SII-SWORD/CoKE huggingface dataset:
TMEM238 protein (TMEM238)
Type: Family

This entry represents a group of eukaryotic transmembrane proteins, TMEM238. Their function is not clear. Proteins in this family are typically between 61 and 153 amino acids in length.
TMEM206 protein (TMEM206)
Type: Family

This entry represents a group of eukaryotic transmembrane proteins, TMEM206. Their function is not clear. Proteins in this family are approximately 350 amino acids in length.
Small integral membrane protein 10 (SMIM10)
Type: Family

The function of small integral membrane protein 10 (SMIM10) is not clear. There are two conserved sequence motifs: FCK and RTL.
Small integral membrane protein 19 (SMIM19)
Type: Family

This family of uncharacterised proteins is found mostly in vertebrates. Proteins in this family are typically around 100 amino acids in length.
Domain of unknown function with conserved HDNR motif (HDNR)
Type: Domain

This domain is found in a group of animal proteins that are typically between 117 and 219 amino acids in length, including Ciliary microtubule inner protein 7 and Testis-expressed protein 36 from humans. There is a conserved HDNR sequence motif.
TMEM117 protein (TMEM117)
Type: Family

This entry represents a group of eukaryotic transmembrane proteins, TMEM117. They are typically between 181 and 504 amino acids in length.
TMEM101 protein (TMEM101)
Type: Family

The function of this family of transmembrane proteins, TMEM101, has not, as yet, been determined. Members of this family remain uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 127 and 257 amino acids in length. These proteins contain eight putative transmembrane helices. This family appears to show some distant sequence similarity with the SURF4 (

) and DoxX (

) families.
Voltage-dependent calcium channel gamma-like subunit (Tmem37)
Type: Family

Voltage-dependent calcium channel gamma-like subunit (also known as Tmem37) has a role in stabilising the calcium channel in an inactivated (closed) state. It is a subunit of the L-type calcium channels that modulate calcium current when coexpressed with CACNA1G (calcium channel, voltage-dependent, T type, alpha 1G subunit) .
FAM216 (FAM216)
Type: Family

This entry represents a group of eukaryotic proteins, FAM216. They are approximately 150 - 270 amino acids in length. In humans, the gene encoding FAM216B protein is located in the position, C13orf30.
TMEM156 protein (TMEM156)
Type: Family

This entry represents a group of eukaryotic transmembrane proteins, TMEM 156. They are approximately 310 amino acids in length. In humans, the gene encoding this protein is located in the chromosomal position, 4p14.
Cilia- and flagella-associated protein 141 (CFAP141)
Type: Family

This entry represents a group of eukaryotic proteins that are typically between 78 and 121 amino acids in length. Proteins in this entry includes human Cilia- and flagella-associated protein 141 (CFAP141, also known as C1orf189 protein). Members of this family may be microtubule inner proteins (MIP) part of the dynein-decorated doublet microtubules (DMTs) in cilia axoneme, which is required for motile cilia beating .
Domain of unknown function DUF4549 (DUF4549)
Type: Domain

This entry represents a domain found in eukaryotic proteins that are typically between 143 and 1871 amino acids in length. The human member of this group is C6orf183.
TMEM220 protein (TMEM220)
Type: Family

This entry represents the transmembrane 220 (TMEM220), which contains a transmembrane helix. The length of this protein is typically between 150 and 160 amino acids. In humans, it is found in the chromosomal position 17p13.1.
Type III secreted effector HopW1-1/HolPsyAE (T3SS_HopW1-1/HolPsyAE)
Type: Family

This is a family of type III effectors derived from the plant pathogen Pseudomonas. The virulence proteins (effectors) are injected into plant cells and induce a resistance response . HopW1-1 (HopPmaA) from Pseudomonas syringae induces the accumulation of the signal molecule salicylic acid (SA) and transcripts of HWI1 (HopW1-1-Induced Gene1) in Arabidopsis .
FAM163 (FAM163)
Type: Family

