SII-SWORD/CoKE huggingface dataset:
Transmembrane protein 191B/C (TMEM191B/C)
Type: Family

Proteins in this family are uncharacterised single-pass membrane proteins found in eukaryotes. Proteins in this family are typically between and 302 amino acids in length. There are two conserved sequence motifs: QDC and RLF. The function of this family is unknown.
STAT6, C-terminal (STAT6_C)
Type: Domain

This family represents the C terminus of mammalian STAT6 (signal transducer and activator of transcription 6). It contains an LXXLL motif which binds to NCOA1 (Nuclear receptor coactivator 1) .
Type IV pilin PilA (Pilin_PilA)
Type: Family

This family consists of proteins which form type IV pili. In Myxococcus xanthus these pili are required for social motility .
Nitrate reductase, alpha subunit, N-terminal (Nitr_red_alph_N)
Type: Domain

This entry represents the N-terminal tail of the respiratory nitrate reductase alpha chain. The nitrate reductase complex is a dimer of heterotrimers each consisting of an alpha, beta and gamma chain. The N-terminal tail of the alpha chain interacts with the beta chain and contributes to the stability of the heterotrimer .
Novel toxin 21 (Ntox21)
Type: Domain

This entry represents an RNase toxin found in bacterial polymorphic toxin systems that is proposed to adopt the BECR (Barnase-EndoU-ColicinE5/D-RelE) fold, with two conserved lysine residues and [DS]xDxxxH, RxG[ST] and RxxD motifs. In bacterial polymorphic toxin systems, the toxin is usually exported by the type 2, type 4, type 5 or type 7 secretion system . This is also referred to as the E. cloacae CdiAC and has been shown to target tRNAs .

The CdiAC proteins carry a variety of sequence-diverse C-terminal domains, which represent a collection of distinct toxins . Many CdiA-CT toxins have nuclease activities. In accord with the structural homology, CdiA-CT cleaves 16S rRNA at the same site as colicin E3 and this nuclease activity is responsible for growth inhibition . These toxins are composed of three domains, each responsible for a distinct step in the cell-killing pathway. The central domain binds specific receptors on the surface of susceptible bacteria, the N-terminal domain mediates translocation across the cell envelope, and the C-terminal domain carries the bacteriocidal activity. This modular structure allows for delivery of diverse C-terminal toxins using conserved translocation and receptor-binding domains .
WASH complex subunit 4, N-terminal (WASH-4_N)
Type: Domain

This entry represents the N-terminal WASH homology domain (WAHD) of WASH complex subunit 4 (WASH4), also known as KIAA1033 or SWIP . This domain comprises the WAHD1 and the TBR (tubulin-binding region) domains . In species such as Drosophila this protein is the only component of the 'complex'. WASH is a complex present at the surface of endosomes that recruits and activates the Arp2/3 complex to induce actin polymerisation .
Bcl-2-modifying factor (BMF)
Type: Family

Bcl-2-modifying factor (BMF) is thought to play a role in inducing apoptosis. It is thought to bind to Bcl-2 proteins . This family of proteins is found in eukaryotes. Proteins in this family are typically between 75 and 190 amino acids in length. There are two conserved sequence motifs: GNA and DQF.
Testis-expressed protein 13 A-D, N-terminal (TEX13A-D_N)
Type: Domain

This entry represents a likely coiled-coil region found at the N-terminal of testis-expressed proteins 13 A-D from vertebrates such as

in homo sapiens, whose function has not, as yet, been determined. However, members are thought to be encoded for by spermatogonially-expressed, germ-cell-specific genes . There are two conserved sequence motifs: FIN and LAL.
Coiled-coil domain-containing protein 167 (CC167)
Type: Family

The function of this family of coiled-coil domain containing proteins, has not as yet been determined. This family of proteins is found in eukaryotes.
Sperm microtubule inner protein 6 (SPMIP6)
Type: Family

