SII-SWORD/CoKE huggingface dataset:
Pfam PF10032: Phosphate transport (Pho88) (family)
Members of this family of proteins are involved in regulating inorganic phosphate transport, as well as telomere length regulation and maintenance. Family members such as SND3 (SRP-independent targeting protein 3, encoded by PHO88, also known as YBR106W) is localized to the endoplasmic reticulum (ER). SND3 works together with SND1 and SND2; these proteins function in parallel with the SRP and GET pathways to target a broad range of substrates to the ER. The SND proteins constitute an alternative targeting route to the ER. SND3/PHO88 was first identified as a Saccharomyces cerevisiae protein involved in inorganic phosphate transport. Functional analysis revealed that Loss of SND3 has been shown to affect secretion of the yeast acid phosphatase.
Pfam PF13366: PD-(D/E)XK nuclease superfamily (domain)
Members of this family belong to the PD-(D/E)XK nuclease superfamily
Pfam PF18864: AbiTii (domain)
Alpha + beta domain. Found fused to the N-terminus of the c2405 family of HEPN domains and in few cases to Ymh.
Pfam PF05411: Equine arteritis virus putative proteinase (family)
These proteins are characterised by a region that has been proposed to have peptidase activity involved in viral polyprotein processing in replication.
Pfam PF04194: Programmed cell death protein 2, C-terminal putative domain (domain)
PDCD2 is localized predominantly in the cytosol of cells situated at the opposite pole of the germinal centre from the centroblasts as well as in cells in the mantle zone. It has been shown to interact with BCL6, an evolutionarily conserved Kruppel-type zinc finger protein that functions as a strong transcriptional repressor and is required for germinal centre development. The rat homologue, Rp8, is associated with programmed cell death in thymocytes.
Pfam PF10763: Protein of unknown function (DUF2584) (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 PF18640: LepB N-terminal domain (domain)
Rab GTPases constitute the largest family of small GTP-binding proteins that act as molecular switches in regulating vesicular transport in eukaryotic cells. LepB is a Rab GTPase-activating protein (GAP) effector found in Legionella pneumophila. This entry represents the N-terminal domain which is followed by a GAP domain.
Pfam PF20908: Ubiquitin-fold modifier 1 specific protease 2, N-terminal (domain)
This domain is found at the N-terminal end of the eukaryotic protein Ubiquitin-fold modifier 1 (Ufm1) specific protease 2 (UfSP2). UfSP2 is a cysteine protease which recognises and hydrolyses the peptide bond at the C-terminal Gly residue of the protein Ufm1, a ubiquitin- like modifier. This protein is organised into two domains: the catalytic C-terminal ([pfam:PF07910]) and a N-terminal showing a six- stranded beta-sheet with five helices. This entry represents the most N-terminal beta-strand.
Pfam PF21000: RMI1, N-terminal helical domain (domain)
The N-terminal domain of RecQ-mediated genome instability protein 1 carries an oligo-nucleotide-binding domain or OB-fold, and forms a stable complex with Bloom syndrome protein BLM and DNA topoisomerase 3-alpha. At the very N-terminal, it has a 3-helix bundle, represented in this entry, which protrudes to one side of the structure and makes extensive hydrophobic contacts with the convex side of the beta-barrel.
Pfam PF13627: Prokaryotic lipoprotein-attachment site (conserved_site)
In prokaryotes, membrane lipoproteins are synthesized with a precursor signal peptide, which is cleaved by a specific lipoprotein signal peptidase (signal peptidase II). The peptidase recognizes a conserved sequence and cuts upstream of a cysteine residue to which a glyceride-fatty acid lipid is attached.
Pfam PF22491: Family of unknown function (DUF6988) (family)
This family of uncharacterised proteins is found mainly in Proteobacteria. These proteins are predicted to adopt an alpha-helical structure. They contain a highly conserved RXXXE-motif and an invariant histidine that may have a functional role.
