SII-SWORD/CoKE huggingface dataset:
Pfam PF18558: Methyltransferase, Helix-turn-helix domain (domain)
This is helix turn helix domain found in polyketide synthases (PKSs) in fungi. They are multidomain enzymes that biosynthesize a wide range of natural products. Family members include citrinin polyketide synthases which contain a C-methyltransferase (CMeT) domain [pfam:PF08242] that adds one or more S-adenosylmethionine (SAM)-derived methyl groups to the carbon framework.
Pfam PF08271: TFIIB zinc-binding (domain)
The transcription factor TFIIB contains a zinc-binding motif near the N-terminus.  This domain is involved in the interaction with RNA pol II and TFIIF and plays a crucial role in selecting the transcription initiation site.  The domain adopts a zinc ribbon like structure.
Wikipedia: A zinc finger is a small protein structural motif that is characterized by the coordination of one or more zinc ions (Zn2+) which stabilizes the fold. It was originally coined to describe the finger-like appearance of a hypothesized structure from the African clawed frog (Xenopus laevis) transcription factor IIIA. However, it has been found to encompass a wide variety of differing protein structures in eukaryotic cells. Xenopus laevis TFIIIA was originally demonstrated to contain zinc and require the metal for function in 1983, the first such reported zinc requirement for a gene regulatory protein followed soon thereafter by the Krüppel factor in Drosophila. It often appears as a metal-binding domain in multi-domain proteins.
Pfam PF09723: Zinc ribbon domain (domain)
This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Pfam PF01196: Ribosomal protein L17 (family)
Large ribosomal subunit protein bL17 (also known as L17) is one of the proteins from the large ribosomal subunit. Bacterial L17 is a protein of 120 to 130 amino-acid residues while yeast YmL8 is twice as large (238 residues). The N-terminal half of YmL8 is collinear with the sequence of L17 from Escherichia coli.
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 PF02943: Ferredoxin thioredoxin reductase catalytic beta chain (domain)
Ferredoxin thioredoxin reductase is a  protein present in organisms performing oxygenic photosynthesis, and plays an important role in the ferredoxin/thioredoxin regulatory chain. It converts an electron signal (photoreduced ferredoxin) to a thiol signal (reduced thioredoxin), regulating enzymes by reduction of specific disulphide groups. It catalyses the light-dependent activation of several photosynthetis enzymes. Ferredoxin thioredoxin reductase is a heterodimer of subunit alpha and subunit beta. Subunit alpha is the variable subunit, and beta is the catalytic chain .
The structure of the beta subunit has been determined and found to fold around the FeS cluster .
Wikipedia: Ferredoxin-thioredoxin reductase EC 1.8.7.2, systematic name ferredoxin:thioredoxin disulfide oxidoreductase, is a [4Fe-4S] protein that plays an important role in the ferredoxin/thioredoxin regulatory chain. It catalyzes the following reaction:2 reduced ferredoxin + thioredoxin disulfide  2 oxidized ferredoxin + thioredoxin thiols + 2 H+
Pfam PF12287: Cytoplasmic activation/proliferation-associated protein-1 C term (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 343 and 708 amino acids in length. This family is the C terminal region of caprin-1. Caprin-1 is a protein involved in regulating cellular proliferation. In mutated phenotypes, the G1 phase of the cell cycle is greatly lengthened, impairing normal proliferation. The C terminal region of caprin-1 contains RGG motifs which are characteristic of RNA binding domains. It is possible that caprin-1 functions through an RNA binding mechanism.
Pfam PF00069: Protein kinase domain (domain)
This entry represents the protein kinase domain containing the catalytic function of protein kinases . This domain is found in serine/threonine-protein kinases, tyrosine-protein kinases and dual specificity protein kinases.
Eukaryotic protein kinases  are enzymes that belong to a very extensive family of proteins which share a conserved catalytic core common with both serine/threonine and tyrosine protein kinases. There are a number of conserved regions in the catalytic domain of protein kinases. In the N-terminal extremity of the catalytic domain there is a glycine-rich stretch of residues in the vicinity of a lysine residue, which has been shown to be involved in ATP binding. In the central part of the catalytic domain there is a conserved aspartic acid residue which is important for the catalytic activity of the enzyme .
Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity :


 * Serine/threonine-protein kinases
 * Tyrosine-protein kinases
 * Dual specificity protein kinases (e.g. MEK -phosphorylates both Thr and Tyr on target proteins)


Protein kinase function is evolutionarily conserved from Escherichia coli to human . Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation . Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved , leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases .
Wikipedia: The protein kinase domain is a structurally conserved protein domain containing the catalytic function of protein kinases. Protein kinases are a group of enzymes that move a phosphate group onto proteins, in a process called phosphorylation. This functions as an on/off switch for many cellular processes, including metabolism, transcription, cell cycle progression, cytoskeletal rearrangement and cell movement, apoptosis, and differentiation. They also function in embryonic development, physiological responses, and in the nervous and immune system. Abnormal phosphorylation causes many human diseases, including cancer, and drugs that affect phosphorylation can treat those diseases.
Pfam PF03475: YiiM-like, 3-alpha helix domain (domain)
This small triple helical domain has been predicted to assume a topology similar to helix-turn-helix domains. These domains are found at the C-terminus of proteins related to [swissprot:P32157].
Pfam PF04869: Uso1 / p115 like vesicle tethering protein, head region (repeat)
Also known as General vesicular transport factor, Transcytosis associated protein (TAP) and Vesicle docking protein, this myosin-shaped molecule consists of an N-terminal globular head region, a coiled-coil tail which mediates dimerisation, and a short C-terminal acidic region.  p115 tethers COP1 vesicles to the Golgi by binding the coiled coil proteins giantin (on the vesicles) and GM130 (on the Golgi), via its C-terminal acidic region.  It is required for intercisternal transport in the golgi stack.  This family consists of part of the head region. The head region is highly conserved, but its function is unknown.  It does not seem to be essential for vesicle tethering.  The N-terminal part of the head region, not within this family, contains context-detected Armadillo/beta-catenin-like repeats ([pfam:PF00514]).
Pfam PF13197: Protein of unknown function (DUF4013) (family)
This is a family of uncharacterised proteins that is found in archaea and bacteria.
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 PF17168: Domain of unknown function (DUF5127) (family)
This domain is found towards the N terminus of Glutaminase A (GtaA), an enzyme from Aspergillus that catalyses the hydrolysis of glutamine to glutamic acid and plays a key role in nitrogen metabolism . It was previously known as DUF5127. Members of this group of proteins are mainly found in fungi and bacteria.
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 PF14375: Cysteine-rich CWC (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 74 and 102 amino acids in length. It contains eight conserved cysteines, including a conserved CWC sequence motif.
Pfam PF12937: F-box-like (domain)
This is an F-box-like family.
Pfam PF18578: Rubisco accumulation factor 1 alpha helical domain (domain)
This is the N-terminal alpha helical domain found in Rubisco accumulation factor1 (Raf1). Raf1 from Arabidopsis thaliana consists of an N-terminal alpha-domain, a flexible linker segment and a C-terminal beta-sheet domain that mediates dimerization. The alpha-domains mediate the majority of functionally important contacts with RbcL (Rubisco large subunits) by bracketing each RbcL dimer at the top and bottom. The alpha-domain alone is essentially inactive.
Pfam PF14924: Microtubule associated protein 10, N-terminal domain (domain)
This domain is found at the N-terminal of MAP10 (Microtubule associated protein 10, also known as MTR120/KIAA1383) from mammals. There are two completely conserved G residues that may be functionally important. It adopts a C2-like fold. MAP10 localises to stabilised MTs during interphase and to the mitotic apparatus during mitosis. It may promote microtubule stability and ensures normal progress of cytokinesis.
Pfam PF04970: Lecithin retinol acyltransferase (domain)
The full-length members of this family, eg [swissprot:P53816], are representatives of a novel class II tumour-suppressor family, designated as H-REV107-like. This domain is the catalytic N-terminal proline-rich region of the protein. The downstream region is a putative C-terminal transmembrane domain which is found to be crucial for cellular localisation, but not necessary for the enzyme activity.  H-REV107-like proteins are homologous to lecithin retinol acyltransferase (LRAT), an enzyme that catalyses the transfer of the sn-1 acyl group of phosphatidylcholine to all-trans-retinol and forming a retinyl ester.
