SII-SWORD/CoKE huggingface dataset:
SESTD1-like, spectrin repeats region (Spectrin_SESTD1)
Type: Domain

This region of spectrin repeats is found in human SEC14 domain and spectrin repeat-containing protein 1 (SESTD1) and similar animal proteins. SESTD1 is a regulator of the transient receptor potential channels TRPC4 and TRPC5 .
ACT domain-containing protein ACR9/10, C-terminal domain (ACT_ACR9/10_C)
Type: Domain

This ACT domain is found at the C-terminal of ACT domain-containing proteins ACR9/10 from from Arabidopsis thaliana and similar plant proteins. They may bind amino acids . Plant ACT DOMAIN REPEAT (ACR) proteins may also serve as nutrient sensors. ACR9 might function as a repressor in glucose (Glc) signalling pathways. It is highly expressed in the leaves, and its expression is downregulated by sugars .
Stabilin-1/2, EGF-like domain (EGF_STAB1-2)
Type: Domain

This entry represents EGF-like domains found in Stabilin-1 and 2 (STAB1/2), proteins that act as a scavenger receptors for acetylated low density lipoproteins. They bind Gram-positive and Gram-negative bacteria and may play a role in defence against bacterial infection . These proteins are also involved in the delivery of newly synthesised CHID1/SI-CLP (stabilin-1 interacting chitinase-like protein) from the biosynthetic compartment to the endosomal/lysosomal system . Members of this group are mainly found in vertebrates.
FHL1/2/3/5, N-terminal LIM domain (LIM_FHL1/2/3/5_N)
Type: Domain

This entry represents the N-terminal LIM domain of Four and a half LIM domains proteins 1/2/3/5 (FHL1/2/3/5) and related animal sequences. FHL3 is recruited by SOX15 to FOXK1 promoters where it acts as a transcriptional coactivator of FOXK1. FHL2 may function as a molecular transmitter linking various signalling pathways to transcriptional regulation. It inhibits the transcriptional activity of FOXO1 and its apoptotic function by enhancing the interaction of FOXO1 with SIRT1 and OXO1 deacetylation .
AAA protein, C-terminal winged helix domain (HTH_AAA)
Type: Domain

This domain is found at the C-terminal end of a group of uncharacterised fungal proteins that contain the AAA ATPase domain

at the N terminus. This domain is predicted to have a winged helix configuration.
GCN1-like, HEAT repeats (HEAT_GCN1_fung)
Type: Domain

This region of HEAT repeats is found in eIF-2-alpha kinase activator GCN1 from Saccharomyces cerevisiae and similar fungal sequences. GCN1 is a ribosome collision sensor that activates a translation quality control pathway when a ribosome has stalled during translation .
Stalled ribosome sensor GCN1-like, N-terminal (GNC1-like_N)
Type: Domain

This entry represents a region that consists of four HEAT repeats found towards the N-terminal of the stalled ribosome sensor GCN1, a ribosome collision sensor that plays a key role in the RNF14-RNF25 translation quality control pathway, a pathway that takes place when a ribosome has stalled during translation, and which promotes ubiquitination and degradation of translation factors on stalled ribosomes . This entry also includes Protein ILITYHIA (ILA) from Arabidopsis, a protein involved in immunity against bacterial infection and in non-host resistance .
RNA-binding domain, fungi (RRM_fung)
Type: Domain

This is a predicted RNA-binding domain, also known as RNA recognition motif (RRM) found in a group of uncharacterised proteins from fungi. This domain is often found associated with
GIL1/IRKI, C-terminal domain (GIL1_IRKI_C)
Type: Domain

This domain is found in the Protein GRAVITROPIC IN THE LIGHT 1 (GIL1), its paralogue IRK-interacting protein (IRKI) from Arabidopsis thaliana and related plant proteins. This domain is predicted to fold into a structure similar to head domain of nucleotide exchange factor GrpE (

). GIL1 is essential for light-dependent randomisation of hypocotyl growth orientation .
GIPC1-3, GH1 domain (GIPC1-3_GH1)
Type: Domain

This entry represents the GIPC homology 1 (GH1) domain found in the GIPC proteins (GAIP interacting protein, C terminus) 1-3, PDZ domain-containing proteins, and similar animal sequences.

