SII-SWORD/CoKE huggingface dataset:
Pfam PF06954: Resistin (family)
This family consists of several mammalian resistin proteins. Resistin is a 12.5-kDa cysteine-rich secreted polypeptide first reported from rodent adipocytes. It belongs to a multigene family termed RELMs or FIZZ proteins. Plasma resistin levels are significantly increased in both genetically susceptible and high-fat-diet-induced obese mice. Immunoneutralisation of resistin improves hyperglycemia and insulin resistance in high-fat-diet-induced obese mice, while administration of recombinant resistin impairs glucose tolerance and insulin action in normal mice. It has been demonstrated that increases in circulating resistin levels markedly stimulate glucose production in the presence of fixed physiological insulin levels, whereas insulin suppressed resistin expression. It has been suggested that resistin could be a link between obesity and type 2 diabetes.
Wikipedia: Resistin also known as adipose tissue-specific secretory factor (ADSF) or C/EBP-epsilon-regulated myeloid-specific secreted cysteine-rich protein (XCP1) is a cysteine-rich peptide hormone derived from adipose tissue that in humans is encoded by the RETN gene.
Pfam PF01656: CobQ/CobB/MinD/ParA nucleotide binding domain (domain)
This family consists of various cobyrinic acid a,c-diamide synthases. These include CbiA [swissprot:P29946] and CbiP [swissprot:Q05597] from  S.typhimurium, and CobQ [swissprot:Q52686] from R. capsulatus. These amidases catalyse amidations to various side chains of  hydrogenobyrinic acid or cobyrinic acid a,c-diamide in the biosynthesis  of cobalamin (vitamin B12) from uroporphyrinogen III. Vitamin B12 is an important cofactor and an essential nutrient for many  plants and animals and is primarily produced by bacteria. The family also contains dethiobiotin synthetases as well as the plasmid partitioning proteins of the MinD/ParA family.
Wikipedia: Cobalamin biosynthesis is the process by which bacteria and archea make cobalamin, vitamin B12. Many steps are involved in converting aminolevulinic acid via uroporphyrinogen III and adenosylcobyric acid to the final forms in which it is used by enzymes in both the producing organisms and other species, including humans who acquire it through their diet.
Pfam PF19243: Family of unknown function (DUF5892) (family)
This is a family of uncharacterised proteins of unknown function predominantly found in Iridoviridae.
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 PF09199: Staphylococcal superantigen-like OB-fold domain (domain)
This OB-fold domain folds into a five-stranded beta-barrel. Members of this family are found in various staphylococcal toxins described as staphylococcal superantigen-like (SSL) proteins that are related to the staphylococcal enterotoxins (SEs) or superantigens. These SSL proteins of which 11 have so far been characterised have a typical SE tertiary structure consisting of a distinct oligonucleotide/oligosaccharide binding (OB-fold), this domain, linked to a beta-grasp domain, family Stap_Strp_tox_C, [pfam:PF02876]. SSLs do not bind to T-cell receptors or major histocompatibility complex class II molecules and do not stimulate T cells. SSLs target components of innate immunity, such as complement, Fc receptors, and myeloid cells 2,3,4,5,6,7,8]. SSL protein 7 (SSL7) is the best characterised of the SSLs and binds complement factor C5 and IgA with high affinity and inhibits the end stage of complement activation and IgA binding to FcalphaR.
Pfam PF15595: Immunity protein 51 (family)
A predicted immunity protein with an alpha+beta fold and a conserved tryptophan and Dx[DE] motif. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Tox-RES or Tox-URI1 families. Proteins containing this domain are present in heterogeneous poly immunity loci in polymorphic toxin systems.
Pfam PF10856: Protein of unknown function (DUF2678) (family)
This 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 PF00501: AMP-binding enzyme (family)
This domain is found in a number of prokaryotic and eukaryotic enzymes, which appear to act via an ATP-dependent covalent binding of AMP to their substrate, share a region of sequence similarity . This region is a Ser/Thr/Gly-rich domain that is further characterised by a conserved Pro-Lys-Gly triplet. This group of enzymes includes luciferase, long chain fatty acid Co-A ligase, long-chain fatty acid transport proteins that also function as acyl-CoA ligases, acetyl-CoA synthetase and various other closely-related synthetases .
