SII-SWORD/CoKE huggingface dataset:
Tumor necrosis factor receptor superfamily member EDAR, death domain (Death_EDAR)
Type: Domain

This entry represents a death domain found in the human Tumor necrosis factor receptor superfamily member EDAR and similar animal proteins. EDAR is a receptor for ectodysplasin A (EDA) isoforms, specifically binding to isoform A1 in humans but not to isoform A2 . This protein family is involved in mediating the activation of key signalling pathways, including NF-kappa-B and JNK, which are crucial for various cellular processes. Additionally, members of this family may promote caspase-independent cell death.
KIN17, C2H2-type zinc finger domain (C2H2-Znf_KIN17)
Type: Domain

This entry represents the C2H2-type zinc finger domain is found at the N terminus of KIN17 , which is involved in RNA binding, and related eukaryotic proteins .

KIN17 is an essential, highly conserved nuclear protein that functions in DNA replication, DNA repair and cell cycle control .
Piezo, transmembrane helical unit (THU_Piezo)
Type: Domain

This entry represents one of the THUs of Piezo proteins from animals and plants, including Piezo-type mechanosensitive ion channel component 1 from mouse (Piezo1).

Piezo is a family of proteins that form mechanosensitive non-specific cation channels whose conductance is higher for Li+, intermediate for Na+ and lowest for Li+. Divalent ions except for Mn2+ permeate the channel but more slowly than monovalent ions and can reduce K+ currents. Members play key roles in cell adhesion, blood vessel formation and vascular structure in both development and adult physiology . These channels have a homotrimeric three-blade propeller-shaped structure that use a cap-motion and plug-and-latch mechanism to gate their ion-conducting pathways . Each protomer consists of 38 TM helices (referred to THUs) that form unusual non-planar blades, and an extracellular cap-like structure (

).
Piezo, TM1-24 (Piezo_TM1-24)
Type: Domain

This entry represents the N-terminal TM segment (TM1-24) which are peripheral part of the blade and exhibit a greater degree of flexibility of these helices relative to TM25-TM36, as apparently, they do not have intracellular supporting structures . Members of this entry are found in animals.

Piezo is a family of proteins that form mechanosensitive non-specific cation channels whose conductance is higher for Li+, intermediate for Na+ and lowest for Li+. Divalent ions except for Mn2+ permeate the channel but more slowly than monovalent ions and can reduce K+ currents. Members play key roles in cell adhesion, blood vessel formation and vascular structure in both development and adult physiology . These channels have a homotrimeric three-blade propeller-shaped structure that use a cap-motion and plug-and-latch mechanism to gate their ion-conducting pathways . Each protomer consists of 38 TM helices (referred to THUs) that form unusual non-planar blades, and an extracellular cap-like structure (

).
Piezo, THU9 and anchor domain (Piezo_THU9_anchor)
Type: Domain

This entry represents a TM segment comprising TM33-36 (THU9) and the anchor domain of Piezo proteins, found towards the C-terminal before the cap domain . Members of this entry are found in animals and plants.

Piezo is a family of proteins that form mechanosensitive non-specific cation channels whose conductance is higher for Li+, intermediate for Na+ and lowest for Li+. Divalent ions except for Mn2+ permeate the channel but more slowly than monovalent ions and can reduce K+ currents. Members play key roles in cell adhesion, blood vessel formation and vascular structure in both development and adult physiology . These channels have a homotrimeric three-blade propeller-shaped structure that use a cap-motion and plug-and-latch mechanism to gate their ion-conducting pathways . Each protomer consists of 38 TM helices (referred to THUs) that form unusual non-planar blades, and an extracellular cap-like structure (

).
FHOD1/3-like, FH3 domain (FH3_FHOD1-3-like)
Type: Domain

This is the FH3 domain of FH1/FH2 domain-containing proteins 1 and 3 from human and related sequences, including ELMOA, Formin-G and Formin-C from Dictyostelium discoideum. FHOD1 is required for the assembly of F-actin structures, such as stress fibres and depends on the Rho-ROCK cascade for its activity. It contributes to the coordination of microtubules with actin fibres and plays a role in elongation . This domain consists of armadillo repeats and mediates the interactions with spectrin repeat 12 (SR12) from Nesprin .
Origin recognition complex subunit 2, RecA-like domain (RecA-like_ORC2)
Type: Domain

This entry represents the RecA-like domain of Origin recognition complex subunit 2 (ORC2) with no predicted ATPase activity .

