SII-SWORD/CoKE huggingface dataset:
Pfam PF19379: Family of unknown function (DUF5954) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001973) is described by MIBiG as an example of the following biosynthetic class, other (unspecified).
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 PF22963: NUP210 Ig-like domain 3 (domain)
This domain is found in the homologues of human Nuclear pore membrane glycoprotein 210 (NUP210). NUP210 is essential for nuclear pore assembly and fusion, nuclear pore spacing, as well as for its structural integrity. NUP210 is composed of multiple immunoglobin-like (Ig-like) domains and forms a ring around the NPC within the NE lumen. The domain represented by this entry is one of these constituent Ig-like domains and has a significant structural similarity to cadherin domains.
Pfam PF08305: NPCBM/NEW2 domain (domain)
This novel putative carbohydrate binding module (NPCBM) domain is found at the N-terminus of glycosyl hydrolase family 98 proteins. This domain has also been called the NEW2 domain.  NPCBM domains found in bacterial conflict systems are predicted to interact with invasive molecules and recruit downstream effectors.
Pfam PF10570: Myelin-PO cytoplasmic C-term p65 binding region (domain)
Myelin protein zero is the major myelin protein in the peripheral central nervous system and is essential for normal myelination. The family is a single-pass transmembrane molecule containing one Ig-like loop in the extracellular domain and this highly basic 69 residue C-terminal cytoplasmic domain which is the region that interacts with protein p65.
Wikipedia: Myelin protein zero is a single membrane glycoprotein which in humans is encoded by the MPZ gene. P0 is a major structural component of the myelin sheath in the peripheral nervous system (PNS). Myelin protein zero is expressed by Schwann cells and accounts for over 50% of all proteins in the peripheral nervous system, making it the most common protein expressed in the PNS. Mutations in myelin protein zero can cause myelin deficiency and are associated with neuropathies like Charcot–Marie–Tooth disease and Dejerine–Sottas disease.
Pfam PF16378: Domain of unknown function (family)
This family around 200 residues locates in the N-terminal of some uncharacterised proteins in various Bacteroides and Alistipes species. The function of this family remains unknown. The N-terminus of this model has been clipped by ~30 residues as it was capturing parts of collagen sequences, [pfam:PF01391].
Pfam PF02897: Prolyl oligopeptidase, N-terminal beta-propeller domain (repeat)
This unusual 7-stranded beta-propeller domain protects the catalytic triad of prolyl oligopeptidase (see [pfam:PF00326]), excluding larger peptides and proteins from proteolysis in the cytosol.
Pfam PF16176: T-box transcription factor-associated (family)
This domain lies downstream of the T-box in many eukaryotic T-box proteins. The exact function is not known.
Pfam PF20258: Aminomethyltransferase beta-barrel domain (domain)
This domain is found at the C-terminus of tRNA(5-methylaminomethyl-2-thiouridine)-methyltransferase which is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine present in the wobble position of some tRNAs.
Pfam PF11237: Protein of unknown function (DUF3038) (family)
This family of proteins with unknown function appear to be restricted to Cyanobacteria.
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 PF04185: Phosphoesterase family (family)
This family includes both bacterial phospholipase C enzymes [ec:3.1.4.3], but also eukaryotic acid phosphatases [ec:3.1.3.2].
Pfam PF01965: DJ-1/PfpI family (domain)
The family includes the protease PfpI [swissprot:Q51732]. This domain is also found in transcriptional regulators such as [swissprot:Q9RJG8].
Pfam PF17861: Laterosporulin defensin-like peptide (domain)
This entry corresponds to a bacteriocin from the bacterium Brevibacillus laterosporus called laterosporulin. This peptide has a defensin-like structure.
Pfam PF12988: TraQ conjugal transfer protein (family)
TraQ is a conjugative transposon lipoprotein. It is a component of the type IV secretion system. TraQ belongs to the immunoglobulin superfamily and shares structural similarity to other proteins involved in pili production for bacterial cell attachment. It appears to be upregulated in the presence of host or other bacterial species vs when in culture.
Pfam PF24702: Family of unknown function (DUF7665) (domain)
This entry represents a family of uncharacterised bacterial protein. Proteins in this family are about 150 residues 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 PF19299: Domain of unknown function (DUF5914) (domain)
This presumed domain is found to the C-terminus of [pfam:PF00355]. This family includes a protein called CrtV that may be a methyltransferase or demethylase.