Pfam PF18677: Archaellum regulatory network B, C-terminal domain (domain)
This is the C-terminal domain found in archeal proteins that carry a von Willebrand factor type A domain such as ArnB from Sulfolobus acidocaldarius. ArnB is involved in negative regulation of the archaellum (former: archaeal flagellum), and the C-terminal domain is phosphorylated by ArnC and ArnD on serine and threonine residues affecting docking of ArnA.
Pfam PF13402: Peptidase M60, enhancin and enhancin-like (domain)
This family of peptidases contains a zinc metallopeptidase motif (HEXXHX(8,28)E) and possesses mucinase activity. It includes the viral enhancins as well as enhancin-like peptidases from bacterial species.  Enhancins are a class of metalloproteases found in some baculoviruses that enhance viral infection by degrading the peritrophic membrane (PM) of the insect midgut. Bacterial enhancins are found to be cytotoxic when compared to viral enhancin, however, suggesting that the bacterial enhancins do not enhance infection in the same way as viral enhancin. Bacterial enhancins may have evolved a distinct biochemical function. These bacterial domains are peptidases targetting host glycoproteins and thus probably play an important role in successful colonisation of both vertebrate mucosal surfaces and the invertebrate digestive tract by both mutualistic and pathogenic microbes. This family has been augmented by a merge with the sequences in the Enhancin Pfam family.
Pfam PF22070: Androglobin, domain V (domain)
Androglobin is a protein with a key role in spermatogenesis. It is required for sperm flagellum formation and maturation of elongating spermatids, both essential for male fertility. Androglobin contains an N-terminal cysteine protease domain that lacks the catalytic cysteine, a tandem of three beta-sandwich domains (domains II,IV,V) and a circularly permuted globin-like domain (domain III) that is inserted between domain II and IV. This entry represents domain V. This domain is predicted to adopt a jelly-roll topology that is observed in galactose-binding domains. It has a significant sequence similarity to domains found in ciliary protein FAP42 and to domain III in calpains. This domain is predicted to contain two large, nearly 80 residues long insertions in the loops both of which likely disordered.
Pfam PF05692: Mycoplasma haemagglutinin (family)
This family consists of several haemagglutinin sequences from Mycoplasma synoviae and Mycoplasma gallisepticum. The major plasma membrane proteins, pMGAs, of Mycoplasma gallisepticum are cell adhesin (hemagglutinin) molecules. It has been shown that the genetic determinants that code for the haemagglutinins are organised into a large family of genes and that only one of these genes is predominately expressed in any given strain.
Pfam PF14800: Domain of unknown function (DUF4481) (family)
This family of unknown function is found in eukaryotes. The human representative is transmembrane protein C9orf91. In mouse it is also known as Tmem268.
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 PF01094: Receptor family ligand binding region (family)
This family includes extracellular ligand binding domains of a wide range of receptors. This family also includes the bacterial amino acid binding proteins of known structure.
Pfam PF10547: P22_AR N-terminal domain (domain)
This domain was identified by Iyer and colleagues.
Pfam PF18838: Large polyvalent protein associated domain 23 (domain)
This is an alpha-helical domain that is usually N-terminal to a metallopeptidase domain. The domain is found in both in polyvalent proteins of conjugative elements and phages/prophages.
Pfam PF10480: Beta-1 integrin binding protein (domain)
ICAP-1 is a serine/threonine-rich protein that binds to the cytoplasmic domains of beta-1 integrins in a highly specific manner, binding to a NPXY sequence motif on the beta-1 integrin. The cytoplasmic domains of integrins are essential for cell adhesion, and the fact that phosphorylation of ICAP-1 by interaction with the cell-matrix implies an important role of ICAP-1 during integrin-dependent cell adhesion. Overexpression of ICAP-1 strongly reduces the integrin-mediated cell spreading on extracellular matrix and inhibits both Cdc42 and Rac1. In addition, ICAP-1 induces release of Cdc42 from cellular membranes and prevents the dissociation of GDP from this GTPase. An additional function of ICAP-1 is to promote differentiation of osteoprogenitors by supporting their condensation through modulating the integrin high affinity state,
Pfam PF03833: DNA polymerase II large subunit DP2, N-terminal (domain)
This entry represents the N-terminal domain of DNA polymerase II large subunit from Pyrococcus abyssi (PolC) and similar sequences mainly found in archaea. This domain shows an alpha beta configuration.
