SII-SWORD/CoKE huggingface dataset:
Pfam PF23140: Podophage GP4 fiber I protein gp80 (family)
This entry represents the Podophage GP4 fiber I protein gp80 and related phage proteins. Bacteriophage tail fibers play a critical role in the early stage of infection by binding to the bacterial surface. In Podophage GP4, five fiber I, each composed of five dimers of gp80 and linked by rope protein, are attached to the five edges of the tail vertex of the icosahedral head of the phage. The structure of gp80 has an unusual barrel-like topology with one strand contributed by the rope protein. The N terminus of gp80 folds into an alpha-helix which is involved in the dimerisation.
Pfam PF10542: Vitelline membrane cysteine-rich region (domain)
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.
Pfam PF20154: Apolipoprotein N-acyltransferase N-terminal domain (domain)
This domain represents the N-terminal transmembrane region of the apolipoprotein N-acyltransferase enzyme. The enzyme catalyzes the phospholipid dependent N-acylation of the N-terminal cysteine of apolipoprotein, the last step in lipoprotein maturation. This entry does not represent the enzymatic domain found at the C-terminus of the protein.
Pfam PF00374: Nickel-dependent hydrogenase (family)
Hydrogenases are enzymes that catalyse the reversible oxidation of hydrogen and are important in anaerobic metabolism. There are various types of metal-containing hydrogenases and can be broadly divided into three groups: Fe ('iron only') hydrogenases; Ni-Fe hydrogenases; and Ni-Fe-Se hydrogenases .

The [NiFe] and [NiFeSe] hydrogenases are heterodimer that consist of a small subunit (S) that contains a signal peptide and a large subunit (L). All the known large subunits seem to be evolutionary related ; they contain two Cys-x-x-Cys motifs; one at their N-terminal end; the other at their C-terminal end. These four cysteines are involved in the binding of nickel . In the [NiFeSe] hydrogenases the first cysteine of the C-terminal motif is a selenocysteine which has experimentally been shown to be a nickel ligand .
Wikipedia: Hydrogenases are enzymes that catalyze the reversible activation of hydrogen and which occur widely in prokaryotes as well as in some eukaryotes. There are various types of hydrogenases, but all of them seem to contain at least one iron-sulphur cluster. They can be broadly divided into two groups: hydrogenases containing nickel and, in some cases, also selenium and those lacking nickel.
Pfam PF11897: Protein of unknown function (DUF3417) (family)
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.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF02202: Tachykinin family (family)
Tachykinins  are a group of biologically active peptides which excite neurons, evoke behavioral responses, are potent vasodilatators and contract (directly or indirectly) many smooth muscles. This family includes many other peptides. Tachykinins, like most other active peptides, are synthesized as larger protein precursors, protachykinins, that are enzymatically converted to their mature forms. Tachykinins are from ten to twelve residues long.
Wikipedia: Tachykinin peptides are one of the largest families of neuropeptides, found from amphibians to mammals. They were so named due to their ability to rapidly induce contraction of gut tissue. The tachykinin family is characterized by a common C-terminal sequence, Phe-X-Gly-Leu-Met-NH2, where X is either an Aromatic or an Aliphatic amino acid. The genes that produce tachykinins encode precursor proteins called preprotachykinins, which are chopped apart into smaller peptides by posttranslational proteolytic processing. The genes also code for multiple splice forms that are made up of different sets of peptides.
Pfam PF00906: Hepatitis core antigen (domain)
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.
Pfam PF06754: Phosphonate metabolism protein PhnG (family)
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.
Pfam PF19138: Transcriptional regulator TbsP-like, N-terminal (domain)
This domain is found at the N-terminal of the putative transcriptional regulator TbsP from Halobacterium volcanii ([swissprot:D4GXF9], also known as HVO_2861) and similar sequences predominantly found in Halobacteria. TbsP is required for adhesion to abiotic surfaces (i.e., biofilm formation) and maintains wild-type cell morphology and motility. This domain shows weak structural similarity with the DNA -binding protein TrmBL2 of P. furiosus ([pfam:PF11495]).
Pfam PF20913: Oxalate Biosynthetic Component A, N-terminal domain (domain)
This domain is found at the N-terminal end of Oxalate Biosynthetic Component A (ObcA) from Burkholderia glumae. ObcA shows a unique structural architecture, with the small N-domain (this entry) inserted into a loop between the first beta-strand and the first alpha-helix of the C-domain barrel fold ([pfam:PF05853]).
Pfam PF08458: Plant pleckstrin homology-like region (domain)
This family describes a pleckstrin homology (PH)-like region found in several plant proteins of unknown function.