The Origin Recognition Complex (ORC) is a six-subunit ATP-dependent DNA-binding complex encoded by ORC1-6 . ORC is a central component for eukaryotic DNA replication, and binds chromatin at replication origins throughout the cell cycle . ORC directs DNA replication throughout the genome and is required for its initiation . ORC bound at replication origins serves as the foundation for assembly of the pre-replicative complex (pre-RC), which includes Cdc6, Tah11 (aka Cdt1), and the Mcm2-7 complex . Pre-RC assembly during G1 is required for replication licensing of chromosomes prior to DNA synthesis during S phase . Cell cycle-regulated phosphorylation of ORC2, ORC6, Cdc6, and MCM by the cyclin-dependent protein kinase Cdc28 regulates initiation of DNA replication, including blocking reinitiation in G2/M phase .

In yeast, ORC also plays a role in the establishment of silencing at the mating-type loci Hidden MAT Left (HML) and Hidden MAT Right (HMR) . ORC participates in the assembly of transcriptionally silent chromatin at HML and HMR by recruiting the Sir1 silencing protein to the HML and HMR silencers .
Origin recognition complex subunit 2, winged-helix domain (WHD_ORC2)
Type: Domain

This entry represents the winged-helix domain (WHD) of Origin recognition complex subunit 2 (ORC2) .

The Origin Recognition Complex (ORC) is a six-subunit ATP-dependent DNA-binding complex encoded by ORC1-6 . ORC is a central component for eukaryotic DNA replication, and binds chromatin at replication origins throughout the cell cycle . ORC directs DNA replication throughout the genome and is required for its initiation . ORC bound at replication origins serves as the foundation for assembly of the pre-replicative complex (pre-RC), which includes Cdc6, Tah11 (aka Cdt1), and the Mcm2-7 complex . Pre-RC assembly during G1 is required for replication licensing of chromosomes prior to DNA synthesis during S phase . Cell cycle-regulated phosphorylation of ORC2, ORC6, Cdc6, and MCM by the cyclin-dependent protein kinase Cdc28 regulates initiation of DNA replication, including blocking reinitiation in G2/M phase .

In yeast, ORC also plays a role in the establishment of silencing at the mating-type loci Hidden MAT Left (HML) and Hidden MAT Right (HMR) . ORC participates in the assembly of transcriptionally silent chromatin at HML and HMR by recruiting the Sir1 silencing protein to the HML and HMR silencers .
FdhE, N-terminal domain (FdhE_N)
Type: Domain

This domain is found at the N-terminal of FdhE from Escherichia coli and similar proteins necessary for formate dehydrogenase activity. This domain shows a mainly α-helical configuration.

This entry contains formate dehydrogenase accessory protein FdhE and its homologues, found largely in proteobacteria, where the fdhE genes are almost always genetically-linked to the structural genes for formate dehydrogenases . FdhE is required for the assembly of formate dehydrogenase although not present in the final complex. In E.coli, FdhE interacts with the catalytic subunits of the respiratory formate dehydrogenases. FdhE is an iron-binding rubredoxin that can adopt monomeric and homodimeric forms. E.coli FdhE interacts with the catalytic subunits, FdnG and FdoG, of the Tat-dependent respiratory formate dehydrogenases. Site-directed mutagenesis has shown that conserved cysteine motifs are essential for the physiological activity of the FdhE protein and are also involved in Fe(III) ligation. The iron likely is redox active, suggesting that the switch from aerobic to anaerobic conditions may be important in modulating FdhE function. Alternatively, FdhE may be involved in an electron transfer reaction, similar to other rubredoxins .
YABBY protein, C-terminal domain (YABBY_C)
Type: Domain

YABBY proteins are a group of plant-specific transcription involved in the specification of abaxial polarity in lateral organs . This entry represents the C-terminal domain of these proteins.
YABBY, N-terminal domain (YABBY_N)
Type: Domain

YABBY proteins are a group of plant-specific transcription involved in the specification of abaxial polarity in lateral organs . This entry represents the N-terminal domain, which is found associated with