This protein family is alternatively named Neuroblastoma-derived secretory proteins. Highly expressed in neuroblastoma compared to other tissues, suggesting that it may be used as a marker for metastasis in bone marrow .
FAM124 (FAM124)
Type: Family

This entry represents a group of eukaryotic proteins that are approximately 480 amino acids in length. FAM124 belongs to the Vicinial Oxygen Chelatase (VOC) superfamily of proteins and is comprised of two tandem α/β domains, which might be enzymatic. Certain FAM124 domains fused to the TRADD-N domain are predicted to have secondarily lost their enzymatic activity and might be involved in protein-protein interactions .
Cancer-associated gene protein 1, N-terminal (CAGE1_N)
Type: Domain

This entry represents the N-terminal region of human Cancer-associated gene 1 protein (CAGE-1) and similar proteins mainly found in vertebrates.

CAGE-1 shows testis-specific expression among normal tissues and displays wide expression in a variety of cancer cell lines and cancer tissues . CAGE-1 is predominantly expressed during post-meiotic stages. It localises to the acrosomal matrix and acrosomal granule showing it to be a component of the acrosome of mammalian spermatids and spermatozoa .
Lysosomal transcription factor, NCU-G1 (NCU-G1)
Type: Family

NCU-G1 is a set of highly conserved nuclear proteins rich in proline with a molecular weight of approximately 44kDa. Especially high levels are detected in human prostate, liver and kidney. NCU-G1 is a dual-function family capable of functioning as a transcription factor as well as a nuclear receptor co-activator by stimulating the transcriptional activity of peroxisome proliferator-activated receptor-alpha (PPAR-alpha) .
ADP-ribosylation factor-like protein 6-interacting protein 6 (ARL6IP6)
Type: Family

ADP-ribosylation factor-like protein 6-interacting protein 6 (ARL6IP6) is a transmembrane helix present in the J2E erythro-leukaemic cell line, but not its myeloid variants. In tissues, ARL-6 mRNA was most abundant in brain and kidney. While ARL-6 protein was predominantly cytosolic, it is known to bind to SEC61-beta subunit of a protein conducting channel SEC61p .
Speriolin, C-terminal (Speriolin_C)
Type: Domain

This entry represents the C terminus of the sperm centrosome protein speriolin .

Speriolin is a sperm centrosome protein that form a complex with CDC20, CDC27 and TUBG1. It interacts with Cdc20 and is only detected in testis in humans . The function of speriolin and speriolin-like proteins is unknown.
Speriolin, N-terminal (Speriolin_N)
Type: Domain

This family represents the N-terminal of the sperm centrosome protein speriolin .
TMEM169 protein (TMEM169)
Type: Family

This entry represents a group of eukaryotic proteins that are approximately 130 amino acids in length. They contain structured transmembrane helices.
Organic solute transporter subunit beta (OSTbeta)
Type: Family

Organic solute transporter subunit beta (OSTbeta, also known as SLC51B) is an essential component of the Ost-alpha/Ost-beta complex, a heterodimer that acts as the intestinal basolateral transporter responsible for bile acid export from enterocytes into portal blood .

OSTbeta is a single-TM domain polypeptide that forms a transporter complex with Ost-alpha protein, which is a 7-transmembrane (TM) domain containing protein. This heterodimerisation is required for the delivery of the complex to the plasma membrane. The OSTalpha-OSTbeta complex serves as a multispecific transporter that may participate in cellular uptake of bile acids, some endogenous and exogenous steroids, and eicosanoids. It functions via a facilitated diffusion mechanism. Interestingly, this transporter also transports dehydroepiandrosterone sulfate (DHEAS) and pregnenolone sulfate (PREGS), which are major excitatory neurosteroids. This suggests a possible function for OSTalpha-OSTbeta complex in the brain .
Domain of unknown function DUF4650 (DUF4650)
Type: Domain

