SII-SWORD/CoKE huggingface dataset:
Pfam PF02961: Barrier to autointegration factor (domain)
The BAF protein has a SAM-domain-like bundle of orthogonally packed alpha-hairpins - one classic and one pseudo helix-hairpin-helix motif.  The protein is involved in the prevention of retroviral DNA integration.
Wikipedia: In molecular biology, barrier-to-autointegration factor (BAF) is a family of essential proteins that is highly conserved in metazoan evolution, and which may act as DNA-bridging proteins. BAF binds directly to double-stranded DNA, to transcription activators, and to inner nuclear membrane proteins, including lamin A filaments that anchor nuclear pore complexes in place, and nuclear LEM-domain proteins that bind to lamin filaments and chromatin. New findings suggest that BAF has structural roles in nuclear assembly and chromatin organization, represses gene expression and might interlink chromatin structure, nuclear architecture and gene regulation in metazoans.
Pfam PF19584: MCAfunc domain (domain)
MCAfunc domain (MCAfunc) is located in the N-terminal region of a mechanosensitive channel protein MID1-COMPLEMENTING ACTIVITY (MCA). MCAfunc represents the provisionally advocated ARPK domain (Amino-terminal domain of Rice putative Protein Kinases), overlapping with the EF hand-like region at the N-terminus. In MCA proteins, MCAfunc has Ca2+ influx activity and is proposed to be a functional domain of MCAs. MCAfunc is exclusively observed in streptophytes and exists not only in MCA but also in E3 ubiquitin ligase-like proteins, ARO3 like proteins and and protein kinases. In the most basal plant lineage, charophytes, MCAfunc is only found in E3 ubiquitin ligase-like proteins and protein of presently unknown function, while MCA proteins are exclusively found in land plants, from bryophytes to angiosperms.
Pfam PF05398: PufQ cytochrome subunit (family)
This family consists of bacterial PufQ proteins. PufQ id required for bacteriochlorophyll biosynthesis serving a regulatory function in the formation of photosynthetic complexes.
Pfam PF24098: Domain of unknown function (DUF7380) (domain)
This domain is found N-terminal in uncharacterised bacterial proteins. It is predicted to adopt a globular structure composed mainly of alpha 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 PF00170: bZIP transcription factor (coiled_coil)
The Pfam entry includes the basic region and the leucine zipper region.
Wikipedia: The Basic Leucine Zipper Domain is found in many DNA binding eukaryotic proteins. One part of the domain contains a region that mediates sequence specific DNA binding properties and the leucine zipper that is required to hold together (dimerize) two DNA binding regions. The DNA binding region comprises a number of basic amino acids such as arginine and lysine. Proteins containing this domain are transcription factors.
Pfam PF03243: Alkylmercury lyase (family)
Alkylmercury lyase ([ec:4.99.1.2]) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate.
Pfam PF12160: Fibrinogen alpha C domain (domain)
This domain family is found in eukaryotes, and is approximately 70 amino acids in length, and the family is found in association with [pfam:PF08702]. This domain is the C terminal domain of fibrinogen in mammals. The domain lies in the C terminal half of the alpha C region in these proteins. The function of the domain is that of intramolecular and intermolecular interactions to form fibrin.
Wikipedia: Fibrinogen is a glycoprotein complex, produced in the liver, that circulates in the blood of all vertebrates. During tissue and vascular injury, it is converted enzymatically by thrombin to fibrin and then to a fibrin-based blood clot. Fibrin clots function primarily to occlude blood vessels to stop bleeding. Fibrin also binds and reduces the activity of thrombin. This activity, sometimes referred to as antithrombin I, limits clotting. Fibrin also mediates blood platelet and endothelial cell spreading, tissue fibroblast proliferation, capillary tube formation, and angiogenesis and thereby promotes revascularization and wound healing.
Pfam PF00889: Elongation factor TS (family)
Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome . EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution.
Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) .
