part of a two gene operon. It affects competence regulation by negatively affecting the transcription of the ComG operon. ComZ contains a leucine zipper motif  .. 
PF10816 Domain of unknown function (DUF2760)<br>Gunasekaran P, Mistry J. Pfam-B_001564 (release 23.0). This is a bacterial family of uncharacterised proteins.. 
PF10817 Protein of unknown function (DUF2563)<br>This family of proteins with unknown function appears to be restricted to Mycobacterium.. 
PF10818 Protein of unknown function (DUF2547)<br>This bacterial family of proteins has no known function.. 
PF10819 Protein of unknown function (DUF2564)     <br>This family of proteins with unknown function appears to be restricted to Bacillus spp.. 
PF10820 Protein of unknown function (DUF2543)<br>This family of proteins with unknown function appear to be restricted to Enterobacteriaceae. The family has a highly conserved sequence.. 
PF10821 Protein of unknown function (DUF2567)<br>This is a bacterial family of proteins with unknown function.. 
PF10823 Protein of unknown function (DUF2568)<br>One member in this family is annotated as yrdB which is part of a four gene operon however currently no function is known.. 
PF10824 Protein of unknown function (DUF2580)<br>This family of proteins with unknown function appears to be mainly found in actinobacteria.. 
PF10825 Protein of unknown function (DUF2752)<br>Gunasekaran P, Mistry J. Pfam-B_001601 (release 23.0). This family is conserved in bacteria. Many members are annotated as being putative membrane proteins.. 
PF10826 Protein of unknown function (DUF2551) <br>This Archaeal family of proteins has no known function.. 
PF10827 Protein of unknown function (DUF2552) <br>This bacterial family of proteins has no known function.. 
PF10828 Protein of unknown function (DUF2570)<br>This is a family of proteins with unknown function.. 
PF10829 Protein of unknown function (DUF2554)<br>This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.. 
PF10830 Protein of unknown function (DUF2553)<br>This family of bacterial proteins has no known function.. 
PF10831 Protein of unknown function (DUF2556)<br>This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.. 
PF10832 Protein of unknown function (DUF2559)<br>This family of proteins appear to be restricted to Enterobacteriaceae. The sequences are annotated as yhfG however currently no function is known.. 
PF10833 Protein of unknown function (DUF2572)<br>This bacterial family of proteins has no known function.. 
PF10834 Protein of unknown function (DUF2560)<br>This family of proteins has no known function.. 
PF10835 Protein of unknown function (DUF2573)<br>Some members in this bacterial family of proteins are annotated as YusU however no function is currently known. This family of proteins appears to be restricted to Bacillus spp.. 
PF10836 Protein of unknown function (DUF2574)  <br>This family of proteins appears to be restricted to Enterobacteriaceae. Members of the family are annotated as yehE however currently no function is known.. 
PF10837 Protein of unknown function (DUF2575)<br>This family of proteins appears to be restricted to Enterobacteriaceae. Members in the family are annotated as yaaY but currently there is no known function.. 
PF10838 Protein of unknown function (DUF2677)<br>Members in this family of proteins are annotated as UL121 however currently no function is known.. 
PF10839 Protein of unknown function (DUF2647)   <br>This eukaryotic family of proteins are annotated as ycf68 but have no known function.. 
PF10840 Protein of unknown function (DUF2645)<br>This family of proteins appear to be restricted to Enterobacteriaceae. Some members in the family are annotated as YjeO however no function for this protein is currently known.. 
PF10841 Protein of unknown function (DUF2644)<br>This family of proteins with unknown function appear to be restricted to Pasteurellaceae.. 
PF10842 Protein of unknown function (DUF2642)<br>This family of proteins with unknown function appear to be restricted to Bacillus spp.. 
PF10843 Protein of unknown function (DUF2578)<br>This is a Saccharomycete family of proteins with unknown function. The protein in S. cerevisiae is strongly induced in response to many stress conditions and is repressed in drug resistant yeast strains.. 
PF10844 Protein of unknown function (DUF2577)<br>This family of proteins has no known function. 
PF10845 Protein of unknown function (DUF2576)<br>The function of this viral family of proteins is unknown.. 
PF10846 Protein of unknown function (DUF2722)<br>This eukaryotic family of proteins has no known function.. 
PF10847 Protein of unknown function (DUF2656)<br>This bacterial family of proteins has no known function.. 
PF10848 Protein of unknown function (DUF2655)<br>This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.. 
PF10849 Protein of unknown function (DUF2654)<br>Some members in this family of proteins are annotated as a-gt.4 however currently no function is known.. 
PF10850 Protein of unknown function (DUF2653)<br>This family of proteins with unknown function appears to be restricted to Bacillus spp.. 
PF10851 Protein of unknown function (DUF2652)   <br>This family of proteins has no known function.. 
PF10852 Protein of unknown function (DUF2651)   <br>This family of proteins with unknown function appears to be restricted to Bacillus spp.. 
PF10853 Protein of unknown function (DUF2650)<br>This family of proteins with unknown function appear to be restricted to Caenorhabditis elegans.. 
PF10854 Protein of unknown function (DUF2649)<br>Members in this family of proteins are annotated as Plectrovirus orf 10 transmembrane proteins however currently no function is known.. 
PF10855 Protein of unknown function (DUF2648)<br>This family of proteins with unknown function appears to be restricted to Bacillales Staphylococcus.. 
PF10856 Protein of unknown function (DUF2678)<br>This family of proteins has no known function.. 
PF10857 Protein of unknown function (DUF2701)<br>This viral family of proteins has no known function.. 
PF10858 Protein of unknown function (DUF2659)<br>This bacterial family of proteins has no known function.. 
PF10859 Protein of unknown function (DUF2660)<br>This is a family of proteins with unknown function.. 
PF10860 Protein of unknown function (DUF2661)<br>This viral family of proteins have no known function.. 
PF10861 Protein of Unknown function (DUF2784)<br>Gunasekaran P, Mistry J. Pfam-B_001600 (release 23.0). This is a family of uncharacterised protein. The function is not known however it is conserved in Bacteria.. 
PF10862 DUF2662;<br>FcoT-like thioesterase domain. Proteins in this family have a HotDog fold. This family was formerly known as domain of unknown function 2662 (DUF2662). The structure of Rv0098 from M. tuberculosis   suggested a thioesterase function. Assays showed that this protein was a thioesterase with a preference for long chain fatty acyl groups  . The maximal Kcat was observed for palmitoyl-CoA although longer and shorter molecules were also cleaved. In solution this protein forms a homo-hexameric complex.. 
PF10863 Protein of unknown function (DUF2702)<br>This eukaryotic family of proteins has no known function.. 
PF10864 Protein of unknown function (DUF2663)<br>Some members in this family of proteins are annotated as YpbF however currently no function is known.. 
PF10865 Domain of unknown function (DUF2703)<br>This family of protein has no known function, but it may be distantly related to the thioredoxin fold. It contains the CXXC motif that is characteristic of thioredoxins.. 
PF10866 Protein of unknown function (DUF2704)<br>This viral family of proteins has no known function.. 
PF10867 Protein of unknown function (DUF2664)<br>This family of proteins is a viral family, annotated as UL96. Currently no function is known.. 
PF10868 Protein of unknown function (DUF2667)<br>This family of proteins with unknown function appears to be restricted to Arabidopsis thaliana.. 
PF10869 Protein of unknown function (DUF2666) <br>This Archaeal family of proteins has no known function.. 
PF10870 Protein of unknown function (DUF2729)<br>This viral family of proteins has no known function.. 
PF10871 Protein of unknown function (DUF2748)<br>This is a bacterial family of proteins with unknown function.. 
PF10872 Protein of unknown function (DUF2740)<br>This family of proteins with unknown function has a highly conserved sequence.. 
PF10873 Protein of unknown function (DUF2668)<br>Members in this family of proteins are annotated as Cysteine and tyrosine-rich protein 1, however currently no function is known.. 
PF10874 Protein of unknown function (DUF2746)<br>This family of proteins has no known function.. 
PF10875 Protein of unknown function (DUF2670)<br>This bacterial family of proteins has no known function.. 
PF10876 Protein of unknown function (DUF2669)<br>This family of proteins has no known function.. 
PF10877 Protein of unknown function (DUF2671)<br>This family of proteins with unknown function appears to be restricted to Rickettsia spp.. 
PF10878 Protein of unknown function (DUF2672)<br>This family of proteins with unknown function appear to be restricted to Rickettsiae.. 
PF10879 Protein of unknown function (DUF2674)<br>This family of proteins with unknown function appears to be conserved to Rickettsia spp.. 
PF10880 Protein of unknown function (DUF2673)<br>This family of proteins with unknown function appears to be restricted to Rickettsiae spp.. 
PF10881 Protein of unknown function (DUF2726)<br>This bacterial family of proteins has no known function.. 
PF10882 DUF2679;<br>This family of proteins with unknown function appear to be related to bacterial PH domains. This family was formerly known as DUF2679.. 
PF10883 Protein of unknown function (DUF2681)<br>This family of proteins is found in bacteria. Proteins in this family are typically between 81 and 117 amino acids in length.. 
PF10884 Protein of unknown function (DUF2683)<br>This family of proteins with unknown function appears to be restricted to Methanosarcinaceae.. 
PF10885 Protein of unknown function (DUF2684)<br>Members in this family of proteins are annotated as yqgD however currently no function is known.. 
PF10886 Protein of unknown function (DUF2685)<br>Members in this family of proteins are annotated as uvdY.-2 which is an open reading frame within uvsY. However currently there is no known function.. 
PF10887 Protein of unknown function (DUF2686)<br>Some members in this family of proteins are annotated as yjfZ however currently no function is known.. 
PF10888 Protein of unknown function (DUF2742)<br>Members in this family of phage proteins are the product of the gene phiRv1, however no function is known.. 
PF10890 Protein of unknown function (DUF2741)<br>Members in this family of proteins are annotated as ubiquinol-cytochrome C reductase however this cannot be confirmed.. 
PF10891 Protein of unknown function (DUF2719)<br>This family of proteins with unknown function appears to be restricted to Nucleopolyhedrovirus.. 
PF10892 Protein of unknown function (DUF2688)<br>Members in this family of proteins are annotated as KleB however currently no function is known.. 
PF10893 Protein of unknown function (DUF2724)<br>This is a family of proteins with unknown function.. 
PF10894 Protein of unknown function (DUF2689)<br>Members in this family of proteins are annotated as TrbD however currently no function is known.. 
PF10895 Protein of unknown function (DUF2715)<br>This family of proteins with unknown function appears to be restricted to Treponema pallidum.. 
PF10896 Protein of unknown function (DUF2714)<br>This family of proteins with unknown function appears to be restricted to Mycoplasmataceae.. 
PF10897 Protein of unknown function (DUF2713)<br>This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.. 
PF10898 Protein of unknown function (DUF2716)<br>This bacterial family of proteins has no known function.. 
PF10899 Protein of unknown function (DUF2743)<br>This is a bacterial family of proteins with unknown function.. 
PF10901 Protein of unknown function (DUF2690)<br>This bacterial family of proteins has no known function.. 
PF10902 Protein of unknown function (DUF2693)<br>This viral family of proteins has no known function.. 
PF10903 Protein of unknown function (DUF2691)<br>This bacterial family of proteins has no known function.. 
PF10904 Protein of unknown function (DUF2694)<br>This family of proteins with unknown function appears to be restricted to Mycobacterium spp.. 
PF10905 Protein of unknown function (DUF2695)<br>This bacterial family of proteins has no known function.. 
PF10906 Protein of unknown function (DUF2697)<br>This is a eukaryotic family of proteins with unknown function.. 
PF10907 Protein of unknown function (DUF2749)<br>This bacterial family of proteins appear to come from the Trb operon however currently no function is known.. 
PF10908 Protein of unknown function (DUF2778)<br>Gunasekaran P, Mistry J. Pfam-B_001575 (release 23.0). This is a bacterial family of uncharacterised proteins.. 
PF10909 Protein of unknown function (DUF2682)<br>This viral family of proteins has no known function.. 
PF10910 Protein of unknown function (DUF2744)<br>This is a viral family of proteins with unknown function.. 
PF10911 Protein of unknown function (DUF2717)<br>Members in this family of proteins are annotated as gene 6.5 protein however currently there is no known function.. 
PF10912 Protein of unknown function (DUF2700)<br>This family of proteins with unknown function appears to be restricted to Caenorhabditis elegans.. 
PF10913 Protein of unknown function (DUF2706)<br>This family of proteins with unknown function appears to be restricted to Rickettsia spp.. 
PF10914 Protein of unknown function (DUF2781)<br>Gunasekaran P, Mistry J. Pfam-B_001738 (release 23.0). This is a eukaryotic family of uncharacterised proteins.  Some of the proteins in this family are annotated as membrane proteins.. 
PF10915 Protein of unknown function (DUF2709)<br>This bacterial family of proteins has no known function.. 
PF10916 Protein of unknown function (DUF2712)<br>This family of proteins with unknown function appear to be restricted to Bacillales.. 
PF10917 Protein of unknown function (DUF2708)<br>This family of proteins with unknown function appears to be restricted to Caenorhabditis elegans.. 
PF10918 Protein of unknown function (DUF2718)<br>This viral family of proteins has no known function.. 
PF10920 Protein of unknown function (DUF2705)<br>This bacterial family of proteins has no known function.. 
PF10921 Protein of unknown function (DUF2710)<br>This family of proteins with unknown function appears to be restricted to Mycobacteriaceae.. 
PF10922 Protein of unknown function (DUF2745)<br>This is a viral family of proteins with unknown function.. 
PF10923 P-loop Domain of unknown function (DUF2791)<br>Gunasekaran P, Mistry J. Pfam-B_001611 (release 23.0). This is a family of proteins found in archaea and bacteria. This domain contains a P-loop motif suggesting it binds to a nucleotide such as ATP.. 
PF10924 Protein of unknown function (DUF2711)<br>Some members in this family of proteins are annotated as ywbB however currently there is no known function.. 
PF10925 Protein of unknown function (DUF2680)<br>Members in this family of proteins are annotated as yckD however currently no function is known.. 
PF10926 Protein of unknown function (DUF2800)<br>Gunasekaran P, Mistry J. Pfam-B_001630 (release 23.0). This is a family of uncharacterised proteins found in bacteria and viruses. Some members of this family are annotated as being Phi APSE P51-like proteins.. 
PF10927 Protein of unknown function (DUF2738)<br>This is a viral family of proteins with unknown function.. 
PF10928 Protein of unknown function (DUF2810)<br>Gunasekaran P, Mistry J. Pfam-B_001682 (release 23.0). This is a bacterial family of uncharacterised proteins.. 
PF10929 Protein of unknown function (DUF2811)<br>Gunasekaran P, Mistry J. Pfam-B_001693 (release 23.0). This is a bacterial family of uncharacterised proteins.. 
PF10930 Protein of unknown function (DUF2737)<br>This family of proteins has no known function.. 
PF10931 Protein of unknown function (DUF2735)<br>Some members in this family of proteins are annotated as glutamine synthetase translation inhibitor however this function can not be confirmed.. 
PF10932 Protein of unknown function (DUF2783)<br>Gunasekaran P, Mistry J. Pfam-B_001590 (release 23.0). This is a bacterial family of uncharacterised protein.. 
PF10933 Protein of unknown function (DUF2827)<br>Gunasekaran P, Mistry J. Pfam-B_001771 (release 23.0). This is a family of uncharacterised proteins found in Burkholderia.. 
PF10934 Protein of unknown function (DUF2634)<br>Some members in this family of proteins are annotated as phage related, xkdS however currently there is no known function.. 
PF10935 Protein of unknown function (DUF2637)<br>This family of proteins has no known function.. 
PF10936 Protein of unknown function DUF2617<br>This bacterial family of proteins has no known function.  . 
PF10937 Protein of unknown function (DUF2638)<br>This family of proteins has no known function.. 
PF10938 YfdX protein<br>YfdX is a protein found in Proteobacteria of unknown function. The protein coding for this gene is regulated by EvgA in E. coli  .. 
PF10939 Protein of unknown function (DUF2631)   <br>This is s bacterial family of proteins with unknown function.. 
PF10940 Protein of unknown function (DUF2618)<br>This bacterial family of proteins has no known function. The sequences within the family are highly conserved.. 
PF10941 Protein of unknown function DUF2620<br>This is a bacterial family of proteins with unknown function.. 
PF10942 Protein of unknown function (DUF2619)<br>This bacterial family of proteins has no known function.. 
PF10943 Protein of unknown function (DUF2632)<br>This is a family of membrane proteins with unknown function.. 
PF10944 Protein of unknown function (DUF2630)<br>This bacterial family of proteins have no known function.. 
PF10945 Protein of unknown function (DUF2629)<br>Some members in this family of proteins are annotated as yhjR however currently no function is known.. 
PF10946 Protein of unknown function DUF2625<br>Some members in this family of proteins are annotated as ybfG however currently no function is known.. 
PF10947 Protein of unknown function (DUF2628)    <br>Some members in this family of proteins are annotated as yigF however currently no function is known.. 
PF10948 Protein of unknown function (DUF2635)<br>This is a family of phage proteins with unknown function.. 
PF10949 Protein of unknown function (DUF2777)<br>This family of proteins with unknown function appears to be restricted to Bacillus cereus.. 
PF10950 Protein of unknown function (DUF2775)<br>This eukaryotic family of proteins has no known function.. 
PF10951 Protein of unknown function (DUF2776)<br>This bacterial family of proteins has no known function.. 
PF10952 Protein of unknown function (DUF2753)<br>This bacterial family of proteins has no known function.. 
PF10953 Protein of unknown function (DUF2754)<br>This family of proteins with unknown function appear to be restricted to Enterobacteriaceae.. 
PF10954 Protein of unknown function (DUF2755)<br>Some members in this family of proteins are annotated as YaiY however no function is known. The family appears to be restricted to Enterobacteriaceae.. 
PF10955 Protein of unknown function (DUF2757)<br>Members in this family of proteins are annotated as YabK however currently no function is known.. 
PF10956 Protein of unknown function (DUF2756)<br>Some members in this family of proteins are annotated yhhA however currently no function is known. The family appears to be restricted to Enterobacteriaceae.. 
PF10957 Protein of unknown function (DUF2758)<br>This family of proteins has no known function.. 
PF10958 Protein of unknown function (DUF2759)<br>This family of proteins with unknown function appear to be restricted to Bacillaceae.. 
PF10959 Protein of unknown function (DUF2761)<br>Members in this family of proteins are annotated as KleF however no function is known.. 
PF10960 Protein of unknown function (DUF2762)<br>Members in this family of proteins are annotated as holin-like protein BhlA however this cannot be confirmed.. 
PF10961 Protein of unknown function (DUF2763)<br>This eukaryotic family of proteins has no known function.. 
PF10962 Protein of unknown function (DUF2764)<br>This bacterial family of proteins has no known function.. 
PF10963 Protein of unknown function (DUF2765)<br>This family of proteins has no known function.. 
PF10964 Protein of unknown function (DUF2766)<br>This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.. 
PF10965 Protein of unknown function (DUF2767)<br>This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.. 
PF10966 Protein of unknown function (DUF2768)<br>This family of proteins with unknown function appear to be restricted to Bacillus spp.. 
PF10967 Protein of unknown function (DUF2769)<br>This family of proteins have no known function.. 
PF10968 Protein of unknown function (DUF2770)<br>Members in this family of proteins are annotated as yceO however currently no function is known.. 
PF10969 Protein of unknown function (DUF2771)<br>This bacterial family of proteins has no known function.. 
PF10970 Protein of unknown function (DUF2772)<br>Members in this family of proteins are annotated as spore germination protein GE however this cannot be confirmed.. 
PF10971 Protein of unknown function (DUF2773)<br>This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.. 
PF10972 Protein of unknown function (DUF2803)<br>Pfam-B_1049 (release 23.0). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.. 
PF10973 Protein of unknown function (DUF2799)<br>Pfam-B_1111 (release 23.0). Some members in this family of proteins are annotated as yfiL which has no known function.. 
PF10974 Protein of unknown function (DUF2804)<br>Pfam-B_1045 (release 23.0). This is a family of proteins with unknown function.. 
PF10975 Protein of unknown function (DUF2802)<br>Pfam-B_1126 (release 23.0). This bacterial family of proteins has no known function.. 
PF10976 Protein of unknown function (DUF2790)<br>Pfam-B_1206 (release 23.0). This family of proteins with unknown function appear to be restricted to Pseudomonadaceae.. 
PF10977 Protein of unknown function (DUF2797)<br>Pfam-B_1162 (release 23.0). This family of proteins has no known function.. 
PF10978 Protein of unknown function (DUF2785)<br>Pfam-B_1219 (release 23.0). Some members in this family are annotated as hypothetical membrane spanning proteins however this cannot be confirmed. The family has no known function.. 
PF10979 Protein of unknown function (DUF2786)<br>Pfam-B_1231 (release 23.0). This family of proteins has no known function.. 
PF10980 Protein of unknown function (DUF2787)<br>Pfam-B_1249 (release 23.0). This bacterial family of proteins has no known function.. 
PF10981 Protein of unknown function (DUF2788)<br>Pfam-B_1255 (release 23.0). This bacterial family of proteins have no known function.. 
PF10982 Protein of unknown function (DUF2789)<br>Pfam-B_1269 (release 23.0). This bacterial family of proteins has no known function.. 
PF10983 Protein of unknown function (DUF2793)<br>Pfam-B_1370 (release 23.0). This is a bacterial family of proteins with unknown function.. 
PF10984 Protein of unknown function (DUF2794)<br>Pfam-B_1384 (release 23.0). This is a bacterial family of proteins with unknown function.. 
PF10985 Protein of unknown function (DUF2805)<br>Pfam-B_001474 (release 23.0). This is a bacterial family of proteins with unknown function.. 
PF10986 Protein of unknown function (DUF2796)<br>Pfam-B_1354 (release 23.0). This bacterial family of proteins has no known function.. 
PF10987 Protein of unknown function (DUF2806)<br>Pfam-B_001505 (release 23.0). This bacterial family of proteins has no known function.. 
PF10988 Protein of unknown function (DUF2807)<br>Pfam-B_001516 (release 23.0). This bacterial family of proteins shows structural similarity to other pectin lyase families. Although structures from this family align with acetyl-transferases, there is no conservation of catalytic residues found. It is likely that the function is one of cell-adhesion. In PDB:3jx8, it is interesting to note that the sequence of contains several well defined sequence repeats, centred around GSG motifs defining the tight beta turn between the two sheets of the super-helix; there are 8 such repeats in the C-terminal half of the protein, which could be grouped into 4 repeats of two.  It seems likely that this family belongs to the superfamily of trimeric autotransporter adhesins (TAAs), which are important virulence factors in Gram-negative pathogens    .  In the case of Parabacteroides distasonis, which is a cmoponent of the normal distal human gut microbiota, TAA-like complexes probably modulate adherence to the host (information derived from TOPSAN).. 
PF10989 Protein of unknown function (DUF2808)<br>Pfam-B_001529 (release 23.0). This family of proteins with unknown function appears to be restricted to Cyanobacteria.. 
PF10990 Protein of unknown function (DUF2809)<br>Pfam-B_001533 (release 23.0). Some members in this family of proteins are annotated as yjgA however currently no function for the protein is known.. 
PF10991 Protein of unknown function (DUF2815)<br>Pfam-B_002212 (release 23.0). This is a phage related family of proteins with unknown function.. 
PF10992 Protein of unknown function (DUF2816)<br>Pfam-B_002257 (release 23.0). This eukaryotic family of proteins has no known function.. 
PF10993 Protein of unknown function (DUF2818)<br>Pfam-B_002280 (release 23.0). This bacterial family of proteins has no known function.. 
PF10994 Protein of unknown function (DUF2817)<br>Pfam-B_002258 (release 23.0). This family of proteins has no known function.. 
PF10995 Protein of unknown function (DUF2819)<br>Pfam-B_002304 (release 23.0). This bacterial family of proteins has no known function.. 
PF10996 Beta-Casp domain<br>The beta-CASP domain is found C terminal to the beta-lactamase domain in pre-mRNA 3'-end-processing endonuclease.  The active site of this enzyme is located at the interface of these two domains  .. 
PF10997 Protein of unknown function (DUF2837)<br>Pfam-B_002349 (release 23.0). This bacterial family of proteins has no known function.. 
PF10998 Protein of unknown function (DUF2838)<br>Pfam-B_002381 (release 23.0). This bacterial family of proteins has no known function.. 
PF10999 Protein of unknown function (DUF2839)<br>Pfam-B_002396 (release 23.0). This bacterial family of unknown function appear to be restricted to Cyanobacteria.. 
PF11000 Protein of unknown function (DUF2840)<br>Pfam-B_002399 (release 23.0). This bacterial family of proteins have no known function.. 
PF11001 Protein of unknown function (DUF2841)<br>Pfam-B_002409 (release 23.0). This family of proteins with unknown function are all present in yeast.. 
PF11002 RFPL defining motif (RDM)<br>Mistry J, Bonnefont J. The RDM domain is found on RFPL (Ret finger protein like) proteins.  In humans, RFPL transcripts can be detected at the onset of neurogenesis in differentiating human embryonic stem cells, and in the developing human neocortex  .  The RDM domain is thought to have emerged from a neofunctionalisation event.  It is found N terminal to the SPRY domain (Pfam:PF00622).. 
PF11003 Protein of unknown function (DUF2842)<br>Pfam-B_002411 (release 23.0). This bacterial family of proteins have no known function.. 
PF11004 DUF2843;<br>3-deoxy-D-manno-oct-2-ulosonic acid (Kdo) hydroxylase. Pfam-B_002426 (release 23.0). This is a family of 3-deoxy-D-manno-oct-2-ulosonic acid 3-hydroxylases, which catalyse the conversion of 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo) to D-glycero-D-talo-oct-2-ulosonic acid (Ko). It contains a potential iron-binding motif, HXDX(n)H (n>40). Hydroxylation activity is iron-dependent  .. 
PF11005 Protein of unknown function (DUF2844)<br>Pfam-B_002433 (release 23.0). This bacterial family of proteins has no known function.. 
PF11006 Protein of unknown function (DUF2845)<br>Pfam-B_002437 (release 23.0). This bacterial family of proteins has no known function.. 
PF11007 Spore coat associated protein JA (CotJA)<br>CotJA is part of the CotJ operon which contains CotJA and CotJC. The operon encodes spore coat proteins. Interaction of CotJA with CotJC is required for the assembly of both CotJA and CotJC into the spore coat  .. 
PF11008 Protein of unknown function (DUF2846)<br>Pfam-B_002451 (release 23.0). Some members in this family of proteins with unknown function are annotated as lipoproteins however this cannot be confirmed.. 
PF11009 Protein of unknown function (DUF2847)<br>Pfam-B_002453 (release 23.0). Some members in this bacterial family of proteins with unknown function are annotated as YtxJ, a putative general stress protein. This cannot be confirmed.. 
PF11010 Protein of unknown function (DUF2848)<br>Pfam-B_002463 (release 23.0). This bacterial family of proteins has no known function.. 
PF11011 Protein of unknown function (DUF2849)<br>Pfam-B_002560 (release 23.0). This bacterial family of proteins has no known function.. 
PF11012 Protein of unknown function (DUF2850)<br>Pfam-B_002587 (release 23.0). This family of proteins with unknown function appear to be restricted to Vibrionaceae.. 
PF11013 Protein of unknown function (DUF2851)<br>Pfam-B_002589 (release 23.0). This bacterial family of proteins has no known function.. 
PF11014 Protein of unknown function (DUF2852)<br>Pfam-B_002611 (release 23.0). This bacterial family of proteins has no known function.. 
PF11015 Protein of unknown function (DUF2853)<br>Pfam-B_002619 (release 23.0). This bacterial family of proteins has no known function.. 
PF11016 Protein of unknown function (DUF2854)<br>Pfam-B_002643 (release 23.0). This family of proteins has no known function.. 
PF11017 Protein of unknown function (DUF2855)<br>Pfam-B_002665 (release 23.0). This family of proteins has no known function.. 
PF11018 Pupal cuticle protein C1<br>Insect cuticles are composite structures whose mechanical properties are optimised for biological function.  The major components are the chitin filament system and the cuticular proteins, and the cuticle's properties are determined largely by the interactions between these two sets of molecules. The proteins can be ordered by species.. 
PF11019 Protein of unknown function (DUF2608)<br>This family is conserved in Bacteria. The function is not known.. 
PF11020 Domain of unknown function (DUF2610)<br>This family is conserved in Proteobacteria. One member is annotated as being elongation factor P but this could not be confirmed. This domain is related to the Ribbon-helix-helix superfamily so may be a DNA-binding protein.. 
PF11021 Protein of unknown function (DUF2613)<br>This is a family of putative small secreted proteins expressed by Actinobacteria. The function is not known.. 
PF11022 Protein of unknown function (DUF2611)<br>This family is conserved in the Dikarya of Fungi. The function is not known.. 
PF11023 Protein of unknown function (DUF2614)<br>This is a family of proteins conserved in the Bacillaceae family. Some members are annotated as being protein YgzB. The function is not known.. 
PF11024 Dispersed gene family protein 1 of Trypanosoma cruzi region 4<br>Pfam-B_187 (release 23.0). This protein is likely to be highly expressed, and is expressed from the sub-telomeric region. However, the function is not known. Other domains on this protein include DGF-1_N, DGF-1_2, and DGF-1_5. This domain is just downstream from the C-terminus, but not the C-terminus of proteins, also annotated as being DGF-1, that constitute family DGF-1_C.. 
PF11025 Glycoprotein GP40 of Cryptosporidium<br>Pfam-B_197 (release 23.0). This family is highly conserved in Cryptosporidium spp.  Many members are annotated as being a 60 kDa glycoprotein.. 
PF11026 Protein of unknown function (DUF2721)<br>Pfam-B_520 (release 23.0). This family is conserved in bacteria. The function is not known.. 
PF11027 Protein of unknown function (DUF2615)<br>This small. approximately 100 residue, family is conserved from worms to humans. It is cysteine-rich with a characteristic FDxCEC sequence motif. The function is not known.. 
PF11028 Protein of unknown function (DUF2723)<br>Pfam-B_590 (release 23.0). This family is conserved in bacteria.  The function is not known.. 
PF11029 DAZ associated protein 2 (DAZAP2)<br>DAZ associated protein 2 has a highly conserved sequence throughout evolution including a conserved polyproline region and several SH2/SH3 binding sites. It occurs as a single copy gene with a four-exon organisation and is located on chromosome 12. It encodes a ubiquitously expressed protein and binds to DAZ and DAZL1 through DAZ repeats [1,2].. 
PF11030 Nucleocapsid protein N   <br>This is the N protein of the nucleocapsid. The nucleocapsid functions to protect the RNA against nuclease degradation and to promote it's reverse transcription  . The NC protein promotes viral RNA dimerisation and encapsidation and initiates reverse transcription by activating the annealing of the primer tRNA to the initiation site  .. 
PF11031 Bacteriophage T holin<br>Bacteriophage effects host lysis with T holin along with an endolysin. T disrupts the membrane allowing sequential events which lead to the attack of the peptidoglycan. T has an usual periplasmic domain which transduces environmental information for the real-time control of lysis timing  .. 
PF11032 Apolipoprotein M (ApoM)<br>ApoM is a 25 kDa plasma protein associated with high-density lipoproteins (HDLs). ApoM is important in the formation of pre-ss-HDL and also in increasing cholesterol efflux from macrophage foam cells  . Lipoproteins consist of lipids solubilized by apolipoproteins. ApoM lacks an external amphipathic motif and is uniquely secreted to plasma without cleavage of its terminal signal peptide  .. 
PF11033 Competence protein J (ComJ)<br>ComJ is a competence specific protein  .. 
PF11034 Protein of unknown function (DUF2823)<br>This family of proteins are possible glucose repressible proteins however this cannot be confirmed. Currently, no function is known.. 
PF11035 Small nuclear RNA activating complex subunit 2-like<br>This family of proteins is SnAPC subunit 2-like. SnAPC allows the transcription of human small nuclear RNA genes to occur by recognition of the proximal sequence element  .. 
PF11036 Virulence promoting factor<br>YqgB encodes adaptive factors that acts in synergy with vqfZ , enabling the bacteria to cope with the physical environment in vivo, facilitating colonisation of the host  .. 
PF11037 Insulin-resistance promoting peptide in skeletal muscle<br>Musclin is a muscle derived secretory peptide which induces insulin resistance in vitro. It encodes a 130 amino acid sequence including a NH(2) terminal 30 amino acid signal sequence. Musclin expression level is tightly regulated by nutritional changes [1,2].. 
PF11038 Dispersed gene family protein 1 of Trypanosoma cruzi region 5<br>Pfam-B_157 (release 23.0). This protein is likely to be highly expressed, and is expressed from the sub-telomeric region. However, the function is not known.  Other domains on this protein include DGF-1_N, DGF-1_2, and DGF-1_4. This domain is just downstream from the C-terminus, but not the C-terminus of proteins, also annotated as being DGF-1, that constitute family DGF-1_C.. 
PF11039 Protein of unknown function (DUF2824)<br>This family of proteins has no known function. Some members in the family are annotated as the P22 head assembly protein gp14 however this cannot be confirmed.. 
PF11040 Dispersed gene family protein 1 of Trypanosoma cruzi C-terminus <br>Pfam-B_30 (release 23.0). This protein is likely to be highly expressed, and is expressed from the sub-telomeric region. However, the function is not known. This is the very C-terminal part of the protein.. 
PF11041 Protein of unknown function (DUF2612)<br>This is a phage protein family expressed from a range of Proteobacteria species. The function is not known.. 
PF11042 Protein of unknown function (DUF2750)<br>Pfam-B_609 (release 23.0). This family is conserved in Proteobacteria. The function is not known.. 
PF11043 Protein of unknown function (DUF2856)<br>Some members in this viral family of proteins with unknown function are annotated as Abc2 however this cannot be confirmed.. 
PF11044 Plectrovirus spv1-c74 ORF 12 transmembrane protein<br>This is a family of proteins expressed by Plectroviruses. The plectroviruses are single-stranded DNA viruses belonging to the Inoviridae. Except that it is a putative transmembrane protein the function is not known.. 
PF11045 Putative inner membrane protein of Enterobacteriaceae<br>This family is conserved in the Enterobacteriaceae. It is a putative inner membrane protein, named YbjM, but the function is not known.. 
PF11046 Transcriptional repressor of hyc and hyp operons<br>This family is conserved in Proteobacteria. It is likely to be the transcriptional repressor molecule for the hyc and hyp operons, which express, amongst others, the protein HycA. This protein may be harnessed for the reduction of technetium oxide, an unwelcome product of radio-nucleotide bioaccumulation. HycA produces formate hydrogenlyase, one of the key proteins necessary for metal compound reduction  .. 
PF11047 Salmonella outer protein D<br>SopD is a type III virulence effector protein whose structure consists of 38% alpha-helix and 26% beta-strand.. 
PF11049 Glycoprotein K1 of Kaposi's sarcoma-associated herpes virus<br>Pfam-B_38 (release 23.0). This is a highly glycosylated cytoplasmic and membrane protein similar to the immunoglobulin receptor family that is expressed as an inducible early-lytic-cycle gene product in primary effusion lymphoma cell-lines. This domain would appear to be the cytoplasmic region of the protein  .. 
PF11050 Virus envelope protein E26<br>E26 is a multifunctional protein. One form of E26 associates with viral DNA or DNA binding proteins, while a second form associates with intracellular membranes  .. 
PF11051 Mannosyltransferase putative<br>Pfam-B_379 (release 23.0). This family is conserved in fungi. Several members are annotated as being alpha-1,3-mannosyltransferase but this could not be confirmed.. 
PF11052 Trans-sialidase of Trypanosoma hydrophobic C-terminal<br>Pfam-B_103 (release 23.0). This is a highly conserved sequence motif that is the very C-terminus of a number of more diverse proteins from Trypanosoma cruzi. All members of the family are annotated putatively as being trans-sialidase but this appears to be a diverse group.. 
PF11053 Terminase DNA packaging enzyme<br>Phage T4 terminase functions in packaging concatemeric DNA. The T4 terminase is composed of a large subunit, gp17 ad a small subunit, gp16. The role of gp16 is not well characterised however it is known that it binds to double-stranded DNA but not single stranded DNA  .. 
PF11054 Sporozoite TA4 surface antigen<br>This family of proteins is a Eukaryotic family of surface antigens. One of the better characterised members of the family is the sporulated TA4 antigen. The TA4 gene encodes a single polypeptide of 25 kDa which contains a 17 and a 8 kD polypeptide  .. 
PF11055 Glucose signalling factor 2<br>Gsf2 is localised to the ER and functions to promote the secretion of certain hexose transporters  .. 
PF11056 Recombination, repair and ssDNA binding protein UvsY<br>UvsY protein enhances the rate of single-stranded-DNA-dependant ATP hydrolysis by UvsX protein. The enhancement of ATP hydrolysis by UvsY protein is shown to result from the ability of UvsY protein to increase the affinity of UvsX protein for single-stranded DNA  .. 
PF11057 Cortexin of kidney<br>In the middle of cortexin protein there is a single membrane-spanning domain which indicates that this protein may be a membrane protein involved in intracellular or extracellular signalling of the kidney or brain, since it is expressed specifically in the kidneys and brain only. The protein is highly conserved among species  . Cortexin is also thought to be important to neurons of both the developing and adult cerebral cortex  .. 
PF11058 Antirestriction protein Ral <br>Ral alleviates restriction and enhances modification by the E.Coli restriction and modification system  .. 
PF11059 Protein of unknown function (DUF2860)<br>Pfam-B_002667 (release 23.0). This bacterial family of proteins has no known function.. 
PF11060 Protein of unknown function (DUF2861)<br>Pfam-B_002683 (release 23.0). This bacterial family of proteins has no known function.. 
PF11061 Protein of unknown function (DUF2862)<br>Pfam-B_003005 (release 23.0). This family of proteins has no known function.. 
PF11062 Protein of unknown function (DUF2863)<br>Pfam-B_002981 (release 23.0). This bacterial family of proteins have no known function.. 
PF11064 Protein of unknown function (DUF2865)<br>Pfam-B_002953 (release 23.0). This bacterial family of proteins has no known function.. 
PF11065 Protein of unknown function (DUF2866)<br>Pfam-B_002950 (release 23.0). This bacterial family of proteins have no known function.. 
PF11066 Protein of unknown function (DUF2867)<br>Pfam-B_002931 (release 23.0). This bacterial family of proteins have no known function.. 
PF11067 Protein of unknown function (DUF2868)<br>Pfam-B_002930 (release 23.0). Some members in this family of proteins with unknown function are annotated as putative membrane proteins. However, this cannot be confirmed.. 
PF11068 DUF2869;<br>Pfam-B_002915 (release 23.0). The structure of a representative of this family has been solved (pdb:4dci) and found to form a tetrameric structure of prefoldin-like architecture with the beta-barrel core and helical coiled coil tentacles. This suggests that this family may act as molecular chaperones.. 
PF11069 Protein of unknown function (DUF2870)<br>Pfam-B_002904 (release 23.0). This is a eukaryotic family of proteins with unknown function.. 
PF11070 Protein of unknown function (DUF2871)<br>Pfam-B_002884 (release 23.0). This family of proteins has no known function.. 
PF11071 Protein of unknown function (DUF2872)<br>Pfam-B_002883 (release 23.0). This bacterial family of proteins has no known function.. 
PF11072 Protein of unknown function (DUF2859)<br>Gunasekaran P, Mistry J. Pfam-B_001915 (release 23.0). This is a bacterial family of uncharacterised proteins.. 
PF11073 Rift valley fever virus non structural protein (NSs) like <br>Gunasekaran P, Mistry J. Pfam-B_001643 (release 23.0). This family contains several Phlebovirus non structural proteins which act as a major determinant of virulence by antagonising interferon beta gene expression  .. 
PF11074 Domain of unknown function(DUF2779)<br>Gunasekaran P, Mistry J. Pfam-B_001581 (release 23.0). This domain is conserved in bacteria. The function is not known.. 
PF11075 Protein of unknown function VcgC/VcgE (DUF2780)<br>Gunasekaran P, Mistry J. Pfam-B_001695 (release 23.0). This is a bacterial family of uncharacterised proteins.. 
PF11076 Putative inner membrane protein YbhQ<br>This family is conserved in Proteobacteria. The function is not known but most members are annotated as being inner membrane protein YbhQ.. 
PF11077 Protein of unknown function (DUF2616)<br>This cysteine-rich family is expressed by the double-stranded Nucleopolyhedrovirus, a member of the Baculoviridae family of dsDNA viruses.  The function is not known.. 
PF11078 Optomotor-blind protein N-terminal region<br>Pfam-B_595 (release 23.0). This family is conserved in Drosophila spp. Optomotor-blind is one of the essential toolkit proteins for coordinating development in diverse animal taxa, and in Drosophila it plays a key role in establishing the abdominal pigmentation pattern, in development of the central nervous system and leg and wing imaginal disc-formation of Drosophila melanogaster. This is the N-terminal region of the protein and does not include the T-box-containing transcription factor that plays a part in DNA-binding.. 
PF11079 Bacterial protein YqhG of unknown function<br>This family of putative proteins is conserved in the Bacillaceae family of the Firmicutes. The function is not known.. 
PF11080 Protein of unknown function (DUF2622)<br>This family is conserved in the Enterobacteriaceae family. Several members are named as YdiZ, a putative cytoplasmic protein. The function is not known.. 
PF11081 Protein of unknown function (DUF2890)<br>Pfam-B_629 (release 23.0). This family is conserved in dsDNA adenoviruses of vertebrates. The function is not known.. 
PF11082 Protein of unknown function (DUF2880)<br>Pfam-B_001492 (release 23.0). This bacterial family of proteins has no known function.. 
PF11083 Lantibiotic streptin immunity protein<br>Pfam-B_43518 (release 22.0). Streptococcal species produce a lantibiotic, streptin, in a similar manner to the production of nisin and subtilin by other lactic acid bacteria, in order to compete against competing bacteria within the environment. The immunity protein protects the bacterium from destruction by its own lantibiotic. In general, there is little homology between the immunity proteins of different genera of bacteria.. 
PF11084 Protein of unknown function (DUF2621)<br>Mistrey J, Coggill P. This family is conserved in the Bacillaceae family.  Several members are named as YneK. The function is not known.. 
PF11085 Conserved membrane protein YqhR<br>This family is conserved in the Bacillaceae family of the Firmicutes. The function is not known.. 
PF11086 Protein of unknown function (DUF2878)<br>Pfam-B_001539 (release 23.0). This bacterial family of proteins has no known function. Some members annotate the proteins as the permease component of a Mn2+/Zn2+ transport system however this cannot be confirmed.. 
PF11087 Protein of unknown function (DUF2881)<br>This viral family of proteins has no known function. Some members are annotated as p34 however this cannot be confirmed.. 
PF11088 Glycoprotein encoding membrane proteins RL5A and RL6<br>RL5A and RL6 are part of the RL11 family which are predicted to encode membrane glycoproteins. Two adjacent open reading frames potentially encode a domain that is the hallmark of proteins encoded by the RL11 family.. 
PF11089 Exopolysaccharide production repressor<br>SyrA is a small protein located in the cytoplasmic membrane that lacks an apparent DNA binding domain. SyrA mediates the transcriptional up-regulation of exo genes involved in the biosynthesis of the symbiotic exopolysaccharide succinoglycan. It does this through a mechanism which requires a two component system  .. 
PF11090 Protein of unknown function (DUF2833)<br>This family of proteins with unknown function are found in the bacteriophage T7. Some of the members of this family are annotated as gene 13 protein.. 
PF11091 Tail-tube assembly protein<br>This tail tube protein is also referred to as Gp48. It is required for the assembly and length regulation of the tail tube of bacteriophage T4  .. 
PF11092 Neuronal protein 3.1 (p311)<br>P311 has several PEST-like motifs and is found in neuron and muscle cells. P311 could have some function in myo-fibroblast transformation and prevention of fibrosis  . It has also been identified as a potential regulator of alveolar generation  .. 
PF11093 Mitochondrial export protein Som1<br>Som1 is a component of the mitochondrial protein export system. The various Som1 proteins exhibit a highly conserved region and a pattern of cysteine residues  . Stabilisation of Som1 occurs through an interaction between Som1 and Imp1, a peptidase required for proteolytic processing of certain proteins during their transport across the mitochondrial membrane  . This suggests that Som1 represents a third subunit of the Imp1 peptidase complex  . 
PF11094 Membrane-associated tegument protein<br>The UL11 gene product of herpes simplex virus is a membrane-associated tegument protein that is incorporated into the HSV virion and functions in viral envelopment  . UL11 is acylated which is crucial for lipid raft association  .. 
PF11095 Gem-associated protein 7 (Gemin7)<br>Gemin7 is a novel component of the survival of motor neuron complex which functions in the assembly of spliceosomal small nuclear ribonucleoproteins. Gemin7 interacts with several Sm proteins of spliceosomal small nuclear ribonucleoproteins, especially SmE  .. 
PF11097 Protein of unknown function (DUF2883)<br>This family of proteins have no known function but appear to be restricted to phage.. 
PF11098 Chlorosome envelope protein C<br>Chlorosomes are light-harvesting antennae found in green bacteria. CsmC is one of the proteins that exists in the chlorosome envelope. CsmC has been shown to exist as a homomultimer with CsmD in the chlorosome envelope  . CsmC is thought to be important in chlorosome elongation and shape  .. 
PF11099 Apoptosis regulator M11L like<br>Apoptosis regulators function to modulate the apoptotic cascades and thereby favour productive viral replication. M11L inhibits mitochondrial-dependant apoptosis by mimicking and competing with host proteins for the binding and blocking of Bak and Bax, two executioner proteins  .. 
PF11100 Conjugal transfer protein TrbE <br>TrbE is essential for conjugation and phage adsorption. It contains four common motifs and one conserved domain  .. 
PF11101 Protein of unknown function (DUF2884)<br>Pfam-B_001481 (release 23.0). Some members in this bacterial family of proteins are annotated as YggN which currently has no known function.. 
PF11102 DUF2886; Cap_synth_GfcC;<br>Group 4 capsule polysaccharide formation lipoprotein gfcB. Pfam-B_1366 (release 23.0). This family includes lipoprotein GfcB (YmcC), involved in group 4 capsule polysaccharide formation  .. 
PF11103 Protein of unknown function (DUF2887)<br>Pfam-B_1330 (release 23.0). This bacterial family of proteins has no known function. These proteins may be distantly related to the PD(D/E)XK superfamily.. 
PF11104 Competence_A;<br>Type IV pilus assembly protein PilM;. The type IV pilus assembly protein PilM is required for competency and pilus biogenesis [1-2]. It binds to PilN and ATP  .. 
PF11105 Arthropod cardioacceleratory peptide 2a<br>CCAP exerts a reversible and dose-dependant cardio-stimulatory effect on the semi-isolated heart of experimental beetles. CCAP also increases free hemolymph sugar concentration in young larvae and adults of the meal-worm beetle  .. 
PF11106 Exopolysaccharide production protein YjbE<br>YjbE is part of a four gene operon which is involved in exopolysaccharide production. The expression of YjbE is higher than the rest of the operon yjbEFGH. It appears to be restricted to Enterobacteriaceae  .. 
PF11107 Fanconi anemia group F protein (FANCF)<br>FANCF regulates its own expression by methylation at both mRNA and protein levels. Methylation-induced inactivation of FANCF has an important role on the occurrence of ovarian cancers by disrupting the FA-BRCA pathway  .. 
PF11108 Viral glycoprotein L<br>GL forms a complex with gH, a glycoprotein known to be essential for entry of HSV-1 into cells and virus-induced cell fusion  . It is a hetero-oligomer of gH and gL which is incorporated into virions and transported to the cell surface which acts during entry of virus into cells  . 
PF11109 Orexigenic neuropeptide Qrfp/P518 <br>Qrfp/P518 has a direct role in maintaining bone mineral density  . Qrfp has also found to be important in energy homeostasis by regulating appetite and energy expenditure in mice  . The c-terminal 28 residues are the functional 26RFa  .. 
PF11110 Baseplate hub distal subunit<br>These baseplate proteins are also referred to as Gp28. Gp28 is the structural component of the central part of the bacteriophage T4 baseplate, which possesses a hydrophobic region and is membrane bound  . Gp28 forms a complex with gp27 which is another structural component of the baseplate  .. 
PF11111 Centromere protein M (CENP-M)<br>The prime candidate for specifying centromere identity is the array of nucleosomes assembles with CENP-A  . CENP-A recruits a nucleosome associated complex (NAC) comprised of CENP-M along with two other proteins  . Assembly of the CENP-A NAC at centromeres is partly dependant on CENP-M. The CENP-A NAC is essential, as disruption of the complex causes errors of chromosome alignment and segregation that preclude cell survival  .. 
PF11112 Pyocin activator protein PrtN<br>PrtN is a transcriptional activator for pyocin synthesis genes  . It activates the expression of various pyocin genes by interaction with the DNA sequences conserved in the 5' noncoding regions of the pyocin genes  .. 
PF11113 Head assembly gene product<br>This head assembly protein is also refereed to as gene product 40 (Gp40). A specific gp20-gp40 membrane insertion structure constitutes the T4 prohead assembly initiation complex  . This protein in T4 stimulates head formation  .. 
PF11114 Minor_capsid; Minor_capsid-2;<br>Minor capsid protein. Most of the members of this family are annotated as being minor capsid proteins. The genomes carrying the genes usually have three similar proteins adjacent to each other, hence this one being named as No.2.. 
PF11115 Protein of unknown function (DUF2623)<br>This family is conserved in the Enterobacteriaceae family. Several members are named as YghW. The function is not known.. 
PF11116 Protein of unknown function (DUF2624)<br>This family is conserved in the Bacillaceae family.  Several members are named as YqfT. The function is not known.. 
PF11117 Protein of unknown function (DUF2626)<br>This family is conserved in the Bacillaceae family.  Several members are named as YqgY. The function is not known.. 
PF11118 Protein of unknown function (DUF2627)<br>This family is conserved in the Bacillaceae family.  Several members are named as YqzF. The function is not known.. 
PF11119 Protein of unknown function (DUF2633)<br>This family is conserved largely in the Bacillaceae family. Several members are named as YfgG. The function is not known.. 
PF11120 Protein of unknown function (DUF2636)<br>This family is conserved in the Enterobacteriaceae family. Several members are named as being YhjT, but the function is not known.. 
PF11121 Protein of unknown function (DUF2639)<br>This family is conserved in the Bacillaceae family.  Several members are named as being YflJ, but the function is not known.. 
PF11122 Inner spore coat protein D<br>This family is conserved in the Enterobacteriaceae family. CotD is an inner spore coat protein that is expressed in the middle phase of mother cell gene expression. Along with CotD, CotH, CotS and CotT it is assumed to assemble into the loose skeleton of the matrix, between the shells of SpoIVA and CotE. Coat proteins do not share much sequence similarity between species, but this does not imply they do not share secondary, tertiary, or quaternary features  .. 
PF11123 DNA packaging protein <br>This DNA packaging protein is also referred to as gene 18 product (gp18). This protein is required for DNA packaging and functions in a complex with gp19  .. 
PF11124 Inorganic phosphate transporter Pho86<br>Pho86p is an ER protein which is produced in response to phosphate starvation. It is essential for growth when phosphate levels are limiting  . Pho86p is also involved in the regulation of Pho84p, a high-affinity phosphate transporter which is localised to the endoplasmic reticulum (ER) in low phosphate medium. When the level of phosphate increases Pho84p is transported to the vacuole. Pho86p is required for packaging of Pho84p in to COPII vesicles  .. 
PF11125 Protein of unknown function (DUF2830)<br>Several members in this viral family of proteins are annotated as lysis proteins.. 
PF11126 Transcriptional regulator DsbA<br>DsbA is a double stranded binding protein found in bacteriophage T4 which is involved in transcriptional regulation. DsbA, along with other viral proteins, interacts with the host RNA polymerase core enzyme enabling initiation of transcription. DsbA acts as an enhancer protein of late genes in vitro. The protein consists of mainly alpha helices  .. 
PF11127 Protein of unknown function (DUF2892)<br>Pfam-B_604 (release 23.0). This family is conserved in bacteria. The function is not known.. 
PF11128 Plant viral coat protein nucleocapsid<br>Pfam-B_645 (release 23.0). This family of nucleocapsid proteins is from ssRNA negative-strand viruses of plant origin.. 
PF11129 Rev protein of equine infectious anaemia virus<br>Pfam-B_124 (release 23.0). The sequence of this family is highly conserved and carries a nuclear export signal from residues 31-55, and RNA binding/nuclear localisation signals of RRDR at residue 76 and KRRRK at residue 159. Rev is an essential regulatory protein required for nucleocytoplasmic transport of incompletely spliced viral mRNAs that encode structural proteins. Rev has been shown to down-regulate the expression of viral late genes and alter sensitivity to Gag-specific cytotoxic-T-lymphocytes (CTL). Equine infectious anaemia virus (EIAV) exhibits a high rate of genetic variation in vivo, and results in a clinically variable disease in infected horses.. 
PF11130 F pilus assembly Type-IV secretion system for plasmid transfer<br>Pfam-B_678 (release 23.0). This family of TraC proteins is conserved in Proteobacteria. TraC is a cytoplasmic, peripheral membrane protein and is one of the proteins encoded by the F transfer region of the conjugative plasmid that is required for the assembly of F pilin into the mature F pilus structure. F pili are filamentous appendages that help establish the physical contact between donor and recipient cells involved in the conjugation process  .. 
PF11131 Rap-phr extracellular signalling<br>PhrC and PhrF stimulate ComA-dependent gene expression to different levels and are both required for full expression of genes activated by ComA, which activates the expression of genes involved in competence development and the production of several secreted products  .. 
PF11132 Transcriptional regulator protein (SplA)<br>The SplA protein functions in trans as a negative regulator of the level of splB-lacZ expression in the developing forespore  .. 
PF11133 Head fiber protein<br>This head fiber protein is also refereed to as Gp8.5. Gp8.5 is a structural protein in phage. It is a dispensable head protein.. 
PF11134 Phage stabilisation protein<br>Members of this family are phage proteins that are probably involved with stabilising the condensed DNA within the capsid  .. 
PF11135 Protein of unknown function (DUF2888)<br>Some members in this family of proteins with unknown function are annotated as immediate early protein ICP-18 however this cannot be confirmed.. 
PF11136 Protein of unknown function (DUF2889)<br>Pfam-B_001473 (release 23.0). This bacterial family of proteins has no known function.. 
PF11137 Protein of unknown function (DUF2909)<br>Pfam-B_764 (release 23.0). This is a family of proteins conserved in Proteobacteria of unknown function.. 
PF11138 Protein of unknown function (DUF2911)<br>Pfam-B_001491 (release 23.0). This bacterial family of proteins has no known function.. 
PF11139 Protein of unknown function (DUF2910)<br>Pfam-B_001487 (release 23.0). Some members in this bacterial family annotate the proteins as cytochrome C biogenesis proteins however this cannot be confirmed. Currently no function for this family is known.. 
PF11140 Protein of unknown function (DUF2913)<br>Pfam-B_001499 (release 23.0). This family of proteins with unknown function appear to be restricted to Gammaproteobacteria.. 
PF11141 Protein of unknown function (DUF2914)<br>Pfam-B_001640 (release 23.0). This bacterial family of proteins has no known function.. 
PF11142 Protein of unknown function (DUF2917)<br>Pfam-B_001647 (release 23.0). This bacterial family of proteins appears to be restricted to Proteobacteria.. 
PF11143 Protein of unknown function (DUF2919)<br>Pfam-B_001684 (release 23.0). This bacterial family of proteins has no known function. Some members are annotated as YfeZ however this cannot be confirmed.. 
PF11144 Protein of unknown function (DUF2920)<br>Pfam-B_001778 (release 23.0). This bacterial family of proteins has no known function.. 
PF11145 Protein of unknown function (DUF2921)<br>Pfam-B_001920 (release 23.0). This eukaryotic family of proteins has no known function.. 
PF11146 Protein of unknown function (DUF2905)<br>Pfam-B_542 (release 23.0). This is a family of bacterial proteins conserved of unknown function.. 
PF11148 Protein of unknown function (DUF2922)<br>Pfam-B_001999 (release 23.0). This bacterial family of proteins has no known function.. 
PF11149 Protein of unknown function (DUF2924)<br>Pfam-B_002010 (release 23.0). This bacterial family of proteins has no known function.. 
PF11150 Protein of unknown function (DUF2927)<br>Pfam-B_739 (release 23.0). This family is conserved in Proteobacteria.  Several members are described as being putative lipoproteins, but otherwise the function is not known.. 
PF11151 Protein of unknown function (DUF2929)<br>Pfam-B_002101 (release 23.0). This family of proteins with unknown function appears to be restricted to Firmicutes.. 
PF11152 Protein of unknown function (DUF2930)<br>Pfam-B_002135 (release 23.0). This family of proteins has no known function.. 
PF11153 Protein of unknown function (DUF2931)<br>Pfam-B_002146 (release 23.0). Some members in this family of proteins are annotated as lipoproteins however this cannot be confirmed. Currently, there is no known function.. 
PF11154 Protein of unknown function (DUF2934)<br>Pfam-B_002301 (release 23.0). This bacterial family of proteins has no known function.. 
PF11155 Domain of unknown function (DUF2935)<br>Pfam-B_002056 (release 23.0). This family of proteins with unknown function appears to be restricted to Firmicutes. The structure of this protein has been solved and each domain is composed of four alpha helices. A metal cluster composed of iron and magnesium lies between the two domains.. 
PF11157 Protein of unknown function (DUF2937)<br>Pfam-B_002314 (release 23.0). This family of proteins with unknown function appears to be restricted to Proteobacteria.. 
PF11158 Protein of unknown function (DUF2938)<br>Pfam-B_002317 (release 23.0). This bacterial family of proteins has no known function. Some members are thought to be membrane proteins however this cannot be confirmed.. 
PF11159 Protein of unknown function (DUF2939)<br>Pfam-B_002321 (release 23.0). This bacterial family of proteins has no known function.. 
PF11160 Protein of unknown function (DUF2945)<br>Pfam-B_002448 (release 23.0). This family of proteins has no known function.. 
PF11161 Protein of unknown function (DUF2946)<br>Pfam-B_002487 (release 23.0). This family of proteins with unknown function appear to be restricted to Proteobacteria.. 
PF11162 Protein of unknown function (DUF2946)<br>Pfam-B_002520 (release 23.0). This family of proteins has no known function.. 
PF11163 Protein of unknown function (DUF2947)<br>Pfam-B_002524 (release 23.0). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.. 
PF11164 Protein of unknown function (DUF2948)<br>Pfam-B_002527 (release 23.0). This family of proteins with unknown function appear to be restricted to Proteobacteria.. 
PF11165 Protein of unknown function (DUF2949)<br>Pfam-B_002571 (release 23.0). This family of proteins with unknown function appear to be restricted to Cyanobacteria.. 
PF11166 Protein of unknown function (DUF2951)<br>Pfam-B_002585 (release 23.0). This family of proteins has no known function. It has a highly conserved sequence.. 
PF11167 Protein of unknown function (DUF2953)<br>Pfam-B_002617 (release 23.0). This family of proteins has no known function.. 
PF11168 Protein of unknown function (DUF2955)<br>Pfam-B_002614 (release 23.0). Some members in this family of proteins with unknown function annotate the proteins as membrane protein. However, this cannot be confirmed.. 
PF11169 Protein of unknown function (DUF2956)<br>Pfam-B_002632 (release 23.0). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.. 
PF11170 Protein of unknown function (DUF2957)<br>Pfam-B_002671 (release 23.0). Some members annotate the proteins to be putative lipoproteins however this cannot be confirmed. Currently no function is known for this family of proteins.. 
PF11171 Protein of unknown function (DUF2958)<br>Pfam-B_002712 (release 23.0). Some members are annotated as lipoproteins however this cannot be confirmed. This family of proteins has no known function.. 
PF11172 Protein of unknown function (DUF2959)<br>Pfam-B_002747 (release 23.0). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.. 
PF11173 Protein of unknown function (DUF2960)<br>Pfam-B_002756 (release 23.0). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.. 
PF11174 Protein of unknown function (DUF2970)<br>Pfam-B_713 (release 23.0). This short family is conserved in Proteobacteria. The function is not known.. 
PF11175 Protein of unknown function (DUF2961)<br>Pfam-B_002770 (release 23.0). This family of proteins has no known function.. 
PF11176 Protein of unknown function (DUF2962)<br>Pfam-B_002773 (release 23.0). This eukaryotic family of proteins has no known function.. 
PF11177 Protein of unknown function (DUF2964)<br>Pfam-B_002804 (release 23.0). This family of proteins with unknown function appears to be restricted to Proteobacteria.. 
PF11178 Protein of unknown function (DUF2963)<br>Pfam-B_002790 (release 23.0). This family of proteins with unknown function appears to be restricted to Mollicutes.. 
PF11179 Protein of unknown function (DUF2967)<br>Pfam-B_002838 (release 23.0). This family of proteins with unknown function appears to be restricted to Drosophila.. 
PF11180 Protein of unknown function (DUF2968)<br>Pfam-B_002850 (release 23.0). This family of proteins has no known function.. 
PF11181 Heat induced stress protein YflT<br>YflT is a heat induced protein.. 
PF11182 Alginate O-acetyl transferase AlgF <br>AlgF is essential for the addition of O-acetyl groups to alginate, an extracellular polysaccharide. The presence of O-acetyl groups plays an important role in the ability of the polymer to act as a virulence factor  .. 
PF11183 Polymyxin resistance protein PmrD<br>PmrB forms a two-component system (TCS) with PmrA that allows Gram-negative bacteria to survive the cationic antimicrobial peptide polymyxin G  . The TCS is linked to another one via the polymyxin resistance protein PmrD. PmrD is the first protein identified to mediate the connectivity between the two TCSs.  It binds to the N terminal domain of the PmrA response regulator which prevents its dephosphorylation, thereby promoting the the transcription of genes involved in polymyxin resistance  .. 
PF11184 Protein of unknown function (DUF2969)<br>Pfam-B_002861 (release 23.0). This family of proteins with unknown function appears to be restricted to Lactobacillales.. 
PF11185 Protein of unknown function (DUF2971)<br>Pfam-B_002776 (release 23.0). This bacterial family of proteins has no known function.. 
PF11186 Protein of unknown function (DUF2972)<br>Pfam-B_002895 (release 23.0). Some members in this family of proteins with unknown function are annotated as sugar transferase proteins, however this cannot be confirmed.. 
PF11187 Protein of unknown function (DUF2974)<br>Pfam-B_002933 (release 23.0). This bacterial family of proteins has no known function.. 
PF11188 Protein of unknown function (DUF2975)<br>Pfam-B_2875 & Pfam-B_3379 (release 23.0) & JH:B0MX27. This family of bacterial proteins have no known function. These proteins are likely to be integral membrane proteins. The proteins contain a highly conserved glutamic acid close to their C-terminus.. 
PF11189 Protein of unknown function (DUF2973)<br>Pfam-B_002929 (release 23.0). Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently they have no known function.. 
PF11190 Protein of unknown function (DUF2976)<br>Pfam-B_002963 (release 23.0). This family of proteins has no known function. Some members are annotated as membrane proteins however this cannot be confirmed.. 
PF11191 Protein of unknown function (DUF2782)<br>Gunasekaran P, Mistry J. Pfam-B_001700 (release 23.0). This is a bacterial family of proteins whose function is unknown.. 
PF11192 Protein of unknown function (DUF2977)<br>Pfam-B_002980 (release 23.0). This family of proteins has no known function.. 
PF11193 Protein of unknown function (DUF2812)<br>Gunasekaran P, Mistry J. Pfam-B_001697 (release 23.0). This is a bacterial family of uncharacterised proteins, however some members of this family are annotated as membrane proteins.. 
PF11195 Protein of unknown function (DUF2829) <br>Gunasekaran P, Mistry J. Pfam-B_001848 (release 23.0). This is a uncharacterised family of proteins found in bacteria and bacteriphages.. 
PF11196 Protein of unknown function (DUF2834)<br>Gunasekaran P, Mistry J. Pfam-B_001850 (release 23.0). This is a bacterial family of uncharacterised proteins.. 
PF11197 Protein of unknown function (DUF2835)<br>Gunasekaran P, Mistry J. Pfam-B_001851 (release 23.0). This is a bacterial family of uncharacterised proteins. One member of this family (Swiss:A4VM42) is annotated as the A subunit of Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV).. 
PF11198 Protein of unknown function (DUF2857)<br>Gunasekaran P, Mistry J. Pfam-B_001886 (release 23.0). This is a bacterial family of uncharacterised proteins.. 
PF11199 Protein of unknown function (DUF2891)<br>Gunasekaran P, Mistry J. Pfam-B_001921 (release 23.0). This is a bacterial family of uncharacterised proteins.. 
PF11200 Protein of unknown function (DUF2981)<br>Pfam-B_003040 (release 23.0). This eukaryotic family of proteins has no known function.. 
PF11201 Protein of unknown function (DUF2982)<br>Pfam-B_003059 (release 23.0). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.. 
PF11202 DUF2983;<br>Phosphoribosyl transferase (PRTase). This PRTase family has a C terminal RNA binding Pelota domain  . These genes are found in the biosynthetic operon associated with the Ter  stress response operon and are predicted to  be involved in the biosynthesis of a ribo- nucleoside involved in stress response  .. 
PF11203 Protein of unknown function (DUF2984)<br>Pfam-B_003006 (release 23.0). Some members in this bacterial family of proteins are annotated as membrane proteins however this cannot be confirmed.. 
PF11204 Protein of unknown function (DUF2985)<br>Pfam-B_003090 (release 23.0). This eukaryotic family of proteins has no known function.. 
PF11205 Protein of unknown function (DUF2987)<br>Pfam-B_003120 (release 23.0). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.. 
PF11207 Protein of unknown function (DUF2989)<br>Pfam-B_003139 (release 23.0). Some members in this bacterial family of proteins are annotated as lipoproteins however this cannot be confirmed.. 
PF11208 Protein of unknown function (DUF2992)<br>Pfam-B_003142 (release 23.0). This bacterial family of proteins has no known function. However, the cis-regulatory yjdF motif, just upstream from the gene encoding the proteins for this family, is a small non-coding RNA, Rfam:RF01764. The yjdF motif is found in many Firmicutes, including Bacillus subtilis. In most cases, it resides in potential 5' UTRs of homologues of the yjdF gene whose function is unknown. However, in Streptococcus thermophilus, a yjdF RNA motif is associated with an operon whose protein products synthesise nicotinamide adenine dinucleotide (NAD+). Also, the S. thermophilus yjdF RNA lacks typical yjdF motif consensus features downstream of and including the P4 stem. Thus, if yjdF RNAs are riboswitch aptamers, the S. thermophilus RNAs might sense a distinct compound that structurally resembles the ligand bound by other yjdF RNAs. On the ohter hand, perhaps these RNAs have an alternative solution forming a similar binding site, as is observed with some SAM riboswitches  .. 
PF11209 Protein of unknown function (DUF2993)<br>Pfam-B_003144 (release 23.0). This family of proteins with unknown function appears to be restricted to Cyanobacteria.. 
PF11210 Protein of unknown function (DUF2996)<br>Pfam-B_003176 (release 23.0). This family of proteins has no known function.. 
PF11211 Protein of unknown function (DUF2997)<br>Pfam-B_003181 (release 23.0). This family of proteins has no known function.. 
PF11212 Protein of unknown function (DUF2999)<br>Pfam-B_003194 (release 23.0). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.. 
PF11213 Protein of unknown function (DUF3006)<br>Pfam-B_003197 (release 23.0). This family of proteins has no known function.. 
PF11214 Mediator complex subunit 2<br>This family of mediator complex subunit 2 proteins is conserved in fungi. Cyclin-dependent kinase CDK8 or Srb10 interacts with and phosphorylates Med2. Post-translational modifications of Mediator subunits are important for regulation of gene expression  .. 
PF11215 Protein of unknown function (DUF3010)<br>Pfam-B_003238 (release 23.0). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.. 
PF11216 Protein of unknown function (DUF3012)<br>Pfam-B_003254 (release 23.0). This family of proteins with unknown function is restricted to Gammaproteobacteria.. 
PF11217 Protein of unknown function (DUF3013)<br>Pfam-B_003257 (release 23.0). This bacterial family of proteins with unknown function appear to be restricted to Firmicutes.. 
PF11218 Protein of unknown function (DUF3011)<br>Pfam-B_003246 (release 23.0). This bacterial family of proteins has no known function. Most members belong to Proteobacteria.. 
PF11219 Protein of unknown function (DUF3014)<br>Pfam-B_003267 (release 23.0). This family of proteins with unknown function appears to be restricted to Proteobacteria.. 
PF11220 Protein of unknown function (DUF3015)<br>Pfam-B_003292 (release 23.0). This bacterial family of proteins has no known function.. 
PF11221 Subunit 21 of Mediator complex<br>Med21 has been known as Srb7 in yeasts, hSrb7 in humans and Trap 19 in Drosophila. The heterodimer of the two subunits Med7 and Med21 appears to act as a hinge between the middle and the tail regions of Mediator  .. 
PF11222 Protein of unknown function (DUF3017)<br>Pfam-B_003304 (release 23.0). This bacterial family of proteins with unknown function appear to be restricted to Actinobacteria.. 
PF11223 Protein of unknown function (DUF3020)<br>This family of fungal proteins is conserved towards the C-terminus of HMG domains. The function is not known.. 
PF11224 Protein of unknown function (DUF3023)<br>Pfam-B_003319 (release 23.0). This bacterial family of proteins with unknown function appear to be restricted to Alphaproteobacteria.. 
PF11225 Protein of unknown function (DUF3024)<br>Pfam-B_003325 (release 23.0). This family of proteins has no known function.. 
PF11226 Protein of unknown function (DUF3022)<br>Pfam-B_003318 (release 23.0). This family of proteins with unknown function appears to be restricted to Proteobacteria.. 
PF11227 Protein of unknown function (DUF3025)<br>Pfam-B_003327 (release 23.0). Some members in this bacterial family of proteins are annotated as transmembrane proteins however this cannot be confirmed. Currently this family of proteins has no known function.. 
PF11228 Protein of unknown function (DUF3027)<br>Pfam-B_003334 (release 23.0). This family of proteins with unknown function appears to be restricted to Actinobacteria.. 
PF11229 Protein of unknown function (DUF3028)<br>Pfam-B_003337 (release 23.0). This eukaryotic family of proteins has no known function.. 
PF11230 Protein of unknown function (DUF3029)<br>Pfam-B_003347 (release 23.0). Some members in this family of proteins are annotated as ykkI. Currently no function is known.. 
PF11231 Protein of unknown function (DUF3034)<br>Pfam-B_003362 (release 23.0). This family of proteins with unknown function appears to be restricted to Proteobacteria.. 
PF11232 Med25_PTOV1;Med25_PTOV-SD2; <br>Mediator complex subunit 25 PTOV activation and synapsin 2. Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species [1-2]. It is arranged into four different sections, a core, a head, a tail and a kinase-active part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function  .  The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA domain, an SD1 - synapsin 1 - domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This family is the combined PTOV and SD2 domains. the PTOV domain being the domain through which Med25 co-operates with the histone acetyltransferase CBP, but the function of the SD2 domain is unclear  .. 
PF11233 Protein of unknown function (DUF3035)<br>Pfam-B_003372 (release 23.0). This family of proteins with unknown function appear to be restricted to Alphaproteobacteria.. 
PF11235 Mediator complex subunit 25 synapsin 1<br>The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA, domain, this SD1 - synapsin 1 - domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This The function of the SD domains is unclear  .. 
PF11236 Protein of unknown function (DUF3037)<br>Pfam-B_003382 (release 23.0). This bacterial family of proteins has no known function.. 
PF11237 Protein of unknown function (DUF3038)<br>Pfam-B_003387 (release 23.0). This family of proteins with unknown function appear to be restricted to Cyanobacteria.. 
PF11238 Protein of unknown function (DUF3039)<br>Pfam-B_003408 (release 23.0). This family of proteins with unknown function appears to be restricted to Actinobacteria.. 
PF11239 Protein of unknown function (DUF3040)<br>Pfam-B_003409 (release 23.0). Some members in this family of proteins with unknown function are annotated as membrane proteins however this cannot be confirmed.. 
PF11240 Protein of unknown function (DUF3042)<br>Pfam-B_003420 (release 23.0). This family of proteins with unknown function appears to be restricted to Firmicutes.. 
PF11241 Protein of unknown function (DUF3043)<br>Pfam-B_003428 (release 23.0). Some members in this family of proteins with unknown function are annotated as membrane proteins. This cannot be confirmed.. 
PF11242 Protein of unknown function (DUF2774)<br>This is a viral family of proteins with unknown function.. 
PF11243 Protein of unknown function (DUF3045)<br>Members in this family of proteins are annotated as gene protein 30.1. Currently no function is known.. 
PF11244 Mediator complex subunit 25 C-terminal NR box-containing<br>The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA, domain, an SD1 - synapsin 1 - domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and this C-terminal NR box-containing domain (646-650) from C69-747. The NR box of MED25 is critical for its recruitment to the promoter, probably through an interaction with pre bound RAR  .. 
PF11245 Protein of unknown function (DUF2544)<br>This is a bacterial family of proteins with unknown function.. 
PF11246 Base plate wedge protein 53<br>The baseplate of bacteriophage T4 controls host cell recognition, attachment, tail sheath contraction and viral DNA ejection. The structure of the baseplate suggests a mechanism of baseplate structural transition during the initial stages of T4 infection. The baseplate is assembled from six identical wedges that surround the central hub. Gp53, along with other T4 gene products, combine sequentially to assemble a wedge  .. 
PF11247 Protein of unknown function (DUF2675) <br>Members in this family of proteins are annotated as Gene protein 5.5. Currently no function is known.. 
PF11248 Protein of unknown function (DUF3046)<br>Pfam-B_3651 (release 23.0). This family of proteins with unknown function appears to be restricted to Actinobacteria.. 
PF11249 Protein of unknown function (DUF3047)<br>Pfam-B_3654 (release 23.0). This bacterial family of proteins has no known function.. 
PF11250 Protein of unknown function (DUF3049)<br>Pfam-B_3659 (release 23.0). This eukaryotic family of proteins has no known function.. 
PF11251 Protein of unknown function (DUF3050)<br>Pfam-B_3661 (release 23.0). This bacterial family of proteins has no known function.. 
PF11252 Protein of unknown function (DUF3051)<br>Pfam-B_3671 (release 23.0). This viral family of proteins has no known function.. 
PF11253 Protein of unknown function (DUF3052)<br>Pfam-B_3674 (release 23.0). This family of proteins with unknown function appears to be restricted to Actinobacteria.. 
PF11254 Protein of unknown function (DUF3053)<br>Pfam-B_3678 (release 23.0). Some members in this family of proteins are annotated as the membrane protein YiaF. No function is currently known.. 
PF11255 Protein of unknown function (DUF3054)<br>Pfam-B_3684 (release 23.0). Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently no function is known.. 
PF11256 Protein of unknown function (DUF3055)<br>Pfam-B_3685 (release 23.0). This family of proteins with unknown function appear to be restricted to Firmicutes.. 
PF11258 Protein of unknown function (DUF3048)<br>Pfam-B_3658 (release 23.0). Some members in this bacterial family of proteins are annotated as YerB. However currently no function is known.. 
PF11259 Protein of unknown function (DUF3060)<br>Pfam-B_3702 (release 23.0). Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed.. 
PF11260 Major ampullate spidroin 1 and 2<br>Pfam-B_001419 (release 23.0). Dragline silk is composed of two proteins, major ampullate spidroin 1 (MaSp1) and major ampullate spidroin 2 (MaSp2)  . MaSp1 contains five alpha-helices  . Only the C-terminus of the proteins are shown.. 
PF11261 Interferon regulatory factor 2-binding protein zinc finger<br>Pfam-B_1430 (release 23.0). IRF-2BP1 and IRF-2BP2 are nuclear transcriptional repressor proteins and can inhibit both enhancer-activated and basal transcription. They both contain N-terminal zinc finger represented in this family and  C-terminal RING finger domains  .. 
PF11262 Transcription factor/nuclear export subunit protein 2<br>Pfam-B_002604 (release 23.0). THO and TREX form a eukaryotic complex which functions in messenger ribonucleoprotein metabolism and plays a role in preventing the transcription-associated genetic instability [1,2]. Tho2, along with four other subunits forms THO  . 
PF11263 Borrelia burgdorferi attachment protein P66 <br>Pfam-B_003349 (release 23.0). P66 is an outer membrane protein in Borrelia burgdorferi, the agent of Lyme disease. P66 has a role in the attachment of Borrelia burgdorferi to human cell-surface receptors  .. 
PF11264 Thylakoid formation protein<br>Pfam-B_003380 (release 23.0). THF1 is localised to the outer plastid membrane and the stroma. THF1 has a role in sugar signalling  . THF1 is also thought to have a role in chloroplast and leaf development  . THF1 has been shown to play a crucial role in vesicle-mediated thylakoid membrane biogenesis  .. 
PF11265 Mediator complex subunit 25 von Willebrand factor type A<br>The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA domain which is this one, an SD2 domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This VWA or von Willebrand factor type A domain when bound to RAR and the histone acetyltransferase CBP is responsible for recruiting Med1 to the rest of the Mediator complex  .. 
PF11266 Protein of unknown function (DUF3066)<br>Pfam-B_3735 (release 23.0). This family of proteins with unknown function appears to be restricted to Cyanobacteria.. 
PF11267 Protein of unknown function (DUF3067)<br>Pfam-B_3740 (release 23.0). This family of proteins has no known function.. 
PF11268 Protein of unknown function (DUF3071)<br>Pfam-B_3805 (release 23.0). Some members in this family of proteins are annotated as DNA-binding proteins however this cannot be confirmed. Currently no function is known.. 
PF11269 Protein of unknown function (DUF3069)<br>Pfam-B_3783 (release 23.0). This family of proteins with unknown function appear to be restricted to Gammaproteobacteria.. 
PF11270 Protein of unknown function (DUF3070)<br>Pfam-B_3804 (release 23.0). This eukaryotic family of proteins has no known function.. 
PF11271 Protein of unknown function (DUF3068)<br>Pfam-B_3769 (release 23.0). Some members in this family of proteins with unknown function are annotated as membrane proteins however this cannot be confirmed.. 
PF11272 Protein of unknown function (DUF3072)<br>Pfam-B_3823 (release 23.0). This bacterial family of proteins has no known function.. 
PF11273 Protein of unknown function (DUF3073)<br>Pfam-B_3852 (release 23.0). This family of proteins with unknown function appears to be restricted to Actinobacteria.. 
PF11274 Protein of unknown function (DUF3074)<br>Pfam-B_3858 (release 23.0). This eukaryotic family of proteins has no known function but appears to be part of the START superfamily.. 
PF11275 Protein of unknown function (DUF3077)<br>Pfam-B_3820 (release 23.0). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.. 
PF11276 Protein of unknown function (DUF3078)<br>Pfam-B_3846 (release 23.0). This bacterial family of proteins has no known function.. 
PF11277 Mediator complex subunit 24 N-terminal<br>This subunit of the Mediator complex appears to be conserved only from insects to humans. It is essential for correct retinal development in fish.  Subunit composition of the mediator contributes to the control of differentiation in the vertebrate CNS as there are divergent functions of the mediator subunits Crsp34/Med27, Trap100/Med24, and Crsp150/Med14  .. 
PF11278 Protein of unknown function (DUF3079)<br>Pfam-B_3866 (release 23.0). This family of proteins with unknown function appears to be restricted to Proteobacteria.. 
PF11279 Protein of unknown function (DUF3080)<br>Pfam-B_3870 (release 23.0). Some members in this family of proteins are annotated as lipoproteins however this cannot be confirmed. Currently this family has no known function.. 
PF11280 Protein of unknown function (DUF3081)<br>Pfam-B_3884 (release 23.0). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.. 
PF11281 Protein of unknown function (DUF3083)<br>Pfam-B_3898 (release 23.0). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.. 
PF11282 Protein of unknown function (DUF3082)<br>Pfam-B_3896 (release 23.0). This family of proteins has no known function.. 
PF11283 Protein of unknown function (DUF3084)<br>Pfam-B_3912 (release 23.0). This bacterial family of proteins has no known function.. 
PF11284 Protein of unknown function (DUF3085)<br>Pfam-B_3922 (release 23.0). This family of proteins with unknown function appears to be restricted to Proteobacteria.. 
PF11285 Protein of unknown function (DUF3086)<br>Pfam-B_3929 (release 23.0). This family of proteins with unknown function appears to be restricted to Cyanobacteria.. 
PF11286 Protein of unknown function (DUF3087)<br>Pfam-B_3938 (release 23.0). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.. 
PF11287 Protein of unknown function (DUF3088)<br>Pfam-B_3952 (release 23.0). This family of proteins with unknown function appears to be restricted to Proteobacteria.. 
PF11288 Protein of unknown function (DUF3089)<br>Pfam-B_3953 (release 23.0). This family of proteins has no known function but appears to have an alpha/beta hydrolase domain and so is likely to be enzymatic.. 
PF11289 Protein of unknown function (DUF3092)<br>Pfam-B_3988 (release 23.0). This viral family of proteins has no known function.. 
PF11290 Protein of unknown function (DUF3090)<br>Pfam-B_3954 (release 23.0). This family of proteins with unknown function appears to be restricted to Actinobacteria.. 
PF11291 Protein of unknown function (DUF3091)<br>Pfam-B_3979 (release 23.0). This eukaryotic family of proteins has no known function.. 
PF11292 Protein of unknown function (DUF3093)<br>Pfam-B_4007 (release 23.0). This family of proteins with unknown function appears to be restricted to Actinobacteria. Some members are annotated as alanine rich membrane proteins however this cannot be confirmed.. 
PF11293 Protein of unknown function (DUF3094)<br>Pfam-B_4017 (release 23.0). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.. 
PF11294 Protein of unknown function (DUF3095)<br>Pfam-B_4020 (release 23.0). Some members in this bacterial family of proteins are annotated as adenylyl cyclase however this cannot be confirmed. Currently no function is known.. 
PF11295 Protein of unknown function (DUF3096)<br>Pfam-B_4028 (release 23.0). This family of proteins with unknown function appears to be restricted to Proteobacteria.. 
PF11296 Protein of unknown function (DUF3097)<br>Pfam-B_4031 (release 23.0). This family of proteins with unknown function appears to be restricted to Actinobacteria.. 
PF11297 Protein of unknown function (DUF3098)<br>Pfam-B_4061 (release 23.0). This bacterial family of proteins has no known function.. 
PF11298 Protein of unknown function (DUF3099)<br>Pfam-B_4064 (release 23.0). Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently no function is known.. 
PF11299 Protein of unknown function (DUF3100)<br>Pfam-B_4068 (release 23.0). Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently no function is known.. 
PF11300 Protein of unknown function (DUF3102)<br>Pfam-B_4016 (release 23.0). This family of proteins has no known function.. 
PF11301 Protein of unknown function (DUF3103)<br>Pfam-B_4046 (release 23.0). This family of proteins with unknown function appear to be restricted to Proteobacteria.. 
PF11302 Protein of unknown function (DUF3104)<br>Pfam-B_4053 (release 23.0). This family of proteins with unknown function appears to be restricted to Cyanobacteria.. 
PF11303 Protein of unknown function (DUF3105)<br>Pfam-B_4062 (release 23.0). Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently no function is known.. 
PF11304 Protein of unknown function (DUF3106)<br>Pfam-B_4069 (release 23.0). Some members in this family of proteins are annotated as transmembrane proteins however this cannot be confirmed. Currently no function is known.. 
PF11305 Protein of unknown function (DUF3107)<br>Pfam-B_3881 (release 23.0). Some members in this family of proteins are annotated as ATP-binding proteins however this cannot be confirmed. Currently no function is known.. 
PF11306 Protein of unknown function (DUF3108)<br>Pfam-B_3856 (release 23.0). This is a bacterial family of putative lipoproteins. The structure for Swiss:Q64U78, PDB:3fzx, the first structural template for this large family including several homologues in the human gut microbiome and in metagenomic datasets, folds into a beta barrel that topologically looks like a small-scale porin (such as FepA). Swiss:Q64U78 is a putative exported protein, and this fold is of the YmcC-like type, with a predicted signal peptide SpI cleavage site AGAMA|QNQDC, and a Phobius server prediction of non-cytoplasmic localisation for amino acids 21-236. The possibility of it being a membrane protein can be ruled out by the hydrophilic nature of the solvent exposed surface outside the barrels. Analysis of sequence conservation suggests that an area near Glu172/Trp206 is potentially interesting. These two residues are also conserved in Dali hit PDB:2in5, a hypothetical lipoprotein classified as a new YmcC-like fold in SCOP (SCOP:159271, with a 12-stranded meander beta-sheet folded into a deformed beta-barrel) despite large structural differences between the two structures, suggesting similarity in function.. 
PF11307 Protein of unknown function (DUF3109)<br>Pfam-B_4077 (release 23.0). This bacterial family of proteins has no known function.. 
PF11308 DUF3111; GHL;<br>Glycosyl hydrolases related to GH101 family, GHL1-GHL3. Pfam-B_4091 (release 23.0). This family of bacterial and lower eukaryote glycosyl hydrolases is related to CAZy family GH101, and is made up of sub-families GHL1-GHL3. In the example Swiss:C02A26, the substrate-binding Asp is residue 596, the nucleophilic Asp is residue 706, and the proton donor Glu is residue 747.. 
PF11309 Protein of unknown function (DUF3112)<br>Pfam-B_4107 (release 23.0). This eukaryotic family of proteins has no known function.. 
PF11310 Protein of unknown function (DUF3113)<br>Pfam-B_4134 (release 23.0). This family of proteins has no known function. It has a highly conserved sequence.. 
PF11311 Protein of unknown function (DUF3114)<br>Pfam-B_4178 (release 23.0). Some members in this family of proteins with unknown function are annotated as cytosolic proteins. This cannot be confirmed.. 
PF11312 Protein of unknown function (DUF3115)<br>Pfam-B_4191 (release 23.0). This eukaryotic family of proteins has no known function.. 
PF11313 Protein of unknown function (DUF3116)<br>Pfam-B_4194 (release 23.0). This family of proteins with unknown function appears to be restricted to Bacillales.. 
PF11314 Protein of unknown function (DUF3117)<br>Pfam-B_4211 (release 23.0). This family of proteins with unknown function appears to be restricted to Actinobacteria.. 
PF11315 Mediator complex subunit 30<br>Pfam-B_28118 (release 23.0). Med30 is a metazoan-specific subunit of Mediator, having no homologues in yeasts.. 
PF11316 DUF3118;<br>Putative rhamnosyl transferase . Pfam-B_4218 (release 23.0). Most members of this family are uncharacterised, but one is a putative side-chain-rhamnosyl transferase  .. 
PF11317 Protein of unknown function (DUF3119)<br>Pfam-B_4223 (release 23.0). This family of proteins has no known function.. 
PF11318 Protein of unknown function (DUF3120)<br>Pfam-B_4230 (release 23.0). This family of proteins with unknown function appears to be restricted to Cyanobacteria.. 
PF11319 Protein of unknown function (DUF3121)<br>Pfam-B_4233 (release 23.0). Some members in this family of proteins with unknown function are annotated as phospholipase proteins however this cannot be confirmed. Currently this family has no known function.. 
PF11320 Protein of unknown function (DUF3122)<br>Pfam-B_4242 (release 23.0). This family of proteins with unknown function appear to be restricted to Cyanobacteria.. 
PF11321 Protein of unknown function (DUF3123)<br>Pfam-B_4246 (release 23.0). This eukaryotic family of proteins has no known function.. 
PF11322 Protein of unknown function (DUF3124)<br>Pfam-B_4248 (release 23.0). This bacterial family of proteins has no known function.. 
PF11323 Protein of unknown function (DUF3125)<br>Pfam-B_4250 (release 23.0). This family of proteins with unknown function appears to be restricted to Staphylococcus.. 
PF11324 Protein of unknown function (DUF3126)<br>Pfam-B_4268 (release 23.0). This family of proteins with unknown function appear to be restricted to Alphaproteobacteria.. 
PF11325 Domain of unknown function (DUF3127)<br>Pfam-B_4273 (release 23.0). This bacterial family of proteins has no known function. However, it does show distant similarity to Pfam:PF00436, with proteins such as Swiss:D1W984 being similar to both families. This suggests that this family may have a DNA-binding function.. 
PF11326 Protein of unknown function (DUF3128)<br>Pfam-B_4309 (release 23.0). This eukaryotic family of proteins has no known function.. 
PF11327 Protein of unknown function (DUF3129)<br>Pfam-B_4316 (release 23.0). This eukaryotic family of proteins has no known function.. 
PF11328 Protein of unknown function (DUF3130<br>Pfam-B_4322 (release 23.0). This bacterial family of proteins has no known function.. 
PF11329 Protein of unknown function (DUF3131)<br>Pfam-B_4335 (release 23.0). This bacterial family of proteins has no known function.. 
PF11330 Protein of unknown function (DUF3132)<br>Pfam-B_4348 (release 23.0). This viral family of proteins are 55kDa. No function is currently known.. 
PF11331 Protein of unknown function (DUF3133)<br>Pfam-B_4400 (release 23.0). This eukaryotic family of proteins has no known function.. 
PF11332 Protein of unknown function (DUF3134)<br>Pfam-B_4408 (release 23.0). This family of proteins with unknown function appears to be restricted to Cyanobacteria.. 
PF11333 Protein of unknown function (DUF3135)<br>Pfam-B_4409 (release 23.0). This family of proteins with unkown function appears to be restricted to Proteobacteria.. 
PF11334 Protein of unknown function (DUF3136)<br>Pfam-B_4419 (release 23.0). This family of proteins with unknown function appear to be restricted to Cyanobacteria.. 
PF11335 Protein of unknown function (DUF3137) <br>Pfam-B_4422 (release 23.0). This bacterial family of proteins has no known function.. 
PF11336 Protein of unknown function (DUF3138)<br>Pfam-B_4423 (release 23.0). This family of proteins with unknown function appear to be restricted to Proteobacteria.. 
PF11337 Protein of unknown function (DUF3139)<br>Pfam-B_4425 (release 23.0). This family of proteins with unknown function appears to be restricted to Firmicutes.. 
PF11338 Protein of unknown function (DUF3140)<br>Pfam-B_4435 (release 23.0). Some members in this family of proteins are annotated as DNA binding proteins. No function is currently known.. 
PF11339 Protein of unknown function (DUF3141)<br>Pfam-B_4443 (release 23.0). This family of proteins with unknown function appears to be restricted to Proteobacteria.. 
PF11340 Protein of unknown function (DUF3142)<br>Pfam-B_4454 (release 23.0). This bacterial family of proteins has no known function.. 
PF11341 Protein of unknown function (DUF3143)<br>Pfam-B_4460 (release 23.0). This family of proteins has no known function.. 
PF11342 Protein of unknown function (DUF3144)<br>Pfam-B_4465 (release 23.0). This family of proteins with unknown function appears to be restricted to Proteobacteria.. 
PF11343 Protein of unknown function (DUF3145)<br>Pfam-B_4467 (release 23.0). This family of proteins with unknown function appear to be restricted to Actinobacteria.. 
PF11344 Protein of unknown function (DUF3146)<br>Pfam-B_4468 (release 23.0). This family of proteins with unknown function appear to be restricted to Cyanobacteria.. 
PF11345 Protein of unknown function (DUF3147)<br>Pfam-B_4475 (release 23.0). Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently no function is known.. 
PF11346 Protein of unknown function (DUF3149)<br>Pfam-B_4495 (release 23.0). This bacterial family of proteins has no known function.. 
PF11347 Protein of unknown function (DUF3148)<br>Pfam-B_4488 (release 23.0). This family of proteins has no known function.. 
PF11348 Protein of unknown function (DUF3150)<br>Pfam-B_4471 (release 23.0). This bacterial family of proteins with unknown function appears to be restricted to Proteobacteria.. 
PF11349 Protein of unknown function (DUF3151)<br>Pfam-B_4506 (release 23.0). This family of proteins with unknown function appears to be restricted to Actinobacteria.. 
PF11350 Protein of unknown function (DUF3152)<br>Pfam-B_4512 (release 23.0). Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently there is no known function.. 
PF11351 Protein of unknown function (DUF3154)<br>Pfam-B_4516 (release 23.0). This family of proteins with unknown function appears to be restricted to Proteobacteria.. 
PF11352 Protein of unknown function (DUF3155)<br>Pfam-B_4534 (release 23.0). This family of proteins with unknown function appears to be restricted to Cyanobacteria.. 
PF11353 Protein of unknown function (DUF3153)<br>Pfam-B_4513 (release 23.0). This family of proteins with unknown function appear to be restricted to Cyanobacteria. Some members are annotated as membrane proteins however this cannot be confirmed.. 
PF11354 Protein of unknown function (DUF3156)<br>Pfam-B_4555 (release 23.0). This family of proteins with unknown function appears to be restricted to Proteobacteria.. 
PF11355 Protein of unknown function (DUF3157)<br>Pfam-B_4561 (release 23.0). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.. 
PF11356 Type IV pilus biogenesis<br>Pfam-B_3750 (release 23.0). Type IV pili are required for auto-agglutination, twitching motility, biofilm formation, adherence and DNA uptake during transformation  . PilP is an inner membrane protein, required for pilus expression and transformation  . PilP interacts with PilQ which suggests that the two proteins may have coordinated activity in functions such as pilus extrusion/retraction  .. 
PF11357 Cell cycle regulatory protein<br>Pfam-B_3875 (release 23.0). Speedy (Spy1) is a cell cycle regulatory protein which activates CDK2, the major kinase that allows progression through G1/S phase and further replication events  . Spy1 expression overcomes a p27-induced cell cycle arrest to allow for DNA synthesis, so cell cycle progression occurs due to an interaction between Spy1 and p27  . Spy1 is also known as Ringo protein A.. 
PF11358 Protein of unknown function (DUF3158)<br>Pfam-B_3964 (release 23.0). Some members in this family of proteins are annotated as integrase regulator R however this cannot be confirmed. This family of proteins with unknown function appear to be restricted to Proteobacteria.. 
PF11359 Glycoprotein UL132<br>Pfam-B_4015 (release 23.0). Glycoprotein UL132 is a low-abundance structural component of Human cytomegalovirus (HCMV)  . The function of this protein is not fully understood.. 
PF11360 Protein of unknown function (DUF3110)<br>Pfam-B_4086 (release 23.0). This family of proteins has no known function.. 
PF11361 Protein of unknown function (DUF3159)<br>Pfam-B_4163 (release 23.0). Some members in this family of proteins with unknown function are annotated as membrane proteins however this cannot be confirmed. Currently this family of proteins has no known function.. 
PF11362 Protein of unknown function (DUF3161)<br>Pfam-B_4173 (release 23.0). This eukaryotic family of proteins has no known function.. 
PF11363 Protein of unknown function (DUF3164)<br>Pfam-B_4249 (release 23.0). This family of proteins has no known function.. 
PF11364 Protein of unknown function (DUF3165)<br>Pfam-B_4331 (release 23.0). Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently there is no known function.. 
PF11365 Protein of unknown function (DUF3166)<br>Pfam-B_4333 (release 23.0). This eukaryotic family of proteins has no known function.. 
PF11367 Protein of unknown function (DUF3168)<br>Pfam-B_4337 (release 23.0). This family of proteins has no known function but is likely to be a component of bacteriophage.. 
PF11368 Protein of unknown function (DUF3169)<br>Pfam-B_4342 (release 23.0). Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently there is no known function.. 
PF11369 Protein of unknown function (DUF3160)<br>Pfam-B_4384 (release 23.0). This family of proteins has no known function.. 
PF11371 Protein of unknown function (DUF3172)<br>Pfam-B_4527 (release 23.0). This family of proteins has no known function.. 
PF11372 Domain of unknown function (DUF3173)<br>Pfam-B_4543 (release 23.0). This family of proteins with unknown function appears to be restricted to Firmicutes. These proteins appear to be distantly related to HHH domains and are therefore likely to be DNA-binding.. 
PF11373 Protein of unknown function (DUF3175)<br>Pfam-B_4566 (release 23.0). This family of proteins with unknown function appears to be restricted to Proteobacteria.. 
PF11374 Protein of unknown function (DUF3176)<br>Pfam-B_4567 (release 23.0). This eukaryotic family of proteins has no known function.. 
PF11375 Protein of unknown function (DUF3177)<br>Pfam-B_4580 (release 23.0). Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently there is no known function.. 
PF11376 Protein of unknown function (DUF3179)<br>Pfam-B_4591 (release 23.0). This family of proteins has no known function.. 
PF11377 Protein of unknown function (DUF3180)<br>Pfam-B_4592 (release 23.0). Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently there is no known function.. 
PF11378 Protein of unknown function (DUF3181)<br>Pfam-B_4595 (release 23.0). This family of proteins has no known function.. 
PF11379 Protein of unknown function (DUF3182)<br>Pfam-B_4440 (release 23.0). This family of proteins with unknown function appears to be restricted to Proteobacteria.. 
PF11380 Protein of unknown function (DUF3184)<br>Pfam-B_4192 (release 23.0). This eukaryotic family of proteins has no known function.. 
PF11381 Protein of unknown function (DUF3185)<br>Pfam-B_4606 (release 23.0). Some members in this bacterial family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently no function is known.. 
PF11382 Protein of unknown function (DUF3186)<br>Pfam-B_4607 (release 23.0). This bacterial family of proteins has no known function.. 
PF11383 Protein of unknown function (DUF3187)<br>Pfam-B_4660 (release 23.0). This family of proteins with unknown function appear to be restricted to Proteobacteria. These proteins are likely to be outer membrane proteins.. 
PF11384 Protein of unknown function (DUF3188)<br>Pfam-B_4573 (release 23.0). This bacterial family of proteins has no known function.. 
PF11385 Protein of unknown function (DUF3189)<br>Pfam-B_4499 (release 23.0). This family of proteins with unknown function appears to be restricted to Firmicutes. 
PF11386 Vitelline envelope receptor for lysin<br>Pfam-B_1349 (release 23.0). VERL, the egg vitelline envelope (VE) receptor for lysin, is a giant unbranched glycoprotein comprising 30% of the vitelline envelope. Lysin binds to VERL and creates a hole as VERL molecules lose cohesion and splay apart. These proteins are important in the mediation of fertilisation  . 
PF11387 Protein of unknown function (DUF2795)<br>Pfam-B_1395 (release 23.0). This family of proteins has no known function.. 
PF11388 Phagosome trafficking protein DotA<br>Pfam-B_001493 (release 23.0). DotA is essential for intracellular growth in Legionella  . DotA is thought to play an important role in regulating initial phagosome trafficking decisions either upon or immediately after macrophage uptake  .. 
PF11389 Leptospira porin protein OmpL1<br>Pfam-B_001515 (release 23.0). OmpL1 is a member of the outer membrane (OM) proteins in the mammalian pathogen Leptospira. Specifically, it is a porin  .. 
PF11390 NADH-dependant formate dehydrogenase delta subunit FdsD<br>Pfam-B_1352 (release 23.0). FdsD is the delta subunit of the enzyme formate dehydrogenase. This subunit may play a role in maintaining the quaternary structure by means of electrostatic interactions with the other subunits  . The delta subunit is not involved in the active centre of the enzyme  .. 
PF11391 Protein of unknown function (DUF2798)<br>Pfam-B_1194 (release 23.0). This family of proteins has no known function.. 
PF11392 Protein of unknown function (DUF2877)<br>Pfam-B_002434 (release 23.0). This bacterial family of proteins are putative carboxylase proteins however this cannot be confirmed.. 
PF11393 Macrophage killing protein with similarity to conjugation protein<br>Pfam-B_002787 (release 23.0). IcmL contains two amphipathic beta-sheet regions, required for the pore-forming ability which may be related to the transfer of this protein into a host cell membrane  . The icmL gene shows significant similarity to plasmid genes involved in conjugation however IcmL is thought to be required for macrophage killing. It is unknown whether conjugation plays a role in macrophage killing  .. 
PF11394 Protein of unknown function (DUF2875)<br>Pfam-B_002814 (release 23.0). This family of proteins with unknown function appear to be restricted to Proteobacteria.. 
PF11395 Protein of unknown function (DUF2873)<br>Pfam-B_002845 (release 23.0). This viral family of proteins has no known function.. 
PF11396 Protein of unknown function (DUF2874)<br>Pfam-B_002962 (release 23.0). This bacterial family of proteins is probably periplasmic and of unknown function.\.     There may be between one and six copies of this domain per sequence.. 
PF11397 Glycosyltransferase (GlcNAc)<br>Pfam-B_002901 (release 23.0). GlcNAc is an enzyme that carries out the first glycosylation step of hydroxylated Skp1, a ubiquitous eukaryotic protein, in the cytoplasm  .. 
PF11398 Protein of unknown function (DUF2813)<br>Pfam-B_002207 (release 23.0). This entry contains YjbD from Escherichia coli (Swiss:P75828), which is annotated as a nucleotide triphosphate hydrolase.. 
PF11399 Protein of unknown function (DUF3192)<br>Pfam-B_002991 (release 23.0). Some members in this family of proteins are annotated as lipoproteins however this cannot be confirmed.. 
PF11401 Tetrabrachion<br>Tetrabrachion forms a parallel right-handed coiled coil structure with hydrophobic interactions and salt bridges forming a thermostable tetrameric structure. It contains large hydrophobic cavities. No function is known for this family of proteins  .. 
PF11402 Antifungal protein<br>Antifungal protein consists of five antiparallel beta strands which are highly twisted creating a beta barrel stabilised by four internal disulphide bridges  . A cationic site adjacent to a hydrophobic stretch on the protein surface may constitute a phospholipid binding site  .. 
PF11403 Yeast metallothionein<br>Metallothioneins are characterised by an abundance of cysteine residues and a lack of generic secondary structure motifs. This protein functions in primary metal storage, transport and detoxification  . For the first 40 residues in the protein the polypeptide wraps around the metal by forming two large parallel loops separated by a deep cleft containing the metal cluster  .. 
PF11404 Potassium voltage-gated channel<br>Fast inactivation of voltage-dependant potassium channels occurs by a 'ball-and-chain'-type mechanism. It controls membrane excitability and signal propagation in central neurons  . Inactivation is regulated by protein phosphorylation where phosphorylation of serine residues leads to a reduction of the fast inactivation  .. 
PF11405 Bromelain_inhib;<br>Bromelain inhibitor VI. Bromelain inhibitor VI is a double-chain inhibitor consisting of a 11-residue and a 41-residue chain. This protein is the 41-residue heavy chain which is joined to the 11-residue chain by disulphide bonds. The inhibitor acts to inhibit the cysteine proteinase bromelain  .. 
PF11406 Antimicrobial peptide tachystatin A<br>Tachystatin A contains a cysteine-stabilised triple-stranded beta-sheet and shows features common to membrane-interactive peptides. Tachystatin A is thought to have an antimicrobial activity similar to defensins.Tachystatin A is also a chitin-binding peptide  .. 
PF11407 Type II restriction enzyme MunI<br>Type II restriction enzyme MunI recognises the palindromic sequence C/AATTG. It makes contact with the DNA via the major groove  .. 
PF11408 Sgs1 RecQ helicase<br>RecQ helicases unwind DNA in an ATP-dependent manner. Sgs1 has a HRDC (helicase and RNaseD C-terminal) domain which modulates the helicase function via auxiliary contacts to DNA  . . 
PF11409 Smad anchor for receptor activation (SARA)<br>Smad proteins mediate transforming growth factor-beta (TGF-beta) signaling from the transmembrane serine-threonine receptor kinases to the nucleus  . SARA recruits Smad2 to the TGF-beta receptors for phosphorylation  .. 
PF11410 Antifungal peptide<br>This peptide has six cysteines involved in three disulphide bonds. It contains a global fold which involves a cysteine-knotted three-stranded antiparallel beta-sheet along with a flexible loop and four beta-reverse turns. It also has an amphiphilic character which is the main structural basis of its biological function  .. 
PF11411 DNA ligase IV<br>DNA ligase IV along with Xrcc4 functions in DNA non-homologous end joining. This process is required to mend double-strand breaks. Upon ligase binding to an Xrcc4 dimer, the helical tails unwind leading to a flat interaction surface  .. 
PF11412 Disulphide bond corrector protein DsbC<br>DsbC rearranges incorrect disulphide bonds during oxidative protein folding. It is activated by the N-terminal domain of DsbD, a transmembrane electron transporter. DsbD binds to a DsbC dimer and selectively activates it using electrons from the cytoplasm  .. 
PF11413 Hypoxia-inducible factor-1<br>HIF-1 is a transcriptional complex and controls cellular systemic homeostatic responses to oxygen availability  . In the presence of oxygen HIF-1 alpha is targeted for proteasomal degradation by pHVL, a ubiquitination complex  .. 
PF11414 Adenomatous polyposis coli tumour suppressor protein<br>The tumour suppressor protein, APC, has a nuclear export activity as well as many different intracellular functions. The structure consists of three alpha-helices forming two separate antiparallel coiled coils  .. 
PF11415 Termicin;<br>Antifungal peptide termicin. Termicin is a cysteine-rich antifungal peptide which exhibits antibacterial activity. A cysteine stabilised alpha beta motif is formed due to an alpha-helical segment and a two-stranded antiparallel beta-sheet  .. 
PF11416 Integral membrane protein Sed5p<br>Sed5p interacts with Sly1p , a positive regulator of intracellular membrane fusion, allowing SM proteins to stay associated with the assembling fusion machinery. This allows for participation in late fusion steps  .. 
PF11417 Loader and inhibitor of phage G40P<br>G39P inhibits the initiation of DNA replication by blocking G40P replicative helicase. G39P has a bipartite stricture consisting of a folded N-terminal domain and an unfolded C-terminal domain. The C terminal is essential for helicase interaction  .. 
PF11418 Phi29 scaffolding protein<br>This protein is also referred to as gp7. The protein contains a DNA-binding function and may halve a role in mediating the structural transition from prohead to mature virus and also scaffold release  .Gp7 is arranged within the capsid as a series of concentric shells  .. 
PF11419 Protein of unknown function (DUF3194)<br>This family of proteins has no known function however the structure has been determined. The protein consists of two alpha-helices packed on the same side of a central beta-hairpin  .. 
PF11420 Bacteriocin subtilosin A<br>Subtilosin A is a bacteriocin from Bacillus subtilis.The protein has a cyclized peptide backbone and forms three cross-liks between the sulphurs of Cys13, Cys7 and Cys4 and the alpha-positions of Phe22,Thr28 and Phe31  .. 
PF11421 ATP synthase F1 beta subunit<br>The NMR solution structure of the protein in SDS micelles was found to contain two helices, an N-terminal amphipathic alpha-helix and a C-terminal alpha-helix separated by a large unstructured internal domain. The N-terminal alpha-helix is the Tom20 receptor binding site whereas the C-terminal alpha-helix is located upstream of the mitochondrial processing peptidase cleavage site  .. 
PF11422 Initiator binding protein 39 kDa<br>IBP39 recognises the initiator which is solely responsible for transcription start site selection. IBP39 contains an N-terminal Inr binding domain connected to a C-terminal domain. The C domain structure indicates that it interacts with the T. vaginalis RNAP II large subunit C-terminal domain. Binding of IBP39 to Inr recruits RNAP II and initiates transcription  .. 
PF11423 Regulatory protein Mnt<br>Mnt is a repressor which is involved in the genetic switch between lysogenic and lytic growth in bacteriophage P22. The C-terminal domain of the protein consists of a dimer of two antiparallel coiled coils with a right handed twist, which is both stronger and has closer inter-helical separation compared with those found in left-handed coiled coils  .. 
PF11424 Protein of unknown function (DUF3195)<br>This archaeal family of proteins has no known function.. 
PF11426 Tn7_TnsC;<br>Tn7 transposition regulator TnsC. TnsC is a molecular switch that regulates transposition and interacts with TnsA which is a component of the transposase. The two proteins interact via the residues 504-555 on TnsC. The TnsA/TnsC interaction is very important in Tn7 transposition  .. 
PF11427 Tc3_transposase;<br>Tc3 is transposase with a specific DNA-binding domain which contains three alpha-helices, two of which form a helix-turn-helix motif which makes four base-specific contacts with the major groove. The N-terminus makes contacts with the minor groove. There is a base specific recognition between Tc3 and the transposon DNA. The DNA binding domain forms a dimer in which each monomer binds a separate transposon end. This implicates that the dimer has a role in synapsis and is necessary for the simultaneous cleavage of both transposon termini  .. 
PF11428 Protein of unknown function (DUF3196)<br>This proteins is the product of the gene MPN330 and is thought to involved in a cellular function that has yet to be characterised. The proteins has 11 helices and a novel fold  . No function is currently known for this protein.. 
PF11429 Colicin D<br>Colicin D is a tRNase which kills sensitive E.coli cells via a specific tRNA cleavage. It targets the four isoaccepting tRNAs for Arg and cleaves the phosphodiester bond between positions 38 and 39 at the 3' junction of the anticodon stem and the loop  .. 
PF11430 Programmed cell death activator EGL-1<br>Initiation of programmed cell death in C.elegans occurs by the binding of EGL-1 to CED-9 which disrupts a complex involving CED-4/CED-9 and allows CED-4 to activate CED-3, a caspase. It is the C terminal domain of EGL-1 which is involved in the formation of the complex with CED-9. The formation of the complex induces structural rearrangements in CED-9 and EGL-1 adopts an extended alpha-helical conformation  .. 
PF11431 Membrane transport protein MerF<br>The mercury transport membrane protein, MerF has a core helix-loop-helix domain. It has two vicinal pairs of cysteine residues which are involved in the transport of Hg(II) across the membrane and are exposed to the cytoplasm  .. 
PF11432 Protein of unknown function (DUF3197)<br>This bacterial family of proteins has no known function.. 
PF11433 Protein of unknown function (DUF3198)<br>Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently, this archaeal family has no known function.. 
PF11434 Chemotaxis-inhibiting protein CHIPS<br>The chemotaxis inhibitory protein, CHIPS, is an excreted virulence factor which acts by binding to C5a and formylated peptide receptor (FPR), blocking phagocyte responses. A fragment of CHIPS, which contains residues 31-121 comprises of an alpha helix packed onto a four stranded anti-parallel beta-sheet. Most of the conserved residues of CHIPS are present in the alpha-helix  .. 
PF11435 RNA binding protein She2p<br>She2p is a RNA binding protein which binds to RNA via a helical hairpin. The protein is required for the actin dependent transport of ASH1 mRNA in yeast, a form of mRNP translocation. ASH1 mRNP requires recognition of zip code elements by the RNA binding protein She2p. She2p contains a globular domain consisting of a bundle of five alpha-helices  .. 
PF11436 Protein of unknown function (DUF3199)<br>Some members in this family of proteins with unknown function are annotated as YqbG however this cannot be confirmed. Currently the proteins has no known function.. 
PF11437 Vanadium-binding protein 2<br>The Vanadium binding protein, Vanabin2, contains four alpha-helices connected by nine disulphide bonds. Vanadium accumulates in Ascidians however the biological reason remains unclear  .. 
PF11438 36-mer N-terminal peptide of the N protein (N36)<br>The arginine-rich motif of the N protein is involved in transcriptional antitermination of phage lambda. N36 forms a complex with boxB RNA by binding tightly to the major groove of the boxB hairpin via hydrophobic and electrostatic interactions forming a bent alpha helix  .. 
PF11439 DUF3200;<br>Type III secretion system filament chaperone CesA. This family represents a chaperone protein for the type III secretion system - TTSS - translocon protein EspA, to prevent the latter's self-polymerisation. The TTSS is a highly specialised bacterial protein secretory pathway, similar in many ways to the flagellar system, that is essential for the pathogenesis of many Gram-negative bacteria. The twenty or so proteins making up the TTSS apparatus, referred to as the needle complex, allow the injection of virulence proteins (known as effectors) directly into the cytoplasm of the eukaryotic host cells they infect; however, the injection process itself is mediated by a subset of extracellular proteins that are secreted by the needle complex to the bacterial surface and assembled into the type III translocon - EspA. EspB and EspD. EspA polymerises into an extracellular filament, and, as with other fibrous proteins, is apt to undergo massive polymerisation when overexpressed. CesA is the secretion chaperone protein that binds to EspA. CesA is dimeric and helical, and it traps EspA in a monomeric state and inhibits its polymerisation.. 
PF11440 DNA alpha-glucosyltransferase<br>The T4 bacteriophage of E.coli protects its DNA via two glycosyltransferases which glucosylate 5-hydroxymethyl cytosines (5-HMC) using UDP-glucose. These two proteins are the retaining alpha-glucosyltransferase (AGT) and the inverting beta-glucosyltransferase (BGT). The proteins in this family are AGT. AGT adopts the GT-B fold and binds both the sugar donor and acceptor to the C-terminal domain. There is evidence for a role of AGT in the base-flipping mechanism and for its specific recognition of the acceptor base  .. 
PF11441 Pilot protein MxiM<br>MxiM, a Shigella pilot protein, is essential for the assembly and membrane association of the Shigella secretin MxiD. MxiM contains an orthologous secretin component and has a specific binding domain for the acyl chains of bacterial lipids  . The C terminal domain of MxiD hinders lipid binding to MxiM  .. 
PF11442 Protein of unknown function (DUF2826)<br>Gunasekaran P, Mistry J. Pfam-B_001753 (release 23.0). This is a family of uncharacterised proteins that is highly conserved in Trypanosoma cruzi.. 
PF11443 Domain of unknown function (DUF2828)<br>Gunasekaran P, Mistry J. Pfam-B_001814 (release 23.0). This is a uncharacterised domain found in eukaryotes and viruses.. 
PF11444 Protein of unknown function (DUF2895)<br>Gunasekaran P, Mistry J. Pfam-B_002001 (release 23.0). This is a bacterial family of uncharacterised proteins.. 
PF11445 Protein of unknown function (DUF2894)<br>Gunasekaran P, Mistry J. Pfam-B_001968 (release 23.0). This is a bacterial family of uncharacterised proteins.. 
PF11446 Protein of unknown function (DUF2897)<br>Gunasekaran P, Mistry J. Pfam-B_002015 (release 23.0). This is a bacterial family of uncharacterised proteins.. 
PF11447 Protein of unknown function (DUF3201)<br>This archaeal family of proteins has no known function.. 
PF11448 Protein of unknown function (DUF3005)<br>Gunasekaran P, Mistry J. Pfam-B_3492 (release 23.0). This is a bacterial family of uncharacterised proteins.. 
PF11449 Protein of unknown function (DUF2899)<br>Gunasekaran P, Mistry J. Pfam-B_002023 (release 23.0). This is a bacterial family of uncharacterised proteins.. 
PF11450 Protein of unknwon function (DUF3008)<br>Gunasekaran P, Mistry J. Pfam-B_3521 (release 23.0). This is a bacterial family of uncharacterised proteins.. 
PF11452 Protein of unknown function (DUF3000)<br>Gunasekaran P, Mistry J. Pfam-B_3481 (release 23.0). This is a bacterial family of uncharacterised proteins.. 
PF11453 Protein of unknown function (DUF2950)<br>Gunasekaran P, Mistry J. Pfam-B_002484 (release 23.0). This is a bacterial family of uncharacterised proteins.. 
PF11454 Protein of unknown function (DUF3016)<br>Gunasekaran P, Mistry J. Pfam-B_3517 (release 23.0). This is a bacterial family of uncharacterised proteins.. 
PF11455 Protein  of unknown function (DUF3018)<br>Gunasekaran P, Mistry J. Pfam-B_3532 (release 23.0). This is a bacterial family of uncharacterised proteins.. 
PF11456 Protein of unknown function (DUF3019)<br>Gunasekaran P, Mistry J. Pfam-B_3539 (release 23.0). This is a bacterial family of uncharacterised proteins.. 
PF11457 Protein of unknown function (DUF3021)<br>Gunasekaran P, Mistry J. Pfam-B_3526 (release 23.0). This is a bacterial family of uncharacterised proteins.. 
PF11458 Membrane-integrating protein Mistic<br>Mistic is an integral membrane protein that folds autonomously into the membrane  .The protein forms a helical bundle with a polar lipid-facing surface. Mistic can be used for high-level production of other membrane proteins in their native conformations  .. 
PF11459 Protein of unknwon function (DUF2893)<br>Gunasekaran P, Mistry J. Pfam-B_001947 (release 23.0). This is a bacterial family of uncharacterised proteins.. 
PF11460 Protein of unknown function (DUF3007)<br>Gunasekaran P, Mistry J. Pfam-B_3514 (release 23.0). This is a family of uncharacterised proteins found in bacteria and eukaryotes.. 
PF11461 Rab interacting lysosomal protein<br>RILP contains a domain which contains two coiled-coil regions and is found mainly in the cytosol. RILP is recruited onto late endosomal and lysosomal membranes by Rab7 and acts as a downstream effector of Rab7. This recruitment process is important for phagosome maturation and fusion with late endosomes and lysosomes  .. 
PF11462 Protein of unknown function (DUF3203)<br>This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.. 
PF11463 R.HinP1I restriction endonuclease<br>Hinp1I is a type II restriction endonuclease, recognising and cleaving a palindromic tetranucleotide sequence (G/CGC) resulting in 2 nt 5' overhanging ends  . HINP1I has a conserved catalytic core domain containing an active site motif SDC18QXK and a DNA-binding domain  .. 
PF11464 Rabenosyn Rab binding domain<br>Rabenosyn-5 (Rbsn) is a multivalent effector with interacts with the Rab family.Rsbn contains distinct Rab4 and Rab5 binding sites within residues 264-500 and 627-784 respectively  . Rab proteins are GTPases involved in the regulation of all stages of membrane trafficking  .. 
PF11465 Natural killer cell receptor 2B4<br>2B4 is a transmembrane receptor which is expressed primarily on natural killer cells. It plays a role in activating NK-mediated cytotoxicity through its interaction with CD48 on target cells in a subset of CD8 T cells  . The structure of 2B4 consists of an immunoglobulin variable domain fold and contains two beta-sheets. One of the beta-sheets, the six-stranded sheet, contains structural features that may have a role in ligand recognition and receptor function  .. 
PF11466 Prion-like protein Doppel<br>Dpl is a homologue related to the prion protein (PrP). Dpl is toxic to neurons and is expressed in the brains of mice that do not express PrP. In DHPC and SDS micelles, Dpl shoes about 40% alpha-helical structure however in aqueous solution it consists of a random coil. The alpha helical segment can adopt a transmembrane localisation also in a membrane  . The unprocessed Dpl protein is thought to posses a possible channel formation mechanism which may be related to toxicity through direct interaction with cell membranes and damage to the cell membrane  .. 
PF11467 Lens epithelium-derived growth factor (LEDGF) <br>LEDGF is a chromatin-associated protein that protects cells from stress-induced apoptosis. It is the binding partner of HIV-1 integrase in human cells. The integrase binding domain (IBD) of LEDGF is a compact right-handed bundle composed of five alpha-helices. The residues essential for the interaction with the integrase are present in the inter-helical loop regions of the bundle structure  .. 
PF11468 Aromatic prenyltransferase Orf2<br>In vivo Orf2 attaches a geranyl group to a 1,3,6,8-tetrahydroxynaphthalene-derived polyketide during naphterpin biosynthesis  . In vitro, Orf2 catalyses carbon-carbon based and carbon-oxygen based prenylation of hydroxyl-containing aromatic acceptors of synthetic, microbial and plant origin  .. 
PF11469 DUF3204;<br>This is a family of archaeal ribonuclease_III proteins.. 
PF11470 TUG;<br>GLUT4 regulating protein TUG. TUG is a GLUT4 regulating protein and functions to retain membrane vesicles containing GLUT4 intracellularly. TUG releases the GLUT4 containing vesicles to the cellular exocytic machinery in response to insulin stimulation which allows translocation to the plasma membrane  . TUG has an N-terminal ubiquitin-like domain (UBL1) which in similar proteins appears to participate in protein-protein interactions  . The region does have a area of negative electrostatic potential and increased backbone motility which leads to suggestions of a potential protein-protein interaction site  .. 
PF11471 DUF3205;<br>Maltoporin periplasmic N-terminal extension. Pollington J, Coggill P. This domain would appear to be the periplasmic, N-terminal extension of the outer membrane maltoporins, Pfam:PF02264, LamB.. 
PF11472 Protein of unknown function (DUF3206)<br>This bacterial family of proteins has no known function.. 
PF11473 RNA binding protein B2<br>B2 is expressed by the insect Flock House virus (FHV) as a counter-defense mechanism against antiviral RNA silencing during infection. In vitro, B2 binds to dsRNA as a dimer and inhibits the cleavage of it by Dicer. B2 blocks cleavage of the FHV genome by Dicer and also the incorporation of FHV small interfering RNAs into the RNA-induced silencing complex  .. 
PF11474 Telomerase reverse transcriptase TEN domain<br>This is the N terminal domain of the protein telomerase reverse transcriptase called TEN. The TEN domain is able to bind both RNA and telomeric DNA and contributes towards telomerase catalysis. The TEN domain has a structure that consists of a core beta sheet surrounded by seven alpha helices and a short beta hairpin  .. 
PF11475 Virion protein N terminal domain <br>This is the N terminal domain of a family of virion proteins which contains a zinc finger domain. Currently no function is known.. 
PF11476 Toxoplasma gondii micronemal protein 1 TgMIC1<br>TgMIC1 is released as part of a complex by Toxoplasma gondii prior to invasion. The complex which consists of TgMIC4-MIC1-MIC6 participates in host cell attachment and penetration and is critical in invasion. This is the C terminal domain of TgMIC1 which has a Galectin-like fold which interacts with and stabilises TgMIC6 providing a mechanism for an exit from the early secretory compartments and trafficking of the complex to micronemes  .. 
PF11477 Sialyltransferase PMO188<br>PMO188 is a sialyltransferase from P.multocida. It transfers sialic acid from cytidine 5'-monophosphonuraminic acid to an acceptor sugar  . It has important catalytic residues such as Asp141, His311, Glu338, Ser355 and Ser356  .. 
PF11478 Antimicrobial chitin binding protein tachystatin B<br>Tachystatin B is an antimicrobial chitin binding peptide and consists of two isotopes B1 and B2.Both structures contain a short antiparallel beta sheet with an inhibitory cysteine knot motif. Tyr(14) and Arg(17) are thought to be the essential residues for chitin binding  .. 
PF11479 RNA silencing suppressor P21<br>P21 is produced by Beet yellows virus to suppress the antiviral silencing response mounted by the host. P21 acts by binding directly to siRNA which is a mediator in the process. P21 has an octameric ring structure with a large central cavity  . . 
PF11480 Colicin-E5 Imm protein<br>Imms bind specifically to cognate colicins in order to protect their host cells  . Imm-E5 is a specific inhibitor protein of colicin E5. It binds to E5 C-terminal ribonuclease domain (CRD) to prevent cell death. The binding mode of E5-CRD and Imm-E5 mimics that of mRNA and tRNA suggesting an evolutionary pathway from the RNA-RNA interaction through the RNA-protein interaction of tRNA/E5-CRD  .. 
PF11482 Protein of unknown function (DUF3208)<br>This bacterial family of proteins has no known function.. 
PF11483 Protein of unknown function (DUF3209)<br>This family of proteins has no known function.. 
PF11485 Protein of unknown function (DUF3211)<br>This archaeal family of proteins has no known function.. 
PF11486 Protein of unknown function (DUF3212)<br>Members in this family of proteins are annotated as YfmB however currently no function for this protein is known.. 
PF11487 Type II restriction enzyme SfiI<br>SfiI is a restriction enzyme that can cleave two DNA sites simultaneously to leave 3-base 3' overhangs. It acts as a homo-tetramer and recognises a specific eight base-paid palindromic DNA sequence. After binding two copies of its recognition sequence, SfiI becomes activated leading to cleavage of all four DNA strands. The structure of SfiI consists of a central twisted beta-sheet surrounded by alpha-helices.. 
PF11488 Transcriptional regulatory protein LGE1<br>This family of proteins is conserved from fungi to human. In yeasts it is involved in the ubiquitination of histones H2A and H2B.  This ubiquitination step is a vital one in the regulation of the transcriptional activity of RNA polymerase II. In S. cerevisiae, Rad6 and Bre1 are present in a complex, also containing Lge1, that is required for H2B ubiquitination. Bre1 is the H2B ubiquitin ligase that interacts with acidic activators, such as Gal4, and recruits Rad6 and its binding partner Lge1 to target promoters  . In S. pombe the equivalent protein to Lge1 appears to be Shf1.. 
PF11489 Protein of unknown function (DUF3210)<br>This is a family of proteins conserved in yeasts. The function is not known. The Schizosaccharomyces pombe member is Swiss:O94497 and the Saccharomyces cerevisiae member is Swiss:P40563.. 
PF11490 DNA_pol3_alph_N;<br>DNA polymerase III polC-type N-terminus II. Pfam-B_853 (release 23.0). This is the second N-terminal domain, NII domain, of the DNA polymerase III polC subunit A that is found only in Firmicutes. DNA polymerase polC-type III enzyme functions as the 'replicase' in low G + C Gram-positive bacteria  .  Purine asymmetry is a characteristic of organisms with a heterodimeric DNA polymerase III alpha-subunit constituted by polC which probably plays a direct role in the maintenance of strand-biased gene distribution; since, among prokaryotic genomes, the distribution of genes on the leading and lagging strands of the replication fork is known to be biased  . It has been predicted that the N-terminus of polC folds into two globular domains, NI and NII. A predicted hydrophobic surface patch suggests this domain may be involved in protein binding  . This domain is associated with DNA_pol3_alpha Pfam:PF07733 and DNA_pol3_a_NI Pfam:PF14480.. 
PF11491 Protein of unknown function (DUF3213)   <br>The backbone structure of this family of proteins has been determined however the function remains unknown. The protein has an alpha and beta structure with a ferredoxin-like fold  .. 
PF11492 Cricket paralysis virus, VP4<br>This is a family of minor capsid proteins, known as VP4, from the dicistroviridae. The dicistroviridae is a group of small, RNA-containing viruses that are closely structurally related to the picornaviridae. VP4 is a short, extended polypeptide chain found within the viral capsid, at the interface between the external protein shell and packaged RNA genome .. 
PF11493 Thylakoid soluble phosphoprotein TSP9<br>The plant-specific protein, TSP9 is phosphorylated and released in response to changing light conditions from the photosynthetic membrane. The protein resembles the characteristics of transcription/translation regulatory factors. The structure of the protein is predicted to consist of a random coil  .. 
PF11494 Ta0938<br>Ta0938 is a protein of unknown function however the structure has been determined. The protein has a novel fold and a putative Zn-binding motif. The structure has two different parts, one region contains a beta sheet flanked by two alpha helices and the other contains a bundle of loops which contain all cysteines in the protein  .. 
PF11495 Archaeal transcriptional regulator TrmB<br>TrmB is an alpha-glucoside sensing transcriptional regulator. The protein is the transcriptional repressor for gene cluster encoding trehalose/maltose ABC transporter in T.litoralis and P.furiosus  . TrmB has lost its DNA binding domain but retained its sugar recognition site. A nonreducing glucosyl residue is shared by all substrates bound to TrmB which suggests that its a common recognition motif  .. 
PF11496 Class II histone deacetylase complex subunits 2 and 3<br>This family of class II histone deacetylase complex subunits HDA2 and HDA3 is found in fungi, The member from S. pombe is referred to as Ccq1 in Swiss:Q10432. These proteins associate with HDA1 to generate the activity of the HDA1 histone deacetylase complex. HDA1 interacts with itself and with the HDA2-HDA3 subcomplex to form a probable tetramer and these interactions are necessary for catalytic activity. The HDA1 histone deacetylase complex is responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. HDA2 and HDA3 have a conserved coiled-coil domain towards their C-terminus  .. 
PF11497 NADH-quinone oxidoreductase chain 15<br>This protein, Nqo15, is a part of respiratory complex 1 which is a complex that plays a central role in cellular energy production in both bacteria and mitochondria. Nqo15 has a similar fold to Frataxin, the mitochondrial iron chaperone. This protein may have a role in iron-sulphur cluster regeneration in the complex. This domain represents more than half the molecular mass of the entire complex  .. 
PF11498 Transcriptional activator LAG-3<br>The C.elegans Notch pathway, involved in the control of growth, differentiation and patterning in animal development, relies on either of the receptors GLP-1 or LIN-12  . Both these receptors promote signalling by the recruitment of LAG-3 to target promoters, where it then acts as a transcriptional activator. LAG-3 works as a ternary complex together with the DNA binding protein, LAG-1  .. 
PF11500 Spindle pole body formation-associated protein<br>This is the central coiled-coil region of cut12 also found in other fungi, barring S. cerevisiae. The full protein has two predicted coiled-coil regions, and one consensus phosphorylation site for p34cdc2 and two for MAP kinase. During fission yeast mitosis, the duplicated spindle pole bodies (SPBs) nucleate microtubule arrays that interdigitate to form the mitotic spindle. Cut12 is localised to the SPB throughout the cell cycle, predominantly around the inner face of the interphase SPB, adjacent to the nucleus  . Cut12 associates with Fin1 and is important in this context for the activity of Plo1  .. 
PF11501 Non structural protein Nsp1<br>Nsp1 is the N-terminal cleavage product from the viral replicase that mediates RNA replication and processing  . The specific function of the protein is unknown however the structure has been determined. The protein has a novel alpha/beta fold formed by a 6 stranded beta barrel with an alpha helix covering one end of the barrel and another helix alongside the barrel  . Nsp1 could be involved in the degradation of mRNA.. 
PF11502 B-cell lymphoma 9 protein<br>The Wnt pathway plays a role in embryonic development, stem cell growth and tumorigenesis. BCL9 associates with beta-catenin and Tcf in the nucleus when the Wnt pathway is stimulated leading to the transactivation of Wnt target genes  .. 
PF11503 Protein of unknown function (DUF3215)<br>This family of proteins with unknown function appears to be restricted to Saccharomycetaceae.. 
PF11504 Colicin Ia<br>Colicins are toxic molecules secreted to kill other bacteria in times of stress. Colicin Ia kills susceptible E.coli cells by binding to the colicin I receptor leading to the formation of a voltage-dependant ion channel. The protein can be divided into three domains, a translocation domain, a receptor binding domain and a channel forming domain  .. 
PF11505 Protein of unknown function (DUF3216)<br>This family of archaeal proteins with unknown function appears to be restricted ton Thermococcaceae.. 
PF11506 Protein of unknown function (DUF3217)<br>This family of proteins with unknown function appears to be restricted to Mycoplasma. Some members in this family of proteins are annotated as MG376 however this cannot be confirmed.. 
PF11507 Ebola virus-specific transcription factor VP30<br>VP30 is a nucleocapsid-associated Ebola virus-specific transcription factor  . It acts by stabilising nascent mRNA in Ebola virus replication. The C terminal domain of VP30 folds into a dimeric helical assembly. VP30 assembles into hexamers in solution by an N-terminal oligomerisation domain which activates the transcription function of the protein. The oligomerisation is mediated by hydrophobic amino acids at 94-112  .. 
PF11508 Protein of unknown function (DUF3218)<br>This family of proteins with unknown function appears to be restricted to Pseudomonas.. 
PF11510 Fanconi Anaemia group E protein FANCE<br>Fanconi Anaemia (FA) is a cancer predisposition disorder. In response to DNA damage, the FA core complex monoubiquitinates the downatream FANCD2 protein. The protein FANCE has an important role in DNA repair as it is the FANCD2-binding protein in the FA core complex so it represents the link between the FA core complex and FANCD2  . The sequence shown is the C terminal domain of the protein which consists predominantly of helices and does not contain any beta-strand. The fold of the polypeptide is a continuous right-handed solenoidal pattern from the N terminal to the C terminal end  .. 
PF11511 Intrinsic membrane protein PufX<br>PufX organises RC-LH1, the photosynthesis reaction centre-light harvesting complex 1 core complex of Rhodobacter sphaeroides  . It also facilitates the exchange of quinol for quinone between the reaction centre and cytochrome bc(1) complexes. In organic solvent, PufX contains two hydrophobic helices which are flanked by unstructured regions and connected by a helical bend  .. 
PF11512 Agrobacterium tumefaciens protein Atu4866<br>Atu4866 is a protein with unknown function from Agrobacterium tumefaciens however the structure has been determined. Atu4866 adopts a streptavidin-like fold and has a beta-barrel/sandwich which is formed by eight antiparallel beta-strands  . Atu4866 has a potential ligand-binding site where is has a stretch of conserved residues on the surface  .. 
PF11513 Thermoplasma acidophilum protein TA0956<br>TA0956 is a protein from Thermoplasma acidophilum which currently has no known function however the structure has been determined. The protein has a two-layered alpha/beta-sandwich topology and is a putative Elongation factor 1-alpha binding motif  .. 
PF11514 Protein of unknown function (DUF3219)<br>This family of proteins with unknown function appears to be restricted to Bacillaceae. Some members in this family of proteins are annotated as YkvR however this cannot be confirmed.. 
PF11515 Mouse development and cellular proliferation protein Cullin-7<br>The Cullin Ring Ligase family member, Cul7, is required for normal mouse development and cellular proliferation. Cul7 has a CPH domain which is a p53 interaction domain. The CPH domain interaction surface of P53 is present in the tetramerisation domain  .. 
PF11516 Protein of unknown function (DUF3120)<br>This family of proteins with unknown function appears to be restricted to Bordetella.. 
PF11517 Nuclear abundant poly(A) RNA-bind protein 2 (Nab2)<br>Nab2 is a yeast heterogeneous nuclear ribonucleoprotein that modulates poly(A) tail length and mRNA. This is the N terminal domain of the protein which mediates interactions with the C-terminal globular domain, Myosin-like protein 1 and the mRNA export factor, Gfd1  .The N-terminal domain of Nab2 shows a structure of a helical fold. The N terminal domain of Nab2 is thought to mediate protein protein interactions that facilitate the nuclear export of mRNA  . An essential hydrophobic Phe73 patch on the N terminal domain is thought to be a important component of the interface between Nab2 and Mlp1  .. 
PF11518 Protein of unknown function (DUF3221)<br>This family of proteins with unknown function appears to be restricted to Bacillus. Some members in this family of proteins are annotated as YobA however this cannot be confirmed. YobA is a protein with unknown function.. 
PF11519 Protein of unknown function (DUF3222)<br>This family of proteins with unknown function appears to be restricted to Rhodopseudomonas.. 
PF11520 Chromatin protein Cren7<br>Cren7 is a chromatin protein found in Crenarchaeota and has a higher affinity for double-stranded DNA than for single-stranded DNA. The protein contains negative DNA supercoils and is associated with genomic DNA in vivo.Cren7 interacts with duplex DNA through a beta-sheet and a long flexible loop. The function has not been completely determined but it is thought that the protein may have a role similar to that of archaeal proteins in Euryarchaea  .. 
PF11521 C-terminal general transcription factor TFIIE alpha<br>TFIIE is compiled of two subunits, alpha and beta. This family of proteins are the C terminal domain of the alpha subunit of the protein which is the largest subunit and contains several functional domains which are important for basal transcription and cell growth. The C terminal end of the protein binds directly to the amino-terminal PH domain of p62/Tfb1 (of IIH) which is involved in the recruitment of the general transcription factor IIH to the transcription preinitiation complex. P53 competes for the same binding site as TFIIE alpha which shows their structural similarity. Like p53, TFIIE alpha 336-439 can activate transcription in vivo  .. 
PF11522 Yeast phosphatidylinositol-4-OH kinase Pik1<br>Pik1 is a regulator of membrane traffic and participates in the mating-pheromone signal-transduction cascade. The protein is localised to the nucleus and cytoplasm in the Golgi. Pik1 is thought to have an actin-independent role in membrane transport  .. 
PF11523 Protein of unknown function (DUF3223)<br>This family of proteins has no known function.. 
PF11524 Selenium binding protein<br>Selenium is an important nutrient that needs to be regulated since lack of the nutrient leads to cell abnormalities and high concentrations are toxic.\. SeBP regulates the level of free selenium in the cell by sequestering the nutrient during transport. SeBP acts as a pentamer and delivers the selenium to the selenophosphate synthetase enzyme  . Each subunit is composed of an alpha helix on top of a four stranded twisted ss sheet, stabilised by hydrogen bonds  .. 
PF11525 Copper resistance protein K<br>CopK is a periplasmic dimeric protein which is strongly up-regulated in the presence of copper, leading to a high periplasmic accumulation  . CopK has two different binding sites for Cu(I), each with a different affinity for the metal. Binding of the first Cu(I) ion induces a conformational change of CopK which involves dissociation of the dimeric apo-protein. Binding of a second Cu(I) further increases the plasticity of the protein. CopK has features that are common with functionally related proteins such as a structure consisting of an all-beta fold and a methionine-rich Cu(I) binding site  .. 
PF11526 Subunit of cleavage factor IA Pcf11<br>Pcf11 is a subunit of an essential polyadenylation factor in Saccharomyces cerevisiae, CFIA. Pcf11 binds to Clp1, another subunit of CFIA whose interaction is responsible for maintaining a tight coupling between the Clp1 nucleotide binding subunit and the other components of the polyadenylation machinery  .. 
PF11527 The ARF-like 2 binding protein BART<br>BART binds specifically to ARL2.GTP with a high affinity however it does not bind to ARL2.GDP. It is thought that this specific interaction is due to BART being the first identified ARL2-specific effector. The function is not completely characterised  . BART is predominantly cytosolic but can also be found to be associated with mitochondria. BART is also involved in binding to the adenine nucleotide transporter ANT1  .. 
PF11528 Protein of unknown function (DUF3224)<br>This bacterial family of proteins has no known function.. 
PF11529 Melampsora lini avirulence protein AvrL567-A<br>AvrL567-A is a protein from the fungal pathogen flax which induces plant disease resistance in flax plants  . The protein has a novel fold  .. 
PF11530 Minor type IV pilin, PilX<br>PilX is a protein from Neissaria meningitidis which is crucial for the formation of bacterial aggregates and adhesion to human cells  . The structure of PilX is similar to all pilins as it has the common alpha/beta roll fold. PilX subunits have surface-exposed motifs which are thought to stabilise bacterial aggregates against pilus retraction. It also illustrates how a minor pilus component can modulate the virulence properties of pili which have a simple composition and structure  .. 
PF11531 Coactivator-associated arginine methyltransferase 1 N terminal<br>CARM1 is an arginine methyltransferase which methylates a variety of different proteins and plays a role in gene expression. This is the N terminal domain of the protein which has a PH domain, normally present to regulate protein-protein interactions.A molecular switch is also present on the N terminal domain  .. 
PF11532 Heterogeneous nuclear ribonucleoprotein M<br>HnRNP M is a splicing regulatory factor that binds to the auxiliary RNA cis-element ISE/ISS-2 which promotes splicing of exon IIIb and silencing of exon IIIC in the fibroblast growth factor receptor 2 (FGFR2)  . By binding to ISE/ISS-3, HnRNP M plays a role in the regulation of alternative splicing in FGFR2 as it induces exon skipping and promotes exon inclusion  .. 
PF11533 Protein of unknown function (DUF3225)<br>This bacterial family of proteins has no known function.. 
PF11534 Hexameric tyrosine-coordinated heme protein (HTHP)<br>HTHP is from the marine bacterium Silicibacter pomeroyi and has peroxidase and catalase activity. HTHP consists of six monomers which each binds a solvent accessible heme group and is stabilised by the interaction of three neighbouring monomers  . The heme iron is penta-coordinated with a tyrosine residue as proximal ligand  .. 
PF11535 Calcium binding<br>CcbP is a Ca(2+) binding protein which, in Anabaena, is thought to bind Ca(2+) by protein surface charge. When bound to Ca(2+), the protein becomes more compact and the level of free calcium decreases. The free Ca(2+) concentration which is regulated by CcbP is critical for the differentiation process  . Calcium signalling is widespread in bacterial species, and prokaryotic cells like eukaryotes are equipped with all the elements to maintain Ca2+ homeostasis  .. 
PF11536 Protein of unknown function (DUF3226)<br>This archaeal family of proteins has no known function.. 
PF11537 Protein of unknown function (DUF3227)<br>This archaeal family of proteins has no known function.. 
PF11539 Protein of unknown function (DUF3228)<br>This family of proteins has no known function.. 
PF11538 Snurportin1<br>Snurportin1 is a novel nuclear import receptor which contains an N-terminal importin beta binding domain which is essential for its function of a snRNP-specific nuclear import receptor  . Snurportin1 interacts with m3G-cap where it enhances the m3G-cap dependent nuclear import of U snRNPs in Xenopus laevis oocytes and digitonin-permeabilized HeLa cells  .. 
PF11540 Cytoplasmic dynein 1 intermediate chain 2<br>Intermediate chain IC 2 forms part of the complex cytoplasmic dynein 1 along with a heavy chain (HC), two light intermediate chains (LICs) and three light chains (LCs). The complex is responsible for hydrolysing ATP to generate force toward the minus end of microtubules  . IC binds to the HC via the N terminal binding domain on the HC and ICs contain binding sites for the LCs. The ICs are responsible for binding to kinetochores and the Golgi apparatus through an interaction with the p150Glued subunit of dynactin which is another complex  . . 
PF11542 Mitochondrial division protein 1<br>Mdv1 is a component of the mitochondrial fission machinery in Saccharomyces cerevisiae. The protein is also involved in peroxisome proliferation  . Mdv1 along with Fis1 is also involved in controlling Dnm-1 dependant devision, a GTPase involved in the mediation of mitochondrial division. In this role, Mdv1 is the linker between Fis1 and Dnm1. Mdv1 plays a key role in the regulation of Dnm1 self-assembly  .. 
PF11543 Nuclear pore localisation protein NPL4<br>Npl4 is part of the heterodimer UN along with Ufd1 which is involved in the recruitment of p97, an AAA ATPase, for tasks involving the ubiquitin pathway. Npl4 has a ubiquitin-like domain which has within its structure a beta-grasp fold with a helical insert  .. 
PF11544 Spindle pole body component Spc42p<br>Spc42p is a 42-kD component of the S.cerevisiae spindle body that localises to the electron dense central region of the SPB  .Spc42p is a phosphoprotein which forms a polymeric layer at the periphery of the SPB central plaque. This functions during SPB duplication and also facilitates the attachment of the SPB to the nuclear membrane  .. 
PF11545 Cell surface heme-binding protein Shp<br>Shp is part of a complex which functions in heme uptake in Streptococcus pyogenes. During which, Shp transfers its heme to HtsA which is a component of an ABC transporter. The heme binding region of Shp contains an immunoglobulin-like beta-sandwich fold and has a unique heme-iron coordination with the axial ligands being two methionine residues from the same Shp molecule  . Surrounding the heme pocket, there is a negative surface which may serve as a docking interface for heme transfer  .. 
PF11546 Staphylococcal complement inhibitor SCIN <br>SCIN is released by Staphylococcus aureus to counteract the host immune defense. The protein binds to and inhibits C3 convertases on the bacterial surface, reducing phagocytosis and blocking downstream effector functions by C3b deposition on its surface  . An 18 residue stretch 31-48 is crucial for SCIN activity  .. 
PF11547 E3 ubiquitin ligase EDD<br>EDD, the ER ubiquitin ligase from the HECT ligases, contains an N-terminal ubiquitin-associated domain which binds ubiquitin. Ubiquitin is recognised by helices alpha-1 and -3 in in the UBA domain. EDD is involved in DNA damage repair pathways and binds to mono-ubiquitinated proteins  .. 
PF11548 Protein-tyrosine phosphatase receptor IA-2<br>IA-2 is a protein-tyrosine phosphatase receptor that upon exocytosis, the cytoplasmic domain is cleaved and moves to the nucleus where it enhances transcription of the insulin gene  . The mature exodomain of IA-2 participates in adhesion to the extracellular matrix and is self-proteolyzed in vitro by reactive oxygen species which may be a new shedding mechanism  .. 
PF11549 Protein transport protein SEC31<br>Sec31 is involved in COPII coat formation as it forms through the sequential binding of three cytoplasmic proteins: Sar1, Sec23/24 and Sec13/31. Sec13/31 is recruited by the pre-budding complex and polymerisation of Sec13/31 occurs to form an octahedral cage that is the outer shell of the COPII coat  . Sec13/31 is a hetero-tetramer which is organised as a linear array of alpha-solenoid and beta-propeller domains to form a rod in which twenty-four copies assemble to form the COPII cub-octahedron  .. 
PF11550 Intracellular growth locus C protein<br>IglC protein is involved in the escape of F.tularensis live vaccine strain  . It has been shown that the expression of IglC is essential for F.tularensis to induce macrophage apoptosis  . IglC adopts a beta-sandwich conformation that has no similarity to any known protein structure  .. 
PF11551 Outer membrane protein Omp28<br>Omp28 is a 28-kDa outer membrane protein from Porphyromonas gingivalis. Omp28 is thought to be a surface adhesion/receptor protein. Omp28 is expressed in a wide distribution of P.gingivalis strains  .. 
PF11553 Protein of unknown function (DUF3231)<br>This bacterial family of proteins has no known function.. 
PF11554 Protein of unknown function (DUF3232)<br>This bacterial family of proteins has no known function.. 
