SII-SWORD/CoKE huggingface dataset:
Transmembrane protein TMEM132, sixth domain (Ig_TMEM132_6th)
Type: Domain

This is the sixth domain of TMEM132 family of proteins. This domain includes a β-hairpin extension which is swapped with the N-terminal domain to complete its β-sandwich fold.

The transmembrane protein 132 family (TMEM132) consists of TMEM132A, TMEM132B, TMEM132C, TMEM132D, TMEM132E. These are transmembrane proteins that regulate neuronal structure and function. In mammalian cells, they may regulate NAP1 in the WAVE regulatory complex (WRC) to finely modulate actin nucleation, cellular cytoskeletal and morphological changes . TMEM132 members have been associated with panic disorders, anxiety and major depressive disorders .

TMEM132A may play a role in embryonic and postnatal development of the brain. It increased resistance to cell death induced by serum starvation in cultured cells. It regulates cAMP-induced GFAP gene expression via STAT3 phosphorylation .

These proteins consist of six globular domains: N-terminal

, 2nd

, 3rd

, 4th

, 5th

and 6th

. The latter three are a tandem of Ig-like domains .

represents the C-terminal region which includes a single transmembrane helix.
Trafficking protein particle complex II-specific subunit 65, IgD1 (IgD1_Trs65)
Type: Domain

This entry represents the IgD1 domain of Trs65 and similar proteins from Saccharomycetales.

This entry includes Trafficking protein particle complex II-specific subunit 65 from Saccharomyces cerevisiae (Trp65), an essential subunit of the TRAPP Golgi trafficking complex . TRAPP subunits are found in three forms-core TRAPP/TRAPPI, TRAPPII, and TRAPPIII and they function in various vesicle trafficking pathways. TRAPPI mediates transport from endoplasmic reticulum to cis-Golgi by tethering COPII-coated vesicles; TRAPPII interacts with COPI-coated vesicles in mammalian cells and aids in endosome-to-Golgi transport, and TRAPPIII plays a unique role in autophagy. TRAPP complexes act as GEFs and play an essential role in catalysing nucleotide exchange for Ypt/Rab GTPase. The three complexes share a core of six different proteins (Bet3, Bet5, Trs20, Trs23, Trs31, and Trs33) that make up core TRAPPI. TRAPPII contains four additional proteins (Trs120, Trs130, Trs65, and Tca17), and TRAPPIII has one additional Trs85 in yeast . While Trp65 has been implicated in cell wall biogenesis and stress response, the role of Trs65 in TRAPPII is supported by the findings that the protein co-localises with Trs130p, and deletion of Trs65 in yeast leads to a conditional lethal phenotype if either one of the other TRAPPII-specific subunits is modified . Trs65 is essential to the formation of TRAPPII dimer and consists of three Ig-like domains (IgD1, IgD2 and IgD3) .
Trafficking protein particle complex II-specific subunit 65, IgD2 (IgD2_Trs65)
Type: Domain

This entry represents the IgD2 domain of Trs65 and similar proteins from Saccharomycetales.

This entry includes Trafficking protein particle complex II-specific subunit 65 from Saccharomyces cerevisiae (Trp65), an essential subunit of the TRAPP Golgi trafficking complex . TRAPP subunits are found in three forms-core TRAPP/TRAPPI, TRAPPII, and TRAPPIII and they function in various vesicle trafficking pathways. TRAPPI mediates transport from endoplasmic reticulum to cis-Golgi by tethering COPII-coated vesicles; TRAPPII interacts with COPI-coated vesicles in mammalian cells and aids in endosome-to-Golgi transport, and TRAPPIII plays a unique role in autophagy. TRAPP complexes act as GEFs and play an essential role in catalysing nucleotide exchange for Ypt/Rab GTPase. The three complexes share a core of six different proteins (Bet3, Bet5, Trs20, Trs23, Trs31, and Trs33) that make up core TRAPPI. TRAPPII contains four additional proteins (Trs120, Trs130, Trs65, and Tca17), and TRAPPIII has one additional Trs85 in yeast . While Trp65 has been implicated in cell wall biogenesis and stress response, the role of Trs65 in TRAPPII is supported by the findings that the protein co-localises with Trs130p, and deletion of Trs65 in yeast leads to a conditional lethal phenotype if either one of the other TRAPPII-specific subunits is modified . Trs65 is essential to the formation of TRAPPII dimer and consists of three Ig-like domains (IgD1, IgD2 and IgD3) .
Trafficking protein particle complex subunit 13, N-terminal (TRAPPC13_N)
Type: Domain

This entry represents the N-terminal domain, which may adopt a β-sandwich fold with an insertion at the very N-terminal consisting of a short β-strand and α-helix connected by a long loop.

