SII-SWORD/CoKE huggingface dataset:
Pfam PF12767: Transcriptional regulator of RNA polII, SAGA, subunit (family)
The yeast SAGA complex is a multifunctional coactivator that regulates transcription by RNA polymerase II. It is formed of five major modular subunits and shows a high degree of structural conservation to human TFTC and STAGA. The complex can also be conceived of as consisting of two histone-fold-containing core subunits, and this family is one of these. As a family it is likely to carry binding regions for interactions with a number of the other components of the complex.
Pfam PF00629: MAM domain, meprin/A5/mu (domain)
An extracellular domain found in many receptors. The MAM domain along with the associated Ig domain in type IIB receptor protein tyrosine phosphatases forms a structural unit (termed MIg) with a seamless interdomain interface. It plays a major role in homodimerisation of the phosphatase ectoprotein and in cell adhesion. MAM is a beta-sandwich consisting of two five-stranded antiparallel beta-sheets rotated away from each other by approx 25 degrees, and plays a similar role in meprin metalloproteinases.
Wikipedia: MAM domain is an evolutionary conserved protein domain. It is an extracellular domain found in many receptors.
Pfam PF05262: Borrelia P83/100 protein (family)
This family consists of several Borrelia P83/P100 antigen proteins.
Pfam PF00258: Flavodoxin (domain)
This domain is found in a number of proteins including flavodoxin and nitric-oxide synthase. Flavodoxins are electron-transfer proteins that function in various electron transport systems. They bind one FMN molecule, which serves as a redox-active prosthetic group  and are functionally interchangeable with ferredoxins. They have been isolated from prokaryotes, cyanobacteria, and some eukaryotic algae. Nitric oxide synthase (1.14.13.39) produces nitric oxide from L-arginine and NADPH. Nitric oxide acts as a messenger molecule in the body.
The flavodoxin-like domain is an around 170-residue domain with a flavin mononucleotide (FMN)-binding site. It is involved in electron transfer reactions .

Structure analyses of several flavodoxin-like domains have shown that it is a wound Î±-Î²-Î± fold with a central 5-stranded parallel hydrophobic Î²-sheet flanked on either side by amphipathic Î±-helices . The FMN is positioned at the tip of the C-terminal side of the Î²-sheet . The fold correlates with a highly conserved, repetitive sequence pattern in which hydrophobic residues cluster in Î²-strands and have a 3-4-residue periodicity in Î±-helices .
Pfam PF16484: Carnitine O-palmitoyltransferase N-terminus (domain)
This domain is found at the N-terminus of carnitine O-palmitoyltransferases. It functions as a regulatory domain and is linked to the catalytic domain ([pfam:PF00755]) via two transmembrane regions.
Pfam PF14771: Domain of unknown function (DUF4476) (family)
This domain is functionally uncharacterised. It is found in eukaryotic and bacterial sequences.
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 PF07714: Protein tyrosine and serine/threonine kinase (domain)
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, and dual specificity protein kinases (e.g.  MEK - phosphorylates both Thr and Tyr on target proteins). This  entry represents the catalytic domain found in a number of serine/threonine- and tyrosine-protein kinases. It does not include  the catalytic domain of dual specificity kinases.
Wikipedia: Receptor tyrosine kinases (RTKs) are the high-affinity cell surface receptors for many polypeptide growth factors, cytokines, and hormones. Of the 90 unique tyrosine kinase genes identified in the human genome, 58 encode receptor tyrosine kinase proteins.
Receptor tyrosine kinases have been shown not only to be key regulators of normal cellular processes but also to have a critical role in the development and progression of many types of cancer. Mutations in receptor tyrosine kinases lead to activation of a series of signalling cascades which have numerous effects on protein expression. The receptors are generally activated by dimerization and substrate presentation. Receptor tyrosine kinases are part of the larger family of protein tyrosine kinases, encompassing the receptor tyrosine kinase proteins which contain a transmembrane domain, as well as the non-receptor tyrosine kinases which do not possess transmembrane domains.