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 PF10783: Protein of unknown function (DUF2599) (family)
This family is conserved in Actinobacteria. 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 PF01716: Manganese-stabilising protein / photosystem II polypeptide (family)
This family consists of the 33 KDa photosystem II polypeptide from the oxygen evolving complex (OEC) of plants and cyanobacteria. The protein is also known as the manganese-stabilising protein as it is associated with the manganese complex of the OEC and may provide the ligands for the complex.
Pfam PF24881: Domain of unknown function (DUF7739) (domain)
This entry includes the Shigella phage Sf6 gene 22 protein [swissprot:Q716F3].
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 PF22075: Family of unknown function (DUF6939) (family)
This is a family of bacterial proteins with unknown function. They share sequence similarity with the N-terminal part of NADAR domain and are predicted to adopt structure that is globally similar to the structure of E.coli protein YbiA, a member of the NADAR domain 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 PF04805: E10-like protein conserved region (family)
Family of poxvirus proteins.
Pfam PF24650: Tal, N-terminal tail tube TT1 domain (domain)
This domain, previously known as DUF7643, is found N-terminal in the tail-associated lysin (Tal, gp59) and related sequences from phages and bacteriophages. gp59 is comprising the tip of the phage tail. The domain represented by this entry is one of the two tail tube domains (TT1 and TT2) that form a quasi-sixfold adapter to the distal tail protein (Dit, gp58) hexamer. These two domains merge into a continuous eight-stranded beta-sheet on one side.
Pfam PF15157: Fusion protein IQCJ-SCHIP1 with IQ-like motif (disordered)
This entry includes eukaryotic fusion proteins. It bridges two adjacent genes that encode distinct proteins, IQCJ, a novel IQ motif containing protein and SCHIP1, a schwannomin interacting protein. It contains a unique calmodulin-binding IQ motif at the N-terminus not shared with its shorter isoform SCHIP1, suggesting a distinctive function for this protein. It is localised to cytoplasm and actin-rich regions, and in differentiated PC12 cells is seen in neurite extensions. It may play a role in action potential conduction in myelinated cells through the organisation of molecular complexes at nodes of Ranvier and axon initial segments. This model covers an N-terminal segment that is mostly disordered and includes the IQ motif.
Pfam PF25109: Polynucleotide kinase PNKP phosphatase domain (domain)
This entry represents the C-terminal domain of the bifunctional enzyme T4 polynucleotide kinase/phosphatase, PNKP (also known as PseT). The PNKP phosphatase domain can catalyse the hydrolytic removal of the 3'-phosphoryl of DNA, RNA and deoxynucleoside 3'-monophosphates.
Pfam PF08189: Meleagrin/Cygnin family (domain)
This family consists of meleagrin and cygnin basic peptides that are isolated from turkey and black swan respectively. Both peptides are low in molecular weight and contains three disulphide bonds with high concentrations of aromatic residues. These peptides show similarity to transferrins and probably play some vital role in avian eggs but the exact function is still unknown.
Pfam PF18244: Cellulose-binding protein CttA N-terminal domain (domain)
This is the N-terminal domain of cellulose-binding protein CttA present in Ruminococcus flavefaciens.  CttA mediates attachment of the bacterial substrate via two carbohydrate-binding modules. The domain is known as the X-module and lacks a true hydrophobic core. Unlike the X-modules in other types of CohE-XDoc complexes it does not contribute to the binding surface. This X-module appears to serve as an extended spacer, which separates the cellulose-binding modules at the N terminus of CttA and the bacterial cell wall. The domain does not share structural similarity with other known X-modules from cellulolytic bacteria but does show similarity to G5-1 module of StrH from S. pneumoniae.
Pfam PF22693: Fungal MACPF-like domain (domain)
This entry represents a MACPF-like domain in uncharacterised proteins primarily found in Fungi.
Pfam PF08315: cwf18 pre-mRNA splicing factor (family)
The cwf18 family is involved in mRNA splicing.  It has been isolated as a subcomplex of the splicosome in Schizosaccharomyces pombe.
Pfam PF03166: MH2 domain (family)
This is the MH2 (MAD homology 2) domain found at the carboxy terminus of MAD related proteins such as Smads. This domain is separated from the MH1 domain by a non-conserved linker region. The MH2 domain mediates interaction with a wide variety of proteins and provides specificity and selectivity to Smad function and also is critical for mediating interactions in Smad oligomers. Unlike MH1, MH2 does not bind DNA. The well-studied MH2 domain of Smad4 is composed of five alpha helices and three loops enclosing a beta sandwich. Smads are involved in the propagation of TGF-beta signals by direct association with the TGF-beta receptor kinase which phosphorylates the last two Ser of a conserved 'SSXS' motif located at the C-terminus of MH2.
