SII-SWORD/CoKE huggingface dataset:
NTF2 fold immunity protein (Imm-NTF2)
Type: Domain

A predicted immunity protein of the NTF2 fold. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, which usually contains toxin domains of the Tox-JAB-2 family .
Toxin in Odyssella and Amoebophilus (Tox-ODYAM1)
Type: Family

A predicted all-α fold toxin present in bacterial polymorphic toxin systems of the endosymbionts Odyssella and Amoebophilus .
Chemotaxis phosphatase CheX-like domain (CheX-like_dom)
Type: Domain

This entry represents a domain found in chemotaxis phosphatase CheX, which is responsible for modulating the bacterial swimming behavioiur in the presence of external chemicals (nutrients and repellents) . CheX is very closely related to the CheC chemotaxis phosphatase, but it dimerises in a different way, via a continuous β sheet between the subunits. CheC and CheX both dephosphorylate CheY, which controls the sense of flagella rotation and thereby determine swimming behavior. The structures of CheX and CheC have been solved .
Kinetochore assembly subunit CENP-C, N-terminal domain (CENP-C_N_dom)
Type: Domain

CENP-C is a vertebrate family that forms a core component of the centromeric chromatin. On depletion of CENP-C, proper formation of both centromeres and kinetochores is prevented. In kinetochores, the KMN (KNL1/Mis12/Ndc80) network regulates kinetochore microtubule binding . The N-terminal of CENP-C is necessary for recruitment of some but not all components of the Mis12 complex to centromeres .
Membrane insertase YidC, N-terminal (Membr_insert_YidC_N)
Type: Domain

YidC is required for the insertion and assembly of the bacterial inner (or only) membrane . This entry represents the N-terminal domain of YidC from Gram-negative bacteria, which includes a large periplasmic domain lacking in YidC members from Gram-positive species. The structure of the periplasmic domain has been solved .
Protein of unknown function DUF4481 (DUF4481)
Type: Family

This family of unknown function is found in eukaryotes. The human representative is transmembrane protein C9orf91. In mouse it is also known as Tmem268.
Membrane insertase YidC/Oxa/ALB, C-terminal (YidC/Oxa/ALB_C)
Type: Domain

This entry represents the C-terminal domain of YidC/Oxa1/ALB proteins from some species and full length protein from other species. Members of this group of proteins are found in bacteria and eukaryotes.

YidC is a bacterial membrane protein which is required for the insertion and assembly of inner membrane proteins . The well-characterised YidC protein from Escherichia coli and its close homologues contain a large N-terminal periplasmic domain (

).

COX18 is a mitochondrial membrane insertase required for the translocation of the C terminus of cytochrome c oxidase subunit II (MT-CO2/COX2) across the mitochondrial inner membrane. It plays a role in MT-CO2/COX2 maturation following the COX20-mediated stabilization of newly synthesized MT-CO2/COX2 protein and before the action of the metallochaperones SCO1/2 .

OXA1 is a mitochondrial inner membrane insertase that mediates the insertion of both mitochondrion-encoded precursors and nuclear-encoded proteins from the matrix into the inner membrane. It links mitoribosomes with the inner membrane .

Plant ALBINO3-like proteins are required for the insertion of some light harvesting chlorophyll-binding proteins (LHCP) into the chloroplast thylakoid membrane .
Colicin M (Colicin_M)
Type: Family

Colicin M is a toxin produced by, and active against, Escherichia coli. It catalyses the hydrolysis of lipid I and lipid II peptidoglycan intermediates, therefore inhibiting peptidoglycan biosynthesis and leading to lysis of the bacterial cells .
DrrA phosphatidylinositol 4-phosphate binding domain (DrrA_P4M)
Type: Domain