This entry represents the C-terminal dimerisation domain found primarily in EF-Tu (EF1A) proteins from bacteria, mitochondria and chloroplasts.
Wikipedia: EF-Ts is one of the prokaryotic elongation factors. It is found in human mitochondria as TSFM. It is similar to eukaryotic EF-1B.
Pfam PF17129: C-terminal domain of metallo-carboxypeptidase (domain)
C-terminal immunoglobulin-like domain of helical cell shape-determining peptidoglycan hydrolases, a metallo-carboxypeptidase. The structural elements of this domain form a Ca2+ binding-channel, the Ca2+ being co-ordinated by six ligand-atoms.
Pfam PF21829: Family of unknown function (DUF6889) (family)
This entry represents a family of small proteins that are largely composed of a single alpha helix. Some members of the family are found on phage. The function of these proteins 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 PF02666: Phosphatidylserine decarboxylase (family)
This is a family of phosphatidylserine decarboxylases, [ec:4.1.1.65].   These enzymes catalyse the reaction: Phosphatidyl-L-serine  phosphatidylethanolamine + CO2. Phosphatidylserine decarboxylase plays  a central role in the biosynthesis of aminophospholipids by converting phosphatidylserine to phosphatidylethanolamine.
Wikipedia: The enzyme phosphatidylserine decarboxylase (EC 4.1.1.65) catalyzes the chemical reactionphosphatidyl-L-serine  phosphatidylethanolamine + CO2
Pfam PF06013: Proteins of 100 residues with WXG (family)
ESAT-6 is a small protein appears to be of fundamental importance in virulence and protective immunity in Mycobacterium tuberculosis. Homologues have been detected in other Gram-positive bacterial species. It may represent a novel secretion system potentially driven by the [pfam:PF01580] domains in the YukA-like proteins.
Pfam PF04033: Domain of unknown function (DUF365) (family)
Archaeal domain 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 PF09057: Second Mitochondria-derived Activator of Caspases (domain)
Second Mitochondria-derived Activator of Caspases promotes apoptosis by activating caspases in the cytochrome c/Apaf-1/caspase-9 pathway, and by opposing the inhibitory activity of inhibitor of apoptosis proteins (XIAP-BIR3). The protein assumes an elongated three-helix bundle structure, and forms a dimer in solution.
Pfam PF00468: Ribosomal protein L34 (family)
Ribosomal protein L34 (also known as Large ribosomal subunit protein bL34) is one of the proteins from the large subunit of the ribosome from bacteria and eukaryotes. It is a small basic protein of 44 to 51 amino-acid residues . L34 belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups: Eubacterial L34, Red algal chloroplast L34 and Cyanelle L34.
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 .
Pfam PF11376: Protein of unknown function (DUF3179) (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 PF16151: Domain of unknown function (DUF4859) (family)
This family consists of uncharacterized proteins around 340 residues in length and is mainly found in various Bacteroides and Prevotella species. The function of this family is unknown.
Pfam PF06824: Metal-independent alpha-mannosidase (GH125) (repeat)
This family, which contains bacterial and fungal glycoside hydrolases, is also known as GH125. They function as metal-independent alpha-mannosidases, with specificity for alpha-1,6-linked non-reducing terminal mannose residues. Structurally this family is part of the 6 hairpin glycosidase superfamily.
Pfam PF02022: Integrase Zinc binding domain (domain)
Integrase mediates integration of a DNA copy of the viral genome into the host chromosome.  Integrase is composed of three domains.  This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain [pfam:PF00665]. The carboxyl terminal domain is a  DNA binding domain [pfam:PF00552].
Wikipedia: Retroviral integrase (IN) is an enzyme produced by a retrovirus that integrates its genetic information into that of the host cell it infects. Retroviral INs are not to be confused with phage integrases (recombinases) used in biotechnology, such as λ phage integrase, as discussed in site-specific recombination.