This entry represents the homologues of Sperm microtubule inner protein 6 (SPMIP6, formerly Spermatid-specific manchette-related protein 1 -SMRP1). SPMIP6 is a sperm-specific microtubule inner protein (MIP) that is found in mammmals. SPMIP6 interacts with alpha-tubulin and associates with protofilament B01 . It may be involved in differentiation or function of ciliated cells .
Keratinocyte differentiation-associated protein (KRTDAP)
Type: Family

Keratinocyte differentiation-associated protein (KRTDAP) is secreted by keratinocytes and may serve as a soluble regulator of keratinocyte differentiation .
Syntaphilin/Syntabulin (Syntaphilin/Syntabulin)
Type: Family

This family consists of the eukaryotic proteins syntaphilin and syntabulin.

Syntaphilin is selectively expressed in the brain. It competes with SNAP-25 for binding to syntaxin-1 and inhibits SNARE complex formation by absorbing free syntaxin-1. In this way, syntaphilin may function as a molecular clamp, controlling free syntaxin-1 availability for the assembly of the SNARE complex, thereby regulating synaptic vesicle exocytosis .

Syntabulin is a microtubule-associated protein that has been implicated in syntaxin transport in neurons. It appears to function as a linker molecule that attaches syntaxin-cargo vesicles to kinesin I, enabling the transport of syntaxin-1 to neuronal processes .
Surfactant-associated protein 2 (SFTA2)
Type: Family

This family of proteins are predicted to possess a signal peptide, indicating that they are secreted . They are found in eukaryotes.
Mucin, catalytic, TM and cytoplasmic tail domain (Mucin_dom)
Type: Domain

This entry represents the non-tandem repeat domain including cleavage site, the transmembrane helix domain, and the cytoplasmic tail of epiglycanin (mucin-21) and related mucins .
Immunity protein 31 (Imm31)
Type: Family

This family consists of predicted immunity proteins with a mostly all-β fold and a conserved GxS motif. These proteins are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Ntox17 or Ntox7 families .
Reductase, C-terminal (Reductase_C)
Type: Domain

This domain occurs at the C terminus of various reductase enzymes, including putidaredoxin reductase, ferredoxin reductase, 3-phenylpropionate/cinnamic acid dioxygenase ferredoxin--NAD(+) reductase component, benzene 1,2-dioxygenase system ferredoxin--NAD(+) reductase subunit, rhodocoxin reductase, biphenyl dioxygenase system ferredoxin--NAD(+) reductase component, rubredoxin-NAD(+) reductase and toluene 1,2-dioxygenase system ferredoxin--NAD(+) reductase component. In putidaredoxin reductase this domain is involved in dimerisation . In the FAD-containing NADH-ferredoxin reductase (BphA4) it is responsible for interaction with the Rieske-type [2Fe-2S] ferredoxin (BphA3) .
Photosynthesis system II assembly factor Ycf48/Hcf136-like domain (PSII_CF48-like_dom)
Type: Domain

This entry represents a domain found in the photosynthesis system II assembly factor YCF48/HCF136 and associated proteins.

The photosynthesis system II (PSII) is a multi-subunit pigment-protein complex responsible for water oxidation during oxygenic photosynthesis . PSII can be found in the thylakoid membrane of chloroplasts and cyanobacteria. Its assembly is regulated by PSII assembly factors including Ycf48/Hcf136, Psb27 and Psb28. Ycf48/Hcf136 contains the BNR repeats and can be found predominantly in the thykaloid membrane. Ycf48/Hcf136 is required for assembly and repair of an early intermediate in PSII assembly that includes D2 (psbD) and cytochrome b559 . This domain can also be found in some YCF48-like proteins that may not affect PSII activity.
Tricorn protease C1 domain (Tricorn_C1)
Type: Domain

This domain is the C1 core domain of tricorn protease. This is a mixed α-β domain .
Late cornified envelope protein (LCE)
Type: Family