.
Ycf2, N-terminal (Ycf2_N)
Type: Domain

This entry, previously known as DUF825, represents the N-temrinal region of Ycf2 protein from Arabidopsis thaliana and related plant proteins. Ycf2 is a component of the Ycf2-FtsHi complex which has been identified as chloroplast import motor. The Ycf2-FtsHi complex is composed of six distinct components. This heterohexameric assembly is organized in a counterclockwise order with components arranged as Ycf2, FtsHi5, FtsHi1, FtsHi2, FtsHi4, and FtsH12 . A collaborative interplay between the Ycf2-FtsHi complex and the TIC (translocon at the inner chloroplast membrane) complex, contributes to the efficient translocation of preproteins into the chloroplasts . This domain is found associated with

.
UPF0261, C-terminal domain (UPF0261_C)
Type: Domain

This entry represents the C-terminal domain of ToMV resistance protein Tm-1 and the uncharacterised UPF0261 proteins. The tomato resistance protein Tm-1, which inhibits replication complex formation through its binding to tomato mosaic virus (ToMV) replication proteins .
Csf1, C-terminal region (Csf1_C)
Type: Domain

This entry represents the C-terminal region of Csf1.

This entry includes Csf1 protein from yeast, which is the orthologue of human BLTP1. These are tube-forming lipid transport proteins which provide phosphatidylethanolamine for glycosylphosphatidylinositol (GPI) anchor synthesis in the endoplasmic reticulum . They belong to the repeating β-groove (RBG) superfamily which are conserved lipid transfer proteins containing long hydrophobic grooves consisting of multiple repeating modules made of five β-sheets followed by a loop .
Renin receptor-like, C-terminal transmembrane spanning segment (Renin_r_C)
Type: Domain

This entry represents the C-terminal region of the human renin receptor, which bears a putative transmembrane spanning segment . The renin receptor is involved in intracellular signal transduction by the activation of the ERK1/ERK2 pathway, and it also serves to increase the efficiency of angiotensinogen cleavage by receptor-bound renin, therefore facilitating angiotensin II generation and action on a cell surface . This domain is also found in the Drosophila homologue, known as dPRR .

Renin receptor is a multifunctional protein which functions as a renin, prorenin cellular receptor and is involved in the assembly of the lysosomal proton-transporting V-type ATPase (V-ATPase) and the acidification of the endo-lysosomal system . Through its function in V-type ATPase (v-ATPase) assembly and acidification of the lysosome it regulates protein degradation and may control different signalling pathways important for proper brain development, synapse morphology and synaptic transmission .
Polynucleotide kinase, PNKP phosphatase domain (HAD_PNKP)
Type: Domain

This entry represents the C-terminal domain of the bifunctional enzyme polynucleotide kinase/phosphatase, PNKP (also known as PseT) from Enterobacteria phage T4. The PNKP phosphatase domain can catalyse the hydrolytic removal of the 3'-phosphoryl of DNA, RNA and deoxynucleoside 3'-monophosphates . Members of this group are found in tailed bacteriophages and bacterial prophages.
DNA replication complex GINS protein PSF1, C-terminal domain (PSF1_C)
Type: Domain

This domain is found C-terminal in the human DNA replication complex GINS protein PSF1 and related proteins. PSF1 is required for correct functioning of the GINS complex, a complex that plays an essential role in the initiation of DNA replication, and progression of DNA replication forks .
DNA replication complex GINS protein PSF2, N-terminal domain (PSF2_N)
Type: Domain

This domain is found N-terminal in the human DNA replication complex GINS protein PSF2 and related eukaryotic proteins. PSF2 is an essential component of of the GINS complex, which plays an essential role in the initiation of DNA replication, and progression of DNA replication forks .
Putative mannosyltransferase YkcA/B-like, C-terminal (YkcA/B-like_C)
Type: Domain

This domain is found at the C-terminal end of the putative mannosyltransferases YkcA and YkcB from Bacillus subtilis and similar sequences. This domain is predicted to adopt an α-β configuration. It is usually found associated with

.
3'-5' exoribonuclease HELZ2, OB-fold domain (OB_HELZ2)
Type: Domain

This domain is found in human 3'-5' exoribonuclease HELZ2 and similar animal proteins. HELZ2 can degrade highly structured RNAs through its concerted ATP-dependent RNA helicase and 3' to 5' exoribonuclease activities .
ABC transporter A family member 2/9/11, C-terminal domain (ABCA2/9/11_C)
Type: Domain

This domain is found towards the C-terminal of ABC transporter A family members 2/9/11 from Arabidopsis thaliana and similar plant proteins. This domain is predicted to adopt a mainly β structure.

