SII-SWORD/CoKE huggingface dataset:
Pfam PF09588: YqaJ-like viral recombinase domain (domain)
This protein family is found in many different bacterial species but is of viral origin. The protein forms an oligomer and functions as a processive alkaline exonuclease that digests linear double-stranded DNA in a Mg(2+)-dependent reaction, It has a preference for 5'-phosphorylated DNA ends. It thus forms part of the two-component SynExo viral recombinase functional unit.
Wikipedia: In molecular biology, the YqaJ refers to the YqaJ/K domain from the skin prophage of the bacterium, Bacillus subtilis. This protein domain, often found in bacterial species, is actually of viral origin. The protein forms an oligomer and functions as an alkaline exonuclease, or in simpler terms, an enzyme that digests double-stranded DNA. It is a reaction which is dependent on Magnesium. It has a preference for 5'-phosphorylated DNA ends. It thus forms part of the two-component SynExo viral recombinase functional unit.
Pfam PF18540: Domain of unknown function (DUF5626) (domain)
This is a domain of unknown function mostly found in firmicutes.
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 PF24551: Probable histone acetyltransferase Rv0428c SH3 domain (domain)
This entry represents the SH3 domain found at the N-terminal of Rv0428c, a probable histone acetyltransferase from Mycobacterium tuberculosis. It may be involved in survival under stress conditions.
Pfam PF11866: Protein of unknown function (DUF3386) (family)
This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are about 220 amino acids in length.
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 PF21193: NMD3 SH3 domain (domain)
A key step in ribosome biogenesis is the nuclear export of pre-ribosomal particles. Nmd3, a highly conserved protein in eukaryotes, is a specific adaptor required for the export of pre-60S particles. This entry represents the second domain in NMD3 which adopts an SH3-fold denoted as RBDII in. The two short alpha-helices in RBDII participate in rRNA recognition.
Pfam PF23566: RTG2 C-terminal domain (domain)
This domain is found C-terminal in the yeast Retrograde regulation protein 2 (RTG2) and related proteins. RTG2 is required for controlling the interorganelle communication between mitochondria, peroxisomes, and the nucleus.  This domain shares significant similarity with known HD/PDEase domains and it is predicted to adopt similar structure.
Pfam PF05153: Myo-inositol oxygenase (family)
MIOX is the enzyme myo-inositol oxygenase.  It catalyses the first committed step in the glucuronate-xylulose pathway, It is a di-iron oxygenase with a key role in inositol metabolism.  The structure reveals a monomeric, single-domain protein with a mostly helical fold that is distantly related to the diverse HD domain superfamily. The structural core is of five alpha-helices that contribute six ligands, four His and two Asp, to the di-iron centre where the two iron atoms are bridged by a putative hydroxide ion and one of the Asp ligands. The substrate is myo-inositol is bound in a terminal substrate-binding mode to a di-iron cluster. Within the structure are two additional proteinous lids that cover and shield the enzyme's active site.
Wikipedia: Inositol oxygenase, also commonly referred to as myo-inositol oxygenase (MIOX), is a non-heme di-iron enzyme that oxidizes myo-inositol to glucuronic acid. The enzyme employs a unique four-electron transfer at its Fe(II)/Fe(III) coordination sites and the reaction proceeds through the direct binding of myo-inositol followed by attack of the iron center by diatomic oxygen. This enzyme is part of the only known pathway for the catabolism of inositol in humans and is expressed primarily in the kidneys. Recent medical research regarding MIOX has focused on understanding its role in metabolic and kidney diseases such as diabetes, obesity and acute kidney injury. Industrially-focused engineering efforts are centered on improving MIOX activity in order to produce glucaric acid in heterologous hosts.
Pfam PF01907: Ribosomal protein L37e (family)
This family includes ribosomal protein L37 from eukaryotes and archaebacteria. The family contains many conserved cysteines and histidines suggesting that this protein may bind to zinc.
Pfam PF15012: Domain of unknown function (DUF4519) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between  and 59 amino acids in length. There are two conserved sequence motifs: KET and VLP. There is a single completely conserved residue P that may be functionally important.
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 PF03071: GNT-I family (family)
Alpha-1,3-mannosyl-glycoprotein beta-1,2-N-acetylglucosaminyltransferase (GNT-I, GLCNAC-T I) [ec:2.4.1.101] transfers N-acetyl-D-glucosamine from  UDP to high-mannose glycoprotein N-oligosaccharide. This is an essential step in the synthesis of complex or hybrid-type N-linked oligosaccharides. The enzyme is an integral membrane protein localised to the Golgi  apparatus, and is probably distributed in all tissues. The catalytic domain is located at the C-terminus.
