SII-SWORD/CoKE huggingface dataset:
Pfam PF16069: Domain of unknown function (DUF4811) (family)
This family of proteins is found in bacteria. Proteins in this family are typically between 188 and 241 amino acids in length. There is a single completely conserved residue Y that may be functionally important.
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 PF11670: Major surface protein 1a (MSP1a) (family)
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.
Pfam PF24203: Phage ProQ C-terminal-like domain (family)
This entry represents a family of uncharacterised phage and bacterial proteins. Structurally the proteins include an N-terminal beta barrel domain that shows some structural similarity to the C-terminal domain of the ProQ RNA-binding domain. That domain has been described as being similar to the Tudor domains.
Pfam PF01824: MatK/TrnK N-terminal (domain)
Group II introns are widespread in plant cell organelles. In vivo, most plant group II introns do not self-splice, but require the assistance of proteinaceous splicing factors, known as maturases. In higher plants, maturases are encoded for in the nuclear genes, but are otherwise encoded by organellar introns. The N-terminal domain of MatK, a maturase encoded in the trnK tRNA gene intron, appears to be a divergent reverse transcriptase domain that has lost most of the conserved sequence motifs typical of functional reverse transcriptases. The function of this domain is not known, but it may be important in RNA splicing.
Wikipedia: Maturase K (matK) is a plant plastidial gene. The protein it encodes is an organelle intron maturase, a protein that splices Group II introns. It is essential for in vivo splicing of Group II introns. Amongst other maturases, this protein retains only a well conserved domain X and remnants of a reverse transcriptase domain.
Pfam PF01728: FtsJ-like methyltransferase (family)
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.
Pfam PF12580: Tripeptidyl peptidase II (family)
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.
Pfam PF12648: TcpE family (domain)
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.
Pfam PF12948: MSP7-like protein C-terminal domain (domain)
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.
Pfam PF13011: leucine-zipper of insertion element IS481 (family)
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.
Pfam PF12706: Beta-lactamase superfamily domain (domain)
This family is part of the beta-lactamase superfamily and is related to [pfam:PF00753].
Pfam PF21355: TRAF/meprin, MATH domain (domain)
Intracellular TRAFs and extracellular meprins share a conserved region of about 180 residues, the the meprin and TRAF homology (MATH) domain which adopts a beta-sandwich structure. This is the MATH domain of TNF receptor-associated factors (TRAFs) and meprins. In TRAFS, it is essential for self-association and receptor interaction. Meprins are mammalian tissue-specific metalloendopeptidases involved developmental, normal and pathological processes.
Pfam PF02106: Fanconi anaemia group C protein (family)
Fanconi anemia (FA) is a human disorder characterised by cancer susceptibility and cellular sensitivity to DNA crosslinks and other damages. The FA complex repairs the interstrand cross-linking (ICL) lesions and coordinates activities of the downstream DNA repair pathway including nucleotide excision repair, translesion synthesis, and homologous recombination. It is required for the monoubiquitylation of FANCD2 and FANCI heterodimer. The FA core complex consists of FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL, FANCM, FANCT (UBET2), FAAP100 and FAAP24 .
This entry represents FANCC .
Wikipedia: Fanconi anemia group C protein is a protein that in humans is encoded by the FANCC gene. This protein delays the onset of apoptosis and promotes homologous recombination repair of damaged DNA. Mutations in this gene result in Fanconi anemia, a human rare disorder characterized by cancer susceptibility and cellular sensitivity to DNA crosslinks and other damages.
Pfam PF17875: RPA43 OB domain in RNA Pol I (domain)
This is OB domain found in RPA43 proteins (DNA-directed RNA polymerase I subunit RPA43, also known as A43) in yeast. Functional analysis of RNA polymerase I show that, subunits A14 and A43 form the heterodimer A14/43, which is distantly related to Rpb4/7 in Pol II and C17/25 in Pol III. Crystal structure analysis show that A43-A14 heterodimer forms the stalk that provides a platform for initiation factors and interacts with newly synthesized RNA.
Pfam PF21824: Mucin-20 protein (repeat)
This entry represents a short repeat from mucin-20 protein that forms a beta solenoid structure in the AlphaFold model.
Pfam PF11816: Domain of unknown function (DUF3337) (family)
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.
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 PF17036: Cellulose biosynthesis protein BcsS (domain)
This is a family of bacterial cellulose biosynthesis proteins. Cellulose is necessary for biofilm formation in bacteria. Structural models show that this protein forms a membrane bound beta barrel structure.