This domain binds to phosphatidylinositol 4-phosphate (PtdIns4P or PI4P) lipids on the cytosolic surface of the phagosomal membrane . It is found in Legionella pneumophila DrrA (also known as sidM), a protein involved in the redirection of endoplasmic reticulum-derived vesicles to the Legionella-containing vacuoles (an intracellular replicative organelle) through the recruitment and activation of the host small guanosine triphosphatase (GTPase) Rab1 .
Fis1, N-terminal tetratricopeptide repeat (Fis1_TPR_N)
Type: Repeat

The mitochondrial fission protein Fis1 consists of two tetratricopeptide repeats. This entry represents the N-terminal tetratricopeptide repeat . Fis1 is an outer mitochondrial membrane protein that plays a role in mitochondrial membrane fission .
Putative flagellar system-associated repeat (SWM_rpt)
Type: Repeat

This repeated unit can occur up to 29 times in outer membrane proteins. It is putatively associated with a novel flagellar system.
Big defensin domain (Defensin_big_dom)
Type: Domain

Big defensins are antimicrobial peptides. They consist of a hydrophobic N-terminal half, which is active against Gram-positive bacteria, and a cationic C-terminal half, which is active against Gram-negative bacteria. The C-terminal half adopts a beta-defensin-like structure .
Fis1, C-terminal tetratricopeptide repeat (Fis1_TPR_C)
Type: Repeat

The mitochondrial fission protein Fis1 consists of two tetratricopeptide repeats. This entry represents the C-terminal tetratricopeptide repeat . Fis1 is an outer mitochondrial membrane protein that plays a role in mitochondrial membrane fission .
Kidney androgen-regulated protein (KAR_prot)
Type: Family

The function of this family is unknown.
Scrapie-responsive protein 1 (SCRG1)
Type: Family

This protein family has an important function in acting against the prion protein, scrapie . This family of proteins is found in eukaryotes. Proteins in this family are approximately 98 amino acids in length.
Transmembrane protein 154 (TMEM154)
Type: Family

The function of this family of transmembrane proteins has not, as yet, been determined. However, it is thought to be a therapeutic target for ovine lentivirus infection . This family of proteins is found in eukaryotes and members are typically between 138 and 320 amino acids in length.
Telomere repeats-binding bouquet formation protein 2 (TERB2)
Type: Family

Telomere repeats-binding bouquet formation protein 2 (TERB2) is a meiosis-specific telomere-associated protein involved in meiotic telomere attachment to the nucleus inner membrane, a crucial step for homologous pairing and synapsis. It is a component of the MAJIN-TERB1-TERB2 complex, which promotes telomere cap exchange by mediating attachment of telomeric DNA to the inner nuclear membrane and replacement of the protective cap of telomeric chromosomes: in early meiosis, the MAJIN-TERB1-TERB2 complex associates with telomeric DNA and the shelterin/telosome complex. During prophase, the complex matures and promotes release of the shelterin/telosome complex from telomeric DNA .
Transmembrane protein 187 (TMEM187)
Type: Family

The function of this family, TMEM187, is not known, however it is predicted to be a multi-pass membrane protein. This protein family is also alternatively named ITBA1. Proteins in this family are found in eukaryotes and are typically between 239 and 267 amino acids in length.
Interleukin-32 (IL-32)
Type: Family

This entry represents interleukin-32, it is a proinflammatory cytokine with a folding structure that does not resemble that of any classical cytokine . It may have a role in a range of diseases, including infections, chronic inflammation, and cancer .
Phosphoinositide-interacting protein (PIRT)
Type: Family

Phosphoinositide-Binding Protein (PIRT) is thought to have a role in positively regulating transient receptor potential vanilloid 1 (TRPV1) channel activity via phosphatidylinositol 4,5-bisphosphate (PIP2) . TRPV1 is a molecular sensor of noxious heat and capsaicin.