Pfam PF23625: Ubiquitin interaction motif (conserved_site)
This entry represents a set of ubiquitin interaction motifs.
Pfam PF20566: eIF4E-associated protein (family)
This fungal family includes eIF4E-associated protein (Eap1) from yeast, which plays a role in cell growth and is implicated in the TOR signaling cascade. Eap1 binds to eIF4E and regulates translation. It competes with eIF4G (the large subunit of the cap-binding complex, eukaryotic initiation factor 4F (eIF4F)) for binding to eIF4E and accelerates mRNA degradation by promoting decapping. It associates with Puf5p and Dhh1p, being essential for Puf5p mediated repression. This family also includes the uncharacterised protein from S. pombe SPCC14G10.04 ([swissprot:O74417]) which has been shown to interact with eIF4E, 4F complex subunits.
Pfam PF23507: YqiM (family)
This protein family includes Protein YqiM from Escherichia coli, a 27-residues micropeptide encoded by a small open reading frame (smORF). Proteins 50 or fewer residues-long have been shown to regulate the functions of larger proteins in a variety of organisms.
Pfam PF09063: Phage PP7 coat protein (domain)
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.
Pfam PF02297: Cytochrome oxidase c subunit VIb (domain)
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.
Wikipedia: The enzyme cytochrome c oxidase or Complex IV is a large transmembrane protein complex found in bacteria, archaea, and the mitochondria of eukaryotes.
Pfam PF15915: GAF and HTH_10 associated domain (domain)
GAF-HTH_assoc domain is always found between GAF-2 and HTH_10 domains on bacterio-opsin activator proteins. The exact function is not known.
Pfam PF20275: C-terminal domain 10 of the ABC-three component (ABC-3C) systems (domain)
C-terminal domains (CTDs) of ABC-3C systems, contain distinct patterns of charged and polar residues and are not yet unifiable with known domains. These domains are found at the C-terminus of the effector component of the systems, which are upstream of the Middle Component and ABC ATPase components on the genome. Due to the typically large size of these CTDs relative to the actual effector and MC domains, the CTDs are predicted to serve as the platform on which the remaining two components assemble. Therewith, conformational changes transmitted by the ABC ATPase-mediated detection of invasive elements like DNA viruses would result in an unfurling and activation of the CTD-associated effector.
Pfam PF13387: Domain of unknown function (DUF4105) (family)
This is a family of uncharacterised bacterial proteins. There is a highly conserved histidine residue and a well-conserved NCT motif.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF22871: AimR transcriptional regulator-like (repeat)
This entry includes AimR transcriptional regulator from Bacillus phage and related sequences found in tailed bacteriophages and prophages. AimR (arbitrium receptor), which is a part of the so-called phage arbitrium system, is a DNA-binding phage regulatory protein that acts as a receptor for a 6-amino acid signaling peptide cleaved rom the C terminus of AimP. AimR controls expression of AimX, the third member of the quorum sensing-like arbitrium system and an inhibitor of phage lysogeny. AimR assembles in an alpha-alpha superhelix fold and accommodates the signaling peptide encircled by its tetratricopeptide repeats, which is reminiscent of RRNPP family members from the quorum-sensing system.
Pfam PF13784: Fic/DOC family N-terminal (family)
This domain is found at the N-terminus of the Fic/DOC family, [pfam:PF02661].
Pfam PF00048: Small cytokines (intecrine/chemokine), interleukin-8 like (domain)
Includes a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity. Structure contains two highly conserved disulfide bonds.
Wikipedia: Chemokines, or chemotactic cytokines, are a family of small cytokines or signaling proteins secreted by cells that induce directional movement of leukocytes, as well as other cell types, including endothelial and epithelial cells. In addition to playing a major role in the activation of host immune responses, chemokines are important for biological processes, including morphogenesis and wound healing, as well as in the pathogenesis of diseases like cancers.
Pfam PF10957: Sporulation protein Cse60 (family)
Cse60 is expressed during sporulation in Bacillus subtilis. Transcription commences around 2h after the start of sporulation and  had an absolute requirement for the transcription factor sigmaE. Cse60 is an acidic product of only 60 residues, whose function is not  known.
Pfam PF11210: Protein of unknown function (DUF2996) (family)
This family of proteins has no known function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF17678: Glycosyl hydrolase family 92 N-terminal domain (domain)
This domain is found at the N-terminus of family 92 glycosyl hydrolase proteins.
Pfam PF22121: Magnetotaxis protein MtxA, C-terminal domain (repeat)
This domain is found at the C-terminal end of Magnetotaxis protein MtxA from Magnetospirillum gryphiswaldense ([swissprot:A4TUL6]) and similar sequences from magnetotactic aquatic proteobacteria. Magnetotaxis is believed to direct the swimming of cells toward growth-favoring microoxic zones in natural waters. This domain shows five anti-parallel alpha-helices-and-turn motifs folded as tetra-trico-peptide repeat (TPR) motifs.
