SII-SWORD/CoKE huggingface dataset:
Protein TIC110, chloroplastic (TIC110)
Type: Family

Chloroplastic protein TIC110 is a component of the Tic complex . It has been proposed to be central to protein translocation across the inner envelope membrane , though this is still controversial .
Putative porin (Porin_6)
Type: Family

This is a family of putative porins from Leptospira species.
Putative phage holin (Phage_holin_Dp1)
Type: Family

This is a family of putative phage-holins from Gram-positive bacteria, largely Firmicutes, with two probable transmembrane segments (TMSs). The member from pneumococcal phage Dp-1 shows lytic activity .
Pathogenicity locus protein HrpK (HrpK)
Type: Family

HrpK1 is a putative Type III secretion system pore-forming bacterial protein. It allows transfer of pathogenic material from bacterial cytoplasm into the plant host cytoplasm.
Putative holin (Holin_9)
Type: Family

This is a family of putative holins from Actinobacteria with three TM regions.
MYND-like zinc finger (Zfn-C6H2)
Type: Domain

This entry represents an unusual zinc-finger similar to Zfn-MYND,

. This zinc-finger is found in the N-terminal of methionine aminopeptidase 1, but it is missing in prokaryotic methionine aminopeptidases. It consists of a C2-C2 zinc-finger motif similar to the RING finger family followed by a C2H2 motif similar to zinc-fingers involved in RNA-binding. In yeast the domain chelates zinc in a 2:1 ratio. The domain is found in yeast, plants and mammals. The domain is necessary for the association of the methionine aminopeptidase with the ribosome and the normal processing of the peptidase .
Small toxic protein BsrE-like (BsrE-like)
Type: Family

This is a family of small proteins (34-48 aa) with a single TM region. Members can exhibit antibacterial activity against Gram-positive bacteria but not against Gram-negative bacteria . Proteins in this entry include BsrG, BsrH and BsrE from Bacillus subtilis. They are the toxic components of the type I toxin-antitoxin (TA) system .
Putative exopolysaccharide exporter (PelG)
Type: Family

This is a family of putative exopolysaccharide transporters like PelG . Most members carry twelve transmembrane regions. The family also contains fusion proteins with glycosyl transferase group 1, which are putative flippase transporters.
Putative type IV secretory system protein (T4SS_TraI)
Type: Family

This is a family of putative Gram-negative, largely proteobacterial, type IV (conjugal DNA-protein transfer or VirB) secretory pathway (IVSP) proteins.
DNA transfer protein (Inj_translocase)
Type: Family

This is a family of putative phage translocases involved in the injectosome mechanism. This entry includes gp20, a component of the phage injection machinery, from Enterobacteria phage P22 .
DDB1- and CUL4-associated factor 17 (DCAF17)
Type: Family

DCAF17 (DDB1- and CUL4-associated factor 17) is a family of proteins found in eukaryotes. It may function as a substrate-receptor for CUL4-DDB1 E3 ubiquitin-protein ligase complex . Mutations in the human protein, otherwise known as C2orf37, are responsible for Woodhouse-Sakati Syndrome. Woodhouse-Sakati Syndrome is a rare autosomal recessive multi-systemic disorder characterised by hypogonadism, alopecia, diabetes mellitus, mental retardation, and extrapyramidal syndrome .
Histidine kinase, N-terminal 7TM region (HisKA_7TM)
Type: Domain

This entry represents a region consisting of seven transmembrane (TM) domains found in Archaea and some bacteria. It is found associated with histidine kinase domains.
Sodium channel modifier 1, zinc-finger (Znf-SCNM1)
Type: Domain

This C2H2 type zinc-finger is found at the N terminus of SCNM1, sodium channel modifier protein 1 . Phylogenetic analysis of these zinc finger sequences places SCNM1 within the U1C subfamily of RNA binding proteins that is commonly found in RNA-processing proteins, suggesting that SCNM1 is involved in splicing activities .
Archaeal histidine kinase, 4TM domain (HisKA_4TM)
Type: Domain