Trafficking protein particle complex subunit 13 (TRAPPC13) is involved in regulating autophagy and survival in response to small molecule compound-induced Golgi stress . It is the mammal homologue of Trs65 from yeast, part of TRAPPII complex which interacts with COPI-coated vesicles in mammalian cells and aids in endosome-to-Golgi transport.
Trafficking protein particle complex subunit 13, C-terminal (TRAPPC13_C)
Type: Domain

This entry represents the C-terminal domain of TRAPPC13 which is predicted to adopt an Ig-like fold.

Trafficking protein particle complex subunit 13 (TRAPPC13) is involved in regulating autophagy and survival in response to small molecule compound-induced Golgi stress . It is the mammal homologue of Trs65 from yeast, part of TRAPPII complex which interacts with COPI-coated vesicles in mammalian cells and aids in endosome-to-Golgi transport.
Trafficking protein particle complex subunit 13, middle domain (TRAPPC13_M)
Type: Domain

This entry represents the middle domain of TRAPPC13 which is predicted to adopt a β-sandwich fold.

Trafficking protein particle complex subunit 13 (TRAPPC13) is involved in regulating autophagy and survival in response to small molecule compound-induced Golgi stress . It is the mammal homologue of Trs65 from yeast, part of TRAPPII complex which interacts with COPI-coated vesicles in mammalian cells and aids in endosome-to-Golgi transport.
Pre-mRNA-splicing factor Syf1/CRNKL1-like, C-terminal HAT-repeats domain (HAT_Syf1_CNRKL1_C)
Type: Domain

This entry includes a group of pre-mRNA-processing factors that are components of the spliceosome that are involved in pre-RNA splicing, including Syf1 from human and its homologues from fungi, crooked neck from Drosophila and its homologues from human and fungi Crooked neck-like protein 1 (CRNKL1/SYF-3) and CFL1, respectively. These proteins contain HAT (Half A TPR) repeats which have a repetitive pattern characterised by three aromatic residues with a conserved spacing. They are structurally and sequentially similar to TPRs . The HAT repeats in these proteins can be divided in three segments, N-terminal, central and C-terminal. This entry represents the C-terminal HAT repeats of these proteins, which make contacts with other proteins in the complex, to stabilise it.
Anti-sigma factor RsgI-like, middle domain (RsgI_M)
Type: Domain

The heat shock genes in B. subtilis can be classified into several groups according to their regulation , and the sigma gene, sigI, of Bacillus subtilis belongs to the group IV heat-shock response genes and has many orthologues in firmicutes . Regulation of sigma factor I is carried out by RsgI from the same operon. This entry represents the middle cytoplasmic region of RsgI, which is found C-terminal to the single transmembrane helix which has been shown to interact directly with Sigma-I .
STING, ligand-binding domain (STING_LBD)
Type: Domain

This entry represents the ligand-binding domain (LBD) of Transmembrane protein 173 which binds to c-di-GMP . Cyclic dinucleotides induce a conformational change to the STING LBD, leading to high-order oligomerization of STING that is essential for triggering the downstream signalling pathways .

Transmembrane protein 173, also known as stimulator of interferon genes protein (STING), is a transmembrane adaptor protein which is involved in innate immune signalling processes. It induces expression of type I interferons (IFN-alpha and IFN-beta) via the NF-kappa-B and IRF3, pathways in response to non-self cytosolic RNA and dsDNA. It consists of an N-terminal transmembrane (TM) and a C-terminal ligand-binding (LBD) domains.
Pre-mRNA-splicing factor Syf1-like, N-terminal HAT-repeats domain (HAT_Syf1-like_N)
Type: Domain

This entry includes a group of pre-mRNA-processing factors that are components of the spliceosome, involved in pre-RNA splicing, including Syf1 from human and its homologues from fungi, CFL1. These proteins contain HAT (Half A TPR) repeats which have a repetitive pattern characterised by three aromatic residues with a conserved spacing. They are structurally and sequentially similar to TPRs . The HAT repeats in these proteins can be divided in three segments, N-terminal, central and C-terminal. This entry represents the N-terminal HAT repeats that in Syf1 and Syf3 contact the U2 core domain via the U2' protein .
STING, transmembrane domain (STING_TM)
Type: Domain

This entry represents the transmembrane domain (TM) of Transmembrane protein 173 which contains a cryptic pocket involved in inter-dimer interactions that mediate the formation of the high-order oligomer .