Pfam PF01801: Cytomegalovirus glycoprotein L (family)
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.
Pfam PF15609: Phosphoribosyl transferase (family)
This PRTase family, and 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.
Pfam PF06738: Putative threonine/serine exporter (domain)
ThrE is a family of bacterial and Archaeal proteins that catalyse the export of L-threonine from the cell. UniProtKB:Q79VD1 has been characterised as being necessary for this export. The domain exhibits 10 putative TMs and catalyses the proton-motive-force-dependent efflux of threonine and serine.
Pfam PF08885: GSCFA family (domain)
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.
Pfam PF19077: Bacterial Ig-like domain (domain)
Presumed domain found as tandem repeats of high sequence identity in bacterial cell surface proteins.
Pfam PF00583: Acetyltransferase (GNAT) family (family)
This family contains proteins with N-acetyltransferase functions such as Elp3-related proteins.
Wikipedia: An acetyltransferase is any of a class of transferase enzymes that transfers an acetyl group in a reaction called acetylation. In biological organisms, post-translational modification of a protein via acetylation can profoundly transform its functionality by altering various properties like hydrophobicity, solubility, and surface attributes. These alterations have the potential to influence the protein's conformation and its interactions with substrates, cofactors, and other macromolecules.
Pfam PF13890: Rab3 GTPase-activating protein catalytic subunit (family)
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.
Pfam PF12142: Polyphenol oxidase middle domain (domain)
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.
Pfam PF05903: PPPDE putative peptidase domain (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).
Pfam PF01957: NfeD-like C-terminal, partner-binding domain (domain)
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.
Pfam PF10025: Uncharacterized conserved protein (DUF2267) (family)
This domain, found in various hypothetical bacterial proteins, has no known function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF12017: Transposable element P transposase-like, HTH domain (domain)
This entry represents the HTH domain of human DNA transposase THAP9 which is homologous to Drosophila P-element transposase.  THAP9 is an active transposase that specifically recognizes the bipartite 5'-TXXGGGX(A/T)-3' consensus motif and mediates transposition. The structure of Drosophila P-element transposase has been solved.
Pfam PF01793: Glycolipid 2-alpha-mannosyltransferase (family)
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.
Pfam PF12552: Protein of unknown function (DUF3741) (family)
This domain family is found in eukaryotes, and is approximately 50 amino acids in length.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF15213: CMT1A duplicated region transcript 4 protein (family)
Charcot-Marie-Tooth disease type 1A (CMT1A) is the most common inherited peripheral neuropathy and one of the best-characterised examples of a submicroscopic genomic disorder. In most cases it is due to a submicroscopic duplication of the 1.4-Mb genomic region in chromosome band 17p12. This putative protein represents the product of transcript 4 in this region .
Pfam PF07806: Nodule-specific GRP repeat (repeat)
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.
Pfam PF00103: Somatotropin hormone family (domain)
Somatotropin is a hormone that plays an important role in growth control. It belongs to a family that includes choriomammotropin (lactogen), its placental analogue; prolactin, which promotes lactation in the mammary gland, and placental prolactin-related proteins; proliferin and proliferin related protein; and somatolactin from various fish . The 3D structure of bovine somatotropin has been predicted using a combination of heuristics and energy minimisation .
Wikipedia: The Somatotropin family is a protein family whose titular representative is somatotropin, also known as growth hormone, a hormone that plays an important role in growth control. Other members include choriomammotropin (lactogen), its placental analogue; prolactin, which promotes lactation in the mammary gland, and placental prolactin-related proteins; proliferin and proliferin related protein; and somatolactin from various fishes. The 3D structure of bovine somatotropin has been predicted using a combination of heuristics and energy minimisation.
Pfam PF02600: Disulfide bond formation protein DsbB (family)
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.
Wikipedia: Disulfide bond formation protein B (DsbB) is a protein component of the pathway that leads to disulfide bond formation in periplasmic proteins of Escherichia coli (P0A6M2) and other bacteria. In Bacillus subtilis it is known as BdbC (O32217).
Pfam PF10509: Galactokinase galactose-binding signature (domain)
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].
Pfam PF12939: Domain of unknown function (DUF3837) (domain)
A small, compact all-alpha helical domain of unknown function. This domain is currently only found in Clostridiales species.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF17196: Protein of unknown function (DUF5133) (family)
This protein of unknown function is part of the Borrelidin synthesis genomic cluster. Borrelidin is a polyketide antibiotic.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.