PF11555 EGFR receptor inhibitor Mig-6<br>When the kinase domain of EGFR binds to segment one of Mitogen induced gene 6 (Mig-6), EGFR becomes inactive due to the conformation it adopts which is Src/CDK like. The binding of the two proteins prevents EGFR acting as a cyclin-like activator for other kinase domains  .The structure of Mig-6(1) consists of alpha helices-G and -H with a polar surface and hydrophobic residues for interactions with EGFR. A critical step for the activation of EGFR is the formation of an asymmetric dimer involving the kinase domains of the protein. Since Mig-6 binds to the kinase domain it blocks this process and EGFR becomes inactive  .. 
PF11556 Erythrocyte binding antigen 175<br>EBA-175 is involved in the formation of a tight junction, a necessary step in invasion. This family represents the region VI which is a cysteine rich domain essential for EBA-175 trafficking. The structure is a homodimer that contains a five-alpha-helical core stabilised by four disulphide bridges  .. 
PF11557 Protein of unknown function (DUF3233)<br>Pfam-B_5068 (release 23.0). This is a bacterial family of uncharacterised proteins.. 
PF11558 Het-s 218-289<br>This family of proteins is residues 218-289 of Het-s, a protein of Podospora anserina. Het-s plays a role in heterokaryon incompatibility which prevents different forms of parasitism  . This region of the protein is the C-terminal end and is unstructured in solution but forms infectious fibrils in vitro which has a structure consisting of a left-handed beta solenoid which contains two windings per molecule  .. 
PF11559 Afadin- and alpha -actinin-Binding<br>This family is found in mammals where it is localised at cell-cell adherens junctions  , and in Sch. pombe and other fungi where it anchors spindle-pole bodies to spindle microtubules  . It is a coiled-coil structure, and in pombe, it is required for anchoring the minus end of spindle microtubules to the centrosome equivalent, the spindle-pole body. The name ADIP derives from the family being composed of Afadin- and alpha -Actinin-Binding Proteins Localised at Cell-Cell Adherens Junctions.. 
PF11560 Lamina-associated polypeptide 2 alpha<br>LAPs are components of the nuclear lamina which supports the nuclear envelope.LAP2alpha is a non-membrane-associated member of the LAP family which is unique. This family of proteins is the C terminal domain of LAP2alpha which consists of residues 459-693 and constitutes a dimeric structure with an antiparallel coiled coil. LAP2alpha is involved in cell-cycle regulation and chromatin organisation and preferentially binds to lamin A/C  .. 
PF11561 Single strand annealing-weakened 1<br>This family of yeast proteins is involved in single-strand-annealing, or SSA. SSA entails multiple steps: end resection and ssDNA formation; annealing of complementary ssDNAs; removal of 3' single-stranded non-homologous tails; gap fill-in synthesis; and ligation. Saw1 in combination with Slx4 catalyses the 3' non-homologous tail removal during recombination. Saw1 interacts physically with Rad1/Rad10, Msh2/Msh3, and Rad52 proteins, and works by targeting Rad1/Rad10 to Rad52-coated recombination intermediates  .. 
PF11563 Protoglobin<br>Pollington J, Eberhardt R. This family includes protoglobin from Methanosarcina acetivorans C2A. It is also found near the N-terminus of the Haem-based aerotactic transducer HemAT in Bacillus subtilis (Swiss:O07621). It is part of the haemoglobin superfamily. Protoglobin has specific loops and an amino-terminal extension which leads to the burying of the haem within the matrix of the protein. Protoglobin-specific apolar tunnels allow the access of O2, CO and NO to the haem distal site  . In HemAT it acts as an oxygen sensor domain  .. 
PF11564 Restriction endonuclease BpuJI - N terminal<br>BpuJI is a restriction endonuclease which recognises the asymmetric sequence 5'-CCCGT and cuts at multiple sites in the surrounding area of the target sequence. This family of proteins is the N terminal domain of BpuJI which has DNA recognition functions. The recognition domain has two subdomains D1 and D2. The recognition of the target sequence occurs through major groove contacts of amino acids on the helix-turn-helix region and the N-terminal arm  .. 
PF11565 Alpha helical Porin B<br>Porin B is a porin from Corynebacterium glutamicum which allows the exchange of material across the mycolic acid layer which is the protective nonpolar barrier. Porin B has an alpha helical core structure consisting of four alpha-helices surrounding a nonpolar interior. There is a disulphide bridge between helices 1 and 4 to form a stable covalently bound ring  . The channel of PorB is oligomeric  .. 
PF11566 Inhibitor_PI31;<br>PI31 proteasome regulator N-terminal. PI31 is a regulatory subunit of the immuno-proteasome which is an inhibitor of the 20 S proteasome in vitro.PI31 is also an F-box protein Fbxo7.Skp1 binding partner which requires an N terminal FP domain in both proteins for the interaction to occur via the FP beta sheets. The structure of PI31 FP domain contains a novel alpha/beta-fold and two intermolecular contact surfaces  . This is the N-terminal domain of the members.. 
PF11567 Plasmodium falciparum UIS3 membrane protein<br>UIS3 is a membrane protein essential for sporozoite development in infected hepatocytes. This family is 130-229 of the Plasmodium falciparum UIS3 protein which is compact and has an all alpha-helical structure.PfUIS3(130-229) interacts with lipids, phospholipid lysosomes, the human liver fatty acid-binding protein and with the lipid phosphatidylethanolamine. The interaction with liver fatty acid-binding protein provides the parasite with a method to import essential fatty acids/lipids during rapid growth phases of sporozoites  .. 
PF11568 Mediator complex subunit 29<br>Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species [1-2]. It is arranged into four different sections, a core, a head, a tail and a kinase-active part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function  . Med29, along with Med11 and Med28, in mammals, is part of the core head-region of the complex. Med29 is the apparent orthologue of the Drosophila melanogaster Intersex protein, which interacts directly with, and functions as a transcriptional coactivator for, the DNA-binding transcription factor Doublesex, so it is likely that mammalian Med29 serves as a target for one or more DNA-binding transcriptional activators  .. 
PF11569 Homeodomain leucine-zipper encoding, Homez<br>Homez contains two leucine zipper-like motifs and an acidic domain and belongs to the superfamily of homeobox-containing proteins. The presence of leucine zippers suggests that Homez can function as a homo or heterodimer in the nucleus  . It is thought that the first leucine zipper and homeodomain 1 (HD1)of Homez is responsible for dimerisation and HD2 has a specific DNA-binding activity. Homez is also thought to function as a transcriptional repressor due to the acidic region in its C-terminal domain  . Homez is involved in a complex regulatory network  .. 
PF11570 Coiled-coil receptor-binding R-domain of colicin E2<br>E2 is a DNase which utilises the outer membrane receptor BtuB to bind to and enter the cell. This family of proteins is E2R135 (residues 321-443) which is the part of E2 which is responsible for binding to BtuB in a coiled coil formation  .. 
PF11571 Mediator complex subunit 27<br>Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species {1-2]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function  . Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. The ubiquitous expression of Med27 mRNA suggests a universal requirement for Med27 in transcriptional initiation. Loss of Crsp34/Med27 decreases amacrine cell number, but increases the number of rod photoreceptor cells  .. 
PF11572 Protein of unknown function (DUF3234)<br>This bacterial family of proteins has no known function. Some members in this family of proteins are annotated as TTHA0547 however this cannot be confirmed.. 
PF11573 Mediator complex subunit 23<br>Med23 is one of the subunits of the Tail portion of the Mediator complex that regulates RNA polymerase II activity. Med23 is required for heat-shock-specific gene expression, and has been shown to mediate transcriptional activation of E1A in mice.. 
PF11574 Protein of unknown function (DUF3235)<br>Some members in this family of proteins with unknown function are annotated as RpfA however this cannot be confirmed.. 
PF11575 FhuF 2Fe-2S C-terminal domain<br>Pfam-B_11690 (release 9.0). This family consists of several bacterial ferric iron reductase protein (FhuF) sequences.\.      FhuF is involved in the reduction of ferric iron in cytoplasmic ferrioxamine B  .  This domain is the C-terminal domain that contains 4 conserved cysteine residues that are found to be part of a 2Fe-2S cluster  .. 
PF11576 Protein of unknown function (DUF3236)<br>This family of proteins with unknown function appears to be restricted to Methanobacteria.. 
PF11577 NF-kappa-B essential modulator NEMO<br>NEMO is a regulatory protein which is part of the IKK complex along with the catalytic IKKalpha and beta kinases. The IKK complex phosphorylates IkappaB targeting it for degradation which results in the release of NF-kappaB which initiates the inflammatory response, cell proliferation or cell differentiation  . NEMO activates the IKK complex's activity by associating with the unphosphorylated IKK kinase C termini.The core domain of NEMO is a dimer which binds to two fragments of IKK  .. 
PF11578 Protein of unknown function (DUF3237)<br>This family of proteins has no known function. 
PF11579 Protein of unknown function (DUF3238)<br>This family of proteins with unknown function appears to be restricted to Bacillus cereus.. 
PF11580 Protein of unknown function (DUF3239)<br>This bacterial family of proteins may be membrane proteins however this cannot be confirmed. Currently there is no known function.. 
PF11581 Antagonist of EGFR signalling, Argos<br>Argos is a natural secreted antagonist of EGFR signalling which functions by binding growth factor ligands that activate EGFR by forming a clamp like structure using three disulphide-bonded beta-sheet domains  .. 
PF11582 Protein of unknown function (DUF3240)<br>This family of proteins with unknown function appears to be restricted to Proteobacteria.. 
PF11583 P-aminobenzoate N-oxygenase AurF<br>AurF is a metalloenzyme which is involved in the biosynthesis of antibiotic aureothin by catalysing the formation of p-nitrobenzoic acid from p-aminobenzoic acid. AurF is a non-heme di-iron monooxygenase which creates nitroarenes via the sequential oxidation of aminoarenes  .. 
PF11584 Proteinaceous host-selective toxin ToxA<br>ToxA is produced by particular Pyrenophora tritici-repentis races and is a proteinaceous host-selective toxin. It is necessary and sufficient to cause cell death in sensitive wheat cultivars  .ToxA adopts a single-domain, beta-sandwich fold which has novel topology. The protein is directly involved in recognition events required for ToxA action. It is thought to be distantly related to FnIII proteins, gaining entry to the host via an integrin-like receptor  .. 
PF11585 Insect antimicrobial peptide, stomoxyn<br>Stomoxyn, localised in the gut epithelium, is an insect antimicrobial peptide which functions in killing a range of microorganisms, parasites and some viruses. Stomoxyn has a structure consisting of a random coil in water however in TFE it adopts a stable helical structure. Stomoxyn is thought to have a similar function to cecropin A from Hyalophora cecropia due to structural similarities  .. 
PF11586 Protein of unknown function (DUF3242)  <br>This protein from Thermotoga maritima is a hypothetical ORFan protein, TM1622, whose structure has been determined. The protein is composed of seven beta strands and three alpha helices  .. 
PF11587 Major prion protein bPrPp - N terminal<br>This family represents the N-terminal domain (1-30) of the bovine prion protein (bPrPp). The proteins structure consists of mainly alpha helices. BPrPp forms a stable helix which inserts in a transmembrane location in the bilayer, with the N -terminal (1-30) functioning as a cell-penetrating peptide  .. 
PF11588 Protein of unknown function (DUF3243)<br>This family of proteins with unknown function appears to be restricted to Firmicutes.. 
PF11589 Domain of unknown function (DUF3244)<br>This domain adopts an immunoglobulin-like beta-sandwich fold  and structurally is most similar to fibronectin.. 
PF11590 DNA polymerase catalytic subunit Pol<br>This family of proteins represents the catalytic subunit, Pol, of the Herpes simplex virus DNA polymerase. Pol binds UL42, making up the DNA polymerase. UL42 is a processivity subunit which binds to the C-terminal of Pol in a similar way that the cell cycle regulator p21 binds to PCNA  .. 
PF11591 Ferredoxin chloroplastic transit peptide<br>The structure of chloroplast ferredoxin in water is unstructured however in a 30:70 molar-ratio mixture of 2,2,2-trifluoroethanol, residues 3 to 13 form an alpha-helix. The rest of the peptide remains unstructured  . This family is the N-terminal of the [2Fe-2S) ferredoxin from C.reinhardtii. This protein catalyses the final reaction in a pathway which allows the production of H(2) from water in the chloroplast  . . 
PF11592 Central core of the bacterial effector protein AvrPto<br>This family of proteins represents the bacterial effector protein AvrPto from Pseudomonas syringae. This is the central core region of the protein which consists of a three-helix bundle motif. AvrPto is part of a type III secretion system from P.syringae which is involved in the bacterial speck disease of tomato. In resistant plants, AvrPto interacts with the host Pto kinase, which elicits an antibacterial defense response. In plants lacking resistance, the Pto kinase is not present and AvrPto acts as a virulence factor, promoting bacterial growth  .. 
PF11593 Mediator complex subunit 3 fungal<br>Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function  . Mediator subunit Hrs1/Med3 is a physical target for Cyc8-Tup1, a yeast transcriptional co-repressor  .. 
PF11594 Mediator complex subunit 28<br>Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species [1-2]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function  . Subunit Med28 of the Mediator may function as a scaffolding protein within Mediator by maintaining the stability of a submodule within the head module, and components of this submodule act together in a gene-regulatory programme to suppress smooth muscle cell differentiation. Thus, mammalian Mediator subunit Med28 functions as a repressor of smooth muscle-cell differentiation, which could have implications for disorders associated with abnormalities in smooth muscle cell growth and differentiation, including atherosclerosis, asthma, hypertension, and smooth muscle tumours  .. 
PF11595 Protein of unknown function (DUF3245)<br>This is a family of proteins conserved in fungi. The function is not known, and there is no S. cerevisiae member.. 
PF11596 Protein of unknown function (DUF3246)<br>This is a small family of fungal proteins one of whose members, Swiss:A3LUS4 from Pichia stipitis is described as being an extremely serine rich protein-mucin-like protein.. 
PF11597 Mediator complex subunit 13 N-terminal<br>Mediator is a large complex of up to 33 proteins that is conserved from plants through fungi to humans - the number and representation of individual subunits varying with species [1-2]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Med13 is part of the ancillary kinase module, together with Med12, CDK8 and CycC, which in yeast is implicated in transcriptional repression, though most of this activity is likely attributable to the CDK8 kinase. The large Med12 and Med13 proteins are required for specific developmental processes in Drosophila, zebrafish, and Caenorhabditis elegans but their biochemical functions are not understood  .. 
PF11598 Cartilage oligomeric matrix protein<br>This family of proteins represents the five-stranded coiled-coil domain of cartilage oligomeric matrix protein (COMP). This region has a binding site between two internal rings formed by Leu37 and Thr40  . 
PF11599 RRNA methyltransferase AviRa<br>This family of proteins represents the methyltransferase AviRa from Streptomyces viridochromogenes. This protein mediates the resistance to the antibiotic avilamycin. AviRa methylates a specific guanine base within the peptidyl-transferase loop of the 23S ribosomal RNA  .. 
PF11600 Chromatin assembly factor 1 complex p150 subunit, N-terminal<br>CAF-1_p150 is a polypeptide subunit of CAF-1, which functions in depositing newly synthesised and acetylated histones H3/H4 into chromatin during DNA replication and repair  . CAF-1_p150 includes the HP1 interaction site, the PEST, KER and ED interacting sites. CAF-1_p150 interacts directly with newly synthesised and acetylated histones through the acidic KER and ED domains. The PEST domain is associated with proteins that undergo rapid proteolysis  .. 
PF11601 Shal-type voltage-gated potassium channels <br>This family of proteins represents Shal-type voltage-gated potassium channels which interact with Kv channel-interacting proteins to modulate cell surface expression and function of Kv4 channels. The interaction of the Shal-type protein Kv4.2 and the Kv interacting protein KChiP1 forms a structure which is like the structure between calmodulin and its target peptides when they interact. Interactions of an N terminal alpha helix in Kv4.2 and a C terminal alpha helix in KChIP1 are essential for the modulation of Kv4.2 by KChIPs  .. 
PF11602 ATPase P4 of dsRNA bacteriophage phi-12<br>P4 is a packaging motor which is involved in the packaging of phi-12 genome into preformed capsids using ATP. P4 is located at the vertices of the icosahedral capsid. ATP drives RNA translocation through cooperative conformational changes  .. 
PF11603 Regulatory protein Sir1<br>Sir1p interacts with the BAH domain of the Orc1p subunit of the origin recognition complex (ORC) resulting in the establishment of silent chromatin at HMR and HML in S.cerevisiae  . The amino acids from the ORC interaction region of Sir1p are presented on a conserved, convex surface that forms a complementary interface with the Orc1 BAH domain, critical for transcriptional silencing  .. 
PF11604 Copper binding periplasmic protein CusF<br>CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein  .. 
PF11605 Vacuolar protein sorting protein 36 Vps36<br>Vps36 is a subunit of ESCRT-II, a protein involved in driving protein sorting from endosomes to lysosomes. The GLUE domain of Vps36 allows for a tight interaction to occur between the protein and Vps28, a subunit of ESCRT-I. This interaction is critical for ubiquitinated cargo progression from early to late endosomes  .. 
PF11606 Family 31 carbohydrate binding protein<br>This family of proteins represents the family 31 carbohydrate-binding module of beta-1,2-xylanase. This protein is from Alcaligenes sp. strain XY-234. The AlcCBM31 module makes a beta-sandwich structure with an immunoglobulin fold and contains two intra-molecular disulfide bonds. AlcCBM31 shows affinity with only beta-1,3-xylan  .. 
PF11607 Protein of unknown function (DUF3247)<br>This family of proteins is the protein product of the gene XC5848 from Xanthomonas campestris. The protein has no known function however its structure has been determined. The protein adopts a Lsm fold however differences with the fold were observed at the N-terminal and internal regions  .. 
PF11608 Limkain b1<br>This family of proteins represents Limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures  .. 
PF11609 Protein of unknown function (DUF3248)<br>This family of proteins is thought to be the product of the gene TT1592 from Thermus thermophilus however this cannot be confirmed. Currently there is no known function.. 
PF11610 Scaffold protein Ste5-Fus5 binding region<br>This family of proteins represents the Fus5 binding region of Ste5. Ste5 functions in the yeast mating pathway and is required for signalling through the mating response MAPK pathway. Ste5 has separate binding sites for each member of the MAPK cascade. This region of Ste5 allosterically activates autophosphroylation of Fus3, a mitogen-activated protein kinase. Auto-activated Fus3 has a negative regulatory role, and promotes Ste5 phosphorylation which leads to a decrease in pathway transcriptional output  .. 
PF11611 TRF2;<br>Domain of unknown function (DUF4352). Members of these family are poutative lipoproteins that fall into the Antigen MPT63/MPB63 (immunoprotective extracellular protein) superfamily.. 
PF11612 GspJ;<br>Type II secretion system (T2SS), protein J. Pollington J, Desvaux M. The T2SJ proteins are pseudopilins, which are targeted to the membrane in E. Coli. T2SJ forms a complex with T2SI (Pfam:PF02501) and T2SK (Pfam:PF03934) which is part of the Type II secretion apparatus involved in the translocation of proteins across the outer membrane in E.coli. The T2SK-I-J complex has quasihelical characteristics  .. 
PF11613 Agonist of corticotropin releasing factor R2, Urocortin-2<br>This family of proteins represents urocortin 2, a member of the corticoliberin family which is a selective agnonist of corticotropin releasing factor 2. The backbone of the protein is mainly alpha-helical but it contains a helix-loop-helix motif  .. 
PF11614 Bre5;<br>IG-like fold at C-terminal of FixG, putative oxidoreductase. Pollington J, Coggill P. This domain is part of a transmembrane protein, FixG, itself part of the FixGHIS operon closely associated with the FixNOPQ operon that is the symbiotically essential cbb3-type haem-copper oxidase complex. FixG expression is induced by oxygen-deprivation. This C-terminal domain adopts an E-set Ig-like fold.. 
PF11615 Protein of unknown function (DUF3249)<br>This family of proteins represents the gene product of the protein CAF4, the yeast protein YKR036c. This protein contains seven WD40 repeats in its C terminus. The function however is unknown  .. 
PF11616 WD repeat binding protein EZH2<br>This family of proteins represents Enhancer of zest homolog 2, (EZH2) a 30 residue peptide which binds to a WD-repeat domain of EED by residues 39-68. EED is a component of PRC2 complex which is involved in gene expression  . This interaction is required for the HMTase activity of PCR2  .. 
PF11617 Protein metal binding site<br>This family of proteins represents a unique protein copper binding site that involves a tryptophan metabolite, kynurenine in the protein MopE. The production of kyneurenin by modification of tryptophan and its involvement in copper binding is an innate property of MopE  .. 
PF11618 Protein of unknown function (DUF3250)<br>This family of proteins represents a protein with unknown function. It may be the C2 domain from KIAA1005 however this cannot be confirmed.. 
PF11619 Transcription factor P53 - C terminal domain<br>This family of proteins is the C terminal domain of the transcription factor P53. While the rest of the protein is quite conserved between the different transcription factors such as p53 and p73, the C terminal domain is highly divergent. The DM-p53 structure is characterized by an additional N-terminal beta-strand and a C-terminal helix  .. 
PF11620 GA-binding protein alpha chain<br>This family of proteins represents the transcription factor GABP alpha. This alpha domain is a five-stranded beta-sheet crossed by a distorted helix termed an OST domain. The surface of the GABP alpha OST domain contains two clusters of negatively-charged residues suggesting there are positively-charged partner proteins. The OST domain binds to the CH1 and CH3 domains of the co-activator histone acetyltransferase CBP/p300, a direct link between GABP and transcriptional machinery has been made  .. 
PF11621 C3 binding domain 4 of IgG-bind protein SBI<br>This family of proteins represents Sbi domain IV which binds the central complement protein C3. Sbi-IV interacts with Sbi-III to induce a consumption of complement via alternative pathway activation  . When not interacting with Sbi-III, Sbi-IV inhibits the alternative pathway without complement consumption. The structure of Sbi-IV consists of a three-helix bundle fold  .. 
PF11622 Protein of unknown function (DUF3251)<br>This family of proteins with unknown function appears to be restricted to Enterobacteriaceae. Some members if this family are annotated as putative lipoprotein YajI however this cannot be confirmed.. 
PF11623 Protein of unknown function (DUF3252)<br>This family of proteins has no known function. Some members are annotated as Ssl0352 however this cannot be confirmed. Currently there is no known function.. 
PF11624 MHC class I-like protein M157<br>This family of proteins represents M157,a divergent form of MHC class I-like proteins which is the protein product of the mouse cytomegalovirus. This protein is unique in its ability to engage both activating (Ly49H) and inhibitory (Ly49I) natural killer cell receptors. M157 is involved in intra- and intermolecular interacts within and between its domains to form a compact MHC-like molecule  .. 
PF11625 Protein of unknown function (DUF3253)<br>This bacterial family of proteins has no known function.. 
PF11626 Rap1_C; TRF2IP; Yippee-Rap1;<br>TRF2-interacting telomeric protein/Rap1 - C terminal domain. This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres  . The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C terminal domain  . Rap1 is otherwise known as TRF2-interacting protein, as it is one of the six subunit components of the Shelterin complex. Shelterin protects telomere ends from attack by DNA-repair mechanisms [2,3,4,5].. 
PF11627 Nuclear factor hnRNPA1<br>This family of proteins represents hnRNPA1, a nuclear factor that binds to Pol II transcripts. The family of hnRNP proteins are involved in numerous RNA-related activities  .. 
PF11628 T-cell surface glycoprotein CD3 zeta chain<br>The incorporation of the zetazeta signalling module requires one basic TCR alpha and two zetazeta aspartic acid TM residues  . The structure of the zetazeta(TM) dimer consists of a left-handed coiled coil with polar contacts. Two aspartic acids are critical for zetazeta dimerisation and assembly with TCR  .. 
PF11629 C terminal SARAH domain of Mst1<br>This family of proteins represents the C terminal SARAH domain of Mst1. SARAH controls apoptosis and cell cycle arrest via the Ras, RASSF, MST pathway. The Mst1 SARAH domain interacts with Rassf1 and Rassf5 by forming a heterodimer which mediates the apoptosis process  .. 
PF11630 Protein of unknown function (DUF3254)<br>This family of proteins is most likely a family of anti-lipopolysaccharide factor proteins however this cannot be confirmed.. 
PF11631 Protein of unknown function (DUF3255)<br>Members in this family of proteins are annotated as YxeF however no function is currently known. The family appears to be restricted to Bacillus.. 
PF11632 Lactococcin G-beta<br>This family of proteins is LcnG-beta, which with LcnG-alpha constitute the two-peptide bacteriocin lactococcin G (LcnG). This family of proteins represents the N terminal domain which has an alpha-helical structure and is amphiphilic. Both peptides have a GxxxG motif which they use for interaction through a helix-helix structure  .. 
PF11633 Nsp3;<br>Single-stranded poly(A) binding domain. This family of proteins represents Nsp3c, the product of ORF1a in group 2 coronavirus. The domain exhibits a macrodomain fold containing the nsp3 residues 528 to 648, with a flexibly extended N-terminal tail from residues 513 to 527 and a C-terminal flexible tail of residues 649 to 651. SUD-M(527-651) binds single-stranded poly(A); the contact area with this RNA on the protein surface, and the electrophoretic mobility shift assays confirm that SUD-M has higher affinity for purine bases than for pyrimidine bases.. 
PF11634 Nuclease inhibitor from bacteriophage T4<br>This family of proteins represents IPI from bacteriophage T4. This protein is a nuclease inhibitor which is injected by T4 to protect its DNA from gmrS/gmrD CT of pathogenic Escherichia coli into the infected host  . The structure of this protein consists of two small beta-sheets flanked by N and C termini by alpha-helices. The protein has a gmrS/gmrD hydrophobic binding site  .. 
PF11635 Mediator complex subunit 16<br>Mediator is a large complex of up to 33 proteins that is conserved from plants through fungi to humans - the number and representation of individual subunits varying with species [1-2]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function.\.   Med16 is one of the subunits of the Tail portion of the Mediator complex and is required for lipopolysaccharide gene-expression  . Several members including the human protein, Swiss:Q9Y2X0, have one or more WD40 domains on them, Pfam:PF00400.. 
PF11636 Troponin I residues 1-32<br>This family of proteins represents the cardiac N-extension of troponin I. This region of the protein (1-32) interacts with the N-lobe of cTnC and modulates myofilament calcium(2) sensitivity  . . 
PF11637 ATP-dependant DNA helicase UvsW<br>This family of proteins represents the DNA helicase UvsW from bacteriophage T4. The protein is a member of the monomeric SF2 helicase superfamily and shows structural homology to the eukaryotic SF2 helicase Rad54. UvsW is thought to have a role in recombination and the rescue of stalled replication forks  .. 
PF11638 DnaA N-terminal domain<br>pdb_2jmp & Jackhmmer:B3CS04. This family of proteins represents the N-terminal domain of DnaA, a protein involved in the initiation of bacterial chromosomal replication. The structure of this domain is known  . It is also found in three copies in some proteins such as Swiss:B5V0X4. The exact function of this domain is uncertain but it has been suggested to play a role in oligomerisation.. 
PF11639 REDY-like protein HapK<br>This family of proteins represents HapK, a protein of unknown function, with two homologues PigK and RedY. The monomer structure of the protein contains a four-stranded anti parallel beta-sheet, three alpha-helices and a short C terminal tail which it uses for dimer formation  . The surface of HapK has a deep cavity with consists of a kinked helix and a beta-four strand. HapK could be involved in prodigiosin biosynthesis, specifically the binding of a bipyrrole intermediate such as HBM or MBM  .. 
PF11640 Telomere-length maintenance and DNA damage repair<br>Pfam-B_6865 (release 23.0). ATM is a large protein kinase, in humans, critical for responding to DNA double-strand breaks (DSBs). Tel1, the orthologue from budding yeast, also regulates responses to DSBs. Tel1 is important for maintaining viability and for phosphorylation of the DNA damage signal transducer kinase Rad53 (an orthologue of mammalian CHK2). In addition to functioning in the response to DSBs, numerous findings indicate that Tel1/ATM regulates telomeres. The overall domain structure of Tel1/ATM is shared by proteins of the phosphatidylinositol 3-kinase (PI3K)-related kinase (PIKK) family, but this family carries a unique and functionally important TAN sequence motif, near its N-terminal, LxxxKxxE/DRxxxL. which is conserved specifically in the Tel1/ATM subclass of the PIKKs. The TAN motif is essential for both telomere length maintenance and Tel1 action in response to DNA damage  . It is classified as an EC:2.7.11.1.. 
PF11641 Glycosylphosphatidylinositol-anchored merozoite surface protein<br>This family of proteins represents the core region of Bd37, a surface antigen of B.divergens which is GPI-anchored at the surface of the merozoite. The structure of the protein consists of mainly alpha folds and has three sub domains  .. 
PF11642 Mite allergen Blo t 5<br>This family of proteins is Blo t 5, an allergen protein from Blomia tropicalis mites. This protein shoes strong reactivity with IgE in asthmatic and rhinitis patients. The structure of the protein contains three alpha helices which form a coiled-coil  .. 
PF11644 Protein of unknown function (DUF3256)<br>This family of proteins with unknown function appears to be restricted to Bacteroidales.. 
PF11645 DUF3257;<br>PD-(D/E)XK endonuclease. This family of endonucleases includes a group I intron-encoded endonuclease  . This family belongs to the PD-(D/E)XK superfamily [2-3].. 
PF11646 Protein of unknown function DUF3258<br>This viral family are possible phage integrase proteins however this cannot be confirmed.. 
PF11647 C-terminal region of Pasteurella multocida toxin residues 569-1285<br>This family represents the C terminal region of Pasteurella multocida toxin (PMT) which displays a Trojan horse-like shape with three domains, C1, C2 and C3. The C3 domain possesses the Cys-His-Asp catalytic triad. PMT is an enzyme toxin carrying the cysteine protease-like catalytic triad which functions on the cytoplasmic face of the plasma membrane of target cells  .. 
PF11648 C-terminal domain of RIG-I<br>This family of proteins represents the regulatory domain RD of RIG-I, a protein which initiates a signalling cascade that provides essential antiviral protection for the host. The RD domain binds viral RNA, activating the RIG-I ATPase by RNA-dependant dimerisation. The structure of RD contains a zinc-binding domain and is thought to confer ligand specificity  .. 
PF11649 Virus neck protein<br>This family of protein represents gene product 14, a major component of the neck in T4-like viruses along with gene product 13. Gene product 14 is rich is beta-sheets. The formation of the neck to the head of the bacteriophage is crucial for the tail attachment  .. 
PF11650 P22 tail accessory factor<br>This tail accessory factor of the P22 virus is also referred to as gene product 4 (Gp4). The proteins structure consists of 60% alpha helices. Gp4 is the first tail accessory factor to be added to newly DNA-filled capsids during P22-morphogenesis. In solution, the protein acts as a monomer and has low structural stability. The interaction of gp4 with the portal protein involves the binding of two non-equivalent sets of six gp4 proteins  . Gp4 acts as a structural adaptor for gp10 and gp26, the other tail accessory factors  .. 
PF11651 P22 coat protein - gene protein 5<br>This family of proteins represents gene product 5 from bacteriophage P22. This protein is involved in the formation of the pro-capsid shells in the bacteriophage. In total, there are 415 molecules of the coat protein which are arranged in an icosahedral shell  .. 
PF11652 Protein of unknown function (DUF3259)<br>This eukaryotic family of proteins has no known function.. 
PF11653 Bacteriophage T7 virion assembly protein<br>This family of proteins represents the gene product 7.3 from T7 bacteriophage. The protein is localised to the tail and is thought to be important in virion assembly. Particles assembled in the absence of the protein fail to adsorb to cells  .. 
PF11654 Protein of unknown function (DUF2665)<br>Some members in this family are annotated as Non classical export proteins, however no specific function is known.. 
PF11655 Protein of unknown function (DUF2589)   <br>This family of proteins has no known function.. 
PF11656 ComReg_Spx;<br>YjbD family (DUF3811). This is a family of proteobacteria proteins of unknown function. This family is unrelated to Pfam:PF03960 which contains a set of transcription factors that are also named YjbD.. 
PF11657 Transcriptional activator TraM <br>TraM is required for quorum dependence. It binds to and in-activates TraR which controls the replication of the tumour-inducing virulence plasmid. TraM interacts in a two-step process with DNA-TraR to form a large, stable anti-activation complex [1,2].. 
PF11658 Protein of unknown function (DUF3260)<br>Pfam-B_003054 (release 23.0). Some members in this family of proteins are annotated as YhjU however this cannot be confirmed. Currently this family has no known function.. 
PF11659 Protein of unknown function (DUF3261)<br>Pfam-B_003077 (release 23.0). This family of proteins with unknown function appears to be restricted to Proteobacteria.. 
PF11660 Protein of unknown function (DUF3262)<br>Pfam-B_003096 (release 23.0). This family of proteins with unknown function appears to be restricted to Proteobacteria.. 
PF11661 Protein of unknown function (DUF2986)<br>Pfam-B_003109 (release 23.0). This family of proteins has no known function.. 
PF11662 Protein of unknown function (DUF3263)<br>Pfam-B_003189 (release 23.0). This family of proteins with unknown function appears to be restricted to Actinobacteria.. 
PF11663 Toxin with endonuclease activity YhaV<br>Pfam-B_003231 (release 23.0). YhaV causes reversible bacteriostasis and is part of a toxin-antitoxin system in Escherichia coli along with PrlF. The toxicity of YhaV is counteracted by PrlF by the formation of a tight complex which binds to the promoter of the prlF-yhaV operon. In vitro, YhaV also has endonuclease activity  .. 
PF11665 Protein of unknown function (DUF3265)<br>Pfam-B_001494 (release 23.0). This family of proteins with unknown function appear to be restricted to Vibrio.. 
PF11666 Protein of unknown function (DUF2933)<br>Pfam-B_002197 (release 23.0). This bacterial family of proteins has no known function.. 
PF11667 Protein of unknown function (DUF3267)<br>Pfam-B_002418 (release 23.0). This family of proteins has no known function.. 
PF11668 HCMV glycoprotein pUL130<br>Pfam-B_002736 (release 23.0). This family of proteins represents pUL130 from Human cytomegalovirus, a glycoprotein secreted from infected cells that is incorporated into the virion envelope as a Golgi-matured form. The protein promotes endothelial cell infection through a producer cell modification of the virion  .. 
PF11669 WW domain-binding protein 1<br>Pfam-B_003402 (release 23.0). This family of proteins represents WBP-1, a ligand of the WW domain of Yes-associated protein. This protein has a proline-rich domain. WBP-1 does not bind to the SH3 domain  .. 
PF11670 Major surface protein 1a (MSP1a)<br>Pfam-B_001532 (release 23.0). MSP1a is part of the A.marginale major surface protein 1 (MSP1) complex and exists as a heterodimer with MSP1b. The complex has adhesive functions in bovine erythrocytes invasion  .. 
PF11671 Complementary sex determiner protein<br>Pfam-B_4678 (release 23.0). This family of proteins represents the complementary sex determiner in the honeybee. In the honeybee, the mechanism of sex determination depends on the csd gene which produces an SR-type protein. Males are homozygous while females are homozygous for the csd gene. Heterozygosity generates an active protein which initiates female development  .. 
PF11672 Protein of unknown function (DUF3268)<br>Pfam-B_4693 (release 23.0). This family of proteins has no known function.. 
PF11673 Protein of unknown function (DUF3269)<br>Pfam-B_4706 (release 23.0). This family of proteins has no known function.. 
PF11674 Protein of unknown function (DUF3270)<br>Pfam-B_4714 (release 23.0). This family of proteins with unknown function appears to be restricted to Streptococcus.. 
PF11675 Protein of unknown function (DUF3271)<br>Pfam-B_4697 (release 23.0). This family of proteins with unknown function appears to be restricted to Plasmodium.. 
PF11676 Protein of unknown function (DUF3272)<br>Pfam-B_4726 (release 23.0). This family of proteins with unknown function appears to be restricted to Streptococcus.. 
PF11677 Protein of unknown function (DUF3273)<br>Pfam-B_4727 (release 23.0). Some members in this family of proteins are annotated as multi-transmembrane proteins however this cannot be confirmed. Currently this family has no known function.. 
PF11678 Protein of unknown function (DUF3274)<br>Pfam-B_4733 (release 23.0). This bacterial family of proteins has no known function.. 
PF11679 Protein of unknown function (DUF3275)<br>Pfam-B_4743 (release 23.0). This family of proteins with unknown function appear to be restricted to Proteobacteria.. 
PF11680 Protein of unknown function (DUF3276)<br>Pfam-B_4744 (release 23.0). This bacterial family of proteins has no known function.. 
PF11681 Protein of unknown function (DUF3277)<br>Pfam-B_4749 (release 23.0). This family of proteins represents a putative bacteriophage protein. No function is currently known.. 
PF11682 Protein of unknown function (DUF3279)<br>Pfam-B_4753 (release 23.0). This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.. 
PF11683 Protein of unknown function (DUF3278)<br>Pfam-B_4766 (release 23.0). This bacterial family of proteins has no known function.. 
PF11684 Protein of unknown function (DUF2380)<br>Pfam-B_4754 (release 23.0). This family of proteins with unknown function appears to be restricted to Proteobacteria.. 
PF11685 Protein of unknown function (DUF3281)<br>Pfam-B_4757 (release 23.0). This family of bacterial proteins has no known function.. 
PF11686 Protein of unknown function (DUF3283)<br>Pfam-B_4778 (release 23.0). This family of proteins with unknown function appears to be restricted to Proteobacteria.. 
PF11687 Domain of unknown function (DUF3284)<br>Pfam-B_4781 (release 23.0). This family of proteins with unknown function appears to be restricted to Firmicutes.. 
PF11688 Protein of unknown function (DUF3285)<br>Pfam-B_4791 (release 23.0). This family of proteins with unknown function appears to be restricted to Cyanobacteria.. 
PF11690 Protein of unknown function (DUF3287)<br>Pfam-B_4801 (release 23.0). This eukaryotic family of proteins has no known function.. 
PF11691 Protein of unknown function (DUF3288)<br>Pfam-B_4815 (release 23.0). This family of proteins with unknown function appears to be restricted to Cyanobacteria.. 
PF11692 Protein of unknown function (DUF3289)<br>Pfam-B_4824 (release 23.0). This family of proteins with unknown function appears to be restricted to Proteobacteria.. 
PF11693 Protein of unknown function (DUF2990)<br>Pfam-B_4826 (release 23.0). This family of proteins represents a fungal protein with unknown function.. 
PF11694 Protein of unknown function (DUF3290)<br>Pfam-B_4838 (release 23.0). This family of proteins with unknown function appears to be restricted to Firmicutes.. 
PF11695 Domain of unknown function (DUF3291)<br>Pfam-B_4872 (release 23.0). This bacterial family of proteins has no known function.. 
PF11696 Protein of unknown function (DUF3292)<br>Pfam-B_4874 (release 23.0). This eukaryotic family of proteins has no known function.. 
PF11697 Protein of unknown function (DUF3293)<br>Pfam-B_4879 (release 23.0). This bacterial family of proteins has no known function.. 
PF11698 V-ATPase subunit H<br>Pfam-B_2481 (release 6.5). The yeast Saccharomyces cerevisiae vacuolar H+-ATPase (V-ATPase) is a multisubunit complex responsible for acidifying organelles. It functions as an ATP dependent proton pump that transports protons across a lipid bilayer.  This domain corresponds to the C terminal domain of the H subunit of V-ATPase.  The N-terminal domain is required for the activation of the complex whereas the C-terminal domain is required for coupling ATP hydrolysis to proton translocation  .. 
PF11699 Mif2;<br>CENP-C_C is a C-terminal family of fungal and eukaryote proteins necessary for centromere formation. CENP-C is the inner-kinetochore centromere (CEN) binding protein.  In the budding-yeast, Mif2, the yeast homologue, binds in the CDEIII region of the centromere, and has been shown to recruit a substantial subset of all inner and outer kinetochore proteins  . Mif2 adopts a cupin fold and is extremely similar both in polypeptide chain conformation and in dimer geometry to the dimerisation domain of a bacterial transcription factor  . The Mif2 dimer appears to be part of an enhanceosome-like structure that nucleates kinetochore assembly in budding yeast  . This C-terminal domain is the region via which CENP-C localises to centromeres throughout the cell cycle 2,3].. 
PF11700 Vacuole effluxer Atg22 like<br>Pfam-B_14077 (release 22.0). Autophagy is a major survival survival mechanism in which eukaryotes recycle cellular nutrients during stress conditions. Atg22, Avt3 and Avt4 are partially redundant vacuolar effluxes, which mediate the efflux of leucine and other amino acids resulting from autophagy  .  This family also includes other transporter proteins.. 
PF11701 Myosin-binding striated muscle assembly central<br>The UNC-45 or small muscle protein 1 of C.elegans is expressed in two forms from different genomic positions in mammals, as a general tissue protein UNC-45a and a specific form Unc-45b expressed only in striated and skeletal muscle. All members carry up to three amino-terminal tetratricopeptide repeat (TPR) domains towards their N-terminal, a UCS domain at the C-terminal that contains a number of Arm repeats Pfam:PF00514 and this central region of approximately 400 residues. Both the general form and the muscle form of UNC-45 function in myotube formation through cell fusion. Myofibril formation requires both GC and SM UNC-45, consistent with the fact that the cytoskeleton is necessary for the development and maintenance of organised myofibrils  . The S. pombe Rng3p, is crucial for cell shape, normal actin cytoskeleton, and contractile ring assembly, and is essential for assembly of the myosin II-containing progenitors of the contractile ring. Widespread defects in the cytoskeleton are found in null mutants of all three fungal proteins  . Mammalian Unc45 is found to act as a specific chaperone during the folding of myosin and the assembly of striated muscle by forming a stable complex with the general chaperone Hsp90. The exact function of this central region is not known  .. 
PF11702 Protein of unknown function (DUF3295)<br>This family is conserved in fungi but the function is not known.. 
PF11703 UPF0506<br>This uncharacterised family is found in Schistosoma genomes. Although uncharacterised it appears to belong to the knottin fold. The sequence is composed of two repeats of a 6 cysteine motif.. 
PF11704 Vesicle coat protein involved in Golgi to plasma membrane transport<br>Pfam-B_3276 (release 23.0), ADDA_17305. In yeast cells this family functions in the regulated delivery of Gap1p (a general amino acid permease) to the cell surface, perhaps as a component of a post-Golgi secretory-vesicle coat complex  . Birt-Hogg-Dube (BHD)4 syndrome is an autosomal dominant disorder characterised by hamartomas of skin follicles, lung cysts, spontaneous pneumothorax, and renal cell carcinoma. Folliculin is the protein from the BHD4 gene and is found to have no significant homology to any other human proteins. It is expressed in most tissues. These same symptoms also occur in TSC or tuberous sclerosis complex, suggesting that the same pathway is involved, and it is likely that the target is the down-stream Tor2 - an essential gene. Folliculin appears to bind Tor2, and down-regulation of Tor2 activity leads to up-regulation of nitrogen responsive genes including membrane transporters and amino acid permeases  .. 
PF11705 DNA-directed RNA polymerase III subunit Rpc31<br>Pfam-B_203281 (release 23.0). RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA pol III-specific, and form the functionally distinct groups (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in S.cerevisiae and H.sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain  .. 
PF11706 CGNR zinc finger<br>Pfam-B_19432 (release 10.0). This family consists of a C-terminal zinc finger domain. It seems likely to be DNA-binding given the conservation of many positively charged residues. The domain is named after a highly conserved motif found in many members of the family.. 
PF11707 Ribosome 60S biogenesis N-terminal<br>Pfam-B_2493 (release 23.0). Npa1p is required for ribosome biogenesis and operates in the same functional environment as Rsa3p and Dbp6p during early maturation of 60S ribosomal subunits  . The protein partners of Npa1p include eight putative helicases as well as the novel Npa2p factor. Npa1p can also associate with a subset of H/ACA and C/D small nucleolar RNPs (snoRNPs) involved in the chemical modification of residues in the vicinity of the peptidyl transferase centre  . The protein has also been referred to as Urb1, and this domain at the N-terminal is one of several conserved regions along the length.. 
PF11708 Pre-mRNA splicing Prp18-interacting factor<br>Pfam-B_999 (release 23.0). The spliceosome, an assembly of snRNAs (U1, U2, U4/U6, and U5) and proteins, catalyses the excision of introns from pre-mRNAs in two successive trans-esterification reactions. Step 2 depends upon integral spliceosome constituents such as U5 snRNA and Prp8 and non-spliceosomal proteins Prp16, Slu7, Prp18, and Prp22. ATP hydrolysis by the DEAH-box enzyme Prp16 promotes a conformational change in the spliceosome that leads to protection of the 3'ss from targeted RNase H cleavage. This change, which probably reflects binding of the 3'ss PyAG in the catalytic centre of the spliceosome, requires the ordered recruitment of Slu7, Prp18, and Prp22 to the spliceosome. There is a close functional relationship between Prp8, Prp18, and Slu7, and Prp18 interacts with Slu7, so that together they recruit Prp22 to the spliceosome. Most members of the family carry a zinc-finger of the CCHC-type upstream of this domain.. 
PF11709 Mitochondrial ribosomal protein subunit <br>Pfam-B_4972 (release 23.0). This family is the mitochondrial ribosomal small-subunit protein Mrp51. Its function is not entirely clear, but deletion of the MRP51 gene completely blocked mitochondrial gene expression.. 
PF11710 G protein-coupled glucose receptor regulating Gpa2<br>Pfam-B_11657 (release 23.0). Git3 is one of six proteins required for glucose-triggered adenylate cyclase activation, and is a G protein-coupled receptor responsible for the activation of adenylate cyclase through Gpa2 - heterotrimeric G protein alpha subunit, part of the glucose-detection pathway. Git3 contains seven predicted transmembrane domains, a third cytoplasmic loop and a cytoplasmic tail  . This is the conserved N-terminus of these proteins, and the C-terminal conserved region is now in family Git3_C.. 
PF11711 Inner membrane protein import complex subunit Tim54<br>Pfam-B_3533 (release 23.0). Mitochondrial function depends on the import of hundreds of different proteins synthesised in the cytosol. Protein import is a multi-step pathway which includes the binding of precursor proteins to surface receptors, translocation of the precursor across one or both mitochondrial membranes, and folding and assembly of the imported protein inside the mitochondrion. Most precursor proteins carry amino-terminal targeting signals, called pre-sequences, and are imported into mitochondria via import complexes located in both the outer and the inner membrane (IM). The IM complex, TIM, is made up of at least two proteins which mediate translocation of proteins into the matrix by removing their signal peptide and another pair of proteins, Tim54 and Tim22, that insert the polytopic proteins, that carry internal targetting information, into the inner membrane  .. 
PF11712 Endoplasmic reticulum-based factor for assembly of V-ATPase<br>Pfam-B_2410 (release 23.0). The yeast vacuolar proton-translocating ATPase (V-ATPase) is the best characterised member of the V-ATPase family. A total of thirteen genes are required for encoding the subunits of the enzyme complex itself and an additional three for providing factors necessary for the assembly of the whole. Vma12 is one of these latter, all three of which are localised to the endoplasmic reticulum  .. 
PF11713 Peptidase C80 family<br>This family belongs to cysteine peptidase family C80.. 
PF11714 Thrombin inhibitor Madanin  <br>Members of this family are the peptidase inhibitor madanin proteins. These proteins were isolated from tick saliva  .. 
PF11715 Nucleoporin Nup120/160<br>Pfam-B_1841 (release 23.0). Nup120 is conserved from fungi to plants to humans, and is homologous with the Nup160 of vertebrates. The nuclear core complex, or NPC, mediates macromolecular transport across the nuclear envelope. Deletion of the NUP120 gene causes clustering of NPCs at one side of the nuclear envelope, moderate nucleolar fragmentation and slower cell growth  . The vertebrate NPC is estimated to contain between 30 and 60 different proteins. most of which are not known. Two important ones in creating the nucleoporin basket are Nup98 and Nup153, and Nup120, in conjunction with Nup 133, interacts with these two and itself plays a role in mRNA export  . Nup160, Nup133, Nup96, and Nup107 are all targets of phosphorylation. The phosphorylation sites are clustered mainly at the N-terminal regions of these proteins, which are predicted to be natively disordered. The entire Nup107-160 subcomplex is stable throughout the cell cycle, thus it seems unlikely that phosphorylation affects interactions within the Nup107-160 subcomplex, but rather that it regulates the association of the subcomplex with the NPC and other proteins  .. 
PF11716 Mycothiol maleylpyruvate isomerase N-terminal domain<br>
PF11717 RNA binding activity-knot of a chromodomain <br>Pfam-B_4165 (release 22.0). This is a novel knotted tudor domain which is required for binding to RNA. The know influences the loop conformation of the helical turn Ht2 - residues 61-6 3- that is located at the side opposite the knot in the tudor domain-chromodomain; stabilisation of Ht2 is essential for RNA binding  .. 
PF11718 Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term<br>Pfam-B_2254 (release 23.0). This is the C-terminal conserved region of the pre-mRNA 3'-end-processing of the polyadenylation factor CPSF-73/CPSF-100 proteins. The exact function of this domain is not known.. 
PF11719 DNA replication and checkpoint protein<br>Pfam-B_1966 (release 23.0). Genome duplication is precisely regulated by cyclin-dependent kinases CDKs, which bring about the onset of S phase by activating replication origins and then prevent relicensing of origins until mitosis is completed. The optimum sequence motif for CDK phosphorylation is S/T-P-K/R-K/R, and Drc1-Sld2 is found to have at least 11 potential phosphorylation sites. Drc1 is required for DNA synthesis and S-M replication checkpoint control. Drc1 associates with Cdc2 and is phosphorylated at the onset of S phase when Cdc2 is activated. Thus Cdc2 promotes DNA replication by phosphorylating Drc1 and regulating its association with Cut5  . Sld2 and Sld3 represent the minimal set of S-CDK substrates required for DNA replication  .. 
PF11720 Peptidase inhibitor I78 family<br>This family includes Aspergillus elastase inhibitor and belongs to MEROPS peptidase inhibitor family I78.. 
PF11721 Di-glucose binding within endoplasmic reticulum<br>Pfam-B_783 (release 23.0) pdb_2jwp. Malectin is a membrane-anchored protein of the endoplasmic reticulum that recognises and binds Glc2-N-glycan. It carries a signal peptide from residues 1-26, a C-terminal transmembrane helix from residues 255-274, and a highly conserved central part of approximately 190 residues followed by an acidic, glutamate-rich region. Carbohydrate-binding is mediated by the four aromatic residues, Y67, Y89, Y116, and F117 and the aspartate at D186.  NMR-based ligand-screening studies has shown binding of the protein to maltose and related oligosaccharides, on the basis of which the protein has been designated "malectin", and its endogenous ligand is found to be Glc2-high-mannose N-glycan  .. 
PF11722 CCCH zinc finger in TRM13 protein<br>This domain is found at the N-terminus of TRM13 methyltransferase proteins. It is presumed to be a zinc binding domain.. 
PF11723 Homotrimeric ring hydroxylase<br>Pfam-B_24837 (release 22.0). This domain is found on aromatic hydroxylating enzymes such as 2-oxo-1,2-dihydroquinoline 8-monooxygenase from Pseudomonas putida and carbazole 1,9a-dioxygenase from Janthinobacterium. These enzymes are homotrimers and are distantly related to the typical oxygenase  .  This domain is found C terminal to the Rieske domain which binds an iron-sulphur cluster.. 
PF11724 YvbH-like oligomerisation region<br>This region is found at the C-terminus of a group of bacterial PH domains. This region is composed of a helical hairpin that appears to mediate oligomerisation based on the known structure. This elaboration of the bacterial PH domain is only found in Bacillales.. 
PF11725 Pathogenicity factor<br>Pfam-B_735 (release 23.0). This family is secreted by gram-negative Gammaproteobacteria such as Pseudomonas syringae of tomato and the fire blight plant pathogen Erwinia amylovora, amongst others. It is an essential pathogenicity factor of approximately 198 kDa. Its injection into the host-plant is dependent upon the bacterial type III or Hrp secretion system  . The family is long and carries a number of predicted functional regions, including an ERMS or endoplasmic reticulum membrane retention signal at both the C- and the N-termini, a leucine-zipper motif from residues 539-560, and a nuclear localisation signal at 1358-1361. this conserved AvrE-family of effectors is among the few that are required for full virulence of many phytopathogenic pseudomonads, erwinias and pantoeas  .. 
PF11726 Protein of unknown function (DUF3296)<br>Pfam-B_768 (release 23.0). This family is expressed in Gammaproteobacteria. One of the E coli members is annotated as yagK, but otherwise the function is not known.. 
PF11727 Invariant surface glycoprotein<br>Pfam-B_785 (release 23.0). This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75. that are found in the mammalian stage of the parasitic protozoan. the sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane alpha-helices and short cytoplasmic domains. they are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite [1,2].. 
PF11728 DUF939 C-terminal domain<br>This region is a presumed intracellular domain found in a set of bacterial presumed transporter proteins. The region is about 160 amino acids in length.. 
PF11729 nodavirus capsid protein <br>Pfam-B_805 (release 23.0). The capsid or coat protein of this family is expressed in Nodaviridae, that are ssRNA positive-strand viruses, with no DNA stage. These viruses are the causative agents of viral nervous necrosis in marine fish.. 
PF11730 Protein of unknown function (DUF3297)<br>Pfam-B_797 (release 23.0). This family is expressed in Proteobacteria and Actinobacteria. The function is not known.. 
PF11731 Pathogenicity locus<br>Pfam-B_826 (release 23.0). Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria  . Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.. 
PF11732 Transcription- and export-related complex subunit<br>Pfam-B_819 (release 23.0). The THO/TREX complex is the transcription- and export-related complex associated with spliceosomes that preferentially deal with spliced mRNAs as opposed to unspliced mRNAs. Thoc2 plays a role in RNA polymerase II (RNA pol II)-dependent transcription and is required for the stability of DNA repeats  . In humans, the TRE complex is comprised of the exon-junction-associated proteins Aly/REF and UAP56 together with the THO proteins THOC1 (hHpr1/p84), Thoc2 (hRlr1), THOC3 (hTex1), THOC5 (fSAP79), THOC6 (fSAP35), and THOC7 (fSAP24). Although much evidence indicates that the function of the TREX complex as an adaptor between the mRNA and components of the export machinery is conserved among eukaryotes, in Drosophila the majority of mRNAs can be exported from the nucleus independently of the THO complex  .. 
PF11733 Non-capsid protein NP1<br>Pfam-B_837 (release 23.0). This family is the non-capsid protein NP1 of the ssDNA, Parvovirinae virus Bocavirus of cattle and humans.. 
PF11734 TilS substrate C-terminal domain<br>This domain is found in the tRNA(Ile) lysidine synthetase (TilS) protein.. 
PF11735 Cryptococcal mannosyltransferase 1 <br>Pfam-B_916 (release 23.0). The capsule of pathogenic fungi is a complex polysaccharide whose formation is determined by a number of enzymes including, most importantly, alpha-1,3-mannosyltransferase 1, EC:2.4.1.-  .. 
PF11736 Protein of unknown function (DUF3299)<br>Pfam-B_876 (release 23.0). This is a family of bacterial proteins of unknown function.. 
PF11737 Protein of unknown function (DUF3300)<br>Pfam-B_886 (release 23.0). This hypothetical bacterial gene product has a long hydrophobic segment and is thus likely to be a membrane protein.. 
PF11738 Protein of unknown function (DUF3298)<br>Pfam-B_854 (release 23.0). This family of bacterial protein C-terminal regions is highly conserved but the function is not known. Several members are annotated as being endo-1,4-beta-xylanase-like, but this could not be confirmed, and the structure can be defined as a heat-shock cognate 70kd protein 44kd ATPase.. 
PF11739 Dicarboxylate transport<br>Pfam-B_935 (release 23.0). In certain bacterial families this protein is expressed from the ydbH gene, and there is a suggestion that this is a form of DctA or dicarboxylate transport protein. Dicarboxylate transport proteins are found in aerobic bacteria which grow on succinate or other C4-dicarboxylates  .. 
PF11740 Plasmid replication region DNA-binding N-term<br>Pfam-B_844 (release 23.0). The broad host-range plasmid RK2 is able to replicate in and be inherited in a stable manner in diverse Gram-negative bacterial species. It encodes a number of co-ordinately regulated operons including a central control korF1 operon that represses the kfrA operon. The KfrA polypeptide is a site-specific DNA-binding protein whose operator overlaps the kfrA promoter. The N-terminus, containing an helix-turn-helix motif, is essential for function. Downstream from this family is an extended coiled-coil domain containing a heptad repeat segment which is probably responsible for formation of multimers, and may provide an example of a bridge to host structures required for plasmid partitioning  .. 
PF11741 AMIN domain<br>Pfam-B_11438 (release 23.0). This N-terminal domain of various bacterial protein families is crucial for the targetting of periplasmic or extracellular proteins to specific regions of the bacterial envelope. AMIN is derived from the N-terminal domain of AmiC, an N-acetylmuramoyl-l-alanine amidase of Escherichia coli which localises to the septal ring during division and plays a key role in the separation of daughter cells.  The AMIN domain is present in several protein families besides amidases suggesting that AMIN may represent a general targetting determinant involved in the localisation of periplasmic protein complexes  .. 
PF11742 Protein of unknown function (DUF3302)<br>Pfam-B_953 (release 23.0). This family of unknown function is expressed by proteobacteria.. 
PF11743 Protein of unknown function (DUF3301)<br>Pfam-B_952 (release 23.0). This family is conserved in Proteobacteria, but the function is not known.. 
PF11744 Aluminium activated malate transporter<br>
PF11745 Protein of unknown function (DUF3304)<br>Pfam-B_956 (release 23.0). This is a family of bacterial proteins of unknown function.. 
PF11746 Protein of unknown function (DUF3303)<br>Pfam-B_958 (release 23.0). Several members are annotated as being LysM domain-like proteins, but these did not match any LysM domains reported in the literature.. 
PF11747 Killing trait<br>Pfam-B_983 (release 23.0). RebB is one of three proteins necessary for the production of R- bodies, refractile inclusion bodies produced by a small number of bacterial species, essential for the expression of the killing trait of the endosymbiont bacteria that produce them for attack upon the host Paramecium. R-bodies are highly insoluble protein ribbons which coil into cylindrical structures in the cell and the genes for their synthesis and assembly are encoded on a plasmid. One of these three proteins is RebB.. 
PF11748 Protein of unknown function (DUF3306)<br>Pfam-B_984 (release 23.0). This family of proteobacterial species proteins has no known function.. 
PF11749 Protein of unknown function (DUF3305)<br>Pfam-B_976 (release 23.0). Several members of this family are annotated as being molybdopterin-guanine dinucleotide biosynthesis protein A; however, this could not be confirmed. The family is found in proteobacteria.. 
PF11750 Protein of unknown function (DUF3307)<br>Pfam-B_1017 (release 23.0). This family of bacterial proteins has no known function.. 
PF11751 Protein of unknown function (DUF3308)<br>Pfam-B_993 (release 23.0). Some members of this family of bacterial proteins are annotated as being one of the several TonB-dependent siderophore receptors, but this could not be confirmed.. 
PF11752 Protein of unknown function (DUF3309)<br>Pfam-B_1113 (release 23.0). This family is conserved in bacteria but its function is not known.. 
PF11753 Protein of unknwon function (DUF3310)<br>Pfam-B_1078 (release 23.0). This is a family of conserved bacteriophage proteins of unknown function.. 
PF11754 Velvet factor<br>Pfam-B_963 (release 23.0). The velvet factor is conserved in many fungal species and is found to have gained different roles depending on the organism's need, expanding the conserved role in developmental programmes  . The velvet factor orthologues can be adapted to the fungal-specific life cycle and may be involved in diverse functions such as sclerotia formation and toxin production, as in A. parasiticus  , nutrition-dependent sporulation, as in A. fumigatus  , or the microconidia-to-macroconidia ratio and cell wall formation, as in the heterothallic fungus Fusarium verticilloides [ .. 
PF11755 Protein of unknown function (DUF3311)<br>Pfam-B_1042 (release 23.0). This is a family of short bacterial proteins of unknown function.. 
PF11756 Nitrous oxide-stimulated promoter<br>Pfam-B_1030 (release 23.0). The function of ygaB is not known but it is a promoter that is stimulated by the presence of nitrous oxide  . It is regulated by the gene-product of the bacterial nsrR gene.. 
PF11757 Suppressor of RNA silencing P21-like<br>Pfam-B_1073 (release 23.0). This is a large family of putative suppressors of RNA silencing proteins, P20-P25, from ssRNA positive-strand viruses such as Closterovirus, Potyvirus and Cucumovirus families. RNA silencing is one of the major mechanisms of defence against viruses, and, in response, some viruses have evolved or acquired functions for suppression of RNA silencing. These counter-defencive viral proteins with RNA silencing suppressor (RSS) activity were originally discovered in the members of plant virus genera Potyvirus and Cucumovirus. Each of the conserved blocks of amino acids found in P21-like proteins corresponds to a computer-predicted alpha-helix, with the most C-terminal element being 42 residues long. This suggests conservation of the predominantly alpha-helical secondary structure in the P21-like proteins.. 
PF11758 Aureocin-like type II bacteriocin<br>This is a small family of type II bacteriocins usually encoded on a plasmid. Characteristically the members are small, cationic, rich in Lys and Try, and bring about a generalised membrane permeabilisation leading to leakage of ions. The family includes aureocin A, lacticins Q and Z, and BhtB as well as an archaeal member.. 
PF11759 Keratin-associated matrix<br>The major structural proteins of mammalian hair are the hair keratin intermediate filaments (KIFs) and the keratin-associated proteins (KRTAPs). In the hair cortex, hair keratins are embedded in an inter-filamentous matrix consisting of KRTAPs which are essential for the formation of a rigid and resistant hair shaft as a result of disulfide bonds between cysteine residues. There are essentially three groups of KRTAPs, viz: the high-sulfur (HS) and ultra-high-sulfur (UHS) KRTAPs (cysteine content: 16-30 and >30 mol%, respectively) and the high-glycine/tyrosine (HGT: 35-60 mol% glycine and tyrosine) KRTAPs.. 
PF11760 Cobalamin synthesis G N-terminal<br>Members of this family are involved in cobalamin synthesis.  The gene encoded by Swiss:P72862 has been designated cbiH but in fact represents a fusion between cbiH and cbiG. As other multi-functional proteins involved in cobalamin biosynthesis catalyse adjacent steps in the pathway, including CysG, CobL (CbiET), CobIJ and CobA-HemD, it is therefore possible that CbiG catalyses a reaction step adjacent to CbiH. In the anaerobic pathway such a step could be the formation of a gamma lactone, which is thought to help to mediate the anaerobic ring contraction process  . Within the cobalamin synthesis pathway CbiG catalyses the both the opening of the lactone ring and the extrusion of the two-carbon fragment of cobalt-precorrin-5A from C-20 and its associated methyl group (deacylation) to give cobalt-precorrin-5B  . The N-terminal of the enzyme is conserved in this family, and the C-terminal and the mid-sections are conserved independently in other families, CbiG_C and CbiG_mid, although the distinct function of each region is unclear.. 
PF11761 Cobalamin biosynthesis central region<br>Members of this family are involved in cobalamin synthesis. The gene encoded by Swiss:P72862 has been designated cbiH but in fact represents a fusion between cbiH and cbiG. As other multi-functional proteins involved in cobalamin biosynthesis catalyse adjacent steps in the pathway, including CysG, CobL (CbiET), CobIJ and CobA-HemD, it is therefore possible that CbiG catalyses a reaction step adjacent to CbiH. In the anaerobic pathway such a step could be the formation of a gamma lactone, which is thought to help to mediate the anaerobic ring contraction process  .. 
PF11762 L-arabinose isomerase C-terminal domain<br>This is a family of L-arabinose isomerases, AraA, EC:5.3.1.4.  These enzymes catalyse the reaction: L-arabinose <=> L-ribulose.  This reaction is the first step in the pathway of L-arabinose utilisation as a carbon source after entering the cell L-arabinose is converted into  L-ribulose by the L-arabinose isomerases enzyme  . This is a C-terminal non catalytic domain.. 
PF11763 Cell-wall adhesin ligand-binding C-terminal<br>Pfam-B_85585 (release 23.0). The DIPSY domain is characterised by the distinctive D*I*PSY motif at the very C-terminus of yeast cell-wall glycoproteins. It appears not to be conserved in any other species, however. In fungi, cell adhesion is required for flocculation, mating and virulence, and is mediated by covalently bound cell wall proteins termed adhesins. Map4, an adhesin required for mating in Schizosaccharomyces pombe, is N-glycosylated and O-glycosylated, and is an endogenous substrate for the mannosyl transferase Oma4p. Map4 has a modular structure with an N-terminal signal peptide, a serine and threonine (S/T)-rich domain that includes nine repeats of 36 amino acids (rich in serine and threonine residues, but lacking glutamines), and a C-terminal DIPSY domain with no glycosyl-phosphatidyl inositol (GPI)-anchor signal. The N-terminal S/T-rich regions, are required for cell wall attachment, but the C-terminal DIPSY domain is required for agglutination and mating in liquid and solid media  .. 
PF11764 COMPASS (Complex proteins associated with Set1p) component N<br>Pfam-B_7375 (release 23.0). The n-SET or N-SET domain is a component of the COMPASS complex, associated with SET1, conserved in yeasts and in other eukaryotes up to humans.  The COMPASS complex functions to methylate the fourth lysine of Histone 3 and for the silencing of genes close to the telomeres of chromosomes  . This domain promotes trimethylation in conjunction with an RRM domain   and is necessary for binding of the Spp1 component of COMPASS into the complex  .. 
PF11765 Hyphally regulated cell wall protein N-terminal<br>The proteins in this family are all fungal and largely annotated as being hyphally regulated cell wall proteins, and several are listed as the enzyme EC:3.2.1.18. This enzyme is acetylneuraminyl hydrolase or exo-alpha-sialidase, that hydrolyses glycosidic linkages of terminal sialic acid residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.. 
PF11766 Cell-wall agglutinin N-terminal ligand-sugar binding <br>This is likely to be the sugar or ligand binding domain of the yeast alpha-agglutinins.. 
PF11767 Histone lysine methyltransferase SET associated<br>Pfam-B_8752 (release 23.0). SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. A subset of SET domains have been called PR domains. The SET domain consists of two regions known as N-SET and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance.  Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure  . This domain is found in fungi associated with SET and N-SET domains.. 
PF11768 Protein of unknown function (DUF3312)<br>Pfam-B_5984 (release 23.0). This is a eukaryotic family of uncharacterised proteins. This family shows similarity to WD40 repeat proteins.. 
PF11769 Protein of unknown function (DUF3313)<br>Pfam-B_1303 (release 23.0). This a bacterial family of proteins which are annotated as putative lipoproteins.. 
PF11770 GRB2-binding adapter (GAPT)<br>This is a family of transmembrane proteins which bind the growth factor receptor-bound protein 2 (GRB2) in B cells  .  In contrast to other transmembrane adaptor proteins, GAPT is not phosphorylated upon BCR ligation.  It associates with GRB2 constitutively through its proline-rich region  .. 
PF11771 Protein of unknown function (DUF3314) <br>This small family contains human, mouse and fish members but the function is not known.. 
PF11772 DNA-directed RNA polymerase subunit beta<br>Pfam-B_4675 (release 23.0). This short 60-residue long bacterial family is the beta subunit of the DNA-directed RNA polymerase, likely to be EC:2.7.7.6. It is membrane-bound and is referred to by the name EpuA.. 
PF11773 Type II secretory pathway pseudopilin <br>Pfam-B_4690 (release 23.0). The secreton (type II secretion) and type IV pilus biogenesis branches of the general secretory pathway in Gram-negative bacteria share many features that suggest a common evolutionary origin. Five components of the secreton, the pseudopilins, are similar to subunits of type IV pili. Pseudopilin PulG is one of the secreton pseudopilins, and is found to assemble into pilus-like bundles  . PulG interacts with proteins H, I and J within the multi-protein complex as well as blocking extracellular secretion and reducing the amount of PulE protein as well as the amounts of PulL, PulM, PulC and PulD when G is over-expressed  . In Klebsiella the pilus-like structure is composed largely of PulG  .. 
PF11774 Lsr2 <br>Lsr2 is a small, basic DNA-bridging protein present in Mycobacterium and related actinomycetes.  It is a functional homologue of the H-NS-like proteins  .  H-NS proteins play a role in nucleoid organisation and also function as a pleiotropic regulator of gene expression   .. 
PF11775 Cobalamin biosynthesis protein CobT VWA domain<br>Pfam-B_10956 (release 9.0). This family consists of several bacterial cobalamin biosynthesis (CobT) proteins. CobT is involved in the transformation of precorrin-3 into cobyrinic acid  . . 
PF11776 Domain of unknown function (DUF3315)<br>This is a Proteobacterial family of uncharacterised proteins. Some of the proteins in this family are annotated as being putative membrane proteins.. 
PF11777 Protein of unknown function (DUF3316)<br>Pfam-B_4718 (release 23.0). This family of bacterial proteins has no known function. Several members are, however, annotated as being putative acyl-CoA synthetase, but this could not be confirmed.. 
PF11778 Septation initiation<br>Pfam-B_41015 (release 23.0). This family is required for activation of the spg1 GTPase signalling cascade which leads to the initiation of septation and the subsequent termination of mitosis. It may act as a scaffold at the spindle pole body to which other components of the spg1 signalling cascade attach in pombe [1,2,3]. In S.cerevisiae it is both required for the proper formation of the spindle pole body outer plaque and may also connect the outer plaque to the central plaque embedded in the nuclear envelope  .. 
PF11779 Protein of unknown function (DUF3317)<br>Pfam-B_3618 (release 23.0). This is a short family of proteins conserved from fungi and plants to human. One each of the human and mouse members is annotated as being androgen down-regulated protein expressed in mouse prostate, with a potential signal transduction function, and all appear to be membrane proteins.. 
PF11780 Protein of unknown function (DUF3318)<br>Pfam-B_1341 (release 23.0). This is a bacterial family of uncharacterised proteins.. 
PF11781 RNA polymerase I-specific transcription initiation factor Rrn7<br>Pfam-B_4705 (release 23.0). Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [1,2]. . 
PF11782 Protein of unknown function (DUF3319)<br>Pfam-B_4745 (release 23.0). This is a family of short bacterial proteins, a few of which are annotated as being minor tail protein. Otherwise the function is unknown.. 
PF11783 Cytochrome c bacterial<br>Pfam-B_4681 (release 23.0). This is a family of long bacterial cytochrome c proteins, found in Proteobacteria and Chlorobi families.. 
PF11784 Protein of unknown function (DUF3320)<br>Pfam-B_4770 (release 23.0). This family is conserved in Proteobacteria and Chlorobi families. Many members are annotated as being putative DNA helicase-related proteins.. 
PF11785 Aft1 osmotic stress response (OSM) domain<br>This domain is found in the transcription factor Aft1 which is required for a wide range of stress responses.  The OSM domain has been shown to be involved in the osmotic stress response  .. 
PF11786 Aft1 HRA domain<br>This domain is found in the transcription factor Aft1 which is required for a wide range of stress responses.  The HRA domain is involved in meiotic recombination.  It has been shown to be necessary and sufficient to activate recombination  .. 
PF11787 Aft1 HRR domain<br>This domain is found in the transcription factor Aft1 which is required for a wide range of stress responses.  The HRR domain is involved in meiotic recombination.  It has been shown to be necessary and sufficient to repress recombination  .. 
PF11788 39S mitochondrial ribosomal protein L46 <br>Pfam-B_1897 (release 23.0). This is the L46 subunit of the mammalian mitochondrial ribosome, conserved from plants and fungi.. 
PF11789 Zinc-finger of the MIZ type in Nse subunit<br>Pfam-B_1696 (release 23.0). Nse1 and Nse2 are novel non-SMC subunits of the fission yeast Smc5-6 DNA repair complex. This family is the zinc-finger domain similar to the MIZ type of zinc-finger  .. 
PF11790 Glycosyl hydrolase catalytic core<br>Pfam-B_1680 (release 23.0), IPR013781. This family is probably a glycosyl hydrolase, and is conserved in fungi and some Proteobacteria. The pombe member is annotated as being from IPR013781.. 
PF11791 Aconitate B N-terminal domain<br>Pfam-B_2605 (release 10.0). This family represents the N-terminal domain of Aconitase B.. 
PF11792 Baculoviridae late expression factor 5 C-terminal domain<br>Pfam-B_5141 (release 7.6). This C-terminal domain is likely to be a zinc-binding domain.. 
PF11793 FANCL C-terminal domain<br>This domain is found at the C-terminus of the Fancl protein in humans which is the putative E3 ubiquitin ligase subunit of the FA complex (Fanconi anaemia). Eight subunits of the Fanconi anaemia gene products form a multisubunit nuclear complex which is required for mono-ubiquitination of a downstream FA protein, FANCD2.. 
PF11794 4-hydroxyphenylacetate 3-hydroxylase N terminal<br>Pfam-B_3148 (release 6.5). HpaB Swiss:Q57160 encodes part of the 4-hydroxyphenylacetate 3-hydroxylase from Escherichia coli  . HpaB is part of a heterodimeric enzyme that also requires HpaC. The enzyme is NADH-dependent and uses FAD as the redox chromophore. This family also includes PvcC Swiss:O30372 may play a role in one of the proposed hydroxylation steps of pyoverdine chromophore biosynthesis  . . 
PF11795 Uncharacterized protein conserved in bacteria N-term (DUF3322)<br>This domain, found in various hypothetical bacterial proteins, has no known function. The family represents just the N-terminus.. 
PF11796 Protein of unknown function N-terminus (DUF3323)<br>Proteins in this entry are encoded within a conserved gene four-gene neighbourhood found sporadically in a phylogenetically broad range of bacteria including: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Beta-proteobacteria).. 
PF11797 Protein of unknown function C-terminal (DUF3324)<br>Pfam-B_7106 (release 9.0). This family consists of several hypothetical bacterial proteins of unknown function.. 
PF11798 IMS family HHH motif<br>Pfam-B_1349 (release 2.1). These proteins are involved in UV protection, eg (Swiss:P07375).. 
PF11799 impB/mucB/samB family C-terminal domain<br>Pfam-B_1349 (release 2.1). These proteins are involved in UV protection (Swiss).. 
PF11800 Replication protein C C-terminal region<br>Pfam-B_4463 (release 6.6). Replication protein C is involved in the early stages of viral DNA replication.. 
PF11801 Tom37 C-terminal domain<br>Pfam-B_30563 (release 22.0). The TOM37 protein is one of the outer membrane proteins that make up the TOM complex for guiding cytosolic mitochondrial beta-barrel proteins from the cytosol across the outer mitochondrial membrane into the intramembrane space. In conjunction with TOM70 it guides peptides without an MTS into TOM40, the protein that forms the passage through the outer membrane  . It has homology with Metaxin-1, also part of the outer mitochondrial membrane beta-barrel protein transport complex  .. 
PF11802 Centromere-associated protein K<br>CENP-K is one of seven new CENP-A-nucleosome distal (CAD) centromere components (the others being CENP-L, CENP-O, CENP-P, CENP-Q, CENP-R and CENP-S) that are identified as assembling on the CENP-A nucleosome associated complex, NAC. The CENP-A NAC is essential, as disruption of the complex causes errors of chromosome alignment and segregation that preclude cell survival despite continued centromere-derived mitotic checkpoint signalling. CENP-K is centromere-associated through its interaction with one or more components of the CENP-A NAC.. 
PF11803 UDP-glucuronate decarboxylase N-terminal<br>Pfam-B_36254 (release 23.0). The N-terminus of the UDP-glucuronate decarboxylases may be involved in localisation to the perinuclear Golgi membrane.. 
PF11804 Protein of unknown function (DUF3325)<br>PFAM-B_2004 (release 23.0). This family of short proteins are functionally uncharacterized. This family is restricted to Alpha-, Beta- and Gamma-proteobacteria.. 
PF11805 Protein of unknown function (DUF3326)<br>PFAM-B_2030 (release 23.0). This protein is functionally uncharacterized. It is about 300-500 amino acids in length.  This family is found in plants and bacteria.. 
PF11806 Domain of unknown function (DUF3327)<br>PFAM-B_2060 (release 23.0). 
PF11807 Domain of unknown function (DUF3328)<br>PFAM-B_2062 (release 23.0). This family of proteins are functionally uncharacterised. This family is only found in eukaryotes.. 
PF11808 Domain of unknown function (DUF3329)<br>PFAM-B_2082 (release 23.0). This family of proteins are functionally uncharacterised. This family is only found in bacteria.. 
PF11809 Domain of unknown function (DUF3330)<br>PFAM-B_2077 (release 23.0). This family of proteins are functionally uncharacterised. This family is only found in bacteria.. 
PF11810 Domain of unknown function (DUF3332)<br>PFAM-B_2104 (release 23.0). This family of proteins are functionally uncharacterised. This family is only found in bacteria.. 
PF11811 Domain of unknown function (DUF3331)<br>PFAM-B_2106 (release 23.0). This family of proteins are functionally uncharacterised. This family is only found in bacteria. Proteins in this family vary in length from 96 to 160 amino acids.. 
PF11812 Domain of unknown function (DUF3333)<br>PFAM-B_2108 (release 23.0). This family of proteins are functionally uncharacterised. This family is only found in bacteria.  This presumed domain is typically between 116 to 159 amino acids in length.. 
PF11813 Protein of unknown function (DUF3334)<br>PFAM-B_2118 (release 23.0). This family of proteins are functionally uncharacterised. This family is only found in bacteria. Proteins in this family are typically between 227 to 238 amino acids in length.. 
PF11814 Peptidase_C39 like family<br>PFAM-B_2152 (release 23.0). 
PF11815 Domain of unknown function (DUF3336)<br>PFAM-B_2157 (release 23.0). This family of proteins are functionally uncharacterised. This family is found in bacteria and eukaryotes. This presumed domain is typically between 143 to 227 amino acids in length.. 
PF11816 Domain of unknown function (DUF3337)<br>PFAM-B_2058 (release 23.0). This family of proteins are functionally uncharacterised. This family is only found in eukaryotes. This presumed domain is typically between 285 to 342 amino acids in length.. 
PF11817 Foie gras liver health family 1<br>Pfam-B_4417 (release 23.0). Mutating the gene foie gras in zebrafish has been shown to affect development; the mutants develop large, lipid-filled hepatocytes in the liver, resembling those in individuals with fatty liver disease  . Foie-gras protein is long and has several well-defined domains though none of them has a known function. We have annotated this one as the first  . The C-terminus of this region contains TPR repeats.. 
PF11818 C-terminal domain of tail specific protease (DUF3340)<br>PFAM-B_2330 (release 23.0). This presumed domain is found at the C-terminus of tail specific proteases. Its function is unknown. This family is found in bacteria and eukaryotes.  This presumed domain is typically between 88 to 187 amino acids in length.. 
PF11819 Domain of unknown function (DUF3338)<br>PFAM-B_2474 (release 23.0). This family of proteins are functionally uncharacterised. This family is found in eukaryotes. This presumed domain is about 130 amino acids in length.. 
PF11820 Protein of unknown function (DUF3339)<br>PFAM-B_2694 (release 23.0). This family of proteins are functionally uncharacterised. This family is found in eukaryotes. Proteins in this family are about 70 amino acids in length.. 
PF11821 Protein of unknown function (DUF3341)<br>PFAM-B_2731 (release 23.0). This family of proteins are functionally uncharacterised. This family is found in bacteria. Proteins in this family are about 170 amino acids in length.. 
PF11822 Domain of unknown function (DUF3342)<br>PFAM-B_2751 (release 23.0). This family of proteins are functionally uncharacterised. This family is found in bacteria. This presumed domain is typically between 170 to 303 amino acids in length. The N-terminal half of this family is a BTB-like domain.. 
PF11823 Protein of unknown function (DUF3343)<br>PFAM-B_2956 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are typically between 78 to 102 amino acids in length.. 
PF11824 Protein of unknown function (DUF3344)<br>PFAM-B_3041 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are typically between 367 to 1857 amino acids in length.. 
PF11825 DUF3345;<br>Nuclear/hormone receptor activator site AF-1. PFAM-B_3322 (release 23.0). Nuclear receptors (NRs) are a family of ligand-inducible transcription factors, and, like other transcription factors, they contain a distinct DNA binding domain that allows for target gene recognition and several activation domains that possess the ability to activate transcription  . One of these activation domains is at the N-terminal, although there are two distinct motifs within this domain, between residues 20-36 and between 74 and the end of this domain, which are the binding regions. One of the co-activators is TIF1beta, which appears to bind at the first motif  .. 
PF11826 Protein of unknown function (DUF3346)<br>PFAM-B_3462 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 231 to 659 amino acids in length.. 
PF11827 Protein of unknown function (DUF3347)<br>PFAM-B_3580 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 169 to 570 amino acids in length.. 
PF11828 Protein of unknown function (DUF3348)<br>PFAM-B_3615 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 244 to 323 amino acids in length.. 
PF11829 Protein of unknown function (DUF3349)<br>PFAM-B_3716 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 99 to 124 amino acids in length.. 
PF11830 Domain of unknown function (DUF3350)<br>PFAM-B_3789 (release 23.0). This domain is functionally uncharacterised. This domain is found in eukaryotes. This presumed domain is typically between 50 to 64 amino acids in length.. 
PF11831 DUF3351;<br>pre-mRNA splicing factor component. PFAM-B_3985 (release 23.0). This family is a region of the Myb-Related Cdc5p/Cef1 proteins, in fungi, and is part of the pre-mRNA splicing factor complex.. 
PF11832 Protein of unknown function (DUF3352)<br>PFAM-B_2160 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 538 to 575 amino acids in length.. 
PF11833 Protein of unknown function (DUF3353)<br>PFAM-B_2231 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 205 to 258 amino acids in length.. 
PF11834 Domain of unknown function (DUF3354)<br>PFAM-B_2265 (release 23.0). This domain is functionally uncharacterised. This domain is found in eukaryotes. This presumed domain is about 60 amino acids in length.. 
PF11835 Domain of unknown function (DUF3355)<br>PFAM-B_2268 (release 23.0). This domain is functionally uncharacterised. This domain is found in eukaryotes. This presumed domain is typically between 111 to 177 amino acids in length.. 
PF11836 Protein of unknown function (DUF3356)<br>PFAM-B_2406 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 104 to 119 amino acids in length.. 
PF11837 Domain of unknown function (DUF3357)<br>PFAM-B_2464 (release 23.0). This domain is functionally uncharacterised. This domain is found in eukaryotes. This presumed domain is typically between 96 to 119 amino acids in length.. 
PF11838 DUF3358;<br>ERAP1-like C-terminal domain. PFAM-B_2558 (release 23.0). This large domain is composed of 16 alpha helices organized as 8  HEAT-like repeats. This domain forms a concave face that faces  towards the active site of the peptidase.. 
PF11839 Protein of unknown function (DUF3359)<br>PFAM-B_2625 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 80 amino acids in length.. 
PF11840 Protein of unknown function (DUF3360)<br>PFAM-B_2754 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 489 to 517 amino acids in length.. 
PF11841 Domain of unknown function (DUF3361)<br>PFAM-B_2780 (release 23.0). This domain is functionally uncharacterised. This domain is found in eukaryotes. This presumed domain is typically between 154 to 168 amino acids in length.. 
PF11842 Domain of unknown function (DUF3362)<br>PFAM-B_2839 (release 23.0). This domain is functionally uncharacterised. This domain is found in bacteria and archaea. This presumed domain is typically between 117 to 158 amino acids in length.. 
PF11843 Protein of unknown function (DUF3363)<br>PFAM-B_2310 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 323 to 658 amino acids in length.. 
PF11844 Domain of unknown function (DUF3364)<br>PFAM-B_2336 (release 23.0). This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 60 amino acids in length.. 
PF11845 Protein of unknown function (DUF3365)<br>PFAM-B_2563 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 198 to 657 amino acids in length.. 
PF11846 Domain of unknown function (DUF3366)<br>PFAM-B_2678 (release 23.0). This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 200 amino acids in length.. 
PF11847 Domain of unknown function (DUF3367)<br>PFAM-B_2726 (release 23.0). This domain is functionally uncharacterised. This domain is found in bacteria and archaea. This presumed domain is typically between 667 to 694 amino acids in length.. 
PF11848 Domain of unknown function (DUF3368)<br>PFAM-B_2745 (release 23.0). This domain is functionally uncharacterised. This domain is found in bacteria and archaea. This presumed domain is about 50 amino acids in length.. 
PF11849 Domain of unknown function (DUF3369)<br>PFAM-B_2927 (release 23.0). This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 170 amino acids in length. The domain appears to be related to the GAF domain.. 
PF11850 Protein of unknown function (DUF3370)<br>PFAM-B_3037 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 452 to 532 amino acids in length.. 
PF11851 Domain of unknown function (DUF3371)<br>PFAM-B_3115 (release 23.0). This domain is functionally uncharacterised. This domain is found in eukaryotes. This presumed domain is typically between 125 to 142 amino acids in length.. 
PF11852 Domain of unknown function (DUF3372)<br>PFAM-B_3259 (release 23.0). This domain is functionally uncharacterised. This domain is found in bacteria and eukaryotes. This presumed domain is about 170 amino acids in length.. 
PF11853 Protein of unknown function (DUF3373)<br>PFAM-B_3442 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 472 to 574 amino acids in length.. 
PF11854 Protein of unknown function (DUF3374)<br>PFAM-B_3548 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 665 to 712 amino acids in length.. 
PF11855 Protein of unknown function (DUF3375)<br>PFAM-B_3589 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 479 to 499 amino acids in length.. 
PF11856 Protein of unknown function (DUF3376)<br>PFAM-B_3667 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 770 to 1142 amino acids in length.. 
PF11857 Domain of unknown function (DUF3377)<br>PFAM-B_3829 (release 23.0). This domain is functionally uncharacterised. This domain is found in eukaryotes. This presumed domain is about 70 amino acids in length.. 
PF11858 Domain of unknown function (DUF3378)<br>PFAM-B_3989 (release 23.0). This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 80 amino acids in length.. 
PF11859 Protein of unknown function (DUF3379)<br>PFAM-B_2469 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 234 to 251 amino acids in length.. 
PF11860 Protein of unknown function (DUF3380)<br>PFAM-B_2757 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria and viruses. Proteins in this family are typically between 194 to 284 amino acids in length. This protein is found associated with Pfam:PF01471.. 
PF11861 Domain of unknown function (DUF3381)<br>PFAM-B_2792 (release 23.0). This domain is functionally uncharacterised. This domain is found in eukaryotes. This presumed domain is typically between 156 to 174 amino acids in length. This domain is found associated with Pfam:PF07780, Pfam:PF01728.. 
PF11862 Domain of unknown function (DUF3382)<br>PFAM-B_2882 (release 23.0). This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 100 amino acids in length. This domain is found associated with Pfam:PF02653.. 
PF11863 Protein of unknown function (DUF3383)<br>PFAM-B_3017 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria and viruses. Proteins in this family are typically between 356 to 501 amino acids in length.. 
PF11864 Domain of unknown function (DUF3384)<br>PFAM-B_3114 (release 23.0). This domain is functionally uncharacterised. This domain is found in eukaryotes. This presumed domain is typically between 422 to 486 amino acids in length. This domain is found associated with Pfam:PF02145.. 
PF11865 Domain of unknown function (DUF3385)<br>PFAM-B_3188 (release 23.0). This domain is functionally uncharacterised. This domain is found in eukaryotes.  This presumed domain is typically between 160 to 172 amino acids in length.  This domain is found associated with Pfam:PF00454, Pfam:PF02260, Pfam:PF02985, Pfam:PF02259 and Pfam:PF08771.. 
PF11866 Protein of unknown function (DUF3386)<br>PFAM-B_3390 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are about 220 amino acids in length.. 
PF11867 Domain of unknown function (DUF3387)<br>PFAM-B_3465 (release 23.0). This domain is functionally uncharacterised. This domain is found in bacteria and archaea. This presumed domain is typically between 255 to 340 amino acids in length. This domain is found associated with Pfam:PF04851, Pfam:PF04313.. 
PF11868 Protein of unknown function (DUF3388)<br>PFAM-B_3650 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 261 to 275 amino acids in length. This protein is found associated with Pfam:PF01842.. 
PF11869 Protein of unknown function (DUF3389)<br>PFAM-B_3739 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 80 amino acids in length.. 
PF11870 Domain of unknown function (DUF3390)<br>PFAM-B_3832 (release 23.0). This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 90 amino acids in length. This domain is found associated with Pfam:PF02589.. 
PF11871 Domain of unknown function (DUF3391)<br>PFAM-B_2190 (release 23.0). This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is typically between 122 to 139 amino acids in length. This domain is found associated with Pfam:PF01966.. 
PF11872 Protein of unknown function (DUF3392)<br>PFAM-B_2322 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 110 amino acids in length.. 
PF11873 Domain of unknown function (DUF3393)<br>PFAM-B_2361 (release 23.0). This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is typically between 188 to 206 amino acids in length. This domain is found associated with Pfam:PF01464.. 
PF11874 Domain of unknown function (DUF3394)<br>PFAM-B_2758 (release 23.0). This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 190 amino acids in length. This domain is found associated with Pfam:PF06808.. 
PF11875 Domain of unknown function (DUF3395)<br>PFAM-B_2767 (release 23.0). This domain is functionally uncharacterised. This domain is found in eukaryotes. This presumed domain is typically between 147 to 176 amino acids in length. This domain is found associated with Pfam:PF00226.. 
PF11876 Protein of unknown function (DUF3396)<br>PFAM-B_2995 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria and viruses. Proteins in this family are typically between 302 to 382 amino acids in length.. 
PF11877 Protein of unknown function (DUF3397)<br>PFAM-B_3446 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 114 to 128 amino acids in length.. 
PF11878 Domain of unknown function (DUF3398)<br>PFAM-B_3712 (release 23.0). This domain is functionally uncharacterised. This domain is found in eukaryotes. This presumed domain is about 100 amino acids in length.. 
PF11879 Domain of unknown function (DUF3399)<br>PFAM-B_3857 (release 23.0). This domain is functionally uncharacterised. This domain is found in eukaryotes.  This presumed domain is about 100 amino acids in length.  This domain is found associated with Pfam:PF02214, Pfam:PF00520.. 
PF11880 Domain of unknown function (DUF3400)<br>PFAM-B_3996 (release 23.0). This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 50 amino acids in length.  This domain is found associated with Pfam:PF02754, Pfam:PF02913, Pfam:PF01565.. 
PF11881 Domain of unknown function (DUF3401)<br>PFAM-B_2478 (release 23.0). This domain is functionally uncharacterised. This domain is found in eukaryotes. This presumed domain is typically between 231 to 250 amino acids in length. This domain is found associated with Pfam:PF02145, Pfam:PF00595.. 
PF11882 Domain of unknown function (DUF3402)<br>PFAM-B_2702 (release 23.0). This domain is functionally uncharacterised. This domain is found in eukaryotes. This presumed domain is typically between 350 to 473 amino acids in length. This domain is found associated with Pfam:PF07923.. 
PF11883 Domain of unknown function (DUF3403)<br>PFAM-B_2739 (release 23.0). This domain is functionally uncharacterised. This domain is found in eukaryotes.  This presumed domain is about 50 amino acids in length.  This domain is found associated with Pfam:PF00069, Pfam:PF08276, Pfam:PF00954, Pfam:PF01453.. 
PF11884 Domain of unknown function (DUF3404)<br>PFAM-B_2879 (release 23.0). This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 260 amino acids in length. This domain is found associated with Pfam:PF02518, Pfam:PF00512.. 
PF11885 Protein of unknown function (DUF3405)<br>PFAM-B_3057 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 636 to 810 amino acids in length.. 
PF11886 Domain of unknown function (DUF3406)<br>PFAM-B_3286 (release 23.0). This domain is functionally uncharacterised. This domain is found in eukaryotes. This presumed domain is about 270 amino acids in length. This domain is found associated with Pfam:PF04548.. 
PF11887 Protein of unknown function (DUF3407)<br>PFAM-B_3559 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 360 to 454 amino acids in length. This protein is found associated with Pfam:PF02470.. 
PF11888 Protein of unknown function (DUF3408)<br>PFAM-B_3594 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 128 to 160 amino acids in length.. 
PF11889 Domain of unknown function (DUF3409)<br>PFAM-B_3824 (release 23.0). This domain is functionally uncharacterised. This domain is found in viruses.  This presumed domain is about 60 amino acids in length.  This domain is found associated with Pfam:PF00271, Pfam:PF05550, Pfam:PF05578.. 
PF11890 Domain of unknown function (DUF3410)<br>PFAM-B_1956 (release 23.0). This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 90 amino acids in length. This domain is found associated with Pfam:PF02826, Pfam:PF00389. This domain has a conserved RRE sequence motif.. 
PF11891 Domain of unknown function (DUF3411)<br>PFAM-B_1986 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 168 to 186 amino acids in length. This domain has a conserved RYQ sequence motif.. 
PF11892 Domain of unknown function (DUF3412)<br>PFAM-B_1106 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is about 120 amino acids in length. This domain is found associated with Pfam:PF03641.. 
PF11893 Domain of unknown function (DUF3413)<br>PFAM-B_1403 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is about 250 amino acids in length. This domain is found associated with Pfam:PF00884.. 
PF11894 Protein of unknown function (DUF3414)<br>PFAM-B_1638 (release 23.0). This family of proteins are functionally uncharacterised. The family is found in eukaryotes and has a conserved LLG sequence motif.. 
PF11895 Domain of unknown function (DUF3415)<br>PFAM-B_1962 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 80 amino acids in length. This domain is found associated with Pfam:PF00141.. 
PF11896 Domain of unknown function (DUF3416)<br>PFAM-B_601 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in bacteria and archaea. This domain is about 190 amino acids in length. This domain is found associated with Pfam:PF00128.. 
PF11897 Protein of unknown function (DUF3417)<br>PFAM-B_724 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are typically between 145 to 860 amino acids in length. This protein is found associated with Pfam:PF00343. This protein has a conserved AYF sequence motif.. 
PF11898 Domain of unknown function (DUF3418)<br>PFAM-B_1028 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is typically between 582 to 594 amino acids in length. This domain is found associated with Pfam:PF07717, Pfam:PF00271, Pfam:PF04408.. 
PF11899 Protein of unknown function (DUF3419)<br>PFAM-B_1329 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 398 to 802 amino acids in length.. 
PF11900 Domain of unknown function (DUF3420)<br>PFAM-B_1362 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 50 amino acids in length. This domain is found associated with Pfam:PF00023.. 
PF11901 Protein of unknown function (DUF3421)<br>PFAM-B_1420 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 119 to 296 amino acids in length.. 
PF11902 Protein of unknown function (DUF3422)<br>PFAM-B_513 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 426 to 444 amino acids in length.. 
PF11903 Protein of unknown function (DUF3423)<br>PFAM-B_670 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 73 to 118 amino acids in length. This protein appears to be related to ribbon-helix-helix DNA-binding domains, suggesting these proteins may also bind DNA.. 
PF11904 DUF3424;<br>PFAM-B_942 (release 23.0). This domain, and the associated ANK family repeat Pfam:PF00023 domain, together act as a chaperone for biogenesis and folding of the DP receptor for prostaglandin D2.. 
PF11905 Domain of unknown function (DUF3425)<br>PFAM-B_1128 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 120 to 143 amino acids in length.. 
PF11906 Protein of unknown function (DUF3426)<br>PFAM-B_1212 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 262 to 463 amino acids in length.. 
PF11907 Domain of unknown function (DUF3427)<br>PFAM-B_1236 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in bacteria and archaea. This domain is typically between 243 to 275 amino acids in length. This domain is found associated with Pfam:PF04851, Pfam:PF00271.. 
PF11909 NADH-quinone oxidoreductase cyanobacterial subunit N<br>The proton-pumping NADH:ubiquinone oxidoreductase catalyzes the electron transfer from NADH to ubiquinone linked with proton translocation across the membrane. It is the largest, most complex and least understood of the respiratory chain enzymes and is referred to as Complex I. The subunit composition of the enzyme varies between groups of organisms. Complex I originating from mammalian mitochondria contains 45 different proteins, whereas in bacteria, the corresponding complex NDH-1 consists of 14 different polypeptides. Homologues of these 14 proteins are found among subunits of the mitochondrial complex I, and therefore bacterial NDH-1 might be considered a model proton-pumping NADH dehydrogenase with a minimal set of subunits. Escherichia coli NDH-1 readily disintegrates into 3 subcomplexes: a water-soluble NADH dehydrogenase fragment (NuoE, -F, and -G),the connecting fragment (NuoB, -C, -D, and -I), and the membrane fragment (NuoA, -H, -J, -K, -L, -M, -N). In cyanobacteria and their descendants, the chloroplasts of green plants, the subunit composition of NDH-1 remains obscure. The genes for eleven subunits NdhA-NdhK, homologous to the NuoA-NuoD and NuoH-NuoN of the E. coli complex, have been found in the genome of Synechocystis sp. PCC 6803 which has a family of 6 ndhD genes and a family of 3 ndhF genes. Two reported multisubunit complexes, NDH-1L and NDH-1M, represent distinct NDH-1 complexes in the thylakoid membrane of Synechocystis 6803 -cyanobacterium. NDH-1L was shown to be essential for photoheterotrophic cell growth, whereas expression of NDH-1M was a prerequisite for CO2 uptake and played an important role in growth of cells at low CO2. Here we report the subunit composition of these two complexes. Fifteen proteins were discovered in NDH-1L including NdhL, a new component of the membrane fragment, and Ssl1690 (designated as NdhO), a novel peripheral subunit  . The cyanobacterial NDH-1 complex contains additional subunits, NdhM and NdhN, compared with the minimal set of the bacterial enzyme and these seem to be specific for thylakoid-located NDH-1 of photosynthetic organisms  .. 
PF11910 Cyanobacterial and plant NDH-1 subunit O<br>The proton-pumping NADH:ubiquinone oxidoreductase catalyzes the electron transfer from NADH to ubiquinone linked with proton translocation across the membrane. It is the largest, most complex and least understood of the respiratory chain enzymes and is referred to as Complex I. The subunit composition of the enzyme varies between groups of organisms. Complex I originating from mammalian mitochondria contains 45 different proteins, whereas in bacteria, the corresponding complex NDH-1 consists of 14 different polypeptides.  Homologues of these 14 proteins are found among subunits of the mitochondrial complex I, and therefore bacterial NDH-1 might be considered a model proton-pumping NADH dehydrogenase with a minimal set of subunits. Escherichia coli NDH-1 readily disintegrates into 3 subcomplexes: a water-soluble NADH dehydrogenase fragment (NuoE, -F, and -G),the connecting fragment (NuoB, -C, -D, and -I), and the membrane fragment (NuoA, -H, -J, -K, -L, -M, -N). In cyanobacteria and their descendants, the chloroplasts of green plants, the subunit composition of NDH-1 remains obscure. The genes for eleven subunits NdhA-NdhK, homologous to the NuoA-NuoD and NuoH-NuoN of the E. coli complex, have been found in the genome of Synechocystis sp. PCC 6803 which has a family of 6 ndhD genes and a family of 3 ndhF genes. Two reported multisubunit complexes, NDH-1L and NDH-1M, represent distinct NDH-1 complexes in the thylakoid membrane of Synechocystis 6803 -cyanobacterium. NDH-1L was shown to be essential for photoheterotrophic cell growth, whereas expression of NDH-1M was a prerequisite for CO2 uptake and played an important role in growth of cells at low CO2. Here we report the subunit composition of these two complexes. Fifteen proteins were discovered in NDH-1L including NdhL, a new component of the membrane fragment, and Ssl1690 (designated as NdhO), a novel peripheral subunit [1, 2]. The three nuclear-encoded subunits NdhM,NdhN and NdhO are vital for the functional integrity of the plastidial complex  .. 
PF11911 Protein of unknown function (DUF3429)<br>PFAM-B_1072 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 147 to 245 amino acids in length.. 
PF11912 Protein of unknown function (DUF3430)<br>PFAM-B_1305 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 209 to 265 amino acids in length.. 
PF11913 Protein of unknown function (DUF3431)<br>PFAM-B_1346 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 291 to 390 amino acids in length. This protein has a conserved NLRC sequence motif.. 
PF11914 Domain of unknown function (DUF3432)<br>PFAM-B_1326 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 100 amino acids in length. This domain is found associated with Pfam:PF00096. This domain has two conserved sequence motifs: YPSPV and PSP.. 
PF11915 Protein of unknown function (DUF3433)<br>PFAM-B_1502 (release 23.0). This is a family of functionally uncharacterised proteins. The family is found in eukaryotes, and represents the conserved central region of the member proteins.. 
PF11916 DUF3434;<br>Vacuolar protein 14 C-terminal Fig4p binding. PFAM-B_1661 (release 23.0). Vac14 is a scaffold for the Fab1 kinase complex, a complex that allows for the dynamic interconversion of PI3P and PI(3,5)P2p (phosphoinositide phosphate (PIP) lipids, that are generated transiently on the cytoplasmic face of selected intracellular membranes). This interconversion is regulated by at least five proteins in yeast: the lipid kinase Fab1p, lipid phosphatase Fig4p, the Fab1p activator Vac7p, the Fab1p inhibitor Atg18p, and Vac14p, a protein required for the activity of both Fab1p and Fig4p. The C-terminal region of Vac14 binds to Fig4p. The full length Vac14 in yeasts is likely to be a protein carrying a succession of HEAT repeats, most of which have now degenerated. This regulatory system is crucial for the proper functioning of the mammalian nervous system.. 
PF11917 Protein of unknown function (DUF3435)<br>PFAM-B_1788 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 435 to 791 amino acids in length. This family is related to Pfam:PF00589 suggesting it may be an integrase enzyme.. 
PF11918 Domain of unknown function (DUF3436)<br>PFAM-B_18 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 50 amino acids in length. This domain is found associated with Pfam:PF03572. This domain has two conserved sequence motifs: DPRL and SYEP.. 
PF11919 Domain of unknown function (DUF3437)<br>PFAM-B_1910 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 142 to 163 amino acids in length.. 
PF11920 Protein of unknown function (DUF3438)<br>PFAM-B_1942 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 276 to 307 amino acids in length.. 
PF11921 Domain of unknown function (DUF3439)<br>PFAM-B_1105 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 46 to 94 amino acids in length. This domain is found associated with Pfam:PF01462, Pfam:PF00560.. 
PF11922 Domain of unknown function (DUF3440)<br>PFAM-B_1674 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is typically between 53 to 190 amino acids in length. This domain is found associated with Pfam:PF01507. This domain has a conserved KND sequence motif.. 
PF11923 Domain of unknown function (DUF3441)<br>PFAM-B_1795 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in archaea and eukaryotes. This domain is typically between 104 to 119 amino acids in length. This domain is found associated with Pfam:PF05833, Pfam:PF05670. This domain has two conserved residues (P and G) that may be functionally important.. 
PF11924 Protein of unknown function (DUF3442)<br>PFAM-B_890 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 334 to 948 amino acids in length.. 
PF11925 Protein of unknown function (DUF3443)<br>PFAM-B_1634 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 400 to 434 amino acids in length. This protein has two conserved sequence motifs: NPV and DNNG.. 
PF11926 Domain of unknown function (DUF3444)<br>PFAM-B_1267 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 210 amino acids in length. This domain is found associated with Pfam:PF00226. This domain has two conserved sequence motifs: FSH and FSH.. 
PF11927 Protein of unknown function (DUF3445)<br>PFAM-B_501 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 264 to 418 amino acids in length. This protein has a conserved RLP sequence motif. This protein has two completely conserved R residues that may be functionally important.. 
PF11928 Domain of unknown function (DUF3446)<br>PFAM-B_833 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 80 to 99 amino acids in length. This domain is found associated with Pfam:PF00096. This domain has a single completely conserved residue P that may be functionally important.. 
PF11929 Domain of unknown function (DUF3447)<br>PFAM-B_10 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 80 amino acids in length.  This domain is found associated with Pfam:PF00023. This domain has a conserved SHN sequence motif. It seems likely that this region represents divergent Ankyrin repeats.. 
PF11931 Domain of unknown function (DUF3449)<br>PFAM-B_769 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 181 to 207 amino acids in length. This domain has two conserved sequence motifs: PIP and CEICG. The domain carries a zinc-finger domain of the C2H2-type.. 
PF11932 Protein of unknown function (DUF3450)<br>PFAM-B_773 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are about 260 amino acids in length.. 
PF11933 Domain of unknown function (DUF3451)<br>PFAM-B_877 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 199 to 238 amino acids in length. This domain is found associated with Pfam:PF06512, Pfam:PF00520. This domain has a conserved ADD sequence motif.. 
PF11934 Domain of unknown function (DUF3452)<br>PFAM-B_1048 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in bacteria and eukaryotes. This domain is typically between 124 to 150 amino acids in length. This domain is found associated with Pfam:PF01858, Pfam:PF01857. This domain has a single completely conserved residue W that may be functionally important.. 
PF11935 Domain of unknown function (DUF3453)<br>PFAM-B_1335 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 239 to 261 amino acids in length.. 
PF11936 Domain of unknown function (DUF3454)<br>PFAM-B_1847 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 60 amino acids in length. This domain is found associated with Pfam:PF00066, Pfam:PF00008, Pfam:PF06816, Pfam:PF07684, Pfam:PF00023.. 
PF11937 Protein of unknown function (DUF3455)<br>PFAM-B_1386 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 174 to 251 amino acids in length.. 
PF11938 TLR4 regulator and MIR-interacting MSAP<br>PFAM-B_1799 (release 23.0). This family of proteins, found from plants to humans, is PRAT4 (A and B), a Protein Associated with Toll-like receptor 4. The Toll family of receptors - TLRs - plays an essential role in innate recognition of microbial products, the first line of defence against bacterial infection  . PRAT4A influences the subcellular distribution and the strength of TLR responses and alters the relative activity of each TLR. PRAT4B regulates TLR4 trafficking to the cell surface and the extent of its expression there   . TLR4 recognizes lipopolysaccharide (LPS), one of the most immuno-stimulatory glycolipids constituting the outer membrane of the Gram-negative bacteria.\.    This family has also been described as a SAP-like MIR-interacting protein family.. 
PF11939 Protein of unknown function (DUF3457)<br>PFAM-B_1822 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 162 to 197 amino acids in length. This protein has a conserved CSL sequence motif.. 
PF11940 Domain of unknown function (DUF3458)<br>PFAM-B_160 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in bacteria, archaea and eukaryotes. This domain is typically between 402 to 419 amino acids in length. This domain is found associated with Pfam:PF01433. This domain has a conserved FSAPV sequence motif.. 
PF11941 Domain of unknown function (DUF3459)<br>PFAM-B_897 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is about 110 amino acids in length. This domain is found associated with Pfam:PF00128, Pfam:PF02922.. 
PF11942 Spt5 transcription elongation factor, acidic N-terminal<br>This is the very acidic N-terminal region of the early transcription elongation factor Spt5  . The Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The actual function of this N-terminal domain is not known although it is dispensable for binding to Spt4  .. 
PF11943 Protein of unknown function (DUF3460)<br>PFAM-B_2362 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 70 amino acids in length. This protein has a conserved WDK sequence motif.. 
PF11944 Protein of unknown function (DUF3461)<br>PFAM-B_2125 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 130 amino acids in length. This protein has two conserved sequence motifs: KFK and HLE.. 
PF11945 DUF3462;<br>WAHD domain of WASH complex. PFAM-B_2071 (release 23.0). This domain forms part of the WASH-complex of domains and proteins that activates the Arp2/3 complex, see Pfam:PF04062. The Arp2/3 complex regulates endocytosis, sorting, and trafficking within the cell. The WAHD domain attaches to the FAM21 proteins via its N-terminal residues and to the microtubules via its C-terminal residues.. 
PF11946 Domain of unknown function (DUF3463)<br>PFAM-B_2277 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in bacteria and archaea. This domain is about 140 amino acids in length. This domain is found associated with Pfam:PF04055. This domain has two conserved sequence motifs: CTPWG and PCYL, plus a highly conserved CxxCxxHC motif.. 
PF11947 Protein of unknown function (DUF3464)<br>PFAM-B_2676 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 137 to 196 amino acids in length.. 
PF11948 Protein of unknown function (DUF3465)<br>PFAM-B_2827 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 131 to 151 amino acids in length. This protein has a conserved HWTH sequence motif.. 
PF11949 Protein of unknown function (DUF3466)<br>PFAM-B_2541 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 564 to 612 amino acids in length.. 
PF11950 Protein of unknown function (DUF3467)<br>PFAM-B_2299 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in bacteria, archaea and viruses. Proteins in this family are typically between 101 to 118 amino acids in length.. 
PF11951 DUF3468;<br>Fungal specific transcription factor domain. PFAM-B_2291 (release 23.0). This family of are likely to be transcription factors. This protein is found in fungi. Proteins in this family are typically between 454 to 826 amino acids in length. This protein is found associated with Pfam:PF00172.. 
PF11952 Protein of unknown function (DUF3469)<br>PFAM-B_2159 (release 23.0). This family of proteins are functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 108 to 439 amino acids in length.. 
PF11953 Domain of unknown function (DUF3470)<br>PFAM-B_2503 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is about 50 amino acids in length. This domain is found associated with Pfam:PF00037. This domain has a single completely conserved residue N that may be functionally important.. 
PF11954 Domain of unknown function (DUF3471)<br>PFAM-B_2961 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in bacteria, archaea and eukaryotes. This domain is typically between 98 to 114 amino acids in length. This domain is found associated with Pfam:PF00144.. 
PF11955 Plant organelle RNA recognition domain<br>Moxon SJ, Barkan A, Coggill P. Pfam-B_1780 (release 8.0). This family, which was previously known as DUF860, has been shown to be a component of group II intron ribonucleoprotein particles in maize chloroplasts. The domain is required for the splicing of the introns with which it associates, and promotes splicing in the context of a heterodimer with the RNase III-domain protein RNC1. All of the members are predicted to localise to mitochondria or chloroplasts  . It seems likely that most PORR proteins function in organellar RNA metabolism  .. 
PF11956 Ankyrin-G binding motif of KCNQ2-3<br>Pfam-B_10256 (release 23.0). Interactions with ankyrin-G are crucial to the localisation of voltage-gated sodium channels (VGSCs) at the axon initial segment and for neurons to initiate action potentials. This conserved 9-amino acid motif ((V/A)P(I/L)AXXE(S/D)D) is required for ankyrin-G binding and functions to localise sodium channels to a variety of 'excitable' membrane domains both inside and outside of the nervous system  . This motif has also been identified in the potassium channel 6TM proteins KCNQ2 and KCNQ3  , that correspond to the M channels that exert a crucial influence over neuronal excitability. KCNQ2/KCNQ3 channels are preferentially localised to the surface of axons both at the axonal initial segment and more distally, and this axonal initial segment targeting of surface KCNQ channels is mediated by these ankyrin-G binding motifs of KCNQ2 and KCNQ3  . KCNQ3 is a major determinant of M channel localisation to the AIS, rather than KCNQ2  . Phylogenetic analysis reveals that anchor motifs evolved sequentially in chordates (NaV channel) and jawed vertebrates (KCNQ2/3)  .. 
PF11957 THO complex subunit 1 transcription elongation factor<br>Pfam-B_2059 (release 23.0). The THO complex plays a role in coupling transcription elongation to mRNA export.  It is composed of subunits THP2, HPR1, THO2 and MFT1  . The THO complex is a nuclear complex that is required for transcription elongation through genes containing tandemly repeated DNA sequences. The THO complex is also part of the TREX (TRanscription EXport) complex that is involved in coupling transcription to export of mRNAs to the cytoplasm [2,3].. 
PF11958 Domain of unknown function (DUF3472)<br>PFAM-B_2598 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in bacteria, eukaryotes and viruses. This domain is typically between 174 to 190 amino acids in length. This domain has a single completely conserved residue G that may be functionally important.. 
PF11959 Domain of unknown function (DUF3473)<br>PFAM-B_3065 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in bacteria and archaea. This domain is about 130 amino acids in length. This domain is found associated with Pfam:PF01522. This domain has two completely conserved residues (P and H) that may be functionally important.. 
PF11960 Domain of unknown function (DUF3474)<br>PFAM-B_3095 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in bacteria and eukaryotes. This domain is typically between 126 to 140 amino acids in length. This domain is found associated with Pfam:PF00487.. 
PF11961 Domain of unknown function (DUF3475)<br>PFAM-B_3098 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 60 amino acids in length.  This domain is found associated with Pfam:PF05003.. 
PF11962 DUF3476;<br>Peptidase_G2, IMC autoproteolytic cleavage domain. PFAM-B_3119 (release 23.0). This domain is found at the very C-terminus of bacteriophage parallel beta-helical tailspike proteins. It carries the enzymic residues that induce autoproteolytic cleavage to bring about maturation of the folding process of the helix in a chaperone-like manner. The domain thus mediates the assembly of a large tailspike protein and then releases itself after maturation. These C-terminal regions that autoproteolytically release themselves after maturation are exchangeable between functionally unrelated N-terminal proteins and have been identified in a number of bacteriophage tailspike proteins  .. 
PF11963 Protein of unknown function (DUF3477)<br>PFAM-B_3147 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in viruses. Proteins in this family are typically between 246 to 7162 amino acids in length. This protein is found associated with Pfam:PF08716, Pfam:PF01661, Pfam:PF05409, Pfam:PF08717, Pfam:PF01831, Pfam:PF08715, Pfam:PF08710.. 
PF11964 DUF3478;<br>PFAM-B_640 (release 23.0). These proteins adopt an alpha/beta SpoIIAA-like fold, similar to that found in STAT (Pfam:PF01740). They adopt open and closed conformations arising from different arrangements of their alpha-2 and alpha-3 helices. They may be membrane associated and may function as carriers of non-polar compounds  .. 
PF11965 Domain of unknown function (DUF3479)<br>PFAM-B_1065 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in bacteria, archaea and eukaryotes. This domain is about 160 amino acids in length. This domain is found associated with Pfam:PF02514.. 
PF11966 Fibronectin-binding repeat<br>Pfam-B_5998 (release 23.0). Streptococcal surface repeat domain - SSURE - is a protein fragment found to bind to extracellular matrix protein fibronectin but not to collagen or submaxillary mucin in Streptococci. Anti-SSURE antibodies recognised the corresponding protein on the surface of streptococcal cells. The full-length proteins are thus fibronectin-binding surface adhesins.. 
PF11967 Recombination protein O N terminal<br>Recombination protein O (RecO) is involved in DNA repair and Pfam:PF00470 pathway recombination.  This domain forms a beta barrel structure.. 
PF11968 Putative methyltransferase (DUF3321)<br>Pfam-B_6141 (release 23.0). This family is broadly conserved, being found in fungi, plants, arthropods and up to primates. it may be a methyltransferase.. 
PF11969 Scavenger mRNA decapping enzyme C-term binding<br>Pfam-B_9894 (release 8.0). This family consists of several scavenger mRNA decapping enzymes (DcpS) and is the C-terminal region. DcpS is a scavenger pyrophosphatase that hydrolyses the residual cap structure following 3' to 5' decay of an mRNA. The association of DcpS with 3' to 5' exonuclease exosome components suggests that these two activities are linked and there is a coupled exonucleolytic decay-dependent decapping pathway. The C-terminal domain contains a histidine triad (HIT) sequence with three histidines separated by hydrophobic residues. The central histidine within the DcpS HIT motif is critical for decapping activity and defines the HIT motif as a new mRNA decapping domain, making DcpS the first member of the HIT family of proteins with a defined biological function.. 
PF11970 G protein-coupled glucose receptor regulating Gpa2 C-term<br>Pfam-B_11657 (release 23.0). Git3 is one of six proteins required for glucose-triggered adenylate cyclase activation, and is a G protein-coupled receptor responsible for the activation of adenylate cyclase through Gpa2 - heterotrimeric G protein alpha subunit, part of the glucose-detection pathway. Git3 contains seven predicted transmembrane domains, a third cytoplasmic loop and a cytoplasmic tail  . This family is the conserved C-terminal domain of the member proteins.. 
PF11971 CAMSAP CH domain<br>This domain is the N-terminal CH domain from the CAMSAP proteins.i. 
PF11972 HTH DNA binding domain<br>Pfam-B_8688 (release 14.0). This is a helix-turn-helix DNA binding domain.. 
PF11973 NQRA C-terminal domain<br>Pfam-B_3622 (release 8.0). This family consists of the C-terminal domain of several bacterial Na(+)-translocating NADH-quinone reductase subunit A (NQRA) proteins.  The Na(+)-translocating NADH: ubiquinone oxidoreductase (Na(+)-NQR) generates an electrochemical Na(+) potential driven by aerobic respiration  .. 
PF11974 Alpha-2-macroglobulin MG1 domain<br>This is the N-terminal MG1 domain from alpha-2-macroglobulin  .. 
PF11975 Family 4 glycosyl hydrolase C-terminal domain<br>
PF11976 Ubiquitin-2 like Rad60 SUMO-like<br>Wood V, Chahwan C, Coggill P. The small ubiquitin-related modifier SUMO-1 is a Ub/Ubl family member, and although SUMO-1 shares structural similarity to Ub, SUMO's cellular functions remain distinct insomuch as SUMO modification alters protein function through changes in activity, cellular localisation, or by protecting substrates from ubiquitination  . Rad60 family members contain functionally enigmatic, integral SUMO-like domains (SLDs). Despite their divergence from SUMO, each Rad60 SLD interacts with a subset of SUMO pathway enzymes: SLD2 specifically binds the SUMO E2 conjugating enzyme (Ubc9)), whereas SLD1 binds the SUMO E1 (Fub2, also called Uba2) activating and E3 (Pli1, also called Siz1 and Siz2) specificity enzymes. Structural analysis of PDB:2uyz reveals a mechanistic basis for the near-synonymous roles of Rad60 and SUMO in survival of genotoxic stress and suggest unprecedented DNA-damage-response functions for SLDs in regulating SUMOylation  . The Rad60 branch of this family is also known as RENi (Rad60-Esc2-Nip45), and biologically it should be two distinct families SUMO and RENi (Rad60-Esc2-Nip45).. 
PF11977 Zc3h12a-like Ribonuclease NYN domain<br>This domain is found in the Zc3h12a protein which has shown to be a ribonuclease that controls the stability of a set of inflammatory genes  . It has been suggested that this domain belongs to the PIN domain superfamily  . This domain has also been identified as part  of the NYN domain family  .. 
PF11978 Shoulder domain<br>This domain is found in the Major Vault Protein and has been called the shoulder domain  . This family includes two bacterial proteins Swiss:A6FXE2 and Swiss:A1ZGE7. This suggests that some bacteria may possess vault particles.. 
PF11979 Domain of unknown function (DUF3480)<br>PFAM-B_2031 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 350 to 362 amino acids in length. This domain is found associated with Pfam:PF01363.. 
PF11980 Domain of unknown function (DUF3481)<br>Pfam-B_2819 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 80 amino acids in length.  This domain is found associated with Pfam:PF00754, Pfam:PF00431, Pfam:PF00629. This domain has two completely conserved residues (Y and E) that may be functionally important.. 
PF11981 Domain of unknown function (DUF3482)<br>PFAM-B_3168 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in bacteria and eukaryotes. This domain is typically between 289 to 301 amino acids in length. This domain is found associated with Pfam:PF01926. THe central region of these proteins contains a hydrophobic region that is similar to Pfam:PF05433.. 
PF11982 Domain of unknown function (DUF3483)<br>PFAM-B_3204 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is about 230 amino acids in length. This domain is found associated with Pfam:PF02754.. 
PF11983 Domain of unknown function (DUF3484)<br>PFAM-B_3216 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is typically between 65 to 81 amino acids in length. This domain is found associated with Pfam:PF02491.. 
PF11984 Protein of unknown function (DUF3485)<br>PFAM-B_3236 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 223 to 526 amino acids in length. This protein is found associated with Pfam:PF09721.. 
PF11985 Protein of unknown function (DUF3486)<br>PFAM-B_3271 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria and viruses. Proteins in this family are about 190 amino acids in length.. 
PF11986 Influenza A Proapoptotic protein<br>PB1-F2 is a protein found in almost all known strains of Influenza A virus - a negative sense ssRNA Orthomyxovirus  . It originates from translation of the viral polymerase gene in an alternative reading frame  . PB1-F2 consists of two independent structural domains, two closely neighboring short helices at the N terminus, and an extended C-terminal helix  .  Although the protein has originally been described to induce apoptosis, it has now been shown that PB1-F2 more likely acts as an apoptosis promoter in concert with other apoptosis-inducing agents  . PB1-F2 promotes apoptosis by localising to the mitochondria where it destabilises the membrane. This will cause release of cytochrome C which activates the caspase cascade of apoptosis through the endogenous pathway  . In this way it acts like the Bcl-2 protein family which are physiological apoptotic regulators in cells  .. 
PF11987 Translation-initiation factor 2<br>IF-2 is a translation initiator in each of the three main phylogenetic domains (Eukaryotes  , Bacteria   and Archaea  ). IF2 interacts with formylmethionine-tRNA, GTP, IF1, IF3 and both ribosomal subunits  . Through these interactions, IF2 promotes the binding of the initiator tRNA to the A site in the smaller ribosomal subunit and catalyses the hydrolysis of GTP following initiation-complex formation  .. 
PF11988 Retrograde transport protein Dsl1 N terminal<br>Dsl1 is a peripheral membrane protein required for transport between the Golgi and the endoplasmic reticulum  . It is localised to the ER membrane, and in vitro it specifically binds to coatomer, the major component of the protein coat of COPI vesicles  . It is comprised primarily of alpha helical bundles  . It complexes with another subunit of the Dsl1p complex called Tip20 which forms heterodimers by pairing the N termini of each protein  .  A central disorganised region between the N and C termini of Dsl1 contains binding sites for coatomer  . The C terminus of Dsl1 contains a binding site to the Sec39 subunit of the Dsl1p complex  .. 
PF11989 Retrograde transport protein Dsl1 C terminal<br>Dsl1 is a peripheral membrane protein required for transport between the Golgi and the endoplasmic reticulum  . It is localised to the ER membrane, and in vitro it specifically binds to coatomer, the major component of the protein coat of COPI vesicles  . Binding sites for coatomer are found on a disorganised region between the C and N termini of Dsl1  . The C terminal domain is involved in binding to the Sec39 subunit of the Dsl1p complex  . The N terminal complexes with another subunit of the Dsl1p complex called Tip20 which forms heterodimers by pairing the N termini of each protein  .. 
PF11990 Protein of unknown function (DUF3487)<br>PFAM-B_2242 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 121 to 136 amino acids in length. This protein has a conserved RLN sequence motif.. 
PF11991 Tryptophan dimethylallyltransferase<br>PFAM-B_2054 (release 23.0). This family of proteins represents tryptophan dimethylallyltransferase (EC:2.5.1.34), which catalyses the first step of ergot alkaloid biosynthesis  . Ergot alkaloids, which are produced by endophyte fungi, can enhance plant host fitness, but also cause livestock toxicosis to host plants. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 390 to 465 amino acids in length.. 
PF11992 Domain of unknown function (DUF3488)<br>PFAM-B_3123 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is typically between 323 to 339 amino acids in length. This domain is found associated with Pfam:PF01841. This domain has a conserved PLW sequence motif. This domain contains 6 transmembrane helices.. 
PF11993 Ribosomal S4P (gammaproteobacterial)<br>PFAM-B_3290 (release 23.0). This family of proteins are ribosomal SSU S4 p proteins. This protein is found in gamma-proteobacteria. Proteins in this family are typically between 162 to 178 amino acids in length.. 
PF11994 Protein of unknown function (DUF3489)<br>PFAM-B_3545 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 84 to 211 amino acids in length. This protein has a single completely conserved residue W that may be functionally important.. 
PF11995 Domain of unknown function (DUF3490)<br>PFAM-B_3558 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 160 amino acids in length. This domain is found associated with Pfam:PF00225. This domain is found associated with Pfam:PF00225. This domain has two conserved sequence motifs: EVE and ESA.. 
PF11996 Protein of unknown function (DUF3491)<br>PFAM-B_3393 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 286 to 3225 amino acids in length. This protein is found associated with Pfam:PF04488. This protein is found associated with Pfam:PF04488.. 
PF11997 Domain of unknown function (DUF3492)<br>PFAM-B_2107 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in bacteria, archaea and eukaryotes. This domain is typically between 259 to 282 amino acids in length. This domain is found associated with Pfam:PF00534. This domain has two conserved sequence motifs: GGVS and EHGIY.. 
PF11998 Protein of unknown function (DUF3493)<br>PFAM-B_3788 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 79 to 331 amino acids in length.. 
PF11999 Protein of unknown function (DUF3494)<br>PFAM-B_3080 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 243 to 678 amino acids in length. This protein has a single completely conserved residue G that may be functionally important.. 
PF12000 DUF3495;<br>Gkycosyl transferase family 4 group. PFAM-B_3335 (release 23.0). This domain is found associated with Pfam:PF00534.. 
PF12001 Domain of unknown function (DUF3496)<br>PFAM-B_3407 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 110 amino acids in length.. 
PF12002 MgsA AAA+ ATPase C terminal<br>The MgsA protein possesses DNA-dependent ATPase and ssDNA annealing activities  . MgsA contributes to the recovery of stalled replication forks and therefore prevents genomic instability caused by aberrant DNA replication  . Additionally, MgsA may play a role in chromosomal segregation  . This is consistent with a report that MgsA co-localises with the replisome and affects chromosome segregation  .  This domain represents the C terminal region of MgsA.. 
PF12003 Domain of unknown function (DUF3497)<br>PFAM-B_3419 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 213 to 257 amino acids in length. This domain is found associated with Pfam:PF02793, Pfam:PF00002, Pfam:PF01825. This domain has a single completely conserved residue W that may be functionally important.. 
PF12004 Domain of unknown function (DUF3498)<br>PFAM-B_3438 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 433 to 538 amino acids in length. This domain is found associated with Pfam:PF00616, Pfam:PF00168. This domain has two conserved sequence motifs: DLQ and PLSFQNP.. 
PF12005 Protein of unknown function (DUF3499)<br>PFAM-B_3439 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 125 to 163 amino acids in length.. 
PF12006 Protein of unknown function (DUF3500)<br>PFAM-B_3479 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 335 to 438 amino acids in length. This protein has a conserved GHH sequence motif. This protein has two completely conserved G residues that may be functionally important.. 
PF12007 Protein of unknown function (DUF3501)<br>PFAM-B_3488 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are about 200 amino acids in length. The structure of protein Swiss:Q63J81 from B. pseudomallei has been solved. This protein contains two domains, domain I (1:31, 46:81) is a helical domain, domain II (32:45,82-193) is a mainly beta protein with a beta barrel. According to crystal contacts the proteins probably functions as a dimer. The gene neighbourhood analysis suggests that this protein may be functionally related to rubrerythrin and ferredoxin. The wedge surface between the two domains might be functionally important. The fold of this protein could best be described as a circularly permuted C2-like fold (details derived from TOPSAN).. 
PF12008 Type I restriction and modification enzyme - subunit R C terminal<br>This enzyme has been characterised and shown to belong to a new family of the type I class of restriction and modification enzymes. This family is involved in bacterial defence by making double strand breaks in specific double stranded DNA sequences, e.g. that of invading bacteriophages. EcoR124 is made up of three subunits, HsdR, HsdS and HsdM. The R subunit has ATPase and restriction endonuclease activity. This domain is the C terminal of the R subunit  .. 
PF12009 Telomerase ribonucleoprotein complex - RNA binding domain<br>Telomeres in most organisms are comprised of tandem simple sequence repeats  . The total length of telomeric repeat sequence at each chromosome end is determined in a balance of sequence loss and sequence addition  . One major influence on telomere length is the enzyme telomerase  . It is a reverse transcriptase that adds these simple sequence repeats to chromosome ends by copying a template sequence within the RNA component of the enzyme  . The RNA binding domain of telomerase - TRBD - is made up of twelve alpha helices and two short beta sheets  . How telomerase and associated regulatory factors physically interact and function with each other to maintain appropriate telomere length is poorly understood. It is known however that TRBD is involved in formation of the holoenzyme (which performs the telomere extension) in addition to recognition and binding of RNA  .. 
PF12010 Domain of unknown function (DUF3502)<br>PFAM-B_3448 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is about 140 amino acids in length. This domain is found associated with Pfam:PF01547.. 
PF12011 Domain of unknown function (DUF3503)<br>PFAM-B_2686 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in viruses. This domain is about 170 amino acids in length. This domain is found associated with Pfam:PF00271.. 
PF12012 Domain of unknown function (DUF3504)<br>PFAM-B_2196 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 156 to 173 amino acids in length.. 
PF12013 Protein of unknown function (DUF3505)<br>PFAM-B_2856 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.. 
PF12014 Domain of unknown function (DUF3506)<br>PFAM-B_3293 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 131 to 148 amino acids in length. This domain has a conserved KLTGD sequence motif.. 
PF12015 Domain of unknown function (DUF3507)<br>PFAM-B_3482 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 180 amino acids in length. This domain has a conserved ENL sequence motif.. 
PF12016 Stonin 2<br>Stonin 2 is involved in clathrin mediated endocytosis  . It binds to Eps15 by its highly conserved NPF motif. The complex formed has been shown to directly associate with the clathrin adaptor complex AP-2, and to localize to clathrin-coated pits (CCPs)  . In addition, stonin2 was recently identified as a specific sorting adaptor for synaptotagmin, and may thus regulate synaptic vesicle recycling  .. 
PF12017 Transposase_37;<br>PFAM-B_3357 (release 23.0). Protein in this family are transposases found in insects. This region is about 230 amino acids in length and is found associated with Pfam:PF05485.. 
PF12018 Domain of unknown function (DUF3508)<br>PFAM-B_3527 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 280 amino acids in length.  This domain has two conserved sequence motifs: GFC and GLL. This family is also known as UPF0704.. 
PF12019 Type II transport protein GspH<br>GspH is involved in bacterial type II export systems  . Like all pilins, GspH has an N terminus alpha helix  . This helix is followed by nine beta strands forming two beta sheets, one of five antiparallel strands and one of four antiparallel strands  . GspH is a minor pseudopilin; it is expressed much less than other pseudopilins in the type II secretion pilus (major pilins)  .  The function and localisation of minor pseudo-pilins are still to be fully unraveled  . It has been suggested that some minor pseudopilins may assemble either into the base or the tip of pili, or both. They function as initiators or regulators of pilus biogenesis and dynamics, and/or as adaptors between various pseudopilin component and other members of the T2SS  .. 
PF12020 TAFA family<br>PFAM-B_3899 (release 23.0). This family of secreted proteins are brain specific and thought to be chemokines  .  These proteins are found in vertebrates. Proteins in this family are typically between 94 to 133 amino acids in length and contain a number of conserved cysteines.. 
PF12021 Protein of unknown function (DUF3509)<br>PFAM-B_2180 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 92 to 110 amino acids in length. This protein has two completely conserved residues (G and R) that may be functionally important.. 
PF12022 Domain of unknown function (DUF3510)<br>PFAM-B_2857 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 130 amino acids in length. This domain is found associated with Pfam:PF06148.. 
PF12023 Domain of unknown function (DUF3511)<br>PFAM-B_3314 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 50 amino acids in length. This domain has two completely conserved residues (Y and K) that may be functionally important.. 
PF12024 Domain of unknown function (DUF3512)<br>PFAM-B_3525 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 231 to 249 amino acids in length. This domain is found associated with Pfam:PF00439.. 
PF12025 Phage protein C<br>PFAM-B_3530 (release 23.0). This family of phage proteins is functionally uncharacterised. Proteins in this family are typically between 68 to 86 amino acids in length.. 
PF12026 Domain of unknown function (DUF3513)<br>PFAM-B_3541 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 192 to 218 amino acids in length. This domain is found associated with Pfam:PF00018, Pfam:PF08824. This domain has a conserved QPP sequence motif.. 
PF12027 Protein of unknown function (DUF3514)<br>PFAM-B_3570 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 368 to 823 amino acids in length.. 
PF12028 Protein of unknown function (DUF3515)<br>PFAM-B_3590 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 166 to 214 amino acids in length. This protein has a conserved RCG sequence motif.. 
PF12029 Domain of unknown function (DUF3516)<br>PFAM-B_3601 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is typically between 460 to 473 amino acids in length. This domain is found associated with Pfam:PF00270, Pfam:PF00271.. 
PF12030 Domain of unknown function (DUF3517)<br>PFAM-B_3933 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 340 amino acids in length. This domain is found associated with Pfam:PF00443.. 
PF12031 Domain of unknown function (DUF3518)<br>PFAM-B_3830 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 260 amino acids in length. This domain is found associated with Pfam:PF01388.. 
PF12032 Regulatory CLIP domain of proteinases<br>CLIP is a regulatory domain which controls the proteinase action of various proteins of the trypsin family, e.g. easter and pap2. The CLIP domain remains linked to the protease domain after cleavage of a conserved residue which retains the protein in zymogen form. It is named CLIP because it can be drawn in the shape of a paper clip. It has many disulphide bonds and highly conserved cysteine residues, and so it folds extensively.    . 
PF12033 Protein of unknown function (DUF3519)<br>PFAM-B_2444 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 117 to 1154 amino acids in length. This protein has a single completely conserved residue Q that may be functionally important.. 
PF12034 Domain of unknown function (DUF3520)<br>PFAM-B_3604 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is about 180 amino acids in length. This domain is found associated with Pfam:PF00092.. 
PF12035 Protein of unknown function (DUF3521)<br>PFAM-B_3612 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 42 to 74 amino acids in length.. 
PF12036 Protein of unknown function (DUF3522)<br>PFAM-B_3665 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 220 to 787 amino acids in length.. 
PF12037 Domain of unknown function (DUF3523)<br>PFAM-B_3746 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 257 to 277 amino acids in length. This domain is found associated with Pfam:PF00004. This domain has a conserved LER sequence motif.. 
PF12038 Domain of unknown function (DUF3524)<br>PFAM-B_3749 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in bacteria and eukaryotes. This domain is about 170 amino acids in length. This domain is found associated with Pfam:PF00534. This domain has two conserved sequence motifs: HENQ and FNS. This domain has a single completely conserved residue S that may be functionally important.. 
PF12039 Protein of unknown function (DUF3525)<br>PFAM-B_3833 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in viruses. Proteins in this family are about 360 amino acids in length.. 
PF12040 Domain of unknown function (DUF3526)<br>PFAM-B_3851 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is typically between 149 to 170 amino acids in length. This domain has a single completely conserved residue P that may be functionally important.. 
PF12041 Transcriptional regulator DELLA protein N terminal<br>Gibberellins are plant hormones which have great impact on growth signalling. DELLA proteins are transcriptional regulators of growth related proteins which are downregulated when gibberellins bind to their receptor GID1. GID1 forms a complex with DELLA proteins and signals them towards 26S proteasome. The N terminal of DELLA proteins contains conserved DELLA and VHYNP motifs which are important for GID1 binding and proteolysis of the DELLA proteins.  . 
PF12042 Tubuliform egg casing silk strands structural domain<br>Spiders use fibroins to make silk strands. This family includes tubuliform silk fibroins which are used to protect egg cases. This domain is a structural domain which is found in repeats of up to 20 in many individuals (although this is not necessarily the case). RP1 makes up structural domains in the N terminal while RP2 makes up structural domains in the C terminal.  . 
PF12043 Domain of unknown function (DUF3527)<br>PFAM-B_3945 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 120 amino acids in length. This domain has a conserved CDCGGWD sequence motif.. 
PF12044 Putative peptidase family<br>PFAM-B_3942 (release 23.0). This family of proteins is functionally uncharacterised. However, it does contain an HEXXH motif characteristic of metallopeptidases. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 625 to 773 amino acids in length.. 
PF12045 Protein of unknown function (DUF3528)<br>PFAM-B_3981 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 185 to 298 amino acids in length. This protein is found associated with Pfam:PF00046.. 
PF12046 Protein of unknown function (DUF3529)<br>PFAM-B_3346 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 176 to 190 amino acids in length.. 
PF12047 Cytosine specific DNA methyltransferase replication foci domain<br>This domain is part of a cytosine specific DNA methyltransferase enzyme. It functions non-catalytically to target the protein towards replication foci. This allows the DNMT1 protein to methylate the correct residues. This domain targets DMAP1 and HDAC2 to the replication foci during the S phase of mitosis. They are thought to have some importance in conversion of critical histone lysine moieties.  . 
PF12048 Protein of unknown function (DUF3530)<br>PFAM-B_2450 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 272 to 336 amino acids in length. These proteins are distantly related to alpa/beta hydrolases so they may act as enzymes.. 
PF12049 Protein of unknown function (DUF3531)<br>PFAM-B_2583 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 149 to 199 amino acids in length.. 
PF12051 Protein of unknown function (DUF3533)<br>PFAM-B_2348 (release 23.0). This family of transmembrane proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 393 to 772 amino acids in length.. 
PF12052 Voltage gated calcium channel subunit beta domain 4Aa N terminal<br>The beta subunit of voltage gated calcium channels is coded for by four genes 1-4. Gene 4 can produce two types of beta4A domain (beta4Aa and beta4Ab) according to how the gene splicing is carried out. This family is part of the beta4Aa N terminal domain. It is made up of an alpha helix and a beta strand. It is thought to regulate the channel properties through protein-protein interactions with non Ca channel proteins.  . 
PF12053 Domain of unknown function (DUF3534)<br>PFAM-B_2753 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 150 amino acids in length. This domain is found associated with Pfam:PF00595. This domain has a conserved GILD sequence motif.. 
PF12054 Domain of unknown function (DUF3535)<br>PFAM-B_2858 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 439 to 459 amino acids in length. This domain is found associated with Pfam:PF00271, Pfam:PF02985, Pfam:PF00176. This domain has two completely conserved residues (P and K) that may be functionally important.. 
PF12055 Domain of unknown function (DUF3536)<br>PFAM-B_3129 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in bacteria and archaea. This domain is typically between 274 to 285 amino acids in length. This domain is found associated with Pfam:PF03065.. 
PF12056 Protein of unknown function (DUF3537)<br>PFAM-B_3199 (release 23.0). This family of transmembrane proteins are functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 427 to 453 amino acids in length.. 
PF12057 Domain of unknown function (DUF3538)<br>PFAM-B_3373 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 120 amino acids in length. This domain is found associated with Pfam:PF00240. This domain has a conserved SDL sequence motif.. 
PF12058 Protein of unknown function (DUF3539)<br>PFAM-B_3564 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 90 amino acids in length. This protein has a conserved NHP sequence motif.. 
PF12059 Protein of unknown function (DUF3540)<br>PFAM-B_2948 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 212 to 238 amino acids in length. This protein has a conserved SCL sequence motif.. 
PF12060 Domain of unknown function (DUF3541)<br>PFAM-B_2172 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is about 230 amino acids in length.. 
PF12061 Protein of unknown function (DUF3542)<br>PFAM-B_2032 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in eukaryotes and viruses. Proteins in this family are typically between 516 to 1283 amino acids in length. This protein is found associated with Pfam:PF00931.. 
PF12062 heparan sulfate-N-deacetylase<br>PFAM-B_2134 (release 23.0). This family of proteins is are heparan sulfate N-deacetylase enzymes. This protein is found in eukaryotes.  This proteinenzyme is often found associated with Pfam:PF00685.. 
PF12063 Domain of unknown function (DUF3543)<br>PFAM-B_2213 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 217 to 291 amino acids in length. This domain is found associated with Pfam:PF00069. This domain has a single completely conserved residue A that may be functionally important.. 
PF12064 Domain of unknown function (DUF3544)<br>PFAM-B_3553 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 198 to 216 amino acids in length. This domain is found associated with Pfam:PF00628, Pfam:PF01753, Pfam:PF00439, Pfam:PF00855.. 
PF12065 Protein of unknown function (DUF3545)<br>PFAM-B_3270 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 60 to 77 amino acids in length. This protein has two completely conserved residues (R and L) that may be functionally important.. 
PF12066 Domain of unknown function (DUF3546)<br>PFAM-B_3237 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 93 to 114 amino acids in length. This domain has two completely conserved Y residues that may be functionally important.. 
PF12067 DUF3547;<br>Sox C-terminal transactivation domain. PFAM-B_3310 (release 23.0). This domain is found at the C-terminus of the Sox family of transcription factors. It is found associated with Pfam:PF00505. It binds to the Armadillo repeats (Pfam:PF00514) in Catenin beta-1 (CTNNB1), which is involved in transcriptional regulation  . It functions as a transactivating domain (TAD)  .. 
PF12068 Domain of unknown function (DUF3548)<br>PFAM-B_3247 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 184 to 216 amino acids in length. This domain is found associated with Pfam:PF00566. This domain is found at the N-terminus of GYP7 proteins.. 
PF12069 Protein of unknown function (DUF3549)<br>PFAM-B_2034 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 340 amino acids in length. This protein has a conserved LDE sequence motif.. 
PF12070 Protein of unknown function (DUF3550/UPF0682)<br>PFAM-B_2472 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 249 to 606 amino acids in length.. 
PF12071 Protein of unknown function (DUF3551)<br>PFAM-B_3610 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 79 to 104 amino acids in length. This protein has a single completely conserved residue C that may be functionally important.. 
PF12072 Domain of unknown function (DUF3552)<br>PFAM-B_3508 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in bacteria, archaea and eukaryotes. This domain is about 200 amino acids in length. This domain is found associated with Pfam:PF00013, Pfam:PF01966. This domain has a single completely conserved residue A that may be functionally important.. 
PF12073 Protein of unknown function (DUF3553)<br>PFAM-B_3361 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 60 amino acids in length. This protein has two conserved sequence motifs: GQVQS and TVNF.. 
PF12074 Domain of unknown function (DUF3554)<br>PFAM-B_2029 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 287 to 356 amino acids in length. This domain is found associated with Pfam:PF02985.. 
PF12075 KN motif<br>PFAM-B_3795 (release 23.0). This small motif is found at the N-terminus of Kank proteins and has been called the KN (for Kank N-terminal) motif. This protein is found in eukaryotes. Proteins in this family are typically between 413 to 1202 amino acids in length. This protein is found associated with Pfam:PF00023. This protein has two conserved sequence motifs: TPYG and LDLDF. Kank1 was obtained by positional cloning of a tumor suppressor gene in renal cell carcinoma, while the other members were found by homology search. The family is involved in the regulation of actin polymerization and cell motility through signaling pathways containing PI3K/Akt and/or unidentified modulators/effectors  .. 
PF12076 WAX2 C-terminal domain<br>Pfam-B_3756  (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 170 amino acids in length.  This domain is found associated with Pfam:PF04116. This domain has a conserved LEGW sequence motif. This region has similarity to short chain dehydrogenases  .. 
PF12077 Transmembrane protein of unknown function (DUF3556)<br>PFAM-B_2567 (release 23.0). This family of transmembrane proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 576 to 592 amino acids in length.. 
PF12078 Domain of unknown function (DUF3557)<br>PFAM-B_2154 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 150 amino acids in length.. 
PF12079 Protein of unknown function (DUF3558)<br>PFAM-B_3489 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 177 to 195 amino acids in length.. 
PF12080 GldM C-terminal domain<br>PFAM-B_3275 (release 23.0). This domain is found in bacteria at the C-terminus of the GldM protein. This domain is typically between 169 to 182 amino acids in length. This domain has two completely conserved residues (Y and N) that may be functionally important. GldM, is named for the member from Cytophaga johnsonae (Flavobacterium johnsoniae), which is required for a type of rapid gliding motility found in certain members of the Bacteriodetes  .. 
PF12081 GldM N-terminal domain<br>PFAM-B_3275 (release 23.0). This domain is found in bacteria at the N-terminus of the GldM protein. This domain is typically between 169 to 182 amino acids in length. This domain has two completely conserved residues (Y and N) that may be functionally important. GldM, is named for the member from Cytophaga johnsonae (Flavobacterium johnsoniae), which is required for a type of rapid gliding motility found in certain members of the Bacteriodetes  .. 
PF12083 Domain of unknown function (DUF3560)<br>PFAM-B_2138 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is about 120 amino acids in length. This domain has a conserved GHHSE sequence motif.. 
PF12084 Protein of unknown function (DUF3561)<br>PFAM-B_2401 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 110 amino acids in length.. 
PF12085 Protein of unknown function (DUF3562)<br>PFAM-B_3549 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 62 to 84 amino acids in length. This protein has two completely conserved residues (A and Y) that may be functionally important.. 
PF12086 Protein of unknown function (DUF3563)<br>PFAM-B_3639 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 50 amino acids in length. This protein has conserved AYL and DLE sequence motifs.. 
PF12087 Protein of unknown function (DUF3564)<br>PFAM-B_3736 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 118 to 142 amino acids in length. This protein has a conserved WSRE sequence motif.. 
PF12088 Protein of unknown function (DUF3565)<br>PFAM-B_3033 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 30 to 78 amino acids in length. This protein has two conserved sequence motifs: WVA and CGH.. 
PF12089 Transmembrane domain of unknown function (DUF3566)<br>PFAM-B_3331 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 136 to 304 amino acids in length. This region represents a transmembrane region found at the C-terminus of the proteins.. 
PF12090 Spt20 family<br>PFAM-B_3386 (release 23.0). This presumed domain is found in the Spt20 proteins from both human and yeast.  The Spt20 protein is part of the SAGA complex which is a large cmplex mediating histone deacetylation. Yeast Spt20 has been shown to play a role in structural integrity of the SAGA complex as as no intact SAGA could be purified in spt20 deletion strains.. 
