SII-SWORD/CoKE huggingface dataset:
Pfam PF15474: Meiotically up-regulated gene family (family)
This protein was identified as being up-regulated during meiosis in S.pombe.  This family of proteins is found in largely in plants and fungi. Proteins in this family are typically between 128 and 920 amino acids in length.
Pfam PF21722: Glycine-rich domain (domain)
This glycine rich region forms a compact hexagonal lattice of polyglycine helices in a variety of likely bacterial and phage surface proteins.
Pfam PF07094: Protein of unknown function (DUF1357) (family)
This family consists of several hypothetical bacterial proteins of around 225 residues in length. Members of this family appear to be specific Borrelia burgdorferi (Lyme disease spirochete). The function of this family is unknown.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF07225: NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4) (family)
This family consists of several NADH-ubiquinone oxidoreductase B15 subunit proteins ([ec:1.6.5.3]).
Wikipedia: Respiratory complex I, EC 7.1.1.2 is the first large protein complex of the respiratory chains of many organisms from bacteria to humans. It catalyzes the transfer of electrons from NADH to coenzyme Q10 (CoQ10) and translocates protons across the inner mitochondrial membrane in eukaryotes or the plasma membrane of bacteria.
Pfam PF04926: Poly(A) polymerase predicted RNA binding domain (domain)
Based on its similarity structurally to the RNA recognition motif this domain is thought to be RNA binding.
Pfam PF00126: Bacterial regulatory helix-turn-helix protein, lysR family (domain)
Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including AmpR, CatM, CatR, CynR, CysB, GltC, IlvY, IrgB, LysR, MetR, NhaR, SyrM, TcbR, TfdS and TrpI . The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-terminal end.
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 PF18116: Sorting Nexin 17 FERM C-terminal domain (domain)
This is the C-terminal domain of sorting nexin 17 (SNX17) present in Homo sapiens. SNX17 localizes to early endosomes where it directly binds NPX(Y/F) motifs in the target receptors to mediate their rates of endocytic internalization, recycling, or degradation. The domain is known as terminal band 4.1/ezrin/radixin/moesin (FERM) domain. The FERM domain binds directly to the common motif, NPX(Y/F), in the cytoplasmic region of its target proteins.
Pfam PF23808: Domain of unknown function (DUF7181) (domain)
This entry represents an uncharacterized protein domain found in bacteriophage proteins, particularly those infecting Salmonella and Dickeya species. The domain is approximately 150 residues in length.  The function of this domain 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 PF08267: Cobalamin-independent synthase, N-terminal domain (domain)
The N-terminal domain and C-terminal domains of cobalamin-independent synthases together define a catalytic cleft in the enzyme.  The N-terminal domain is thought to bind the substrate, in particular, the negatively charged polyglutamate chain.  The N-terminal domain is also thought to stabilise a loop from the C-terminal domain.
Pfam PF16020: Deltamethrin resistance (family)
This presumed domain is found in the deltamethrin-resistance protein prag01 from Culex pipiens pallens.
Pfam PF24591: Phage YunG-like protein (domain)
This entry represents a small family of uncharacterised phage proteins. These proteins show structural similarity to the B. subtilis YunG protein and appear to conserve a putative catalytic triad of cys, his and asp. Structure predictions suggest that these proteins may form homodimers.
Pfam PF23405: APC4, WD40 domain C-terminal half (repeat)
Apc4 is a component of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated E3 ubiquitin ligase that controls progression through mitosis and the G1 phase of the cell cycle. This complex acts by ubiquitination and degradation of target proteins. Apc4 consists of a beta-propeller that is split by      a long alpha-helical domain ([pfam:PF12816]) which generate an L-shaped molecule. APC4 interacts with APC5; the N-terminal of APC1  serves to stabilise the union between APC4 and APC5, both of which lie towards the bottom-front of the APC. This entry represents the C-terminal half of the beta-propeller of ACP4 from animals.
Pfam PF19468: Family of unknown function (DUF6005) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000942) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). This family  includes a protein from the petrobactin biosynthetic gene cluster  from Bacillus anthracis str. Ames.