GIPC1-3 may act as scaffold proteins linking heterotrimeric G-proteins to seven-transmembrane-type WNT receptor or to receptor tyrosine kinases . They might play key roles in carcinogenesis and embryogenesis through modulation of growth factor signalling and cell adhesion . GIPCs are proteins with a GIPC homology 1 (GH1) domain, a central PDZ domain and a GH2 domain.
ACT domain-containing protein ACR2/9/10, N-terminal domain (ACR2/9/10_N)
Type: Domain

This is the ACT domain found at the N-terminal of ACT domain-containing protein ACR2/9/10 from Arabidopsis thaliana and similar plant proteins. They may bind amino acids . Plant ACT DOMAIN REPEAT (ACR) proteins may also serve as nutrient sensors. ACR9 might function as a repressor in glucose (Glc) signalling pathways. It is highly expressed in the leaves, and its expression is downregulated by sugars .
Glucose-1-phosphate adenylyltransferase/Bifunctional protein GlmU-like, C-terminal hexapeptide (GlmU/GlgC-like_hexapep)
Type: Domain

This domain is found at the C-terminal end of bacterial and plant glucose-1-phosphate adenylyltransferases (GlgC) and Bifunctional protein GlmU, including GlmU from Streptococcus pneumoniae. This domain is responsible for the transfer of acetyl group from acetyl coenzyme A to glucosamine-1-phosphate (GlcN-1-P) to produce N-acetylglucosamine-1-phosphate (GlcNAc-1-P). It consists of hexapeptide repeats that form a left-handed β-helix .
Acyl-CoA-binding domain-containing protein 4-6, C-terminal (ACBP4-6_C)
Type: Domain

This entry represents a long α-helix found at the C terminus of the cytosolic acyl-CoA-binding domain-containing proteins 4/5 (ACBP4/5) from Arabidopsis and ACBP6 from rice. They play a role in the biosynthesis of membrane lipids including galactolipids and phospholipids. They bind medium- and long-chain acyl-CoA esters with very high affinity . ACBPs also play a role in stress responses, such as drought, cold, heat, salinity, oxidative stress, and pathogen attacks . These proteins have a Kelch repeats β-propeller in the middle region and an acyl CoA binding domain at the N-terminal (

).
Teneurin, TTR-like domain (TEN_TTR-like)
Type: Domain

This entry represents the transthyretin-like (TTR-like) domain found in animal teneurins, ancient cell-cell adhesion receptors that are vital for brain development and synapse organisation .

Teneurins are a family of phylogenetically conserved transmembrane glycoproteins expressed during pattern formation and morphogenesis . Originally discovered as ten-m and ten-a in Drosophila melanogaster, the teneurin family is conserved from Caenorhabditis elegans (ten-1) to vertebrates, in which four paralogs exist (teneurin-1 to -4 or odz-1 to -4). Their distinct domain architecture is highly conserved between invertebrate and vertebrate teneurins, particularly in the extracellular part. The intracellular domains of Ten-a, Ten-m/Odz and C. elegans Ten-1 are significantly different, both in size and structure, from the comparable domains of vertebrate teneurins, but the extracellular domains of all of these proteins are remarkably similar.