PF12091 Protein of unknown function (DUF3567)<br>PFAM-B_3056 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 90 amino acids in length. This protein has a conserved EIVDK sequence motif.. 
PF12092 Protein of unknown function (DUF3568)<br>PFAM-B_3573 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 130 amino acids in length.. 
PF12093 Coronavirus NS8 protein<br>Pfam-B_2038 (Release 23.0). This family of proteins is functionally uncharacterised. This protein is found in coronaviruses. Proteins in this family are typically between 39 to 121 amino acids in length. This protein has two conserved sequence motifs: EDPCP and INCQ.. 
PF12094 Protein of unknown function (DUF3570)<br>PFAM-B_3745 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 396 to 444 amino acids in length.. 
PF12095 Protein of unknown function (DUF3571)<br>PFAM-B_3506 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 85 to 97 amino acids in length.. 
PF12096 Protein of unknown function (DUF3572)<br>PFAM-B_2130 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 100 amino acids in length.. 
PF12097 Protein of unknown function (DUF3573)<br>PFAM-B_2286 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 372 to 530 amino acids in length.. 
PF12098 Protein of unknown function (DUF3574)<br>PFAM-B_3542 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria and viruses. Proteins in this family are typically between 144 to 163 amino acids in length. This protein has a conserved TPRF sequence motif.. 
PF12099 Protein of unknown function (DUF3575)<br>PFAM-B_2229 (release 23.0). This family of proteins are functionally uncharacterised. This family is only found in bacteria.  Proteins in this family are typically between 187 to 236 amino acids in length.. 
PF12100 Domain of unknown function (DUF3576)<br>PFAM-B_2102 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is about 100 amino acids in length. This domain has a single completely conserved residue G that may be functionally important.. 
PF12101 Protein of unknown function (DUF3577)<br>PFAM-B_2116 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 143 to 307 amino acids in length.. 
PF12102 Domain of unknown function (DUF3578)<br>PFAM-B_2328 (release 23.0). This presumed domain is functionally uncharacterised. This domain is found in bacteria and archaea. This domain is typically between 177 to 191 amino acids in length.. 
PF12103 Surface lipoprotein of Spirochaetales order<br>Lipl32 is an outer membrane surface lipoprotein of Leptospira like bacteria.. 
PF12104 T cell CD4 receptor C terminal region<br>This domain is the C terminal domain of the CD4 T cell receptor. The C terminal domain is the cytoplasmic domain which relays the signal for T cell activation. This process involves co-receptor internalisation. This domain is involved in binding to the N terminal of Lck co-receptor in a Zn2+ clasp structure.. 
PF12105 SpoU, rRNA methylase, C-terminal<br>PFAM-B_2024 (release 23.0). This domain is found in bacteria. This domain is about 60 amino acids in length. This domain is found in association with Pfam:PF00588. This domain has a conserved LFE sequence motif. Some members of the Pfam family SpoU_methylase, Pfam:PF00588, carry this very distinctive sequence region at their extreme C-terminus. The exact function of this region is not known.. 
PF12106 Colicin C terminal ribonuclease domain<br>Colicin is a protein produced by bacteria with Col plasmids. Its function is to attack E. coli through actions on its inner membrane ion channels or through ribonuclease or deoxyribonuclease actions. The C terminal domain is the ribonuclease domain. It specifically cleaves tRNA anticodons which recognise codons in the form NAY (N:any nucleotide, A:adenosine, Y:pyrimidine) which corresponds to Tyrosine, Histidine, Asparagine and Aspartic Acid. E5-CRD can be referred to as an RNA restriction enzyme that specifically recognizes and cleaves single-stranded GU sequences.  . 
PF12107 Plasminogen (Pg) ligand in fibrinolytic pathway<br>Pg is an important mediator of angiostatin production in the fibrinolytic pathway. Pg is made up of five subunit kringle molecules (Pg-K1 to Pg-K5), of which the first three make the protein angiostatin. VEK-30 is a domain of the group A streptococcal protein PAM. It binds to Pg-K2 of angiostatin and activates the molecule to mediate its anti-angiogenic effects. VEK-30 binds to angiostatin via a C terminal lysine with argininyl and glutamyl side chain residues known as a 'through space isostere'.  . 
PF12108 Splicing factor SF3a60 binding domain<br>This domain is found in eukaryotes. This domain is about 30 amino acids in length. This domain has a single completely conserved residue Y that may be functionally important. SF3a60 makes up the SF3a complex with SF3a66 and SF3a120. This domain is the binding site of SF3a60 for SF3a120. The SF3a complex is part of the spliceosome, a protein complex involved in splicing mRNA after transcription.. 
PF12109 CXCR4 Chemokine receptor N terminal<br>CXCR4 and its ligand stromal cell-derived factor-1 (a.k.a. CXCL12) are essential for proper fetal development. CXCR4 is also the major coreceptor for T-tropic strains of human immunodeficiency virus 1 (HIV-1), and SDF-1 inhibits HIV-1 infection. Additionally, SDF-1 and CXCR4 mediate cancer cell migration and metastasis. The N terminal domain of most chemokine receptors is the ligand binding domain and so the N terminal domain of CXCR4 is the binding site for SDF-1.  . 
PF12110 Nuclear protein 96<br>Nup96 (often known by the name of its yeast homolog Nup145C) is part of the Nup84 heptameric complex in the nuclear pore complex. Nup96 complexes with Sec13 in the middle of the heptamer. The function of the heptamer is to coat the curvature of the nuclear pore complex between the inner and outer nuclear membranes. Nup96 is predicted to be an alpha helical solenoid. The interaction between Nup96 and Sec13 is the point of curvature in the heptameric complex.    . 
PF12111 Polyribonucleotide phosphorylase C terminal<br>PNPase regulates the expression of small non-coding RNAs that control expression of outer-membrane proteins. The enzyme also affects complex processes, such as the tissue-invasive virulence of Salmonella enterica and the regulation of a virulence-factor secretion system in Yersinia. In Escherichia coli, PNPase is involved in the quality control of ribosomal RNA precursors and is required for growth following cold shock. This family contains the C terminal protomer domain of the PNPase core.  The function of the C terminal protomer is to catalyse phosphorolysis through its two active sites.  . 
PF12112 Protein of unknown function (DUF3579)<br>PFAM-B_2027 (release 23.0). This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 98 to 126 amino acids in length. This protein has a conserved FRP sequence motif.. 
PF12113 SVM protein signal sequence<br>PFAM-B_2829 (release 23.0). This region is presumed to be a signal peptide sequence found in Sequence-variable mosaic (SVM) proteins  . This domain is found in phytoplasmas. This presumed signal sequence is about 30 amino acids in length.. 
PF12114 Period protein 2/3C-terminal region<br>PFAM-B_2037 (release 23.0). This domain is found in eukaryotes. This domain is typically between 164 to 200 amino acids in length. This domain is found associated with Pfam:PF08447.. 
PF12115 Salivary protein of 15kDa inhibits CD4+ T cell activation<br>PFAM-B_2039 (release 23.0). This is a family of 15kDa salivary proteins from Acari Arachnids that is induced on feeding and assists the parasite to remain attached to its arthropod host. By repressing calcium fluxes triggered by TCR engagement, Salp15 inhibits CD4+ T cell activation. Salp15 shows weak similarity to Inhibin A, a member of the TGF-beta superfamily that inhibits the production of cytokines and the proliferation of T cells.. 
PF12116 Stage III sporulation protein D<br>PFAM-B_2045 (release 23.0). This stage III sporulation protein is a small DNA-binding family that is essential for gene expression of the mother-cell compartment during sporulation. The domain is found in bacteria and viruses, and is about 40 amino acids in length. It has a conserved RGG sequence motif.. 
PF12117 DUF_B2046;<br>Protein of unknown function (DUF3580). PFAM-B_2046 (release 23.0). This domain is found in viruses, and is about 120 amino acids in length. It is found in association with Pfam:PF01057.. 
PF12118 SprA-related family<br>PFAM-B_2057 (release 23.0). This protein is found in bacteria. Proteins in this family are typically between 234 to 465 amino acids in length. There is a conserved GEV sequence motif.Most members are annotated as being SprA-related.. 
PF12119 Protein of unknown function (DUF3581)<br>PFAM-B_2081 (release 23.0). This protein is found in bacteria. Proteins in this family are about 240 amino acids in length.. 
PF12120 DNApol_Rpb2_rif; RNApol_Rpb2_rif;<br>Rifampin ADP-ribosyl transferase. This protein is found in bacteria. Proteins in this family are typically between 136 to 150 amino acids in length. The opportunistic pathogen Mycobacterium smegmatis is resistant to rifampin because of the presence of a chromosomally encoded rifampin ADP-ribosyltransferase (Arr-ms). Arr-ms is a small enzyme whose activity thus renders rifamycin antibiotics ineffective  .. 
PF12121 Dermaseptin<br>This protein is found in eukaryotes. Proteins in this family are typically between 30 to 76 amino acids in length. This protein is found associated with Pfam:PF03032. This domain is part of a dermaseptin protein which is used as an antimicrobial agent. The full protein is almost completely defined in an alpha helical domain. It creates high levels of disorder at the level of the phospholipid head group of bacterial membranes suggesting that it partitions into the bilayer where it severely disrupts membrane packing.. 
PF12122 Protein of unknown function (DUF3582)<br>PFAM-B_2087 (release 23.0). This domain is found in bacteria, and is approximately 130 amino acids in length. It is found associated with Pfam:PF01694. There is a conserved ASW sequence motif. This domain has a single completely conserved residue F that may be functionally important.. 
PF12123 N-acetylmuramoyl-l-alanine amidase<br>This domain is found in bacteria and viruses. This domain is about 50 amino acids in length. This domain is classified with the enzyme classification code EC:3.5.1.28. This domain is the C terminal of the enzyme which hydrolyses the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides.. 
PF12124 Coronavirus polyprotein cleavage domain<br>This domain is found in SARS coronaviruses, and is about 70 amino acids in length. It is found associated with various other coronavirus proteins due to the polyprotein nature of most viral translation. PL2pro is a domain of the non-structural protein nsp3. The domain performs three of the cleavages required to separate the translated polyprotein into its distinct proteins.. 
PF12125 D domain of beta-TrCP<br>This domain is found in eukaryotes, and is approximately 40 amino acids in length. It is found associated with Pfam:PF00646, Pfam:PF00400. The protein that contains this domain functions as a ubiquitin ligase. Ubiquitination is required to direct proteins towards the proteasome for degradation. This protein is part of the WD40 class of F box proteins. The D domain of these F box proteins is involved in mediating the dimerisation of the protein.  Dimerisation is necessary to polyubiquitinate substrates so this D domain is vital in directing substrates towards the proteasome for degradation.. 
PF12126 Protein of unknown function (DUF3583)<br>PFAM-B_2092 (release 23.0). This domain is found in eukaryotes, and is typically between 302 and 338 amino acids in length. It is found in association with Pfam:PF00097 and Pfam:PF00643. Most members are promyelocytic leukemia proteins, and this family lies towards the C-terminus.. 
PF12127 SigmaW regulon antibacterial<br>PFAM-B_2114 (release 23.0). This protein is found in bacteria. Proteins in this family are about 330 amino acids in length. The operon from which this protein is derived confers immunity for the host species to a broad range of antibacterial compounds, unlike the specific immunity proteins that are linked to and co-regulated with their antibiotic-synthesis proteins.. 
PF12128 Protein of unknown function (DUF3584)<br>PFAM-B_2142 (release 23.0). This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 943 to 1234 amino acids in length. This family contains a P-loop motif suggesting it is a nucleotide binding protein. It may be involved in replication.. 
PF12129 Male germ-cell putative homeodomain transcription factor<br>PFAM-B_2140 (release 23.0). This domain is found in bacteria and eukaryotes, and is typically between 101 and 140 amino acids in length. Phtf proteins do not display any sequence similarity to known or predicted proteins, but their conservation among species suggests an essential function. The 84 kDa Phtf1 protein is an integral membrane protein, anchored to a cell membrane by six to eight trans-membrane domains, that is associated with a domain of the endoplasmic reticulum (ER) juxtaposed to the Golgi apparatus. It is present during meiosis and spermiogenesis, and, by the end of spermiogenesis, is released from the mature spermatozoon within the residual bodies  . Phtf1 enhances the binding of FEM1B -feminisation homologue 1B - to cell membranes. Fem-1 was initially identified in the signaling pathway for sex determination, as well as being implicated in apoptosis, but its biochemical role is still unclear, and neither FEM1B nor PHTF1 is directly implicated in apoptosis in spermatogenesis. It is the ANK domain of FEM1B that is necessary for the interaction with the N-terminal region of Phtf1  .. 
PF12130 Protein of unknown function (DUF3585)<br>PFAM-B_2156 (release 23.0). This domain is found in eukaryotes. This domain is typically between 135 and 149 amino acids in length and is found associated with Pfam:PF00307.. 
PF12131 Protein of unknown function (DUF3586)<br>PFAM-B_2164 (release 23.0). This domain is found in eukaryotes. This domain is about 80 amino acids in length and is found associated with Pfam:PF08246, and Pfam:PF00112.. 
PF12132 Protein of unknown function (DUF3587)<br>PFAM-B_2181 (release 23.0). This protein is found in viruses. Proteins in this family are typically between 209 and 248 amino acids in length.. 
PF12133 Open reading frame 6 from SARS coronavirus<br>PfamB-2188 (release 23.0). This family is found in Coronaviruses. Proteins in this family are typically between 42 to 63 amino acids in length.. 
PF12134 PRP8 domain IV core<br>This domain is found in eukaryotes, and is about 20 amino acids in length. It is found associated with Pfam:PF10597, Pfam:PF10596, Pfam:PF10598, Pfam:PF08083, Pfam:PF08082, Pfam:PF01398, Pfam:PF08084. There is a conserved LILR sequence motif. The domain is a selenomethionine domain in a subunit of the spliceosome. The function of PRP8 domain IV is believed to be interaction with the splicosomal core.. 
PF12135 Sialidase enzyme penultimate C terminal domain<br>This domain is found in bacteria and eukaryotes, and is about 30 amino acids in length. The protein from which this domain is found is a sialidase enzyme which is used by virulent bacteria as a toxin. It is the penultimate C terminal domain.. 
PF12136 RNA polymerase Rpo13 subunit HTH domain<br>This domain is found in archaea, and is about 40 amino acids in length. It has a single completely conserved residue E that may be functionally important. It is found in the archaeal DNA dependent RNA polymerase. The domain is a 'helix-turn-helix' (HTH) domain in the Rpo13 subunit of the RNA polymerase. This domain is involved in downstream DNA binding, and the entire subunit has also been implicated in contacting transcription factor II B.. 
PF12137 RNA polymerase recycling family C-terminal<br>PFAM-B_2201 (release 23.0). This domain is found in bacteria. This domain is about 360 amino acids in length. This domain is found associated with Pfam:PF00271, Pfam:PF00176. The function of this domain is not known, but structurally it forms an alpha-beta fold in nature with a central beta-sheet flanked by helices and loops, the beta-sheet being mainly antiparallel and flanked by four alpha helices, among which the two longer helices exhibit a coiled-coil arrangement.. 
PF12138 Spherulation-specific family 4<br>PFAM-B_2198 (release 23.0). This protein is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 250 and 398 amino acids in length.  There is a conserved NPG sequence motif and there are two completely conserved G residues that may be functionally important. Starvation will often induce spherulation - the production of spores - and this process may involve DNA-methylation. Changes in the methylation of spherulin4 are associated with the formation of spherules, but these changes are probably transient. Methylation of the gene accompanies its transcriptional activation, and spherulin4 mRNA is only detectable in late spherulating cultures and mature spherules. It is a spherulation-specific protein.. 
PF12139 Adenosine-5'-phosphosulfate reductase beta subunit<br>PFAM-B_2202 (release 23.0). This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 112 to 142 amino acids in length. This family is found in association with Pfam:PF00037, and has a conserved FPIRTT sequence motif. The whole beta subunit has the enzymic properties of EC:1.8.99.2.. 
PF12140 Protein of unknown function (DUF3588)<br>PFAM-B_2205 (release 23.0). This family of proteins is found in eukaryotes. Proteins in this family are typically between 129 and 866 amino acids in length, and the family is found in association with Pfam:PF02820. The exact function of this family is not known.. 
PF12141 Protein of unknown function (DUF3589)<br>PFAM-B_2240 (release 23.0). This family of proteins is found in eukaryotes. Proteins in this family are typically between 541 and 717 amino acids in length. The function of this family is not known,. 
PF12142 Polyphenol oxidase middle domain<br>PFAM-B_2219 (release 23.0). This domain family is found in bacteria and eukaryotes, and is approximately 50 amino acids in length, and the family is found in association with Pfam:PF00264. Most members are annotated as being polyphenol oxidases, and many are from plants or plastids. There is a conserved DWL sequence motif which gives the family its name.. 
PF12143 Protein of unknown function (DUF_B2219)<br>PFAM-B_2219 (release 23.0). This domain family is found in eukaryotes, and is typically between 138 and 152 amino acids in length. and the family is found in association with Pfam:PF00264. Many members are plant or plastid polyphenol oxidases, and there is a highly conserved sequence motif: KFDV, from which the name derives. This is the C-terminal domain of these oxidases.. 
PF12144 Eukaryotic Mediator 12 catenin-binding domain<br>PFAM-B_2250 (release 23.0). 
PF12145 Eukaryotic Mediator 12 subunit domain<br>PFAM-B_2250 (release 23.0). This domain is found in eukaryotes, and is typically between 325 and 354 amino acids in length. The function of this particular region of the Mediator subunit Med12 is not known, but there is a conserved sequence motif: LCEWAV, from which the name derives.. 
PF12146 Putative lysophospholipase<br>PFAM-B_2243 (release 23.0). This domain is found in bacteria and eukaryotes and is approximately 110 amino acids in length. It is found in association with Pfam:PF00561. Many members are annotated as being lysophospholipases, and others as alpha-beta hydrolase fold-containing proteins.. 
PF12147 Hydrolase_5;<br>Putative methyltransferase. PFAM-B_2243 (release 23.0). This domain is found in bacteria and eukaryotes and is approximately 110 amino acids in length. It is found in association with Pfam:PF00561. The family shows homology to methyltransferases.. 
PF12148 Protein of unknown function (DUF3590)<br>This domain is found in eukaryotes, and is typically between 83 and 97 amino acids in length. It is found in association with Pfam:PF00097, Pfam:PF02182, Pfam:PF00628, Pfam:PF00240. There are two conserved sequence motifs: RAR and NYN. The domain is part of the protein NIRF which has zinc finger and ubiquitinating domains. The function of this domain is likely to be mainly structural, however this has not been confirmed.. 
PF12149 Herpes simplex virus virion protein 16 C terminal<br>This domain is found in viruses, and is about 30 amino acids in length. It is found in association with Pfam:PF02232. This domain is the C terminal of the HSV virion protein 16. This protein is a transcription promoter. The C terminal domain is the carboxyl subdomain of the acidic transcriptional activation domain. The protein binds to DNA binding proteins to carry out its function. Such proteins include TATA binding protein, CBP, TBP-binding protein, etc.. 
PF12150 Cytosolic motility protein<br>This domain family is found in eukaryotes, and is approximately 50 amino acids in length. These proteins are found in nematodes. They complex with MSP (major sperm protein) to allow motility. Their action is quite similar to the action of bacterial actin molecules.. 
PF12151 Mannan-binding protein<br>This domain family is found in bacteria, and is approximately 40 amino acids in length, There is a single completely conserved residue G that may be functionally important. The domain occurs in two types of proteins. In mannan binding proteins  , it forms a homodimeric molecule which complexes into a homo-octamer. In thiamidases it occurs without repeats but in the presence of other domains. MVL is distinct amongst other oligomannoside binding proteins in that it exhibits specificity for certain tetrasaccharides. Each molecule of MVL has four distinct carbohydrate binding sites.. 
PF12152 Eukaryotic translation initiation factor 4G1<br>This domain is found in eukaryotes, and is about 80 amino acids in length. It is found in association with Pfam:PF02854. This domain is part of the protein eIF_4G. It binds to eIF_4E by wrapping around its N terminal to form the eIF_4F complex. This complex binds various eIF_4E-BPs (binding proteins) to regulate initiation of translation.. 
PF12153 LPS binding domain of CAP18 (C terminal)<br>This domain family is found in eukaryotes, and is approximately 30 amino acids in length, and the family is found in association with Pfam:PF00666. CAP18 is a protein which is derived from rabbit granulocytes. It has two domains, an N terminal DUF and a C terminal Gram negative LPS binding domain. This domain is the C terminal domain.. 
PF12154 Glycoprotein B N-terminal antigenic domain of HCMV<br>PFAM-B_2260 (release 23.0). This domain is found in viruses, and is approximately 40 amino acids in length. The domain is found in association with Pfam:PF00606. There are two conserved sequence motifs: SVS and TSS. This family is the amino-terminal antigenic domain of glycoprotein B of human cytomegalovirus.. 
PF12155 NADH dehydrogenase subunit 2 N-terminal<br>PFAM-B_2270 (release 23.0). This domain is found in eukaryotes, and is approximately 90 amino acids in length. It is found associated with Pfam:PF00361. All members are annotated as being NADH dehydrogenase subunit 2, and this region is the N-terminus.. 
PF12156 Putative metal-binding domain of cation transport ATPase<br>PFAM-B_2287 (release 23.0). This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with Pfam:PF00403, Pfam:PF00122, Pfam:PF00702. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.. 
PF12157 Protein of unknown function (DUF3591)<br>PFAM-B_2298 (release 23.0). This domain is found in eukaryotes and is typically between 445 to 462 amino acids in length. Most members are annotated as being transcription initiation factor TFIID subunit 1, and this region is the conserved central portion of these proteins.. 
PF12158 Protein of unknown function (DUF3592)<br>PFAM-B_2016 (release 23.0). This family of proteins is functionally uncharacterised.This family of proteins is found in  bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 150 and 242 amino acids in length.. 
PF12159 Protein of unknown function (DUF3593)<br>PFAM-B_2028 (release 23.0). This family of proteins is functionally uncharacterised.This family of proteins is found in  bacteria and eukaryotes. Proteins in this family are typically between 98 and 228 amino acids in length. There is a conserved LHG sequence motif.. 
PF12160 Fibrinogen alpha C domain<br>This domain family is found in eukaryotes, and is approximately 70 amino acids in length, and the family is found in association with Pfam:PF08702. This domain is the C terminal domain of fibrinogen in mammals. The domain lies in the C terminal half of the alpha C region in these proteins. The function of the domain is that of intramolecular and intermolecular interactions to form fibrin.. 
PF12161 HsdM N-terminal domain<br>PFAM-B_2036 (release 23.0). This domain is found at the N-terminus of the methylase subunit of Type I DNA methyltransferases. This domain family is found in bacteria and archaea, and is typically between 123 and 138 amino acids in length. The family is found in association with Pfam:PF02384. Mutations in this region of EcoKI methyltransferase Swiss:P08957 abolish the normally strong preference of this system for methylating hemimethylated substrate  .  The structure of this domain has been shown to be all alpha-helical.. 
PF12162 STAT1 TAZ2 binding domain<br>This domain family is found in eukaryotes, and is approximately 20 amino acids in length, and the family is found in association with Pfam:PF02865, Pfam:PF00017, Pfam:PF01017, Pfam:PF02864. This domain is the C terminal domain of STAT1. This domain binds selectively to the TAZ2 domain of CRB (CREB-binding protein). In this process it becomes a transcriptional activator and can initiate transcription of certain genes.. 
PF12163 DNA replication regulator<br>This family of proteins is found exclusively in epsilon-proteobacteria. Proteins in this family are approximately 180 amino acids in length. The structure of HobA is a modified Rossmann fold consisting of a five-stranded parallel beta-sheet (beta1-5) flanked on one side by alpha-2, alpha-3 and alpha-6 helices and alpha-4 and alpha-5 on the other. The alpha-1 helix is extended away from and has minimal interaction with the globular part of the protein. Four monomers interact to form a tetrameric molecule. Four calcium atoms bind to the tetramer and these binding sites may have functional relevance. The function of HobA is to regulate DNA replication and its does this by binding to DNA-A, but the exact mechanism of how this regulation occurs is purely speculative. 
PF12164 SporV_proteinAA;<br>Stage V sporulation protein AA. This domain family is found in bacteria - primarily Firmicutes, and is approximately 90 amino acids in length. There is a single completely conserved residue G that may be functionally important. Most annotation associated with this domain suggests that it is involved in the fifth stage of sporulation, however there is little publication to back this up.. 
PF12165 Domain of unknown function (DUF3594)<br>PFAM-B_2040 (release 23.0). This presumed domain is functionally uncharacterised.This domain family is found in  eukaryotes, and is approximately 140 amino acids in length. The family is found in association with Pfam:PF00628.. 
PF12166 Protein of unknown function (DUF3595)<br>PFAM-B_2166 (release 23.0). This family of proteins is functionally uncharacterised.This family of proteins is found in  eukaryotes. Proteins in this family are typically between 578 and 2525 amino acids in length.. 
PF12167 Domain of unknown function (DUF3596)<br>PFAM-B_2234 (release 23.0). This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 90 amino acids in length. The family is found in association with Pfam:PF00589. It is likely that this domain acts to bind DNA.. 
PF12168 DNA polymerase III subunits tau domain IV DnaB-binding<br>PFAM-B_2296 (release 23.0). This domain family is found in bacteria, and is approximately 80 amino acids in length. The family is found in association with Pfam:PF00004. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau.. 
PF12169 DNA polymerase III subunits gamma and tau domain III<br>PFAM-B_2296 (release 23.0). This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with Pfam:PF00004. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau.. 
PF12170 DNA polymerase III tau subunit V interacting with alpha<br>PFAM-B_2296 (release 23.0). This domain family is found in bacteria, and is approximately 140 amino acids in length. The family is found in association with Pfam:PF00004. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau. The extreme C-terminal region of this domain 5 is the part which interacts with the alpha subunit of the DNA polymerase III holoenzyme.. 
PF12171 Zinc-finger double-stranded RNA-binding<br>PFAM-B_2302 (release 23.0). This domain family is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation.. 
PF12172 Rubredoxin-like zinc ribbon domain (DUF35_N)<br>Pfam-B_1390 (release 4.2). This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins.  The domain is duplicated in Swiss:O53566.  The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment.. 
PF12173 Bacteriocin class IIc cyclic gassericin A-like<br>PfamB_170026 (release 23.0), manual. This class of bacteriocins was previously described as class V. The members include gassericin A, acidocin B and butyrovibriocin AR10, all of which are hydrophobic cyclical structures  . The N- and C-termini are covalently linked, and the circular molecule is resistant to several proteases and peptidases  . The immunity protein that protects Lactobacillus gasseri from the toxic effects of its bacteriocin, gassericin A, has been identified. It is found to be a small positively-charged hydrophobic peptide of 53 amino acids containing a putative transmembrane segment   - a structure unlike that of the more common immunity proteins as found in Pfam:PF08951.. 
PF12174 RCD1-SRO-TAF4 (RST) plant domain<br>Overmyer K, Coggill P. Pfam-B_8550 (release 23.0). This domain is found in plant RCD1, SRO and TAF4 proteins, hence its name of RST. It is required for interaction with multiple plant transcription factors. Radical-Induced Cell Death1 (RCD1) is an important regulator of stress and hormonal and developmental responses in Arabidopsis thaliana, as is its closest homologue, SRO1 - Similar To RCD-One1. TBP-Associated Factor 4 (TAF4) and TAF4-b are components of the transcription initiation factor complex TFIID.. 
PF12175 White spot syndrome virus structural envelope protein VP<br>This family of proteins is found in viruses. Proteins in this family are approximately 210 amino acids in length. There is a conserved NNT sequence motif.  These proteins are structural envelope proteins in viruses. This is the beta barrel C terminal domain. There is a protruding N terminal domain which completes the proteins. Three of four envelope proteins in white spot syndrome virus share sequence homology with each other and are present in this family - VP24, VP26 and VP28. VP19 is the other major envelope protein but shares no sequence homology with the other proteins. These proteins are essential for entry into cells of the crustacean host.. 
PF12176 Methanol-cobalamin methyltransferase B subunit<br>This family of proteins is found in bacteria and archaea. Proteins in this family are approximately 460 amino acids in length. MtaB folds as a TIM barrel and contains a novel zinc-binding motif. Zinc(II) lies at the bottom of a funnel formed at the C-terminal beta-barrel end and ligates to two cysteinyl sulfurs (Cys-220 and Cys-269) and one carboxylate oxygen (Glu-164). The function of this protein is to catalyse the cleavage of the C O bond in methanol by an SN2 mechanism. It complexes with MtaA and MtaC to perform this function.. 
PF12177 Prohormone convertase enzyme<br>This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with Pfam:PF01483, Pfam:PF00082. There are two completely conserved residues (Y and D) that may be functionally important. This protein is the C terminal domain of a prohormone convertase enzyme which targets hormones in dense core secretory granules. This C terminal tail domain is the domain responsible for targeting these dense core secretory granules. The domain adopts an alpha helical structure. . 
PF12178 Chromosome passenger complex (CPC) protein INCENP N terminal<br>This domain family is found in eukaryotes, and is approximately 40 amino acids in length. INCENP is a regulatory protein in the chromosome passenger complex. It is involved in regulation of the catalytic protein Aurora B. It performs this function in association with two other proteins - Survivin and Borealin. These proteins form a tight three-helical bundle. The N terminal domain is the domain involved in formation of this three helical bundle.. 
PF12179 I-kappa-kinase-beta NEMO binding domain<br>This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with Pfam:PF00069. These proteins are involved in inflammatory reactions. They cause release of NF-kappa-B into the nucleus of inflammatory cells and upregulation of transcription of proinflammatory cytokines. They perform this function by phosphorylating I-kappa-B proteins which are targeted for degradation to release NF-kappa-B. This kinase (I-kappa-kinase-beta) is found in association with IKK-alpha and NEMO (NF-kappa-B essential modulator). This domain is the binding site of IKK-beta for NEMO.. 
PF12180 TSG101 and ALIX binding domain of CEP55<br>This domain family is found in eukaryotes, and is approximately 40 amino acids in length. This domain is the active domain of CEP55. CEP55 is a protein involved in cytokinesis, specifically in abscission of the plasma membrane at the midbody. To perform this function, CEP55 complexes with ESCRT-I (by a Proline rich sequence in its TSG101 domain) and ALIX. This is the domain on CEP55 which binds to both TSG101 and ALIX. It also acts as a hinge between the N and C termini. This domain is called EABR.. 
PF12181 DNA binding domain of the motility gene repressor (MogR)<br>This domain family is found in bacteria, and is approximately 150 amino acids in length. MogR is involved in repression of transcription of the flagellar gene in Listeria bacteria. This allows a phenotypical switch from an extracellular bacterium to an intracellular pathogen. MogR binds AT rich flagellar gene promoter regions upstream of the flagellar gene. These regions follow the pattern 5'-TTTTNNNNNAAAA-3'. This domain is the DNA binding domain of MogR.. 
PF12182 Lipoprotein;<br>Bacterial lipoprotein. This domain family is found in bacteria, and is approximately 60 amino acids in length. There is a single completely conserved Y residue that may be functionally important. This domain is from a bacterial lipoprotein, a major virulence factor in Gram negative bacteria.. 
PF12183 Restriction endonuclease NotI<br>This family of proteins is found in bacteria. Proteins in this family are typically between 270 and 341 amino acids in length. There is a conserved CPF sequence motif. The type IIP restriction enzyme, NotI, is a homodimer that recognizes the 8 bp DNA sequence 5'-GC/GGCCGC-3' and cleaves both strands of DNA to create 5', 4 base cohesive overhangs.. 
PF12185 Nup358/RanBP2 E3 ligase domain<br>This domain family is found in eukaryotes, and is approximately 60 amino acids in length. The family is found in association with Pfam:PF00638, Pfam:PF00641, Pfam:PF00160. There are two conserved sequence motifs: TFFC and EDF. Nup358/RanBP2 is a nucleoporin involved in ubiquitination of many different protein targets from various cellular pathways. It complexes with Ubc9, SUMO-1 and RanGAP1 to perform this function. This is the ligase domain which binds to Ubc9.. 
PF12186 Acyl-CoA dehydrogenase C terminal<br>This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with Pfam:PF02770, Pfam:PF00441, Pfam:PF02771. There is a conserved ARRL sequence motif. The C terminal domain is an alpha helical domain. The flavin ring of Acyl-CoA dehydrogenase is buried in the crevice between the two alpha helical domains and the beta-sheet domain of one subunit, and the adenosine pyrophosphate moiety is stretched into the subunit junction of a neighbouring subunit, composed of two C terminal domains.. 
PF12187 Viral/Archaeal nuclease<br>This family of proteins is found in archaea and viruses. Proteins in this family are typically between 211 and 244 amino acids in length. These proteins are nucleases from fusseloviruses and sulfolobus archaea.. 
PF12188 STAT2_Cterm;<br>Signal transducer and activator of transcription 2 C terminal. This domain family is found in eukaryotes, and is approximately 60 amino acids in length. The family is found in association with Pfam:PF02865, Pfam:PF00017, Pfam:PF01017, Pfam:PF02864. There is a conserved DLP sequence motif. STATs are involved in transcriptional regulation and are the only regulators known to be modulated by tyrosine phosphorylation. STAT2 forms a trimeric complex with STAT1 and IRF-9 (Interferon Regulatory Factor 9), on activation of the cell by interferon, which is called ISGF3 (Interferon-stimulated gene factor 3). The C terminal domain of STAT2 contains a nuclear export signal (NES) which allows export of STAT2 into the cytoplasm along with any complexed molecules.. 
PF12189 Single-strand DNA-binding protein<br>This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. There is a conserved IELE sequence motif. VirE1 is an acidic chaperone protein which binds to VirE2, a ssDNA binding protein. These proteins are virulence factors of the plant pathogens Agrobacteria. VirE1 competes for the ssDNA binding site of VirE2.. 
PF12190 Fungal protease inhibitor<br>This protein family is found in eukaryotes, and is approximately 50 amino acids in length. These proteins are fungal protease inhibitors.. 
PF12191 Tumour necrosis factor receptor stn_TNFRSF12A_TNFR domain<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 129 and 184 amino acids in length. This is the stn_TNFRSF12A_TNFR domain from the tumour necrosis factor receptor. The function of this domain is unknown.. 
PF12192 Fungal calcium binding protein<br>This domain is found in eukaryotes, and is approximately 60 amino acids in length. There is a single completely conserved residue C that may be functionally important. This is a calcium binding domain from the fungal protein CBP (calcium binding protein). This protein is a virulence factor with unknown virulence mechanisms. CBP complexes as a highly intertwined homodimer. Each monomer is comprised of four alpha helices which adopt the saposin fold, characteristic of a protein family that binds to membranes and lipids.. 
PF12193 Sulf_coatprot_C;<br>Sulfolobus virus coat protein C terminal. This domain family is found in viruses, and is approximately 70 amino acids in length. It is the C terminal of a coat protein in sulfolobus viruses.. 
PF12194 ste5minscaffold;<br>Protein kinase Fus3-binding. This domain family is found in eukaryotes, and is approximately 190 amino acids in length. This domain is the penultimate C terminal domain from the protein ste5 which co-catalyses the phosphorylation of fus3 by ste7. It is involved in the MAPK pathways. This domain is the minimal scaffold domain of ste5. It binds to the mitogen activated protein kinase fus3 before it is phosphorylated.. 
PF12195 Endosialidase; Endobetabarrel;<br>Beta barrel domain of bacteriophage endosialidase. This domain family is found in bacteria and viruses, and is approximately 80 amino acids in length.This domain is the beta barrel domain of bacteriophage endosialidase which represents the one of the two sialic acid binding sites of the enzyme. The domain is nested in the beta propeller domain of the endosialidase enzyme. The endosialidase protein complexes to form homotrimeric molecules.. 
PF12196 FHA Ki67 binding domain of hNIFK<br>This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with Pfam:PF00076. There are two conserved sequence motifs: TPVCTP and LERRKS. This domain is found on the human nucleolar protein hNIFK. It binds to the fork-head-associated domain of human Ki67. High-affinity binding requires sequential phosphorylation by two kinases, CDK1 and GSK3, yielding pThr238, pThr234 and pSer230. This interaction is involved in cell cycle regulation.. 
PF12197 Bacillus cereus group antimicrobial protein<br>This domain is found in bacteria, and is approximately 40 amino acids in length. This domain is found in bacillus cereus group bacteria. It is an antimicrobial protein.. 
PF12198 Theoretical tuberculin protein<br>This domain family is found in bacteria, and is approximately 30 amino acids in length. This protein is a theoretical model of the tuberculin protein from Mycobacterium tuberculosis.. 
PF12199 Extracellular fibrinogen binding protein C terminal<br>This domain family is found in bacteria, and is approximately 70 amino acids in length. There is a conserved VLK sequence motif. It is the C terminal domain of bacterial extracellular fibrinogen binding protein. It contains a helical motif involved in complement regulation. This motif binds to complement and changes its conformation to a form which cannot activate downstream components of the complement cascade.. 
PF12200 Domain of unknown function (DUF3597)<br>This family of proteins is found in bacteria, eukaryotes and viruses.  Proteins in this family are typically between 126 and 281 amino acids in length. The function of this domain is unknown. The structure of this domain has been found to contain five helices with a long flexible loop between helices one and two.. 
PF12201 Bcl2-interacting killer, BH3-domain containing<br>This is a family of pro-apoptotic Bcl-x proteins, B cell leukaemia/lymphoma 2, or BIKs.  BIK proteins rely for their activity upon an intact BH3 domain lying between residues 48 and 80, as in UniProt:Q13323.. 
PF12202 Oxidative-stress-responsive kinase 1 C terminal<br>This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with Pfam:PF00069. There is a single completely conserved residue F that may be functionally important. OSR1 is involved in the signalling cascade which activates Na/K/2Cl cotransporter during osmotic stress. This domain is the C terminal domain of OSR1 which recognises a motif (Arg-Phe-Xaa-Val) on the OSR1-activating protein WNK1.. 
PF12203 Glutamine rich N terminal domain of histone deacetylase 4<br>This domain is found in eukaryotes, and is approximately 90 amino acids in length. The family is found in association with Pfam:PF00850. The domain forms an alpha helix which complexes to form a tetramer. The glutamine rich domains have many intra- and inter-helical interactions which are thought to be involved in reversible assembly and disassembly of proteins. The domain is part of histone deacetylase 4 (HDAC4) which removes acetyl groups from histones. This restores their positive charge to allow stronger DNA binding thus restricting transcriptional activity.. 
PF12204 Domain of unknown function (DUF3598)<br>This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 230 and 398 amino acids in length. These proteins are formed entirely from B sheets which form a barrel structure similar to those seen in the lipocalin superfamily.. 
PF12205 G protein-coupled receptor kinase-interacting protein 1 C term<br>This domain family is found in eukaryotes, and is approximately 120 amino acids in length. The family is found in association with Pfam:PF01412, Pfam:PF00023, Pfam:PF08518. GIT1 plays an important role in cell adhesion, motility, cytoskeletal remodeling and membrane trafficking. To perform this function, it localises p21-activated kinase (PAK) and PAK-interactive exchange factor to focal adhesions. Its activation is regulated by interaction between its paxillin-binding C terminal and the LD motifs of paxillin. The C terminal folds into a four helix bundle.. 
PF12206 Domain of unknown function (DUF3599)<br>This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length. This domain is the phage-like element pbsx protein xkdh.. 
PF12207 Domain of unknown function (DUF3600)<br>This family of proteins is found in bacteria. Proteins in this family are approximately 230 amino acids in length. This domain is the C terminal of the putative ecf-type sigma factor negative effector.. 
PF12208 Domain of unknown function (DUF3601)<br>This domain family is found in bacteria, and is approximately 80 amino acids in length.. 
PF12209 Leucine permease transcriptional regulator helical domain<br>This domain family is found in eukaryotes, and is approximately 80 amino acids in length. The family is found in association with Pfam:PF03399. This domain is a helical domain in the middle of leucine permease transcriptional regulator.. 
PF12210 Hepatocyte growth factor-regulated tyrosine kinase substrate<br>This domain family is found in eukaryotes, and is approximately 100 amino acids in length. The family is found in association with Pfam:PF00790, Pfam:PF01363, Pfam:PF02809. This domain is the helical region of Hrs which forms the core complex of ESCRT with STAM.. 
PF12211 Low molecular weight S layer protein N terminal<br>This family of proteins is found in bacteria. Proteins in this family are typically between 328 and 381 amino acids in length. There is a conserved LGDG sequence motif. Clostridial species have a layer of surface proteins surrounding their membrane. This layer is comprised of a high molecular weight protein and a low molecular weight protein. This domain is the N terminal domain of the low molecular weight protein. It is a structural domain.. 
PF12212 Piwi/Argonaute/Zwille siRNA-binding domain<br>This domain family is found in bacteria and archaea, and is approximately 50 amino acids in length. There is a conserved LKDIL sequence motif. There is a single completely conserved residue L that may be functionally important. This domain is part of an Argonaute protein. It is an siRNA binding domain.. 
PF12213 DNA polymerases epsilon N terminal<br>This domain is found in eukaryotes, and is approximately 70 amino acids in length. The family is found in association with Pfam:PF04042. There is a single completely conserved residue F that may be functionally important. This domain is the N terminal domain of DNA polymerase epsilon subunit B. It forms a primarily alpha helical structure in which four helices are arranged in two hairpins with connecting loops containing beta strands which form a short parallel sheet. DNA polymerase epsilon is required in DNA replication for synthesis of the leading strand. This domain has close structural relation to AAA+ protein C terminal domains.. 
PF12214 Cell cycle regulated microtubule associated protein<br>PFAM-B_2368 (release 23.0). This domain is found in eukaryotes. This domain is typically between 127 to 182 amino acids in length. This domain is found associated with Pfam:PF06886. This domain is found in the protein TPX2 (a.k.a p100) which is involved in cell cycling. It is only expressed between the start of the S phase and completion of cytokinesis. The microtubule-associated protein TPX2 has been reported to be crucial for mitotic spindle formation. This domain is close to the C terminal of TPX2. The protein importin alpha regulates the activity of TPX2 by binding to the nuclear localisation signal in this domain.. 
PF12215 beta-Glucocerebrosidase 2 N terminal<br>PFAM-B_2416 (release 23.0). This domain is found in bacteria, archaea and eukaryotes. This domain is typically between 320 to 354 amino acids in length. This domain is found associated with Pfam:PF04685. This domain is found in the protein beta-Glucocerebrosidase 2. It is found just after the extreme N terminus. This protein is located in the ER. The N terminal is thought to be the luminal domain while the C terminal is the cytosolic domain. The catalytic domain of GBA-2 is unknown.. 
PF12216 Immune evasion protein<br>PFAM-B_2496 (release 23.0). This protein is found in archaea and viruses. Proteins in this family are typically between 265 to 342 amino acids in length. The proteins in this family are or are related to the m04 encoded protein gp34 of pathogenic microorganisms such as murine cytomegalovirus. m06 and m152 genes are expressed earlier in the intracellular replication phases of these microorganism' life cycles. They function to inhibit MHC-1 loading and export. gp34 is theorized to prevent immune reactions from NK cells which would ordinarily recognise and attack cells lacking MHC.. 
PF12217 Catalytic beta propeller domain of bacteriophage endosialidase<br>This domain family is found in bacteria and viruses, and is typically between 443 and 460 amino acids in length. This domain is the highly conserved beta propeller of bacteriophage endosialidase which represents the catalytically active part of the enzymes. This core domain forms stable SDS-resistant trimers. There is a nested beta barrel domain in this domain (Pfam:PF12195). The endosialidase protein complexes to form a homotrimeric molecule.. 
PF12218 N terminal extension of bacteriophage endosialidase<br>This domain family is found in bacteria and viruses, and is approximately 70 amino acids in length. This domain is found in the bacteriophage protein endosialidase. The two N-terminal domains (this domain and the beta propeller) assemble in the compact 'cap' whereas the C-terminal domain forms an extended tail-like structure. The very N-terminal part of the 'cap' region (residues 246 to 312) holds the only alpha-helix of the protein and is presumably the residual part of the deleted N-terminal head-binding domain. The endosialidase protein complexes to form homotrimeric molecules.. 
PF12219 Catalytic domain of bacteriophage endosialidase<br>This domain family is found in bacteria and viruses, and is approximately 160 amino acids in length. There are two conserved sequence motifs: VSR and YGA. This domain is the C terminal domain of the bacteriophage protein endosialidase. The endosialidase protein forms homotrimeric molecules and this domain complexes into a tail-spike stalk. The stalk region folds in a triple beta-helix that is interrupted by a small triple beta-prism domain. The tail-spike is a multifunctional protein device used by the phage to fulfill the following functions: (i) to adsorb to the bacterial polySia capsule (ii) to de-polymerise the capsule to gain access to the outer bacterial membrane, and finally (iii) to mediate tight adhesion to the membrane, a prerequisite for the initiation of the infection cycle.. 
PF12220 U1 small nuclear ribonucleoprotein of 70kDa MW N terminal<br>PFAM-B_2533 (release 23.0). This domain is found in eukaryotes. This domain is about 90 amino acids in length. This domain is found associated with Pfam:PF00076. This domain is part of U1 snRNP, which is the pre-mRNA binding protein of the penta-snRNP spliceosome complex. It extends over a distance of 180 A from its RNA binding domain, wraps around the core domain of U1 snRNP consisting of the seven Sm proteins and finally contacts U1-C, which is crucial for 5'-splice-site recognition.. 
PF12221 Bacterial membrane protein N terminal<br>PFAM-B_2550 (release 23.0). This domain is found in bacteria. This domain is typically between 65 to 81 amino acids in length. This domain is found associated with Pfam:PF01145. This domain is the N terminal of the bacterial membrane protein HflK. HflK complexes with HflC to form a membrane protease which is modulated by the GTPase HflX. The N terminal domain of HflK is the membrane spanning region which anchors the protein in the bacterial membrane.. 
PF12222 Peptide N-acetyl-beta-D-glucosaminyl asparaginase amidase A<br>PFAM-B_2578 (release 23.0). This family of proteins is found in bacteria, archaea and eukaryotes.  Proteins in this family are typically between 558 and 775 amino acids in length. There is a conserved TGG sequence motif. PNGase A is a protein which cleaves glycopeptides.. 
PF12223 Protein of unknown function (DUF3602)<br>PFAM-B_2582 (release 23.0). This domain family is found in eukaryotes, and is typically between 78 and 89 amino acids in length.. 
PF12224 Putative amidoligase enzyme<br>This family of proteins are likely to act as amidoligase enzymes   Protein in this family are found in conserved gene neighborhoods encoding a glutamine amidotransferase-like thiol peptidase (in proteobacteria) or an Aig2 family cyclotransferase protein (in firmicutes)  .. 
PF12225 Methylene-tetrahydrofolate reductase C terminal<br>PFAM-B_2600 (release 23.0). This family is found in bacteria and archaea, and is approximately 100 amino acids in length. There is a conserved NGPCGG sequence motif. This family is the C terminal of methylene-tetrahydrofolate reductase. This protein reduces FAD using the reducing equivalents from reduced FAD, subsequently reduces tetrahydrofolate. The C terminal of MTHFR contains the FAD binding site and is the catalytic portion of the enzyme.. 
PF12226 Turkey astrovirus capsid protein<br>PFAM-B_2608 (release 23.0). This family of proteins is found in viruses. Proteins in this family are typically between 241 and 261 amino acids in length. These proteins are capsid proteins from various astrovirus strains.. 
PF12227 Protein of unknown function (DUF3603)<br>PFAM-B_2609 (release 23.0). This protein is found in bacteria and eukaryotes. Proteins in this family are about 250 amino acids in length.. 
PF12228 Protein of unknown function (DUF3604)<br>PFAM-B_2610 (release 23.0). This family of proteins is found in bacteria. Proteins in this family are typically between 621 and 693 amino acids in length.. 
PF12229 Putative peptidoglycan binding domain<br>
PF12230 Pre-mRNA splicing factor PRP21 like protein<br>PFAM-B_2642 (release 23.0). This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with Pfam:PF01805. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form.. 
PF12231 Rap1-interacting factor 1 N terminal<br>Assefa S, Gavin OL, Eberhardt R. PFAM-B_2647 (release 23.0). This domain family is found in eukaryotes, and is typically between 135 and 146 amino acids in length. Rif1 is a protein which interacts with Rap1 to regulate telomere length. Interaction with telomeres limits their length. The N terminal region contains many HEAT- and ARMADILLO- type repeats. These are helical folds which form extended curved proteins or RNA interface surfaces.. 
PF12232 Myogenic determination factor 5<br>PFAM-B_2654 (release 23.0). This domain family is found in eukaryotes, and is approximately 70 amino acids in length. The family is found in association with Pfam:PF00010, Pfam:PF01586. There is a conserved CSD sequence motif. Myf5 is responsible for directing cells to the skeletal myocyte lineage during development. Myf5 is likely to act in a similar way to the other MRF4 proteins such as MyoD which perform the same function. These are histone acetyltransferases and histone deacetylases which activate and repress genes involved in the myocyte lineage.. 
PF12233 Human adult T cell leukemia/lymphoma virus protein<br>PFAM-B_2655 (release 23.0). This family of proteins is found in viruses. Proteins in this family are approximately 100 amino acids in length. p12I binds to the immature beta and gamma-c chains of the interleukin-2 receptor retarding their translocation to the plasma membrane. p12I forms dimers which bind to these chains.. 
PF12234 RAVE protein 1 C terminal<br>PFAM-B_2692 (release 23.0). This domain family is found in eukaryotes, and is typically between 621 and 644 amino acids in length. This family is the C terminal region of the protein RAVE (regulator of the ATPase of vacuolar and endosomal membranes). Rav1p is involved in regulating the glucose dependent assembly and disassembly of vacuolar ATPase V1 and V0 subunits.. 
PF12235 Fragile X-related 1 protein C terminal<br>PFAM-B_2701 (release 23.0). This domain family is found in eukaryotes, and is typically between 126 and 160 amino acids in length. The family is found in association with Pfam:PF05641, Pfam:PF00013. This family is the C terminal region of the fragile X related 1 protein FXR1P. FXR1P contains two KH domains and a RGG box that are characteristic motifs in RNA-binding proteins as well as nuclear localization and export signals. FXR1P is thought to regulate mRNA transport and translation.. 
PF12236 Bacteriophage head to tail connecting protein<br>PFAM-B_2709 (release 23.0). This family of head-tail connector proteins is found in bacteria and viruses. Proteins in this family are typically between 516 and 555 amino acids in length.  This protein is found in Phage T7 and T3 among others.. 
PF12237 Phosphorylated CTD interacting factor 1 WW domain<br>PFAM-B_2805 (release 23.0). This domain family is found in bacteria and eukaryotes, and is approximately 180 amino acids in length. This domain is the WW domain of PCIF1. PCIF1 interacts with phosphorylated RNA polymerase II carboxy-terminal domain (CTD). The WW domain of PCIF1 can directly and preferentially bind to the phosphorylated CTD compared to the unphosphorylated CTD. PCIF1 binds to the hyperphosphorylated RNAP II (RNAP IIO) in vitro and in vivo. Double immunofluorescence labeling in HeLa cells demonstrated that PCIF1 and endogenous RNAP IIO are co-localized in the cell nucleus. Thus, PCIF1 may play a role in mRNA synthesis by modulating RNAP IIO activity.. 
PF12238 Merozoite surface antigen 2c<br>PFAM-B_2755 (release 23.0). This family of proteins is found in eukaryotes. Proteins in this family are typically between 263 and 318 amino acids in length. There is a conserved SFT sequence motif. MSA-2 is a plasma membrane glycoprotein which can be found in Babesia bovis species.. 
PF12239 Protein of unknown function (DUF3605)<br>PFAM-B_2795 (release 23.0). This family of proteins is found in eukaryotes and viruses. Proteins in this family are typically between 161 and 256 amino acids in length.. 
PF12240 Angiomotin C terminal<br>PFAM-B_2808 (release 23.0). This domain family is found in eukaryotes, and is typically between 197 and 211 amino acids in length. This family is the C terminal region of angiomotin. Angiomotin regulates the action of angiogenesis inhibitor angiostatin  . The C terminal region of angiomotin appears to be involved in directing the protein chemotactically  .. 
PF12241 Trans-2-enoyl-CoA reductase catalytic region<br>Vella Briffa B, Coggill P. Pfam-B_10602 (release 10.0). This family of trans-2-enoyl-CoA reductases, EC:1.3.1.44, carries the the catalytic sites of the enzyme, characterised by the conserved sequence motifs: YNThhhFxK, and YShAPxR. In Euglena where the enzyme has been characterised it catalyses the reduction of enoyl-CoA to acyl-CoA in an unusual fatty acid pathway in mitochondria. the whole path performs a malonyl-CoA independent synthesis of fatty acids leading to accumulation of wax esters, which serve as the sink for electrons stemming from glycolytic ATP synthesis and pyruvate oxidation.. 
PF12242 NAD(P)H binding domain of trans-2-enoyl-CoA reductase<br>Vella Briffa B, Coggill P. Pfam-B_10602 (release 10.0). This family carries the region of the enzyme trans-2-enoyl-CoA reductase, EC:1.3.1.44, which binds NAD(P)H. The activity of the enzyme was characterised in Euglena where an unusual fatty acid synthesis path-way in the mitochondria performs a malonyl-CoA independent synthesis of fatty acids leading to accumulation of wax esters, which serve as the sink for electrons stemming from glycolytic ATP synthesis and pyruvate oxidation. The full enzyme catalyses the reduction of enoyl-CoA to acyl-CoA. The binding site is conserved as GA/CSpGYG, where p is any polar residue  .. 
PF12243 CTD kinase subunit gamma CTK3<br>Pfam-B_12814 (release 23.0). The C-terminal domain kinase (CTDK-1), is a three-subunit complex comprised of Ctk1, Ctk2, and Ctk3, that plays a key role in regulation of transcription and translation and in coordinating these two processes. Both Ctk2 and Ctk3 are regulated at the level of protein turnover, and are unstable proteins processed through a ubiquitin-proteasome pathway. Their physical interaction is required to protect both subunits from degradation, and both Ctk2 and Ctk3 are required for Ctk1 CTD kinase activation  . The mammalian P-TEFb is mirrored by the combined complexes in yeast of the CTDK1 and the Bur1/2  .. 
PF12244 Protein of unknown function (DUF3606)<br>PFAM-B_2813 (release 23.0). This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.. 
PF12245 DUF3607;<br>Bacterial Ig-like domain (group 3). PFAM-B_2816 (release 23.0). This family consists of bacterial domains with an Ig-like fold. Members of this family are found in a variety of bacterial surface proteins.. 
PF12246 Temperature dependent protein affecting M2 dsRNA replication<br>PFAM-B_2862 (release 23.0). This domain family is found in eukaryotes, and is typically between 231 and 255 amino acids in length. There is a single completely conserved residue P that may be functionally important. MKT1 is required for maintenance of K2 toxin above 30 degrees C in strains with the L-A-HN variant of the L-A double-stranded RNA virus of Saccharomyces cerevisiae. MKT1 is a 93 kDa protein with serine-rich regions and the retroviral protease signature, DTG. This family is the C terminal region of MKT1.. 
PF12247 Temperature dependent protein affecting M2 dsRNA replication<br>PFAM-B_2862 (release 23.0). This domain family is found in eukaryotes, and is typically between 231 and 255 amino acids in length. There is a single completely conserved residue P that may be functionally important. MKT1 is required for maintenance of K2 toxin above 30 degrees C in strains with the L-A-HN variant of the L-A double-stranded RNA virus of Saccharomyces cerevisiae. MKT1 is a 93 kDa protein with serine-rich regions and the retroviral protease signature, DTG. This family is the N terminal region of MKT1.. 
PF12248 Farnesoic acid 0-methyl transferase<br>PFAM-B_2872 (release 23.0). This domain family is found in bacteria and eukaryotes, and is approximately 110 amino acids in length.Farnesoic acid O-methyl transferase (FAMeT) is the enzyme that catalyses the formation of methyl farnesoate (MF) from farnesoic acid (FA) in the biosynthetic pathway of juvenile hormone (JH).. 
PF12249 Arabinofuranosyltransferase A C terminal<br>PFAM-B_2900 (release 23.0). This domain family is found in bacteria, and is typically between 179 and 190 amino acids in length. This family is the C terminal region of AftA. The enzyme catalyses the addition of the first key arabinofuranosyl residue from the sugar donor beta-D-arabinofuranosyl-1-monophosphoryldecaprenol to the galactan domain of the cell wall, thus priming the galactan for further elaboration by the arabinofuranosyltransferases. The C terminal region is predicted to be directed towards the periplasm.. 
PF12250 Arabinofuranosyltransferase N terminal<br>PFAM-B_2900 (release 23.0). This domain family is found in bacteria, and is typically between 430 and 441 amino acids in length. This family is the N terminal region of AftA. The enzyme catalyses the addition of the first key arabinofuranosyl residue from the sugar donor beta-D-arabinofuranosyl-1-monophosphoryldecaprenol to the galactan domain of the cell wall, thus priming the galactan for further elaboration by the arabinofuranosyltransferases. The N terminal region has been predicted to span 11 transmembrane regions.. 
PF12251 snRNA-activating protein of 50kDa MW C terminal<br>PFAM-B_2919 (release 23.0). This domain family is found in eukaryotes, and is typically between 196 and 207 amino acids in length. There is a conserved CEH sequence motif. SNAP50 is part of the snRNA-activating protein complex which activates RNA polymerases II and III. There is a cysteine-histidine cluster which contains two possible zinc finger motifs.. 
PF12252 Dot/Icm substrate protein<br>PFAM-B_2926 (release 23.0). This family of proteins is found in bacteria. Proteins in this family are typically between 397 and 1543 amino acids in length. This family is the SidE protein in the Dot/Icm pathway of Legionella pneumophila bacteria. There is little literature describing the family.. 
PF12253 CAF1B;<br>Chromatin assembly factor 1 subunit A. The CAF-1 or chromatin assembly factor-1 consists of three subunits, and this is the first, or A  . The A domain is uniquely required for the progression of S phase in mouse cells  , independent of its ability to promote histone deposition   but dependent on its ability to interact with HP1 - heterochromatin protein 1-rich heterochromatin domains next to centromeres that are crucial for chromosome segregation during mitosis. This HP1-CAF-1 interaction module functions as a built-in replication control for heterochromatin, which, like a control barrier, has an impact on S-phase progression in addition to DNA-based checkpoints  .. 
PF12254 DNA polymerase alpha subunit p180 N terminal<br>PFAM-B_2966 (release 23.0). This domain family is found in eukaryotes, and is approximately 70 amino acids in length. The family is found in association with Pfam:PF00136, Pfam:PF08996, Pfam:PF03104. This family is the N terminal of DNA polymerase alpha subunit p180 protein. The N terminal contains the catalytic region of the alpha subunit.. 
PF12255 Insecticide toxin TcdB middle/C-terminal region<br>PFAM-B_3032 (release 23.0). This domain family is found in bacteria, and is approximately 150 amino acids in length. The family is found in association with Pfam:PF03534. This family is the C-terminal-sided middle region of the bacterial insecticide toxin TcdB.. 
PF12256 Insecticide toxin TcdB middle/N-terminal region<br>PFAM-B_3032 (release 23.0). This domain family is found in bacteria and archaea, and is typically between 164 and 180 amino acids in length. The family is found in association with Pfam:PF05593. This family is the N-terminal-sided middle region of the bacterial insecticide toxin TcdB. This region appears related to the FG-GAP repeat Pfam:PF01839.. 
PF12257 Protein of unknown function (DUF3608)<br>PFAM-B_3083 (release 23.0). This domain family is found in eukaryotes, and is approximately 280 amino acids in length. The family is found in association with Pfam:PF00610.. 
PF12258 Microcephalin protein<br>PFAM-B_3105 (release 23.0). This family of proteins is found in eukaryotes. Proteins in this family are typically between 384 and 835 amino acids in length. Microcephalin is involved in determining the size of the brain in animals. It is a protein, which if expressed homozygously causes the organism to have the condition microcephaly. Organisms expressing the mutated form of this protein in a homozygous manner develop a condition called microcephaly - a drastically reduced brain mass and volume. Microcephalin is predicted to contain three BRCA1 C-terminal domains, the first of which is the probable microcephaly mutation site.. 
PF12259 Protein of unknown function (DUF3609)<br>PFAM-B_3173 (release 23.0). This domain family is found in eukaryotes and viruses, and is typically between 348 and 360 amino acids in length.. 
PF12260 Protein-kinase domain of FAM69<br>Assefa S, Gavin OL, Coggill P. PFAM-B_3196 (release 23.0). This is the C-terminal region of a family of FAM69 proteins from Metazoa and Viridiplantae that are active protein-kinases. The family members have a short transmembrane helix close to the N-terminus, and thereafter are highly enriched with cysteines. FAM69 proteins are localised to the endoplasmic reticulum. Many members also have a short EF-hand, calcium-binding, domain just upstream of the kinase domain. The exact function of the more N-terminal family is uncertain.. 
PF12261 Thermostable hemolysin<br>PFAM-B_3198 (release 23.0). This family of proteins is found in bacteria. Proteins in this family are typically between 200 and 228 amino acids in length. T_hemolysin is a pore-forming toxin of bacteria, able to lyse erythrocytes from a number of mammalian species.. 
PF12262 Bacterial virulence factor lipase N-terminal<br>PFAM-B_3205 (release 23.0). This domain family is found in bacteria, and is typically between 258 and 271 amino acids in length. There are two conserved sequence motifs: DGT and DGWST. This family is the N-terminal region of bacterial virulence factor lipase. The N-terminal region contains a potential signalling sequence.. 
PF12263 Protein of unknown function (DUF3611)<br>PFAM-B_3207 (release 23.0). This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 180 and 205 amino acids in length. There are two completely conserved residues (W and G) that may be functionally important.. 
PF12264 VSL_protease; Peptidase_C03;<br>Waikavirus capsid protein 1. Assefa S, Gavin OL, Eberhardt R. PFAM-B_3208 (release 23.0). The rice tungro spherical waikavirus polyprotein is cleaved into 7 proteins, including three capsid proteins, by the tungro spherical virus-type peptidase Pfam:PF12381. This family represents the capsid protein 1 [1,2].. 
PF12265 Histone-binding protein RBBP4 or subunit C of CAF1 complex<br>Pfam-B_318 (release 23.0). The CAF-1 complex is a conserved heterotrimeric protein complex that promotes histone H3 and H4 deposition onto newly synthesized DNA during replication or DNA repair; specifically it facilitates replication-dependent nucleosome assembly with the major histone H3 (H3.1). This domain is an alpha helix which sits just upstream of the WD40 seven-bladed beta-propeller in the human RbAp46 protein. RbAp46 folds into the beta-propeller and binds histone H4 in a groove formed between this N-terminal helix and an extended loop inserted into blade six  .. 
PF12266 Protein of unknown function (DUF3613)<br>PFAM-B_3240 (release 23.0). This family of proteins is found in bacteria. Proteins in this family are typically between 94 and 126 amino acids in length.. 
PF12267 Protein of unknown function (DUF3614)<br>PFAM-B_3244 (release 23.0). This family of proteins is found in viruses. Proteins in this family are typically between 162 and 495 amino acids in length.. 
PF12268 Protein of unknown function (DUF3612)<br>PFAM-B_3220 (release 23.0). This domain family is found in bacteria, and is approximately 180 amino acids in length. The family is found in association with Pfam:PF01381.. 
PF12269 CpG binding protein zinc finger C terminal domain<br>PFAM-B_3253 (release 23.0). This domain family is found in eukaryotes, and is approximately 240 amino acids in length. This domain is the zinc finger domain of a CpG binding DNA methyltransferase protein. It contains a CxxC motif which forms the zinc finger and binds to DNA.. 
PF12270 Cytochrome c oxidase subunit IV<br>PFAM-B_3280 (release 23.0). This family of proteins is found in bacteria. Proteins in this family are approximately 140 amino acids in length. This family is the fourth subunit of the cytochrome c oxidase complex. This subunit does not have a catalytic capacity but instead, is required for assembly and/or stability of the complex.. 
PF12271 Chitin synthase III catalytic subunit<br>PFAM-B_3298 (release 23.0). This family of proteins is found in eukaryotes. Proteins in this family are typically between 288 and 332 amino acids in length. This family is the catalytic domain of chitin synthase III. Chitin is a major component of fungal cell walls and this enzyme is responsible for its formation.. 
PF12272 Protein of unknown function (DUF3610)<br>PFAM-B_3173 (release 23.0). This domain family is found in eukaryotes, and is typically between 146 and 160 amino acids in length. There are two conserved sequence motifs: FNN and IDS.. 
PF12273 Chitin synthesis regulation, resistance to Congo red<br>Pfam-B_2935 (release 23.0). RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall  . RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5  .. 
PF12274 Protein of unknown function (DUF3615)<br>PFAM-B_3306 (release 23.0). This domain family is found in bacteria and eukaryotes, and is typically between 86 and 97 amino acids in length. There is a conserved FAE sequence motif. There is a single completely conserved residue F that may be functionally important.. 
PF12275 Protein of unknown function (DUF3616)<br>PFAM-B_3338 (release 23.0). This family of proteins is found in bacteria. Proteins in this family are typically between 335 and 392 amino acids in length. There is a conserved GLRGPV sequence motif.. 
PF12276 Protein of unknown function (DUF3617)<br>PFAM-B_3343 (release 23.0). This family of proteins is found in bacteria. Proteins in this family are typically between 155 and 179 amino acids in length. There is a single completely conserved residue C that may be functionally important.. 
PF12277 Protein of unknown function (DUF3618)<br>PFAM-B_3350 (release 23.0). This domain family is found in bacteria, and is approximately 50 amino acids in length.. 
PF12278 Sex determination protein N terminal<br>PFAM-B_3366 (release 23.0). This family of proteins is found in eukaryotes. Proteins in this family are typically between 168 and 410 amino acids in length. This family is the N terminal end of the sex determination protein of many different animals. It plays a role in the gender determination of around 20% of all animals.. 
PF12279 Protein of unknown function (DUF3619)<br>PFAM-B_3353 (release 23.0). This protein is found in bacteria. Proteins in this family are about 140 amino acids in length. This protein has two conserved sequence motifs: AAR and DDLP.. 
PF12280 Brain specific membrane anchored protein<br>PFAM-B_3398 (release 23.0). This family of proteins is found in eukaryotes. Proteins in this family are typically between 285 and 331 amino acids in length. BSMAP has a putative transmembrane domain and is predicted to be a type I membrane glycoprotein.. 
PF12281 Protein of unknown function (DUF3620)<br>PFAM-B_3384 (release 23.0). This family of proteins is found in bacteria. Proteins in this family are typically between 281 and 358 amino acids in length. There are two completely conserved residues (G and P) that may be functionally important.. 
PF12282 Signal transduction histidine kinase<br>PFAM-B_3401 (release 23.0). This domain is found in bacteria. This domain is about 150 amino acids in length. This domain is found associated with Pfam:PF07568, Pfam:PF08448, Pfam:PF02518. This domain has a single completely conserved residue P that may be functionally important. This family is mostly annotated as a histidine kinase involved in signal transduction but there is little published evidence to support this.. 
PF12283 Bacteriophage protein K<br>PFAM-B_3455 (release 23.0). This family of proteins is found in viruses. Proteins in this family are approximately 60 amino acids in length. This family is a protein expressed by bacteriophages which has an unknown function. There is evidence that it is non-essential for in vivo production of a mature phage.. 
PF12284 Hox protein A13 N terminal<br>PFAM-B_3464 (release 23.0). This family of proteins is found in eukaryotes. Proteins in this family are typically between 149 and 306 amino acids in length. The family is found in association with Pfam:PF00046. This family is the N terminal of the Hox gene protein involved in formation of the digital arch of the hands and feet as well as in correct genital formation. Mutation of the protein is associated with hand-foot-genital syndrome.. 
PF12285 Protein of unknown function (DUF3621)<br>PFAM-B_3468 (release 23.0). This family of proteins is found in viruses. Proteins in this family are typically between 49 and 62 amino acids in length. There are two conserved sequence motifs: QPLDLS and EQQ.. 
PF12286 Protein of unknown function (DUF3622)<br>PFAM-B_3490 (release 23.0). This family of proteins is found in bacteria. Proteins in this family are typically between 72 and 107 amino acids in length. There is a conserved VSK sequence motif.. 
PF12287 Cytoplasmic activation/proliferation-associated protein-1 C term<br>PFAM-B_3504 (release 23.0). This family of proteins is found in eukaryotes. Proteins in this family are typically between 343 and 708 amino acids in length. This family is the C terminal region of caprin-1. Caprin-1 is a protein involved in regulating cellular proliferation. In mutated phenotypes, the G1 phase of the cell cycle is greatly lengthened, impairing normal proliferation. The C terminal region of caprin-1 contains RGG motifs which are characteristic of RNA binding domains. It is possible that caprin-1 functions through an RNA binding mechanism.. 
PF12288 Carboxysome shell peptide mid-region<br>PFAM-B_3507 (release 23.0). This domain family is found in bacteria and eukaryotes, and is approximately 430 amino acids in length. This family is annotated frequently as a carboxysome shell peptide, however there is little publication to confirm this.. 
PF12289 Rotavirus VP1 structural protein<br>PFAM-B_3516 (release 23.0). This domain family is found in viruses, and is approximately 50 amino acids in length. The family is found in association with Pfam:PF02123. VP1 is a structural protein of the inner core layer of the rotavirus virion. It complexes with VP2 and Vp3 to form this layer.. 
PF12290 topoisom_IIA_B; Topoisom_IIA_B;<br>Protein of unknown function (DUF3802). PFAM-B_3547 (release 23.0). This family of proteins is found in bacteria. Proteins in this family are typically between 114 and 143 amino acids in length. There is a conserved KNLFD sequence motif.. 
PF12291 Protein of unknown function (DUF3623)<br>PFAM-B_3578 (release 23.0). This family of proteins is found in bacteria. Proteins in this family are typically between 261 and 345 amino acids in length.. 
PF12292 Protein of unknown function (DUF3624)<br>PFAM-B_3603 (release 23.0). This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There is a conserved GRC sequence motif.. 
PF12293 Protein of unknown function (DUF3625)<br>PFAM-B_3621 (release 23.0). This family of proteins is found in bacteria. Proteins in this family are typically between 327 and 360 amino acids in length.. 
PF12294 Protein of unknown function (DUF3626)<br>PFAM-B_3627 (release 23.0). This family of proteins is found in bacteria. Proteins in this family are typically between 294 and 374 amino acids in length.. 
PF12295 Symplekin tight junction protein C terminal<br>PFAM-B_3634 (release 23.0). This domain family is found in eukaryotes, and is approximately 180 amino acids in length. There is a single completely conserved residue P that may be functionally important. Symplekn has been localized, by light and electron microscopy, to the plaque associated with the cytoplasmic face of the tight junction-containing zone (zonula occludens) of polar epithelial cells and of Sertoli cells of testis. However, both the mRNA and the protein can also be detected in a wide range of cell types that do not form tight junctions. Careful analyses have revealed that the protein occurs in all these diverse cells in the nucleoplasm, and only in those cells forming tight junctions is it recruited, partly but specifically, to the plaque structure of the zonula occludens. . 
PF12296 Hydrophobic surface binding protein A<br>PFAM-B_3635 (release 23.0). This protein is found in eukaryotes. Proteins in this family are typically between 171 to 275 amino acids in length. Although the HsbA amino acid sequence suggests that HsbA may be hydrophilic, HsbA adsorbed to hydrophobic PBSA (Polybutylene succinate-co-adipate) surfaces in the presence of NaCl or CaCl2. When HsbA was adsorbed on the hydrophobic PBSA surfaces, it promoted PBSA degradation via the CutL1 polyesterase. CutL1 interacts directly with HsbA attached to the hydrophobic QCM electrode surface. These results suggest that when HsbA is adsorbed onto the PBSA surface, it recruits CutL1, and that when CutL1 is accumulated on the PBSA surface, it stimulates PBSA degradation.. 
PF12297 Ellis van Creveld protein 2 like protein<br>PFAM-B_3668 (release 23.0). This family of proteins is found in eukaryotes. Proteins in this family are typically between 571 and 1310 amino acids in length. There are two conserved sequence motifs: LPA and ELH. EVC2 is implicated in Ellis van Creveld chondrodysplastic dwarfism in humans. Mutations in this protein can give rise to this congenital condition. LIMBIN is a protein which shares around 80% sequence homology with EVC2 and it is implicated in a similar condition in bovine chondrodysplastic dwarfism.. 
PF12298 Eukaryotic mitochondrial regulator protein <br>PFAM-B_3672 (release 23.0). This family of proteins is found in eukaryotes. Proteins in this family are typically between 168 and 381 amino acids in length. Bot1p localizes to the mitochondria in live cells and cofractionates with purified mitochondrial ribosomes. Bot1p has a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery. Observations also indicate that in fission yeast, alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms.. 
PF12299 Protein of unknown function (DUF3627)<br>PFAM-B_3687 (release 23.0). This domain family is found in bacteria and viruses, and is approximately 90 amino acids in length. The family is found in association with Pfam:PF02498.. 
PF12300 Protein of unknown function (DUF3628)<br>PFAM-B_3692 (release 23.0). This domain family is found in bacteria, and is typically between 153 and 183 amino acids in length. The family is found in association with Pfam:PF00270, Pfam:PF00271.. 
PF12301 CD99 antigen like protein 2<br>PFAM-B_3714 (release 23.0). This family of proteins is found in eukaryotes. Proteins in this family are typically between 165 and 237 amino acids in length. CD99L2 and CD99 are involved in trans-endothelial migration of neutrophils in vitro and in the recruitment of neutrophils into inflamed peritoneum.. 
PF12302 Protein of unknown function (DUF3629)<br>PFAM-B_3723 (release 23.0). This family of proteins is found in eukaryotes. Proteins in this family are typically between 256 and 292 amino acids in length.. 
PF12304 Beta-casein like protein<br>PFAM-B_3744 (release 23.0). This protein is found in eukaryotes. Proteins in this family are typically between 216 to 240 amino acids in length. This protein has two conserved sequence motifs: VLR and TRIY. BCLP is associated with cell morphology and a regulation of growth pattern of tumor. It is found in adenocarcinomas of uterine cervical tissues.. 
PF12305 Protein of unknown function (DUF3630)<br>PFAM-B_3766 (release 23.0). This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length. There is a single completely conserved residue D that may be functionally important.. 
PF12306 Inclusion body protein<br>PFAM-B_3786 (release 23.0). This family of proteins is found in bacteria. Proteins in this family are typically between 173 and 191 amino acids in length. PixA is thought to be specifically produced in Xenorhabdus nematophila. It is an inclusion body protein.. 
PF12307 Protein of unknown function (DUF3631)<br>PFAM-B_3787 (release 23.0). This protein is found in bacteria. Proteins in this family are typically between 180 to 701 amino acids in length.. 
PF12308 Neurogenesis glycoprotein<br>PFAM-B_3817 (release 23.0). This domain family is found in eukaryotes, and is approximately 100 amino acids in length. The family is found in association with Pfam:PF02191. There are two conserved sequence motifs: SAQ and VQN. Noelin-1 is a glycoprotein which is secreted mainly by postmitotic neurogenic tissues in the developing central and peripheral nervous systems, first appearing after neural tube closure. It is likely that it forms large multimeric complexes.It has a divergent function in neurogenesis. In animal caps neuralized by expression of noggin, co-expression of Noelin-1 causes expression of neuronal differentiation markers several stages before neurogenesis normally occurs in this tissue. Finally, only secreted forms of the protein can activate sensory marker expression, while all forms of the protein can induce early neurogenesis.. 
PF12309 KIF-1 binding protein C terminal<br>PFAM-B_3821 (release 23.0). This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 365 and 621 amino acids in length. There is a conserved LLP sequence motif. KBP is a binding partner for KIF1Balpha that is a regulator of its transport function and thus represents a type of kinesin interacting protein.. 
PF12310 Transcription factor protein N terminal<br>PFAM-B_3835 (release 23.0). This domain family is found in eukaryotes, and is approximately 110 amino acids in length. The family is found in association with Pfam:PF00178. There is a conserved PAVIVE sequence motif. Elf-1 is an immune cell specific transcription factor. It is found in T cells, B cells, megakaryocytes,and mast cells and is involved in the control of transcription for various immune proteins. These include IL-2, GM-CSF, IL-5, IL-2 receptor alpha chain, and CD4 in T cells, IgH, blk, and lyn in B cells, TdT in T and B cells, IL-3 in megakaryocytes, and SCL and Fc-epsilon-RI alpha chain in mast cells.. 
PF12311 Protein of unknown function (DUF3632)<br>PFAM-B_3839 (release 23.0). This domain family is found in eukaryotes, and is approximately 170 amino acids in length. There is a conserved ALE sequence motif.. 
PF12312 NeA_polyprotein;<br>Nepovirus subgroup A polyprotein . PFAM-B_3843 (release 23.0). This family of proteins is found in viruses. Proteins in this family are typically between 259 and 1110 amino acids in length. The family is found in association with Pfam:PF03688, Pfam:PF03689, Pfam:PF03391. This family is one of the polyproteins expressed by Nepoviruses in subgroup A.. 
PF12313 NPR1/NIM1 like defence protein C terminal<br>PFAM-B_3871 (release 23.0). This family of proteins is found in eukaryotes. Proteins in this family are typically between 251 and 588 amino acids in length. The family is found in association with Pfam:PF00023, Pfam:PF00651. There are two conserved sequence motifs: LENRV and DLN. NPR1 (NIM1) is a defence protein in many plant species.. 
PF12314 Inner membrane complex protein<br>PFAM-B_3921 (release 23.0). This domain is found in bacteria and eukaryotes. This domain is about 120 amino acids in length. This family is the inner membrane complex of parasitic organisms. This is a cytoskeletal structure associated with the pellicle of these parasites.. 
PF12315 Protein of unknown function (DUF3633)<br>PFAM-B_3949 (release 23.0). This domain family is found in bacteria and eukaryotes, and is approximately 210 amino acids in length. The family is found in association with Pfam:PF00412.. 
PF12316 Segment polarity protein dishevelled (Dsh) C terminal<br>PFAM-B_3969 (release 23.0). This domain family is found in eukaryotes, and is typically between 177 and 207 amino acids in length. The family is found in association with Pfam:PF00778, Pfam:PF02377, Pfam:PF00610, Pfam:PF00595. The segment polarity gene dishevelled (dsh) is required for pattern formation of the embryonic segments. It is involved in the determination of body organisation through the Wingless pathway (analogous to the Wnt-1 pathway).. 
PF12317 Intraflagellar transport complex B protein 46 C terminal<br>PFAM-B_3974 (release 23.0). This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.. 
PF12318 Membrane bound FAD containing D-sorbitol dehydrogenase <br>PFAM-B_3647 (release 23.0). This family of proteins is found in bacteria. Proteins in this family are typically between 168 and 189 amino acids in length. There is a conserved ALM sequence motif. This family is a membrane protein (FAD-SLDH) involved in oxidation of D-sorbitol to L-sorbose.. 
PF12319 Tryptophan-Threonine-rich plasmodium antigen C terminal<br>PFAM-B_3676 (release 23.0). This protein is found in eukaryotes. Proteins in this family are typically between 254 to 536 amino acids in length. This family is the C terminal of a surface antigen of malarial Plasmodium species. It is currently being targeted for use as part of a subunit vaccine against Plasmodium falciparum, the main species involved in causing human malaria.. 
PF12320 Type 5 capsule protein repressor C-terminal domain<br>PFAM-B_3790 (release 23.0). This domain is found in bacteria and archaea. This domain is about 90 amino acids in length. This domain is found associated with Pfam:PF00149. SbcD works in complex with SbdC (SbcDC) which is a transcription regulator. It down-regulates transcription of arl and mgr to inhibit type 5 capsule protein production. It acts as part of the SOS pathway of bacteria.. 
PF12321 Protein of unknown function (DUF3634)<br>PFAM-B_3607 (release 23.0). This family of proteins is found in bacteria. Proteins in this family are typically between 103 and 114 amino acids in length.. 
PF12322 T4 bacteriophage base plate protein<br>PFAM-B_3861 (release 23.0). This protein is found in viruses. Proteins in this family are typically between 208 to 249 amino acids in length. This protein has a single completely conserved residue S that may be functionally important. This family includes the two base plate proteins in T4 bacteriophages. These are gp51 and gp26, encoded by late genes.. 
PF12323 HTH_14;<br>Helix-turn-helix domain. Pfam-B_1210 (release 3.0) & Pfam-B_4602 (Release 7.5). This is the N terminal helix-turn-helix domain of Transposase_2 Pfam:PF01385.. 
PF12324 Helix-turn-helix domain of alkylmercury lyase<br>Pfam-B_3505 (release 6.5). Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This is the N terminal helix-turn-helix domain associated with Pfam:PF03243.. 
PF12325 TATA element modulatory factor 1 TATA binding<br>Pfam-B_97264 (release 23.0). This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes  . The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs  . TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal   and plant   cells. The Rab6-binding domain appears to be the same region as this C-terminal family  .. 
PF12326 N-glycosylation protein<br>Pfam-B_29822 (release 23.0). This family is not required for survival of S.cerevisiae, but its deletion leads to heightened sensitivity to oxidative stress. It appears to be involved in N-glycosylation, and resides in the endoplasmic reticulum.. 
PF12327 FtsZ family, C-terminal domain<br>This family includes the bacterial FtsZ family of proteins. Members of this family are involved in polymer formation. FtsZ is the polymer-forming protein of bacterial cell division. It is part of a ring in the middle of the dividing cell that is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ is a GTPase, like tubulin. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea.. 
PF12328 Rpp20 subunit of nuclear RNase MRP and P<br>Pfam-B_33537 (release 23.0). The nuclear RNase P of Saccharomyces cerevisiae is made up of at least nine protein subunits; Pop1, Pop3, Pop4, Pop5, Pop6, Pop7, Pop8, Rpr2 and Rpp1. Many of these subunits seem to be present also in the RNase MRP, with the exception of Rpr2 (Rpp21) which is unique to RNase P. Human nuclear RNase P and MRP appear to contain at least 10 protein subunits, Rpp14, Rpp20, Rpp21, Rpp25, Rpp29, Rpp30, Rpp38, Rpp40, hPop1 and hPop5, although there is recent evidence that not all of these subunits are shared between P and MRP. Archaeal RNase P has at least four protein subunits homologous to eukaryotic RNase P/MRP proteins  . In the yeast RNase P, Pop6 and Pop7 (the Rpp20 homologue) interact with each other and they are both interaction partners of Pop4  ; in the human MRP Rpp25 and Rpp20 interact with each other   and Rpp25 binds to Rpp29 (Pop4)  .. 
PF12329 TATA element modulatory factor 1 DNA binding<br>This is the middle region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures. . The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein.  TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal   and plant   cells.. 
PF12330 Domain of unknown function (DUF3635)<br>This family may be a potential Haspin-related leucine-zipper. A leucine zipper was proposed to be present towards the C-terminus of human Haspin, (up-stream of the current family)  ; however, as this domain would appear to span several helices and be largely within a loop structure  , the actual zipper might be further downstream, and be this family, which is the very C-terminal part of the Sch. pombe sequence.. 
PF12331 Protein of unknown function (DUF3636) <br>This domain family is found in eukaryotes, and is approximately 160 amino acids in length.. 
PF12333 Rix1 complex component involved in 60S ribosome maturation<br>This domain family is found in eukaryotes, and is typically between 91 and 105 amino acids in length. This family is the N terminal of Ipi1, a component of the Rix1 complex which works in conjunction with Rea1 to mature the 60S ribosome.. 
PF12334 Rickettsia outer membrane protein B <br>This domain family is found in bacteria, and is approximately 220 amino acids in length. The family is found in association with Pfam:PF03797. This family is the middle region of one of the outer membrane proteins of Rickettsia which is involved in adhesion to eukaryotic cells for uptake.. 
PF12335 Myotubularin protein <br>This domain family is found in eukaryotes, and is approximately 220 amino acids in length. The family is found in association with Pfam:PF02141, Pfam:PF03456, Pfam:PF03455. This family is the middle region of SBF2, a member of the myotubularin family. Myotubularin-related proteins have been suggested to work in phosphoinositide-mediated signalling events that may also convey control of myelination. Mutations of SBF2 are implicated in Charcot-Marie-Tooth disease.. 
PF12336 SOX transcription factor<br>This domain family is found in eukaryotes, and is approximately 80 amino acids in length. The family is found in association with Pfam:PF00505. There are two conserved sequence motifs: KKDK and LPG. This family is made up of SOX transcription factors. These are involved in upregulation of nestin, a neural promoter.. 
PF12337 Protein of unknown function (DUF3637) <br>This domain family is found in viruses, and is approximately 70 amino acids in length. The family is found in association with Pfam:PF00073, Pfam:PF08935.. 
PF12338 Ribulose-1,5-bisphosphate carboxylase small subunit<br>This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with Pfam:PF00101. There is a conserved APF sequence motif. There are two completely conserved residues (L and P) that may be functionally important. This family is the small subunit of ribulose-1,5-bisphosphate.. 
PF12339 DNA-J related protein <br>This domain family is found in bacteria, and is approximately 130 amino acids in length. The family is found in association with Pfam:PF00226. There is a conserved YYLD sequence motif. Mostof the sequences in this family are annotated as DNA-J related proteins but there is little publication to back this up.. 
PF12340 Protein of unknown function (DUF3638)<br>This domain family is found in eukaryotes, and is approximately 230 amino acids in length. There are two conserved sequence motifs: LLE and NMG.. 
PF12341 Protein of unknown function (DUF3639) <br>This domain family is found in eukaryotes, and is approximately 30 amino acids in length. The family is found in association with Pfam:PF00400. There are two completely conserved residues (E and R) that may be functionally important.. 
PF12342 Protein of unknown function (DUF3640) <br>This family of proteins is found in viruses. Proteins in this family are typically between 25 and 211 amino acids in length.. 
PF12343 Cold shock protein DEAD box A<br>This domain family is found in bacteria, and is typically between 68 and 89 amino acids in length. The family is found in association with Pfam:PF00270, Pfam:PF00271, Pfam:PF03880. This family is the C terminal region of DEAD box A, a protein expressed under conditions of cold shock which is involved in various cellular processes such as transcription, translation and DA recombination.. 
PF12344 Ultra-violet resistance protein B<br>This domain family is found in bacteria, archaea and eukaryotes, and is approximately 40 amino acids in length. The family is found in association with Pfam:PF00271, Pfam:PF02151, Pfam:PF04851. There are two conserved sequence motifs: YAD and RRR. This family is the C terminal region of the UvrB protein which conveys mutational resistance against UV light to various different species.. 
PF12345 Protein of unknown function (DUF3641) <br>This domain family is found in bacteria and eukaryotes, and is approximately 140 amino acids in length. The family is found in association with Pfam:PF04055. This family consists of proteins which are commonly annotated as Radical SAM domains but there is little annotation to back this up.. 
PF12346 HJURP_repeat;<br>Holliday junction recognition protein-associated repeat. Vertebral Holliday junction recognition proteins carry an SCM3 domain at their N-terminus as do the eukaryotic fungi, but they also carry this central, conserved region. The function of this family is not known. Further downstream there is also a repeated domain, also of unknown function. Investigation of Scm3 and associated proteins is likely to be directly relevant to understanding the mechanism of HJURP-mediated CENP-A chromatin assembly at human centromeres.. 
PF12347 HJURP_repeat;<br>Holliday junction regulator protein family C-terminal repeat. Although this family is conserved in the Holliday junction regulator, HJURP, proteins in higher eukaryotes, alongside an Scm3, Pfam:PF10384, family, its exact function is not known. The C-terminal region of Scm3 proteins has been evolving rapidly, and this short repeat at the C-terminal end can be present in up to two copies in the higher eukaryotes.. 
PF12348 CLASP N terminal<br>This region is found at the N terminal of CLIP-associated proteins (CLASPs).\.   CLASPs are widely conserved microtubule plus-end-tracking proteins that regulate the stability of dynamic microtubules   .  In yeast, Drosophila, and Xenopus, a single CLASP orthologue is present.  In mammals, a second paralogue (CLASP2) exists which has some functional overlap with CLASP1  .. 
PF12349 SREBP-CAP_SSD;<br>Sterol-sensing domain of SREBP cleavage-activation. Sterol regulatory element-binding proteins (SREBPs) are membrane-bound transcription factors that promote lipid synthesis in animal cells. They are embedded in the membranes of the endoplasmic reticulum (ER) in a helical hairpin orientation and are released from the ER by a two-step proteolytic process. Proteolysis begins when the SREBPs are cleaved at Site-1, which is located at a leucine residue in the middle of the hydrophobic loop in the lumen of the ER  . Upon proteolytic processing SREBP can activate the expression of genes involved in cholesterol biosynthesis and uptake. SCAP stimulates cleavage of SREBPs via fusion of the their two C-termini  . This domain is the transmembrane region that traverses the membrane eight times and is the sterol-sensing domain of the cleavage protein  . WD40 domains are found towards the C-terminus.. 
PF12350 CTD kinase subunit gamma CTK3 C-terminus<br>Pfam-B_12814 (release 23.0). The C-terminal domain kinase (CTDK-1), is a three-subunit complex comprised of Ctk1, Ctk2, and Ctk3, that plays a key role in regulation of transcription and translation and in coordinating these two processes. Both Ctk2 and Ctk3 are regulated at the level of protein turnover, and are unstable proteins processed through a ubiquitin-proteasome pathway. Their physical interaction is required to protect both subunits from degradation, and both Ctk2 and Ctk3 are required for Ctk1 CTD kinase activation  . The mammalian P-TEFb is mirrored by the combined complexes in yeast of the CTDK1 and the Bur1/2  . It is not clear what independent function this C-terminal domain has.. 
PF12351 Ca2+ regulator and membrane fusion protein Fig1<br>During the mating process of yeast cells, two Ca2+ influx pathways become activated. The resulting elevation of cytosolic free Ca2+ activates downstream signaling factors that promote long term survival of unmated cells.  Fig1 is a regulator of the low affinity Ca2+ influx system (LACS)  , and is also required for efficient membrane fusion during yeast mating  .. 
PF12352 Snare region anchored in the vesicle membrane C-terminus<br>Within the SNARE proteins interactions in the C-terminal half of the SNARE helix are critical to the driving of membrane fusion; whereas interactions in the N-terminal half of the SNARE domain are important for promoting priming or docking of the vesicle Pfam:PF05008.. 
PF12353 Eukaryotic translation initiation factor 3 subunit G <br>This domain family is found in eukaryotes, and is approximately 130 amino acids in length. The family is found in association with Pfam:PF00076. This family is subunit G of the eukaryotic translation initiation factor 3. Subunit G is required for eIF3 integrity.. 
PF12354 Bacterial adhesion/invasion protein N terminal<br>This domain family is found in bacteria, and is approximately 60 amino acids in length. The family is found in association with Pfam:PF00560, Pfam:PF08191, Pfam:PF09479. There are two completely conserved residues (I and F) that may be functionally important. Internalin mediates bacterial adhesion and invasion of epithelial cells in the human intestine through specific interaction with its host cell receptor E-cadherin. This family is the N terminal of internalin, the cap domain of the protein. The cap domain is conserved between different internalin types. The cap domain does not interact with E cadherin, therefore its function is presumably structural: capping the hydrophobic core.. 
PF12355 Down syndrome cell adhesion molecule C terminal <br>This domain family is found in eukaryotes, and is approximately 120 amino acids in length. The family is found in association with Pfam:PF00047, Pfam:PF07679, Pfam:PF00041. The Down syndrome cell adhesion molecule (Dscam) belongs to a family of cell membrane molecules involved in the differentiation of the nervous system. This is the C terminal cytoplasmic tail region of Dscam.. 
PF12356 Protein of unknown function (DUF3643) <br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 217 and 4852 amino acids in length. There is a conserved TLA sequence motif.. 
PF12357 Phospholipase D C terminal <br>This domain family is found in eukaryotes, and is approximately 70 amino acids in length. The family is found in association with Pfam:PF00168, Pfam:PF00614. There is a conserved FPD sequence motif.  This family is the C terminal of phospholipase D. PLD is a major plant lipid-degrading enzyme which is involved in signal transduction.. 
PF12358 Protein of unknown function (DUF3644) <br>This domain family is found in bacteria, and is typically between 65 and 80 amino acids in length.. 
PF12359 Protein of unknown function (DUF3645) <br>This domain family is found in eukaryotes, and is approximately 40 amino acids in length. There is a conserved HPD sequence motif.. 
PF12360 Paired box protein 7 <br>This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with Pfam:PF00046, Pfam:PF00292.  Pax7 belongs to a family of genes that encode paired-box-containing transcription factors involved in the control of developmental processes. Pax7 has a distinct role in the specification of myogenic satellite cells.. 
PF12361 Duffy-antigen binding protein <br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 449 and 1061 amino acids in length. The family is found in association with Pfam:PF05424. There are two conserved sequence motifs: NKNGG and QKHDF. This family is part of the Duffy-antigen binding protein of Plasmodium spp. This protein is an antigen on these parasites which enable them to invade erythrocytes.. 
PF12362 DNA polymerase III gamma and tau subunits C terminal<br>This domain family is found in bacteria, and is approximately 120 amino acids in length. The family is found in association with Pfam:PF00004. The proteins in this family are frequently annotated as the gamma and tau subunits of DNA polymerase III, however there is little accompanying literature to back this up.. 
PF12363 Phage protein <br>This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 119 and 164 amino acids in length. The proteins in this family are frequently annotated as phage proteins, however there is little accompanying literature to back this up or to describe the nature of these phage proteins.. 
PF12364 Protein of unknown function (DUF3648) <br>This family of proteins is found in eukaryotes and viruses. Proteins in this family are typically between 53 and 3115 amino acids in length. There are two completely conserved residues (A and F) that may be functionally important.. 
PF12365 Protein of unknown function (DUF3649) <br>This domain family is found in bacteria and eukaryotes, and is approximately 30 amino acids in length.. 
PF12366 Cancer susceptibility candidate 1 <br>This domain family is found in eukaryotes, and is typically between 216 and 263 amino acids in length. Casc1 has many SNPs associated with cancer susceptibility.. 
PF12367 Pyruvate ferredoxin oxidoreductase beta subunit C terminal<br>This domain family is found in bacteria and archaea, and is approximately 70 amino acids in length. The family is found in association with Pfam:PF02775. There are two completely conserved residues (A and G) that may be functionally important. PFO is involved in carbon dioxide fixation via a reductive TCA cycle. It forms a heterodimer (alpha/beta). The beta subunit has binding motifs for Fe-S clusters and thiamine pyrophosphate.. 
PF12368 Protein of unknown function (DUF3650) <br>This domain family is found in bacteria, and is approximately 30 amino acids in length. The family is found in association with Pfam:PF00581. There is a single completely conserved residue N that may be functionally important.. 
PF12369 Gonadotropin hormone receptor transmembrane region <br>This domain family is found in eukaryotes, and is approximately 70 amino acids in length. The family is found in association with Pfam:PF00560, Pfam:PF00001. There are two completely conserved C residues that may be functionally important. This family contains the transmembrane region of Follicular stimulating hormone and leutenizing hormone - the two major gonadotropin hormone receptors. These receptors are G protein coupled receptors involved in development and maturation of germ cells in both fecund genders. The transmembrane region is conserved between the two different receptors while the extracellular ligand binding domains are less well conserved.. 
PF12371 Protein of unknown function (DUF3651)<br>This domain family is found in eukaryotes, and is approximately 70 amino acids in length. This family is frequently annotated as a membrane protein but there is little associated literature to back this up.. 
PF12372 Huntingtin protein region <br>This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with Pfam:PF02985. This family is in the middle region of the Huntingtin protein associated with Huntington's disease. The protein is of unknown function, however it is known that a polyglutamine (CAG) repeat in the gene coding for it results in the development of Huntington's disease.. 
PF12373 Major surface glycoprotein 2 C terminal<br>This domain family is found in eukaryotes, and is approximately 30 amino acids in length. The family is found in association with Pfam:PF02349. This family is the C terminal of major surface glycoprotein 2 of virulent bacteria. It is a virulence factor antigen.. 
PF12374 Double-sex mab3 related transcription factor 1<br>This domain family is found in eukaryotes, and is typically between 61 and 73 amino acids in length. The family is found in association with Pfam:PF00751. This family is a transcription factor involved in sex determination. The proteins in this family contain a zinc finger-like DNA-binding motif, DM domain.. 
PF12375 Phage protein<br>This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 112 and 194 amino acids in length.. 
PF12376 Protein of unknown function (DUF3654) <br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 193 and 612 amino acids in length.. 
PF12377 Duffy binding protein N terminal <br>This domain family is found in eukaryotes, and is approximately 70 amino acids in length. The family is found in association with Pfam:PF05424. This family contains the N terminus of the Duffy receptor binding domain.. 
PF12378 Trypsin-sensitive surface-exposed protein<br>This domain family is found in bacteria, and is typically between 67 and 79 amino acids in length. This family contains trypsin-sensitive surface-exposed proteins called cytadhesins. Cytadhesins are virulence factor proteins which mediate attachment of bacterial cells to host cells for invasion.. 
PF12379 Protein of unknown function (DUF3655) <br>This domain family is found in viruses, and is approximately 70 amino acids in length. The family is found in association with Pfam:PF08716, Pfam:PF01661, Pfam:PF05409, Pfam:PF06471, Pfam:PF08717, Pfam:PF06478, Pfam:PF09401, Pfam:PF06460, Pfam:PF08715, Pfam:PF08710.. 
PF12380 Gill-associated viral 3C-like peptidase<br>a positive-stranded RNA virus of prawns, that has been called yellow head virus protease and gill-associated virus 3C-like peptidase. The GAV cysteine protease is predicted to be the key enzyme in the processing of the GAV replicase polyprotein precursors, pp1a and pp1ab. This protease employs a Cys(2968)-His(2879) catalytic dyad.. 
PF12381 Tungro spherical virus-type peptidase<br>This is the protease for self-cleavage of the positive single-stranded polyproteins of a number of plant viral genomes. The protease activity of the polyprotein is at the C-terminal end, adjacent to the putative RNA polymerase.. 
PF12382 Retrotransposon peptidase<br>This is a small family of fungal retroviral aspartyl peptidases.. 
PF12383 Severe acute respiratory syndrome coronavirus 3b protein<br>This family of proteins is found in viruses. Proteins in this family are typically between 32 and 154 amino acids in length. This family contains the SARS coronavirus 3b protein which is predominantly localized in the nucleolus, and induces G0/G1 arrest and apoptosis in transfected cells.. 
PF12384 Ty3 transposon peptidase<br>Ty3 is a gypsy-type, retrovirus-like, element found in the budding yeast. The Ty3 aspartyl protease is required for processing of the viral polyprotein into its mature species.. 
PF12385 Papain-like cysteine protease AvrRpt2<br>This is a family of cysteine proteases, found in actinobacteria, protobacteria and firmicutes. Papain-like cysteine proteases play a crucial role in plant-pathogen/pest interactions. On entering the host they act on non-self substrates, thereby manipulating the host to evade proteolysis  . AvrRpt2 from Pseudomonas syringae pv. tomato DC3000 triggers resistance to P. syringae-2-dependent defence responses, including hypersensitive cell death, by cleaving the Arabidopsis RIN4 protein which is monitored by the cognate resistance protein RPS2  .. 
PF12386 Pseudomurein endo-isopeptidase Pei<br>This peptidase has the catalytic triad C-H-D at the C-terminal end, a triad similar to that in thiol proteases and animal transglutaminases. It catalyses the in vitro lysis of M. marburgensis cells under reducing conditions and exhibits characteristics of metal-activated peptidases.. 
PF12387 Pestivirus NS2 peptidase<br>The pestivirus NS2 peptidase is responsible for single cleavage between NS2 and NS3 of the bovine viral diarrhea virus polyprotein, a cleavage that is correlated with cytopathogenicity  . The peptidase is activated by its interaction with 'J-domain protein interacting with viral protein' - Jiv. [2, 1].. 
PF12388 Dual-action HEIGH metallo-peptidase<br>The catalytic triad for this family of proteases is HE-H-H, which in many members is in the sequence motif HEIGH.. 
PF12389 Camelysin metallo-endopeptidase<br>
PF12390 Selenocysteine synthase N terminal<br>This domain family is found in bacteria, and is approximately 40 amino acids in length. The family is found in association with Pfam:PF03841.  There is a single completely conserved residue P that may be functionally important. This family is the N terminal region of selenocysteine synthase which catalyses the conversion of seryl-tRNA(Sec) into selenocysteyl-tRNA(Sec).. 
PF12391 Protocatechuate 3,4-dioxygenase beta subunit N terminal<br>This domain family is found in bacteria, and is approximately 40 amino acids in length. The family is found in association with Pfam:PF00775.  There are two completely conserved residues (Y and R) that may be functionally important. This family is the N terminal region of the beta subunit of protocatechuate 3,4-dioxidase. This enzyme utilizes a mononuclear, non-heme Fe3+ centre to catalyse metabolic cellular reactions.. 
PF12392 Collagenase <br>This domain family is found in bacteria, archaea and eukaryotes, and is approximately 120 amino acids in length. The family is found in association with Pfam:PF01136.. 
PF12393 Dr family adhesin <br>This domain family is found in bacteria, and is approximately 20 amino acids in length. The family is found in association with Pfam:PF04619. This family is the Dr-family adhesin expressed by uropathogenic E. coli.. 
PF12394 Protein of unknown function (DUF3657) <br>This domain family is found in eukaryotes, and is approximately 60 amino acids in length. The family is found in association with Pfam:PF05057.. 
PF12395 Protein of unknown function <br>This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with Pfam:PF08874. There are two completely conserved residues (D and R) that may be functionally important.. 
PF12396 Protein of unknown function (DUF3659) <br>This domain family is found in bacteria and eukaryotes, and is approximately 70 amino acids in length.. 
PF12397 U3 small nucleolar RNA-associated protein 10 <br>This domain family is found in eukaryotes, and is approximately 120 amino acids in length. The family is found in association with Pfam:PF08146. This family is the protein associated with U3 snoRNA which is involved in the processing of pre-rRNA.. 
PF12398 Receptor serine/threonine kinase <br>This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with Pfam:PF00954, Pfam:PF01453, Pfam:PF00069, Pfam:PF08276. There is a conserved ELPL sequence motif.. 
PF12399 Branched-chain amino acid ATP-binding cassette transporter<br>This domain family is found in bacteria, archaea and eukaryotes, and is approximately 30 amino acids in length. The family is found in association with Pfam:PF00005. There is a conserved AYLG sequence motif. This family is the C terminal of an ATP dependent branched-chain amino acid transporter.. 
PF12400 Vaculolar membrane protein <br>This domain family is found in eukaryotes, and is typically between 123 and 138 amino acids in length.. 
PF12401 Protein of unknown function (DUF2662) <br>This domain family is found in bacteria, and is approximately 120 amino acids in length. The family is found in association with Pfam:PF00498.. 
PF12402 NocA-like zinc-finger protein 1<br>This domain family is found in eukaryotes, and is typically between 42 and 57 amino acids in length. There is a conserved GAY sequence motif.  There is a single completely conserved residue G that may be functionally important. Nlz1 self-associated via its C terminus, interacted with Nlz2, and bound to histone deacetylases.. 
PF12403 Paired-box protein 2 C terminal<br>This domain family is found in eukaryotes, and is approximately 110 amino acids in length. The family is found in association with Pfam:PF00292. This family is the C terminal of the paired-box protein 2 which is a transcription factor involved in embryonic development and organogenesis.. 
PF12404 Peptidase <br>This domain family is found in bacteria, and is approximately 80 amino acids in length. The family is found in association with Pfam:PF00883. There is a conserved WAF sequence motif.. 
PF12406 Surface protein <br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 131 and 312 amino acids in length.. 
PF12407 Homeobox protein <br>This domain family is found in eukaryotes, and is approximately 30 amino acids in length. The family is found in association with Pfam:PF00046. This family is a homeobox protein involved in differentiation of embryonic cells to form the abdominal region.. 
PF12408 Ribose-5-phosphate isomerase <br>This domain family is found in bacteria, and is approximately 50 amino acids in length. The family is found in association with Pfam:PF02502. There are two completely conserved residues (D and F) that may be functionally important.. 
PF12409 P_ATPase;<br>P5-type ATPase cation transporter. This domain family is found in eukaryotes, and is typically between 110 and 126 amino acids in length. The family is found in association with Pfam:PF00122, Pfam:PF00702. P-type ATPases comprise a large superfamily of proteins, present in both prokaryotes and eukaryotes, that transport inorganic cations and other substrates across cell membranes.. 
PF12410 Poxvirus DNA dependent RNA polymerase 30kDa subunit <br>This family of proteins is found in viruses. Proteins in this family are typically between 193 and 259 amino acids in length. The family is found in association with Pfam:PF01096. There are two conserved sequence motifs: GIEYSKD and LRY. This family is N terminal of the 30 kDa subunit of poxvirus DNA-d-RNA-pol. It has structural similarity to the eukaryotic transcriptional elongation factor SII.. 
PF12411 Choline sulfatase enzyme C terminal <br>This domain family is found in bacteria, eukaryotes and viruses, and is approximately 60 amino acids in length. The family is found in association with Pfam:PF00884. There are two completely conserved residues (R and W) that may be functionally important. This family is the C terminal of choline sulfatase, the enzyme responsible for catalysing the conversion of choline-O-sulfate and, at a lower rate, phosphorylcholine, into choline.. 
PF12412 Protein of unknown function (DUF3667)<br>This domain family is found in bacteria and eukaryotes, and is approximately 50 amino acids in length. There is a single completely conserved residue P that may be functionally important.. 
PF12413 Homeobox protein distal-less-like N terminal <br>This domain family is found in eukaryotes, and is approximately 80 amino acids in length. The family is found in association with Pfam:PF00046. This family is the N terminal of a homeobox protein involved in embryonic development and adult neural regeneration.. 
PF12414 Calcitonin gene-related peptide regulator C terminal<br>This domain family is found in eukaryotes, and is typically between 69 and 99 amino acids in length. The family is found in association with Pfam:PF00076. This family is the C terminal of Fox-1, a protein involved in the regulation of calcitonin gene-related peptide to mediate the neuron-specific splicing pattern. Fox-1, with Fox-2, functions to repress exon 4 inclusion.. 
PF12415 Poxvirus DNA dependent RNA polymerase<br>This domain family is found in viruses, and is approximately 30 amino acids in length. The family is found in association with Pfam:PF04566, Pfam:PF00562, Pfam:PF04567, Pfam:PF04560, Pfam:PF04565. This family is the second largest subunit of the poxvirus DNA dependent RNA polymerase. It has structural similarity to the second-largest RNA polymerase subunits of eubacteria, archaebacteria, and eukaryotes.. 
PF12416 Cep120 protein<br>This family includes the Cep120 protein which is associated with centriole structure and function  .. 
PF12417 Zinc finger protein <br>This domain family is found in eukaryotes, and is typically between 64 and 80 amino acids in length.. 
PF12418 Acyl-CoA dehydrogenase N terminal <br>This domain family is found in bacteria and eukaryotes, and is approximately 30 amino acids in length. The family is found in association with Pfam:PF02770, Pfam:PF00441, Pfam:PF02771. This family is one of the enzymes involved in AcylCoA interaction in beta-oxidation.. 
PF12419 SNF2 Helicase protein <br>This domain family is found in bacteria, archaea and eukaryotes, and is approximately 140 amino acids in length. The family is found in association with Pfam:PF00271, Pfam:PF00176. Most of the proteins in this family are annotated as SNF2 helicases but there is little accompanying literature to confirm this.. 
PF12420 Protein of unknown function <br>This domain family is found in eukaryotes, and is typically between 96 and 116 amino acids in length.. 
PF12421 Fibronectin type III protein <br>This domain family is found in bacteria and viruses, and is typically between 126 and 146 amino acids in length. The family is found in association with Pfam:PF09327, Pfam:PF00041. There are two completely conserved G residues that may be functionally important. Many of the proteins in this family are annotated as fibronectin type III however there is little accompanying literature to confirm this.. 
PF12422 Condensin II non structural maintenance of chromosomes subunit<br>This domain family is found in eukaryotes, and is approximately 150 amino acids in length. This family is part of a non-SMC subunit of condensin II which is involved in maintenance of the structural integrity of chromosomes. Condensin II is made up of SMC (structural maintenance of chromosomes) and non-SMC subunits. The non-SMC subunits bind to the catalytic ends of the SMC subunit dimer. The condensin holocomplex is able to introduce superhelical tension into DNA in an ATP hydrolysis- dependent manner, resulting in the formation of positive supercoils in the presence of topoisomerase I and of positive knots in the presence of topoisomerase II.. 
PF12423 Kinesin protein 1B<br>This domain family is found in eukaryotes, and is approximately 50 amino acids in length. The family is found in association with Pfam:PF00225, Pfam:PF00498. KIF1B is an anterograde motor for transport of mitochondria in axons of neuronal cells.. 
PF12424 Plasma membrane calcium transporter ATPase C terminal<br>This domain family is found in eukaryotes, and is approximately 60 amino acids in length. The family is found in association with Pfam:PF00689, Pfam:PF00122, Pfam:PF00702, Pfam:PF00690. There is a conserved QTQ sequence motif. This family is the C terminal of a calcium transporting ATPase located in the plasma membrane.. 
PF12425 Protein of unknown function (DUF3673) <br>This domain family is found in eukaryotes, and is approximately 50 amino acids in length.. 
PF12426 RNA dependent RNA polymerase<br>This domain family is found in viruses, and is approximately 40 amino acids in length. There is a conserved MFNLKF sequence motif. There are two completely conserved residues (E and P) that may be functionally important.. 
PF12427 Branched-chain amino acid aminotransferase <br>This domain family is found in bacteria, and is typically between 23 and 35 amino acids in length. The family is found in association with Pfam:PF01063. There is a conserved TRT sequence motif.. 
PF12428 Protein of unknown function (DUF3675) <br>This domain family is found in eukaryotes, and is approximately 120 amino acids in length. The family is found in association with Pfam:PF00097. There are two completely conserved residues (R and L) that may be functionally important.. 
PF12429 Protein of unknown function (DUF3676) <br>This domain family is found in eukaryotes, and is approximately 230 amino acids in length.. 
PF12430 Abscisic acid G-protein coupled receptor <br>This domain family is found in eukaryotes, and is typically between 177 and 216 amino acids in length. This family is part of the abscisic acid (ABA) G-protein coupled receptor. ABA is a stress hormone in plants.. 
PF12431 Transcriptional regulator <br>This domain family is found in bacteria, and is approximately 30 amino acids in length. The family is found in association with Pfam:PF00072.  There is a single completely conserved residue G that may be functionally important. CitT is a transcriptional regulator which allows transcription of the citM gene which codes for the secondary transporter in the Mg-citrate transport complex.. 
PF12432 Protein of unknown function (DUF3677) <br>This domain family is found in eukaryotes, and is approximately 80 amino acids in length.. 
PF12433 Parvovirus non-structural protein 1 <br>This family of proteins is found in viruses. Proteins in this family are typically between 109 and 668 amino acids in length. Parvoviral NSPs regulate host gene expression through histone acetylation.. 
PF12434 Malate dehydrogenase enzyme <br>This domain family is found in bacteria, and is approximately 30 amino acids in length. The family is found in association with Pfam:PF00390, Pfam:PF03949, Pfam:PF01515. There is a conserved AAL sequence motif.  There is a single completely conserved residue R that may be functionally important. Malate dehydrogenase is one of the enzymes involved in the citric acid cycle in mitochondria. It converts malate to oxaloacetate using NAD as a cofactor.. 
PF12435 Protein of unknown function (DUF3678) <br>This domain family is found in eukaryotes, and is approximately 40 amino acids in length.. 
PF12436 USP7;<br>ICP0-binding domain of Ubiquitin-specific protease 7. This domain is one of two C-terminal domains on the much longer ubiquitin-specific proteases. This particular one is found to interact with the herpesvirus 1 trans-acting transcriptional protein ICP0/VMW110.. 
PF12437 Glutamine synthetase type III N terminal <br>This domain family is found in bacteria and eukaryotes, and is approximately 160 amino acids in length. The family is found in association with Pfam:PF00120. This family is the N terminal region of glutamine synthetase type III which is one of the enzymes responsible for generation of glutamine through conversion glutamate to glutamine by the incorporation of ammonia (NH3).. 
PF12438 Protein of unknown function (DUF3679) <br>This domain family is found in bacteria, and is approximately 60 amino acids in length.. 
PF12439 Glycogen debranching enzyme N terminal<br>This domain family is found in bacteria and archaea, and is typically between 218 and 229 amino acids in length. The family is found in association with Pfam:PF06202. Glycogen debranching enzyme catalyses the debranching of amylopectin in glycogen. This is done by transferring three glucose subunits of glycogen from one parallel chain to another. This has the effect of enabling the glucose residues to become more accessible for glycolysis.. 
PF12440 Melanoma associated antigen family N terminal <br>This domain family is found in eukaryotes, and is typically between 82 and 96 amino acids in length. The family is found in association with Pfam:PF01454. This family is the N terminal of various melanoma associated antigens. These are tumour rejection antigens which are expressed on HLA-A1 of tumour cells and they are recognised by cytotoxic T lymphocytes (CTLs).. 
PF12441 Protein of unknown function (DUF3680) <br>This domain family is found in bacteria and archaea, and is approximately 40 amino acids in length.. 
PF12442 Protein of unknown function (DUF3681) <br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 112 and 212 amino acids in length. There is a single completely conserved residue G that may be functionally important.. 
PF12443 AT-hook-containing transcription factor<br>This domain family is found in eukaryotes, and is approximately 110 amino acids in length. This family contains a transcription factor which regulates the expression of the costimulatory molecules on lymphocytes.. 
PF12444 Sox developmental protein N terminal <br>This domain family is found in eukaryotes, and is typically between 69 and 88 amino acids in length. The family is found in association with Pfam:PF00505. There are two conserved sequence motifs: YDW and PVR. This family contains Sox8, Sox9 and Sox10 proteins which have structural similarity. Sox proteins are involved in developmental processes.. 
PF12445 Flagellin protein <br>This domain family is found in bacteria, and is typically between 125 and 147 amino acids in length. The family is found in association with Pfam:PF00669, Pfam:PF00700. There are two completely conserved G residues that may be functionally important. This family is the flagellin motor protein which confers motility to bacterial cells.. 
PF12446 Protein of unknown function (DUF3682)<br>This domain family is found in eukaryotes, and is typically between 125 and 136 amino acids in length.. 
PF12447 Protein of unknown function (DUF3683)<br>This domain family is found in bacteria, and is approximately 120 amino acids in length. The family is found in association with Pfam:PF02754, Pfam:PF01565, Pfam:PF02913.. 
PF12448 Kinesin associated protein<br>This domain family is found in eukaryotes, and is typically between 143 and 173 amino acids in length. The family is found in association with Pfam:PF04849. This family is a region of the protein milton. Milton recruits the heavy chain of kinesin to mitochondria to allow the motor movement function of kinesin.. 
PF12449 Protein of unknown function (DUF3684) <br>This domain family is found in eukaryotes, and is typically between 1072 and 1090 amino acids in length.. 
PF12450 von Willebrand factor <br>This domain family is found in bacteria, and is approximately 100 amino acids in length. The family is found in association with Pfam:PF00092. There are two conserved sequence motifs: STF and DVD.  There are two completely conserved residues (E and N) that may be functionally important. In hemostasis, platelet adhesion to the damaged vessel wall is mediated by several proteins, including von Willebrand factor. In solution vWF becomes immobilized via its A3 domain on the fibrillar collagen of the vessel wall and acts as an intermediary between collagen and the platelet receptor glycoprotein Ibalpha (GPIbalpha), which is the only platelet receptor that does not require prior activation for bond formation.. 
PF12451 Vacuolar protein sorting protein 11 C terminal<br>This domain family is found in eukaryotes, and is approximately 50 amino acids in length. Vps 11 is one of the evolutionarily conserved class C vacuolar protein sorting genes (c-vps: vps11, vps16, vps18, and vps33), whose products physically associate to form the c-vps protein complex required for vesicle docking and fusion.. 
PF12452 Protein of unknown function (DUF3685) <br>This domain family is found in bacteria and eukaryotes, and is approximately 190 amino acids in length. There are two completely conserved residues (L and D) that may be functionally important.. 
PF12453 Protein tyrosine phosphatase N terminal <br>This domain family is found in eukaryotes, and is approximately 30 amino acids in length. The family is found in association with Pfam:PF00041. There is a single completely conserved residue L that may be functionally important. This family consists of various protein tyrosine phosphatase haematopoietic receptors, e.g. CD45, which dephosphorylate growth stimulating proteins. This limits growth signalling in haematopoietic cells.. 
PF12454 GPI-anchored cell wall organization protein<br>This domain family is found in eukaryotes, and is approximately 40 amino acids in length. Ecm33 is an essential cell wall component and is important for cell wall integrity.. 
PF12455 Dynein associated protein <br>This domain family is found in eukaryotes, and is approximately 280 amino acids in length. The family is found in association with Pfam:PF01302. There is a single completely conserved residue E that may be functionally important. Dynactin has been associated with Dynein, a kinesin protein which is involved in organelle transport, mitotic spindle assembly and chromosome segregation. Dynactin anchors Dynein to specific subcellular structures.. 
PF12456 Inositol phosphatase <br>This domain family is found in eukaryotes, and is approximately 120 amino acids in length. The family is found in association with Pfam:PF02383. hSac2 functions as an inositol polyphosphate 5-phosphatase.. 
PF12457 Tuftelin interacting protein N terminal <br>This domain family is found in eukaryotes, and is typically between 99 and 114 amino acids in length. The family is found in association with Pfam:PF08697, Pfam:PF01585. There are two completely conserved residues (G and F) that may be functionally important. TIP is involved in enamel assembly by interacting with one of the major proteins responsible for biomineralisation of enamel - tuftelin.. 
PF12458 ATPase involved in DNA repair <br>This domain family is found in bacteria, and is approximately 450 amino acids in length. There are two conserved sequence motifs: DVF and SPNGED.. 
PF12459 D-Ala-teichoic acid biosynthesis protein<br>This family of proteins is found in bacteria. Proteins in this family are approximately 50 amino acids in length. There are two completely conserved residues (L and Y) that may be functionally important.. 
PF12460 MMS19_N;<br>RNAPII transcription regulator C-terminal. MMS19 is required for both nucleotide excision repair (NER) and RNA polymerase II (RNAP II) transcription  . This C-terminal domain, along with the N-terminal, MMS19_N, form part of a silencing complex in fission yeast that contains Dos2, Rik1, Mms19 and Cdc20 (the catalytic subunit of DNA polymerase-epsilon). This complex regulates RNA polymerase II (RNA Pol II) activity in heterochromatin and is required for DNA replication and heterochromatin assembly  . This domain apparently shares homology with some HEAT repeat sequences.. 
PF12461 Protein of unknown function (DUF3688) <br>This domain family is found in bacteria and viruses, and is typically between 79 and 104 amino acids in length. There is a conserved YRW sequence motif. There is a single completely conserved residue Y that may be functionally important.. 
PF12462 Nucleolin_N;<br>DNA helicase IV / RNA helicase N terminal. This domain family is found in bacteria, and is approximately 170 amino acids in length. This family is found in bacterial DNA helicase IV, at the N-terminus of Pfam:PF00580.. 
PF12463 Protein of unknown function (DUF3689) <br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 399 and 797 amino acids in length.. 
PF12464 Maltose acetyltransferase <br>This domain family is found in bacteria, archaea and eukaryotes, and is approximately 50 amino acids in length. The family is found in association with Pfam:PF00132. Mac uses acetyl-CoA as acetyl donor to acetylated cytoplasmic maltose.. 
PF12465 Proteasome beta subunits C terminal <br>This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with Pfam:PF00227. There is a conserved GTT sequence motif. There is a single completely conserved residue Y that may be functionally important. This family includes the C terminal of the beta-type subunits of the proteasome, a multimeric complex that degrades proteins into peptides as part of the MHC class I-mediated Ag-presenting pathway.. 
PF12466 Glutamate dehydrogenase N terminal<br>This domain family is found in bacteria, and is approximately 60 amino acids in length. The family is found in association with Pfam:PF05088.  There is a conserved ALR sequence motif. Glutamate dehydrogenase (GDH) is a homohexameric, mitochondrial enzyme that reversibly catalyses the oxidative deamination of L-glutamate to 2-oxoglutarate using either NADP(H) or NAD(H) with comparable efficacy.. 
PF12467 Cucumber mosaic virus 1a protein family<br>This domain family is found in viruses, and is typically between 156 and 171 amino acids in length. The family is found in association with Pfam:PF01443, Pfam:PF01660. 1a protein is the major virulence factor of the cucumber mosaic virus (CMV). The Ns strain of CMV causes necrotic lesions to Nicotiana spp. while other strains cause systemic mosaic. The determinant of the pathogenesis of these different strains is the specific amino acid residue at the 461 residue of the 1a protein.. 
PF12468 Type III secretion system leucine rich repeat protein  <br>This domain family is found in bacteria, and is approximately 50 amino acids in length. There are two completely conserved residues (Y and W) that may be functionally important. This family consists of leucine-rich repeat proteins involved in type III secretion.. 
PF12469 CRISPR-associated protein <br>This domain family is found in bacteria and archaea, and is typically between 101 and 138 amino acids in length. The proteins in this family are frequently annotated as CRISPR-associated proteins however there is little accompanying literature to confirm this.. 
PF12470 Suppressor of Fused Gli/Ci N terminal binding domain<br>This domain family is found in eukaryotes, and is typically between 192 and 219 amino acids in length. The family is found in association with Pfam:PF05076. There is a conserved HGRHFT sequence motif. This family is the C terminal domain of the Suppressor of Fused protein (Su(fu)). Su(fu) is a repressor of the Gli and Ci transcription factors of the Hedgehog signalling cascade. It functions by binding these proteins and preventing their translocation to the nucleus. The C terminal domain is only found in eukaryotic Su(fu) proteins; it is not present in bacterial homologues. The C terminal domain binds to the N terminal of Gli/Ci while the N terminal of Su(fu) binds to the C terminal of Gli/Ci. This dual binding mechanism is likely an evolutionary advancement in this signalling cascade which is not present in bacterial homologues.. 
PF12471 GTP cyclohydrolase N terminal <br>This domain family is found in bacteria and eukaryotes, and is approximately 190 amino acids in length. This family is the N terminal of GTP cyclohydrolase, the rate limiting enzyme in the synthesis of tetrahydrobiopterin.. 
PF12472 Phage related protein<br>This domain family is found in bacteria and viruses, and is approximately 60 amino acids in length.. 
PF12473 Kinesin protein <br>This domain family is found in eukaryotes, and is typically between 131 and 151 amino acids in length. The family is found in association with Pfam:PF00225, Pfam:PF00498. There is a single completely conserved residue W that may be functionally important.. 
PF12474 Polo kinase kinase <br>This domain family is found in eukaryotes, and is approximately 140 amino acids in length. The family is found in association with Pfam:PF00069. Polo-like kinase 1 (Plx1) is essential during mitosis for the activation of Cdc25C, for spindle assembly, and for cyclin B degradation. This family is Polo kinase kinase (PKK) which phosphorylates Polo kinase and Polo-like kinase to activate them. PKK is a serine/threonine kinase.. 
PF12475 Amdovirus non-structural protein <br>This domain family is found in viruses, and is approximately 50 amino acids in length. This family contains proteins of each of the four types of Amdovirus non-structural protein.. 
PF12476 Protein of unknown function (DUF3696)<br>This domain family is found in bacteria and archaea, and is approximately 50 amino acids in length.. 
PF12477 Sex factor F TraW protein N terminal<br>This domain family is found in bacteria, and is approximately 30 amino acids in length. There is a single completely conserved residue G that may be functionally important. The traW gene of the E. coli K-12 sex factor, F, encodes one of the numerous proteins required for conjugative transfer of this plasmid.. 
PF12478 Ubiquitin-associated protein 2 <br>This domain family is found in eukaryotes, and is approximately 30 amino acids in length. The family is found in association with Pfam:PF00627. There are two conserved sequence motifs: AVEMPG and QFG.. 
PF12479 Protein of unknown function (DUF3698) <br>This domain family is found in eukaryotes, and is typically between 89 and 105 amino acids in length.. 
PF12480 Protein of unknown function (DUF3699) <br>This domain family is found in eukaryotes, and is approximately 80 amino acids in length.. 
PF12481 Aluminium induced protein <br>This domain family is found in eukaryotes, and is approximately 120 amino acids in length. There are two conserved sequence motifs: YGL and LRDR. This family is related to GATase enzyme domains.. 
PF12482 Phage integrase protein<br>This domain family is found in bacteria, and is approximately 100 amino acids in length. The family is found in association with Pfam:PF00589.. 
PF12483 E3 Ubiquitin ligase<br>This domain family is found in bacteria, archaea and eukaryotes, and is typically between 150 and 163 amino acids in length. There is a single completely conserved residue E that may be functionally important. GIDE is an E3 ubiquitin ligase which is involved in inducing apoptosis.. 
PF12484 Polymorphic PE/PPE proteins C terminal<br>This domain family is found in bacteria, and is approximately 90 amino acids in length. The family is found in association with Pfam:PF00823.  There is a conserved SVP sequence motif. There is a single completely conserved residue W that may be functionally important. The proteins in this family are PE/PPE proteins implicated in immunostimulation and virulence.. 
PF12485 Lymphocyte signaling adaptor protein<br>This domain family is found in eukaryotes, and is typically between 144 and 156 amino acids in length. The family is found in association with Pfam:PF07647, Pfam:PF07653. There is a conserved LGKK sequence motif. SLY contains a Src homology 3 domain and a sterile alpha motif, suggesting that it functions as a signaling adaptor protein in lymphocytes.. 
PF12486 ImpA domain protein <br>This family of proteins is found in bacteria. Proteins in this family are typically between 207 and 469 amino acids in length. The family is found in association with Pfam:PF06812.. 
PF12487 Protein of unknown function (DUF3703) <br>This family of proteins is found in bacteria. Proteins in this family are typically between 113 and 135 amino acids in length.. 
PF12488 Protein of unknown function (DUF3704) <br>This domain family is found in eukaryotes, and is approximately 30 amino acids in length.. 
PF12489 Nuclear coactivator<br>This domain family is found in eukaryotes, and is typically between 127 and 138 amino acids in length. This family is ARA70, a nuclear coactivator which interacts with peroxisome proliferator-activated receptor gamma (PPARgamma) to regulate transcription and the addition of the PPARgamma ligand (prostaglandin J2) enhances this interaction.. 
PF12490 Breast carcinoma amplified sequence 3 <br>This domain family is found in eukaryotes, and is typically between 229 and 245 amino acids in length. The proteins in this family have been shown to be proto-oncogenes implicated in the development of breast cancer.. 
PF12491 Apolipoprotein B100 C terminal<br>This domain family is found in eukaryotes, and is approximately 60 amino acids in length. There are two conserved sequence motifs: QLS and LIDL. ApoB100 has an essential role in the assembly and secretion of triglyceride-rich lipoproteins and lipids transport.. 
PF12493 Protein of unknown function (DUF3709)<br>This domain family is found in bacteria, and is approximately 30 amino acids in length. There are two conserved sequence motifs: RCLMK and LIEL.. 
PF12494 Protein of unknown function (DUF3695) <br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 157 and 192 amino acids in length. There is a single completely conserved residue D that may be functionally important.. 
PF12495 Vegetative insecticide protein 3A N terminal <br>This family of proteins is found in bacteria. Proteins in this family are typically between 170 and 789 amino acids in length. The family is found in association with Pfam:PF02018. Vip3A represents a novel class of proteins insecticidal to lepidopteran insect larvae.. 
PF12496 Bcl2-/adenovirus E1B nineteen kDa-interacting protein 2<br>This domain family is found in eukaryotes, and is typically between 119 and 133 amino acids in length. There is a conserved HGGY sequence motif. This family is Bcl2-/adenovirus E1B nineteen kDa-interacting protein 2. It interacts with pro- and anti- apoptotic molecules in the cell.. 
PF12497 Estrogen receptor beta<br>This domain family is found in eukaryotes, and is approximately 110 amino acids in length. The family is found in association with Pfam:PF00104, Pfam:PF00105. There is a conserved IPS sequence motif.  There are two completely conserved residues (Y and W) that may be functionally important. ERbeta binds estrogens with an affinity similar to that of ERalpha, and activates expression of reporter genes containing estrogen response elements in an estrogen-dependent manner. ERbeta acts as a transcription factor once bound to its ligand and it can dimerise with ERalpha.. 
PF12498 Basic leucine-zipper C terminal<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 174 and 411 amino acids in length. The family is found in association with Pfam:PF00170. There is a conserved KVK sequence motif. There is a single completely conserved residue K that may be functionally important. Various bZIP proteins have been found and shown to play a role in seed-specific gene expression. bZIP binds to the alpha-globulin gene promoter, but not to promoters of other major storage genes such as glutelin, prolamin and albumin.. 
PF12499 Pherophorin <br>This domain family is found in eukaryotes, and is typically between 147 and 160 amino acids in length. The proteins in this family are frequently annotated as pherophorins however there is little accompanying literature to confirm this.. 
PF12500 DUF3706;<br>TRSP domain C terminus to PRTase_2 . Anantharaman V, Gavin OL. This domain occurs C terminus to PRTase_2 and has a highly conserved GXXE and TRSP signatures  . It is found in bacteria.  These genes are found in the biosynthetic operon associated with the Ter  stress response operon and are predicted to  be involved in the biosynthesis of a ribo- nucleoside involved in stress response  .. 
PF12501 Phosphate ATP-binding cassette transporter<br>This domain family is found in bacteria, and is typically between 143 and 173 amino acids in length. The family is found in association with Pfam:PF00528. There is a single completely conserved residue P that may be functionally important.. 
PF12502 Protein of unknown function (DUF3710) <br>This family of proteins is found in bacteria. Proteins in this family are typically between 237 and 284 amino acids in length. There are two conserved sequence motifs: DLG and DGPRW.. 
PF12503 Cucumber mosaic virus 1a protein C terminal <br>This domain family is found in viruses, and is approximately 90 amino acids in length. The family is found in association with Pfam:PF01443, Pfam:PF01660. There is a conserved GLG sequence motif. 1a protein is the major virulence factor of the cucumber mosaic virus (CMV). The Ns strain of CMV causes necrotic lesions to Nicotiana spp. while other strains cause systemic mosaic. The determinant of the pathogenesis of these different strains is the specific amino acid residue at the 461 residue of the 1a protein.. 
PF12505 Protein of unknown function (DUF3712)<br>This domain family is found in eukaryotes, and is approximately 130 amino acids in length.. 
PF12506 Protein of unknown function (DUF3713)<br>This family of proteins is found in bacteria. Proteins in this family are typically between 92 and 1225 amino acids in length. There is a single completely conserved residue S that may be functionally important.. 
PF12507 Human Cytomegalovirus UL139 protein<br>This family of proteins is found in eukaryotes and viruses. Proteins in this family are approximately 140 amino acids in length. UL139 product shared sequence homology with human CD24, a signal transducer modulating B-cell activation responses, and the sequences in the G1c variant of UL139 contained a specific attachment site of prokaryotic membrane lipoprotein lipid.. 
PF12508 Protein of unknown function (DUF3714) <br>This domain family is found in bacteria, and is approximately 200 amino acids in length.. 
PF12509 Protein of unknown function (DUF3715)<br>This domain family is found in eukaryotes, and is approximately 170 amino acids in length.. 
PF12510 Smoothelin cytoskeleton protein<br>This domain family is found in eukaryotes, and is approximately 50 amino acids in length. The family is found in association with Pfam:PF00307. Smoothelin is a cytoskeletal protein specifically expressed in differentiated smooth muscle cells and has been shown to co-localize with smooth muscle alpha actin.. 
PF12511 Protein of unknown function (DUF3716) <br>This domain family is found in eukaryotes, and is approximately 60 amino acids in length.. 
PF12512 Protein of unknown function (DUF3717) <br>This family of proteins is found in bacteria. Proteins in this family are typically between 75 and 117 amino acids in length. There is a conserved AIN sequence motif. There are two completely conserved residues (L and Y) that may be functionally important.. 
PF12513 Mitochondrial degradasome RNA helicase subunit C terminal<br>This domain family is found in bacteria and eukaryotes, and is approximately 50 amino acids in length. The family is found in association with Pfam:PF00271. The yeast mitochondrial degradosome (mtEXO) is an NTP-dependent exoribonuclease involved in mitochondrial RNA metabolism. mtEXO is made up of two subunits: an RNase (DSS1) and an RNA helicase (SUV3). These co-purify with mitochondrial ribosomes.. 
PF12514 Protein of unknown function (DUF3718)<br>This domain family is found in bacteria and viruses, and is approximately 70 amino acids in length. There is a single completely conserved residue C that may be functionally important. . 
PF12515 Ca2+-ATPase N terminal autoinhibitory domain<br>This domain family is found in eukaryotes, and is approximately 50 amino acids in length. The family is found in association with Pfam:PF00689, Pfam:PF00122, Pfam:PF00702, Pfam:PF00690. There is a conserved RRFR sequence motif. There are two completely conserved residues (F and W) that may be functionally important. This family is the N terminal autoinhibitory domain of an endosomal Ca2+-ATPase.. 
PF12516 Protein of unknown function (DUF3719)<br>This domain family is found in eukaryotes, and is approximately 70 amino acids in length. There is a conserved HLR sequence motif. There are two completely conserved residues (W and H) that may be functionally important.. 
PF12517 Protein of unknown function (DUF3720) <br>This domain family is found in eukaryotes, and is approximately 100 amino acids in length. There are two completely conserved A residues that may be functionally important.. 
PF12518 Protein of unknown function<br>This domain family is found in bacteria and eukaryotes, and is approximately 30 amino acids in length. There is a conserved WMPC sequence motif. There are two completely conserved residues (A and C) that may be functionally important.. 
PF12519 Protein of unknown function (DUF3722) <br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 415 and 473 amino acids in length.. 
PF12520 Protein of unknown function (DUF3723) <br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 374 and 1069 amino acids in length. There is a conserved LGF sequence motif.. 
PF12521 Protein of unknown function (DUF3724) <br>This domain family is found in viruses, and is approximately 20 amino acids in length. The family is found in association with Pfam:PF00073. There is a single completely conserved residue Y that may be functionally important.. 
PF12522 Cytomegalovirus glycoprotein N terminal<br>This domain family is found in viruses, and is approximately 30 amino acids in length. The family is found in association with Pfam:PF03554. This family is an envelope glycoprotein of human cytomegalovirus (HCMV).. 
PF12523 Protein of unknown function (DUF3725)<br>This domain family is found in viruses, and is approximately 70 amino acids in length. The family is found in association with Pfam:PF01577. There is a conserved FLE sequence motif.. 
PF12524 dsDNA virus glycoprotein L C terminal <br>This domain family is found in viruses, and is typically between 55 and 80 amino acids in length. The family is found in association with Pfam:PF05259. This family is the C terminal of glycoprotein L from various types of double stranded DNA viruses (dsDNA).. 
PF12525 Protein of unknown function (DUF3726) <br>This domain family is found in bacteria and eukaryotes, and is approximately 80 amino acids in length. There is a single completely conserved residue E that may be functionally important.. 
PF12526 Protein of unknown function (DUF3729) <br>This family of proteins is found in viruses. Proteins in this family are typically between 145 and 1707 amino acids in length. The family is found in association with Pfam:PF01443, Pfam:PF01661, Pfam:PF05417, Pfam:PF01660, Pfam:PF00978. There is a single completely conserved residue L that may be functionally important.. 
PF12527 Protein of unknown function (DUF3727) <br>This domain family is found in bacteria and eukaryotes, and is approximately 100 amino acids in length.. 
PF12528 Prepilin peptidase dependent protein C (DUF3728)<br>This family of proteins is found in bacteria. Proteins in this family are typically between 106 and 121 amino acids in length. The family is found in association with Pfam:PF07963. There are two completely conserved C residues that may be functionally important. This family is frequently annotated as prepilin peptidase dependent protein C.. 
PF12529 Xylosyltransferase C terminal <br>This domain family is found in eukaryotes, and is typically between 169 and 183 amino acids in length. The family is found in association with Pfam:PF02485. There is a single completely conserved residue G that may be functionally important. Xylosyltransferases are enzymes involved in the biosynthesis of the glycosaminoglycan linker region in proteoglycans.. 
PF12530 Protein of unknown function (DUF3730) <br>This domain family is found in eukaryotes, and is typically between 220 and 262 amino acids in length.. 
PF12531 DNA-K related protein <br>This domain family is found in bacteria, and is approximately 250 amino acids in length. There are two conserved sequence motifs: RPG and WRR. The proteins in this family are frequently annotated as DNA-K related proteins however there is little accompanying literature to confirm this.. 
PF12532 Protein of unknown function (DUF3732)<br>This domain family is found in bacteria and eukaryotes, and is typically between 180 and 198 amino acids in length. There is a conserved DQP sequence motif.. 
PF12533 Neuronal helix-loop-helix transcription factor <br>This domain family is found in eukaryotes, and is approximately 80 amino acids in length. The family is found C-terminal to Pfam:PF00010. There is a single completely conserved residue W that may be functionally important. Neuronal basic helix-loop-helix (bHLH) transcription factors such as neuroD and neurogenin have been shown to play important roles in neuronal development.. 
PF12534 Leucine-rich repeat containing protein 8 <br>This domain family is found in eukaryotes, and is approximately 60 amino acids in length. The family is found in association with Pfam:PF00560. There are two completely conserved residues (W and Y) that may be functionally important. Many of the proteins in this family are annotated as leucine-rich repeat containing protein 8 however there is little accompanying literature to back this up.. 
PF12535 Hydrolase of X-linked nucleoside diphosphate N terminal <br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 847 and 5344 amino acids in length. These enzymes hydrolyse the molecular motif of a nucleoside diphosphate linked to some other moiety, X.. 
PF12536 Patatin phospholipase <br>This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with Pfam:PF01734. There are two completely conserved residues (F and G) that may be functionally important. The proteins in this family are frequently annotated as patatin family phospholipases however there is little accompanying literature to confirm this.. 
PF12537 Protein of unknown function (DUF3735)<br>This domain family is found in eukaryotes, and is approximately 70 amino acids in length. There is a conserved LSG sequence motif. There is a single completely conserved residue G that may be functionally important.. 
PF12538 DNA transporter <br>This domain family is found in bacteria, and is typically between 107 and 121 amino acids in length. The family is found in association with Pfam:PF01580. The FtsK/SpoIIIE family of DNA transporters are responsible for translocating missegregated chromosomes after the completion of cell division.. 
PF12539 Chromosome segregation protein Csm1/Pcs1<br>Saccharomyces cerevisiae Csm1 is part of the monopolin complex. Csm1 forms a complex with Mde4 and promotes monoorientation during meiosis  .  Csm1 also plays a mitotic role in DNA replication  .  This family also contains the Schizosaccharomyces pombe homologue to Csm1, Pcs1.  Pcs1 forms a complex with Mde4 and acts in the central kinetochore domain to clamp microtubule binding sites together  .  The two complexes (Csm1/Lrs4 and Pcs1/Mde4) contribute to the prevention of merotelic attachment  .. 
PF12540 Protein of unknown function (DUF3736)<br>This domain family is found in eukaryotes, and is typically between 135 and 160 amino acids in length.. 
PF12541 Protein of unknown function (DUF3737) <br>This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 281 and 297 amino acids in length.. 
PF12542 Pre-mRNA splicing factor<br>This domain family is found in eukaryotes, and is approximately 100 amino acids in length. The family is found in association with Pfam:PF10197. There is a single completely conserved residue Y that may be functionally important. Cwc25 has been identified to associate with pre-mRNA splicing factor Cef1/Ntc85, a component of the Prp19-associated complex (NTC) involved in spliceosome activation. Cwc25 is neither tightly associated with NTC nor required for spliceosome activation, but is required for the first catalytic reaction.. 
PF12543 Protein of unknown function (DUF3738)<br>This family of proteins is found in bacteria. Proteins in this family are typically between 251 and 457 amino acids in length.. 
PF12544 Lysine-2,3-aminomutase <br>This domain family is found in bacteria, archaea and eukaryotes, and is typically between 111 and 127 amino acids in length. The family is found in association with Pfam:PF04055. LAM catalyses the interconversion of L-alpha-lysine and L-beta-lysine, which proceeds by migration of the amino group from C2 to C3 concomitant with cross-migration of the 3-pro-R hydrogen of L-alpha-lysine to the 2-pro-R position of L-beta-lysine.. 
PF12545 Filamentous haemagglutinin family outer membrane protein<br>This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with Pfam:PF05860.. 
PF12546 Blue/Ultraviolet sensing protein C terminal<br>This domain family is found in eukaryotes, and is typically between 113 and 125 amino acids in length. The family is found in association with Pfam:PF03441, Pfam:PF00875. Cryptochromes are blue/ultraviolet-A light sensing photoreceptors involved in regulating various growth and developmental responses in plants.. 
PF12547 Capicua transcriptional repressor modulator <br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 49 and 781 amino acids in length. There is a conserved IQT sequence motif. ATXN1 directly binds Capicua and modulates Capicua repressor activity in Drosophila and mammalian cells. The polyglutamine expanded mutant type of ATXN-1 does not bind Capicua with as high affinity as wild-type ATXN-1. It is associated with spinocerebellar ataxia type 1 (SCA1).. 
PF12548 Sulfatase protein<br>This domain family is found in eukaryotes, and is typically between 144 and 173 amino acids in length. The family is found in association with Pfam:PF00884.. 
PF12549 Tyrosine hydroxylase N terminal <br>This domain family is found in eukaryotes, and is approximately 30 amino acids in length. There is a single completely conserved residue G that may be functionally important. Tyrosine hydroxylase converts L-tyrosine to L-DOPA in the catecholamine synthesis pathway.. 
PF12550 Transcriptional activator of glycolytic enzymes<br>This domain family is found in eukaryotes, and is approximately 80 amino acids in length. This family is activates the transcription of glycolytic enzymes.. 
PF12551 Poly-beta-hydroxybutyrate polymerase N terminal<br>This domain family is found in bacteria and eukaryotes, and is approximately 50 amino acids in length. The family is found in association with Pfam:PF07167, Pfam:PF00561. There is a single completely conserved residue W that may be functionally important. PHBC is the third enzyme of the poly-beta-hydroxybutyrate biosynthetic pathway.. 
PF12552 Protein of unknown function (DUF3741)<br>This domain family is found in eukaryotes, and is approximately 50 amino acids in length.. 
PF12553 Protein of unknown function (DUF3742)<br>This domain family is found in bacteria, and is approximately 50 amino acids in length. There is a single completely conserved residue Y that may be functionally important.. 
PF12554 DUF3743;<br>Mitotic-spindle organizing gamma-tubulin ring associated. The name MOZART is derived from letters of 'mitotic-spindle organizing proteins associated with a ring of gamma-tubulin'. This family operates as part of the gamma-tubulin ring complex, gamma-TuRC, one of the complexes necessary for chromosome segregation. This complex is located at centrosomes and mediates the formation of bipolar spindles in mitosis; it consists of six subunits. However, unlike the other four known subunits, this family does not carry the conserved 'Spc97-Spc98' GCP domain, so the TUBCGP nomenclature cannot be used for it. MOZART1 is required for gamma-TuRC recruitment to centrosomes  .. 
PF12555 Thiamine pyrophosphokinase C terminal<br>This domain family is found in bacteria, and is approximately 50 amino acids in length. The proteins in this family catalyses the pyrophosphorylation of thiamine in yeast and synthesizes thiamine pyrophosphate (TPP), a thiamine coenzyme.. 
PF12556 Cobaltochelatase CobS subunit N terminal <br>This domain family is found in bacteria, and is approximately 40 amino acids in length. The family is found in association with Pfam:PF07728.  There are two completely conserved residues (P and F) that may be functionally important. This family is the N terminal of the CobS subunit of cobaltochelatase. Cobaltochelatase belongs to the AAA+ superfamily of proteins. CobS and CobT form a chaperone like complex.. 
PF12557 Cob(I)alamin adenosyltransferase N terminal <br>This domain family is found in bacteria and eukaryotes, and is approximately 20 amino acids in length. The family is found in association with Pfam:PF02572. Cob(I)alamin adenosyltransferase adenosylates Co(I) in an ATP-dependent manner in the conversion of aquacobalamin to its coenzyme form. This is the third step in this process, after two steps involved in the reduction of Co(III) to Co(I).. 
PF12558 ATP-binding cassette cobalt transporter<br>This domain family is found in bacteria, and is approximately 70 amino acids in length. The family is found in association with Pfam:PF00005.  There is a conserved REP sequence motif. There is a single completely conserved residue P that may be functionally important. The proteins in this family are frequently annotated as ABC Cobalt transporters however there is little accompanying literature to confirm this.. 
PF12559 Serine endopeptidase inhibitors<br>This family includes both microviridins and marinostatins. It seems likely that in both cases it is the C-terminus which becomes the active inhibitor after post-translational modifications of the full length, pre-peptide. it is the ester linkages within the key, 12-residue. region that circularise the molecule giving it its inhibitory conformation [1, 2, 3].. 