Pfam PF09631: Sen15 protein (domain)
The Sen15 subunit of the tRNA intron-splicing endonuclease is one of the two structural subunits of this hetero-tetrameric enzyme. Residues 36-157 of this subunit possess a novel homodimeric fold.  Each monomer consists of three alpha-helices and a mixed antiparallel/parallel beta-sheet. Two monomers of Sen15 fold with two monomers of Sen34, one of the two catalytic subunits, to form an alpha2-beta2 tetramer as part of the functional endonuclease assembly.
Pfam PF12058: PII-interacting protein X (family)
This protein family includes PII-interacting protein X (PipX) from Synechococcus elongatus and similar proteins found in cyanobacteria. PipX modulates the expression of genes involved in nitrogen assimilation by interacting with the global nitrogen transcription factor NtcA and the signal transduction protein PII. It is involved in several regulatory pathways. The crystal structure of this protein shows a tudor-like domain (TLD), formed by a highly bent beta-sheet that mediates the interactions with both PII and NtcA, and two C-terminal helices.
Pfam PF21708: Galactocerebrosidase, C-terminal lectin domain (domain)
This domain is found at the C-terminal end of Galactocerebrosidase from Mus musculus (GALCERase) and similar proteins predominantly found in animals and bacteria. GALCERase hydrolyses the galactose ester bonds of glycolipids such as galactosylceramide and galactosylsphingosine. It is responsible for the lysosomal catabolism of galactosylceramide, a major lipid in myelin, kidney and epithelial cells of small intestine and colon. This protein is organised into three domains, all of them contributing residues to the substrate- binding pocket. This entry represents the lectin domain, which is not present in other lysosomal enzymes, is likely to be be involved in processes that are not found in related enzymes. Mutations in this domain lead to Krabbe disease.
Pfam PF16542: PNKP adenylyltransferase domain, ligase domain (domain)
PNKP_ligase is a classical ligase nucleotidyltransferase module of bacteria. PNKP (polynucleotide 5'-kinase/3'-phosphatase) is the end-healing and end-sealing component of an RNA-repair system present in diverse bacteria from ten different phyla. RNA breakage by site-specific 'ribotoxins' is an ancient mechanism by which microbes respond to cellular stress and distinguish self from non-self. Ribotoxins are trans-esterifying endonucleases that generate 5'-OH and 2',3' cyclic phosphate termini. Repair of this type of RNA damage is feasible via sequential enzymatic end-healing and end-sealing steps.
Pfam PF09922: Cell wall-active antibiotics response LiaF, C-terminal (repeat)
This domain is found in various prokaryotic proteins, including cell wall-active antibiotic response proteins. This entry includes protein product of the yvqF gene, LiaF, located immediately upstream of vraS. It is associated with glycopeptide resistance in Staphylococcus aureus. This domain has been described as toast rack from its structural resemblance.
Pfam PF11346: Protein of unknown function (DUF3149) (family)
This bacterial family of proteins has no known function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF09074: Mer2 (family)
Mer2 (Rec107) forms part of a complex  that is required for meiotic double strand DNA break formation.  Mer2 increases in abundance and is phosphorylated during the prophase phase of cell division. Blocking double strand break formation results in delayed dephosphorylation and dissociation of Mer2 from the chromosome.
Pfam PF02017: CIDE-N domain (domain)
This domain is found in CAD nuclease [swissprot:O76075] , ICAD [swissprot:O00273] the inhibitor of CAD nuclease. The two proteins interact through this domain.
Pfam PF22166: ArnR1-like, winged-helix domain (domain)
This entry represents a WH-like domain present in ArnR1-like proteins (PDB:2pg4). ArnR1-like transcription factors have been implicated in regulating the expression of components found in both the archaeal adhesive pilus and UV-inducible pili systems.
Pfam PF04916: Phospholipase B (family)
Phospholipase B (PLB) catalyses the hydrolytic cleavage of both acylester bonds of glycerophospholipids.  This family of PLB enzymes has been identified in mammals, flies and nematodes but not in yeast.  In Drosophila this protein was named LAMA for laminin ancestor since it is expressed in the neuronal and glial precursors that surround the lamina.
Pfam PF14290: Succinate dehydrogenase subunit 5, mitochondrial (family)
Complex II [succinate dehydrogenase (succinate-ubiquinone oxidoreductase); SDH] is the only enzyme shared by both the electron transport chain and the tricarboxylic acid (TCA) cycle in mitochondria. In plants, this complex is considered unusual because it has accessory subunits (SDH5-SDH8), in addition to the catalytic subunits of SDH found in all eukaryotes (SDH1- SDH4). This family represents the accessory complex II subunit Succinate dehydrogenase subunit 5 mitochondrial, from plants.
