SII-SWORD/CoKE huggingface dataset:
Pfam PF09385: Histidine kinase N terminal (domain)
This domain is found at the N terminal of sensor histidine kinase proteins.
Wikipedia: In molecular biology, a two-component regulatory system serves as a basic stimulus-response coupling mechanism to allow organisms to sense and respond to changes in many different environmental conditions. Two-component systems typically consist of a membrane-bound histidine kinase that senses a specific environmental stimulus, and a corresponding response regulator that mediates the cellular response, mostly through differential expression of target genes. Although two-component signaling systems are found in all domains of life, they are most common by far in bacteria, particularly in Gram-negative and cyanobacteria; both histidine kinases and response regulators are among the largest gene families in bacteria. They are much less common in archaea and eukaryotes; although they do appear in yeasts, filamentous fungi, and slime molds, and are common in plants, two-component systems have been described as "conspicuously absent" from animals.
Pfam PF13171: Protein of unknown function (DUF4004) (family)
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.
Pfam PF17628: Inclusion membrane protein D (family)
The chlamydial inclusion membrane is extensively modified by the insertion of type III secreted effector proteins. These inclusion membrane proteins (Incs) have two major characteristics: an N-terminal type III secretion signal that is necessary for their secretion out of the bacterium and a hydrophobic region consisting of at least two trans-membrane helices that allows insertion into the inclusion membrane. Generally, both the N- and C-terminal regions of the Inc are exposed to the host cell cytosol. This family has members such as the IncD proteins found in Chlamydia trachomatis. This C. trachomatis effector protein IncD has been shown to recruit the lipid transfer protein CERT to the inclusion membrane by directly interacting with CERT PH domain, which mediates the FFAT motif-dependent recruitment of the ER-resident protein VAPB (vesicle-associated membrane protein-associated protein) to the inclusion.
Pfam PF08872: KGK domain (domain)
This presumed domain is found in one or two copies in cyanobacterial proteins. It is named after a short sequence motif.
Pfam PF07934: 8-oxoguanine DNA glycosylase, N-terminal domain (family)
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.
Wikipedia: 8-Oxoguanine glycosylase, also known as OGG1, is a DNA glycosylase enzyme that, in humans, is encoded by the OGG1 gene. It is involved in base excision repair. It is found in bacterial, archaeal and eukaryotic species.
Pfam PF11461: Rab interacting lysosomal protein (family)
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.
Pfam PF01486: K-box region (family)
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.
Pfam PF19697: Atg11 middle domain (domain)
This domain represents the region comprised between residues 522 and 583 from fission yeast protein Atg11, which is necessary and sufficient for Atg11 autophagy function and for supporting Atg1 kinase activity as it harbours an Atg1-binding domain at the N-terminal and a homodimerisation domain at the C-terminal. The N-terminal part contains the conserved aromatic residues Phe and Tyr necessary for the direct and specific interaction with the tMIT domain of Atg1. This interaction is required for the autophagy function of Atg11. The C-terminal part of this domain, residues 546-583, is predicted to adopt a coiled-coil conformation which mediates Atg11 homodimerisation. It seems to be conserved among Schizosaccharomyces.
Pfam PF01144: Coenzyme A transferase (domain)
This family consists of 3-oxoacid CoA-transferases and related CoA-transferases from family I.
Coenzyme A (CoA) transferases belong to an evolutionary conserved  family of enzymes catalyzing the reversible transfer of CoA from one carboxylic acid to another. They have been identified in many prokaryotes and in mammalian tissues. The bacterial enzymes are heterodimer of two subunits (A and B) of about 25 Kd each while eukaryotic SCOT consist of a single chain which is colinear with the two bacterial subunits.