The large C-terminal extracellular domain consists of eight EGF-like repeats (see

), a region of conserved cysteines and unique YD-repeats. The N-terminal intracellular domain of vertebrate teneurins contains two EF-hand-like calcium-binding motifs and two polyproline regions involved in protein-protein interactions, followed by a single-span transmembrane domain. The intracellular domain is linked to the cytoskeleton through its interaction with the adaptor protein CAP/ponsin and can be cleaved near (or possibly in) the transmembrane domain and transported to the nucleus , giving teneurins the potential to act as transcription factors

,

]. There is considerable divergence between intracellular domains of invertebrate and vertebrate teneurins as well as between different invertebrate proteins .

Teneurin proteins are involved in the development and function of the nervous system . They are ancient cell-cell adhesion receptors that play a vital role in establishing precise connectivity within the nervous system, including the formation of topographic projections, dendrite morphogenesis, and axon targeting . These proteins mediate both homophilic and heterophilic cell-cell adhesion, which is essential for synapse assembly and the formation of neural circuits. They also act as ligands for specific receptors, contributing to axon guidance and intracellular signal transduction. Additionally, certain members are implicated in gene transcription regulation, cytoskeleton reorganisation, and neuroplasticity. Teneurins may also contribute to the differentiation of specific cell types, and play roles in stress response and neuroprotection. Their functions are fundamental to neural development and the establishment of proper nervous system connectivity .
Teneurin, NHL domain (TEN_NHL)
Type: Domain

This entry represents the NHL six-bladed β-propeller domain found in teneurins which packs against the TTR, FN and shell domains with the bottom face and is held in place by the FN domain which acts as a wedge to position the NHL at an angle perpendicular to the YD-shell domain . The top face of the NHL propeller contains extended loops, stabilised by five disulphide bonds, which are highly conserved among vertebrates members .

Teneurins are a family of phylogenetically conserved transmembrane glycoproteins expressed during pattern formation and morphogenesis . Originally discovered as ten-m and ten-a in Drosophila melanogaster, the teneurin family is conserved from Caenorhabditis elegans (ten-1) to vertebrates, in which four paralogs exist (teneurin-1 to -4 or odz-1 to -4). Their distinct domain architecture is highly conserved between invertebrate and vertebrate teneurins, particularly in the extracellular part. The intracellular domains of Ten-a, Ten-m/Odz and C. elegans Ten-1 are significantly different, both in size and structure, from the comparable domains of vertebrate teneurins, but the extracellular domains of all of these proteins are remarkably similar.

The large C-terminal extracellular domain consists of eight EGF-like repeats (see

), a region of conserved cysteines and unique YD-repeats. The N-terminal intracellular domain of vertebrate teneurins contains two EF-hand-like calcium-binding motifs and two polyproline regions involved in protein-protein interactions, followed by a single-span transmembrane domain. The intracellular domain is linked to the cytoskeleton through its interaction with the adaptor protein CAP/ponsin and can be cleaved near (or possibly in) the transmembrane domain and transported to the nucleus , giving teneurins the potential to act as transcription factors

,

]. There is considerable divergence between intracellular domains of invertebrate and vertebrate teneurins as well as between different invertebrate proteins .

Teneurin proteins are involved in the development and function of the nervous system . They are ancient cell-cell adhesion receptors that play a vital role in establishing precise connectivity within the nervous system, including the formation of topographic projections, dendrite morphogenesis, and axon targeting . These proteins mediate both homophilic and heterophilic cell-cell adhesion, which is essential for synapse assembly and the formation of neural circuits. They also act as ligands for specific receptors, contributing to axon guidance and intracellular signal transduction. Additionally, certain members are implicated in gene transcription regulation, cytoskeleton reorganisation, and neuroplasticity. Teneurins may also contribute to the differentiation of specific cell types, and play roles in stress response and neuroprotection. Their functions are fundamental to neural development and the establishment of proper nervous system connectivity .
Teneurin, YD-shell (TEN_YD-shell)
Type: Domain

This entry represents the YD-shell domain found in Teneurins which forms a hollow tube, consisting of a single up-and-down spiralling β-sheet with 78 strands and shows similarity to structures of bacterial toxin complexes TcB-TcC. This domain is the most most structurally conserved region of Teneurins and the TcB-TcC toxin complexes . This big domain comprises YD or rearrangement hotspot (Rhs) repeats.