PF12560 Protein of unknown function (DUF3745)<br>This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with Pfam:PF00097, Pfam:PF10426.. 
PF12561 ToxR activated gene A lipoprotein<br>This domain family is found in bacteria, and is approximately 140 amino acids in length. The family is found in association with Pfam:PF10462. There is a conserved GAG sequence motif. This family is a bacterial lipoprotein.. 
PF12562 Protein of unknown function (DUF3746)<br>This domain family is found in viruses, and is approximately 40 amino acids in length. The family is found in association with Pfam:PF04595.. 
PF12563 Hemolytic toxin N terminal<br>This domain family is found in bacteria, and is approximately 190 amino acids in length. The family is found in association with Pfam:PF07968, Pfam:PF00652. This family is a bacterial virulence factor - hemolysin - which forms pores in erythrocytes and causes them to lyse.. 
PF12564 Type III restriction/modification enzyme methylation subunit<br>This domain family is found in bacteria, and is approximately 60 amino acids in length. The family is found in association with Pfam:PF01555.  There are two completely conserved residues (F and S) that may be functionally important. This family is a bacterial phage resistance protein. It functions in a type III restriction/modification enzyme complex. It is part of the methylation subunit of the complex. It binds DNA and methylates it.. 
PF12565 Protein of unknown function (DUF3747)<br>This family of proteins is found in bacteria. Proteins in this family are typically between 215 and 413 amino acids in length. There is a conserved DSNGYS sequence motif.. 
PF12566 Protein of unknown function (DUF3748)<br>This domain family is found in bacteria and eukaryotes, and is approximately 120 amino acids in length.. 
PF12567 Leukocyte receptor CD45<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 77 and 1130 amino acids in length. The family is found in association with Pfam:PF00041. CD45 plays a critical role in T-cell receptor (TCR)-mediated signaling. CD45 interacts with SKAP55 which is a transcriptional activator of IL-2.. 
PF12568 Acetyltransferase (GNAT) domain<br>This domain family is found in bacteria, and is approximately 40 amino acids in length. The proteins in this family are acetyltransferases of the GNAT family.. 
PF12569 NMDA receptor-regulated protein 1 <br>This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with Pfam:PF07719, Pfam:PF00515. There is a single completely conserved residue L that may be functionally important. NARP1 is the mammalian homologue of a yeast N-terminal acetyltransferase that regulates entry into the G(0) phase of the cell cycle.. 
PF12570 Protein of unknown function (DUF3750)<br>This family of proteins is found in bacteria. Proteins in this family are typically between 175 and 265 amino acids in length.. 
PF12571 Phage tail-collar fibre protein<br>This domain family is found in bacteria and viruses, and is approximately 160 amino acids in length. There are two completely conserved residues (K and W) that may be functionally important. The members are annotated as being putative phage tail or tail-collar proteins.. 
PF12572 Protein of unknown function (DUF3752)<br>This domain family is found in eukaryotes, and is typically between 140 and 163 amino acids in length.. 
PF12573 2-oxoisovalerate dehydrogenase E1 alpha subunit N terminal<br>This domain family is found in bacteria, and is approximately 40 amino acids in length. The family is found in association with Pfam:PF00676.  There are two conserved sequence motifs: VPEP and RPG. This family is the alpha subunit of the E1 component of 2-oxoisovalerate dehydrogenase. This is the enzyme complex responsible for metabolism of pyruvate, 2-oxoglutarate, branched chain 2-oxo acids and acetoin. The E1 component is a heterotetramer of alpha2beta2. The homodimerised beta subunits are flanked by two alpha subunits in a 'vise' structure.. 
PF12574 120 KDa Rickettsia surface antigen<br>This domain family is found in bacteria, and is approximately 40 amino acids in length. This family is a Rickettsia surface antigen of 120 KDa which may be used as an antigen for immune response against the bacterial species.. 
PF12575 Protein of unknown function (DUF3753)<br>This family of proteins is found in viruses. Proteins in this family are approximately 70 amino acids in length. There is a conserved YLK sequence motif. There are two completely conserved residues (D and F) that may be functionally important.. 
PF12576 Protein of unknown function (DUF3754)<br>This domain family is found in bacteria, archaea and eukaryotes, and is typically between 135 and 166 amino acids in length. There is a single completely conserved residue P that may be functionally important.. 
PF12577 PPAR gamma N-terminal region<br>Peroxisome proliferator-activated receptors (PPAR) are nuclear hormone receptors that control the expression of genes involved in lipid homeostasis in mammals.  This sequence region is found at the N-terminus of these proteins. The family is found in association with Pfam:PF00104, Pfam:PF00105. It is not clear if this region is a separate protein domain.. 
PF12578 Myotubularin-associated protein<br>This domain family is found in eukaryotes, and is typically between 115 and 138 amino acids in length. Myotubularin is a dual-specific phosphatase that dephosphorylates phosphatidylinositol 3-phosphate and phosphatidylinositol (3,5)-bisphosphate. 3-PAP is a catalytically inactive member of the myotubularin gene family, which coprecipitates lipid phosphatidylinositol 3-phosphate-3-phosphatase activity from lysates of human platelets.. 
PF12579 Protein of unknown function (DUF3755)<br>This domain family is found in eukaryotes, and is approximately 40 amino acids in length. There is a single completely conserved residue N that may be functionally important.. 
PF12580 Tripeptidyl peptidase II <br>This domain family is found in bacteria and eukaryotes, and is approximately 190 amino acids in length. The family is found in association with Pfam:PF00082. Tripeptidyl peptidase II (TPPII) is a crucial component of the proteolytic cascade acting downstream of the 26S proteasome in the ubiquitin-proteasome pathway. It is an amino peptidase belonging to the subtilase family removing tripeptides from the free N terminus of oligopeptides.. 
PF12581 Protein of unknown function (DUF3756)<br>This domain family is found in viruses, and is approximately 40 amino acids in length.. 
PF12582 Protein of unknown function (DUF3757)<br>This family of proteins is found in bacteria. Proteins in this family are typically between 94 and 154 amino acids in length.. 
PF12583 Tripeptidyl peptidase II N terminal<br>This domain family is found in bacteria and eukaryotes, and is approximately 190 amino acids in length. The family is found in association with Pfam:PF00082. Tripeptidyl peptidase II (TPPII) is a crucial component of the proteolytic cascade acting downstream of the 26S proteasome in the ubiquitin-proteasome pathway. It is an amino peptidase belonging to the subtilase family removing tripeptides from the free N terminus of oligopeptides.. 
PF12584 DUF3758;<br>Trafficking protein particle complex subunit 10, TRAPPC10. This domain forms part of the TRAPP complex for mediating vesicle docking and fusion in the Golgi apparatus. The fungal version is referred to as Trs130, and an alternative vertebrate alias is TMEM1 [1,2].. 
PF12585 Protein of unknown function (DUF3759)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 107 and 132 amino acids in length. There is a single completely conserved residue H that may be functionally important.. 
PF12586 Protein of unknown function (DUF3760)<br>This domain family is found in eukaryotes, and is typically between 46 and 64 amino acids in length.. 
PF12587 Protein of unknown function (DUF3761)<br>This family of proteins is found in bacteria. Proteins in this family are typically between 100 and 157 amino acids in length.. 
PF12588 Phophatidylserine decarboxylase <br>This domain family is found in bacteria and eukaryotes, and is approximately 140 amino acids in length. The family is found in association with Pfam:PF02666. Phosphatidylserine decarboxylase (PSD) is an important enzyme in the synthesis of phosphatidylethanolamine in both prokaryotes and eukaryotes.. 
PF12589 Methyltransferase involved in Williams-Beuren syndrome<br>This domain family is found in eukaryotes, and is typically between 72 and 83 amino acids in length. The family is found in association with Pfam:PF08241. This family is made up of S-adenosylmethionine-dependent methyltransferases  . The proteins are deleted in Williams-Beuren syndrome (WBS), a complex developmental disorder with multisystemic manifestations including supravalvular aortic stenosis (SVAS) and a specific cognitive phenotype  .. 
PF12590 Acyl-ATP thioesterase<br>This domain family is found in bacteria and eukaryotes, and is typically between 120 and 131 amino acids in length. The family is found in association with Pfam:PF01643. The plant acyl-acyl carrier protein (ACP) thioesterases (TEs) have roles in fatty acid synthesis.. 
PF12591 Protein of unknown function (DUF3762)<br>This domain family is found in viruses, and is approximately 80 amino acids in length. The family is found in association with Pfam:PF05533.. 
PF12592 Protein of unknown function (DUF3763)<br>This domain family is found in bacteria, and is approximately 60 amino acids in length. The family is found in association with Pfam:PF07728. There is a single completely conserved residue F that may be functionally important.. 
PF12593 Microcystin synthetase C terminal<br>This domain family is found in bacteria, and is approximately 40 amino acids in length. The family is found in association with Pfam:PF08242, Pfam:PF00501. There is a conserved YAN sequence motif. Microcystins form a large family of small cyclic heptapeptides harbouring extensive modifications in amino acid residue composition and functional group chemistry. These peptide hepatotoxins contain a range of non-proteinogenic amino acids and unusual peptide bonds, and are typically N-methylated. They are synthesized on large enzyme complexes consisting of non-ribosomal peptide synthetases and polyketide synthases. This family is made up of the C terminal of microcystin synthetase, one of the proteins involved in this synthesis pathway.. 
PF12594 Protein of unknown function (DUF3764)<br>This family of proteins is found in bacteria. Proteins in this family are typically between 89 and 101 amino acids in length.. 
PF12595 Rhomboid serine protease<br>This domain family is found in eukaryotes, and is approximately 210 amino acids in length. The family is found in association with Pfam:PF01694. Rhomboid is a seven-transmembrane spanning protein that resides in the Golgi and acts as a serine protease to cleave Spitz.. 
PF12596 87kDa_TransP;<br>This domain family is found in eukaryotes, and is typically between 78 and 110 amino acids in length. The family is found in association with Pfam:PF05485. There are two completely conserved residues (D and G) that may be functionally important. This family is an 87kDa transposase protein which catalyses both the precise and imprecise excision of a nonautonomous P transposable element.. 
PF12597 Protein of unknown function (DUF3767)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 112 and 199 amino acids in length.. 
PF12598 T-box transcription factor<br>This domain family is found in eukaryotes, and is typically between 77 and 89 amino acids in length. The family is found in association with Pfam:PF00907. There are two completely conserved residues (S and P) that may be functionally important. T-box genes encode transcription factors involved in morphogenesis and organogenesis of vertebrates and invertebrates. 
PF12599 Protein of unknown function (DUF3768)<br>This family of proteins is found in bacteria. Proteins in this family are typically between 108 and 129 amino acids in length. There are two conserved sequence motifs: NDP and RVLT.. 
PF12600 Protein of unknown function (DUF3769)<br>This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 560 and 931 amino acids in length.. 
PF12601 Rubivirus non-structural protein<br>This domain family is found in viruses, and is approximately 70 amino acids in length. The family is found in association with Pfam:PF05407. The rubella virus (RUB) nonstructural (NS) protein (NSP) ORF encodes a protease that cleaves the NSP precursor (240 kDa) at a single site to produce two products.. 
PF12602 Fertility inhibition protein N terminal<br>This domain family is found in bacteria, and is typically between 62 and 102 amino acids in length. The family is found in association with Pfam:PF04352. The FinOP (fertility inhibition) system of F-like plasmids consists of an antisense RNA (FinP) and a 22 kDa protein (FinO) which act in concert to prevent the translation of TraJ, the positive regulator of the transfer operon.. 
PF12603 Protein of unknown function (DUF3770)<br>This domain family is found in viruses, and is approximately 250 amino acids in length. The family is found in association with Pfam:PF04196.. 
PF12604 Tail fiber protein gp37 C terminal<br>This domain family is found in bacteria and viruses, and is typically between 49 and 166 amino acids in length. The family is found in association with Pfam:PF03906. In T-even phages, gp37 and gp38 are components of the tail fiber that are critical for phage-host interaction.. 
PF12605 Casein kinase 1 gamma C terminal<br>This domain family is found in eukaryotes, and is typically between 54 and 99 amino acids in length. The family is found in association with Pfam:PF00069. CK1gamma is a membrane-bound member of the CK1 family. Gain-of-function and loss-of-function experiments show that CK1gamma is both necessary and sufficient to transduce LRP6 signalling in vertebrates and Drosophila cells.. 
PF12606 Tumour necrosis factor receptor superfamily member 19<br>This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 49 and 288 amino acids in length.  There are two completely conserved residues (K and Y) that may be functionally important. The members of tumor necrosis factor receptor (TNFR) superfamily have been designated as the "guardians of the immune system" due to their roles in immune cell proliferation, differentiation, activation, and death (apoptosis). The messenger RNA of RELT is especially abundant in hematologic tissues such as spleen, lymph node, and peripheral blood leukocytes as well as in leukemias and lymphomas. RELT is able to activate the NF-kappaB pathway and selectively binds tumor necrosis factor receptor-associated factor 1.. 
PF12607 Protein of unknown function (DUF3772)<br>This domain family is found in bacteria, and is approximately 60 amino acids in length. The family is found in association with Pfam:PF00924.. 
PF12608 Protein of unknown function (DUF3773)<br>This family of proteins is found in bacteria and eukaryotes. Proteins in this family are approximately 110 amino acids in length.. 
PF12609 Wound-induced protein<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 81 and 97 amino acids in length. The proteins in the family are often annotated as wound-induced proteins however there is little accompanying literature to confirm this.. 
PF12610 Suppressor of cytokine signalling<br>This domain family is found in bacteria and eukaryotes, and is approximately 60 amino acids in length. The family is found in association with Pfam:PF07525, Pfam:PF00017. The suppressors of cytokine signaling (SOCS) family play important roles in regulating a variety of signal transduction pathways that are involved in immunity, growth and development of organisms.. 
PF12611 Protein of unknown function (DUF3766)<br>This domain family is found in bacteria, and is approximately 20 amino acids in length. There is a conserved FTNID sequence motif. There is a single completely conserved residue T that may be functionally important.. 
PF12612 Tubulin folding cofactor D C terminal<br>This domain family is found in eukaryotes, and is typically between 182 and 199 amino acids in length. The family is found in association with Pfam:PF02985. There is a single completely conserved residue R that may be functionally important. Tubulin folding cofactor D does not co-polymerise with microtubules either in vivo or in vitro, but instead modulates microtubule dynamics by sequestering beta-tubulin from GTP-bound alphabeta-heterodimers in microtubules.. 
PF12613 Flagellin structural protein<br>This domain family is found in bacteria, and is approximately 60 amino acids in length. The family is found in association with Pfam:PF00669, Pfam:PF00700. This family is the bacterial flagellin structural protein. It is involved with cell motility.. 
PF12614 Ribosome recycling factor <br>This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 130 amino acids in length. There are two conserved sequence motifs: LPS and LKR. Overproduction of ribosome recycling factor (RRF) reduces tna operon expression and increases the rate of cleavage of TnaC-tRNA(2)(Pro), relieving the growth inhibition associated with plasmid-mediated tnaC overexpression.. 
PF12615 F sex factor protein N terminal<br>This domain family is found in bacteria, and is typically between 96 and 107 amino acids in length. The family is found in association with Pfam:PF10412. TraD is a cytoplasmic membrane protein with possible DNA binding domains. It is part of the bacterial F sex factor complex.. 
PF12616 Protein of unknown function (DUF3775)<br>This domain family is found in bacteria, and is approximately 80 amino acids in length. There is a single completely conserved residue G that may be functionally important.. 
PF12617 Iron-Sulfur binding protein C terminal<br>This domain family is found in bacteria and eukaryotes, and is typically between 179 and 201 amino acids in length. The family is found in association with Pfam:PF00037. LdpA (light-dependent period) plays a role in controlling the redox state in cyanobacteria to modulate its. circadian clock. LdpA is a protein with Iron-Sulfur cluster-binding motifs.. 
PF12618 Protein of unknown function (DUF3776)<br>This domain family is found in eukaryotes, and is approximately 100 amino acids in length.. 
PF12619 Mini-chromosome maintenance protein 2<br>This domain family is found in eukaryotes, and is typically between 138 and 153 amino acids in length. The family is found in association with Pfam:PF00493. Mini-chromosome maintenance (MCM) proteins are essential for DNA replication. These proteins use ATPase activity to perform this function.. 
PF12620 Protein of unknown function (DUF3778)<br>This domain family is found in eukaryotes, and is typically between 48 and 61 amino acids in length. There is a conserved LRF sequence motif.. 
PF12621 Phosphate metabolism protein <br>This domain family is found in eukaryotes, and is approximately 100 amino acids in length. The family is found in association with Pfam:PF02714. There are two completely conserved residues (W and D) that may be functionally important. This family is likely to be involved in phosphate metabolism however there is little accompanying literature to confirm this.. 
PF12622 mRNA biogenesis factor<br>The full-length Wbp11 proteins carry several copies of a PPGPPP motif throughout their length. This motif is thought to be necessary for folding of the molecule as it helps to bind the WW domain, Wbp11, Pfam:PF09429  . This domain together with Wbp11 may function as components of an mRNA factory in the nucleus.. 
PF12623 RNA repair, ligase-Pnkp-associating, region of Hen1<br>This domain is the N-terminal region of the bacterial Hen1 protein.  This protein forms stable hetero-tetramer with Pnkp. The hetero-tetramer was able to repair transfer RNAs cleaved by ribotoxins in vitro  . This domain provides the ligase activity of the hetero-tetramer.. 
PF12624 N-terminal region of Chorein, a TM vesicle-mediated sorter<br>Pfam-B_PB000002 (release 24.0). Although mutations in the full-length vacuolar protein sorting 13A (VPS13A) protein in vertebrates lead to the disease of chorea-acanthocytosis, the exact function of any of the regions within the protein is not yet known. This region is the proposed leucine zipper at the N-terminus. The full-length protein is a transmembrane protein with a presumed role in vesicle-mediated sorting and intracellular protein transport.. 
PF12625 Arabinose-binding domain of AraC transcription regulator, N-term<br>Pfam-B_PB000001 (release 24.0). AraC is a bacterial transcriptional regulatory protein with a DNA-binding domain at the C-terminus, HTH_AraC, Pfam:PF00165, and this dimerisation domain which harbours the arabinose-binding pocket at the N-terminus. AraC positively and negatively regulates expression of the proteins required for the uptake and catabolism of the sugar L-arabinose 1,2,3].. 
PF12626 Polymerase A arginine-rich C-terminus<br>Pfam-B_105 (release 24.0). The C-terminus of polymerase A in E coli is arginine-rich and is necessary for full functioning of the enzyme.. 
PF12627 Probable RNA and SrmB- binding site of polymerase A<br>Pfam-B_105 (release 24.0). This region encompasses much of the RNA and SrmB binding motifs on polymerase A.. 
PF12628 Falstatin, cysteine peptidase inhibitor<br>This family of peptidase inhibitors is expressed from plasmodial protozoal species. Falstatin is found to be a potent reversible inhibitor of the P. falciparum cysteine proteases falcipain-2 and falcipain-3, as well as other parasite- and non-parasite-derived cysteine proteases, but is only a relatively weak inhibitor of the P. falciparum cysteine proteases falcipain-1 and dipeptidyl aminopeptidase 1. Thus, P. falciparum requires expression of falstatin to limit proteolysis by certain host or parasite cysteine proteases during erythrocyte invasion.. 
PF12629 Poxvirus poly(A) polymerase C-terminal domain<br>This domain is found at the C-terminus of the pox virus PolyA polymerase protein  .. 
PF12630 Poxvirus poly(A) polymerase N-terminal domain<br>This domain is found at the N-terminus of the pox virus Poly(A) polymerase protein  . According to SCOP this domain contains a helix-hairpin-helix motif.. 
PF12631 Catalytic cysteine-containing C-terminus of GTPase, MnmE<br>Pfam-B_102 (release 24.0). This short C-terminal region contains the only cysteine present in these proteins. It is proposed that MnmE is a tRNA-modifying enzyme and that Cys-451 functions as a catalytic residue in the modification reaction.. 
PF12632 Mysoin-binding motif of peroxisomes<br>Vezatin is a peroxisome transmembrane receptor that is involved in membrane-membrane and cell-cell adhesions. In the movement of peroxisomes it binds to class V   and class VIIa   myosins to guide the organelle through the microtubules   and allow pathogens to internalise themselves into host cells  . Vezatin is crucial for spermatozoan production  . In mouse cells it interacts with the cadherin-catenin complex bridging it to the C-terminal FERM domain of myosin VIIA  .. 
PF12633 Adenylate cyclase NT domain<br>
PF12634 Inheritance of peroxisomes protein 1<br>Inp1 is a family of peripheral membrane proteins of peroxisomes. Inp1p binds Pex25p, Pex30p, and Vps1p, all of which are involved in controlling peroxisome division. The levels of Inp1p vary with the cell cycle, and Inp1 acts as a factor that retains peroxisomes in cells and controls peroxisome division  . Inp1p promotes the retention of peroxisomes in mother cells and buds of budding yeast by attaching peroxisomes to as-yet-unidentified cortical structures  .. 
PF12635 Protein of unknown function (DUF3780)<br>This family of proteins is functionally uncharacterised.This family of proteins is found in bacteria. Proteins in this family are typically between 189 and 206 amino acids in length. There are two conserved sequence motifs: PEERWWL and GWR. This family is found in a very sporadic set of bacterial species, suggesting that it may have been horizontally transferred. One protein is annotated as plasmid borne.. 
PF12636 Protein of unknown function (DUF3781)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 82 and 98 amino acids in length. There are two conserved sequence motifs: GKNWY and ITA.. 
PF12637 TSCPD domain<br>This family of proteins is found in bacteria, archaea and viruses.  The domain is found in isolation in many proteins where it has a conserved C-terminal motif TSCPD after which the domain is named.  Most copies of the domain possess 4 conserved cysteines that may be part of an Iron-sulfur cluster. This domain is found at the C-terminus of some ribonucleoside-diphosphate reductase enzymes.. 
PF12638 Staygreen protein<br>This family of proteins have been implicated in chlorophyll degradation [1,2]. Intriguingly members of this family are also found in non-photosynthetic bacteria.. 
PF12639 Colicin-DNAse;<br>DNase/tRNase domain of colicin-like bacteriocin. Colicin-like bacteriocins are complex structures with an N-terminal beta-barrel translocation domain (Pfam:PF09000), a long double-alpha-helical receptor-binding domain (Pfam:PF11570) and this C-terminal RNAse/DNase domain with endonuclease activity. Their competitor bacteriocidal action is by a process that involves binding to a surface receptor, entering the cell, and, finally, killing it. The lethal action of colicin E3 is a specific cleavage in the ribosomal decoding A site. The crystal structure of colicin E3 reveals a Y-shaped molecule with the receptor binding domain forming a 100 Angstrom long stalk and the two globular heads of the translocation domain and this catalytic domain comprising the two arms  .. 
PF12640 UPF0489 domain<br>This family is probably an enzyme which is related to the Arginase family.. 
PF12641 Flavodoxin domain<br>This family represents a flavodoxin domain.. 
PF12642 Conjugative transposon protein TcpC<br>This family of proteins are annotated as conjugative transposon protein TcpC. The transfer clostridial plasmid (tcp) locus is part of some conjugative antibiotic resistance and virulence plasmids. TcpC was one of five genes whose products had low-level sequence identity to Tn916 proteins, having similarity to ORF13 homologues from Tn916, Tn5397, and CW459tet  .\.  This family of proteins is found in bacteria. Proteins in this family are typically between 302 and 351 amino acids in length.. 
PF12643 MazG-like family<br>This family of short proteins are distantly related to the MazG enzyme. This suggests that these proteins are enzymes that catalyse a related reaction.. 
PF12644 Protein of unknown function (DUF3782)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 91 and 186 amino acids in length.. 
PF12645 Helix-turn-helix domain<br>This domain appears to be a helix-turn-helix domain suggesting that this might be a transcriptional regulatory protein. Some members of this family are annotated as conjugative transposon domains.. 
PF12646 Domain of unknown function (DUF3783)<br>This presumed domain is functionally uncharacterised. This domain family is found in bacteria, archaea and eukaryotes, and is approximately 60 amino acids in length.. 
PF12647 RNHCP domain<br>This family of proteins is found in bacteria. Proteins in this family are typically between 94 and 143 amino acids in length. There is a conserved RNHCP sequence motif.. 
PF12648 TcpE family<br>This family of proteins includes TcpE a conjugative transposon membrane protein.This family of proteins is found in bacteria. Proteins in this family are typically between 122 and 168 amino acids in length.. 
PF12650 Domain of unknown function (DUF3784)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 96 and 110 amino acids in length.. 
PF12651 Ribbon-helix-helix domain<br>This short bacterial protein contains a ribbon-helix-helix domain that is likely to be DNA-binding.. 
PF12652 CotJB protein<br>CotJ is a sigma E-controlled operon involved in the spore coat of Bacillus subtilis  . This protein has been identified as a spore coat protein  .. 
PF12653 Protein of unknown function (DUF3785)<br>
PF12654 Domain of unknown function (DUF3786)<br>Pfam-B_16102 (release 23.0) . This presumed domain is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 201 and 257 amino acids in length. Some proteins also contains an iron-sulfur cluster.. 
PF12655 Domain of unknown function (DUF3787)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in Clostridia. Proteins in this family are approximately 60 amino acids in length. There is a conserved TAAW sequence motif that may be functionally important.. 
PF12656 DExH-box splicing factor binding site<br>Pfam-B_900 (release 24.0). Yeast Spp2, a G-patch protein and spliceosome component, interacts with the ATP-dependent DExH-box splicing factor Prp2  . As this interaction involves the G-patch sequence in Spp2 and is required for the recruitment of Prp2 to the spliceosome before the first catalytic step of splicing, it is proposed that Spp2 might be an accessory factor that confers spliceosome specificity on Prp2  .. 
PF12657 Transcription factor IIIC subunit delta N-term<br>In humans there are six subunits of transcription factor IIIC, and this one is the 90 kDa subunit; whereas in fungi the complex resolves into nine different subunits and this is No. 9 in yeasts  . The whole subunit is involved in RNA polymerase III-mediated transcription. It is possible that this N-terminal domain interacts with TFIIIC subunit 8  .. 
PF12658 Telomere capping, CST complex subunit<br>Stn1 and Ten1 are DNA-binding proteins with specificity for telomeric DNA substrates and both protect chromosome termini from unregulated resection and regulate telomere length. Stn1 complexes with Ten1 and Cdc13 to function as a telomere-specific replication protein A (RPA)-like complex  . These three interacting proteins associate with the telomeric overhang in budding yeast, whereas a single protein known as Pot1 (protection of telomeres-1) performs this function in fission yeast, and a two-subunit complex consisting of POT1 and TPP1 associates with telomeric ssDNA in humans. S.pombe has Stn1- and Ten1-like proteins that are essential for chromosome end protection. Stn1 orthologues exist in all species that have Pot1, whereas Ten1-like proteins can be found in all fungi. Fission yeast Stn1 and Ten1 localise at telomeres in a manner that correlates with the length of the ssDNA overhang, suggesting that they specifically associate with the telomeric ssDNA. Two separate protein complexes are required for chromosome end protection in fission yeast.  Protection of telomeres by multiple proteins with OB-fold domains is conserved in eukaryotic evolution  . Ten1 is one of the three components of the CST complex, which, in conjunction with the Shelterin complex helps protect telomeres from attack by DNA-repair mechanisms  .. 
PF12659 Telomere capping C-terminal wHTH<br>This domain consists of tandem winged helix-turn-helix motifs. Stn1 and Ten1 are DNA-binding proteins with specificity for telomeric DNA substrates and both protect chromosome termini from unregulated resection and regulate telomere length. Stn1 complexes with Ten1 and Cdc13 to function as a telomere-specific replication protein A (RPA)-like complex  . These three interacting proteins associate with the telomeric overhang in budding yeast, whereas a single protein known as Pot1 (protection of telomeres-1) performs this function in fission yeast, and a two-subunit complex consisting of POT1 and TPP1 associates with telomeric ssDNA in humans. S.pombe has Stn1- and Ten1-like proteins that are essential for chromosome end protection. Stn1 orthologues exist in all species that have Pot1, whereas Ten1-like proteins can be found in all fungi. Fission yeast Stn1 and Ten1 localise at telomeres in a manner that correlates with the length of the ssDNA overhang, suggesting that they specifically associate with the telomeric ssDNA. Two separate protein complexes are required for chromosome end protection in fission yeast. Protection of telomeres by multiple proteins with OB-fold domains is conserved in eukaryotic evolution  .. 
PF12660 Putative zinc-finger of transcription factor IIIC complex<br>This zinc-finger domain is at the very C-terminus of a number of different TFIIIC subunit proteins. This domain might be involved in protein-DNA and/or protein-protein interactions  .. 
PF12661 Human growth factor-like EGF<br>Wouters M, Coggill P. hEGF, or human growth factor-like EGF, domains have six conserved residues disulfide-bonded into the characteristic 'ababcc' pattern. They are involved in growth and proliferation of cells, in proteins of the Notch/Delta pathway, neurogulin and selectins. hEGFs are also found in mosaic proteins with four-disulfide laminin EGFs such as aggrecan and perlecan.  The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal Cys residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In hEGFs the C-terminal thiol resides in the beta-turn, resulting in shorter loop-lengths between the Cys residues of disulfide 'c', typically C[8-9]XC.  These shorter loop-lengths are also typical of the four-disulfide EGF domains, laminin ad integrin.  Tandem hEGF domains have six linking residues between terminal cysteines of adjacent domains. hEGF domains may or may not bind calcium in the linker region. hEGF domains with the consensus motif CXD4X[F,Y]XCXC are hydroxylated exclusively in the Asp residue.. 
PF12662 Complement Clr-like EGF-like<br>Wouters M, Coggill P. cEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteristic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL receptor. The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal cysteine residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In cEGFs the C-terminal thiol resides on the C-terminal beta-sheet, resulting in long loop-lengths between the cysteine residues of disulfide 'c', typically C[10+]XC. These longer loop-lengths may have arisen by selective cysteine loss from a four-disulfide EGF template such as laminin or integrin.  Tandem cEGF domains have five linking residues between terminal cysteines of adjacent domains. cEGF domains may or may not bind calcium in the linker region. cEGF domains with the consensus motif CXN4X[F,Y]XCXC are hydroxylated exclusively on the asparagine residue.. 
PF12663 Protein of unknown function (DUF3788)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 137 and 149 amino acids in length. This family may be distantly related to RelE proteins.. 
PF12664 Protein of unknown function (DUF3789)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length. There are two completely conserved residues (V and C) that may be functionally important.. 
PF12666 PrgI family protein<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 116 and 146 amino acids in length. This protein is found in an operon that is part of a Type IV secretion system.. 
PF12667 NigD-like protein<br>JCSG target Q5LAY5_BACFN. This family of proteins is functionally uncharacterised. This family of proteins is found in Bacteroides species. Proteins in this family are typically between 234 and 260 amino acids in length. These proteins possess an N-terminal lipoprotein attachment site. The family includes NigD a protein found in the Nig operon that encodes a bacteriocin called nigrescin. It has been suggested that NigD may be the immunity protein for nigrescin (NigC) because it is directly downstream  .. 
PF12668 Protein of unknown function (DUF3791)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 71 and 125 amino acids in length.. 
PF12669 Virus attachment protein p12 family<br>This family of proteins are related to Virus attachment protein p12 from the African swine fever virus. The family appears to contain an N-terminal signal peptide followed by a short cysteine rich region. The cysteine rich region is extremely variable and it is possible that only the N-terminal region is homologous.. 
PF12670 Protein of unknown function (DUF3792)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 130 amino acids in length. These proteins are integral membrane proteins.. 
PF12671 Putative amidase domain<br>
PF12672 Protein of unknown function (DUF3793)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 187 and 211 amino acids in length. There are two conserved sequence motifs: PHE and LGYP.. 
PF12673 Domain of unknown function (DUF3794)<br>This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 90 amino acids in length. The family is found in association with Pfam:PF01476.. 
PF12674 Putative zinc ribbon domain<br>This domain appears to be a zinc binding DNA-binding domain.. 
PF12675 Protein of unknown function (DUF3795)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 99 and 171 amino acids in length. This protein is likely to be zinc binding given the conserved cysteines.. 
PF12676 Protein of unknown function (DUF3796)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length.. 
PF12677 Domain of unknown function (DUF3797)<br>This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.. 
PF12678 RING-H2 zinc finger<br>There are 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding. The protein, of which this domain is the conserved region, participates in diverse functions relevant to chromosome metabolism and cell cycle control  .. 
PF12679 ABC-2 family transporter protein<br>This family is related to the ABC-2 membrane transporter family  .. 
PF12680 SnoaL-like domain<br>This family contains a large number of proteins that share the SnoaL fold.. 
PF12681 Glyoxalase-like domain<br>This domain is related to the Glyoxalase domain Pfam:PF00903.. 
PF12682 Flavodoxin<br>This is a family of flavodoxins.  Flavodoxins are electron transfer proteins that carry a molecule of non-covalently bound FMN.. 
PF12683 Protein of unknown function (DUF3798)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 247 and 417 amino acids in length. Most of the proteins in this family have an N-terminal lipoprotein attachment site. These proteins have distant similarity to periplasmic ligand binding families such as Pfam:PF02608, which suggests that this family have a similar role.. 
PF12684 PDDEXK-like domain of unknown function (DUF3799)<br>Jackhmmer:JCSG target 392282. This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 265 and 420 amino acids in length. It appears that these proteins are distantly related to the PDDEXK superfamily and so these domains are likely to be nucleases. This family has a C-terminal cysteine cluster similar to that found in Pfam:PF01930.. 
PF12685 SpoIIIAH-like protein<br>Stage III sporulation protein AH (SpoIIIAH) is a protein that is involved in forespore engulfment. It forms a channel with SpoIIIAH that is open on the forespore end and closed (or gated) on the mother cell end. This allows sigma-E-directed gene expression in the mother-cell compartment of the sporangium to trigger the activation of sigma-G forespore-specific gene expression by a pathway of intercellular signaling.  This family of proteins is found in bacteria, archaea and eukaryotes and so must have a wider function that in sporulation.  Proteins in this family are typically between 174 and 223 amino acids in length.. 
PF12686 Protein of unknown function (DUF3800)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea, eukaryotes and viruses.  Proteins in this family are typically between 215 and 302 amino acids in length. There is a DE motif at the N-terminus and a QXXD motif at the C-terminus that may be functionally important.. 
PF12687 Protein of unknown function (DUF3801)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 158 and 187 amino acids in length. This family includes the PcfB protein.. 
PF12688 Tetratrico peptide repeat<br>BH0479 of Bacillus halodurans is a hypothetical protein which contains a tetratrico peptide repeat (TPR) structural motif. The TPR motif is often involved in mediating protein-protein interactions.  This protein is likely to function as a dimer. The first 48 amino acids are not present in the clone construct. This Pfam entry includes tetratricopeptide-like repeats not detected by the Pfam:PF00515, Pfam:PF07719, Pfam:PF07720 and Pfam:PF07221 models.. 
PF12689 Acid Phosphatase<br>This family contains phosphatase enzymes and other proteins of the HAD superfamily.  It includes MDP-1 which is a eukaryotic magnesium-dependent acid phosphatase [1-2].. 
PF12690 Intracellular proteinase inhibitor<br>This is a bacterial domain which has been named BsuPI in Bacillus subtilis.\.      This domain is found in Swiss:P39804, where it has been suggested to regulate the major intracellular proteinase (ISP-1) activity in vivo  .  The structure of proteins in this family adopt a beta barrel topology.. 
PF12691 Minor capsid protein from bacteriophage<br>This family is from one of three adjacent genes, all of which are involved in formation of the minor phage capsid.. 
PF12692 S-adenosyl-L-methionine methyltransferase<br>This domain is found in bacterial proteins.  The structure of the proteins in this family suggest that they function as a methyltransferase.. 
PF12693 GspL periplasmic domain<br>This domain is the periplasmic domain of the GspL/EpsL family proteins. These proteins are involved in type II secretion systems.. 
PF12694 Putative molybdenum carrier<br>The structure of proteins in this family contain central beta strands with flanking alpha helices.  The structure is similar to that of a molybdenum cofactor carrier protein.. 
PF12695 Alpha/beta hydrolase family<br>Jackhmmer:Q186B9_CLOD6. This family contains a diverse range of alpha/beta hydrolase enzymes.. 
PF12696 TraM recognition site of TraD and TraG<br>Pfam-B_1146 (release 5.4). This family includes both TraG and TraD as well as VirD4 proteins. TraG is essential for DNA transfer in bacterial conjugation.  These proteins are thought to mediate interactions between the DNA-processing (Dtr) and the mating pair formation (Mpf) systems  . This domain interacts with the relaxosome component TraM via the latter's tetramerisation domain. TraD is a hexameric ring ATPase that forms the cytoplasmic face of the conjugative pore  .. 
PF12697 Alpha/beta hydrolase family<br>Jackhmmer:Q186D8_CLOD6. This family contains alpha/beta hydrolase enzymes of diverse specificity.. 
PF12698 ABC-2 family transporter protein<br>Jackhmmer:Q17ZU3_CLOD6. This family is related to the ABC-2 membrane transporter family Pfam:PF01061  .. 
PF12699 phiKZ-like phage internal head proteins<br>Hardies SC, Coggill P. Phage internal head proteins (IP) are proteins that are encoded by a bacteriophage and assembled into the mature virion inside the capsid head.  The most analogous characterised IP proteins are those of bacteriophage T4, which are known to be proteolytically processed during phage maturation, and then subsequently injected into the host cell during infection. The phiKZ_IP family consists of internal head proteins encoded by phiKZ-like phages.  Each phage encodes three to six members of this family  .  Members of the family reside in the head   and are cleaved during phage maturation to separate an N-terminal propeptide from a C-terminal domain.  The C-terminal domain remains in the mature capsid.  The N-terminal propeptide domain is either mostly or completely removed from the mature capsid. In one case, an unrelated polypeptide is embedded in the propeptide and also remains in the mature capsid.  The phiKZ-like IP proteins are not discernibly homologous to the T4 IP proteins, and it is not known if the phiKZ-like IP proteins are injected into the host cell, or have some other function within the head. The alignment and HMM model exclude most of the propeptide region, but include the cleavage sites.  The first 100 residues, including the cleavage sites, constitute the most conservative part of the seed alignment.. 
PF12700 HlyD family secretion protein<br>Jackhmmer:Q182V7_CLOD6. This family is related to Pfam:PF00529.. 
PF12701 Scd6-like Sm domain<br>The Scd6-like Sm domain is found in Scd6p from S. cerevisiae, Rap55 from the newt Pleurodeles walt, and its orthologs from fungi,  animals, plants and apicomplexans  . The domain is also found in  Dcp3p and the human EDC3/FLJ21128 protein where it is fused to the  the Rossmanoid YjeF-N domain [1,2]. In addition both EDC3 and Scd6p are found fused to the FDF domain [1,2].. 
PF12702 DUF3803;<br>JCSG_target_392987_3hty Pfam-B_17140 (release 24.0). This is a family of proteins of 115 residues on average.  The family has two highly conserved tryptophan residues. The fold is very similar to the lipocalin-like fold from several comparable structures.. 
PF12703 Toxin of toxin-antitoxin type 1 system<br>Gardner P, Coggill P. This family is the toxin of a type 1 toxin-antitoxin system which is found in a relatively widespread range of bacterial species. The species distribution suggests frequent horizontal gene transfer.  In a type 1 system, as characterised for the plasmid-encoded E coli hok/sok system, the toxin-encoding stable mRNA encodes a protein which rapidly leads to cell death unless the translation is suppressed by a short-lived small RNA. The plasmid-encoded module prevents the growth of plasmid-free offspring, thus ensuring the persistence of the plasmid in the population. Plasmid-free cells arising after cell-division will be killed because the stable mRNA toxin is present while the comparably unstable anti-toxin is rapidly degraded. Where the system is transcribed chromosomally, the mechanism is poorly understood  .. 
PF12704 MacB-like periplasmic core domain<br>This family represents the periplasmic core domain found in a variety of ABC transporters. The structure of this family has been solved for the MacB protein  . Some structural similarity was found to the periplasmic domain of the AcrB multidrug efflux transporter.. 
PF12705 PD-(D/E)XK nuclease superfamily<br>Jackhmmer:Q18AP1_CLOD6. Members of this family belong to the PD-(D/E)XK nuclease superfamily. 
PF12706 Beta-lactamase superfamily domain<br>Jackhmmer:Q189N7_CLOD6. This family is part of the beta-lactamase superfamily and is related to Pfam:PF00753.. 
PF12707 Protein of unknown function (DUF3804)<br>This family is approximately 130 residues.  Dali search indicates this protein carries a NTF2-fold with a hydrophobic cavity as a structural homologue to 1JB2, 2R4I, 3FSD and 2UX0.  In this hydrophobic cavity, Arg 118 provides the H-bonding force to hold a PEG molecule from crystallisation. The interface interaction suggests that the biomolecule of Swiss:Q46KI2 is a dimer. Two members of the family are annotated as putative EF-Tu domain 2 but there is no match to this family so this is likely to be a false assignment. There are two highly conserved tryptophan residues towards the C-terminal end of the family.. 
PF12708 Pectate lyase superfamily protein<br>Jackhmmer:Q184L0_CLOD6. This family of proteins possesses a beta helical structure like Pectate lyase.  This family is most closely related to glycosyl hydrolase family 28.. 
PF12709 Central kinetochore-associated<br>This is a family of proteins integrally involved in the central kinetochore. Slk19 is a yeast member and it may play an important role in the timing of nuclear migration. It may also participate, directly or indirectly, in the maintenance of centromeric tensile strength during mitotic stagnation, for instance during activation of checkpoint controls, when cells need to preserve nuclear integrity until cell cycle progression can be resumed  .. 
PF12710 haloacid dehalogenase-like hydrolase<br>Jackhmmer:Q18AI1_CLOD6. 
PF12711 Kinesin motor<br>This family is closely related to Kinesin-related, Pfam:PF06548.. 
PF12712 Domain of unknown function (DUF3805)<br>This family represent the N-terminal domain of the structure. In two related Bacteroides species the gene lies immediately upstream from a putative ATP binding component of an ATP transporter and a putative histidinol phosphatase. The structure of this domain is strikingly similar to the N-terminal structure of 1tui, also of unknown function. The domain carries four conserved tryptophan residues.. 
PF12713 Domain of unknown function (DUF3806)<br>This family represent the C-terminal domain of the structure. In two related Bacteroides species the gene lies immediately upstream from a putative ATP binding component of an ATP transporter and a putative histidinol phosphatase. The structure of this domain is strikingly similar to the N-terminal structure of 1ma7 whose C-terminal domain is a phage integrase, Pfam:PF00589.. 
PF12714 TILa domain<br>Pfam-B_897 (release 5.2). This cysteine rich domain occurs along side the TIL Pfam:PF01826 domain and is likely to be a distantly related relative.. 
PF12715 Abhydrolase family<br>This is a family of probable bacterial abhydrolases.. 
PF12716 Nuclear pore assembly and biogenesis<br>This is a family of conserved fungal proteins involved in nuclear pore assembly  . Apq12 is an integral membrane protein of the nuclear envelope (NE) and endoplasmic reticulum. Its absence leads to a partial block in mRNA export and cold-sensitive defects in the growth and localisation of a subset of nucleoporins, particularly those asymmetrically localised to the cytoplasmic fibrils  . The defects in nuclear pore assembly appear to be due to defects in regulating membrane fluidity  .. 
PF12717 non-SMC mitotic condensation complex subunit 1<br>Pfam-B_410 (release 24.0). The three non-SMC (structural maintenance of chromosomes) subunits of the mitotic condensation complex are Cnd1-3. The whole complex is essential for viability and the condensing of chromosomes in mitosis.. 
PF12718 Tropomyosin like<br>This family is a set of eukaryotic tropomyosins. Within the yeast Tmp1 and Tmp2, biochemical and sequence analyses indicate that Tpm2p spans four actin monomers along a filament, whereas Tpmlp spans five.  Despite its shorter length, Tpm2p can compete with Tpm1p for binding to F-actin. Over-expression of Tpm2p in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1p. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis  . The family also contains higher eukaryote Tmp3 members.. 
PF12719 Nuclear condensing complex subunits, C-term domain<br>Pfam-B_484 (release 24.0). The Cnd1-3 proteins are the three non-SMC (structural maintenance of chromosomes) proteins that go to make up the mitotic condensation complex along with the two SMC protein families, XCAP-C and XCAP-E, (or in the case of fission yeast, Cut3 and Cut14). The five-member complex seems to be conserved from yeasts to vertebrates. This domain is the C-terminal, cysteine-rich domain of Cnd3. The complex shuttles between the nucleus, during mitosis, and the cytoplasm during the rest of the cycle. Thus this family is made up of the C-termini of XCAP-Gs, Ycg1 and Ycs5 members.. 
PF12720 Protein of unknown function (DUF3807)<br>This is a family of conserved fungal proteins of unknown function.. 
PF12721 RIP homotypic interaction motif<br>RIP proteins are receptor-interacting serine/threonine-protein kinases or cell death proteins  . This interacting domain is involved in virus recognition. The RHIM domain is necessary for the recruitment of RIP and RIP3 by the IFN-inducible protein DNA-dependent activator of IRFs (DAI), also known as DLM-1 or Z-DNA binding protein (ZBP1). Both the RIP kinases contribute to DAI-induced NF-kappaB activation. RIP3 undergoes auto phosphorylation on binding to DAI  .. 
PF12722 High-temperature-induced dauer-formation protein<br>Hid1 (high-temperature-induced dauer-formation protein 1) represents proteins of approximately 800 residues long and is conserved from fungi to humans. It contains up to seven potential transmembrane domains separated by regions of low complexity. Functionally it might be involved in vesicle secretion or be an inter-cellular signalling protein or be a novel insulin receptor  .. 
PF12723 Protein of unknown function (DUF3809)<br>Jackhmmer:NP_295729.1. This family of proteins is functionally uncharacterised. This family of proteins is found in Deinococci bacteria. Proteins in this family are typically between 117 and 157 amino acids in length.. 
PF12724 Flavodoxin domain<br>Jackhmmer:Q186N5_CLOD6. This is a family of flavodoxins.  Flavodoxins are electron transfer proteins that carry a molecule of non-covalently bound FMN.. 
PF12725 Protein of unknown function (DUF3810)<br>Jackhmmer:Q185R6_CLOD6. This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 333 and 377 amino acids in length. There is a conserved HEXXH sequence motif that is characteristic of metallopeptidases. This family may therefore belong to an as yet uncharacterised family of peptidase enzymes.. 
PF12726 SEN1 N terminal<br>Pfam-B_2547 (release 24.0). This domain is found at the N terminal of the helicase SEN1. SEN1 is a Pol II termination factor for noncoding RNA genes  . The N terminal of SEN1, unlike the C terminal, is not required for growth  .. 
PF12727 PBP superfamily domain<br>Jackhmmer:Q18A58_CLOD6. This family belongs to the periplasmic binding domain superfamily. It is often associated with a helix-turn-helix domain.. 
PF12728 Helix-turn-helix domain<br>Jackhmmer:Q18A58_CLOD6. This domain is a DNA-binding helix-turn-helix domain.. 
PF12729 4HB_MCP_2;<br>Four helix bundle sensory module for signal transduction. This family is a four helix bundle that operates as a ubiquitous sensory module in prokaryotic signal-transduction. The 4HB_MCP is always found between two predicted transmembrane helices indicating that it detects only extracellular signals. In many cases the domain is associated with a cytoplasmic HAMP domain suggesting that most proteins carrying the bundle might share the mechanism of transmembrane signalling which is well-characterised in E coli chemoreceptors.. 
PF12730 ABC-2 family transporter protein<br>Jackhmmer:Q18D57_CLOD6. This family is related to the ABC-2 membrane transporter family Pfam:PF01061  .. 
PF12731 Mating-type protein beta 1<br>Pfam-B_4610 (release 8.0). This domain is found in some fungi and is the C-terminus of a homeodomain-containing transcription factor protein involved in mating.. 
PF12732 YtxH-like protein<br>Jackhmmer:Q18C91_CLOD6. This family of proteins is found in bacteria. Proteins in this family are typically between 100 and 143 amino acids in length. The N-terminal region is the most conserved. Proteins is this family are functionally uncharacterised.. 
PF12733 Cadherin-like beta sandwich domain<br>Aravind L, Coggill P. This domain is found in several bacterial, metazoan and chlorophyte algal proteins.  A profile-profile comparison recovered the cadherin domain and a comparison of the predicted structure of this domain with the crystal structure of the cadherin showed a congruent seven stranded secondary structure. The domain is widespread in bacteria and seen in the firmicutes, actinobacteria, certain proteobacteria, bacteroides and chlamydiae with an expansion in Clostridium. In contrast, it is limited in its distribution in eukaryotes suggesting that it was derived through lateral transfer from bacteria. In prokaryotes, this domain is widely fused to other domains such as FNIII (Fibronectin Type III), TIG, SLH (S-layer homology), discoidin, cell-wall-binding repeat domain and alpha-amylase-like glycohydrolases. These associations are suggestive of a carbohydrate-binding function for this cadherin-like domain. In animal proteins it is associated with an ATP-grasp domain.. 
PF12734 Cysteine-rich TM module stress tolerance<br>Aravind L, Coggill P. The members of this family are short cysteine-rich membrane proteins that most probably dimerise together to form a transmembrane sulfhydryl-lined pore. The CYSTM module is always present at the extreme C-terminus of the protein in which it is present. Furthermore, like the yeast prototypes, the majority of the proteins also possess a proline/glutamine-rich segment upstream of the CYSTM module that is likely to form a polar, disordered head in the cytoplasm. The presence of an atypical well-conserved acidic residue at the C-terminal end of the TM helix suggests that this might interact with a positively charged moiety in the lipid head group. Consistently across the eukaryotes, the different versions of the CYSTM module appear to have roles in stress-response or stress-tolerance, and, more specifically, in resistance to deleterious substances, implying that thes might be general functions of the whole family.. 
PF12735 TRAPP trafficking subunit Trs65<br>This family is one of the subunits of the TRAPP Golgi trafficking complex  . TRAPP subunits are found in two different sized complexes, TRAPP I and TRAPP II. While both complexes contain the same seven subunits, Bet3p, Bet5p, Trs20p, Trs23p, Trs31p, Trs33p and Trs85p, with TRAPPC human equivalents, TRAPP II has the additional three subunits ,Trs65p, Trs120p and Trs130p  . While it has been implicated in cell wall biogenesis and stress response, the role of Trs65 in TRAPP II is supported by the findings that the protein co-localises with Trs130p, and deletion of TRS65 in yeast leads to a conditional lethal phenotype if either one of the other TRAPP II-specific subunits is modified  . Furthermore, the trs65 mutant has reduced Ypt31/32p guanine nucleotide exchange, GEF, activity  .. 
PF12736 Cell-cycle sustaining, positive selection, <br>Aravind L, Coggill P. The 'CABIT' domain (for 'cysteine-containing, all- in Themis') is found in a newly identified gene family that has three mammalian homologues (Themis, Icb1 and 9130404H23Rik) that encode proteins with two CABIT domains and a highly conserved proline-rich region. In contrast, Fam59A, Fam59B and related proteins from mammals to cnidarians, including the insect Serrano proteins, have a single copy of the CABIT domain, a proline-rich region and often a C-terminal SAM (sterile-motif) domain. Multiple-sequence alignment has predicted that the CABIT domain adopts an all-strand structure with at least 12 strands, ie a dyad of six-stranded beta-barrel units. The CABIT domain contains a nearly absolutely conserved cysteine residue which is likely to be central to its function. CABIT domain proteins function downstream of tyrosine kinase signalling and interact with GRB2.. 
PF12737 C-terminal domain of homeodomain 1<br>Pfam-B_4610 (release 8.0). Mating in fungi is controlled by the loci that determine the mating type of an individual, and only individuals with differing mating types can mate. Basidiomycete fungi have evolved a unique mating system, termed tetrapolar or bifactorial incompatibility, in which mating type is determined by two unlinked loci; compatibility at both loci is required for mating to occur. The multi-allelic tetrapolar mating system is considered to be a novel innovation that could have only evolved once, and is thus unique to the mushroom fungi. This domain is C-terminal to the homeodomain transcription factor region.. 
PF12738 twin BRCT domain<br>Pfam-B_181 (release 24.0). This is a BRCT domain that appears in duplicate in most member sequences. BRCT domains are peptide- and phosphopeptide-binding modules. BRCT domains are present in a number of proteins involved in DNA checkpoint controls and DNA repair [1,2].. 
PF12739 ER-Golgi trafficking TRAPP I complex 85 kDa subunit<br>This family is one of the subunits of the TRAPP Golgi trafficking complex. TRAPP subunits are found in two different sized complexes, TRAPP I and TRAPP II, and this Trs85 is in the smaller complex. TRAPP I, but Not TRAPP II, functions in ER-Golgi transport  . Trs85p was reported to function in the cytosol-to-vacuole targeting pathway, suggesting a role for this subunit in autophagy as well as in secretion  . The overall architecture of TRAPP I shows the other components to be Bet3p (TRAPPC3), Bet5p (TRAPPC1), Trs20p (TRAPPC2) , Trs23p (TRAPPC4), Trs31p (TRAPPC5), Trs33p (TRAPPC6a and b) and Trs85p.. 
PF12740 Chlorophyllase enzyme<br>This family consists of several chlorophyllase and chlorophyllase-2 (EC:3.1.1.14) enzymes. Chlorophyllase (Chlase) is the first enzyme involved in chlorophyll (Chl) degradation and catalyses the hydrolysis of an ester bond to yield chlorophyllide and phytol  . The family includes both plant and Amphioxus members.. 
PF12741 Susd and RagB outer membrane lipoprotein <br>This is a family of SusD-like proteins, one member of which, BT1043 (Swiss:Q8A8X4), is an outer membrane lipoprotein involved in host glycan metabolism. The structures of this and SusD-homologues in the family are dominated by tetratrico peptide repeats that may facilitate association with outer membrane beta-barrel transporters required for glycan uptake. The structure of BT1043 complexed with N-acetyllactosamine reveals that recognition is mediated via hydrogen bonding interactions with the reducing end of beta-N-acetylglucosamine, suggesting a role in binding glycans liberated from the mucin polypeptide. Mammalian distal gut bacteria have an expanded capacity to utilize glycans. In the absence of dietary sources, some species rely on host-derived mucosal glycans. The ability of Bacteroides thetaiotaomicron, a prominent human gut symbiont, to forage host glycans contributes to both its ability to persist within an individual host and its ability to be transmitted naturally to new hosts at birth.. 
PF12742 Gryzun, putative Golgi trafficking<br>Members of this family are involved in Golgi trafficking.. 
PF12743 Oestrogen-type nuclear receptor final C-terminal <br>This is the very C-terminal region of a subfamily of nuclear receptors that includes oestrogen receptors and other subfamily 3 group A members. The actual function of this region is not known, but the domain is absent from all the other types of nuclear receptors. Oestrogen receptors modulate AP-1-dependent transcription   through two distinct mechanisms: via protein-protein interactions on DNA; and via non-genomic actions. The mechanism used depends on the cellular localisation of the receptor. In addition to the more extensively studied cross-talk on DNA, additional non-genomic actions might be very important in target tissues in which membrane-associated ERs are found. These non-genomic actions probably contribute to the overall physiological responses mediated by ligand-bound ERs   and might possibly be mediated via this C-terminal domain.. 
PF12744 Autophagy protein Atg19, Atg8-binding<br>Autophagy is generally known as a process involved in the degradation of bulk cytoplasmic components that are non-specifically sequestered into an autophagosome, where they are sequestered into double-membrane vesicles and delivered to the degradative organelle, the lysosome/vacuole, for breakdown and eventual recycling of the resulting macromolecules. In contrast to autophagy, however, the Cvt pathway is a highly selective process that involves the sequestration of at least two specific cargos that are resident vacuolar hydrolases, aminopeptidase I (Ape1) and alpha-mannosidase (Ams1). These proteins are sequestered within a double-membrane vesicle, termed a Cvt vesicle. The Cvt vesicle is fairly consistent in size, and is much smaller than the autophagosome, being 140-160 nm in diameter. The prApe1 is sequestered within either Cvt vesicles or autophagosomes, depending on the nutrient conditions, and delivered to the vacuole. Autophagy and the Cvt pathway are topologically and mechanistically similar and share most of the same machinery. The Ape1 complex is ultimately enwrapped within either Cvt vesicles or autophagosomes at the perivacuolar PAS. The receptor protein Atg19 binds to the Ape1 complex through the prApe1 propeptide to form the Cvt complex in the cytosol. In the absence of Atg19, prApe1 can form an Ape1 complex, but does not localise at the PAS. Atg19 is a peripheral membrane protein with differing binding sites for both Ape1 and Ams1. The Atg8-binding region in the yeast proteins is this very C-terminal residues  .. 
PF12745 Anticodon binding domain of tRNAs<br>Pfam-B_20896 (release 24.0). This is an HGTP_anticodon binding domain, found largely on Gcn2 proteins which bind tRNA to down regulate translation in certain stress situations.. 
PF12746 GNAT acetyltransferase<br>Many of the members are annotated s being Zwittermicin A resistance proteins, whereas others are listed as being GNAT acetyltransferases.  The family has similarities to the GNAT acetyltransferase family.. 
PF12747 DdrB-like protein<br>This family includes the Deinococcus DdrB protein which is a ssDNA binding protein. This family also includes some possibly distantly related cyanobacterial proteins. However, these are not strongly supported. The structure of DdrB is known.. 
PF12749 Eukaryotic metallothionein<br>This is a family of eukaryotic metallothioneins.. 
PF12750 Maff2 family<br>Jackhmmer:Q187G1_CLOD6. This family of short membrane proteins are related to the protein Maff2. Maff2 lies just outside the direct repeats of a tetracycline resistance transposable element. This protein may contain transmembrane helices.. 
PF12751 Vacuolar segregation subunit 7<br>Pfam-B_10847 (release 24.0). Vac7 is localised at the vacuole membrane, a location which is consistent with its involvement in vacuole morphology and inheritance  . Vac7 has been shown to function as an upstream regulator of the Fab1 lipid kinase pathway  . The Fab1 lipid p[pathway is important for correct regulation of membrane trafficking events.. 
PF12752 SUZ domain<br>The SUZ domain is a conserved RNA-binding domain found in eukaryotes and enriched in positively charged amino acids. It was first characterized in the C.elegans protein Szy-20 where it has been shown to bind RNA and allow their localization to the centrosome. Warning- the domain has a compositionally biased character.. 
PF12753 Nuclear pore complex subunit Nro1<br>Pfam-B_4826 (release 24.0). 
PF12754 Cell-cycle control medial ring component<br>During size-dependent cell cycle transitions controlled by the ubiquitous cyclin-dependent kinase Cdk1, Blt1 has been shown to co-localise with Cdr2 in the medial interphase nodes, as well as with Mid1 which was previously shown to localise to similar interphase structures. Physical interactions between Blt1-Mid1, Blt1-Cdr2 and Cdr2-Mid1 were detected, indicating that medial cortical nodes are formed by the ordered, Cdr2-dependent assembly of multiple interacting proteins during interphase. Q5KIH8.1/10-346; Q5KIH8.1/10-90;. 
PF12755 Vacuolar 14 Fab1-binding region<br>Vac14 is a scaffold for the Fab1 kinase complex, a complex that allows for the dynamic interconversion of PI3P and PI(3,5)P2p (phosphoinositide phosphate (PIP) lipids, that are generated transiently on the cytoplasmic face of selected intracellular membranes). This interconversion is regulated by at least five proteins in yeast: the lipid kinase Fab1p, lipid phosphatase Fig4p, the Fab1p activator Vac7p, the Fab1p inhibitor Atg18p, and Vac14p, a protein required for the activity of both Fab1p and Fig4p. This domain appears to be the one responsible for binding to Fab1. The full length Vac14 in yeasts is likely to be a protein carrying a succession of HEAT repeats, most of which have now degenerated. This regulatory system is crucial for the proper functioning of the mammalian nervous system.. 
PF12756 C2H2 type zinc-finger (2 copies)<br>Pfam-B_88 (release 24.0). This family contains two copies of a C2H2-like zinc finger domain.. 
PF12757 Protein of unknown function (DUF3812)<br>Pfam-B_8029 (release 24.0). This is a family of fungal proteins whose function is not known.. 
PF12758 Protein of unknown function (DUF3813)<br>PfamB_1273 (release 24.0). This is an uncharacterised family of Bacillus proteins.. 
PF12759 InsA_C;<br>InsA C-terminal domain. This short domain is found at the C-terminus of the InsA protein. This domain contains a helix-turn-helix domain.. 
PF12760 Zn_ribbon_3;<br>Transposase zinc-ribbon domain. Pfam-B_3 (Release 24.0). This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It is likely a zinc-binding beta ribbon domain that could bind the DNA.. 
PF12761 E3;<br>Actin cytoskeleton-regulatory complex protein END3. Pfam-B_51079 (release 24.0). Endocytosis is accomplished through the sequential recruitment at endocytic sites of proteins that drive cargo sorting, membrane invagination and vesicle release  . End3p is part of the coat module protein complex Pan1, along with Pan1p, Sla1p, and Sla2p  . The proteins in this complex are regulated by phosphorylation events. End3p also regulates the cortical actin cytoskeleton [3,4]. The subunits of the Pan1 complex are homologous to mammalian intersectin.. 
PF12762 Transposase_38;<br>ISXO2-like transposase domain. Pfam-B_3 (Release 24.0). This domain probably functions as an integrase that is found in a wide variety of transposases, including ISXO2.. 
PF12763 efhand_3;<br>Cytoskeletal-regulatory complex EF hand. Pfam-B_51079 (release 24.0). This is an efhand family from the N-terminal of actin cytoskeleton-regulatory complex END3 and similar proteins from fungi and closely related species.. 
PF12764 Glycine-rich region of argonaut<br>Pfam-B_7248 (release 24.0). This domain is often found at the very N-terminal of argonaut-like proteins.. 
PF12765 HEAT repeat associated with sister chromatid cohesion<br>Pfam-B_443 (release 24.0). This HEAT repeat is found most frequently in sister chromatid cohesion proteins such as Nipped-B. HEAT repeats are found tandemly repeated in many proteins, and they appear to serve as flexible scaffolding on which other components can assemble.. 
PF12766 Pyridoxamine 5'-phosphate oxidase<br>Pfam-B_2486 (release 24.0). Pyridoxamine 5'-phosphate oxidase catalyses the oxidation of pyridoxamine-5-P (PMP) and pyridoxine-5-P (PNP) to pyridoxal-5-P (PLP), the terminal step in the de novo biosynthesis of PLP in Escherichia coli and part of the salvage pathway of this coenzyme in both E. coli and mammalian cells. This region is the flavoprotein FMN-binding domain.. 
PF12767 Transcriptional regulator of RNA polII, SAGA, subunit<br>Pfam-B_319 (release 24.0). The yeast SAGA complex is a multifunctional coactivator that regulates transcription by RNA polymerase II [1,2]. It is formed of five major modular subunits and shows a high degree of structural conservation to human TFTC and STAGA  . The complex can also be conceived of as consisting of two histone-fold-containing core subunits, and this family is one of these. As a family it is likely to carry binding regions for interactions with a number of the other components of the complex.. 
PF12768 Cortical protein marker for cell polarity<br>Pfam-B_2071 (release 24.0). Diploid yeast cells repeatedly polarize and bud from their poles, due probably to the presence of highly stable membrane markers, and Rax2 is one such marker. It is inherited immutably at the cell cortex for multiple generations, and has a half-life exceeding several generations. The persistent inheritance of cortical protein markers would provide a means of coupling a cell's history with the future development of a precise morphogenetic form  . Both Rax1 and Rax2 localise to the distal pole as well as to the division site and they interact both with each other and with Bud8p and Bud9p in the establishment and/or maintenance of the cortical markers for bipolar budding  . thus Rax2 is likely to control cell polarity during vegetative growth, and in fission yeast this is done by regulating the localisation of for3p  .. 
PF12769 Domain of unknown function (DUF3814)<br>Pfam-B_10 (release 24.0). This is a domain of unknown function.  It is often found in combination with Pfam:PF05222, Pfam:PF01262 and Pfam:PF02233 on alanine dehydrogenase and pyridine nucleotide transhydrogenase enzymes.. 
PF12770 CHAT domain<br>Pfam-B_4 (Release 24.0). These proteins appear to be related to peptidases in peptidase clan CD that includes the caspases. This domain has been termed the CHAT domain for Caspase HetF Associated with Tprs. This family has been identified as a sister group to the separins  .. 
PF12771 Starch-binding associating with outer membrane<br>JCSG structure (Target 390167). SusD is a secreted starch-binding protein with an N-terminal lipid tail that allows it to associate with the outer membrane.. 
PF12772 Growth hormone receptor binding<br>Pfam-B_7 (release 24.0). Growth hormone receptor binding protein is produced either by proteolysis of the GHR (growth hormone receptor) at the cell surface thereby releasing its extracellular domain, the GHBP (growth hormone-binding protein), or, in rodents, by alternative processing of the GHR transcript. The sheddase proteolytic enzyme responsible for the cleavage is TACE (tumour necrosis factor-alpha-converting enzyme) [1,2]. Growth hormone (GH) binding to GH receptor (GHR) is the initial step that leads to the physiological functions of the hormone  . The biological effects of GHBP are determined by the serum levels of growth hormone (GH), which can vary. Low levels of GH can result in a dwarf phenotype and have been positively correlated with an increased life expectancy. High levels of GH can lead to gigantism or a clinical syndrome termed acromegaly and have been implicated in diabetic eye and kidney damage  .. 
PF12773 Double zinc ribbon<br>Pfam-B_12 (Release 24.0). This family consists of a pair of zinc ribbon domains.. 
PF12774 Hydrolytic ATP binding site of dynein motor region D1<br>Pfam-B_14 (release 24.0). the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D1 unit of the motor and contains the hydrolytic ATP binding site  . . 
PF12775 P-loop containing dynein motor region D3<br>Pfam-B_14 (release 24.0). the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D3 and is an ATP binding site  .. 
PF12776 Myb/SANT-like DNA-binding domain<br>Pfam-B_16 (Release 24.0). This presumed domain appears to be related to other Myb/SANT like DNA binding domains. In particular Pfam:PF10545 seems most related.  This family is greatly expanded in plants and appears in several proteins annotated as transposon proteins.. 
PF12777 Microtubule-binding stalk of dynein motor<br>Pfam-B_14 (release 24.0). the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This family is the region between D4 and D5 and is the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component  .. 
PF12778 PXPV repeat (3 copies)<br>Pfam-B_15 (Release 24.0). This short repeat is found in multiple copies in a variety of Burkholderia proteins. The function of this region is unknown.. 
PF12779 YXWGXW repeat (2 copies)<br>Pfam-B_15 (Release 24.0). This short repeat contains the motif YXWXXGXW where X can be any amino acid.  It is generally found in 2-5 copies in short secreted bacterial proteins. Its function is as yet unknown.. 
PF12780 P-loop containing dynein motor region D4<br>Pfam-B_14 (release 24.0). The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D4 ATP-binding region of the motor  .. 
PF12781 ATP-binding dynein motor region D5<br>Pfam-B_14 (release 24.0). The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution.  This particular family is the D5 ATP-binding region of the motor, but has lost its P-loop  .. 
PF12782 Invertebrate innate immunity transcript family<br>Pfam-B_9 (release 24.0). The immune response of the purple sea urchin appears to be more complex than previously believed in that it uses immune-related gene families homologous to vertebrate Toll-like and NOD/NALP-like receptor families as well as C-type lectins and a rudimentary complement system. In addition, the species also produces this unusual family of mRNAs, also known as 185/333, which is strongly upregulated in response to pathogen challenge  .. 
PF12783 Guanine nucleotide exchange factor in Golgi transport N-terminal<br>Pfam-B_13 (release 24.0). The full-length Sec7 functions proximally in the secretory pathway as a protein binding scaffold for the coat protein complexes COPII-COPI. The COPII-COPI-protein switch is necessary for maturation of the vesicular-tubular cluster, VTC, intermediate compartments for Golgi compartment biogenesis. This N-terminal domain however does not appear to be binding either of the COP or the ARF  .   . 
PF12784 PD-(D/E)XK nuclease family transposase<br>Pfam-B_5 (Release 24.0). Members of this family belong to the PD-(D/E)XK nuclease superfamily  . These proteins are transposase proteins.. 
PF12785 Variant erythrocyte surface antigen-1<br>Pfam-B_22 (release 24.0). This family represents the N-terminal of the variant erythrocyte surface antigen 1, versions a and b, of Babesia. Babesia bovis is a tick-borne, intra-erythrocytic, protozoal parasite of cattle that shares many lifestyle parallels with the most virulent of the human malarial parasites, Plasmodium falciparum. Babesia uses antigenic variation to establish consistent infections of long duration. The two variants of VESA1, a and b, are expressed from different but closely related genes, and variation is achieved through the involvement of a segmental gene conversion mechanism and low-frequency epigenetic in situ switching of transcriptional activity from the VESA1 gene-pair to a possible other gene pair.. 
PF12786 GB virus C genotype envelope<br>Pfam-B_19 (release 24.0). This the envelope protein from the ssRNA GB virus genotype C.. 
PF12787 EcsC protein family<br>Jackhmmer:Q186V8_CLOD6. Proteins in this family are related to EcsC from B. subtilis. This protein is found in an operon with EcsA and EcsB which are components of an ABC transport system  . The function of this protein is unknown.. 
PF12788 YmaF family<br>This family of proteins contain 6 HXH motifs and is named after the B. subtilis YmaF protein.\.  It seems likely that these are involved in metal binding. The function of this protein is unknown.. 
PF12789 Phage tail repeat like<br>This family largely contains proteins from the eukaryote Trichomonas vaginalis.  These proteins contain multiple HXH repeats. Some proteins in this family are annotated as having phage tail repeats. The function of this family is unknown.. 
PF12790 Type VI secretion lipoprotein<br>Pfam-B_27 (release 24.0). One of the virulence mechanisms of E coli is the production of toxins which it produces from dedicated machineries called secretion systems. Seven secretion systems have been described, which assemble from 3 to upto more than 20 subunits. These secretion systems derive from or have co-evolved with bacterial organelles such as ABC transporters (type I), type IV pili (type 2), flagella (type 3), or conjugative machines (type IV). The type VI secretion system (T6SS) is present in most pathogens that have contact with animals, plants, or humans. SciN is a lipoprotein tethered to the outer membrane and expressed in the periplasm of E coli and is essential for T6S-dependent secretion of the Hcp-like SciD protein and for biofilm formation.. 
PF12791 Anti-sigma factor N-terminus<br>Borovok I, Coggill P. The heat shock genes in B. subtilis can be classified into several groups according to their regulation  , and the sigma gene, sigI, of Bacillus subtilis belongs to the group IV heat-shock response genes and has many orthologues in the bacterial phylum Firmicutes  . Regulation of sigma factor I is carried out by RsgI from the same operon, and this N-terminal cytoplasmic portion of RsgI ('upstream' of the single transmembrane helix) has been shown to interact directly with Sigma-I  .. 
PF12792 CSS motif domain associated with EAL <br>This family with its characteristic highly conserved CSS sequence motif is found N-terminal to the EAL, Pfam:PF00563, domain in many cyclic diguanylate phosphodiesterases.. 
PF12793 Sugar transport-related sRNA regulator N-term<br>Pfam-B_33 (release 24.0). Small, non-coding RNA molecules play important regulatory roles in a variety of physiological processes in bacteria. SgrR_N is the N-terminus of a family of proteins which regulate the transcription of these sRNAs, in particular SgrS. SgrR_N contains a helix-turn-helix motif characteristic of winged-helix DNA-binding transcriptional regulators. SgrS is a small RNA required for recovery from glucose-phosphate stress in bacteria  . In examining the regulation of sgrR expression it was found that SgrR negatively auto-regulates its own transcription in the presence and absence of stress, and thus SgrR coordinates the response to glucose-phosphate stress by binding specifically to sgrS promoter DNA  .. 
PF12794 Mechanosensitive ion channel inner membrane domain 1<br>Pfam-B_24 (release 24.0). The small mechanosensitive channel, MscS, is a part of the turgor-driven solute efflux system that protects bacteria from lysis in the event of osmotic shock. The MscS protein alone is sufficient to form a functional mechanosensitive channel gated directly by tension in the lipid bilayer. The MscS proteins are heptamers of three transmembrane subunits with seven converging M3 domains, and this domain is one of the inner membrane domains.. 
PF12795 Mechanosensitive ion channel porin domain<br>Pfam-B_24 (release 24.0). The small mechanosensitive channel, MscS, is a part of the turgor-driven solute efflux system that protects bacteria from lysis in the event of osmotic shock. The MscS protein alone is sufficient to form a functional mechanosensitive channel gated directly by tension in the lipid bilayer. The MscS proteins are heptamers of three transmembrane subunits with seven converging M3 domains, and this MscS_porin is towards the N-terminal of the molecules. The high concentration of negative charges at the extracellular entrance of the pore helps select the cations for efflux.. 
PF12796 Ankyrin repeats (3 copies)<br>Jackhmmer:Q183I8_CLOD6. 
PF12797 4Fe-4S binding domain<br>This superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases.  Structure of the domain is an alpha-antiparallel beta sandwich.. 
PF12798 4Fe-4S binding domain<br>This superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases.  Structure of the domain is an alpha-antiparallel beta sandwich.. 
PF12799 Leucine Rich repeats (2 copies)<br>Leucine rich repeats are short sequence motifs present in a number of proteins with diverse functions and cellular locations. These repeats are usually involved in protein-protein interactions.  Each Leucine Rich Repeat is composed of a beta-alpha unit. These units form elongated non-globular structures. Leucine Rich Repeats are often flanked by cysteine rich domains.. 
PF12800 4Fe-4S binding domain<br>This superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases.  Structure of the domain is an alpha-antiparallel beta sandwich.. 
PF12801 4Fe-4S binding domain<br>Superfamily includes proteins containing  domains which bind to iron-sulfur clusters. Members  include bacterial ferredoxins, various dehydrogenases, and various reductases.  Structure of the domain is an alpha-antiparallel beta sandwich.. 
PF12802 MarR family<br>The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR.  A large number of compounds induce transcription of the mar operon.  This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds  . The structure of MarR is known   and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif.. 
PF12803 mRNA (guanine-7-)methyltransferase (G-7-MTase)<br>The Sendai virus RNA-dependent RNA polymerase complex, which consists of L and P proteins, participates in the synthesis of viral mRNAs that possess a methylated cap structure. The N-terminal of the L protein acts as the RNA-dependent RNA polymerase part of the molecule, family Paramyx_RNA_pol, Pfam:PF00946. This domain is the C-terminal part of the L protein and it catalyses cap methylation through its mRNA (guanine-7-)methyltransferase (G-7-MTase) activity  .. 
PF12804 MobA-like NTP transferase domain<br>This family includes the MobA protein (Molybdopterin-guanine dinucleotide biosynthesis protein A). The family also includes a wide range of other NTP transferase domain.. 
PF12805 FUSC-like inner membrane protein yccS<br>Pfam-B_45 (release 24.0). This family has similarities to the fusaric acid resistance protein family. The proteins are lodged in the inner membrane.. 
PF12806 Acetyl-CoA dehydrogenase C-terminal like<br>Pfma-B_46 (release 24.0). this domain would appear to be the very C-terminal region of many bacterial acetyl-CoA dehydrogenases.. 
PF12807 Translation initiation factor eIF3 subunit 135<br>Translation initiation factor eIF3 is a multi-subunit protein complex required for initiation of protein biosynthesis in eukaryotic cells. The complex promotes ribosome dissociation, the binding of the initiator methionyl-tRNA to the 40 S ribosomal subunit, and mRNA recruitment to the ribosome. The protein product from TIF31 genes in yeast is p135 which associates with the eIF3 but does not seem to be necessary for protein translation initiation  .. 
PF12808 Mto1_bdg;<br>Micro-tubular organiser Mto1 C-term Mto2-binding region. Wood V, Coggill P, Eberhardt R. Pfam-B_28820 (release 24.0). The C-terminal region of the micro-tubular organiser protein 1 (mto1) is the binding domain for attachment to Mto2p.The full-length Mto1 protein is required for microtubule nucleation from non-spindle pole body MTOCs in fission yeast  . The interaction of Mto2p with this region of Mto1 is critical for anchoring the cytokinetic actin ring to the medial region of the cell and for proper coordination of mitosis with cytokinesis  .. 
PF12809 Eukaryotic metallothionein<br>This is a family of eukaryotic metallothioneins.. 
PF12810 Glycine rich protein<br>This family of proteins is greatly expanded in Trichomonas vaginalis. The proteins are composed of several glycine rich motifs interspersed through the sequence. Although many proteins have been annotated by similarity in the family these annotations given the biased composition of the sequences these are unlikely to be functionally relevant.. 
PF12811 Bax inhibitor 1 like <br>The Bax-inhibitor-1 region of the receptor molecules is conserved from bacteria to humans.. 
PF12812 PDZ-like domain<br>Pfam-B_17100 (release 24.0). PDZ domains are found in diverse signalling proteins in bacteria, yeasts, plants, insects and vertebrates. this is a family of PDZ-like domains from bacteria, plants and fungi.. 
PF12813 XPG domain containing<br>Pfam-B_10579 (release 24.0). This family is largely of fungal proteins and is related to the XP-G protein family.. 
PF12814 Meiotic cell cortex C-terminal pleckstrin homology<br>Pfam-B_1220 (release 24.0). The PH domain of these largely fungal proteins is necessary for the cortical localisation of the protein during meiosis, since the overall function of the protein is to anchor dynein at the cell cortex during the horsetail phase. During prophase I of fission yeast, horsetail nuclear movement occurs, and this starts when all the telomeres become bundled at the spindle pole body - SPB. Subsequent to this, the nucleus undergoes a dynamic oscillation, resulting in elongated nuclear morphology. Horsetail nuclear movement is thought to be predominantly due to the pulling of astral microtubules that link the SPB to cortical microtubule-attachment sites at the opposite end of the cell; the pulling force is believed to be provided by cytoplasmic dynein and dynactin.. 
PF12815 Spt5 C-terminal nonapeptide repeat binding Spt4<br>Pfam-B_197031 (release 23.0). The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe  . The repeat has a characteristic TPA motif.. 
PF12816 Golgi CORVET complex core vacuolar protein 8<br>Pfam-B_90 (release 24.0). Vps8 is one of the Golgi complex components necessary for vacuolar sorting  . Eukaryotic cells contain a highly dynamic endo-membrane system, in which individual organelles keep their identity despite continuous vesicle generation and fusion. Vesicles that bud from a donor membrane are targeted and delivered to each individual organelle, where they release their cargo after fusion with the acceptor membrane. Vps8 is the core component of the endosomal tethering complex CORVET (class C core vacuole/endosome tethering).  Vps8 co-operates with Vps21-GTP to mediate endosomal clustering in a reaction that is dependent on Vps3. Vps8 is the only CORVET subunit that is enriched on late endosomes, suggesting that it is a marker for the maturation of late endosomes. Late endosomes form intralumenal vesicles, and the resulting multivesicular bodies fuse with the vacuole to release their cargoes  .. 
PF12818 dsDNA viral tegument protein<br>Pfam-B_48 (release 24.0). This is a family of tegument proteins from double-stranded DNA herpesvirus and related viral species.. 
PF12819 Carbohydrate-binding protein of the ER<br>Pfam-B_41 (release 24.0). Malectin is a membrane-anchored protein of the endoplasmic reticulum that recognises and binds Glc2-N-glycan. The domain is found on a number of plant receptor kinases.. 
PF12820 Serine-rich domain associated with BRCT<br>Pfam-B_51 (release 24.0). This domain is found on BRCA1 proteins.. 
PF12821 Protein of unknown function (DUF3815)<br>This family of membrane proteins is functionally uncharacterised.. 
PF12822 Protein of unknown function (DUF3816)<br>This family of proteins is functionally uncharacterised but are likely to be membrane transporters. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 177 and 208 amino acids in length. A subset of this family  is associated with the TM1506 proteins. In this context, transport through the channel is predicted to be regulated by the TM1506 protein by either regulating redox potential or modification of substrates  . 
PF12823 Domain of unknown function (DUF3817)<br>Pfam-B_123 (release 24.0). This domain is of unknown function.  It is sometimes found adjacent to Pfam:PF07690 and Pfam:PF03176 which are both transporter domains.. 
PF12824 Mitochondrial ribosomal protein subunit L20<br>Pfam-B_1364 (release 24.0). This family is the essential mitochondrial ribosomal protein subunit L20 of fungi.. 
PF12825 Domain of unknown function in PX-proteins (DUF3818)<br>Pfam-B_972 (release 24.0). This domain is found on proteins carrying a PX domain. Its function is unknown.. 
PF12826 Helix-hairpin-helix motif<br>Jackhmmer:DISA_CLOD6. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain  .. 
PF12827 Peroxisomal biogenesis protein family<br>Pfam-B_15020 (release 24.0). Peroxin-22 is a integral peroxisomal membrane protein family. The N-terminus is in the matrix and the C-terminus is in the cytosol. The N-terminus carries a 25-amino acid peroxisome membrane-targeting signal. It interacts with the ubiquitin-conjugating peripheral peroxisomal membrane enzyme Pex4p anchoring it at the peroxisomal membrane. Both Pex proteins are involved at the same stage of peroxisome biogenesis.. 
PF12828 PX-associated<br>Pfam-B_972 (release24,0). This domain is associated with the PX domain.. 
PF12829 Transcriptional regulation of mitochondrial recombination<br>Pfam-B_7788 (release 24.0). This family is involved in the transcriptional regulation of recombination in the mitochondria,. 
PF12830 Sister chromatid cohesion C-terminus<br>Pfam-B_443 (release 24.0). This domain lies towards the C-terminus of nipped-B or sister chromatid cohesion proteins.. 
PF12831 FAD dependent oxidoreductase<br>PfamB_47 (release 24.0). This family of proteins contains FAD dependent oxidoreductases and related proteins.. 
PF12832 MFS_1 like family<br>Pfam-B_20770 (release 24.0). In fungal members this domain is found at the C-terminus of putative transporter proteins.. 
PF12833 Helix-turn-helix domain<br>
PF12834 Integrase_l_N;<br>Phage integrase, N-terminal. Pfam-B_50 (release 24.0). This is a family of DNA-binding prophage integrases. It is found largely in Proteobacteria.. 
PF12835 Integrase<br>Pfam-B_50 (release 24.0). This is a family of DNA-binding prophage integrases found in Proteobacteria.. 
PF12836 Helix-hairpin-helix motif<br>The HhH domain is a short DNA-binding domain  .. 
PF12837 4Fe-4S binding domain<br>This superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases.  Structure of the domain is an alpha-antiparallel beta sandwich.. 
PF12838 4Fe-4S dicluster domain<br>Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases.  Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters.. 
PF12840 Helix-turn-helix domain<br>This domain represents a DNA-binding Helix-turn-helix domain found in transcriptional regulatory proteins.. 
PF12841 YvrJ protein family<br>This family of short proteins are related to B. subtilis YvrJ protein. None of the members of this family have been functionally characterised.. 
PF12842 Domain of unknown function (DUF3819)<br>Pfam-B_986 (release 24.0). This is an uncharacterised domain that is found on the CCR4-Not complex component Not1.  Not1 is a global regulator of transcription that affects genes positively and negatively and is thought to regulate transcription factor TFIID  .. 
PF12843 Protein of unknown function (DUF3820)<br>Pfam-B_72 (release 24.0). This a bacterial family that is functionally uncharacterised.. 
PF12844 Helix-turn-helix domain<br>Members of this family contains a DNA-binding helix-turn-helix domain.. 
PF12845 TBD domain<br>The Tbk1/Ikki binding domain (TBD) is a 40 amino acid domain able to bind kinases, has been found to be essential for poly(I:C)-induced IRF activation  . The domain is found in SINTBAD, TANK and NAP1 protein. This domain is predicted to form an a-helix with residues essential for kinase binding clustering on one side  .. 
PF12846 AAA-like domain<br>This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.. 
PF12847 Methyltransferase domain<br>Protein in this family function as methyltransferases.. 
PF12848 ABC transporter<br>This domain is related to Pfam:PF00005.. 
PF12849 PBP superfamily domain<br>This domain belongs to the periplasmic binding protein superfamily.. 
PF12850 Calcineurin-like phosphoesterase superfamily domain<br>Members of this family are part of the Calcineurin-like phosphoesterase superfamily.. 
PF12851 TET_DSBH;<br>Oxygenase domain of the 2OGFeDO superfamily . A double-stranded beta helix (DSBH) fold domain of the 2-oxoglutarate (2OG)-Fe(II)-dependent dioxygenase (2OGFeDO) superfamily found in  various eukaryotes, bacteria and bacteriophages  . Members of this  family catalyze nucleic acid modifications, such as thymidine hydroxylation during base J synthesis in kinetoplastids  , and the conversion of 5 methyl-cytosine (5-mC) to 5-hydroxymethyl-cytosine  (hmC)  , or further oxidation to 5-formylcytosine (5fC) and  5-carboxylcytosine (5caC)  . Metazoan TET proteins contain a  cysteine-rich region inserted into the core of the DSBH fold.  Vertebrate TET proteins are oncogenes that are mutated in various  myeloid cancers  . Fungal and algal versions of this family are  linked to a predicted transposase and show lineage-specific  expansions  .. 
PF12852 Cupin<br>Pfam-B_918 (release 24.0). This is a family of bacterial and eukaryotic proteins that belong to the Cupin superfamily.  Some of the proteins in this family are annotated as being members of the AraC family of transcription factors, in which case this domain corresponds to the ligand binding domain.. 
PF12853 C-terminal of NADH-ubiquinone oxidoreductase 21 kDa subunit<br>This family is the C-terminal domain of NADH-ubiquinone oxidoreductase 21 kDa subunits from fungi.. 
PF12854 PPR repeat<br>Pfam-B_105542 (release 24.0). This family matches additional variants of the PPR repeat that were not captured by the model for Pfam:PF01535. The exact function is not known.. 
PF12855 Life-span regulatory factor<br>Pfam-B_42039 (release 24.0). This family is involved in the chronological life-span of S. cerevisiae. Over-expression leads to an extended viability of wild-type strains, indicating a role in regulation.. 
PF12856 Anaphase-promoting complex subunit 9<br>Apc9 is one of the subunits of the anaphase-promoting complex, or cyclosome  , which is essential for regulating entry into anaphase and exit from mitosis. The APC is a ubiquitin-protein ligase complex. All APC subunits are members of the cullin family proteins, which bind to a ring-finger subunit via a conserved cullin domain  . The APC is made up of four parts, the third of which is a tetratricopeptide repeat arm (TPR) that contains Apc9  .. 
PF12857 TOBE-like domain<br>Pfam-B_1384 (release 24.0). The TOBE domain   (Transport-associated OB) always occurs  as a dimer as the C-terminal strand of each domain is supplied by the partner. Probably involved in the recognition of small ligands such as molybdenum (eg Swiss:P46930) and sulfate (Swiss:P16676). Found in ABC transporters immediately  after the ATPase domain.. 
PF12859 Anaphase-promoting complex subunit 1<br>Apc1 is the largest of the subunits of the anaphase-promoting complex or cyclosome. The anaphase-promoting complex is a multiprotein subunit E3 ubiquitin ligase complex that controls segregation of chromosomes and exit from mitosis in eukaryotes [1,2]. Infection of human fibroblasts with human cytomegalovirus (HCMV) leads to cell cycle dysregulation, which is associated with the inactivation of the anaphase-promoting complex  .. 
PF12860 PAS fold<br>Pfam-B_21375 (release 24.0). The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs  . The PAS fold appears in archaea, eubacteria and eukarya.. 
PF12861 Anaphase-promoting complex subunit 11 RING-H2 finger<br>Apc11 is one of the subunits of the anaphase-promoting complex or cyclosome  . The APC subunits are cullin family proteins with ubiquitin ligase activity  . Polyubiquitination marks proteins for degradation by the 26S proteasome and is carried out by a cascade of enzymes that includes ubiquitin-activating enzymes (E1s), ubiquitin-conjugating enzymes (E2s), and ubiquitin ligases (E3s). Apc11 acts as an E3 enzyme and is responsible for recruiting E2s to the APC and for mediating the subsequent transfer of ubiquitin to APC substrates in vivo. In Saccharomyces cerevisiae this RING-H2 finger protein defines the minimal ubiquitin ligase activity of the APC, and the integrity of the RING-H2 finger is essential for budding yeast cell viability  .. 
PF12862 Anaphase-promoting complex subunit 5<br>Apc5 is a subunit of the anaphase-promoting complex/cyclosome (APC/C) which is a multi-subunit ubiquitin ligase that mediates the proteolysis of cell cycle proteins in mitosis and G1.  Apc5, although it does not harbour a classical RNA binding domain, Apc5 binds the poly(A) binding protein (PABP), which directly binds the internal ribosome entry site (IRES) of growth factor 2 mRNA. PABP was found to enhance IRES-mediated translation, whereas Apc5 over-expression counteracted this effect. In addition to its association with the APC/C complex, Apc5 binds much heavier complexes and co-sediments with the ribosomal fraction [1,2]. The N-terminus of Afi1 serves to stabilise the union between Apc4 and Apc5, both of which lie towards the bottom-front of the APC  . This region of the Apc5 member proteins carries a TPR-like motif.. 
PF12863 Domain of unknown function (DUF3821)<br>This is a domain largely confined to sequences from Methanomicrobiales found on putative lipases. The function is not known.. 
PF12864 Protein of unknown function (DUF3822)<br>This is a family of uncharacterised bacterial proteins. However, structural-similarity searches indicate the family takes on an actin-like ATPase fold.. 
PF12866 Protein of unknown function (DUF3823)<br>This is a family of uncharacterised proteins from Bacteroidetes. It has characteristic DN and DR sequence-motifs. The function is not known.. 
PF12867 DinB superfamily<br>The DinB family are an uncharacterised family of potential enzymes. The structure of these proteins is composed of a four helix bundle  .. 
PF12868 Domain of unknwon function (DUF3824)<br>This is a repeating domain found in fungal proteins. It is proline-rich, and the function is not known.. 
PF12869 tRNA_anti-like<br>JCSG_target_390051_3f1z. This is a family of bacterial, archeael and viral proteins that is related to the tRNA_anti family Pfam:PF01336. The major characteristic of families like tRNA_anti is their OB-fold, and many of them bind DNA.. 
PF12870 Lumazine-binding domain<br>JCSG_target_391926_3k7c. This is a family of putative lipoproteins from bacteria.  Many members of the family are defined as having a lumazine-binding domain. Lumazine is a fluorescent accessory protein having 6,7-dimethyl-8-(1'-D-ribityl) lumazine (DMRL) as its authentic chromophore; it modulates the emission of bacterial luciferase to shorter wavelengths with increasing luminous strength. The family is related to the NTF2-like transpeptidase family.. 
PF12871 Pre-mRNA-splicing factor 38-associated hydrophilic C-term<br>This domain is a hydrophilic region found at the C-terminus of plant and metazoan pre-mRNA-splicing factor 38 proteins.  The function is not known.. 
PF12872 OST_LOTUS;<br>OST-HTH/LOTUS domain. A predicted RNA-binding domain found in insect Oskar and vertebrate TDRD5/TDRD7 proteins that nucleate or organize structurally related ribonucleoprotein (RNP) complexes, the polar granule and nuage, is poorly understood   . The domain adopts the winged helix-turn-  helix fold and bind RNA with a potential specificity for dsRNA  .In  eukaryotes this domain is often combined in the same polypeptide with protein-protein- or lipid- interaction domains that might play a role in anchoring these proteins to specific cytoskeletal structures. Thus, proteins with this domain might have a key role in the recognition and localization of dsRNA, including miRNAs, rasiRNAs and piRNAs hybridized to their targets. In other cases, this domain is fused to ubiquitin-binding, E3 ligase and ubiquitin-like domains indicating a previously under-appreciated role for ubiquitination in regulating the assembly and stability of nuage-like RNP complexes. Both bacteria and eukaryotes encode a conserved family of proteins that combines this predicted RNA-binding domain with a previously uncharacterized RNAse domain belonging to the superfamily that includes the 5'->3' nucleases, PIN and NYN domains  .. 
PF12873 Domain of unknown function (DUF3825)<br>Potential uncharacterized enzymatic domain associated with bacterial Pfam:PF12872 domains.  Has conserved residues suggestive of an enzymatic role probably related to RNA metabolism.. 
PF12874 Zinc-finger of C2H2 type<br>This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found in multiple copies in a wide range of proteins from plants to metazoans. Some member proteins, particularly those from plants, are annotated as being RNA-binding.. 
PF12875 Protein of unknown function (DUF3826)<br>JCSG_target_393061_3g6i. This is a putative sugar-binding family.. 
PF12876 Sugar-binding cellulase-like<br>JCSG_target_394744_3gyc. This is a putative cellulase family.. 
PF12877 Domain of unknown function (DUF3827)<br>Zenonos ZA, Mistry J. This family contains the Swiss:Q9HCM3 protein which has been found to be fused fused to BRAF gene in many cases of pilocytic astrocytomas. The fusion is due mainly to a tandem duplication of 2 Mb at 7q34 [1-2].  Although nothing is known about the function of Swiss:Q9HCM3 protein, the BRAF protein is a well characterised oncoprotein. It is a serine/threonine protein kinase which is implicated in MAP/ERK signalling, a critical pathway for the regulation of cell division, differentiation and secretion [1-3].. 
PF12878 SICA extracellular beta domain<br>The SICA (schizont-infected cell agglutination) proteins of P. knowlesi, one of the variant antigen gene families, are associated with parasitic virulence. These proteins are comprised of multiple domains, with the extracellular domains occurring at different frequencies.  There can be between 1 and 10 copies of this cysteine-rich domain  .. 
PF12879 SICA C-terminal inner membrane domain <br>The SICA (schizont-infected cell agglutination) proteins of P. knowlesi, one of the variant antigen gene families, are associated with parasitic virulence. These proteins are comprised of multiple domains, with the extracellular domains occurring at different frequencies.  The C-terminal domain is thought to remain in the erythrocyte, found juxtaposition to the single transmembrane domain.  To date, all full length proteins contain a single copy of this domain  .. 
PF12881 NUT protein N terminus<br>Zenonos ZA, Mistry J. This family includes the NUT protein. The gene encoding for NUT protein (Nuclear Testis protein) is found fused to BRD3 or BRD4 genes, in some aggressive types of carcinoma, due to chromosomal translocations [1-2]. Proteins of the BRD family contain two bromodomains that bind transcriptionally active chromatin through associations with acetylated histones H3 and H4 [1-2]. Such proteins are crucial for the regulation of cell cycle progression. On the other hand, little is known about NUT protein. NUT is known to have a Nuclear Export Sequence (NES) as well as a Nuclear Localization Signal (NLS), both located towards the C-terminal end of the protein [1-2]. A fused NUT-GFP protein showed either cytoplasmic or nuclear localization, suggesting that it is subject to nuclear/cytoplasmic shuttling. Consistent with this possibility, treatment with leptomycin B an inhibitor of CRM1-dependent nuclear export resulted in re-distribution of NUT-GFP to the nucleus [3-4]. Inspection of NUT revealed a C-terminal sequence similar to known nuclear export sequences (NES) which are often regulated by phosphorylation [3-4].. 
PF12882 NUT protein C terminal<br>Zenonos ZA, Mistry J. This family includes the NUT protein. The gene encoding for NUT protein (Nuclear Testis protein) is found fused to BRD3 or BRD4 genes, in some aggressive types of carcinoma, due to chromosomal translocations [1-2]. Proteins of the BRD family contain two bromodomains that bind transcriptionally active chromatin through associations with acetylated histones H3 and H4 [1-2]. Such proteins are crucial for the regulation of cell cycle progression. On the other hand, little is known about NUT protein. NUT is known to have a Nuclear Export Sequence (NES) as well as a Nuclear Localization Signal (NLS) [1-2], both located C-terminal to this domain. A fused NUT-GFP protein showed either cytoplasmic or nuclear localization, suggesting that it is subject to nuclear/cytoplasmic shuttling. Consistent with this possibility, treatment with leptomycin B an inhibitor of CRM1-dependent nuclear export resulted in re-distribution of NUT-GFP to the nucleus [3-4]. Inspection of NUT revealed a C-terminal sequence similar to known nuclear export sequences (NES) which are often regulated by phosphorylation [3-4].. 
PF12883 Protein of unknown function (DUF3828)<br>JCSG_target_392985_3kzt. This is a family of bacterial proteins of unknown function.. 
PF12884 Transducer of regulated CREB activity, N terminus<br>Zenonos ZA, Mistry J. This family includes the N terminal region of TORC proteins. TORC (Transducer of regulated CREB activity) is a protein family of coactivators that enhances the activity of CRE-depended transcription via a phosphorylation-independent interaction with the bZIP DNA binding/dimerisation domain of CREB (cAMP Response Element-Binding)  . The proteins display a highly conserved predicted N-terminal coiled-coil domain and an invariant sequence matching a protein kinase A (PKA) phosphorylation consensus sequence (RKXS)  . The coiled-coil structure interacts with the bZIP domain of CREB  . This interaction may occur via ionic bonds because it is disrupted under high-salt conditions  . In addition to CREB-binding, the N-terminal region plays a role in the tetramer formation of TORCs  , but the physiological function of the multimeric complex has not been clarified yet.. 
PF12885 Transducer of regulated CREB activity middle domain<br>Zenonos ZA, Mistry J. This family includes the region between the N and C terminus of TORC proteins. TORC (Transducer of regulated CREB activity) is a protein family of coactivators that enhances the activity of CRE-depended transcription via a phosphorylation-independent interaction with the bZIP DNA binding/dimerisation domain of CREB (cAMP Response Element-Binding)  . Although the C- and N- terminal domains of these proteins have been well characterised [1-2], no functional role has been assigned to the central region, yet.. 
PF12886 Transducer of regulated CREB activity, C terminus<br>Zenonos ZA, Mistry J. This family includes the C terminal region of TORC proteins. TORC (Transducer of regulated CREB activity) is a protein family of coactivators that enhances the activity of CRE-depended transcription via a phosphorylation-independent interaction with the bZIP DNA binding/dimerisation domain of CREB (cAMP Response Element-Binding)  . The C terminus region is negatively charged, resembling the transcription activation domains. When this domain, from all three human TORC proteins, was expressed as fusion proteins with the DNA-binding domain of GAL4 (GAL4-BD), and tested for induction of a minimal promoter linked to GAL4-binding sites (UAS-GAL4), UAS-GAL4 was potently induced by GAL4-BD fusions containing the C-terminal portion of all three human TORCs  .. 
PF12887 SICA extracellular alpha domain<br>The SICA (schizont-infected cell agglutination) proteins of P. knowlesi, one of the variant antigen gene families, are associated with parasitic virulence. These proteins are comprised of multiple domains, with the extracellular domains occurring at different frequencies.  This domain is typically found at the N-terminus, with 1 or 2 copies per protein.  The domain is cysteine-rich domain  and similar to PFAM:PF12878  .. 
PF12888 Lipid-binding putative hydrolase<br>JCSG_target_393040_3h3i. This is a small family of lipid-binding proteins found in Bacteroidetes.. 
PF12889 Protein of unknown function (DUF3829)<br>JCSG_target_393163_3iee. This is a small family of proteins from several bacterial species, whose function is not known. It may, however, be related to the GvpL_GvpF family of proteins, Pfam:PF06386.. 
PF12890 Dihydro-orotase-like<br>This is a small family of dihydro-orotase-like proteins from various bacteria.. 
PF12891 Glycoside hydrolase family 44<br>This is a family of bacterial glycoside hydrolases formerly known as cellulase family J, and now known as Cel44A. It is one of the major enzymatic components of the cellulosome of Clostridium thermocellum strain F1 and of many other Firmicutes.. 
PF12892 T surface-antigen of pili<br>The FCT and equivalent region genes of Streptococcus pyogenes and other related bacteria encode surface proteins that include fibronectin- and collagen-binding proteins and the serological markers known as T antigens. Some of these proteins give rise to pilus-like appendages  . The FctA family is found in many Firmicutes and related bacteria. In S. pyogenes, the pili have a role in bacterial adherence and colonisation of human tissues  .. 
PF12893 Putative lumazine-binding<br>This is a family of uncharacterised proteins. However, the family belongs to the NTF2-like superfamily of various enzymes, and some of the members of the family are putative dehydrogenases.. 
PF12894 Anaphase-promoting complex subunit 4 WD40 domain<br>Apc4 contains an N-terminal propeller-shaped WD40 domain.The N-terminus of Afi1 serves to stabilise the union between Apc4 and Apc5, both of which lie towards the bottom-front of the APC,. 
PF12895 Anaphase-promoting complex, cyclosome, subunit 3<br>Apc3, otherwise known as Cdc27, is one of the subunits of the anaphase-promoting complex or cyclosome. The anaphase-promoting complex is a multiprotein subunit E3 ubiquitin ligase complex that controls segregation of chromosomes and exit from mitosis in eukaryotes [1, 2]. The protein members of this family contain TPR repeats just as those of Apc7 do, and it appears that these TPR units bind the C-termini of the APC co-activators CDH1 and CDC20  .. 
PF12896 Anaphase-promoting complex, cyclosome, subunit 4<br>Apc4 is one of the larger of the subunits of the anaphase-promoting complex or cyclosome. This family represents the long domain downstream of the WD40 repeat/s that are present on the Apc4 subunits. The anaphase-promoting complex is a multiprotein subunit E3 ubiquitin ligase complex that controls segregation of chromosomes and exit from mitosis in eukaryotes [1,2]. Results in C.elegans show that the primary essential role of the spindle assembly checkpoint is not in the chromosome segregation process itself but rather in delaying anaphase onset until all chromosomes are properly attached to the spindle.  the APC/C is likely to be required for all metaphase-to-anaphase transitions in a multicellular organism  .. 
PF12897 Alanine-glyoxylate amino-transferase<br>JCSG_target_390749_3ez1. These proteins catalyse the reversible transfer of an amino group from the amino acid substrate to an acceptor alpha-keto acid  . They require pyridoxal 5'-phosphate (PLP) as a cofactor to catalyse this reaction. Trans-amination reactions are of central importance in amino acid metabolism and in links to carbohydrate and fat metabolism. This class of aminotransferases acts as dimers in a head-to-tail configuration  .. 
PF12898 Stc1 domain<br>The domain contains 8 conserved cysteines that may bind to zinc. In S. pombe this protein acts as a protein linker which links the chromatin modifying CLRC complex to RNAi by tethering it to the RITS complex. The region is reported as a LIM domain here, but has a slightly different arrangement of its CxxC pairs from the Pfam LIM domain Pfam:PF00412, hence why it is not part of that family  . The tandem zinc-finger structure could mediate protein-protein interactions.. 
PF12899 Alkaline and neutral invertase<br>This is a family of bacterial and plant alkaline and neutral invertases, EC:3.2.1.26, previously known as Invertase_neut Pfam:PF04853.. 
PF12900 Pyridoxamine 5'-phosphate oxidase<br>Pyridoxamine 5'-phosphate oxidase is a FMN flavoprotein that catalyses the oxidation of pyridoxamine-5-P (PMP) and pyridoxine-5-P (PNP) to pyridoxal-5-P (PLP).  This entry contains several pyridoxamine 5'-phosphate oxidases, and related proteins.. 
PF12901 SUZ-C motif<br>The SUZ-C domain is a conserved motif found in one or more copies in several RNA-binding proteins. It is always found at the C-terminus of the protein and appear to be required for localization of the protein to specific subcellular structures. It was first characterized in the C.elegans protein Szy-20 which localizes to the centrosome. It is widely distributed in eukaryotes.. 
PF12902 Ferritin-like<br>JCSG_target_390707_3hli. This is a family of bacterial ferritin-like substances that also includes a C-terminal domain of VioB, polyketide synthase enzymes, that make up one of the key components of the violacein biosynthesis pathway. Violacein is a purple-coloured, broad-spectrum antibacterial pigment.. 
PF12903 Protein of unknown function (DUF3830)<br>JCSG_target_392654_3kop. This is a family of bacterial and archaeal proteins, the structure for one of whose members has been characterised. PDB:3kop from Swiss:A0JVT3 probably adopts a new hexameric form compared to previous structures. The putative active is near the domain interface. 3kop is most closely related, structurally to PDB:1zx8, where the potential active site is located near residues E51 and Y53 (conserved in 1zx8). Beyond the two residues above, the other residues are not conserved. Also the shape of the active site differs from that of 1zx8. PDB:1zx8 belongs to family DUF369. Pfam:PF04126, which is part of the cyclophilin-like clan.. 
PF12904 Putative collagen-binding domain of a collagenase <br>JCSG_target_393067_3kzs. This domain is likely to be the collagen-binding domain of a family of bacterial collagenase enzymes. It is the C-terminal part of the PDB:3kzs structure determined from Swiss:Q8A905 (information derived from TOPSAN).. 
PF12905 Endo-alpha-N-acetylgalactosaminidase<br>Virulence of pathogenic organisms such as the Gram-positive Streptococcus pneumoniae is largely determined by the ability to degrade host glycoproteins and to metabolise the resultant carbohydrates. This family is the enzymatic region, EC:3.2.1.97, of the cell surface proteins that specifically cleave Gal-beta-1,3-GalNAc-alpha-Ser/Thr (T-antigen, galacto-N-biose), the core 1 type O-linked glycan common to mucin glycoproteins. This reaction is exemplified by the S. pneumoniae protein Swiss:B2DRU5, where Asp764 is the catalytic nucleophile-base and Glu796 the catalytic proton donor.. 
PF12906 RING-variant domain<br>
PF12907 Zinc-binding<br>This is small family of metazoan zinc-binding proteins.. 
PF12909 Protein of unknown function (DUF3832)<br>JCSG_target_391895_3k6q. This is a family of proteins from bacteria and archaea of unknwon function. The N-terminal part of the structure from Swiss:Q0AZ30 shows remote homology to the N-terminus of the bacterial toxin/antitoxin 'addiction module', and the C-terminus is distantly related to the TTHA1013/TTHA0281 superfamily.. 
PF12910 Antitoxin of toxin-antitoxin stability system N-terminal<br>JCSG_target_391895_3k6q. This domain appears to be the N-terminus of the RelB antitoxin of toxin-antitoxin stability system or prevent-host death system. Together RelE toxin and the RelB antitoxin form a non-toxic complex.  Although toxin-antitoxin gene cassettes were first found in plasmids, it is clear that these loci are abundant in free-living prokaryotes, including many pathogenic bacteria, and these toxin-antitoxin loci provide a control mechanism that helps free-living prokaryotes cope with nutritional stress [1,2].. 
PF12911 N-terminal TM domain of oligopeptide transport permease C<br>Pfam-B_1473 (release 24.0). Oligopeptide permeases (Opp) have been identified in numerous gram-negative and -positive bacteria. These transport systems belong to the superfamily of highly conserved ATP-binding cassette transporters. Typically, Opp importers comprise a complex of five proteins. The oligopeptide-binding protein OppA is responsible for the capture of peptides from the external medium. Two integral highly hydrophobic membrane spanning proteins, OppB and OppC, form a channel through the membrane used for peptide translocation.  This N-terminal domain appears to be the first TM domain of the molecule  .. 
PF12912 N-term_NLPC_P60;<br>NLPC_P60 stabilising domain, N term. Pfam-B_845 (release 24.0). This domain, at the N-terminus, appears to be the stabilising domain for the structure from Swiss:Q72DN3, PDB:3m1u, which is a four-domain protein. The next domain is an SH3b1, the third an SH3b2 and the last, the C-terminal region, the catalytic domain of the cysteine-peptidase type, ie family NLPC_P60, Pfam:PF00877 (details derived from TOPSAN).. 
PF12913 SH3 domain of the SH3b1 type<br>JCSG_target_405735_3m1u. This domain appears to be an SH3 domain of the SH3b1-type, and is just C-terminal to an N-terminal domain that is probably the stabilising domain for the structure from Swiss:Q72DN3, PDB:3m1u, which is a four-domain protein. The next domain is an SH3b2 and the last, the C-terminal region, is the catalytic domain of the cysteine-peptidase type, ie family NLPC_P60, Pfam:PF00877 (details derived from TOPSAN).. 
PF12914 SH3 domain of SH3b2 type<br>JCSG_target_405735_3m1u. This domain appears to be an SH3 domain of the SH3b2-type, and is the second SH3 domain to be found, downstream of an N-terminal domain that is probably the stabilising domain, for the structure from Swiss:Q72DN3, PDB:3m1u, which is a four-domain protein.  The last, the C-terminal region, is the catalytic domain of the cysteine-peptidase type, ie family NLPC_P60, Pfam:PF00877 (details derived from TOPSAN).. 
PF12915 Protein of unknown function (DUF3833)<br>Pfam-B_259 (release 24.0). This is a family of uncharacterised proteins found in Proteobacteria.. 
PF12916 Protein of unknown function (DUF3834)<br>This family is likely to be related to solute-binding lipo-proteins.. 
PF12917 HD_1;<br>HD containing hydrolase-like enzyme . This is a family of bacterial and archaeal hydrolases.. 
PF12918 TcdB toxin N-terminal helical domain<br>This is a short helical bundle domain found associated with the catalytic domain of the TcdB toxin from C. difficile  . The function of this domain is unknown, but it may be involved in substrate recognition.. 
PF12919 TcdA/TcdB catalytic glycosyltransferase domain<br>This domain represents the N-terminal glycosyltransferase from a set of toxins found in some bacteria. This domain in TcdB glycosylates the host RhoA protein.. 
PF12920 TcdA/TcdB pore forming domain<br>This family represents the most conserved region within the C. difficile Toxin A and Toxin B pore forming region.. 
PF12921 Mitochondrial ATPase expression<br>ATP13 is necessary for the expression of subunit 9 of mitochondrial ATPase. The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria  .. 
PF12922 non-SMC mitotic condensation complex subunit 1, N-term<br>Pfam-B_15091 (release 24.0). The three non-SMC (structural maintenance of chromosomes) subunits of the mitotic condensation complex are Cnd1-3. The whole complex is essential for viability and the condensing of chromosomes in mitosis. This is the conserved N-terminus of the subunit 1.. 
PF12923 Ribosomal RNA-processing protein 7 (RRP7)<br>Pfam-B_1057 (release 24.0). RRP7 is an essential protein in yeast that is involved in pre-rRNA processing and ribosome assembly  .  It is speculated to be required for correct assembly of rpS27 into the pre-ribosomal particle [1-2].. 
PF12924 Copper-binding of amyloid precursor, CuBD<br>This short domain, part of the extra-cellular N-terminus of the amyloid precursor protein, APP, can bind both copper and zinc, CuBD.  The structure of Cu2+-bound CuBD reveals that the metal ligands are His147, His151, Tyr168 and two water molecules, which are arranged in a square pyramidal geometry. The structure of Cu+-bound CuBD is almost identical to the Cu2+-bound structure except for the loss of one of the water ligands. The geometry of the site is unfavourable for Cu+, thus providing a mechanism by which CuBD could readily transfer Cu ions to other proteins.. 
PF12925 E2 domain of amyloid precursor protein<br>The E2 domain is the largest of the conserved domains of the amyloid precursor protein. The structure of E2 consists of two coiled-coil sub-structures connected through a continuous helix, and bears an unexpected resemblance to the spectrin family of protein structures.E 2 can reversibly dimerise in solution, and the dimerisation occurs along the longest dimension of the molecule in an antiparallel orientation, which enables the N-terminal substructure of one monomer to pack against the C-terminal substructure of a second monomer. The high degree of conservation of residues at the putative dimer interface suggests that the E2 dimer observed in the crystal could be physiologically relevant. Heparin sulfate proteoglycans, the putative ligands for the precursor present in extracellular matrix, bind to E2 at a conserved and positively charged site near the dimer interface  .. 
PF12926 Mitotic-spindle organizing gamma-tubulin ring associated<br>FAM128A and FAM128B proteins have been re-named MOZART2A and B. The name MOZART is derived from letters of 'mitotic-spindle organizing proteins associated with a ring of gamma-tubulin'. This family operates as part of the gamma-tubulin ring complex, gamma-TuRC, one of the complexes necessary for chromosome segregation. This complex is located at centrosomes and mediates the formation of bipolar spindles in mitosis; it consists of six subunits. However, unlike the other four known subunits, the MOZART proteins, both 1 and 2, do not carry the conserved 'Spc97-Spc98' GCP domain, so the TUBCGP nomenclature cannot be used for it. The exact function of MOZART2 is not clear  .. 
PF12927 Domain of unknown function (DUF3835)<br>Pfam-B_14632 (release 24.0). This is a C-terminal domain conserved in fungi.. 
PF12928 tRNA-splicing endonuclease subunit sen54 N-term<br>Pfam-B_644 (release 24.0). This is an N-terminal family of archaeal and metazoan sen54 proteins that forms one of the tRNA-splicing endonuclease subunits.. 
PF12929 Stretch-activated Ca2+-permeable channel component<br>Pfam-B_1244 (release 24.0). MID1 is a yeast Saccharomyces cerevisiae gene encoding a plasma membrane protein required for Ca2+ influx induced by the mating pheromone, alpha-factor. Mid1 protein plays a crucial role in supplying Ca2+ during the mating process. Mid1 is composed of 548-amino-acid residues with four hydrophobic regions named H1, H2, H3 and H4, and two cysteine-rich regions (C1 and C2) at the C-terminal. This family contains the H3, H4, C1 and C2 regions. suggesting that H1 is a signal sequence responsible for the alpha-factor-induced Mid1 delivery to the plasma membrane. The region from H1 to H3 is required for the localisation of Mid1 in the plasma and ER membranes. Trafficking of Mid1-GFP to the plasma membrane is dependent on the N-glycosylation of Mid1 and the transporter protein Sec12. This findings suggests that the trafficking of Mid1-GFP to the plasma membrane requires a Sec12-dependent pathway from the ER to the Golgi, and that Mid1 is recruited via a Sec6- and Sec7-independent pathway from the Golgi to the plasma membrane.. 
PF12930 Family of unknown function (DUF3836)<br>Family of uncharacterised proteins found in Bacteroidales species. Test.. 
PF12931 Sec23-binding domain of Sec16<br>Sec16 is a multi-domain vesicle coat protein. The C-terminal region is the part that binds to Sec23, a COPII vesicle coat protein. This association is part of the transport vesicle coat structure  .. 
PF12932 Vesicle coat trafficking protein Sec16 mid-region<br>Sec16 is a multi-domain vesicle coat protein. This central region is the functional part of the molecules and thus is vital for the family's role in mediating the movement of protein-cargo between the organelles of the secretory pathway  .. 
PF12933 FTO catalytic domain<br>This domain is the catalytic AlkB-like domain from the FTO protein  . This domain catalyses a demethylase activity with a preference for 3-methylthymidine.. 
PF12934 FTO C-terminal domain<br>This domain is found at the C-terminus of the FTO protein which was shown to be associated with increased BMI and obesity risk in humans.  The N-terminal domain of this protein is a DNA demethylase and this domain is found to associate with the N-terminal domain in the crystal structure  . This domain is alpha helical with three helices that form a bundle  .. 
PF12935 Vesicle coat trafficking protein Sec16 N-terminus<br>Sec16 is a multi-domain vesicle coat protein. The overall function of Sec16 is in mediating the movement of protein-cargo between the organelles of the secretory pathway. Over-expression of truncated mutants of only the N-terminus are lethal, and this portion does not appear to be essential for function so may act as a stabilising region  .. 
PF12936 KRI1-like family C-terminal<br>Pfam-B_8372 (release 7.7). The yeast member of this family (Kri1p) is found to be required for 40S ribosome biogenesis in the nucleolus  . This is the C-terminal domain of the family.. 
PF12937 F-box-like<br>Pfam-B_22368 (release 24.0). This is an F-box-like family.. 
PF12938 M domain of GW182<br>
PF12939 Domain of unknown function (DUF3837)<br>A small, compact all-alpha helical domain of unknown function. This domain is currently only found in Clostridiales species. . 
PF12940 Recombination-activation protein 1 (RAG1)<br>This famiy contains recombination activating protein 1, which is the catalytic component of the RAG complex.  The RAG complex is a multi-protein complex that mediates DNA cleavage during V(D)J (variable-diversity-joining) recombination  .  RAG1 mediates DNA-binding to the conseved recombination signal sequences (RSS)  .  Many of the proteins in this family are fragments.. 
PF12941 DUF3838;<br>HCV NS5a protein C-terminal region. This is a family of proteins found in the hepatitis C virus. This family contains the C-terminal region of the NS5A protein.  CC The molecular function of the non-structural 5a protein is uncertain.  The NS5a protein is phosphorylated when expressed in mammalian cells.  It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR, Swiss:P19525.. 
PF12942 Archaeal ammonia monooxygenase subunit A (AmoA)<br>This is an archeael family that contains ammonia monooxygenase subunit A.  Ammonia monooxygenase is an enzyme that oxidises ammonia to nitrite and nitrate, thus playing a significant role in the nitrogen cycle.  Ammonia-oxidising archaea (AOA) are widespread in marine environments  .. 
PF12943 Protein of unknown function (DUF3839)<br>This is a family of uncharacterised proteins that are found in Trichomonas.. 
PF12944 Protein of unknown function (DUF3840)<br>This is a family of uncharacterised proteins found in hepatitis A viruses.. 
PF12945 Flagellar protein YcgR<br>Mistry J, Auchincloss A. This domain is found N terminal to Pfam:PF07238.  Proteins which contain YcgR domains are known to interact with the flagellar switch-complex proteins FliG and FliM.  This interaction results in a reduction of torque generation and induces CCW motor bias  .  This family contains members not captured by Pfam:PF07317.. 
PF12946 MSP1 EGF domain 1<br>This EGF-like domain is found at the C-terminus of the malaria parasite MSP1 protein. MSP1 is the merozoite surface protein 1. This domain is part of the C-terminal fragment that is proteolytically processed from the the rest of the protein and is left attached to the surface of the invading parasite.. 
PF12947 EGF domain<br>This family includes a variety of EGF-like domain homologues. This family includes the C-terminal domain of the malaria parasite MSP1 protein  .. 
PF12948 MSP7-like protein C-terminal domain<br>MSP7 is a protein family the malaria parasite that has been found to be associated with processed fragments from the MSP1 protein in a complex involved in red blood cell invasion.. 
PF12949 SAP_2;<br>Mistry J, Sazer S, Wood V. This is a HeH domain.  HeH domains form helix-extended loop-helix (HeH) structures.\.       This domain is closely related to Pfam:PF03020 and Pfam:PF02037.. 
PF12950 TaqI-like C-terminal specificity domain<br>This domain is found at the C-terminus of the TaqI protein and is involved in DNA-binding and substrate recognition.. 
PF12951 Autotransporter-associated beta strand repeat<br>This model represent a core 32-residue region of a class of bacterial protein repeat found in one to 30 copies per protein. Most proteins with a copy of this repeat have domains associated with membrane autotransporters (Pfam:PF03797). The repeats occur with a periodicity of 60 to 100 residues. A pattern of sequence conservation is that every second residue is well-conserved across most of the domain. These repeats as likely to have a beta-helical structure.. 
PF12952 Domain of unknown function (DUF3841)<br>This presumed domain is around 190 amino acids in length. As yet no function has been given to any member of the family.. 
PF12953 Domain of unknown function (DUF3842)<br>This short protein is found mainly in firmicute bacteria. It is functionally uncharacterised.. 
PF12954 Protein of unknown function (DUF3843)<br>JCSG - Joint Center for Structural Genomics. A family of uncharacterized proteins found by clustering human gut metagenomic sequences  .. 
PF12955 Domain of unknown function (DUF3844)<br>This presumed domain is found in fungal species.  It contains 8 largely conserved cysteine residues. This domain is found in proteins that are thought to be found in the endoplasmic reticulum.. 
PF12956 Domain of Unknown Function with PDB structure<br>JCSG structure PDB:3GF6. Member PDB:3GF6 has statistically significant similarity  to TNF-like jelly roll fold may indicate an immunomodulatory  function  or a bioadhesion role . 
PF12957 Domain of unknown function (DUF3846)<br>JCSG - Joint Center for Structural Genomics. A family of uncharacterized proteins found by clustering human gut metagenomic sequences  . This domain is found associated with an Pfam:PF07275 like domain. This suggests that this family may also be involved in evading host restriction.. 
PF12958 Protein of unknown function (DUF3847)<br>JCSG - Joint Center for Structural Genomics. A family of uncharacterized proteins found by clustering human gut metagenomic sequences  .. 
PF12959 Protein of unknown function (DUF3848)<br>JCSG - Joint Center for Structural Genomics. A family of uncharacterized proteins found by clustering human gut metagenomic sequences  . This domain frequently seen with DUF3849.. 
PF12960 Protein of unknown function (DUF3849)<br>JCSG-Joint Centrer for Structural Genomics. A family of uncharacterized proteins found by clustering human gut metagenomic sequences  . This domain frequently seen with DUF3848.. 
PF12961 Domain of Unknown Function with PDB structure (DUF3850)<br>JCSG structure PDB:3IUW. The search results from NCBI sequence alignment indicates a conserved domain belonging to ASCH superfamily  . Dali searching results show that the protein is a structurally similar to the PUA domain, suggesting it may be involved in RNA recognition. It has been reported that the deletion of PUA genes results in impaired growth (RluD) and competitive disadvantage (TruB) in Escherichia coli.  Suggestions have been put forward that, apart from their usual catalytic role, certain PUS enzymes (e.g. TruB) may also act as chaperones for RNA folding. The interface interaction indicates that the biomolecule of protein NP_809782.1 should be a dimer.. 
PF12962 Protein of unknown function (DUF3851)<br>JCSG - Joint Center for Structural Genomics. A family of uncharacterised proteins found by clustering human gut metagenomic sequences  .. 
PF12963 Protein of unknown function (DUF3852)<br>JCSG - Joint Center for Structural Genomics. A family of uncharacterized proteins found by clustering human gut metagenomic sequences  . This domain frequently seen with DUF3848.. 
PF12964 Protein of unknown function (DUF3853)<br>JCSG - Joint Center for Structural Genomics. A family of uncharacterized proteins found by clustering human gut metagenomic sequences  .. 
PF12965 Domain of unknown function (DUF3854)<br>JCSG - Joint Center for Structural Genomics. A family of uncharacterised proteins found by clustering human gut metagenomic sequences  . This domain is likely to be related to the Toprim domain.. 
PF12966 N-ATPase, AtpR subunit <br>Membrane protein with three predicted transmembrane segments, two of which contain conserved Arg residues. AtpR genes are found in the N-ATPase (archaeal-type F1-Fo-ATPase) operons and are predicted to interact with the conserved Glu/Asp residues in the c subunits, regulating the assembly and/or function of the membrane-embedded ring of 'c' (proteolipid) subunits (PFAM:PF00137).. 
PF12967 Domain of Unknown Function with PDB structure (DUF3855)<br>JCSG structure PDB:1O22. Family based on orphan protein (TM0875) from Thermotoga maritima that has been structurally determined as PDB:1022. The TM0875 gene of Thermotoga maritima encodes a hypothetical protein NP_228683   of unknown function. Analysis of TM0875 genomic context reveals the presence of MMT1 (a predicted Co/Zn/Cd cation transporter) and an inactive homolog of metal-dependent proteases. 1O22 shows weak structural similarity with the phosphoribosylformylglycinamidine synthase 1t4a (Dali Z-scr=4.6), the yggU protein (PDB structure:1n91; with DALI Z-scr=3), and with the thioesterase superfamily member (PDB structure 2cy9 - found using FATCAT), even though they have very low sequence identity.. 
PF12968 Domain of Unknown Function (DUF3856)<br>JCSG structure PDB:2HR2. TPR-like protein. The 2hr2 structure belongs to the SCOP all alpha class, TPR-like superfamily, CT2138-like family. A DALI search gives hits with the putative peptidyl-prolyl isomerase 2fbn (Z=16), the SGTA protein (Z=16), the PLCR protein 2qfc (Z=16), a putative FK506-binding protein (PDB:1qz2-A; DALI Z-score 15.3; RMSD 2.9; 16% sequence identity within 132 superimposed residues), and with the tetratricopeptide repeats of the protein phosphatase 5 (PDB:2bug; DALI Z-score 15.1; RMSD 2.5; 19% sequence identity within 117 superimposed residues).. 
PF12969 Domain of Unknown Function with PDB structure (DUF3857)<br>JCSG structure PDB:3KD4. This family is based on the first domain of the PDB structure PDB:3KD4(residues 1-228). It is structurally similar to domains in other hydrolases, eg. M1 family aminopeptidase (3ebi, Z=10, rmsd 3.6A for 152 CA, seq id 12%), despite lack of any significant sequence similarity.. 
PF12970 Domain of Unknown Function with PDB structure (DUF3858)<br>JCSG structure PDB:3KD4. This family is based on the third domain of the PDB structure 3KD4(residues 410-525).  It is structurally similar to part of neuropilin-2 (Z=4.6, rmsd 3.6A for 83 CA, 7% seq id).  This domain and the second domain appears to be part of peptide-n-glycanase (1x3w, 2g9f).. 
PF12971 Alpha-N-acetylglucosaminidase (NAGLU) N-terminal domain<br>Pfam-B_6295 (release 7.7). Alpha-N-acetylglucosaminidase, a lysosomal enzyme required for the stepwise degradation of heparan sulfate  . Mutations on the alpha-N-acetylglucosaminidase (NAGLU) gene can lead to Mucopolysaccharidosis type IIIB (MPS IIIB; or Sanfilippo syndrome type B) characterised by neurological dysfunction but relatively mild somatic manifestations  . The structure shows that the enzyme is composed of three domains.  This N-terminal domain has an alpha-beta fold  .. 
PF12972 Alpha-N-acetylglucosaminidase (NAGLU) C-terminal domain<br>Pfam-B_6295 (release 7.7). Alpha-N-acetylglucosaminidase, a lysosomal enzyme required for the stepwise degradation of heparan sulfate  . Mutations on the alpha-N-acetylglucosaminidase (NAGLU) gene can lead to Mucopolysaccharidosis type IIIB (MPS IIIB; or Sanfilippo syndrome type B) characterised by neurological dysfunction but relatively mild somatic manifestations  . The structure shows that the enzyme is composed of three domains.  This C-terminal domain has an all alpha helical fold  .. 
PF12973 ChrR Cupin-like domain<br>Members of this family are part of the cupin superfamily. This family includes the transcriptional activator ChrR.. 
PF12974 ABC transporter, phosphonate, periplasmic substrate-binding protein <br>This is a family of periplasmic proteins which are part of the transport system for alkylphosphonate uptake.. 
PF12975 Domain of unknown function (DUF3859)<br>This short domain is functionally uncharacterised.. 
PF12976 Domain of Unknown Function with PDB structure (DUF3860)<br>JCSG structure PDB:2OD5. A protein family created to cover PDB:2OD5. 2OD5 is a hypothetical protein (JCVI_PEP_1096688149193) from an environmental metagenome (unidentified marine microbe).. 
PF12977 Domain of Unknown Function with PDB structure (DUF3861)<br>JCSG structure PDB:3CJL. The 3cjl structure is likely a representative of a new fold with some resemblance to 3-helical bundle folds such as the serum albumin-like fold of SCOP. No significant hits reported by a Dali search. This protein is the first structural representative of a small (about 60 proteins) family of proteins that are found among proteo- and enterobacteria (REF http://www.topsan.org/Proteins/JCSG/3CJL).. 
PF12978 Domain of Unknown Function with PDB structure (DUF3862)<br>JCSG structure PDB:3D4E. PDB:3D4E shared structural similarity to beta-lactamase inhibitory proteins (BLIP) which already include 1XXM, 1S0W, 1JTG, 2G2U, 2G2W, 2B5R, and 3due. All of structures are involved in beta-lactamase inhibitor complex.  (REF http://www.topsan.org/Proteins/JCSG/3d4e). 
PF12979 Domain of Unknown Function with PDB structure (DUF3863)<br>JCSG structure PDB:3LM3. Domain based on 1-364 domain of PDB:3LM3 which is encoded by the BDI_3119 gene from Parabacteroides distasonis atcc 8503.. 
PF12980 Domain of Unknown Function with PDB structure (DUF3864)<br>JCSG structure PDB:3LM3. Domain based on 366-449 domain of PDB:3LM3 which is encoded by the BDI_3119 gene from Parabacteroides distasonis atcc 8503.. 
PF12981 Domain of Unknown Function with PDB structure (DUF3865)<br>JCSG structure PDB:3B5P. Family based of PDB:3B5P encoded by ZP_00108531 from nitrogen-fixing cyanobacterium Nostoc punctiforme pcc 73102 is a CADD-like protein of unknown function. Superposition between protein structures encoded by CT610 from Chlamydia trachomatis (PDB code 1rwc), pyrroloquinolinquinone synthase C (PqqC, PDB code 1otv) and ZP_00108531 revealed that putative active sites in CT610 and ZP_00108531 are identical. ( REF: http://www.topsan.org/Proteins/JCSG/3B5P).. 
PF12982 Protein of unknown function (DUF3866)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 352 and 374 amino acids in length.. 
PF12983 Protein of unknown function (DUF3867)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 190 amino acids in length.. 
PF12984 Domain of unknown function, B. Theta Gene description (DUF3868)<br>Ellrott K, Bakolitsa C. Bacteroides thetaiotaomicron: BT_1065. Based on Bacteroides thetaiotaomicron gene BT_1065, a putative uncharacterized protein As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), It appears to be upregulated in the presence of host or other bacterial species vs when in culture [1,2].. 
PF12985 Domain of unknown function (DUF3869)<br>Ellrott K, Bakolitsa C. JCSG structure PDB:3KOG. A family based on the N-terminal domain of 3KOG, which shows weak but consistent remote homology with adhesive families such as immunoglobulins and cadherins, suggesting it might form an attachment module.. 
PF12986 Domain of unknown function (DUF3870)<br>Ellrott K, Bakolitsa C. JCSG structure PDB:3KOG. A family based on the C-terminal domain of 3KOG which shows structural similarity to pore-forming proteins   , suggesting it may have a lytic function. . 
PF12987 Domain of unknown function, B. Theta Gene description (DUF3871)<br>Ellrott K, Bakolitsa C. Bacteroides thetaiotaomicron: BT_2984. Based on Bacteroides thetaiotaomicron gene BT_2984, a putative uncharacterized protein  As seen in gene expression experiments  (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231). It appears to be upregulated in the presence of host or other bacterial species vs when in culture [1,2].. 
PF12988 Domain of unknown function, B. Theta Gene description (DUF3872)<br>Ellrott K, Bakolitsa C. Bacteroides thetaiotaomicron: BT_2593. Based on Bacteroides thetaiotaomicron gene BT_2593, a conserved protein found in a conjugate transposon. As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231). It appears to be upregulated in the presence of host or other bacterial species vs when in culture [1,2].. 
PF12989 Domain of unknown function, B. Theta Gene description (DUF3873)<br>Ellrott K, Bakolitsa C. Bacteroides thetaiotaomicron: BT_2286. Based on Bacteroides thetaiotaomicron gene BT_2286, a putative uncharacterized protein.  As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), it appears to be upregulated in the presence of host or other bacterial species vs when in culture [1,2].. 
PF12990 Domain of unknonw function from B. Theta Gene description (DUF3874)<br>Ellrott K, Bakolitsa C. Bacteroides thetaiotaomicron: BT_4228. Based on Bacteroides thetaiotaomicron gene BT_4228, a putative uncharacterized protein  As seen in gene expression experiments  (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), It appears to be upregulated in the presence of host or other bacterial species vs when in culture [1,2].. 
PF12991 Domain of unknown function, B. Theta Gene description (DUF3875)<br>Ellrott K, Bakolitsa C. Bacteroides thetaiotaomicron: BT_4769. Based on Bacteroides thetaiotaomicron gene BT_4769, a conserved protein found in a conjugate transposon. As seem in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231). It appears to be upregulated in the presence of host or other bacterial species vs when in culture [1,2].. 
PF12992 Domain of unknown function, B. Theta Gene description (DUF3876)<br>Ellrott K, Bakolitsa C. Bacteroides thetaiotaomicron: BT_0092. Based on Bacteroides thetaiotaomicron gene BT_0092, a conserved protein found in a conjugate transposon. As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), it appears to be upregulated in the presence of host or other bacterial species vs when in culture [1,2].. 
PF12993 Domain of unknown function, E. rectale Gene description (DUF3877)<br>Ellrott K, Bakolitsa C. Bacteroides thetaiotaomicron: EUBREC_0237. Based on Eubacterium rectale gene EUBREC_0237.  As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14737), it appears to be upregulated in the presence of Bacteroides thetaiotaomicron vs when isolated in culture  .. 
PF12994 Domain of unknown function, E. rectale Gene description (DUF3878)<br>Ellrott K, Bakolitsa C. Bacteroides thetaiotaomicron: EUBREC_0973. Based on Eubacterium rectale gene EUBREC_0973. As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14737). it appears to be upregulated in the presence of Bacteroides thetaiotaomicron vs when isolated in culture  .. 
PF12995 Domain of unknown function, E. rectale Gene description (DUF3879)<br>Ellrott K, Bakolitsa C. Bacteroides thetaiotaomicron: EUBREC_1343. Based on Eubacterium rectale gene EUBREC_1343.  As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14737), it appears to be upregulated in the presence of Bacteroides thetaiotaomicron vs when isolated in culture  .. 
PF12996 DUF based on E. rectale Gene description (DUF3880)<br>Ellrott K, Bakolitsa C. Bacteroides thetaiotaomicron: EUBREC_3218. Based on Eubacterium rectale gene EUBREC_3218.  As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14737),  It appears to be upregulated in the presence of  Bacteroides thetaiotaomicron vs when isolated in culture  .. 
PF12997 Domain of unknown function, E. rectale Gene description (DUF3881)<br>Ellrott K, Bakolitsa C. Bacteroides thetaiotaomicron: EUBREC_3695. Based on Eubacterium rectale gene EUBREC_3695.  As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14737), it appears to be upregulated in the presence of Bacteroides thetaiotaomicron vs when isolated in culture  .. 
PF12998 Inhibitor of growth proteins N-terminal histone-binding<br>Pfam-B_205 (release 24.0). Histones undergo numerous post-translational modifications, including acetylation and methylation, at residues which are then probable docking sites for various chromatin remodelling complexes. Inhibitor of growth proteins (INGs) specifically bind to residues that have been thus modified. INGs carry a well-characterised C-terminal PHD-type zinc-finger domain, binding with lysine 4-tri-methylated histone H3 (H3K4me3), as well as this N-terminal domain that binds unmodified H3 tails. Although these two regions can bind histones independently, together they increase the apparent association of the ING for the H3 tail.. 
PF12999 Glucosidase II beta subunit-like<br>The sequences found in this family are similar to a region found in the beta-subunit of glucosidase II (Swiss:P14314), which is also known as protein kinase C substrate 80K-H (PRKCSH). The enzyme catalyses the sequential removal of two alpha-1,3-linked glucose residues in the second step of N-linked oligosaccharide processing  . The beta subunit is required for the solubility and stability of the heterodimeric enzyme, and is involved in retaining the enzyme within the endoplasmic reticulum  .. 
PF13000 Acetyl-coenzyme A transporter 1<br>The mouse Acatn is a 61 kDa hydrophobic protein with six to 10 transmembrane domains. It appears to promote 9-O-acetylation in gangliosides.. 
PF13001 Proteasome stabiliser<br>Pfam-B_682 (release 24.0). The proteasome consists of two subunits, and the capacity of the proteasome to degrade protein depends crucially on the interaction between these two subunits. This interaction is affected by a wide range of factors including metabolites, such as ATP, and proteasome-associated proteins such as Ecm29. Ecm29 stabilises the interaction between the two subunits.. 
PF13002 Arrestin_N terminal like<br>This is a family of proteins related to the Arrestin_N terminal family.. 
PF13003 Ribosomal protein L1<br>This family includes putative ribosomal L1 and L10 proteins and fragments.. 
PF13004 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal<br>The BACON (Bacteroidetes-Associated Carbohydrate-binding Often N-terminal) domain is an all-beta domain found in diverse architectures, principally in combination with carbohydrate-active enzymes and proteases. These architectures suggest a carbohydrate-binding function which is also supported by the nature of BACON's few conserved amino-acids. The phyletic distribution of BACON and other data tentatively suggest that it may frequently function to bind mucin.. 
PF13005 HTH_Tnp_IS66;<br>zinc-finger binding domain of transposase IS66 . This is a zinc-finger region of the N-terminus of the insertion element IS66 transposase.. 
PF13006 Insertion element 4 transposase N-terminal<br>This family represents the N-terminal region of proteins carrying the transposase enzyme, DDE_Tnp_1 (that was Transposase_11), Pfam:PF01609, at the C-terminus. The full-length members are Insertion Element 4, IS4. Within the collection of E.coli strains, ECOR, the number of IS4 elements varies from zero to 14, with an average of 5 copies/strain  .. 
PF13007 Transposase C of IS166 homeodomain<br>This is a leucine-zipper-like or homeodomain-like region of transposase TnpC of insertion element IS66.. 
PF13008 Zinc-binding domain of Paramyxoviridae V protein<br>The Paramyxoviridae, which include such respiroviruses as para-influenzae and measles, produce phosphoproteins - protein P - that are integral to the polymerase transcription-replication complex. Protein P consists of two functionally distinct moieties, an N-terminal PNT, and a C-terminal PCT  . The P gene region transcribes proteins from all three ORFs, and the V protein consists of the PNT moiety and a more C-terminal 2-zinc-binding domain. This conserved region consists of the two-zinc-binding section sandwiched between beta sheets 6 and 7 of the overall V protein. It is the binding of this core domain of V protein with the DDB1 protein (part of the ubiquitin-ligase complex) of eukaryotes which represents the key element of the virus-host protein interaction  . In the Henipavirus family which includes Nipah and Hendra viruses, the V protein is able to block IFN (interferon) signalling by preventing IFN-induced STAT phosphorylation and nuclear translocation  .  The P gene of morbillivirus is co-transcriptionally edited leading to a V protein being produced.. 
PF13009 Putative phage integrase<br>Pfam-B_5288 (release 24.0). This family is found in association with IS elements.. 
PF13010 Primase helical domain<br>This alpha helical domain is found in a set of bacterial plasmid replication proteins  . The domain is found to the C-terminus of the primase/polymerase domain. Mutants of this domain are defective in template binding, dinucleotide formation and conformation change prior to DNA extension  .. 
PF13011 leucine-zipper of insertion element IS481<br>This is the upstream region of the conjoined ORF AB of insertion element 481. The significance of IS481 in the detection of Bordetella pertussis is discussed in  . The B portion of the ORF AB carries the transposase activity in family rve, PFAM:PF00665.. 
PF13012 Maintenance of mitochondrial structure and function<br>This is C-terminal to the Mov24 region of the yeast proteasomal subunit Rpn11 and seems likely to regulate the mitochondrial fission and tubulation processes, ie the outer mitochondrial membrane proteins. This function appears to be unrelated to the proteasome activity of the N-terminal region  .. 
PF13013 F-box-like domain<br>The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.. 
PF13014 KH domain<br>KH motifs bind RNA in vitro  . This RNA-binding domain is required for the efficient anchoring of ASH1-mRNA to the distal tip of the daughter cell. ASH1 is a specific repressor of transcription that localizes asymmetrically to the daughter cell nucleus.  RNA localisation is a widespread mechanism for achieving localised protein synthesis  .. 
PF13015 Glucosidase II beta subunit-like protein<br>The sequences found in this family are similar to a region found in the beta-subunit of glucosidase II (Swiss:P14314), which is also known as protein kinase C substrate 80K-H (PRKCSH). The enzyme catalyses the sequential removal of two alpha-1,3-linked glucose residues in the second step of N-linked oligosaccharide processing  . The beta subunit is required for the solubility and stability of the heterodimeric enzyme, and is involved in retaining the enzyme within the endoplasmic reticulum  . The beta-subunit confers substrate specificity for di- and monoglucosylated glycans on the glucose-trimming activity of the alpha-subunit  .. 
PF13016 Cys-rich Gliadin N-terminal<br>This is a cysteine-rich N-terminal region of gliadin and avenin plant proteins. The exact function is not known.. 
PF13017 piRNA pathway germ-plasm component<br>Maelstrom is a germ-plasm component protein, that is shown to be functionally involved in the piRNA pathway. It is conserved throughout Eukaryota, though it appears to have been lost from all examined teleost fish species.  The domain architecture shows that it is coupled with several DNA- and RNA- related domains such as HMG box, SR-25-like and HDAC_interact domains.  Sequence analysis and fold recognition have found a distant similarity between Maelstrom domain and the DnaQ 3'-5' exonuclease family with the RNase H fold (Exonuc_X-T, Pfam:PF00929); notably, that the Maelstrom domains from basal eukaryotes contain the conserved 3'-5' exonuclease active site residues (Asp-Glu-Asp-His-Asp, DEDHD). However, the animal and some amoeba maelstrom contain another set of conserved residues (Glu-His-His-Cys-His-Cys, EHHCHC). This evolutionary link together with structural examinations leads to the hypothesis that Maelstrom domains may have a potential nuclease-transposase activity or RNA-binding ability that may be implicated in piRNA biogenesis. A protein function evolution mode, namely "active site switch", has been proposed  , in which the amoeba Maelstrom domains are the possible evolutionary intermediates due to their harbouring of the specific characteristics of both 3'-5' exonuclease and Maelstrom domains.. 
PF13018 Extended Signal Peptide of Type V secretion system<br>Coggill P, Desvaux M. This conserved domain is called ESPR for Extended Signal Peptide Region. It is present at the N-terminus of the signal peptides of proteins belonging to the Type V secretion systems, including the autotransporters (T5aSS), TpsA exoproteins of the two-partner system (T5bSS) and trimeric autotransporters (TAAs). So far, the ESPR is present only in Gram-negative bacterial proteins originating from the classes Beta- and Gamma-proteobacteria. ESPR severely impairs inner membrane translocation, suggesting that it adopts a particular conformation or it interacts with a cytoplasmic or inner membrane co-factor, prior to exportation. Deletion of ESPR causes mis-folding of the TAAs passenger domain in the periplasm , substantially impairing its translocation across the outer membrane  .. 
PF13019 Ubiquitin-like;<br>Telomere stability and silencing. Pfam-B_2457 (release 24.0). Sde2 has been identified in fission yeast as an important factor in telomere formation and maintenance. This is a more N-terminal domain on these nuclear proteins, and is essential for telomeric silencing and genomic stability.. 
PF13020 Domain of unknown function (DUF3883)<br>This is a domain is uncharacterised.  It is found on restriction endonucleases.. 
PF13021 Domain of unknown function (DUF3885)<br>Pfam-B_1173 (release 24.0). A putative Rac prophage DNA binding protein. This domain family is found in bacteria, and is approximately 40 amino acids in length. There is a conserved YDDRG sequence motif. There is a single completely conserved residue D that may be functionally important.. 
PF13022 Helix-turn-helix of insertion element transposase<br>This is a family of largely phage proteins which are likely to be a helix-turn-helix insertion elements.. 
PF13023 HD domain<br>HD domains are metal dependent phosphohydrolases.. 
PF13024 Protein of unknown function (DUF3884)<br>Pfam-B_1352 (release 24.0). This family of proteins is functionally uncharacterised. However several proteins are annotated as Tagatose 1,6-diphosphate aldolase, but evidence to support this could not be found. This family of proteins is found in bacteria. Proteins in this family are typically between 61 and 106 amino acids in length. There are two completely conserved residues (Y and F) that may be functionally important.. 
PF13025 Protein of unknown function (DUF3886)<br>Pfam-B_1536 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There are two completely conserved L residues that may be functionally important.. 
PF13026 Protein of unknown function (DUF3887)<br>Pfam-B_1534 (release 24.0). This family of lipoproteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 128 and 167 amino acids in length. The proteins in this family contain an N-terminal lipid attachment site.. 
PF13027 Protein of unknown function (DUF3888)<br>Pfam-B_1080 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 111 and 149 amino acids in length.. 
PF13028 Protein of unknown function (DUF3889)<br>Pfam-B_1146 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length. There are two completely conserved residues (A and Y) that may be functionally important.. 
PF13029 Domain of unknown function (DUF3890)<br>Pfam-B_1148 (release 24.0). This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 70 amino acids in length.. 
PF13030 Protein of unknown function (DUF3891)<br>Pfam-B_1216 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are approximately 250 amino acids in length.. 
PF13031 Protein of unknown function (DUF3892)<br>Pfam-B_1252 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 87 and 104 amino acids in length.. 
PF13032 Domain of unknown function (DUF3893)<br>Pfam-B_1590 (release 24.0). This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is typically between 123 and 144 amino acids in length. There is a single completely conserved residue E that may be functionally important.. 
PF13033 Protein of unknown function (DUF3894)<br>Pfam-B_1594 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 66 and 79 amino acids in length. There are two conserved sequence motifs: FNIC and MALLNLT.. 
PF13034 Protein of unknown function (DUF3895)<br>Pfam-B_1598 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length. There are two completely conserved residues (Y and L) that may be functionally important.. 
PF13035 Protein of unknown function (DUF3896)<br>Pfam-B_1603 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length.. 
PF13036 Protein of unknown function (DUF3897)<br>This is a bacterial family of uncharacterised proteins.   Some of the proteins in this family are annotated as putative lipoproteins.. 