PIRT is predicted to be a multi-pass membrane protein and is located in the cell membrane .
Transmembrane protein 89 (TMEM89)
Type: Family

The function of this family of transmembrane proteins, TMEM89, has not, as yet, been determined. This family of proteins is found in eukaryotes. Proteins are approximately 159 amino acids in length.
G6B family (G6B)
Type: Family

G6b-B is a unique platelet ITIM-containing receptor that is highly expressed in mature megakaryocytes and platelets . It inhibits platelet aggregation and activation by agonists such as ADP and collagen-related peptide. It appears to operate in a calcium-independent manner . It is a type I transmembrane protein that consists of a single N-glycosylated immunoglobulin-variable (IgV)-like domain in its extracellular region, a single transmembrane domain and a cytoplasmic tail containing an ITIM and an immunoreceptor tyrosine-based switch motif (ITSM) . The human G6B gene encodes a number of splice forms that are translated into both cell-surface and secreted isoforms. Cell-surface isoforms G6B-A and G6B-B have the same extracellular N-terminal Ig-like domain but differ in their C-terminal cytoplasmic tails. The extracellular matrix heparan sulfate (HS) proteoglycan perlecan was identified as a G6b-B binding partner . Subsequent in vitro biochemical studies and a cell-based genetic screen demonstrated that the interaction is specifically mediated by the HS chains of perlecan .
Macro-like domain (Macro-like_dom)
Type: Domain

This domain is an ADP-ribose binding module. It is found predominantly in yeast proteins. Some members in this domain family also contain the A1pp domain and are putative ADP-ribose-1''-monophosphatase that converts ADP-ribose-1''-monophosphate to ADP-ribose .
Domain of unknown function DUF4466 (DUF4466)
Type: Domain

This is a domain of unknown function found in proteins from bacteroidetes.
PTHB1, N-terminal domain (PHTB1_N_dom)
Type: Domain

This entry represents the N-terminal domain of PTHB1 (also known as BBS9) protein found also in PTHB1 homolog from C. elegans.

PTHB1 (also known as Bardet-Biedl syndrome 9 protein, BBS9) forms a part of the BBSome complex, which is required for ciliogenesis . PTHB1 is the major binding subunit of the IFT38 C-terminal tail, which assists the BBSome in some of its roles .
PTHB1, GAE domain (PHTB1_GAE_dom)
Type: Domain

This entry represents the gamma-adaptin ear (GAE) domain of PTHB1 protein.

PTHB1 (also known as Bardet-Biedl syndrome 9 protein, BBS9) forms a part of the BBSome complex, which is required for ciliogenesis . PTHB1 is the major binding subunit of the IFT38 C-terminal tail, which assists the BBSome in some of its roles .
Domain of unknown function with cystatin-like fold DUF4467 (DUF4467)
Type: Domain

A large family of predicted lipoproteins from Gram-positive bacteria have this domain, which has a cystatitin-like fold, suggesting that they belong to the NTF2-like superfamily, despite a lack of any detectable sequence similarity to other families in the superfamily.
Staphopain proregion (Staphopain_pro)
Type: Domain

This domain is the proregion of the cysteine protease staphopain. Like many papain type peptidases, staphopain is synthesised as an inactive precursor and cleavage of the proregion is required for activation. This proregion has a half-barrel or barrel-sandwich hybrid fold. The proregion blocks the active site cleft of the mature enzyme on one side of the nucleophilic cysteine .
Ubiquitin/SUMO-activating enzyme ubiquitin-like domain (UAE_UbL_dom)
Type: Domain

This is the C-terminal domain of ubiquitin-activating enzyme and SUMO-activating enzyme 2. It is structurally similar to ubiquitin. This domain is involved in E1-SUMO-thioester transfer to the SUMO E2 conjugating protein .
AP2-coincident, C-terminal domain (ACDC)
Type: Domain

This domain is found at the C terminus of apicomplexan proteins containing the AP2 domain.
Zc3h12a-like Ribonuclease NYN domain (RNase_Zc3h12a_2)
Type: Domain

This entry represents a divergent form of the NYN-domain containing RNAse family .
Domain of unknown function DUF4454 (DUF4454)
Type: Domain

This domain is found at the C terminus of a small subgroup of proteins from Gram-positive Clostridiales that also carry a YARHG domain (

