SII-SWORD/CoKE huggingface dataset:
Pfam PF01017: STAT transcription factor, coiled-coil domain (domain)
STAT proteins (Signal Transducers and Activators of Transcription) are a family of transcription factors that are specifically activated to regulate gene transcription when cells encounter cytokines and growth factors. STATs share 6 structurally and functionally conserved domains including: an N-terminal domain (ND) that strengthens interactions between STAT dimers on adjacent DNA-binding sites; a coiled-coil STAT domain (CCD) that is implicated in protein-protein interactions; a DNA-binding domain (DBD) with an immunoglobulin-like fold similar to p53 tumour suppressor protein; an EF-hand-like linker domain connecting the DNA-binding and SH2 domains; an SH2 domain that acts as a phosphorylation-dependent switch to control receptor recognition and DNA-binding; and a C-terminal transactivation domain. This entry represents the coiled-coil domain (CCD)
Wikipedia: Members of the signal transducer and activator of transcription (STAT) protein family are intracellular transcription factors that mediate many aspects of cellular immunity, proliferation, apoptosis and differentiation. They are primarily activated by membrane receptor-associated Janus kinases (JAK). Dysregulation of this pathway is frequently observed in primary tumors and leads to increased angiogenesis which enhances the survival of tumors and immunosuppression. Gene knockout studies have provided evidence that STAT proteins are involved in the development and function of the immune system and play a role in maintaining immune tolerance and tumor surveillance.
Pfam PF20914: DNA polymerase III subunit alpha, C-terminal domain (domain)
This domain is found at the C-terminal end of DNA polymerase III subunit alpha and similar proteins from Proteobacteria and Actinobacteria. This protein, which is the replicative DNA polymerase, consists of six domains that form an irregular pyramid around a central cavity. The C-terminal domain lies on top of this structure.
Pfam PF22860: Domain of unknown function (DUF7017) (repeat)
This entry represents a domain consisting of TPR repeats found at the N-terminal of of group of uncharacterised sequences predominantly from bacteria, which seem to be related to TOTE conflict systems as they are associated with [pfam:PF22708].
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 PF06884: Protein of unknown function (DUF1264) (family)
This family contains a number of bacterial and eukaryotic proteins of unknown function that are approximately 200 residues long. Some family members are annotated as putative lipoproteins.
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 PF22988: Lysine-specific demethylase 3B, PWWP domain (domain)
This domain is found in Lysine-specific demethylase 3B (KDM3B, also known as JmjC domain-containing histone demethylation protein 2B or JHDM2B) and related proteins. KDM3B is a histone demethylase that specifically demethylates lysine at position 9 of histone H3. This enzyme plays a central role in histone code. This domain is predicted to adopt an open beta-barrel with an SH3-like topology. It has detectable sequence and structural similarity to PWWP reader domains of LEDGF and ZMYND8 known to recognise the histone H3 methylation marks of lysine at position 36.
Pfam PF23940: Domain of unknown function (DUF7275) (domain)
This entry represents the central alpha helical domain from a large family of uncharacterised phage proteins that typically contain three domains.
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 PF18473: Urease subunit beta-alpha linker domain (domain)
This domain is present in bacterial ureases and corresponds to the gap region between the C-terminus of the beta-chain Urease beta subunit [pfam:PF00699] and the N-terminus of the alpha-chain Urease alpha-subunit, N-terminal domain [pfam:PF00449]. It is suggested that this region is required for the stability of the putative transmembrane beta-barrel, and might be the reason for bacterial urease (B. pasteurii) not being lethal to insects.
Pfam PF06676: Protein of unknown function (DUF1178) (family)
This family consists of several hypothetical bacterial proteins of around 150 residues in length. 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 PF02659: Putative manganese efflux pump (family)
MntP is a family of bacterial proteins with a signal peptide and four transmembrane domains. It is a putative manganese efflux pump, since deletion of the gene leads to profound manganese sensitivity and elevated intracellular manganese levels in bacteria. Manganese is a highly important trace nutrient for organisms from bacteria to humans, and acts as an important element in the defence against oxidative stress and as an enzyme cofactor.