Transmembrane protein 173, also known as stimulator of interferon genes protein (STING), is a transmembrane adaptor protein which is involved in innate immune signalling processes. It induces expression of type I interferons (IFN-alpha and IFN-beta) via the NF-kappa-B and IRF3, pathways in response to non-self cytosolic RNA and dsDNA. It consists of an N-terminal transmembrane (TM) and a C-terminal ligand-binding (LBD) domains.
TMEM131L, third Ig-like domain (Ig_TMEM131L_3)
Type: Domain

This entry represents the third Ig-like domain of TMEM131L and the fourth in TMEM131.

Transmembrane protein 131-like (TMEM131L) was identified as a negative regulator of thymocyte proliferation that acts through mixed Wnt-dependent and independent mechanisms. It has two isoforms, L and S, which have different subcellular localisation. L isoform, the membrane-associated form, inhibits canonical Wnt/beta-catenin signalling through the induction of lysosome-dependent degradation of the active phosphorylated form of the LRP6 coreceptor. This protein was firstly described as containing three conserved homology domains (CHD1, 2 and 3), a transmembrane region and a C-terminal serine-rich region . Using structure prediction models from AlphaFold, it has been possible to identify the CHDs as Ig-like domains.

TMEM131 is a collagen binding transmembrane protein involved in collagen secretion by recruiting the ER-to-Golgi transport complex TRAPPIII . Human TMEM131 is predicted to contain eight Ig-like domains.
TMEM131L, fourth Ig-like domain (Ig_TMEM131L_4)
Type: Domain

This entry represents the fourth Ig-like domain of TMEM131L while in TMEM131 represents the seventh one.

Transmembrane protein 131-like (TMEM131L) was identified as a negative regulator of thymocyte proliferation that acts through mixed Wnt-dependent and independent mechanisms. It has two isoforms, L and S, which have different subcellular localisation. L isoform, the membrane-associated form, inhibits canonical Wnt/beta-catenin signalling through the induction of lysosome-dependent degradation of the active phosphorylated form of the LRP6 coreceptor. This protein was firstly described as containing three conserved homology domains (CHD1, 2 and 3), a transmembrane region and a C-terminal serine-rich region . Using structure prediction models from AlphaFold, it has been possible to identify the CHDs as Ig-like domains.

TMEM131 is a collagen binding transmembrane protein involved in collagen secretion by recruiting the ER-to-Golgi transport complex TRAPPIII . Human TMEM131 is predicted to contain eight Ig-like domains.
TMEM131L, fifth Ig-like domain (TMEM131L_Ig_5)
Type: Domain

This entry represents the fifth Ig-like domain of TMEM131L which is eighth in TMEM131.

Transmembrane protein 131-like (TMEM131L) was identified as a negative regulator of thymocyte proliferation that acts through mixed Wnt-dependent and independent mechanisms. It has two isoforms, L and S, which have different subcellular localisation. L isoform, the membrane-associated form, inhibits canonical Wnt/beta-catenin signalling through the induction of lysosome-dependent degradation of the active phosphorylated form of the LRP6 coreceptor. This protein was firstly described as containing three conserved homology domains (CHD1, 2 and 3), a transmembrane region and a C-terminal serine-rich region . Using structure prediction models from AlphaFold, it has been possible to identify the CHDs as Ig-like domains.

TMEM131 is a collagen binding transmembrane protein involved in collagen secretion by recruiting the ER-to-Golgi transport complex TRAPPIII . Human TMEM131 is predicted to contain eight Ig-like domains.
Succinylglutamate desuccinylase/Aspartoacylase, catalytic domain (AstE_AspA_cat)
Type: Domain

This entry represents the catalytic domain found in Succinylglutamate desuccinylase (AstE), aspartoacylase (AspA) and related enzymes. AstE catalyses the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway whereas AspA cleaves acylaspartate into a fatty acid and aspartate. Mutations in human AspA lead to Canavan disease . The domain represented by this entry contains the residues which are essential for catalysis and has structural similarity to catalytic domains of enzymes that are members of the Zn-dependent exopeptidases clan .
EML-like, first beta-propeller domain (Beta-prop_EML_1st)
Type: Domain

This entry represents the first β-propeller domain of echinoderm microtubule-associated protein (EMAP)-like (EML) proteins . This model completes the first β-propeller of the TAPE pair in EMLs. In some members, such as EML5 and EML6, there are three TAPE pairs.