Pfam PF00234: Protease inhibitor/seed storage/LTP family (domain)
This family is composed of trypsin-alpha amylase inhibitors, seed  storage proteins and lipid transfer proteins from plants.
Wikipedia: Plant lipid transfer proteins, also known as plant LTPs or PLTPs, are a group of highly-conserved proteins of about 7-9kDa found in higher plant tissues. As its name implies, lipid transfer proteins facilitate the shuttling of phospholipids and other fatty acid groups between cell membranes. LTPs are divided into two structurally related subfamilies according to their molecular masses: LTP1s (9 kDa) and LTP2s (7 kDa). Various LTPs bind a wide range of ligands, including fatty acids with a C10–C18 chain length, acyl derivatives of coenzyme A, phospho- and galactolipids, prostaglandin B2, sterols, molecules of organic solvents, and some drugs.
Pfam PF23424: Family of unknown function (DUF7112) (family)
This family represents a group of proteins from halobacteria. It has several conserved R, D W and Y residues. Members are predicted to show a mainly beta configuration.
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 PF13694: Sec63/Sec62 complex-interacting family (family)
This is a family of closely related Hph proteins that are integral endoplasmic reticulum (ER) membrane proteins required for yeast survival under environmental stress conditions. They interact with several subunits of the Sec63/Sec62 complex that mediates post-translational translocation of proteins into the ER. Cells with mutant Hph1 and Hph2 proteins revealed phenotypes resembling those of mutants defective for vacuolar proton ATPase (V-ATPase) activity. The yeast V-ATPase is a multisubunit complex whose function, structure, and assembly have been well characterized. Cells with impaired V-ATPase activity fail to acidify the vacuole, cannot grow at alkaline pH, and are sensitive to high concentrations of extracellular calcium.
Pfam PF15621: Proline-rich submaxillary gland androgen-regulated family (family)
SMR is a family of proteins found in eukaryotes. The family of SMR proteins is expressed in the submaxillary gland. SMR members may play a role in protection or detoxification.
Pfam PF08619: Alkali metal cation/H+ antiporter Nha1 C terminus (family)
The C terminus of the plasma membrane Nha1 antiporter plays an important role in the immediate cell response to hypo-osmotic shock which prevents an execessive loss of ions and water. This  domain is found with [pfam:PF00999].
Pfam PF04591: Protein of unknown function, DUF596 (family)
This family contains several uncharacterised proteins.
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 PF16556: Interleukin-17 receptor, fibronectin-III-like domain 1 (domain)
IL17R_fnIII_D1 is the first of two fibronectin 3-like domains on interleukin-17 receptor proteins A and B. The tow fnIII domains are linked and together bind two molecules of IL-17 at one of its receptor-binding interfaces.  This allows the other interface to bind to another receptor, thus allowing the IL-17 family of homodimeric cytokines to coordinate two different receptors.
Pfam PF04833: COBRA-like protein (family)
This is a family of plant proteins designated COBRA-like (COBL) proteins. The 12 Arabidopsis members of the family are all GPI-linked. Some members of this family are annotated as phytochelatin synthase, but these annotations are incorrect.
Pfam PF18728: AbiV (domain)
AbiV-like HEPN
Pfam PF00548: 3C cysteine protease (picornain 3C) (family)
Picornaviral proteins are expressed as a single polyprotein which is cleaved by the viral 3C cysteine protease.
Pfam PF11065: Protein of unknown function (DUF2866) (family)
This bacterial family of proteins have 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 PF13219: Protein of unknown function (DUF4027) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length. There is a conserved CLGGF sequence motif.
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 PF06176: Lipopolysaccharide core biosynthesis protein (WaaY) (family)
This family consists of several bacterial lipopolysaccharide core biosynthesis proteins (WaaY or RfaY). The waaY, waaQ, and waaP genes are located in the central operon of the waa (formerly rfa) locus on the chromosome of Escherichia coli. This locus contains genes whose products are involved in the assembly of the core region of the lipopolysaccharide molecule. WaaY is the enzyme that phosphorylates HepII in this system.