PF13037 Domain of unknown function (DUF3898)<br>Pfam-B_1179 (release 24.0). This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 90 amino acids in length. There are two conserved sequence motifs: DFG and FEKG.. 
PF13038 Domain of unknown function (DUF3899)<br>Pfam-B_1174 (release 24.0). Putative Tryptophanyl-tRNA synthetase.. 
PF13039 Protein of unknown function (DUF3900)<br>Pfam-B_1279 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 360 amino acids in length.. 
PF13040 Protein of unknown function (DUF3901)<br>Pfam-B_1316 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 50 amino acids in length. There is a single completely conserved residue L that may be functionally important.. 
PF13041 PPR repeat family <br>This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins.\.   The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR  .. 
PF13042 Protein of unknown function (DUF3902)<br>Pfam-B_1357 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 170 amino acids in length. There is a conserved LGI sequence motif.. 
PF13043 Domain of unknown function (DUF3903)<br>Pfam-B_1600 (release 24.0). This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 40 amino acids in length.. 
PF13044 Protein of unknown function (DUF3904)<br>Pfam-B_1386 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in viruses. Proteins in this family are typically between 437 and 448 amino acids in length.. 
PF13045 Protein of unknown function (DUF3905)<br>Pfam-B_1447 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length.. 
PF13046 Protein of unknown function (DUF3906)<br>Pfam-B_1532 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. There is a conserved EKK sequence motif.. 
PF13047 Protein of unknown function (DUF3907)<br>Pfam-B_1274 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 160 amino acids in length. There is a conserved AYTG sequence motif.. 
PF13048 Protein of unknown function (DUF3908)<br>Pfam-B_1533 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 140 amino acids in length. There is a single completely conserved residue Y that may be functionally important.. 
PF13049 Protein of unknown function (DUF3910)<br>Pfam-B_1539 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length.. 
PF13050 Protein of unknown function (DUF3911)<br>Pfam-B_1540 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length.. 
PF13051 Protein of unknown function (DUF3912)<br>Pfam-B_1615 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length.. 
PF13052 Protein of unknown function (DUF3913)<br>Pfam-B_1619 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length.. 
PF13053 Protein of unknown function (DUF3914)<br>Pfam-B_1562 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length. There are two conserved sequence motifs: KFDIR and DLW.. 
PF13054 Protein of unknown function (DUF3915)<br>Pfam-B_1549 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length.. 
PF13055 Protein of unknown function (DUF3917)<br>Pfam-B_1608 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length.. 
PF13056 Protein of unknown function (DUF3918)<br>Pfam-B_1567 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length. There are two completely conserved residues (G and R) that may be functionally important.. 
PF13057 Protein of unknown function (DUF3919)<br>Pfam-B_1479 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 251 and 262 amino acids in length. There is a conserved YLNG sequence motif.. 
PF13058 Protein of unknown function (DUF3920)<br>Pfam-B_1595 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 140 amino acids in length.. 
PF13059 Protein of unknown function (DUF3992)<br>Pfam-B_1628 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 87 and 98 amino acids in length.. 
PF13060 Protein of unknown function (DUF3921)<br>Pfam-B_1624 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length.. 
PF13061 Protein of unknown function (DUF3923)<br>Pfam-B_1586 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length.. 
PF13062 Protein of unknown function (DUF3924)<br>Pfam-B_1601 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length.. 
PF13063 Protein of unknown function (DUF3925)<br>Pfam-B_1644 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length.. 
PF13064 Protein of unknown function (DUF3927)<br>Pfam-B_1668 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 50 amino acids in length. There is a conserved SVL sequence motif. There is a single completely conserved residue D that may be functionally important.. 
PF13065 Protein of unknown function (DUF3928)<br>Pfam-B_1675 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length.. 
PF13066 Protein of unknown function (DUF3929)<br>Pfam-B_1716 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length.. 
PF13067 Protein of unknown function (DUF3930)<br>Pfam-B_1721 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 51 and 67 amino acids in length.. 
PF13068 Protein of unknown function (DUF3932)<br>Pfam-B_1731 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length.. 
PF13069 Protein of unknown function (DUF3933)<br>Pfam-B_1720 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length.. 
PF13070 Protein of unknown function (DUF3934)<br>Pfam-B_1719 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length. There are two conserved sequence motifs: GTG and SKG.. 
PF13071 Protein of unknown function (DUF3935)<br>Pfam-B_1715 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There are two conserved sequence motifs: FVF and LGV.. 
PF13072 Protein of unknown function (DUF3936)<br>Pfam-B_1705 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length. There is a conserved GKAW sequence motif. There is a single completely conserved residue G that may be functionally important.. 
PF13073 Protein of unknown function (DUF3937)<br>Pfam-B_1711 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length.. 
PF13074 Protein of unknown function (DUF3938)<br>Pfam-B_1607 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 130 amino acids in length.. 
PF13075 Protein of unknown function (DUF3939)<br>Pfam-B_1535 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 150 amino acids in length.. 
PF13076 Protein of unknown function (DUF3940)<br>Pfam-B_1673 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 50 amino acids in length.. 
PF13077 Protein of unknown function (DUF3909)<br>Pfam-B_1537 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length.. 
PF13078 Protein of unknown function (DUF3942)<br>Pfam-B_1722 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 130 amino acids in length.. 
PF13079 Protein of unknown function (DUF3916)<br>Pfam-B_1564 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 170 amino acids in length. There is a single completely conserved residue S that may be functionally important.. 
PF13080 Protein of unknown function (DUF3926)<br>Pfam-B_1663 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 46 and 63 amino acids in length. There is a single completely conserved residue P that may be functionally important.. 
PF13081 Domain of unknown function (DUF3941)<br>Pfam-B_1728 (release 24.0). This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 30 amino acids in length. There is a conserved YSK sequence motif.. 
PF13082 Protein of unknown function (DUF3931)<br>Pfam-B_1734 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length.. 
PF13083 KH domain<br>
PF13084 Domain of unknown function (DUF3943)<br>This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 110 amino acids in length.. 
PF13085 2Fe-2S iron-sulfur cluster binding domain<br>The 2Fe-2S ferredoxin family have a general core structure consisting of beta(2)-alpha-beta(2) which abeta-grasp type fold. The domain is around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated.. 
PF13086 AAA domain<br>This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.. 
PF13087 AAA domain<br>This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.. 
PF13088 BNR repeat-like domain<br>This family of proteins contains BNR-like repeats suggesting these proteins may act as sialidases.. 
PF13089 Polyphosphate kinase N-terminal domain<br>Splitting PF02503 into domains. Polyphosphate kinase (Ppk) catalyses the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate molecules.. 
PF13090 Polyphosphate kinase C-terminal domain<br>Splitting PF02503 into domains. Polyphosphate kinase (Ppk) catalyses the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate molecules. This C-terminal domain has a structure similar to phospholipase D.. 
PF13091 PLD-like domain<br>
PF13092 Kinetochore complex Sim4 subunit Fta1<br>CENP-L is one of the components that assembles onto the CENP-A-nucleosome distal (CAD) centromere. The centromere, which is the basic element of chromosome inheritance, is epigenetically determined in mammals. CENP-A, the centromere-specific histone H3 variant, assembles an array of nucleosomes and it is this that seems to be the prime candidate for specifying centromere identity. CENP-A nucleosomes directly recruit a proximal CENP-A nucleosome associated complex (NAC) comprised of CENP-M, CENP-N and CENP-T, CENP-U(50), CENP-C and CENP-H. Assembly of the CENP-A NAC at centromeres is dependent on CENP-M, CENP-N and CENP-T. Additionally, there are seven other subunits which make up the CENP-A-nucleosome distal (CAD) centromere, CENP-K, CENP-L, CENP-O, CENP-P, CENP-Q, CENP-R and CENP-S, also assembling on the CENP-A NAC  . Fta1 is the equivalent component of the fission yeast Sim4 complex  . The centromere, which is the basic element of chromosome inheritance, is epigenetically determined in mammals.. 
PF13093 CENP-U;<br>Kinetochore complex Fta4 of Sim4 subunit, or CENP-50. Fission yeast has three kinetochore protein complexes. Two complexes, Sim4 and Ndc80-MIND-Spc7 (NMS), are constitutive components, whereas the third complex, DASH, is transiently associated with kinetochores only in mitosis and is required for precise chromosome segregation. The Sim4 complex functions as a loading dock for the DASH complex. Sim4 consists of a number of different proteins including Ftas 1-7 and Dad1  .. 
PF13094 CENP-Q, a CENPA-CAD centromere complex subunit<br>CENP-Q is one of the components that assembles onto the CENPA-nucleosome distal (CAD) centromere. The centromere, which is the basic element of chromosome inheritance, is epigenetically determined in mammals. CENP-A, the centromere-specific histone H3 variant, assembles an array of nucleosomes and it is this that seems to be the prime candidate for specifying centromere identity. CENPA nucleosomes directly recruit a proximal CENPA-nucleosome-associated complex (NAC) comprised of CENP-M, CENP-N and CENP-T, CENP-U(50), CENP-C and CENP-H. Assembly of the CENPA NAC at centromeres is dependent on CENP-M, CENP-N and CENP-T. Additionally, there are seven other subunits which make up the CENPA-nucleosome distal (CAD) centromere, CENP-K, CENP-L, CENP-O, CENP-P, CENP-Q, CENP-R and CENP-S, also assembling on the CENP-A NAC  . Fta7 is the equivalent component of the fission yeast Sim4 complex  .. 
PF13095 Kinetochore Sim4 complex subunit FTA2<br>Fission yeast has three kinetochore protein complexes. Two complexes, Sim4 and Ndc80-MIND-Spc7 (NMS), are constitutive components, whereas the third complex, DASH, is transiently associated with kinetochores only in mitosis and is required for precise chromosome segregation. The Sim4 complex functions as a loading dock for the DASH complex. Sim4 consists of a number of different proteins including Ftas 1-7 and Dad1  . The equivalent higher eukaryotic protein is CENP-P. The centromere, which is the basic element of chromosome inheritance, is epigenetically determined in mammals. CENP-A, the centromere-specific histone H3 variant, assembles an array of nucleosomes and it is this that seems to be the prime candidate for specifying centromere identity. CENP-A nucleosomes directly recruit a proximal CENP-A nucleosome associated complex (NAC) comprised of CENP-M, CENP-N and CENP-T, CENP-U(50), CENP-C and CENP-H. Assembly of the CENP-A NAC at centromeres is dependent on CENP-M, CENP-N and CENP-T. Additionally, there are seven other subunits which make up the CENP-A-nucleosome distal (CAD) centromere, CENP-K, CENP-L, CENP-O, CENP-P, CENP-Q, CENP-R and CENP-S, also assembling on the CENP-A NAC  .. 
PF13096 ShortName;<br>CENP-A-nucleosome distal (CAD) centromere subunit, CENP-P. CENP-P is one of the components that assembles onto the CENP-A-nucleosome distal (CAD) centromere. The centromere, which is the basic element of chromosome inheritance, is epigenetically determined in mammals. CENP-A, the centromere-specific histone H3 variant, assembles an array of nucleosomes and it is this that seems to be the prime candidate for specifying centromere identity. CENP-A nucleosomes directly recruit a proximal CENP-A nucleosome associated complex (NAC) comprised of CENP-M, CENP-N and CENP-T, CENP-U(50), CENP-C and CENP-H. Assembly of the CENP-A NAC at centromeres is dependent on CENP-M, CENP-N and CENP-T. Additionally, there are seven other subunits which make up the CENP-A-nucleosome distal (CAD) centromere, CENP-K, CENP-L, CENP-O, CENP-P, CENP-Q, CENP-R and CENP-S, also assembling on the CENP-A NAC  . Fta7 is the equivalent component of the fission yeast Sim4 complex  .. 
PF13097 CENP-A nucleosome associated complex (NAC) subunit<br>CENP-U is one of the components that assembles onto the CENP-A-nucleosome associated complex (NAC). The centromere, which is the basic element of chromosome inheritance, is epigenetically determined in mammals. CENP-A, the centromere-specific histone H3 variant, assembles an array of nucleosomes and it is this that seems to be the prime candidate for specifying centromere identity. CENP-A nucleosomes directly recruit a proximal CENP-A nucleosome associated complex (NAC) comprised of CENP-M, CENP-N and CENP-T, CENP-U(50), CENP-C and CENP-H. Assembly of the CENP-A NAC at centromeres is dependent on CENP-M, CENP-N and CENP-T. Additionally, there are seven other subunits which make up the CENP-A-nucleosome distal (CAD) centromere, CENP-K, CENP-L, CENP-O, CENP-P, CENP-Q, CENP-R and CENP-S, also assembling on the CENP-A NAC  . FTA4 is the equivalent component of the fission yeast Sim4 complex. . 
PF13098 Thioredoxin-like domain<br>
PF13099 Domain of unknown function (DUF3944)<br>This short domain is sometimes found N terminal to Pfam:PF03981.. 
PF13100 OstA-like protein<br>This is a family of OstA-like proteins that are related to  Pfam:PF03968.. 
PF13101 Protein of unknown function (DUF3945)<br>JCSG - Joint Center for Structural Genomics. A family of uncharacterized proteins found by clustering human gut metagenomic sequences  . This is a C-terminal repeated region.. 
PF13102 DUF3946;<br>Phage integrase SAM-like domain. JCSG - Joint Center for Structural Genomics. A family of uncharacterized proteins found by clustering human gut metagenomic sequences  . This family appears related to the N-terminal domain of phage integrases.. 
PF13103 TonB C terminal<br>This family contains TonB members that are not captured by Pfam:PF03544.. 
PF13104 Protein of unknown function (DUF3956)<br>Pfam-B_1228 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length.. 
PF13105 Protein of unknown function (DUF3959)<br>Pfam-B_1424 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 260 amino acids in length.. 
PF13106 Domain of unknown function (DUF3961)<br>Pfam-B_1483 (release 24.0). This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 40 amino acids in length.. 
PF13107 Protein of unknown function (DUF3964)<br>Pfam-B_1516 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length. There are two conserved sequence motifs: FYF and AFW.. 
PF13108 Protein of unknown function (DUF3969)<br>Pfam-B_1576 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length.. 
PF13109 AsmA-like C-terminal region<br>Jackhammer-O25308 (H pylori). This family is similar to the C-terminal of the AsmA protein of E. coli.. 
PF13110 Protein of unknown function (DUF3966)<br>Pfam-B_1525 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 86 amino acids in length.. 
PF13111 Protein of unknown function (DUF3962)<br>Pfam-B_1505 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 233 and 796 amino acids in length. There is a conserved FSY sequence motif.. 
PF13112 Protein of unknown function (DUF3965)<br>Pfam-B_1524 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 380 amino acids in length.. 
PF13113 Protein of unknown function (DUF3970)<br>Pfam-B_1596 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. There is a conserved NPKY sequence motif.. 
PF13114 RecO N terminal<br>This entry contains members that are not captured by  Pfam:PF11967.. 
PF13115 YtkA-like<br>
PF13116 Protein of unknown function<br>Jackhammer_O25308 (H.pylori). Some members of this family are related to the AsmA family proteins.. 
PF13117 Cag pathogenicity island protein Cag12<br>This is a Proteobacterial family of Cag pathogenicity island proteins.. 
PF13118 Protein of unknown function (DUF3972) <br>This is a Proteobacterial family of unknown function.  Some of the proteins in this family are annotated as being kinesin-like proteins.. 
PF13119 Domain of unknown function (DUF3973)<br>Pfam-B_1636 (release 24.0). This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 40 amino acids in length. There is a conserved YCI sequence motif.. 
PF13120 Domain of unknown function (DUF3974)<br>Pfam-B_1643 (release 24.0). This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 130 amino acids in length.. 
PF13121 Domain of unknown function (DUF3976)<br>Pfam-B_1743 (release 24.0). This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 40 amino acids in length.. 
PF13122 Protein of unknown function (DUF3977)<br>Pfam-B_1744 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length.. 
PF13123 Protein of unknown function (DUF3978)<br>Pfam-B_1745 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 150 amino acids in length.. 
PF13124 Protein of unknown function (DUF3963)<br>Pfam-B_1512 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 42 and 85 amino acids in length. There is a conserved DIQKW sequence motif.. 
PF13125 Protein of unknown function (DUF3958)<br>Pfam-B_1404 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length. There are two conserved sequence motifs: RLF and TWH.. 
PF13126 Protein of unknown function (DUF3975)<br>Pfam-B_1736 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length.. 
PF13127 Protein of unknown function (DUF3955)<br>Pfam-B_966 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 68 and 87 amino acids in length. There are two completely conserved residues (G and E) that may be functionally important.. 
PF13128 Protein of unknown function (DUF3954)<br>Pfam-B_934 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 60 amino acids in length.. 
PF13129 Protein of unknown function (DUF3953)<br>Pfam-B_875 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 47 and 76 amino acids in length.. 
PF13130 Domain of unknown function (DUF3952)<br>Pfam-B_704 (release 24.0). This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 110 amino acids in length. There is a conserved VMSAS sequence motif.. 
PF13131 Protein of unknown function (DUF3951)<br>Pfam-B_698 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 56 and 71 amino acids in length. There is a conserved YTP sequence motif.. 
PF13132 Domain of unknown function (DUF3950)<br>Pfam-B_688 (release 24.0). This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 30 amino acids in length. There is a conserved NFS sequence motif.. 
PF13133 Protein of unknown function (DUF3949)<br>Pfam-B_636 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 69 and 87 amino acids in length.. 
PF13134 Protein of unknown function (DUF3948)<br>Pfam-B_550 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length.. 
PF13135 Protein of unknown function (DUF3947)<br>Pfam-B_493 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length.. 
PF13136 Protein of unknown function (DUF3984)<br>Pfam-B_3236 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 393 and 442 amino acids in length.. 
PF13137 Protein of unknown function (DUF3983)<br>Pfam-B_2658 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 40 amino acids in length. There is a conserved AWRN sequence motif.. 
PF13138 Protein of unknown function (DUF3982)<br>Pfam-B_2022 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 47 and 73 amino acids in length. There are two conserved sequence motifs: EKL and EIP.. 
PF13139 Domain of unknown function (DUF3981)<br>Pfam-B_1754 (release 24.0). This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 110 amino acids in length.. 
PF13140 Domain of unknown function (DUF3980)<br>Pfam-B_1748 (release 24.0). This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 90 amino acids in length.. 
PF13141 Protein of unknown function (DUF3979)<br>Pfam-B_1747 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length.. 
PF13142 Domain of unknown function (DUF3960)<br>Pfam-B_1431 (release 24.0). This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is typically between 72 and 89 amino acids in length.. 
PF13143 Protein of unknown function (DUF3986)<br>Pfam-B_362 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length.. 
PF13144 SAF-like<br>The members of this family are similar to those in the SAF family, and include flagellar basal-body proteins and pilus-assembly proteins.. 
PF13145 PPIC-type PPIASE domain<br>
PF13146 TRL-like protein family<br>This family includes the Swiss:O87326 TRL protein that is found in a locus that includes several tRNAs.  The function of this protein is not known  . The proteins in this family usually have a lipoprotein attachment site at their N-terminus.. 
PF13147 Amidohydrolase<br>This family of enzymes are a part of a large metal dependent hydrolase superfamily  . The family includes Adenine deaminase EC:3.5.4.2 that hydrolyses adenine to form hypoxanthine and ammonia. Adenine deaminases reaction is important for adenine utilisation as a purine and also as a nitrogen source  . This family also includes dihydroorotase and N-acetylglucosamine-6-phosphate deacetylases, EC:3.5.1.25 These enzymes catalyse the reaction N-acetyl-D-glucosamine 6-phosphate + H2O <=> D-glucosamine 6-phosphate + acetate. This family includes the catalytic domain of urease alpha subunit  . Dihydroorotases (EC:3.5.2.3) are also included [4-5].. 
PF13148 Protein of unknown function (DUF3987)<br>JCSG - Joint Center for Structural Genomics. A family of uncharacterised proteins found by clustering human gut metagenomic sequences  .. 
PF13149 Protein of unknown function (DUF3988)<br>JCSG - Joint Center for Structural Genomics. A family of uncharacterised proteins found by clustering human gut metagenomic sequences  .. 
PF13150 Protein of unknown function (DUF3989)<br>JCSG - Joint Center for Structural Genomics. A family of uncharacterised proteins found by clustering human gut metagenomic sequences  .. 
PF13151 Protein of unknown function (DUF3990)<br>JCSG - Joint Center for Structural Genomics. A family of uncharacterised proteins found by clustering human gut metagenomic sequences  .. 
PF13152 Protein of unknown function (DUF3967)<br>Pfam-B_1529 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 173 and 249 amino acids in length.. 
PF13153 Protein of unknown function (DUF3985)<br>Pfam-B_3329 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 50 amino acids in length.. 
PF13154 Protein of unknown function (DUF3991)<br>This family of proteins is often associated with family Toprim, Pfam:PF01751.. 
PF13155 Toprim-like<br>This is a family or Toprim-like proteins.. 
PF13156 Restriction endonuclease<br>Prokaryotic family found in type II restriction enzymes containing the hallmark (D/E)-(D/E)XK active site. Presence of catalytic residues implicates this region in the enzymatic cleavage of DNA [1,2]. 
PF13157 Protein of unknown function (DUF3992)<br>Pfam-B_480 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 98 and 122 amino acids in length. There is a single completely conserved residue T that may be functionally important.. 
PF13158 Protein of unknown function (DUF3993)<br>Pfam-B_782 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 160 amino acids in length.. 
PF13159 Domain of unknown function (DUF3994)<br>Pfam-B_903 (release 24.0). This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is typically between 97 and 111 amino acids in length.. 
PF13160 Protein of unknown function (DUF3995)<br>Pfam-B_958 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 138 and 149 amino acids in length. There are two completely conserved residues (W and P) that may be functionally important.. 
PF13161 Protein of unknown function (DUF3996)<br>Pfam-B_998 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 172 and 203 amino acids in length.. 
PF13162 Protein of unknown function (DUF3997)<br>Pfam-B_1597 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 140 amino acids in length.. 
PF13163 Protein of unknown function (DUF3999)<br>Pfam-B_2128 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 440 and 470 amino acids in length. There is a single completely conserved residue D that may be functionally important.. 
PF13164 Protein of unknown function (DUF4002)<br>Pfam-B_3350 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes and viruses. Proteins in this family are typically between 112 and 125 amino acids in length. There are two completely conserved C residues that may be functionally important.. 
PF13165 Protein of unknown function (DUF4001)<br>Pfam-B_3337 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 50 amino acids in length. There are at least two pairs of cysteine residues in this short family of proteins.. 
PF13166 AAA domain<br>This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease  .. 
PF13167 GTP-binding GTPase N-terminal<br>This is the N-terminal region of GTP-binding HflX-like proteins. The full-length members bind and interact with the 50S ribosome and are GTPases, hydrolysing GTP/GDP/ATP/ADP. This N-terminal region is necessary for stability of the whole protein.. 
PF13168 Poxvirus B22R protein C-terminal<br>Pfam-B_3510 (release 7.3). This is the highly conserved C-terminal region of poxvirus proteins from eg, Fowlpox virus, Myxoma virus, Lumpy skin disease, Variola virus and other members of the Poxviridae family of double-stranded, no-RNA stage poxviruses.. 
PF13169 Poxvirus B22R protein N-terminal<br>Pfam-B_3510 (release 7.3). This is the highly conserved N-terminal region of poxvirus proteins from eg, Fowlpox virus, Myxoma virus, Lumpy skin disease, Variola virus and other members of the Poxviridae family of double-stranded, no-RNA stage poxviruses.. 
PF13170 Protein of unknown function (DUF4003)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 327 and 345 amino acids in length.. 
PF13171 Protein of unknown function (DUF4004)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 210 amino acids in length.. 
PF13172 PepSY-associated TM helix<br>This family represents a conserved TM helix found in bacteria and archaea.. 
PF13173 AAA domain<br>This family of domains contain a P-loop motif that is characteristic of the AAA superfamily.. 
PF13174 Tetratricopeptide repeat<br>
PF13175 AAA ATPase domain<br>This family of domains contain a P-loop motif that is characteristic of the AAA superfamily.. 
PF13176 Tetratricopeptide repeat<br>
PF13177 DNA polymerase III, delta subunit<br>DNA polymerase III, delta subunit (EC 2.7.7.7) is required for, along with delta' subunit, the assembly of the processivity factor beta(2) onto primed DNA in the DNA polymerase III holoenzyme-catalysed reaction  . The delta subunit is also known as HolA.. 
PF13178 Protein of unknown function (DUF4005)<br>Pfam-B_2171 (release 24.0). This is a C-terminal region of plant IQ-containing putative calmodulin-binding proteins.. 
PF13179 Family of unknown function (DUF4006)<br>This is a family of short, approx 65 residue-long, bacterial proteins of unknown function.. 
PF13180 PDZ domain<br>
PF13181 Tetratricopeptide repeat<br>
PF13182 Protein of unknown function (DUF4007)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 284 and 326 amino acids in length. This domain is found associated with Pfam:PF01507 in some proteins, suggesting a functional link.. 
PF13183 4Fe-4S dicluster domain<br>Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases.  Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters.. 
PF13184 NusA-like KH domain<br>
PF13185 GAF domain<br>
PF13186 DUF4008;<br>Iron-sulfur cluster-binding domain. This domain occurs as an additional C-terminal iron-sulfur cluster binding domain in many radical SAM domain, Pfam:PF04055 proteins. The domain occurs in a number of proteins that modify a protein to become an active enzyme, or a peptide to become a ribosomal natural product. The domain is named SPASM because it occurs in the maturases of Subilitosin, PQQ, Anaerobic Sulfatases, and Mycofactocin.. 
PF13187 4Fe-4S dicluster domain<br>
PF13188 PAS domain<br>
PF13189 Cytidylate kinase-like family<br>This family includes enzymes related to cytidylate kinase.. 
PF13190 PDGLE domain<br>This short presumed domain is usually found on its own. However, it is also found associated with Pfam:PF01891 suggesting it may have a role in cobalt uptake. The domain is named after a short motif found within many members of the family.. 
PF13191 AAA ATPase domain<br>This family of domains contain a P-loop motif that is characteristic of the AAA superfamily.. 
PF13192 Thioredoxin domain<br>
PF13193 DUF4009;<br>AMP-binding enzyme C-terminal domain. Mistry J, Eberhardt R. This is a small domain that is found C terminal to Pfam:PF00501. It has a central beta sheet core that is flanked by alpha helices.. 
PF13194 Domain of unknown function (DUF4010)<br>This is a family of putative membrane proteins found in archaea and bacteria.\.  It is sometimes found C terminal to Pfam:PF02308.. 
PF13195 Protein of unknown function (DUF4011)<br>This family of proteins is found in archaea and bacteria. Many members are annotated as being putative DNA helicase-related proteins.. 
PF13196 Protein of unknown function (DUF4012)<br>This is a family of uncharacterised proteins found in archaea and bacteria.. 
PF13197 Protein of unknown function (DUF4013)<br>This is a family of uncharacterised proteins that is found in archaea and bacteria.. 
PF13198 Protein of unknown function (DUF4014)<br>Pfam-B_4873 (release 24.0). This is a bacterial and viral family of uncharacterised proteins.. 
PF13199 Glycosyl hydrolase family 66<br>Pfam-B_3959 (Release 24.0). This family is a set of glycosyl hydrolase enzymes including cycloisomaltooligosaccharide glucanotransferase (EC:2.4.1.-) and dextranase (EC:3.2.1.11) activities.. 
PF13200 Putative glycosyl hydrolase domain<br>Pfam-B_597 (Release 24.0). This domain is related to other known glycosyl hydrolases suggesting this domain is also involved in carbohydrate break down.. 
PF13201 Putative glycoside hydrolase xylanase<br>This is a family of putative bacterial xylanases. Comparative structural data from TOPSAN indicates there to be a C-terminal carbohydrate binding domain similar to those of carbohydrate enzymes such as glucanase and xylanase. There is also structural similarity of the N-terminal domain, according to TOPSAN, to endo-1,4-beta-xylanase (from Streptomyces sviceus) and beta-xylosidase (from Magnetospirillum magnetotacticum MS-1). The N-terminal domain fold is an immunoglobulin-like beta-sandwich.. 
PF13202 EF_hand_3;<br>
PF13203 Putative metallopeptidase domain<br>This domain, found in various hypothetical bacterial proteins, has no known function. However, it is related to Pfam:PF01435.. 
PF13204 Hydrolase_6;<br>Protein of unknown function (DUF4038). A family of putative cellulases. . 
PF13205 Bacterial Ig-like domain<br>
PF13206 Trypanosomal VSG domain<br>This family represents the B-type variant surface glycoproteins from trypanosomal parasites. This family is related to Pfam:PF00913.. 
PF13207 AAA domain<br>
PF13208 DUF4016;<br>Anantharaman V, Aldam G, Mistry J. The TerB-N domain is found N terminus to TerB, and TerB-C containing proteins  . It has a predominantly alpha-helical structure and contains an absolutely conserved glutamate  . The presence of a conserved acidic residue suggests that it might chelate metal like TerB  . These proteins occur in an two-gene operon containing an AAA+ ATPase and SF-II DNA helicase suggesting a role in stress  stress response or phage defense  .. 
PF13209 Protein of unknown function (DUF4017)<br>Pfam-B_2009 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length.. 
PF13210 Domain of unknown function (DUF4018)<br>Pfam-B_2010 (release 24.0). This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 190 amino acids in length.. 
PF13211 Protein of unknown function (DUF4019)<br>Pfam-B_2012 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 130 and 183 amino acids in length. There is a single completely conserved residue E that may be functionally important.. 
PF13212 Domain of unknown function (DUF4020)<br>Pfam-B_2014 (release 24.0). This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is typically between 176 and 195 amino acids in length.. 
PF13213 Protein of unknown function (DUF4021)<br>Pfam-B_2025 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. There is a conserved YGM sequence motif.. 
PF13214 Protein of unknown function (DUF4022)<br>Pfam-B_2027 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 73 and 85 amino acids in length.. 
PF13215 Protein of unknown function (DUF4023)<br>Pfam-B_2030 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length. There is a conserved KLP sequence motif.. 
PF13216 Protein of unknown function (DUF4024)<br>Pfam-B_2031 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length. There is a conserved RDE sequence motif.. 
PF13217 Protein of unknown function (DUF4025)<br>Pfam-B_2033 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. There is a conserved EGT sequence motif.. 
PF13218 Protein of unknown function (DUF4026)<br>Pfam-B_2037 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 450 amino acids in length. The family is found in association with Pfam:PF10077.. 
PF13219 Protein of unknown function (DUF4027)<br>Pfam-B_2038 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length. There is a conserved CLGGF sequence motif.. 
PF13220 Protein of unknown function (DUF4028)<br>Pfam-B_2040 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 67 and 93 amino acids in length. There are two conserved sequence motifs: IVKI and YVKKWF.. 
PF13221 Protein of unknown function (DUF4029)<br>Pfam-B_2041 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 95 and 119 amino acids in length.. 
PF13222 Protein of unknown function (DUF4030)<br>Pfam-B_2044 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 164 and 197 amino acids in length.. 
PF13223 Protein of unknown function (DUF4031)<br>Pfam-B_2059 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 91 and 130 amino acids in length. There is a conserved HYD sequence motif.. 
PF13224 Domain of unknown function (DUF4032)<br>Pfam-B_2062 (release 24.0). This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 170 amino acids in length. The family is found in association with Pfam:PF06293.. 
PF13225 Domain of unknown function (DUF4033)<br>Pfam-B_2072 (release 24.0). This presumed domain is functionally uncharacterised. This domain family is found in bacteria and eukaryotes, and is approximately 80 amino acids in length.. 
PF13226 Domain of unknown function (DUF4034)<br>Pfam-B_2075 (release 24.0). This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 280 amino acids in length. There is a conserved PRW sequence motif.. 
PF13227 Protein of unknown function (DUF4035)<br>Pfam-B_2076 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 67 and 93 amino acids in length.. 
PF13228 Domain of unknown function (DUF4037)<br>Pfam-B_2110 (release 24.0). This presumed domain is functionally uncharacterised. This domain family is found in bacteria and eukaryotes, and is approximately 100 amino acids in length. There is a single completely conserved residue P that may be functionally important.. 
PF13229 Right handed beta helix region<br>This region contains a parallel beta helix region that shares some similarity with Pectate lyases.. 
PF13230 GATase_II;<br>Glutamine amidotransferases class-II. This family captures members that are not found in Pfam:PF00310.. 
PF13231 Dolichyl-phosphate-mannose-protein mannosyltransferase<br>This family contains members that are not captured by Pfam:PF02366.. 
PF13232 LYR-motif-like;<br>This is a family of proteins carrying the LYR motif of family Complex1_LYR, Pfam:PF05347, likely to be involved in Fe-S cluster biogenesis in mitochondria.. 
PF13233 Complex1_LYR-like<br>This is a family of proteins carrying the LYR motif of family Complex1_LYR, Pfam:PF05347, likely to be involved in Fe-S cluster biogenesis in mitochondria.. 
PF13234 rRNA-processing arch domain<br>Pfam-B_8473 (release 24). 
PF13236 Clustered mitochondria<br>The CLU domain (CLUstered mitochondria) is a eukaryotic domain found in proteins from fungi, protozoa, plants to humans. It is required for correct functioning of the mitochondria and mitochondrial transport [1,2] although the exact function of the domain is unknown  . In Dictyostelium the full-length protein is required for a very late step in fission of the outer mitochondrial membrane   suggesting that mitochondria are transported along microtubules, as in mammalian cells, rather than along actin filaments, as in budding yeast  . Disruption of the protein-impaired cytokinesis and caused mitochondria to cluster at the cell centre  . It is likely that CLU functions in a novel pathway that positions mitochondria within the cell based on their physiological state. Disruption of the CLU pathway may enhance oxidative damage, alter gene expression, cause mitochondria to cluster at microtubule plus ends, and lead eventually to mitochondrial failure  .. 
PF13237 4Fe-4S dicluster domain<br>This family includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich.. 
PF13238 AAA domain<br>
PF13239 2TM domain<br>This short region contains two transmembrane alpha helices that are found associated with a wide range of other domains.  This domain may be involved in cell lysis or peptidoglycan turnover.. 
PF13240 zinc-ribbon domain<br>This family consists of a single zinc ribbon domain, ie half of a pair as in family DZR. Pfam:PF12773.. 
PF13241 Hydrolase_like;<br>Putative NAD(P)-binding. This domain is found in fungi, plants, archaea and bacteria.. 
PF13242 HAD-hyrolase-like<br>
PF13243 Prenyltransferase-like<br>
PF13244 Domain of unknown function (DUF4040)<br>
PF13245 Part of AAA domain<br>
PF13246 Putative hydrolase of sodium-potassium ATPase alpha subunit<br>This is a putative hydrolase of the sodium-potassium ATPase alpha subunit.. 
PF13247 4Fe-4S dicluster domain<br>Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases.  Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters.. 
PF13248 zinc-ribbon domain<br>This family consists of a single zinc ribbon domain, ie half of a pair as in family DZR. Pfam:PF12773.. 
PF13249 Prenyltransferase-like<br>
PF13250 Domain of unknown function (DUF4041)<br>Pfam-B_2162 (release 24.0). This presumed domain is functionally uncharacterised. This domain family is found in bacteria, archaea and viruses, and is approximately 60 amino acids in length. The family is found in association with Pfam:PF10544.. 
PF13251 Domain of unknown function (DUF4042)<br>Pfam-B_2172 (release 24.0). This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is approximately 180 amino acids in length.. 
PF13252 Protein of unknown function (DUF4043)<br>Pfam-B_2174 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 369 and 424 amino acids in length. There is a single completely conserved residue G that may be functionally important.. 
PF13253 Protein of unknown function (DUF4044)<br>Pfam-B_2177 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 42 and 56 amino acids in length. There is a single completely conserved residue M that may be functionally important.. 
PF13254 Domain of unknown function (DUF4045)<br>Pfam-B_2180 (release 24.0). This presumed domain is functionally uncharacterised. This domain family is found in bacteria and eukaryotes, and is typically between 384 and 430 amino acids in length.. 
PF13255 Protein of unknown function (DUF4046)<br>Pfam-B_2182 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 64 and 331 amino acids in length.. 
PF13256 Domain of unknown function (DUF4047)<br>Pfam-B_2183 (release 24.0). This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 130 amino acids in length. There are two conserved sequence motifs: TEA and FPKT.. 
PF13257 Domain of unknown function (DUF4048)<br>Pfam-B_2186 (release 24.0). This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is typically between 228 and 257 amino acids in length.. 
PF13258 Domain of unknown function (DUF4049)<br>Pfam-B_2191 (release 24.0). This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is typically between 310 and 324 amino acids in length.. 
PF13259 Protein of unknown function (DUF4050)<br>Pfam-B_2193 (release 24.0). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 109 and 173 amino acids in length. There are two conserved sequence motifs: IPL and FLVD.. 
PF13260 Protein of unknown function (DUF4051)<br>Pfam-B_2194 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length.. 
PF13261 Protein of unknown function (DUF4052)<br>Pfam-B_2197 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 220 amino acids in length.. 
PF13262 Protein of unknown function (DUF4054)<br>Pfam-B_2204 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 120 and 152 amino acids in length.. 
PF13263 PHP-associated<br>This is a subunit, probably the alpha, of bacterial and eukaryotic DNA polymerase III, associated with the PHP domain, Pfam:PF02811.. 
PF13264 Domain of unknown function (DUF4055)<br>Pfam-B_2501 (release 24.0). This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 140 amino acids in length.. 
PF13265 Protein of unknown function (DUF4056)<br>Pfam-B_2502 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 355 and 380 amino acids in length.. 
PF13266 Protein of unknown function (DUF4057)<br>Pfam-B_2503 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 279 and 322 amino acids in length.. 
PF13267 Protein of unknown function (DUF4058)<br>Pfam-B_2520 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 244 and 264 amino acids in length.. 
PF13268 Protein of unknown function (DUF4059)<br>Pfam-B_2521 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. There is a conserved DKT sequence motif.. 
PF13269 Protein of unknown function (DUF4060)<br>Pfam-B_2524 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. There are two conserved sequence motifs: VEVV and SYVAT.. 
PF13270 Domain of unknown function (DUF4061)<br>Pfam-B_2526 (release 24.0). This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is approximately 90 amino acids in length. There is a conserved AFG sequence motif.. 
PF13271 Domain of unknown function (DUF4062)<br>Pfam-B_2536 (release 24.0). This presumed domain is functionally uncharacterised. This domain family is found in bacteria, archaea and eukaryotes, and is approximately 80 amino acids in length. There is a conserved SST sequence motif.. 
PF13272 Protein of unknown function (DUF4063)<br>Pfam-B_3026 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 95 and 123 amino acids in length. There is a conserved RRA sequence motif.. 
PF13273 Protein of unknown function (DUF4064)<br>
PF13274 Protein of unknown function (DUF4065)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea and viruses. Proteins in this family are typically between 155 and 202 amino acids in length.. 
PF13275 S4 domain<br>The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4.. 
PF13276 HTH-like domain<br>This domain contains a predicted helix-turn-helix suggesting a DNA-binding function.. 
PF13277 YmdB-like protein<br>This family of putative phosphoesterases contains the B. subtilis protein YmdB Swiss:O31775.. 
PF13278 Putative amidotransferase<br>This domain contains similarities to other amidotransferase families such as Pfam:PF00117. Some members of the family lack the likely catalytic residues.. 
PF13279 Thioesterase-like superfamily<br>This family contains a wide variety of enzymes, principally thioesterases. These enzymes are part of the Hotdog fold superfamily  .. 
PF13280 WYL domain<br>This presumed domain is around 170 amino acids in length.\.    It is found to the C-terminus of a DNA-binding helix-turn-helix domain. This domain may be involved in binding to an as yet unknown ligand that allows a transcriptional regulation response to that molecule. There are a number of proteins that contain two tandem copies of this domain such as Swiss:Q47P13. This suggests that this domain may form a dimeric arrangement.. 
PF13281 Domain of unknown function (DUF4071)<br>Pfam-B_2008 (release 24.0). This domain is found at the N-terminus of many serine-threonine kinase-like proteins.. 
PF13282 Domain of unknown function (DUF4070)<br>Pfam-B_2005 (release 24.0). This is a bacterial domain often found at the C-terminus of Radical_SAM methylases.. 
PF13283 Bacteriophage N adsorption protein A C-term<br>Pfam-B_2015 (release 24.0). The function of this domain is unknown but it is found at the C-terminus of bacteriophage N4 adsorption protein A, in association with an N-terminal region of TPR repeats.. 
PF13284 Domain of unknown function (DUF4072)<br>Pfam-B_2021 (release 24.0). This short domain is normally found at the very N-terminus of Hyrdrolases Pfam:PF00702.. 
PF13285 Domain of unknown function (DUF4073)<br>Pfam-B_2039 (release 24.0). This family is frequently found at the C-terminus of bacterial proteins carrying the family, Metallophos Pfam:PF00149.. 
PF13286 Phosphohydrolase-associated domain<br>Pfam-B_2016 (release 24.0). This domain is found on bacterial and archaeal metal-dependent phosphohydrolases.. 
PF13287 Fn3 associated<br>
PF13288 DXP reductoisomerase C-terminal domain<br>This is the C-terminal domain of the 1-deoxy-D-xylulose-5-phosphate reductoisomerase enzyme. This domain forms a left handed super-helix.. 
PF13289 SIR2-like domain<br>This family of proteins are related to the sirtuins.. 
PF13290 Chitobiase/beta-hexosaminidase C-terminal domain<br>
PF13291 ACT domain<br>ACT domains bind to amino acids and regulate associated enzyme domains. These ACT domains are found at the C-terminus of the RelA protein.. 
PF13292 1-deoxy-D-xylulose-5-phosphate synthase<br>This family contains 1-deoxyxylulose-5-phosphate synthase (DXP synthase), an enzyme which catalyses the thiamine pyrophosphoate-dependent acyloin condensation reaction between carbon atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate, to yield 1-deoxy-D- xylulose-5-phosphate, a precursor in the biosynthetic pathway to isoprenoids, thiamine (vitamin B1), and pyridoxol (vitamin B6).. 
PF13293 Domain of unknown function (DUF4074)<br>Pfam-B_2050 (release 24.0). This family is found at the C-terminal of Homeobox proteins in Metazoa.. 
PF13294 Domain of unknown function (DUF4075)<br>Pfam-B_2028 (release 24.0). The members of this family are putative mature parasite-infected erythrocyte surface antigen protein from Bacillus spp.. 
PF13295 Domain of unknown function (DUF4077)<br>Pfam-B_2043 (release 24.0). This is the N-terminal region of methyl-accepting chemotaxis proteins from Bacillus spp. The function is not known.. 
PF13296 Putative type VI secretion system Rhs element Vgr<br>Pfam-B_2052 (release 24.0). This is a family of putative type VI secretion system Rhs element Vgr proteins from Proteobacteria.. 
PF13297 DUF4076; Sde2_C;<br>Telomere stability C-terminal. Pfam-B_2053 (release 24.0). This short C-terminal domain is found in higher eukaryotes further downstream from the Sde2 family, Pfam:PF13019. It is found in all Sde2-related proteins except those from fission yeast, fly, and mosquito. Its exact function in telomere formation and maintenance has not yet been established.. 
PF13298 DNA polymerase Ligase (LigD)<br>This is the N terminal region of ATP dependant DNA ligase.. 
PF13299 Cleavage and polyadenylation factor 2 C-terminal<br>Pfam-B_2065 (release 24.0). This family lies at the C-terminus of many fungal and plant cleavage and polyadenylation specificity factor subunit 2 proteins. The exact function of the domain is not known, but is likely to function as a binding domain for the protein within the overall CPSF complex  .. 
PF13300 Domain of unknown function (DUF4078)<br>Pfam-B_3305 (release 24.0). This family is found from fungi to humans, but its exact function is not known.. 
PF13301 Protein of unknown function (DUF4079)<br>This is an uncharacterised family of proteins.. 
PF13302 Acetyltransferase (GNAT) domain<br>This domain catalyses N-acetyltransferase reactions.. 
PF13303 Phosphotransferase system, EIIC<br>The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. The sugar-specific permease of the PTS consists of three domains (IIA, IIB and IIC). The IIC domain catalyses the transfer of a phosphoryl group from IIB to the sugar substrate.. 
PF13304 AAA domain<br>
PF13305 WHG domain<br>This presumed domain is around 80 amino acids in length.  It is found to the C-terminus of a DNA-binding helix-turn-helix domain. This domain may be involved in binding to an as yet unknown ligand that allows a transcriptional regulation response to that molecule.  The domain is named WHG after three conserved residues near the C-terminus of the domain.. 
PF13306 Leucine rich repeats (6 copies)<br>This family includes a number of leucine rich repeats. This family contains a large number of BSPA-like surface antigens from Trichomonas vaginalis.. 
PF13307 Helicase C-terminal domain<br>This domain is the second of two tandem AAA domains found in a wide variety of helicase enzymes.. 
PF13308 YARHG domain<br>This presumed extracellular domain is about 70 amino acids in length. It is named YARHG after a conserved motif in the sequence. This domain is associated with peptidases and bacterial kinase proteins. Its molecular function is unknown.. 
PF13309 HTH domain<br>This domain is a helix-turn-helix domain that is likely to act as a DNA-binding domain.. 
PF13310 Virulence protein RhuM family<br>There are currently no experimental data for members of this group or their homologues. However, these proteins are implicated in virulence/pathogenicity because RhuM is encoded in the SPI-3 pathogenicity island in Salmonella typhimurium [1-2].. 
PF13311 Protein of unknown function (DUF4080)<br>JCSG - Joint Center for Structural Genomics. A family of uncharacterized proteins found by clustering  human gut metagenomic sequences  .. 
PF13312 Domain of unknown function (DUF4081)<br>Pfam-B_2088 (release 24.0). This domain is often found N-terminal to the GNAT acetyltransferase domain, Pfam:PF00583 and FR47, Pfam:PF08445.. 
PF13313 Domain of unknown function (DUF4082)<br>Pfam-B_2054 (release 24.0). This family appears to be a parallel beta-helix repeated region that sits between successive Cadherin domains, Pfam:PF00028.. 
PF13314 Domain of unknown function (DUF4083)<br>Pfam-B_2061 (release 24.0). This is a family of very short, approximately 60 residue, proteins from Firmicutes, that are all putatively annotated as being MutT/Nudix. However, the characteristic Nudix motif of GX(5)EX(7)REUXEE is absent.. 
PF13315 Protein of unknown function (DUF4085)<br>Pfam-B_2570 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 101 and 269 amino acids in length.. 
PF13316 Protein of unknown function (DUF4087)<br>Pfam-B_3066 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 140 and 280 amino acids in length. There is a conserved RCGW sequence motif.. 
PF13317 Protein of unknown function (DUF4088)<br>Pfam-B_3345 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 258 and 300 amino acids in length.. 
PF13318 Protein of unknown function (DUF4089)<br>Pfam-B_3700 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length.. 
PF13319 Protein of unknown function (DUF4090)<br>Pfam-B_3702 (release 24.0). This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length.. 
PF13320 Domain of unknown function (DUF4091)<br>Pfam-B_3704 (release 24.0). This presumed domain is functionally uncharacterised. This domain family is found in bacteria, archaea and eukaryotes, and is approximately 70 amino acids in length. There is a single completely conserved residue G that may be functionally important.. 
PF13321 Domain of unknown function (DUF4084)<br>Pfam-B_2026 (release 24.0). This family of Firmicute proteins is frequently associated with the EAL, GGDEF and PAS families, Pfam:PF00563, Pfam:PF00990, and Pfam:PF00989. The exact function is not known.. 
PF13322 Domain of unknown function (DUF4092)<br>Pfam-B_2068 (release 24.0). This family is found in Proteobacteria. The function is not known.. 
PF13323 N-terminal domain with HPIH motif<br>Pfam-B_2165 (release 24.0). This family is found in fungi on proteins carrying the PAS, Pfam:PF00989, domain. There is a well-conserved characteristic HPIH motif, but the function is not known.. 
PF13324 Grap2 and cyclin-D-interacting<br>Pfam-B_2169 (release 24.0). GCIP, or Grap2 and cyclin-D-interacting protein, is found in eukaryotes, and in the protein Swiss:O95273, residues 149-190 constitute a helix-loop-helix domain, residues 190-240 an acidic region, and 240-261 a leucine zipper domain. GCIP interacts with full-length Grap2 protein and with the COOH-terminal unique and SH3 domains (designated QC domain) of Grap2. It is potentially involved in the regulation of cell differentiation and proliferation through Grap2 and cyclin D-mediated signalling pathways  . In mice, it is involved in G1/S-phase progression of hepatocytes, which in older animals is associated with the development of liver tumours. In vitro it acts as an inhibitory HLH protein, for example, blocking transcription of the HNF-4 promoter. In its function as a cyclin D1-binding protein it is able to reduce CDK4-mediated phosphorylation of the retinoblastoma protein and to inhibit E2F-mediated transcriptional activity  . GCIP has also been shown to have interact physically with Rad (Ras associated with diabetes), Rad being important in regulating cellular senescence  .. 
PF13325 N-terminal region of micro-spherule protein<br>Pfam-B_2099 (release 24.0). This domain is found in plants and higher eukaryotes, and is the N-terminal region of micro-spherule proteins which repress the transactivation activities of Nrf1 (p45 nuclear factor-erythroid 2 (p45 NF-E2)-related factor 1)  . In conjunction with DIPA the full-length protein acts as a transcription repressor  . The exact function of the region is not known.. 
PF13326 Photosystem II Pbs27<br>This family of proteins contains Pbs27, a highly conserved component of photosystem II.  Pbs27 is comprised of four helices arranged in a right handed up-down-up-down fold, with a less ordered region located at the N-terminus  .. 
PF13327 Type III secretion system subunit<br>Pfam-B_2123 (release 24.0). This is a family of bacterial putative type III secretion apparatus proteins associated with the locus of enterocyte effacement (LEE).. 
PF13328 HD domain<br>HD domains are metal dependent phosphohydrolases.. 
PF13329 Autophagy-related protein 2 CAD motif<br>Pfam-B_2170 (release 24.0). The Atg2 protein, an integral membrane protein, is required for a range of functions including the regulation of autophagy in conjunction with the Atg1-Atg13 complex. Atg2 binds Atg9. The precise function of this region, with its characteristic highly conserved CAD sequence motif, is not known.. 
PF13330 Mucin-2 protein WxxW repeating region<br>Pfam-B_2205 (release 24.0). This family is repeating region found on mucins 2 and 5. The function is not known, but the repeat can be present in up to 32 copies, as in Swiss:C3Y5K5, from Branchiostoma floridae. The region carries a highly conserved WxxW sequence motif and also has at least six well conserved cysteine residues.. 
PF13331 Domain of unknown function (DUF4093)<br>This domain lies at the C-terminus of primase proteins carrying the TOPRIM, Pfam:PF01751, domain. The exact function of the domain is not known.. 
PF13332 Haemagluttinin repeat<br>
PF13333 Integrase core domain<br>
PF13334 Domain of unknown function (DUF4094)<br>Pfam-B_2504 (release 24.0). This domain is found in plant proteins that often carry a galactosyltransferase domain, Pfam:PF01762, at their C-terminus.. 
PF13335 Magnesium chelatase, subunit ChlI<br>This is a family of putative bacterial magnesium chelatase subunit ChlI proteins. The domain lacks the P-loop region present at the N-terminal of Mg_chelatase, Pfam:PF01078.. 
PF13336 Acetyl-CoA hydrolase/transferase C-terminal domain<br>This family contains several enzymes which take part in pathways involving acetyl-CoA. Acetyl-CoA hydrolase EC:3.1.2.1 (Swiss:P32316) catalyses the formation of acetate from acetyl-CoA, CoA transferase (CAT1) EC:2.8.3.- (Swiss:P38946) produces succinyl-CoA, and acetate-CoA transferase EC:2.8.3.8 (Swiss:Q59323) utilises acyl-CoA and acetate to form acetyl-CoA.. 
PF13337 Putative ATP-dependent Lon protease<br>This is a family of proteins that are annotated as ATP-dependent Lon proteases.. 
PF13338 Domain of unknown function (DUF4095)<br>
PF13339 Apoptosis antagonizing transcription factor<br>Pfam-B_2199 (release 24.0). The N-terminal and leucine-zipper region of the apoptosis antagonizing transcription factor-Che1.. 
PF13340 Putative transposase of IS4/5 family (DUF4096)<br>
PF13341 RAG2 PHD domain<br>This domain is found at the C-terminus of the RAG2 protein. The structure of this domain has been shown bound to histone H3 trimethylated at lysine 4 (H3K4me3)  .. 
PF13342 C-terminal repeat of topoisomerase<br>
PF13343 Bacterial extracellular solute-binding protein<br>This family includes bacterial extracellular solute-binding proteins.. 
PF13344 Haloacid dehalogenase-like hydrolase<br>This family is part of the HAD superfamily.. 
PF13345 Domain of unknown function (DUF4098)<br>This domain is a C-terminal repeat found in many bacterial species.. 
PF13346 ABC-2 family transporter protein<br>This family is related to the ABC-2 membrane transporter family Pfam:PF01061  .. 
PF13347 MFS/sugar transport protein<br>This family is part of the major facilitator superfamily of membrane transport proteins.. 
PF13348 Tyrosine phosphatase family C-terminal region<br>
PF13349 Domain of unknown function (DUF4097)<br>
PF13350 Tyrosine phosphatase family<br>This family is closely related to the Pfam:PF00102 and Pfam:PF00782 families.. 
PF13351 Protein of unknown function (DUF4099)<br>JCSG - Joint Center for Structural Genomics. A family of uncharacterized proteins found by clustering human gut metagenomic sequences  . The C-terminal repeat region of this family is DUF4098, Pfam:PF13345.. 
PF13352 Protein of unknown function (DUF4100)<br>This is a family of uncharacterised proteins found in Physcomitrella.. 
PF13353 4Fe-4S single cluster domain<br>This family includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich.. 
PF13354 Beta-lactamase enzyme family<br>This family is closely related to Beta-lactamase, Pfam:PF00144, the serine beta-lactamase-like superfamily, which contains the distantly related Pfam:PF00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.. 
PF13355 Protein of unknown function (DUF4101)<br>This is a family of uncharacterised proteins, and is sometimes found in combination with Pfam:PF00226.. 
PF13356 Domain of unknown function (DUF4102)<br>This presumed domain is found at the N-terminus of a wide variety of phage integrase proteins.. 
PF13358 DDE superfamily endonuclease<br>This family of proteins are related to Pfam:PF00665 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 contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction.. 
PF13359 DDE_4;<br>DDE superfamily endonuclease. This family of proteins are related to Pfam:PF00665 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 contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction.. 
PF13360 PQQ-like domain<br>This domain contains several repeats of the PQQ repeat.. 
PF13361 UvrD-like helicase C-terminal domain<br>This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold.. 
PF13362 Toprim domain<br>The toprim domain is found in a wide variety of enzymes involved in nucleic acid manipulation  .. 
PF13363 Beta-galactosidase, domain 3<br>This is the second domain of the five-domain beta-galactosidase enzyme that altogether catalyses the hydrolysis of beta(1-3) and beta(1-4) galactosyl bonds in oligosaccharides as well as the inverse reaction of enzymatic condensation and trans-glycosylation. This domain has an Ig-like fold  .. 
PF13364 Beta-galactosidase jelly roll domain<br>This domain is found in beta galactosidase enzymes.  It has a jelly roll fold  .. 
PF13365 Trypsin-like peptidase domain<br>This family includes trypsin like peptidase domains.. 
PF13366 PD-(D/E)XK nuclease superfamily<br>Members of this family belong to the PD-(D/E)XK nuclease superfamily. 
PF13367 Protease prsW family<br>This is a family of putative peptidases, possibly belonging to the MEROPS M79 family. Swiss:B7GHM8, PrsW, appears to be a member of a widespread family of membrane proteins that includes at least one previously known protease. PrsW appears to be responsible for Site-1 cleavage of the RsiW anti-sigma factor, the cognate anti-sigma factor, and it senses antimicrobial peptides that damage the cell membrane and other agents that cause cell envelope stress, The three acidic residues, E75, E76 and E95 in Swiss:B7GHM8, appear to be crucial since their mutation to alanine renders the protein inactive. Based on predictions of the bioinformatics programme TMHMM it is likely that these residues are located on the extracytoplasmic face of PrsW placing them in a position to act as a sensor for cell envelope stress  .. 
PF13368 Topoisomerase C-terminal repeat<br>This domain is repeated up to five times to form the C-terminal region of bacterial topoisomerase immediately downstream of the zinc-finger motif.. 
PF13369 Transglutaminase-like superfamily<br>
PF13370 4Fe-4S single cluster domain<br>
PF13371 Tetratricopeptide repeat<br>
PF13372 DUF4104;<br>Coggill P, Eberhardt R. This domain forms an 18-stranded beta-barrel pore which is likely to act as an alginate export channel  .. 
PF13373 DUF2407 C-terminal domain<br>Pfam-B_17915 (release 21.0). This is a family of proteins found in fungi. The function is not known. There is a characteristic GFDRL sequence motif.. 
PF13374 Tetratricopeptide repeat<br>
PF13375 RnfC Barrel sandwich hybrid domain<br>This domain is part of the barrel sandwich hybrid superfamily. It is found at the N-terminus of the RnfC Electron transport complex protein. It appears to be most related to the N-terminal NQRA domain (Pfam:PF05896).. 
PF13376 Bacteriocin-protection, YdeI or OmpD-Associated<br>This is a family of archaeal and bacterial proteins predicted to be periplasmic. YdeI is important for resistance to polymyxin B in broth and for bacterial survival in mice upon oral, but not intraperitoneal inoculation, suggesting a role for YdeI in the gastrointestinal tract of mice  . Production of the ydeI gene is regulated by the Rcs (regulator of capsule synthesis) phospho-relay system pathway independently of RcsA, and additionally transcription of the protein is regulated by the stationary-phase sigma factor, RpoS (sigma-S)  . YdeI confers protection against cationic AMPs (Antimicrobial peptides) or bacteriocins in conjunction with the general porin Omp, thus justifying its name of OmdA, for OmpD-Associated protein  .. 
PF13377 Periplasmic binding protein-like domain<br>Thi domain is found in a variety of transcriptional regulatory proteins. It is related to bacterial periplasmic binding proteins, although this domain is unlikely to be found in the periplasm. This domain likely acts to bind a small molecule ligand that the DNA-binding domain responds to.. 
PF13378 Enolase C-terminal domain-like<br>This domain appears at the C-terminus of many of the proteins that carry the MR_MLE, Pfam:PF01188 and MR_MLE_N Pfam:PF02746 domains.  EC:4.2.1.40.. 
PF13379 NMT1-like family<br>This family is closely related to the Pfam:PF09084 family.. 
PF13380 CoA binding domain<br>This domain has a Rossmann fold and is found in a number of proteins including succinyl CoA synthetases, malate and ATP-citrate ligases.. 
PF13382 Adenine deaminase C-terminal domain<br>This family represents a C-terminal region of the adenine deaminase enzyme.. 
PF13383 Methyltransferase domain<br>This family appears to be a methyltransferase domain.. 
PF13384 Homeodomain-like domain<br>
PF13385 Concanavalin A-like lectin/glucanases superfamily<br>This domain belongs to the Concanavalin A-like lectin/glucanases superfamily.. 
PF13386 Cytochrome C biogenesis protein transmembrane region <br>Coggill P, Eberhardt R. 
PF13387 Domain of unknown function (DUF4105)<br>This is a family of uncharacterised bacterial proteins. There is a highly conserved histidine residue and a well-conserved NCT motif.. 
PF13388 Protein of unknown function (DUF4106)<br>This family of proteins are found in large numbers in the Trichomonas vaginalis proteome.  The function of this protein is unknown.. 
PF13389 Protein of unknown function (DUF4107)<br>This family of putative proteins are found in Trichomonas vaginalis in large numbers.\.  The function of this protein is unknown.. 
PF13390 Protein of unknown function (DUF4108)<br>This family of putative proteins are found in Trichomonas vaginalis in large numbers.\.  The function of this protein is unknown.. 
PF13391 HNH endonuclease<br>Pfam-B_14 (Rel 25.0). 
PF13392 HNH endonuclease<br>This is a zinc-binding loop of Fold group 7   as found in endo-deoxy-ribonucleases and HNH nucleases.. 
PF13393 Histidyl-tRNA synthetase<br>This is a family of class II aminoacyl-tRNA synthetase-like and ATP phosphoribosyltransferase regulatory subunits.. 
PF13394 4Fe-4S single cluster domain<br>
PF13395 HNH endonuclease<br>This HNH nuclease domain is found in CRISPR-related proteins.. 
PF13396 Phospholipase_D-nuclease N-terminal<br>This family is often found at the very N-terminus of proteins from the phospholipase_D-nuclease family, PLDc, Pfam:PF00614. However, a large number of members are full-length within this family.. 
PF13397 Domain of unknown function (DUF4109)<br>This is a family of bacterial proteins with several highly conserved characteristic sequence motifs, such as: APR, WxC and ERR. The function is not known.. 
PF13398 Peptidase M50B-like<br>This is a family of bacterial and plant peptidases in the same family as MEROPS:M50B.. 
PF13399 LytR cell envelope-related transcriptional attenuator<br>This family appears at the C-terminus of members of the LytR_cpsA_psr, Pfam:PF03816, family. 
PF13400 Putative Flp pilus-assembly TadE/G-like<br>This is an N-terminal domain on a family of putative Flp pilus-assembly proteins. The exact function is not known. The Flp-pilus biogenesis genes include the Tad genes, and some members of this family are putatively assigned as being TadG [1,2].. 
PF13401 AAA domain<br>
PF13402 Peptidase M60-like family<br>This family of peptidases contains a zinc metallopeptidase motif (HEXXHX(8,28)E) and possesses mucinase activity  .. 
PF13403 Hint domain<br>This domain is found in inteins.. 
PF13404 AsnC-type helix-turn-helix domain<br>
PF13405 EF_hand_4;<br>
PF13406 Transglycosylase SLT domain<br>This family is related to the SLT domain Pfam:PF01464.. 
PF13407 Periplasmic binding protein domain<br>This domain is found in a variety of bacterial periplasmic binding proteins.. 
PF13408 Recombinase zinc beta ribbon domain<br>This short bacterial protein contains a zinc ribbon domain that is likely to be DNA-binding. This domain is found in site specific recombinase proteins. This family appears most closely related to Pfam:PF04606.. 
PF13409 Glutathione S-transferase, N-terminal domain<br>This family is closely related to Pfam:PF02798.. 
PF13410 Glutathione S-transferase, C-terminal domain<br>This domain is closely related to Pfam:PF00043.. 
PF13411 MerR HTH family regulatory protein<br>
PF13412 Winged helix-turn-helix DNA-binding<br>
PF13413 Helix-turn-helix domain<br>This domain is a helix-turn-helix domain that probably binds to DNA.. 
PF13414 TPR repeat<br>
PF13415 Galactose oxidase, central domain<br>
PF13416 Bacterial extracellular solute-binding protein<br>This family includes bacterial extracellular solute-binding proteins.. 
PF13417 Glutathione S-transferase, N-terminal domain<br>
PF13418 Galactose oxidase, central domain<br>
PF13419 Haloacid dehalogenase-like hydrolase<br>
PF13420 Acetyltransferase (GNAT) domain<br>
PF13421 SPFH domain-Band 7 family<br>
PF13422 Domain of unknown function (DUF4110)<br>Pfam-B_8504 (release 24.0). This is a family that is found predominantly at the C-terminus of Kelch-containing proteins. However, the exact function of this region is not known.. 
PF13423 Ubiquitin carboxyl-terminal hydrolase<br>
PF13424 Tetratricopeptide repeat<br>
PF13425 O-antigen ligase like membrane protein<br>
PF13426 PAS domain<br>
PF13427 Domain of unknown function (DUF4111)<br>Although the exact function of this domain is not known it frequently appears downstream of the family, Nucleotidyltransferase, Pfam:PF01909. It is also found in species associated with methicillin-resistant bacteria.. 
PF13428 Tetratricopeptide repeat<br>
PF13429 Tetratricopeptide repeat<br>
PF13430 Domain of unknown function (DUF4112)<br>This family has several highly conserved GD sequence-motifs of unknown function. The family is found in bacteria, archaea and fungi.. 
PF13431 Tetratricopeptide repeat<br>
PF13432 Tetratricopeptide repeat<br>
PF13433 Periplasmic binding protein domain<br>This domain is found in a variety of bacterial periplasmic binding proteins.. 
PF13434 L_oxygenase;<br>L-lysine 6-monooxygenase (NADPH-requiring). This is family of Rossmann fold oxidoreductases that catalyses the NADPH-dependent hydroxylation of lysine at the N6 position, EC:1.14.13.59.. 
PF13435 Cytochrome c554 and c-prime<br>This family is a tetra-haem cytochrome involved in the oxidation of ammonia. It is found in both phototrophic and denitrifying bacteria.. 
PF13436 Glycine-zipper containing OmpA-like membrane domain<br>
PF13437 HlyD family secretion protein<br>This is a family of largely bacterial haemolysin translocator HlyD proteins.. 
PF13438 Domain of unknown function (DUF4113)<br>Although the function is not known this domain occurs almost invariably at the very C-terminus of the IMS family DNA-polymerase repair proteins, IMS, Pfam:PF00817.. 
PF13439 Glycosyltransferase Family 4<br>
PF13440 Polysaccharide biosynthesis protein<br>
PF13441 YMGG-like Gly-zipper<br>
PF13442 Cytochrome C oxidase, cbb3-type, subunit III <br>
PF13443 Cro/C1-type HTH DNA-binding domain<br>This is a helix-turn-helix domain that probably binds to DNA.. 
PF13444 Acetyltransferase (GNAT) domain<br>This family contains proteins with N-acetyltransferase functions.. 
PF13445 zf-RING_LisH;<br>RING-type zinc-finger. Pfam-B_49 (release 24.0). This zinc-finger is a typical RING-type of plant ubiquitin ligases  .. 
PF13446 A repeated domain in UCH-protein<br>Pfam-B_2127 (release 24.0). This is a repeated domain found in de-ubiquitinating proteins. It's exact function is not known although it is likely to be involved in the binding of the Ubps in the complex with Rsp5 and Rup1.. 
PF13447 Seven times multi-haem cytochrome CxxCH<br>This domain carries up to seven CxxCH repeated sequence motifs, characteristic of multi-haem cytochromes.. 
PF13448 Domain of unknown function (DUF4114)<br>This is a repeated domain that is found towards the C-terminal of many different types of bacterial proteins. There are highly conserved glutamate and aspartate residues suggesting that this domain might carry enzymic activity.. 
PF13449 Esterase-like activity of phytase<br>This is a repeated domain that carries several highly conserved Glu and Asp residues indicating the likelihood that the domain incorporates the enzymic activity of the PLC-like phospho-diesterase part of the proteins. . 
PF13450 NAD(P)-binding Rossmann-like domain<br>
PF13451 Probable zinc-binding domain<br>This is a probable zinc-binding domain with two CxxC sequence motifs, found in various families of bacteria.. 
PF13452 zf-MaoC;<br>N-terminal half of MaoC dehydratase. It is clear from the structures of bacterial members of MaoC dehydratase, Pfam:PF01575, that the full-length functional dehydratase enzyme is made up of two structures that dimerise to form a whole. Divergence of the N- and C- monomers in higher eukaryotes has led to two distinct domains, this one and MaoC_dehydratas. However, in order to function as an enzyme both are required together.. 
PF13453 Transcription factor zinc-finger<br>
PF13454 FAD-NAD(P)-binding<br>
PF13455 Meiotically up-regulated gene 113<br>Pfam-B_48720 (release 24.0). This is a family of fungal proteins found to be up-regulated in meiosis.. 
PF13456 Reverse transcriptase-like<br>This domain is found in plants and appears to be part of a retrotransposon.. 
PF13457 SH3-like domain<br>
PF13458 Periplasmic binding protein<br>This family includes a diverse range of periplasmic binding proteins.. 
PF13459 4Fe-4S single cluster domain<br>
PF13460 NADH(P)-binding <br>
PF13461 Cell-wall surface anchor repeat<br>
PF13462 Thioredoxin<br>
PF13463 Winged helix DNA-binding domain<br>
PF13464 Domain of unknown function (DUF4115)<br>This short domain is often found at the C-terminus of proteins containing a helix-turn-helix domain. The function of this domain is unknown.. 
PF13465 Zinc-finger double domain<br>
PF13466 STAS domain<br>The STAS (after Sulphate Transporter and AntiSigma factor antagonist) domain is found in the C-terminal region of Sulphate transporters and bacterial antisigma factor antagonists. It has been suggested that this domain may have a general NTP binding function  .. 
PF13467 Ribbon-helix-helix domain<br>This short bacterial protein contains a ribbon-helix-helix domain that is likely to be DNA-binding.. 
PF13468 Glyoxalase-like domain<br>This domain is related to the Glyoxalase domain Pfam:PF00903.. 
PF13469 Sulfotransferase family<br>
PF13470 PIN domain<br>Members of this family of bacterial domains are predicted to be RNases (from similarities to 5'-exonucleases).. 
PF13471 Transglutaminase-like superfamily<br>This family includes uncharacterised proteins that are related to the transglutaminase like domain Pfam:PF01841.. 
PF13472 GDSL-like Lipase/Acylhydrolase family<br>This family of presumed lipases and related enzymes are similar to Pfam:PF00657.. 
PF13473 Cupredoxin-like domain<br>The cupredoxin-like fold consists of a beta-sandwich with 7 strands in 2 beta-sheets, which is arranged in a Greek-key beta-barrel.. 
PF13474 SnoaL-like domain<br>This family contains a large number of proteins that share the SnoaL fold.. 
PF13475 Domain of unknown function (DUF4116)<br>
PF13476 AAA domain<br>
PF13477 Glycosyl transferase 4-like<br>
PF13478 XdhC Rossmann domain<br>This entry is the rossmann domain found in the Xanthine dehydrogenase accessory protein.. 
PF13479 AAA domain<br>This AAA domain is found in a wide variety of presumed phage proteins.. 
PF13480 Acetyltransferase (GNAT) domain<br>This family contains proteins with N-acetyltransferase functions.. 
PF13481 AAA domain<br>This AAA domain is found in a wide variety of presumed DNA repair proteins.. 
PF13482 RNase_H superfamily<br>
PF13483 Beta-lactamase superfamily domain<br>This family is part of the beta-lactamase superfamily and is related to Pfam:PF00753.. 
PF13484 4Fe-4S double cluster binding domain<br>
PF13485 Peptidase MA superfamily<br>
PF13486 Reductive dehalogenase subunit<br>This family is most frequently associated with a Fer4 iron-sulfur cluster towards the C-terminal region.. 
PF13487 HD domain<br>HD domains are metal dependent phosphohydrolases.. 
PF13488 Glycine zipper<br>
PF13489 Methyltransferase domain<br>This family appears to be a methyltransferase domain.. 
PF13490 Putative zinc-finger<br>This is a putative zinc-finger found in some anti-sigma factor proteins.. 
PF13491 Domain of unknown function (DUF4117)<br>This family is frequently found on DNA-translocase FtsK proteins at the N-terminus. The function is not known but might well be enzymatic.. 
PF13492 GAF domain<br>
PF13493 Domain of unknown function (DUF4118)<br>This domain is found in a wide variety of bacterial signalling proteins. It is likely to be a transmembrane domain involved in ligand sensing.. 
PF13494 Domain of unknown function, B. Theta Gene description (DUF4119)<br>Ellrott K, Bakolitsa C. Bacteroides thetaiotaomicron: BT_0594. Based on Bacteroides thetaiotaomicron gene BT_0594, a putative uncharacterised protein. As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), it appears to be upregulated in the presence of host or vs when in culture [1,2]. 
PF13495 Phage_integr_N2;<br>Phage integrase, N-terminal SAM-like domain. 
PF13496 Domain of unknown function (DUF4120)<br>Ellrott K, Bakolitsa C. Bacteroides thetaiotaomicron: BT_2585. Based on Bacteroides thetaiotaomicron gene BT_2585, a putative uncharacterised protein.  As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), it appears to be upregulated in the presence of host or vs when in culture [1,2].. 
PF13497 Domain of unknown function (DUF4121)<br>Ellrott K, Bakolitsa C. Bacteroides thetaiotaomicron: BT_2588. Based on Bacteroides thetaiotaomicron gene BT_2588, a putative uncharacterised protein. As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), it appears to be upregulated in the presence of host or vs when in culture [1,2].. 
PF13498 Domain of unknown function (DUF4122)<br>Ellrott K, Bakolitsa C. Bacteroides thetaiotaomicron: BT_2607. Based on Bacteroides thetaiotaomicron gene BT_2607, a putative uncharacterized protein. As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), it appears to be upregulated in the presence of host or vs when in culture [1,2].. 
PF13499 EF_hand_5;<br>
PF13500 AAA domain<br>This domain is found in a number of proteins involved in cofactor biosynthesis such as dethiobiotin synthase and cobyric acid synthase. This domain contains a P-loop motif.. 
PF13501 Sulfur oxidation protein SoxY<br>This domain is found in the sulfur oxidation protein SoxY. It is closely related to the Desulfoferrodoxin family Pfam:PF01880. Dissimilatory oxidation of thiosulfate is carried out by the ubiquitous sulfur-oxidizing (Sox) multi-enzyme system. In this system, SoxY plays a key role, functioning as the sulfur substrate-binding protein that offers its sulfur substrate, which is covalently bound to a conserved C-terminal cysteine, to another oxidizing Sox enzyme  . The structure of this domain shows an Ig-like fold  .. 
PF13502 AsmA-like C-terminal region<br>This family is similar to the C-terminal of the AsmA protein of E.  coli.. 
PF13503 Domain of unknown function (DUF4123)<br>This presumed domain is functionally uncharacterised. It is about 120 amino acids in length and contains several conserved motifs that may be functionally important.  This domain is sometimes associated with the FHA domain.. 
PF13504 Leucine rich repeat<br>
PF13505 Outer membrane protein beta-barrel domain<br>This domain is found in a wide range of outer membrane proteins. This domain assumes a membrane bound beta-barrel fold.. 
PF13506 Glycosyl transferase family 21<br>This is a family of ceramide beta-glucosyltransferases - EC:2.4.1.80.. 
PF13507 CobB/CobQ-like glutamine amidotransferase domain<br>This family captures members that are not found in Pfam:PF00310, Pfam:PF07685 and Pfam:PF13230.. 
PF13508 Acetyltransferase (GNAT) domain<br>This domain catalyses N-acetyltransferase reactions.. 
PF13509 S1 domain<br>The S1 domain was originally identified as a repeat motif in the ribosomal S1 protein. It was later identified in a wide range of proteins. The S1 domain has an OB-fold structure. The S1 domain is involved in nucleic acid binding.. 
PF13510 2Fe-2S iron-sulfur cluster binding domain<br>The 2Fe-2S ferredoxin family have a general core structure consisting of beta(2)-alpha-beta(2) which a beta-grasp type fold. The domain is around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated. This cluster appears within sarcosine oxidase proteins.. 
PF13511 Domain of unknown function (DUF4124)<br>This presumed domain is found in a variety of bacterial proteins. It is found associated at the N-terminus associated with other domains such as the SLT domain and glutaredoxin domains in some proteins. The function of this domain is unknown, but it may have an Ig-like fold.. 
PF13512 Tetratricopeptide repeat<br>
PF13513 HEAT-like repeat<br>The HEAT repeat family is related to armadillo/beta-catenin-like repeats (see Pfam:PF00514). These EZ repeats are found in subunits of cyanobacterial phycocyanin lyase and other proteins and probably carry out a scaffolding role.. 
PF13514 AAA domain<br>This domain is found in a number of double-strand DNA break proteins. This domain contains a P-loop motif.. 
PF13515 Fusaric acid resistance protein-like<br>
PF13516 Leucine Rich repeat<br>
PF13517 Repeat domain in Vibrio, Colwellia, Bradyrhizobium and Shewanella<br>This domain of about 100 residues is found in multiple (up to 35) copies in long proteins from several species of Vibrio, Colwellia, Bradyrhizobium, and Shewanella (hence the name VCBS) and in smaller copy numbers in proteins from several other bacteria. The large protein size and repeat copy numbers, species distribution, and suggested activities of several member proteins suggests a role for this domain in adhesion (TIGR).. 
PF13518 Helix-turn-helix domain<br>This helix-turn-helix domain is often found in transposases and is likely to be DNA-binding.. 
PF13519 von Willebrand factor type A domain<br>
PF13520 Amino acid permease<br>
PF13521 AAA domain<br>
PF13522 Glutamine amidotransferase domain<br>This domain is a class-II glutamine amidotransferase domain found in a variety of enzymes, such as asparagine synthetase and glutamine--fructose-6-phosphate transaminase.. 
PF13523 Acetyltransferase (GNAT) domain<br>This domain catalyses N-acetyltransferase reactions.. 
PF13524 Glycosyl transferases group 1<br>
PF13525 Outer membrane lipoprotein<br>This outer membrane lipoprotein carries a TPR-like region towards its N-terminal. YfiO in E.coli is one of three outer membrane lipoproteins that form a multicomponent YaeT complex in the outer membrane of Gram-negative bacteria that is involved in the targeting and folding of beta-barrel outer membrane proteins. YfiO is the only essential lipoprotein component of the complex. It is required for the proper assembly and/or targeting of outer membrane proteins to the outer membrane. Through its interactions with NlpB it maintains the functional integrity of the YaeT complex.. 
PF13526 Protein of unknown function (DUF4125)<br>
PF13527 Acetyltransferase (GNAT) domain<br>This domain catalyses N-acetyltransferase reactions.. 
PF13528 Glycosyl transferase family 1<br>
PF13529 Peptidase_C39 like family<br>
PF13530 Sterol carrier protein domain<br>
PF13531 Bacterial extracellular solute-binding protein<br>This family includes bacterial extracellular solute-binding proteins.. 
PF13532 2OG-Fe(II) oxygenase superfamily<br>
PF13533 Biotin-lipoyl like<br>
PF13534 4Fe-4S dicluster domain<br>This family includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich.. 
PF13535 ATP-grasp domain<br>This family includes a diverse set of enzymes that possess ATP-dependent carboxylate-amine ligase activity.. 
PF13536 Multidrug resistance efflux transporter<br>This is a membrane protein family acting as a multidrug resistance efflux transporter.. 
PF13537 Glutamine amidotransferase domain<br>This domain is a class-II glutamine amidotransferase domain found in a variety of enzymes such as asparagine synthetase and glutamine-fructose-6-phosphate transaminase.. 
PF13538 UvrD-like helicase C-terminal domain<br>This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold.. 
PF13539 D-alanyl-D-alanine carboxypeptidase<br>This family resembles VanY, Pfam:PF02557, which is part of the peptidase M15 family.. 
PF13540 Regulator of chromosome condensation (RCC1) repeat<br>
PF13541 Subunit ChlI of Mg-chelatase<br>
PF13542 Helix-turn-helix domain of transposase family ISL3<br>
PF13543 SAM like domain present in kinase suppressor RAS 1<br>
PF13544 Type IV pilin N-term methylation site GFxxxE<br>This short sequence motif appears a the N-terminus of type IV prokaryotic filamentous adhesins or pilins. The N-terminal residue, which is methylated, is hydrophobic (generally a phenylalanine or a methionine), and this leader peptide is hydrophilic. The fifth residue of the mature sequence is a glutamate which seems to be required for the methylation step.. 
PF13545 Crp-like helix-turn-helix domain<br>This family represents a crp-like helix-turn-helix domain that is likely to bind DNA.. 
PF13546 DDE superfamily endonuclease<br>This family of proteins are related to Pfam:PF00665 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 contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction.. 
PF13547 GTA TIM-barrel-like domain<br>This domain is found in the gene transfer agent protein.  An unusual system of genetic exchange exists in the purple nonsulfur bacterium Rhodobacter capsulatus. DNA transmission is mediated by a small bacteriophage-like particle called the gene transfer agent (GTA) that transfers random 4.5-kb segments of the producing cell's genome to recipient cells, where allelic replacement occurs  . The genes involved in this process appear to be found widely in bacteria  . According to the SUPERFAMILY database this domain has a TIM barrel fold.. 
PF13548 Domain of unknown function (DUF4126)<br>
PF13549 ATP-grasp domain<br>This family includes a diverse set of enzymes that possess ATP-dependent carboxylate-amine ligase activity.. 
PF13550 Putative phage tail protein<br>This putative domain is found in the large gene transfer agent protein. These produce defective phage like particles. This domain is similar to other phage-tail protein families.. 
PF13551 Winged helix-turn helix<br>This helix-turn-helix domain is often found in transferases and is likely to be DNA-binding.. 
PF13552 Protein of unknown function (DUF4127)<br>This family of uncharacterised bacterial proteins are about 500 amino acids in length.. 
PF13553 Function to find<br>Weichenberger CX, D'Osualdo A. Joint Center of Structural Genomics (JCSG). The function to find (FIIND) was initially discovered in two proteins, NLRP1 (aka NALP1, CARD7, NAC, DEFCAP) and CARD8 (aka TUCAN, Cardinal)\.    . NLRP1 is a member of the Nod-like receptor (NLR) protein  superfamily and is involved in apoptosis and inflammation. To date,  it is the only NLR protein known to have a FIIND domain. The FIIND\. domain is also present in the CARD8 protein where, like in NLRP1,  it is followed by a C-terminal CARD domain. Both proteins are described\.     to form an "inflammasome", a macro-molecular complex able to process  caspase 1 and activate pro-IL1beta  . The FIIND domain is present\. in only a very small subset of the kingdom of life, comprising  primates, rodents (mouse, rat), carnivores (dog) and a few more,\.  such as horse. The function of this domain is yet to be determined. Publications describing the newly discovered NLRP1 protein  failed to identify it as a separate domain; for example, it was taken as part of the adjacent leucine rich repeat domain (LRR)  .  Upon discovery of CARD8 it was noted that the N-terminal region  shared significant sequence identity with an undescribed region in  NLRP1  . Before getting its final name, FIIND  , this domain  was termed NALP1-associated domain (NAD)  .. 
PF13554 Bacteriophage related domain of unknown function<br>Wahab A, Serrano P, Geralt M, Wuthrich K. Bordetella bronchiseptica RB50 PDB:2L25. The three-dimesnional structure of NP_888769.1 (PDB:2L25) reveals\.      a tail terminator protein gpU fold, which suggests that    the protein could have a bacteriophage origin.. 
PF13555 P-loop containing region of AAA domain<br>
PF13556 PucR C-terminal helix-turn-helix domain<br>This helix-turn-helix domain is often found at the C-terminus of PucR-like transcriptional regulators such as Swiss:O32138 and is likely to be DNA-binding.. 
PF13557 Putative MetA-pathway of phenol degradation<br>
PF13558 Putative exonuclease SbcCD, C subunit<br>Possible exonuclease SbcCD, C subunit, on AAA proteins.. 
PF13559 Domain of unknown function (DUF4129)<br>This presumed domain is found at the C-terminus of proteins that contain a transglutaminase core domain. The function of this domain is unknown. The domain has a conserved TXXE motif.. 
PF13560 Helix-turn-helix domain<br>This domain is a helix-turn-helix domain that probably binds to DNA.. 
PF13561 Enoyl-(Acyl carrier protein) reductase<br>
PF13562 Sugar nucleotidyl transferase<br>This is a probable sugar nucleotidyl transferase family.. 
PF13563 2'-5' RNA ligase superfamily<br>This family contains proteins related to Pfam:PF02834. These proteins are likely to be enzymes, but they may not share the RNA ligase activity.. 
PF13564 DoxX-like family<br>This family of uncharacterised proteins are related to DoxX Pfam:PF07681.. 
PF13565 Homeodomain-like domain<br>
PF13566 Domain of unknown function (DUF4130<br>
PF13567 Domain of unknown function (DUF4131)<br>This domain is frequently found to the N-terminus of the Competence domain, Pfam:PF03772.. 
PF13568 Outer membrane protein beta-barrel domain<br>This domain is found in a wide range of outer membrane proteins. This domain assumes a membrane bound beta-barrel fold.. 
PF13569 Domain of unknown function (DUF4132)<br>This domain might be involved in the biosynthesis of the molybdopterin cofactor in E.coli.. 
PF13570 YWTD;<br>Coggill P, Eberhardt R. 
PF13571 Domain of unknown function (DUF4133)<br>Ellrott K, Bakolitsa C. Bacteroides thetaiotaomicron: BT_0094. Based on Bacteroides thetaiotaomicron gene BT_0094, a putative uncharacterized protein as seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), It appears to be upregulated in the presence of host or vs when in culture   .. 
PF13572 Domain of unknown function (DUF4134)<br>Ellrott K, Bakolitsa C. Bacteroides thetaiotaomicron: BT_0095. Based on Bacteroides thetaiotaomicron gene BT_0095, a putative uncharacterized protein As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), It appears to be upregulated in the presence of host or vs when in culture   .. 
PF13573 PbH1;<br>Coggill P, Eberhardt R. This repeat occurs several times in SprB, a cell surface protein involved in gliding motility in the bacterium Flavobacterium johnsoniae  . 
PF13574 Metallo-peptidase family M12B Reprolysin-like<br>This zinc-binding metallo-peptidase has the characteristic binding motif HExxGHxxGxxH of Reprolysin-like peptidases of family M12B.. 
PF13575 Domain of unknown function (DUF4135)<br>This presumed domain is functionally uncharacterised. This domain family is found in bacteria and archaea, and is approximately 380 amino acids in length. The family is found in association with Pfam:PF05147. This domain may be involved in synthesis of a lantibiotic compound.. 
PF13576 Pentapeptide repeats (9 copies)<br>
PF13577 SnoaL-like domain<br>This family contains a large number of proteins that share the SnoaL fold.. 
PF13578 Methyltransferase domain<br>This family appears to be a methyltransferase domain.. 
PF13579 Glycosyl transferase 4-like domain<br>
PF13580 SIS domain<br>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.. 
PF13581 Histidine kinase-like ATPase domain<br>
PF13582 Metallo-peptidase family M12B Reprolysin-like<br>This zinc-binding metallo-peptidase has the characteristic binding motif HExxGHxxGxxH of Reprolysin-like peptidases of family M12B.. 
PF13583 Metallo-peptidase family M12B Reprolysin-like<br>This zinc-binding metallo-peptidase has the characteristic binding motif HExxGHxxGxxH of Reprolysin-like peptidases of family M12B.. 
PF13584 Oxygen tolerance<br>This family of proteins carries up to three membrane spanning regions and is involved in tolerance to oxygen in in Bacteroides spp.. 
PF13585 C-terminal domain of CHU protein family<br>The function of this C-terminal domain is not known; there are several conserved tryptophan and asparagine residues.. 
PF13586 Transposase DDE domain<br>Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis.. 
PF13587 N-terminal domain of DJ-1_PfpI family<br>This domain is found at the N-terminus of proteins from the DJ-1_PfpI family, Pfam:PF01965. The exact function is not known.. 
PF13588 Type I restriction enzyme R protein N terminus (HSDR_N)<br>This family consists of a number of N terminal regions found in type I restriction enzyme R (HSDR) proteins. Restriction and modification (R/M) systems are found in a wide variety of prokaryotes and are thought to protect the host bacterium from the uptake of foreign DNA  . Type I restriction and modification systems are encoded by three genes: hsdR, hsdM, and hsdS. The three polypeptides, HsdR, HsdM, and HsdS, often assemble to give an enzyme (R2M2S1) that modifies hemimethylated DNA and restricts unmethylated DNA  .. 
PF13589 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase<br>This family represents, additionally, the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90.. 
PF13590 Domain of unknown function (DUF4136)<br>This domain is found in bacterial lipoproteins. The function is not known.. 
PF13591 MerR HTH family regulatory protein<br>
PF13592 Winged helix-turn helix<br>This helix-turn-helix domain is often found in transferases and is likely to be DNA-binding.. 
PF13593 SBF-like CPA transporter family (DUF4137)<br>These family members are membrane transporter proteins of the CPA and AT superfamily.. 
PF13594 Amidohydrolase<br>This family of enzymes are a part of a large metal dependent hydrolase superfamily  . The family includes Adenine deaminase EC:3.5.4.2 that hydrolyses adenine to form hypoxanthine and ammonia. Adenine deaminases reaction is important for adenine utilisation as a purine and also as a nitrogen source  . This family also includes dihydroorotase and N-acetylglucosamine-6-phosphate deacetylases, EC:3.5.1.25 These enzymes catalyse the reaction N-acetyl-D-glucosamine 6-phosphate + H2O <=> D-glucosamine 6-phosphate + acetate. This family includes the catalytic domain of urease alpha subunit  . Dihydroorotases (EC:3.5.2.3) are also included [4-5].. 
PF13595 Domain of unknown function (DUF4138)<br>Ellrott K, Bakolitsa C. Bacteroides thetaiotaomicron: BT_4780. Based on Bacteroides thetaiotaomicron gene BT_4780, a putative uncharacterized protein. As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), it appears to be upregulated in the presence of host or vs when in culture [1,2].. 
PF13596 PAS domain<br>
PF13597 Anaerobic ribonucleoside-triphosphate reductase<br>
PF13598 Domain of unknown function (DUF4139)<br>This family is usually found at the C-terminus of proteins.. 
PF13599 Pentapeptide repeats (9 copies)<br>
PF13600 N-terminal domain of unknown function (DUF4140)<br>This family is often found at the N-terminus of its member proteins, with DUF4139, Pfam:PF13598, at the C-terminus.. 
PF13601 Winged helix DNA-binding domain<br>
PF13602 Zinc-binding dehydrogenase<br>
PF13603 Leucyl-tRNA synthetase, Domain 2<br>This is a family of the conserved region of Leucine-tRNA ligase or Leucyl-tRNA synthetase, EC:6.1.1.4.. 
PF13604 AAA domain<br>This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.. 
PF13605 Domain of unknown function (DUF4141)<br>Ellrott K, Bakolitsa C. Bacteroides thetaiotaomicron: BT_4772. Based on Bacteroides thetaiotaomicron gene BT_4772, a putative uncharacterized protein. As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), it appears to be upregulated in the presence of host or vs when in culture [1,2].. 
PF13606 Ankyrin repeat<br>Ankyrins are multifunctional adaptors that link specific proteins to the membrane-associated, spectrin- actin cytoskeleton. This repeat-domain is a 'membrane-binding' domain of up to 24 repeated units, and it mediates most of the protein's binding activities.. 
PF13607 Succinyl-CoA ligase like flavodoxin domain<br>This domain contains the catalytic domain from Succinyl-CoA ligase alpha subunit and other related enzymes. A conserved histidine is involved in phosphoryl transfer.. 
PF13608 Protein P3 of Potyviral polyprotein<br>This is the P3 protein section of the Potyviridae polyproteins. The function is not known except that the protein is essential to viral survival.. 
PF13609 Gram-negative porin<br>
PF13610 DDE domain<br>This DDE domain is found in a wide variety of transposases including those found in IS240, IS26, IS6100 and IS26.. 
PF13611 Serine peptidase of plant viral polyprotein, P1<br>Rawlings N, Coggill P. This family is the P1 protein of the Potyviridae polyproteins that is a serine peptidase at the N-terminus. The catalytic triad in Swiss:Q65730, the ssRNA positive-strand Brome streak mosaic rymovirus, is His-311, Asp-322 and Ser-355.. 
PF13612 Transposase DDE domain<br>Transposase proteins are necessary for efficient DNA transposition.  This domain is a member of the DDE superfamily, which contains three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction  .. 
PF13613 DDE_4_2;<br>Helix-turn-helix of DDE superfamily endonuclease. This domain is the probable DNA-binding region of transposase enzymes, necessary for efficient DNA transposition. Most of the members derive from the IS superfamily IS5 and rather fewer from IS4.. 
PF13614 AAA domain<br>This family includes a wide variety of AAA domains including some that have lost essential nucleotide binding residues in the P-loop.. 
PF13615 Putative alanine racemase<br>This is a family of eukaryotic proteins which are putatively alanine racemase.. 
PF13616 PPIC-type PPIASE domain<br>Rotamases increase the rate of protein folding by catalysing the interconversion of cis-proline and trans-proline.. 
PF13617 YnbE-like lipoprotein<br>This family includes lipoproteins similar to E. coli YnbE Swiss:P64448. Protein in this family are typically 60 amino acids in length and contain an N-terminal lipid attachment site, which has been included in the alignment to increase sensitivity. The specific function of these proteins is unknown.. 
PF13618 Gluconate 2-dehydrogenase subunit 3<br>This family corresponds to subunit 3 of the Gluconate 2-dehydrogenase enzyme that catalyses the conversion of gluconate to 2-dehydro-D-gluconate   EC:1.1.99.3.. 
PF13619 KTSC domain<br>This short domain is named after Lysine tRNA synthetase C-terminal domain. It is found at the C-terminus of some Lysyl tRNA synthetases as well as a single domain in bacterial proteins. The domain is about 60 amino acids in length and contains a reasonably conserved YXY motif in the centre of the sequence. The function of this domain is unknown but it could be an RNA binding domain.. 
PF13620 Carboxypeptidase regulatory-like domain<br>
PF13621 Cupin-like domain<br>This cupin like domain shares similarity to the JmjC domain.. 
PF13622 Thioesterase-like superfamily<br>This family contains a wide variety of enzymes, principally thioesterases. These enzymes are part of the Hotdog fold superfamily  .. 
PF13623 SurA N-terminal domain<br>This domain is found at the N-terminus of the chaperone SurA. It is a helical domain of unknown function. The C-terminus of the SurA protein folds back and forms part of this domain also but is not included in the current alignment.. 
PF13624 SurA N-terminal domain<br>This domain is found at the N-terminus of the chaperone SurA. It is a helical domain of unknown function. The C-terminus of the SurA protein folds back and forms part of this domain also but is not included in the current alignment.. 
PF13625 Helicase conserved C-terminal domain<br>This domain family is found in a wide variety of helicases and helicase-related proteins.. 
PF13627 Prokaryotic lipoprotein-attachment site<br>In prokaryotes, membrane lipoproteins are synthesized with a precursor signal peptide, which is cleaved by a specific lipoprotein signal peptidase (signal peptidase II). The peptidase recognizes a conserved sequence and cuts upstream of a cysteine residue to which a glyceride-fatty acid lipid is attached  .. 
PF13628 Domain of unknown function (DUF4142)<br>This is a bacterial family of unknown function.. 
PF13629 Pilus formation protein N terminal region<br>
PF13630 SdpI/YhfL protein family<br>This family of proteins includes the SdpI and YhfL proteins from B. subtilis. The SdpI protein is a multipass integral membrane protein that protects toxin-producing cells from being killed. Killing is mediated by the exported toxic protein SdpC an extracellular protein that induces the synthesis of an immunity protein  .. 
PF13631 Cytochrome b(N-terminal)/b6/petB<br>
PF13632 Glycosyl transferase family group 2<br>Members of this family of prokaryotic proteins include putative glucosyltransferases, which are involved in bacterial capsule biosynthesis   .. 
PF13633 Prokaryotic N-terminal methylation site<br>This short motif directs methylation of the conserved phenylalanine residue.  It is most often found at the N-terminus of pilins and other proteins involved in secretion, see Pfam:PF00114, Pfam:PF05946, Pfam:PF02501 and Pfam:PF07596. It is often described as TypeIV_pilin_GFxxxE.. 
PF13634 Nucleoporin FG repeat region<br>This family includes a number of FG repeats that are found in nucleoporin proteins. This family includes the yeast nucleoporins Nup116, Nup100, Nup49, Nup57 and Nup 145.. 
PF13635 Domain of unknown function (DUF4143)<br>This domain is almost always found C-terminal to an ATPase core family.. 
PF13636 pre-rRNA processing and ribosome biogenesis<br>This family represents an evolutionarily conserved sequence motif of a set of proteins that are involved in pre-rRNA processing and ribosome biogenesis in S. cerevisiae.. 
PF13637 Ankyrin repeats (many copies)<br>
PF13638 PIN domain<br>Members of this family of bacterial domains are predicted to be RNases (from similarities to 5'-exonucleases).. 
PF13639 Ring finger domain<br>
PF13640 2OG-Fe(II) oxygenase superfamily<br>This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily  .. 
PF13641 Glycosyltransferase like family 2<br>Members of this family of prokaryotic proteins include putative glucosyltransferase, which are involved in bacterial capsule biosynthesis   .. 
PF13642 protein structure with unknown function<br>Serrano P, Geralt M, Mohanty B, Horst R, Wuthrich K. Shewanella amazonensis SB2B PDB:2L6O. A family based on the three-dimensional structure of YP_926445.1 (PDB:2L6O). 
PF13643 Domain of unknown function (DUF4145)<br>This domain is found in a variety of restriction endonuclease enzymes. The exact function of this domain is uncertain.. 
PF13644 DKNYY family<br>This family represents a group of proteins found enriched in fusobacteria. These proteins contain many repeats of a DKNXXYY motif. The repeats are spaced at about 35 amino acid residues intervals. These proteins are likely to be associated with the membrane. The specific function of these proteins is unknown.. 
PF13645 L,D-transpeptidase catalytic domain<br>This family is related to Pfam:PF03734.. 
PF13646 HEAT repeats<br>This family includes multiple HEAT repeats.. 
PF13647 Glycosyl hydrolase family 80 of chitosanase A<br>Naumoff D, Coggill P. This is a small family of bacterial chitosanases.. 
PF13648 Lipocalin-like domain<br>
PF13649 Methyltransferase domain<br>This family appears to be a methyltransferase domain.. 
PF13650 Aspartyl protease<br>This family consists of predicted aspartic proteases, typically from 180 to 230 amino acids in length, in MEROPS clan AA. This model describes the well-conserved 121-residue C-terminal region. The poorly conserved, variable length N-terminal region usually contains a predicted transmembrane helix.. 
PF13651 Adenine-specific methyltransferase EcoRI<br>This methylase recognizes the double-stranded sequence GAATTC, causes specific methylation on A-3 on both strands, and protects the DNA from cleavage by the EcoRI endonuclease.. 
PF13652 Domain of unknown function (DUF4146)<br>This is a family of short proteins which appear to be pre-cursors. All members are from Pseudomonas spp. The function is not known.. 
PF13653 Glycerophosphoryl diester phosphodiesterase family<br>This family also includes glycerophosphoryl diester phosphodiesterases as well as agrocinopine synthase, the similarity to GDPD has been noted  . This family appears to have weak but not significant matches to mammalian phospholipase C Pfam:PF00388, which suggests that this family may adopt a TIM barrel fold.. 
PF13654 AAA domain<br>This family includes a wide variety of AAA domains including some that have lost essential nucleotide binding residues in the P-loop.. 
PF13655 N-terminal domain of reverse transcriptase<br>This domain is found at the N-terminus of bacterial reverse transcriptases.. 
PF13656 RNA polymerase Rpb3/Rpb11 dimerisation domain<br>The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer.  The dimerisation domain of the alpha subunit/Rpb3 is interrupted by an insert domain (Pfam:PF01000).  Some of the alpha subunits also contain iron-sulphur binding domains (Pfam:PF00037).  Rpb11 is found as a continuous domain.  Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp. Many of the members of this family carry only the N-terminal region of Rpb11.. 
PF13657 HipA N-terminal domain<br>This domain is found to the N-terminus of HipA-like proteins.  It is also found in isolation in some proteins.. 
PF13659 Methyltransferase domain<br>This family contains methyltransferase domains.. 
PF13660 Domain of unknown function (DUF4147)<br>This domain is frequently found at the N-terminus of proteins carrying the glycerate kinase-like domain MOFRL, Pfam:PF05161.. 
PF13661 2OG-Fe(II) oxygenase superfamily<br>This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily  .. 
PF13662 Toprim domain<br>The toprim domain is found in a wide variety of enzymes involved in nucleic acid manipulation  .. 
PF13663 Domain of unknown function (DUF4148)<br>
PF13664 Domain of unknown function (DUF4149)<br>
PF13665 Domain of unknown function (DUF4150)<br>
PF13667 ThiC-associated domain <br>This domain is most frequently found at the N-terminus of the ThiC family of proteins, Pfam:PF01964. The function is not known.. 
PF13668 Ferritin-like domain<br>This family contains ferritins and other ferritin-like proteins such as members of the DPS family and bacterioferritins.. 
PF13669 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily<br>
PF13670 Peptidase propeptide and YPEB domain<br>This region is likely to have a protease inhibitory function (personal obs:C Yeats).  The name is derived from Peptidase & Bacillus subtilis YPEB.. 
PF13671 AAA domain<br>This family of domains contain only a P-loop motif, that is characteristic of the AAA superfamily. Many of the proteins in this family are just short fragments so there is no Walker B motif.. 
PF13672 Protein phosphatase 2C<br>Protein phosphatase 2C is a Mn++ or Mg++ dependent protein serine/threonine phosphatase.. 
PF13673 Acetyltransferase (GNAT) domain<br>This family contains proteins with N-acetyltransferase functions such as Elp3-related proteins.. 
PF13675 Type IV pili methyl-accepting chemotaxis transducer N-term<br>This domain is found on many type IV pili methyl-accepting chemotaxis transducer proteins where there is also a HAMP, signature towards the C-terminus.. 
PF13676 TIR domain<br>This is a family of bacterial Toll-like receptors.. 
PF13677 Membrane MotB of proton-channel complex MotA/MotB <br>This is the MotB member of the E.coli MotA/MotB proton-channel complex that forms the stator of the bacterial membrane flagellar motor. Key residues act as a plug to prevent premature proton flow. The plug is in the periplasm just C-terminal to the MotB TM, consisting of an amphipathic alpha helix flanked by Pro-52 and Pro-65, eg in Swiss:D3V2T1. In addition to the Pro residues, Ile-58, Tyr-61, and Phe 62 are also essential for plug function   .. 
PF13678 NFkB-p65-degrading zinc protease<br>Rawlings N, Coggill P. This family of bacterial metallo-peptidases is thought to compromise the inflammatory response by degrading p65 thereby down-regulating the NF-kappaB signalling pathway  . NF-kappa-B is a pleiotropic transcription factor which is present in almost all cell types and is involved in many biological processes such as inflammation, immunity, differentiation, cell growth, tumorigenesis and apoptosis. NF-kappa-B is a homo- or heterodimeric complex formed by the Rel-like domain-containing proteins RELA/p65, RELB, NFKB1/p105, NFKB1/p50, REL and NFKB2/p52; and the heterodimeric p65-p50 complex appears to be most abundant one.. 
PF13679 Methyltrans_27;<br>Methyltransferase domain. This family appears to be a methyltransferase domain.. 
PF13680 Protein of unknown function (DUF4152)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in archaea. Proteins in this family are approximately 230 amino acids in length. The structure of PF2046 from pyrococcus furiosus has been solved.  It shows an RNaseH like fold that conserves critical catalytic residues  . This suggests that these proteins may cleave nucleic acid.. 
PF13681 Type IV pilus assembly protein PilX C-term<br>This family is likely to be the C-terminal region of type IV pilus assembly PilX or PilW proteins.. 
PF13682 MCPsignal_assoc;<br>Chemoreceptor zinc-binding domain. The chemoreceptor zinc-binding domain (CZB) is found in bacterial signal transduction proteins - most frequently receptors involved in chemotaxis and motility, but also in c-di-GMP signalling and nitrate/nitrite-sensing. Originally discovered in the cytoplasmic chemoreceptor TlpD from Helicobacter pylori, it is often found C-terminal to the MCPsignal domain in cytoplasmic chemoreceptor proteins. The CZB domain contains a core sequence motif, Hxx[WFYL]x21-28Cx[LFMVI]Gx[WFLVI]x18-27HxxxH. The highly-conserved H-C-H-H residues of this motif are believed to coordinate zinc; mutating the latter two histidines of the motif to alanines abolishes Zn binding. This domain binds zinc with high affinity, with a Kd in the femtomolar range. Although the function of the CZB domain is not yet known, scientists have speculated that it may function as either an unknown signal input domain, based on its frequent association with signalling output domains, or as a domain that helps to stabilise protein tertiary or quaternary structure.. 
PF13683 Integrase core domain<br>
PF13684 Dihydroxyacetone kinase family<br>This is the kinase domain of the dihydroxyacetone kinase family.. 
PF13685 Iron-containing alcohol dehydrogenase<br>
PF13686 DsrE/DsrF/DrsH-like family<br>DsrE is a small soluble protein involved in intracellular sulfur  reduction  . The family also includes YrkE proteins.. 
PF13687 Domain of unknown function (DUF4153)<br>Members of this family are annotated as putative inner membrane proteins.. 
PF13688 Peptidase_M84;<br>Metallo-peptidase family M12. 
PF13689 Domain of unknown function (DUF4154)<br>This family of proteins is found in bacteria. Proteins in this family are typically between 172 and 207 amino acids in length. Many members are annotated as valyl-tRNA synthetase but this could not be confirmed.. 
PF13690 Chemotaxis phosphatase CheX<br>CheX is very closely related to the CheC chemotaxis phosphatase, but it dimerises in a different way, via a continuous beta sheet between the subunits. CheC and CheX both dephosphorylate CheY, although CheC requires binding of CheD to achieve the activity of CheX. The ability of bacteria to modulate their swimming behaviour in the presence of external chemicals (nutrients and repellents) is one of the most rudimentary behavioural responses known, but the the individual components are very sensitively tuned  .. 
PF13691 tRNase Z endonuclease<br>This is family of tRNase Z enzymes, that are closely related structurally to the Lactamase_B family members. tRNase Z is the endonuclease that is involved in tRNA 3'-end maturation through removal of the 3'-trailer sequences from tRNA precursors. The fission yeast Schizosaccharomyces pombe contains two candidate tRNase Zs encoded by two essential genes. The first, Swiss:Q10155, is targeted to the nucleus and has an SV40 nuclear localisation signal at its N-terminus, consisting of four consecutive arginine and lysine residues between residues 208 and 211 (KKRK) that is critical for the NLS function. The second, Swiss:P87168, is targeted to the mitochondria, with an N-terminal mitochondrial targeting signal within the first 38 residues  .. 
PF13692 Glycosyl transferases group 1<br>
PF13693 Winged helix-turn-helix DNA-binding<br>
PF13694 Sec63/Sec62 complex-interacting family<br>This is a family of closely related Hph proteins that are integral endoplasmic reticulum (ER) membrane proteins required for yeast survival under environmental stress conditions. They interact with several subunits of the Sec63/Sec62 complex that mediates post-translational translocation of proteins into the ER. Cells with mutant Hph1 and Hph2 proteins revealed phenotypes resembling those of mutants defective for vacuolar proton ATPase (V-ATPase) activity. The yeast V-ATPase is a multisubunit complex whose function, structure, and assembly have been well characterized. Cells with impaired V-ATPase activity fail to acidify the vacuole, cannot grow at alkaline pH, and are sensitive to high concentrations of extracellular calcium  .. 
PF13695 Zinc-binding domain<br>This is a family with several pairs of CxxC motifs possibly representing a multiple zinc-binding region. Only one pair of cysteines is associated with a highly conserved histidine residue.. 
PF13696 Zinc knuckle<br>This is a zinc-binding domain of the form CxxCxxxGHxxxxC from a variety of different species.. 
PF13698 Domain of unknown function (DUF4156)<br>The function of this family is unknown but members are annotated as putative lipoprotein outer membrane proteins.. 
PF13699 Domain of unknown function (DUF4157)<br>This presumed domain is functionally uncharacterised. This domain family is found in bacteria, archaea and eukaryotes, and is approximately 80 amino acids in length. This domain contains an HEXXH motif that is characteristic of many families of metallopeptidases. However, no peptidase activity has been shown for this domain.. 
PF13700 Domain of unknown function (DUF4158)<br>The exact function of this domain is not clear, but it frequently occurs as an N-terminal region of transposase 3 or IS3 family of insertion elements.. 
PF13701 Transposase DDE domain group 1<br>Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis.. 
PF13702 Lysozyme-like<br>
PF13703 PepSY-associated TM helix<br>This family represents a conserved TM helix found in bacteria and archaea.. 
PF13704 Glycosyl transferase family 2<br>Members of this family of prokaryotic proteins include putative glucosyltransferases,. 
PF13705 TRC8 N-terminal domain<br>This region is found at the N-terminus of the TRC8 protein Swiss:Q8WU17. TRC8 is an E3 ubiquitin-protein ligase also known as RNF139. This region contains 12 transmembrane domains. This region has been suggested to contain a sterol sensing domain  . It has been found that TRC8 protein levels are sterol responsive and that it binds and stimulates ubiquitylation of the endoplasmic reticulum anchor protein INSIG  .. 
PF13706 PepSY-associated TM helix<br>This family represents a conserved TM helix found in bacteria and archaea.. 
PF13707 RloB-like protein<br>This family includes the RloB protein that is found within a bacterial restriction modification operon.  This family includes the AbiLii protein that is found as part of a plasmid encoded phage abortive infection mechanism  . Deletion within abiLii abolished the phage resistance. The family includes some proteins annotated as CRISPR Csm2 proteins.. 
PF13708 Methyltransferase domain<br>This family contains methyltransferase domains.. 
PF13709 Domain of unknown function (DUF4159)<br>Members of this family are hypothetical proteins. TM prediction shows them to have two transmembrane regions, with a cytosolic region of about 25 amino acids between the two, and an N-terminus outside the membrane.. 
PF13710 ACT domain<br>ACT domains bind to amino acids and regulate associated enzyme domains. These ACT domains are found at the C-terminus of the RelA protein.. 
PF13711 Domain of unknown function (DUF4160)<br>
PF13712 Glycosyltransferase like family<br>Members of this family of prokaryotic proteins include putative glucosyltransferases, which are involved in bacterial capsule biosynthesis.. 
PF13713 Transcription factor BRX N-terminal domain<br>The BREVIS RADIX (BRX) domain was characterised as being a transcription factor in plants regulating the extent of cell proliferation and elongation in the growth zone of the root [1,2].  BRX is rate limiting for auxin-responsive gene-expression by mediating cross-talk with the brassino-steroid pathway.  BRX has a ubiquitous, although quantitatively variable role in modulating the growth rate in both the root and the shoot  . This family features a short region, also alpha-helical, N-terminal to the repeated alpha-helices of family BRX, Pfam:PF08381  . BRX is expressed in the vasculature and is rate-limiting for transcriptional auxin action  .. 
PF13714 Phosphoenolpyruvate phosphomutase<br>This domain includes the enzyme Phosphoenolpyruvate phosphomutase (EC:5.4.2.9). This protein Swiss:O86937 has been characterised as catalysing the formation of a carbon-phosphorus bond by converting phosphoenolpyruvate (PEP) to phosphonopyruvate (P-Pyr)  . This enzyme has a TIM barrel fold.. 
PF13715 Cna_B_2;<br>Domain of unknown function (DUF4480). Coggill P, Eberhardt R. This domain family is found in bacteria, archaea and eukaryotes, and is approximately 90 amino acids in length. The family is found in association with Pfam:PF07715 and Pfam:PF00593. There is a single completely conserved residue G that may be functionally important.. 
PF13716 Divergent CRAL/TRIO domain<br>This family includes divergent members of the CRAL-TRIO domain family. This family includes ECM25 that contains a divergent CRAL-TRIO domain identified by Gallego and colleagues  .. 
PF13717 zinc-ribbon domain<br>This family consists of a single zinc ribbon domain, ie half of a pair as in family DZR, Pfam:PF12773.. 
PF13718 GNAT acetyltransferase 2<br>Coggill P, Eberhardt R. This domain has N-acetyltransferase activity [1,2]. It has a GCN5-related N-acetyltransferase (GNAT) fold  .. 
PF13719 zinc-ribbon domain<br>This family consists of a single zinc ribbon domain, ie half of a pair as in family DZR, Pfam:PF12773.. 
PF13720 Udp N-acetylglucosamine O-acyltransferase; Domain 2<br>This is domain 2, or the C-terminal domain, of Udp N-acetylglucosamine O-acyltransferase.  This enzyme is a zinc-dependent enzyme that catalyses the deacetylation of UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine to form UDP-3-O-(R-hydroxymyristoyl)glucosamine and acetate.. 
PF13721 SecD export protein N-terminal TM region<br>This domain appears to be the fist transmembrane region of the SecD export protein. SecD is directly involved in protein secretion and important for the release of proteins that have been translocated across the cytoplasmic membrane.. 
PF13722 C-terminal domain on CstA (DUF4161)<br>This domain is found at the C=terminal of most known CstA domain-containing proteins. The function is not known.. 
PF13723 Beta-ketoacyl synthase, N-terminal domain<br>
PF13724 DNA-binding domain<br>Coggill P, Eberhardt R. Pfam-B_65234 (release 24.0). This domain, often found on ovate proteins, binds to single-stranded and double-stranded DNA. Binding to DNA is not sequence-specific  .. 
PF13725 Possible tRNA binding domain<br>Coggill P, Eberhardt R. This domain, found at the C-terminus of tRNA(Met) cytidine acetyltransferase, may be involved in tRNA-binding  .. 
PF13726 Na+-H+ antiporter family<br>This family includes integral membrane proteins, some of which are NA+-H+ antiporters  .. 
PF13727 CoA-binding domain<br>
PF13728 F plasmid transfer operon protein<br>TraF protein undergoes proteolytic processing associated with export. The 19 amino acids at the amino terminus of the polypeptides appear to constitute a typical membrane leader peptide - not included in this family, while the remainder of the molecule is predicted to be primarily hydrophilic in character  . F plasmid TraF and TraH are required for F pilus assembly and F plasmid transfer, and they are both localised to the outer membrane in the presence of the complete F transfer region, especially TraV, the putative anchor  .. 
PF13729 F plasmid transfer operon, TraF, protein<br>
PF13730 Helix-turn-helix domain<br>
PF13731 WxL domain surface cell wall-binding<br>The WxL motif appears in two or three copies in these bacterial proteins   and confers a cell surface localisation function. It seems likely that this region is the cell wall-binding domain of gram-positive bacteria, and may interact with the peptidoglycan  .. 
PF13732 Domain of unknown function (DUF4162)<br>This domain is found at the C-terminus of bacterial ABC transporter proteins. The function is not known.. 
PF13733 N-terminal region of glycosyl transferase group 7<br>This is the N-terminal half of a family of galactosyltransferases from a wide range of Metazoa with three related galactosyltransferases activities, all three of which are possessed by one sequence in some cases.  EC:2.4.1.90, N-acetyllactosamine synthase; EC:2.4.1.38, Beta-N-acetylglucosaminyl-glycopeptide beta-1,4- galactosyltransferase; and EC:2.4.1.22 Lactose synthase. Note that N-acetyllactosamine synthase is a component of Lactose synthase along with alpha-lactalbumin, in the absence of alpha-lactalbumin EC:2.4.1.90 is the catalysed reaction.. 
PF13734 Spi protease inhibitor<br>This family includes the inhibitor Spi and the pro-peptides of streptopain (SpeB).  SpeB is produced as a 43 kDa pre-pro-protein, which is secreted via the recently described Sec secretory pathway Exportal. There is tight coupling between this inhibitor and its associated protease: the gene for the inhibitor Spi is located directly downstream from the gene for the streptococcal cysteine protease SpeB, and the sequence of the inhibitor is very similar to that of the SpeB propeptide. This is an example of an inhibitor molecule that is a structural homologue of the cognate propeptide, and is genetically linked to the protease gene  .. 
PF13735 tRNA nucleotidyltransferase domain 2 putative<br>
PF13737 Transposase DDE domain<br>Transposase proteins are necessary for efficient DNA transposition.  This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis.. 
PF13738 Pyridine nucleotide-disulphide oxidoreductase<br>
PF13739 Domain of unknown function (DUF4163)<br>The structure of this domain is and alpha-beta-two layer sandwich, identified from a Fervidobacterium nodosum Rt17-B1 like protein. The function is not known except that it is found in association with Heat-shock cognate 70kd protein 44kd ATPase, Pfam:PF11738.. 
PF13740 ACT domain<br>ACT domains bind to amino acids and regulate associated enzyme domains.. 
PF13741 Mitochondrial ribosomal protein S25<br>PfamB-B_2836 (release 25.0). This is the family of fungal 37S mitochondrial ribosomal S25 proteins.. 
PF13742 OB-fold nucleic acid binding domain<br>This family contains OB-fold domains that bind to nucleic acids.. 
PF13743 Thioredoxin<br>
PF13744 Helix-turn-helix domain<br>Members of this family contains a DNA-binding helix-turn-helix domain.. 
PF13745 HxxPF-repeated domain<br>This family is found in non-ribosomal peptide synthetase proteins, and can occur up to twelve times.. 
PF13746 4Fe-4S dicluster domain<br>This family includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich.. 
PF13747 Domain of unknown function (DUF4164)<br>This is a family of short, approx 100 residue-long, bacterial proteins of unknown function. There is several conserved LE/LD sequence pairs.. 
PF13748 ABC transporter transmembrane region<br>This family represents a unit of six transmembrane helices.. 
PF13749 ATP-dependent DNA helicase recG C-terminal<br>This domain may well interact selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.. 
PF13750 Bacterial Ig-like domain (group 3)<br>This family consists of bacterial domains with an Ig-like fold. Members of this family are found in a variety of bacterial surface proteins.. 
PF13751 Transposase DDE domain<br>Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis.. 
PF13752 Domain of unknown function (DUF4165)<br>
PF13753 Putative flagellar system-associated repeat<br>This family appears to be a repeated unit that can occur up to 29 times in these outer membrane proteins. It is putatively associated with a novel flagellar system.. 
PF13754 Bacterial Ig-like domain (group 3)<br>This family consists of bacterial domains with an Ig-like fold. Members of this family are found in a variety of bacterial surface proteins.. 
PF13755 Sensor N-terminal transmembrane domain<br>Coggill P, Eberhardt R. This domain is found at the N-terminus of the sensor component of the two-component regulatory system. It includes a transmembrane region and part of the periplasmic region, which is likely to be involved in stimulus sensing  .. 
PF13756 Stimulus-sensing domain<br>Coggill P, Eberhardt R. This domain is found in the periplasmic region of the sensor component of the two-component regulatory system. The periplasmic region is likely to be involved in stimulus sensing  .. 
PF13757 Vault protein inter-alpha-trypsin domain<br>Inter-alpha-trypsin inhibitors (ITIs) consist of one light chain and a variable set of heavy chains.  ITIs play a role in extracellular matrix (ECM) stabilisation and tumour metastasis as well as in plasma protease inhibition  .  The vault protein inter-alpha-trypsin (VIT) domain described here is found to the N-terminus of a von Willebrand factor type A domain (Pfam:PF00092) in ITI heavy chains (ITIHs) and their precursors.. 
PF13758 Prefoldin subunit<br>This family includes prefoldin subunits that are not detected by Pfam:PF02996.. 
PF13759 Putative 2OG-Fe(II) oxygenase<br>Coggill P, Eberhardt R. This family has structural similarity to the 2OG-Fe(II) oxygenase superfamily.. 
PF13761 Domain of unknown function (DUF4166)<br>Coggill P, Eberhardt R. This domain is often found at the C-terminus of proteins containing Pfam:PF03435.. 
PF13762 Mitochondrial splicing apparatus component<br>MNE1 is a novel component of the mitochondrial splicing apparatus responsible for the processing of a COX1 group I intron in yeast  . Yeast cells lacking MNE1 are deficient in intron splicing in the gene encoding the Cox1 subunit of cytochrome oxidase but do contain wild-type levels of the bc1 complex.. 
PF13763 Domain of unknown function (DUF4167)<br>
PF13764 E3 ubiquitin-protein ligase UBR4<br>This is a family of E£ ubiquitin ligase enzymes.. 
PF13765 SPRY-associated domain<br>SPRY and PRY domains occur on PYRIN proteins. Their function is not known.. 
PF13766 2-enoyl-CoA Hydratase C-terminal region<br>This is the C-terminal region of enoyl-CoA hydratase.. 
PF13767 Domain of unknown function (DUF4168)<br>
PF13768 von Willebrand factor type A domain<br>
PF13769 Virulence factor<br>This domain is found in conserved virulence factors  . It is often found in association with Pfam:PF02985 and Pfam:PF08712.. 
PF13770 Domain of unknown function (DUF4169)<br>
PF13771 PHD-like zinc-binding domain<br>The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains.  The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH.. 
PF13772 AIG2-like family<br>This family is found in bacteria and metazoa.. 
PF13773 Domain of unknown function (DUF4170)<br>
PF13774 Regulated-SNARE-like domain<br>Longin is one of the approximately 26 components required for transporting proteins from the ER to the plasma membrane, via the Golgi apparatus. It is necessary for the steps of the transfer from the ER to the Golgi complex  . Longins are the only R-SNAREs that are common to all eukaryotes, and they are characterised by a conserved N-terminal domain with a profilin-like fold called a longin domain  .. 
PF13775 Domain of unknown function (DUF4171)<br>This short family is frequently found at the N-terminus of Homeobox proteins.. 
PF13776 Domain of unknown function (DUF4172)<br>The family is often found in association with Pfam:PF02661.. 
PF13777 Domain of unknown function (DUF4173)<br>This domain of unknown function contains multiple predicted transmembrane domains.. 
PF13778 Domain of unknown function (DUF4174)<br>This domain of unknown function is found in a putative tumour suppressor gene   and in a ligand for the the urokinase-type plasminogen activator receptor, which plays a role in cellular migration and adhesion [2,3].. 
PF13779 Domain of unknown function (DUF4175)<br>
PF13780 Domain of unknown function (DUF4176)<br>
PF13781 DoxX-like family<br>This family of uncharacterised proteins are related to DoxX Pfam:PF07681.. 
PF13782 Stage V sporulation protein AB<br>This family of proteins is required for sporulation  .. 
PF13783 Domain of unknown function (DUF4177)<br>
PF13784 Fic/DOC family N-terminal<br>This domain is found at the N-terminus of the Fic/DOC family, Pfam:PF02661.. 
PF13785 Domain of unknown function (DUF4178)<br>
PF13786 Domain of unknown function (DUF4179)<br>
PF13787 Protein of unknown function with HXXEE motif<br>This domain contains an HXXEE motif, another conserved histidine and a YXPG motif. Its function is unknown.. 
PF13788 Domain of unknown function (DUF4180)<br>
PF13789 Domain of unknown function (DUF4181)<br>
PF13790 Domain of unknown function (DUF4182)<br>This protein of unknown function contains a number of highly conserved cysteine residues, which may form disulphide bonds.. 
PF13791 Sigma factor regulator C-terminal<br>This family is the C-terminal domain of a sigma factor regulator, this may represent a sensory domain  .. 
PF13792 Sulfate transporter N-terminal domain with GLY motif<br>This domain is found usually at the N-terminus of sulfate-transporter proteins. It carries a highly conserved GLY sequence motif, but the function of the domain is not known.. 
PF13793 N-terminal domain of ribose phosphate pyrophosphokinase<br>This family is frequently found N-terminal to the Pribosyltran, Pfam:PF00156.. 
PF13794 tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE)-like<br>
PF13795 HupE / UreJ protein<br>These proteins contain many conserved histidines that may be involved in nickel binding.. 
PF13796 Putative sensor<br>This family is often found at the N-terminus of proteins containing Pfam:PF07730 and Pfam:PF02518. The N-termini of proteins containing these two domains often function in stimulus sensing.. 
PF13797 Post-transcriptional regulator<br>This family includes post-transcriptional regulators  .. 
PF13798 Protein of unknown function with PCYCGC motif<br>This domain contains a PCYCGC motif and four other conserved cysteines. Its function is unknown.. 
PF13799 Domain of unknown function (DUF4183)<br>This domain of unknown function contains a highly conserved ING motif.. 
PF13800 Sigma factor regulator N-terminal<br>Coggill P, Eberhardt R. This domain is found near the N-terminus of a sigma factor regulator. The N-terminus is responsible for interaction with the sigma factor  .. 
PF13801 Heavy-metal resistance<br>This is a metal-binding protein which is involved in resistance to heavy-metal ions [1,2]. The protein forms a four-helix hooked hairpin, consisting of two long alpha helices each flanked by a shorter alpha helix. It binds a metal ion in a type-2 like centre  . It contains two copies of an LTXXQ motif.. 
PF13802 Galactose mutarotase-like<br>This family is found N-terminal to glycosyl-hydrolase domains, and appears to be similar to the galactose mutarotase superfamily.. 
PF13803 Domain of unknown function (DUF4184)<br>This domain of unknown function contains several highly conserved histidines.. 
PF13804 Retro-transcribing viruses envelope glycoprotein<br>This family comes from human endogenous retrovirus K envelope glycoproteins.. 
PF13805 Eisosome component PIL1<br>In the budding yeast, S. cerevisiae, Pil1 and another cytoplasmic protein, Lsp1, together form large immobile assemblies at the plasma membrane that mark sites for endocytosis, called eisosomes.  Endocytosis functions to recycle plasma membrane components, to regulate cell-surface expression of signalling receptors and to internalise nutrients in all eukaryotic cells.. 
PF13806 Rieske-like [2Fe-2S] domain<br>
PF13807 G-rich domain on putative tyrosine kinase<br>This domain is found between two families, Wzz, Pfam:PF02706 and CbiA Pfam:PF01656. There is a highly conserved GNVR sequence motif which characterises this domain. The function is not known.. 
PF13808 DDE_Tnp_1-associated<br>This domain is frequently found N-terminal to the transposase, IS family DDE_Tnp_1, Pfam:PF01609 and its relatives.. 
PF13809 Tubulin like<br>Many of the residues conserved in Tubulin, Pfam:PF00091, are also highly conserved in this family.. 
PF13810 Domain of unknown function (DUF4185)<br>
PF13811 Domain of unknown function (DUF4186)<br>
PF13812 Pentatricopeptide repeat domain<br>This family matches additional variants of the PPR repeat that were not captured by the model for Pfam:PF01535. The exact function is not known.. 
PF13813 Membrane bound O-acyl transferase family<br>
PF13814 Replication-relaxation<br>This family includes proteins which are essential for plasmid replication   and plasmid DNA relaxation  .. 
PF13815 Iguana/Dzip1-like DAZ-interacting protein N-terminal<br>The DAZ gene-product - Deleted in Azoospermia - and a closely related sequence are required early in germ-cell development in order to maintain germ-cell populations. This family is the N-terminal region that is the only part of the protein in some fungi and lower metazoa.. 
PF13816 Haem-containing dehydratase<br>This family includes aldoxime dehydratase, EC:4.99.1.5. This is a haem-containing enzyme, which catalyses the dehydration of aldoximes to their corresponding nitrile  . It also includes phenylacetaldoxime dehydratase, EC:4.99.1.7. This haem-containing enzyme catalyses the dehydration of Z-phenylacetaldoxime to phenylacetonitrile  . The enzyme forms an elliptic beta barrel, composed of eight beta-strands, flanked by alpha-helices  .. 
PF13817 IS66 C-terminal element<br>
PF13820 Putative nucleic acid-binding region<br>This is a family of putative nucleic acid-binding proteins. Several members are annotated as being nuclear receptor coactivator 6 proteins but this could not be confirmed.. 
PF13821 Domain of unknown function (DUF4187)<br>This family is found at the very C-terminus of proteins that carry a G-patch domain, Pfam:PF01585.  The domain is short and cysteine-rich.. 
PF13822 Acyl-CoA carboxylase epsilon subunit<br>This family includes the epsilon subunits of propionyl-CoA carboxylase, EC:6.4.1.3, and acetyl-CoA carboxylase, EC:6.4.1.2. These enzymes are involved in the biosynthesis of long-chain fatty acids. The epsilon subunit is necessary for an efficient interaction between the alpha and beta subunits of these enzymes  .. 
PF13823 Alcohol dehydrogenase GroES-associated<br>This short domain is frequently found at the N-terminus of the alcohol dehydrogenase GroES-like domain, Pfam: PF08240.. 
PF13824 Zinc-finger of mitochondrial splicing suppressor 51<br>Mss51 regulates the expression of cytochrome oxidase, so this domain is probably DNA-binding.. 
PF13825 Paramyxovirus structural protein V/P N-terminus<br>This family consists of several Paramyxoviridae structural protein P and V sequences  . From a structural point of view, P is the best-characterised protein of the replicative complex. P is organised into two moieties that are functionally and structurally distinct: a C-terminal moiety (PCT) and an N-terminal moiety (PNT). PCT is the most conserved in sequence and contains all regions required for virus transcription, whereas PNT, which is poorly conserved, provides several additional functions required for replication  . P protein plays a crucial role in the enzyme by positioning L onto the N/RNA template through an interaction with the C-terminal domain of N. Without P, L is not functional. The N, P, and L proteins of SeV and measles and mumps viruses are functionally equivalent. However, sequence identity between proteins from these viruses is limited, and the viruses have been placed in different genera (Respirovirus, Morbilivirus, and Rubulavirus, respectively).  SeV P protein (568 aa) is a modular protein with distinct functional domains. The N-terminal part of P (PNT) is a chaperone for N and prevents it from binding to non-viral RNA in the infected cell  .. 
PF13826 Domain of unknown function (DUF4188)<br>
PF13827 Domain of unknown function (DUF4189)<br>This domain of unknown function contains six well-conserved cysteine residues.. 
PF13828 Domain of unknown function (DUF4190)<br>This integral membrane domain is functionally uncharacterised. One of the membrane helices contains two GXXG motifs that are usually associated with dimerisation.. 
PF13829 Domain of unknown function (DUF4191)<br>
PF13830 Domain of unknown function (DUF4192)<br>
PF13831 PHD-finger<br>PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains  .  Several PHD fingers have been identified as binding modules of methylated histone H3  .. 
PF13832 PHD-zinc-finger like domain<br>
PF13833 EF_hand_6;<br>
PF13834 Domain of unknown function (DUF4193)<br>This domain of unknown function contains four conserved cysteines and a conserved histidine, including a CXXXXH motif.. 
PF13835 Domain of unknown function (DUF4194)<br>
PF13836 Domain of unknown function (DUF4195)<br>This family is found at the N-terminus of metazoan proteins that carry PHD-like zinc-finger domains. The function is not known.. 
PF13837 Myb/SANT-like DNA-binding domain<br>This presumed domain appears to be related to other Myb/SANT-like DNA binding domains. In particular Pfam:PF10545 seems most related.  This family is greatly expanded in plants and appears in several proteins annotated as transposon proteins.. 
PF13838 Clathrin-H-link<br>This short domain is found on clathrins, and often appears on proteins directly downstream from the Clathrin-link domain Pfam:PF09268.. 
PF13839 GDSL/SGNH-like Acyl-Esterase family found in Pmr5 and Cas1p<br>    N-terminal C rich potential sugar binding domain followed by the  PC-Esterase domain  .. 
PF13840 ACT domain <br>The ACT domain is a structural motif of 70-90 amino acids that functions in the control of metabolism, solute transport and signal transduction. They are thus found in a variety of different proteins in a variety of different arrangements  . In mammalian phenylalanine hydroxylase the domain forms no contacts but promotes an allosteric effect despite the apparent lack of ligand binding  .. 
PF13841 Beta defensin<br>The beta defensins are antimicrobial peptides implicated in the resistance of epithelial surfaces to microbial colonisation  .. 
PF13842 DDE_Tnp_1-like zinc-ribbon<br>This zinc-ribbon domain is frequently found at the C-terminal of proteins derived from transposable elements.. 
PF13843 Transposase IS4<br>
PF13844 Glycosyl transferase family 41<br>This family of glycosyltransferases includes O-linked beta-N-acetylglucosamine (O-GlcNAc) transferase, an enzyme which catalyses the addition of O-GlcNAc to serine and threonine residues [1,2]. In addition to its function as an O-GlcNAc transferase, human OGT, Swiss:O15294, also appears to proteolytically cleave the epigenetic cell-cycle regulator HCF-1  .. 
PF13845 Septum formation<br>This domain is found in a protein which is predicted to play a role in septum formation during cell division  .. 
PF13846 Domain of unknown function (DUF4196)<br>Pfam-B_104093 (release 24.0). This is a short region of ccdc82_homologues that is conserved from Schizo. pombe up to humans.  The function is not known.. 
PF13847 Methyltransferase domain<br>This family appears to be have methyltransferase activity.. 
PF13848 Thioredoxin-like domain<br>
PF13850 Endoplasmic Reticulum-Golgi Intermediate Compartment (ERGIC)<br>This family is the N-terminal of ERGIC proteins  , ER-Golgi intermediate compartment clusters, otherwise known as Ervs, and is associated with family COPIIcoated_ERV, Pfam:PF07970.. 
PF13851 Growth-arrest specific micro-tubule binding<br>This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localisation of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages  . Gas8 is a microtubule-binding protein localised to regions of dynein regulation in mammalian cells.. 
PF13852 Protein of unknown function (DUF4197)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 228 and 249 amino acids in length.. 
PF13853 Olfactory receptor<br>The members of this family are transmembrane olfactory receptors.. 
PF13854 Kelch motif<br>The kelch motif was initially discovered in Kelch (Swiss:Q04652). In this protein there are six copies of the motif.  It has been shown that Swiss:Q04652 is related to Galactose Oxidase   for which a structure has been solved  . The kelch motif forms a beta sheet.  Several of these sheets associate to form a beta propeller structure   as found in Pfam:PF00064, Pfam:PF00400 and Pfam:PF00415.. 
PF13855 Leucine rich repeat<br>Jackhmer:JCS-Target417241. 
PF13856 ATP-binding sugar transporter from pro-phage<br>Members of this short family are putative ATP-binding sugar transporter-like protein.. 
PF13857 Ankyrin repeats (many copies)<br>
PF13858 Protein of unknown function (DUF4199)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 167 and 182 amino acids in length.. 
PF13859 BNR repeat-like domain<br>This family of proteins contains BNR-like repeats suggesting these proteins may act as sialidases.. 
PF13860 FlgD Ig-like domain<br>This domains has an immunoglobulin like beta sandwich fold. It is found in the FlgD protein the flagellar hook capping protein. THe structure for this domain shows that it is inserted within a TUDOR like beta barrel domain  .. 
PF13861 FlgD Tudor-like domain<br>This domain has a tudor domain-like beta barrel fold. It is found in the FlgD protein the flagellar hook capping protein. The structure for this domain shows that it contains a nested Ig-like domain within it  .  However in some firmicute proteins this inserted domain is absent such as Q67K21.. 
PF13862 p21-C-terminal region-binding protein<br>This family of p21-binding proteins is important as a modulator of p21 activity. The domain binds the C-terminal region of p21 in a ternary complex with CDK2, which results in inhibition of the kinase activity of CDK2.. 
PF13863 Domain of unknown function (DUF4200)<br>This family is found in eukaryotes. It is a coiled-coil domain of unknwon function.. 
PF13864 Calmodulin-binding<br>
PF13865 C-terminal duplication domain of Friend of PRMT1<br>Fop, or Friend of Prmt1, proteins are conserved from fungi and plants to vertebrates. There is little that is actually conserved except for this C-terminal LDXXLDAYM region where X is any amino acid). The Fop proteins themselves are nuclear proteins localised to regions with low levels of DAPI, with a punctate/speckle-like distribution. Fop is a chromatin-associated protein and it colocalises with facultative heterochromatin. It is is critical for oestrogen-dependent gene activation  .. 
PF13866 SAP30 zinc-finger<br>SAP30 is a subunit of the histone deacetylase complex, and this domain is a zinc-finger. Solution of the structure shows a novel fold comprising two beta-strands and two alpha-helices with the zinc organising centre showing remote resemblance to the treble clef motif. In silico analysis of the structure revealed a highly conserved surface dominated by basic residues. NMR-based analysis of potential ligands for the SAP30 zn-finger motif indicated a strong preference for nucleic acid substrates. The zinc-finger of SAP3 probably functions as a double-stranded DNA-binding motif, thereby expanding the known functions of both SAP30 and the mammalian Sin3 co-repressor complex  .. 
PF13867 Sin3 binding region of histone deacetylase complex subunit SAP30<br>This C-terminal domain of the SAP30 proteins appears to be the binding region for Sin3.. 
PF13868 Tumour suppressor, Mitostatin<br>Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement.  The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs)  .. 
PF13869 Nucleotide hydrolase<br>Nudix hydrolases are found in all classes of organism and hydrolyse a wide range of organic pyrophosphates, including nucleoside di- and triphosphates, di-nucleoside and diphospho-inositol polyphosphates, nucleotide sugars and RNA caps, with varying degrees of substrate specificity.. 
PF13870 Domain of unknown function (DUF4201)<br>This is a family of coiled-coil proteins from eukaryotes. The function is not known.. 
PF13871 Helicase_C-like<br>Strawberry notch proteins carry DExD/H-box groups and Helicase_C domains. These proteins promote the expression of diverse targets, potentially through interactions with transcriptional activator or repressor complexes  .. 
PF13872 P-loop containing NTP hydrolase pore-1<br>
PF13873 Myb/SANT-like DNA-binding domain<br>This presumed domain appears to be related to other Myb/SANT like DNA binding domains.  This family is greatly expanded in arthropods and higher eukaryotes.. 
PF13874 Nucleoporin complex subunit 54<br>This is the human Nup54 subunit of the nucleoporin complex, equivalent to Nup57 of yeast. Nup54, Nup58 and Nup62 all have similar affinities for importin-beta. It seems likely that they are the only FG-repeat nucleoporins of the central channel, and as such they would form a zone of equal affinity spanning the central channel.  The diffusion of importin-beta import complexes through the central channel may be a stochastic process as the affinities are similar, whereas movement from cytoplasmic fibrils to the central channel and from the central channel to the nuclear basket would be facilitated by the subtle differences in affinity between them [1,2].. 
PF13875 Domain of unknown function (DUF4202)<br>This family of proteins is found in bacteria, archaea and eukaryotes.  Proteins in this family are typically between 187 and 205 amino acids in length. There are two conserved sequence motifs: LED and KMS. The function of these proteins is unknown, although many are incorrectly annotated as glutamyl tRNA synthetases.. 
PF13876 Phage protein (N4 Gp49/phage Sf6 gene 66) family<br>This family of phage proteins is functionally uncharacterised. The family includes bacteriophage Sf6 gene 66 Swiss:Q716B1 as well as phage N4 GP49 protein Swiss:A0MZD7. Proteins in this family are typically between 87 and 154 amino acids in length. There is a conserved NGF sequence motif.. 
PF13877 Potential Monad-binding region of RPAP3<br>This domain is found at the C-terminus of RNA-polymerase II-associated proteins.  These proteins bind to Monad and are involved in regulating apoptosis.\. They contain TPR-repeats towards the N_terminus.. 
PF13878 zinc-finger of acetyl-transferase ESCO<br>
PF13879 KIAA1430 homologue<br>This is a family of KIAA1430 homologues.  The function is not known.. 
PF13880 ESCO1/2 acetyl-transferase<br>
PF13881 Ubiquitin-2 like Rad60 SUMO-like<br>
PF13882 Bravo-like intracellular region<br>This is the very C-terminal intracellular region of neural adhesion molecule L1 proteins that are also known as Bravo or NrCAM. It lies upstream of the IG and Fn3 domains and has the highly conserved motif FIGEY.  The function is not known.. 
PF13883 Pyridoxamine 5'-phosphate oxidase<br>
PF13884 Chaperone of endosialidase<br>This is the very C-terminal, chaperone, domain of the bacteriophage protein endosialidase. It releases itself, via the serine-lysine dyad at the N-terminus, from the remainder of the end-tail-spike. Cleavage occurs after the threonine which is the final residue of the End-tail-spike family, Pfam:PF12219. The endosialidase protein forms homotrimeric molecules in bacteriophages  . The catalytic dyad allows this portion of the molecule to be cleaved from the more N-terminal region such that the latter can fold and presumably bind to DNA.. 
PF13885 Keratin, high sulfur B2 protein<br>
PF13886 Domain of unknown function (DUF4203)<br>This is the N-terminal region of 7tm proteins.  The function is not known.. 
PF13887 Myelin gene regulatory factor -C-terminal domain 1<br>This domain is found just downstream of Peptidase_S74, Pfam:PF13884.  The function is not known.. 
PF13888 Myelin gene regulatory factor C-terminal domain 2<br>This domain is found further downstream of Peptidase_S74, Pfam:PF13884, and MRF_C1, Pfam:PF13887.  The function is not known.. 
PF13889 DUF4204;<br>Chromosome segregation during meiosis. The proteins come from eukaryotes, plants and animals, and are necessary for chromosome segregation during meiosis.. 
PF13890 Rab3 GTPase-activating protein catalytic subunit<br>This family is the probable catalytic subunit of the GTPase activating protein that has specificity for Rab3 subfamily (RAB3A, RAB3B, RAB3C and RAB3D). It is likely to convert active Rab3-GTP to the inactive form Rab3-GDP.  Rab3 proteins are involved in regulated exocytosis of neurotransmitters and hormones. The Rab3 GTPase-activating complex is a heterodimer composed of RAB3GAP and RAB3-GAP150. This complex interacts with DMXL2 [1,2,3].. 
PF13891 Potential DNA-binding domain<br>This domain is likely to be the DNA-binding domain of chromatin re-modelling proteins and helicases.. 
PF13892 DNA-binding domain<br>DBINO is a DNA-binding domain found on global transcription activator SNF2L1 proteins and chromatin re-modelling proteins.. 
PF13893 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)<br>JCSG:Target_421317_RF20609A. The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins.. 
PF13894 C2H2-type zinc finger<br>This family contains a number of divergent C2H2 type zinc fingers.. 
PF13895 Immunoglobulin domain<br>This domain contains immunoglobulin-like domains.. 
PF13896 Glycosyl-transferase for dystroglycan<br>This glycosyl-transferase brings about the glycosylation of the  alpha-dystroglycan subunit. Dystroglycan is an integral member of the skeletal muscular dystrophin glycoprotein complex, which links dystrophin to proteins in the extracellular matrix [1,2].. 
PF13897 Golgi-dynamics membrane-trafficking<br>Sec14-like Golgi-trafficking  domain The GOLD domain is always found combined with lipid- or membrane-association domains  .. 
PF13898 Domain of unknown function (DUF4205)<br>The proteins in this family are uncharacterised but often named FAM188B.. 
PF13899 Thioredoxin-like<br>Thioredoxins are small enzymes that participate in redox reactions, via the reversible oxidation of an active centre disulfide bond.. 
PF13900 Putative binding domain<br>This short domain is often found nested inside other longer domains. The function is not known, but the domain carries a highly conserved GVQW motif. The members are rich in proline and cysteine. This may be a binding domain.. 
PF13901 Domain of unknown function (DUF4206)<br>This is a family of cysteine-rich proteins. Many members also carry a pleckstrin-homology domain, Pfam:PF00169. 
PF13902 R3H-associated N-terminal domain<br>This family is found at the N-terminus of R3H, Pfam:PF01424, domain-containing proteins.  The function is not known.. 
PF13903 PMP-22/EMP/MP20/Claudin tight junction<br>Members of this family are claudins, that form tight junctions between cells.. 
PF13904 Domain of unknown function (DUF4207)<br>This family is found in eukaryotes; it has several conserved tryptophan residues. The function is not known.. 
PF13905 Thioredoxin-like<br>Thioredoxins are small enzymes that participate in redox reactions, via the reversible oxidation of an active centre disulfide bond.. 
PF13906 C-terminus of AA_permease<br>This is the C-terminus of AA-permease enzymes that is not captured by the models Pfam:PF00324 and Pfam:PF13520.. 
PF13907 Domain of unknown function (DUF4208)<br>This domain is found at the C-terminus of chromodomain-helicase-DNA-binding proteins.  The exact function of the domain is undetermined.. 
PF13908 Wnt and FGF inhibitory regulator<br>Shisa is a transcription factor-type molecule that physically interacts with immature forms of the Wnt receptor Frizzled and the FGF receptor within the endoplasmic reticulum to inhibit their post-translational maturation and trafficking to the cell surface.. 
PF13909 C2H2-type zinc-finger domain<br>
PF13910 Domain of unknown function (DUF4209)<br>This short domain is found in bacteria and eukaryotes, though not in yeasts or Archaea. It carries a highly conserved RNxxxHG sequence motif.. 
PF13911 AhpC/TSA antioxidant enzyme<br>This family contains proteins related to alkyl hydro-peroxide reductase (AhpC) and thiol specific antioxidant (TSA).. 
PF13912 C2H2-type zinc finger<br>
PF13913 zinc-finger of a C2HC-type<br>This family contains a number of divergent C2H2 type zinc fingers.. 
PF13914 Phostensin PP1-binding and SH3-binding region<br>Phostensin has been identified as a PP1 regulatory protein binding PP1 at the KISF motif. The domain also appears to carry an incomplete incomplete SH3-binding domain PxRxP further upstream. It is likely that Phostensin targets PP1 to the F-actin cytoskeleton  . Phostensin binds to actin and decreases the elongation and depolymerisation rates of actin filament pointed ends  .. 
PF13915 Domain of unknown function (DUF4210)<br>This short domain is found in fungi, plants and animals, and the proteins appear to be necessary for chromosome segregation during meiosis.. 
PF13916 PP1-regulatory protein, Phostensin N-terminal<br>Phostensin has been identified as a PP1 regulatory protein binding protein. This domain is N-terminal to the PP1- and SH3-binding regions though may carry an additional SH3-binding motif. It is likely that Phostensin targets PP1 to the F-actin cytoskeleton  .  Phostensin binds to actin and decreases the elongation and depolymerisation rates of actin filament pointed ends  .. 