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 PF20162: Septation protein etd1 (family)
This family includes the Septation protein etd1 from Schizosaccharomyces pombe, which activates the  GTPase Spg1 to trigger signaling through the septum initiation network (SIN) pathway and onset of cytokinesis. The proper regulation of Etd1 is crucial for both activation of Spg1 in anaphase and inactivation of Spg1 when cytokinesis is complete. It was suggested that Etd1 is the functional homologue of budding yeast Lte1 as they have the same function but a very low sequence similarity.
Pfam PF18659: Cell-traversal protein for ookinetes and sporozoites (domain)
Cell-traversal protein for ookinetes and sporozoites (CelTOS) is a conserved protein that is essential for traversal of malaria parasites in both the mosquito vector and human host and is therefore critical for malaria transmission and disease pathogenesis. It specifically binds phosphatidic acid commonly present within the inner leaflet of plasma membranes, and potently disrupts liposomes composed of phosphatidic acid by forming pores.  CelTOS resembles class I viral membrane fusion glycoproteins and a bacterial pore-forming toxin with roles in membrane binding and disruption. CelTOS forms an alpha helical dimer that resembles a tuning fork.  Structure analysis indicate that it has a distinct structural architecture with two subdomains that independently resemble membrane binding and/or disrupting proteins and could simultaneously act during disruption.
Pfam PF19613: Family of unknown function (DUF6118) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 222 and 245 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 PF03797: Autotransporter beta-domain (domain)
Secretion of protein products occurs by a number of different pathways in bacteria.  One of these pathways known as the type V pathway was first described for the IgA1 protease. The protein component that mediates secretion through the outer membrane is contained within the secreted protein itself, hence the proteins secreted in this way are called autotransporters. This family corresponds to the presumed integral membrane beta-barrel domain that transports the protein. This domain is found at the C terminus of the proteins it occurs in.  The N terminus contains the variable passenger domain that is translocated across the membrane.  Once the passenger domain is exported it is cleaved auto-catalytically in some proteins, in others a different protease is used and in some cases no cleavage occurs.
Wikipedia: In molecular biology, an autotransporter domain is a structural domain found in some bacterial outer membrane proteins. The domain is always located at the C-terminal end of the protein and forms a beta-barrel structure. The barrel is oriented in the membrane such that the N-terminal portion of the protein, termed the passenger domain, is presented on the cell surface. These proteins are typically virulence factors, associated with infection or virulence in pathogenic bacteria.
Pfam PF09132: BmKX (domain)
Members of this family assume a structure adopted by most short-chain scorpion toxins, consisting of a cysteine-stabilised alpha/beta scaffold consisting of a short 3-10-helix and a two-stranded antiparallel beta-sheet. They are predominantly found in short-chain scorpion toxins, and their biological method of action has not, as yet, been defined.
Pfam PF17287: POTRA domain (domain)
This POTRA domain is found in ShlB-like proteins.
Pfam PF24229: Staphylococcus phage terminal repeat-encoded protein TreK (family)
This entry represents a terminal repeat-encoded protein (TreK) found in Twort-like Staphylococcus phages. Twort-like viruses are members of the Myoviridae family and are characterized by large genomes (>125 kb) with a low G+C content (30-31%) and terminally redundant ends. These terminal repeats are several thousand base pairs long and may influence the host range. The TreK protein is encoded within these terminal repeat regions. Twort-like phages are known for their broad host range and strictly lytic life cycle, making them suitable candidates for phage therapy against Staphylococcus aureus infections. This domain is often found in various Staphylococcus phages, particularly those belonging to the Herelleviridae family. The protein is typically around 90-95 amino acids in length. While its exact function remains unknown, its conservation among Twort-like phages suggests it plays an important role in phage biology, possibly related to host range determination or genome packaging.  Structure prediction shows these proteins form a globular domain that includes a 5 stranded highly curved beta sheet with a C-terminal helix.