CoA-transferases are found in organisms from all kingdoms of life. They catalyse reversible transfer reactions of coenzyme A groups from CoA-thioesters to free acids. There are at least three families of CoA-transferases, which differ in sequence and reaction mechanism:


 * Family I consists of CoA-transferases for 3-oxoacids (2.8.3.5, 2.8.3.6), short-chain fatty acids (2.8.3.8, 2.8.3.9) and glutaconate (2.8.3.12). Most use succinyl-CoA or acetyl-CoA as CoA donors.
 * Family II consists of the homodimeric alpha-subunits of citrate lyase and citramalate lyase (2.8.3.10, 2.8.3.11). These enzymes catalyse the transfer of acyl carrier protein (ACP) with a covalently bound CoA derivative, but can accept free CoA thioesters as well.
 * Family III consists of formyl-CoA:oxalate CoA-transferase , succinyl-CoA:(R)-benzylsuccinate CoA-transferase , (E)-cinnamoyl-CoA:(R)-phenyllactate CoA-transferase , succinyl-CoA:mesaconate CoA-transferase  and butyrobetainyl-CoA:(R)-carnitine CoA-transferase . These CoA-transferases occur in prokaryotes and eukaryotes, and catalyse CoA-transfer reactions in a highly substrate-and stereo-specific manner .
Pfam PF23559: Disease resistance protein Winged helix domain (domain)
This entry represents a winged helix-turn-helix domain found in plant Resistance proteins.
Pfam PF12323: Helix-turn-helix domain (family)
This is the N terminal helix-turn-helix domain of Transposase_2 [pfam:PF01385].
Wikipedia: Helix-turn-helix is a DNA-binding domain (DBD). The helix-turn-helix (HTH) is a major structural motif capable of binding DNA. Each monomer incorporates two α helices, joined by a short strand of amino acids, that bind to the major groove of DNA. The HTH motif occurs in many proteins that regulate gene expression. It should not be confused with the helix–loop–helix motif.
Pfam PF05768: Glutaredoxin-like domain (DUF836) (domain)
These proteins are related to the [pfam:PF00462] family. This entry includes several viral glutaredoxins and many related bacterial and eukaryotic proteins of unknown function. The best characterised member is G4L ([swissprot:P68460]) from Vaccinia virus (strain Western Reserve/WR) (VACV), which is necessary for virion morphogenesis and replication. This is a cytoplasmic protein which functions as a shuttle in a redox pathway between membrane-associated E10R and L1R or F9L.
Pfam PF23792: CD1375-like protein (domain)
This entry represents a short uncharacterized domain of about 50 residues. It is found in phage proteins from a variety of phages infecting Bacilli or Clostridia bacteria. Structural predictions suggest it adopts an alpha helical fold. Its function is currently unknown.
Pfam PF07397: Repeat of unknown function (DUF1502) (repeat)
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.
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 PF08842: Fimbrillin-A associated anchor proteins Mfa1 and Mfa2 (family)
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.
Pfam PF11549: Protein transport protein SEC31 (family)
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.
Pfam PF12631: MnmE helical domain (family)
The tRNA modification GTPase MnmE consists of three domains. An N-terminal domain, a helical domain and a GTPase domain which is nested within the helical domain. This family represents the helical domain.
Pfam PF20616: Capsule biosynthesis GfcC, N-terminal (domain)
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. This entry represents D2 domain found at the N-terminal.
Pfam PF05030: SSXT protein (N-terminal region) (family)
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.
Pfam PF01491: Frataxin-like domain (domain)
This family contains proteins that have a domain related to the globular C-terminus of Frataxin the protein that is mutated in Friedreich's ataxia.  This domain is found in a family of bacterial proteins.        The function of this domain is currently unknown. It has been suggested that this family is involved in iron transport.
Wikipedia: In molecular biology, the frataxin-like domain is a protein domain found in proteins including eukaryotic frataxin and bacterial CyaY.
Pfam PF17294: Uncharacterised lipoprotein family (domain)
The proteins in this family all have an N-terminal lipoprotein attachment motif. No member of this family has been functionally characterised.