This is a family of late cornified envelope proteins that are expressed in skin . They are precursors of the cornified envelope of the stratum corneum, the outermost layer of the epidermis.
Psoriasis susceptibility 1 candidate 1 (SEEK1)
Type: Family

This family is considered a candidate for susceptibility to psoriasis .
DNA polymerase beta, palm domain (DNA_pol_B_palm_palm)
Type: Domain

The catalytic region of DNA polymerase beta is split into three domains. An N-terminal fingers domain, a central palm domain and a C-terminal thumb domain. This entry represents the palm domain .
Effector protein NleD-like (Effector_pro_NleD-like)
Type: Family

This entry represents Escherichia coli effector protein NleD-like proteins.
LAMTOR1/MEH1 (LAMTOR1/MEH1)
Type: Family

LAMTOR1 is a family of eukaryotic proteins that have otherwise been referred to as Lipid raft adaptor protein p18, Late endosomal/lysosomal adaptor and MAPK and MTOR activator 1, and Protein associated with DRMs and endosomes.

LAMTOR1 regulates the mTOR (mammalian target of rapamycin) pathway, a signaling cascade that promotes cell growth in response to growth factors, energy levels, and amino acids. LAMTOR1 is part of the Ragulator complex, recruits the Rag GTPases and the mTORC1 complex to lysosomes, a key step in activation of the TOR signaling cascade by amino acids . LAMTOR1 is responsible for anchoring the Ragulator complex to membranes. It may regulate both the recycling of receptors through endosomes and the MAPK signaling pathway through recruitment of some of its components to late endosomes . It may be involved in cholesterol homeostasis regulating LDL uptake and cholesterol release from late endosomes/lysosomes. It may also play a role in RHOA activation .

This family also includes Saccharomyces cerevisiae MEH1 (Ego1), a component of the EGO complex. The EGO complex and the Rag-Ragulator complex are structurally related . The yeast EGO complex consists of Gtr1, Gtr2, Ego1, and Ego3, localises to the endosomal and vacuolar membranes, and plays a crucial role in cell growth and autophagy regulation through amino acid signals that activate TORC1 . MEH1 (GSE2) is also a component of the GSE complex, which is required for proper sorting of amino acid permease Gap1 .
Pre-mRNA-splicing factor Ntr2 (Ntr2)
Type: Family

This entry represents the pre-mRNA-splicing factor Ntr2.

In Saccharomyces cerevisiae, Ntr1 and Ntr2 (nineTeen complex-Related proteins) formed a stable complex with DExD/H-box RNA helicase Prp43, which is involved in disassembly of the spliceosome and release of the excised intron in its branched, lariat form . Ntr1 is required for the association of Prp43 with the excised intron complex prior to its release and recycling of the splicing factors . Ntr2 can associate with late splicing complexes independently of Ntr1 but is not by itself sufficient to activate the intron release function of Prp43 .
Hypothetical glycosyl hydrolase 6 (GHL6)
Type: Family

This is a family of hypothetical glycoside hydrolases.
PTIP-associated protein 1 (PA1)
Type: Family

PTIP-associated protein 1 (PA1), also known as PAXIP1-associated-protein-1, is found in eukaryotes. PA1 and PTIP form a stable complex, which is recruited to DNA damage sites via the RNF8-dependent pathway and is required for cell survival in response to DNA damage .
Testis-specific serine kinase substrate (TSKS)
Type: Family

Testis-specific serine kinase substrate (TSKS) is expressed in the testis and is downregulated in cancerous testicular tissue, in comparison with adjacent normal tissue. TSKS expression is very low to undetectable in seminoma, teratocarcinoma, embryonal, and Leydig cell tumours, while high in testicular tissue adjacent to tumours which contain pre-malignant carcinoma in situ . Recently it has been shown in human testis to be localised to the equatorial segment of ejaculated human sperm. The finding of a TSKS family member in mature sperm suggests that this family of kinases might play a role in sperm function . TSKS is localised during spermiogenesis to the centrioles of post-meiotic spermatids, where it reaches its greatest concentration during the period of flagellogenesis .
Refilin family (Refilin)
Type: Family