).
Leucine-binding protein domain (Leu-bd)
Type: Domain

This domain is found in periplasmic binding proteins, mainly belonging to the leucine-binding and Leu/Ile/Val-binding proteins. The periplasmic leucine-binding protein is the primary receptor for the leucine transport system in Escherichia coli .
Periplasmic binding protein-like I (Peripla_BP_I)
Type: Homologous_superfamily

Periplasmic binding protein-like I domains are similar in architecture to the those included in group II, but partly differ in topology. They consist of two similar intertwined globular subdomains, both exhibiting very similar supersecondary structures which consist of a central β-sheet flanked on either side by two or three helices .
Spt6 acidic, N-terminal domain (Spt6_acidic_N_dom)
Type: Domain

The N terminus of Spt6 is highly acidic. The full Spt6 protein is a transcription regulator, but the exact function of this acidic region is not certain.
Folliculin-interacting protein, N-terminal domain (FNIP_N_dom)
Type: Domain

This domain is found at the N terminus of folliculin-interacting proteins .
Folliculin-interacting protein, middle domain (FNIP_mid_dom)
Type: Domain

This is the middle domain of folliculin-interacting proteins , which may have a role in energy and/or nutrient sensing.
Folliculin-interacting protein, C-terminal domain (FNIP_C_dom)
Type: Domain

This is the C terminus of folliculin-interacting proteins, which may have a role in energy and/or nutrient sensing. This region is responsible for binding to folliculin .
Putative Flp pilus-assembly TadG-like, N-terminal (Tad_N)
Type: Domain

This is an N-terminal domain on a family of putative Flp pilus-assembly proteins. The exact function is not known. The Flp-pilus biogenesis genes include the Tad genes, and some members of this family are putatively assigned as being TadG .
Helix-turn-helix DNA-binding domain of Spt6 (Spt6_HTH_DNA-bd_dom)
Type: Domain

This helix-turn-helix represents the first of two DNA-binding domains on the Spt6 proteins
.
Domain of unknown function DUF4455 (DUF4455)
Type: Domain

Proteins with this domain are found in bacteria and eukaryotes. There are two completely conserved residues (W and P) that may be functionally important.
JAB domain, prokaryotic (JAB_dom_prok)
Type: Domain

This entry represents the JAB domain in prokaryotes. The domain is widely found in bacteria, archaea and phages. Its function is still not clear. However, in eukaryotes, JAB domain has been found in metalloenzymes that function as the ubiquitin isopeptidase/deubiquitinase in the ubiquitin-based signaling and protein turnover pathways . Prokaryotic proteins containing JAB domains are predicted to have a similar role in their cognates of the ubiquitin modification pathway . A distinct family, the RadC-like JAB domains are widespread in bacteria and are predicted to function as nucleases . In halophilic archaea, the JAB domain shows strong gene-neighbourhood associations with a nucleotidyltransferase suggesting a role in nucleotide metabolism .

The archaeal (H. volcanii) JAB (also known as JAMM) domain containing protein, HvJAMM1, has been characterised . It cleaves ubiquitin-like small archaeal modifier proteins (SAMP1/2) from protein conjugates .
FAM91, N-terminal domain (FAM91_N_dom)
Type: Domain

This domain is found at the N terminus of proteins from the FAM91 family.
Retinal degeneration protein 3 (RD3)
Type: Family

In humans, Retinal degeneration protein 3 (RD3) is found preferentially expressed in the retina . Mutations in RD3 causes Leber Congenital Amaurosis type 12 ,which is a severe dystrophy of the retina, typically becoming evident in the first years of life .
Restriction of telomere capping protein 4, C-terminal (RTC4_C)
Type: Domain

This entry represents the C-terminal domain of the RTC4 (restriction of telomere capping protein 4) protein from yeasts. In Saccharomyces cerevisiae, deletion of RTC4 affects the cell response to telomere uncapping . This domain is also found in proteins that contain a DNA-binding myb domain.
Mso1, N-terminal domain (Mso1_N_dom)
Type: Domain