Pfam PF08094: Conotoxin TVIIA/GS family (family)
This family consists of conotoxins isolated from the venom  of cone snail Conus tulipa and Conus geographus. Conotoxin  TVIIA, isolated from Conus tulipa displays little sequence  homology with other well-characterised pharmacological  classes of peptides, but displays similarity with conotoxin GS, a peptide from Conus geographus. Both these peptides  block skeletal muscle sodium channels and also share  several biochemical features and represent a distinct subgroup  of the four-loop conotoxins.
Pfam PF03829: PTS system glucitol/sorbitol-specific IIA component (family)
This entry consists of glucitol-specific transporters, and occur both in Gram-negative and Gram-positive bacteria. The system in Escherichia coli consists of a IIA protein and a IIBC protein. This family is specific for the IIA component.
Pfam PF05181: XPA protein C-terminus (domain)
Xeroderma pigmentosum (XP)  is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30kDa nuclear protein called XPA (or XPAC) . The sequence of the XPA protein is conserved from higher eukaryotes  to yeast (gene RAD14) . XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section.
This entry represents the uncharacterised C-terminal domain of the XPA protein.
Pfam PF05908: Poly-gamma-glutamate hydrolase (domain)
This family consists of a number of bacterial and phage proteins that function as gamma-PGA hydrolase enzymes. Structurally the protein in this family adopted an open alpha/beta mixed core structure with a seven-stranded parallel/anti-parallel beta-sheet. This structure shows similarity to mammalian carboxypeptidase A and related enzymes.
Pfam PF02284: Cytochrome c oxidase subunit Va (domain)
Cytochrome c oxidase, a 13 sub-unit complex, [ec:1.9.3.1] is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of cytochrome c oxidase subunit Va.
Pfam PF12941: HCV NS5a protein C-terminal region (family)
This is a family of proteins found in the hepatitis C virus. This family contains the C-terminal region of the NS5A protein. CC The molecular function of the non-structural 5a protein is uncertain.  The NS5a protein is phosphorylated when expressed in mammalian cells.  It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR, [swissprot:P19525].
Wikipedia: NS5 may refer to:
Pfam PF05734: Herpesvirus protein of unknown function (DUF832) (family)
This family consists of several herpesvirus 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 PF01462: Leucine rich repeat N-terminal domain (family)
Leucine Rich Repeats [pfam:PF00560] are short sequence motifs present in a number of proteins with diverse functions and cellular locations. Leucine Rich Repeats are often flanked by cysteine rich domains. This domain is often found at the N-terminus of tandem leucine rich repeats.
Wikipedia: A leucine-rich repeat (LRR) is a protein structural motif that forms an α/β horseshoe fold. It is composed of repeating 20–30 amino acid stretches that are unusually rich in the hydrophobic amino acid leucine. These tandem repeats commonly fold together to form a solenoid protein domain, termed leucine-rich repeat domain. Typically, each repeat unit has beta strand-turn-alpha helix structure, and the assembled domain, composed of many such repeats, has a horseshoe shape with an interior parallel beta sheet and an exterior array of helices. One face of the beta sheet and one side of the helix array are exposed to solvent and are therefore dominated by hydrophilic residues. The region between the helices and sheets is the protein's hydrophobic core and is tightly sterically packed with leucine residues.
Pfam PF07523: Bacterial Ig-like domain (group 3) (domain)
This family consists of bacterial domains with an Ig-like fold. Members of this family are found in a variety of bacterial surface proteins.
Pfam PF11284: Protein of unknown function (DUF3085) (family)
This family of proteins with unknown function appears to be restricted to 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 PF14725: Domain of unknown function (DUF4466) (family)
This is a domain of unknown function found in proteins from bacteroidetes.
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 PF13589: Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase (domain)
This family represents, additionally, 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 PF04142: Nucleotide-sugar transporter (family)
This family of membrane proteins transport nucleotide sugars from the cytoplasm into Golgi vesicles.  [swissprot:P78382] transports CMP-sialic acid, [swissprot:P78381] transports UDP-galactose and [swissprot:Q9Y2D2] transports UDP-GlcNAc.