This N-terminal domain of putative signal-transducing histidine-kinases consists of 4 transmembrane (TM) segments and it is found in Archaea.
Coiled-coil domain-containing protein 168, N-terminal (CCDC168_N)
Type: Domain

This domain corresponds to the N-terminal region of eukaryotic coiled-coil proteins 168. There are up to 17, on average 6, copies of this domain in most members.
Sodium channel modifier 1, acidic C-terminal domain (SCNM1_acidic)
Type: Domain

This entry represents the C-terminal acidic region of eukaryotic sodium channel modifier protein 1 (SCNM1). Deletion of this region affects the splicing and normal activity of the sodium channel Nav1.6 from gene Scn8a . SCNM1 belongs to the U1C subfamily of RNA binding proteins that is commonly found in RNA-processing proteins, suggesting that SCNM1 is involved in splicing activities. SCNM1 and LUC7L2 associate with the mammalian spliceosomal subunit U1 snRNP .
Trafficking protein particle complex subunit 14 (TRAPPC14)
Type: Family

TRAPPC14 (also known as MAP11) is a microtubule associated protein that regulates preciliary trafficking of Rabin8 (a guanine nucleotide exchange factor for Rab8) and ciliogenesis . It is a specific subunit of the TRAPP (transport protein particle) II complex, a highly conserved vesicle tethering complex that functions in late Golgi trafficking as a membrane tether . TRAPPC14 is dispensable for TRAPPII complex integrity but mediates Rabin8 association with the TRAPPII complex . It also modulates YAP1 activity as transcriptional regulator . Mutations in the MAP11 gene cause microcephaly in humans and zebrafish .
PDZK1-interacting protein 1/SMIM24 (PDZK1IP1/SMIM24)
Type: Family

PDZK1-interacting protein 1 (PDZK1IP1, MAP17) is a small non-glycosylated two-pass membrane protein that is overexpressed in many tumours of different origins, including carcinomas .

This entry also includes small integral membrane protein 24 (SMIM24) from mammals and proximal tubules-expressed gene protein (pteg) from Xenopus. The function of SMIM24 is not clear. Pteg is essential for pronephric mesoderm specification and tubulogenesis .
BCL-6 corepressor, non-ankyrin-repeat domain (BCOR)
Type: Domain

This domain is found in eukaryotes, and is approximately 220 amino acids in length. It lies just upstream of the ankyrin-repeat region at the C terminus of BCL-6 corepressor proteins. The function of this domain is not known.
Dipicolinate synthase subunit A, N-terminal (DpaA_N)
Type: Domain

This entry represents the N-terminal domain of dipicolinate synthase subunit A. Dipicolinic acid is a small polar molecule that accumulates to high concentrations in bacterial endospores .
Coiled-coil domain-containing protein 117 (CCDC117)
Type: Family

CCDC117 is a family of coiled-coil proteins found in eukaryotes. Proteins in this family are typically between 203 and 279 amino acids in length. There is a conserved MELV sequence motif. The function is not known.
Glycosyl hydrolase family 63, N-terminal (Glyco_hydro_63N)
Type: Domain

Glycoside hydrolases are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. More than 100 different families of glycoside hydrolases have been defined based on sequence similarity.

This entry represents the N-terminal β sandwich domain found in glycosyl hydrolase family 63 proteins . Glycosyl hydrolase family 63 is a family of eukaryotic enzymes that catalyse the specific cleavage of the non-reducing terminal glucose residue from Glc(3)Man(9)GlcNAc(2).
Small VCP/p97-interacting protein (SVIP)
Type: Family