This protein family includes the actin regulators, Refilin A and B. Refilin (also known as Cfm or FAM101) is thought to stabilise peri-nuclear actin filament bundles, important in fibroblasts. Refilin is important as changes in localisation and shape in the nucleus plays a role in cellular and developmental processes . Refilins are essential partner molecules of Filamin B involved in regulating differentiation and proliferation of chondryocytes .
DDB1- and CUL4-associated factor 16 (DCAF16)
Type: Family

DDB1- and CUL4-associated factor 16 (DCAF16) may function as a substrate receptor for the CUL4-DDB1 E3 ubiquitin-protein ligase complex .
Ribosome-assembly protein 3, C-terminal (Rsa3_C)
Type: Domain

This entry represents the C-terminal domain of 60S ribosome-assembly proteins from fungi .
JAB-like toxin 1 (Toxin-JAB1)
Type: Family

Structurally, the JAB domain is related to the nucleotide deaminase and binds a zinc-ion in a similar structural location . This entry represents a family of predicted JAB-like toxins .
Spermatogenesis-associated protein 19, mitochondrial (SPATA19)
Type: Family

Spermatogenesis-associated protein 19 may have a role in spermiogenesis .
Junctional cadherin 5-associated protein (JCAD)
Type: Family

Junctional cadherin 5-associated protein (JCAD) is a component of VE-cadherin-based cell-cell junctions in endothelial cells . The cell-cell or adherens junction is an adhesion complex that plays a crucial role in the organisation and function of epithelial and endothelial cellular sheets. These junctions join the actin cytoskeleton to the plasma membrane to form adhesive contacts between cells or between cells and extracellular matrix. The junctions also mediate both cell adhesion and cell-signalling. JCAD localises close to the apical membrane in epithelial cells.
AP-5 complex subunit zeta-1 (AP5Z1)
Type: Family

AP-5 complex subunit zeta-1 is a component of the fifth Adaptor-Protein complex (AP-5) . Adaptor protein (AP) complexes facilitate the trafficking of cargo from one membrane compartment of the cell to another by recruiting other proteins to particular types of vesicles. AP-5 is involved in trafficking proteins from endosomes towards other membranous compartments . There are genetic links between AP-5 and hereditary spastic paraplegia, a group of human genetic disorders characterised by progressive spasticity in the lower limbs .
Otospiralin (Otospiralin)
Type: Family

Otospiralin, has a role in maintaining the neurosensory epithelium of the inner ear . Otospiralin is also expressed in the central nervous system, where could be involved in signalling pathways and play a role in repair mechanisms .
Protein LIN37 (LIN37)
Type: Family

This entry represent LIN37 and related proteins from animals and plants. In humans, LIN37 is a component of the DREAM (MuvB/DRM) complex, which represses cell cycle-dependent genes in quiescent cells and plays a role in the cell cycle-dependent activation of G2/M genes .
Uncharacterised protein family UPF0449 (UPF0449)
Type: Family

This family of proteins is found in eukaryotes and it is functionally uncharacterised. Proteins in this family have a conserved LPTRP sequence motif.
Immunity protein 53 (Imm53)
Type: Family

This family consists of predicted immunity proteins with an α+β fold and a conserved tryptophan, and WE and PGW motifs. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Ntox24 or Ntox10 families .
Integrase repeat unit (Integrase_rpt)
Type: Repeat

This repeat is found on integrase proteins in up to 15 copies. The function is not known.
Trimeric autotransporter adhesin, tryptophan-ring motif (TAA-Trp-ring)
Type: Domain

Pathogenic bacteria adhere to the host cell surface using a family of outer membrane (OM) proteins called Trimeric Autotransporter Adhesins (TAAs). TAAs cosist of an N-terminal 'passenger' domain followed by a C-terminal translocation unit/membrane anchor. The 'passenger' domain has a modular structure consisting of a secretion sequence, a head region that facilitates binding to the host cell surface, and a stalk region.