Teneurins are a family of phylogenetically conserved transmembrane glycoproteins expressed during pattern formation and morphogenesis . Originally discovered as ten-m and ten-a in Drosophila melanogaster, the teneurin family is conserved from Caenorhabditis elegans (ten-1) to vertebrates, in which four paralogs exist (teneurin-1 to -4 or odz-1 to -4). Their distinct domain architecture is highly conserved between invertebrate and vertebrate teneurins, particularly in the extracellular part. The intracellular domains of Ten-a, Ten-m/Odz and C. elegans Ten-1 are significantly different, both in size and structure, from the comparable domains of vertebrate teneurins, but the extracellular domains of all of these proteins are remarkably similar.

The large C-terminal extracellular domain consists of eight EGF-like repeats (see

), a region of conserved cysteines and unique YD-repeats. The N-terminal intracellular domain of vertebrate teneurins contains two EF-hand-like calcium-binding motifs and two polyproline regions involved in protein-protein interactions, followed by a single-span transmembrane domain. The intracellular domain is linked to the cytoskeleton through its interaction with the adaptor protein CAP/ponsin and can be cleaved near (or possibly in) the transmembrane domain and transported to the nucleus , giving teneurins the potential to act as transcription factors

,

]. There is considerable divergence between intracellular domains of invertebrate and vertebrate teneurins as well as between different invertebrate proteins .

Teneurin proteins are involved in the development and function of the nervous system . They are ancient cell-cell adhesion receptors that play a vital role in establishing precise connectivity within the nervous system, including the formation of topographic projections, dendrite morphogenesis, and axon targeting . These proteins mediate both homophilic and heterophilic cell-cell adhesion, which is essential for synapse assembly and the formation of neural circuits. They also act as ligands for specific receptors, contributing to axon guidance and intracellular signal transduction. Additionally, certain members are implicated in gene transcription regulation, cytoskeleton reorganisation, and neuroplasticity. Teneurins may also contribute to the differentiation of specific cell types, and play roles in stress response and neuroprotection. Their functions are fundamental to neural development and the establishment of proper nervous system connectivity .
GPI inositol-deacylase, transmembrane domain (PGAP1_TMD)
Type: Domain

This domain is found at the C-terminal end of GPI inositol-deacylase (BST1, also known as PGAP1) and related proteins from vertebrates and fungi. This transmembrane domain (TMD) consists of 10 transmembrane helices that are mostly perpendicular to the membrane, with the exception of a long TMH4 which crosses the membrane diagonally .

PGAP1 is an endoplasmic reticulum membrane protein with a catalytic serine-containing motif that is conserved in a number of lipases. PGAP1 functions as a GPI inositol-deacylase; this deacylation is important not only for the efficient transport of GPI-anchored proteins from the endoplasmic reticulum to the Golgi body but also for efficient degradation of misfolded GPI-anchored proteins in the ER .
Agd3, C-terminal domain (Agd3_C)
Type: Domain

This entry represents the C-terminal domain of the exopolysaccharide deacetylase Agd3 from Aspergillus fumigatus (

) a protein required for biofilm formation . It forms six β-strands in a seven-stranded β-sandwich, whose function is unknown .
Agd3, deacetylase domain (Agd3_CE)
Type: Domain

This entry represents the carbohydrate esterase (CE) domain of the exopolysaccharide deacetylase Agd3 from Aspergillus fumigatus (

), a protein required for biofilm formation . This domain has structural similarity to members of the carbohydrate esterase family (CE4) but the amino acid sequences is too divergent and constitutes a founding member of a CE family .
Agd3, CBM87 (CBM87_Agd3)
Type: Domain