Pfam PF03091: CutA1 divalent ion tolerance protein (domain)
Several gene loci with a possible involvement in cellular tolerance to copper have been identified. One such locus in eubacteria and  archaebacteria, cutA, is thought to be  involved in cellular tolerance to a wide variety of divalent cations other than copper. The cutA locus consists of two operons, of one and two genes. The CutA1 protein is a cytoplasmic protein, encoded by the single-gene operon and has been linked to divalent cation tolerance. It has no recognised structural motifs. This family also contains putative proteins from eukaryotes (human and Drosophila).
Pfam PF08748: Phage tail assembly chaperone (domain)
This is a family of phage tail assembly chaperone proteins largely from phage T1 Gp40.
Pfam PF23328: Shavenoid isoform B N-terminal domain (domain)
This entry represents a small beta strand domain that contains six conserved cysteines that likely form three disulphide bridges.  This domain is found in an extracellular context in a variety of proteins. This includes a small number of putative odorant receptors as well as proteins annotated as shavenoid proteins. In particular it is found at the N-terminus of shavenoid isoform B from drosophila [swissprot:B7YZF2].
Pfam PF21372: Topoisomerase I, zinc finger (domain)
This entry represents a zinc ribbon domain found at the C-terminal of topoisomerase I from bacteria (it corresponds to D6 described in. Topoisomerase I has an essential function in preventing hypernegative supercoiling of DNA. The C-terminal domains bind ssDNA to recognise the accumulation of negative supercoils in duplex DNA.
Pfam PF16834: Shu complex component Csm2, DNA-binding (domain)
CSM2 is one of the components of the yeast Shu complex that maintains genomic stability during replication. CSM2 complexes first with Psy3, and their L2 loops confer the DNA-binding activity to the Shu complex.  The Shu complex binds to recombination sites and is required for Rad51 assembly and function during meiosis. The heterodimer of Psy3-Csm2 stabilises the Rad51-single-stranded DNA complex independently of nucleotide cofactor because Psy3-Csm2 is a structural mimic of the Rad51-dimer.
Pfam PF08469: Nucleoside triphosphatase I C-terminal (family)
This viral domain is found to the C-terminus of Poxvirus nucleoside triphosphatase phosphohydrolase I (NPH I,) together with the helicase conserved C-terminal domain ([pfam:PF00271]).
Pfam PF01136: Peptidase family U32 (family)
This is a group of peptidases belonging to MEROPS peptidase family U32 (clan U-). They are classified as collagenases as they are present in bacterial collagenases, involved in bacterial infection. For example, Porphyromonas gingivalis PrtC (Bacteroides gingivalis) , is an enzyme that degrades type I collagen and that seems to require a metal cofactor, or Helicobacter pylori HP0169, another Peptidase U32 protein is required for colonisation of mouse gut.

Novel functions of peptidase U32 proteins have been found, suggesting that these peptidases are involved in diverse cellular processes. The conservation of a CX6CX15CX3/4C motif in several U32 proteases indicates that these proteins bind [Fe-S] clusters. RlhA, a member of the U32 protease family involved in the C-hydroxylation of a cytidine on E. coli 23S rRNA is a Fe-S protein related to iron metabolism . TrhP (tRNA hydroxylation protein P), a member of this family, is involved in prephenate-dependent formation of 5-hydroxyuridine (ho5U) modification at position 34 in tRNAs, the first step in 5-methoxyuridine (mo5U) biosynthesis, which is important for tRNA hydroxylation ensuring the efficient decoding during protein synthesis . UbiU-UbiV are involved in ubiquinone biosynthesis in which the 4Fe-4S clusters bind to each protein have a role in electron transfer chains in hydroxylation reactions .
The peptidases families associated with clan U-have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported.
Pfam PF03209: PUCC protein (family)
This protein is required for high-level transcription of the PUC operon.
Pfam PF05662: Coiled stalk of trimeric autotransporter adhesin (conserved_site)
This short motif is found in invasins and haemagglutinins, normally associated with ([pfam:PF05658]).
Wikipedia: In molecular biology, trimeric autotransporter adhesins (TAAs), are proteins found on the outer membrane of Gram-negative bacteria. Bacteria use TAAs in order to infect their host cells via a process called cell adhesion. TAAs also go by another name, oligomeric coiled-coil adhesins, which is shortened to OCAs. In essence, they are virulence factors, factors that make the bacteria harmful and infective to the host organism.