This domain lies to the C terminus of the ubiquitin-specific peptidase-like proteins from veterbrates (

). Many peptidases require exosites (a secondary binding site that is remote from the active site) to recognise physiological substrates. This domain might be acting as the exosite for the peptidase.
Izumo sperm-egg fusion protein (IZUMO)
Type: Family

IZUMO is a protein with a single immunoglobulin (Ig) domain. Its expression has been found to be testis-specific . IZUMO is not detectable on the surface of fresh sperm, but becomes exposed after an exocytotic process, the acrosome reaction, has occurred. It is thought to bind to putative Izumo receptors on the oocyte. Studies have shown that knock-out mice (Izumo-/- males) were sterile despite normal mating behaviour and ejaculation, indicating the importance of the protein in fertilisation . IZUMO is a typical type I membrane glycoprotein with one immunoglobulin-like domain and a putative N-glycoside link motif (Asn 204) . It contains cysteine residues thought to form a disulphide bridge, and a conserved GCL sequence motif.
AP-3 complex subunit beta, C-terminal domain (AP3B_C)
Type: Domain

This domain lies at the C terminus of the clathrin-adaptor protein complex-3 beta-1 subunit. The AP-3 complex is associated with the Golgi region of the cell, as well as with more peripheral structures. Loss of functional AP-3 complex leads to defects in the function of lysosomes and lysosome-related organelles . The AP-3 complex seems to be involved in the trafficking of lysosomal membrane proteins from endosomes .
COP9 signalosome complex, subunit 9, metazoa (CSN9_metazoa)
Type: Family

This entry includes COP9 signalosome complex subunit 9, a component of the COP9 signalosome complex (CSN), which is conserved in all eukaryotes. The CSN complex is an essential regulator of the largest family of E3 ubiquitin ligases, the cullin-RING-ubiquitin ligases (CRLs). The CSN complex deactivates CRL by removing the ubiquitin-like tag NEDD8 (deneddylation) from the cullin subunit, or by binding to the deneddylated CRL, and preventing it interacting with E2 enzymes and ubiquitination substrates .
AP-5 complex subunit sigma-1 (AP-5_subunit_s1)
Type: Family

This family of proteins are subunits of the adaptor protein complex AP-5, which is involved in endosomal sorting and has links with hereditary spastic paraplegia . It is required for efficient homologous recombination DNA double-strand break repair .
Tumour suppressor candidate 2 (FUS1)
Type: Family

Tumour suppressor candidate 2 (also known as Fus1) gene is identified in the human chromosome 3p21.3 region where allele losses and genetic alterations occur early and frequently for many human cancers . FUS1 protein induces apoptosis through the activation of the intrinsic mitochondrial-dependent and Apaf-1-associated pathways and inhibits the function of protein tyrosine kinases including EGFR, PDGFR, AKT, c-Abl, and c-Kit . In lung cancer cells, Fus1 can modulate their chemosensitivity and enhance the antitumour activity of a conventional chemotherapeutic drug, cisplatin .
AP-3 complex subunit beta 1, serine-rich domain (AP3B1_Ser)
Type: Domain

This short low-complexity, highly serine-rich domain lies on clathrin-adaptor complex 3 beta-1 subunit proteins.
Protein of unknown function DUF4514 (DUF4514)
Type: Family

This family of uncharacterised proteins are found in mammals, including TMEM273 from humans.
Tuberoinfundibular peptide of 39 residues (TIP39)
Type: Family

This entry represents Tuberoinfundibular peptide of 39 residues (TIP39), which is a potent and selective agonist of the parathyroid hormone 2 receptor (PTH2R) . In human, TIP39 expression was detected by RT-PCR in the brain, trachea, fetal liver, kidney and heart. In the brain, TIP39 is expressed in only three sites, the medial and lateral parts of the subparafascicular area in the caudal thalamus, and the medial paralemnsical nucleus in the lateral pons . The TIP39-PTH2R system is a unique neuropeptide-receptor system that plays a role in limbic, endocrine, viscerosensory, and auditory functions .
Tube, Death domain (Tube_Death)
Type: Domain