Wikipedia: The Manganese (Mn2+) Exporter (MntP) Family is a member of the Lysine Exporter (LysE) Superfamily. The MntP family is a small family whose members have been found in bacteria and archaea. MntP proteins are of about 200 amino acyl residues with 6 putative transmembrane segments (TMSs). The Conserved Domain Database (CDD) recognized two DUF204 repeats, each repeat having 3 TMSs. A representative list of proteins belonging to the MntP family can be found in the Transporter Classification Database.
Pfam PF00296: Luciferase-like monooxygenase (domain)
Bacterial luciferase is a flavin monooxygenase that catalyses the oxidation of long-chain aldehydes and releases energy in the form of visible light, and which uses flavin as a substrate rather than a cofactor . Bacterial luciferase is an alpha/beta (LuxA/LuxB) heterodimer, where each individual subunit folds into a single TIM (Î²/Î±)8-barrel domain. There are structural similarities between bacterial luciferase and nonfluorescent flavoproteins (LuxF, FP390), alkanesulphonate monooxygenase (SsuD), and coenzyme F420-dependent terahydromethanopterin reductase, which make up clearly related families with somewhat different folds .
Wikipedia: Luciferase is a generic term for the class of oxidative enzymes that produce bioluminescence, and is usually distinguished from a photoprotein. The name was first used by Raphaël Dubois who invented the words luciferin and luciferase, for the substrate and enzyme, respectively. Both words are derived from the Latin word lucifer, meaning "lightbearer", which in turn is derived from the Latin words for "light" (lux) and "to bring or carry" (ferre).
Pfam PF03703: Bacterial PH domain (domain)
Domain found in uncharacterised family of membrane proteins. 1-3 copies found in each protein, with each copy flanked by transmembrane helices. Members of this family have a PH domain like structure.
Wikipedia: Pleckstrin homology domain or (PHIP) is a protein domain of approximately 120 amino acids that occurs in a wide range of proteins involved in intracellular signaling or as constituents of the cytoskeleton.
Pfam PF07160: Spindle and kinetochore-associated protein 1 (family)
Spindle and kinetochore-associated protein 1 (SKA1) is a component of the SKA1 complex (consists of Ska1, Ska2, and Ska3/Rama1), a microtubule-binding subcomplex of the outer kinetochore that is essential for proper chromosome segregation. It is required for  timely anaphase onset during mitosis, when chromosomes undergo  bipolar attachment on spindle microtubules leading to silencing of  the spindle checkpoint.
Pfam PF20662: Conserved oligomeric Golgi complex subunit 4, C-terminal (repeat)
COG4 is a component of the conserved oligomeric Golgi (COG) complex which mediates the proper glycosylation of proteins trafficking through the Golgi apparatus. It is included in the CATCHR (complexes associated with tethering containing helical rods) family, which includes components of the exocyst, COG, GARP, and DSL1 complexes, sharing structural and functional features, such as the alpha-helical bundles at the C-terminal and a N-terminal coiled-coil region. This is the C-terminal domain which contains the key Arginine residue that stabilises this domain and it is required for the proper glycosylation of cell surface proteins.
Pfam PF09500: Putative thioesterase (yiiD_Cterm) (domain)
This entry consists of a broadly distributed uncharacterised domain often found as a standalone protein. The member from Shewanella oneidensis is described from crystallography work as a putative thioesterase because it belongs to the HotDog clan of enzymes. About half of the members of this family are fused to an Acetyltransf_1 domain [pfam:PF00583].