This entry includes mammalian SVIP, small VCP/p97-interacting protein and its orthologues from yeast. SVIP was identified by yeast two-hybrid screening to be an interactive partner of VCP/p97. Mammalian VCP/p97 and its yeast counterpart Cdc48 participate in the formation of organelles, including the endoplasmic reticulum (ER), Golgi apparatus, and nuclear envelope. SVIP has been identified as an endogenous inhibitor of endoplasmic reticulum-associated degradation . Over-expression of SVIP caused the formation of large vacuoles that seemed to be derived from the ER . Proteins in this family have two putative coiled-coil regions and are approximately 80 amino acids in length.
DNA replication complex GINS protein SLD5, C-terminal (SLD5_C)
Type: Domain

DNA replication complex GINS protein SLD5 is a component of the GINS tetrameric protein complex, which is involved in both initiation and elongation stages of eukaryotic chromosome replication . It is essential for the maintenance of genomic integrity, GINS plays a central role in coordinating DNA replication with cell cycle checkpoints and is involved in cell growth. It has been associated with NK cell deficiency and neutropenia .

This entry represents the C-terminal domain of SLD5. This region is important in the assembly of the GINS complex.
Protein kinase G, rubredoxin domain (PknG_rubred)
Type: Domain

This rubredoxin domain is found in the N-terminal of protein kinase G, and is essential for kinase activity .
Growth factor receptor NTRK, leucine rich repeat C-terminal (NTRK_LRRCT)
Type: Domain

This entry represents the Leucine Rich Repeat C-terminal (LRRCT) capping motif found in growth factor receptors, such as NTRK1 (also known as
Trk-A) .
Protein kinase G, tetratricopeptide repeat containing domain (PknG_TPR)
Type: Domain

This domain is found in the C terminus of protein kinase G and contains a tetratricopeptide repeat (TPR) .
Melanoregulin (Melanoregulin)
Type: Family

Melanoregulin (MREG) is a putative membrane fusion regulator that forms a complex with peripherin-2 . It is required for lysosome maturation and plays a role in intracellular trafficking . Melanoregulin is involved in the retrograde melanosome transport in melanocytes, which is dependent on the dynein-dynactin motor complex , and is a negative regulator of melanosome intercellular transfer . Palmitoylation serves to stably anchor melanoregulin in the melanosome membrane .
Annelid erythrocruorin linker subunit, C-terminal (Eryth_link_C)
Type: Domain

This domain is found in linker subunits of the giant extracellular hemoglobin (erythrocruorin) respiratory complex in annelid worms . In Lumbricus terrestris, the erythrocruorin complex consists of 144 hemoglobin subunits and 36 non-hemoglobin ('linker') subunits that are crucial for the formation of the complete complex . This C-terminal globular domain in linker subunits is involved in trimerization, and also interacts with globins and other C-terminal globular linker domains of neighbouring trimers .
Glucose dehydrogenase, C-terminal (Glu_dehyd_C)
Type: Domain

This entry represents the C-terminal domain of glucose dehydrogenase.

Glucose 1 dehydrogenase (

) belongs to the medium-chain alcohol dehydrogenase superfamily and requires zinc for catalysis . It catalyses the NAD(P)(+)-dependent oxidation of D-glucose to D-gluconate via gluconolactone. It is involved in the degradation of glucose through a modified version of the Entner-Doudoroff pathway in Halobacteria and a non-phosphorylative variant of the Entner-Doudoroff pathway in other organisms.

This entry includes a group of glucose 1 dehydrogenases from archaea.
Phthiocerol/phthiodiolone dimycocerosyl transferase, C-terminal (PapA_C)
Type: Domain

This entry represents the C-terminal domain of phthiocerol/phthiodiolone dimycocerosyl transferase (PapA5) from Mycobacterium tuberculosis. PapA5 catalyses diesterification of phthiocerol and phthiodiolone with mycocerosic acids, the final step in the phthiocerol and phthiodiolone dimycocerosate esters (PDIM) synthesis .
Domain of unknown function DUF4708 (DUF4708)
Type: Domain

This uncharacterised domain is found in eukaryotes.
E3 ubiquitin-protein ligase makorin 1, C-terminal (MKRN1_C)
Type: Domain