Pfam PF15723: Motility quorum-sensing regulator, toxin of MqsA (domain)
MqsR_toxin is a family of bacterial toxins that act as an mRNA interferase. MqsR is the gene most highly upregulated in E. coli persister cells and it plays an essential role in biofilm regulation and cell signalling. It forms part of a bacterial toxin-antitoxin TA system, and as expected for a TA system, the expression of the MqsR toxin leads to growth arrest, while co-expression with its antitoxin, MqsA, rescues the growth arrest phenotype. In addition, MqsR associates with MqsA to form a tight, non-toxic complex and both MqsA alone and the MqsR:MqsA2:MqsR complex bind and regulate the mqsR promoter. The structure of MqsR shows that is is a member of the RelE/YoeB family of bacterial RNases that are structurally and functionally characterised bacterial toxins.y characterized bacterial toxins.
Pfam PF03320: Bacterial fructose-1,6-bisphosphatase, glpX-encoded (family)
Gluconeogenesis is an important metabolic pathway, which produces glucose from noncarbohydrate precursors such as organic acids, fatty acids, amino acids, or glycerol. Fructose-1,6-bisphosphatase, a key enzyme of gluconeogenesis, is found in all organisms, and five different classes of these enzymes have been identified.
This entry represents the class 2 fructose-1,6-bisphosphatases, which include GlpX and YggF of Escherichia coli (strain K12), which show different catalytic properties. The crystal structure of GlpX has been determined in a free state and in the complex with a substrate (fructose 1,6-bisphosphate) or inhibitor (phosphate). The crystal structure of the ligand-free GlpX revealed a compact, globular shape with two Î±/Î²-sandwich domains. The core fold of GlpX is structurally similar to that of Li+-sensitive phosphatases suggesting that they have a common evolutionary origin and catalytic mechanism. The structure of the GlpX complex with fructose 1,6-bisphosphate revealed that the active site is located between two domains and accommodates several conserved residues coordinating two metal ions and the substrate. A third metal ion is bound to phosphate 6 of the substrate. Inorganic phosphate strongly inhibited activity of both GlpX and YggF, and the crystal structure of the GlpX complex with phosphate demonstrated that the inhibitor molecule binds to the active site. Alanine replacement mutagenesis of GlpX identifies 12 conserved residues important for activity and suggested that Thr(90) is the primary catalytic residue .
A number of the proteins in this entry, particularly those from algae are bi functional and can catalyzes the hydrolysis of fructose 1,6-bisphosphate and sedoheptulose 1,7-bisphosphate to fructose 6-phosphate and sedoheptulose 7-phosphate, respectively.
Pfam PF24902: NUP210, Ig-like domain 9 (domain)
This domain is found in human Nuclear pore membrane glycoprotein 210 (NUP210), which is essential for nuclear pore assembly and fusion, nuclear pore spacing, as well as structural integrity. NUP210 is composed of multiple immunoglobin-like (Ig-like) domains and forms a ring around the NPC within the NE lumen.
Pfam PF21029: Regulator of MON1-CCZ1 complex, N-terminal (repeat)
This is the N-terminal beta-propeller of Regulator of MON1-CCZ1 complex (RMC1). RMC1 is a component of the the CCZ1-MON1 complex, which functions as a guanine exchange factor (GEF) for RAB7 during endocytic and autophagic flux to the lysosome. This region may function analogously to the WIPI proteins to bind phosphoinositides at the membrane.
Pfam PF12661: Human growth factor-like EGF (domain)
hEGF, or human growth factor-like EGF, domains have six conserved residues disulfide-bonded into the characteristic 'ababcc' pattern. They are involved in growth and proliferation of cells, in proteins of the Notch/Delta pathway, neurogulin and selectins. hEGFs are also found in mosaic proteins with four-disulfide laminin EGFs such as aggrecan and perlecan.  The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal Cys residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In hEGFs the C-terminal thiol resides in the beta-turn, resulting in shorter loop-lengths between the Cys residues of disulfide 'c', typically C[]XC.  These shorter loop-lengths are also typical of the four-disulfide EGF domains, laminin ad integrin.  Tandem hEGF domains have six linking residues between terminal cysteines of adjacent domains. hEGF domains may or may not bind calcium in the linker region. hEGF domains with the consensus motif CXD4X[F,Y]XCXC are hydroxylated exclusively in the Asp residue.