Pfam PF08625: Utp13 specific WD40 associated domain (domain)
Utp13 is a component of the five protein Pwp2 complex that forms part of a stable particle subunit independent of the U3 small nucleolar ribonucleoprotein that is essential for the initial assembly steps of the 90S pre-ribosome. Pwp2 is capable of interacting directly with the 35 S pre-rRNA 5' end.
Pfam PF08645: Polynucleotide kinase 3 phosphatase (family)
Polynucleotide kinase 3 phosphatases play a role in the repair of single breaks in DNA induced by DNA-damaging agents such as gamma radiation and camptothecin.
Pfam PF08384: Pro-opiomelanocortin, N-terminal region (family)
This family features the N-terminal peptide of pro-opiomelanocortin (NPP). It is thought to represent an important pituitary peptide, given its high yield from pituitary glands, and exhibits a potent in vitro aldosterone-stimulating activity.
Pfam PF07204: Orthoreovirus membrane fusion protein p10 (family)
This family consists of several Orthoreovirus membrane fusion protein p10 sequences.  p10 is thought to be a multifunctional protein that plays a key role in virus-host interaction.
Pfam PF06208: Borna disease virus G protein (family)
This family consists of Borna disease virus G glycoprotein sequences. Borna disease virus (BDV) infection produces a variety of clinical diseases, from behavioural illnesses to classical fatal encephalitis. G protein is important for viral entry into the host cell.
Wikipedia: The Borna disease viruses 1 and 2 are members of the species Mammalian 1 orthobornavirus and cause Borna disease in mammals.
Pfam PF15731: Antitoxin component of bacterial toxin-antitoxin system, MqsA (domain)
MqsA_antitoxin is a family of prokaryotic proteins that act as antidotes to the mRNA interferase MqsR.  It has a zinc-binding at the very N-terminus indicating its DNA-binding capacity. MqsR is the gene most highly upregulated in E. Colo MqsR_toxin is a family of bacterial toxins that act as an mRNA interferase. MqsR is the gene most highly upregulated in E. coli persister cells and it plays an essential role in biofilm regulation and cell signalling. It forms part of a bacterial toxin-antitoxin TA system, and as expected for a TA system, the expression of the MqsR toxin leads to growth arrest, while co-expression with its antitoxin, MqsA, rescues the growth arrest phenotype. In addition, MqsR associates with MqsA to form a tight, non-toxic complex and both MqsA alone and the MqsR:MqsA2:MqsR complex bind and regulate the mqsR promoter. The structure of MqsR shows that is is a member of the RelE/YoeB family of bacterial RNases that are structurally and functionally characterised bacterial toxins.
Wikipedia: A toxin-antitoxin system consists of a "toxin" and a corresponding "antitoxin", usually encoded by closely linked genes. The toxin is usually a protein while the antitoxin can be a protein or an RNA. Toxin-antitoxin systems are widely distributed in prokaryotes, and organisms often have them in multiple copies. When these systems are contained on plasmids – transferable genetic elements – they ensure that only the daughter cells that inherit the plasmid survive after cell division. If the plasmid is absent in a daughter cell, the unstable antitoxin is degraded and the stable toxic protein kills the new cell; this is known as 'post-segregational killing' (PSK).
Pfam PF05305: Protein of unknown function (DUF732) (family)
This family consists of several uncharacterised Mycobacterium tuberculosis and leprae 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 PF05028: Poly (ADP-ribose) glycohydrolase (PARG), Macro domain fold (domain)
Poly(ADP-ribose) glycohydrolase (PARG), is a ubiquitously expressed exo- and endoglycohydrolase which mediates oxidative and excitotoxic neuronal death. It catalyses hydrolysis of the O-glycosidic linkages of ADP-ribose polymers, which reverses the effects of poly(ADP-ribose). This entry represents the Macro domain fold localised in the C-terminal end of PARG catalytic domain from animals and plants.
Pfam PF04561: RNA polymerase Rpb2, domain 2 (domain)
RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure.  This domain is also known as the lobe domain.  DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble.  Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).
Pfam PF17554: Family of unknown function (DUF5466) (family)
This is a family of unknown function found in Enterobacteria phage T7.