This domain is found at the C terminus of makorins, a family of eukaryotic putative ribonucleoproteins with a distinctive array of zinc-finger motifs . Makorin-1 (MKRN1) plays an important role in modulating the homeostasis of telomere-length through a dynamic balance involving the stability of the protein hTERT . MKRN1 has been shown to be a a transcriptional co-regulator and an E3 ligase. It functions simultaneously as a differentially negative regulator of p53 and p21, preferentially leading cells to p53-dependent apoptosis by suppressing p21 . The exact function of the C-terminal region has not been determined.
Transmembrane protein 82 (TMEM82)
Type: Family

Transmembrane protein 82 (TMEM82) is a family of proteins found in eukaryotes. The function is not known.
Voltage-dependent L-type calcium channel, IQ-associated domain (GPHH_dom)
Type: Domain

This entry represents a domain found in voltage-dependent L-type calcium channel proteins from eukaryotes. The domain is closely associated with the IQ-domain (

).
Coiled-coil domain-containing protein 73 (CCDC73)
Type: Family

CCDC73 is a family of eukaryotic coiled-coil domain-containing proteins. The function is not known. The alternative name is sarcoma antigen NY-SAR-79.
Domain of unknown function DUF4709 (DUF4709)
Type: Domain

This domain is found in eukaryotes, and is approximately 110 amino acids in length. There is a conserved QQL sequence motif.

It is sometimes found C-terminal to (

).
Phosphoribosylformylglycinamidine subunit PurL, C-terminal (PurL_C)
Type: Domain

This is the C-terminal subdomain of the FGAM (formylglycinamidine ribonucleotide) synthetase domain found in PurL (also known as phosphoribosylformylglycinamidine synthase subunit II) from Thermatoga and related species. PurL catalyses the ATP-dependent synthesis of formylglycinamidine ribonucleotide (FGAM) from formylglycinamide ribonucleotide (FGAR) and glutamine, the fourth step of the purine biosynthetic pathway .

Two forms of PurL have been characterised, large and small. Large PurL is present in most Gram-negative bacteria and eukaryotes and consists of a single polypeptide chain comprised of an N-terminal domain, an FGAM synthetase domain, and a glutaminase domain, with a putative ammonia channel located between the active sites of the latter two. Small PurL, present in Gram-positive bacteria and archaea, is structurally homologous to the FGAM synthetase domain of large PurL, and forms a complex with two additional gene products, PurQ and PurS .

The FGAM synthetase domain is divided into four subdomains: A1 and A2 which make up the core of the enzyme and B1 and B2, which represent the N-terminal and C-terminal subdomains, respectively .
MAPK-interacting and spindle-stabilising protein (MISS)
Type: Family

MAPK-interacting and spindle-stabilising protein (MISS) is rich in prolines and has four potential MAPK-phosphorylation sites, a MAPK-docking site, a PEST sequence (PEST motif) and a bipartite nuclear localisation signal. The endogenous protein accumulates during mouse meiotic maturation and is found as discrete dots on the MII (meiosis metaphase II) spindle. MISS is the first example of a physiological MAPK-substrate that is stabilised in MII that specifically regulates MII spindle integrity during the cytostatic factor (CSF) arrest .
Major capsid protein, N-terminal (Capsid_N)
Type: Domain

This is the N-terminal domain of the major capsid protein in several dsDNA viruses .
FokI, D3 domain (FokI_D3)
Type: Domain

This entry represents the subdomain D3 of FokI. D1 and D2 make almost all of the base-specific contacts with the DNA. D3 is most similar to CAP and related proteins such as histone H5, HNF-3gamma and the biotin operon repressor (BirA). Despite this similarity, D3 barely touches the DNA .

Type IIS restriction endonuclease FokI (

) is a member of an unusual class of bipartite restriction enzymes that recognises the double-stranded DNA sequence 5'-GGATG-3' and cleave DNA phosphodiester groups 9 base pairs away on this strand and 13 base pairs away on the complementary strand . FokI contains amino- and carboxy-terminal domains corresponding to the DNA-recognition and cleavage functions, respectively.