PF13917 Zinc knuckle<br>The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag  proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.. 
PF13918 PLD-like domain<br>
PF13919 Asx-hm;<br>Iyer LM, Aravind L, Godzik A, Coggill P. A conserved alpha helical domain with a characteristic LXXLL motif    . The LXXLL motif is detected in diverse transcription  factors, coactivators and corepressors and is implicated in mediating interactions between them  . The ASXH domain is found in animals, fungi and plants   and is predicted to play a role in mediating contact between transcription factors and chromatin-associated complexes. In Drosophila Asx and Human ASXL1, the ASXH domain is predicted to mediate interactions with the Calypso and BAP1 deubiquitinases (DUBs) which further belong to the UCHL5/UCH37 clade  of DUBs  .. 
PF13920 Zinc finger, C3HC4 type (RING finger)<br>
PF13921 Myb-like DNA-binding domain<br>This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family  .. 
PF13922 PHD domain of transcriptional enhancer, Asx<br>This is the DNA-binding domain on the additional sex combs-like 1 proteins. The Asx protein acts as an enhancer of trithorax and polycomb in displaying bidirectional homoeotic phenotypes in Drosophila, suggesting that it is required for maintenance of both activation and silencing of Hox genes. Asx is required for normal adult haematopoiesis and its function depends on its cellular context.. 
PF13923 Zinc finger, C3HC4 type (RING finger)<br>
PF13924 Lipocalin-like domain<br>This family includes domains distantly related to lipocalins. However, they do contain the important GXW motif in the first strand. The protein in this family include aln5 Swiss:B6SEG2 which is involved in biosynthesis of alnumycin  . The family also includes the ZFK protein from Trypanosoma brucei which is a protein kinase. This domain is at the C-terminus of that protein  . The domain is also found as the C-terminal domain in StiJ a protein involved in producing stigmatellin. This domain has been assumed to catalyse a final cyclisation reaction  .. 
PF13925 con80 domain of Katanin<br>The con80 domain of katanin is the C-terminal region of the protein that binds to the N-terminal domain of katanin-p60, the catalytic ATPase. The complex associates with a specific subregion of the mitotic spindle leading to increased microtubule disassembly and targeting of p60 to the spindle poles  .  The assembly and function of the mitotic spindle requires the activity of a number of microtubule-binding proteins. Katanin, a heterodimeric microtubule-severing ATPase, is found localized at mitotic spindle poles. A proposed model is that katanin is targeted to spindle poles through a combination of direct microtubule binding by the p60 subunit and through interactions between the WD40 domain and an unknown protein  .. 
PF13926 Domain of unknown function (DUF4211)<br>
PF13927 Immunoglobulin domain<br>This family contains immunoglobulin-like domains.. 
PF13928 Flocculin type 3 repeat<br>This repeat is found in the Flocculation protein FLO9 Swiss:P39712 close to its C-terminus.. 
PF13929 mRNA stabilisation<br>This domain is an mRNA stabilisation factor  .. 
PF13930 DNA/RNA non-specific endonuclease<br>
PF13931 Kinesin-associated microtubule-binding<br>This domain binds to micotubules [1,2].. 
PF13932 GidA associated domain 3<br>The GidA associated domain 3 is a motif that has been identified at the C-terminus of protein GidA. It consists of 4 helices, the last three being rather short and forming small bundle at the top end of the first longer one. It is here named helical domain 3 because in GidA it is preceded by two other C-terminal helical domain (based on crystal structures [1,2]). GidA is an tRNA modification enzyme found in bacteria and mitochondrial. Based on mutational analysis this domain has been suggested to be implicated in binding of the D-stem of tRNA   and to be responsible for the interaction with protein MnmE  . Structures of GidA in complex with either tRNA or MnmE are missing. Reported to bind to Pfam family MnmE, Pfam:PF12631.. 
PF13933 Putative peptidase family<br>This family of putative peptidases are closely related to the M35 family Pfam:PF02102. In this family the metal binding HEXXH motif is replaced with HRXXH. The exact function of these proteins is unknown. Members of this family are found to be fungal allergens.. 
PF13934 Nuclear pore complex assembly<br>ELYS (embryonic large molecule derived from yolk sac) is conserved from fungi such Aspergillus nidulans and Schizosaccharomyces pombe to human  . It is important for the assembly of the nuclear pore complex  .. 
PF13935 Ead/Ea22-like protein<br>This family contains phage proteins and bacterial proteins that are likely to represent integrated phage proteins. This family includes the Lambda phage Ea22 early protein as well as the Bacteriophage P22 Ead protein.. 
PF13936 Helix-turn-helix domain<br>This helix-turn-helix domain is often found in transferases and is likely to be DNA-binding.. 
PF13937 Domain of unknown function (DUF4212)<br>This family includes several putative integral membrane proteins.. 
PF13938 Domain of unknown function (DUF4213)<br>This domain of unknown function has an enolase N-terminal domain-like fold. Its genomic context suggests that it may have a role in anaerobic vitamin B12 biosynthesis. This domain is often found at the N-terminus of proteins containing DUF364, Pfam:PF04016.. 
PF13939 Toxin TisB, type I toxin-antitoxin system<br>TisB (toxicity-induced by SOS B) is an SOS-induced toxic peptide. It is a hydrophobic membrane-spanning protein which inhibits cell growth  . Its expression is inhibited by the antisense RNA IstR-1, which acts as an antitoxin  .. 
PF13940 Toxin Ldr, type I toxin-antitoxin system<br>This family includes the Ldr (long direct repeat) toxins. In Escherichia coli there are four Ldr toxins, LdrA, LdrB, LdrC and LdrD. These toxins inhibit cell growth, decrease cell viability and cause nucleoid condensation. LdrD expression is inhibited by the antisense RNA RdlD, which functions as an antitoxin  .. 
PF13941 MutL protein<br>This small family includes, GlmL/MutL from Clostridium tetanomorphum and Clostridium cochlearium. GlmL is located between the genes for the two subunits, epsilon (GlmE) and sigma (GlmS), of the coenzyme-B12-dependent glutamate mutase (methylaspartate mutase), the first enzyme in a pathway of glutamate fermentation. Members shows significant sequence similarity to the hydantoinase branch of the hydantoinase/oxoprolinase family  .. 
PF13942 YfhG lipoprotein<br>This family includes the YfhG protein from E. coli Swiss:P0AD44. Members of this family have an N-terminal lipoprotein attachment site. The members of this family are functionally uncharacterized.. 
PF13943 WPP domain<br>
PF13944 Lipocalin-like domain<br>Jackhmmer:JCSG_Target393211_GS13544C. 
PF13945 Salt tolerance down-regulator<br>NST1 is a family of proteins that seem to be involved, directly or indirectly, in the salt sensitivity of some cellular functions in yeast. It does this without affecting sodium accumulation. It negatively affects salt-tolerance through an interaction with the splicing factor Msl1p. This interaction stresses the importance of efficient RNA processing under salt stress conditions  .. 
PF13946 Domain of unknown function (DUF4214)<br>Pfam-B_781 (release 24.0). This domain is found on a variety of different proteins including transferases, and allergen V5/Tpx-1 related proteins.. 
PF13947 Wall-associated receptor kinase galacturonan-binding<br>This cysteine-rich GUB_WAK_bind domain is the extracellular part of this serine/threonine kinase that binds to the cell-wall pectins.. 
PF13948 Domain of unknown function (DUF4215)<br>The function of this family is unknown.. 
PF13949 ALIX V-shaped domain binding to HIV <br>The binding of the LYPxL motif of late HIV p6Gag and EIAV p9Gag to this domain is necessary for viral budding.This domain is generally central between an N-terminal Bro1 domain, Pfam:PF03097 and a C-terminal proline-rich domain. The retroviruses thus used this domain to hijack the ESCRT system of the cell.. 
PF13950 UDP-glucose 4-epimerase C-term subunit<br>This domain is the very C-terminal subunit of UDP-glucose 4-epimerase.. 
PF13952 Domain of unknown function (DUF4216)<br>This DUF is sometimes found at the C-terminal end of proteins carrying a Transposase_21 domain, Pfam:PF02992.. 
PF13953 PapC C-terminal domain<br>The PapC C-terminal domain is a structural domain found at the C-terminus of the E. coli PapC protein. Pili are assembled using the chaperone usher system. In E.coli this is composed of the chaperone PapD and the usher PapC. This domain represents the C-terminal domain from PapC and its homologues. This domain has a beta-sandwich structure similar to the plug domain of PapC  .. 
PF13954 PapC N-terminal domain<br>The PapC N-terminal domain is a structural domain found at the N-terminus of the E. coli PapC protein. Pili are assembled using the chaperone usher system. In E.coli this is composed of the chaperone PapD and the usher PapC. This domain represents the N-terminal domain from PapC and its homologues. This domain is involved in substrate binding  .. 
PF13955 Toxin Fst, type I toxin-antitoxin system<br>Fst (faecalis plasmid stabilization toxin), also known as RNA I, is a toxic peptide. Its N-terminus forms a transmembrane alpha helix, its C terminus is disordered and is likely to be cytosolic. Its translation is inhibited by the antisense RNA, RNA II, which acts as an antitoxin [1,2].. 
PF13956 Toxin Ibs, type I toxin-antitoxin system<br>The Ibs (induction brings stasis) proteins are a family of toxic peptides. Their expression is inhibited by the Sib antisense RNAs, which act as antitoxins  .. 
PF13957 Toxin YafO, type II toxin-antitoxin system<br>YafO is a toxin which inhibits protein synthesis. It acts as a ribosome-dependent mRNA interferase. It forms part of a type II toxin-antitoxin system, where the YafN protein acts as an antitoxin [1,2]. This domain forms complexes with yafN antitoxins containing Pfam:PF02604.. 
PF13958 Toxin ToxN, type III toxin-antitoxin system<br>ToxN acts as a toxin, it is part of a type III toxin-antitoxin system. It acts as a ribosome independent endoribonuclease. It interacts with, and is inhibited by, the RNA antitoxin, ToxI [1,2]. Three ToxN monomers bind to three ToxI monomers to create a trimeric ToxN-ToxI complex  .. 
PF13959 Domain of unknown function (DUF4217)<br>This short domain is found at the C-terminus of many helicase proteins.. 
PF13960 Domain of unknown function (DUF4218)<br>
PF13961 Domain of unknown function (DUF4219)<br>This domain is very short and is found at the N-terminal of many Gag-pol polyprotein and related proteins. There is a highly conserved YxxWxxxM sequence motif.. 
PF13962 Domain of unknown function<br>The PGG domain is named for the highly conserved sequence motif found at the startt of the domain. The function is not known.. 
PF13963 Transposase-associated domain<br>
PF13964 Kelch motif<br>
PF13965 dsRNA-gated channel SID-1<br>This is a family of proteins that are transmembrane dsRNA-gated channels. They passively transport dsRNA into cells and do not act as ATP-dependent pumps  . They are required for systemic RNA interference [2,3].. 
PF13966 zinc-binding in reverse transcriptase<br>This domain would appear to be a zinc-binding region of a putative reverse transcriptase.. 
PF13967 Late exocytosis, associated with Golgi transport <br>This family represents the first three transmembrane regions of 11-TM proteins involved in vesicle transport. In S. cerevisiae these proteins are members of the yeast facilitator superfamily and are integral membrane proteins localised to the cell periphery, in particular to the bud-neck region. The distribution is consistent with a role in late exocytosis which is in agreement with the proteins' ability to substitute for the function of Sro7p, required for the sorting of the protein Enap1 into Golgi-derived vesicles destined for the cell surface  .. 
PF13968 Domain of unknown function (DUF4220)<br>This family is found in plants and is often associated with DUF294, Pfam:PF04578.. 
PF13969 Pab87 octamerisation domain<br>This domain was first characterised as the C-terminal domain of Pab87 serine protease from Pyrococcus abyssi  . The domain is reported to play a crucial role in Pab87 octamerisation and active site compartmentalisation. Its up-and-down 8-stranded beta-barrel 3D structure is reminiscent of the one found in lipocalins.. 
PF13970 Domain of unknown function (DUF4221)<br>JCSG_target-390208:A6KZ57. This family of bacterial proteins contains highly conserved asparagine and cysteine residues.\.  The function is not known.. 
PF13971 MEI4-Rec24;<br>Meiosis-specific protein Mei4. Wood V, Coggill P, Eberhardt R. Pfam-B_78600 (release 24.0). This family of meiosis specific proteins is required for correct meiotic chromosome segregation and recombination  . It is required for meiotic DNA double-strand break (DSB) formation  .. 
PF13972 Bacterial transcriptional repressor<br>This family of bacterial transcriptional repressors is characterised by the short approximately 50 amino acid stretch of residues constituting the helix-turn-helix DNA binding motif, around the YRFhY motif. The target proteins that are repressed are involved in the transcriptional control of multi-drug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity.  The regulatory network in which TetR itself is involved is in being released in the presence of tetracycline, binding to the target operator, and repressing tetA transcription  .. 
PF13973 Domain of unknown function (DUF4222)<br>This short protein is likely to be of phage origin. For example it is found in the Swiss:B6DZ51 Enterobacteria phage YYZ-2008. It is largely found in enteric bacteria. The molecular function of this protein is unknown.. 
PF13974 YebO-like protein<br>This short protein is uncharacterized. It seems likely to be of phage origin as it is found in Swiss:Q9MCU2 and Swiss:Q9MCS4. The protein is also found in a variety of enteric bacteria.. 
PF13975 gag-polyprotein putative aspartyl protease<br>This family of putative aspartyl proteases is found pre-dominantly in retroviral proteins.. 
PF13976 GAG-pre-integrase domain<br>This domain is found associated with retroviral insertion elements and lies just upstream of the integrase region on the polyproteins.. 
PF13977 Bacterial transcriptional repressor<br>This family of bacterial transcriptional repressors is characterised by the short approximately 50 amino acid stretch of residues constituting the helix-turn-helix DNA binding motif, around the YRFhY motif. The target proteins that are repressed are involved in the transcriptional control of multi-drug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity  . Another target protein is BetI, an osmoprotectant which controls the choline-glycine betaine pathway in E.coli  .. 
PF13978 Protein of unknown function (DUF4223)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. These proteins are likely to be lipoproteins (attachment site currently included in alignment).. 
PF13979 SopA-like catalytic domain<br>This domain is found in the E. coli Type III secretion effector proteins SopA and NleL [1,2]. These proteins have been shown to act as E3 ubiquitin ligase enzymes. This domain contains the active site cysteine residue.. 
PF13980 Uncharacterised protein family (UPF0370)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. There is a conserved DWP sequence motif.. 
PF13981 SopA-like central domain<br>This domain is found in the E. coli Type III secretion effector proteins SopA and NleL [1,2]. These proteins have been shown to act as E3 ubiquitin ligase enzymes.. 
PF13982 YbfN-like lipoprotein<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length. Members of this family are lipoproteins.. 
PF13983 YsaB-like lipoprotein<br>This family of proteins is functionally uncharacterised. These proteins are related to E.coli YsaB Swiss:Q0TBP2. This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length. These proteins are lipoproteins.. 
PF13984 MsyB protein<br>The MsyB protein has been found to be able to restore protein export defects caused by a temperature-sensitive secY or secA mutation  . However, its exact molecular function is still unknown, but it may play a role in protein export. Proteins in this family are approximately 120 amino acids in length. This family of proteins is found in bacteria.. 
PF13985 YbgS-like protein<br>This family of proteins is functionally uncharacterised. The family includes the YbgS protein from E. coli Swiss:P0AAV6. This family of proteins is found in bacteria. Proteins in this family are approximately 130 amino acids in length. Some members of this family are annotated as homeobox protein, but this annotation cannot be verified.. 
PF13986 Domain of unknown function (DUF4224)<br>This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. The protein is likely to be of phage origin and is found as protein Gp02 Swiss:C8CLF5 in the Xylella phage Xfas53  .. 
PF13987 YedD-like protein<br>This family of proteins related to the YedD protein is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 140 amino acids in length. These proteins are lipoproteins.. 
PF13988 Protein of unknown function (DUF4225)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 182 and 282 amino acids in length.. 
PF13989 YejG-like protein<br>The YejG protein family is a group of functionally uncharacterised proteins related to Swiss:P0AD21. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length.. 
PF13990 YjcZ-like protein<br>This family of proteins is functionally uncharacterised. The family includes the YjcZ protein from E. coli Swiss:P39267. This family of proteins is found in enteric bacteria. Proteins in this family are approximately 300 amino acids in length. There are two conserved sequence motifs: FGD and MPR.. 
PF13991 BssS protein family<br>The BssS protein family is a group of proteins that are involved in regulation of biofilm formation  .  Proteins in this family are approximately 80 amino acids in length.. 
PF13992 YecR-like lipoprotein<br>The YecR-like family of lipoproteins includes the YecR protein from E. coli Swiss:P76308. This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 110 amino acids in length.. 
PF13993 YccJ-like protein<br>The YccJ-like family of proteins includes the E. coli YccJ protein   Swiss:P0AB14 which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length.. 
PF13994 PgaD-like protein<br>This family includes the PgaD protein from E. coli Swiss:P69432. The homopolymer poly-beta-1,6-N-acetyl-D-glucosamine (beta-1,6-GlcNAc; PGA) serves as an adhesin for the maintenance of biofilm structural stability in eubacteria. The pgaABCD operon is required for its synthesis and export. It has been shown that PgaD is essential for this process  .. 
PF13995 YebF-like protein<br>The YebF-like protein family appears to be a group of colicin immunity proteins. As well as YebF the family includes cmi, the colicin M immunity protein  . This domain family is found in bacteria, and is approximately 80 amino acids in length. The alignment contains two conserved cysteine residues that form a disulphide bond in the solved structure  .. 
PF13996 YobH-like protein<br>The YobH-like protein family includes the YobH protein from E. coli Swiss:Q2MB16 which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. There are two conserved sequence motifs: GYG and GLGL.. 
PF13997 YqjK-like protein<br>The YqjK-like protein family includes the E. coli YqjK protein Swiss:Q47710 which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length. There is a single completely conserved residue R that may be functionally important.. 
PF13998 MgrB protein<br>The MgrB protein is a short lipoprotein.  The mgrB gene has a mg2+ responsive promoter  . Deletion of mgrB results in a potent increase in PhoP-regulated transcription  . The PhoQ/PhoP signaling system responds to low magnesium and the presence of certain cationic antimicrobial peptides. Over-expression of mgrB decreased transcription at both high and low concentrations of magnesium. Localization and bacterial two-hybrid studies suggest that MgrB resides in the inner-membrane and interacts directly with PhoQ. This domain family is found in bacteria, and is approximately 40 amino acids in length. There are two conserved sequence motifs: CDQ and GIC.. 
PF13999 MarB protein<br>The MarB protein is found in the multiple antibiotic resistance (mar) locus in Escherichia coli. The MarB protein is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. There is a conserved GSDKSD sequence motif.. 
PF14000 DNA packaging protein FI<br>This family includes the lambda phage DNA-packaging protein FI. Proteins in this family are typically between 124 and 140 amino acids in length.  There is a conserved EEE sequence motif.. 
PF14001 YdfZ protein<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. There is a conserved YDRNRN sequence motif. The E. coli protein has been shown to bind selenium  .. 
PF14002 YniB-like protein<br>The YniB-like protein family includes the E. coli YniB protein Swiss:P76208 which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 180 amino acids in length. This family of proteins are integral membrane proteins.. 
PF14003 YlbE-like protein<br>The YlbE-like protein family includes the B. subtilis protein YlbE Swiss:O34958 which is functionally uncharacterised. This family of cytosolic proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. There is a conserved WYR sequence motif.. 
PF14004 Protein of unknown function (DUF4227)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length.. 
PF14005 YpjP-like protein<br>The YpjP-like protein family includes the B. subtilis YpjP protein Swiss:P54172 which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 200 amino acids in length.. 
PF14006 YqzL-like protein<br>The YqzL-like protein family includes the B. subtilis YqzL protein Swiss:C0H452 which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 50 amino acids in length.. 
PF14007 YtpI-like protein<br>The YtpI-like protein family includes the B. subtilis YtpI protein Swiss:O34922 which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 73 and 101 amino acids in length.. 
PF14008 Iron/zinc purple acid phosphatase-like protein C<br>This domain is found at the C-terminus of Purple acid phosphatase proteins.. 
PF14009 Domain of unknown function (DUF4228)<br>This domain is found in plants. The function is not known.. 
PF14010 Phosphoenolpyruvate carboxylase<br>This family of phosphoenolpyruvate carboxylases is based on seqeunces not picked up by the model for PEPcase, PF00311. Most of the family members are from Archaea.. 
PF14011 EspG family<br>This family of proteins contains the the EspG1, EspG2 and EspG3 proteins from M. tuberculosis.  These proteins are involved in the ESAT-6 secretion system 1 (ESX-1) of Mycobacterium tuberculosis which is important for virulence and intercellular spread  . Proteins in this family are typically between 254 and 295 amino acids in length.. 
PF14012 Protein of unknown function (DUF4229)<br>This family of integral membrane proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 95 and 122 amino acids in length.. 
PF14013 MT0933-like antitoxin protein<br>This family of proteins contains the MT0933 protein Swiss:O05901 which has been identified as an antitoxin to /protein MT0934  . This family of proteins is found in bacteria. Proteins in this family are typically between 61 and 90 amino acids in length.. 
PF14014 Protein of unknown function (DUF4230)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 203 and 228 amino acids in length.. 
PF14015 Protein of unknown function (DUF4231)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 148 and 288 amino acids in length.. 
PF14016 Protein of unknown function (DUF4232)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 177 and 242 amino acids in length. Many members of this family are lipoproteins.. 
PF14017 Protein of unknown function (DUF4233)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 122 and 147 amino acids in length. Proteins in this family are integral membrane proteins.. 
PF14018 Domain of unknown function (DUF4234)<br>This presumed integral membrane protein domain is functionally uncharacterised. This domain family is found in bacteria and archaea, and is approximately 70 amino acids in length.. 
PF14019 Protein of unknown function (DUF4235)<br>This family of integral membrane proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 88 and 119 amino acids in length.. 
PF14020 Protein of unknown function (DUF4236)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 69 and 402 amino acids in length.. 
PF14021 Protein of unknown function (DUF4237)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 123 and 781 amino acids in length.. 
PF14022 Protein of unknown function (DUF4238)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 274 and 374 amino acids in length.. 
PF14023 Protein of unknown function (DUF4239)<br>Jackhmmer:Catenulispora acidiphila . This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 254 and 270 amino acids in length.. 
PF14024 Protein of unknown function (DUF4240)<br>This presumed domain is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 169 and 263 amino acids in length. This domain is often associated with the WGR domain Pfam:PF05406.. 
PF14025 Protein of unknown function (DUF4241)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 205 and 315 amino acids in length. There is a conserved GDG sequence motif at the C-terminus.. 
PF14026 Protein of unknown function (DUF4242)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 90 and 170 amino acids in length. There is a single completely conserved residue C that may be functionally important.. 
PF14027 Protein of unknown function (DUF4243)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 348 and 477 amino acids in length.. 
PF14028 SpaB C-terminal domain<br>This presumed domain is found at the C-terminus of the SpaB protein Swiss:P39774. SpaB is involved in the synthesis of the lantibiotic subtilin.\.   This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 317 and 1029 amino acids in length. The family is often found in association with Pfam:PF04737, Pfam:PF04738. This domain is found in isolation in some proteins. This domain is also found in EpiB involved in epidermin biosynthesis.. 
PF14029 Protein of unknown function (DUF4244)<br>Jackhmmer:Catenulispora acidiphila . This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 66 and 95 amino acids in length. There is a conserved EYA sequence motif.. 
PF14030 Protein of unknown function (DUF4245)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 188 and 235 amino acids in length.. 
PF14031 Putative serine dehydratase domain<br>This domain is found at the C-terminus of yeast D-serine dehydratase  . Structures have been solved for two bacterial members of this family. The yeast protein has been shown to be a zinc dependant enzyme.. 
PF14032 PknH-like extracellular domain<br>This domain is functionally uncharacterised. It is found as the periplasmic domain of the bacterial protein kinase PknH  . The domain is also found in isolation in numerous proteins, for example the lipoproteins lpqQ, lprH, lppH and lpqA from M. tuberculosis. This family of proteins is found in bacteria. Proteins in this family are typically between 214 and 268 amino acids in length. There are two completely conserved C residues that are likely to form a disulphide bond.  A second pair of cysteines are less well conserved probably form a second disulphide bond. It seems likely that this domain functions to bind some as yet unknown ligand.. 
PF14033 Protein of unknown function (DUF4246)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and fungi. Proteins in this family are typically between 392 and 644 amino acids in length.. 
PF14034 Sporulation protein YtrH<br>This family of proteins is involved in sporulation. It may contribute to the formation and stability of the thick peptidoglycan layer between the two membranes of the spore, known as the cortex  . In Bacillus subtilis its expression is regulated by sigma-E  .. 
PF14035 YlzJ-like protein<br>The YlzJ-like protein family includes the B. subtilis YlzJ protein Swiss:C0H413, which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 61 and 72 amino acids in length. There are two completely conserved residues (L and G) that may be functionally important.. 
PF14036 YlaH-like protein<br>The YlaH-like protein family includes the B. subtilis YlaH protein Swiss:O07632, which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length. There is a conserved LGFA sequence motif.. 
PF14037 YoqO-like protein<br>The YoqO-like protein family includes the B. subtilis YoqO protein Swiss:O31923, which is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 120 amino acids in length. There are two completely conserved residues (I and Y) that may be functionally important.. 
PF14038 YqzE-like protein<br>The YqzE-like protein family includes the B. subtilis YqzE protein Swiss:O32020, which is functionally uncharacterised. It is a part of the ComG operon, which is regulated by the competence transcription factor ComK  .  This family of proteins is found in bacteria. Proteins in this family are typically between 49 and 66 amino acids in length.. 
PF14039 YusW-like protein<br>The YusW-like protein family includes the B. subtilis YusW protein Swiss:O32189, which is functionally uncharacterised. This family of proteins is found in bacteria, and is approximately 90 amino acids in length.. 
PF14040 Deoxyribonuclease NucA/NucB<br>Members of this family act as deoxyribonucleases  .. 
PF14041 LppP/LprE lipoprotein<br>The family includes putative lipoproteins LppP and LprE from species of Mycobacterium. LppP is required for optimal growth of M. tuberculosis  .. 
PF14042 Domain of unknown function (DUF4247)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 143 and 271 amino acids in length.. 
PF14043 WVELL protein<br>This family includes the B. subtilis YfjH protein Swiss:O31578, which is functionally uncharacterised.  This is not a homologue of E. coli YfjH, a synonym for IscX, which belongs to Pfam:PF04384.  This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length and contain a highly conserved WVELL motif.. 
PF14044 NETI protein<br>This family includes the B. subtilis YebG protein Swiss:O34700, which is functionally uncharacterised. This is not a homologue of E. coli YebG, which belongs to Pfam:PF07130. This family of proteins is found in bacteria.  Proteins in this family are typically between 42 and 66 amino acids in length and contain a conserved NETI motif.. 
PF14045 YIEGIA protein<br>This family includes the B. subtilis YphB protein Swiss:P50742, which is functionally uncharacterised. Its expression is regulated by the sporulation transcription factor sigma-F, however it is not essential for sporulation or germination  . This is not a homologue of E. coli YphB, which belongs to Pfam:PF01263.\.    This family of proteins is found in bacteria. Proteins in this family are typically between 276 and 300 amino acids in length and contain a conserved YIEGIA motif.. 
PF14046 Nuclear receptor repeat<br>Joint Center of Structural Genomics (JCSG). This is a repeat domain involved in dimerisation of nuclear receptors proteins and in transcriptional regulation in general. It contains a  Leu-Xaa-Xaa-Leu-Leu motif which has been characterized for the orphan  nuclear receptor Dax-1, which represses the constitutively expressed  protein Ad4BP/SF-1. The LXXLL motif plays in important role in binding of Dax-1 to Ad4BP/SF-1  . The domain is subject to structure\. determination by the Joint Center of Structural Genomics.. 
PF14047 Dppa2/4 conserved region<br>Joint Center of Structural Genomics (JCSG). This domain has been characterized in the finding of a developmental pluripotency associated gene (Dppa) in the lower vertebrate Xenopus laevis  . Previous to this discovery, Dppa genes were known only in higher vertebrates. The domain is subject to structure determination by the Joint Center of Structural Genomics.. 
PF14048 C-terminal domain of methyl-CpG binding protein 2 and 3<br>Joint Center of Structural Genomics (JCSG). CpG-methylation is a frequently occurring epigenetic modification of vertebrate genomes resulting in transcriptional repression. This domain was found at the C-terminus of the methyl-CpG-binding domain (MBD) containing proteins MBD2   and MBD3  , the latter was shown to not bind directly to methyl-CpG DNA but rather interact with components of the NuRD/Mi2 complex  , an abundant deacetylase complex. The domain is subject to structure determination by the Joint Center of Structural Genomics.. 
PF14049 Dppa2/4 conserved region in higher vertebrates<br>Joint Center of Structural Genomics (JCSG). Developmental pluripotency associated genes (Dppa) in lower vertebrates have remained undetected until the discovery of a Dppa homologue in Xenopus laevis  , reporting a new domain termed Dppa2/4 conserved region (DCR). In higher vertebrate Dppa proteins the DCR domain is located next to the here-reported domain. The domain is subject to structure determination by the Joint Center of Structural Genomics.. 
PF14050 N-terminal conserved domain of Nudc.<br>Joint Center of Structural Genomics (JCSG). The N-terminus of nuclear distribution gene C homolog (NUDC) proteins contains a highly conserved region consisting of a predicted three helix bundle. In the human homolog this segment has been targeted for structure determination by the Joint Center for Structural Genomics.  NUDC forms a complex with other NUD proteins and is involved in several cellular division activities. Recently it was shown that NUDC regulates platelet-activating factor (PAF) acetylhydrolase with PAF being a pro-inflammatory secondary lipidic messenger  .. 
PF14051 N-terminal domain of DPF2/REQ.<br>Joint Center of Structural Genomics (JCSG). This putative domain has been detected on the human DPF2 protein and was subsequently targeted for structure determination by the Joint Center for Structural Genomics (JCSG). Possibly, the C-terminus extends by 30 amino acids and forms a separate domain. DPF2 interacts with estrogen related receptor alpha (Err-alpha), an orphan receptor which acts as a regulator in energy metabolism  .  It was also identified as an adaptor molecule that links nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kappa-B) dimer RelB/p52 and switch/sucrose-nonfermentable (SWI/SNF) chromatin remodeling factor  .. 
PF14052 Capsule assembly protein Wzi<br>Many bacteria are covered in a layer of surface-associated polysaccharide called the capsule. These capsules can be divided into four groups depending upon the organisation of genes responsible for capsule assembly, the assembly pathway and regulation  . This family plays a role in group 1 capsule biosynthesis. It is likely to be involved in the later stages of capsule assembly. It is likely to consist of a beta-barrel structure  .. 
PF14053 Domain of unknown function (DUF4248)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 73 and 86 amino acids in length.. 
PF14054 Domain of unknown function (DUF4249)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 279 and 365 amino acids in length. There are two completely conserved residues (C and G) that may be functionally important.. 
PF14055 NVEALA protein<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 75 and 92 amino acids in length. There is a conserved NVEALA sequence motif.. 
PF14056 Domain of unknown function (DUF4250)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. There are two completely conserved residues (N and R) that may be functionally important.. 
PF14057 GGGtGRT protein<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are approximately 330 amino acids in length and contain many highly conserved residues including a GGGtGRT motif.. 
PF14058 PcfK-like protein<br>The PcfK-like protein family includes the Enterococcus faecalis PcfK protein Swiss:Q82YK9 which is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 137 and 257 amino acids in length. There are two completely conserved residues (D and L) that may be functionally important.. 
PF14059 Domain of unknown function (DUF4251)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 164 and 196 amino acids in length.. 
PF14060 Domain of unknown function (DUF4252)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 154 and 182 amino acids in length.. 
PF14061 Polycomb-like MTF2 factor 2<br>Joint Center of Structural Genomics (JCSG). Mammalian Polycomb-like gene MTF2/PCL2 forms a complex with Polycomb repressive complex-2 (PRC2) and collaborates with PRC1 to achieve repression of Hox gene expression  . The human MTF2 gene is expressed in three splicing variants, each of them contains the short C-terminal domain defined here. The domain is subject to structure determination by the Joint Center of Structural Genomics.. 
PF14062 Domain of unknown function (DUF4253)<br>This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 110 amino acids in length.. 
PF14063 Protein of unknown function (DUF4254)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 195 and 207 amino acids in length.. 
PF14064 HmuY protein<br>HmuY is a novel heme-binding protein   that recruits heme from host carriers and delivers it to its cognate outer-membrane transporter, the TonB-dependent receptor HmuR.\.    This family of proteins is found in bacteria. Proteins in this family are typically between 214 and 278 amino acids in length.. 
PF14065 Protein of unknown function (DUF4255)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 190 and 320 amino acids in length.. 
PF14066 Protein of unknown function (DUF4256)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 190 amino acids in length.. 
PF14067 LssY C-terminus<br>This domain is found at the C-terminus of Legionella LssY proteins, which may be a part of the type I secretion system  . This domain is functionally uncharacterised. This domain is found in bacteria, and is typically between 182 and 195 amino acids in length. It is often found in association with Pfam:PF09335 and PF01569. There are two completely conserved residues (P and W) that may be functionally important.. 
PF14068 Putative membrane protein<br>This family of bacterial proteins is functionally uncharacterised.  Proteins in this family are approximately 100 amino acids in length. There is a conserved FGIGF sequence motif, and many members are putative membrane proteins.. 
PF14069 Stage VI sporulation protein F<br>The sporulation-specific SpoVIF (YjcC) protein of Bacillus subtilis is essential for the development of heat-resistant spores. Its expression is governed by SigK [1,2].. 
PF14070 Putative motility protein<br>This family of proteins is regulated in B. subtilis by SigD, and is likely to be involved in motility or flagellin production, Proteins in this family are approximately 60 amino acids in length, and contain two highly conserved asparagine residues.. 
PF14071 Putative coat protein<br>This is a family of putative bacterial coat proteins. Proteins in this family are approximately 140 amino acids in length.. 
PF14072 DNA-sulfur modification-associated<br>This is family of bacterial proteins likely to be necessary for binding to DNA and recognising the modification sites.  Members are found in bacteria, archaea and on viral plasmids, and are typically between 354 and 474 amino acids in length. There is a conserved DGQHR sequence motif.. 
PF14073 Centrosome localisation domain of Cep57<br>The CLD or centrosome localisation domain of Cep57 is found at the N-terminus, and lies approximately between residues 58 and 239. This region lies within the first alpha-helical coiled-coil segment of Cep57, and localises to the centrosome internally to gamma-tubulin, suggesting that it is either on both centrioles or on a centromatrix component.  This N-terminal region can also multimerise with the N-terminus of other Cep57 molecules.  The C-terminal part, Family Cep57_MT_bd, Pfam:PF06657, is the microtubule-binding region of Cep57.. 
PF14074 Protein of unknown function (DUF4257)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length.. 
PF14075 Ubinuclein conserved middle domain<br>Joint Center of Structural Genomics (JCSG). Ubinuclein 1 and 2 (UBN1, UBN2) are members of a histone chaperone  complex involved in the formation of a certain type of facultative  heterochromatin, called senescence-associated heterochromatin foci  (SAHF)    . The domain described here is conserved in many  eukaryotes such as human, rat, drosophila, and zebra-fish and has been  targeted for protein structure determination by the Joint Center  for Structural Genomics.. 
PF14076 Domain of unknown function (DUF4258)<br>Jackhmmer:Chitinophaga pinensis . This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 95 and 124 amino acids in length.. 
PF14077 Alternative WD40 repeat motif<br>Joint Center of Structural Genomics (JCSG). WD repeats are short subdomains of about 40 amino acids and fold into 4 antiparallel beta hairpins. This domain here has been detected on the C-terminus of WD repeat-containing protein 18 during target selection by the Joint Center for Structural Genomics.. 
PF14078 Domain of unknown function (DUF4259)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 118 and 145 amino acids in length.. 
PF14079 Domain of unknown function (DUF4260)<br>This family of integral membrane proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 114 and 126 amino acids in length. There is a conserved GLK sequence motif.. 
PF14080 Domain of unknown function (DUF4261)<br>This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 80 amino acids in length.. 
PF14081 Domain of unknown function (DUF4262)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 147 and 227 amino acids in length. Swiss:Q50763 is incorrectly annotated as the KatG protein.. 
PF14082 Domain of unknown function (DUF4263)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 244 and 403 amino acids in length.. 
PF14083 PGDYG protein<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 150 amino acids in length. There is a conserved PGDYG motif.. 
PF14084 Protein of unknown function (DUF4264)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length.. 
PF14085 Domain of unknown function (DUF4265)<br>Jackhmmer:Chitinophaga pinensis . This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 139 and 168 amino acids in length.. 
PF14086 Domain of unknown function (DUF4266)<br>This presumed lipoprotein domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 50 amino acids in length.. 
PF14087 Domain of unknown function (DUF4267)<br>This family of integral membrane proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 126 and 142 amino acids in length.. 
PF14088 Domain of unknown function (DUF4268)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 151 and 387 amino acids in length.. 
PF14089 KinB-signalling pathway activation in sporulation<br>This family of small proteins is found in the membrane and is necessary for kinase KinB signalling during sporulation. There is a conserved GFF sequence motif. The initiation of sporulation in Bacillus subtilis is dependent on the phosphorylation of the Spo0A transcription factor mediated by the phospho-relay and by two major kinases, KinA and KinB.. 
PF14090 Helix-turn-helix domain<br>This helix-turn-helix domain is often found in phage proteins and is likely to be DNA-binding.. 
PF14091 Domain of unknown function (DUF4269)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 176 and 187 amino acids in length. There is a conserved KTE sequence motif.. 
PF14092 Domain of unknown function (DUF4270)<br>This family of lipoproteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 444 and 534 amino acids in length.. 
PF14093 Domain of unknown function (DUF4271)<br>This family of integral membrane proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 221 and 326 amino acids in length.. 
PF14094 Domain of unknown function (DUF4272)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 221 and 399 amino acids in length.. 
PF14096 Domain of unknown function (DUF4274)<br>This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 80 amino acids in length.. 
PF14097 Stage V sporulation protein AE1<br>Members of this family are all described as putative stage V sporulation protein AE, although this could not be confirmed. Proteins in this family are approximately 190 amino acids in length.. 
PF14098 Small, acid-soluble spore protein I<br>This family of proteins is putatively assigned as a small, acid-soluble spore protein 1.  Proteins in this family are approximately 70 amino acids in length. There is a conserved LPGLGV sequence motif.. 
PF14099 Polysaccharide lyase<br>This family includes heparin lyase I, EC:4.2.2.7.\.   Heparin lyase I depolymerises heparin by cleaving the glycosidic linkage next to an iduronic acid moiety [1,2]. The structure of heparin lyase I consists of a beta-jelly roll domain with a long, deep substrate-binding groove and an unusual thumb domain containing many basic residues extending from the main body of the enzyme  . This family also includes glucuronan lyase, EC:4.2.2.14  . The structure glucuronan lyase is a beta-jelly roll  .. 
PF14100 Methane oxygenase PmoA<br>This family is a putative methane oxygenase  . 
PF14101 Domain of unknown function (DUF4275)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 140 amino acids in length.. 
PF14102 Capsule biosynthesis CapC<br>This family of proteins play a role in capsule biosynthesis. They are essential for gamma-polyglutamic acid (PGA) production  .. 
PF14103 Domain of unknown function (DUF4276)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 190 and 224 amino acids in length. There is a single completely conserved residue E that may be functionally important.. 
PF14104 Domain of unknown function (DUF4277)<br>This presumed domain is functionally uncharacterised. This domain family is found in bacteria and archaea, and is approximately 110 amino acids in length. There is a conserved NGLGF sequence motif.. 
PF14105 Domain of unknown function (DUF4278)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 58 and 136 amino acids in length. There is a single completely conserved residue R that may be functionally important.. 
PF14106 Domain of unknown function (DUF4279)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 134 and 145 amino acids in length.. 
PF14107 Domain of unknown function (DUF4280)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 129 and 456 amino acids in length. There is a single completely conserved residue C that may be functionally important.. 
PF14108 Domain of unknown function (DUF4281)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 147 and 232 amino acids in length. There are two completely conserved residues (W and P) that may be functionally important.. 
PF14109 GldH lipoprotein<br>Members of this protein family are predicted lipoproteins, exclusive to the Bacteroidetes phylum. Proteins in this family are typically between 155 and 167 amino acids in length. Members include GldH, a protein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii  . Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Not all Bacteroidetes with members of this protein family may have gliding motility.. 
PF14110 Domain of unknown function (DUF4282)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 93 and 155 amino acids in length. There is a single completely conserved residue E that may be functionally important.. 
PF14111 Domain of unknown function (DUF4283)<br>This domain family is found in plants, and is approximately 100 amino acids in length. Considering the very diverse range of other domains it is associated with it is possible that this domain is a binding/guiding region.  There are two highly conserved tryptophan residues.. 
PF14112 Domain of unknown function (DUF4284)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 124 and 142 amino acids in length.. 
PF14113 Domain of unknown function (DUF4285)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 157 and 206 amino acids in length.. 
PF14114 Domain of unknown function (DUF4286)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 100 and 112 amino acids in length.. 
PF14115 YuzL-like protein<br>The YuzL-like protein family includes the B. subtilis YuzL protein Swiss:C0H3R0 which is functionally uncharacterised. This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 50 amino acids in length.. 
PF14116 YyzF-like protein<br>The YyzF-like protein family includes the B. subtilis YyzF protein Swiss:C0H3T9 which is functionally uncharacterised.  This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length.. 
PF14117 Domain of unknown function (DUF4287)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 70 and 180 amino acids in length.. 
PF14118 YfzA-like protein<br>The YfzA-like protein family includes the B. subtilis YfzA protein Swiss:C0H3X6 which is functionally uncharacterised.  This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length.. 
PF14119 Domain of unknown function (DUF4288)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length.. 
PF14120 YhzD-like protein<br>The YhzD-like protein family includes the B. subtilis YhzD protein Swiss:C0H3Y1 which is functionally uncharacterised.  This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. There is a conserved GKL sequence motif.. 
PF14121 Domain of unknown function (DUF4289)<br>This family of membrane bet-barrel proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 655 and 722 amino acids in length. Swiss:Q2S343 is identified by Gene3D as a membrane bound beta-barrel.. 
PF14122 YokU-like protein<br>The YokU-like protein family includes the B. subtilis YokU protein Swiss:C0H434 which is functionally uncharacterised.  This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There are two conserved CXXC sequence motifs.. 
PF14123 Domain of unknown function (DUF4290)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 200 and 221 amino acids in length. There are two conserved sequence motifs: EYGR and KLWD.. 
PF14124 Domain of unknown function (DUF4291)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 190 and 214 amino acids in length. There are two conserved sequence motifs: VYQAY and RMTW.. 
PF14125 Domain of unknown function (DUF4292)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 243 and 287 amino acids in length.. 
PF14126 Domain of unknown function (DUF4293)<br>This family of integral membrane proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 136 and 154 amino acids in length.. 
PF14127 Domain of unknown function (DUF4294)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 192 and 226 amino acids in length.. 
PF14128 Domain of unknown function (DUF4295)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 50 amino acids in length. There are two completely conserved residues (K and Y) that may be functionally important.. 
PF14129 Domain of unknown function (DUF4296)<br>This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 90 amino acids in length.. 
PF14130 Domain of unknown function (DUF4297)<br>This presumed domain is functionally uncharacterised. This domain family is found in bacteria and archaea, and is typically between 207 and 221 amino acids in length.. 
PF14131 Domain of unknown function (DUF4298)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 94 and 105 amino acids in length. There are two completely conserved residues (Y and D) that may be functionally important.. 
PF14132 Domain of unknown function (DUF4299)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 275 and 313 amino acids in length. There are two conserved sequence motifs: RGF and DAY. There are two completely conserved residues (P and D) that may be functionally important.. 
PF14133 Domain of unknown function (DUF4300)<br>This family of lipoproteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 281 and 303 amino acids in length. There are two conserved sequence motifs: NCR and PYQ.. 
PF14134 Domain of unknown function (DUF4301)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 505 and 516 amino acids in length.. 
PF14135 Domain of unknown function (DUF4302)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 344 and 443 amino acids in length. There are two completely conserved residues (R and L) that may be functionally important.. 
PF14136 Domain of unknown function (DUF4303)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 169 and 192 amino acids in length.. 
PF14137 Domain of unknown function (DUF4304)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 154 and 223 amino acids in length.. 
PF14138 Cytochrome c oxidase assembly protein COX16<br>This family represents homologues of COX16   which has been shown to be involved in assembly of cytochrome oxidase  . Protein in this family are typically between 106 and 134 amino acids in length.. 
PF14139 YpzG-like protein<br>The YpzG-like protein family includes the B. subtilis YpzG protein Swiss:C0H444 which is functionally uncharacterised.  This family of proteins is found in bacteria. Proteins in this family are approximately 50 amino acids in length. There is a conserved QVNG sequence motif.. 
PF14140 YpzI-like protein<br>The YpzI-like protein family includes the B. subtilis YpzI protein Swiss:C0H446 which is functionally uncharacterised.  This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length.. 
PF14141 YqzM-like protein<br>The YqzM-like protein family includes the B. subtilis YqzM protein Swiss:C0H453 which is functionally uncharacterised.  This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length.. 
PF14142 YrzO-like protein<br>The YrzO-like protein family includes the B. subtilis YrzO protein Swiss:C0H458 which is functionally uncharacterised.  This family of proteins is found in bacteria. Proteins in this family are approximately 50 amino acids in length.. 
PF14143 YrhC-like protein<br>The YrhC-like protein family includes the B. subtilis YrhC protein Swiss:O05395 which is functionally uncharacterised. YrhC is on the same operon as the MccA and MccB genes, which are involved in the conversion of methionine to cysteine.  Expression of this operon is repressed in the presence of sulphate or cysteine  . This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length.. 
PF14144 Seed dormancy control<br>This family of plant proteins appears to be a highly specific controller seed dormancy.. 
PF14145 YrhK-like protein<br>The YrhK-like protein family includes the B. subtilis YrhK protein Swiss:O05401 which is functionally uncharacterised.  Its expression is under the control of the motility sigma factor sigma-D  .  This domain family is found in bacteria, archaea and eukaryotes, and is approximately 60 amino acids in length.. 
PF14146 Domain of unknown function (DUF4305)<br>This family includes the B. subtilis YdiK protein Swiss:O05524, which is functionally uncharacterised.  This is not a homologue of E. coli YdiK, which belongs to Pfam:PF01594.  This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length.. 
PF14147 Sporulation protein YhaL<br>This family of proteins is involved in sporulation. In B. subtilis its expression is regulated by the early mother-cell-specific transcription factor sigma-E  .. 
PF14148 YhdB-like protein<br>The YhdB-like protein family includes the B. subtilis YhdB protein Swiss:O07530, which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 57 and 82 amino acids in length. There are two conserved sequence motifs: LMVRT and FLHAY.. 
PF14149 YhfH-like protein<br>The YhfH-like protein family includes the B. subtilis YhfH protein Swiss:O07606, which is functionally uncharacterised. Its expression is repressed by the Spx paralogue MgsR, which regulates genes involved in stress response  .  This family of proteins is found in bacteria. Proteins in this family are typically between 42 and 53 amino acids in length.. 
PF14150 YesK-like protein<br>The YesK-like protein family includes the B. subtilis YesK protein Swiss:O31514, which is functionally uncharacterised.  Its expression is regulated by the sporulation-specific sigma factor sigma-E  .  This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length.. 
PF14151 YfhD-like protein<br>The YfhD-like protein family includes the B. subtilis YfhD protein Swiss:O31572, which is functionally uncharacterised.  Its expression is regulated by the sporulation-specific sigma factor sigma-F  .  This family of proteins is found in bacteria. Proteins in this family are approximately 50 amino acids in length. There is a single completely conserved residue E that may be functionally important.. 
PF14152 YfhE-like protein<br>The YfhE-like protein family includes the B. subtilis YfhE protein Swiss:O31573, which is functionally uncharacterised.  Its expression may be regulated by the sigma factor sigma-B, which regulates the expression of stress-response proteins  .  This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length. There is a conserved QEV sequence motif.. 
PF14153 Spore coat protein CotO<br>Bacillus spores are protected by a protein shell consisting of over 50 different polypeptides, known as the coat.  This family of proteins has an important morphogenetic role in coat assembly, it is involved in the assembly of at least 5 different coat proteins including CotB, CotG, CotS, CotSA and CotW. It is likely to act at a late stage of coat assembly  .. 
PF14154 Domain of unknown function (DUF4306)<br>This family includes the B. subtilis YjdJ protein Swiss:O05524, which is functionally uncharacterised.  This is not a homologue of E. coli YjdJ, which belongs to Pfam:PF00583.  This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 95 and 152 amino acids in length.. 
PF14155 Domain of unknown function (DUF4307)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 132 and 153 amino acids in length. There is a single completely conserved residue C that may be functionally important.. 
PF14156 Antirepressor AbbA<br>This family inactivates the repressor AbrB, which represses genes switched on during the transition from the exponential to the stationary phase of growth.  It binds to AbrB and prevents it from binding to DNA  .. 
PF14157 YmzC-like protein<br>The YmzC-like protein family includes the B. subtilis YmzC protein Swiss:O31797, which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 91 amino acids in length. There is a conserved ELR sequence motif.. 
PF14158 YndJ-like protein<br>The YndJ-like protein family includes the B. subtilis YndJ protein Swiss:O31813, which is functionally uncharacterised. This family is found in bacteria and archaea, and is typically between 222 and 269 amino acids in length. There are two completely conserved G residues that may be functionally important.. 
PF14159 DUF4308;<br>CAAD domains of cyanobacterial aminoacyl-tRNA synthetase. This domain is present in aminoacyl-tRNA synthetases (aaRSs), enzymes that couple tRNAs to their cognate amino acids  . aaRSs from cyanobacteria containing the CAAD (for cyanobacterial aminoacyl-tRNA synthetases appended domain) protein domains are localised in the thylakoid membrane. The domain bears two putative transmembrane helices and is present in glutamyl-, isoleucyl-, leucyl-, and valyl-tRNA synthetases, the latter of which has probably recruited the domain more than once during evolution.. 
PF14160 Centrosome-associated C terminus<br>This is the C-terminus of a family of proteins that colocalise with the centrosome/microtubule organisation centre in interphase and at the spindle poles in mitosis.. 
PF14161 Centrosome-associated N terminus<br>This is the N-terminus of a family of proteins that colocalise with the centrosome/microtubule organisation centre in interphase and at the spindle poles in mitosis.. 
PF14162 YozD-like protein<br>The YozD-like protein family includes the B. subtilis YozD protein Swiss:O31863, which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length.. 
PF14163 Superinfection exclusion protein B<br>This family includes superinfection exclusion proteins. These proteins prevent the growth of superinfecting phage which are insensitive to repression. It aborts lytic development of superinfecting phage [1-3].. 
PF14164 YqzH-like protein<br>The YqzH-like protein family includes the B. subtilis YqzH protein Swiss:O32014, which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length.. 
PF14165 YtzH-like protein<br>The YtzH-like protein family includes the B. subtilis YtzH protein Swiss:O32066, which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There is a conserved DIL sequence motif.. 
PF14166 YueH-like protein<br>The YueH-like protein family includes the B. subtilis YueH protein Swiss:O32093, which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length.. 
PF14167 YfkD-like protein<br>The YfkD-like protein family includes the B. subtilis YfkD protein Swiss:O34579, which is functionally uncharacterised.  Its expression is regulated by the sigma factor sigma-B, which regulates the expression of stress-response proteins, and by the forespore-specific sigma factor sigma-G [1,2]. This family of proteins is found in bacteria. Proteins in this family are typically between 254 and 265 amino acids in length.. 
PF14168 YjzC-like protein<br>The YjzC-like protein family includes the B. subtilis YjzC protein Swiss:O34585, which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length.. 
PF14169 Cold-inducible protein YdjO<br>This family includes the B. subtilis YdjO protein Swiss:O34759, which is functionally uncharacterised. This is not a homologue of E. coli YdjO, Swiss:P76210.  B. subtilis YdjO is cold-inducible  . Its expression is induced by the extracytoplasmic function sigma factor sigma-W  .  This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length.. 
PF14171 Toxin SpoIISA, type II toxin-antitoxin system<br>SpoIISA is a toxin which causes lysis of vegetatively growing cells.  It forms part of a type II toxin-antitoxin system, where the SpoIISB protein, Pfam:PF14185, acts as an antitoxin. It is a transmembrane protein, with a cytoplasmic domain accounting for approximately two-thirds of the protein. The structure of the cytoplasmic domain resembles that of the GAF domains, Pfam: PF01590. SpoIISB binds to the cytoplasmic domain of SpoIISA with high affinity  .. 
PF14172 Domain of unknown function (DUF4309)<br>This family includes the B. subtilis YjgB protein Swiss:O34960, which is functionally uncharacterised. This is not a homologue of E. coli YjgB, Swiss: P27250. Expression of B. subtilis YjgB is regulated by the alternative transcription factor sigma-B  . This family is found in bacteria, and is approximately 140 amino acids in length.. 
PF14173 ComG operon protein 7<br>This family is required for DNA-binding during transformation of competent bacterial cells  .. 
PF14174 YycC-like protein<br>The YycC-like protein family includes the B. subtilis YycC protein Swiss:P37481, which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 50 amino acids in length. There is a conserved HIL sequence motif.. 
PF14175 YaaC-like Protein<br>The YaaC-like protein family includes the B. subtilis YaaC protein Swiss:P37526, which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 320 and 333 amino acids in length.. 
PF14176 YxiJ-like protein<br>The YxiJ-like protein family includes the B. subtilis YxiJ protein Swiss:P42320, which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length.. 
PF14177 YkyB-like protein<br>The YkyB-like protein family includes the B. subtilis YkyB protein Swiss:P42430, which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 150 amino acids in length. There are two conserved sequence motifs: NRHAKTA and HLG.. 
PF14178 YppF-like protein<br>The YppF-like protein family includes the B. subtilis YppF protein Swiss:P50834, which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. There is a conserved LLDF sequence motif.. 
PF14179 YppG-like protein<br>The YppG-like protein family includes the B. subtilis YppG protein Swiss:P50835, which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 115 and 181 amino acids in length. There are two completely conserved residues (F and G) that may be functionally important.. 
PF14181 YqfQ-like protein<br>The YqfQ-like protein family includes the B. subtilis YqfQ protein Swiss:P54474, also known as VrrA, which is functionally uncharacterised.  This family of proteins is found in bacteria. Proteins in this family are typically between 146 and 237 amino acids in length. There are two conserved sequence motifs: QYGP and PKLY.. 
PF14182 YgaB-like protein<br>The YgaB-like protein family includes the B. subtilis YgaB protein Swiss:P71080, which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length.. 
PF14183 YwpF-like protein<br>The YwpF-like protein family includes the B. subtilis YwpF protein Swiss:P94588, which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 146 and 167 amino acids in length. There is a conserved IIN sequence motif.. 
PF14184 Regulatory protein YrvL<br>YrvL prevents expression and activity of the YrvI sigma factor. It may function as an anti-sigma factor [1,2]. 
PF14185 Antitoxin SpoIISB, type II toxin-antitoxin system <br>Members of this family act as antitoxins. They bind to the SpoIISA toxin, Pfam:PF14171. They are disordered proteins which adopt structure only when bound to SpoIISA  .. 
PF14186 Cytoskeletal adhesion<br>This is the C-terminal domain of the axin-interacting protein family, and is a distinct version of the C2 domain. This domain is critical for interactions with cytoskeletal in the context of cellular adhesion points  .. 
PF14187 Domain of unknown function (DUF4310)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 214 and 231 amino acids in length.. 
PF14188 Domain of unknown function (DUF4311)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 260 amino acids in length.. 
PF14189 Domain of unknown function (DUF4312)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 99 and 118 amino acids in length.. 
PF14190 Domain of unknown function (DUF4313)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 136 and 171 amino acids in length.. 
PF14191 YodL-like<br>The YodL-like protein family includes the B. subtilis YodL protein Swiss:O30472, which is functionally uncharacterised. This domain family is found in bacteria, and is approximately 100 amino acids in length. There are two completely conserved residues (Y and D) that may be functionally important.. 
PF14192 Domain of unknown function (DUF4314)<br>This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is typically between 56 and 93 amino acids in length.. 
PF14193 Domain of unknown function (DUF4315)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length.. 
PF14194 Cysteine-rich VLP<br>This presumed domain is functionally uncharacterised. This domain family is found in bacteria and eukaryotes, and is approximately 60 amino acids in length. It contains 6 conserved cysteines and a conserved VLP sequence motif.. 
PF14195 Domain of unknown function (DUF4316)<br>This domain is functionally uncharacterised. This domain is found in bacteria, and is typically between 56 and 95 amino acids in length.. 
PF14196 L-2-amino-thiazoline-4-carboxylic acid hydrolase<br>This family of enzymes catalyses the conversion of L-2-amino-delta2-thiazoline-4-carboxylic acid (L-ATC) to N-carbamoyl-L-cysteine  . It cleaves the carbon-sulphur bond in the ring structure of L-ATC to produce N-carbamoyl-L-cysteine  .. 
PF14197 Centrosome localisation domain of PPC89 <br>The N-terminal region of the fission yeast spindle pole body protein PPC89 has low similarity to the human Cep57 protein. The CLD or centrosome localisation domain of Cep57 and PPC89 is found at the N-terminus. This region localises to the centrosome internally to gamma-tubulin, suggesting that it is either on both centrioles or on a centromatrix component. This N-terminal region can also multimerise with the N-terminus of other Cep57 molecules.  The C-terminal part, Family Cep57_MT_bd, Pfam:PF06657, is the microtubule-binding region of Cep57 and PPC89.. 
PF14198 Transposon-encoded protein TnpV<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 114 and 125 amino acids in length.. 
PF14199 Domain of unknown function (DUF4317)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 225 and 451 amino acids in length. There is a single completely conserved residue P that may be functionally important.. 
PF14200 Ricin-type beta-trefoil lectin domain-like<br>
PF14201 Domain of unknown function (DUF4318)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. There is a single completely conserved residue F that may be functionally important.. 
PF14202 Transposon-encoded protein TnpW<br>This family of proteins is found in bacteria. Proteins in this family are typically between 54 and 75 amino acids in length. There is a single completely conserved residue G that may be functionally important.. 
PF14203 Domain of unknown function (DUF4319)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. There are two completely conserved residues (E and K) that may be functionally important.. 
PF14204 Ribosomal L18 C-terminal region<br>This domain is the C-terminal end of ribosomal L18/L5 proteins.. 
PF14205 Cysteine-rich KTR<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 60 amino acids in length. There are 4 conserved cysteines and a conserved KTR sequence motif.. 
PF14206 Cysteine-rich CPCC<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea, eukaryotes and viruses.  Proteins in this family are typically between 68 and 104 amino acids in length. There are six conserved cysteines and a conserved CPCC sequence motif.. 
PF14207 DpnD/PcfM-like protein<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 57 and 153 amino acids in length. There are two completely conserved residues (E and A) that may be functionally important.. 
PF14208 Domain of unknown function (DUF4320)<br>This family of proteins is found in bacteria. Proteins in this family are typically between 120 and 131 amino acids in length. There are two completely conserved residues (G and Y) that may be functionally important.. 
PF14209 Domain of unknown function (DUF4321)<br>This family of proteins is functionally uncharacterised.  It is found in bacteria, and is approximately 50 amino acids in length.. 
PF14210 Domain of unknown function (DUF4322)<br>This presumed domain is functionally uncharacterised. This domain family is found in archaea, and is approximately 60 amino acids in length. There is a conserved QTV sequence motif.. 
PF14213 Domain of unknown function (DUF4325)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 99 and 341 amino acids in length.. 
PF14214 Helitron helicase-like domain at N-terminus<br>This family is found in Helitrons, recently recognised eukaryotic transposons that are predicted to amplify by a rolling-circle mechanism. In many instances a protein-coding gene is disrupted by their insertion.. 
PF14215 bHLH-MYC and R2R3-MYB transcription factors N-terminal<br>This is the N-terminal region of a family of MYB and MYC transcription factors. The DNA-binding HLH domain is further downstream, Pfam:PF00010. Members of the MYB and MYC family regulate the biosynthesis of phenylpropanoids in several plant species (DOI:10.1007/s11295-009-0232-y).. 
PF14216 Domain of unknown function (DUF4326)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 100 and 162 amino acids in length. There are two completely conserved residues (P and C) that may be functionally important.. 
PF14217 Domain of unknown function (DUF4327)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length.. 
PF14218 Circadian oscillating protein COP23<br>This family includes the circadian oscillating protein COP23 from Cyanothece sp. (strain PCC 8801), Swiss:Q54702. The levels of this peripheral membrane protein display a circadian oscillation  .. 
PF14219 Domain of unknown function (DUF4328)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 218 and 342 amino acids in length.. 
PF14220 Domain of unknown function (DUF4329)<br>This domain is functionally uncharacterised.  It is found in bacteria and eukaryotes, and is approximately 130 amino acids in length. It is often found in association with Pfam:PF05593 and Pfam:PF03527. There is a single completely conserved residue D and a highly conserved HTH motif which may be functionally important.. 
PF14221 Domain of unknown function (DUF4330)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 165 and 177 amino acids in length. There is a single completely conserved residue G that may be functionally important.. 
PF14222 Cell morphogenesis N-terminal<br>This family is the conserved N-terminal region of proteins that are involved in cell morphogenesis.. 
PF14223 gag-polypeptide of LTR copia-type<br>This family is found in Plants and fungi, and contains LTR-polyproteins, or retrotransposons of the copia-type.. 
PF14224 Domain of unknown function (DUF4331)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 223 and 526 amino acids in length. There is a conserved FPY sequence motif.. 
PF14225 Cell morphogenesis C-terminal<br>This family is the conserved C-terminal region of proteins that are involved in cell morphogenesis.. 
PF14226 non-haem dioxygenase in morphine synthesis N-terminal<br>This is the highly conserved N-terminal region of proteins with 2-oxoglutarate/Fe(II)-dependent dioxygenase activity.. 
PF14227 gag-polypeptide of LTR copia-type<br>This family is found in Plants and fungi, and contains LTR-polyproteins, or retrotransposons of the copia-type.. 
PF14228 Cell morphogenesis central region<br>This family is the conserved central region of proteins that are involved in cell morphogenesis.. 
PF14229 Domain of unknown function (DUF4332)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 134 and 356 amino acids in length. This domain contains helix-hairpin-helix motifs.. 
PF14230 Domain of unknown function (DUF4333)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 140 and 255 amino acids in length. There are two completely conserved C residues that may be functionally important.. 
PF14231 GXWXG protein<br>This domain is found in bacteria and eukaryotes, and is approximately 60 amino acids in length. There is a conserved GXWXG motif. This domain is frequently found at the N-terminus of Pfam:PF14232.. 
PF14232 Domain of unknown function (DUF4334)<br>This domain family is found in bacteria and eukaryotes, and is approximately 60 amino acids in length. This domain is frequently found at the C-terminus of Pfam:PF14231.. 
PF14233 Domain of unknown function (DUF4335)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 204 and 480 amino acids in length. There are two completely conserved residues (G and D) that may be functionally important.. 
PF14234 Domain of unknown function (DUF4336)<br>
PF14235 Domain of unknown function (DUF4337)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 187 and 201 amino acids in length. There is a single completely conserved residue Q that may be functionally important.. 
PF14236 Domain of unknown function (DUF4338)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 206 and 475 amino acids in length.. 
PF14237 Domain of unknown function (DUF4339)<br>This domain is found in bacteria, archaea and eukaryotes, and is approximately 50 amino acids in length. There are two completely conserved residues (G and W) that may be functionally important.. 
PF14238 Domain of unknown function (DUF4340)<br>This domain is found in bacteria, and is typically between 183 and 196 amino acids in length.. 
PF14239 RRXRR protein<br>This domain is found in bacteria, eukaryotes and viruses, and is approximately 180 amino acids in length. It contains a conserved RRXRR motif. It is often found in association with Pfam:PF01844.. 
PF14240 YHYH protein<br>This domain family is found in bacteria, eukaryotes and viruses, and is typically between 141 and 198 amino acids in length. There is a conserved YHYH sequence motif.. 
PF14241 Domain of unknown function (DUF4341)<br>This domain family is found in bacteria, archaea and eukaryotes, and is approximately 60 amino acids in length. The family is found in association with Pfam:PF04143. There are a number of conserved glycine residues that may be functionally important.. 
PF14242 Domain of unknown function (DUF4342)<br>This family of proteins is found in bacteria. Proteins in this family are typically between 97 and 206 amino acids in length. There is a single completely conserved residue P that may be functionally important.. 
PF14243 Domain of unknown function (DUF4343)<br>This domain family is found in bacteria, eukaryotes and viruses, and is typically between 127 and 142 amino acids in length.. 
PF14244 gag-polypeptide of LTR copia-type<br>This family is found in Plants and fungi, and contains LTR-polyproteins, or retrotransposons of the copia-type.. 
PF14245 Type IV pilin PilA<br>Jackhmmer:Q59589, Jackhmmer:B0C6E0. This family consists of proteins which form type IV pili. In M. xanthus these pili are required for social motility [1,2].. 
PF14246 AefR-like transcriptional repressor, C-terminal region<br>This family comprises the C-terminal domain of transcriptional regulators of the TetR family. It includes the AefR transcriptional regulator from P. syringae  . It is found in association with Pfam:PF00440.. 
PF14247 Domain of unknown function (DUF4344)<br>This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 247 and 291 amino acids in length. There is a conserved EED sequence motif.. 
PF14248 Domain of unknown function (DUF4345)<br>This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 125 and 141 amino acids in length. There is a single completely conserved residue E that may be functionally important.. 
PF14249 Tocopherol cyclase<br>This family contains tocopherol cyclases. These enzymes are involved in the synthesis of tocopherols and tocotrienols (vitamin E)  .. 
PF14250 AbrB-like transcriptional regulator<br>This family of DNA-binding proteins is likely to act as a transcriptional regulator  . This family does not include E.coli AbrB, Swiss:P75747, which belongs to Pfam:PF05145.. 
PF14251 Domain of unknown function (DUF4346)<br>This family of proteins is found in bacteria, archaea and eukaryotes.  Proteins in this family are typically between 127 and 502 amino acids in length. There are two conserved sequence motifs: LDP and DHA. Many members of this family have been annotated as dihydropteroate synthases, however no experimental evidence can be found for this and Swiss:Q57571 has been shown not to possess dihydropteroate synthase activity  .. 
PF14252 Domain of unknown function (DUF4347)<br>This domain family is found in bacteria and eukaryotes, and is approximately 160 amino acids in length. There are two completely conserved residues (C and G) that may be functionally important.. 
PF14253 Bacteriophage abortive infection AbiH<br>This family of proteins confers resistance to bacteriophage  .. 
PF14254 Domain of unknown function (DUF4348)<br>
PF14255 Cysteine-rich CPXCG<br>This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. There are 5 conserved cysteines which occur in a CPXCG motif and a DCXXCCXP motif.. 
PF14256 YwiC-like protein<br>The YwiC-like protein family includes the B. subtilis YwiC protein Swiss:P46909, which is functionally uncharacterised. This domain family is found in bacteria, and is approximately 130 amino acids in length. There is a single completely conserved residue G that may be functionally important.. 
PF14257 Domain of unknown function (DUF4349)<br>This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 282 and 353 amino acids in length.  There is a single completely conserved residue D that may be functionally important.. 
PF14258 Domain of unknown function (DUF4350)<br>This domain family is found in bacteria, archaea and eukaryotes, and is approximately 70 amino acids in length.. 
PF14259 RNA recognition motif (a.k.a. RRM, RBD, or RNP domain)<br>JCSG:Target_421663_WS20613B. 
PF14260 C4-type zinc-finger of DNA polymerase delta<br>In fission yeast this zinc-finger domain appears is the region of Pol3 that binds directly to the B-subunit, Cdc1  .  Pol delta is a hetero-tetrameric enzyme comprising four evolutionarily well-conserved proteins: the catalytic subunit Pol3 and three smaller subunits Cdc1, Cdc27 and Cdm1  .. 
PF14261 Domain of unknown function (DUF4351)<br>This domain is found in bacteria, and is approximately 60 amino acids in length.. 
PF14262 Domain of unknown function (DUF4353)<br>This family is found in bacteria and archaea, and is typically between 262 and 279 amino acids in length.. 
PF14263 Domain of unknown function (DUF4354)<br>JCSG:Target416839_SP17692A. Several members of this family are annotated as being ATP/GTP-binding site motif A (P-loop) proteins, but this could not be confirmed. The one PDB:3NRF structure solved for this family exhibits an immunoglobin-like beta-sandwich fold.  Crystal packing suggests that a tetramer is a significant oligomerisation state, and a disulfide bridge is formed between Cys 125 at the C-terminal end of the monomer, and Cys 69.. 
PF14264 Glucosyl transferase GtrII<br>This family includes glucosyl transferase II from the Shigella phage SfII, Swiss:O21944, which mediates seroconversion of S. flexneri when the phage is integrated into the host chromosome  .. 
PF14265 Domain of unknown function (DUF4355)<br>This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 180 and 214 amino acids in length.. 
PF14266 Domain of unknown function (DUF4356)<br>This family of proteins is found in bacteria. Proteins in this family are approximately 540 amino acids in length.. 
PF14267 Domain of unknown function (DUF4357)<br>This domain family is found in bacteria and archaea, and is approximately 60 amino acids in length. There are two completely conserved residues (G and W) that may be functionally important.. 
PF14268 YoaP-like<br>The YoaP-like domain is found at the C-terminus of the B. subtilis YoaP protein Swiss:O34983.  It is found in bacteria and archaea, and is approximately 40 amino acids in length. The family is found in association with Pfam:PF00583. There is a single completely conserved residue A that may be functionally important.. 
PF14269 Arylsulfotransferase (ASST)<br>JCSG:Target416597_Pfam-B_1234 (release 25.0). 
PF14270 Domain of unknown function (DUF4358)<br>This domain family is found in bacteria, and is approximately 110 amino acids in length.. 
PF14271 Domain of unknown function (DUF4359)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 130 amino acids in length. There are two completely conserved residues (P and S) that may be functionally important.. 
PF14272 Glycine-rich SFCGS<br>This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length. There are a number of highly conserved motifs including an SFCGSGGAGA motif.. 
PF14273 Domain of unknown function (DUF4360)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 200 and 228 amino acids in length. There is a conserved GCP sequence motif near the N-terminus.. 
PF14274 Domain of unknown function (DUF4361)<br>JCSG:Target_416718_SP15308B. 
PF14275 Domain of unknown function (DUF4362)<br>This family of proteins is found in bacteria. Proteins in this family are typically between 93 and 146 amino acids in length. There is a conserved IRIV sequence motif.. 
PF14276 Domain of unknown function (DUF4363)<br>This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length.. 
PF14277 Domain of unknown function (DUF4364)<br>This family of proteins is found in bacteria and archaea. Proteins in this family are approximately 180 amino acids in length.. 
PF14278 Transcriptional regulator C-terminal region<br>JCSG:Target403231_MJ9673J Pfam-B_17743 (release 25.0). This domain is a tetracycline repressor, domain 2, or C-terminus.. 
PF14279 HNH endonuclease<br>This domain is related to other HNH domain families such as Pfam:PF01844. Suggesting that these proteins have a nucleic acid cleaving function.. 
PF14280 Domain of unknown function (DUF4365)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, eukaryotes and viruses. Proteins in this family are typically between 182 and 530 amino acids in length. There is a single completely conserved residue D that may be functionally important.. 
PF14281 PD-(D/E)XK nuclease superfamily<br>Members of this family belong to the PD-(D/E)XK nuclease superfamily.. 
PF14282 FlxA-like protein<br>This family includes FlxA from E. coli, Swiss:P77609. The expression of FlxA is regulated by the FliA sigma factor, a transcription factor specific for class 3 flagellar operons. However FlxA is not required for flagellar function or formation  .. 
PF14283 Domain of unknown function (DUF4366)<br>This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 227 and 387 amino acids in length.. 
PF14284 PcfJ-like protein<br>The PcfJ-like protein family includes the E. faecalis PcfJ protein Swiss:Q5G3N2, which is functionally uncharacterised.  It is found in bacteria and viruses, and is typically between 159 and 170 amino acids in length. There is a conserved HCV sequence motif.. 
PF14285 Domain of unknown function (DUF4367)<br>This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 229 and 435 amino acids in length.. 
PF14286 DHHW protein<br>This family of proteins is found in bacteria. Proteins in this family are typically between 366 and 404 amino acids in length. There is a conserved DHHW motif.. 
PF14287 Domain of unknown function (DUF4368)<br>This domain family is found in bacteria, and is approximately 70 amino acids in length. The family is found in association with Pfam:PF00239 and Pfam:PF07508. There is a single completely conserved residue G that may be functionally important.. 
PF14288 1,3-beta-glucan synthase subunit FKS1, domain-1<br>The FKS1_dom1 domain is likely to be the 'Class I' region just N-terminal to the first set of transmembrane helices that is involved in 1,3-beta-glucan synthesis itself  . This family is found on proteins with family Glucan_synthase, Pfam:PF02364.. 
PF14289 Domain of unknown function (DUF4369)<br>This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with Pfam:PF00578.. 
PF14290 Domain of unknown function (DUF4370)<br>
PF14291 Domain of unknown function (DUF4371)<br>
PF14292 SusE outer membrane protein<br>This family includes the SusE outer membrane protein from Bacteroides thetaiotaomicron, Swiss:Q45769. This protein has a role in starch utilisation, but is not essential for growth on starch  .. 
PF14293 YWFCY protein<br>This family is found in bacteria, and is approximately 60 amino acids in length. There is a conserved YWFCY motif. It is often found in association with Pfam:PF02534.. 
PF14294 Domain of unknown function (DUF4372)<br>This domain family is found in bacteria, and is approximately 80 amino acids in length. The family is found in association with Pfam:PF01609.  There is a single completely conserved residue G that may be functionally important.. 
PF14295 PAN domain<br>
PF14296 O-antigen polysaccharide polymerase Wzy<br>This family includes O-antigen polysaccharide polymerases  . These enzymes link O-units via a glycosidic linkage to form a long O-antigen  . These enzymes vary in specificity and sequence  .. 
PF14297 Domain of unknown function (DUF4373)<br>This domain is found in bacteria, eukaryotes and viruses, and is approximately 90 amino acids in length.. 
PF14298 Domain of unknown function (DUF4374)<br>This family of proteins is found in bacteria. Proteins in this family are typically between 406 and 466 amino acids in length.. 
PF14299 Phloem protein 2<br>Phloem protein 2 (PP2) is one of the most abundant and enigmatic proteins in the phloem sap. PP2 is translocated in the assimilate stream where its lectin activity or RNA-binding properties can exert effects over long distances  .. 
PF14300 Domain of unknown function (DUF4375)<br>This family of proteins is found in bacteria. Proteins in this family are typically between 156 and 204 amino acids in length. There is a single completely conserved residue G that may be functionally important.. 
PF14301 Domain of unknown function (DUF4376)<br>This domain family is found in bacteria and viruses, and is approximately 110 amino acids in length.. 
PF14302 Domain of unknown function (DUF4377)<br>This domain family is found in bacteria and archaea, and is approximately 80 amino acids in length.. 
PF14303 No apical meristem-associated C-terminal domain<br>This domain is found in a number of different types of plant proteins including NAM-like proteins.. 
PF14304 Transcription termination and cleavage factor C-terminal<br>The C-terminal section of CSTF proteins is a discreet structure is crucial for mRNA 3'-end processing. This domain interacts with Pcf11 and possibly PC4, thus linking CstF2 to transcription, transcriptional termination, and cell growth.. 
PF14305 Glycos_tran_Wfd;<br>Eberhardt R, Iyer LM, Abhiman S, Burroughs AM, Aravind L. A member of the ATP-grasp fold predicted to be involved in the  biosynthesis of cell surface polysaccharides such as the O-antigen  in proteobacteria, the capsule in firmicutes and the polyglutamate chain of teichuronopeptide  . . 
PF14306 PUA-like domain<br>This PUA like domain is found at the N-terminus of ATP-sulfurylase enzymes.. 
PF14307 Glycosyltransferase WbsX<br>Members of this family are found in within O-antigen biosynthesis clusters in Gram negative bacteria, where they are predicted to function as glycosyltransferases [1,2].. 
PF14308 X-domain of DnaJ-containing<br>IN certain plant and yeast proteins, the DnaJ-1 proteins have a three-domain structure.  The x-domain lies between the N-terminal DnaJ and the C-terminal Z domains. The exact function is not known.. 
PF14309 Domain of unknown function (DUF4378)<br>
PF14310 Fibronectin type III-like domain<br>This domain has a fibronectin type III-like structure  . It is often found in association with Pfam:PF00933 and Pfam:PF01915. Its function is unknown.. 
PF14311 Domain of unknown function (DUF4379)<br>This domain is found in bacteria, eukaryotes and viruses, and is approximately 60 amino acids in length. It contains a CXXCXH motif and a CPXC motif.. 
PF14312 FG-GAP repeat<br>
PF14313 N-terminal region of Paramyxovirinae phosphoprotein (P)<br>The soyouz module moiety is the N-terminal region of the phosphoprotein (P) from the subfamily Paramyxovirinae of the family Paramyxoviridae viruses. The main genera in this subfamily include the Rubulaviruses, avulaviruses, respiroviruses, henipaviruses, and morbilliviruses, all of which are enveloped viruses with a non-segmented, negative, single-stranded RNA genome encapsidated by the nucleoprotein (N) within a helical nucleocapsid.. 
PF14314 Virus-capping methyltransferase<br>This is the methyltransferase region of the Mononegavirales single-stranded RNA viral RNA polymerase enzymes. This region is involved in the mRNA-capping of the virion particles.. 
PF14315 Domain of unknown function (DUF4380)<br>This family of proteins is found in bacteria, archaea and eukaryotes.  Proteins in this family are typically between 288 and 372 amino acids in length. There are two completely conserved residues (G and E) that may be functionally important.. 
PF14316 Domain of unknown function (DUF4381)<br>This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 158 and 180 amino acids in length.. 
PF14317 YcxB-like protein<br>The YcxB-like protein family includes the B. subtilis YcxB protein Swiss:Q08793, which is a functionally uncharacterised transmembrane protein.  This family of proteins is found in bacteria, and is approximately 60 amino acids in length.. 
PF14318 Mononegavirales mRNA-capping region V<br>This V domain of L RNA-polymerase carries a new motif, GxxTx(n)HR, that is essential for mRNA cap formation. Nonsegmented negative-sense (NNS) RNA viruses, Mononegavirales, cap their mRNA by an unconventional mechanism. Specifically, 5'-monophosphate mRNA is transferred to GDP derived from GTP through a reaction that involves a covalent intermediate between the large polymerase protein L and mRNA. The V region is essential for this process  .. 
PF14319 Transposase zinc-binding domain<br>This domain is likely to be a zinc-binding domain. It is found at the N-terminus of transposases belonging to the IS91 family.. 
PF14320 Phosphoprotein P region PCT disordered<br>The N-terminal half of the phosphoprotein P of the Paramyxovirinae viruses.  The very first 60 residues have been built as the family Soyouz-module, Pfam:PF14313. The remaining part of the region, here, is disordered, and is liable to induced folding under the right physiological conditions. The region undergoes an unstructured-to-structured transition upon binding to Measles virus tail, C, unstructured region.. 
PF14321 Domain of unknown function (DUF4382)<br>This family is found in bacteria and archaea, and is typically between 142 and 161 amino acids in length.. 
PF14322 Starch-binding associating with outer membrane<br>JCSG:Target390309 Jackhmmer:Q8A1B4. SusD is a secreted starch-binding protein with an N-terminal lipid tail that allows it to associate with the outer membrane.. 
PF14323 GxGYxY sequence motif in domain of unknown function<br>This family carries a characteristic sequence motif, GxGYxYP, but is of unknown function. Associated families are sugar-processing domains.. 
PF14324 PINIT domain<br>The PINIT domain is a protein domain that is found in PIAS proteins  . The PINIT domain is about 180 amino acids in length.. 
PF14325 Domain of unknown function (DUF4383)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 137 and 164 amino acids in length.. 
PF14326 Domain of unknown function (DUF4384)<br>This presumed domain is functionally uncharacterised. This domain family is found in bacteria and archaea, and is approximately 80 amino acids in length.. 
PF14327 Hinge domain of cleavage stimulation factor subunit 2<br>The hinge domain of cleavage stimulation factor subunit 2 proteins, CSTF2, is necessary for binding to the subunit CstF-77 within the polyadenylation complex and subsequent nuclear localisation. This suggests that nuclear import of a pre-formed CSTF complex is an essential step in polyadenylation. Accurate and efficient polyadenylation is essential for transcriptional termination, nuclear export, translation, and stability of eukaryotic mRNAs. CSTF2 is an important regulatory subunit of the polyadenylation complex.. 
PF14328 Domain of unknown function (DUF4385)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 149 and 163 amino acids in length.. 
PF14329 Domain of unknown function (DUF4386)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 214 and 245 amino acids in length.. 
PF14330 Domain of unknown function (DUF4387)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are approximately 110 amino acids in length. There is a conserved RSKN sequence motif.. 
PF14331 ImcF-related N-terminal domain<br>This domain is found in bacterial ImcF (intracellular multiplication and human macrophage-killing) proteins. It is found to the N-terminus of the ImcF-related domain, Pfam:PF06761.. 
PF14332 Domain of unknown function (DUF4388)<br>This domain family is found in bacteria, and is typically between 102 and 135 amino acids in length.. 
PF14333 Domain of unknown function (DUF4389)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 104 and 223 amino acids in length. There is a single completely conserved residue R that may be functionally important.. 
PF14334 Domain of unknown function (DUF4390)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 192 and 203 amino acids in length.. 
PF14335 Domain of unknown function (DUF4391)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 220 and 257 amino acids in length.. 
PF14336 Domain of unknown function (DUF4392)<br>This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 282 and 585 amino acids in length. There are two completely conserved G residues that may be functionally important.. 
PF14337 Domain of unknown function (DUF4393)<br>This family of proteins is found in bacteria, archaea and viruses.  Proteins in this family are typically between 254 and 285 amino acids in length.. 
PF14338 Mrr N-terminal domain<br>This domain is found at the N-terminus of the Mrr restriction endonuclease catalytic domain, Pfam:PF04471 [1,2]. Fold recognition analysis predicts that it is a diverged member of the winged helix variant of helix turn helix proteins. It may play a role in DNA sequence recognition  .. 
PF14339 Domain of unknown function (DUF4394)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 262 and 476 amino acids in length.. 
PF14340 Domain of unknown function (DUF4395)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 142 and 168 amino acids in length. There are two completely conserved C residues that may be functionally important.. 
PF14341 PilX N-terminal<br>This domain is found at the N-terminus of the PilX prepilin-like proteins which are involved in type 4 fimbrial biogenesis  .. 
PF14342 Domain of unknown function (DUF4396)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 167 and 310 amino acids in length.. 
PF14343 PrcB C-terminal<br>This domain is found at the C-terminus of Treponema denticola PrcB, Swiss:B8YNY4. PrcB interacts with the PrtP protease (dentilisin) and is required for the stability of the protease complex  .. 
PF14344 Domain of unknown function (DUF4397)<br>This presumed domain is functionally uncharacterised. This domain family is found in bacteria, archaea and eukaryotes, and is approximately 120 amino acids in length.. 
PF14345 GDYXXLXY protein<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 171 and 199 amino acids in length.  It contains a conserved GDYXXLXY motif.. 
PF14346 Domain of unknown function (DUF4398)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 127 and 269 amino acids in length.. 
PF14347 Domain of unknown function (DUF4399)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 135 and 1079 amino acids in length.. 
PF14348 Domain of unknown function (DUF4400)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 209 and 249 amino acids in length. There is a single completely conserved residue P that may be functionally important.. 
PF14349 Motility related/secretion protein<br>This domain is found repeated three times in the N-terminal half of the gliding motility-related SprA proteins. The role of this domain in motility is uncertain  . It is also found in proteins required for secretion  .. 
PF14350 Beta protein<br>This family includes the beta protein from Bacteriophage T4, Swiss:P13057. Beta protein prevents the gop protein, Swiss:P13058, from killing the bacterial host cell  .. 
PF14351 Domain of unknown function (DUF4401)<br>This family of proteins is found in bacteria. Proteins in this family are typically between 357 and 735 amino acids in length. The family is found in association with Pfam:PF09925.  There is a single completely conserved residue K that may be functionally important.. 
PF14352 Domain of unknown function (DUF4402)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 155 and 182 amino acids in length.. 
PF14353 CpXC protein<br>This presumed domain is functionally uncharacterised. This domain is found in bacteria and archaea, and is typically between 122 and 134 amino acids in length. It contains four conserved cysteines forming two CpXC motifs.. 
PF14354 Restriction alleviation protein Lar<br>This family includes the restriction alleviation protein Lar encoded by the Rac prophage of Escherichia coli, Swiss:P33229. This protein modulates the activity of the Escherichia coli restriction and modification system  .. 
PF14355 Abortive infection C-terminus<br>This domain is found at the C-terminus of the Lactococcus lactis abortive infection protein Abi-859, Swiss:Q48620. This protein confers bacteriophage resistance  .. 
PF14356 Domain of unknown function (DUF4403)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 455 and 518 amino acids in length. There is a single completely conserved residue W that may be functionally important.. 
PF14357 Domain of unknown function (DUF4404)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There are two completely conserved residues (P and G) that may be functionally important.. 
PF14358 Domain of unknown function (DUF4405)<br>This presumed domain is functionally uncharacterised. This domain family is found in bacteria and archaea, and is approximately 50 amino acids in length. There are two conserved histidines that may be functionally important. This family is N-terminally truncated compared to other members of the clan.. 
PF14359 Domain of unknown function (DUF4406)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 98 and 145 amino acids in length.. 
PF14360 PAP2 superfamily C-terminal<br>This family is closely related to the C-terminal a region of PAP2.. 
PF14361 RsbT co-antagonist protein rsbRD N-terminal domain<br>This domain is found at the N-terminus of a number of anti-sigma-factor antagonist proteins including B. subtilis RsbRD, Swiss:P54504. These proteins are negative regulators of the general stress transcription factor sigma(B)  . It is found in association with Pfam:PF01740.. 
PF14362 Domain of unknown function (DUF4407)<br>This family of proteins is found in bacteria. Proteins in this family are typically between 366 and 597 amino acids in length. There is a single completely conserved residue R that may be functionally important.. 
PF14363 Domain associated at C-terminal with AAA<br>This domain is found in association with the AAA family, Pfam:PF00004.. 
PF14364 Domain of unknown function (DUF4408)<br>This domain is found at the N-terminus of member of the DUF761 family Pfam:PF05553. Many members are plant proteins.. 
PF14365 Domain of unknown function (DUF4409)<br>
PF14366 Domain of unknown function (DUF4410)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 187 and 238 amino acids in length.. 
PF14367 Domain of unknown function (DUF4411)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 153 and 170 amino acids in length. There is a single completely conserved residue D that may be functionally important.. 
PF14368 Probable lipid transfer<br>The members of this family are probably involved in lipid transfer. The family has several highly conserved cysteines, paired in various ways.. 
PF14369 zinc-finger<br>
PF14370 C-terminal topoisomerase domain<br>This domain is found at the C-terminal of topoisomerase and other similar enzymes.. 
PF14371 Domain of unknown function (DUF4412)<br>This presumed domain is functionally uncharacterised. This domain family is found in bacteria, archaea and eukaryotes, and is typically between 75 and 104 amino acids in length.. 
PF14372 Domain of unknown function (DUF4413)<br>This domain is part of an RNase-H fold section of longer proteins some of which are transposable elements possibly of the Pong type, since some members are putative Tam3 transposases.. 
PF14373 Superinfection immunity protein<br>This family includes the E. coli bacteriophage T4 superinfection immunity (imm) protein, Swiss:P08986. When E. coli is sequentially infected with two T-even type bacteriophage the DNA of the superinfecting phage is excluded from the host, into the periplasmic space. The immunity protein plays a role in this process  .. 
PF14374 60S ribosomal protein L4 C-terminal domain<br>This family is found at the very C-terminal of 60 ribosomal L4 proteins.. 
PF14375 Cysteine-rich CWC<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 74 and 102 amino acids in length. It contains eight conserved cysteines, including a conserved CWC sequence motif.. 
PF14376 Haem-binding domain<br>This domain contains a potential haem-binding motif, CXXCH  . This family is found in association with Pfam:PF00034 and Pfam:PF03150.. 
PF14377 Domain of unknown function (DUF4414)<br>This family is frequently found on DNA binding proteins of the URE-B1 type and on ligases.. 
PF14378 PAP2 superfamily<br>
PF14379 MYB-CC type transfactor, LHEQLE motif<br>This family is found towards the C-terminus of Myb-CC type transcription factors, and carries a highly conserved LHEQLE sequence motif.. 
PF14380 Wall-associated receptor kinase C-terminal<br>This WAK_assoc domain is cysteine-rich and lies C-terminal to the binding domain, GUB_WAK_bind, Pfam:PF13947.. 
PF14381 Ethylene-responsive protein kinase Le-CTR1<br>EDR1 regulates disease resistance and ethylene-induced senescence, and is also involved in stress response signalling and cell death regulation  .. 
PF14382 ECR11_N;<br>Exosome complex exonuclease RRP4 N-terminal region. ECR1_N is an N-terminal region of the exosome complex exonuclease RRP proteins. It is a G-rich domain which structurally is a rudimentary single hybrid fold with a permuted topology.. 
PF14383 DUF761-associated sequence motif <br>This family is found frequently at the N-terminus of family DUF3741, Pfam:PF12552.. 
PF14384 Domain of unknown function (DUF4415)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 82 and 104 amino acids in length.. 
PF14385 Domain of unknown function (DUF4416)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 176 and 187 amino acids in length. There is a conserved DPG sequence motif.. 
PF14386 Domain of unknown function (DUF4417)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 220 and 340 amino acids in length. There is a single completely conserved residue G that may be functionally important.. 
PF14387 Domain of unknown function (DUF4418)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 132 and 150 amino acids in length.. 
PF14388 Domain of unknown function (DUF4419)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, eukaryotes and viruses. Proteins in this family are typically between 348 and 454 amino acids in length.. 
PF14389 Leucine-zipper of ternary complex factor MIP1<br>This leucine-zipper is towards the N-terminus of MIP1 proteins. These proteins, here largely from plants, are subunits of the TORC2 (rictor-mTOR) protein complex controlling cell growth and proliferation  . The leucine-zipper is likely to be the region that interacts with plant MADS-box factors  ,. 
PF14390 Domain of unknown function (DUF4420)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 310 and 334 amino acids in length.. 
PF14391 Domain of unknown function (DUF4421)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 336 and 370 amino acids in length.. 
PF14392 Zinc knuckle<br>The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. This particular family is found in plant proteins.. 
PF14393 Domain of unknown function (DUF4422)<br>This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 255 and 371 amino acids in length.. 
PF14394 Domain of unknown function (DUF4423)<br>This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 170 amino acids in length.. 
PF14395 Phage phiEco32-like COOH.NH2 ligase-type 2<br>Iyer LM, Abhiman S, Burroughs AM, Aravind L. A family of COOH-NH2 ligases/GCS superfamily found in the neighborhood of YheC/D-like ATP-grasp and the CotE family of proteins in the firmicutes. Contextual analysis suggests that it might be involved in cell wall modification and spore coat biosynthesis  .. 
PF14396 Cystic fibrosis TM conductance regulator (CFTR), regulator domain<br>
PF14397 Sugar-transfer associated ATP-grasp<br>Iyer LM, Abhiman S, Burroughs AM, Aravind L. A member of the ATP-grasp fold predicted to be involved in the  biosynthesis of cell surface polysaccharides  .. 
PF14398 YheC/D like ATP-grasp<br>Iyer LM, Abhiman S, Burroughs AM, Aravind L. A member of the ATP-grasp fold predicted to be involved in the  modification/biosynthesis of spore-wall and capsular proteins  .. 
PF14399 BtrH;<br>NlpC/p60-like transpeptidase. Iyer LM, Abhiman S, Burroughs AM, Aravind L, Eberhardt R. Members of this family are often found in the gene neighbourhood, or fused to, non-ribosomal peptide synthetases. They are predicted to function as transpeptidases in peptide metabolite biosynthesis  .. 
PF14400 Inactive transglutaminase fused to 7 transmembrane helices<br>Iyer LM, Abhiman S, Burroughs AM, Aravind L. A family of inactive transglutaminases fused to seven transmembrane  helices. The transglutaminase domain is predicted to be extracellularly  located. Members of this family are associated in gene neighborhoods with a pepsin-like peptidase and an ATP-grasp of the RimK-family. The  ATP-grasp is predicted to modify the 7TM protein or a cofactor that  interacts with it  .. 
PF14401 RimK-like ATPgrasp N-terminal domain<br>Iyer LM, Abhiman S, Burroughs AM, Aravind L. An uncharacterized alpha+beta fold domain that is mostly fused to a RimK-like ATP-grasp and is found in bacteria and euryarchaea. Members of this family are almost always associated in gene  neighborhoods with a GNAT-like acetyltransferase fused to a  papain-like petidase. Additionally M20-like peptidases, GCS2,  4Fe-4S Ferredoxins, a distinct metal-sulfur cluster protein and ribosomal proteins are found in the gene neighborhoods. Contextual analysis suggests a role for these in peptide biosynthesis  .. 
PF14402 7 transmembrane helices usually fused to an inactive transglutaminase<br>Iyer LM, Abhiman S, Burroughs AM, Aravind L. A family of seven transmembrane helices fused to an inactive  transglutaminase domain. The transglutaminase domain is predicted to be extracellularly located. Members of this family are associated in gene neighborhoods with a pepsin-like peptidase and an ATP-grasp of the RimK-family. The ATP-grasp is predicted to modify the 7TM protein or a cofactor that interacts with it  .. 
PF14403 Circularly permuted ATP-grasp type 2 <br>Iyer LM, Abhiman S, Burroughs AM, Aravind L. Circularly permuted ATP-grasp prototyped by Roseiflexus RoseRS_2616  that is associated in gene neighborhoods with a GCS2-like COOH-NH2  ligase, alpha/beta hydrolase fold peptidase, GAT-II -like  amidohydrolase, and M20 peptidase. Members of this family are  predicted to be involved in the biosynthesis of small peptides  .. 
PF14404 Ribosomally synthesized peptide in Streptomyces species<br>Iyer LM, Abhiman S, Burroughs AM, Aravind L. A ribosomally synthesized peptide related to microviridin and  marinostatin, usually in the gene neighborhood of one or more  RimK-like ATP-grasp. The gene-context suggests that it is further modified by the ATP-grasp. The peptide is predicted to  function in a defensive or developmental role, or as an antibiotic  .. 
PF14406 Ribosomally synthesized peptide in Bacteroidetes<br>Iyer LM, Abhiman S, Burroughs AM, Aravind L. Ribosomally synthesized peptide that is usually in the gene  neighborhood of a RimK-like ATP-grasp, and an ABC ATPase fused to\. a papain-like domain. It is often present in multiple tandem  gene copies. The gene contexts suggest that it is modified by the  ATP-grasp as in the biosynthesis of microviridin and marinostatin.  They might function in defense or development or as peptide antibiotics  .. 
PF14407 Ribosomally synthesized peptide prototyped by Frankia Franean1_4349.<br>Iyer LM, Abhiman S, Burroughs AM, Aravind L. Ribosomally synthesized peptide linked to cyclases in chloroflexi.  It may have a link to cyclic nucleotide signaling  .. 
PF14408 Ribosomally synthesized peptide in actinomycetes<br>Iyer LM, Abhiman S, Burroughs AM, Aravind L. Ribosomally synthesized peptide that is usually in the gene  neighborhood of a RimK-like ATP-grasp and an aspartyl-O-methylase. Gene contexts suggest that it is further modified by the ATP-grasp  and the methylase. It might function in defense or development, or  as a peptide antibiotic  .. 
PF14409 Ribosomally synthesized peptide in Herpetosiphon<br>Iyer LM, Abhiman S, Burroughs AM, Aravind L. Ribosomally synthesized peptide that is usually in the gene  neighborhood of a RimK-like ATP-grasp, and an ABC ATPase fused to a papain-like domain. It is often present in multiple tandem gene  copies. Gene contexts suggest that it is modified by the ATP=grasp. It might function in defense or development, or as a peptide antibiotic  .. 
PF14410 HNH/ENDO VII superfamily nuclease with conserved GHE residues<br>Zhang D, Iyer LM, Aravind L. A predicted nuclease of the HNH/EndoVII superfamily of the treble  clef fold which is closely related to the NucA-like family. The  name is derived from the conserved G, H and E residues. It is found in several bacterial polymorphic toxin systems  . Some GH-E members preserve the conserved cysteines of the treble-clef  suggesting that they might represent potential evolutionary  intermediates from a classical HNH domain to the derived NucA-like  form  .. 
PF14411 A nuclease of the HNH/ENDO VII superfamily with conserved LHH<br>Zhang D, Iyer LM, Aravind L. LHH is a predicted nuclease of the HNH/ENDO VII superfamily of the  treble clef fold. The name is derived from the conserved motif, LHH. It is found in bacterial polymorphic toxin systems   and functions as a toxin module. Like WHH and AHH, LHH nuclease contain 4 conserved  histidines of which, the first one is predicted to bind metal-ion  and other three ones are involved in activation of water molecule for hydrolysis.. 
PF14412 A nuclease family of the HNH/ENDO VII superfamily with conserved AHH<br>Zhang D, Iyer LM, Aravind L. AHH is a predicted nuclease of the HNH/ENDO VII superfamily of the  treble clef fold. The name is derived from the conserved motif, AHH. It is found in bacterial polymorphic toxin systems   and functions as a toxin module. Like WHH and LHH, the AHH nuclease contains 4  conserved histidines of which, the first one is predicted to bind  a metal-ion and the other three ones are involved in activation of a water molecule for hydrolysis.. 
PF14413 Thg1 C terminal domain<br>Thg1 polymerases contain an additional region of conservation  C-terminal to the core palm domain that comprise of 5 helices and two strands  . This region has several well-conserved charged residues  including a basic residue found towards the end of the first helix  of this unit might contribute to the Thg1-specific active site  . This C-terminal module of Thg1 is predicted to form a helical bundle  that functions equivalently to the fingers of the other nucleic acid  polymerases, probably in interacting with the template HtRNA  .. 
PF14414 A nuclease of the HNH/ENDO VII superfamily with conserved WHH<br>Zhang D, Iyer LM, Aravind L;. WHH is a predicted nuclease of the HNH/ENDO VII superfamily of the  treble clef fold. The name is derived from the conserved motif WHH. It is found in bacterial polymorphic toxin systems   and functions as a toxin module. WHH is the shortest version of HNH nuclease families. Like AHH and LHH, the WHH nuclease contains 4 conserved histidines of which the first one is predicted to bind a metal-ion  and other three ones are involved in activation of water molecule for hydrolysis  .. 
PF14415 Domain of unknown function (DUF4424)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 310 and 361 amino acids in length.. 
PF14416 PMR5 N terminal Domain<br>The plant family with PMR5, ESK1, TBL3 etc have a N-terminal   C rich predicted sugar binding domain followed by the PC-Esterase (acyl esterase) domain  .. 
PF14417 MEDS: MEthanogen/methylotroph, DcmR Sensory domain<br>MEDS is prototyped by DcmR and is likely to function with the PocR domain in certain organisms in sensing hydrocarbon derivatives    The MEDS domain occurs fused to Histidine Kinase and as standalone version  . Sequence analysis shows that it is a catalytically  inactive version of the P-loop NTPase domain of the RecA superfamily  .. 
PF14418 OST-HTH Associated domain<br>OHA occurs with OST-HTH  . . 
PF14419 SPOUT_MTase_11;<br>AF2226-like SPOUT RNA Methylase fused to THUMP. SPOUT superfamily RNA methylase fused to RNA binding THUMP domain  .. 
PF14420 Clr5 domain<br>This domain is found at the N-terminus of the Clr5 protein which has been shown to be involved in silencing in fission yeast. This domain has been found to often be associated with proteins that contain ankyrin repeats and large regions of disordered sequence  .. 
PF14421 CDD_CDA_1;<br>A distinct subfamily of CDD/CDA-like deaminases. Iyer LM, Zhang D, Aravind L. A distinct branch of the CDD/CDA-like deaminases prototyped by  Leishmania LmjF36.5940. Members of this family are widely distributed across several microbial eukaryotes such as kinetoplastids,  chlorophyte algae, stramenopiles and the alveolate Perkinsus. Domain  architectures suggest that these proteins might possess mRNA editing  or DNA mutagenizing activity  .. 
PF14423 Immunity protein Imm5<br>Iyer LM, Zhang D, Aravind L.. A predicted Immunity protein, with an all-alpha fold, present in bacterial polymorphic toxin systems as an immediate neighbor of  the toxin   .. 
PF14424 DEAM-TOXIN1;<br>The  BURPS668_1122 family of deaminases. Iyer LM, Zhang D, Aravind L. A member of the nucleic acid/nucleotide deaminase superfamily  prototyped by Burkholderia BURPS668_1122  . Members of this family are found as toxins in polymorphic toxin systems in a wide range of bacteria and in the eukaryote Perkinsus. Members of this family typically possess a DxE catalytic motif in Helix-2 of the core fold instead of the more common C[H]xE motif.  The Perkinsus versions are predicted to be inactive  .. 
PF14425 Immunity protein Imm3<br>Iyer LM, Zhang D, Aravind L. A predicted Immunity protein, with a mostly all-alpha fold, present  in bacterial polymorphic toxin systems as an immediate gene neighbor  of the toxin gene   .. 
PF14426 Immunity protein Imm2<br>Iyer LM, Zhang D, Aravind L. A predicted Immunity protein, with a mostly all-alpha fold, present  in bacterial polymorphic toxin systems as an immediate gene neighbor  of the toxin gene  .. 
PF14427 Pput2613-DEAM;<br>Pput_2613-like deaminase. Iyer LM, Zhang D, Aravind L. A member of the nucleic acid/nucleotide deaminase superfamily  prototyped by Pseudomonas Pput_2613  . Members of this family are predicted to function as toxins in bacterial polymorphic toxin  systems   .. 
PF14428 SCP1201-DEAM;<br>SCP1.201-like deaminase. Iyer LM, Zhang D, Aravind, L. A member of the nucleic acid/nucleotide deaminase superfamily  prototyped by Streptomyces SCP1.201  . Members of this family are predicted to function as toxins in bacterial polymorphic toxin  systems  .. 
PF14429 C2 domain in Dock180 and Zizimin proteins<br>The Dock180/Dock1 and Zizimin proteins are atypical GTP/GDP exchange factors for the small GTPases Rac and Cdc42 and are implicated  cell-migration and phagocytosis. Across all Dock180 proteins, two regions are conserved: C-terminus termed CZH2 or DHR2 (or the  Dedicator of cytokinesis) whereas CZH1/DHR1 contain a new family of the C2 domain   .. 
PF14430 Immunity protein Imm1<br>Iyer LM, Zhang D, Aravind L. A predicted immunity protein, with an alpha+beta fold and a conserved C-terminal tryptophan residue. The protein is present in a wide range of bacteria in polymorphic toxin systems as an immediate gene  neighbor of the toxin gene  .. 
PF14431 YwqJ-like deaminase<br>Iyer LM, Zhang D, Aravind L. A member of the nucleic acid/nucleotide deaminase superfamily  prototyped by Bacillus YwqJ  . Members of this family are present in a wide phyletic range of bacteria and a few basidiomycetes. Bacterial versions are predicted to function as toxins in bacterial  polymorphic toxin systems  .. 
PF14432 DYW_Deaminase;<br>DYW family of nucleic acid deaminases. Iyer LM, Zhang D, Aravind, L. A family of nucleic acid  deaminases prototyped by the plant PPR DYW proteins that are implicated in chloroplast and mitochondrial RNA transcript maturation by numerous C to U editing events  . The  name derives from the DYW motif present at the C-terminus of the  classical plant PPR DYW deaminases. Members of this family are  present in bacteria, plants, Naegleria, and fungi  . Plants and  Naegleria show lineage-specific expansions of this family. The  classical DYW family contain an additional C-terminal metal-binding  cluster composed of 2 histidines and a CxC motif and are often fused to PPR repeats. Ascomycete versions, which are independent lateral  transfers, contain a large insert within the domain and are often fused to ankyrin repeats. Bacterial versions are predicted to  function as toxins in polymorphic toxin systems  .. 
PF14433 SUKH-3 immunity protein<br>Zhang D, Iyer LM, Aravind L. This family belongs to the SUKH superfamily and functions as immunity proteins in bacterial toxin systems  .. 
PF14434 Immunity protein Imm6<br>Iyer LM, Zhang D, Aravind L. A predicted immunity protein, with an alpha+beta fold (mostly alpha  helices). The protein is present in polymorphic toxin systems as an  immediate gene neighbor of the toxin gene  .. 
PF14435 SUKH-4 immunity protein<br>Zhang D, Iyer LM, Aravind L. This family belongs to the SUKH superfamily and functions as immunity proteins in bacterial toxin systems  .. 
PF14436 Bacterial EndoU nuclease<br>Zhang D, Iyer LM, Aravind L. This is a bacterial verion of EndoU nuclease. It is found at C-terminal region of polymorphic toxin proteins. . 
PF14437 MafB19-like deaminase<br>Iyer LM, Zhang D, Aravind L. A member of the nucleic acid/nucleotide deaminase superfamily  prototyped by Neisseria MafB19  . Members of this family are present in a wide phyletic range of bacteria and are predicted to function as toxins in bacterial polymorphic toxin systems  .. 
PF14438 Ataxin 2 SM domain<br>Anantharaman V, Eberhardt R. This SM domain is found in Ataxin-2  .. 
PF14439 Bd3614-like deaminase<br>Iyer LM, Zhang D, Aravind L. A member of the nucleic acid/nucleotide deaminase superfamily  prototyped by Bdellovibrio Bd3614  . They are typified by a  distinct N-terminal globular domain. The Bdellovibrio version occurs in a predicted operon with a 23S rRNA G2445-modifying  methylase suggesting that it might be involved in RNA editing  .. 
PF14440 Xanthomonas XOO_2897-like deaminase<br>Iyer LM, Zhang D, Aravind L. A member of the nucleic acid/nucleotide deaminase superfamily  prototyped by Xanthomonas XOO_2897  . Members of this family are present in a wide phyletic range of bacteria and are predicted to function as toxins in bacterial polymorphic toxin systems  . The Xanthomonas XOO_2897 lack an immunity protein and is predicted  to be deployed against its eukaryotic host  .. 
PF14441 OTT_1508-like deaminase<br>Iyer LM, Zhang D, Aravind L, Eberhardt R. A member of the nucleic acid/nucleotide deaminase superfamily  prototyped by Orientia OTT_1508  . Members of this family are present in a wide phyletic range of bacteria,including several intracellular parasites and eukaryotes such as fungi, Leishmania,  Selaginella, and some apicomplexa. In bacteria, these deaminases are predicted to function as toxins in bacterial polymorphic toxin  systems  . Versions in intracellular bacteria lack immunity proteins and are likely to be deployed against their eukaryotic hosts. Eukaryotic versions are predicted to function as nucleic acid (either DNA or RNA) deaminases. Among eukaryotes, some fungi show  lineage-specific expansions of this family. Many fungal versions are  fused to a distinct N-terminal globular domain. Various fungal  versions are fused to domains involved in chromatin function.  Apicomplexan versions are fused to tRNA guanine transglycosylase  domain  . . 
PF14442 Bd3614-N;<br>Bd3614-like deaminase N-terminal. Iyer LM, Zhang D, Aravind L. This is a globular domain that occurs N-terminal to the Bd3614-like deaminases, which are predicted to be involved in RNA editing  .. 
PF14443 DBC1<br>DBC1 and it homologs from diverse eukaryotes are a catalytically  inactive version of the Nudix hydrolase (MutT) domain  . DBC1 is predicted to bind NAD metabolites and regulate the activity of SIRT1 or related deacetylases by sensing the soluble products or substrates of the NAD-dependent deacetylation reaction  .. 
PF14444 S1-like<br>S1-like RNA binding domain found in DBC1  . 
PF14445 Prokaryotic RING finger family 2<br>Burroughs AM, Iyer LM, Aravind L. RING finger family found sporadically in bacteria and archaea, and  associated with other components of the ubiquitin-based signaling  and degradation system, including ubiquitin and the E1 and E2  proteins. The bacterial versions contain transmembrane helices  .. 
PF14446 Prokaryotic RING finger family 1<br>Burroughs AM, Iyer LM, Aravind L. RING finger family found sporadically in bacteria and archaea, and  associated in gene neighborhoods with other components of the  ubiquitin-based signaling and degradation system, including  ubiquitin, the E1 and E2 proteins and the JAB-like metallopeptidase.  The bacterial versions contain transmembrane helices  .. 
PF14447 Prokaryotic RING finger family 4<br>Burroughs AM, Iyer LM, Aravind L. RING finger family domain found sporadically in bacteria. The finger is fused to an N-terminal alpha-helical domain, ROT/Trove-like repeats and a C-terminal TerD domain  . The architecture suggests a possible role in an RNA-processing complex  .. 
PF14448 NUC_N;<br>Zhang D, Iyer LM, Aravind L, Eberhardt R. Zhang D, Iyer LM, Aravind L. This is a conserved short region that is found in many bacterial polymorphic toxin proteins  . It is often located before C-terminal nuclease domains  .. 
PF14449 Pre-toxin TG<br>Zhang D, Iyer LM, Aravind L, Eberhardt R. Zhang D, Iyer LM, Aravind L. PT-TG is a conserved region found in many bacterial toxin proteins. It could function as a linker that links N-terminal secretion-related domain and C-terminal toxin domain. It contains a TG motif  . . 
PF14450 Cell division protein FtsA<br>Pfam-B_1177 (release 5.4). FtsA is essential for bacterial cell division, and co-localises to  the septal ring with FtsZ. It has been suggested that the interaction of FtsA-FtsZ has arisen through coevolution in different bacterial strains  .  The FtsA protein contains two structurally related  actin-like ATPase domains which are also structurally related to the ATPase domains of HSP70 (see PF00012). FtsA has a SHS2 domain  PF02491 inserted in to the RnaseH fold PF02491  .. 
PF14451 Mut7-C ubiquitin<br>Iyer LM, Burroughs AM, Aravind L, Eberhardt R. This member of the ubiquitin superfamily is found at the N-terminus of Mut7-C like RNAses, suggestive of an RNA-binding role  .. 
PF14452 Bac_multiUb;<br>Iyer LM, Burroughs AM, Aravind L, Eberhardt R. A ubiquitin superfamily domain that is often present in multiple  tandem copies in the same polypeptide. Members of this family are associated in gene neighborhoods, or on occasions fused to, bacterial homologs of components of ubiquitin-dependent modification  system such as the E1, E2 and JAB metallopeptidase enzymes and a distinct metal-binding domain  . The E2/UBC fold domain appears to be  inactive. The JAB domain in these operons is usually fused to  the E1 domain  .. 
PF14453 ThiS-like ubiquitin <br>Iyer LM, Burroughs AM, Aravind L. A member of the ubiquitin superfamily that is often fused to the  ThiF-like (E1)- ubiquitin activating enzyme and is present in gene neighborhoods with components of the thiamine biosynthesis pathway  .. 
PF14454 Prokaryotic Ubiquitin<br>Iyer LM, Burroughs AM, Aravind L. A Ubiquitin-superfamily protein that is present across several  bacterial lineages, and found in gene neighborhoods with components of the ubiquitin modification system such as the E1, E2 and JAB  proteins, and a novel alpha-helical protein, which is predicted  to be enzymatic  .. 
PF14455 Predicted metal binding domain<br>Iyer LM, Burroughs AM, Aravind L. A predicted metal-binding domain that is found in gene-neighborhood associations with genes encoding components of the bacterial homologs of the ubiquitin modification pathway including the E1, E2, JAB  metallopeptidase and ubiquitin proteins. The domain is characterised  by a conserved motif with a CxxxxxEYHxxxxH signature.. 
PF14456 Alpha-helical domain 2<br>Iyer LM, Burroughs AM, Aravind L. An alpha-helical domain found in gene neighborhoods encoding genes  containing bacterial homologs of components of the ubiquitin  modification pathway such as the E1, E2, Ub and JAB peptidase  proteins.. 
PF14457 Prokaryotic E2 family A<br>Iyer LM, Burroughs AM, Aravind L. A member of the E2/UBC superfamily of proteins found in several bacteria. The active site residues are very similar to the eukaryotic E2 proteins [1,2]. Members of this family are usually fused to E1 and JAB domains C-terminal to the E2 domain. The protein is usually in the gene neighborhood of a gene encoding a distinct metallobetalactamase family protein  .. 
PF14460 Prokaryotic E2 family D<br>Iyer LM, Burroughs AM, Aravind L. A member of the E2/UBC superfamily of proteins found in several  bacteria. Members of this family lack the conserved histidine  of the classical E2-fold. However, they have an absolutely conserved histidine carboxyl-terminal to the conserved cysteine [1,2]. Members  of this family are usually present in a conserved gene neighborhood  with genes encoding members of the Ub modification pathway such as  the E1, Ub and JAB proteins. These neighborhoods also contain a  gene encoding a rapidly diverging alpha-helical protein  .. 
PF14459 Prokaryotic E2 family C<br>Iyer LM, Burroughs AM, Aravind L. A divergent member of the E2/UBC superfamily of proteins found in  bacteria. Members of the family contain a conserved cysteine in place of the histidine of the classical E2/UBC proteins [1,2]. Members of this family are usually fused to an E1 domain at their C-terminus. The protein is usually in the gene neighborhood of a gene encoding a JAB peptidase and another encoding a predicted metal binding domain  .. 
PF14461 Prokaryotic E2 family B<br>Iyer LM, Burroughs AM, Aravind L. A member of the E2/UBC superfamily of proteins found in several  bacteria. The active site residues are  similar to the eukaryotic E2 proteins but lack the conserved asparagine [1,2]. Members of this family are usually fused to an E1 domain at the C-terminus. The protein is usually in the gene neighborhood of a gene encoding  a member of the pol-beta nucleotidyltransferase superfamily  . Many of the operons in this family are in ICE-like mobile elements and plasmids  .. 
PF14462 Prokaryotic E2 family E<br>Iyer LM, Burroughs AM, Aravind L. A member of the E2/UBC superfamily of proteins found in diverse bacteria. Analysis of the active site residues suggest that members of this family are inactive as they lack the characteristic catalytic residues of the E2 enzymes [1,2]. They are usually fused  to or in the neighborhood of a multi/poly ubiquitin domain protein. Other proteins of the ubiquitin modification pathway such as  the E1 and JAB proteins are also found in its gene neighborhood along with a distinct predicted metal-binding protein.. 
PF14463 E1 N-terminal domain<br>Iyer LM, Burroughs AM, Aravind L. An uncharacterized alpha/beta domain fused to E1 proteins. This protein is usually present in gene neighborhoods with genes  encoding a JAB protein and a predicted metal-binding protein. In related E1 proteins, the E1-N domain is replaced by an E2/UBC superfamily domain  .. 
PF14464 Prokaryotic homologs of the JAB domain<br>Iyer LM, Burroughs AM, Aravind L. These are metalloenzymes that function as the ubiquitin isopeptidase/ deubiquitinase in the ubiquitin-based signaling and protein turnover pathways in eukaryotes  . Prokaryotic JAB domains are predicted to  have a similar role in their cognates of the  ubiquitin modification pathway [2,3]. The domain is widely found in bacteria,  archaea and phages where they are present in several gene contexts  in addition to those that correspond to the prokaryotic cognates of the eukaryotic Ub pathway. Other contexts in which JAB domains are present include gene neighbor associations with ubiquitin fold  domains in cysteine and siderophore biosynthesis, and phage tail  morphogenesis, where they are shown or predicted to process the  associated ubiquitin [2,4]. A distinct family, the RadC-like JAB domains are widespread in bacteria and are predicted to function as nucleases  . In halophilic archaea the JAB domain shows strong  gene-neighborhood associations with a nucleotidyltransferase  suggesting a role in nucleotide metabolism  .. 
PF14465 NFRKB Winged Helix-like<br>de novo domain prediction, confirmed by X-ray structure determination. This domain covers regions 370-495 of human nuclear factor related  to kappaB binding (NFRKB) protein.. 
PF14466 Domain of unknown function (DUF4425) <br>BVU_3708 from Bacteroides vulgatus, JCSG target GS13500. A small family of bacterial proteins, found in several  Bacteroides species. Structure determination (NMR and Xray) shows an immunoglobulin beta barrel fold.\. Multiple homologs have been found  in human gut metagenomics data sets.. 
PF14467 Domain of unknown function (DUF4426)<br>Pseudomonas aeruginosa PA0388, JCSG target SP19004A. Members of this entry are found mostly  in g-proteobacteria, especially in Vibrio. Strangely enough, there seems to be one eukaryotic homolog in Nematostella vectensis (NEMVEDRAFT_v1g226006), where the PA0388-like domain is fused with a domain homogous to the Methionine biosynthesis protein MetW (see below). In several Pseudomonas species, but also in Vibrio vulnificus and Azotobacter vinelandii PA0388 homologs are genomic neighbors of Nucleoside 5-triphosphatase  RdgB (dHAPTP, dITP, XTP-specific) (EC 3.6.1.15) and Methionine  biosynthesis protein MetW. On the other hand, in most Vibrio  species it appears as a part of a conserved operon involved in possible response to stress.. 
PF14468 Protein of unknown function (DUF4427)<br>PSYMP_19184 [Pseudomonas syringae pv. morsprunorum str. M302280PT]. This domain is often found at the C-terminal of proteins with  Pfam:PF10899 domain, for instance in STY1911 protein from a  multiple drug resistant Salmonella enterica serovar Typhi CT18.. 
PF14469 28 kDa A-kinase anchor <br>Jaroszewski L, Godzik A. Q86UN6 A-kinase anchor protein 14 isoform a [Homo sapiens]. 28 kDa AKAP (AKAP28) is highly enriched in human airway axonemes.  The mRNA for AKAP28 is up-regulated as primary airway cells  differentiate and is specifically expressed in tissues containing  cilia and/or flagella  . Homologs of AKAP28 are present in all  animals and in some, including mice the AKAP28-like domain are  preceded by another uncharacterized domain . 
PF14470 Bacterial PH domain<br>Proteins in this family are distantly related to PH domains.. 
PF14471 Domain of unknown function (DUF4428)<br>This putative zinc finger domain is found in uncharacterised bacterial proteins.. 
PF14472 Domain of unknown function (DUF4429)<br>This presumed domain is functionally uncharacterised. This domain family is found in bacteria, archaea and viruses, and is approximately 90 amino acids in length.  This domain is often found in two tandem copies.. 
PF14473 RD3 protein<br>RD3 is a human protein that is found preferentially expressed in the retina  .  Mutations in RD3 causes Leber Congenital Amaurosis type 12  .. 
PF14474 RTC4-like domain<br>This presumed domain is found in the RTC4 protein from yeasts. In Saccharomyces cerevisiae, Cdc13 binds telomeric DNA to recruit telomerase and to "cap" chromosome ends. RTC4 was identified in a screen to identify novel proteins and pathways that cap telomeres, or that respond to uncapped telomeres  . This domain is also found in proteins that contain a DNA-binding myb domain.. 
PF14475 Sec1-binding region of Mso1<br>Mso1p is a component of the secretory vesicle docking complex whose function is closely associated with that of Sec1p. It is a small hydrophilic protein that is enriched in the microsomal membrane fraction  , and this binding domain is towards the N-terminus of Mso1. The yeast Sec1p protein functions in the docking of secretory transport vesicles to the plasma membrane  .  Mso1p and Sec1p interact at sites of exocytosis and the Mso1p-Sec1p interaction site depends on a functional Rab GTPase Sec4p and its GEF Sec2p  . The C-terminal region of Mso1 (not built) assists in targetting Sec1 to the sites of polarised membrane transport  .. 
PF14476 Petal formation-expressed<br>Pfam-B_480 (release 25.0). The members of this plant family from Arabidopsis thaliana appear to be proteins found in the chloroplast, expressed in the pollen tube during the petal differentiation and expansion stage. The function is not known.. 
PF14477 Membrane-polarising domain of Mso1<br>Mso1p is a component of the secretory vesicle docking complex whose function is closely associated with that of Sec1p. It is a small hydrophilic protein that is enriched in the microsomal membrane fraction  . The yeast Sec1p protein functions in the docking of secretory transport vesicles to the plasma membrane  . Mso1p and Sec1p interact at sites of exocytosis and the Mso1p-Sec1p interaction site depends on a functional Rab GTPase Sec4p and its GEF Sec2p  . This C-terminal region of Mso1 assists in targetting Sec1 to the sites of polarised membrane transport, the SNARES and Sec4  .. 
PF14478 Domain of unknown function (DUF4430)<br>JCSG-Target:417407-SP17946A. Although this family has overlaps with SLBB, the majority of its sequences are unique. Several family members, eg UniProtKB:A0RGA8, that do not overlap have an LPXTG-cell wall anchor at their C-terminus, a SSF_Family 10_polysaccharide_lyase or Glycosyltransferase structure associated with them in the middle region, as shown by InterPro, as well as this domain at the N-terminus.. 
PF14479 Prion-inhibition and propagation<br>Greenwald J, Coggill P. Pfam-B_407 (release 25.0). This N-terminal region, HeLo, has a prion-inhibitory effect in cis on its own prion-forming domain (PFD) and in trans on HET-s prion propagation  . The domain is found exclusively in the fungal kingdom. Its structure, as it occurs in the HET-s/HET-S proteins, consists of two bundles of alpha-helices that pack into a single globular domain  .  The domain boundary determined from its structure and from protease-resistance experiments overlaps with the C-terminal prion-forming domain of HET-s (PF11558  . The HeLo domains of HET-s and HET-S are very similar and their few differences (and not the prion-forming domains) determine the compatibility-phenotype of the fungi in which the proteins are expressed. The mechanism of the HeLo domain-function in heterokaryon-incompatibility is still under investigation, however the HeLo domain is found in similar protein architectures as other cell death and apoptosis-inducing domains. The only other HeLo protein to which a function has been associated is LopB from L. maculans  .  Although its specific role in L. maculans is unknown, LopB- mutants have impaired ability to form lesions on oilseed rape. The HeLo domain is not related to the HET domain (PF06985) which is another domain involved in heterokaryon incompatibility.. 
PF14480 DNA polymerase III polC-type N-terminus I<br>Pfam-B_853 (release 23.0). This is the first N-terminal domain, NI domain, of the DNA polymerase III polC subunit A that is found only in Firmicutes. DNA polymerase polC-type III enzyme functions as the 'replicase' in low G + C Gram-positive bacteria  .  Purine asymmetry is a characteristic of organisms with a heterodimeric DNA polymerase III alpha-subunit constituted by polC which probably plays a direct role in the maintenance of strand-biased gene distribution; since, among prokaryotic genomes, the distribution of genes on the leading and lagging strands of the replication fork is known to be biased  . It has been predicted that the N-terminus of polC folds into two globular domains, NI and NII. A predicted patch of elecrostatic potential at the surface of this domain suggests a possible involvement in nucleic acid binding  . This domain is associated with DNA_pol3_alpha Pfam:PF07733 and DNA_pol3_a_NI Pfam:PF11490.. 
PF14481 Type 4 fimbrial biogenesis protein PilY2<br>Jaroszewski L, Godzik A. Pseudomonas aeruginosa PAO1 gene PA4555, JCSG target SP18988A. Members of this family were experimentally shown to be involved  in fimbrial biogenesis, but its exact role appears to be unknown.. 
PF14482 Cut8 proteasome-binding domain<br>In Schizosaccharomyces pombe, Cut8 is a nuclear envelope protein that physically interacts with and tethers 26S proteasome in the nucleus resulting in the nuclear accumulation of proteasome  . Cut8 comprises three functional domains. An N-terminal lysine-rich segment (this entry) which binds to the proteasome when ubiquitinated, a central dimerisation domain (Pfam:PF14483) and a C-terminal six-helix bundle (Pfam:PF08559), which shows structural similarity to 14-3-3 phosphoprotein-binding domains. The six-helix bundle is necessary for liposome and cholesterol binding  . Cut8 is a proteasome substrate and the N-terminal segment is polyubiquitinated and functions as a degron tag. Ubiquitination of the amino N-terminal segment is essential to the function of Cut8  . Lysine residues in the N-terminal segment of Cut8 are required for physical interaction with proteasome  . In fission yeast the function of Cut8 has been demonstrated to be regulated by ubiquitin-conjugating Rhp6/Ubc2/Rad6 and ligating enzymes Ubr1  . Cut8 homologues have been identified in Drosophila melanogaster, Anopheles gambiae and Dictyostelium discoideum  .. 
PF14483 Cut8 dimerisation domain<br>In Schizosaccharomyces pombe, Cut8 is a nuclear envelope protein that physically interacts with and tethers 26S proteasome in the nucleus resulting in the nuclear accumulation of proteasome  . Cut8 comprises three functional domains. An N-terminal lysine-rich segment (Pfam:PF14482) which binds to the proteasome when ubiquitinated, a central dimerisation domain (this entry) and a C-terminal six-helix bundle (Pfam:PF08559), which shows structural similarity to 14-3-3 phosphoprotein-binding domains. The six-helix bundle is necessary for liposome and cholesterol binding  . Cut8 is a proteasome substrate and the N-terminal segment is polyubiquitinated and functions as a degron tag. Ubiquitination of the amino N-terminal segment is essential to the function of Cut8  . Lysine residues in the N-terminal segment of Cut8 are required for physical interaction with proteasome  . In fission yeast the function of Cut8 has been demonstrated to be regulated by ubiquitin-conjugating Rhp6/Ubc2/Rad6 and ligating enzymes Ubr1  . Cut8 homologues have been identified in Drosophila melanogaster, Anopheles gambiae and Dictyostelium discoideum  .. 
PF14484 Fish-specific NACHT associated domain<br>This domain is frequently found associated with the NACHT domain (Pfam:PF05729) in fish and other vertebrates  .. 
PF14485 Domain of unknown function (DUF4431)<br>
PF14486 Domain of unknown function (DUF4432)<br>JCSG_target390294_A6THE6. 
PF14487 Domain of unknown function (DUF4433)<br>This family of proteins is found in bacteria, archaea and eukaryotes.  Proteins in this family are typically between 201 and 230 amino acids in length. There is a single completely conserved residue E that may be functionally important. This family is distantly similar to Pfam:PF01885 suggesting these may be ADP-ribosylases.. 
PF14488 Domain of unknown function (DUF4434)<br>JCSG_Target_393000_GS13553A. 
PF14489 QueF-like protein<br>This protein is involved in the biosynthesis of queuosine.  In some proteins this domain appears to be fused to Pfam:PF06508.. 
PF14490 Helix-hairpin-helix containing domain<br>This presumed domain contains at least one helix-hairpin-helix motif. This domain is often found in RecD helicases.. 
PF14491 Protein of unknown function (DUF4435)<br>This presumed domain is functionally uncharacterised. This domain is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 285 and 362 amino acids in length. This domain is sometimes associated with AAA domains.. 
PF14492 Elongation Factor G, domain II<br>This domain is found in Elongation Factor G. It shares a similar structure with domain V (Pfam:PF00679).. 
PF14493 Helix-turn-helix domain<br>This presumed domain is found at the C-terminus of a large number of helicase proteins.. 
PF14494 Domain of unknown function (DUF4436)<br>Pfam-B_6430 (release 25.0). This is a family of membrane and transmembrane proteins from mycobacterial and related species. The function is not known.. 
PF14495 Cytochrome c-550 domain<br>This domain is a heme binding cytochrome known as cytochrome c550, or cytochrome c549, or PsbV  .. 
PF14496 C-terminal novel E3 ligase, LRR-interacting<br>Jackhmmer:E7K2H2_PDB:3ckd. This NEL or novel E3 ligase domain is found at the C-terminus of bacterial virulence factors. Its sequence is different from those of the eukaryotic HECT and RING-finger E3 ligases, and it subverts the host ubiquitination process. At the N-terminus of the family-members there is a series of LRR repeats, and the NEL domain interacts with the most N-terminal repeat. The key residue for the ligation step is the cysteine, eg found at position 386 in UniProtKB:E7K2H2. The LRR section sequesters this active site until invasion has occurred  .. 
PF14497 Glutathione S-transferase, C-terminal domain<br>This domain is closely related to Pfam:PF00043.. 
PF14498 Glycosyl hydrolase family 65, N-terminal domain<br>This domain represents a domain found to the N-terminus of the glycosyl hydrolase 65 family catalytic domain.. 
PF14499 Domain of unknown function (DUF4437)<br>This family of proteins is found in bacteria. Proteins in this family are typically between 152 and 283 amino acids in length.. 
PF14500 Dos2-interacting transcription regulator of RNA-Pol-II<br>This domain, along with the C-terminal part, Pfam:PF12460  , is an essential component of a silencing complex in fission yeast that contains Dos2, Rik1, Mms19 and Cdc20 (the catalytic subunit of DNA polymerase-epsilon). This complex regulates RNA polymerase II (RNA Pol II) activity in heterochromatin and is required for DNA replication and heterochromatin assembly  .. 
PF14501 GHKL domain<br>This family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90.. 
PF14502 Helix-turn-helix domain<br>
PF14503 YhfZ C-terminal domain<br>This domain is often found in association with the helix-turn-helix domain HTH_41 (Pfam:PF14502). It includes YhfZ proteins from Escherichia coli and Shigella flexneri.. 
PF14504 CAP-associated N-terminal<br>JCSG:target_417453-SP18049A. The function of this domain is unknown, but it is found towards the N-terminus of bacterial proteins carrying the CAP domain, Pfam:PF00188. All members that do not otherwise carry an additional Cu_amine_oxidN1, Pfam:PF07833, domain are likely to be extracellular as they start with a signal-peptide. Most other non-bacterial proteins with the CAP domain are allergenic  .. 
PF14505 Domain of unknown function (DUF4438)<br>
PF14506 CppA N-terminal<br>This is the N-terminal domain of the CppA protein found in species of Streptococcus. CppA is a putative C3-glycoprotein degrading proteinase, involved in pathogenicity [1,2]. It is often found associated with Pfam:PF14507.. 
PF14507 CppA C-terminal<br>This is the C-terminal domain of the CppA protein found in species of Streptococcus. CppA is a putative C3-glycoprotein degrading proteinase, involved in pathogenicity [1,2]. It is often found associated with Pfam:PF14506.. 
PF14508 Glycosyl-hydrolase 97 N-terminal<br>This N-terminal domain of glycosyl-hydrolase-97  contributes part of the active site pocket. It is also important for contact with the catalytic and C-terminal domains of the whole [2,3].. 
PF14509 Glycosyl-hydrolase 97 C-terminal, oligomerisation<br>Glycosyl-hydrolase-97 is made up of three tightly linked and highly conserved globular domains.  The C-terminal domain is found to be necessary for oligomerisation of the whole molecule in order to create the active-site pocket and the Ca++-binding site.. 
PF14510 ABC-transporter extracellular N-terminal<br>Pfam-B_101 (release 25.0). This domain is found at the N-terminus of ABC-transporter proteins from fungi, plants to higher eukaryotes. It would appear to be an extracellular domain.. 
PF14511 Type II restriction endonuclease EcoO109I<br>Coggill P, Eberhardt R. pdb_1wtd-Jackhmmer:Q9RPJ3. This is a family of Type II restriction endonucleases.. 
PF14512 Putative TM nitroreductase<br>Jackhmmer:Q9X1S2_pdb:1vkw. Compared with the more traditional NADH oxidase/flavin reductase family, this family is a duplication, consisting of two similar domains arranged as the subunits of the dimeric NADH oxidase/flavin reductase with one conserved active site.. 
PF14513 Diacylglycerol kinase N-terminus<br>This domain is found at the N-terminus of diacylglycerol kinases.. 
PF14514 Transcriptional regulator, TetR, C-terminal<br>This family comprises proteins that belong to the TetR family of transcriptional regulators. This family features the C-terminal region of these sequences, which does not include the N-terminal helix-turn-helix.. 
PF14515 Haem-oxygenase-associated N-terminal helices<br>Jackhmmer:Q9HY91, pdb_3bjdA. This domain represents a pair of alpha helices, which are found at the N-terminus of some Haem-oxygenase globular domain.. 
PF14516 AAA-like domain<br>This family of proteins are part of the AAA superfamily.. 
PF14517 Tachylectin<br>This family of lectins binds N-acetylglucosamine and N-acetylgalactosamine and may be involved in innate immunity [1-3]. It has a five-bladed beta-propeller structure with five carbohydrate-binding sites, one per beta sheet  .. 
PF14518 Iron-containing redox enzyme<br>Pfam-B_412 (release 26.0). The CADD, Chlamydia protein associating with death domains, crystal structure reveals a dimer of seven-helical bundles. Each bundle contains a di-iron centre adjacent to an internal cavity that forms an active site similar to that of methane mono-oxygenase hydrolase  .. 
PF14519 Macro-like domain<br>Jachmmer_A6ZME4, pdb_1njr. This domain is an ADP-ribose binding module.  It is found in a number of yeast proteins.. 
PF14520 Helix-hairpin-helix domain<br>
PF14521 Lysine-specific metallo-endopeptidase <br>Pfam-B_2237 (release 26.0), pdb_1g12 . This is the catalytic region of aspzincins, a group of lysine-specific metallo-endopeptidases in the MEROPS:M35 family. They exhibit the following active-site architecture. The active site is composed of two helices and a loop region and includes the HExxH and GTxDxxYG motifs. In UniProt:P81054, His117, His121 and Asp130 coordinate to the catalytic zinc ligands. An electrostatically negative region composed of Asp154 and Glu157 attracts a positively charged Lys side chain of a substrate in a specific manner  .. 
PF14522 Cytochrome c7<br>This family includes cytochromes c7 and c7-type. In cytochromes c7 all three haems are bis-His co-ordinated. In c7-type the last haem is His-Met co-ordinated  .. 
PF14523 Syntaxin-like protein<br>This domain includes syntaxin-like domains including from the Vam3p protein  .. 
PF14524 Wzt C-terminal domain<br>This domain is found at the C-terminus of the Wzt protein  . The crystal structure of C-Wzt(O9a) reveals a beta sandwich with an immunoglobulin-like topology that contains the O-antigenic polysaccharide binding pocket. This domain is often associated with  the ABC-transporter domain.. 
PF14525 AraC-binding-like domain<br>This domain is related to the AraC ligand binding domain Pfam:PF02311.. 
PF14526 Integron-associated effector binding protein<br>This family contains Cass2 from Vibrio cholerae, an integron-associated protein that has been shown   to bind cationic drug compounds with submicromolar affinity. Cass2 has been proposed to be representative of a larger family of independent effector-binding proteins associated with lateral gene transfer within Vibrio and other closely-related species.. 
PF14527 WhiA LAGLIDADG-like domain<br>This domain is found within the sporulation regulator WhiA.  It is a LAGLIDADG superfamily like domain [1-2].. 
PF14528 LAGLIDADG-like domain<br>This domain is part of the LAGLIDADG superfamily  .. 
PF14529 Endonuclease-reverse transcriptase <br>This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes.\. These are enzymes largely from class EC:2.7.7.49.. 
PF14530 Domain of unknown function (DUF4439)<br>This domain has a ferritin-like fold.. 
PF14531 Kinase-like<br>This family includes the pseudokinases ROP2 and ROP8 from Toxoplasma gondii (Swiss:Q06AK3 and Swiss:O15693). These proteins have a typical bilobed protein kinase fold, but lack catalytic actvity  .. 
PF14532 Sigma-54 interaction domain<br>
PF14533 Ubiquitin-specific protease C-terminal<br>Pfam-B_1954 (release 25.0). This C-terminal domain on many long ubiquitin-specific proteases has no known function.. 
PF14534 Domain of unknown function (DUF4440)<br>
PF14535 AMP-binding enzyme C-terminal domain<br>This is a small domain that is found C terminal to Pfam:PF00501. It has a central beta sheet core that is flanked by alpha helices.. 
PF14536 Domain of unknown function (DUF4441)<br>Pfam-B_1275 (release 25.0). This family is largely made up of uncharacterised proteins from the Ciliophora.  The function is not known.. 
PF14537 Cytochrome c3<br>
PF14538 Raptor N-terminal CASPase like domain<br>This domain is found at the N-terminus of the Raptor protein. It has been identified to have a CASPase like structure  . It conserves the characteristic cys/his dyad of the caspases suggesting it may have a peptidase activity.. 
PF14539 Domain of unknown function (DUF4442)<br>This family of proteins is found in bacteria, archaea and eukaryotes.  Proteins in this family are typically between 139 and 165 amino acids in length.  There is a conserved PYF sequence motif. There is a single completely conserved residue N that may be functionally important.. 
PF14540 Nucleotidyltransferase-like<br>Structural comparisons with PDB:1kny indicate that this N-terminal domain resembles a nucleotidyltransferase fold.. 
PF14541 Xylanase inhibitor C-terminal<br>The N- and C-termini of the members of this family are jointly necessary for creating the catalytic pocket necessary for cleaving xylasnase.  Phytopathogens produce xylanase that destroys plant cells, so its destruction through proteolysis is vital for plant-survival.. 
PF14542 GCN5-related N-acetyl-transferase<br>This family of GCN5-related N-acetyl-transferases bind both CoA and acetyl-CoA. They are characterised by highly conserved glycine, a cysteine residue in the acetyl-CoA binding site near the acetyl group, their small size compared with other GNATs and a lack of of an obvious substrate-binding site.  It is proposed that they transfer an acetyl group from acetyl-CoA to one or more unidentified aliphatic amines via an acetyl (cysteine) enzyme intermediate. The substrate might be another macromolecule.. 
PF14543 Xylanase inhibitor N-terminal<br>The N- and C-termini of the members of this family are jointly necessary for creating the catalytic pocket necessary for cleaving xylanase.\.       Phytopathogens produce xylanase that destroys plant cells, so its destruction through proteolysis is vital for plant-survival.. 
PF14544 Domain of unknown function (DUF4443)<br>This is a family of archaeal proteins. The domain is a putative gyrase domain.. 
PF14545 BCAP_N;<br>Dof, BCAP, and BANK (DBB) motif,. PROSITE, Pfam-B_2980 (release 26.0). The DBB domain is named from the Drosophila (Downstream of FGFR - Dof, also known as Heartbroken or Stumps) protein, the BANKS and BCAP, both signalling in B-cell pathway, proteins. This domain defines a minimal region required for mediating Dof dimerisation. Since this domain can interact both with itself and with a region in the C-terminal part of the molecule, it may mediate either intermolecular or intramolecular interactions  . Mutants lacking this domain disrupt FGFR signal transduction and fibroblast growth-factor signalling  .. 
PF14547 Hydrophobic seed protein<br>This domain has a four-helix bundle structure. It contains four disulfide bonds, of which three function to keep the C- and N-terminal parts of the molecule in place  .. 
PF14549 DNA-binding transcriptional regulator Cro<br>Bacteriophage P22 Cro protein represses genes normally expressed in early phage development and is necessary for the late stage of lytic growth.  It does this by binding to the OL and OR operator-regions normally used by the repressor protein for lysogenic maintenance.. 
PF14550 Putative phage protease XkdF<br>Pfam-B_5816 (release 26.0). This domain is largely found on phage proteins.  In a number of cases the domain is associated with a SAM-dependent methyltransferase.. 
PF14551 MCM N-terminal domain<br>This family contains the N-terminal region of MCM proteins.  This region is composed of three structural domains. Firstly a four helical bundle, secondly a zinc binding motif and thirdly an OB-like fold  .. 
PF14552 Tautomerase enzyme<br>CATH:3c6vA00, Pfam-B_819 (release 26.0). 
PF14553 YqbF, hypothetical protein domain<br>This N-terminal domain is found in Bacillus and related spp. The function is not known.. 
PF14554 VEGF heparin-binding domain<br>This short domain is found at the C-terminus of VEGF. It has been shown to have heparin binding activity.. 
PF14555 UBA-like domain<br>
PF14556 AF2331-like<br>AF2331-like is a 11-kDa orphan protein of unknown function from Archaeoglobus fulgidus. The structure consists of an alpha + beta fold formed by an unusual homodimer, where the two core beta-sheets are interdigitated, containing strands alternating from both subunits. AF2331 contains multiple negatively charged surface clusters and is located on the same operon as the basic protein AF2330. It is suggested that AF2331 and AF2330 may form a charge-stabilized complex in vivo, though the role of the negatively charged surface clusters is not clear.. 
PF14557 Putative AphA-like transcriptional regulator<br>Members of this family are putative transcriptional regulators that appear to be related to the Pfam:PF03551 family. This family includes AphA-like members.. 
PF14558 ML-like domain<br>This domain is distantly similar to Pfam:PF02221 and conserves its pattern of conserved cysteines. This suggests that this domain may be involved in lipid binding.. 
PF14559 Tetratricopeptide repeat<br>
PF14560 Ubiquitin-like domain<br>This entry contains ubiquitin-like domains [1-2].. 
PF14561 Tetratricopeptide repeat<br>
PF14562 Restriction endonuclease BglI<br>This restriction endonuclease binds DNA as a dimer. BglI recognises and cleaves the interrupted DNA sequence GCCNNNNNGGC and cleaves between the fourth and fifth unspecified base pair to produce 3' overhanging ends  .. 
PF14563 Domain of unknown function (DUF4444)<br>This domain family is found in bacteria, and is approximately 40 amino acids in length. There is a conserved LIPL sequence motif. There are two completely conserved G residues that may be functionally important.. 
PF14564 Membrane binding<br>This family includes the C-terminal domain of Dictyostelium discoideum Calcium-dependent cell adhesion molecule 1 (Swiss:P54657), which has an immunoglobulin-like fold. It tethers the protein to the cell membrane  .. 
PF14565 Interleukin 22 IL-10-related T-cell-derived-inducible factor<br>Interleukin-22 is distantly related to interleukin (IL)-10, and is produced by activated T cells. IL-22 is a ligand for CRF2-4, a member of the class II cytokine receptor family.. 
PF14566 Inositol hexakisphosphate<br>Pfam-B_194 (release 26.0). Inositol hexakisphosphate, often called phytate, is found in abundance in seeds and acting as an inorganic phosphate reservoir. Phytases are phosphatases that hydrolyze phytate to less-phosphorylated myo-inositol derivatives and inorganic phosphate. The active-site sequence (HCXXGXGR) of the phytase identified from the gut micro-organism Selenomonas ruminantium forms a loop (P loop) at the base of a substrate binding pocket that is characteristic of protein tyrosine phosphatases (PTPs). The depth of this pocket is an important determinant of the substrate specificity of PTPs. In humans this enzyme is thought to aid bone mineralization and salvage the inositol moiety prior to apoptosis  .. 
PF14567 SMI1-KNR4 cell-wall<br>Pfam-B_7167 (release 26.0). Members of this family are related to the SMI1/KNR4-like or SUKH superfamily of proteins.. 
PF14568 SMI1-KNR4 cell-wall<br>Pfam-B_725 (releawse 26.0). Members of this family are related to the SMI1/KNR4-like or SUKH superfamily of proteins.. 
PF14569 Zinc-binding RING-finger<br>This RING/U-box type zinc-binding domain is frequently found in the catalytic subunit (irx3) of cellulose synthase. The enzymic class is EC:2.4.1.12, whereby the synthase removes the glucose from UDP-glucose and adds it to the growing cellulose, thereby releasing UDP. The domain-structure is treble-clef like (PDB:1weo).. 
PF14570 RING/Ubox like zinc-binding domain<br>
PF14571 Stress-induced protein Di19, C-terminal<br>C-terminal domain of Di19, a protein that increases the sensitivity of plants to environmental stress, such as salinity, drought, osmotic stress and cold. the protein is also induced by an increased supply of stress-related hormones such as abscisic acid ABA and ethylene  . There is a zinc-finger at the N-terminus, zf-Di19, Pfam:PF05605.. 
PF14572 Phosphoribosyl synthetase-associated domain<br>pdb_2c4k; Jackhmmer:Q14558. This family includes several examples of enzymes from class EC:2.7.6.1, phosphoribosyl-pyrophosphate transferase.. 
PF14573 Acyl-carrier<br>
PF14574 Domain of unknown function (DUF4445)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 525 and 664 amino acids in length. The family is found in association with Pfam:PF00111.. 
PF14575 Ephrin type-A receptor 2 transmembrane domain<br>Epha2_TM represents the left-handed dimer transmembrane domain of of EphA2 receptor.  This domain oligomerises and is important for the active signalling process.. 
PF14576 Sieve element occlusion N-terminus<br>Sieve element occlusion (SEO) proteins, or forisomes, are phloem proteins which accumulate during sieve element differentiation  . This domain represents the N-terminus of SEO proteins.. 
PF14577 Sieve element occlusion C-terminus<br>Sieve element occlusion (SEO) proteins, or forisomes, are phloem proteins which accumulate during sieve element differentiation  . This domain represents the C-terminus of SEO proteins.. 