This entry also includes Cilia- and flagella-associated protein 44, EMAP and Ciliary WD repeat-containing protein ctxp80.

EML proteins contribute to the formation of the mitotic spindle and interphase microtubule network . In these proteins, the β-propellers are intimately associated as a pair, which was defined as a tandem atypical propeller in EMLs (TAPE) domain. There is a hydrophobic core between the propellers, which corresponds to the HELP motif (

) that contributes blades 1 and 14 buried at the interface and joins them .
WDR90, 4th beta-propeller domain (Beta-prop_WDR90_4th)
Type: Domain

This entry represents the fourth β-propeller domain found in WD repeat-containing protein 90 from mouse and human. WDR90 proteins constitute an evolutionary conserved central core microtubule triplet component that is essential for maintaining the inner centriolar scaffold components in centrioles . This entry also includes Cilia- and flagella-associated protein 52 from Chlamydomonas reinhardtii which may play a role in cell growth and/or survival.
WDR90/POC16, second beta-propeller domain (Beta-prop_WDR90_POC16_2nd)
Type: Domain

This entry represents the second β-propeller domain found in WD repeat-containing protein 90 (WDR90) from animals, and the homologue protein POC16 from Chlamydomonas reinhardtii. WDR90 is proposed to be localised in the centriole and required for ciliogenesis . The similarities between WDR90 and the flagellar inner B-microtubule protein FAP52/WDR16 lead to the proposal that the WD40 domains of WDR90 might be located within the B-microtubule of the centriole triplet .
EML-like, second beta-propeller domain (Beta-prop_EML-like_2nd)
Type: Domain

This entry represents β-propeller domains of echinoderm microtubule-associated protein (EMAP)-like (EML) proteins . This model completes the second β-propeller of the TAPE pair in EMLs. In some members, such as EML5 and EML6, there are three TAPE pairs. The first β-propeller of the pair is represented in

.

This entry also includes Superkiller complex protein 8 from Xenopus laevis, LST8 homologue from Drosophila melanogaster, Cilia- and flagella-associated protein 57 (CFA57) from animals, among others. In CFA57, this entry covers the second β-propeller domain, a protein that associates with components of the nexin-dynein regulatory complex (N-DRC), a key regulator of ciliary/flagellar motility, and might act as an inner dynein arm (IDA) hub or linkage . This entry also includes will decrease acetylation (wda) in Drosophila melanogaster.

EML proteins contribute to the formation of the mitotic spindle and interphase microtubule network . In these proteins, the β-propellers are intimately associated as a pair, which was defined as a tandem atypical propeller in EMLs (TAPE) domain. There is a hydrophobic core between the propellers, which corresponds to the HELP motif (

) that contributes blades 1 and 14 buried at the interface and joins them .
Proteasome adapter and scaffold protein ECM29, HEAT-repeat domain (HEAT_ECM29)
Type: Domain

This entry represents a HEAT-repeat domain found in ECM29, an adapter/scaffolding protein that binds to the 26S proteasome, motor proteins and other compartment specific proteins . This domain is found in the C-terminal half of ECM29, which binds kinesin and myosin .
ECM29, ARM-like repeats domain (ARM_ECM29)
Type: Domain

This is a region of armadillo-like repeats found in human Proteasome adapter and scaffold protein ECM29 and similar protein sequences found in animals and some uncharacterised plant and fungal proteins. ECM29 binds to the 26S proteasome, motor proteins and other compartment specific proteins. This entry is often found C-terminal to

.
ARMC5-like, ARM-repeats domain (ARM_ARMC5)
Type: Domain

This entry represents the ARM-repeats domain of ARMC5 from animal, a protein involved in fetal development, T-cell function and adrenal gland growth homeostasis. It negatively regulates adrenal cells survival. It plays a role in steroidogenesis, modulates steroidogenic enzymes expression and cortisol production . This domain is also found in human ARMC3 and a group of uncharacterised proteins mainly from vertebrates and arthropods.
ATP-dependent RecD2 DNA helicase, OB-fold domain (RecD2_N_OB)
Type: Domain

This entry represents a domain which is found N-terminal in ATP-dependent RecD2 DNA helicase (also known as YrrC) and related bacterial proteins. RecD2 may favour replication restart by preventing RecA from binding to blocked replication forks, avoiding unnecessary recombination during replication restart. It fuctions as a negative modulator of the RecA-ssDNA filament, may dissasemble RecA threads and is able to act as both a positive and negative regulator of strand exchange . This domain is predicted to adopt a β-barrel with an OB-fold topology.
Spike glycoprotein G, central domain, rhabdovirus (Rhabdo_glycop_CD)
Type: Domain

This entry represents the central domain (CD) which consists of domains I (β-sheet rich) and II (α-helical) ).