Pfam PF01060: Transthyretin-like family (family)
TTR-52 was called family 2 in, and has weak similarity to transthyretin (formerly called pre-albumin) which transports thyroid hormones. The specific function of this protein is as a bridging molecule in apoptosis cross-linking dying cells to phagocytes. TTR-52 bridges by cross-linking surface-exposed phosphatidylserine (PtdSer) on apoptotic cells to the CED-1 receptor, a transmembrane receptor, on phagocytes. TTR-52 has an open beta-barrel-like structure.
Pfam PF04998: RNA polymerase Rpb1, domain 5 (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).  This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound.
Pfam PF09446: VMA21-like domain (domain)
This presumed short domain appears to contain two potential transmembrane helices. VMA21 is localised in the ER where it is needed as an accessory factor for assembly of the V0 component of the vacuolar ATPase.
Pfam PF06312: Neurexophilin (family)
This family consists of mammalian neurexophilin proteins. Mammalian brains contain four different neurexophilin proteins. Neurexophilins form a family of related glycoproteins that are proteolytically processed after synthesis and bind to alpha-neurexins. The structure and characteristics of neurexophilins indicate that they function as neuropeptides that may signal via alpha-neurexins.
Pfam PF13052: Protein of unknown function (DUF3913) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length.
Pfam PF03150: Di-haem cytochrome c peroxidase (family)
This is a family of distinct cytochrome c peroxidases (CCPs) that contain two haem groups. Similar to other cytochrome c peroxidases, they reduce hydrogen peroxide to water using c-type haem as an oxidisable substrate. However, since they possess two, instead of one, haem prosthetic groups, bacterial CCPs reduce hydrogen peroxide without the need to generate semi-stable free radicals. The two haem groups have significantly different redox potentials. The high potential (+320 mV) haem feeds electrons from electron shuttle proteins to the low potential (-330 mV) haem, where peroxide is reduced (indeed, the low potential site is known as the peroxidatic site). The CCP protein itself is structured into two domains, each containing one c-type haem group, with a calcium-binding site at the domain interface. This family also includes MauG proteins, whose similarity to di-haem CCP was previously recognised.
Wikipedia: In molecular biology, the di-haem cytochrome c peroxidase family is a group of distinct cytochrome c peroxidases (CCPs) that contain two haem groups. Similar to other cytochrome c peroxidases, they reduce hydrogen peroxide to water using c-type haem as an oxidizable substrate. However, since they possess two, instead of one, haem prosthetic groups, this family of bacterial CCPs reduce hydrogen peroxide without the need to generate semi-stable free radicals. The two haem groups have significantly different redox potentials. The high potential haem feeds electrons from electron shuttle proteins to the low potential haem, where peroxide is reduced. The CCP protein itself is structured into two domains, each containing one c-type haem group, with a calcium-binding site at the domain interface. This family also includes MauG proteins, whose similarity to di-haem CCP was previously recognised.
Pfam PF04655: Aminoglycoside/hydroxyurea antibiotic resistance kinase (family)
The aminoglycoside phosphotransferases achieve inactivation of their antibiotic substrates by phosphorylation utilising ATP. Likewise hydroxyurea is inactivated by phosphorylation of the hydroxy group in the hydroxylamine moiety.
Pfam PF22196: HdrB-like C-terminal domain (domain)
This entry represents a domain found at the C-terminal end of poorly characterised proteins similar to HdrB from Helicobacter sp.
Pfam PF10979: Protein of unknown function (DUF2786) (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 PF22943: Putative helix-turn-helix domain (domain)
This entry represents a putative helix-turn-helix domain that may be involved in DNA binding.
Pfam PF14501: GHKL domain (domain)
This family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90.
Wikipedia: The GHKL domain is an evolutionary conserved protein domain. It is an ATPase domain found in several ATP-binding proteins such as histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins.