The TAA-head_Trp-ring is the tryptophan-ring motif of some Gram-negative Enterobacteriaceae TAAs. The Trp-ring folds into a β-meander type on the top of the head domain of its TAA. In conjunction with the GIN domain it is thought to be the region of the head that adheres to fibronectin .
Transcription elongation factor Spt6, YqgF domain (Spt6_YqgF)
Type: Domain

The YqgF domain of Spt6 proteins is homologous to the E.coli Holliday junction resolvase RuvC , but its putative catalytic site lacks the carboxylate side chains critical for coordinating magnesium ions that mediate phosphodiester bond-cleavage .
Cilia BBSome complex subunit 10 (BBIP10)
Type: Family

The BBSome (so-named after the association with Bardet-Biedl syndrome) is a complex of 8 subunits that lies at the base of the flagellar microtubule structure. The precise function of the all the individual components in cilia formation is unclear; however, they function to promote loading of cargo to the ciliary axoneme .
Dynein assembly factor 3, C-terminal domain (DNAAF3_C)
Type: Domain

This domain of unknown function is found in a number of proteins, including dynein assembly factor 3 (DNAAF3), which is required for the assembly of axonemal inner and outer dynein arms. DNAAF3 is involved in preassembly of dyneins into complexes before their transport into cilia .
Ciliogenesis and planar polarity effector 1 (CPLANE1)
Type: Family

This family of proteins, which is found in eukaryotes, has no known function. However, mutations in the gene lead to Joubert's Syndrome, a ciliopathy characterised by a distinctive mid-hindbrain malformation, developmental delay with hypotonia, ocular-motor apraxia, and breathing abnormalities .
Proline-rich protein 15 (PRR15)
Type: Family

This is a family of proteins found in eukaryotes that consists of proline-rich 15 (PRR15) and proline-rich 15-like proteins. PRR15 is expressed almost exclusively in post-mitotic cells both during foetal development and in adult tissues, such as the intestinal epithelium and the testis. Its expression in mouse and human gastrointestinal tumours is linked, directly or indirectly, to the disruption of the Wnt signaling pathway .
Bacterial toxin 46 (Ntox46)
Type: Domain

Proteins in this family are mostly uncharacterised. However, this family includes a predicted toxin found in bacterial polymorphic toxin systems. The toxin possesses an α+β fold with a conserved glutamine residue and a [KR]STxxPxxDxx[ST] motif. In bacterial polymorphic toxin systems, the toxin is exported by the type 2 or type 6 secretion system .
RAVE subunit 2/Rogdi (RAVE2/Rogdi)
Type: Family

This is a family of conserved proteins which have been suggested as containing leucine-zipper domains. A leucine zipper domain is a region of 30 amino acids with leucines repeating every seven or eight residues; these proteins do have many such leucines. The representative protein in Drosophila comes from the gene ROGDI. This group includes Rav2 (RAVE complex subunit 2) from yeast. The RAVE complex is required for stable assembly of the vacuolar ATPase complex V-ATPase .

Mutations in human ROGDI cause Kohlschütter-Tönz syndrome (KTS), which is an autosomal-recessive disease characterised by the combination of epilepsy, psychomotor regression, and amelogenesis imperfecta .
Paramyxovirus structural protein P/V, N-terminal domain (Paramyxo_P/V_N)
Type: Domain

The replicative complex of Paramyxoviridae consists of proteins N, P and L. Transcription and replication are carried out on the N/RNA template by a RNA-dependent RNA polymerase complex, made of the phosphoprotein (P) and the large protein (L). P is organised into two moieties that are functionally and structurally distinct: a C-terminal moiety (PCT) and an N-terminal moiety (PNT). PCT is the most conserved in sequence and contains all regions required for virus transcription, whereas PNT, which is poorly conserved, provides several additional functions required for replication . P protein plays a crucial role in the enzyme by positioning L onto the N/RNA template through an interaction with the C-terminal domain of N. Without P, L is not functional. The N-terminal part of P (PNT) is a chaperone for N and prevents it from binding to non-viral RNA in the infected cell .