Pfam PF02697: Putative antitoxin (family)
Proteins in this family are possibly the antitoxin component of a VAPBC-like toxin-antitoxin (TA) module, which is widespread in the in both archaea and bacteria.
Pfam PF11163: Protein of unknown function (DUF2947) (family)
This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
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 PF25126: Domain of unknown function (DUF7818) (domain)
This domain is found towards the C terminus of human NEDD4 -binding protein 2 (N4BP2), which has 5'-polynucleotide kinase and nicking endonuclease activity and may play a role in DNA repair or recombination. This domain is often found associated with [pfam:PF25124] and [pfam:PF08590].
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 PF00228: Bowman-Birk serine protease inhibitor family (domain)
This family of eukaryotic proteinase inhibitors, belongs to MEROPS inhibitor family I12, clan IF. They predominantly inhibit serine peptidases of the S1 family (IPR001254) . They play a role in defense response against pathogens and insects, but they also have been studied as therapeutic treatment in cancer and inflammatory disorders . Exceptionally, cowpea trypsin inhibitor inhibits a cathepsin L-like cysteine proteinase CPL-1 from the nematode Heterodera glycines .

The Bowman-Birk inhibitor family  is one of the numerous families of serine proteinase inhibitors. They have a duplicated structure and generally possess two distinct inhibitory sites. These inhibitors are primarily found in plants and in particular in the seeds of legumes as well as in cereal grains. In cereals they exist in two forms, one of which is a duplication of the basic structure . Proteins of the Bowman-Birk inhibitor family of serine proteinase inhibitors interact with the enzymes they inhibit via an exposed surface loop that adopts the canonical proteinase inhibitory conformation. The resulting non-covalent complex renders the proteinase inactive. This inhibition mechanism is common for the majority of serine proteinase inhibitor proteins and many analogous examples are known. A particular feature of the Bowman-Birk inhibitor protein, however, is that the interacting loop is a particularly well-defined disulphide-linked short Î²-sheet region .
Wikipedia: In molecular biology, the Bowman–Birk protease inhibitor family of proteins consists of eukaryotic proteinase inhibitors, belonging to MEROPS inhibitor family I12, clan IF. They mainly inhibit serine peptidases of the S1 family, but also inhibit S3 peptidases.
Pfam PF20834: Domain of unknown function (DUF6842) (domain)
This domain is found in Hypothetical protein lpg2422 from Legionella pneumophila. It adopts an helical bundle fold. Its function is unknown.
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 PF18025: Alpha-(1,3)-fucosyltransferase FucT N-terminal domain (domain)
This is the N-terminal domain of the alpha chain found in Helicobacter pylori Fucosyltransferase protein which is involved in the production of Lewis x trisaccharide, a major component of lipopolysaccharide. The N-terminal domain contains the catalyst base, Glu-95 which is equivalent to the Asp-100 of other members of the glycosyltransferases-B family. The domain contains the pocket where LacNAc binds. The domain is composed of 2-10 heptad repeats and a conserved N-terminal alpha-beta-alpha motif which has little sequence similarity to the conserved N-terminal motif in other glycosyltransferases.
Wikipedia: A fucosyltransferase is an enzyme that transfers an L-fucose sugar from a GDP-fucose donor substrate to an acceptor substrate. The acceptor substrate can be another sugar such as the transfer of a fucose to a core GlcNAc (N-acetylglucosamine) sugar as in the case of N-linked glycosylation, or to a protein, as in the case of O-linked glycosylation produced by O-fucosyltransferase. There are various fucosyltransferases in mammals, the vast majority of which, are located in the Golgi apparatus. The O-fucosyltransferases have recently been shown to localize to the endoplasmic reticulum (ER).
Pfam PF21688: FAD-dependent protein, C-terminal domain-like (domain)
This domain is found towards the C-terminal of a group of bacterial and archaeal FAD-linked dehydrogenases, whose exact function is not yet clear.