PF14578 Elongation factor Tu domain 4<br>Elongation factor Tu consists of several structural domains, and this is usually the fourth.. 
PF14579 Helix-hairpin-helix motif<br>The HHH domain is a short DNA-binding domain  .. 
PF14580 Leucine-rich repeat<br>
PF14581 SseB protein C-terminal domain<br>This family consists of several SseB proteins which appear to be found exclusively in Enterobacteria. SseB is known to enhance serine-sensitivity in Escherichia coli   and is part of the Salmonella pathogenicity island 2 (SPI-2) translocon  .\. This presumed domain is found at the C-terminus of SseB proteins.. 
PF14582 Metallophosphoesterase, calcineurin superfamily<br>Members of this family are part of the Calcineurin-like phosphoesterase superfamily.. 
PF14583 Oligogalacturonate lyase<br>This is a family of oligogalacturonate lyases, referred to more generally as pectate lyase family 22.  These proteins fold into 7-bladed beta-propellers.. 
PF14584 Protein of unknown function (DUF4446)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 165 and 176 amino acids in length.. 
PF14585 CagY type 1 repeat<br>This repeat is found at the N-terminus of the CagY proteins - part of the CAG pathogenicity island - and involved in delivery of the protein CagA into host cells ( ).. 
PF14586 Class I Histocompatibility antigen, NKG2D ligand, domains 1 and 2<br>Members of this family are known as retinoic-acid-inducible proteins. They are ligands for the activating immunoreceptor NKG2D, which is widely expressed on natural killer cells, T cells, and macrophages.. 
PF14587 O-Glycosyl hydrolase family 30<br>
PF14588 YjgF/chorismate_mutase-like, putative endoribonuclease<br>YjgF_Endoribonuc is a putative endoribonuclease. The structure is of beta-alpha-beta-alpha-beta(2) domains common both to bacterial chorismate mutase and to members of the YjgF family. These proteins form trimers with a three-fold symmetry with three closely-packed beta-sheets. The YjgF family is a large, widely distributed family of proteins of unknown biochemical function that are highly conserved among eubacteria, archaea and eukaryotes  .. 
PF14589 Polysulfide reductase<br>CATH:2vpzC00, Pfam-B_200168. Bacterial polysulfide reductase is an integral membrane protein complex responsible for quinone-coupled reduction of polysulfide, a process important in extreme environments such as deep-sea vents and hot springs. Polysulfides are a class of compounds composed of chains of sulfur atoms, which in their simplest form are present as an anion with general formula Sn(2-). In nature, polysulfides are found in particularly high concentrations in extreme volcanic or geothermically active environments. Here, the reduction and oxidation of polysulfides are vital processes for many bacteria and are essential steps in the global sulfur cycle. In particular, the reduction of polysulfide to hydrogen sulfide in these environments is usually linked to energy-generating respiratory processes, supporting growth of many microorganisms, particularly hyperthermophiles.. 
PF14590 Domain of unknown function (DUF4447)<br>This family of proteins is found in bacteria. Proteins in this family are approximately 170 amino acids in length.. 
PF14591 NTP_transf_5;<br>Members of this family are of unknown function.. 
PF14592 Chondroitinase B<br>This family includes chondroitinases. These enzymes cleave the glycosaminoglycan dermatan sulfate  .. 
PF14593 PH domain<br>
PF14594 Siphovirus ReqiPepy6 Gp37-like protein<br>This family includes numerous phage proteins from Siphoviruses. The function of this protein is uncertain, but it is related to Pfam:PF06605. In Rhodococcus phage ReqiPepy6 this protein is called Gp37  .. 
PF14595 Thioredoxin<br>
PF14596 STAT6 C-terminal<br>This family represents the C-terminus of mammalian STAT6 (Signal transducer and activator of transcription 6), it contains an LXXLL motif which binds to NCOA1 (Nuclear receptor coactivator 1)  .. 
PF14597 Metallo-beta-lactamase superfamily<br>This is a small family of putative metal-dependent hydrolases.. 
PF14598 PAS domain<br>This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), which binds to an LXXLL motif in the C-terminal region of STAT6 (Signal transducer and activator of transcription 6)  .. 
PF14599 Zinc-ribbon<br>This is a typical zinc-ribbon finger, with each pair of zinc-ligands coming from more-or-less either side of two knuckles. It is found in eukaryotes.. 
PF14600 Cellulose-binding domain<br>This C-terminal domain belongs to the CAZy family of carbohydrate-binding domains that are associated with glycosyl-hydrolases. It is suggested to bind cellulose.. 
PF14601 DNA_binding protein, TFX, C-term<br>This is the C-terminal region of TFX-like DNA-binding proteins.. 
PF14602 Hexapeptide repeat of succinyl-transferase<br>
PF14603 Helically-extended SH3 domain<br>This domain is the 70 C-terminal residues of ADAP - Adhesion and de-granulation promoting adapter protein. It shows homology to SH3 domains; however, conserved residues of the fold are absent.  It thus represents an altered SH3 domain fold. An N-terminal, amphipathic, helix makes extensive contacts to residues of the regular SH3 domain fold thereby creating a composite surface with unusual surface properties. The domain can no longer bind conventional proline-rich peptides  . There are key phosphorylation sites within the two hSH3 domains and it would appear that binding at these sites does not materially affect the folding of these regions although the equilibrium towards the unfolded state may be slightly altered  . The binding partners of the hSH3 domains are still unknown  .. 
PF14604 Variant SH3 domain<br>Jackhmmer, JCSG:target_422527. 
PF14605 Nup53/35/40-type RNA recognition motif<br>Jackhmmer, JCSG:target_422743. 
PF14606 GDSL-like Lipase/Acylhydrolase family<br>Jackhmmer, JCSG:target_416889. 
PF14607 N-terminus of Esterase_SGNH_hydro-type<br>Jackhmmer, JCSG_target_416889. This domain lies upstream of SGNH hydrolase, but its function is not known. There is a highly conserved GxDLY sequence-motif.. 
PF14608 Zinc finger C-x8-C-x5-C-x3-H type<br>Pfam-B_880 (release 26.0). This is a zinc-finger of the type C-x8-C-x5-C-x3-H.. 
PF14609 gamma-Tubulin ring complex non-core subunit mod21 <br>Pfam-B_276835 (release 26.0). GCP5-Mod21 is a non-core subunit of the larger gamma-tubulin ring complex that effects microtubule nucleation from both centrosomal and non-centrosomal sites. This subunit, unlike GCP2 and and GCP3 and others, is not thought to be essential for viability in the fission yeast, and may not be expressed in very high concentrations.  Fission yeast can form a large gamma-Tubulin complex C similar to that found in higher eukaryotes and this complex is important for maintaining normal levels of microtubule nucleation in vivo  .. 
PF14610 GPI-anchored_2;<br>Protein of unknown function (DUF4448). Pfam-B_5686 (release 26.0). This is a family of predicted membrane glycoproteins from fungi. However there appears, visually, to be some similarity with the family of GPI-anchored fungal proteins, Pfam:PF10342.. 
PF14611 Mitochondrial inner-membrane-bound regulator<br>Pfam-B_1679 (release 26.00. SLS is a fungal domain found bound to the mitochondrial inner-membrane  . It reacts physically with fungal Kar2p to promote translocation across the endoplasmic-reticulum membrane. This action appeared to be mediated via the promotion of the Sec63p-mediated activation of Kar2p's ATPase activity. This indicates that the Sls1p protein is a GrpE-like protein in the endoplasmic reticulum. In S.cerevisiae the SLS1 gene (ScSLS1) is not essential but is also involved in ERAD and folding [2,3].. 
PF14612 IEC3 subunit of the Ino80 complex, chromatin re-modelling<br>Pfam-B_3771 (release 26.0). This is a family of fungal chromatin re-modelling proteins found in one of the chromatin-central complexes, Ino80. The function was identified in Schizosaccharomyces pombe but there is no orthologue in S. cerevisiae. . 
PF14613 Protein of unknown function (DUF4449)<br>Pfam-B_1378 (release 26.0). This is a fungal DUF of unknown function.. 
PF14614 Domain of unknown function (DUF4450)<br>JCSG:Target_393004-GS13576A. This is a family of bacterial proteins of unknown function.. 
PF14615 Ribosome-assembly protein 3<br>Pfam-B_11864 (release 26.0). This is a family of 60S ribosome-assembly proteins, from fungi.. 
PF14616 Domain of unknown function (DUF4451)<br>Pfam-B_5126 (release 26.0). This is family of fungal proteins up-regulated during meiosis.. 
PF14617 U3-containing 90S pre-ribosomal complex subunit<br>Pfam-B_3046 (release 26.0). This is a family of fungal and plant CMS1-like proteins. The family has similarity to the DEAD-box helicases. . 
PF14618 Domain of unknown function (DUF4452)<br>Pfam-B_6056 (release 26.0). This fungal family has no known function. However, it is rich in paired, as CXXC, cysteines and histidines, but these do not fall in the conformation that might suggest zinc-binding.. 
PF14619 Snf2-ATP coupling, chromatin remodelling complex<br>Pfam-B_4045 (release 26.0). This domain appears to play a crucial role in chromatin remodelling for yeast SWI/SNF. It binds histones. It is required for mobilising nucleosomes and lies within the catalytic subunit of the yeast SWI/SNF. It is found to be universally conserved  .. 
PF14620 YpeB sporulation<br>Pfam-B_309 (release 26.0). YPEB is a protein that is necessary for the functioning of SleB during spore-cortex hydrolysis.. 
PF14621 RFX5 DNA-binding domain<br>Pfam-B_20855 (release 26.0). RFX5 and RFXAP reveals molecular details associated with MHCII gene expression.. 
PF14622 Ribonuclease-III-like<br>Pfam-B_6419 (release 26.0). Members of this family are involved in rDNA transcription and rRNA processing. They probably also cleave a stem-loop structure at the 3' end of U2 snRNA to ensure formation of the correct U2 3' end; they are involved in polyadenylation-independent transcription termination. Some members may be mitochondrial ribosomal protein subunit L15, others may be 60S ribosomal protein L3.. 
PF14623 Hint-domain<br>This short domain is a conserved region of intein-containing proteins from lower eukaryotes. 
PF14624 VWA / Hh  protein intein-like<br>Buerglin T, Coggill P. VWA-Hint proteins carry this conserved domain of around 300 residues, now named the Vwaint domain. Such proteins do not seem to have a signal peptide for secretion. Generally, this domain lies between the N-terminal VWA domain and the more C-terminal 'Vint'-type Hint domain. The exact function of this domain is not known.. 
PF14625 Lustrin, cysteine-rich repeated domain<br>This repeated domain is found in proteins from lower eukaryotes in lustrin, perlucin, pearl nacre, and other similar protein-types. Each repeat lies between Kunitz-BPTI repeats, in certain species, which are also cysteine-rich. The cysteines may form the disulfide bonds observed for other members of this superfamily.. 
PF14626 Zc3h12a-like Ribonuclease NYN domain<br>This family is found to be a divergent form of the NYN-domain- containing RNAse family.. 
PF14627 Domain of unknown function (DUF4453)<br>This short domain is found only on a small subgroup of proteins from Gram-negative Proteobacteria that also carry a YARHG domain, Pfam:PF13308. They carry three conserved tryptophan and three conserved cysteine residues.. 
PF14628 Domain of unknown function (DUF4454)<br>This C-terminal domain is found only on a small subgroup of proteins from Gram-positive Clostridiales that also carry a YARHG domain, Pfam:PF13308.. 
PF14629 Origin recognition complex (ORC) subunit 4 C-terminus<br>This entry represents the C-terminus of origin recognition complex subunit 4 [1,2].. 
PF14630 Origin recognition complex (ORC) subunit 5 C-terminus<br>This entry represents the C-terminus of origin recognition complex subunit 5  .. 
PF14631 Fanconi anaemia protein FancD2 nuclease<br>The Fanconi anaemia protein FancD2 is a nuclease necessary for the repair of DNA interstrand-crosslinks.. 
PF14632 Acidic N-terminal SPT6<br>pfam-B_9510 (release 26.0). The N-terminus of SPT6 is highly acidic. The full SPT6 protein is a transcription regulator, but the exact function of this acidic region is not certain.. 
PF14633 SH2 domain<br>pfam-B_9510 (release 26.0). 
PF14634 zinc-RING finger domain<br>
PF14635 Helix-hairpin-helix motif\<br>Pfam-B_9510 (release 26.0). 
PF14636 Folliculin-interacting protein N-terminus<br>This is the N-terminus of folliculin-interacting proteins [1,2].. 
PF14637 Folliculin-interacting protein middle domain<br>This is the middle domain of folliculin-interacting proteins [1,2].. 
PF14638 Folliculin-interacting protein C-terminus<br>This is the C-terminus of folliculin-interacting proteins [1,2]. This region is responsible for binding to folliculin  .. 
PF14639 Holliday-junction resolvase-like of SPT6 <br>Pfam-B_9510 (release 26.0). The YqgF domain of SPT6 proteins is homologous to the E.coli RuvC   but its putative catalytic site lacks the carboxylate side chains critical for coordinating magnesium ions that mediate phosphodiester bond-cleavage  . 
PF14640 Transmembrane protein 223<br>
PF14641 HtH;<br>Helix-turn-helix DNA-binding domain of SPT6. Pfam-B_9510 (release 26.0). This helix-turn-helix represents the first of two DNA-binding domains on the SPT6 proteins.. 
PF14642 FAM47 family<br>The function of this Chordate family of proteins is not known.. 
PF14643 Domain of unknown function (DUF4455)<br>This domain family is found in bacteria and eukaryotes, and is approximately 480 amino acids in length. There are two completely conserved residues (W and P) that may be functionally important.. 
PF14644 Domain of unknown function (DUF4456)<br>This domain family is found in bacteria and eukaryotes, and is approximately 210 amino acids in length. There is a single completely conserved residue E that may be functionally important.. 
PF14645 Chibby family<br>This family includes the eukaryotic chibby proteins. These proteins inhibit the wingless/Wnt pathway by binding to beta-catenin and inhibiting beta-catenin-mediated transcriptional activation. Chibby is Japanese for small, and is named after the RNAi phenotype seen in Drosophila  .. 
PF14646 MYCBP-associated protein family<br>This family of eukaryotic proteins includes the mammalian MYCBP-associated proteins. These proteins may be synaptic processes   and may have a role in spermatogenesis  .. 
PF14647 FAM91 N-terminus<br>
PF14648 FAM91 C-terminus<br>
PF14649 Spatacsin C-terminus<br>This family includes the C-terminus of spatacsin.. 
PF14650 FAM75 family<br>
PF14651 Lipocalin / cytosolic fatty-acid binding protein family<br>Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The family also encompasses the enzyme prostaglandin D synthase (EC:5.3.99.2).. 
PF14652 Domain of unknown function (DUF4457)<br>This family of proteins is found in eukaryotes. It is found repeated several times in the vertebrate KIAA0556 proteins.. 
PF14653 Insulin growth factor-like family<br>This family includes the insulin growth factor-like proteins. These proteins are potential ligands for the IGFLR1 cell membrane receptor  .. 
PF14654 Mucin_C;<br>Mucin, catalytic, TM and cytoplasmic tail region. Pfam-B_ 91014 (release 26.0). This family represents the non-tandem repeat domain including cleavage site, the transmembrane helix domain, and the cytoplasmic tail of epiglycanin and related mucins  .. 
PF14655 Rab3 GTPase-activating protein regulatory subunit N-terminus<br>This family includes the N-terminus of the Rab3 GTPase-activating protein non-catalytic subunit. Rab3 GTPase-activating protein is a GTPase activating protein with specificity for Rab3 subfamily  .. 
PF14656 Rab3 GTPase-activating protein regulatory subunit C-terminus<br>This family includes the N-terminus of the Rab3 GTPase-activating protein non-catalytic subunit. Rab3 GTPase-activating protein is a GTPase activating protein with specificity for Rab3 subfamily  .. 
PF14657 AP2-like DNA-binding integrase domain<br>This family includes AP2-like domains found in a variety of phage integrase proteins.  Presumably these domains are DNA-binding.. 
PF14658 efhand_7;<br>
PF14659 Phage integrase, N-terminal SAM-like domain<br>This domain is found in a variety of phage integrase proteins.. 
PF14660 Domain of unknown function (DUF4458)<br>this domain is found in tandem repeats on the N-terminus of secreted LRR proteins from human associated Bacteroidetes domain boundaries are based on the JCSG solved 3D structure of JCSG target SP16667A (BT_0210). 
PF14661 HAUS augmin-like complex subunit 6 N-terminus<br>This family includes the N-terminus of HAUS augmin-like complex subunit 6. The HAUS augmin-like complex contributes to mitotic spindle assembly, maintenance of chromosome integrity and completion of cytokinesis [1-2].. 
PF14662 Coiled-coil region of CCDC155<br>This is a small family of eukaryotic proteins of unknown function.ThiS is the central coiled-coil region.. 
PF14663 Rapamycin-insensitive companion of mTOR RasGEF_N domain<br>Pfam-B_389 (release 26.0). Rictor appears to serve as a scaffolding protein that is important for maintaining mTORC2 integrity. The mammalian target of rapamycin (mTOR) is a conserved Ser/Thr kinase that forms two functionally distinct complexes, mTROC1 and mTORC2, important for nutrient and growth-factor signalling. This region is the more conserved central section that may include several individual domains. Rictor can be inhibited in the short-term by rapamycin.. 
PF14664 Rapamycin-insensitive companion of mTOR, N-term<br>Pfam-B_389 (release 26.0). Rictor appears to serve as a scaffolding protein that is important for maintaining mTORC2 integrity. The mammalian target of rapamycin (mTOR) is a conserved Ser/Thr kinase that forms two functionally distinct complexes, mTROC1 and mTORC2, important for nutrient and growth-factor signalling. This region is the N-terminal conserved section that may include several individual domains. Rictor can be inhibited in the short-term by rapamycin.. 
PF14665 Rapamycin-insensitive companion of mTOR, phosphorylation-site<br>Pfam-B_389 (release 26.0). Rictor appears to serve as a scaffolding protein that is important for maintaining mTORC2 integrity. The mammalian target of rapamycin (mTOR) is a conserved Ser/Thr kinase that forms two functionally distinct complexes, mTROC1 and mTORC2, important for nutrient- and growth-factor signalling. This short region is the phoshorylation site.  Rictor does interact with 14-3-3 in a Thr1135-dependent manner. Rictor can be inhibited by short-term rapamycin treatment showing that Thr1135 is an mTORC1-regulated site.. 
PF14666 Rapamycin-insensitive companion of mTOR, middle domain<br>Pfam-B_389 (release 26.0). Rictor appears to serve as a scaffolding protein that is important for maintaining mTORC2 integrity. The mammalian target of rapamycin (mTOR) is a conserved Ser/Thr kinase that forms two functionally distinct complexes, mTROC1 and mTORC2, important for nutrient and growth-factor signalling. This region is the more conserved central section that may include several individual domains. Rictor can be inhibited in the short-term by rapamycin.. 
PF14667 Polysaccharide biosynthesis C-terminal domain<br>This family represents the C-terminal integral membrane region of polysaccharide biosynthesis proteins.. 
PF14668 Rapamycin-insensitive companion of mTOR, domain 5<br>Pfam-B_389 (release 26.0). Rictor appears to serve as a scaffolding protein that is important for maintaining mTORC2 integrity. The mammalian target of rapamycin (mTOR) is a conserved Ser/Thr kinase that forms two functionally distinct complexes, mTROC1 and mTORC2, important for nutrient and growth-factor signalling. These long eukaryotic proteins carry several well-conserved domains, and this is No.5.. 
PF14669 Putative aspartate racemase<br>Pfam-B_34791 (release 26.0). This is a small family of vertebrate putative aspartate racemases. The family lies on TOPAZ 1 proteins.. 
PF14670 Coagulation Factor Xa inhibitory site<br>Jackhmmer CATH:3kl6_B_0. This short domain on coagulation enzyme factor Xa is found to be the target for a potent inhibitor of coagulation, TAK-442  .. 
PF14671 Dual specificity protein phosphatase, N-terminal half<br>Jackhmeer:CATH:1ohe_A_01. The active core of the dual specificity protein phosphatase is made up of two globular domains both with the DSP-like fold. This family represents the N-terminal half of the core. These domains are arranged in tandem, and are associated via an extensive interface to form a single globular whole. The conserved PTP signature motif (Cys-[X]5-Arg) that defines the catalytic centre of all PTP-family members is located within the C-terminal domain, family DSPc, Pfam:PF00782. Although the centre of the catalytic site is formed from DSPc, two loops from the N-terminal domain, DSPn, also contribute to the catalytic site, facilitating peptide substrate specificity  .. 
PF14672 Late cornified envelope <br>This is a family of late cornified envelope proteins that are expressed in skin  .. 
PF14673 Domain of unknown function (DUF4459)<br>Pfam-B_10980 (release 26.0). This family appears only on sequences from Salmonella spp.  These sequences also all carry a YARHG domain, Pfam:PF13308.. 
PF14674 FANCI solenoid 1 cap<br>This is the solenoid 1 cap (S1-cap) domain of the Fanconi anemia group I protein  .. 
PF14675 FANCI solenoid 1<br>This is the solenoid 1 (S1) domain of the Fanconi anemia group I protein  .. 
PF14676 FANCI solenoid 2<br>This is the solenoid 2 (S2) domain of the Fanconi anemia group I protein  .. 
PF14677 FANCI solenoid 3<br>This is the solenoid 3 (S3) domain of the Fanconi anemia group I protein  .. 
PF14678 FANCI solenoid 4<br>This is the solenoid 4 (S4) domain of the Fanconi anemia group I protein  .. 
PF14679 FANCI helical domain 1<br>This is the helical domain 1 (HD1) of the Fanconi anemia group I protein  .. 
PF14680 FANCI helical domain 2<br>This is the helical domain 2 (HD2) of the Fanconi anemia group I protein  .. 
PF14681 Uracil phosphoribosyltransferase<br>This family includes the enzyme uracil phosphoribosyltransferase (EC:2.4.2.9). This enzyme catalyzes the first step of UMP biosynthesis.. 
PF14682 Sporulation initiation phospho-transferase B, C-terminal<br>Sporulation initiation phospho-transferase B or SpoOB is part of a phospho-relay that initiates sporulation in Bacillus subtilis. Spo0B is a two-domain protein consisting of an N-terminal alpha-helical hairpin domain and a C-terminal alpha/beta domain, represented by this family. Two subunits of Spo0B dimerise by a parallel association of helical hairpins to form a novel four-helix bundle from which the active histidine - involved in the auto-phosphorylation - protrudes. In the phospho-relay, the signal-receptor histidine kinases are dephosphorylated by a common response regulator, Spo0F. Spo0B then takes phosphorylated Spo0F as substrate hereby mediating the transfer of a phosphoryl group to Spo0A, the ultimate transcription factor.. 
PF14683 Polysaccharide lyase family 4, domain III<br>CBM-like is domain III of rhamnogalacturonan lyase (RG-lyase). The full-length protein specifically recognises and cleaves alpha-1,4 glycosidic bonds between l-rhamnose and d-galacturonic acids in the backbone of rhamnogalacturonan-I, a major component of the plant cell wall polysaccharide, pectin. This domain possesses a jelly roll beta-sandwich fold structurally homologous to carbohydrate binding modules (CBMs), and it carries two sulfate ions and a hexa-coordinated calcium ion.. 
PF14684 Tricorn protease C1 domain<br>This domain is the C1 core domain of tricorn protease. This is a mixed alpha-beta domain  .. 
PF14685 Tricorn protease PDZ domain<br>This domain is the PDZ domain of tricorn protease  .. 
PF14686 Polysaccharide lyase family 4, domain II<br>FnIII-like is domain II of rhamnogalacturonan lyase (RG-lyase). The full-length protein specifically recognises and cleaves alpha-1,4 glycosidic bonds between l-rhamnose and d-galacturonic acids in the backbone of rhamnogalacturonan-I, a major component of the plant cell wall polysaccharide, pectin. This domain displays an immunoglobulin-like or more specifically Fibronectin-III type fold and shows highest structural similarity to the C-terminal beta-sandwich subdomain of the pro-hormone/propeptide processing enzyme carboxypeptidase gp180 from duck. It serves to assist in producing the deep pocket, with domain III, into which the substrate fits  .. 
PF14687 Domain of unknown function (DUF4460)<br>This domain family is found in eukaryotes, and is typically between 103 and 119 amino acids in length. There is a conserved HPD sequence motif. There are two completely conserved residues (N and F) that may be functionally important.. 
PF14688 Domain of unknown function (DUF4461)<br>This domain family is found in eukaryotes, and is approximately 310 amino acids in length.. 
PF14689 Sensor_kinase_SpoOB-type, alpha-helical domain<br>Sporulation initiation phospho-transferase B or SpoOB is part of a phospho-relay that initiates sporulation in Bacillus subtilis. Spo0B is a two-domain protein consisting of an N-terminal alpha-helical hairpin domain and a C-terminal alpha/beta domain. Two subunits of Spo0B dimerise by a parallel association of helical hairpins to form a novel four-helix bundle from which the active histidine - involved in the auto-phosphorylation - protrudes. In the phospho-relay, the signal-receptor histidine kinases are dephosphorylated by a common response regulator, Spo0F. Spo0B then takes phosphorylated Spo0F as substrate thereby mediating the transfer of a phosphoryl group to Spo0A, the ultimate transcription factor. The exact function of this alpha-helical domain is not known; it does not always occur just as the N-terminal domain of SPOB_ab, Pfam:PF14682. SCOP describes this domain as a histidine kinase-like fold lacking the kinase ATP-binding site.. 
PF14690 zinc-finger of transposase IS204/IS1001/IS1096/IS1165<br>
PF14691 Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster<br>Domain II of the enzyme dihydroprymidine dehydrogenase binds FAD. Dihydroprymidine dehydrogenase catalyses the first and rate-limiting step of pyrimidine degradation by converting pyrimidines to the corresponding 5,6- dihydro compounds  . This domain carries two Fe4-S4 clusters.. 
PF14692 Domain of unknown function (DUF4462)<br>This domain family is found in eukaryotes, and is approximately 30 amino acids in length.. 
PF14693 ShortName;<br>Ribosomal protein TL5, C-terminal domain. This family contains the C-terminal domain of ribosomal protein TL5. The N-terminal domain, which binds to 5S rRNA, is contained in family Ribosomal_L25p, Pfam:PF01386. Full length (N- and C-terminal domain) homologues of TL5 are also known as CTC proteins. TL5 or CTC are not found in Eukarya or Archaea. In some Bacteria, including E. coli, this ribosomal subunit occurs as a single domain protein (named Ribosomal subunit L25), where the only domain is homologous to TL5 N-terminal domain (hence included in family Pfam:PF01386). The function of the C-terminal domain of TLC is at present unknown.. 
PF14694 Lines N-terminus<br>This family represents the N-terminus of protein lines  . In Drosophila this protein is involved in embryonic segmentation and may function as a transcriptional regulator [2-3].. 
PF14695 Lines C-terminus<br>This family represents the C-terminus of protein lines  . In Drosophila this protein is involved in embryonic segmentation and may function as a transcriptional regulator [2-3].. 
PF14696 Hydroxyphenylpyruvate dioxygenase, HPPD, N-terminal <br>This domain is one of two barrel-shaped regions that together form the active enzyme, 4-hydroxyphenylpyruvic acid dioxygenase, EC:1.13.11.27. As can be deduced from the disposition of the various Glyoxalase families, _2, _3 and _4 in Pfam, Pfam:PF00903, Pfam:PF12681, Pfam:PF13468, Pfam:PF13669, these two regions are similar to be indicative of a gene-duplication event. At the individual sequence level slight differences in conformation have given rise to slightly different functions. In the case of UniProt:P80064, 4-hydroxyphenylpyruvic acid dioxygenase catalyses the formation of homogentisate from 4-hydroxyphenylpyruvate, and the pyruvate part of the HPPD substrate (4-hydroxyphenylpyruvate), derived from L-tyrosine, and the O2 molecule occupy the three free coordination sites of the catalytic iron atom in the C-terminal domain. In plants and photosynthetic bacteria, the tyrosine degradation pathway is crucial because homogentisate, a tyrosine degradation product, is a precursor for the biosynthesis of photosynthetic pigments, such as quinones or tocopherols  .. 
PF14697 4Fe-4S dicluster domain<br>Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases.  Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters.. 
PF14698 Argininosuccinate lyase C-terminal<br>This domain is found at the C-terminus of argininosuccinate lyase [1-2].. 
PF14699 N-terminal domain from the human glycogen debranching enzyme<br>Jcakhammer:GDE_HUMAN. this domain is found on the very N-terminal of eukaryotic variant\.      of the glycogen debranching enzyme (GDE), where it is immediately  followe by the aldolase-like domain. The eukaryotic GDE performs  two functions: 4-α-D-glucanotransferase (EC 2.4.1.25) and  Amylo-α-1,6-glucosidase (EC 3.2.1.33), performed by the,  respectively N- and C- terminal halfs of eukaryotic GDE enzyme hGDE_N domain is involved in the glucosyltransferase activity,  probably\.     as a substrate binding module (by analogy to other  glucosyltransferases). 
PF14700 DNA-directed RNA polymerase N-terminal<br>This is the N-terminal domain of DNA-directed RNA polymerase. This domain has a role in interaction with regions of upstream promoter DNA and the nascent RNA chain, leading to the processivity of the enzyme  . In order to make mRNA transcripts the RNA polymerase undergoes a transition from the initiation phase (which only makes short fragments of RNA) to an elongation phase. This domain undergoes a structural change in the transition from initiation to elongation phase. The structural change results in abolition of the promoter binding site, creation of a channel accommodating the heteroduplex in the active site and formation of an exit tunnel which the RNA transcript passes through after peeling off the heteroduplex  .. 
PF14701 glucanotransferase domain of human glycogen debranching enzyme<br>Jackhammer:GDE_HUMAN. this is a glucanotransferase catalytic domain of the eukaryotic  variant of the glycogen debranching enzyme (GDE).\. The eukaryotic GDEs performs two functions: 4-α-D-glucanotransferase  (EC 2.4.1.25) and Amylo-α-1,6-glucosidase (EC 3.2.1.33),\. performed by the, respectively N- and C- terminal halfs of  eukaryotic GDE enzymes. hDGE_amylase domain is a catalytic domain responsible for the glucanotransferase function. It belongs to the  alpha-amylase clan and is predicted to have a structure of a 8  stranded alpha/beta barrel (TIM barreal) where strands are  interuppted by long loops and additional mini-domains. In most other amylases, the catalytic domain is followed by a beta- barrel substrate binding domain, but presence of such domain cannot  be verified in the human (and other eukaryotic) GDE enzymes. 
PF14702 central domain of human glycogen debranching enzyme<br>Jackhammer:GDE_HUMAN. this is a central domain of the eukaryotic variant      of the glycogen debranching enzyme (GDE). The eukaryotic GDE performs   two functions: 4-α-D-glucanotransferase (EC 2.4.1.25) and  Amylo-α-1,6-glucosidase (EC 3.2.1.33), performed by the,  respectively N- and C- terminal halfs of eukaryotic GDE enzyme The hGDE_central domain follows the glucanotransferas domain and  precedes the glucosidase (GDE_N) domain. It is very likely that the current definition contains two or more domains, by analogy  with baterial GDEs, this domain should be involved in substrate  binding either for the N-terminal glucanotransferase  and/or the the C-terminal glucosidase (or both) . 
PF14703 Domain of unknown function (DUF4463)<br>This is a cytosolic (predicted) domain present in integral membrane  proteins, such as TM63C_HUMAN TRANSMEMBRANE PROTEIN 63C. This domain usually preceeds a DUF221 (PF02714)domain and follows  a RSN1_TM (PF13967) Fold recognition programs consistenly and with high significance  predict this domain to be distantly homologous to RNA binding  proteins from the RRM clan.. 
PF14704 Dermatopontin<br>Members of this family mediate cell adhesion via cell surface integrin binding  . They also induce haemagglutination and aggregation of amebocytes [2-3].. 
PF14705 Costars<br>This domain is found both alone and at the C-terminus of actin-binding Rho-activating protein (ABRA). It binds to actin, and in muscle regulates the actin cytoskeleton and cell motility [1-2]. It has a winged helix-like fold consisting of three alpha-helices and four antiparallel beta strands. Unlike typical winged helix proteins it does not bind to DNA, but contains a hydrophobic groove which may be responsible for interaction with other proteins  .. 
PF14706 Transposase DNA-binding<br>This domain occurs at the C-terminus of transposases including E. coli tnpA (Swiss:Q46731). TnpA encodes a transposase and an inhibitor protein, the inhibitor only differs from the transposase by the absence of the N-terminal 55 amino acids, which includes most of this domain  . This domain consists of alpha helices and turns, and functions as a DNA-binding domain  .. 
PF14707 C-terminal region of aryl-sulfatase<br>
PF14709 double strand RNA binding domain from DEAD END PROTEIN 1<br>A C-terminal domain in human dead end protein 1 (DND1_HUMAN) homologous to double strand RNA binding domains (PF00035, PF00333)   . 
PF14710 Respiratory nitrate reductase alpha N-terminal<br>This is the N-terminal tail of the respiratory nitrate reductase alpha chain. The nitrate reductase complex is a dimer of heterotrimers each consisting of an alpha, beta and gamma chain. The N-terminal tail of the alpha chain interacts with the beta chain and contributes to the stability of the heterotrimer  .. 
PF14711 Respiratory nitrate reductase beta C-terminal<br>This domain occurs near the C-terminus of the respiratory nitrate reductase beta chain. The nitrate reductase complex is a dimer of heterotrimers each consisting of an alpha, beta and gamma chain. This domain plays a role in the interactions between subunits and shielding of the Fe-S clusters  . 
PF14712 Snapin/Pallidin<br>This family of proteins includes Snapin, this protein is associated with the SNARE complex, which mediates synaptic vesicle docking and fusion  . It also includes the yeast snapin-like protein SNN1, which is a part of a complex involved in endosomal cargo sorting  . The family also includes pallidin, a component of a complex involved in biogenesis of lysosome-related organelles  .. 
PF14713 Domain of unknown function (DUF4464)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 224 and 241 amino acids in length. There is a conserved YID sequence motif.. 
PF14714 KH-domain-like of EngA bacterial GTPase enzymes, C-terminal<br>The KH-like domain at the C-terminus of the EngA subfamily of essential bacterial GTPases has a unique domain structure position. The two adjacent GTPase domains (GD1 and GD2), two domains of family MMR_HSR1, Pfam:PF01926, pack at either side of the C-terminal domain.  This C-terminal domain resembles a KH domain but is missing the distinctive RNA recognition elements. Conserved motifs of the nucleotide binding site of GD1 are integral parts of the GD1-KH domain interface, suggesting the interactions between these two domains are directly influenced by the GTP/GDP cycling of the protein. In contrast, the GD2-KH domain interface is distal to the GDP binding site of GD2.. 
PF14715 N-terminal domain of cytochrome oxidase-cbb3, FixP <br>Pfam-B_28684 (release 26.0). This is the N-terminal domain of FixP, the cytochrome oxidase type-cbb3. the exact function is not known.. 
PF14716 Helix-hairpin-helix domain<br>
PF14717 Domain of unknown function (DUF4465)<br>JCSG structure SP13250B. A large family of uncharacterized proteins mostly from  human gut bacteroides, but also some environmental  and water bacteria (Planctomycetes) as well as  metagenomic samples Most proteins from this family are secreted or  located on the outer surface and may participate  in cell-cell interactions or cell-nutrient interactions This function is supported by a solved structure of a Bacteroides ovatus homolog, which adapts a galactose binding (jelly-roll) beta barrel structure. 
PF14718 Soluble lytic murein transglycosylase L domain<br>Soluble lytic murein transglycosylase (SLT) consists of three domains, an N-terminal U domain, an L domain (linker domain) and a C-terminal domain (C). The L domain may be involved in the interaction of the enzyme with peptidoglycan  .. 
PF14719 Phosphotyrosine interaction domain (PTB/PID)<br>
PF14720 NiFe/NiFeSe hydrogenase small subunit C-terminal<br>This domain is found at the C-terminus of hydrogenase small subunits including periplasmic [NiFeSe] hydrogenase small subunit, uptake hydrogenase small subunit and periplasmic [NiFe] hydrogenase small subunit. This C-terminal domain binds two of the three iron-sulfur clusters in this enzyme [1-3].. 
PF14721 Apoptosis-inducing factor, mitochondrion-associated, C-term<br>Jackhmmer:JCSG-Target_422903. This C-terminal domain appears to be a dimerisation domain of the mitochondrial apoptosis-inducing factor 1.  protein. The domain also appears at the C-terminus of FAD-dependent pyridine nucleotide-disulfide oxidoreductases. Apoptosis inducing factor (AIF) is a bifunctional mitochondrial flavoprotein critical for energy metabolism and induction of caspase-independent apoptosis. On reduction with NADH, AIF undergoes dimerisation and forms tight, long-lived FADH2-NAD charge-transfer complexes proposed to be functionally important.. 
PF14722 SSFA2_N;<br>Ki-ras-induced actin-interacting protein-IP3R-interacting domain. This family includes the N-terminus of the actin-interacting protein sperm-specific antigen 2, or KRAP (Ki-ras-induced actin-interacting protein)  .  This region is found to be the residues that interact with inositol 1,4,5-trisphosphate receptor (IP3R). KRAP was first localised as a membrane-bound form with extracellular regions suggesting it might be involved in the regulation of filamentous actin and signals from the outside of the cells  . It has now been shown to be critical for the proper subcellular localisation and function of IP3R. Inositol 1,4,5-trisphosphate receptor functions as the Ca2+ release channel on specialised endoplasmic reticulum membranes, so the subcellular localisation of IP3R is crucial for its proper function  .. 
PF14723 Sperm-specific antigen 2 C-terminus<br>This family includes the C-terminus of the actin-interacting protein sperm-specific antigen 2  .. 
PF14724 Mitochondrial-associated sphingomyelin phosphodiesterase<br>The GO annotation for this family indicates that it is a single-pass membrane protein, and it appears to be found in mitochondrial membranes. Sphingolipids play important roles in regulating cellular responses, and although mitochondria contain sphingolipids, direct regulation of their levels in mitochondria or mitochondria-associated membranes is mostly unclear. Sphingomyelin phosphodiesterases catalyse the hydrolysis of sphingomyelin to ceramide and phosphocholine, and these metabolites are involved in signalling pathways.. 
PF14725 Domain of unknown function (DUF4466)<br>Jackhmmer-JCSG:target_419245-SP18803A. 
PF14726 Rotatin, an armadillo repeat protein, centriole functioning <br>Pfma-B_645 (release 26.0). Rotatin and its homologues such as Ana3 in Drosophila are found to be essential for centriole function  . A deficiency of rotatin in mice leads to randomised heart tube looping, defects in embryonic turning  , and abnormal expression of HNF3beta, lefty, and nodal. Thus it is required for left-right and axial patterning. Ana3 - the Drosophila homologue - is present in centrioles and basal bodies, is required for the structural integrity of both centrioles and basal bodies and for centriole cohesion. Rotatin also localises to centrioles and basal bodies and appears to be essential for cilia function  . This family represents the N-terminal domain.. 
PF14727 PTHB1 N-terminus<br>This family includes the N-terminus of PTHB1 protein. This protein forms a part of the BBSome complex, which is required for ciliogenesis  .. 
PF14728 PTHB1 C-terminus<br>This family includes the C-terminus of PTHB1 protein. This protein forms a part of the BBSome complex, which is required for ciliogenesis  .. 
PF14729 Domain of unknown function with cystatin-like fold (DUF4467) <br>JCSG target SP18127A; Pfam-B_491 (release 26.0). Large family of predicted lipoproteins from Gram-positive bacteria Experimentally determined structure shows a cystatitin-like fold, allowing us to classify this family in the NFT2 clan, despite lack of any detectable sequence similarity between members of this family and other families in this clan. 
PF14730 Domain of unknown function (DUF4468) with TBP-like fold<br>Jackhammer: JCSG target SP13279C. A large family of (predicted) secreted proteins with unknown functions from human gut and oral cavity.\. Typically forms a N-terminal domain with FMN binding  domain at the C-terminus. Experimentaly determined 3D structure of this domain shows a variant of a TATA box binding - like fold, but no detectable  sequence similarity to other proteins with this fold. 
PF14731 Staphopain proregion<br>This domain is the proregion of the cysteine protease staphopain. Like many papain type peptidases, staphopain is synthesised as an inactive precursor and cleavage of the proregion is required for activation. This proregion has a half-barrel or barrel-sandwich hybrid fold. The proregion blocks the active site cleft of the mature enzyme on one side of the nucleophilic cysteine  . 
PF14732 Ubiquitin/SUMO-activating enzyme ubiquitin-like domain<br>This is the C-terminal domain of ubiquitin-activating enzyme and SUMO-activating enzyme 2. It is structurally similar to ubiquitin. This domain is involved in E1-SUMO-thioester transfer to the SUMO E2 conjugating protein  .. 
PF14733 AP2-coincident C-terminal<br>Woodcroft B, Eberhardt R. This family is found at the C-terminus of apicomplexan proteins containing the AP2 domain (Pfam:PF00847).. 
PF14734 Domain of unknown function (DUF4469) with IG-like fold<br>Jackhammer:JCSG target GS13689A. A C-terminal domain in a large family of (predicted) secreted proteins with uknown functions from human gut bacteroides. 
PF14735 HAUS augmin-like complex subunit 4<br>This family includes HAUS augmin-like complex subunit 4. The HAUS augmin-like complex contributes to mitotic spindle assembly, maintenance of chromosome integrity and completion of cytokinesis [1-2].. 
PF14736 N_Asn_aminohyd;<br>Protein N-terminal asparagine amidohydrolase. This family of enzymes catalyse the deamindation of N-terminal asparagines in peptides and proteins to aspartic acid [1-2].. 
PF14737 Domain of unknown function (DUF4470)<br>This family is conserved from fungi to Metazoa and includes plants.  The function is not known, but several members have zinc-finger domain, zf-MYND, Pfam:PF01753, at their very C-terminus. Others are also associated with DUF1279, Pfam:PF06916.. 
PF14738 Solute carrier (proton/amino acid symporter), TRAMD3 or PAT1<br>PAT1 (proton amino acid transporter 1), also known as TRAMD3 of AAT-1, is the molecular correlate of the intestinal imino acid carrier. It is a proton-amino acid co-transporter having a stoichiometry of 1:1. Due to its mechanism, PAT1 activity increases at acidic pH, which correlates well with the acidic micro-climate close to the brush-border in the intestine. Glycine, proline, and alanine are the preferred substrates of the transporter. The maximum velocity is similar for the three substrates. All substrates are transported with low affinity, showing Km values in the range of 2-10 mM. The transporter does not discriminate between L- and D-isoforms of these amino acids; in addition, beta-alanine is transported with similar affinity as alpha-alanine. Similar to the IMINO transporter, the amino acid analog MeAIB is recognized by PAT1. The transporter is strongly expressed in the small intestine, colon, kidney, and brain.. 
PF14739 Domain of unknown function (DUF4472)<br>This family is specific to the Chordates. Some members also carry Kinesin-motor domains at their N-terminus, Kinesin, Pfam:PF00225.. 
PF14740 Domain of unknown function (DUF4471)<br>This family is conserved from fungi to Metazoa and includes plants.  The function is not known, but several members have zinc-finger domain, zf-MYND, Pfam:PF01753, at their very C-terminus. Others are also associated with DUF1279, Pfam:PF06916. This domain is more C-terminal in many members to DUF4470, Pfam:PF14737.. 
PF14741 N-terminal glycosyl-hydrolase-114-associated domain<br>Naumoff D, Coggill P. This short domain is also a very small family found at the N-terminus of GH114, glycosyl-hydrolases.. 
PF14742 N-terminal domain of (some) glycogen debranching enzymes<br>Jackhammer:YP_001865398. This domain is found on the N-terminal of some glycogen debranching  enzymes and is usually followed by the GDE_C (PF06202) and in this  sense it is analogous (but probably not homologous) to the GDE_N  (PF12439). Its exact function is unknown. 
PF14743 DNA ligase OB-like domain<br>This domain has an OB-like fold, but does not appear to be related to Pfam:PF03120. It is found at the C-terminus of the ATP dependent DNA ligase domain Pfam:PF01068 [1-3].. 
PF14744 WASH complex subunit 7<br>This family is the central, conserved region of proteins that form subunit 7 of the WASH complex  . In species such as Drosophila this protein is the only component of the 'complex'. This complex is a nucleation promoting factor necessary for the activation of Arp2/3 that nucleates and organises actin filaments by associating with a pre-existing filament to induce the assembly of a branching filament.  WASH thus effectively nucleates actin on endosomes  .. 
PF14745 WASH complex subunit 7, N-terminal<br>This family is the conserved N-terminal region of proteins that form subunit 7 of the WASH complex  . In species such as Drosophila this protein is the only component of the 'complex'. This complex is a nucleation promoting factor necessary for the activation of Arp2/3 that nucleates and organises actin filaments by associating with a pre-existing filament to induce the assembly of a branching filament.  WASH thus effectively nucleates actin on endosomes  .. 
PF14746 WASH complex subunit 7, C-terminal<br>This family is the conserved C-terminal region of proteins that form subunit 7 of the WASH complex  . In species such as Drosophila this protein is the only component of the 'complex'. This complex is a nucleation promoting factor necessary for the activation of Arp2/3 that nucleates and organises actin filaments by associating with a pre-existing filament to induce the assembly of a branching filament.  WASH thus effectively nucleates actin on endosomes  . The C-terminus is predicted to include a transmembrane region.. 
PF14747 Domain of unknown function (DUF4473)<br>Pfam-B_8489 (release 26.0). This short family is largely confined to Caenorhabditis proteins. The function is not known. There are two well-conserved aspartate residues.. 
PF14748 Pyrroline-5-carboxylate reductase dimerisation<br>Pyrroline-5-carboxylate reductase consists of two domains, an N-terminal catalytic domain (Pfam:PF03807) and a C-terminal dimerisation domain. This is the dimerisation domain  .. 
PF14749 Acyl-coenzyme A oxidase N-terminal<br>Acyl-coenzyme A oxidase consists of three domains. An N-terminal alpha-helical domain, a beta sheet domain (Pfam:PF02770) and a C-terminal catalytic domain (Pfam:PF01756). This entry represents the N-terminal alpha-helical domain  .. 
PF14750 Integrator complex subunit 2<br>This family of proteins are subunits of the integrator complex involved in snRNA transcription and processing  .. 
PF14751 Domain of unknown function (DUF4474)<br>Jackhmmer:JCSG target SP18061A. Domain found on N-termina of few families of uncharacterized  Clostridia proteins. Typically followed by a proline-rich domain  or other kinds of repeats. 
PF14752 Retinol binding protein receptor<br>Proteins in this family function as retinol binding protein receptors  .. 
PF14753 Domain of unknown function (DUF4475)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 99 and 305 amino acids in length.. 
PF14754 PPRSV-IRF3_ant;<br>Papain-like auto-proteinase. Pfam-B_8065 (release 26.0). The replicase polyproteins of the Nidoviruses such as, porcine arterivirus PRRSV, equine arterivirus EAV, human coronavirus 229E, and severe acute respiratory syndrome coronavirus (SARS-CoV), are predicted to be cleaved into 14 non-structural proteins (nsps) by the nsp4 main proteinase Pfam:PF05579 and three accessory proteinases residing in nsp1-alpha, nsp1-beta and nsp2. This family is the two nsp1 proteins that together act in a papain-like way to separate off the rest of the various functional domains of the polyprotein. Once inside the host cell, this nsp1 interferes with the regulation of interferon, thereby enabling the virus to replicate.. 
PF14755 Intracellular membrane remodeller <br>Pfam-B_2813 (release 26.0). This domain represents subunit nsp3 of the RNA-arteriviruses, such as porcine arterivirus PRRSV and equine arterivirus EAV, and is a tetraspanning transmembrane protein that contains a cluster of four highly conserved cysteine residues. These are predicted to reside in the first luminal domain of the protein. Arterivirus nsp3 proteins are uniformly predicted to contain four transmembrane helices, with the N and C termini of the protein residing in the cytoplasm. NSP3 are localised to the ER and appear to be essential for formation of double-membrane vesicles that originate from the ER during the life-cycle of the virus.. 
PF14756 Peptidase_C33-associated domain<br>Pfam-B_535 (release 26.0). The nsps or non-structural protein subunits of the arteriviral polyproteins such as porcine arterivirus PRRSV and equine arterivirus EAV are auto-cleaved into functional units. the function of this particular domain is not known.. 
PF14757 Immunogenic region of nsp2 protein of arterivirus polyprotein<br>Pfam-B_58 (release 26.0). This domain is in a non-essential part of the nsp2 (non-structural protein) subunit section of the arterivirus polyprotein. This domain carries seven small sequence-regions that are predicted to be potential B-cell epitopes.. 
PF14758 Non-essential region of nsp2 of arterivirus polyprotein <br>Pfam-B_6704 (release 26.0) . This non-essential region of the nsp2 subunit of the arterivirus polyprotein of such as porcine arterivirus PRRSV and equine arterivirus EAV may offer immunogneic surfaces to B-cells. It is associated with Peptidase_C33, Pfam:PF05412.. 
PF14759 Reductase C-terminal<br>This domain occurs at the C-terminus of various reductase enzymes, including putidaredoxin reductase, ferredoxin reductase, 3-phenylpropionate/cinnamic acid dioxygenase ferredoxin--NAD(+) reductase component, benzene 1,2-dioxygenase system ferredoxin--NAD(+) reductase subunit, rhodocoxin reductase, biphenyl dioxygenase system ferredoxin--NAD(+) reductase component, rubredoxin-NAD(+) reductase and toluene 1,2-dioxygenase system ferredoxin--NAD(+) reductase component. In putidaredoxin reductase this domain is involved in dimerisation  . In the FAD-containing NADH-ferredoxin reductase (BphA4) it is responsible for interaction with the Rieske-type [2Fe-2S] ferredoxin (BphA3)  .. 
PF14760 Rnk N-terminus<br>This domain occurs at the N-terminus of Rnk, an RNA polymerase-interacting protein of the GreA/GreB family (Pfam:PF01272). It has a coiled coil structure  .. 
PF14761 Hermansky-Pudlak syndrome 3<br>This domain is at the N-terminus of these vertebrate proteins. This region carries the clathrin-binding motif LLDFE at residues 172-176 in SwissProt:Q969F9. There is also reference to a human Mendelian disease at MIM:614072  .. 
PF14762 Hermansky-Pudlak syndrome 3, middle region<br>This domain is downstream of the N-terminus of these vertebrate proteins. This region carries a number of tyrosine sorting motifs and one of two di-leucine sorting boxes at residues 542-548 well as a peroxisomal matrix targetting motif at residues 614-623 in SwissProt:Q969F9. There is also reference to a human Mendelian disease at MIM:614072  .. 
PF14763 Hermansky-Pudlak syndrome 3, C-terminal<br>This domain is downstream of the mid domain family, Pfam:PF14762, of these vertebrate proteins. This region carries a number of tyrosine sorting motifs and the second of two di-leucine sorting boxes at residues 711-717 well as the ER membrane-retention signal KKPL at residues 1000-1003 in SwissProt:Q969F9. There is also reference to a human Mendelian disease at MIM:614072  .. 
PF14764 AP-5 complex subunit, vesicle trafficking<br>This family would appear to be the second of the two larger subunits of the fifth Adaptor-Protein complex, AP-5. Adaptor protein (AP) complexes facilitate the trafficking of cargo from one membrane compartment of the cell to another by recruiting other proteins to particular types of vesicles. AP-5 is involved in trafficking proteins from endosomes towards other membranous compartments  . There are genetic links between AP-5 and hereditary spastic paraplegia, a group of human genetic disorders characterised by progressive spasticity in the lower limbs  .. 
PF14765 Polyketide synthase dehydratase<br>Pfam-B_852 (release 26.0). This is the dehydratase domain of polyketide synthases  . Structural analysis shows these DH domains are double hotdogs in which the active site contains a histidine from the N-terminal hotdog and an aspartate from the C-terminal hotdog. Studies have uncovered that a substrate tunnel formed between the DH domains may be essential for loading substrates and unloading products  .. 
PF14766 Replication protein A interacting N-terminal<br>This family of proteins represents the N-terminal domain of replication protein A (RPA) interacting protein.  RPA interacting protein is involved in the import of RPA into the nucleus. The N-terminal domain is responsible for interaction with importin beta [1-2].. 
PF14767 Replication protein A interacting middle<br>This family of proteins represents the middle domain of replication protein A (RPA) interacting protein.  RPA interacting protein is involved in the import of RPA into the nucleus. This domain is responsible for interaction with RPA [1-2].. 
PF14768 Replication protein A interacting C-terminal<br>This family of proteins represents the C-terminal domain of replication protein A (RPA) interacting protein.  RPA interacting protein is involved in the import of RPA into the nucleus. The C-terminal domain is a putative zinc finger [1-2].. 
PF14769 Flagellar C1a complex subunit C1a-32<br>Jackhmmer:Q6P047, Pfam-B_2704 (release26.0). This family represents one small subunit, C1a-32, of the C1a projection (the seventh projection of flagellar)  . Numerous studies have indicated that each of the seven projections associated with the central pair of microtubules in flagellar plays a distinct role in regulating eukaryotic ciliary/flagellar motility. The C1a projection is a complex of proteins including PF6, C1a-86, C1a-34, C1a-32, C1a-18, and calmodulin. C1a projection is involved in modulating flagellar beat frequency and this is mediated via the C1a-34, C1a-32, and C1a-18 sub-complex by modulating the activity of both the inner and outer dynein arms  .. 
PF14770 Transmembrane protein 18<br>The function of this family is not known, however it is predicted to be a three-pass membrane protein.. 
PF14771 Domain of unknown function (DUF4476)<br>
PF14772 Sperm tail<br>NYD-SP28 is expressed in a development-dependent manner, localised in spermatogenic cell cytoplams and human spermatozoa tail.  It is post-translationally modified during sperm capacitation and ultimately contributes to the success of fertilisation  .. 
PF14773 Helicase-associated putative binding domain, C-terminal<br>Jackhmmer:A4D997, Pfam-B_8865 (release 26.0). The function of this short, serine-rich C-terminal region is not known. However, as it is frequently found at the very C-terminus of P-loop containing nucleoside triphosphate hydrolases, it might possibly be a binding domain.. 
PF14774 FAM177 family<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 134 and 205 amino acids in length.. 
PF14775 Sperm tail C-terminal domain<br>NYD-SP28 is expressed in a development-dependent manner, localised in spermatogenic cell cytoplams and human spermatozoa tail.  It is post-translationally modified during sperm capacitation and ultimately contributes to the success of fertilisation  . This short region is found at the very C-terminus of family members of family NYD-SP28, Pfam:PF14772.. 
PF14776 Cation-channel complex subunit UNC-79<br>This family is a component of a cation-channel complex.. 
PF14777 Cilia BBSome complex subunit 10<br>Jackhmmer:A8MTZ0, Pfam-B_35417 (release 26.0). The BBSome (so-named after the association with Bardet-Biedl syndrome) is a complex of 8 subunits that lies at the base of the flagellar microtubule structure. The precise function of the all the individual components in cilia formation is unclear, however they function to promote loading of cargo to the ciliary axoneme  . BBIP10 localises to the primary cilium, and is present exclusively in ciliated organisms. It is required for cytoplasmic microtubule polymerisation and acetylation, two functions not shared with any other BBSome subunits. BBIP10 physically interacts with HDAC6. BBSome-bound BBIP10 may therefore function to couple acetylation of axonemal microtubules and ciliary membrane growth  . The primary cilium, a slim microtubule-based organelle that projects from the surface of vertebrate cells has crucial roles in vertebrate development and human genetic diseases. Cilia are required for the response to developmental signals, and evidence is accumulating that the primary cilium is specialised for Hedgehog (Hh) signal transduction. Formation of cilia, in turn, is regulated by other signalling pathways, possibly including the planar cell polarity pathway. The connections between cilia and developmental signalling have begun to clarify the basis of human diseases associated with ciliary dysfunction  .. 
PF14778 Olfactory receptor 4-like<br>In C.elegans, odr-4 and odr-8 are required for localising a subset of odorant GPCRs to the cilia of olfactory neurons  . Olfactory receptors (ORs) are synthesised in endoplasmic reticulum of the olfactory neurons, trafficked to the cell surface membrane and transported to the tip of the olfactory cilium, where they bind with odorants. Various accessory proteins are required for proper targetting of different ORs to the cell membrane. ODR-4 was the first accessory protein to be described.. 
PF14779 Ciliary BBSome complex subunit 1<br>The BBSome (so-named after the association with Bardet-Biedl syndrome) is a complex of 8 subunits that lies at the base of the flagellar microtubule structure. The precise function of the all the individual components in cilia formation is unclear, however they function to promote loading of cargo to the ciliary axoneme  . The primary cilium, a slim microtubule-based organelle that projects from the surface of vertebrate cells has crucial roles in vertebrate development and human genetic diseases. Cilia are required for the response to developmental signals, and evidence is accumulating that the primary cilium is specialised for Hedgehog (Hh) signal transduction. Formation of cilia, in turn, is regulated by other signalling pathways, possibly including the planar cell polarity pathway. The connections between cilia and developmental signalling have begun to clarify the basis of human diseases associated with ciliary dysfunction  . BBS1 predominantly localizes to the basal body and or transitional zone of ciliated cells. It has been found in a heptameric complex with BBS2, BBS5, BBS7, BBS8, and BBS9, termed the BBSome. Mutations in BBS1 can lead to retinal inadequacy  .. 
PF14780 Domain of unknown function (DUF4477)<br>Jackhmmer:Q6NW34, Pfam-B_4074 (release 26.0). 
PF14781 Ciliary BBSome complex subunit 2, N-terminal<br>Pfam-B_5448 (release 26.0). The BBSome (so-named after the association with Bardet-Biedl syndrome) is a complex of 8 subunits that lies at the base of the flagellar microtubule structure. The precise function of the all the individual components in cilia formation is unclear, however they function to promote loading of cargo to the ciliary axoneme  . The primary cilium, a slim microtubule-based organelle that projects from the surface of vertebrate cells has crucial roles in vertebrate development and human genetic diseases. Cilia are required for the response to developmental signals, and evidence is accumulating that the primary cilium is specialised for Hedgehog (Hh) signal transduction. Formation of cilia, in turn, is regulated by other signalling pathways, possibly including the planar cell polarity pathway. The connections between cilia and developmental signalling have begun to clarify the basis of human diseases associated with ciliary dysfunction  . BBS2 is one of the three Bardet-Biedl syndrome subunits that is required for leptin receptor signalling in the hypothalamus, and BBS2 and 4 are also required for the localisation of somatostatin receptor 3 and melanin-concentrating hormone receptor 1 into neuronal cilia  .. 
PF14782 Ciliary BBSome complex subunit 2, C-terminal<br>Pfam-B_5884 (release 26.0). The BBSome (so-named after the association with Bardet-Biedl syndrome) is a complex of 8 subunits that lies at the base of the flagellar microtubule structure. The precise function of the all the individual components in cilia formation is unclear, however they function to promote loading of cargo to the ciliary axoneme  . The primary cilium, a slim microtubule-based organelle that projects from the surface of vertebrate cells has crucial roles in vertebrate development and human genetic diseases. Cilia are required for the response to developmental signals, and evidence is accumulating that the primary cilium is specialised for Hedgehog (Hh) signal transduction. Formation of cilia, in turn, is regulated by other signalling pathways, possibly including the planar cell polarity pathway. The connections between cilia and developmental signalling have begun to clarify the basis of human diseases associated with ciliary dysfunction  . BBS2 is one of the three Bardet-Biedl syndrome subunits that is required for leptin receptor signalling in the hypothalamus, and BBS2 and 4 are also required for the localisation of somatostatin receptor 3 and melanin-concentrating hormone receptor 1 into neuronal cilia  .. 
PF14783 Ciliary BBSome complex subunit 2, middle region<br>Pfam-B_5884 (release 26.0). The BBSome (so-named after the association with Bardet-Biedl syndrome) is a complex of 8 subunits that lies at the base of the flagellar microtubule structure. The precise function of the all the individual components in cilia formation is unclear, however they function to promote loading of cargo to the ciliary axoneme  . The primary cilium, a slim microtubule-based organelle that projects from the surface of vertebrate cells has crucial roles in vertebrate development and human genetic diseases. Cilia are required for the response to developmental signals, and evidence is accumulating that the primary cilium is specialised for Hedgehog (Hh) signal transduction. Formation of cilia, in turn, is regulated by other signalling pathways, possibly including the planar cell polarity pathway. The connections between cilia and developmental signalling have begun to clarify the basis of human diseases associated with ciliary dysfunction  . BBS2 is one of the three Bardet-Biedl syndrome subunits that is required for leptin receptor signalling in the hypothalamus, and BBS2 and 4 are also required for the localisation of somatostatin receptor 3 and melanin-concentrating hormone receptor 1 into neuronal cilia  .. 
PF14784 C-terminal domain of the ECSIT protein<br>Jackhammer:Q9BQ95:268-396. This family represents the C-terminal domain of the evolutionarily conserved signaling intermediate in Toll pathway protein, an adapter protein of the Toll-like and IL-1 receptor signaling pathway, which is involved in the activation of NF-kappa-B via MAP3K1. This domain is missing in isoform 2. Fold recognition suggests that this domain may be distantly homologous to the pleckstrin homology domain. 
PF14785 Maltose transport system permease protein MalF P2 domain<br>This is the second periplasmic domain (P2 domain) of the maltose transport system permease protein MalF [1-2].. 
PF14786 DEATH_2;<br>CATH:1d2z_B_00, Pfam-B_14779 (release 26.0). This Tube-Death domain has an insertion between helices 2 and 3, and a C-terminal tail compared with the Death domain of Pelle proteins in Drosophila. The two N-terminal Death domains of the serine/threonine kinase Pelle and the adaptor protein Tube interact to form a six-helix bundle fold arranged in an open-ended linear array with plastic interfaces mediating their interactions. This interaction leads to the nuclear translocation of the transcription factor Dorsal and activation of zygotic patterning genes during Drosophila embryogenesis, and is assisted by the significant and indispensable contacts in the heterodimer contributed by the insertion and C-terminal tail described above  .. 
PF14787 GAG-polyprotein viral zinc-finger<br>
PF14788 EF hand<br>
PF14789 Tetrahydrodipicolinate N-succinyltransferase middle<br>This is the middle domain of 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase  .. 
PF14790 Tetrahydrodipicolinate N-succinyltransferase N-terminal<br>This is the N-terminal domain of 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase  .. 
PF14791 DNA polymerase beta thumb <br>The catalytic region of DNA polymerase beta is split into three domains. An N-terminal fingers domain, a central palm domain and a C-terminal thumb domain. This entry represents the thumb domain  .. 
PF14792 DNA polymerase beta palm <br>The catalytic region of DNA polymerase beta is split into three domains. An N-terminal fingers domain, a central palm domain and a C-terminal thumb domain. This entry represents the palm domain  .. 
PF14793 Domain of unknown function (DUF4478)<br>This domain is found in bacteria, and is approximately 110 amino acids in length. It is found in association with Pfam:PF03641 and Pfam:PF11892.. 
PF14794 Domain of unknown function (DUF4479)<br>This domain family is found in bacteria, and is approximately 70 amino acids in length. The family is found in association with Pfam:PF01588.. 
PF14795 Leucine-tRNA synthetase-specific domain<br>This short region is found only in leucyl-tRNA synthetases. It is flexibly linked to the enzyme-core by beta-ribbons structures  . 
PF14796 Clathrin-adaptor complex-3 beta-1 subunit C-terminal<br>Pfam-B_195384 (release 26.0). This domain lies at the C-terminus of the clathrin-adaptor protein complex-3 beta-1 subunit. The AP-3 complex is associated with the Golgi region of the cell as well as with more peripheral structures. The AP-3 complex may be directly involved in trafficking to lysosomes or alternatively it may be involved in another pathway, but that mis-sorting in that pathway may indirectly lead to defects in pigment granules  .. 
PF14797 Serine-rich region of AP3B1, clathrin-adaptor complex<br>Pfam-B_195384 (release 26.0). This short low-complexity, highly serine-rich region lies on clathrin-adaptor complex 3 beta-1 subunit proteins, between family Adaptin_N, Pfam:PF01602 and a C-terminal domain, AP3B1_C,Pfam:PF14796.. 
PF14798 Calcium homeostasis modulator<br>This family of proteins control cytosolic calcium concentration. They are transmembrane proteins which may be pore-forming ion channels  .. 
PF14799 FAM195 family<br>
PF14800 Domain of unknown function (DUF4481)<br>
PF14801 tRNA methyltransferase complex GCD14 subunit N-term<br>This is the N-terminal domain of GCD14, itself a subunit of the tRNA methyltransferase complex that is required for 1-methyladenosine modification and maturation of initiator methionyl-tRNA  . The exact function of the N-terminus is not known but it is necessary for maintaining the overall folding and for full enzymatic activity.. 
PF14802 TMEM192 family<br>The function of this family of transmembrane proteins is unknown. In vertebrates, proteins in this family are located in the lysosomal membrane and late endosome [1-2]. In Arabidopsis, a member of this family has been found to weakly interact with FRIGIDA, a determinant of flowering time  .. 
PF14803 Nudix N-terminal<br>Ths domain occurs at the N-terminus of several Nudix (Nucleoside Diphosphate linked to X) hydrolases.. 
PF14804 Jag N-terminus<br>This domain is found at the N-terminus of proteins containing Pfam:PF13083 and Pfam:PF01424, including the jag proteins.. 
PF14805 Tetrahydrodipicolinate N-succinyltransferase N-terminal<br>This is the N-terminal domain of 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase  .. 
PF14806 Coatomer beta subunit appendage platform<br>This family is found at the C-terminus of the coatamer beta subunit proteins (Beta-coat proteins). It is a platform domain on the appendage that carries a highly conserved tryptophan.. 
PF14807 Adaptin AP4 complex epsilon appendage platform<br>Pfam-B_21377 (release 26.0). This domain is found at the C terminal of clathrin-adaptor epsilon subunit, and at the C-terminus of the appendage on the platform domain.. 
PF14808 TMEM164 family<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 214 and 330 amino acids in length. There are two conserved sequence motifs: LNPCH and DPF.. 
PF14809 C1 domain of tRNA-guanine transglycosylase dimerisation<br>This short region of the tRNA-guanine transglycosylase enzyme acts as the dimerisation domain of the whole protein  .. 
PF14810 Patch-forming domain C2 of tRNA-guanine transglycosylase<br>Domain C2 of tRNA-guanine transglycosylase is formed by a four-stranded anti-parallel beta-sheet lined with two alpha helices. It has conserved basic residues on the surface of the beta-sheets as does the C-terminal domain PUA, Pfam:PF01472. The catalytic domain, TGT has conserved basic residues on the outer surface of the N-terminal three-stranded beta sheet, which closes the barrel, and it is postulated that these basic residues from the three domains form a continuous, positively charged patch to which the tRNA binds  .. 
PF14811 Protein of unknown function TPD sequence-motif<br>This is a family of eukaryotic proteins of unknown function.  A few members have an associated zinc-finger domain. All members carry a highly conserved TPD sequence-motif.. 
PF14812 Transmembrane domain of transglycosylase PBP1 at N-terminal<br>CATH:3fwl_A_01, Pfam-B_367 (release 26.0). This is the N-terminal, transmembrane, domain of the transglycosylases ()penicillin-binding proteins), the multi-domain membrane proteins essential for cell wall synthesis that are targeted by penicillin antibiotics. The TM domain is a single helix, several of whose residues lie in close proximity to hydrophobic residues in the TGT domain. The TM helix seems to be necessary for stabilizing the protein-membrane interaction, and the resulting orientation limits the interaction between PBPb1 and lipid II in the membrane in a 2D lateral diffusion fashion  .. 
PF14813 NADH dehydrogenase 1 beta subcomplex subunit 2<br>This family represents an accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis [1-2].. 
PF14814 Bifunctional transglycosylase second domain<br>UB2H is the second domain of the transglycosylases, or penicillin-binding proteins PBP1bs)), the multi-domain membrane proteins essential for cell wall synthesis that are targeted by penicillin antibiotics. The exact function of the UB2H domain is uncertain, but it may act as the binding component of PBP1b with different binding partners, or it may participate in the regulation between DNA repair and/or synthesis and cell wall formation during the bacterial cell cycle  .. 
PF14815 NUDIX domain<br>
PF14816 Family of unknown function, FAM178<br>
PF14817 HAUS augmin-like complex subunit 5<br>This family includes HAUS augmin-like complex subunit 5. The HAUS augmin-like complex contributes to mitotic spindle assembly, maintenance of chromosome integrity and completion of cytokinesis [1-2].. 
PF14818 Domain of unknown function (DUF4482)<br>This family is found in eukaryotes, and is approximately 140 amino acids in length. The family is found in association with Pfam:PF11365.. 
PF14819 Nitrile reductase, 7-cyano-7-deazaguanine-reductase N-term<br>The QueF monomer is made up of two ferredoxin-like domains aligned together with their beta-sheets that have additional embellishments. This subunit is composed of a three-stranded beta-sheet and two alpha-helices. QueF reduces a nitrile bond to a primary amine. The two monomer units together create suitable substrate-binding pockets  .. 
PF14820 Small proline-rich 2<br>This family of small proteins is rich in proline, cysteine and glutamate. They contain a tandemly repeated nonamer, PKCPEPCPP  . They are components of the cornified envelope of keratinocytes  .. 
PF14821 Threonine synthase N terminus<br>This domain is found at the N-terminus of many threonine synthase enzymes  .. 
PF14822 Vasohibin<br>This family of proteins function as angiogenesis inhibitors in animals [1-2].. 
PF14823 Sirohaem biosynthesis protein C-terminal<br>This domain is the C-terminus of a multifunctional enzyme which catalyses the biosynthesis of sirohaem. Both of the catalytic activities of this enzyme (precorrin-2 dehydrogenase EC:1.3.1.76) and sirohydrochlorin ferrochelatase (EC:4.99.1.4) are located in the N-terminal domain of this enzyme, Pfam:PF13241  .. 
PF14824 Sirohaem biosynthesis protein central<br>This is the central domain of a multifunctional enzyme which catalyses the biosynthesis of sirohaem. Both of the catalytic activities of this enzyme (precorrin-2 dehydrogenase EC:1.3.1.76) and sirohydrochlorin ferrochelatase (EC:4.99.1.4) are located in the N-terminal domain of this enzyme, Pfam:PF13241  .. 
PF14825 Domain of unknown function (DUF4483)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 203 and 326 amino acids in length. There is a single completely conserved residue N that may be functionally important.. 
PF14826 FACT complex subunit SPT16 N-terminal lobe domain<br>The FACT or facilitator of chromatin transcription complex binds to and alters the properties of nucleosomes. This family represents the N-terminal lobe of the NTD, or N-terminal domain, and acts as a protein-protein interaction domain presumably with partners outside of the FACT complex  . Knockout of the whole NTD domain, 1-450 residues in UniProt:P32558, in yeast serves to tender the cells sensitive to DNA replication stress but is not lethal. The C-terminal half of NTD is structurally similar to aminopeptidases, and the most highly conserved surface residues line a cleft equivalent to the aminopeptidase substrate-binding site, family peptidase_M24, Pfam:PF00557  .. 
PF14827 Sensory domain of two-component sensor kinase<br>CATH:3by8_A_00, Pfam-B_120 (release 26.0). Cache_3 is the periplasmic sensor domains of sensor histidine kinase of E. coli DcuS. This domain forms one of the components of the two-component signalling system that allows bacteria to adapt to changing environments. The ability of bacteria to monitor and adapt to their environment is crucial to their survival, and two-component signal transduction systems mediate most of these adaptive responses. One component is a histidine kinase sensor - this domain - most commonly part of a homodimeric transmembrane sensor protein, and the second component is a cytoplasmic response regulator. The two components interact in tandem through a phospho-transfer cascade  .. 
PF14828 Amnionless<br>The amnionless protein forms a complex with cubilin. This complex is necessary for vitamin B12 uptake  .. 
PF14829 Glycerol-3-phosphate acyltransferase N-terminal<br>GPAT_N is the N-terminal domain of glycerol-3-phosphate acyltransferases, and it forms a four-helix bundle  . Glycerol-3-phosphate (1)-acyltransferase(G3PAT) catalyses the incorporation of an acyl group from either acyl-acyl carrier proteins or acyl-CoAs into the sn-1 position of glycerol 3-phosphate to yield 1-acylglycerol-3-phosphate. G3PATs can either be selective, preferentially using the unsaturated fatty acid, oleate (C18:1), as the acyl donor, or non-selective, using either oleate or the saturated fatty acid, palmitate (C16:0), at comparable rates. The differential substrate-specificity for saturated versus unsaturated fatty acids seen within this enzyme family has been implicated in the sensitivity of plants to chilling temperatures  . The exact function of this domain is not known. it lies upstream of family Acyltransferase, Pfam:PF01553.. 
PF14830 Haemocyanin beta-sandwich<br>This antiparallel beta sandwich domain occurs in mollusc haemocyanins. Each mollusc haemocyanin contains several globular oxygen binding functional units. Each unit consists of an alpha-helical copper binding domain (Pfam:PF00264) and an antiparallel beta sandwich domain [1-2].. 
PF14831 Domain of unknown function (DUF4484)<br>KOGs (KOG4704), PF09804. This domain is found, in a few members, a the the C-terminus of family Avl9, Pfam:PF09794. The function is not known.. 
PF14832 Putative oxalocrotonate tautomerase enzyme<br>4-oxalocrotonate tautomerase enzyme is involved in the anthranilate synthase pathway.1. 
PF14833 NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase<br>3-Hydroxyisobutyrate is a central metabolite in the valine catabolic pathway, and is reversibly oxidized to methylmalonate semi-aldehyde by a specific dehydrogenase belonging to the 3-hydroxyacid dehydrogenase family. The reaction is NADP-dependent and this region of the enzyme binds NAD. The NAD-binding domain of 6-phosphogluconate dehydrogenase adopts a Rossmann fold  .. 
PF14834 Glutathione S-transferase, C-terminal domain<br>GST conjugates reduced glutathione to a variety of targets including S-crystallin from squid, the eukaryotic elongation factor 1-gamma, the HSP26 family of stress-related proteins and auxin-regulated proteins in plants.  Stringent starvation proteins in E. coli are also included in the alignment but are not known to have GST activity. The glutathione molecule binds in a cleft between N and C-terminal domains. The catalytically important residues are proposed to reside in the N-terminal domain  .. 
PF14835 zf-RING of BARD1-type protein<br>The RING domain of the breast and ovarian cancer tumour-suppressor BRCA1 interacts with multiple cognate proteins, including the RING protein BARD1. Proper function of the BRCA1 RING domain is critical, as evidenced by the many cancer-predisposing mutations found within this domain. A dimer is formed between the RING domains of BRCA1 and BARD1. The BRCA1-BARD1 structure provides a model for its ubiquitin ligase activity, illustrates how the BRCA1 RING domain can be involved in associations with multiple protein partners and provides a framework for understanding cancer-causing mutations at the molecular level  . The corresponding BRCA1-RING domain is on family zf-C3HC4_2, Pfam:PF13923.. 
PF14836 Ubiquitin-like domain<br>This ubiquitin-like domain is found in several ubiquitin carboxyl-terminal hydrolases   and in gametogenetin-binding protein.. 
PF14837 Integrator complex subunit 5 N-terminus<br>This family of proteins represents the N-terminus of subunit 5 of the integrator complex involved in snRNA transcription and processing  .. 
PF14838 Integrator complex subunit 5 C-terminus<br>This family of proteins represents the C-terminus of subunit 5 of the integrator complex involved in snRNA transcription and processing  .. 
PF14839 DOR family<br>This family of proteins regulate autophagy and gene transcription  .. 
PF14840 Processivity clamp loader gamma complex DNA pol III C-term<br>This domain lies at the C-terminus of the delta subunit of the DNA polymerase III clamp loader gamma complex. Within the complex the several C-terminal domains, of gamma, delta and delta' form a helical scaffold, on which the rest of he subunits are hung. The gamma complex, an AAA+ ATPase, is the bacterial homologue of the eukaryotic replication factor C that loads the sliding clamp (beta, homologous to PCNA) onto DNA.. 
PF14841 FliG middle domain<br>This is the middle domain of the flagellar rotor protein FliG [1-2].. 
PF14842 FliG N-terminal domain<br>This is the N-terminal domain of the flagellar rotor protein FliG  .. 
PF14843 Growth factor receptor domain IV<br>This is the fourth extracellular domain of receptor tyrosine protein kinases. Interaction between this domain and the furin-like domain (Pfam:PF00757) regulates the binding of ligands to the receptor L domains (Pfam:PF01030)  .. 
PF14844 PH domain associated with Beige/BEACH<br>This PH domain is found in proteins containing the Beige/BEACH domain (Pfam:PF02138), it immediately precedes the Beige/BEACH domain  .. 
PF14845 beta-acetyl hexosaminidase like<br>
PF14846 Domain of unknown function (DUF4485)<br>This family is found in eukaryotes, and is approximately 90 amino acids in length.. 
PF14847 Ras-binding domain of Byr2<br>CATH:1k8r_B_00, Pfam-B_3317 (release 26.0). This domain is the binding/interacting region of several protein kinases, such as the Schizosaccharomyces pombe Byr2. Byr2 is a Ser/Thr-specific protein kinase acting as mediator of signals for sexual differentiation in S. pombe by initiating a MAPK module, which is a highly conserved element in eukaryotes. Byr2 is activated by interacting with Ras, which then translocates the molecule to the plasma membrane. Ras proteins are key elements in intracellular signaling and are involved in a variety of vital processes such as DNA transcription, growth control, and differentiation. They function like molecular switches cycling between GTP-bound 'on' and GDP-bound 'off' states  .. 
PF14848 DNA-binding domain<br>JCSG_Target_393235 / GS13689A, Pfam-B_2593 (release 26.0). 
PF14849 YidC periplasmic domain<br>This is the periplasmic domain of YidC, a bacterial membrane protein which is required for the insertion and assembly of inner membrane proteins [1,2].. 
PF14850 DNA-binding domain of Proline dehydrogenase<br>This domain lies at the N-terminus of bifunctional proline-dehydrogenases and is found to bind DNA.. 
PF14851 FAM176 family<br>Members of the FAM176 family regulate autophagy and apoptosis [1-2].. 
PF14852 Fis1 N-terminal tetratricopeptide repeat<br>The mitochondrial fission protein Fis1 consists of two tetratricopeptide repeats. This domain is the N-terminal tetratricopeptide repeat [1-2]. 
PF14853 Fis1 C-terminal tetratricopeptide repeat<br>The mitochondrial fission protein Fis1 consists of two tetratricopeptide repeats. This domain is the C-terminal tetratricopeptide repeat [1-2]. 
PF14854 Leucine rich adaptor protein <br>
PF14855 Pilus-assembly fibrillin subunit, chaperone<br>Pfam-B_9717 (release 26.0). PapJ is part of the Pap pilus assembly complex that plays an auxiliary role by ensuring the proper integration of PapA into the fimbrial shaft. PapA is the major shaft protein of the pilus.. 
PF14856 Ecp2;<br>Pathogen effector; putative necrosis-inducing factor. Stergiopoulos I, Coggill P. The domain corresponds to the mature part of the Ecp2 effector protein from the tomato pathogen Cladopsorium fulvum. Effectors are low molecular weight proteins that are secreted by bacteria, oomycetes and fungi to manipulate their hosts and adapt to their environment. Ecp2 is a 165 amino acid secreted protein that was originally identified as a virulence factor in C. fulvum, since disruption reduces virulence of the fungus on tomato plants. We have recently determined that Ecp2 is a member of a novel, widely distributed and highly diversified within the fungal kingdom multigene superfamily, which we have designated Hce2, for Homologs of C. fulvum Ecp2 effector. Although Ecp2 is present in most organisms as a small secreted protein, the mature part of this protein can be found fused to other protein domains, including the fungal Glycoside Hydrolase family 18, Glyco_hydro_18 Pfam:PF00704 and other, unknown, protein domains. The intrinsic function of Ecp2 remains unknown but it is postulated by   that it is a necrosis-inducing factor in plants that serves pathogenicity on the host.. 
PF14857 TMEM151 family<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 338 and 558 amino acids in length.. 
PF14858 Domain of unknown function (DUF4486)<br>This domain family is found in eukaryotes, and is typically between 542 and 565 amino acids in length.. 
PF14859 Colicin M<br>Colicin M is a toxin produced by, and active against, Escherichia coli. It catalyses the hydrolysis of lipid I and lipid II peptidoglycan intermediates, therefore inhibiting peptidoglycan biosynthesis and leading to lysis of the bacterial cells  .. 
PF14860 DrrA phosphatidylinositol 4-phosphate binding domain<br>This domain binds to phosphatidylinositol 4-phosphate. It is found in Legionella pneumophila DrrA, a protein involved in the redirection of endoplasmic reticulum-derived vesicles to the Legionella-containing vacuoles [1,2].. 
PF14861 Plant antimicrobial peptide<br>This family includes plant antimicrobial peptides [1-2]. They adopt an alpha-helical hairpin fold stabilised by two disulphide bonds  .. 
PF14862 Big defensin<br>Big defensins are antimicrobial peptides. They consist of a hydrophobic N-terminal half, which is active against Gram-positive bacteria, and a cationic C-terminal half, which is active against Gram-negative bacteria. The C-terminal half adopts a beta-defensin-like structure [1,2].. 
PF14863 Alkyl sulfatase dimerisation<br>This domain is found in alkyl sulfatases such as the Pseudomonas aeruginosa SDS hydrolase (Swiss:Q9I5I9), where it acts as a dimerisation domain  . 
PF14864 Alkyl sulfatase C-terminal<br>This domain is found at the C-terminus of alkyl sulfatases. Together with the N-terminal catalytic domain, this domain forms a hydrophobic chute and may recruit hydrophobic substrates  .. 
PF14865 Macin<br>The macins are antimicrobial proteins [1-3]. They form a disulphide-stabilised alpha-beta motif  .. 
PF14866 Potassium channel toxin<br>This family includes scorpion potassium channel toxins [1-2].. 
PF14867 Lantibiotic alpha<br>Lantibiotics are two-component lanthionine-containing peptide antibiotics active on Gram-positive bacteria [1-2].. 
PF14868 Domain of unknown function (DUF4487)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 209 and 938 amino acids in length. There is a conserved WCF sequence motif. There is a single completely conserved residue W that may be functionally important.. 
PF14869 Domain of unknown function (DUF4488)<br>Pfam_7936 (release 26.0). In most members this family covers almost the whole sequence, but a few member-sequences also carry a TonB_C domain, PF03544.. 
PF14870 PSII_YCF48;<br>Photosynthesis system II assembly factor YCF48. Pfam-B_547 (release 26.0). YCF48 is one of several assembly factors of the photosynthesis system II. The photosynthesis system II occurs in Cyanobacteria that are Gram-negative bacteria performing oxygenic photosynthesis. One of the three membranes surrounding these bacteria is the inner thylakoid membrane (TM) system that is localised within the cell and houses the large pigment-protein complexes of the photosynthetic electron transfer chain, i.e. Photosystem (PS) II, PSI, the cytochrome b6f complex, and the ATP synthase. YCF48 is necessary for efficient assembly and repair of the PSII  . YCF48 is found predominantly in the thykaloid membrane  . It is a BNR repeat protein.. 
PF14871 Hypothetical glycosyl hydrolase 6<br>GHL6 is a family of hypothetical glycoside hydrolases.. 
PF14872 Hypothetical glycoside hydrolase 5<br>GHL5 is a family of hypothetical glycoside hydrolases.. 
PF14873 N-terminal domain of BNR-repeat neuraminidase<br>Pfam-B_13890 (release 26.0). This domain is usually found at the N-terminus of the BNR-repeat neuraminidase protein family.. 
PF14874 Flagellar-associated PapD-like<br>Pfam-B_1987 (release 26.0). This domain is a putative PapD periplasmic pilus chaperone protein family.. 
PF14875 N-term cysteine-rich ER, FAM69<br>The FAM69 family of cysteine-rich type II transmembrane proteins localise to the endoplasmic reticulum (ER) in cultured cells, probably via N-terminal di-arginine motifs. These proteins carry at least 14 luminal cysteines which are conserved in all FAM69s. There are currently few indications of the involvement of FAM69 members in human diseases  . It would appear that FAM69 proteins are predicted to be have a protein kinase structure and function. Analysis of three-dimensional structure models and conservation of the classic catalytic motifs of protein kinases in four of human FAM69 proteins suggests they might have retained catalytic phosphotransferase activity. An EF-hand Ca2+-binding domain, inserted within the structure of the kinase domain, suggests they function as Ca2+-dependent kinases (unpublished).. 
PF14876 RSF1P;<br>Respiratory growth transcriptional regulator. Pfam-B_36578 (release 26.0). This is a family of transcriptional regulators that determine the transition from fermentative activity to growth on glycerol  .. 
PF14877 Mitochondrial translation initiation factor<br>Pfam-B_22619 (release 26.0). This is a family of mitochondrial initiation factors IF3.. 
PF14878 Death-like domain of SPT6<br>Pfam-B_9510 (release 26.0). This DLD domain maintains the characteristic overall topology of death domains, as it consists of a six-helix bundle with three stacked antiparallel helices and an additional helix inserted between the final two helices of the bundle. Although it is unlikely that the Spt6 DLD functions in an apoptotic process in yeast, its prominent location and the observation that it displays the most highly conserved region of the Spt6 surface suggest that it mediates important intermolecular interactions [1,2].. 
PF14879 Domain of unknown function (DUF4489)<br>Pfam-B_28643 (release 26.0). 
PF14880 Cytochrome oxidase c assembly<br>Pfam-B_122767 (release 26.0). COX14 plays an essential role in cytochrome oxidase assembly. The COX14 product is a low-molecular weight membrane protein of mitochondria, but it is not a subunit of cytochrome oxidase  . Orthology-prediction methods have identified the vertebrate C12orf62 orthologues to be orthologues of the yeast COX14  .. 
PF14881 Tubulin domain<br>This family includes the tubulin alpha, beta and gamma chains, as well as the bacterial FtsZ family of proteins. Misato from Drosophila and Dml1p from fungi are descendants of an ancestral tubulin-like protein, and exhibit regions with similarity to members of a GTPase family that includes eukaryotic tubulin and prokaryotic FtsZ. Dml1p and Misato have been co-opted into a role in mtDNA inheritance in yeast, and into a cell division-related mechanism in flies, respectively. Dml1p might additionally function in the partitioning of the mitochondrial organelle itself, or in the segregation of chromosomes, thereby explaining its essential requirement. This domain subject to extensive post-translational modifications.. 
PF14882 Hypothetical glycosyl hydrolase 12<br>GHL12 is a family of hypothetical glycoside hydrolases.. 
PF14883 Hypothetical glycosyl hydrolase family 13<br>GHL13 is a family of hypothetical glycoside hydrolases.. 
PF14884 Type I membrane glycoproteins cell-cell fusogen<br>Podbilewicz B, Coggill P. Podbilewicz B,  , Pfam-B_25631 (release 26.0). EFF-AFF was first identified when EFF1 mutants were found to block cell fusion in all epidermal and vulval epithelia in the worm  . However, fusion between the anchor cell and the utse syncytium that establishes a continuous uterine-vulval tube proceeds normally in eff-1 mutants and thus Aff1 was established as necessary for this and the fusion of heterologous cells in C. elegans  . The transmembrane forms of FF proteins, like most viral fusogens, possess an N-terminal signal sequence followed by a long extracellular portion, a predicted transmembrane domain, and a short intracellular tail. A striking conservation in the position and number of all 16 cysteines in the extracellular portion of FF proteins from different nematode species suggests that these proteins are folded in a similar 3D structure that is essential for their fusogenic activity  . C. elegans AFF-1 and EFF-1 proteins are essential for developmental cell-to-cell fusion and can merge insect cells. Thus FFs comprise an ancient family of cellular fusogens that can promote fusion when expressed on a viral particle  .. 
PF14885 Hypothetical glycosyl hydrolase family 15<br>GHL15 is a family of hypothetical glycoside hydrolases.. 
PF14886 FAM183A and FAM183B related<br>The function of this family of metazoan sequences is not known.. 
PF14887 HMG (high mobility group) box 5<br>Nucleolar transcription factor/upstream binding factor contains six HMG box domains. This is the fifth HMG box domain in these proteins. This domain has lost DNA-binding ability  .. 
PF14888 Penicillin-binding protein Tp47 domain C<br>Domain C is the largest domain in this unusual penicillin-binding protein PBP), Tp47. This domain is mainly characterised by an immunoglobulin fold with two opposing beta-sheets that form the typical barrel-like structure. In contrast to the classical immunoglobulin fold, however, this has an additional beta-strand inserted after strand 3. Also, the strands are connected by rather large loops. Helices are inserted between strands 2 and 3 and between strands 4 and 5. Domain C interacts with domain B via a surface that has a slightly concave, goblet-like shape. Tp47 is unusual in that it displays β-lactamase activity, and thus it does not fit the classical structural and mechanistic paradigms for PBPs, and thus Tp47 appears to represent a new class of PBP  .. 
PF14889 Penicillin-binding protein Tp47 domain a<br>This is the first domain in this unusual penicillin-binding protein PBP), Tp47 is mainly composed of beta-strands and is sequentially non-contiguous. The first three domains in Tp47 interact with each other through intimate domain-domain interfaces. Domain A contacts domain B through its N-terminal segment. Domain A also interacts tightly with domain C, Tp47 is unusual in that it displays β-lactamase activity, and thus it does not fit the classical structural and mechanistic paradigms for PBPs, and thus Tp47 appears to represent a new class of PBP  . . 
PF14890 Intein splicing domain<br>Inteins are segments of protein which excise themselves from a precursor protein and mediate the rejoining of the remainder of the precursor (the extein). Most inteins consist of a splicing domain which is split into two segments by a homing endonuclease domain. This domain represents the splicing domain  .. 
PF14891 Effector protein<br>This family of proteins contains an HEXXH motif, typical of zinc metallopeptidases. The family includes the E. coli effector protein NleD, which cleaves and inactivates c-Jun N-terminal kinase (JNK)  .. 
PF14892 Domain of unknown function (DUF4490)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 101 and 220 amino acids in length. In mice, a member of this family whose expression is induced by p53 may play a role in DNA damage response  .. 
PF14893 PNMA<br>The PNMA family includes paraneoplastic antigens Ma 1, 2 and 3, found in the serum of patients with paraneoplastic neurological disorders [1,2]. The family also includes modulator of apoptosis 1, which has a role in death receptor-dependent apoptosis  .. 
PF14894 Lsm C-terminal<br>This domain is found at the C-terminus of archaeal Lsm (like-Sm) proteins  .. 
PF14895 Protein phosphatase 1 inhibitor<br>This family of proteins interacts with and inhibits the phosphatase activity of protein phosphatase 1 (PP1) complexes  .. 
PF14896 EmbC C-terminal domain<br>Pfam-B_4670 (release 7.5). Arabinosyltransferase is involved in arabinogalactan (AG) biosynthesis pathway in mycobacteria. AG is a component of the   macromolecular assembly of the mycolyl-AG-peptidoglycan complex of the cell wall. This enzyme has important clinical applications as it is believed to be the target of the antimycobacterial drug Ethambutol  . This domain represents the C-terminal extracellular domain that is likely to bind to carbohydrate  .. 
PF14897 EpsG family<br>This family of proteins are related to the EpsG protein from B. subtilis Swiss:P71056. These proteins are likely glycosyl transferases belonging to the membrane protein GT-C clan.. 
PF14898 Domain of unknown function (DUF4491)<br>This family of proteins is found in bacteria. Proteins in this family are typically between 94 and 107 amino acids in length. There is a conserved EYY sequence motif.. 
PF14899 Domain of unknown function (DUF4492)<br>This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. The function of these proteins is unknown.. 
PF14900 Domain of unknown function (DUF4493)<br>This family of proteins is found in bacteria. Proteins in this family are typically between 264 and 710 amino acids in length. Many of these proteins have a lipid attachment site suggesting they are lipoproteins.. 
PF14901 Cleavage inducing molecular chaperone<br>Coggill P, Hetherington K. Pfam-B_1192 (release 26.0). Jiv90 is a fragment of the DnaJ protein in eukaryotes and in J-domain protein interacting with viral protein (Jiv) located in the N terminal region of the pestivirus viral polypeptide.  The viral protein interacts stably with non structural (NS) protein NS2, causing a conformational change in NS2-NS3 and stimulates NS2-NS3 cleavage in trans. Cleavage of NS2-NS3 increases cytopathogenicity and consequently aids viral replication. Jiv therefore acts as a regulating cofactor for NS2 auto-protease. The efficient release of NS3 from the viral polypeptide by Jiv is considered crucial to the pestivirus cytopathogenicity  . In eukaryotes, it usually lies 40 residues downstream of DnaJ family Pfam:PF00226. However, the function in eukaryotes is still unknown.. 
PF14902 Domain of unknown function (DUF4494)<br>This family of proteins is found in bacteria. Proteins in this family are typically between 154 and 172 amino acids in length. There are two conserved sequence motifs: VDA and EAE. There is a single completely conserved residue E that may be functionally important.. 
PF14903 WG containing repeat<br>
PF14904 Family of unknown function<br>Coggill P, Hetherington K. Function of this protein family is not known.. 
PF14905 Outer membrane protein beta-barrel family<br>This family includes proteins annotated as TonB dependent receptors. But it is also likely to contain other membrane beta barrel proteins of other functions.. 
PF14906 Domain of unknown function (DUF4495)<br>This domain family is found in eukaryotes, and is typically between 322 and 336 amino acids in length. There are two conserved sequence motifs: QMW and DLW. Proteins in this family vary in length from 793 to 1184 amino acids.. 
PF14907 Uncharacterised nucleotidyltransferase<br>This family is likely to be an uncharacterised group of nucleotidyltransferases.. 
PF14908 Domain of unknown function (DUF4496)<br>This domain family is found in eukaryotes, and is typically between 134 and 154 amino acids in length. Proteins in this family vary in length between 264 and 772 amino acid residues.. 
PF14909 Spermatogenesis-assoc protein 6<br>This domain family is found in eukaryotes, and is approximately 140 amino acids in length. The family has similarity to the motor domain of kinesin related proteins and with the Caenorhabditis elegans neural calcium sensor protein (NCS�2).. 
PF14910 S-phase genomic integrity recombination mediator, N-terminal<br>MMS22L (Methyl methanesulfonate-sensitivity protein 22-like) is found in yeast, plants and vertebrates, and is integrally concerned with DNA forking and repair mechanisms during replication.  MMS22L complexes with TONSL and this complex accumulates at regions of ssDNA associated with distressed replication forks or at processed DNA breaks. Its depletion results in high levels of endogenous DNA double-strand breaks caused by an inability to complete DNA synthesis after replication fork collapse  . Thus the complex mediates recovery from replication stress and homologous recombination in vertebrates, yeasts and plants [2,3]. This family is the more N-terminal region of the proteins.. 
PF14911 S-phase genomic integrity recombination mediator, C-terminal<br>MMS22L (Methyl methanesulfonate-sensitivity protein 22-like) is found in yeast, plants and vertebrates, and is integrally concerned with DNA forking and repair mechanisms during replication.  MMS22L complexes with TONSL and this complex accumulates at regions of ssDNA associated with distressed replication forks or at processed DNA breaks. Its depletion results in high levels of endogenous DNA double-strand breaks caused by an inability to complete DNA synthesis after replication fork collapse  . Thus the complex mediates recovery from replication stress and homologous recombination in vertebrates, yeasts and plants [2,3]. This family is the more C-terminal region of the proteins.. 
PF14912 Testicular haploid expressed repeat<br>This repeat is the only conserved part of the THEG proteins from vertebrate spermatids. Both human and mouse THEG are specifically expressed in the nucleus of haploid male germ cells and are involved in the regulation of nuclear functions [1,2].  Although the differential gene expression of THEG in spermatid-Sertoli cell co-culture supports the relevance of germ cell-Sertoli cell interaction for gene regulation during spermatogenesis, THEG was not found to be essential for spermatogenesis in mice  .. 
PF14913 DPCD protein family<br>Coggill P, Hetherington K. This protein is a found in eukaryotes and a mutation in this protein is thought to cause Primary Ciliary Dyskinesia (PCD)  . This protein is 203 amino acids in length, 23 kDa in size and its function remains unknown. The gene that encodes this protein is a candidate gene for PCD and is expressed during ciliogenesis. PCD affects the airways and reproductive organs, and probing Northern blots show DPCD expression in humans is highest in the testes. Additionally, there is no indication of major splice variants  .. 
PF14914 LRRC37A/B like protein 1 C-terminal domain<br>Coggill P, Hetherington K. This family represents the C-terminal domain of the putative Leucine Rich Repeat Containing protein 37A or protein 37B (LRRC37A/B) found in eukaryotes. The Leucine Rich Repeats (LRR) lies in the central region. The gene that encodes this protein is found in the chromosomal position 17q11.2, and its microdeletion results in the disease, neurofibromatosis type-1 (NF1)  . The function of the protein, LRRC37B is unknown, however experimental data shows expression in the aorta, heart, skeletal muscle, liver and brain during gestation  .. 
PF14915 CCDC144C protein coiled-coil region<br>Coggill P, Hetherington K. This family includes the human protein CCDC144C and the ankyrin repeat domain-containing protein 26-like 1 found in eukaryotes. Its function remains unknown, however, it is known to contain a coiled-coil domain which corresponds to this region. The ankyrin repeat which features in this protein is a common amino acid motif.. 
PF14916 Coiled-coil domain of unknown function<br>This domain family is found in eukaryotes, and is approximately 60 amino acids in length. The function is not known and the proteins carry no other domains.. 
PF14917 Coiled coil protein 74, C terminal<br>Pfam-B_23141 (release 26.0). This is a C-terminal conserved domain of coiled-coil proteins from vertebrates. The function is not known. Expression levels in humans are elevated in breast cancer [].. 
PF14918 MDM2-binding<br>MTBP, or MDM2-binding protein, binds to MDM2. The MDM2 protein, through its interaction with p53, plays an important role in the regulation of the G1 checkpoint of the cell cycle  . MTBP promotes MDM2-mediated ubiquitination and degradation of p53 and also MDM2 stabilisation in an MDM2 RING finger-dependent manner  . MTBP differentially regulates the E3 ubiquitin ligase activity of MDM2 towards two of its most critical targets (itself and p53) and in doing so significantly contributes to MDM2-dependent p53 homeostasis in unstressed cells  . MTBP inhibits cancer cell migration by interacting with a protein involved in cell motility. This motility protein is alpha-actinin-4 (ACTN4)  . It is unclear which regions of MTBP interact with which binding-partner. See PF14919, PF14920. . 
PF14919 MDM2-binding<br>MTBP, or MDM2-binding protein, binds to MDM2. The MDM2 protein, through its interaction with p53, plays an important role in the regulation of the G1 checkpoint of the cell cycle  . MTBP promotes MDM2-mediated ubiquitination and degradation of p53 and also MDM2 stabilisation in an MDM2 RING finger-dependent manner  . MTBP differentially regulates the E3 ubiquitin ligase activity of MDM2 towards two of its most critical targets (itself and p53) and in doing so significantly contributes to MDM2-dependent p53 homeostasis in unstressed cells  . MTBP inhibits cancer cell migration by interacting with a protein involved in cell motility. This motility protein is alpha-actinin-4 (ACTN4)  . It is unclear which regions of MTBP interact with which binding-partner.  See PF14918, PF14920.. 
PF14920 MDM2-binding<br>MTBP, or MDM2-binding protein, binds to MDM2. The MDM2 protein, through its interaction with p53, plays an important role in the regulation of the G1 checkpoint of the cell cycle  . MTBP promotes MDM2-mediated ubiquitination and degradation of p53 and also MDM2 stabilisation in an MDM2 RING finger-dependent manner  . MTBP differentially regulates the E3 ubiquitin ligase activity of MDM2 towards two of its most critical targets (itself and p53) and in doing so significantly contributes to MDM2-dependent p53 homeostasis in unstressed cells  . MTBP inhibits cancer cell migration by interacting with a protein involved in cell motility. This motility protein is alpha-actinin-4 (ACTN4)  . It is unclear which regions of MTBP interact with which binding-partner.  See PF14918, PF14919.. 
PF14921 Adenomatosis polyposis coli down-regulated 1<br>The domain is duplicated in most members of this family. APCDD is directly regulated by the beta-catenin/Tcf complex, and its elevated expression promotes proliferation of colonic epithelial cells in vitro and in vivo  . APCDD1 has an N-terminal signal-peptide and a C-terminal transmembrane region.  The domain is rich in cysteines, there being up to 12 such residues, a structural motif important for interaction between Wnt ligands and their receptors. APCDD1 is expressed in a broad repertoire of cell types, indicating that it may regulate a diverse range of biological processes controlled by Wnt signalling  .. 
PF14922 Protein of unknown function<br>This is a family of eukaryotic proteins. Most members carry a highly distinctive, conserved sequence motif of FWWh, where h represents a hydrophobic residue. The function of the family is not known.. 
PF14923 Coiled-coil protein 142<br>The function of this coiled-coil domain-containing family is not known. It is found in eukaryotes.. 
PF14924 Protein of unknown function (DUF4497)<br>This domain family is found in eukaryotes, and is typically between 107 and 123 amino acids in length. There are two completely conserved G residues that may be functionally important.. 
PF14925 Domain of unknown function<br>Members of this family carry two distinct, highly conserved sequence motifs, CPPPLYYTHL and HPHLAWLY. The family is found in eukaryotes, and the function is not known. This family lies at the C-terminus of members.. 
PF14926 Domain of unknown function (DUF4498)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 203 and 308 amino acids in length.. 
PF14927 Neurensin<br>The neurensin family includes the neuronal membrane proteins neurensin-1 and neurensin-2  . Neurensin-1 plays a role in neurite extension  .. 
PF14928 Short tail fibre protein receptor-binding domain<br>This domain is a receptor binding domain found on bacteriophage short tail fibre proteins. It contains a zinc-binding site and a potential lipopolysaccharide-binding site  .. 
PF14929 TAF RNA Polymerase I subunit A<br>Coggill P, Hetherington K. TATA box binding protein associated factor RNA Polymerase I subunit A is found in eukaryotes and is encoded by the gene TAF1A in humans. Its function is to aid transcription of DNA into RNA by binding to the promoter at the -10 TATA box site. It is a component of the transcription factor SL1/TIF-IB complex, involved in PIC assembly (preinitiation complex) during RNA polymerase I-dependent transcription. The rate of PIC formation depends on the rate of association of this protein. This protein also stabilises nucleolar transcription factor 1/UBTF on rDNA.. 
PF14930 Quinohemoprotein amine dehydrogenase, alpha subunit domain II<br>This is the second domain of the alpha subunit of quinohemoprotein amine dehydrogenase [1,2]. 
PF14931 Intraflagellar transport complex B, subunit 20<br>IFT20 is subunit 20 of the intraflagellar transport complex B  . The intraflagellar transport complex assembles and maintains eukaryotic cilia and flagella. IFT20 is localised to the Golgi complex and is anchored there by the Golgi polypeptide, GMAP210, whereas all other subunits except IFT172 localise to cilia and the peri-basal body or centrosomal region at the base of cilia [1,2,3].  IFT20 accompanies Golgi-derived vesicles to the point of exocytosis near the basal bodies where the other IFT polypeptides are present, and where the intact IFT particle is assembled in association with the inner surface of the cell membrane.  Passage of the IFT complex then follows, through the flagellar pore recognition site at the transition region, into the ciliary compartment.  There also appears to be a role of intraflagellar transport (IFT) polypeptides in the formation of the immune synapse in non ciliated cells. The flagellum, in addition to being a sensory and motile organelle, is also a secretory organelle  . A number of IFT components are expressed in haematopoietic cells, which have no cilia, indicating an unexpected role of IFT proteins in immune synapse-assembly and intracellular membrane trafficking in T lymphocytes; this suggests that the immune synapse could represent the functional homologue of the primary cilium in these cells [6,7].. 
PF14932 HAUS augmin-like complex subunit 3<br>This domain is subunit three of the augmin complex found from Drosophila to humans  . The HAUS-augmin complex is made up of eight subunits.\.   The augmin complex interacts with gamma-TuRC, and attenuation of this interaction severely impairs spindle MT generation. Furthermore, we provide evidence that human augmin plays critical and non-redundant roles in the kinetochore-MT attachment and also central spindle formation during anaphase in human cells.The HAUS complex is required for mitotic spindle assembly and for maintenance of centrosome integrity  .. 
PF14933 CEP19-like protein<br>Coggill P, Hetherington K. This family includes the centrosomal protein of 19 kDa found in eukaryotes. In humans, it is encoded for by the gene CEP19 which is also known as C3orf34. These proteins localize in the centrosomes. Centrosomes are dynamic organelles that assemble around the centrioles. They organise the microtubule cytoskeleton and mitotic spindle apparatus and are required for cell division and cell migration. C3orf34 localizes near the centrosome in early interphase, to spindle poles during mitosis, and to distinct foci oriented towards the midbody at telophase  .. 
PF14934 Domain of unknown function (DUF4499)<br>Coggill P, Hetherington K. This family contains a protein found in eukaryotes. Transmembrane protein C10orf57 is encoded for by the gene chromosome 10 open reading frame 57 (C10orf57) located in chromosomal position 10q22.3. The exact function of this protein is still unknown, however it is thought to be an integral membrane protein. The protein sequence is 123 amino acids in length and has a mass of approximately 14.2 kDa.  The family also includes some longer proteins that possess an N-terminal dehydrogenase domain, Pfam:PF01073.. 
PF14935 Transmembrane protein 138<br>Coggill P, Hetherington L. This family of proteins is found in eukaryotes and members are approximately 160 amino acids in length. There are two conserved sequence motifs: YYY and DPR. This transmembrane protein belongs to a family found in eukaryotes and is involved in the biogenesis and degradation of ciliated cells  . Mutations in this protein cause the disease Joubert syndrome(JBTS) where the cilia becomes non-motile. Ciliopathy can be severe since cilia provide the cell with large amounts of information through signals. Ciliopathy can affect cell behaviour as the appropriate signals between the cell and its environment are not made, which can affect cell survival.. 
PF14936 Tumour protein p53-inducible protein 11<br>Coggill P, Hetherington K. TP53 is a tumour suppressor gene, when switched on it suppresses tumour development by inducing stable growth arrest or cell apoptosis  . The tumour protein TP53 inducible protein 11 encoded for by the gene TP53I11, has a protein sequence of 189 amino acids in length and 21 kDa in mass. The role of this protein is thought to negatively regulate cell proliferation in response to stress, and therefore suppress tumour formation  .. 
PF14937 Domain of unknown function (DUF4500)<br>Coggill P, Hetherington K. This family is found in eukaryotes. The function of this protein remains unknown. The gene which encodes for this protein is named chromosome 6 open reading frame 162 (C6orf162) and is found between the chromosomal positions 6q15-q16.1. It is thought that this protein may be an important part of membrane function.. 
PF14938 Soluble NSF attachment protein, SNAP<br>The soluble NSF attachment protein (SNAP) proteins are involved in vesicular transport between the endoplasmic reticulum and Golgi apparatus  . They act as adaptors between SNARE (integral membrane SNAP receptor) proteins and NSF (N-ethylmaleimide-sensitive factor)  . They are structurally similar to TPR repeats  .. 
PF14939 ShortName;<br>DDB1-and CUL4-substrate receptor 15, WD repeat. DCAFs, Ddb1- and Cul4-associated factors, are substrate receptors for the Cul4-Ddb1 Ubiquitin Ligase. There are 18 different factors, the majority of which are WD40-repeat-proteins  .. 
PF14940 Transmembrane 219<br>Coggill P, Hetherington K. This protein belongs to a family found in eukaryotes.  Proteins in this family are typically between 240 and 315 amino acids in length. The domains in this family vary in length from 202 to 249 amino acids. Its exact function remains unknown, however, it is thought to have a role as a transmembrane protein. More specifically, it is possible that this transmembrane protein may have a role as an insulin-like growth factor binding protein 3-receptor (IGFBP-3R). This receptor binds to the ligand, insulin growth factor 3, which is a p53-induced, apoptosis factor important for cancer prevention  .. 
PF14941 Transcriptional regulator, Out at first<br>Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between 198 and 332 amino acids in length. The domains in this family vary in length from 239 to 242 amino acids. The gene, OAF (out at first), which encodes this protein, has a promoter which may help mediate regulation of neighbouring genes  . An alternative name for this protein is HCV NS5A-transactivated protein 13 target protein 2, which stands for Hepatitis C virus nonstructural 5A-transactivated protein 13 target protein 2. NS5A inhibits double-stranded-RNA-activated protein kinase (PKR) activity, which is thought to allow Hepatitis C Virus replication to continue in the presence of an alpha interferon (IFN)induced antiviral response  .. 
PF14942 Organelle biogenesis, Muted-like protein<br>Coggill P, Hetherington P. The protein is a coiled-coil protein and belongs to a family found in eukaryotes. It undergoes alternative splicing forming two isoforms.  The larger isoform is 187 amino acids long in protein sequence length and 21 kDa in mass. The smaller isoform is 110 amino acids long in protein sequence length and 12 kDa in mass. This protein associates with other proteins in order to form biogenesis of lysosome-related organelles complex-1 BLOC1 complex. BLOC-1 is required for the normal biogenesis of specialized organelles of the endosomal-lysosomal system  .. 
PF14943 Mitochondrial ribosome subunit S26<br>This family of proteins corresponds to mitochondrial ribosomal subunit S26 in eukaryotes  . 
PF14944 Tongue Cancer Chemotherapy Resistant Protein 1<br>Coggill P, Hetherington K. This family of proteins are found in eukaryotes. Tongue Cancer Chemotherapy Resistant-associated Protein 1 (TCRP1) is resistant to the chemotherapy drug, cisplatin, which induces apoptosis in tumour cells. There is suggestion that TCRP1 can be targeted to reverse chemotherapy resistance. The precise mechanism of TCRP1 inducing resistance against chemotherapy is still not clear, but it is thought that TCRP1 alters cell signalling pathways affecting apoptosis or DNA repair capacity. Proteins in this family are typically between 194 and 235 amino acids in length  .. 
PF14945 Normal lung function maintenance, Low in Lung Cancer 1 protein<br>Coggill P, Hetherington K. This protein is part of a family found in eukaryotes. It is 137 amino acids long in protein sequence length and mass is approximately 15.7 kDa. The protein is present in the normal lung epithelium, but absent or downregulated in most primary non-small lung cancers. The gene is known as Low in Lung Cancer 1 (LLC1). This protein is thought to have a role in the maintenance of normal lung function and its absence may lead to lung tumourigenesis  .. 
PF14946 Domain of unknown function (DUF4501)<br>Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between 167 and 308 amino acids in length. The exact function of this protein remains unknown, but it is thought to be a single-pass membrane protein. This family contains many highly conserved cysteine residues.. 
PF14947 Winged helix-turn-helix<br>This winged helix-turn-helix domain contains an extended C-terminal alpha helix which is responsible for dimerisation of this domain  .. 
PF14948 RESP18 domain<br>This domain is found in the glucocorticoid-responsive protein regulated endocrine-specific protein 18 (RESP18) and in the N-terminal extracellular region of receptor-type tyrosine-protein phosphatases containing the protein-tyrosine phosphatase receptor IA-2 domain (Pfam:PF11548) [1,2].. 
PF14949 ARF7 effector protein C-terminus<br>This family represents the C-terminus of the ARF7 effector protein (ARF7EP). ARF7EP interacts with ADP-ribosylation factor-like protein 14 and unconventional myosin-Ie and through this interaction controls movement of MHC-II-containing vesicles along the actin cytoskeleton in dendritic cells  . It contains a conserved CXCXXXXCXXCXXXCXXCXXXXCXXXCXC motif in it's C-terminal half.. 
PF14950 Domain of unknown function (DUF4502)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 181 and 876 amino acids in length.. 
PF14951 Domain of unknown function (DUF4503)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 313 and 876 amino acids in length.. 
PF14952 Putative treble-clef, zinc-finger, Zn-binding<br>This domain resembles the zinc-binding domain of prokaryotic topoisomerases, family DNA_ligase_ZBD Pfam:PF03119. The function of the eukaryotic proteins it is carried on is not known.. 
PF14953 Domain of unknown function (DUF4504)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 253 and 329 amino acids in length. There are two conserved sequence motifs: LLGYP and SFS.. 
PF14954 Limb expression 1<br>This entry represents the limb expression 1 (LIX1) family  .. 
PF14955 Mitochondrial ribosome subunit S24<br>This family of proteins corresponds to mitochondrial ribosomal subunit S24 in eukaryotes [1-2].. 
PF14956 Domain of unknown function (DUF4505)<br>This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 166 and 225 amino acids in length.. 
PF14957 Cdc42 effector<br>The Cdc42 effector (CEP) or binder of Rho GTPases (BORG) proteins are involved in the organisation of the actin cytoskeleton  . They may function as negative regulators of Rho GTPase signaling  .. 
PF14958 Domain of unknown function (DUF4506)<br>This domain family is found in eukaryotes, and is approximately 140 amino acids in length.. 
PF14959 gamma-Secretase-activating protein C-term<br>GSAP, or gamma-secretase-activating protein, also known as PION, regulates gamma-secretase activity. The holo-protein is a large, approx 850 residue protein that is rapidly cleaved to an active 16 kDa C-terminal fragment that is the stable, predominant form. GSAP is expressed in inclusion bodies and is important in brain function. It dramatically and selectively increases neurotoxic beta-Amyloid production in the brain through a mechanism involving its interactions with both gamma-secretase and its substrate, the amyloid precursor protein C-terminal fragment (APP-CTF). Accumulation of neurotoxic beta-Amyloid is a major hallmark of Alzheimer's disease.  Formation of beta-Amyloid is catalysed by gamma-secretase, a protease with numerous substrates that catalyses the intra-membrane cleavage of integral membrane proteins such as Notch receptors and APP (beta-amyloid precursor protein)  .  The secondary structure of GSAP is largely alpha-helical, lacking well-defined tertiary structure. GSAP represents a type of gamma-secretase regulator that directs enzyme specificity by interacting with a specific substrate  .. 
PF14960 ATP synthase regulation<br>Members of this family are subunits of mitochondrial ATP synthase (F-ATPase) [1-2] and vacuolar ATPase (V-ATPase)  . In F-ATPase, this subunit regulates mitochondrial ATP synthase population  .. 
PF14961 Broad-minded protein<br>Broad-minded protein (BROMI) interacts with cell cycle-related kinase (CCRK), together these proteins regulate ciliary membrane and axonemal growth  .. 
PF14962 Mitochondria Localisation Sequence<br>Coggill P, Hetherington K. This family contains a protein found in eukaryotes. Proteins in this family are typically between 240 and 613 amino acids in length. The family is found in association with Pfam:PF07992. This protein family is an N-terminal domain for the mitochondrial localisation sequence for an apoptosis-inducing factor  . The protein is also known as Corneal endothelium-specific protein 1 or as Ovary-specific acidic protein. It is thought to be important for membrane function and is expressed in the ovary and corneal endothelium.. 
PF14963 Calcium signal-modulating cyclophilin ligand<br>Calcium signal-modulating cyclophilin ligand was originally identified in a screen for cyclophilin B-interacting proteins. It is likely to be involved in calcium signalling  . It has also been shown to interact with many other signalling molecules including proto-oncogene tyrosine-protein kinase LCK, tumor necrosis factor receptor superfamily member 13B and EGFR [2-4].. 
PF14964 Domain of unknown function (DUF4507)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 346 and 434 amino acids in length.. 
PF14965 Negative regulator of p53/TP53<br>Coggill P, Hetherington K. This family of transmembrane proteins is found in eukaryotes. Proteins in this family are typically between 213 and 245 amino acids in length. It is found in various tissues, including the brain, liver and kidneys. It was first discovered as a functional unknown gene, murine brain I3 (BRI3). This protein is also known as HCCRBP-1 and it plays a role in tumourigenesis, as it binds to an oncogene, HCCR-1, and acts as a negative regulator of p53/TP53 tumour suppressor. BRI3BP induces tumourigenesis by activating protein kinase C (PKC) activity but decreasing the pro-apoptotic PKC-alpha and PKC-delta isoform levels. BRI3BP is over-expressed in many tumours  .. 
PF14966 DNA repair REX1-B<br>This family of proteins includes Chlamydomonas reinhardtii REX1-B (Required for Excision 1-B) which is involved in a light-independent DNA repair pathway  .. 
PF14967 FAM70 protein<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 241 and 349 amino acids in length. The function of this family is unknown.. 
PF14968 Coiled coil protein 84<br>The function of this coiled-coil domain-containing family is not known. It is found in eukaryotes.. 
PF14969 Domain of unknown function (DUF4508)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 117 and 253 amino acids in length.. 
PF14970 Domain of unknown function (DUF4509)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 212 and 449 amino acids in length. There is a conserved WLL sequence motif.. 
PF14971 Domain of unknown function (DUF4510)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 242 and 452 amino acids in length. There are two conserved sequence motifs: LEA and WMD.. 
PF14972 Mitochondrial morphogenesis regulator<br>This family of proteins regulate mitochondrial morphogenesis via a mechanism which is independent of mitofusins and dynamin-related protein 1  .. 
PF14973 TERF1-interacting nuclear factor 2 N-terminus<br>This is the N-terminus of TERF1-interacting nuclear factor 2. It is required for the formation of the shelterin complex. The shelterin complex is involved in the protection and maintenance of telomeres [1-3].. 
PF14974 Domain of unknown function (DUF4511)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 116 and 127 amino acids in length.. 
PF14975 Domain of unknown function (DUF4512)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 74 and 104 amino acids in length. There are two completely conserved residues (C and P) that may be functionally important.. 
PF14976 FAM72 protein<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 145 and 264 amino acids in length. The function of this family is unknown.. 
PF14977 FAM194 protein<br>This family is found in eukaryotes, and is approximately 210 amino acids in length. There is a conserved YPSG sequence motif. The function of this family is unknown.. 
PF14978 Mitochondrial ribosome protein 63<br>This family of proteins is present in the intact 55S subunit of the mitochondrial ribosome. It is not known if it belongs to the 28S or to the 39S subunit  .. 
PF14979 Transmembrane 52<br>This family of transmembrane proteins is found in eukaryotes. Proteins in this family are typically between 160 and 236 amino acids in length. There is a conserved LLCG sequence motif. The function of this family is unknown.. 
PF14980 TIP39 peptide<br>
PF14981 FAM165 family<br>This family of proteins known as FAM165 are found in eukaryotes. Members of this family are as yet uncharacterised. Proteins in this family are typically short membrane proteins between 55 and 70 amino acids in length.. 
PF14982 UPF0731 family<br>The UPF0731 family of uncharacterised proteins is found in mammals.. 
PF14983 Domain of unknown function (DUF4513)<br>This family of uncharacterised proteins is found in chordates.. 
PF14984 CD24 protein<br>
PF14985 TM140 protein family<br>This family of uncharacterised membrane proteins are called transmembrane protein 140. They are found in mammals.. 
PF14986 Domain of unknown function (DUF4514)<br>This family of uncharacterised proteins are found in mammals.. 
PF14987 NADH dehydrogenase 1 alpha subcomplex subunit 3<br>This family of proteins are accessory subunits of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I). This subunit is not believed to be catalytic [1-2].. 
PF14988 Domain of unknown function (DUF4515)<br>This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 198 and 469 amino acids in length. There are two completely conserved L residues that may be functionally important.. 
PF14989 Coiled-coil domain containing 32<br>Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between 160 and 188 amino acids in length. The gene that encodes this protein is C15orf57 but its protein product is called Protein CCDC32 (Coiled-coil domain containing 32). The exact function of this protein is still unknown.. 
PF14990 Domain of unknown function (DUF4516)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 56 and 69 amino acids in length.. 
PF14991 Protein melan-A<br>
PF14992 TMCO5 family<br>The TMCO5 family includes human transmembrane and coiled-coil domain-containing proteins 5A and 5B.. 
PF14993 Neuropeptide S precursor protein<br>
PF14994 Testis-specific gene 13 protein<br>This family of uncharacterised proteins are found in chordates. In humans this gene is found to be expressed specifically in the testes.. 
PF14995 Transmembrane protein<br>Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between 138 and 164 amino acids in length. There are two completely conserved residues (H and E) that may be functionally important and four transmembrane helices. The domains in this family vary in length from 124 to 126 amino acids. The precise function of the protein family is still unknown.. 
PF14996 Retinal Maintenance<br>Coggill P, Hetherington K. RMP is encoded for by a gene, C8orf37. Mutations in the gene cause two types of retinal dystrophies: cone-rod dystrophy type 16 (CORD16) and retinitis pigmentosa type 64 (RP64). CORD16 affects the cone receptors which detect red, green or blue wavelengths of light and RP64 affects the cone receptors first and then the rod receptors. Both of these affect the photo-receptors in the eye leading to colour blindness or blindness respectively  .. 
PF14997 CECR6/TMEM121 family<br>This family includes Cat eye syndrome critical region protein 6, a protein which has been identified in a screen for candidate genes for the developmental disorder Cat Eye Syndrome (CES)  . It also includes the TMEM121 transmembrane proteins. The function of this family is unknown.. 
PF14998 Transcription Regulator<br>Coggill P, Hetherington K. The precise function of this family is not clear, but it is thought to play a role in somitogenesis, development and transcriptional repression. Ripply is also known by an alternative name, Bowline. Bowline, is an associate protein of the transcriptional co-repressor XGrg-4  . This family contains two conserved sequence motifs: WRPW and FPVQATI. The WRPW motif is thought to be required for binding to tle/groucho proteins  . Ripply3 is also known as Down Syndrome Critical Region Protein 6 homolog  .  This family of proteins is found in eukaryotes. Proteins in this family are typically between 109 and 154 amino acids in length.. 
PF14999 Shadow of prion protein, neuroprotective<br>Coggill P, Hetherington K. This protein family is a Prion-like protein and its function is neuroprotective and similar to PrP(C)-like. Shadoo is mainly expressed in the brain, and highly expressed in the hippocampus, the area of the brain which co-ordinates memory as well as spatial memory and navigation. This protein may also alter the biological actions of normal and abnormal Prion Protein (PrP) which lead to lethal neurodegenerative diseases  . This family of proteins is found in eukaryotes. Proteins in this family are approximately 150 amino acids in length, of which the first 90 are alanine rich.. 
PF15000 Tumour suppressor candidate 2<br>This family of proteins are candidate tumour suppressors [1-2].. 
PF15001 AP-5 complex subunit sigma-1<br>This family of proteins are subunits of the adaptor protein complex AP-5  .. 
PF15002 ERK and JNK pathways, inhibitor<br>Coggill P, Hetherington K. This coiled-coiled domain, CCDC134, is a secretory protein that inhibits Mitogen activated protein kinase (MAPK) pathways such as Raf-1/MEK/ERK and JNK/SAPK but not p38.  CCDC134 is widely expressed in normal adult tissues, tumour tissues and cell lines, which shows its importance in cell signal transduction pathways, transcription regulation and therefore cell survival  . Additionally, CCDC134 is known to bind to a transcription adaptor, hADA2a, which forms part of the general control nonderepressible 5 (GCN5) histone acetyltransferase complex. Acetylation usually 'switches genes on' for transcription. Moreover, knocking out CCDC134 suppressed hADA2a-induced cell apoptosis activity and G1/S cell cycle arrest suggesting its importance in cell survival  . This family of proteins is found in eukaryotes. Proteins in this family are typically between 188 and 257 amino acids in length. This family is a coiled-coil domain containing protein 134 (CCDC134) whereby the coiled-coiled domain is a ubiquitous motif involved in oligomerisation.. 
PF15003 HAUS augmin-like complex subunit 2 <br>Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between 203 and 291 amino acids in length. HAUS augmin-like complex subunit 2 is alternatively called centrosomal protein of 27 kDa (CEP27). It localized in the microtubule organising centre, the centrosome. These microtubules are part of the cytoskeleton and give the cell its shape, provides it with a platform for motility and are crucial for mitosis  .  This protein is part of the HAUS augmin-like complex. This interacts with the gamma-tubulin ring complex (gamma-TuRC) which is required for spindle generation. HAUS2 may also increase the tension between spindle and kinetochore allowing for chromosome segregation during mitosis  . This protein is involved in mitotic spindle assembly, maintenance of centrosome integrity and completion of cytokinesis.. 
PF15004 Myeloma-overexpressed-like<br>This family of proteins is found in eukaryotes. It includes human myeloma-overexpressed gene 2 protein. Proteins in this family are typically between 45 and 74 amino acids in length. There are two conserved sequence motifs: MKP and DEMF. The function of this family is unknown.. 
PF15005 Izumo sperm-egg fusion<br>Coggill P, Hetherington K. Izumo is a molecule with a single immunoglobulin (Ig) domain. It is thought that Izumo bind to putative Izumo receptors on the oocyte. Izumo is not detectable on the surface of fresh sperm but becomes exposed only after an exocytotic process, the acrosome reaction, has occurred. Studies have shown that knock-out mice (Izumo-/- males) were sterile despite normal mating behaviour and ejaculation, indicating the importance of the protein in fertilization  .  There are cysteine residues thought to form a disulphide bridge. Izumo is a typical type I membrane glycoprotein with one immunoglobulin-like domain and a putative N-glycoside link motif (Asn 204)  . There is a conserved GCL sequence motif. Izumo expression has been found to be testis-specific [1,2]. This family of proteins is found in eukaryotes and are typically between 193 and 305 amino acids in length.. 
PF15006 Domain of unknown function (DUF4517)<br>Coggill P, Hetherington K. The function of this protein remains unknown. This family of proteins is found in eukaryotes and are typically between 160 and 182 amino acids in length.. 
PF15007 Centrosomal spindle body, CEP44<br>Coggill P, Hetherington K. CEP44 is a coiled coil domain found localised in the centrosome and spindle poles.. 
PF15008 Domain of unknown function (DUF4518)<br>Coggill P, Hetherington K. The precise function of this protein family is unknown but it is thought to be involved in apoptosis regulation.. 
PF15009 Transmembrane protein 173<br>Transmembrane protein 173, also known as stimulator of interferon genes protein (STING), is a transmembrane adaptor protein which is involved in innate immune signalling processes. It induces expression of type I interferons (IFN-alpha and IFN-beta) via the NF-kappa-B and IRF3, pathways in response to non-self cytosolic RNA and dsDNA [1-4].. 
PF15010 Putative cell signalling<br>Coggill P, Hetherington K. The precise function of this protein family is unknown, however studies have shown it undergoes Protein N-myristoylation; a type of lipid modification in eukaryotic and viral proteins. Protein N-myristoylation is usually an irreversible co-translational protein modification which is useful in cell signal transduction pathways  . This indicates that FAM131 may have some sort of role in cell signalling due to its ability to be myristoylated. This family of proteins is found in eukaryotes and are typically between 257 and 361 amino acids in length.. 
PF15011 Casein Kinase 2 substrate<br>Coggill P, Hetherington K. It is suggested that CK2S (C10orf109) is important in the regulation of cancer cell proliferation. Studies have indicated that CK2S is the downstream target of a protein kinase, casein kinase 2 (CK2), which is upregulated in cancer cells. CK2S has been found to be upregulated in cancer cells. The precise mechanism of CK2 targetting CK2S is not well characterised. It is found to be localised in the nucleus and cytoplasm  . This family of proteins is found in eukaryotes. Proteins in this family are typically between 160 and 221 amino acids in length. There is a single completely conserved residue P that may be functionally important.. 
PF15012 Domain of unknown function (DUF4519)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between  and 59 amino acids in length. There are two conserved sequence motifs: KET and VLP. There is a single completely conserved residue P that may be functionally important.. 
PF15013 CCSMST1 family<br>This family of proteins was discovered in a screen of Bos taurus placental ESTs. The B. taurus member of this family was named cattle cerebrum and skeletal muscle-specific transcript 1  . This family of proteins is found in eukaryotes. Proteins in this family are typically between 97 and 157 amino acids in length. There is a single completely conserved residue D that may be functionally important. The function of this family is unknown.. 
PF15014 Ceroid-lipofuscinosis neuronal protein 5<br>
PF15015 Spermatogenesis-associated, N-terminal<br>NYD-SP12, also known as SPATA16, is a germ-cell specific participant in the Golgi apparatus, and its expression is confined to spermatogenic epithelium, not being found in interstitial cells  . Computer analysis of the protein-sequence showed that NYD-SP12 contains a cluster of phosphorylation sites for protein kinase C as well as for cyclic nucleotide-dependent protein kinases [2,3]. It is postulated that since the mutation of some Golgi apparatus’ proteins are responsible for male infertility that NYD-SP12 might play a role in modification and sorting of acrosomal enzymes  . OMIM:102530.. 
PF15016 Domain of unknown function (DUF4520)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 197 and 638 amino acids in length.This is the C-terminal domain of the member proteins.. 
PF15017 Drug resistance and apoptosis regulator<br>Coggill P, Hetherington K. AF1q is an oncogenic factor involved in leukaemia development, thyroid tumourigenesis, and breast cancer metastasis. AF1q plays a critical role in the regulation of apoptosis and drug resistance. Initially identified as a mixed-lineage leukaemia fusion partner (MLL11) in infant acute myelomonocytic leukemia carrying t(1;11)(q21;q23) translocation. It is located in chromosome 1 band 21  . AF1Q may be a novel mediator of metastasis promotion in human breast cancer through regulation of the MMP pathway and RhoC expression  .This family of proteins is found in eukaryotes. Proteins in this family are typically between 25 and 482 amino acids in length.. 
PF15018 TRP-interacting helix<br>Coggill P, Hetherington K. This highly conserved motif is thought to be a transmembrane helix that binds to transient receptor potential (TRP) calcium channel. It is known that proline-rich proteins inactivate tannins found in food compounds, and it is putatively thought that PRR24 does too. This is important since tannins often inhibit the uptake of iron  .  InaF is a protein required for TRP calcium channel function in Drosophila [2,3]. TRP-related channels have been suggested to mediate store-operated calcium entry, important for Ca2+ homeostasis in a wide variety of cell types  .  The amino acid sequence of PRR-24 contains two completely conserved Y residues that may be functionally important. This domain family is found in eukaryotes, and is approximately 40 amino acids in length.. 
PF15019 FTDALS;<br>C9orf72-like protein family. Coggill P, Hetherington K. The precise function of this family is unknown but members have been found to be localised in the cytoplasm of brain tissue. Defects in the gene, C9orf72, are the cause of frontotemporal dementia and/or amyotrophic lateral sclerosis (FTDALS) which is an autosomal dominant neurodegenerative disorder. The disorder is caused by a large expansion of a GGGGCC hexa-nucleotide within the first C9orf72 intron located between the first and the second non-coding exons. The expansion leads to the loss of transcription of one of the two transcripts encoding isoform 1 and to the formation of nuclear RNA foci  . This domain family is found in eukaryotes, and is typically between 230 and 250 amino acids in length. There is a single completely conserved residue F that may be functionally important.. 
PF15020 Cation channel sperm-associated protein subunit delta<br>The CATSPER (cation channel of sperm) complex is a tetrameric complex consisting of CATSPER1, CATSPER2, CATSPER3 and CATSPER4, it functions as an alkalinisation-activated calcium channel. This complex requires several auxiliary subunits, including CATSPERD. CATSPERD is essential for the cation channel function and may play a role in channel assembly or transport  .. 
PF15021 Protein of unknown function (DUF4521)<br>This family of vertebrate proteins is functionally uncharacterised. The family includes the Chromosome 20 protein C20orf196.. 
PF15022 Protein of unknown function (DUF4522)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in mammals. In human this protein is known as C4orf36.. 
PF15023 Protein of unknown function (DUF4523)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in mammals.. 
PF15024 Glycosyltransferase family 18<br>Enzymes belonging to glycosyltransferase family 18 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase) contribute to the creation of branches in complex-type N-glycans. This domain is responsible for the catalytic activity of the enzyme  .. 
PF15025 Domain of unknown function (DUF4524)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 197 and 638 amino acids in length.This is the N-terminal domain of the member proteins. The human gene is from C5orf34.. 
PF15026 FAM74 protein<br>This family of uncharacterised proteins are found in humans and are known as FAM74 proteins. Members of this family contain several short protein repeats.. 
PF15027 Domain of unknown function (DUF4525)<br>This domain is found in eukaryotes. It is often found at the N-terminus of glycosyltransferase family 18 enzymes (Pfam:PF15024). It is also found in coiled-coil domain-containing protein 126.. 
PF15028 Pre-T-cell antigen receptor<br>The pre-T-cell antigen receptor (pre-TCR), expressed by immature thymocytes, has a pivotal role in early T-cell development, including TCR beta-selection, survival and proliferation of CD4(-)CD8(-) double-negative thymocytes, and subsequent alpha/beta T-cell lineage differentiation  . This protein contains an immunoglobulin domain  .. 
PF15029 Protein of unknown function (DUF4526)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in mammals and includes the human integral membrane protein TMEM174 protein.. 
PF15030 Protein of unknown function (DUF4527)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in vertebrates.. 
PF15031 Domain of unknown function (DUF4528)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 95 and 154 amino acids in length. This family includes Human C15orf61.. 
PF15032 Protein of unknown function (DUF4529)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. The proteins contain a conserved VLPPLK sequence motif.. 
PF15033 Kinocilin protein<br>This family of kinocilin proteins is found in vertebrate. In mouse it has been shown that this protein is expressed primarily in the kinocilium of sensory cells in the inner ear  .. 
PF15034 KRTAP type 7 family<br>This family of keratin associated proteins are found in vertebrate.. 
PF15035 Ciliary rootlet component, centrosome cohesion<br>
PF15036 Interleukin 34<br>
PF15037 Interleukin-17 receptor extracellular region<br>This domain is found at the N-terminus (extracellular region) of interleukin-17 receptor C and Interleukin-17 receptor E. This is the presumed ligand-binding domain  . Human putative interleukin-17 receptor E-like consists only of this domain.. 
PF15038 Jiraiya<br>Jiraiya inhibits bone morphogenetic protein (BMP) signaling during embryogenesis  . The human member of this family is TMEM221.. 
PF15039 Domain of unknown function (DUF4530)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically around 140 amino acids in length. The human member of this family is C19orf69.. 
PF15040 Humanin family<br>This family of proteins is found exclusively in humans. Humanin is a short anti-apoptotic peptide that interacts with Bax  .. 
PF15041 Domain of unknown function (DUF4531)<br>This family of uncharacterised proteins is found in mammals. This family includes the human protein C19orf71.. 
PF15042 Late cornified envelope-like proline-rich protein 1<br>This family of uncharacterised proteins is found in mammals.. 
PF15043 CB1 cannabinoid receptor-interacting protein 1<br>This family of proteins interacts with cannabinoid receptor 1 (CNR1) and attenuates CNR1-mediated tonic inhibition of voltage-gated calcium channels  .. 
PF15044 Mitochondrial function, CLU-N-term<br>CLU_N is the N-terminal domain of the Clueless protein, also known as TIF31-like in other organisms.  The function of this domain is not known. It family is found in association with Pfam:PF13236.. 
PF15045 Clathrin-binding box of Aftiphilin, vesicle trafficking<br>Aftiphilin forms a stable complex with p200 and gamma-synergin. This family contains a clathrin box, with two identified clathrin-binding motifs.  This family of proteins is found in eukaryotes.. 
PF15046 Protein of unknown function (DUF4532)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes.. 
PF15047 Protein of unknown function (DUF4533)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in mammals. This family includes two human proteins: C12orf60 and C12orf69.. 
PF15048 Organic solute transporter subunit beta protein<br>
PF15049 Protein of unknown function (DUF4534)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in mammals. Proteins in this family are typically between 170 and 190 amino acids in length. The protein includes the human integral membrane TMEM217 protein.. 
PF15050 SCIMP protein<br>This family contains the SCIMP proteins which are a a transmembrane adaptor protein involved in major histocompatibility complex class II signaling  .. 
PF15051 FAM198 protein<br>This family of proteins is found in eukaryotes. The function of this family is unknown. Murine FAM198B is downregulated by FGFR signalling  .. 
PF15052 TMEM169 protein family<br>Coggill P, Hetherington K. This domain is thought to be structured transmembrane helices and includes the intermediary cytoplasmic domain. It is found in eukaryotes, and is approximately 130 amino acids in length.. 
PF15053 Mjmu-R1-like protein family<br>Coggill P, Hetherington K. This protein family is thought to have a role in spermatogenesis. This family of proteins is found in eukaryotes. In humans, it is found in chromosome 17 open reading frame 75 (C17orf75). Proteins in this family are typically between 217 and 399 amino acids in length.. 
PF15054 Domain of unknown function (DUF4535)<br>Coggill P, Hetherington K. This family includes the uncharacterised protein C7orf73 that is found in eukaryotes. Members are generally less than 100 residues in length. Although the precise function of the domain is still unknown, members have a predicted N-terminal signal peptide sequence which suggests they are short secreted peptides.. 
PF15055 Domain of unknown function (DUF4536)<br>Coggill P, Hetherington K. This domain family is thought to be a transmembrane helix. It is found in eukaryotes, and is approximately 50 amino acids in length. In humans, it is located in the chromosomal position, C9orf123.. 
PF15056 Neuritin protein family<br>Coggill P, Hetherington K. The domain family Neuritin1 (NRN1) is a GPI-anchored protein expressed in post-mitotic-differentiating neurons in the developing nervous system  . NRN1 is a glutamate and neurotrophin receptor target encoding a neuronal protein that functions extracellularly to modulate neurite outgrowth (OMIM:607409).\.   This family of proteins is found in eukaryotes. Proteins in this family are typically between and 158 amino acids in length.. 
PF15057 Domain of unknown function (DUF4537)<br>The function of this domain family is unknown. It is found in eukaryotes, and is typically between 119 and 141 amino acids in length. In humans, it is found in the chromosomal position C11orf16.. 
PF15058 Speriolin N terminus<br>This family represents the N-terminus of the sperm centrosome protein speriolin [1-2].. 
PF15059 Speriolin C-terminus<br>This family represents the C-terminus of the sperm centrosome protein speriolin [1-2].. 
PF15060 Differentiation and proliferation regulator<br>Coggill P, Hetherington K. Pancreatic progenitor cell differentiation and proliferation factor-like protein (PPDFL) is alternatively named Exocrine differentiation and proliferation factor-like protein. PPDFL regulates exocrine cell fate. This protein is highly expressed in exocrine progenitor cells which eventually differentiate to form exocrine pancreatic cells  .. 
PF15061 Domain of unknown function (DUF4538)<br>Coggill P, Hetherington K. This protein family is thought to be a transmembrane helix. Its function remains unknown. This family of proteins is found in eukaryotes. Proteins in this family are typically between 58 and 87 amino acids in length.. 
PF15062 Haemopoietic lineage transmembrane helix<br>Coggill P, Hetherington K. ADP-ribosylation factor-like protein 6-interacting protein 6 (ARP6) is a transmembrane helix present in the J2E erythro-leukaemic cell line, but not its myeloid variants. In tissues, ARL-6 mRNA was most abundant in brain and kidney. While ARL-6 protein was predominantly cytosolic, it is known to bind to SEC61-beta subunit of a protein conducting channel SEC61p  .. 
PF15063 Thyroid cancer protein 1<br>Thyroid cancer protein 1 (TC1) is thought to decrease in apoptosis and increase cell proliferation. It is found to be expressed in thyroid papillary carcinoma  . This suggests its importance in thyroid cancer. The molecular mechanism of TC1, involves up-regulating cell signalling through ERK-1/2 signalling pathway and it positively regulates transition between the G1 and S phase in the cell cycle  . It is thought to positively regulate Wnt/beta-catenin signalling pathway by interacting with its repressor  . In humans, it is located in the chromosomal position, C8orf4. This family of proteins is found in eukaryotes and contains a conserved NIF sequence motif.. 
PF15064 Cation channel sperm-associated protein subunit gamma<br>This family represents the gamma subunit of the CATSPER, or cation channel sperm-associated protein complex. The complex appears only to be expressed in the flagellum of sperm. The complex is activated at alkaline intracellular pH, and being restricted to the flagellum is the mediating calcium channel.. 
PF15065 Lysosomal transcription factor, NCU-G1<br>NCU-G1 is a set of highly conserved nuclear proteins rich in proline with a molecular weight of approximately 44 kDa. Especially high levels are detected in human prostate, liver and kidney. NCU-G1 is a dual-function family capable of functioning as a transcription factor as well as a nuclear receptor co-activator by stimulating the transcriptional activity of peroxisome proliferator-activated receptor-alpha (PPAR-alpha)  .. 
PF15066 Cancer-associated gene protein 1 family<br>CAGE-1 is a family of proteins overexpressed in tumour tissues compared with surrounding tissues. CAGE-1 gene showed testis-specific expression among normal tissues and displayed wide expression in a variety of cancer cell lines and cancer tissues  .  CAGE-1 is predominantly expressed during post-meiotic stages. It localises to the acrosomal matrix and acrosomal granule showing it to be a component of the acrosome of mammalian spermatids and spermatozoa  .. 
PF15067 FAM124 family<br>Coggill P, Hetherington K. The exact function of this protein family remains unknown. This family of proteins is found in eukaryotes. Proteins in this family are approximately 480 amino acids in length. There is a conserved LFL sequence motif.. 
PF15068 FAM101 family<br>This protein family includes the actin regulators, Refilin A and B, however the exact function of this protein family remains unknown. Refilin is thought to stabilise peri-nuclear actin filament bundles, important in fibroblasts. Refilin is important as changes in localisation and shape in the nucleus plays a role in cellular and developmental processes  .. 
PF15069 FAM163 family<br>Coggill P, Hetherington K. This protein family is alternatively named Neuroblastoma-derived secretory proteins. Highly expressed in neuroblastoma compared to other tissues, suggesting that it may be used as a marker for metastasis in bone marrow  .. 
PF15070 Putative golgin subfamily A member 2-like protein 5<br>The function of the GOLGA2L5 protein family remains unknown. This family of proteins is thought to be found in the Golgi apparatus of eukaryotes. Proteins in this family are typically between and 840 amino acids in length.. 
PF15071 Transmembrane family 220, helix<br>Coggill P, Hetherington K. Transmembrane 220 (TMEM220) is a domain of unknown function. It is thought to be a transmembrane helix. The length of this protein is typically between 150 and 160 amino acids. In humans, it is found in the chromosomal position 17p13.1.. 
PF15072 Domain of unknown function (DUF4539)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 230 and 625 amino acids in length.. 
PF15073 Domain of unknown function (DUF4540)<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between 109 and 302 amino acids in length. In humans, it is found in the chromosomal position, C7orf72.. 
PF15074 Domain of unknown function (DUF4541)<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between 100 and 163 amino acids in length. There is a conserved KLHRDDR sequence motif. There is a single completely conserved residue Y that may be functionally important. In humans, the gene is found in the chromosomal location, C5orf49.. 
PF15075 Domain of unknown function (DUF4542)<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between 123 and 173 amino acids in length. There is a conserved IPPYN sequence motif. The gene that encodes this protein in humans, is found in the chromosomal position, C17orf98.. 
PF15076 Domain of unknown function (DUF4543)<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between and 90 amino acids in length. The human member of this family is C17orf67.. 
PF15077 Domain of unknown function (DUF4544)<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between 118 and 256 amino acids in length. The human member of this family is C11orf85.. 
PF15078 Domain of unknown function (DUF4545)<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between and 417 amino acids in length. The human member of this family is C1orf141.. 
PF15079 Domain of unknown function (DUF4546)<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between 88 and 212 amino acids in length. The human member of this family is C1orf49.. 
PF15080 Domain of unknown function (DUF4547)<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between 144 and 206 amino acids in length. The human member of this family is C3orf43.. 
PF15081 Domain of unknown function (DUF4548)<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between and 178 amino acids in length. The human member of this family is C1orf105.. 
PF15082 Domain of unknown function (DUF4549)<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between 143 and 1871 amino acids in length. The human member of this family is C6orf183.. 
PF15083 Colipase-like<br>Eberhardt RY, Coggill P, Hetherington K. This is a family of colipase-like proteins.. 
PF15084 Domain of unknown function (DUF4550)<br>This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is approximately 100 amino acids in length. This domain contains an N-terminal HXE motif.. 
PF15085 Neuropeptide FF<br>Eberhardt RY, Coggill P, Hetherington K. 
PF15086 Uncharacterised protein family UPF0542<br>This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. There is a conserved LSWKL sequence motif. This family includes human protein C5orf43.. 
PF15087 Protein of unknown function (DUF4551)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in metazoa. This family includes human protein C12orf56.. 
PF15088 NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial<br>Eberhardt RY, Coggill P, Hetherington K. 
PF15089 Domain of unknown function (DUF4552)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in vertebrates. Proteins in this family are typically between 425 and 649 amino acids in length.. 
PF15090 Domain of unknown function (DUF4553)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in vertebrates. This family includes the human protein C10orf12.. 
PF15091 Domain of unknown function (DUF4554)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in some vertebrates. This family includes human protein C11orf80.. 
PF15092 Uncharacterised protein family UPF0728<br>This family of proteins is functionally uncharacterised. This family of proteins is found in metazoa. There is a conserved GPY sequence motif.. 
PF15093 Domain of unknown function (DUF4555)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in metazoa.This family includes the human protein C7orf31.. 