Pfam PF16007: Domain of unknown function (DUF4777) (family)
This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is approximately 70 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 PF16746: BAR domain of APPL family (domain)
BAR_12 is the BAR coiled-coil domain at the N-terminus of APPL or adaptor protein containing PH domain, PTB domain, and leucine zipper motif proteins in higher eukaryotes. This BAR domain contains four helices whereas the other classical BAR domains contain only three helices. The first three helices form an antiparallel coiled-coil, while the fourth helix, is unique to APPL1. BAR domains take part in many varied biological processes such as fission of synaptic vesicles, endocytosis, regulation of the actin cytoskeleton, transcriptional repression, cell-cell fusion, apoptosis, secretory vesicle fusion, and tissue differentiation.
Wikipedia: Bar or BAR may refer to:
Pfam PF05255: Uncharacterised protein family (UPF0220) (family)
This family of proteins is functionally uncharacterised.
Pfam PF05331: Protein of unknown function (DUF742) (family)
This family consists of several uncharacterised Streptomyces proteins as well as one from Mycobacterium tuberculosis. The function of these proteins 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 PF04732: Intermediate filament head (DNA binding) region (family)
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.
Wikipedia: Intermediate filaments (IFs) are cytoskeletal structural components found in the cells of vertebrates, and many invertebrates. Homologues of the IF protein have been noted in an invertebrate, the cephalochordate Branchiostoma.
Pfam PF02210: Laminin G domain (domain)
This family includes the Thrombospondin N-terminal-like domain, a Laminin G subfamily.
Wikipedia: Laminins are a family of glycoproteins of the extracellular matrix of all animals. They are major constituents of the basement membrane, namely the basal lamina. Laminins are vital to biological activity, influencing cell differentiation, migration, and adhesion.
Pfam PF09992: Phosphodiester glycosidase (domain)
This is a family conserved from bacteria to humans. The structure of a member from Bacteroides has been crystallised and modelled onto the luminal region of the human member of the family, the transmembrane glycoprotein N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase. There is some conservation of potentially functional residues, implying that in the bacterial members this family acts in some way as a phosphodiester glycosidase. The human protein is also present, so the eukaryotic members are likely to be catalysing the second step in the formation of the mannose 6-phosphate targeting signal on lysosomal enzyme oligosaccharides.
Pfam PF02414: Borrelia ORF-A (family)
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.
Pfam PF22014: Family of unknown function (DUF6932) (family)
This is a family of uncharacterised bacterial proteins. They are remotely related to nucleotidyltransferases and share similar active site architecture.
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 PF19928: Domain of unknown function (DUF6391) (domain)
This domain of unknown function is found in uncharacterised proteins from bacteria, mainly from Cyanobacteria. It contains the conserved sequence motifs LEHAT, GF, CGTN and QxxxTT.
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 PF18676: MBG domain (YGX type) (domain)
This domain is found in a variety of bacterial extracellular proteins. This domain is related to the MBG domain ([pfam:PF17883]).  But it replaces the characteristic YDG motif close the N-terminus with a YGX motif.
Pfam PF20161: VpsR domain (family)
VpsR appears superficially to be a response regulator, based on extension of its alignment to response regulators AlgB and NrtC all the way to the N-terminus.  Instead of being a response regulator with a histidine kinase partner, the sigma-54-dependent transcription factor VpsR directly binds to cyclic-di-GMP. Its regulon includes genes for the biosynthesis of the biofilm matrix component called Vibrio polysaccharide (VPS).
Pfam PF07435: YycH protein (family)
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.
Pfam PF23894: SV2A/B/C luminal domain (repeat)
This entry represents the luminal domain found in synaptic vesicle protein 2 A, B and C (SV2A, SV2B and SV2C) from animals. SV2s are specific to vesicles that undergo calcium-regulated secretion and are essential for normal nervous system function, particularly for neurotransmission. SV2s have also been identified as targets for botulinum neurotoxins (BoNTs) serotypes A, D, E and F. In the case of VS2C, this domain interacts directly and allows BoNT/A transport into host cells.
Pfam PF14276: Domain of unknown function (DUF4363) (family)
This family of proteins is found in bacteria. Proteins in this family are approximately 120 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 PF01950: Fructose-1,6-bisphosphatase (family)
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.