Wikipedia: The EGF-like domain is an evolutionary conserved protein domain, which derives its name from the epidermal growth factor where it was first described. It comprises about 30 to 40 amino-acid residues and has been found in a large number of mostly animal proteins. Most occurrences of the EGF-like domain are found in the extracellular domain of membrane-bound proteins or in proteins known to be secreted. An exception to this is the prostaglandin-endoperoxide synthase. The EGF-like domain includes 6 cysteine residues which in the epidermal growth factor have been shown to form 3 disulfide bonds. The structures of 4-disulfide EGF-domains have been solved from the laminin and integrin proteins. The main structure of EGF-like domains is a two-stranded β-sheet followed by a loop to a short C-terminal, two-stranded β-sheet. These two β-sheets are usually denoted as the major (N-terminal) and minor (C-terminal) sheets. EGF-like domains frequently occur in numerous tandem copies in proteins: these repeats typically fold together to form a single, linear solenoid domain block as a functional unit.
Pfam PF14115: YuzL-like protein (disordered)
The YuzL-like protein family includes the B. subtilis YuzL protein [swissprot:C0H3R0] which is functionally uncharacterised. This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 50 amino acids in length.
Pfam PF02040: Arsenical pump membrane protein (family)
Arsenic is a toxic metalloid whose trivalent and pentavalent ions inhibit a variety of biochemical processes. Operons that encode arsenic resistance have been found in multicopy plasmids from both Gram-positive and Gram-negative bacteria . The resistance mechanism is encoded from a single operon, which houses an anion pump. The pump has two polypeptide components: a catalytic subunit (the ArsA protein), which functions as an oxyanion-stimulated ATPase; and an arsenite export component (the ArsB protein), which is associated with the inner membrane . The ArsA and ArsB proteins are thought to form a membrane complex that functions as an anion-translocating ATPase.

The ArsB protein is distinguished by its overall hydrophobic character, in keeping with its role as a membrane-associated channel. Sequence analysis reveals the presence of 13 putative transmembrane (TM) regions.
Wikipedia: Arsenite resistance (Ars) efflux pumps of bacteria may consist of two proteins, ArsB and ArsA, or of one protein. ArsA proteins have two ATP binding domains and probably arose by a tandem gene duplication event. ArsB proteins all possess twelve transmembrane spanners and may also have arisen by a tandem gene duplication event. Structurally, the Ars pumps resemble ABC-type efflux pumps, but there is no significant sequence similarity between the Ars and ABC pumps. When only ArsB is present, the system operates by a pmf-dependent mechanism, and consequently belongs in TC subclass 2.A. When ArsA is also present, ATP hydrolysis drives efflux, and consequently the system belongs in TC subclass 3.A. ArsB therefore appears twice in the TC system but ArsA appears only once. These pumps actively expel both arsenite and antimonite.
Pfam PF21802: CRISPR-associated Cas3 subtype I-F/YPEST-like, C-terminal domain (domain)
This domain is found at the C-terminal end of CRISPR-associated nuclease/helicase Cas3 subtype I-F/YPEST from Pseudomonas aeruginosa. Cas3 contains an HD nuclease domain ([pfam:PF18019]), RecA1, RecA2, a long linker region, and this C-terminal domain. This domain shows two alpha-helices and two six-stranded beta-blades.
Pfam PF15982: N-terminal cysteine-rich region of Transmembrane protein 135 (domain)
TMEM135_C_rich is a family of putative peroxisomal membrane proteins found in eukaryotes.  This is the highly conserved N-terminal region that has several highly conserved cysteine residues. The domain is associated with family Tim17, [pfam:PF02466].