Pfam PF12666: PrgI family protein (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 116 and 146 amino acids in length. This protein is found in an operon that is part of a Type IV secretion system.
Pfam PF06905: Fas apoptotic inhibitory molecule (FAIM1) (family)
This family consists of several fas apoptotic inhibitory molecule (FAIM1) proteins. FAIM expression is upregulated in B cells by anti-Ig treatment that induces Fas-resistance, and overexpression of FAIM diminishes sensitivity to Fas-mediated apoptosis of B and non-B cell lines. FAIM1 is highly evolutionarily conserved and is widely expressed in murine tissues, suggesting that FAIM plays an important role in cellular physiology.
Pfam PF22154: Elongation factor SelB, second winged-helix domain (domain)
This domain is found in Elongation factor SelB from Aquifex aeolicus and similar bacterial proteins. SelB is a selenocysteine(Sec)-specific elongation factor that brings the selenocysteinyl-tRNA(Sec) to the ribosome. It consists of three EF-Tu-like domains (D1-3, where [pfam:PF00009] is the first one), followed by four winged-helix domains (WHD1-4). This entry represents the second winged-helix domain (WHD2).
Pfam PF18144: Second Messenger Oligonucleotide or Dinucleotide Synthetase domain (domain)
Nucleotide synthetase enzyme of the DNA polymerase beta superfamily. Experimental studies have demonstrated cGAMP synthetase activity in the Vibrio cholerae DncV protein, a member of the SMODS family. The diversity inherent to the SMODS family suggests members of the family could generate a range of nucleotides, cyclic and/or linear. The nucleotide second messengers generated by the SMODS domains are predicted to activate effectors in a class of conflict systems reliant on the production and sensing of the nucleotide second messengers.
Pfam PF09159: Mitochondrial resolvase Ydc2 / RNA splicing MRS1 (domain)
Members of this family adopt a secondary structure consisting of two beta sheets and one alpha helix, arranged as a beta-alpha-beta motif.  Each beta sheet has five strands, arranged in a 32145 order, with the second strand being antiparallel to the rest. Mitochondrial resolvase Ydc2 is capable of resolving Holliday junctions and cleaves DNA after 5'-CT-3' and 5'-TT-3' sequences.  This family also contains the mitochondrial RNA-splicing protein MRS1 which is involved in the excision of group I introns.
Wikipedia: In molecular biology, the protein domain, Ydc2, is a Holliday junction resolvase from the fission yeast Schizosaccharomyces pombe that is involved in the maintenance of mitochondrial DNA.
Pfam PF23814: Family of unknown function (DUF7185) (family)
This entry represents an uncharacterized protein found in various mycobacteriophages. The protein is typically around 80 to 100 amino acids in length. It is found in phages belonging to cluster B, such as the Bclasvirinae and Coopervirus genera. The function of this protein is currently 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 PF10800: Protein of unknown function (DUF2528) (family)
This family of proteins has no known function. Some of the sequences are annotated as ea10 however the function of this protein 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 PF03048: UL92 family (family)
Members of this family, found in several herpesviruses, include EBV BDLF4 [swissprot:P03223], HCMV UL92 [swissprot:P16798], HHV8 31 [swissprot:P88920],  HSV6 U63 [swissprot:P24440]. Their function is unknown. The N terminus of this protein contains 6 conserved cysteines and histidines that might form a zinc binding domain (A Bateman pers. obs.).
Pfam PF17727: CtsR C-terminal dimerization domain (domain)
This family consists of several Firmicute transcriptional repressor of class III stress genes (CtsR) proteins. CtsR of L. monocytogenes negatively regulates the clpC, clpP and clpE genes belonging to the CtsR regulon. This entry corresponds to the C-terminal dimerization domain.
Pfam PF21618: Oligosaccharyl transferase, Peripheral 1 domain (domain)
This domain is found in Oligosaccharyl transferase from Pyrococcus furiosus (OST, also known as AglB-L) and similar archaeal sequences. OST catalyses the co-translational transfer of an oligosaccharide from a lipid donor to an asparagine residue in nascent polypeptide chains. This protein is organised into four regions: a N-terminal half ([pfam:PF02516]), the central core (CC) domain that includes the IS (insert) domain ([pfam:PF18246]) and two peripheral domains, P1 (this entry) and P2 ([pfam:PF18235]). This domain, which consists mainly of beta-strands, encircles the central core domain.
Pfam PF03252: Herpesvirus UL21 (family)
The UL21 protein appears to be a dispensable component in herpesviruses.