The recognition domain is made of three smaller subdomains (D1, D2 and D3) which are evolutionarily related to the helix-turn-helix-containing DNA-binding domain of the catabolite gene activator protein CAP .
Alpha-glycerophosphate oxidase, C-terminal (DAO_C)
Type: Domain

This entry represents the C-terminal cap domain of alpha-glycerophosphate oxidase, also known as glycerol-3-phosphate oxidase (

) . This domain shows an overall negative electrostatic surface, thought to be involved in substrate recognition.
Replication protein A, OB domain (REPA_OB_2)
Type: Domain

Replication protein A contains two OB domains in it's DNA binding region. This is the second of the OB domains .
Cyclin, C-terminal domain 2 (Cyclin_C_2)
Type: Domain

Cyclins contain two domains of similar all-alpha fold. This domain corresponds to the C-terminal domain of some cyclins, including cyclin C and cyclin H .
Spermatogenesis-associated protein 9 (SPATA9)
Type: Family

SPATA9, spermatogenesis-associated protein 9, or testis development protein NYD-SP16, is a family of eukaryotic proteins associated with sperm production. It is highly expressed in human testis and contains one transmembrane domain. Its localisation indicates it is likely to play an important role in testicular development and spermatogenesis and may be an important factor in male infertility .
C-terminal associated domain of TOPRIM (TOPRIM_C)
Type: Domain

This domain is found as the C-terminal extension of the TOPRIM domain (

)
.
Bcl-2-binding component 3 (Bbc3)
Type: Family

PUMA (p53 upregulated modulator of apoptosis), also known as Bbc3 (Bcl-2-binding component 3), is a critical mediator of p53-dependent and -independent apoptosis . PUMA transduces death signals primarily to the mitochondria. It is induced in cells after p53 activation. It binds to Bcl-2, localises to the mitochondria to induce cytochrome c release, and activates the rapid induction of apoptosis . PUMA is capable of inhibiting all the five major anti-apoptotic Bcl-2-like proteins (Mcl-1, Bcl-2, Bcl-XL, Bcl-W and A1) . The binding of PUMA to the inhibitory members of the Bcl-2 family via its BH3 domain results in the displacement of the proteins Bax and/or Bak, and seems to be a critical regulatory step in the induction of apoptosis .
GTP binding protein, second domain (GTP-binding_2)
Type: Domain

This entry represents a domain located C-terminal to

in a group of GTP binding proteins. In Ribosome-interacting GTPase 1 from Saccharomyces cerevisiae (Rgb1) this entry represents a region of the G domain that contains the G3 and G4 motifs and folds as an independent domain emerging from the G domain, with an α/β configuration. It is essential for the full activity of the proteiin .
Phosphogluconate dehydrogenase (decarboxylating) , C-terminal (PGDH_C)
Type: Domain

This entry represents the C-terminal domain of putative bacterial phosphogluconate dehydrogenase proteins.
Protein of unknown function DUF5085 (DUF5085)
Type: Family

This protein is believed to be involved in the type VII secretion system.
Protein of unknown function DUF5084 (DUF5084)
Type: Family

This protein is believed to be involved in the type VII secretion system.
Required for drug-induced death protein 1 (RDD1)
Type: Family

This family of proteins is found in eukaryotes and includes Required for drug-induced death protein 1 (RDD1) which regulates drug efflux through modulation of ABCB1 localization and activity .
Protein of unknown function DUF4711 (DUF4711)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 130 and 288 amino acids in length.
Fibronectin type III domain, fungi (Fn3_2)
Type: Domain

This fibronectin type III domain is found in fungal chitin biosynthesis protein CHS5 where, together with the neighbouring BRCT domain (

), it binds to the Arf1 GTPase .
Protein of unknown function DUF4712 (DUF4712)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 133 and 267 amino acids in length.
Small integral membrane protein 5/18/22 (SMIM5/18/22)
Type: Family