The adaptor protein Tube and kinase Pelle are essential components in Drosophila Toll signalling pathway . This Tube-Death domain has an insertion between helices 2 and 3, and a C-terminal tail compared with the Death domain of Pelle proteins in Drosophila. The two N-terminal Death domains of the serine/threonine kinase Pelle and the adaptor protein Tube interact to form a six-helix bundle fold arranged in an open-ended linear array with plastic interfaces mediating their interactions. This interaction leads to the nuclear translocation of the transcription factor Dorsal and activation of zygotic patterning genes during Drosophila embryogenesis, and is assisted by the significant and indispensable contacts in the heterodimer contributed by the insertion and C-terminal tail described above .
DNA polymerase beta, thumb domain (PolB_thumb)
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 thumb domain .
TMEM192 family (TMEM192)
Type: Family

The function of this family of transmembrane proteins is unknown. In vertebrates, proteins in this family are located in the lysosomal membrane and late endosome . In Arabidopsis, a member of this family (protein FIP1) has been found to weakly interact with FRIGIDA, a determinant of flowering time .
TERF1-interacting nuclear factor 2, N-terminal domain (TINF2_N)
Type: Domain

This entry represents the N-terminal domain of TERF1-interacting nuclear factor 2 (TINF2). It is a component of the shelterin complex (telosome), which is involved in the protection and maintenance of telomeres . TINF2 plays a role in shelterin complex assembly . In humans, one of its isoforms may have an additional role in tethering telomeres to the nuclear matrix .
Nudix hydrolase, N-terminal (Nudix_N)
Type: Domain

Ths domain occurs at the N terminus of several Nudix (Nucleoside Diphosphate linked to X) hydrolases, such as chloroplastic nudix hydrolase 23 from Arabidopsis thaliana (also known as AtNUDT23). AtNUDT23 mediates the hydrolysis of some nucleoside diphosphate derivatives and can use FAD and ADP-ribose as substrates .
tRNA-guanine transglycosylase, patch-forming domain C2 (TGT_C2)
Type: Domain

Domain C2 of tRNA-guanine transglycosylase is formed by a four-stranded anti-parallel β-sheet lined with two α helices. It has conserved basic residues on the surface of the β-sheets as does the C-terminal domain PUA (

). The catalytic domain of TGT has conserved basic residues on the outer surface of the N-terminal three-stranded β sheet, which closes the barrel. It is postulated that these basic residues from the three domains form a continuous, positively charged patch to which the tRNA binds .
RESP18 domain (RESP18_dom)
Type: Domain

This domain is found in the glucocorticoid-responsive protein regulated endocrine-specific protein 18 (RESP18) and in the N-terminal extracellular region of receptor-type tyrosine-protein phosphatases IA-2 (RPTPN) and RPTPN2 .
CDAN1-interacting nuclease 1 (CDIN1)
Type: Family

This is a family of proteins includes CDIN1 from human, and homologues. CDIN1 is thought to play a role in erythroid cell differentiation .
Some family members have an associated zinc-finger domain. All members carry a highly conserved TPD sequence-motif.
APCDD1 domain (APCDD1_dom)
Type: Domain

APCDD1 is directly regulated by the beta-catenin/Tcf complex, and its elevated expression promotes proliferation of colonic epithelial cells in vitro and in vivo . APCDD1 has an N-terminal signal-peptide and a C-terminal transmembrane region. This domain is duplicated in most members of the family. The domain is rich in cysteines, there being up to 12 such residues, a structural motif important for interaction between Wnt ligands and their receptors. APCDD1 is expressed in a broad repertoire of cell types, indicating that it may regulate a diverse range of biological processes controlled by Wnt signalling .
Ewing's tumour-associated antigen 1 (ETAA1)
Type: Family