Pfam PF06107: Bacterial protein of unknown function (DUF951) (family)
This family consists of several short hypothetical bacterial proteins of unknown function. Structural modelling suggests this domain may bind nucleic acids.
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 PF12871: Pre-mRNA-splicing factor 38-associated hydrophilic C-term (domain)
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.
Pfam PF18537: Carbon monoxide dehydrogenase subunit alpha N-terminal domain (domain)
Acetyl-coenzyme A (CoA) synthase/carbon monoxide dehydrogenase (ACS/CODH) is a bifunctional enzyme that catalyzes the reversible reduction of CO2 to CO (CODH activity). This entry is for the N-terminal domain found in ACS/CODH subunit alpha.
Pfam PF13715: CarboxypepD_reg-like domain (domain)
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].
Pfam PF01732: Mycoplasma peptidase (DUF31) (domain)
This domain is found in various uncharacterised proteins and putative lipoproteins from mycoplasmas. Although its function is not clear, it has been suggested that this is a serine protease domain; sequence analysis revealed that the amino acid sequence is similar to that of serine proteases. It is related to pathogenicity as this domain is present in proteins encoded by animal and human pathogenic Mycoplasmas. It has been proposed that the Ig binding protein M may function together with this domain playing a role in evading host Ig-mediated defense against the MIB-MIP (mycoplasma Ig binding protein (MIB) and mycoplasma Ig protease (MIP)) system, which is a novel mechanism that protects mycoplasma against host immune response.
Pfam PF17320: Family of unknown function (DUF5363) (family)
This is a family of unknown function found in Gammaproteobacteri.
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 PF24346: Domain of unknown function (DUF7507) (domain)
This domain of unknown function is found in multiple copies in a number of bacterial proteins. It is closely related to domains represented by DUF11 ([pfam:PF01345]). Similarly to DUF11, this domain contains a conserved N-terminal lysine and a C-terminal asparagine with central aspartate/glutamate residues suggesting that it may contain an isopeptide bond. In addition, it contains a semi-conserved TNTGNV sequence motif in which a highly conserved asparagine probably plays a role in stabilising the rod structure formed by repetitive copies of this domain.
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 PF24755: YcgB (domain)
This entry represents a presumed domain found at the C-terminal of the uncharacterised protein YcgB from E.coli and related sequences. It may adopt a fold consisting of four beta-strands and an alpha-helix.
Pfam PF13145: PPIC-type PPIASE domain (domain)
Peptidyl-prolyl cis-trans isomerase (5.2.1.8) (PPIase or rotamase) is an enzyme that accelerates protein folding by catalysing the cis-trans isomerisation of proline imidic peptide bonds in oligopeptides . Most characterised PPiases belong to two families, the cyclophilin-type and the the FKBP-type. A third family has been discovered . So far, the only biochemically characterised member of this family is the Escherichia coli protein parvulin (gene ppiC), a small (92 residues) cytoplasmic enzyme that prefers amino acid residues with hydrophobic side chains like leucine and phenylalanine in the P1 position of the peptides substrates.

This entry represents a conserved region that contains a serine which could play a role in the catalytic mechanism of these enzymes. This domain is present in Periplasmic chaperone PpiD that were originally thought to be peptidyl-prolyl isomerases but it was shown later that they lack such activity .
Wikipedia: Prolyl isomerase is an enzyme found in both prokaryotes and eukaryotes that interconverts the cis and trans isomers of peptide bonds with the amino acid proline. Proline has an unusually conformationally restrained peptide bond due to its cyclic structure with its side chain bonded to its secondary amine nitrogen. Most amino acids have a strong energetic preference for the trans peptide bond conformation due to steric hindrance, but proline's unusual structure stabilizes the cis form so that both isomers are populated under biologically relevant conditions. Proteins with prolyl isomerase activity include cyclophilin, FKBPs, and parvulin, although larger proteins can also contain prolyl isomerase domains.