Pfam PF08119: Scorpion acidic alpha-KTx toxin family (family)
This family consists of acidic alpha-KTx short chain scorpion toxins. These toxins named parabutoxins, block voltage-gated K channels and have extremely low pI values. Furthermore, they lack the crucial pore-plugging lysine. In addition, the second important residue of the dyad, the hydrophobic residue (Phe or Tyr) is also missing.
Pfam PF21739: Family of unknown function (DUF6866) N-terminal domain (domain)
This entry represents the N-terminal alpha+beta domain found in DUF6866 family proteins. The function of these proteins is unknown. Proteins in this family are primarily found in Proteobacteria.
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 PF13146: TRL-like protein family (domain)
This family includes the [swissprot:O87326] TRL protein that is found in a locus that includes several tRNAs.  The function of this protein is not known. The proteins in this family usually have a lipoprotein attachment site at their N-terminus.
Pfam PF14523: Syntaxin-like protein (domain)
This entry includes syntaxin-like domains. Syntaxins are the prototype family of SNARE proteins. They usually consist of three main regions - a C-terminal  transmembrane region, a central SNARE domain which is  characteristic of and conserved in all syntaxins, and an N-terminal domain that is featured in this entry.
Pfam PF19238: Radical SAM-like domain (domain)
This family represents a set of radical SAM like domains that are often found associated with [pfam:PF04459].
Pfam PF13717: zinc-ribbon domain (domain)
This family consists of a single zinc ribbon domain, ie half of a pair as in family DZR, [pfam:PF12773].
Pfam PF14942: Organelle biogenesis, Muted-like protein (family)
The protein is a coiled-coil protein and belongs to a family found in eukaryotes. It undergoes alternative splicing forming two isoforms.  The larger isoform is 187 amino acids long in protein sequence length and 21 kDa in mass. The smaller isoform is 110 amino acids long in protein sequence length and 12 kDa in mass. This protein associates with other proteins in order to form biogenesis of lysosome-related organelles complex-1 BLOC1 complex. BLOC-1 is required for the normal biogenesis of specialized organelles of the endosomal-lysosomal system.
Pfam PF05907: CXXC motif containing zinc binding protein, eukaryotic (family)
This family consists of a number of eukaryotic proteins including CXXC motif containing zinc binding protein (previously known as UPF0587 protein C1orf123). The crystal structure reveals that the protein binds a Zn2+ ion in a tetrahedral coordination with four Cys residues from two CxxC motifs. CXXC motif containing zinc binding protein was initially identified as an interaction partner for the heavy metal-associated (HMA) domain of CCS (copper chaperone for superoxide dismutase). However, it was shown that only misfolded mutant forms, lacking part of the zinc-binding sites, interact with CCS.
Pfam PF09594: Glycosyltransferase family 87 (family)
The enzymes in this family are glycosyltransferases. PimE is involved in phosphatidylinositol mannoside (PIM) synthesis, a major class of glycolipids in all mycobacteria. PimE is a polyprenol-phosphate-mannose-dependent mannosyltransferase that transfers the fifth mannose of PIM. The family also includes alpha(1-->3) arabinofuranosyltransferase, invloved in the synthesis of of mycobacterial arabinogalactan.
Pfam PF14069: Stage VI sporulation protein F (family)
The sporulation-specific SpoVIF (YjcC) protein of Bacillus subtilis is essential for the development of heat-resistant spores. Its expression is governed by SigK.
Pfam PF21768: AF_1763-like, C-terminal domain (domain)
This domain is found at the C-terminal end of a group of prokaryotic proteins, including the putative lipase AF_1763 from Archaeoglobus fulgidus. This protein contains a C-terminal lipid binding domain, which is formed by two layers of seven beta-strands. This entry represents the second half of this domain.
Pfam PF22671: Tail sheath protein Gp18 domain III N-terminal region (domain)
This entry represents the N-terminal segment of domain III from the phage tail sheath protein Gp18 y similar sequences. Domain III is completed by [pfam:PF04984] with an overall structure consisting of a beta-sheet with five parallel and one anti-parallel beta-strands plus six alpha-helices, which surround the beta-sheet.