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 PF01509: TruB family pseudouridylate synthase (N terminal domain) (family)
Members of this family are involved in modifying bases in RNA molecules.  They carry out the conversion of uracil bases to pseudouridine. This family includes TruB, a pseudouridylate synthase that specifically converts uracil 55 to pseudouridine in most tRNAs. This family also includes Cbf5p that modifies rRNA.
Pfam PF05925: Enterobacterial virulence protein IpgD (family)
This family consists of several enterobacterial IpgD like virulence factor proteins. In the Gram-negative pathogen Shigella flexneri, the virulence factor IpgD is translocated directly into eukaryotic cells and acts as a potent inositol 4-phosphatase that specifically dephosphorylates phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P(2)] into phosphatidylinositol 5-monophosphate [PtdIns(5)P] that then accumulates. Transformation of PtdIns(4,5)P(2) into PtdIns(5)P by IpgD is responsible for dramatic morphological changes of the host cell, leading to a decrease in membrane tether force associated with membrane blebbing and actin filament remodelling.
Pfam PF02962: 5-carboxymethyl-2-hydroxymuconate isomerase (domain)
5-carboxymethyl-2-hydroxymuconate isomerase transforms 5-carboxymethyl-2-hydroxy-muconic acid into 5-oxo-pent-3-ene-1,2,5-tricarboxylic acid during the third step of the homoprotocatechuate catabolic pathway . Homoprotocatechuate (HPC; 3,4-dihydroxyphenylacetate) is catabolized to Krebs cycle intermediates via extradiol (meta-) cleavage and the necessary enzymes are chromosomally encoded in a variety of bacteria . 5-carboxymethyl-2-hydroxymuconate isomerase is probably a dimer of two identical subunits . A comparison of the N-terminal half of the isomerase/decarboxylase sequence from the pathway (both encoded by the gene hpcE), with the second half showed significant similarity. This suggests that a duplication may have occurred to produce a bifunctional gene .
Pfam PF10849: Protein of unknown function (DUF2654) (family)
Some members in this family of proteins are annotated as a-gt.4 however currently no function is 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 PF12226: Turkey astrovirus capsid protein (family)
This family of proteins is found in viruses. Proteins in this family are typically between 241 and 261 amino acids in length. These proteins are capsid proteins from various astrovirus strains.
Pfam PF24050: Phage T4 Cef protein family (domain)
This entry represents proteins that are related to the phage T4 cef protein. This protein adopts a compact globular domain composed of 5 beta strands and one alpha helix. The beta strands adopt the order 1-5-4-3-2 with the alpha helix found between strands 1 and 2. This family shows structural similarity to [pfam:PF24005].
Pfam PF17751: SKICH domain (domain)
The SKICH domains of SKIP and PIPP mediate plasma membrane localisation. The functions of the SKICH domains of NDP52 and CALCOCO1 are not known.
Pfam PF00152: tRNA synthetases class II (D, K and N) (domain)
The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction . These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel Î²-sheet fold flanked by Î±-helices , and are mostly dimeric or multimeric, containing at least three conserved regions . However, tRNA binding involves an Î±-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c .
This entry includes the asparagine, aspartic acid and lysine tRNA synthetases.
Wikipedia: Aminoacyl-tRNA synthetases, class II is a family of proteins. These proteins catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have a limited sequence homology.
Pfam PF02743: Cache domain (domain)
Double cache domain 1 covers the last three strands from the membrane distal PAS-like domain, the first two strands of the membrane proximal domain, and the connecting elements  between the two domains. This domain when present in chemoreceptors recognise several signals such as proteinogenic amino acids, GABA, Histamine and polyamines, decanoic acid, Autoinducer-2, purine derivatives, quaternary amines, citrate and taurine, among others. When associated with histidine kinases, it recognises C3/C4-dicarboxylic acids, Spermine, guanosine and Autoinducer-2 (Mantilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1 https://doi.org/10.1093/femsre/fuab043).