Pfam PF12131: Protein of unknown function (DUF3586) (family)
This domain is found in eukaryotes. This domain is about 80 amino acids in length and is found associated with [pfam:PF08246], and [pfam:PF00112].
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 PF25048: TEP-1 C-terminal beta-propeller (repeat)
This entry represents the beta-propeller found at the C-terminal of Telomerase protein component 1 (TEP1), a component of the telomerase ribonucleoprotein complex that is essential for the replication of chromosome termini. It is also a component of the ribonucleoprotein vaults particle, a multi-subunit structure involved in nucleo-cytoplasmic transport.
Pfam PF08403: Amino acid permease N-terminal (family)
This domain is found to the N-terminus of the amino acid permease domain ([pfam:PF00324]) in metazoan Na-K-Cl cotransporters.
Pfam PF02076: Pheromone A receptor (family)
G protein-coupled receptors (GPCRs) constitute a vast protein family that encompasses a wide range of functions, including various autocrine, paracrine and endocrine processes. They show considerable diversity at the sequence level, on the basis of which they can be separated into distinct groups . The term clan can be used to describe the GPCRs, as they embrace a group of families for which there are indications of evolutionary relationship, but between which there is no statistically significant similarity in sequence . The currently known clan members include rhodopsin-like GPCRs (Class A, GPCRA), secretin-like GPCRs (Class B, GPCRB), metabotropic glutamate receptor family (Class C, GPCRC), fungal mating pheromone receptors (Class D, GPCRD), cAMP receptors (Class E, GPCRE) and frizzled/smoothened (Class F, GPCRF) . GPCRs are major drug targets, and are consequently the subject of considerable research interest. It has been reported that the repertoire of GPCRs for endogenous ligands consists of approximately 400 receptors in humans and mice . Most GPCRs are identified on the basis of their DNA sequences, rather than the ligand they bind, those that are unmatched to known natural ligands are designated by as orphan GPCRs, or unclassified GPCRs .
GPCR Fungal pheromone mating factor receptors form a distinct family of G-protein-coupled receptors, and are also known as Class D GPCRs.

The Fungal pheromone mating factor receptors STE2 and STE3 are integral membrane proteins that may be involved in the response to mating factors on the cell membrane . The amino acid sequences of both receptors contain high proportions of hydrophobic residues grouped into 7 domains,in a manner reminiscent of the rhodopsins and other receptors believed tointeract with G-proteins. However, while a similar 3D framework has been proposed to account for this, there is no significant sequence similarity either between STE2 and STE3, or between these and the rhodopsin-type family: the receptors thereofore bear their own unique '7TM' signatures which is why they have been given their own GPCR group: Class D Fungal mating pheromone receptors.
This entry represents the STE3-type family of fungal pheromone mating factor receptors. The STE3 gene of Saccharomyces cerevisiae (Baker's yeast) is the cell-surface receptor that binds the 13-residue lipopeptide a-factor. Several related fungal pheromone receptor sequences are known: these include pheromone B alpha 1 and B alpha 3, and pheromone B beta 1 receptors from Schizophyllum commune; pheromone receptor 1 from Ustilago hordei; and pheromone receptors 1 and 2 from Ustilago maydis. Members of the family share about 20% sequence identity.
Pfam PF24472: KDM8-like, N-terminal ARM repeats (repeat)
This region of armadillo (ARM)-like repeats is found at the N-terminal end of human Bifunctional peptidase and arginyl -hydroxylase JMJD5 (also known as KDM8) and similar animal proteins. KDM8 functions both as an endopeptidase and 2-oxoglutarate-dependent monooxygenase.
Pfam PF14990: Domain of unknown function (DUF4516) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 56 and 69 amino acids in length.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF07677: A-macroglobulin receptor binding domain (domain)
This family includes the receptor binding domain region of the alpha-2-macroglobulin family.
Wikipedia: α2-Macroglobulin (α2M) or alpha-2-macroglobulin is a large plasma protein found in the blood. It is mainly produced by the liver, and also locally synthesized by macrophages, fibroblasts, and adrenocortical cells. In humans it is encoded by the A2M gene.