Pfam PF16924: Dipicolinate synthase subunit A N-terminal domain (domain)
This entry represents the N-terminal domain of dipicolinate synthase subunit A. Dipicolinic acid is a small polar molecule that accumulates to high concentrations in bacterial endospores .
Pfam PF04797: Herpesvirus dUTPase protein (family)
This family of proteins are found in Herpesvirus proteins.  This family includes proteins called ORF10 and ORF11 amongst others. However, these proteins seem to be related to other dUTPases [pfam:PF00692] suggesting that these proteins are also dUTPases (Bateman A pers. obs.).
Pfam PF18598: Tetracyclin repressor-like, C-terminal domain (domain)
This is a C-terminal TetR regulatory domain found in QsdR proteins (quorum-sensing degradation regulation).
Pfam PF08295: Sin3 family co-repressor (domain)
This domain is found on transcriptional regulators.  It forms interactions with histone deacetylases.
Pfam PF21846: Domain of unknown function (DUF6905) (domain)
Members of this family are annotated in SwissProt as Putative glycerol transporters SwissProt:Q92EU1. Members of the family contain four potential transmembrane helices.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF10806: SAM35, subunit of SAM coomplex (family)
SAM35 is a family of fungal proteins found in the peripheral mitochondrial outer membrane. It is essential for cell viability. It forms a subunit of the SAM (sorting and assembly machinery) complex and is crucial for the assembly of the precursors of Tom40 and porin, the outer membrane beta-barrel proteins involved in mitochondrial biogenesis. SAM35 is required in order for the Sam50 subunit of the SAM complex to bind outer membrane substrate proteins.
Pfam PF07093: SGT1 protein (family)
This family consists of several eukaryotic SGT1 proteins. Human SGT1 or hSGT1 is known to suppress GCR2 and is highly expressed in the muscle and heart. The function of this family is unknown although it has been speculated that SGT1 may be functionally analogous to the Gcr2p protein of Saccharomyces cerevisiae which is known to be a regulatory factor of glycolytic gene expression.
Pfam PF12921: Mitochondrial ATPase expression (family)
ATP13 is necessary for the expression of subunit 9 of mitochondrial ATPase. The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria.
Pfam PF03198: Glucanosyltransferase (domain)
This is a family of glycosylphosphatidylinositol-anchored beta(1-3)glucanosyltransferases. The active site residues in the Aspergillus fumigatus example [swissprot:B0XT72] are the two glutamate residues at 160 and 261.
Wikipedia: In molecular biology, glycoside hydrolase family 72 is a family of glycoside hydrolases.
Pfam PF10767: Inner membrane protein YbjO, dehydrogenase-like (family)
This family of proteins includes the Inner membrane protein YbjO which appears to be restricted to Enterobacteriaceae. From AlphaFold structure predictions, it has been suggested that these proteins may function as dehydrogenases.
Pfam PF03160: Calx-beta domain (domain)
The calx-Î² motif is present as a tandem repeat in the cytoplasmic domains of Calx Na-Ca exchangers, which are used to expel calcium from cells. This motif overlaps domains used for calcium binding and regulation. The calx-Î² motif is also present in the cytoplasmic tail of mammalian integrin-beta4, which mediates the bi-directional transfer of signals across the plasma membrane, as well as in some cyanobacterial proteins. This motif is also found in Fras1/Frem family of extracellular proteins (extracellular matrix organizing protein FRAS1 and FRAS1-related extracellular matrix proteins FRAM1, 2 and 3) required for proper organogenesis during embryonic development and whose mutations lead to Fraser Syndrome, a rare congenital disorder characterised by multisystem malformation usually comprising abnormal brain formation, cryptophthalmos, syndactyly and renal defects . This motif contains a series of Î²-strands and turns that form a self-contained Î²-sheet .