This family of proteins is found in eukaryotes, where members are expressed at high levels in the brain, liver kidney and Ewing tumour cell lines . Proteins in this family are typically between 648 and 898 amino acids in length.
Kidney-associated antigen 1 (KAAG1)
Type: Family

KAAG1, kidney-associated antigen 1, or RU2AS (RU2 antisense gene protein) has been found in mammals. It is expressed in testis and kidney, and, at lower levels, in urinary bladder and liver. It is expressed by a high proportion of tumours of various histologic origin, including melanomas, sarcomas and colorectal carcinomas .
Transmembrane protein 237 (TMEM237)
Type: Family

This entry represents a group of eukaryotic proteins that aid the production of new cilia in ciliogenesis. Mutations in the human protein cause a disease named Joubert syndrome type 14 (JBTS14), which is an autosomal recessive disorder characterised by severe mental retardation, hypotonia, breathing abnormalities in infancy, and dysmorphic facial features . Loss of the mammalian TMEM237 results in defective ciliogenesis and deregulation of Wnt signaling . Proteins in this family are typically between 203 and 512 amino acids in length. There are two completely conserved G residues that may be functionally important.
CAP-associated domain (CAP_assoc)
Type: Domain

The function of this domain is unknown, but it is found towards the N terminus of bacterial proteins carrying the CAP domain,

. All members that do not carry an additional copper amine oxidase N-terminal domain (

) are likely to be extracellular, as they start with a signal-peptide. Most other non-bacterial proteins with the CAP domain are allergenic .
Rhamnogalacturonan lyase, domain III (RG-lyase_III)
Type: Domain

This is domain III of rhamnogalacturonan lyase (RG-lyase). The full-length protein specifically recognises and cleaves alpha-1,4 glycosidic bonds between l-rhamnose and d-galacturonic acids in the backbone of rhamnogalacturonan-I, a major component of the plant cell wall polysaccharide, pectin. This domain possesses a jelly roll β-sandwich fold structurally homologous to carbohydrate binding modules (CBMs), and it carries two sulfate ions and a hexa-coordinated calcium ion .
Centrosomal protein of 19kDa (CEP19)
Type: Family

This entry represents the centrosomal protein of 19kDa (CEP19, also known as C3orf34) from eukaryotes. It was identified by complementary proteomics methods . It associates with the mother centriole in early interphase. It localises to spindle poles during mitosis, and to distinct foci oriented towards the midbody at telophase . Its function is not clear.
Rhamnogalacturonan lyase, domain II (RG-lyase_II)
Type: Domain

This entry represents domain II of rhamnogalacturonan lyase (RG-lyase). The full-length protein specifically recognises and cleaves alpha-1,4 glycosidic bonds between l-rhamnose and d-galacturonic acids in the backbone of rhamnogalacturonan-I, a major component of the plant cell wall polysaccharide, pectin. This domain displays an immunoglobulin-like or more specifically Fibronectin-III type fold and shows highest structural similarity to the C-terminal β-sandwich subdomain of the pro-hormone/propeptide processing enzyme carboxypeptidase gp180 from duck. It serves to assist in producing the deep pocket, with domain III, into which the substrate fits .
Tricorn protease, PDZ domain (Tricorn_PDZ)
Type: Domain

This entry represents the PDZ domain of tricorn protease . The tricorn protease is a protease that forms massive proteasome-like capsids with a hollow chamber . Typically, it consists of the β-propeller, PDZ and catalytic domains.
Protein Lines, C-terminal (Lines_C)
Type: Domain

This family represents the C terminus of protein lines . In Drosophila, this protein is involved in embryonic segmentation and may function as a transcriptional regulator .
Cilia- and flagella-associated protein 300 (CFAP300)
Type: Family

CFAP300 is a cilia- and flagella-associated protein that is essential for assembly of dynein arms. Mutations in the CFAP300 gene (C11orf70) cause defective cilia motility and primary ciliary dyskinesia .
FAM227 Protein (FAM227)
Type: Family