Pfam PF24537: Fungal C2H2 zinc finger (domain)
This is a presumed C2H2-type zinc finger domain found in a group of fungal uncharacterised proteins.
Pfam PF13129: Protein of unknown function (DUF3953) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 47 and 76 amino acids in length.
Pfam PF20094: GWxTD domain (domain)
This domain is found in uncharacterised proteins from bacteria, mainly in Bacteroidetes. This domain is approximately 180 amino acids in length and it is rich in aromatic residues, with Trp, Tyr, or Phe as the majority amino acids in the most-conserved residue positions.
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 PF04819: Family of unknown function (DUF716) (family)
This family is equally distributed in both metazoa and plants. Annotation associated with [swissprot:Q9SLW7] suggest that it may be involved in response to viral attack in plants.  However, no clear function has been assigned to this family.
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 PF24360: Domain of unknown function (DUF7516) (domain)
This domain is found in a group of uncharacterised metazoan proteins. It has a detectable sequence similarity to HTH winged helix domains and it is predicted to adopt similar structure. In some proteins, this domain is found two copies and usually associated with [pfam:PF24359].
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 PF02662: Methyl-viologen-reducing hydrogenase, delta subunit (family)
This family consist of methyl-viologen-reducing hydrogenase, delta subunit / heterodisulphide reductase.  No specific functions have been assigned to this  subunit.  The aligned region corresponds to almost the entire delta chain sequence and contains 4 conserved cysteine residues.  However, in  two Archaeoglobus sequences this region corresponds to only the C-terminus of these proteins [swissprot:O29030] and [swissprot:029595].
Pfam PF04045: Arp2/3 complex, 34 kD subunit p34-Arc (family)
Arp2/3 protein complex has been implicated in the control of actin polymerisation in cells. The human complex consists of seven subunits which include the actin related Arp2 and Arp3, and five others referred to as p41-Arc, p34-Arc, p21-Arc, p20-Arc, and p16-Arc.  This family represents the p34-Arc subunit.
Pfam PF24134: Domain of unknown function (DUF7401) (domain)
This entry represents a domain of unknown function found towards the centre of some PRiA4b ORF-3-like proteins from bacteria, such as SwissProt:A0A068QX925. This domain is generally associated to PriA4_ORF3 ([pfam:PF07929]) 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 PF13191: AAA ATPase domain (domain)
This family of domains contain a P-loop motif that is characteristic of the AAA superfamily.
Wikipedia: AAA proteins are a large group of protein family sharing a common conserved module of approximately 230 amino acid residues. This is a large, functionally diverse protein family belonging to the AAA+ protein superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent remodeling or translocation of macromolecules.
Pfam PF15427: S100P-binding protein (family)
S100PBPR is a family of proteins found in eukaryotes, and localised to cell nuclei where S100P is also present, and the two proteins co-immunoprecipitate. S100P is a member of the S100 family of calcium-binding proteins and there have been several recent reports of its over-expression in pancreatic ductal adenocarcinoma. In situ hybridisation shows S100PBPR transcripts to be found in islet cells but not duct cells of the healthy pancreas. An interaction between S100P and S100PBPR may be involved in early pancreatic cancer.
Pfam PF08395: 7tm Chemosensory receptor (family)
This family includes a number of insect chemosensory receptors encoded by gustatory and odorant receptors genes, including A. gambiae and D. melanogaster. They are seven-transmembrane ligand-gated ion channels, showing high sequence divergence, consistent with an ancient origin for the family.
Pfam PF20594: Domain of unknown function (DUF6794) (domain)
This domain is functionally uncharacterised, found in bacteria. It is around 120 amino acids in length. There is a conserved sequence motif GxxxRN.
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 PF19776: Family of unknown function (DUF6262) (family)
This family of proteins, functionally uncharacterised, is found in bacteria. Proteins in this family are typically between 124 and 143 amino acids in length. Some members included in this family are hypothetical transposases, associated with transposon Tn554. There is a conserved sequence GV/LSR/K and a highly conserved tyrosine residue.
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 PF03588: Leucyl/phenylalanyl-tRNA protein transferase (family)
Leucyl/phenylalanyl-tRNA--protein transferase 2.3.2.6 transfers a Leu or Phe to the amino end of certain proteins to enable degradation. The N-terminal residue controls the biological half-life of many proteins via the N-end rule pathway.