This entry represents a small family of single-pass membrane proteins described as small integral membrane proteins, including SMIM5/18/22 which have been described as variants of the Cancer-Associated Small Integral Membrane Open reading frame 1 (CASIMO1), a small open reading frame (sORF)-encoded protein (also known as a microprotein). CASIMO1 controls cell proliferation and interacts with squalene epoxidase (SQLE) modulating lipid droplet formation. CASIMO1 RNA is overexpressed predominantly in hormone receptor-positive breast tumors, and its knockdown has been shown to decrease proliferation in multiple breast cancer cell lines. Loss of CASIMO1 disturbs the organization of the actin cytoskeleton, leads to inhibition of cell motility, and stalls the cell cycle in the G0/G1 phase. CASIMO1 interacts with SQLE, a key enzyme in cholesterol synthesis and a known oncogene in breast cancer .
FAM27D/FAM27E (FAM27D/FAM27E)
Type: Family

FAM27 is a family of proteins found in eukaryotes. Proteins in this family are typically between 57 and 131 amino acids in length.
Chitin biosynthesis protein Chs5, N-terminal (Chs5_N)
Type: Domain

This domain is found at the N-terminal of the fungal chitin biosynthesis protein Chs5 . It functions as a dimerisation domain .

Chs5/6 is a multi-protein complex conserved in fungi that interacts with chitin synthase III (Chs3p) and is involved in its transport to the cell surface from the trans-Golgi network, functioning as an exomer cargo adapter. Chs5p appears to form a complex with Chs6p and its paralogues Bch1p, Bud7p, and Bch2p. In this complex, Chs5p may act as a central scaffold . The N-terminal domain characterised by this model forms a homodimer and has been shown to interact with Chs6p and Bch1p. It may function as a flexible hinge domain that allows the exomer to interact with both proteins and the Golgi membrane as the latter undergoes changes in curvature during the formation of transport vesicles . The dimerisation domain sits N-terminally to a conserved FBE (FN3-BRCT) unit, which binds Arf1 and is involved in the recruitment of the exomer to the membrane .
Protein of unknown function DUF4714 (DUF4714)
Type: Family

Proteins in this family are described as leucine-rich single-pass membrane protein 2. They are found in eukaryotes and are typically between 143 and 164 amino acids in length.
Serine-threonine protein phosphatase, N-terminal (STPPase_N)
Type: Domain

This domain is often found N-terminal to

in serine-threonine protein phosphatases .
Protein of unknown function DUF5083 (DUF5083)
Type: Family

This protein is believed to be involved in the type VII secretion system.
Testis-expressed sequence 38 protein (TEX38)
Type: Family

Testis-expressed sequence 38 is a family of proteins found in eukaryotes. Proteins in this family are typically between 152 and 232 amino acids in length.
Protein of unknown function DUF4715 (DUF4715)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are approximately 150 amino acids in length. The proteins are also known as coiled-coil domain-containing protein 182 (CCDC182).
TSSK6-activating co-chaperone protein (SSTK-IP)
Type: Family

SSTK-IP, SSTK-interacting protein or TSSK6-activating co-chaperone, is a family of proteins found in eukaryotes. SSTK-IP directly binds to HSP70, is found associated with HSP70 and HSP90 in cells, and facilitates HSP90-dependent enzymatic activation of SSTK. SSTK is a small serine/threonine kinase expressed post-meiotically and essential for male fertility along with two other serine threonine kinases. SSTK is one of the smallest protein kinases, consisting only of N- and C-lobes of a kinase catalytic domain, and forms stable associations with heat shock protein (HSP) 70 and 90. SSTK-IP, its interacting protein, represents a germ cell-specific co-chaperone critical to the HSP90-mediated activation of SSTK .
Heparin-sulfate lyase, N-terminal (Hepar_II_III_N)
Type: Domain

This is the N-terminal domain of heparin-sulfate lyase. It is a toroid-like domain . Heparin-sulfate lyase specifically cleaves heparan sulfate-rich regions of acidic polysaccharides .