Wikipedia: In molecular biology, the cache domain is an extracellular protein domain that is predicted to have a role in small-molecule recognition in a wide range of proteins, including the animal dihydropyridine-sensitive voltage-gated Ca2+ channel alpha-2delta subunit, and various bacterial chemotaxis receptors. The name Cache comes from CAlcium channels and CHEmotaxis receptors. This domain consists of an N-terminal part with three predicted strands and an alpha-helix, and a C-terminal part with a strand dyad followed by a relatively unstructured region. The N-terminal portion of the (unpermuted) Cache domain contains three predicted strands that could form a sheet analogous to that present in the core of the PAS domain structure. Cache domains are particularly widespread in bacteria such as Vibrio cholerae. The animal calcium channel alpha-2delta subunits might have acquired a part of their extracellular domains from a bacterial source. The Cache domain appears to have arisen from the GAF-PAS fold despite their divergent functions.
Pfam PF09570: SinI restriction endonuclease (family)
This family includes the SinI (recognises and cleaves G^GWCC) restriction endonuclease.
Pfam PF23343: Replication-associated protein ORF2/G2P (family)
This entry represents a group of Replication-associated proteins including ORF2 from Spiroplasma virus 4 (SpV4) and G2P from phages, such as Xanthomonas phage phiLf and Bdellovibrio phage phiMH2K. These proteins play an essential role in viral DNA replication; they bind the origin of replication and cleaves the dsDNA replicative form I (RFI) and becomes covalently bound to it via phosphotyrosine bond, generating the dsDNA replicative form II (RFII). After one round of rolling circle synthesis, protein G2P is linked to the newly synthesized ssDNA and joins the ends of the displaced strand to generate a circular single-stranded molecule ready to be packed into a virion.
Pfam PF07849: Protein of unknown function (DUF1641) (family)
Archaeal and bacterial hypothetical proteins are found in this family, with the region in question  being approximately 40 residues long.
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 PF17663: Family of unknown function (DUF5525) (family)
This is a family of unknown function found in Chordata.
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 PF16998: 17 kDa outer membrane surface antigen (family)
17kDa_Anti_2 is a surface protein that is found in several Proteobacteria species.
Pfam PF02014: Reeler domain (family)
The reeler or reelin domain is a ~170 amino acid module, which has been identified in the amino terminus of the extracellular matrix proteins reelin and F-spondin (renamed Spon1) . The reelin domain is found in association with other modules, such as the thrombospondin type I repeat (TSP1), the spondin domain, the fibronectin type III domain or the Kunitz trypsin protease inhibitor domain. Its function is not yet known .
Extracellular matrix (ECM) proteins play an important role in early cortical development, specifically in the formation of neural connections and in controlling the cyto-architecture of the central nervous system. The product of the reeler gene in mouse is reelin,a large extracellular protein secreted by pioneer neurons that coordinates cell positioning during neurodevelopment . F-spondin and mindin are a family of matrix-attached adhesion molecules that share structural similarities and overlapping domains of expression. Both F-spondin and mindin promote adhesion and outgrowth of hippocampal embryonic neurons and bind to a putative receptor(s) expressed on both hippocampal and sensory neurons .
Wikipedia: Reeler domain  is a protein domain. Extracellular matrix (ECM) proteins play an important role in early cortical development, specifically in the formation of neural connections and in controlling the cytoarchitecture of the central nervous system. The product of the reeler gene in mouse is reelin, a large extracellular protein secreted by pioneer neurons that coordinates cell positioning during neurodevelopment. F-spondin and mindin are a family of matrix-attached adhesion molecules that share structural similarities and overlapping domains of expression. Both F-spondin and mindin promote adhesion and outgrowth of hippocampal embryonic neurons and bind to a putative receptor(s) expressed on both hippocampal and sensory neurons.
Pfam PF00851: Helper component proteinase (family)
This protein is found in genome polyproteins of potyviruses.
Pfam PF06762: Lipase maturation factor (family)
This family of transmembrane proteins includes the lipase maturation factor, LMF1. Lipoprotein lipase and hepatic lipase require LMF1 to fold into their active states. It acts as a chaperone required for maturation and transport of active lipoprotein lipase (LPL), through the secretory pathway.