Pfam PF01686: Adenovirus penton base protein (family)
This family consists of various adenovirus penton base proteins, from both the Mastadenoviradae having mammalian hosts and the Aviadenoviradae having avian hosts. The penton base is a major structural protein forming part of the penton which consists of a base and a fibre, the pentons hold a morphologically prominent position at the vertex capsomer in the adenovirus particle. In mammalian adenovirus there is only one tail on each base where as in avian adenovirus there are two.
Pfam PF03532: OMS28 porin (family)
The outer membrane-spanning (Oms) proteins of Borrelia burgdorferi have been isolated and their porin activities characterised; 0.6-nS porin activity was found to reside in a 28kDa protein, designated Oms28 . The gene sequence of oms28 was found to encode a 257-amino-acid precursor protein with a putative 24-amino-acid leader peptidase I signal sequence . The Oms28 protein partly fractionated to the outer membrane, and was characterised by an average single-channel conductance of 1.1 nS in a planar lipid bilayer assay, confirming Oms28 to be a porin .
Pfam PF08988: Type III secretion system, cytoplasmic E component of needle (family)
T3SS_needle_E is a family of proteins from the operon that builds and controls the needle of the injection system of type III secretion. The YscE protein, produced by the pathogen Yersinia, assumes a secondary structure composed of two anti-parallel alpha-helices separated by a flexible loop. The family is cytoplasmic and may help to stabilise and prevent early polymerisation of the needle-protein F.
Wikipedia: The type III secretion system is one of the bacterial secretion systems used by bacteria to secrete their effector proteins into the host's cells to promote virulence and colonisation. While the type III secretion system has been widely regarded as equivalent to the injectisome, many argue that the injectisome is only part of the type III secretion system, which also include structures like the flagellar export apparatus. The T3SS is a needle-like protein complex found in several species of pathogenic gram-negative bacteria.
Pfam PF05742: Transport and Golgi organisation 2 (family)
In eukaryotes this family is predicted to play a role in protein secretion and Golgi organisation. In plants this family includes [swissprot:A9X6Y0], which is involved in water permeability in the cuticles of fruit. [swissprot:P54797] has been found to be expressed during early embryogenesis in mice. This protein contains a conserved NRDE motif. This gene has been characterised in Drosophila melanogaster and named as transport and Golgi organisation 2, hence the name Tango2.
Pfam PF21747: YpoC-like protein (domain)
This family of proteins contains the B. subtilis YpoC protein [swissprot:P39789]. It is largely confined to bacilli 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 PF09887: Uncharacterized protein conserved in archaea (DUF2114) (domain)
This domain, found in various hypothetical archaeal 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 PF07185: Protein of unknown function (DUF1404) (family)
This family consists of several archaeal proteins of around 180 residues in length. Members of this family seem to be found exclusively in Sulfolobus tokodaii and Sulfolobus solfataricus. 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 PF20507: Family of unknown function (DUF6733) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 240 and 250 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 PF17758: Proteasomal ATPase OB N-terminal domain (domain)
This is N-terminal interdomain (ID), oligonucleotide binding (OB) domain of proteasomal ATPase.
Pfam PF06955: Xyloglucan endo-transglycosylase (XET) C-terminus (family)
This family represents the C-terminus (approximately 60 residues) of plant xyloglucan endo-transglycosylase (XET). Xyloglucan is the predominant hemicellulose in the cell walls of most dicotyledons. With cellulose, it forms a network that strengthens the cell wall. XET catalyses the splitting of xyloglucan chains and the linking of the newly generated reducing end to the non-reducing end of another xyloglucan chain, thereby loosening the cell wall. Note that all family members contain the [pfam:PF00722] domain.
Wikipedia: In molecular biology, the xyloglucan endo-transglycosylase (XET) is an enzyme that is involved in the metabolism of xyloglucan, which is a component of plant cell walls. This enzyme is part of glycoside hydrolase family 16.
Pfam PF00082: Subtilase family (domain)
Subtilases are a family of serine proteases. They appear to have independently and convergently evolved an Asp/Ser/His catalytic triad, like that found in the trypsin serine proteases (see [pfam:PF00089]). Structure is an alpha/beta fold containing a 7-stranded parallel beta sheet, order 2314567.
Wikipedia: The sedolisin family of peptidases are a family of serine proteases structurally related to the subtilisin (S8) family. Well-known members of this family include sedolisin ("pseudomonalisin") found in Pseudomonas bacteria, xanthomonalisin ("sedolisin-B"), physarolisin as well as animal tripeptidyl peptidase I. It is also known as sedolysin or  serine-carboxyl peptidase. This group of enzymes contains a variation on the catalytic triad: unlike S8 which uses Ser-His-Asp, this group runs on Ser-Glu-Asp, with an additional acidic residue Asp in the oxyanion hole.
Pfam PF14083: PGDYG protein (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 150 amino acids in length. There is a conserved PGDYG motif.
Pfam PF11276: Protein of unknown function (DUF3078) (family)
This bacterial 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 PF23287: Transcription elongation factor SPT5, seventh KOW domain (domain)
This entry includes Transcription elongation factor SPT5, a component of the elongation factor DRB-sensitivity inducing factor (DSIF) that plays multiple roles during transcription. SPT5 is a multidomain protein consisting of an N-terminal NusG domain ([pfam:PF03439]), tandem of KOW domains and and a mobile C-terminal-repeat region. The KOW domains differ in number between yeast, which has five, and animals, which have seven. This entry represents the seventh KOW domain of Spt5 from animals, which is located at the very C-terminal of the sequences. The KOW domains of these proteins play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and they are also involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.
Pfam PF02690: Na+/Pi-cotransporter (family)
This is a family of mainly mammalian type II renal Na+/Pi-cotransporters with other related sequences from lower eukaryotes and bacteria some of  which are also Na+/Pi-cotransporters.  In the kidney the type II renal Na+/Pi-cotransporters protein allows re-absorption of filtered Pi in the  proximal tubule.
Pfam PF02686: Glu-tRNAGln amidotransferase C subunit (family)
This is a family of Glu-tRNAGln amidotransferase C subunits. The Glu-tRNA Gln amidotransferase enzyme itself is an important translational fidelity mechanism replacing incorrectly charged Glu-tRNAGln with the correct Gln-tRANGln via transmidation of the misacylated Glu-tRNAGln. This activity supplements the lack  of glutaminyl-tRNA synthetase activity in gram-positive eubacterteria, cyanobacteria, Archaea, and organelles. This entry includes the C subunit of the bacterial/archaeal aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferases and eukaryotic Glu-tRNAGln amidotransferases (GatC).
Pfam PF20318: Family of unknown function (DUF6613) (family)
This family of proteins is functionally uncharacterised. However, the contain an N-terminal [pfam:PF07963] suggesting these may be pilin proteins. This family of proteins is found in bacteria. Proteins in this family are typically between 203 and 237 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 PF24006: SCAP N-terminal (domain)
This entry represents a domain found at the N-terminal of SCAP (Sterol regulatory element-binding protein cleavage-activating protein). SCAP is a key player in the sterol regulatory element-binding protein (SREBP) pathway that controls the cellular homeostasis of sterol. It consists of a luminal domain, eight transmembrane segments from which TM2-TM6 corresponds to the SSD ([pfam:PF12349]) and a WD40 domain at the C-terminal. This entry represents the luminal domain of SCAP, which binds cholesterol.
Pfam PF05973: Phage derived protein Gp49-like (DUF891) (domain)
This family consists of hypothetical bacterial proteins of unknown function as well as phage Gp49 proteins.
Pfam PF01011: PQQ enzyme repeat (repeat)
The family represent a single repeat of a beta propeller. This propeller has been found in several enzymes which utilise pyrrolo-quinoline quinone as a prosthetic group.