Pfam PF07019: EMC6 (family)
This family consists of several Rab5-interacting proteins (RIP5 or Rab5ip) including ER membrane protein complex subunit 6 (EMC6) and RCAF1. The ras-related GTPase rab5 is rate-limiting for homotypic early endosome fusion. Rab5ip represents a novel rab5 interacting protein that may function on endocytic vesicles as a receptor for rab5-GDP and participate in the activation of rab5. EMC6 interacts with Rab5A and BECN1/Beclin 1 and regulates autophagosome formation. EMC6 is part of the EMC complex, required for efficient folding of proteins in the ER and for post-translational membrane insertion of tail-anchored (TA) proteins.
Pfam PF17667: Fungal protein kinase (domain)
This domain appears to be a variant of the protein kinase domain that is found in a variety of fungal species.
Pfam PF03265: Deoxyribonuclease II (family)
Deoxyribonuclease II (3.1.22.1) hydrolyses DNA under acidic conditions with a preference for double-stranded DNA. It catalyses the endonucleolytic cleavage of DNA to 3'-phosphomononucleotide and 3'-phosphooligonucleotide end-products. The enzyme may play a role in apoptosis. This family also includes hypothetical proteins from Caenorhabditis elegans.
Pfam PF10311: Increased loss of mitochondrial DNA protein 1 (family)
This is a family of proteins of approximately 200 residues that are conserved in fungi. Ilm1 is part of the peroxisome, a complex that is the sole site of beta-oxidation in Saccharomyces cerevisiae and known to be required for optimal growth in the presence of fatty acid. Ilm1 may participate in the control of the C16/C18 ratio since it interacts strongly with Mga2p, a transcription factor that controls expression of Ole1, the sole fatty acyl desaturase in S. cerevisiae responsible for conversion of the saturated fatty acids stearate (C18) and palmitate (C16) to oleate and palmitoleate, respectively.
Pfam PF08824: Serine rich protein interaction domain (domain)
This is a serine rich domain that is found in the docking protein p130(cas) (Crk-associated substrate).  This domain folds into a four helix bundle which is associated with protein-protein interactions.
Pfam PF07929: Plasmid pRiA4b ORF-3-like protein (family)
Members of this family are similar to the protein product of ORF-3 ([swissprot:Q44206]) found on plasmid  pRiA4 in the bacterium Agrobacterium rhizogenes.  This plasmid is responsible for tumourigenesis at  wound sites of plants infected by this bacterium, but the ORF-3 product does not seem to be involved in the pathogenetic process. Other proteins found in this family are annotated as being putative TnpR resolvases ([swissprot:Q9LCU7], [swissprot:Q50439]), but no  further evidence was found to back this. Moreover,  another member of this family is described as a probable  lexA repressor ([swissprot:Q7UEI4]) and in fact carries a LexA  DNA binding domain ([pfam:PF01726]), but no references were  found to expand on this.
Pfam PF09658: CRISPR-associated protein (Cas_Csx9) (family)
Clusters of short DNA repeats with nonhomologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognisable features. This family is known as CRISPR (short for Clustered, Regularly Interspaced Short Palindromic Repeats). A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This entry describes archaeal proteins encoded in cas gene regions.
Pfam PF06599: Protein of unknown function (DUF1139) (family)
This family consists of several hypothetical Fijivirus 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 PF11387: Protein of unknown function (DUF2795) (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 PF21292: EME1/MUS81, C-terminal (domain)
EME1 and MUS81 form a complex that acts as a structure-specific endonuclease, playing an important role in rescuing stalled replication forks and resolving the meiotic recombination intermediates in eukaryotes. Both consist of a central nuclease domain ([pfam:PF02732]), two repeats of the helix-hairpin-helix (HhH) motif and a linker helix. This entry represents the C-terminal HhH domain of EME1 and MUS81. Similar to EME1-MUS81, human MUS81-EME2 cleaves 3'-flaps, replication forks and nicked Holliday junctions, and exhibits limited endonuclease activity with intact Holliday junctions.