Pfam PF18365: Phosphoinositide phosphatase C-terminal domain (domain)
This domain is found in the C-terminal region of effector protein SidP present in Legionella longbeachae. SidP functions as a PI-3-phosphatase specifically hydrolyzing PI(3)P and PI(3,5)P2. This C-terminal domain is rich with glutamate residues.
Pfam PF10325: Serpentine type 7TM GPCR chemoreceptor Srz (family)
Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srz is a solo families amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srz appear to be under strong adaptive evolutionary pressure.
Pfam PF17558: Androgenic gland hormone (family)
This family contains members such as the Androgenic gland hormone (AGH) of the woodlouse, Armadillidium vulgare. AGH is a heterodimeric glycopeptide synthesized and secreted from androgenic glands. It is responsible for sex differentiation in crustaceans and contains 4 disulfide bonds.
Pfam PF03133: Tubulin-tyrosine ligase family (family)
Tubulins and microtubules are subjected to several post-translational modifications of which the reversible detyrosination/tyrosination of the carboxy-terminal end of most alpha-tubulins has been extensively analysed. This modification cycle involves a specific carboxypeptidase and the activity of the tubulin-tyrosine ligase (TTL). The true physiological function of TTL has so far not been established. Tubulin-tyrosine ligase (TTL) catalyses the ATP-dependent post-translational addition of a tyrosine to the carboxy terminal end of detyrosinated alpha-tubulin. In normally cycling cells, the tyrosinated form of tubulin predominates. However, in breast cancer cells, the detyrosinated form frequently predominates, with a correlation to tumour aggressiveness. On the other hand, 3-nitrotyrosine has been shown to be incorporated, by TTL, into the carboxy terminal end of detyrosinated alpha-tubulin. This reaction is not reversible by the carboxypeptidase enzyme. Cells cultured in 3-nitrotyrosine rich medium showed evidence of altered microtubule structure and function, including altered cell morphology, epithelial barrier dysfunction, and apoptosis.  Bacterial homologs of TTL are predicted to form peptide tags. Some of these are fused to a 2-oxoglutarate Fe(II)-dependent  dioxygenase domain.
Pfam PF19456: MobI protein (family)
MobI is conserved across conjugative plasmids of incompatibility group C (IncC), integrative conjugative elements of the SXT/R391 family and numerous genomic islands mobilized by IncC plasmids. Alongside a relaxase of the MOBH1 family, this protein is essential to conjugative transfer of these elements and is likely a relaxosome component involved in recognition of the origin of transfer.
Pfam PF11878: Dedicator of cytokinesis C/D, N terminal (domain)
This entry represents the N-terminal domain of the DOCK-C subfamily (DOCK 6, 7, 8) and DOCK-D subfamily (DOCK 9, 10, 11). DOCK family members are evolutionarily conserved guanine nucleotide exchange factors (GEFs) for Rho-family GTPases, required during several cellular processes, such as cell motility and phagocytosis. DOCK proteins are categorised into four subfamilies based on their sequence homology: DOCK-A (DOCK1/180, 2, 5), DOCK-B subfamily (DOCK3, 4), DOCK-C subfamily (DOCK6, 7, 8), DOCK-D subfamily (DOCK9, 10, 11).
Pfam PF06170: Protein of unknown function (DUF983) (family)
This family consists of several bacterial proteins of unknown 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 PF13293: Domain of unknown function (DUF4074) (family)
This family is found at the C-terminal of Homeobox proteins in Metazoa.
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 PF10990: Protein of unknown function (DUF2809) (family)
Some members in this family of proteins are annotated as yjgA however currently no function for the protein is 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 PF22369: GLMA-like, second domain (domain)
This entry represents the second domain of exo-beta-D-glucosaminidase GLMA from Thermococcus kodakarensis and similar archaeal proteins, just before the C-terminal domain ([pfam:PF22345]). It is an exo-type enzyme that specifically cleaves the non-reducing terminal glycosidic bond of chitooligosaccharides, being involved in chitin degradation.