SII-SWORD/CoKE huggingface dataset:
Pfam PF19625: Family of unknown function (DUF6130) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 137 and 161 amino acids in length. There are two conserved sequence motifs: NLRI and HVTVDD.
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 PF13647: Glycosyl hydrolase family 80 of chitosanase A (domain)
This is a small family of bacterial chitosanases. These have lysozyme-like activity.
Wikipedia: In molecular biology, glycoside hydrolase family 80 is a family of glycoside hydrolases.
Pfam PF04031: Las1-like (family)
Las1 is an essential nuclear protein involved in cell morphogenesis and cell surface growth.
Pfam PF23201: Domain of unknown function (DUF7062) (domain)
This domain is found in a group of uncharacterised proteins from digenean 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 PF17396: Domain of unknown function (DUF1611_N) Rossmann-like domain (domain)
This entry represents a domain found at the N-terminal end of a group of prokaryotic proteins that includes A0A2T1AE85 from Tritonibacter scottomollicae (DgcN), an N-acetyltransferase responsible for N-acetylation of D-Glutamate, an essential component of bacterial peptidoglycans. DgcN consists of two distinct domains. This domain adopts a Rossman-like fold, with four Î²-strands composing a hydrogen-bonded Î²-sheet and six Î±-helices .
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 PF07024: ImpE protein (family)
This family consists of several bacterial proteins including ImpE ([swissprot: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.
Pfam PF10697: Protein of unknown function (DUF2502) (family)
Members of this family are all Gammaproteobacteria. The function is not known.
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 PF10953: Protein of unknown function (DUF2754) (family)
This family of proteins with unknown function appear to be restricted to Enterobacteriaceae.
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 PF15746: TMEM215 family (family)
This family of proteins is found in eukaryotes. Proteins in this family are approximately 230 amino acids in length.
Pfam PF07598: Protein of unknown function (DUF1561) (family)
A family of paralogous proteins in Leptospira interrogans.
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 PF19152: Family of unknown function (DUF5834) (family)
This family represents an uncharacterised protein  that is associated with the thiocillin biosynthetic  gene cluster.
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 PF14106: Domain of unknown function (DUF4279) (family)
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.
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 PF24555: Centrosomal protein of 85 kDa-like, CC4 coiled-coil domain (domain)
This domain is found in human Centrosomal protein of 85 kDa (CEP85) and similar animal proteins. CEP85 functions as a regulator of centriole duplication through a direct interaction with STIL, a key factor involved in the early steps of centriole formation. This entry represents the coiled-coil domain within the C-terminal region (cc4) that binds directly to the STIL N-terminal domain.
Pfam PF16937: Type III secretion system translocator protein, HrpF (family)
T3SS_HrpK1 is a family of putative Type III secretion system pore-forming bacterial proteins. These allow transfer of pathogenic material from bacterial cytoplasm into the plant host cytoplasm.
Pfam PF23935: Domain of unknown function (DUF7271) (domain)
This domain is found in the homologues of uncharacterised soybean proteins.
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 PF18498: Domain of unknown function (DUF5618) (domain)
This is a domain of unknown function found in bacteria.
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 PF01040: UbiA prenyltransferase family (family)
The UbiA family of prenyltransferases includes bacterial 4-hydroxybenzoate octaprenyltransferase (gene ubiA); yeast mitochondrial para-hydroxybenzoate--polyprenyltransferase (gene COQ2); protohaem IX farnesyltransferase (haem O synthase) from yeast and mammals (gene COX10), and from bacteria (genes cyoE or ctaB) ; and 2-acylphloroglucinol 4-prenyltransferase and 2-acyl-4-prenylphloroglucinol 6-prenyltransferase from plant chloroplasts which catalyse prenylation steps in the beta-bitter acid pathway . These are integral membrane proteins, which probably contain seven transmembrane segments.

Archaeal family members include lycopene elongase/hydratase - this type of enzyme has been shown to be involved in bacterioruberin synthesis in Halobacterium salinarum and Haloferax volcanii .
Pfam PF14193: Domain of unknown function (DUF4315) (family)
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.
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 PF05984: Cytomegalovirus UL20A protein (family)
This family consists of several Cytomegalovirus UL20A proteins. UL20A is thought to be a glycoprotein.
Pfam PF09468: Ydr279p protein family (RNase H2 complex component) wHTH domain (domain)
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.
Pfam PF01030: Receptor L domain (repeat)
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.
Pfam PF14253: Bacteriophage abortive infection AbiH (family)
This family of proteins confers resistance to bacteriophage.
Pfam PF14424: The BURPS668_1122 family of deaminases (family)
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.
Pfam PF21721: Phage tail fibre adhesin Gp38 N-terminal domain (domain)
This entry represents the N-terminal domain from several Gp38 proteins from T-even-like phages. This domain interacts with the Gp37 tail fiber protein.
Pfam PF01054: Mouse mammary tumour virus superantigen (family)
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.
Pfam PF06189: 5'-nucleotidase (family)
This family consists of both eukaryotic and prokaryotic 5'-nucleotidase sequences ([ec:3.1.3.5]).
Pfam PF14911: S-phase genomic integrity recombination mediator, C-terminal (family)
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. This family is the more C-terminal region of the proteins.
Pfam PF02892: BED zinc finger (domain)
The BED finger, which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain .

Some proteins known to contain a BED domain are listed below:


 * Animal, fungal and plant AC1 and Hobo-like transposases.
 * Caenorhabditis elegans protein dpy-20, a predicted cuticular-gene transcriptional regulator.
 * Drosophila BEAF (boundary element-associated factor), which is thought to be involved in chromatin insulation.
 * Drosophila DREF, a transcriptional regulator for S-phase genes.
 * Tobacco 3AF1 and tomato E4/E8-BP1, which are light- and ethylene-regulated DNA binding proteins that contain two BED fingers .
Wikipedia: In molecular biology the BED-type zinc finger domain is a protein domain which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF, thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. Most genes in this family are believed to have evolved from the hAT family of DNA transposons.
Pfam PF00488: MutS domain V (domain)
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.
Pfam PF12078: Domain of unknown function (DUF3557) (family)
This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 150 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 PF18693: TRAM domain (domain)
This is a C-terminal TRAM (after TRM2, a family of uridine methylases, and MiaB) domain found in the methylthiotransferases RimO enzymes that catalyze the conversion of aspartate to 2-methylthio-aspartate (msD) in the S12 protein near the decoding center in prokaryotic ribosomes. The TRAM domain in RimO, contains five anti-parallel beta-strands and docks on the surface of the Radical-SAM domain at the distal edge of its open TIM-barrel from its conserved [4Fe-4S] cluster.
Pfam PF04885: Stigma-specific STIG1-like protein family (family)
This family represents the Stig1 cysteine rich plant protein. The STIG1 gene is developmentally regulated and expressed specifically in the stigmatic secretory zone.  The STIG1 family is involved in various plant-specific functions, including the regulation of cell death, promotion of pollen tube growth, and modification of the interface between embryo and endosperm during seed development. Members of the family are typically cysteine-rich proteins that may undergo processing to perform their roles. For instance, a processed peptide of GRI induces cell death dependent on superoxide and salicylic acid, while STIG1 promotes pollen tube growth and binds phosphoinositol lipids, triggering an intracellular reactive oxygen species elevation. The family is also essential for the formation of structures like the embryo sheath and for the normal separation of embryo and endosperm tissues. This region contains three cystein-rich subdomains.
Pfam PF19873: Family of unknown function (DUF6346) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000223) is described by MIBiG as an example of the following biosynthetic class, polyketide, rabelomycin biosynthetic  gene cluster from uncultured bacterium BAC AB649/1850. This  family appears to be predominantly found in Actinobacteria.
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 PF15481: Chondroitin proteoglycan 4 (family)
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.
Pfam PF22190: TTHA0829-like ACT domain (domain)
This entry represents the ACT domain found at the C-terminal of TTHA0829, a hypothetical protein from Thermus thermophilus HB8. This protein may act as a cell-stress sensor or a metabolite acceptor. This protein contains a CBS ([pfam:PF00571]) at the N-terminal. TTHA0829 can form dimers or tetramers through several inter-domain interactions.
Pfam PF08313: SCA7, zinc-binding domain (domain)
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.
Pfam PF16759: DNA ligase 3 BRCT domain (domain)
The BRCT domain of DNA ligase 3 (LIG3) binds to the C-terminal BRCT domain of the scaffolding protein X-ray repair cross-complementing protein 1 (XRCC1) and mediates homo- and heterodimerisation.
Pfam PF06445: GyrI-like small molecule binding domain (domain)
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.
Pfam PF13365: Trypsin-like peptidase domain (domain)
This family includes trypsin-like peptidase domains.
Pfam PF09415: CENP-S associating Centromere protein X (domain)
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.
Pfam PF19034: RNase LS, bacterial toxin DBD domain (domain)
RnlA toxin is an RNase LS and a putative toxin of a bacterial toxin-antitoxin pair. Toxin-antitoxin systems consist of a stable toxin and an unstable antitoxin. In this case, a novel type II system, RnlA is the stable toxin that causes inhibition of cell growth and rapidly degrades T4 late mRNAs to prevent their expression, and this is neutralised by the activity of the unstable antitoxin RnlB. This entry represents the C-terminal DBD domain, responsible for the RNA cleavage activity and toxicity. Through interaction between DBDs, RnlA dimerises in solution. T4 Dmd binds to DBD for inhibition of RnlA toxicity and RnlB also inhibits the toxicity of DBD.
Pfam PF00091: Tubulin/FtsZ family, GTPase domain (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.
Wikipedia: Tubulin in molecular biology can refer either to the tubulin protein superfamily of globular proteins, or one of the member proteins of that superfamily. α- and β-tubulins polymerize into microtubules, a major component of the eukaryotic cytoskeleton. It was discovered and named by Hideo Mōri in 1968. Microtubules function in many essential cellular processes, including mitosis. Tubulin-binding drugs kill cancerous cells by inhibiting microtubule dynamics, which are required for DNA segregation and therefore cell division.