This entry represents the PNT domain, found in several Paramyxoviridae (mainly Morbillivirus) structural protein P and V sequences . V is a non-structural protein translated from an edited mRNA that contains an extra G residue.
Putative type VI secretion system, Rhs element associated Vgr domain (T6SS_Rhs_Vgr_dom)
Type: Domain

Rsh (rearrangement hot-spot) elements are repetitious sequences identified in certain Escherichia coli strains. These elements are genetic composites, each containing a Rhs core sequence that is conserved from one element to another. As reservoirs of sequence repetition, Rhs elements mediate major chromosomal rearrangements. Eight distinct Rhs elements have identified in E. coli strains .

This domain is found in putative type VI secretion system Rhs element-associated Vgr proteins from Proteobacteria.
Eisosome component PIL1/LSP1 (PIL1/LSP1)
Type: Family

In the budding yeast, S. cerevisiae, Pil1 and another cytoplasmic protein, Lsp1, together form large immobile assemblies at the plasma membrane that mark sites for endocytosis, called eisosomes . Endocytosis functions to recycle plasma membrane components, to regulate cell-surface expression of signalling receptors and to internalise nutrients in all eukaryotic cells.
Cation channel sperm-associated auxiliary subunit gamma (CATSPERG)
Type: Family

This family represents the gamma subunit (CATSPERG) of the complex CatSper .

The CatSper (cation channel of sperm) complex is a tetrameric complex consisting of CATSPER1, CATSPER2, CATSPER3 and CATSPER4 that functions as an alkalinisation-activated calcium channel. This complex is involved in sperm cell hyperactivation, a process needed for sperm motility, which is essential late in the preparation of sperm for fertilisation . This complex requires four auxiliary subunits (beta, gamma, delta and epsilon), which play a role in channel assembly . These are multidomain proteins which share a similar domain organisation.
Transmembrane protein 190 (TMEM190)
Type: Family

This entry represents the transmembrane protein 190 (TMEM190) family. In mice, this protein may play an indirect role in sperm-oocyte fusion .
Thiol:disulfide interchange protein DsbD, N-terminal domain (DsbDN)
Type: Domain

Folding of secreted proteins within the periplasm of Escherichia coli requires the formation of disulfide bonds, a process that is dependent on the Dsb (disulfide bond) proteins. The reduction of Dsb proteins DsbC, DsbE, and DsbG occurs by transport of electrons from cytoplasmic thioredoxin to the C-terminal thioredoxin-like domain of DsbD (DsbDC). The N-terminal domain of DsbD (DsbDN) is capable of forming disulfides with oxidized DsbC, DsbE, or DsbG as well as with reduced DsbD . This entry represents DsbDN .
Centromere protein T (CENP-T)
Type: Family

This entry represents the centromere protein T (CENP-T). CENP-T is a component of the CENPA-NAC (nucleosome-associated) complex, which plays a central role in assembly of kinetochore proteins, mitotic progression and chromosome segregation . CENP-T and CENP-W form a complex that is directly involved in establishment of centromere chromatin structure coordinately with CENP-A . Histone-fold-containing CENP-T-W and CENP-S-X complexes can form a stable CENP-T-W-S-X heterotetramer. Structural analysis of the CENP-T-W-S-X complex suggests that it can form a unique nucleosome-like structure to generate contacts with DNA .
Centrosomal protein of 126kDa (CEP126)
Type: Family

Centrosomal protein of ~126kDa (CEP126), previously known as KIAA1377 , localises to the centrosome, pericentriolar satellites and the base of the primary cilium. It is an important regulator of centrosomal function. Cep126 is necessary for microtubule (MT) organisation, association of the MT array with the centrosome, and is also required for the formation of the primary cilium .