Pfam PF20969: MASE11 (domain)
This entry represents the membrane-associated sensor domain 11 (MASE11), a predicted transmembrane domain that has been found in association with HD-GYP ([pfam:PF01966]), PAS ([pfam:PF13426]), GAF ([pfam:PF01590]) and GGDEF ([pfam:PF00990])-EAL ([pfam:PF00563]) domains. It is also present in sensor histidine kinases with various domain architectures.
Pfam PF20132: Family of unknown function (DUF6522) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 88 and 99 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 PF17178: Membrane-associated sensor (family)
MASE5 is a family of bacterial membrane-associated sensor domains. It is an integral membrane sensor domain found in various GGDEF domain proteins, including a diguanylate cyclase DgcY (EcSMS35_1716) from multidrug-resistant environmental isolate Escherichia coli SMS-3-5.
Pfam PF01560: Hepatitis C virus non-structural protein E2/NS1 (family)
The hypervariable region of the E2/NS1 region of hepatitis C virus varies greatly between viral isolates. E2 is thought to encode a structurally unconstrained envelope protein.
Pfam PF03488: Nematode insulin-related peptide beta type (domain)
The insulin family of proteins groups together several evolutionarily related active peptides : these include insulin , relaxin , insect prothoracicotropic hormone (bombyxin) , insulin-like growth factors (IGF1 and IGF2) , mammalian Leydig cell-specific insulin-like peptide (gene INSL3), early placenta insulin-like peptide (ELIP) (gene INSL4), locust insulin-related peptide (LIRP), molluscan insulin-related peptides (MIP), and Caenorhabditis elegans insulin-like peptides. The 3D structures of a number of family members have been determined . The fold comprises two polypeptide chains (A and B) linked by two disulphide bonds: all share a conserved arrangement of 4 cysteines in their A chain, the first of which is linked by a disulphide bond to the third, while the second and fourth are linked by interchain disulphide bonds to cysteines in the B chain.

Insulin is found in many animals, and is involved in the regulation of normal glucose homeostasis. It also has other specific physiological effects, such as increasing the permeability of cells to monosaccharides, amino acids and fatty acids, and accelerating glycolysis and glycogen synthesis in the liver . Insulin exerts its effects by interaction with a cell-surface receptor, which may also result in the promotion of cell growth .
This entry represents Caenorhabditis elegans insulin-like peptides , beta type.
Pfam PF18009: 4Fe-4S iron-sulfur cluster binding domain (domain)
This is the C-terminal domain found in Deinococcus radiodurans protein DR2241 (a Ribosomal protein S2-related protein). This domain has been shown to harbour the sequence motifs CxxC and CxxxC which bind a [4Fe-4S] iron-sulphur cluster. Together with the preceding domain, it is heavily involved in the tetramer formation.
Pfam PF18269: T3SS EscN ATPase C-terminal domain (domain)
This is the C-terminal domain of the EscN protein family of ATPases that form part of the Type III secretion system (T3SS) present in Escherichia coli. T3SS is a macromolecular complex that creates a syringe-like apparatus extending from the bacterial cytosol across three membranes to the eukaryotic cytosol. This process is essential for pathogenicity. EscN is a functionally unique ATPase that provides an inner-membrane recognition gate for the T3SS chaperone-virulence effector complexes as well as a potential source of energy for their subsequent secretion.The C-terminal domain of T3SS ATPases mediates binding with multiple contact points along the chaperone.
Pfam PF18880: Uracil-DNA glycosylase inhibitor (family)
Uracil-DNA glycosylase inhibitor (UGI) found in Bacillus subtilis phage, is an inhibitor that inactivates the host uracil-DNA glycosylase (UDG), also known as (UNG) uracil-DNA N-glycosylase. UDG is a highly conserved enzyme responsible for the initiation of uracil-base excision repair (1). UGI forms a tight non-covalent bond to UDG, completely inhibiting it from binding to DNA by inserting its beta-1 strand into the conserved DNA-binding groove of the enzyme (2). In complex with UDG, UGI folds into an alpha-beta-alpha sandwich structure formed by five-stranded antiparallel beta-strands and two helices (3).
Pfam PF21394: Beta-ketoacyl synthase-like, N-terminal (domain)
This is the N-terminal adenylation (A) domain of bacterial beta-ketoacyl synthases. This domain selects the alpha-keto acid that then adenylates and transfer to the PCP domain.
Pfam PF21641: NarE (family)
This is a group of short bacterial sequences that includes NarE from Neisseria meningitidis. NarE is a protein with predicted ADP-ribosyltransferase activity. It shows an alpha-beta structure.