Mso1 is a probable component of the secretory vesicle docking complex. It interacts with Sec1, which is a Sm-like protein involved in docking and fusion of exocytic vesicles . The Sec1 binding domain has been identified in the N-terminal region of Mso1 . This entry represents the N-terminal region (including the Sec1 binding domain) of Mso1.
EfeO-type cupredoxin-like domain (EfeO_Cupredoxin)
Type: Domain

The cupredoxin-like fold consists of a β-sandwich with 7 strands in 2 β-sheets, which is arranged in a Greek-key β-barrel.

EfeO is a periplasmic protein with a cupredoxin N-terminal domain from the EfeUOB iron uptake system . This entry represents an EfeO-type cupredoxin-like domain.
FAM91, C-terminal domain (FAM91_C_dom)
Type: Domain

This entry represents the C-terminal domain of FAM91 proteins.
Glycosyltransferase subfamily 4-like, N-terminal domain (Glyco_trans_4-like_N)
Type: Domain

MshA belongs to the GT-B structural family of glycosyltransferases whose members have a two-domain structure with both domains exhibiting a Rossman-type fold . This entry represents the N-terminal domain found in MshA and the subfamily 4 of glycosyltransferases family 1.
Protein of unknown function DUF4577 (DUF4577)
Type: Family

The function of this family of proteins, has not, as yet, been determined. This family of proteins is found in eukaryotes and includes human coiled-coil domain-containing transmembrane protein C7orf53.
Protein of unknown function DUF4616 (DUF4616)
Type: Family

This protein family is found in eukaryotes and includes human uncharacterised protein C14orf93.
Protein of unknown function DUF4652 (DUF4652)
Type: Family

This family of uncharacterised proteins from Clostridia and Bacilli classes has an unusual structure of three β propeller repeats that do not form a barrel, as in well known 6-, 7- etc β propeller barrels, but instead are stacked in a three-layer β-sheet sandwich. The function of all the proteins from this family is unknown.
Spatacsin (Spatacsin)
Type: Family

Defects in the spatacsin gene are the cause of spastic paraplegia 11, a neurodegenerative disorder characterised by a slow, gradual, progressive weakness and spasticity of the lower limbs . Human and rat spacticin protein has been shown to be expressed in the central nervous system, particularly in cortical and spinal motor neurons as well as in retina .
Protein of unknown function DUF4553 (DUF4553)
Type: Family

This family of proteins is functionally uncharacterised. It is found in vertebrates and includes the human protein C10orf12.
Protein of unknown function DUF4651 (DUF4651)
Type: Family

This is a family of short, secreted proteins specific to the Streptococcus genus, with distant homologues, not recognised by this entry, found in other cocci. In all sequenced genomes, proteins from this family appear in a conserved genomic context with an thioredoxin, tRNA synthase and tRNA binding protein, but the functional implication of this is unclear.
Protein of unknown function DUF4578 (DUF4578)
Type: Family

This family of proteins is found in eukaryotes and includes human protein C11orf52.
Spatacsin, C-terminal domain (Spatacsin_C_dom)
Type: Domain

This entry represents the C-terminal domain of spatacsin. Defects in the spatacsin gene are the cause of spastic paraplegia 11 .
Protein of unknown function DUF4505 (DUF4505)
Type: Family

This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 166 and 225 amino acids in length.
Transmembrane protein 254 (TMEM254)
Type: Family

This family consists of proteins found in eukaryotes, including the human protein C10orf57 (also known as transmembrane protein 254). The exact function of this protein is still unknown; however, it is thought to be an integral membrane protein. The family also includes some longer proteins that possess an N-terminal dehydrogenase domain (