The glycoprotein G from rhabdoviruses, such as rabies virus (RABV), Mokola virus (MOKV) and European bat lyssavirus 1 (EBLV) attaches the virus to host cellular receptor, and induces endocytosis of the virion. It forms the glycoprotein spike which is made up of a trimer of G proteins. Each protomer of the trimer is composed of three domains: a membrane-distal pleckstrin homology domain (PH), a membrane-proximal fusion domain (FD) and a laterally positioned central domain (CD) .

Different families of ssRNA negative-strand viruses contain glycoproteins responsible for forming spikes on the surface of the virion. The glycoprotein spike is made up of a trimer of glycoproteins. These proteins are frequently abbreviated to G protein. Channel formed by glycoprotein spike is thought to function in a similar manner to Influenza virus M2 protein channel, thus allowing a signal to pass across the viral membrane to signal for viral uncoating .
Glycoprotein G, PH domain, rhabdovirus (PH_Rhabdo_glycop)
Type: Domain

This entry represents the PH domain (also known as the neck domain) .

The glycoprotein G from rhabdoviruses, such as rabies virus (RABV), Mokola virus (MOKV) and European bat lyssavirus 1 (EBLV) attaches the virus to host cellular receptor, and induces endocytosis of the virion. It forms the glycoprotein spike which is made up of a trimer of G proteins. Each protomer of the trimer is composed of three domains: a membrane-distal pleckstrin homology domain (PH), a membrane-proximal fusion domain (FD) and a laterally positioned central domain (CD) .

Different families of ssRNA negative-strand viruses contain glycoproteins responsible for forming spikes on the surface of the virion. The glycoprotein spike is made up of a trimer of glycoproteins. These proteins are frequently abbreviated to G protein. Channel formed by glycoprotein spike is thought to function in a similar manner to Influenza virus M2 protein channel, thus allowing a signal to pass across the viral membrane to signal for viral uncoating .
INO80 complex subunit 3-like, middle region (Iec3-like_M)
Type: Domain

This entry represents the middle region of a group of fungal sequences that are homologues of the INO80 complex subunit 3 (Iec3) from S.pombe. They differ in this region that is absent on the S.pombe homologue which only consists of an α-helix. According to structure predictions, this section may adopt an arrangement of short helices connected by loops. The C-terminal region is disordered.
AP-5 complex subunit zeta-1, ARM repeats domain (AP5Z1_ARM)
Type: Domain

This entry represents a region of ARM-repeats in human AP-5 complex subunit zeta-1.

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 . AP5Z1 is part of AP-5, a probable fifth adaptor protein complex that may be involved in endosomal transport. This protein has been associated with hereditary spastic paraplegia .
CATSPERD, Ig-like domain (Ig-like_CATSPERD)
Type: Domain

This entry represents a Ig-like domain found in the central region of the delta subunit (CATSPERD) .

The CATSPER (cation channel of sperm) complex is a tetrameric complex consisting of CATSPER1, CATSPER2, CATSPER3 and CATSPER4, it 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.
TRAPP14, C-terminal (TRAPP14_C)
Type: Domain

This entry includes Trafficking protein particle complex subunit 14 (TRAPP14), which is a specific subunit of the TRAPP (transport protein particle) II complex, a conserved vesicle tethering complex that functions in late Golgi trafficking as a membrane tether . This entry represents the C-terminal domain which is predicted to adopt an Ig-like fold.
TRAPP14, N-terminal (TRAPP14_N)
Type: Domain

This entry includes Trafficking protein particle complex subunit 14 (TRAPP14), a specific subunit of the TRAPP (transport protein particle) II complex, a conserved vesicle tethering complex that functions in late Golgi trafficking as a membrane tether . This entry represents the N-terminal region consisting of two domains which are predicted to adopt an Ig-like fold, where distant amino acids in the sequence contribute to different β-sheets in the structure.
CCR4-NOT transcription complex subunit 1-like, NOT1 connector (CNOT1-like_NOT1_connector)
Type: Domain

This entry represents a region of human CCR4-NOT transcription complex subunit 1 (CNOT1), an scaffolding component of the CCR4-NOT complex, which is one of the major cellular mRNA deadenylases. This region shows several repeats of the HEAT type . Members of this group are predominantly found in animals and fungal and uncharacterised plant sequences.