Wikipedia: The enzyme fructose bisphosphatase (EC 3.1.3.11; systematic name D-fructose-1,6-bisphosphate 1-phosphohydrolase) catalyses the conversion of fructose-1,6-bisphosphate to fructose 6-phosphate in gluconeogenesis and the Calvin cycle, which are both anabolic pathways:D-fructose 1,6-bisphosphate + H2O = D-fructose 6-phosphate + phosphate
Pfam PF01578: Cytochrome C assembly protein (family)
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 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. CcmF forms a working module with CcmH and CcmI, CcmFHI, and itself is unlikely to bind haem directly.
Wikipedia: In molecular biology, the cytochrome c assembly protein family includes various proteins involved in cytochrome c assembly from mitochondria and bacteria. Members of this family include: CycK from Rhizobium leguminosarum, CcmC from Escherichia coli and Paracoccus denitrificans, and orf240 from Triticum aestivum (Wheat) mitochondria. The members of this family are probably integral membrane proteins with six predicted transmembrane helices that may comprise the membrane component of an ABC transporter complex. This transporter may be necessary for transport of some component needed for cytochrome c assembly. One member, R. leguminosarum CycK, contains a putative haem-binding motif. Wheat orf240 also contains a putative haem-binding motif and is a proposed ABC transporter with c-type haem as its proposed substrate. However it seems unlikely that all members of this family transport haem or c-type apocytochromes because P. denitrificans CcmC transports neither.
Pfam PF19160: SPARK (domain)
This entry is typically found as an extracellular domain of plant receptor-like kinases, many of which play a role in signalling during plant-fungal symbiosis. The precise function of this entry is unknown (Montero H et.al. PNAS June 22, 2021 118 (25) e2105281118).
Pfam PF22642: Cell-division inhibitor MinC, N-terminal domain-like (domain)
This entry represents the N-terminal domain of MinC and related proteins. MinC is a cell division inhibitor that blocks the formation of polar Z ring septums. It consists of two domains. The N-terminal domain interacts with FtsZ and inhibits FtsZ polymerization while the C-terminal interacts with MinD and inhibits the bundling of FtsZ filaments.
Pfam PF16984: Group 7 allergen (domain)
This entry contains proteins that cause an allergic reaction in humans. Common symptoms of mite allergy are bronchial asthma, allergic rhinitis and conjunctivitis .
Pfam PF23484: YBR126W-A (family)
This protein family includes the uncharacterised protein YBR126W-A from Saccharomyces cerevisiae, a micropeptide encoded by a small open reading frame (smORF). YBR126W-A is predicted to adopt an alpha-helical structure.
Pfam PF01418: Helix-turn-helix domain, rpiR family (domain)
This domain contains a helix-turn-helix motif. The best characterised member of this family is [swissprot:P39266]. RpiR is a regulator of the expression of rpiB gene.
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 PF08866: Putative amino acid metabolism (domain)
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.
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 PF12350: CTD kinase subunit gamma CTK3 C-terminus (domain)
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.
Pfam PF13891: Potential DNA-binding domain (domain)
This domain is likely to be the DNA-binding domain of chromatin re-modelling proteins and helicases.
Pfam PF11713: Peptidase C80 family (domain)
This family belongs to cysteine peptidase family C80.
Wikipedia: Clostridioides difficile toxin B (TcdB) is a cytotoxin produced by the bacteria Clostridioides difficile. It is one of two major kinds of toxins produced by C. difficile, the other being a related enterotoxin. Both are very potent and lethal.
Pfam PF22217: Acyl-CoA dehydrogenase 11 C-terminal domain-like (domain)
Acyl-CoA dehydrogenase 11 (ACDH-11) sequesters C11/C12-chain fatty acids and prevents these fatty acids from activating nuclear hormone receptors and driving fat-7 expression. This enzyme consists of four domains, of which the C-terminal, represented by this entry, folds into a four-helical up-and-down bundle.
Pfam PF21237: Eukaryotic Pus10, N-terminal (domain)
This is the N-terminal domain of eukaryotic tRNA pseudouridine synthase Pus10. Pus10 has different functions depending on its subcellular location: involved in miRNA processing in the nucleus and acts as a tRNA pseudouridylate synthase in the cytoplasm. This domain functions as an accessory RNA-binding domain regarding the presence of a THUMP domain, similarly to other pseudouridine synthases ([pfam:PF02926]). This entry does not include archaeal Pus10, the N-terminal domain of eukaryotic Pus10 is much larger than that of archaeal Pus10.