Wikipedia: In molecular biology, the calx-beta motif is a protein motif which is present as a tandem repeat in the cytoplasmic domains of Calx sodium-calcium exchangers, which are used to expel calcium from cells. This motif overlaps domains used for calcium binding and regulation. The calx-beta motif is also present in the cytoplasmic tail of mammalian integrin-beta4, which mediates the bi-directional transfer of signals across the plasma membrane, as well as in some cyanobacterial proteins. This motif contains a series of beta-strands and turns that form a self-contained beta-sheet.
Pfam PF19777: Family of unknown function (DUF6263) (family)
This family of proteins found in bacteria is functionally uncharacterised. Proteins in this family are typically between 298 and 349 amino acids in length. There is a conserved sequence pattern PxxxI/VxxGxxW.
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 PF08339: RTX C-terminal domain (family)
This family describes the C-terminal region of various bacterial haemolysins and leukotoxins, which belong to the RTX family of toxins. These are produced by various Gram negative bacteria, such as E. coli ([swissprot:P09983]) and Actinobacillus pleuropneumoniae ([swissprot:P15377]). RTX toxins may interact with lipopolysaccharide (LPS) to functionally impair and eventually kill leukocytes. This region is found in association with the RTX N-terminal domain ([pfam:PF02382]) and multiple hemolysin-type calcium-binding repeats ([pfam:PF00353]).
Pfam PF11933: Cytoplasmic domain of voltage-gated Na+ ion channel (family)
This is a large cytoplasmic domain towards the start of voltage-dependent sodium ion channel proteins in eukaryotes. It is found closely associated with [pfam:PF06512] and [pfam:PF00520].
Pfam PF13973: Domain of unknown function (DUF4222) (domain)
This short protein is likely to be of phage origin. For example it is found in the [swissprot:B6DZ51] Enterobacteria phage YYZ-2008. It is largely found in enteric bacteria. The molecular function of this protein is unknown.
Pfam PF10683: Hermes transposase DNA-binding domain (domain)
This domain confers specific DNA-binding on Hermes transposase.
Pfam PF17671: Family of unknown function (DUF5531) (family)
This is a family of unknown function found in Mammalia. Family members have one or several predicted 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 PF00064: Neuraminidase (repeat)
Neuraminidases cleave sialic acid residues from glycoproteins. Belong to the sialidase family - but this alignment does not generalise to the other sialidases. Structure is a 6-sheet beta propeller.
Wikipedia: Viral neuraminidase is a type of neuraminidase found on the surface of influenza viruses that enables the virus to be released from the host cell. Neuraminidases are enzymes that cleave sialic acid groups from glycoproteins. Viral neuraminidase was discovered by Alfred Gottschalk at the Walter and Eliza Hall Institute in 1957. Neuraminidase inhibitors are antiviral agents that inhibit influenza viral neuraminidase activity and are of major importance in the control of influenza.
Pfam PF12754: Get5, N-terminal domain (domain)
This entry represents the N-terminal domain of Get5 from Aspergillus fumigatus and similar proteins found mainly in Ascomycetes. Get5 is a component of the get4/get5/sgt2 sorting complex involved in the GET (guided entry of TA proteins) pathway that leads to the insertion of tail-anchored proteins into the endoplasmic reticulum.
Pfam PF19266: Contractile injection system tube protein (family)
This protein is part of a contractile injection system. This family includes the Pvc7 protein from the Photorhabdus asymbiotica virulence cassette (PVC). Pvc7 is made of a tube protein (this entry) and an additional LysM domain. The equivalents of these two parts in T4 phage are gp48 and gp53, respectively.
Pfam PF10705: Chloroplast protein precursor Ycf15 putative (family)
In some species of plants the ycf15 gene is probably not a protein-coding gene because the protein in these species has premature stop codons. Most of the members of the family are hypothetical or uncharacterised.