This entry represents a group of eukaryotic proteins that carry a highly distinctive, conserved sequence motif of FWWh, where h represents a hydrophobic residue.
MDN2-binding protein, C-terminal domain (MTBP_C)
Type: Domain

This entry represents the C-terminal domain of the MDM2-binding protein (MTBP). MDM2 is an E3 ubiquitin-protein ligase that mediates ubiquitination of p53, leading to its degradation by the proteasome . MTBP inhibits autoubiquitination of MDM2, thereby enhancing MDM2 stability, and this promotes MDM2-mediated ubiquitination of p53 and its subsequent degradation . Mouse MTBP also inhibits cancer cell migration by interacting with alpha-actinin-4 (ACTN4) .
Argininosuccinate lyase, C-terminal (Arg_succ_lyase_C)
Type: Domain

This domain is found at the C terminus of argininosuccinate lyase .

Argininosuccinate lyase (ASL,

) participates in arginine synthesis in all organisms catalysing the reversible breakdown of argininosuccinate to arginine and fumarate. The reaction is also part of the urea cycle . The crystal structures of ASLs from several species have been studied, in particular the duck delta1 and delta2 eye lens crystallins, which are inactive and active homologues of ASL, respectively .
MDM2-binding protein, central domain (MTBP_central)
Type: Domain

This entry represents the central domain of the MDM2-binding protein (MTBP). MDM2 is an E3 ubiquitin-protein ligase that mediates ubiquitination of p53, leading to its degradation by the proteasome . MTBP inhibits autoubiquitination of MDM2, thereby enhancing MDM2 stability, and this promotes MDM2-mediated ubiquitination of p53 and its subsequent degradation . Mouse MTBP also inhibits cancer cell migration by interacting with alpha-actinin-4 (ACTN4) .
MDM2-binding protein, N-terminal domain (MTBP_N)
Type: Domain

This entry represents the N-terminal domain of the MDM2-binding protein (MTBP). MDM2 is an E3 ubiquitin-protein ligase that mediates ubiquitination of p53, leading to its degradation by the proteasome . MTBP inhibits autoubiquitination of MDM2, thereby enhancing MDM2 stability, and this promotes MDM2-mediated ubiquitination of p53 and its subsequent degradation . Mouse MTBP also inhibits cancer cell migration by interacting with alpha-actinin-4 (ACTN4) .
Coiled coil protein 74, C-terminal (CCDC74_C)
Type: Domain

This entry represents the C-terminal conserved domain of coiled-coil proteins from animals. Its function is not known.
LRRC37A/B like protein 1, C-terminal (LRRC37AB_C)
Type: Domain

This entry represents the C-terminal domain of the putative Leucine Rich Repeat Containing protein 37A or protein 37B (LRRC37A/B) found in eukaryotes. The Leucine Rich Repeats (LRR) lies in the central region. The gene that encodes this protein is found in the chromosomal position 17q11.2, and its microdeletion results in the disease, neurofibromatosis type-1 (NF1) . The function of the protein, LRRC37B is unknown, however experimental data shows expression in the aorta, heart, skeletal muscle, liver and brain during gestation .
MMS22-like, C-terminal (MMS22L_C)
Type: Domain

This entry represents the C-terminal of the MMS22L (Methyl methanesulfonate-sensitivity protein 22-like) protein.
Protein MMS22-like, N-terminal (MMS22L_N)
Type: Domain

This entry represents the N-terminal of the MMS22L (Methyl methanesulfonate-sensitivity protein 22-like) protein.

Methyl methanesulfonate-sensitivity protein 22-like (MMS22L) is a component of the MMS22L-TONSL complex, a complex that stimulates the recombination-dependent repair of stalled or collapsed replication forks . The MMS22L-TONSL complex is required to maintain genome integrity during DNA replication by promoting homologous recombination-mediated repair of replication fork-associated double-strand breaks . It may act by mediating the assembly of RAD51 filaments on ssDNA .