This entry represents the carbohydrate binding module (CBM) domain found at the N-terminal of the exopolysaccharide deacetylase Agd3 from Aspergillus fumigatus (

), a protein required for biofilm formation . This is the founding member of CBM family 87 .
TEP-1, C-terminal beta-propeller (Beta-prop_TEP1_C)
Type: Domain

This entry represents the β-propeller found at the C-terminal of Telomerase protein component 1 (TEP1), a component of the telomerase ribonucleoprotein complex that is essential for the replication of chromosome termini . It is also a component of the ribonucleoprotein vaults particle, a multi-subunit structure involved in nucleo-cytoplasmic transport .
TEP-1, second beta-propeller (Beta-prop_TEP1_2nd)
Type: Domain

This entry represents the second of three presumed β-propeller domains found at the C-terminal of Telomerase protein component 1 (TEP1), a component of the telomerase ribonucleoprotein complex that is essential for the replication of chromosome termini . It is also a component of the ribonucleoprotein vaults particle, a multi-subunit structure involved in nucleo-cytoplasmic transport .
Tetratricopeptide repeat protein 21A/21B, second ARM domain (ARM_TT21_2nd)
Type: Domain

This entry represents the second ARM-repeats domain found towards the N-terminal of Tetratricopeptide repeat protein 21A (TTC21A) and 21B (TTC21B) from human and its homologues.

TTC21A/B are intraflagellar transport (IFT)-associated proteins required for spermatogenesis. TTC21A is involved in sperm flagellar formation and intraflagellar transport . TTC21B is a component of the IFT complex A (IFT-A), which is required for retrograde ciliary transport. Intraflagellar transport (IFT) is required for cilium assembly and trafficking within cilia . Several diseases results from mutations in the TTC21B gene including nephronophthisis 12, short-rib thoracic dysplasia 4 with or without polydactyly, and Joubert syndrome 11 .
Tetratricopeptide repeat protein 21A/21B, N-terminal ARM repeat (ARM_TT21_N)
Type: Domain

This entry represents the N-terminal segment of ARM repeats of Tetratricopeptide repeat protein 21A (TTC21A) and 21B (TTC21B) from human and its homologues.

TTC21A/B are intraflagellar transport (IFT)-associated proteins required for spermatogenesis. TTC21A is involved in sperm flagellar formation and intraflagellar transport . TTC21B is a component of the IFT complex A (IFT-A), which is required for retrograde ciliary transport. Intraflagellar transport (IFT) is required for cilium assembly and trafficking within cilia . Several diseases results from mutations in the TTC21B gene including nephronophthisis 12, short-rib thoracic dysplasia 4 with or without polydactyly, and Joubert syndrome 11 .
Tetratricopeptide repeat protein 21A/21B, C-terminal ARM domain (ARM_TT21_C)
Type: Domain

This entry represents the C-terminal ARM-repeats domain of Tetratricopeptide repeat protein 21A (TTC21A) and 21B (TTC21B)from human and its homologues.

TTC21A/B are intraflagellar transport (IFT)-associated proteins required for spermatogenesis. TTC21A is involved in sperm flagellar formation and intraflagellar transport . TTC21B is a component of the IFT complex A (IFT-A), which is required for retrograde ciliary transport. Intraflagellar transport (IFT) is required for cilium assembly and trafficking within cilia . Several diseases results from mutations in the TTC21B gene including nephronophthisis 12, short-rib thoracic dysplasia 4 with or without polydactyly, and Joubert syndrome 11 .
Tetratricopeptide repeat protein 21A/21B, fifth ARM repeats domain (ARM_TT21_5th)
Type: Domain

This is the fifth ARM-repeats domain found towards the C-terminal end of Tetratricopeptide repeat protein 21A (TTC21A) and 21B (TTC21B)from human and its homologues.

TTC21A/B are intraflagellar transport (IFT)-associated proteins required for spermatogenesis. TTC21A is involved in sperm flagellar formation and intraflagellar transport . TTC21B is a component of the IFT complex A (IFT-A), which is required for retrograde ciliary transport. Intraflagellar transport (IFT) is required for cilium assembly and trafficking within cilia . Several diseases results from mutations in the TTC21B gene including nephronophthisis 12, short-rib thoracic dysplasia 4 with or without polydactyly, and Joubert syndrome 11 .
Tetratricopeptide repeat protein 21A/21B, fourth ARM domain (ARM_TT21_4th)
Type: Domain

This entry represents the forth ARM-repeats domain found around the middle of Tetratricopeptide repeat protein 21A (TTC21A) and 21B (TTC21B) from human and its homologues.

TTC21A/B are intraflagellar transport (IFT)-associated proteins required for spermatogenesis. TTC21A is involved in sperm flagellar formation and intraflagellar transport . TTC21B is a component of the IFT complex A (IFT-A), which is required for retrograde ciliary transport. Intraflagellar transport (IFT) is required for cilium assembly and trafficking within cilia . Several diseases results from mutations in the TTC21B gene including nephronophthisis 12, short-rib thoracic dysplasia 4 with or without polydactyly, and Joubert syndrome 11 .
IFT122, zinc ribbon domain (Zn_ribbon_IFT122)
Type: Domain

This zinc ribbon domain is found in the human Intraflagellar transport protein 122 homolog (IFT122) and related animal proteins. IFT122 contains two zinc ribbon domains toward the C-terminal. This one is the first of the pair.

Intraflagellar transport protein 122 homolog IFT122 is one of the core components (together with WDR19/IFT144 and IFT140) of the IFT-A complex which is required for retrograde ciliary transport and entry into cilia of G protein-coupled receptors (GPCRs), being involved in cilia function and/or assembly . IFT-A polymerises interacts with IFT-B, and uses an array of β-propeller and TPR domains to create 'carriages' of the IFT train that engage TULP adaptor proteins .
AHK4/CRE1/WOL, first receiver domain (Receiver_AHK4/CRE1_1st)
Type: Domain

This entry represents the first receiver domain found in AtHK4 (also known as CRE1 and WOL) from Arabidopsis thaliana, CRE1 from Medicago truncatula (

) and its homologues from plants such as AtHK2, AtHK3, OsHK5 and OsHK6 . AtHK4/CRE1 is a cytokinin (CK) receptor. Alternative splicing of AtHK4/CRE1 results in fine-tuning the cytokinin signalling pathway . It functions as a histidine kinase and transmits the stress signal to a downstream MAPK cascade. This domain mediates dimerisation through 3D domain swapping, which suggests that a considerable change of conformation must occur upon the phosphorylation reaction to allow HPt (histidine-containing phosphotransfer protein) binding .
Importin-9, central HEAT repeats (HEAT_IPO9_central)
Type: Domain

This entry represents the central HEAT repeat domain found in the human Importin-9 and the yeast orthologue Importin subunit beta-5. Importin-9 is a nuclear transport receptor that mediates nuclear import of proteins, such as histones, proteasome and actin . It consists of 20 tandem HEAT repeats . This entry represents a central segment of HEAT repeats which includes repeats 7-8 that are part of interface 2 that interacts with a five-residue segment of the H2B N-terminal tail described in .
TNRC18/BAHCC1-like, SH3 domain (TNRC18_BAHCC1-like_SH3)
Type: Domain

This SH3 domain is found immediately N-terminal to the Tudor domain (

) in human Trinucleotide repeat-containing gene 18 protein (TNRC18), BAH and coiled-coil domain-containing protein 1 (BAHCC1) and similar proteins mainly found in vertebrates and arthropods. TNRC18 is a chromatin regulator that recognises histone H3 lysine 9 to mediate the silencing of endogenous retroviruses class I . BAHCC1 is highly expressed in human acute leukemia and interacts with transcriptional co-repressors .