PF15094 Domain of unknown function (DUF4556)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in vertebrates. This family includes human protein C1orf127.. 
PF15095 Interleukin 33<br>Eberhardt RY, Coggill P, Hetherington K. 
PF15096 G6B family<br>Eberhardt RY, Coggill P, Hetherington K. 
PF15097 Immunoglobulin J chain<br>Eberhardt RY, Coggill P, Hetherington K. 
PF15098 TMEM89 protein family<br>The function of this family of transmembrane proteins, TMEM89, has not, as yet, been determined. Members of this family are as yet uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are approximately 159 amino acids in length.. 
PF15099 Phosphoinositide-interacting protein family<br>Eberhardt RY, Coggill P, Hetherington K. The function of this family, PIRT, is not known, however it is predicted to be a multi-pass membrane protein. This family of proteins is thought to have a role in positively regulating TRPV1 channel activity via phosphatidylinositol 4,5-bisphosphate (PIP2). This family of proteins is found in eukaryotes. Proteins in this family are located in the cell membrane  . Proteins in this family are approximately 140 amino acids in length.. 
PF15100 TMEM187 protein family<br>Eberhardt RY, Coggill P, Hetherington K. The function of this family, TMEM187, is not known, however it is predicted to be a multi-pass membrane protein. Members of this family are as yet uncharacterised. This protein family is also alternatively named ITBA1. This family of proteins are found in eukaryotes. Proteins in this family are typically between 239 and 267 amino acids in length.. 
PF15101 Domain of unknown function (DUF4557)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. There is a conserved TVF sequence motif.. 
PF15102 TMEM154 protein family<br>Eberhardt RY, Coggill P, Hetherington K. The function of this family of transmembrane proteins has not, as yet, been determined. However, it is thought to be a therapeutic target for ovine lentivirus infection  . This family of proteins is found in eukaryotes and members are typically between 138 and 320 amino acids in length.. 
PF15103 G0/G1 switch protein 2<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins regulate apoptosis by binding to Bcl-2 and preventing the formation of the anti-apoptotic BAX-BCL2 heterodimers  .. 
PF15104 Domain of unknown function (DUF4558)<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between 78 and 121 amino acids in length. One member is annotated as being a flagellar associated protein.. 
PF15105 TMEM61 protein family<br>Eberhardt RY, Coggill P, Hetherington K. The function of this family of transmembrane proteins has not, as yet, been determined. Members of this family remain uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 150 and 211 amino acids in length.. 
PF15106 TMEM156 protein family<br>Eberhardt RY, Coggill P, Hetherington K. The function of this family of transmembrane proteins, TMEM 156, has not, as yet, been determined. Members of this family are as yet uncharacterised. This family of proteins are found in eukaryotes. Proteins in this family are approximately 310 amino acids in length. In humans, the gene encoding this protein is located in the chromosomal position, 4p14.. 
PF15107 FAM216B protein family<br>Eberhardt RY, Coggill P, Hetherington K. The function of this family of proteins, FAM216B, has not, as yet, been determined. Members of this family are as yet uncharacterised. This family of proteins are found in eukaryotes. Proteins in this family are approximately 150 amino acids in length. In humans, the gene encoding this protein is located in the position, C13orf30.. 
PF15108 Voltage-dependent calcium channel gamma-like subunit protein family<br>Eberhardt RY, Coggill P, Hetherington K. This family of transmembrane proteins, TMEM37, has a role in stabilising the calcium channel in an inactivated (closed) state. It is a subunit of the L-type calcium channels. This family of proteins are found in eukaryotes. Proteins in this family are approximately 210 amino acids in length.. 
PF15109 TMEM125 protein family<br>Eberhardt RY, Coggill P, Hetherington K. The function of this family of transmembrane proteins, TMEM125, has not, as yet, been determined. Members of this family are as yet uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 55 and 232 amino acids in length.. 
PF15110 TMEM141 protein family<br>Eberhardt RY, Coggill P, Hetherington K. The function of this family of transmembrane proteins, TMEM141, has not, as yet, been determined. Members of this family remain uncharacterised. TMEM141 protein family is found in eukaryotes. Proteins in this family are typically between 103 and 124 amino acids in length. There are two completely conserved residues (C and W) that may be functionally important.. 
PF15111 TMEM101 protein family<br>Eberhardt RY, Coggill P, Hetherington K. The function of this family of transmembrane proteins, TMEM101, has not, as yet, been determined. Members of this family remain uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 127 and 257 amino acids in length.. 
PF15112 Domain of unknown function (DUF4559)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. This family includes human protein CXorf38.. 
PF15113 TMEM117 protein family<br>Eberhardt RY, Coggill P, Hetherington K. The function of this family of transmembrane proteins has not, as yet, been determined. Members of this family are as yet uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 181 and 504 amino acids in length.. 
PF15114 Uncharacterised protein family UPF0640<br>This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 70 and 80 amino acids in length. There are two conserved sequence motifs: PGK and YRFLP.. 
PF15115 Domain of unknown function with conserved HDNR motif<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between 117 and 219 amino acids in length. There is a conserved HDNR sequence motif. The function is not known.. 
PF15116 CAMPATH-1 antigen<br>Eberhardt RY, Coggill P, Hetherington K. 
PF15117 Uncharacterised protein family UPF0697   <br>This family of uncharacterised proteins is found in vertebrates. Proteins in this family are typically around 100 amino acids in length.. 
PF15118 Domain of unknown function (DUF4560)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 66 and 78 amino acids in length. There are two conserved sequence motifs: FCK and RTL.. 
PF15119 Apolipoprotein C4<br>Eberhardt RY, Coggill P, Hetherington K. 
PF15120 Domain of unknown function (DUF4561)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes.. 
PF15121 TMEM71 protein family<br>Eberhardt RY, Coggill P, Hetherington K. The function of this family, TMEM71, is not known, however it is predicted to be a transmembrane protein. This family of proteins is found in eukaryotes and located in the cell membrane. Proteins in this family vary between 41 and 291 amino acids in length.. 
PF15122 TMEM206 protein family<br>Eberhardt RY, Coggill P, Hetherington K. The function of this family of transmembrane proteins, TMEM206, has not, as yet, been determined. Members of this family are remain uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are approximately 350 amino acids in length.. 
PF15123 Domain of unknown function (DUF4562)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. There is a conserved HRYQNPW sequence motif. This family includes the human protein C4orf45.. 
PF15124 Domain of unknown function (DUF4563)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. This family includes the human protein C3orf24.. 
PF15125 TMEM238 protein family<br>Eberhardt RY, Coggill P, Hetherington K. The function of this family of transmembrane proteins, TMEM238; has not, as yet, been determined. Members of this family are as yet uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 61 and 153 amino acids in length.. 
PF15127 Protein of unknown function (DUF4565)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes.  This family includes the human protein C2orf88.. 
PF15128 T-cell leukemia translocation-altered<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is required for osteoclastogenesis  .. 
PF15129 FAM150 family<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins known as FAM150 is found in eukaryotes. Members of this family are as yet uncharacterised. Proteins in this family are approximately 143 amino acids in length. The function of this family has not, as yet, been determined, however it is predicted to be a secretory protein family.. 
PF15130 Domain of unknown function (DUF4566)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. This family includes human protein C6orf62.. 
PF15131 Domain of unknown function (DUF4567)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in some mammals.. 
PF15132 Domain of unknown function (DUF4568)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes.. 
PF15133 Domain of unknown function (DUF4569)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes.  This family includes human protein CXorf21.. 
PF15134 Domain of unknown function (DUF4570)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. . 
PF15135 Uncharacterised protein UPF0515<br>This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes.  There are two conserved sequence motifs: PLT and HSC.. 
PF15136 Uncharacterised protein family UPF0449<br>This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes.  There is a conserved LPTRP sequence motif.. 
PF15137 Domain of unknown function (DUF4571)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in vertebrate. This family includes human protein C21orf62.. 
PF15138 Syncollin<br>Eberhardt RY, Coggill P, Hetherington K. This family has a role in zymogen granule exocytosis [1-2].. 
PF15139 Domain of unknown function (DUF4572)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 160 and 220 amino acids in length.. 
PF15140 Domain of unknown function (DUF4573)<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically approximately 360 amino acids in length.. 
PF15141 Domain of unknown function (DUF4574)<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between  and 86 amino acids in length.. 
PF15142 INCA1<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins inhibits cyclin-dependent kinase activity [1-2].. 
PF15143 Domain of unknown function (DUF4575)<br>This family of uncharacterised proteins is found in eukaryotes.. 
PF15144 Domain of unknown function (DUF4576)<br>This family of uncharacterised proteins is found in eukaryotes.. 
PF15145 Domain of unknown function (DUF4577)<br>Eberhardt RY, Coggill P, Hetherington K. The function of this family of proteins, has not, as yet, been determined. Members of this family are as yet uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically 128 amino acids in length.. 
PF15146 Fanconi anemia-associated <br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins plays a role in the Fanconi anemia-associated DNA damage response  .. 
PF15147 Domain of unknown function (DUF4578)<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between 44 and 137 amino acids in length.. 
PF15148 Apolipoprotein F<br>Eberhardt RY, Coggill P, Hetherington K. 
PF15149 Cation channel sperm-associated protein subunit beta protein family<br>Eberhardt RY, Coggill P, Hetherington K. The function of this family of transmembrane proteins, CATSPERB, has not, as yet, been determined. However, it is thought to play a role in sperm hyperactivation by associating with CATSPER1  . This family of proteins is found in eukaryotes. Proteins in this family are typically between 220 and 1107 amino acids in length.. 
PF15150 Phorbol-12-myristate-13-acetate-induced<br>Eberhardt RY, Coggill P, Hetherington K. This family carries a BH3 domain between residues 23 and 40.. 
PF15151 Response gene to complement 32 protein family<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between 44 and 130 amino acids in length. There is a conserved KLGDT sequence motif.. 
PF15152 Kisspeptin<br>Eberhardt RY, Coggill P, Hetherington K. 
PF15153 Cytokine-like protein 1<br>Eberhardt RY, Coggill P, Hetherington K. The function of this family of proteins, CYTL1, has not, as yet, been determined. However it is thought to be a secretory protein expressed in CD34+ haemopoietic cells  . This family of proteins is found in eukaryotes. Proteins in this family are typically between 134 and 145 amino acids in length. There are two conserved sequence motifs: PPTCYSR and DDC.. 
PF15155 MORF4 family-associated protein1<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between and 127 amino acids in length.. 
PF15156 Ceroid-lipofuscinosis neuronal protein 6<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between 190 and 310 amino acids in length.. 
PF15157 IQ-like<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins includes Human IQ domain-containing protein J (IQCJ).. 
PF15158 Domain of unknown function (DUF4579)<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between 192 and 239 amino acids in length. The human member of this family is C8orfK29.. 
PF15159 Phosphatidylinositol N-acetylglucosaminyltransferase subunit Y<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins represents subunit Y of the GPI-N-acetylglucosaminyltransferase (GPI-GnT) complex. It may regulate activity of the complex by binding the catalytic subunit, PIG-A  .. 
PF15160 Spermatogenesis-associated serine-rich protein 1<br>Eberhardt RY, Coggill P, Hetherington K. Spermatogenesis-associated serine-rich protein 1 is a serine-rich protein differentially expressed during spermatogenesis  .. 
PF15161 Neuropeptide-like<br>Eberhardt RY, Coggill P, Hetherington K. This family contains putative neuropeptides  .. 
PF15162 Domain of unknown function (DUF4580)<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between 63 and 185 amino acids in length.. 
PF15163 Meiosis-expressed<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is essential for spermiogenesis  .. 
PF15164 Williams-Beuren syndrome chromosomal region 28 protein homologue<br>WBS28 is an integral membrane family. These proteins have been identified as being linked to Williams-Beuren syndrome, OMIM:194050.  This family of proteins is found in eukaryotes, and are typically 266 amino acids in length.. 
PF15165 Meiotic recombination protein REC114-like<br>Eberhardt RY, Coggill P, Hetherington K. REC114-like members are necessary for meiotic DNA double-strand break formation. It functions in conjunction with Mei4. This family of proteins is found in eukaryotes. Proteins in this family are typically between 43 and 259 amino acids in length.. 
PF15167 Domain of unknown function (DUF4581)<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically 131 amino acids in length.. 
PF15168 Triple QxxK/R motif-containing protein family<br>Eberhardt RY, Coggill P, Hetherington K. TRIQK member-proteins share a characteristic triple repeat of the sequence QXXK/R, as well as a hydrophobic C-terminal region. Xenopus and mouse triqk genes are broadly expressed throughout embryogenesis, and mtriqk is also generally expressed in mouse adult tissues. TRIQK proteins are localized to the endoplasmic reticulum membrane.  This family is found in eukaryotes and members are typically between and 86 amino acids in length.. 
PF15169 Domain of unknown function (DUF4564)<br>This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. This family includes the human protein C17orf62.. 
PF15170 Calcium/calmodulin-dependent protein kinase II inhibitor<br>Eberhardt RY, Coggill P, Hetherington K. CaM-KIIN is the inhibitor of Calcium/calmodulin-dependent protein kinase II (CaMKII). CaMKII plays a central part in long-term potentiation, which underlies some forms of learning and memory. CaM-KIIN is a natural, specific inhibitor of CaMKII  . This family is found in eukaryotes.. 
PF15171 Neuropeptide secretory protein family, NPQ, spexin<br>Eberhardt RY, Coggill P, Hetherington K. Spexin, alternatively named NPQ, is a peptide hormone and is derived from a pro-hormone. This family of proteins has a role in inducing stomach wall contraction and is expressed in the submucosal layer of the mouse oesophagus and stomach. Spexin, like most peptide hormones, is a ligand for G-protein coupled receptors  . Spexin is also thought to have a role in controlling arterial blood pressure as well as salt and water balance  .. 
PF15172 Prolactin-releasing peptide<br>Eberhardt RY, Coggill P, Hetherington K. 
PF15173 FAM180 family<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between 117 and 182 amino acids in length. There are two conserved sequence motifs: ELAS and DFE. The function of this family is unknown.. 
PF15174 Prion-related protein testis-specific<br>Eberhardt RY, Coggill P, Hetherington K. PRNT is a family of prion-related proteins expressed in the testis [1,2].  This family of proteins is found in eukaryotes. Proteins in this family are typically between 52 and 94 amino acids in length.. 
PF15175 Spermatogenesis-associated protein 24<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins bind to DNA and to TBP (TATA box binding protein), TATA-binding protein (TBP)-related protein 2 (TRF2) and several polycomb factors. It is likely to function as a transcription regulator [1-2].. 
PF15176 Leucine-rich repeat family 19 TM domain<br>Eberhardt RY, Coggill P, Hetherington K. LRR19-TM is the single-span transmembrane region of LRRC19, a leucine-rich repeat protein family. LRRC19 functions as a transmembrane receptor inducing pro-inflammatory cytokines. This suggests its role in innate immunity  . This family of proteins is found in eukaryotes.. 
PF15177 Interleukin-28A<br>Eberhardt RY, Coggill P, Hetherington K. The protein family, Interleukin-28A, plays an important role in modulating the immune system. This protein family is induced by viral infection and interacts with a class II receptor  . This family of proteins is found in eukaryotes. Proteins in this family are typically between 145 and 195 amino acids in length.. 
PF15178 Mitochondrial import receptor subunit TOM5 homolog<br>Eberhardt RY, Coggill P, Hetherington K. This is a family of transmembrane proteins thought to form part of the pre-protein translocase complex of the outer mitochondrial membrane (TOM complex)  . This family of proteins is found in eukaryotes. Proteins in this family are approximately 50 amino acids in length.. 
PF15179 Myc target protein 1<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is regulated by the c-Myc oncoprotein. It regulates the expression of several other c-Myc target genes  .. 
PF15180 Neuropeptides B and W<br>Eberhardt RY, Coggill P, Hetherington K. The function of this family, NPBW, which includes Neuropeptides B and W, is thought to be involved in activating G-protein coupled receptors, GPR7 and GPR8. It is thought to play a regulatory role in the organisation of neuroendocrine signals accessing the anterior pituitary gland. It is predicted that this effect will stimulate the increase in water-drinking and food-intake. This suggests it plays a role in the hypothalamic response to stress. This family of proteins is found in eukaryotes [1,2].. 
PF15181 Spermatid-specific manchette-related protein 1<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins, SMRP1, is thought to have a role in spermatogenesis and may be involved in differentiation or function of ciliated cells  . This family of proteins is found in eukaryotes. Proteins in this family are typically approximately 260 amino acids in length.. 
PF15182 Otospiralin<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins, Otospiralin, has a role in maintaining the neurosensory epithelium of the inner ear [1,2]. This family of proteins is found in eukaryotes. Proteins in this family are approximately 90 amino acids in length.. 
PF15183 Melanocortin-2 receptor accessory protein family<br>Eberhardt RY, Coggill P, Hetherington K. This family is thought to be involved in cell trafficking. It is required for MC2R expression in certain cell types, suggesting that it is involved in the processing, trafficking or function of MC2R. MRAP may be involved in the intracellular trafficking pathways in adipocyte cells  . This family of proteins is found in eukaryotes. Proteins in this family are typically between 47 and 205 amino acids in length.. 
PF15184 Mitochondrial import receptor subunit TOM6 homolog<br>Eberhardt RY, Coggill P, Hetherington K. TOMM6 forms part of the pre-protein translocase complex of the outer mitochondrial membrane (TOM complex)  . This family of proteins is found in eukaryotes. Proteins in this family are typically between 43 and 74 amino acids in length.. 
PF15185 Bcl-2-modifying factor, apoptosis<br>Eberhardt RY, Coggill P, Hetherington K. BMF is thought to play a role in inducing apoptosis.  It is thought to bind to Bcl-2 proteins  . This family of proteins is found in eukaryotes. Proteins in this family are typically between 75 and 190 amino acids in length. There are two conserved sequence motifs: GNA and DQF.. 
PF15186 Testis-expressed sequence 13 protein family<br>Eberhardt RY, Coggill P, Hetherington K. The function of this family of proteins has not, as yet, been determined. However, members are thought to be encoded for by spermatogonially-expressed, germ-cell-specific genes  . This family of proteins is found in eukaryotes. Proteins in this family are typically between 177 and 384 amino acids in length. There are two conserved sequence motifs: FIN and LAL.. 
PF15187 Oesophageal cancer-related gene 4<br>Eberhardt RY, Coggill P, Hetherington K. Augurin is alternatively named oesophageal cancer-related gene 4 protein. The function of this family of transmembrane proteins, is to induce the senescence of oligodendrocyte and neural precursor cells, characterised by G1 arrest, RB1 dephosphorylation and accelerated CCND1 and CCND3 proteasomal degradation  . Augurin has been found to stimulate the release of ACTH via the release of hypothalamic CRF  . This family of proteins is found in eukaryotes. Proteins in this family are typically 145 amino acids in length.. 
PF15188 Coiled-coil domain-containing protein 167<br>Eberhardt RY, Coggill P, Hetherington K. The function of this family of coiled-coil domains, has not, as yet, been determined. Members of this family remain uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between and 103 amino acids in length.. 
PF15189 Domain of unknown function (DUF4582)<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between 126 and 788 amino acids in length. In humans, it is encoded for on the chromosomal position, C17orf104.. 
PF15190 Domain of unknown function (DUF4583)<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins, also known as UPF0694, is found in eukaryotes. Proteins in this family are around 135 amino acids in length. In humans, it is found on the chromosomal position, C14orf109.. 
PF15191 Synaptonemal complex central element protein 3<br>Eberhardt RY, Coggill P, Hetherington K. 
PF15192 TMEM213 family<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between and 154 amino acids in length. The function of this family is unknown.. 
PF15193 FAM24 family<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between and 101 amino acids in length. There are two conserved sequence motifs: FDLRT and CLY. The function of this family is unknown.. 
PF15194 TMEM191C family<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between and 302 amino acids in length. There are two conserved sequence motifs: QDC and RLF. The function of this family is unknown.. 
PF15195 TMEM210 family<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between and 149 amino acids in length. The function of this family is unknown.. 
PF15196 Activator of apoptosis harakiri<br>Eberhardt RY, Coggill P, Hetherington K. 
PF15197 Leukemia-associated protein 2<br>Eberhardt RY, Coggill P, Hetherington K. 
PF15198 Dexamethasone-induced<br>Eberhardt RY, Coggill P, Hetherington K. 
PF15199 D-amino acid oxidase activator<br>Eberhardt RY, Coggill P, Hetherington K. 
PF15200 Keratinocyte differentiation-associated<br>Eberhardt RY, Coggill P, Hetherington K. 
PF15201 Progressive rod-cone degeneration<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is involved in vision  .. 
PF15202 Adipogenin<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is involved in the stimulation of adipocyte differentiation and development  .. 
PF15203 TMEM95 family<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between 102 and 231 amino acids in length. There is a conserved LGG sequence motif. The function of this family is unknown.. 
PF15204 Kita-kyushu lung cancer antigen 1<br>Eberhardt RY, Coggill P, Hetherington K. This is a family of cancer antigens  .. 
PF15205 Placenta-specific protein 9<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins was identified as being enriched in placenta  .. 
PF15206 FAM209 family<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between and 170 amino acids in length. The function of this family is unknown.. 
PF15207 TMEM240 family<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between 54 and 175 amino acids in length. The function of this family is unknown.. 
PF15208 Rab15 effector<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins has a role in receptor recycling from the endocytic recycling compartment  .. 
PF15209 Interleukin 31<br>Eberhardt RY, Coggill P, Hetherington K. 
PF15210 Surfactant-associated protein 2<br>Eberhardt RY, Coggill P, Hetherington K. 
PF15211 VEGF co-regulated chemokine 1<br>Eberhardt RY, Coggill P, Hetherington K. 
PF15212 Spermatogenesis-associated protein 19, mitochondrial<br>Eberhardt RY, Coggill P, Hetherington K. 
PF15213 CMT1A duplicated region transcript 4 protein<br>Eberhardt RY, Coggill P, Hetherington K. 
PF15214 Peroxisomal testis-specific protein 1<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is testis-specific  .. 
PF15215 Follicular dendritic cell secreted peptide<br>Eberhardt RY, Coggill P, Hetherington K. 
PF15216 Thymic stromal lymphopoietin<br>Eberhardt RY, Coggill P, Hetherington K. 
PF15217 TSC21 family<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is testis-specific  .. 
PF15218 Spermatogenesis-associated protein 25<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins may be involved in spermatogenesis  .. 
PF15219 Testis-expressed 12<br>Eberhardt RY, Coggill P, Hetherington K. 
PF15220 Hypoxia-inducible lipid droplet-associated <br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins stimulate intracellular lipid accumulation, function as autocrine growth factors and enhance cell growth [1-2].. 
PF15221 Lens epithelial cell protein LEP503<br>Eberhardt RY, Coggill P, Hetherington K. This protein may be involved in lens epithelial cell differentiation [1-2].. 
PF15222 Kidney androgen-regulated <br>Eberhardt RY, Coggill P, Hetherington K. The function of this family is unknown.. 
PF15223 Domain of unknown function (DUF4584)<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are approximately 835 amino acids in length. The family is found in association with Pfam:PF02437.. 
PF15224 Scrapie-responsive protein 1<br>Eberhardt RY, Coggill P, Hetherington K. This protein family has an important function in acting against the prion protein, Scrapie [1,2].This family of proteins is found in eukaryotes. Proteins in this family are approximately 98 amino acids in length.. 
PF15225 Interleukin 32<br>Eberhardt RY, Coggill P, Hetherington K. 
PF15226 HCF-1 beta-propeller-interacting protein family<br>Eberhardt RY, Coggill P, Hetherington K. HPIP is a small cellular polypeptide that binds to the beta-propeller domain of HCF-1. HPIP regulates HCF-1 activity by modulating its subcellular localisation. HCF-1 is a cellular protein required by VP16 to activate the herpes simplex virus- immediate-early genes. VP16 is a component of the viral tegument and, after release into the cell, binds to HCF-1 and translocates to the nucleus to form a complex with the POU domain protein Oct-1 and a VP16-responsive DNA sequence. HPIP-mediated export may provide the pool of cytoplasmic HCF-1 required for import of virion-derived VP16 into the nucleus  .. 
PF15227 zinc finger of C3HC4-type, RING<br>This is a family of primate-specific Ret finger protein-like (RFPL) zinc-fingers of the C3HC4 type. Ret finger protein-like proteins are primate-specific target genes of Pax6, a key transcription factor for pancreas, eye and neocortex development  . This domain is likely to be DNA-binding  . This zinc-finger domain together with the RDM domain, Pfam:PF11002, forms a large zinc-finger structure of the RING/U-Box superfamily. RING-containing proteins are known to exert an E3 ubiquitin protein ligase activity with the zinc-finger structure being mandatory for binding to the E2 ubiquitin-conjugating enzyme  .. 
PF15228 Death-associated protein<br>Eberhardt RY, Coggill P, Hetherington K. 
PF15229 POM121 family<br>Eberhardt RY, Coggill P, Hetherington K. 
PF15230 Serine/arginine repetitive matrix protein C-terminus<br>Eberhardt RY, Coggill P, Hetherington K. This domain is found near to the C-terminus of Serine/arginine repetitive matrix proteins 3 and 4.. 
PF15231 Variable charge X/Y family<br>Eberhardt RY, Coggill P, Hetherington K. The variable charge X/Y (VCX/VCY) family of proteins has members on the Human X and Y chromosomes, is expressed in male germ calls and may play a role in spermatogenesis or in sex ratio distortion  .. 
PF15232 Domain of unknown function (DUF4585)<br>Eberhardt RY, Coggill P, Hetherington K. The function of this protein domain family is yet to be characterised. It is putatively thought to lie in the C-terminal domain of the DNA nucleotide repair protein, Xeroderma pigmentosa complementation group A (XPA). The function of XPA is to bind to DNA and repair any mismatched base pairs.  This domain family is often found in eukaryotes, and is approximately 70 amino acids in length. There is a conserved DPE sequence motif. In humans, this protein is encoded for in the chromosomal position, Chromosome 5 open reading frame 65. Mutations in the gene lead to myelodysplastic syndromes, where there is inefficient stem cell production in the bone marrow. This suggests that the protein may have a role in forming blood cells  .. 
PF15233 Synaptonemal complex central element protein 1<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins includes synaptonemal complex central element protein 1, a component of the synaptonemal complex involved in meiosis, and synaptonemal complex central element protein 1-like, which may be involved in meiosis [1-2].. 
PF15234 Linker for activation of T-cells<br>Eberhardt RY, Coggill P, Hetherington K. 
PF15235 G protein-regulated inducer of neurite outgrowth C-terminus<br>Eberhardt RY, Coggill P, Hetherington K. This represents the C-terminus of the G protein-regulated inducer of neurite outgrowth proteins  .. 
PF15236 Coiled-coil domain-containing protein 66<br>Eberhardt RY, Coggill P, Hetherington K. This protein family, named Coiled-coil domain-containing protein 66 (CCDC) refers to a protein domain found in eukaryotes, and is approximately 160 amino acids in length. CCDC66 protein is detected mainly in the inner segments of photoreceptors in many vertebrates including mice and humans. It has been found in dogs, that a mutation in the CCDC66 gene causes generalized progressive retinal atrophy (gPRA). This shows that the protein encoded for by this gene is vital for healthy vision and guards against photoreceptor cell degeneration. The structure of CCDC66 proteins includes a heptad repeat pattern which contains at least one coiled-coil domain. There are at least two or more alpha-helices which form a cable-like structure  .. 
PF15237 PTRF/SDPR family<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins includes muscle-related coiled-coil protein (MURC), protein kinase C delta-binding protein (PRKCDBP), polymerase I and transcript release factor (PTRF) and serum deprivation-response protein (SDPR). MURC activates the Rho/ROCK pathway  . PRKCDBP appears to act as an immune potentiator  . PTRF is involved in caveolae formation and function  . SDPR is involved in the targetting of protein kinase Calpha to caveolae  .. 
PF15238 FAM181<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between 256 and 426 amino acids in length.. 
PF15239 Domain of unknown function (DUF4586)<br>Eberhardt RY, Coggill P, Hetherington K. This protein family, refers to a domain of unknown function. The precise role of this protein domain remains to be elucidated. This family of proteins is found in eukaryotes and are typically between 256 and 320 amino acids in length. There is a single completely conserved residue, phenylalanine (F), that may be functionally important. In humans, the protein is found in the position, chromosome 4 open reading frame 47.. 
PF15240 Proline-rich<br>Eberhardt RY, Coggill P, Hetherington K. This family includes several eukaryotic proline-rich proteins.. 
PF15241 Cylicin N-terminus<br>Eberhardt RY, Coggill P, Hetherington K. This is the N-terminus of cylicin proteins, which may play a role in spermatid differentiation  .. 
PF15242 Family of FAM53<br>Eberhardt RY, Coggill P, Hetherington K. The FAM53 protein family refers to a family of proteins, which bind to a transcriptional regulator that modulates cell proliferation  . It is known to be highly important in neural tube development  . It is found in eukaryotes and is typically between 303 and 413 amino acids in length.. 
PF15243 Anaphase-promoting complex subunit 15<br>Eberhardt RY, Coggill P, Hetherington K. This is a component of the anaphase promoting complex/cyclosome  .. 
PF15244 Hydroxy-steroid dehydrogenase<br>Eberhardt RY, Coggill P, Hetherington K. This family also goes by the name of Spermatogenesis-associated protein 7 or SPAT7. It is an aldo-keto reductase (AKR) human type 3 3-alpha-hydroxy-steroid dehydrogenase (H3-alpha-HSD3, AKR1C2), and it plays a crucial role in the regulation of the intracellular concentrations of testosterone and 5-alpha-dihydrotestosterone (5-alpha-DHT), two steroids directly linked to the aetiology and the progression of many prostate diseases and cancer [1,2]. Mutations in the gene cause Leber congenital amaurosis (LCA) and juvenile retinitis pigmentosa (RP), the most common hereditary causes of visual impairment in infants and children  .. 
PF15245 Transcription cofactor vestigial-like protein 4<br>Eberhardt RY, Coggill P, Hetherington K. These proteins act as transcriptional enhancer factor (TEF-1) cofactors  .. 
PF15246 Nck-associated protein 5, Peripheral clock protein<br>Eberhardt RY, Coggill P, Hetherington K. NCKAP5 is short for Nck-associated protein 5, which is also known as the Peripheral clock protein. NCKAP5 is a protein family, which interacts with the SH3-containing region of the adaptor protein Nck. Nck is a protein that interacts with receptor tyrosine kinases and guanine nucleotide exchange factor Sos. The role of Nck can be thought of as similar to Grb2. The role of NCKAP5 is to assist Nck with its adaptor protein role  .. 
PF15247 Histone RNA hairpin-binding protein RNA-binding domain<br>Eberhardt RY, Coggill P, Hetherington K. This family represents the RNA-binding domain of histone RNA hairpin-binding protein  .. 
PF15248 Domain of unknown function (DUF4587)<br>Eberhardt RY, Coggill P, Hetherington K. This protein family is a domain of unknown function. The precise function of this protein domain remains to be elucidated. This domain family is found in eukaryotes, and is typically between 64 and 79 amino acids in length. There are two conserved sequence motifs: QNAQ and HHH. In humans, it is found in the position, chromosome 21 open reading frame 58.. 
PF15249 Glioma tumor suppressor candidate region<br>Eberhardt RY, Coggill P, Hetherington K. This domain family is found in eukaryotes, and is typically between 105 and 124 amino acids in length. There is a single completely conserved residue F that may be functionally important. Mutations in the gene for this protein in humans leads to the development of oligodendrogliomas  . There is evidence that these protein interacts with SH3 domains  .. 
PF15250 Raftlin<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins plays a role in the formation and/or maintenance of lipid rafts  .. 
PF15251 Domain of unknown function (DUF4588)<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between 200 and 274 amino acids in length. There is a conserved LYK sequence motif. There is a single completely conserved residue A that may be functionally important.. 
PF15252 Domain of unknown function (DUF4589)<br>Eberhardt RY, Coggill P, Hetherington K. This protein family is a domain of unknown function. The precise function of the protein domain remains to be elucidated. This family of proteins is found in eukaryotes and are typically between 215 and 293 amino acids in length. The protein contains two conserved sequence motifs: SSS and KST.. 
PF15253 SCL-interrupting locus protein N-terminus<br>Eberhardt RY, Coggill P, Hetherington K. 
PF15254 Coiled-coil domain-containing protein 14<br>Eberhardt RY, Coggill P, Hetherington K. This protein family, Coiled-coil domain-containing protein 14 (CCDC14) is a domain of unknown function. This family of proteins is found in eukaryotes. Proteins in this family are typically between 301 and 912 amino acids in length.. 
PF15255 WASH complex subunit CAP-Z interacting, central region<br>Eberhardt RY, Coggill P, Hetherington K. This domain is found on WASH complex subunits FAM21 and CAP-ZIP proteins, as well as on VPEF (vaccinia virus penetration factor). This family of proteins is found in eukaryotes. Proteins in this family are typically between 305 and 1321 amino acids in length. The exact function of this region is not known.. 
PF15256 SPATIAL<br>Eberhardt RY, Coggill P, Hetherington K. SPATIAL (stromal protein associated with thymii and lymph node) proteins may be involved in spermatid differentiation  .. 
PF15257 Domain of unknown function (DUF4590)<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins remains to be characterised and is a domain of unknown function. This domain family is found in eukaryotes, and is approximately 120 amino acids in length. There are two conserved sequence motifs: CCE and PCY. In humans, the gene encoding this protein lies in the position, chromosome 1 open reading frame 173.. 
PF15258 Protein family of FAM222A<br>Eberhardt RY, Coggill P, Hetherington K. This protein family, FAM222A are a domain of unknown function. This family of proteins is found in eukaryotes and are typically between 411 and 562 amino acids in length. In humans, the gene encoding this protein domain lies in the position, chromosome 12 open reading frame 34.. 
PF15259 G-2 and S-phase expressed 1<br>Eberhardt RY, Coggill P, Hetherington K. This family is the N-terminus of GTSE1 proteins. GTSE-1 (G2 and S phase-expressed-1) protein is specifically expressed during S and G2 phases of the cell cycle. It is mainly localised to the microtubules and when overexpressed delays the G2 to M transition. the full protein negatively regulates p53 transactivation function, protein levels, and p53-dependent apoptosis.  This domain family is found in eukaryotes, and is approximately 140 amino acids in length. There is a conserved FDFD sequence motif.. 
PF15260 Protein family FAM219A<br>Eberhardt RY, Coggill P, Hetherington K. This protein family, FAM219A is a domain of unknown function. This protein family has been found in eukaryotes. Proteins in this family are typically between 144 and 191 amino acids in length. There are two conserved sequence motifs: QLL and LDE.. 
PF15261 Domain of unknown function (DUF4591)<br>Eberhardt RY, Coggill P, Hetherington K. This protein family is a domain of unknown function. It is found in eukaryotes, and is approximately 120 amino acids in length. In humans, the gene encoding this protein lies in the position chromosome 11 open reading frame 63.. 
PF15262 Domain of unknown function (DUF4592)<br>Eberhardt RY, Coggill P, Hetherington K. This protein family is a domain of unknown function, which lies to the N-terminus of the protein. This domain family is found in eukaryotes, and is typically between 114 and 130 amino acids in length. There are two completely conserved residues (L and A) that may be functionally important. In humans, the gene that encodes this protein lies in the position, chromosome 2 open reading frame 55.. 
PF15263 Domain of unknown function (DUF4593)<br>Eberhardt RY, Coggill P, Hetherington K. This protein family is a putative uncharacterised protein family. Its existence is uncertain and its precise function is unknown. This family of proteins is thought to be found in eukaryotes. Proteins in this family are estimated to be around 155 amino acids in length.. 
PF15264 Tumour suppressing sub-chromosomal transferable candidate 4<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is expressed from a gene cluster where in humans the TSSC4 gene is not imprinted [1,2]. This same cluster is associated with the Beckwith-Wiedermann syndrome  .  This domain family is found in eukaryotes, and is typically between 120 and 147 amino acids in length. There is a conserved YSL sequence motif.. 
PF15265 FAM186A;<br>Eberhardt RY, Coggill P, Hetherington K. This protein family is a domain of unknown function.  This family of proteins is found in eukaryotes and are typically between 441 and 534 amino acids in length.. 
PF15266 Domain of unknown function (DUF4594)<br>Eberhardt RY, Coggill P, Hetherington K. This protein family is a domain of unknown function. The protein family is found in eukaryotes, and is typically between 170 and 183 amino acids in length.In humans, the gene encoding this protein lies in the position, chromosome 15 open reading frame 52.. 
PF15268 Dapper<br>Eberhardt RY, Coggill P, Hetherington K. This is a family of signalling proteins [1-2]. They act in a diverse range of signaling pathways and have a range of binding partners. They act as homo- and heterodimers  .. 
PF15269 Zinc-finger<br>Eberhardt RY, Coggill P, Hetherington K. this is a family of eukaryotic zinc-fingers.. 
PF15270 Metallo-carboxypeptidase inhibitor <br>Pfam-B_261362 (release 26.0). ACI44, a metallo-carboxypeptidase inhibitor, is one member of a battery of selective inhibitors protecting roundworms of the genus Ascaris, common parasites of the human gastrointestinal tract, from host enzymes and the immune system  .. 
PF15271 Spindle pole body component BBP1, Mps2-binding protein<br>Pfam-B_31027 (release 26.0). This N-terminal domain of BBP1, a spindle pole body component, interacts directly, though transiently, with the polo-box domain of Cdc5p. full length BBP1 localises at the cytoplasmic side of the central plaque periphery of the spindle pole body (SPB) and plays an important role in inserting a duplication plaque into the nuclear envelope and assembling a functional inner plaque  . Although not a membrane protein itself, BBP1 binds to Mps2 as well as to Spc29 and the half-bridge protein Kar1, thus providing a model for how the SPB core is tethered within the nuclear envelope and to the half-bridge  .. 
PF15272 Spindle pole body component BBP1, C-terminal<br>Pfam-B_58229 (release 26.0). This C-terminal domain of BBP1, a spindle pole body component, carries coiled-coils that are necessary for the localisation of BBP1 to the spindle pole body (SPB)  . Although not a membrane protein itself, BBP1 binds to Mps2 as well as to Spc29 and the half-bridge protein Kar1, thus providing a model for how the SPB core is tethered within the nuclear envelope and to the half-bridge  . 
PF15273 NHS-like<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins includes Nance-Horan syndrome protein (NHS)  .. 
PF15274 Muscular LMNA-interacting protein<br>Eberhardt RY, Coggill P, Hetherington K. MLIP is a Muscle-enriched A-type Lamin-interacting Protein, an innovation of amniotes, and is expressed ubiquitously and most abundantly in heart, skeletal, and smooth muscle. MLIP interacts directly and co-localises with lamin A and C in the nuclear envelope. MLIP also co-localises with promyelocytic leukemia (PML) bodies within the nucleus. PML, like MLIP, is only found in amniotes, suggesting that a functional link between the nuclear envelope and PML bodies may exist through MLIP  .. 
PF15275 PEHE domain<br>Eberhardt RY, Coggill P, Hetherington K. This domain was first identified in drosophila MSL1 (male-specific lethal 1)  . In drosophila it binds to the histone acetyltransferase males-absent on the first protein (MOF) and to protein male-specific lethal-3 (MSL3) [2-3].. 
PF15276 Protein phosphatase 1 binding<br>Eberhardt RY, Coggill P, Hetherington K. This domain contains a protein phosphatase 1 (PP1) binding site  .. 
PF15277 Exocyst complex component SEC3 N-terminal PIP2 binding PH<br>This is the N-terminal domain of fungal and eukaryotic Sec3 proteins. Sec3 is a component of the exocyst complex that is involved in the docking of exocytic vesicles with fusion sites on the plasma membrane.This N-terminal domain contains a cryptic pleckstrin homology (PH) fold, and all six positively charged lysine and arginine residues in the PH domain predicted to bind the PIP2 head group are conserved. The exocyst complex is essential for many exocytic events, by tethering vesicles at the plasma membrane for fusion. In fission yeast, polarised exocytosis for growth relies on the combined action of the exocyst at cell poles and myosin-driven transport along actin cables  .. 
PF15278 Sec3 exocyst complex subunit<br>This small Sec3 C-terminal domain family is based around the fission yeast protein, and is rather shorter than the budding yeast/vertebrate domain Sec3_C, family. Pfam:PF09763. In fact it is only this coiled-coil region that they carry in common. The full length fission yeast, UniProtKB:Q10324, protein Sec3 is redundant with Exo70 for viability and for the localisation of other exocyst subunits, suggesting that these components act as exocyst tethers at the plasma membrane. Sec3, Exo70 and Sec5 are transported by the myosin V Myo52 along actin cables. The exocyst holo-complex, including Sec3 and Exo70, is present on exocytic vesicles, which can reach cell poles by either myosin-driven transport or random walk  .. 
PF15279 Sine oculis-binding protein<br>Eberhardt RY, Coggill P, Hetherington K. SOBP is associated with syndromic and nonsyndromic intellectual disability. It carries a zinc-finger of the zf-C2H2 type at the N-terminus, and a highly characteristic C-terminal PhPhPhPhPhPh motif. The deduced 873-amino acid protein contains an N-terminal nuclear localisation signal (NLS), followed by 2 FCS-type zinc finger motifs, a proline-rich region (PR1), a putative RNA-binding motif region, and a C-terminal NLS embedded in a second proline-rich motif.  SOBP is expressed in various human tissues, including developing mouse brain at embryonic day 14. In postnatal and adult mouse brain SOBP is expressed in all neurons, with intense staining in the limbic system. Highest expression is in layer V cortical neurons, hippocampus, pyriform cortex, dorsomedial nucleus of thalamus, amygdala, and hypothalamus. Postnatal expression of SOBP in the limbic system corresponds to a time of active synaptogenesis  . the family is also referred to as Jackson circler, JXC1. In seven affected siblings from a consanguineous Israeli Arab family with mental retardation, anterior maxillary protrusion, and strabismus mutations were found in this protein [1,2].. 
PF15280 Protein aurora borealis N-terminus<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is required for the activation of the protein kinase Aurora-A  .. 
PF15281 Consortin C-terminus<br>Eberhardt RY, Coggill P, Hetherington K. Consortin is a trans-Golgi network cargo receptor involved in targeting connexins to the plasma membrane  .. 
PF15282 BMP-2-inducible protein kinase C-terminus<br>Eberhardt RY, Coggill P, Hetherington K. This family represents the C-terminus of BMP2K and related proteins [1-2].. 
PF15283 Domain of unknown function (DUF4595) with porin-like fold<br>JCSG target SP16885A/PDB 4ghb. Large family of predicted secreted proteins mostly from  CFG group, but also from Burkholderia, Pseudomonas and Streptomyces. Function of these proteins is not known. A 3D structure of a representative of this family from  Bacteroides uniformis was solved by JCSG and deposited to PDB as 4ghb. There is some overlap with RHS-repeat (PF05593) family despite lack of obvious repeats in the structure. 
PF15284 Phage-encoded virulence factor<br>Pfam-B_45688 (release 26). PAGK represents a new of virulence factors that is translocated into the host cytoplasm via bacterial outer membrane vesicles (OMV). Members are small proteins composed of ¡­70 amino acids. In Salmonella they are secreted independently of the SPI-2 type-III secretion system, T3SS. The OMV functions as a vehicle for transferring virulence determinants to the cytoplasm of the infected host cell. OMVs are released from the cell envelopes of Gram-negative bacteria and comprise a variety of outer membrane and periplasmic constituents, including proteins, phospholipids, lipopolysaccharides, and DNA  .. 
PF15285 Beclin-1 BH3 domain, Bcl-2-interacting<br>The BH3 domain is a short motif known to bind to Bcl-xLs. This interaction is important in apoptosis.. 
PF15286 Apoptosis regulator M11, B cell 2 leukaemia/lymphoma like<br>Pfam:PF02180.  Bcl-2_3 is a small family of eukaryotic proteins associated with autophagy. The family is found in association with Pfam:PF00452,. 
PF15287 KRBA1 family repeat<br>KRBA1 is a short repeating motif found in mammalian proteins. It is characterised by a highly conserved sequence of residues, SSPLxxLxxCLK.  The function of the repeat, which can be present in up to seven copies, is unknown as is the function of the full length proteins.. 
PF15288 Zinc knuckle<br>This Zinc knuckle is found in FAM90A mammalian proteins.. 
PF15289 Regulatory factor X-associated C-terminal binding domain<br>This C-terminal domain of Regulatory factor X-associated protein binds to RFXANK [1,2], the Ankyrin-repeat regulatory factor X proteins. RFXA is part of the RFX complex, Mutants of either RFXAP or RFXANK protein fail to bind to each other. RFX5 binds only to the RFXANK-RFXAP scaffold and not to either protein alone, and neither the scaffold nor RFX5 alone can bind DNA. The binding of the RFXANK-RFXAP scaffold to RFX5 leads to a conformational change in the latter that exposes the DNA-binding domain of RFX5. The DNA-binding domain of RFX5 anchors the RFX complex to MHC class II X and S promoter boxes  .. 
PF15290 Golgi-localised syntaxin-1-binding clamp<br>Eberhardt RY, Coggill P, Hetherington K. Syntaphilin or Syntabulin is a family of eukaryotic proteins. Syntaphilin binds to syntaxin-1 thereby inhibiting SNARE complex formation by absorbing free syntaxin-1. So it is a syntaxin-1 clamp that controls SNARE assembly.. 
PF15291 Dermcidin, antibiotic peptide<br>Dermcidin is a family of peptides produced in the sweat to protect against pathogenic Gram-positive bacteria.. 
PF15292 Treslin N-terminus<br>Eberhardt RY, Coggill P, Hetherington K. This family represents the N-terminus of treslin, a checkpoint regulator which plays a role in DNA replication preinitiation complex formation [1-2].. 
PF15293 Nuclear fragile X mental retardation-interacting protein 2<br>Eberhardt RY, Coggill P, Hetherington K. 
PF15294 Leucine zipper<br>Eberhardt RY, Coggill P, Hetherington K. This family includes Leucine zipper transcription factor-like protein 1 (LZTFL1)   and Leucine zipper protein 2 (LUZP2)  .. 
PF15295 Coiled-coil domain-containing protein 50  N-terminus<br>Eberhardt RY, Coggill P, Hetherington K. 
PF15296 Codanin-1 C-terminus<br>Eberhardt RY, Coggill P, Hetherington K. This domain is found near to the C-terminus of codanin-1  . . 
PF15297 Cytoskeleton-associated protein 2 C-terminus<br>Eberhardt RY, Coggill P, Hetherington K. This family includes the C-terminus of CKAP2 and CKAP2L. CKAP2 is a microtubule associated protein which stabilises microtubules  .. 
PF15298 AJAP1/PANP C-terminus<br>Eberhardt RY, Coggill P, Hetherington K. This family includes the C-terminus of adherens junction-associated protein 1 (AJAP1) and of PILR-associating neural protein (PANP). AJAP1 inhibits cell adhesion and migration  . PANP is a ligand for the immune inhibitory receptor paired immunoglobulin-like type 2 receptor alpha  .. 
PF15299 Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8<br>Eberhardt RY, Coggill P, Hetherington K. This domain is found in amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8 protein  .. 
PF15300 INTS6/SAGE1/DDX26B/CT45 C-terminus<br>Eberhardt RY, Coggill P, Hetherington K. This domain is found at the C-terminus of integrator complex subunit 6 (INTS6), sarcoma antigen 1 (SAGE1), protein DDX26B (DDX26B) and members of the cancer/testis antigen family 45.. 
PF15301 SLAIN motif-containing family<br>Eberhardt RY, Coggill P, Hetherington K. The SLAIN motif containing family is named after the presence of a SLAIN motif in SLAIN1  . They are a family of microtubule plus-end tracking proteins  .. 
PF15302 P33 mono-oxygenase<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins contains a flavine-containing mono-oxygenase motif. It may have a role in the regulation of neuronal survival, differentiation and axonal outgrowth  .. 
PF15303 E3 ubiquitin-protein ligase Arkadia N-terminus<br>Eberhardt RY, Coggill P, Hetherington K. This domain is found at the N-terminus of E3 ubiquitin-protein ligase Arkadia  .. 
PF15304 A-kinase anchor protein 2 C-terminus<br>Eberhardt RY, Coggill P, Hetherington K. This family includes the C-terminus of A-kinase anchor protein 2 (AKAP2). It includes the site where the regulatory subunits (RII) of protein kinase AII binds  .. 
PF15305 Intraflagellar transport protein 43<br>Eberhardt RY, Coggill P, Hetherington K. Intraflagellar transport protein 43 (IFT43) is a subunit of the IFT complex A (IFT-A) machinery of primary cilia  .. 
PF15306 LIN37<br>Eberhardt RY, Coggill P, Hetherington K. LIN37 is a component of the DREAM (or LINC) complex which represses cell cycle-dependent genes in quiescent cells and plays a role in the cell cycle-dependent activation of G2/M genes [1-2].. 
PF15307 Sperm acrosome-associated protein 7<br>SPACA7 is a family of eukaryotic proteins expressed in the testes. Proteins in this family are typically between 104 and 195 amino acids in length. There is a conserved DEIL sequence motif. The function is not known.. 
PF15308 CEP170 C-terminus<br>Eberhardt RY, Coggill P, Hetherington K. This family includes the C-terminus of centrosomal protein of 170 kDa (CEP170)  .. 
PF15309 ALMS motif<br>Eberhardt RY, Coggill P, Hetherington K. This domain is found at the C-terminus of Alstrom syndrome protein 1 (ALMS1), KIAA1731 and C10orf90 [1-2].. 
PF15310 Vitamin A-deficiency (VAD) rat model signalling<br>VAD1-2 is a family of proteins found in eukaryotes. The family is expressed in testes and is involved in signalling during spermatogenesis.. 
PF15311 Hydrolethalus syndrome protein 1 C-terminus<br>Eberhardt RY, Coggill P, Hetherington K. 
PF15312 Junctional sarcoplasmic reticulum protein<br>JSRP, junctional sarcoplasmic reticulum protein 1, or junctional-face membrane protein of 45 kDa homologue, is a family of eukaryotic proteins. The family is to the junctional face membrane of the skeletal muscle sarcoplasmic reticulum (SR); it colocalises with its Ca2+-release channel (the ryanodine receptor), and interacts with calsequestrin and the skeletal-muscle dihydro-pyridine receptor Cav1. It is key for the functional expression of voltage-dependent Ca2+ channels.. 
PF15313 Hexamethylene bis-acetamide-inducible protein<br>Eberhardt RY, Coggill P, Hetherington K. HEXIM is a transcriptional regulator that functions as a general RNA polymerase II transcription inhibitor. In cooperation with 7SK snRNA it sequesters P-TEFb in a large inactive 7SK snRNP complex preventing RNA polymerase II phosphorylation and subsequent transcriptional elongation. HEXIM may also regulate NF-kappa-B, ESR1, NR3C1 and CIITA-dependent transcriptional activity.. 
PF15314 Proline-rich acidic protein 1, pregnancy-specific uterine<br>PRAP, or proline-rich acidic protein 1, is a family of eukaryotic proteins. PRAP is abundantly expressed in the epithelial cells of the human liver, kidney, gastrointestinal tract, and cervix. It is significantly down-regulated in hepatocellular carcinoma and right colon adenocarcinoma compared with the respective adjacent normal tissues. In the mouse it is expressed in the epithelial cells of the mouse and rat gastrointestinal tracts, and pregnant mouse uterus. This article describes the isolation, distribution, and functional characterization of the human homologue. PRAP was abundantly expressed in the epithelial cells of the human liver, kidney, gastrointestinal tract, and cervix. PRAP plays an important role in maintaining normal growth suppression  .. 
PF15315 Facioscapulohumeral muscular dystrophy candidate 2<br>This family of proteins is found in eukaryotes. The family is localised close to the D4Z4 repeats on chromosome 4 and 10 that are associated with the autosomal dominant facioscapulohumeral muscular dystrophy (FSHD). FRG2 are transcriptionally upregulated in FSHD myoblast cultures suggesting involvement in the pathogenesis of FSHD  .. 
PF15316 MyoD family inhibitor<br>Eberhardt RY, Coggill P, Hetherington K. Members of this family inhibits the transactivation activity of the MyoD family of myogenic factors  . They affect axin-mediated regulation of the Wnt and JNK signaling pathways  , and regulate expression from viral promoters  .. 
PF15317 Cardiac transcription factor regulator, Developmental protein<br>Eberhardt RY, Coggill P, Hetherington K. The family of proteins are cardiac transcription regulators, named Lbh, short for Limb, bud and heart. They regulate embryological development in the heart  .  More specifically, in humans, they may act as transcriptional activators in MAPK signaling pathway to mediate cellular functions  . This family of proteins is found in eukaryotes. Proteins in this family are typically between 92 and 116 amino acids in length.. 
PF15318 Putative Bcl-2 like protein of testis<br>This family of proteins is found in eukaryotes. The family may represent a set of Bcl-2-like proteins involved in apoptosis, see UniProt:Q9BQM9.. 
PF15319 RAD9, RAD1, HUS1-interacting nuclear orphan protein<br>RHINO, or RAD9, RAD1, HUS1-interacting nuclear orphan, is a family of eukaryotic proteins  . Under genotoxic stresses such as ionizing radiation during the S phase, RHINO plays a role in DNA damage response signalling. It is recruited to sites of DNA damage through interaction with the 9-1-1 cell-cycle checkpoint response complex and TOPBP1 in a ATR-dependent (ataxia telangiectasia and Rad3-related) manner. It is required for the progression of the G1 to S phase transition of breast cancer cells, and it is known to play a role in the stimulation of CHEK1 phosphorylation. It interacts with RAD9A, RAD18, TOPBP1 and UBE2N  .. 
PF15320 mRNA cap methylation, RNMT-activating mini protein<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 102 and 154 amino acids in length. There is a single completely conserved residue D that may be functionally important.  RAM is a family of eukaryotic proteins that are an obligate component of the mammalian cap methyltransferase, RNMT (RNA guanine-7 methyltransferase). RAM consists of an N-terminal RNMT-activating domain and a C-terminal RNA-binding domain. Either RAM or RNMT independently have rather weak binding affinity for RNA, but together their RNA affinity is significantly increased. RAM is necessary for efficient cap methylation, maintaining mRNA expression levels, for mRNA translation and for cell viability.. 
PF15321 ATPase family AAA domain containing 4<br>ATAD4 is a family of proteins is found in eukaryotes. The family is also known as PRR15L, or proline-rich 15-like. ATAD4 is expressed almost exclusively in post-mitotic cells both during foetal development and in adult tissues, such as the intestinal epithelium and the testis. Its expression in mouse and human gastrointestinal tumours is linked, directly or indirectly, to the disruption of the Wnt signaling pathway.. 
PF15322 Protein missing in infertile sperm 1, putative<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 249 and 341 amino acids in length.. 
PF15323 Developmental protein<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins are found in eukaryotes. These proteins have an important role to play in developmental biology, particularly embryogenesis. It plays an important role in cell survival and axial pattern  . It is also thought to be a crucial subunit in the tRNA splicing ligase complex . Proteins in this family are typically between 141 and 232 amino acids in length. There are two conserved sequence motifs: HPE and PQR.. 
PF15324 Hedgehog signalling target<br>Eberhardt RY, Coggill P, Hetherington K. TALPID3 is a family of eukaryotic proteins that are targets for Hedgehog signalling. Mutations in this gene noticed first in chickens lead to multiple abnormalities of development.. 
PF15325 Modulator of retrovirus infection<br>MRI, or modulator of retrovirus infection, is a family of eukaryotic proteins that regulate the activity of the proteasome in the uncoating of retroviruses  .. 
PF15326 Testis expressed sequence 15<br>TEX15 is a family of eukaryotic proteins that is required for chromosomal synapsis and meiotic recombination. TEX15 regulates the loading of DNA repair proteins onto sites of double-stranded-breaks and, thus, its absence causes a failure in meiotic recombination  . Two polymorphisms in the TEX15 gene could be considered the genetic risk factors for spermatogenic failure in the Chinese Han population  .. 
PF15327 Tankyrase binding protein C terminal domain<br>Eberhardt RY, Coggill P, Hetherington K. This protein domain family is found at the C-terminal end of the Tankyrase binding protein in eukaryotes. The precise function of this protein is still unknown. However, it is known interacts with the enzyme tankyrase, a telomeric poly(ADP-ribose) polymerase, by binding to it. Tankyrin catalyses poly(ADP-ribose) chain formation onto proteins. More specifically, it binds to the ankyrin domain in tankyrase  . The protein domain is approximately 170 amino acids in length and contains two conserved sequence motifs: FPG and LKA.. 
PF15328 Putative GRINL1B complex locus protein 2<br>Eberhardt RY, Coggill P, Hetherington K. This protein family is named Putative GRINL1B complex locus protein 2. GRINL1B is short for: glutamate receptor, ionotropic, N-methyl D-aspartate-like 1B. The name indicates what sort of receptor it is thought to be, a ligand gated ion channel specific to the neurotransmitter Glutamate. This family of proteins is found in eukaryotes. Proteins in this family are typically between 325 and 463 amino acids in length. The protein is thought to be the product of a pseudogene with a role in helping assemble a gene transcription unit  .. 
PF15330 SHP2-interacting transmembrane adaptor protein, SIT<br>SIT, or SHP2-interacting transmembrane adaptor protein, is a disulfide-linked dimer that regulates human T Cell activation.. 
PF15331 Cellular tumour antigen p53-inducible 5<br>TP53IP5 suppresses cell growth, and its intracellular location and expression change in a cell-cycle-dependent manner.. 
PF15332 Lck-interacting transmembrane adapter 1<br>LIME1 is a family of eukaryotic transmembrane adaptors. It plays an important role in linking BCR stimulation to B-cell activation and is expressed in primary B cells. LIME localises to lipid rafts in T cells in response to TCR stimulation  , and is phosphorylated by Lck and recruits signalling molecules such as Lck, PI3K, Grb2, Gads, and SHP-2  . LIME acts as the transmembrane adaptor linking BCR-induced membrane-proximal signalling to B-cell activation  .. 
PF15333 TATA box-binding protein-associated factor 1D<br>TAF1D is a family of eukaryotic proteins that are members of the SL1 complex The SL1 complex includes TBP and TAF1A, TAF1B and TAF1C, and plays a role in RNA polymerase I transcription [1,2]. Alternatives names have included 'JOSD3, Josephin domain containing 3'.. 
PF15334 Aurora kinase A and ninein interacting protein<br>AIB is a family of eukaryotic proteins necessary for the adequate functioning of Aurora-A, a protein involved in chromosome alignment, centrosome maturation, mitotic spindle assembly and aspects of tumourigenesis. AIB is likely to act as a regulator of Aurora-A activity.. 
PF15335 Caspase activity and apoptosis inhibitor 1<br>CAAP1, or caspase activity and apoptosis inhibitor 1, is a family of eukaryotic proteins involved in the regulation of apoptosis. It modulates a caspase-10 dependent mitochondrial caspase-3/9 feedback amplification loop.. 
PF15336 Autism susceptibility gene 2 protein<br>Auts2, or FBRSL2, Fibrosin-1-like protein 2, is a family of eukaryotic proteins associated both with a susceptibility to autism   and with influencing the number of corpora lutea produced by breeding sows  .. 
PF15337 Vascular protein family Vasculin-like 1<br>Eberhardt RY, Coggill P, Hetherington K. GC-rich promoter-binding protein 1-like 1 or Vasculin-like protein family 1, is likely to be a transcription factor. The domain family is found in eukaryotes, and is approximately 90 amino acids in length.. 
PF15338 p53-regulated apoptosis-inducing protein 1<br>TPIP1 is a family of eukaryotic proteins whose expression is induced by wild-type p53. Ectopically expressed TPIP1, which is localised within mitochondria, leads to apoptotic cell death through dissipation of mitochondrial A(psi)m. Phosphorylation of p53 Ser-46 regulates the transcriptional activation of TPIP1, thereby mediating p53-dependent apoptosis.. 
PF15339 Acrosome formation-associated factor<br>Afaf is a family of single pass type I membrane proteins. Afaf is a vesicle factor derived from the early endosome trafficking pathway that is involved in the biogenesis of the acrosome on the maturing spermatozoon head.. 
PF15340 Cooperator of PRMT5 family<br>COPR5 is a family of histone H4-binding proteins expressed in the nucleus. It interacts with the N-terminus of histone H4 thereby mediating the association between histone H4 and PRMT5, PRMT5, the Janus kinase-binding protein 1 that catalyses the formation of symmetric dimethyl-arginine residues in proteins. COPR5 is specifically required for histone H4 'Arg-3' methylation mediated by PRMT5, but not histone H3 'Arg-8' methylation, suggesting that it modulates the substrate specificity of PRMT5. This family of proteins is found in eukaryotes.. 
PF15341 Ribosome biogenesis protein SLX9<br>Eberhardt RY, Coggill P, Hetherington K. SLX9 is present in pre-ribosomes from an early stage and is implicated in the processing events that remove the ITS1 spacer sequences. In eukaryotes, biogenesis of ribosomes starts in the nucleolus with transcription by RNA polymerase I of a large precursor RNA molecule, called 35S pre-rRNA in yeast, in which the 18S, 5.8S, and 25S mature rRNAs reside, while RNA polymerase III transcribes a 3'-extended pre-5S rRNA. The 35S precursor also contains external transcribed spacer elements (5' and 3'-ETS) at either end as well as internal transcribed spacers (ITS1 and ITS2) that separate the mature sequences  .. 
PF15342 FAM212 family<br>Eberhardt RY, Coggill P, Hetherington K. This domain family is found in eukaryotes, and is approximately 60 amino acids in length.. 
PF15343 Decidual protein induced by progesterone family<br>DEPP is a family of proteins expressed in various tissues, including pancreas, placenta, ovary, testis and kidney. High levels are found during the first trimester.  Its expression is induced by progesterone, testosterone and, to a much lower extent, oestrogen. The family is alternatively known as fasting-induced gene protein, FIG.. 
PF15344 FAM217 family<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 329 and 507 amino acids in length. There is a conserved YPDFLP sequence motif.. 
PF15345 Transmembrane protein 51<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 233 and 253 amino acids in length.. 
PF15346 Arginine and glutamate-rich 1<br>ARGLU, arginine and glutamate-rich 1 protein family, is required for the oestrogen-dependent expression of ESR1 target genes. It functions in cooperation with MED1. The family of proteins is found in eukaryotes.. 
PF15347 Phosphoprotein associated with glycosphingolipid-enriched<br>PAG, or Cbp/PAG (Csk binding protein/phospho-protein associated with glycosphingolipid-enriched microdomains) is a transmembrane family that has a negative regulatory role in T-cell activation through being an adapter for C-terminal Src kinase, Csk. This family of proteins is found in eukaryotes.. 
PF15348 Gemini of Cajal bodies-associated protein 8<br>Eberhardt RY, Coggill P, Hetherington K. GEMIN8 proteins are found in the nuclear bodies called gems (Gemini of Cajal bodies) that are often in proximity to Cajal (coiled) bodies themselves. They are also found in the cytoplasm  . The family is part of the SMN (survival motor neurone) complex that plays an essential role in spliceosomal snRNP assembly in the cytoplasm and is required for pre-mRNA splicing in the nucleus. GEMIN8 binds directly to SMN1 and mediates the interaction of the GEMIN6-GEMIN7 heterodimer  .. 
PF15349 DDB1- and CUL4-associated factor 16<br>DCA16 is a family of eukaryotic proteins that interacts with DDB1 and CUL4A. The family may function as a substrate receptor for the CUL4-DDB1 E3 ubiquitin-protein ligase complex  .. 
PF15350 Ewing's tumour-associated antigen 1 homologue<br>This family of proteins is found in eukaryotes, where members are expressed at high levels in the brain, liver kidney and Ewing tumour cell lines. Proteins in this family are typically between 648 and 898 amino acids in length.. 
PF15351 Junctional protein associated with coronary artery disease<br>JCAD is a component of VE-cadherin-based cell-cell junctions in endothelial cells.  The cell-cell or adherens junction is an adhesion complex that plays a crucial role in the organisation and function of epithelial and endothelial cellular sheets. These junctions join the actin cytoskeleton to the plasma membrane to form adhesive contacts between cells or between cells and extracellular matrix. The junctions also mediate both cell adhesion and cell-signalling. JCAD localises close to the apical membrane in epithelial cells. This family is found in eukaryotes.. 
PF15352 Susceptibility to monomelic amyotrophy<br>This family of proteins is associated with a susceptibility to monomelic amyotrophy.. 
PF15353 Headcase protein family homologue<br>Eberhardt RY, Coggill P, Hetherington K. HECA was characterised first in Drosophila where it regulates the proliferation and differentiation of cells during adult morphogenesis. In humans, HECA affects cell cycle progression and proliferation in head and neck cancer cells. It by slows down cell division of oral squamous cell carcinoma cells and may thereby act as a tumour-suppressor in head and neck cancers.   . 
PF15354 Kidney-associated antigen 1<br>KAAG1, kidney-associated antigen 1, or RU2AS (RU2 antisense gene protein) has been found in mammals. It is expressed in testis and kidney, and, at lower levels, in urinary bladder and liver. It is expressed by a high proportion of tumours of various histologic origin, including melanomas, sarcomas and colorectal carcinomas.. 
PF15355 Stretch-responsive small skeletal muscle X protein, Chisel<br>The murine X-linked gene Chisel (Csl/Smpx) is selectively expressed in cardiac and skeletal muscle cells. It localises to the costameric cytoskeleton of muscle cells through its association with focal adhesion proteins, where it may participate in regulating the dynamics of actin through the Rac1/p38 kinase pathway. Thus it is implicated in the maintenance of muscle integrity and in responses to biomechanical stress.. 
PF15356 Psoriasis susceptibility locus 2<br>SPR1 is psoriasis susceptibility locus 2 protein family.. 
PF15357 Psoriasis susceptibility 1 candidate 1<br>This family is considered a candidate for susceptibility to psoriasis.. 
PF15358 Testis-specific serine kinase substrate<br>TSKS, testis-specific serine kinase substrate, is expressed in the testis and is downregulated in cancerous testicular tissue, in comparison with adjacent normal tissue. TSKS expression is very low to undetectable in seminoma, teratocarcinoma, embryonal, and Leydig cell tumours, while high in testicular tissue adjacent to tumours which contain pre-malignant carcinoma in situ  . Recently it has been shown in human testis to be localised to the equatorial segment of ejaculated human sperm. The finding of a TSKS family member in mature sperm suggests that this family of kinases might play a role in sperm function  . TSKS is localised during spermiogenesis to the centrioles of post-meiotic spermatids, where it reaches its greatest concentration during the period of flagellogenesis  .. 
PF15359 Carnitine deficiency-associated protein 3<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between 128 and 251 amino acids in length. CDV3 is also known as TPP36 - tyrosine-phosphorylated protein 36. The function is not known.. 
PF15360 APJ endogenous ligand<br>Apelin is among the most potent stimulators of cardiac contractility known. The apelin-APJ signaling pathway is an important novel mediator of cardiovascular control  . Apelin is an adipokine secreted by adipocytes where it is co-expressed with apelin receptor (APJ) in adipocytes.  It suppresses adipogenesis through MAPK kinase/ERK dependent pathways and prevents lipid droplet fragmentation, thereby inhibiting basal lipolysis through AMP kinase dependent enhancement of perilipin expression. It also inhibits hormone-stimulated acute lipolysis through decreasing perilipin phosphorylation. Apelin induces a decrease of free fatty acid release via its dual inhibition on adipogenesis and lipolysis  . As a vaso-active and vascular cell growth-regulating peptide Apelin is a target of the BMP pathway, the TGF-beta/bone morphogenic protein (BMP) system - a major pathway for angiogenesis  .. 
PF15361 Resistance to inhibitors of cholinesterase homologue 3<br>Eberhardt RY, Coggill P, Hetherington K. RIC3 is a protein associated with nicotinic acetylcholine receptors (nAChRs), neurotransmitter-gated ion channels expressed at the neuromuscular junction and within the central and peripheral nervous systems. It can enhance functional expression of multiple nAChR subtypes. RIC3 promotes functional expression of homomeric alpha-7 and alpha-8 nicotinic acetylcholine receptors at the cell surface.. 
PF15362 Enamelin<br>ENAMELIN is involved in the mineralisation and structural organisation of enamel. It is necessary for the extension of enamel during the secretory stage of dental enamel formation. The proteins are expressed in teeth, particularly in odontoblasts, ameloblasts and cementoblasts.. 
PF15363 Domain of unknown function (DUF4596)<br>Eberhardt RY, Coggill P, Hetherington K. This domain family is found in eukaryotes, and is approximately 50 amino acids in length. There is a conserved ELET sequence motif. There are two completely conserved residues (S and E) that may be functionally important.. 
PF15364 PAXIP1-associated-protein-1 C term PTIP binding protein<br>Eberhardt RY, Coggill P, Hetherington K. This protein domain family is the C-terminal domain of PAXIP1-associated-protein-1, which also goes by the name PTIP-associated protein 1. This family of proteins is found in eukaryotes. The function of this protein is to localise at the site of DNA damage and form foci with PTIP at the DNA break point. Furthermore, studies have shown that depletion of PA1 increases cellular sensitivity to ionizing radiation. Proteins in this family are typically between 122 and 254 amino acids in length  .. 
PF15365 Proline-rich nuclear receptor coactivator<br>Eberhardt RY, Coggill P, Hetherington K. The PNRC family, proline-rich nuclear receptor coactivator, is found in eukaryotes, and is approximately 60 amino acids in length. There is a conserved YAG sequence motif.. 
PF15366 Domain of unknown function (DUF4597)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 63 and 76 amino acids in length. There is a conserved TPPTPT sequence motif.. 
PF15367 Calcium-binding and spermatid-specific protein 1<br>CABS1 is a family of proteins found in eukaryotes. It is also known as NYD-SP26. It binds calcium and is specifically expressed in the elongate spermatids and then localised into the principal piece of flagella of matured spermatozoa.. 
PF15368 Spermatogenesis family BioT2<br>BioT2 is a family of eukaryotic proteins expressed only in the testes. BioT2 is found abundantly in five types of murine cancer cell lines, suggesting it plays a role in testes development as well as tumourigenesis [1,2,3].. 
PF15369 Uncharacterised protein KIAA1328<br>Eberhardt RY, Coggill P, Hetherington K. This function of this protein family remains uncharacterised. This family of proteins is found in eukaryotes.. 
PF15370 Domain of unknown function (DUF4598)<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between 159 and 251 amino acids in length.. 
PF15371 Domain of unknown function (DUF4599)<br>The function of this family of eukaryotic proteins is not known.. 
PF15372 Domain of unknown function (DUF4600)<br>
PF15373 Domain of unknown function (DUF4601)<br>Eberhardt RY, Coggill P, Hetherington K. This protein family is a domain of unknown function, which is found in eukaryotes. In humans, the gene encoding this protein is found in the position, chromosome 19 open reading frame 45.. 
PF15374 Coiled-coil domain-containing protein 71L<br>Eberhardt RY, Coggill P, Hetherington K. The protein family, Coiled-coil domain-containing protein 71L, is a domain of unknown function, which is found in eukaryotes.. 
PF15375 Domain of unknown function (DUF4602)<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between 173 and 294 amino acids in length. This family includes Human C1orf131.. 
PF15376 Domain of unknown function (DUF4603)<br>Eberhardt RY, Coggill P, Hetherington K. This protein family is a domain of unknown function. In particular, this domain lies at the C-terminal end of a protein found in eukaryotes.. 
PF15377 Domain of unknown function (DUF4604)<br>Eberhardt RY, Coggill P, Hetherington K. This protein family is a domain of unknown function, which is found in eukaryotes. Proteins in this family are typically between 141 and 174 amino acids in length and contain a conserved LSF sequence motif.. 
PF15378 Domain of unknown function (DUF4605)<br>Eberhardt RY, Coggill P, Hetherington K. This protein family is a domain of unknown function, which is found in eukaryotes. Proteins in this family are typically between 82 and 137 amino acids in length.. 
PF15379 Domain of unknown function (DUF4606)<br>This domain family is found in eukaryotes, and is approximately 100 amino acids in length.. 
PF15380 Domain of unknown function (DUF4607)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 207 and 359 amino acids in length.. 
PF15381 Domain of unknown function (DUF4608)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 85 and 157 amino acids in length.. 
PF15382 Domain of unknown function (DUF4609)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 70 and 139 amino acids in length.. 
PF15383 Transmembrane protein 237<br>Eberhardt RY, Coggill P, Hetherington K. This protein family is found in eukaryotes. The function of this protein is to aid the production of new cilia in ciliogenesis. Mutations in the protein cause a disease, named Joubert syndrome type 14 (JBTS14) and also affect cell signalling using the Wnt pathway . Proteins in this family are typically between 203 and 512 amino acids in length. There are two completely conserved G residues that may be functionally important.. 
PF15384 Domain of unknown function (DUF4610)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 164 and 206 amino acids in length. There is a conserved NPG sequence motif.. 
PF15385 Specifically androgen-regulated gene protein<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes, the function of this protein is still unknown but it is thought to be an androgen receptor. Protein expression is up-regulated in the presence of androgens, but not in the presence of glucocorticoids. SARG tends to be highly expressed in prostate tissue  . Proteins in this family are typically between 340 and 587 amino acids in length. There is a conserved EETI sequence motif.. 
PF15386 PRR14;<br>Drosophila Tantalus-like. Iyer LM, Aravind L, Eberhardt RY, Coggill P, Hetherington K. An alpha+beta fold domain found in metazoan proteins such as   Drosophila Tantalus  . Drosophila Tantalus binds the chromatin protein Additional sex combs (Asx) and also binds DNA in vitro  .. 
PF15387 Domain of unknown function (DUF4611)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 71 and 100 amino acids in length. There is a conserved AKR sequence motif.. 
PF15388 Protein Family FAM117<br>Eberhardt RY, Coggill P, Hetherington K. This protein family is a domain of unknown function found in eukaryotes. Proteins in this family are typically between 269 and 453 amino acids in length. There are two conserved sequence motifs: RRT and TQT.. 
PF15389 Domain of unknown function (DUF4612)<br>Eberhardt RY, Coggill P, Hetherington K. This protein family is a domain of unknown function, which is found in eukaryotes. Proteins in this family are typically between 109 and 323 amino acids in length.. 
PF15390 Domain of unknown function (DUF4613)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 625 and 725 amino acids in length.. 
PF15391 Domain of unknown function (DUF4614)<br>This domain family is found in eukaryotes, and is approximately 180 amino acids in length. There is a conserved EALT sequence motif.. 
PF15392 Joubert syndrome-associated<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is domain of unknown function, which is found in eukaryotes. However, mutations in the gene lead to Joubert's Syndrome, indicating that the protein that the gene encodes for is vital for correct ciliogenesis .. 
PF15393 Domain of unknown function (DUF4615)<br>Eberhardt RY, Coggill P, Hetherington K. This protein family is a domain of unknown function, which is found in eukaryotes. Proteins in this family are typically between 161 and 229 amino acids in length. There is a single completely conserved residue F that may be functionally important.. 
PF15394 Domain of unknown function (DUF4616)<br>Eberhardt RY, Coggill P, Hetherington K. This protein family is a domain of unknown function found at the C-terminal domain of the proteins. This protein family is found in eukaryotes. Proteins in this family are typically between 166 and 538 amino acids in length.. 
PF15395 Domain of unknown function (DUF4617)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 702 and 1745 amino acids in length.. 
PF15396 Protein Family FAM60A<br>Eberhardt RY, Coggill P, Hetherington K. This protein family, FAM60A is a family of proteins is found in eukaryotes. It is known to be a cell cycle protein that binds to the promoter of a gene transcription repressor complex, named SIN4-HDAC complex. This means that FAM60A has an important role to play in 'switching on' gene expression  . Proteins in this family are typically between 179 and 324 amino acids in length.. 
PF15397 Domain of unknown function (DUF4618)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 238 and 363 amino acids in length. There are two conserved sequence motifs: EYP and KCTPD.. 
PF15398 Domain of unknown function (DUF4619)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 128 and 299 amino acids in length.. 
PF15399 Domain of unknown function (DUF4620)<br>
PF15400 Testis-expressed sequence 33 protein family<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 147 and 280 amino acids in length. There are two conserved sequence motifs: NIRH and SYT. The function is not known.. 
PF15401 Tryptophan-ring motif of head of Trimeric autotransporter adhesin<br>TAA-head_Trp-ring is the tryptophan-ring motif of some Gram-negative Enterobacteriaceae. The Trp-ring folds into a beta-meander type on the top of the head domain of its trimeric autotransporter adhesin proteins. In conjunction with the GIN domain it is thought to be the region of the head that adheres to fibronectin.. 
PF15402 N-terminus of kinetochore NMS complex subunit Spc7<br>
PF15403 HiaBD2_N domain of Trimeric autotransporter adhesin (GIN)<br>HiaBD2_N may represent the GIN domain of the Head region of TAAs - trimeric autotransporter adhesins. Not all TAAs carry this domain; however, in those that do, the GIN in combination with the Trp-ring domain is necessary for adhesion to fibronectin in the host cell.. 
PF15404 Pleckstrin homology domain<br>This Pleckstrin homology domain is found in some fungal species.. 
PF15405 Pleckstrin homology domain<br>This Pleckstrin homology domain is found in some fungal species.. 
PF15406 Pleckstrin homology domain<br>This Pleckstrin homology domain is found in some fungal species.. 
PF15407 Sporulation protein family 7<br>Pfam-B_51974 (release 26.0). Spo7_2 constitutes a different set of fungal and related species from those found in Spo7.  This domain is found in general at the N-terminus. In many members the domain is associated with a Pleckstrin-homology - PH - domain.. 
PF09061 Stirrup<br>Bio::Pfam::PfamLiveDBManager=HASH(0x4ef6130). The Stirrup domain, found in the prokaryotic protein ribonucleotide reductase, has a molecular mass of 9 kDa and is folded into an alpha/beta structure. It allows for binding of the reductase to DNA via electrostatic interactions, since it has a predominance of positive charges distributed on its surface  .. 
PF15408 Pleckstrin homology domain<br>This Pleckstrin homology domain is found in some fungal species.. 
PF15409 Pleckstrin homology domain<br>This Pleckstrin homology domain is found in some fungal species.. 
PF15410 Pleckstrin homology domain<br>This Pleckstrin homology domain is found in some fungal species.. 
PF15411 Pleckstrin homology domain<br>This Pleckstrin homology domain is found in some fungal species.. 
PF15412 Binding domain of Nse4/EID3 to Nse3-MAGE<br>This family includes Nse4 and EID3 members  , that bind over this region to the Nse3 pocket, in MAGE family Pfam:PF01454  .. 
PF15413 Pleckstrin homology domain<br>This Pleckstrin homology domain is found in some fungal species.. 
PF15414 Protein of unknown function (DUF4621)<br>JCSG:Target_394740-GS13541A. This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 350 amino acids in length.. 
PF15415 Protein of unknown function (DUF4622)<br>JCSG:Target_390149-GS13960A. This family of proteins is found in bacteria. Proteins in this family are typically between 348 and 360 amino acids in length.. 
PF15416 Domain of unknown function (DUF4623)<br>This family of proteins is found in bacteria. Proteins in this family are approximately 470 amino acids in length. There are two conserved sequence motifs: HLL and RYL.. 
PF15417 Domain of unknown function (DUF4624)<br>JCSG:Target_390388-GS13780A. This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 150 amino acids in length.. 
PF15418 Domain of unknown function (DUF4625)<br>JCSG:Target_390125-GS13882B. This family contains a likely bacterial Ig-like fold, suggesting it may be a family of lipoproteins.. 
PF15419 Leukemia NUP98 fusion partner 1<br>This family of proteins includes leukemia NUP98 fusion partner 1, the gene encoding this protein is involved in a chromosomal translocation with the NUP98 locus in a form of T-cell acute lymphoblastic leukemia  .. 
PF15420 Alpha/beta-hydrolase family N-terminus<br>This is the N-terminal transmembrane domain of a family of alpha/beta hydrolases which may function as lipases. The C-terminal domain (Pfam:PF10081) is the catalytic domain  .. 
PF15421 Putative polysaccharide deacetylase<br>JCSG:Target_416920-SP13771A. 
PF15422 Domain of unknown function (DUF4626)<br>
PF15423 FLYWCH-type zinc finger-containing protein<br>This family is the N-terminus of some FLYWCH-zinc-finger proteins, found in eukaryotes. The family is found in association with Pfam:PF04500. There are two conserved sequence motifs: EQE and QEPS.. 
PF15424 Odontogenic ameloblast-associated family<br>
PF15425 Domain of unknown function (DUF4627)<br>This family of proteins is found in bacteria. Proteins in this family are approximately 230 amino acids in length. There is a conserved WYK sequence motif.. 
PF15427 S100P-binding protein<br>S100PBPR is a family of proteins found in eukaryotes, and localised to cell nuclei where S100P is also present, and the two proteins co-immunoprecipitate. S100P is a member of the S100 family of calcium-binding proteins and there have been several recent reports of its over-expression in pancreatic ductal adenocarcinoma. In situ hybridisation shows S100PBPR transcripts to be found in islet cells but not duct cells of the healthy pancreas. An interaction between S100P and S100PBPR may be involved in early pancreatic cancer.. 
PF15428 Immunity protein 14<br>A predicted immunity protein with mostly all-beta fold and several conserved hydrophobic residues. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, usually containing a domain of the Tox-URI1 or Tox-HNH family  . The protein is also found heterogeneous polyimmunity loci.. 
PF15429 Domain of unknown function (DUF4628)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 152 and 673 amino acids in length.. 
PF15430 Single domain von Willebrand factor type C<br>
PF15431 Transmembrane protein 190<br>
PF15432 Accessory Sec secretory system ASP3<br>Sec-ASP3 is family of bacterial proteins involved in the Sec secretory system. The family forms part of the accessory SecA2/SecY2 system specifically required to export GspB, a serine-rich repeat cell-wall glycoprotein adhesin encoded upstream in the same operon.. 
PF15433 Mitochondrial 28S ribosomal protein S31<br>Eberhardt RY, Coggill P, Hetherington K. MRP-S31 is the mitochondrial 28S ribosomal subunit S31. This family of proteins is found in eukaryotes. Proteins in this family are typically between 246 and 395 amino acids in length. There are two conserved sequence motifs: RHFMELV and GLSKN.. 
PF15434 Family 104<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 113 and 185 amino acids in length. There is a conserved SLQ sequence motif.. 
PF15435 UNC119-binding protein C5orf30 homologue<br>UNC119_bdg is a family of eukaryotic proteins that probably plays a role in trafficking of proteins, via interaction with unc119 family cargo adapters. The family may play a role in ciliary membrane localisation.. 
PF15436 Plasminogen-binding protein pgbA N-terminal<br>PGBA_N is an N-terminal family of bacterial proteins that bind plasminogen. This activity was identified in In Helicobacter pylori where it is thought to contribute to the virulence of this bacterium. Both PgbA and PgbB are surface-exposed proteins that mediate binding to plasminogen such that it can be converted into plasmin in the presence of a Pg activator.. 
PF15437 Plasminogen-binding protein pgbA C-terminal<br>PGBA_C is an C-terminal family of bacterial proteins that bind plasminogen. This activity was identified in Helicobacter pylori where it is thought to contribute to the virulence of this bacterium.  Both PgbA and PgbB are surface-exposed proteins that mediate binding to plasminogen such that it can be converted into plasmin in the presence of a plasminogen activator.. 
PF15438 Antigenic membrane protein of phytoplasma<br>Phyto-Amp is a family of phytopathogenic wall-less bacterial antigenic membrane proteins  . The bacteria are limited to the phloem and pose a major threat to agriculture worldwide. They are transmitted in a persistent, propagative manner by phloem-sucking Hemipteran insects. Phytoplasma membrane proteins are in direct contact with hosts and are assumed to be involved in determining vector specificity. Phyto-Amp is thought to be one family of proteins that mediates such specificity. The proteins appear to be encoded by circular extrachromosomal elements, at least one of which is a plasmid  .. 
PF15439 Neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adapter<br>NYAP_N is an N-terminal family of eukaryotic proteins that are substrates of tyrosine kinase in the brain. When first identified, the family members were referred to as unconventional myosin XVI, or Myr 8  . However, proteins have now been identified as being integrally involved in neuronal function and morphogenesis. The family is involved in both the activation of phosphoinositide 3-kinase (PI3K) and the recruitment of the downstream effector WAVE complex to the close vicinity of PI3K; it also appears to regulate the brain size and neurite outgrowth in mice  .. 
PF15440 THRAP3/BCLAF1 family<br>This family includes thyroid hormone receptor-associated protein 3 (THRAP3), which is a spliceosome component and a subunit of the TRAP complex which plays a role in pre-mRNA splicing and in mRNA decay  . It also includes the transcriptional repressor Bcl-2-associated transcription factor 1 (BCLAF1)  .. 
PF15441 Rho guanine nucleotide exchange factor 5/35<br>This family includes Rho guanine nucleotide exchange factor 5   and Rho guanine nucleotide exchange factor 35.. 
PF15442 Domain of unknown function (DUF4629)<br>This domain family is found in eukaryotes, and is approximately 150 amino acids in length. There are two conserved sequence motifs: MHML and LGKK.. 
PF15443 Domain of unknown function (DUF4630)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 124 and 286 amino acids in length.. 
PF15444 Transmembrane protein 247<br>This family of transmembrane proteins is found in eukaryotes. Proteins in this family are typically between 197 and 222 amino acids in length. The function of this family is unknown.. 
PF15445 acidic terminal segments, variant surface antigen of PfEMP1<br>ATS is the intracellular and relatively conserved acidic terminal segment of the Plasmodium falciparum erythrocyte membrane protein-1 (PfEMP1)  . this domain appears to be present in all variants of the highly polymorphic PfEMP1 proteins.. 
PF15446 PHD/FYVE-zinc-finger like domain<br>Pfam-B_5236 (release 26.0). This family appears to be a combination domain of several consecutive zinc-binding regions.. 
PF15447 N-terminal segments of PfEMP1<br>NTS, the N-terminal segment, is the most variable part of the variant surface antigen family of Plasmodium falciparum, the erythrocyte membrane protein-1 (PfEMP1) proteins. PfEMP1 is an important target for protective immunity and is implicated in the pathology of malaria through its ability to adhere to host endothelial receptors  . A structural and functional study of the N-terminal domain of PfEMP1 from the VarO variant comprising the N-terminal segment (NTS) and the first DBL domain (DBL1α1), shows this region is directly implicated in rosetting.  NTS, previously thought to be a structurally independent component of PfEMP1, forms an integral part of the DBL1α domain that is found to be the important heparin-binding site  . This family is closely associated with PFEMP, Pfam:PF03011, and Duffy_binding, Pfam:PF05424.. 
PF15448 N-terminal segments of P. falciparum erythrocyte membrane protein<br>NTS_2 is a family of the most variable part of the variant surface antigen family of Plasmodium falciparum, the erythrocyte membrane protein-1 (PfEMP1)  . However, in this group of proteins conservation is high. PfEMP1 is an important target for protective immunity and is implicated in the pathology of malaria through its ability to adhere to host endothelial receptors.. 
PF15449 Retinal protein<br>This family of proteins is found in the photoreceptor cells of the retina [1,2]. Mutations of the gene encoding this protein have been associated with retinal disorders such as retinitis pigmentosa and late-onset progressive retinal atrophy [1-4]. The function of this family of proteins is unknown, but it is likely to be important in the development and function of the retina [2-3].. 
PF15450 Domain of unknown function (DUF4631)<br>This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 394 and 668 amino acids in length.. 
PF15451 Domain of unknown function (DUF4632)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 59 and 190 amino acids in length.. 
PF15452 Neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adapter<br>NYAP_C is a C-terminal family of eukaryotic proteins that are substrates of tyrosine kinase in the brain. When first identified, the family members were referred to as unconventional myosin XVI, or Myr 8  . However, proteins have now been identified as being integrally involved in neuronal function and morphogenesis. The family is involved in both the activation of phosphoinositide 3-kinase (PI3K) and the recruitment of the downstream effector WAVE complex to the close vicinity of PI3K; it also appears to regulate the brain size and neurite outgrowth in mice  .. 
PF15453 Protein incorporated later into Tight Junctions<br>Pilt is a family of eukaryotic tight junction-proteins that binds to guanylate-kinase. Pilt is a component of TJs (Tight junctions) rather than AJs (Adhesin junctions). The protein is incorporated into TJs after TJ strands are formed, thereby suggesting the name Pilt for 'protein incorporated later into TJs'. Pilt binds to the guanylate-kinase region of hDlg otherwise known as Disk large homologue  .. 
PF15454 Late endosomal/lysosomal adaptor and MAPK and MTOR activator<br>LAMTOR is a family of eukaryotic proteins that have otherwise been referred to as Lipid raft adaptor protein p18, Late endosomal/lysosomal adaptor and MAPK and MTOR activator 1, and Protein associated with DRMs and endosomes. It is found to be one of three small proteins constituting the Rag complex or Ragulator that interact with each other, localise to endosomes and lysosomes, and play positive roles in the MAPK pathway. The complex does this by interacting with the Rag GTPases, recruiting them to lysosomes, and bringing about mTORC1 activation.. 
PF15455 Proline-rich 19<br>This family includes proline-rich protein 19.. 
PF15456 Up-regulated During Septation<br>Uds1 is a domain family is found mostly in fungi, and is typically between 120 and 138 amino acids in length. The GO annotation for the S.pombe protein describes the protein as barrier septum assembly involved in cell cycle cytokinesis, GO:0071937. Many of the uncharacterised members are listed as being involucrin repeat proteins, but this can not be substantiated.. 
PF15457 Type III T3SS secreted effector HopW1-1/HopPmaA<br>HopW1-1 is a family of bacterial modular P. syringae Avr effectors that induce accumulation of the signal molecule salicylic acid (SA) and the transcripts of HWI1 (HOPW1-1-INDUCED GENE1) in Arabidopsis. Thus HopW1-1 elicits a resistance response in Arabidopsis  .. 
PF15458 Nineteen complex-related protein 2<br>NTR2 or Nineteen complex-related protein 2 is a family of largely fungal and plant proteins that form a complex with the DExD/H-box RNA helicase Prp43. Along with NTR1 it is an accessory factor of Prp43 in catalysing spliceosome disassembly.  Disassembly of the spliceosome after completion of the splicing reaction is necessary for recycling of splicing factors to promote efficient splicing  . NTR2 and NTR1 associate with a post-splicing complex containing the excised intron and the spliceosomal U2, U5, and U6 snRNAs, that supports a link with a late stage in the pre-mRNA splicing process  .. 
PF15459 60S ribosome biogenesis protein Rrp14<br>Pfam-B_10508 (release 26.0). RRP14 is a family of nucleolar 60S ribosomal biogenesis proteins from eukaryotes. RRP14 functions in ribosome synthesis as it is required for the maturation of both small and large subunit rRNAs and it helps to prevent premature cleavage of the pre-rRNA at site C2  . It also plays a role in cell polarity and/or spindle positioning 2],. 
PF15460 Something about silencing, SAS, complex subunit 4<br>SAS4 is a family of largely fungal silencing regulators. This silencing is mediated by chromatin. SAS4 specifically silences the yeast mating-type genes HML and HMR  . SAS4 is found to be one subunit of a complex, the SAS complex, that interacts with chromatin assembly factor Asf1p, and asf1 mutants show silencing defects similar to mutants in the SAS complex. Thus, ASF1-dependent chromatin-assembly may mediate the role of the SAS complex in silencing  . Co-expression of Sas2, SAS4, and Sas5 in Escherichia coli leads to formation of a stable SAS complex that acetylates histones. SAS4 is essential for the acetyltransferase activity of Sas2, and Sas5 is also important  .. 
PF15461 Beta-carotene 15,15'-dioxygenase<br>BCD is a family of bacterial and archaeal proteins is found in bacteria and archaea that catalyse or regulate the conversion of beta-carotene to retinal  . Characterisation of BCD proteins shows them to cleave beta-carotene at its central double bond (15,15′) to yield two molecules of all-trans-retinal. However, the oxygen atom of retinal originated not from water but from molecular oxygen, suggesting that the enzyme was a beta-carotene 15,15′-dioxygenase, rather than a mono-oxygenase that catalyzes the same biochemical reaction [2,3].. 
PF15462 Bartter syndrome, infantile, with sensorineural deafness (Barttin)<br>Barttin is a family of mammalian proteins that are chloride ion channel beta-subunits crucial for renal Cl-re-absorption and inner ear K+ secretion. Bartter syndrome is a term covering a heterogeneous group of autosomal recessive salt-losing nephropathies that are caused by disturbed transepithelial sodium chloride re-absorption in the distal nephron. Mutations in the BCD proteins lead to sensorial deafness.. 
PF15463 Extracellular mutant protein 11<br>ECM11 is a family of largely fungal proteins. ECM11 interacts with Cdc6, an essential protein involved in the initiation of DNA replication, and is a nuclear protein involved in maintaining chromatin structure  . It was previously identified as a protein involved in yeast cell wall biogenesis and organisation, but is also found to be required in meiosis where its function is related to DNA replication and crossing-over  .. 
PF15464 Domain of unknown function (DUF4633)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 94 and 123 amino acids in length.. 
PF15465 Domain of unknown function (DUF4634)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 98 and 133 amino acids in length.. 
PF15466 Domain of unknown function (DUF4635)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 120 and 154 amino acids in length. There are two conserved sequence motifs: LEQ and DLE.. 
PF15467 Secretogranin-3<br>Secretogranin_3 is a family of vertebrate proteins that is one of the granin family. Granins are rich in acidic amino acids, exhibit aggregation at low pH, and possess a high capacity for calcium binding. Because granins are restricted in their localisation to secretory granules of neuroendocrine cells, two interesting characteristics of their sorting mechanisms have been observed.  These are, first, that they aggregate on low pH/high calcium concentrations and second that two of them carry an N-terminal disulfide loop, mutations in which lead to mis-sorting. Thus, granins are thought to be essential for the sorting of secretory proteins at the trans-Golgi network. Chromogranin A (CgA) binds to SGIII in secretory granules of endocrine cells  . SGIII directly binds to cholesterol components of the secretory granule membrane and targets CgA to secretory granules in pituitary and pancreatic endocrine cells  . Mutations in the SGIII gene may influence the risk of obesity through possible regulation of hypothalamic neuropeptide secretion  .. 
PF15468 Domain of unknown function (DUF4636)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 196 and 244 amino acids in length.. 
PF15469 Exocyst complex component Sec5<br>Pfam-B_353125 (release 26.0). This Sec5 family of eukaryotic proteins conserved is not representing the Sec5-Ral binding site.. 
PF15470 Domain of unknown function (DUF4637)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 142 and 178 amino acids in length.. 
PF15471 Transmembrane protein family 171<br>This family of proteins is found in eukaryotes. TMEM171 is also known as parturition-related protein 2. Proteins in this family are typically between 242 and 326 amino acids in length.. 
PF15472 Domain of unknown function (DUF4638)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 240 and 272 amino acids in length.. 
PF15473 PEST, proteolytic signal-containing nuclear protein family<br>Eberhardt RY, Coggill P, Hetherington K. PCNP is a PEST-containing nuclear protein that is ubiquitinated by NIRF, a Np95/ICBP90-like RING finger protein. PEST sequences, which are rich in proline (P), glutamic acid (E), serine (S) and threonine (T), are found in a number of short-lived proteins, such as transcription factors and cell cycle-associated proteins. Their function is generally controlled by proteolysis, mostly via ubiquitin-mediated degradation. Thus, NIRF and PCNP are a ubiquitin ligase and its substrate, respectively, that may constitute a novel signalling pathway with some relation to cell proliferation  .. 
PF15474 Meiotically up-regulated gene family<br>This protein was identified as being up-regulated during meiosis in S.pombe.  This family of proteins is found in largely in plants and fungi. Proteins in this family are typically between 128 and 920 amino acids in length.. 
PF15475 Transmembrane protein C12orf23, UPF0444<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 94 and 119 amino acids in length.. 
PF15476 Histone deacetylase complex subunit SAP25<br>SAP25 is a family of proteins found in eukaryotes. SAP25 is a core component of the mSin3 co-repressor complex whose subcellular location is regulated by PML. mSin3, the transcriptional co-repressor, is associated with histone deacetylases (HDACs) and is utilised by many DNA-binding transcriptional repressors. SAP25 is a nucleo-cytoplasmic shuttling protein that is actively exported from the nucleus by a CRM1-dependent mechanism. It binds to the PAH1 domain of mSin3A, associates with the mSin3A-HDAC complex in vivo, and represses transcription when tethered to DNA [1,2].. 
PF15477 Small acidic protein family<br>This domain family is found in eukaryotes, and is approximately 70 amino acids in length. There is a single completely conserved residue G that may be functionally important.. 
PF15478 Family of unknown function with LKAAEAR motif<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 119 and 235 amino acids in length. There is a conserved LKAAEAR sequence motif.. 
PF15479 Domain of unknown function (DUF4639)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 161 and 601 amino acids in length.. 
PF15480 Domain of unknown function (DUF4640)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 99 and 306 amino acids in length.. 
PF15481 Chondroitin proteoglycan 4<br>CPG4 is a domain family found in nematodes of one of nine core chondroitin proteoglycans. Vertebrates produce multiple chondroitin sulfate proteoglycans that play important roles in development and tissue mechanics. In the nematode Caenorhabditis elegans, the chondroitin chains lack sulfate but nevertheless play essential roles in embryonic development and vulval morphogenesis. CPG4 has the largest predicted mass of the C. elegans CPGs at 84 kDa. The majority of its 35 predicted glycosaminoglycan attachment sites reside in the COOH-terminal half of the protein, of which four sites were confirmed by DTT modification  . The family is rich in conserved cysteines.. 
PF15482 Coiled-coil domain-containing glutamate-rich protein family 1<br>This is a family of coiled-coil family proteins found in eukaryotes. Proteins in this family are typically between 160 and 397 amino acids in length.. 
PF15483 Domain of unknown function (DUF4641)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 201 and 519 amino acids in length.. 
PF15484 Domain of unknown function (DUF4642)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 115 and 196 amino acids in length.. 
PF15485 Domain of unknown function (DUF4643)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 254 and 462 amino acids in length.. 
PF15486 Domain of unknown function (DUF4644)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 143 and 191 amino acids in length.. 
PF15487 FAM220 family<br>This protein family is a domain of unknown function which is found in eukaryotes. Proteins in this family are typically between 217 and 277 amino acids in length. There are two completely conserved residues (S and L) that may be functionally important.. 
PF15488 Domain of unknown function (DUF4645)<br>This family of proteins is found in eukaryotes. Proteins in this family are typically between 200 and 298 amino acids in length.. 
PF15489 CST, telomere maintenance, complex subunit CTC1<br>Pfam-B_19246 (release 26.0). CTC1 is one of the three components of the CST complex that assists Shelterin to protect the ends of telomeres from attack by DNA-repair mechanisms. Mutations in human CTC1 have been recognised as contributing to cerebroretinal microangiopathy.. 
PF15490 Telomere-capping, CST complex subunit<br>Ten1_2 is a family of primarily plant and vertebrate telomere-capping proteins that is evolutionarily related to the mostly fungal family of Ten1, Pfam:PF12658.. 
PF15491 CST, telomere maintenance, complex subunit CTC1<br>CTC1 is one of the three components of the CST complex that assists Shelterin to protect the ends of telomeres from attack by DNA-repair mechanisms. This family largely represents sequences from plants species.. 
PF15492 Neuroblastoma-amplified sequence, N terminal<br>Nbas_N is an N-terminal family of metazoan sequences. This domain lies at the N-terminal of several WD40-containing proteins. The human protein is over-expressed in neuroblastoma cells  .. 
PF15493 Domain of unknown function, YrpD<br>JCSG:Target-418961/SP17457A. This family of proteins is found in bacteria. Proteins in this family are typically between 236 and 351 amino acids in length. The member from Bacillus subtilis, UniProtKB:O05411, is named YrpD.. 
PF15494 Scavenger receptor cysteine-rich domain<br>SRCR_2 is a scavenger receptor cysteine-rich domain family found largely on vertebrate sequences up-stream of the trypsin-like transmembrane serine protease, Spinesin.. 
PF15495 Major fimbrial subunit protein type IV, Fimbrillin, C-terminal<br>JCSG:Target-417041/SP13489F. Fimbrillin_C is a C-terminal family of major fimbrial subunit protein type IV proteins largely from Bacillus species. The family is associated with family P_gingi_FimA, Pfam:PF06321.. 
PF15496 Domain of unknown function (DUF4646)<br>Pfam-B_61885 (release 26.0). This is a family of proteins largely from fungi.  The function is not known.. 
PF15497 snRNA-activating protein complex subunit 19, SNAPc subunit 19<br>Eberhardt RY, Coggill P, Hetherington K. SNAPc19 is a family of proteins found in eukaryotes. It is one of the five core components of the snRNA-activating protein complex or SNAPc that helps direct the nucleation of RNA polymerases II and III. The core RNA polymerase II snRNA promoters consist of a single essential element, the proximal sequence element (PSE), whereas the core RNA polymerase III snRNA promoters consist of both a PSE and a TATA box. The SNAPc binds to the PSE of both of these. SNAPc recognises the PSE sequence common to all human snRNA genes, irrespective of polymerase specificity. SNAPc is also known as the PSE transcription factor (PTF) or PSE-binding protein (PBP). The human SNAP19 and SNAP45 subunits are dispensable for transcription in vitro and are not as widely conserved as the other three, SNAP190, SNAP43 and SNAP50, suggesting that these vertebrate-specific SNAPc subunits may have adapted specialised regulatory roles for snRNA gene transcription  .. 
PF15498 Nephrin and CD2AP-binding protein, Dendrin<br>Eberhardt RY, Coggill P, Hetherington K. Dendrin is a family of eukaryotic proteins found in the podocytes of the kidneys. Dendrin, originally identified in telencephalic dendrites, is a constituent of the slit diaphragm, SD, complex of podocytes, where it directly binds to nephrin and CD2AP. Kidney podocytes and their slit diaphragms (SDs) form the final barrier to urinary protein loss. SD proteins also participate in intracellular signalling pathways. Dendrin appears to prevent programmed cell death (apoptosis) through its binding to nephrin. The SD protein nephrin serves as a component of a signalling complex that directly links podocyte junctional integrity to actin cytoskeletal dynamics. Thus, dendrin is identified as an SD family with proapoptotic signalling properties that accumulates in the podocyte nucleus in response to glomerular injury.. 
PF15499 Ubiquitin-specific peptidase-like, SUMO isopeptidase<br>Rawlings N, Coggill P. Peptidase_C98 is a small family of SUMO - small ubiquitin-related modifier - isopeptidases found in eukaryotes.  Reversible attachment of SUMO is an essential protein modification in all eukaryotic cells, The family neither binds nor cleaves ubiquitin, but is a potent SUMO isopeptidase, and the invariant residues required for SUMO binding and cleavage, in UniProtKB:Q5W0Q7, are Cys-236, His-456 and Asp-472, all of which are fully conserved in the family. Member proteins are low-abundance proteins that colocalise with coilin in Cajal bodies. Peptidase_C98 depletion does not affect global sumoylation, but causes striking coilin mis-localisation and impairs cell proliferation, functions that are not dependent on the catalytic activity. Thus, Peptidase_C98 represents a third type of SUMO protease, with essential functions in Cajal body biology.. 
PF15500 Putative RNase-like toxin<br>A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an alpha+beta fold and conserved cysteine, . 
PF15501 Nuclear protein MDM1<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is present in the nucleus  . The function of MDM1 is not known.. 
PF15502 M-phase-specific PLK1-interacting protein<br>Eberhardt RY, Coggill P,. 
PF15503 PPP1R35;<br>Protein phosphatase 1 regulatory subunit 35 C-terminus. Eberhardt RY, Coggill P,. This is the C-terminus of protein phosphatase 1 regulatory subunit 35. This protein interacts with and inhibits the serine/threonine-protein phosphatase PPP1CA  .. 
PF15504 Domain of unknown function (DUF4647)<br>Eberhardt RY, Coggill P. This family of proteins is found in eukaryotes. Proteins in this family are typically between 282 and 480 amino acids in length.. 
PF15505 Domain of unknown function (DUF4648)<br>Eberhardt RY, Coggill P. This family of proteins is found in eukaryotes. Proteins in this family are typically between 115 and 207 amino acids in length.. 
PF15506 OCC1 family<br>Eberhardt RY, Coggill P. The human member of this family, overexpressed in colon carcinoma 1 protein (Swiss:Q8TAD7) has been shown to be overexpressed in several colon carcinomas  .. 
PF15507 Domain of unknown function (DUF4649)<br>Pfam-B_83 (release 26.0). This family of Firmicute sequences has members that are annotated as ribose-phosphate pyrophosphokinase; however there is no evidence for this attribution. Member proteins are all shorter than 100 residues in length.. 
PF15508 beta subunit of N-acylethanolamine-hydrolyzing acid amidase<br>De Vivo M, Coggill P. NAAA-beta is a family of vertebral sequences that form the beta subunit of vertebral N-acylethanolamine-hydrolyzing acid amidase, a member of the choloylglycine hydrolase acid ceramidase family. The alpha subunit is represented by family CBAH, Pfam:PF02275.. 
PF15509 Domain of unknown function (DUF4650)<br>Pfam-B_31507 (release 26.0). This family of vertebrate proteins lies to the C-terminus of Ubiquitin-specific peptidase-like protein family peptidase_C98, Pfam:PF15499. It might be acting as the exosite for the peptidase.. 
PF15510 Centromere kinetochore component W<br>Pfam-B_49340 (release 26.0). CENP-W is a family of vertebral kinetochore proteins that associates directly with CENP-T. CENP-W members are histone-fold proteins. The histone fold region is critical for binding to centromeric DNA. Importantly, the CENP-T-W complex does not directly associate with CENP-A, but with histone H3 in the centromere region. CENP-T and -W form a hetero-tetramer with CENP-S and -X and bind to a ~100 bp region of nucleosome-free DNA forming a nucleosome-like structure. The DNA-CENP-T-W-S-X complex is likely to be associated with histone H3-containing nucleosomes rather than with CENP-nucleosomes.. 
PF15511 Centromere kinetochore component CENP-T<br>Pfam-B_9162 (release 26.0). CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore.  Importantly, the CENP-T-W complex does not directly associate with CENP-A, but with histone H3 in the centromere region. CENP-T and -W form a hetero-tetramer with CENP-S and -X and bind to a ~100 bp region of nucleosome-free DNA forming a nucleosome-like structure.  The DNA-CENP-T-W-S-X complex is likely to be associated with histone H3-containing nucleosomes rather than with CENP-nucleosomes.. 
PF15512 Chromatin assembly factor complex 1 subunit p60, C-terminal<br>Pfam-B_74766 (release 26.0). CAF-1_p60_C is a family of vertebral proteins that is involved in chromatin assembly. CAF-1_p60 is one of the three subunits of the CAF-1 complex, and this domain binds to the C-terminal region of CAF-1_p150, family Pfam:PF12253. The N-terminal part of the CAF-1_p60 proteins is a WD-repeat structure, Pfam:PF00400.. 
PF15513 Domain of unknown function (DUF4651)<br>JCSG target SP18156A . family of short, secreted proteins specific to the Streptococcus genus, with distant homologs, not recognized by this HMM, found in other cocci. In all sequenced genomes, proteins from  this family appear in a conserved genomic context with an thioredoxin, tRNA synthase and tRNA binding protein, but the functional implication of this is unclear. 
PF15514 Restriction endonuclease ThaI<br>This family of restriction endonucleases belongs to the PD-(D/E)XK superfamily. It cuts the recognition site CG^CG leaving blunt ends  .. 
PF15515 MvaI/BcnI restriction endonuclease family<br>This family of proteins includes the restriction endonucleases MvaI and BcnI. These enzymes both function as monomers. MvaI cleaves the sequence CC/WGG, where W is an A or a T nucleotide, leaving sticky ends. BcnI cleaves the sequence CC/SGG, where S is G or C, leaving sticky ends [1-2].. 
PF15516 BpuSI N-terminal domain<br>This is the N-terminal (nuclease) domain of the BpuSI restriction endonuclease  .. 
PF15517 TBP-interacting protein N-terminus<br>This is the N-terminal restriction endonuclease-like domain found in several archaeal TATA-binding protein (TBP)-interacting proteins  .. 
PF15518 L protein N-terminus<br>This endonuclease domain is found at the N-terminus of many bunyavirus L proteins  .. 
PF15519 linker between RRM2 and RRM3 domains in RBM39 protein<br>Jackhmmer:Q14498, residues 339-411. A conserved linker between the second and the third RRM domain in human RBM39 (CAPER) protein, also present in other RNA binding proteins, especially those involved in RNA splicing. This linker was implicated in interactions with ESR1 and ESR2. Preliminary results from JCSG suggest that this is a structured domain with a well defined fold.. 
PF15520 Putative toxin 40<br>A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an alpha+beta fold that is usually exported by the type 2 secretion system  .
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PF15521 Putative toxin 41<br>A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin contains two structural domains, an N-terminal alpha/beta domain and a C-terminal all-beta domain. The domain contains conserved GxR, RxxxoH GxE and GxxH motifs and a conserved histidine residue. In bacterial polymorphic toxin systems, the toxin is usually exported by the Photorhabdus virulence cassette (PVC)-type export system  .
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PF15522 Putative toxin 42<br>A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an alpha+beta fold that is usually exported by the Photorhabdus virulence cassette (PVC)-type export system  .
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PF15523 Putative toxin 44<br>A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an all-alpha helical fold and conserved [DNE]xxH motif and arginine residue. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 6, or Photorhabdus virulence cassette (PVC)-type secretion system  .
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PF15524 Putative toxin 45<br>A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses a mostly all-beta fold and a conserved ExD motif and a histidine residue. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 7 or TcdB/TcaC-type secretion system  .
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PF15525 Domain of unknown function (DUF4652)<br>JCSG target SP18005A. This family of uncharacterised proteins from Clostridia and Bacilli classes has an unusual structure of three beta propeller repeats that do not form a barrel, as in well known 6-, 7- etc beta propeller barrels, but instead are stacked in a three-layer beta-sheet sandwich. The function of all the proteins from this family is unknown.. 
PF15526 Putative toxin 46<br>An RNase toxin found in bacterial polymorphic toxin systems that is proposed to adopt the BECR (Barnase-EndoU-ColicinE5/D-RelE) fold, with two conserved lysine residues and and [DS]xDxxxH, RxG[ST] and RxxD motifs. In bacterial polymorphic toxin systems, the toxin is usually exported by the type 2, type 4, type 5 or type 7 secretion system  . This is also referred to as the E. cloacae CdiAC and has been shown to target tRNAs.
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PF15527 Putative toxin 47<br>A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses a mostly beta fold and two conserved histidines, two aspartates and a glutamate residue. In bacterial polymorphic toxin systems, the toxin is usually exported by the type 5 secretion system  .
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PF15528 Putative toxin 48<br>A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an all-beta fold and conserved ND and DxxR motifs and a histidine residue. In bacterial polymorphic toxin systems, the toxin is exported by the type 2 or TcdB/TcaC secretion system  .
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PF15529 Putative toxin 49<br>A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an all-beta fold and conserved ND and DxxR motifs and a histidine residue. In bacterial polymorphic toxin systems, the toxin is exported by the type 2 or TcdB/TcaC secretion system. Interestingly, the toxin is also found in type-II toxin-antitoxin systems  .
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PF15530 Putative toxin 50<br>A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses a mostly all-beta fold and conserved FGPY motif and a histidine residue. In bacterial polymorphic toxin systems, the toxin is exported by the type 2 or type 5 secretion system  .
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PF15531 Putative toxin 51<br>A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an alpha+beta fold and conserved aspartate and glutamate residues, and an RxW motif. In bacterial polymorphic toxin systems, the toxin is exported by the type 2 or type 7 secretion system  .
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PF15532 Putative toxin 53<br>A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an all-beta fold and two conserved histidines present in an RxH and THIP motif. The domain additionally has a highly conserved arginine residue. In bacterial polymorphic toxin systems, the toxin is usually exported by the type 2, type 6 or type 7 secretion system  .
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PF15533 Putative toxin 54<br>A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an alpha+beta fold and [DN]xHxxK and DxxxD motifs. It is usually exported by the Type 2 secretory system  .
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PF15534 Putative toxin 56<br>A predicted RNase toxin found in bacterial polymorphic toxin systems that is proposed to adopt the BECR (Barnase-EndoU-ColicinE5/D-RelE) fold, and contains a conserved histidine residue and a KH motif. In bacterial polymorphic toxin systems, the toxin is usually exported by the type 2 secretion system  .
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PF15535 Putative toxin 57<br>A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an all-beta fold and a conserved glutamate residue, and [KR] and Hx[DH] motifs. In bacterial polymorphic toxin systems, the toxin is exported by the type 2 or type 7 secretion system  .
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PF15536 Putative toxin 58<br>A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an all-beta fold and conserved aspartate, arginine, histidine and cysteine residues that is usually exported by the Photorhabdus virulence cassette (PVC)-type export system  .
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PF15537 Putative toxin 59<br>A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an alpha+beta fold with two conserved histidine residues. In bacterial polymorphic toxin systems, the toxin is usually exported by the type 2 or TcdB/TcaC-type secretion system  . A  of this, the Pseudomonas RhsT-C has been experimentally characterized.
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PF15538 Putative toxin 61<br>A predicted toxin domain found in bacterial polymorphic toxin systems. The toxin possesses an alpha+beta fold with a conserved glutamine residue and a [KR]STxxPxxDxx[ST] motif. In bacterial polymorphic toxin systems, the toxin is exported by the type 2 or type 6 secretion system  .
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PF15539 CAF1 complex subunit p150, region binding to CAF1-p60 at C-term<br>CAF1-p150_C2 is part of the binding region of the CAF1 complex p150 subunit to the p60 subunit. The CAF1 complex is essential in human cells for the de novo deposition of histones H3 and H4 at the DNA replication fork [1,2].. 
PF15540 Putative toxin 62<br>A predicted RNase toxin found in bacterial polymorphic toxin systems that is proposed to adopt the BECR (Barnase-EndoU-ColicinE5/D-RelE) fold, and contains a two conserved aspartates, a glutamate, a histidine and an arginine residue and an RT motif. In bacterial polymorphic toxin systems, the toxin is usually exported by the type 2, type 6 or type 7 secretion system  .
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PF15541 Putative toxin 63<br>A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an alpha+beta fold that is usually exported by the Photorhabdus virulence cassette (PVC)-type export system  .
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PF15542 Putative toxin 64<br>A predicted RNase toxin found in bacterial polymorphic toxin systems that is proposed to adopt the BECR (Barnase-EndoU-ColicinE5/D-RelE) fold, and contains two conserved histidine, a serine, two lysine, and a threonine residue and a HxVP motif. In bacterial polymorphic toxin systems, the toxin is usually exported by the type 2, type 6, type 7, and MuF-type secretion system  .
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PF15543 Putative toxin 65<br>A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an alpha+beta fold that is usually exported by the Photorhabdus virulence cassette (PVC)-type export system  .
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PF15544 Putative toxin 66<br>A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an alpha+beta fold that is usually exported by the Photorhabdus virulence cassette (PVC)-type export system  .
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PF15545 Putative toxin 67<br>A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an alpha+beta fold and HxR and HxxxH motifs that is usually exported by the type 2 and type 6 secretion system  .
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PF15546 Domain of unknown function (DUF4653)<br>Eberhardt RY, Coggill P. This family of proteins is found in eukaryotes. Proteins in this family are typically between 93 and 229 amino acids in length.. 
PF15547 Domain of unknown function (DUF4654)<br>Eberhardt RY, Coggill P. This family of proteins is found in eukaryotes. Proteins in this family are typically between 145 and 169 amino acids in length. There is a conserved IDC sequence motif.. 
PF15548 Domain of unknown function (DUF4655)<br>Eberhardt RY, Coggill P. This family of proteins is found in eukaryotes. Proteins in this family are typically between 533 and 570 amino acids in length.. 
PF15549 DPPA3;<br>PGC7/Stella/Dppa3 domain . Iyer LM, Aravind L, Eberhardt RY, Coggill P. The domain belongs to a fast evolving family known only from the placental mammals [1-3]. The PGC7/Stella/Dppa3 protein protects imprinted regions from demethylation post-fertilization  . This suggests that it might bind methylated DNA sequences directly  . The conserved core includes a postively charged helical segment and a C-terminal CXCXXC motif that is predicted to chelate a metal ion  . Most placental mammals contain 3-6 paralogs of this domain family. The CXCXXC motif is also conserved in a subset of fungal MBD4-like proteins  .. 
PF15550 Draxin<br>Eberhardt RY, Coggill P. This family of proteins inhibit Wnt signaling and act as chemorepulsive axon guidance molecules [1-2].. 
PF15551 Domain of unknown function (DUF4656)<br>Eberhardt RY, Coggill P. This family of proteins is found in eukaryotes. Proteins in this family are typically between 286 and 398 amino acids in length.. 
PF15552 Domain of unknown function (DUF4657)<br>Eberhardt RY, Coggill P. This family of proteins is found in eukaryotes. Proteins in this family are typically between 305 and 370 amino acids in length.. 
PF15553 Testis-expressed protein 19<br>Eberhardt RY, Coggill P. This family of proteins is expressed in testis  .. 
PF15554 FSIP1 family<br>Eberhardt RY, Coggill P. 
PF15555 Domain of unknown function (DUF4658)<br>Eberhardt RY, Coggill P. This family of proteins is found in eukaryotes. Proteins in this family are typically between 129 and 161 amino acids in length.. 
PF15556 ZW10 interactor<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between 127 and 281 amino acids in length.. 
PF15557 CAF1 complex subunit p150, region binding to PCNA<br>CAF1-p150_N is part of the N-terminus of the CAF1 complex p150 subunit that binds to PCNA - proliferating cell nuclear antigen. The PCNA mediates the connection between CAF-1 and the DNA replication fork. The CAF1 complex is essential in human cells for the de novo deposition of histones H3 and H4 at the DNA replication fork [1,2].. 
PF15558 Domain of unknown function (DUF4659)<br>Eberhardt RY, Coggill P. This family of proteins is found in eukaryotes. Proteins in this family are typically between 427 and 674 amino acids in length. There are two completely conserved residues (D and I) that may be functionally important.. 
PF15559 Domain of unknown function (DUF4660)<br>Eberhardt RY, Coggill P. This family of proteins is found in eukaryotes. Proteins in this family are typically between 93 and 189 amino acids in length.. 
PF15560 Immunity protein 8<br>A predicted immunity protein with an alpha+beta fold and several conserved charged and hydrophobic residues. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, usually containing a domain of the Tox-URI2 family  . The protein is also found in heterogeneous polyimmunity loci.
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PF15561 Immunity protein 9<br>A predicted immunity protein with an alpha+beta fold and several conserved polar and hydrophobic residues. Proteins containing this domain are present in heterogeneous polyimmunity loci in polymorphic toxin systems  . 
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PF15562 Immunity protein 10<br>A predicted immunity protein with two transmembrane helices, and a WxW motif and a conserved arginine between the two helices. Proteins containing this domain are present in heterogeneous polyimmunity loci in polymorphic toxin systems  . 
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PF15563 Immunity protein 11<br>A predicted immunity protein with an alpha+beta fold and a conserved HxxRN motif. Proteins containing this domain are present in heterogeneous polyimmunity loci in polymorphic toxin systems  . 
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PF15564 Immunity protein 13<br>A predicted immunity protein with an alpha+beta fold. Proteins containing this domain are present in heterogeneous polyimmunity loci of polymorphic toxin systems  
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PF15565 Immunity protein 16<br>A predicted immunity protein with a mostly alpha-helical fold and a conserved DxG motif. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, usually containing a domain of the Tox-SHH family of HNH/Endonuclease VII fold nucleases  .
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PF15566 Immunity protein 18<br>A predicted immunity protein with an alpha+beta fold and a conserved histidine residue. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, usually containing a domain of the Ntox12 or Ntox37 or Notx 7 families  .
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PF15567 Immunity protein 19<br>A predicted immunity protein with an alpha+beta fold and a conserved tryptophan residue. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, usually containing a protease domain such as Tox-PL1 and Ntox40. In some instances, it is also fused to a papain-like toxin, ADP-ribosyl glycohydrolase and a S8-like peptidase  . Based on these associations the domain is likely to be a protease inhibitor.
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PF15568 Immunity protein 20<br>A predicted immunity protein with an alpha+beta fold and conserved GR, and GxK motifs. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, usually containing a domain of the Tox-URI2 family of nucleases  .
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PF15569 Immunity protein 21<br>A predicted immunity protein with an alpha+beta fold and conserved phenylalanine and tryptophan residues and a GGD motif. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, usually containing a domain of the Ntox19 family  .
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PF15570 Immunity protein 24<br>A predicted immunity protein with an alpha+beta fold with conserved tryptophan, proline, aspartate, serine and arginine residues. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, usually containing a domain of the Tox-AHH family of HNH/Endonuclease VII fold nucleases  . The gene for this toxin is also found in heterogeneous polyimmunity loci.
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PF15571 Immunity protein 25<br>A predicted immunity protein with an alpha+beta fold. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, usually containing a domain of the Tox-URI1, Tox-URI2 or Tox-ParBL1 families  . The gene for this toxin is also found in heterogeneous polyimmunity loci that show variations in structure even between closely related strains.
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PF15572 Immunity protein 26<br>A predicted immunity protein with an alpha+beta fold and a conserved C-terminal tryptophan residue. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, usually containing a domain of the Tox-ColE3 family  .
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PF15573 Immunity protein 27<br>A predicted immunity protein with an alpha+beta fold and a conserved KxGDxxK motif. Proteins containing this domain are present in heterogeneous polyimmunity loci in polymorphic toxin systems  .
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PF15574 Immunity protein 28<br>A predicted immunity protein with an all alpha-helical fold and a conserved HRG motif. Proteins containing this domain are present in heterogeneous polyimmunity loci in polymorphic toxin systems  .
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PF15575 Immunity protein 29<br>A predicted immunity protein with an all alpha-helical fold and a conserved proline residue. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, usually containing a domain of the Tox-REAse-1 or Tox-REase-6 families  .
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PF15576 Domain of unknown function (DUF4661)<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are typically between 281 and 302 amino acids in length.. 
PF15577 Spc7_C2<br>Spc7_C2 is a short family to the C-terminus of fungal Spc7 proteins. The Ndc80-MIND-Spc7 complex plays a role in kinetochore function during late meiotic prophase and throughout the mitotic cell cycle  . The N-terminal region of Spc7 co-localises with the mitotic spindle, and it has been argued that Spc7 has the potential to associate with spindle microtubules and that this association is regulated by the C-terminal part of the Spc7 protein [2,3]. However, this family represents only the conserved region towards the end of the C-terminus; the majority of the C-terminal part is in family Spc7, Pfam:PF08317.. 
PF15578 Domain of unknown function (DUF4662)<br>Eberhardt RY, Coggill P, Hetherington K. This family of proteins is found in eukaryotes. Proteins in this family are approximately 290 amino acids in length.. 
PF15579 Immunity protein 32<br>A predicted immunity protein with an alpha+beta fold and conserved tryptophan and phenylalanine residues, and a GT motif. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, usually containing a domain of the Tox-REase-5 family  .. 
PF15580 Immunity protein 33<br>A predicted immunity protein with an alpha+beta fold and a conserved tryptophan, and WE and PGW motifs. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, usually containing a domain of the Ntox24 or Ntox10 families  .. 
PF15581 Immunity protein 35<br>A predicted immunity protein with an alpha+beta fold and YxxxD, WxG, KxxxE motifs. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene  .. 
PF15582 Immunity protein 40<br>A predicted immunity protein with an alpha+beta fold and a conserved YxC motif. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, which usually contains toxin domains of the Tox-JAB1 family  . The immunity protein typically contains a signal peptide and a lipobox.. 
PF15583 Immunity protein 41<br>A predicted immunity protein with an alpha+beta fold and a conserved glutamate residue. The domain is often fused to one or more immunity domains in polyimmunity proteins  . . 
PF15584 Immunity protein 44<br>A predicted immunity protein with a mostly all-beta fold and GxxE, WxDxRY motifs and a glutamate residue. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, which usually contains toxin domains of the Ntox48 family. This domain is often fused to the Imm71 immunity domain  .. 
PF15585 Immunity protein 46<br>A predicted immunity protein with an alpha+beta fold and a conserved GxaG motif. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, usually containing a Tox-REase-3 domain  . . 
PF15586 Immunity protein 47<br>A predicted immunity protein with an alpha+beta fold and a conserved Wea (a: aromatic) motif. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, usually containing a domain of the Ntox7 family  . . 
PF15587 Immunity protein 48<br>A predicted immunity protein with an alpha+beta fold and a conserved lysine residue. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, usually containing a domain of the Tox-URI2 family  . The protein is also found in heterogeneous polyimmunity loci.. 
PF15588 Immunity protein 7<br>A predicted immunity protein with a mostly all-beta fold and a conserved arginine residue. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, usually containing a Pput_2613 deaminase domain  . The protein is also found in heterogeneous polyimmunity loci.
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PF15589 Immunity protein 12<br>A predicted immunity protein with an alpha+beta fold and conserved WxG and YxxxC motif. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, usually containing a domain of the NGO1392-family of HNH/Endonuclease VII fold nucleases  . 
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PF15590 Immunity protein 15<br>A predicted immunity protein with an alpha+beta fold and a conserved aspartate and GGxP motif. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, usually containing a domain of the Ntox10 or Tox-ParB families  .. 
PF15591 Immunity protein 17<br>A predicted immunity protein with a mostly all-beta fold and a conserved GxS motif. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, usually containing a domain of the Ntox17 or Ntox7 families  .
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PF15592 Immunity protein 22<br>A predicted immunity protein with an alpha+beta fold and a conserved SF motif and tryptophan residue. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, usually containing a domain of the Ntox21, Ntox29 or Tox-ART-RSE-like ADP-ribosyltransferase families  .
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PF15593 Immunity protein 23<br>A predicted immunity protein with an alpha+beta fold. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, usually containing a domain of the Ntox18 family  .
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PF15594 Immunity protein 30<br>A predicted immunity protein with an all-beta fold. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, usually containing a domain of the Tox-HHH or Ntox24 families  .. 
PF15595 Immunity protein 31<br>A predicted immunity protein with an alpha+beta fold and a conserved tryptophan and Dx[DE] motif. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, usually containing a domain of the Tox-RES or Tox-URI1 families. Proteins containing this domain are present in heterogeneous polyimmunity loci in polymorphic toxin systems  .. 
PF15596 Immunity protein 34<br>A predicted immunity protein with a mostly alpha-helical fold and conserved aspartate and cysteine residues and an SE motif. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, usually containing a domain of the LD-peptidase or Tox-Caspase families  .. 
PF15597 Immunity protein 36<br>A predicted immunity protein with an alpha+beta fold and a conserved [DE]R motif. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, which usually contains toxin domains of the Ntox13 or Ntox40 families  . In some proteins this domain is fused to the Imm38 -like (PFAM:PF15599) immunity domain.. 
PF15598 Immunity protein 37<br>A predicted immunity protein with an alpha+beta fold and a conserved arginine. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, which usually contains toxin domains of the Ntox40 family  .. 
PF15599 Immunity protein 38<br>A predicted immunity protein with an alpha+beta fold and a conserved E+G and ExxY motifs. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, which usually contains toxin domains of the Ntox40, Tox-CdiAC and Tox-ARC families  . The protein is also found in polyimmunity loci in polymorphic toxin systems.. 
PF15600 Immunity protein 39<br>A predicted immunity protein with an alpha+beta fold and a conserved DxEA motif and arginine residue. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, which usually contains toxin domains of the Tox-ColD family  .. 
PF15601 Immunity protein 42<br>A predicted immunity protein with an alpha+beta fold and conserved tyrosine and tryptophan residues. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, which usually contains toxin domains of the Tox-REase-10 family  .. 
PF15602 Immunity protein 43<br>A predicted immunity protein with a mostly alpha-helical fold and conserved arginine and phenylalanine residues. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, which usually contains toxin domains of the Ntox48 family  . This domain is often fused to the Imm72 immunity domain.. 
PF15603 Immunity protein 45<br>A predicted immunity protein with an alpha+beta fold. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, which usually contains toxin domains of the Tox-ARC family. This domain is also found in heterogeneous polyimmunity loci  .. 
PF15604 Putative toxin 43<br>A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses a most all-alpha helical fold and a conserved HxxD motif. In bacterial polymorphic toxin systems, the toxin is usually exported by the type 2, type 6, type 7 or Photorhabdus virulence cassette (PVC)-type secretion systems  .
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PF15605 Putative toxin 52<br>A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an all alpha-helical fold and conserved aspartate and glutamate residues, and K[DE] and[DN]HxxE motifs. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 5 or type 7 secretion system  .
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PF15606 Putative toxin 55<br>A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an all-alpha helical fold and conserved lysine and cysteine residues, and GNxxD and WxCxH motifs. In bacterial polymorphic toxin systems, the toxin is exported by the type 2 or type 6 secretion system  .
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PF15607 Putative toxin 60<br>A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an all-alpha-helical fold with conserved DxK, GNxxxG, and DxxxD motifs. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 6 or type 7 secretion system  .
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PF15608 PELOTA RNA binding domain<br>This RNA binding Pelota domain   is at the C terminus of a PRTase family  . These PRTase+Pelota genes are found in the biosynthetic  operon associated with the Ter stress response operon and are  predicted to be involved  in the biosynthesis of a ribo-nucleoside  involved in stress response  . . 
PF15609 Phosphoribosyl transferase<br>This PRTase family, with C terminal TRSP domain, are related to  OPRTases  , and are predicted to use Orotate as substrate. These genes are found in the biosynthetic operon associated with the Ter  stress response operon and are predicted to  be involved in the biosynthesis of a ribo- nucleoside involved in stress response  .. 
PF15610 PRTase ComF-like<br>This PRTase family is related to the ComF PRTases  . These genes are found in the smaller biosynthetic operon associated with the Ter  stress response operon and are predicted to  be involved in the biosynthesis of a ribo- nucleoside involved in stress response  .. 
PF15611 EH_Signature domain<br>This domain with a strongly conserved glutamate at the N-terminus  and a histidine at the C-terminus  , is found in a SWI2/SNF2 four gene operon  . Its strict-neighborhood association with\.     SWI2/SNF2 ATPase strongly suggests a function in conjunction with it  . The other genes in the operon are a OmpA protein and a TM protein  . This has a DNA related function along with the TerY-P triad  .. 
PF15612 WSTF, HB1, Itc1p, MBD9 motif 1<br>A conserved alpha helical motif that along with the WHIM2 and  WHIM3 motifs, and the DDT domain comprise an alpha helical module  found in diverse eukaryotic chromatin proteins  .Based on the  Ioc3 structure, this module is inferred to interact with nucleosomal  linker DNA and the SLIDE domain of ISWI proteins   .  The resulting complex forms a protein ruler that measures out the  spacing between two adjacent nucleosomes  . The conserved basic  residue in WHIM1 is involved in packing with the DDT motif. The  module shows a great domain architectural diversity and is often  combined with other modified histone peptide recognizing and  DNA binding domains, some of which discriminate methylated DNA  .   . 
PF15613 WSTF, HB1, Itc1p, MBD9 motif 2<br>A conserved alpha helical motif that along with the WHIM1 and WHIM3 motifs, and the DDT domain comprise an alpha helical module found in diverse eukaryotic chromatin proteins  . Based on the Ioc3 structure, this module is inferred to interact with nucleosomal  linker DNA and the SLIDE domain of ISWI proteins   . The resulting complex forms a protein ruler that measures out the  spacing between two adjacent nucleosomes  . The acidic residue from the GxD signature of WHIM2 is a major determinant of the  interaction between the ISWI and WHIM motifs. The N-terminal portion of the WHIM2 motif also contacts the inter-nucleosomal linker DNA. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognizing and DNA binding domains, some of which discriminate methylated DNA  .. 
PF15614 WSTF, HB1, Itc1p, MBD9 motif 3<br>A conserved alpha helical motif that along with the WHIM1 and WHIM2 motifs, and the DDT domain comprise an alpha helical module found in diverse eukaryotic chromatin proteins  . Based on the Ioc3 structure, this module is inferred to interact with nucleosomal  linker DNA and the SLIDE domain of ISWI proteins   . The resulting complex forms a protein ruler that measures out the  spacing between two adjacent nucleosomes  . WHIM3 along with  WHIM2-N constitutes the inter-nucleosomal linker DNA binding site in the major groove of DNA. The module shows a great domain  architectural diversity and is often combined with other modified  histone peptide recognizing and DNA binding domains, some of which  discriminate methylated DNA  .. 
PF15615 TerB-C domain<br>TerB-C occurs C terminal of TerB in TerB-N containing proteins. This domain displays multiple conserved acidic residues (TerBC)  . The  presence of conserved acidic residues in both TerB-N and TerB-C  suggests that they, like the TerB domain, might also chelate metals. These two domains might also occur together in the same protein independently of TerB  .. 
PF15616 TerY-C metal binding domain<br>TerY-C is found C terminal to TerY-like vWA domains in some proteins  . It has 8 conserved metal chelating cysteines or  histidines  . It occasionaly occurs as solos  .. 
PF15617 C-C_Bond_Lyase of the TIM-Barrel fold<br>This family of TIM-Barrel fold C-C bond lyase is related to Citrate -lyase. These genes are found in the biosynthetic operon, with other  enzymatic domains, associated with the Ter  stress response operon  and are predicted to  be involved in the biosynthesis of a ribo- nucleoside involved in stress response  .. 
PF15619 Ciliary protein causing Leber congenital amaurosis disease<br>Eberhardt RY, Coggill P, Hetherington K. Lebercilin is a family of eukaryotic ciliary proteins. Mutations in the gene, LCA5, are implicated in the disease Leber congenital amaurosis. In photoreceptors, lebercilin is uniquely localised at the cilium that bridges the inner and outer segments. Lebercilin functions as an integral element of selective protein transport through photoreceptor cilia.  Lebercilin specifically interacts with the intraflagellar transport (IFT), and disruption of IFT can lead to Leber congenital amaurosis.. 
PF15620 Centromere assembly component CENP-C middle DNMT3B-binding region<br>Pfam-B_64009 (release 26.0). CENP-C is a component of the centromere assembly complex in eukaryotes. CENP-C recruits the DNA methyltransferases DNMT3B, in order to establish the necessary epigenetic DNA-methylation essential for maintenance of chromatin structure and genomic stability.  This middle region of CENP-C is the binding-domain for DNMT3B. Binding of CENP-C and DNMT3B to DNA occurs at both centromeric and peri-centromeric satellite repeats.  CENP-C and DNMT3B regulate the histone code in these regions [1,2].. 
PF15621 Proline-rich submaxillary gland androgen-regulated family<br>Eberhardt RY, Coggill P, Hetherington K. SMR is a family of proteins found in eukaryotes. The family of SMR proteins is expressed in the submaxillary gland. SMR members may play a role in protection or detoxification.. 
PF15622 Kinetochore assembly subunit CENP-C N-terminal<br>Pfam-B_21609 (release 26.0). CENP-C is a vertebrate family that forms a core component of the centromeric chromatin. On depletion of CENP-C proper formation of both centromeres and kinetochores is prevented. The N-terminal of CENP-C is necessary for recruitment of some but not all components of the Mis12 complex of the kinetochore [1,2].. 
PF15623 Cancer/testis gene family 47<br>Eberhardt RY, Coggill P, Hetherington K. CT47 is a family of proteins found in eukaryotes. Proteins in this family are typically between 262 and 291 amino acids in length. There is a conserved HIL sequence motif. The function of this family is not known.. 
PF15624 Kinetochore CENP-C fungal homologue, Mif2, N-terminal<br>PB002175 (release 26.0). Mif2_N is a family of fungal proteins homologous to mammalian CENP-C. On depletion of CENP-C proper formation of both centromeres and kinetochores is prevented. The N-terminal of CENP-C is necessary for recruitment of some but not all components of the Mis12 complex of the kinetochore [1,2].. 
PF15625 CC2D2A N-terminal C2 domain<br>Many ciliary proteins are involved in ciliogenesis and implicated for ciliophathies. A recent study has shown that many of them contain various new versions of C2 domains which are predicted to mediate membrane localizations for Y-shaped linkers of transition\. zone of cilia  . This is the first C2 domain of ciliary CC2D2A  proteins which also have another C2 domain (CC2D2AC-C2) and  a new inactive transglutaminase-like peptidase domain (CC2D2A-TGL).. 
PF15626 single CXXC unit<br>This is a solo version of the zf-CXXC domain with a conserved  CXXCXXCX(n)C, zinc-binding motif. This is, thus far,  only detected  in the plant lineage in diverse chromatin proteins  .  Structural  comparisons show that the mono-CXXC is homologous to the structural- zinc binding domain of medium chain dehydrogenases  . The regular  zf-CXXC domain binds nonmethyl-CpG dinucleotides.. 
PF15627 CEP76 C2 domain<br>Many ciliary proteins are involved in ciliogenesis and implicated for ciliophathies. A recent study has shown that many of them contain various new versions of C2 domains which are predicted to mediate membrane localizations for Y-shaped linkers of transition zone of cilia  . This is the new C2 domain that is contained by ciliary  CEP76  proteins  .. 
PF15628 RRM in Demeter<br>This is a predicted RRM-fold domain present at the C-terminus of  Demeter-like glycoslyases  . These proteins  are involved in  DNA demethylation in plants where they catalyze removal of the 5mC  base and subsequently cleave the backbone through lyase activity.  Orthologs of Demeter are present in plants and stramenopiles. The RRM fold domain is predicted to facilitate interaction of the catalytic  domain with ssDNA or regulatory RNA  .. 
PF15629 Permuted single zf-CXXC unit <br>This is a permuted version of a single unit of the zf-CXXC domain  that is detected in the Demeter-like proteins of land plants.  Structural comparisons show that the mono-CXXC is homologous to  the structural-zinc binding domain of medium chain dehydrogenases   . The classical zf-CXXC domain binds nonmethyl-CpG dinucleotides.. 
PF15630 Kinetochore component CENP-S<br>CENP-S is a family of vertebral and fungal kinetochore component proteins. CENP-S complexes with CENP-X to form a stable CENP-T-W-S-X heterotetramer.. 
PF15631 NTF2 fold immunity protein<br>A predicted immunity protein of the NTF2 fold. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, which usually contains toxin domains of the Tox-NucA family  . This domain is also fused to ankyrin repeats and the PFAM:PF14025.. 
PF15632 ATP-grasp in the biosynthetic pathway with Ter operon<br>This ATP-grasp family is related to carbamoyl phosphate synthetase. These genes are found in the biosynthetic operon associated with the Ter  stress response operon and are predicted to  be involved in the biosynthesis of a ribo-nucleoside involved in stress response  . In press. Mol. BioSyst. 2012, DOI:10.1039/C2MB25239B. "Ter-dependent stress response systems: novel pathways related to  metal sensing, production of a nucleoside-like metabolite, and  DNA-processing" Anantharaman V, Iyer LM, Aravind L;. 
PF15633 HYD1 signature containing ADP-ribosyltransferase<br>A predicted toxin of the ADP-ribosyltransferase superfamily present in bacterial polymorphic toxin systems. The domain has characteristic histidine, tyrosine and aspartate residues that comprise the active site. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 6, or type 7 secretion system  .. 
PF15634 HYE1 signature containing ADP-ribosyltransferase<br>A predicted toxin of the ADP-ribosyltransferase superfamily present in bacterial polymorphic toxin systems. The domain has characteristic histidine, tyrosine and glutamate residues that comprise the active site  .. 
PF15635 GHH signature containing HNH/Endo VII superfamily nuclease toxin  2<br>A predicted toxin of the HNH/Endonuclease VII fold present in bacterial polymorphic toxin systems with a characteristic s[AGP]HH signature motif. In bacterial polymorphic toxin systems, the toxin is exported by the type 2 or type secretion system  .. 
PF15636 GHH signature containing HNH/Endo VII superfamily nuclease toxin<br>A predicted toxin of the HNH/Endonuclease VII fold present in bacterial polymorphic toxin systems with a characteristic sG[HQ]H signature motif. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 6, type 7 or TcdB/TcaC-type secretion system. The metazoan teneurin proteins possess an inactive  of this domain at their C-terminus  .. 
PF15637 HNH/Endo VII superfamily nuclease toxin with a HHH motif<br>A predicted toxin of the HNH/Endonuclease VII fold present in bacterial polymorphic toxin systems with characteristic conserved s[GD]xxR and HHH motifs. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 5, type 6, type 7 or Photorhabdus virulence cassette (PVC)-type secretion system  .. 
PF15638 Metallopeptidase toxin 2<br>A zincin-like metallopeptidase domain found in bacterial polymorphic toxin systems  .. 
PF15639 Metallopeptidase toxin 3<br>A zincin-like metallopeptidase domain found in bacterial polymorphic toxin systems  .. 
PF15640 Metallopeptidase toxin 4<br>A zincin-like metallopeptidase domain found in bacterial polymorphic toxin systems  .. 
PF15641 Metallopeptidase toxin 5<br>A zincin-like metallopeptidase domain found in bacterial polymorphic toxin systems  .. 
PF15642 Toxin in Odyssella and Amoebophilus<br>A predicted all-alpha fold toxin present in bacterial polymorphic toxin systems of the endosymbionts Odyssella and Amoebophilus  .. 
PF15643 Papain fold toxin 2<br>A papain fold toxin domain found in bacterial polymorphic toxin systems  . . 
PF15644 Papain fold toxin 1<br>A papain fold toxin domain found in bacterial polymorphic toxin systems. In these systems they might function either as a releasing peptidase or toxin  .. 
PF15645 Dermonecrotoxin of the Papain-like fold<br>A papain fold toxin domain found in bacterial polymorphic toxin systems  . . 
PF15646 Restriction endonuclease fold toxin 2<br>A predicted toxin of the restriction endonuclease fold present in bacterial polymorphic toxin systems. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 7 or PrsW-peptidase dependent secretion system  .. 
PF15647 Restriction endonuclease fold toxin 3<br>A predicted toxin of the restriction endonuclease fold present in bacterial polymorphic toxin systems. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 6, type 7 or PrsW-peptidase dependent secretion system  .. 
PF15648 Restriction endonuclease fold toxin 5<br>A predicted toxin of the restriction endonuclease fold present in bacterial polymorphic toxin systems. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 5, type 6, or PrsW-peptidase dependent secretion system. Versions of this domain are also found in caudoviruses  .. 
PF15649 Restriction endonuclease fold toxin 7<br>A predicted toxin of the restriction endonuclease fold present in bacterial polymorphic toxin systems. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 5, type 6, or type 7 secretion system  .. 
PF15650 Restriction endonuclease fold toxin 9<br>A predicted toxin of the restriction endonuclease fold present in bacterial polymorphic toxin systems. In bacterial polymorphic toxin systems, the toxin is exported by the type 2 or type 7 secretion system  .. 
PF15651 Salivary glad secreted protein domain toxin<br>An alpha+beta fold domain with four conserved cysteine residues and a conserved [DE}xx[ND] motif. This domain is mainly present at the c-terminus of RHS repeats containing proteins in insects and crustaceans. Although no bacterial homologs have been identified, the domain architecture suggests an origin from bacterial polymorphic toxin systems  . . 
PF15652 HNH/Endo VII superfamily toxin with a SHH signature<br>A predicted toxin of the HNH/Endonuclease VII fold present in bacterial polymorphic toxin systems with two conserved histidine residues. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 5, type 6 or type 7 secretion system  .. 
PF15653 URI fold toxin 2<br>A predicted toxin of the URI nuclease fold present in bacterial polymorphic toxin systems. In bacterial polymorphic toxin systems, the toxin is exported by the type 2 or type 6 secretion system  .. 
PF15654 Toxin with a conserved tryptophan and TIP tripeptide motif<br>A predicted toxin domain with two membrane spanning alpha helices and RxxR, Wx[ST]IP motifs. The domain is present in bacterial polymorphic toxin systems. The toxin is usually exported by the type 2 or Photorhabdus virulence cassette (PVC)-type secretion system  .. 
PF15655 NTF2 fold immunity protein<br>A predicted immunity protein of the NTF2 fold. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, which usually contains toxin domains of the Tox-JAB-2 family  .. 
PF15656 Toxin with a H, D/N and C signature<br>A predicted alpha/beta fold peptidase domain with a strongly conserved triad of a histidine, aspartate/asparagine and cysteine residues that are predicted to comprise the active site of the predicted peptidase. Proteins bearing this predicted toxin domain are particularly common in both intracellular and extracellular pathogens  .. 
PF15657 HNH/Endo VII superfamily nuclease toxins<br>A predicted toxin of the HNH/Endonuclease VII fold present in bacterial polymorphic toxin systems with a characteristic conserved [ED]H motif and two histidine residues. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 5, type 6, type 7 or Photorhabdus virulence cassette (PVC)-type secretion system  .. 
PF15658 Latrotoxin C-terminal domain<br>A toxin domain present in arthropod alphaproteobacterial, gammaproteobacterial endosymbionts and also at the C-termini of the latrotoxins of the black widow spider. The domain is characterized by a conserved, hydrophobic helix and is predicted to associate with the cell membrane  .. 
PF15659 JAB-like toxin  1<br>
PF15660 Immunity protein 49<br>