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 PF09787: Golgin subfamily A member 5 (coiled_coil)
Members of this family of proteins are involved in maintaining Golgi structure. They stimulate the formation of Golgi stacks and ribbons, and are involved in intra-Golgi retrograde transport. Two main interactions have been characterised: one with RAB1A that has been activated by GTP-binding and another with isoform CASP of CUTL1.
Pfam PF21588: AP5B1, middle domain (repeat)
AP5B1 is part of the AP-5 adaptor protein complex, which may be involved in endosomal transport. This entry represents the central domain which consists of a repeated all-helical arrangement.
Pfam PF23252: PARP14, fifth type I KH domain (domain)
This domain is found in human Protein mono-ADP-ribosyltransferase PARP14 and related proteins. PARP14 is a large multidomain protein which in the N-terminal half contains a series of consecutive RRM and KH domains that are known to be nucleic acid-binding. PARP14 is involved in multiple signaling pathways linked to cancer, inflammation, and infection. PARP14 is an ADP-ribosyltransferase that mediates mono-ADP-ribosylation of glutamate residues on target proteins. In contrast to PARP1 and PARP2, it is not able to mediate poly-ADP-ribosylation. The domain represented by this entry is a KH domain found fifth in the human PARP14.
Pfam PF21518: Spindle assembly abnormal protein 5, implico domain (domain)
This domain is found in Spindle assembly abnormal protein 5 from Caenorhabditis elegans (Sas-5), which is essential for daughter- centriole formation. The implico domain shows three alpha-helices and adopt a globular dimeric configuration.
Pfam PF07861: WisP family N-Terminal Region (family)
This family is found at the N-terminus of the Tropheryma whipplei WisP family proteins ().
Pfam PF18785: Invertebrate-AID/APOBEC-deaminase (family)
A classical AID/APOBEC-like deaminases found in lophotrochozoans, echinoderms and cnidarians.
Pfam PF08870: DNA sulphur modification protein DndE (domain)
DndE is a small protein of 126 residues. It is a putative carboxylase homologous to NCAIR synthetase. It is encoded by an operon that is  associated with a sulphur-based modification to DNA.
Pfam PF00419: Fimbrial protein (domain)
This domain is found in bacterial proteins that are involved in regulation of length and mediation of adhesion of fimbriae. Fimbriae (also called pili), are polar filaments radiating from the surface of the bacterium to a length of 0.5-1.5 micrometers, that enable bacteria to colonize the epithelium of specific host organs. Fimbriae are also responsible to promote virulence .
Pfam PF17280: Family of unknown function (DUF5345) (family)
This is a family of unknown function. It is found mostly in Bacteria. Members of this family are predicted to contain 2 trans-membrane regions.
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 PF04780: Protein of unknown function (DUF629) (family)
This family represents a region of several plant proteins of unknown  function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the 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 PF11292: Protein of unknown function (DUF3093) (family)
This family of proteins with unknown function appears to be restricted to Actinobacteria. Some members are annotated as alanine rich membrane proteins however this cannot be confirmed.
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 PF16959: Renal amino acid transporter (domain)
Collectrin is a single-pass transmembrane protein that is homologous to the C-terminal region of human angiotensin-converting enzyme 2, ACE2, SwissProt:Q9BYF1, found in Peptidase_M2 [pfam:PF01401]. Collectrin is critical for normal amino acid reabsorption in the kidney.
Pfam PF21112: CsgH protein (domain)
CsgH is a Curli-like protein found in proteobacteria and Bacteroidetes. These proteins adopt a seven stranded beta sandwich fold. CsgH is a functional homologue of CsgC and is a potent inhibitor of CsgA amyloid formation.
Pfam PF02700: Phosphoribosylformylglycinamidine (FGAM) synthase (family)
This family forms a component of the de novo purine biosynthesis pathway.
Pfam PF01159: Ribosomal protein L6e (family)
This family represents large ribosomal subunit protein eL6 which are found in eukaryotes, including mammalian eL6 (which was previously known as L6 and TAX-responsive enhancer element binding protein 107 , Saccharomyces cerevisiae (Baker's yeast) ribosomal protein eL6A/B (also known as YL16A/YL16B); and Mesembryanthemum crystallinum (Common ice plant) eL6 (also known as YL16-like). These proteins have 175 (yeast) to 287 (mammalian) amino acids.
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .