SII-SWORD/CoKE huggingface dataset:
Pfam PF10187: FAM192A/Fyv6, N-terminal domain (domain)
This is a the N-terminal domain of the mammalian PIP30/FAM192A protein and the fungal Fyv6 protein. PIP30/FAM192A acts as a regulator PA28-gamma, a nuclear activator of the 20S proteasome. PIP30 favors PA28-gamma interaction with the 20S proteasome while inhibiting its association with coilin, a central component of nuclear Cajal bodies. Fyv6 is involved in telomere length regulation and required for survival upon exposure to K1 killer toxin. It promotes fully efficient non-homologous end-joining (NHEJ) by a mechanism activated in postdiauxic/stationary phase.
Pfam PF14722: Ki-ras-induced actin-interacting protein-IP3R-interacting domain (family)
This family includes the N-terminus of the actin-interacting protein sperm-specific antigen 2, or KRAP (Ki-ras-induced actin-interacting protein).  This region is found to be the residues that interact with inositol 1,4,5-trisphosphate receptor (IP3R). KRAP was first localised as a membrane-bound form with extracellular regions suggesting it might be involved in the regulation of filamentous actin and signals from the outside of the cells. It has now been shown to be critical for the proper subcellular localisation and function of IP3R. Inositol 1,4,5-trisphosphate receptor functions as the Ca2+ release channel on specialised endoplasmic reticulum membranes, so the subcellular localisation of IP3R is crucial for its proper function.
Pfam PF00003: 7 transmembrane sweet-taste receptor of 3 GCPR (domain)
This is a domain of seven transmembrane regions that forms the C-terminus of some subclass 3 G-coupled-protein receptors. It is often associated with a downstream cysteine-rich linker domain, NCD3G [pfam:PF07562], which is the human sweet-taste receptor, and the N-terminal domain, ANF_receptor [pfam:PF01094]. The seven TM regions assemble in such a way as to produce a docking pocket into which such molecules as cyclamate and lactisole have been found to bind and consequently confer the taste of sweetness.
Wikipedia: The class C G-protein-coupled receptors are a class of G-protein coupled receptors that include the metabotropic glutamate receptors and several additional receptors.
Pfam PF00007: Cystine-knot domain (domain)
The family comprises glycoprotein hormones and the C-terminal domain of various extracellular proteins.  It is believed to be involved in disulfide-linked dimerisation.
Wikipedia: A cystine knot is a protein structural motif containing three disulfide bridges. The sections of polypeptide that occur between two of them form a loop through which a third disulfide bond passes, forming a rotaxane substructure. The cystine knot motif stabilizes protein structure and is conserved in proteins across various species. There are three types of cystine knot, which differ in the topology of the disulfide bonds:The growth factor cystine knot (GFCK)
inhibitor cystine knot (ICK) common in spider and snail toxins
Cyclic Cystine Knot, or cyclotide
Pfam PF10845: Protein of unknown function (DUF2576) (family)
The function of this viral family of 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 PF15377: Domain of unknown function (DUF4604) (family)
This protein family is a domain of unknown function, which is found in eukaryotes. Proteins in this family are typically between 141 and 174 amino acids in length and contain a conserved LSF 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 PF04009: Protein of unknown function (DUF356) (family)
Members of this family are around 120 amino acids in length and are found in some archaebacteria.  The function of this family is unknown.  However it contains a conserved motif IHPPAH that may be involved in its 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 PF03896: Translocon-associated protein (TRAP), alpha subunit (family)
The alpha-subunit of the TRAP complex (TRAP alpha also known as signal sequence receptor 1/alpha subunit, SSRA)) is a single-spanning membrane protein of the endoplasmic reticulum (ER) which is found in proximity of nascent polypeptide chains translocating across the membrane. TRAP complex consists of four subunits (alpha, beta, gamma, delta) and localises in the ER membrane. It associates with the Sec61 translocon as a heterotetramer. It also interacts with palmitoylated calnexin (CALX), the interaction is required for efficient folding of glycosylated proteins. TRAP complex may also be involved in endoplasmic reticulum-associated degradation. TRAP-alpha plays a critical role in the biosynthesis of insulin, being involved in preproinsulin translocation and proinsulin trafficking which may contribute to the pathogenesis of type 2 diabetes. This entry also includes IRC22 from fungi, which show sequence and structural similarities with TRAP-alpha. The function of IRC22 is not yet known.
Pfam PF16386: Domain of unknown function (family)
This family around 100 residues locates in the N-terminal of some uncharacterized proteins and glucuronyl hydrolases in various Bacteroides species. The function of this family remains unknown.
Pfam PF16946: OMPG-porin 1 family (domain)
Porin_OmpG_1_2 is a family of putative porins of the OmpG-type. these are channels without solute specificity.
Pfam PF06378: Protein of unknown function (DUF1071) (family)
This family consists of several hypothetical bacterial and phage 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 PF09638: Ph1570 protein (domain)
This is a hypothetical protein from Pyroccous horikoshii of unknown function.       It contains six alpha helices and eight beta strands and is thought to be monomeric.
Pfam PF14041: LppP/LprE lipoprotein (family)
The family includes putative lipoproteins LppP and LprE from species of Mycobacterium. LppP is required for optimal growth of M. tuberculosis.
Pfam PF04822: Takusan (family)
This domain is named takusan, which is a Japanese word meaning 'many'. Members of this family regulate synaptic activity.
Pfam PF10091: Putative glucoamylase (repeat)
The structure of UniProt:Q5LIB7 has an alpha/alpha toroid fold and is similar structurally to a number of glucoamylases. Most of these structural homologues are glucoamylases, involved in breaking down complex sugars (e.g. starch). The biologically relevant state is likely to be monomeric. The putative active site is located at the centre of the toroid with a well defined large cavity.
Pfam PF08733: PalH/RIM21 (family)
PalH (also known as RIM21) is a transmembrane protein required for proteolytic cleavage of Rim101/PacC transcription factors which are activated by C terminal proteolytic processing. Rim101/PacC family proteins play a key role in pH-dependent responses and PalH has been implicated as a pH sensor.
Pfam PF21185: RecBCD enzyme subunit RecD, N-terminal domain (domain)
This domain is found in RecBCD enzyme subunit RecD from Escherichia coli and in similar proteins mostly found in Gammaproteobacteria. RecD is a 5'-3' helicase that comprises three domains. This entry represents the N-terminal domain of RecD, which forms the principal interface between RecD and domain 2B of RecC and leads to the conformational change in RecD that has significant effects on the conformation of the RecC subunit.
Pfam PF08585: RMI1, N-terminal OB-fold domain (domain)
This is the OB-fold domain found at the N-terminal of RecQ-mediated genome instability protein 1 (RMI1), which forms a stable complex with Bloom syndrome protein BLM and DNA topoisomerase 3-alpha.
Pfam PF09019: EcoRII C terminal (domain)
The C-terminal catalytic domain of the Restriction Endonuclease EcoRII has a restriction endonuclease-like fold with a central five-stranded mixed beta-sheet surrounded on both sides by alpha-helices. It cleaves DNA specifically at single 5' CCWGG sites.
Wikipedia: Restriction endonuclease (REase) EcoRII is an enzyme of restriction modification system (RM) naturally found in Escherichia coli, a Gram-negative bacteria. Its molecular mass is 45.2 kDa, being composed of 402 amino acids.
Pfam PF13087: AAA domain (domain)
This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
Wikipedia: AAA proteins are a large group of protein family sharing a common conserved module of approximately 230 amino acid residues. This is a large, functionally diverse protein family belonging to the AAA+ protein superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent remodeling or translocation of macromolecules.
Pfam PF01202: Shikimate kinase (domain)
Shikimate kinase (2.7.1.71) catalyses the fifth step in the biosynthesis of aromatic amino acids from chorismate (the so-called shikimate pathway) . The enzyme catalyses the following reaction:

ATP + shikimate = ADP + shikimate-3-phosphate

The protein is found in bacteria (gene aroK or aroL), plants and fungi (where it is part of a multifunctional enzyme that catalyses five consecutive steps in this pathway). In 1994, the 3D structure of shikimate kinase was predicted to be very close to that of adenylate kinase, suggesting a functional similarity as well as an evolutionary relationship . This prediction has since been confirmed experimentally. The protein is reported to possess an Î±/Î² fold, consisting of a central sheet of five parallel Î²-strands flanked by Î±-helices. Such a topology is very similar to that of adenylate kinase .

The N terminus of threonine synthase-like 1 from metazoan shares protein sequence similarity with shikimate kinase and is included in this entry. However, their functions may be different.
Wikipedia: Shikimate kinase (EC 2.7.1.71) is an enzyme that catalyzes the ATP-dependent phosphorylation of shikimate to form shikimate 3-phosphate. This reaction is the fifth step of the shikimate pathway, which is used by plants and bacteria to synthesize the common precursor of aromatic amino acids and secondary metabolites. The systematic name of this enzyme class is ATP:shikimate 3-phosphotransferase. Other names in common use include shikimate kinase (phosphorylating), and shikimate kinase II.
Pfam PF17033: Carboxypeptidase controlling helical cell shape catalytic (domain)
This is the peptidase domain of a D,L-carboxypeptidase.  The active site residues are Arg86, Glu222 and the metal ligands, in the peptidase domain, are Gln46, Glu49 and His128 in UniProtKB:O25708.  The protein binds many zinc ions and a calcium ion and there are other metal binding sites.  The catalytic activity is the release of m-Dpm from the peptide muramyl-Ala-gamma-D-Glu-m-Dpm; this is probably the precursor of the cell wall cross-linking peptide.
Pfam PF20758: 2B protein soluble domain (domain)
This domain is found in the membrane-targeting protein 2B from Human hepatitis A virus. This protein, which is the soluble region of the virus, plays a key role in the rearrangement of host intracellular membranes, part of the viral infection process of this picornavirus. The soluble domain of this protein (this entry) is organized into two subdomains: the N-terminal adopts a pseudo-beta-barrel shape with five beta strands that fold into a curved antiparallel beta sheet, and two beta strands prolonged by a beta-hairpin; the C-terminal consists of four alpha helices forming an helical bundle. This structure shows great similarity to the beta-barrel domain of enteroviral 2A proteins.
Pfam PF17806: Sarcosine oxidase A3 domain (domain)
This short domain is found in Heterotetrameric Sarcosine Oxidase's alpha A3 domain. This domain binds to FMN in sarcosine oxidase. This domain is related to [pfam:PF04324] but lacks its iron binding cysteine residues.
Pfam PF13187: 4Fe-4S dicluster domain (family)
Ferredoxins are a group of iron-sulphur proteins which mediate electron transfer in a wide variety of metabolic reactions. Ferredoxins can be divided into several subgroups depending upon the physiological nature of the iron-sulphur cluster(s). One of these subgroups are the 4Fe-4S ferredoxins, which are found in bacteria and which are thus often referred as 'bacterial-type' ferredoxins. The structure of these proteins  consists of the duplication of a domain of twenty six amino acid residues; each of these domains contains four cysteine residues that bind to a 4Fe-4S centre.

Several structures of the 4Fe-4S ferredoxin domain have been determined . The clusters consist of two interleaved 4Fe- and 4S-tetrahedra forming a cubane-like structure, in such a way that the four iron occupy the eight corners of a distorted cube. Each 4Fe-4S is attached to the polypeptide chain by four covalent Fe-S bonds involving cysteine residues.

A number of proteins have been found  that include one or more 4Fe-4S binding domains similar to those of bacterial-type ferredoxins.

The pattern of cysteine residues in the iron-sulphur region is sufficient to detect this class of 4Fe-4S binding proteins. This entry represents the whole domain.

Note: In some bacterial ferredoxins, one of the two duplicated domains has lost one or more of the four conserved cysteines. The consequence of such variations is that these domains have either lost their iron-sulphur binding property or bind to a 3Fe-3S centre instead of a 4Fe-4S centre.
Pfam PF24256: Family of unknown function (DUF7457) (family)
This entry represents a small family of uncharacterised phage proteins. This family includes gene 78 from Phage Bxb1.
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 PF02101: Ocular albinism type 1 protein (family)
G-protein coupled receptor 143 (also known as ocular albinism type 1, OA1) is a receptor for tyrosine, L-DOPA and dopamine. After binding to L-DOPA, it stimulates Ca2+ influx into the cytoplasm, increases secretion of the neurotrophic factor SERPINF1 and relocalises beta arrestin at the plasma membrane; this ligand-dependent signaling occurs through a G(q)-mediated pathway in melanocytic cells .
Wikipedia: G-protein coupled receptor 143, also known as Ocular albinism type 1 (OA1) in humans, is a conserved integral membrane protein with seven transmembrane domains and similarities with G protein-coupled receptors (GPCRs) that is expressed in the eye and epidermal melanocytes. This protein encoded by the GPR143 gene, whose variants can lead to Ocular albinism type 1.
Pfam PF05379: Carlavirus endopeptidase (domain)
A peptidase involved in auto-proteolysis of a polyprotein from the plant pathogen blueberry scorch carlavirus (BBScV). Corresponds to Merops family C23.
Pfam PF11502: B-cell lymphoma 9 protein (family)
The Wnt pathway plays a role in embryonic development, stem cell growth and tumorigenesis. BCL9 associates with beta-catenin and Tcf in the nucleus when the Wnt pathway is stimulated leading to the transactivation of Wnt target genes.
Pfam PF12669: FeoB-associated Cys-rich membrane protein (family)
Members of this family typically are small proteins encoded next to FeoB, part of a ferrous iron uptake system. They consist of a highly hydrophobic predicted membrane segment, followed by a short, Cys-rich region, for an average length of less than sixty amino acids. In some cases, member proteins are fusion proteins, with the region described by this family occurring as a C-terminal extension to FeoB.
Pfam PF18561: Endoribonuclease Regnase 1/ ZC3H12 C-terminal domain (domain)
This is the C-terminal domain found in regnase-1, an RNase that directly cleaves mRNAs of inflammatory genes such as IL-6 and IL-12p40, and negatively regulates cellular inflammatory responses. The C-terminal domain is composed of three alpha helices and resembles ubiquitin associated protein 1 in structure.
Pfam PF18956: Family of unknown function (DUF5699) (family)
The function of DUF5699 is not clear.
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 PF09207: Yeast killer toxin (domain)
Members of this family, which are produced by Williopsis fungi, adopt a secondary structure consisting of eight strands in two beta sheets, in a Greek-key topology.
Pfam PF24860: FdhE, C-terminal domain (domain)
This is the C-terminal domain of FdhE from Escherichia coli and similar proteins necessary for formate dehydrogenase activity. This domain is found associated with [pfam:PF04216] and [pfam:PF24859].
Pfam PF00210: Ferritin-like domain (domain)
This family contains ferritins and other ferritin-like proteins such as members of the DPS family and bacterioferritins.
Wikipedia: Ferritin is a universal intracellular and extracellular protein that stores iron and releases it in a controlled fashion. The protein is produced by almost all living organisms, including archaea, bacteria, algae, higher plants, and animals. It is the primary intracellular iron-storage protein in both prokaryotes and eukaryotes, keeping iron in a soluble and non-toxic form. In humans, it acts as a buffer against iron deficiency and iron overload.
Pfam PF06622: SepQ protein (family)
This family consists of several enterobacterial SepQ proteins from Escherichia coli and Citrobacter rodentium. The function of this family is unclear.
Pfam PF14412: A nuclease family of the HNH/ENDO VII superfamily with conserved AHH (family)
AHH is a predicted nuclease of the HNH/ENDO VII superfamily of the  treble clef fold. The name is derived from the conserved motif, AHH. It is found in bacterial polymorphic toxin systems and functions as a toxin module. Like WHH and LHH, the AHH nuclease contains 4  conserved histidines of which, the first one is predicted to bind       a metal-ion and the other three ones are involved in activation of a water molecule for hydrolysis.
Pfam PF14441: OTT_1508-like deaminase (family)
A member of the nucleic acid/nucleotide deaminase superfamily prototyped by Orientia OTT_1508. Members of this family are present in a wide phyletic range of bacteria,including several intracellular parasites and eukaryotes such as fungi, Leishmania,  Selaginella, and some apicomplexa. In bacteria, these deaminases are predicted to function as toxins in bacterial polymorphic toxin  systems. Versions in intracellular bacteria lack immunity proteins and are likely to be deployed against their eukaryotic hosts. Eukaryotic versions are predicted to function as nucleic acid (either DNA or RNA) deaminases. Among eukaryotes, some fungi show  lineage-specific expansions of this family. Many fungal versions are  fused to a distinct N-terminal globular domain. Various fungal  versions are fused to domains involved in chromatin function. Apicomplexan versions are fused to tRNA guanine transglycosylase domain.
Pfam PF13349: Toastrack DUF4097 (repeat)
This an all-beta structure with a twenty-residue repeat with a highly conserved repeating GD, gly-asp, motif that has been described as Toastrack DUF4097, whose function is unknown. It has been suggested to form part of a bacterial adhesin. Toastrack has been transferred from bacteria to certain eukaryotes, such as FAM185A from human and its orthologues in animals and other eukaryotes.
Pfam PF01226: Formate/nitrite transporter (family)
Proteins in this entry belong to the Formate-Nitrite Transporter (FNT) family and includes the nitrite transport protein NirC and formate channel FocA. They have a pentameric architecture with structural similarity to aquaporins and glyceroporins. Proteins in this family transport the structurally related compounds, formate and nitrite.
Wikipedia: The Formate-Nitrite Transporter (FNT) Family belongs to the Major Intrinsic Protein (MIP) Superfamily. FNT family members have been sequenced from Gram-negative and Gram-positive bacteria, archaea, yeast, plants and lower eukaryotes. The prokaryotic proteins of the FNT family probably function in the transport of the structurally related compounds, formate and nitrite.
Pfam PF01522: Polysaccharide deacetylase (family)
This domain is found in polysaccharide deacetylase. This family of polysaccharide deacetylases includes NodB (nodulation protein B from  Rhizobium) which is a chitooligosaccharide deacetylase. It also includes chitin deacetylase from yeast, and endoxylanases which hydrolyses glucosidic bonds in xylan.
Pfam PF17309: Family of unknown function (DUF5356) (family)
This is a family of unknown function found in Chromadorea.
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 PF10992: Epiplasmin protein (family)
This entries covers epiplasmins, a multigene family in Paramecium. They make up a scale structure called the epiplasm under the cell membrane.