Pfam PF03834: Binding domain of DNA repair protein Ercc1 (rad10/Swi10) (family)
Ercc1 and XPF (xeroderma pigmentosum group F-complementing protein) are two structure-specific endonucleases of a class of seven containing an ERCC4 domain.  Together they form an obligate complex that functions primarily in nucleotide excision repair (NER), a versatile pathway able to detect and remove a variety of DNA lesions induced by UV light and environmental carcinogens, and secondarily in DNA interstrand cross-link repair and telomere maintenance. This domain in fact binds simultaneously to both XPF and single-stranded DNA; this ternary complex explains the important role of Ercc1 in targeting its catalytic XPF partner to the NER pre-incision complex.
Pfam PF06993: Protein of unknown function (DUF1304) (domain)
This family consists of several hypothetical bacterial proteins of around 120 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 PF17473: Family of unknown function (DUF5426) (family)
This is a family of unknown function found in Mycoplasma.
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 PF23769: WD repeat-containing protein 75 second beta-propeller (repeat)
This entry represents the second beta-propeller found in WD repeat-containing protein 75 (WDR75) from animals. WDR75 has a crucial positive role in ribosome biogenesis and its malfunction activates p53, leading to cellular senescence. The function of this domain is unknown. This entry also represents the second beta-propeller domain of U3 small nucleolar RNA-associated protein 13 and 17 (UTP13 and UTP17), which are WDR75 orthologs from yeast.
Pfam PF22495: RsaL-like HTH domain (domain)
This is a helix-turn-helix (HTH) domain found in quorum-sensing regulator RsaL and related proteins.
Pfam PF00328: Histidine phosphatase superfamily (branch 2) (family)
The histidine phosphatase superfamily is so named because catalysis centres on a conserved His residue that is transiently phosphorylated during the catalytic cycle.  Other conserved residues contribute to a 'phosphate pocket' and interact with the phospho group of substrate before, during and after its transfer to the His residue. Structure and sequence analyses show that different families contribute different additional residues to the 'phosphate pocket' and, more surprisingly, differ in the position, in sequence and in three dimensions, of a catalytically essential acidic residue.  The superfamily may be divided into two main branches.The smaller branch 2 contains predominantly eukaryotic proteins.  The catalytic functions in members include phytase, glucose-1-phosphatase and multiple inositol polyphosphate phosphatase.  The in vivo roles of the mammalian acid phosphatases in branch 2 are not fully understood, although activity against lysophosphatidic acid and tyrosine-phosphorylated proteins has been demonstrated.
Wikipedia: In biochemistry, a phosphatase is an enzyme that uses water to cleave a phosphoric acid monoester into a phosphate ion and an alcohol. Because a phosphatase enzyme catalyzes the hydrolysis of its substrate, it is a subcategory of hydrolases. Phosphatase enzymes are essential to many biological functions, because phosphorylation and dephosphorylation serve diverse roles in cellular regulation and signaling. Whereas phosphatases remove phosphate groups from molecules, kinases catalyze the transfer of phosphate groups to molecules from ATP. Together, kinases and phosphatases direct a form of post-translational modification that is essential to the cell's regulatory network.
Pfam PF23663: SCAN domain-containing protein 3-like zinc finger (domain)
This zinc finger domain is found in human SCAN domain-containing protein 3 (SCAND3) and similar animal proteins. SCAND3 is a candidate prognostic marker for non-small cell lung cancer.
Pfam PF15665: Family with sequence similarity 184, A and B (coiled_coil)
The function of FAM184 is not known.
Pfam PF10161: Putative mitochondrial precursor protein (family)
This is a family of small conserved proteins found from nematodes to humans. The C-terminal region is rich in asparagine. Members are putatively assigned to be mitochondrial precursor proteins but this could not be confirmed.