).
Melanocortin-2 receptor accessory protein family (MRAP)
Type: Family

This family of proteins is found in eukaryotes. Melanocortin-2 receptor accessory protein (MRAP) is required for MC2R expression in certain cell types, suggesting that it is involved in the processing, trafficking or function of MC2R. MRAP may be involved in the intracellular trafficking pathways in adipocyte cells .
DNA polymerase III PolC-type, N-terminal domain I (DNA_PolC-type_N_I)
Type: Domain

This entry represent the first N-terminal domain, NI domain, of the DNA polymerase III PolC subunit A. DNA polymerase PolC-type III enzyme functions as the 'replicase' in low G + C Gram-positive bacteria . It has been predicted that the N terminus of PolC folds into two globular domains, NI and NII. A predicted patch of elecrostatic potential at the surface of this domain suggests a possible involvement in nucleic acid binding . This domain is associated with DNA polymerase III, alpha subunit (

) and DNA polymerase III PolC-like, N-terminal domain II (

).
Protein of unknown function DUF4624 (DUF4624)
Type: Family

This family of proteins is functionally uncharacterised and is found in bacteria. Proteins in this family are approximately 150 amino acids in length.
Protein of unknown function DUF4658 (DUF4658)
Type: Family

This family of proteins is found in eukaryotes and includes human transmembrane protein C14orf180. Proteins in this family are typically between 129 and 161 amino acids in length.
Domain of unknown function DUF4484 (DUF4484)
Type: Domain

This domain is often found at the the C terminus of

. Its function is not known.
Tautomerase, cis-CaaD-like (Cis-CaaD-like)
Type: Domain

Cis-3-chloroacrylic acid dehalogenase (cis-CaaD) represents the first characterised member of a new family in the tautomerase superfamily . It is not a 4-oxalocrotonate (4-OT) tautomerase, but it probably resulted from an independent duplication of a 4-OT-like sequence . cis-CaaD is part of a bacterial pathway for the degradation of the soil fumigant 1,3-dichloropropene .
Chibby family (Chibby_fam)
Type: Family

This family from eukaryotes includes the chibby proteins and spermatid-associated protein (Spert). Chibby proteins inhibit the wingless/Wnt pathway by binding to beta-catenin and inhibiting beta-catenin-mediated transcriptional activation. Chibby is Japanese for small, and is named after the RNAi phenotype seen in Drosophila . Spermatid-associated protein is expressed in the flower-like structure in spermatids and its function is unclear .
Snapin/Pallidin/Snn1 (Snapin/Pallidin/Snn1)
Type: Family

This family of proteins includes snapin, which is associated with the SNARE complex that mediates synaptic vesicle docking and fusion . This family also includes the yeast snapin-like protein, Snn1, which is a part of a complex involved in endosomal cargo sorting , and pallidin - a component of a complex involved in biogenesis of lysosome-related organelles .
Apolipoprotein C-IV (APOC4)
Type: Family

Apolipoprotein C-IV, also known as apolipoprotein C4, may play a role in lipid metabolism .
TMEM213 family (TMEM213)
Type: Family

This family of proteins is found in eukaryotes. The function of this family is unknown.
FAM24 family (FAM24)
Type: Family

This family of proteins is found in eukaryotes. There are two conserved sequence motifs: FDLRT and CLY. The function of this family is unknown.
TMEM210 family (TMEM210)
Type: Family

This family of proteins is found in eukaryotes. The function of this family is unknown.
Small acidic protein-like domain (SMAP_dom)
Type: Domain

This domain is found in eukaryotes, and is approximately 70 amino acids in length. It contains a single completely conserved residue G that may be functionally important. It is found in some uncharacterised proteins, including some described as small acidic protein.
Spexin (Spexin)
Type: Family

Spexin, alternatively named NPQ, is a peptide hormone and is derived from a pro-hormone. This family of proteins has a role in inducing stomach wall contraction and is expressed in the submucosal layer of the mouse oesophagus and stomach. Spexin, like most peptide hormones, is a ligand for G-protein coupled receptors . Spexin is also thought to have a role in controlling arterial blood pressure as well as salt and water balance .