ABCA9 mediates the transport of acyl-CoAs and/or free fatty acids to the endoplasmic reticulum. It has no effect on the selectivity of fatty acid incorporation into triacylglycerol or further desaturation steps .

ABCA2, also known as ATH1, can control Arabidopsis rosette habit when it is induced. ATH1 induction prevents rosette internode elongation by maintaining the shoot apical meristem (SAM) rib zone area inactive and requires inactivation of photomorphogenesis inhibitors, including PHYTOCHROME INTERACTING FACTOR (PIF) proteins .
R13L1/DRL21-like, LRR repeat region (LRR_R13L1-DRL21)
Type: Domain

This entry represents a region of leucine-rich repeats (LRRs) found in R13L1, DRL21 from Arabidopsis thaliana and related plant proteins. R13L1 and DRL21 are likely disease resistance proteins. DRL21 has adenylate cyclase activity .
Ribophorin II, C-terminal domain (Ribophorin_II_C)
Type: Domain

This domain is found at the C-terminal of human Ribophorin II (RPN2, also known as dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2), a subunit of the oligosaccharyl transferase (OST) complex that catalyses the first step in protein N-glycosylation. This domain shows a non-compact all-α configuration and is often found associated to

,

and

.
Mcm10, C-terminal zinc binding motif (Znf_Mcm10_C)
Type: Domain

This is the C-terminal zinc binding motif of Mcm10, an eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha. This motif is structurally similar to the zinc-ribbon domain found in the N-terminal domain of eukaryotic and archaeal MCM helicases .
Ribosome maturation factor RimM, PRC barrel domain (PRC_RimM)
Type: Domain

This entry represents a PRC-barrel domain found in the RimM protein family. The RimM family comprises ribosome maturation factors essential for the final assembly of the 30S ribosomal subunit, particularly the head region. These proteins facilitate the efficient processing of 16S rRNA and may function both before and after RbfA during 16S rRNA maturation. RimM proteins have a specific affinity for free 30S ribosomal subunits but not for 70S ribosomes. The PRC barrel domain within these proteins binds to ribosomal protein uS19, playing a crucial role in the assembly process. In some organisms, RimM is one of several proteins, including Era, RbfA, and RsgA/YjeQ, that assist in the late stages of 30S subunit assembly, ensuring the correct assembly of head-associated ribosomal proteins and preventing the accumulation of precursor rRNA forms .
Heparan sulfate-N-deacetylase, N-terminal domain (HSNSD_N)
Type: Domain

This entry represents the N-terminal domain of Bifunctional heparan sulfate N-deacetylase/N-sulfotransferases, which is related to the N-terminal domain of Agd3 from A. fumigatus , a carbohydrate binding module (CBM), the founding member of CBM family 87. This domain is found associated with

.
Patellin-1-6, C-terminal GOLD domain (PATL1-6_C_GOLD)
Type: Domain

This GOLD domain is found at the C-terminal end of Patellin-1-6 from Arabidopsis thaliana (PATL1-6) and similar plant proteins. PATL1 is a carrier protein that may be involved in membrane -trafficking events associated with cell plate formation during cytokinesis. It binds to some hydrophobic molecules and promotes their transfer between the different cellular sites . This domain is predicted to adopt a compact β-sandwich fold.
PAC1-like, LisH-like dimerisation domain (PAC1-like_LisH-like_dom)
Type: Domain

This entry represents a presumed LisH-like dimerisation domain found at the N terminus of the Nuclear distribution protein PAC1 and related proteins, including Lissencephaly-1 homolog (Lis1) and Nuclear distribution protein nudF. PAC1 is the yeast homologue of Lis1, which positively regulates the activity of the minus-end directed microtubule motor protein dynein . Lis1 is required for neuronal cell differentiation and is involved in the regulation of nuclear migration in hypodermal precursor cells .
FdhE, C-terminal domain (FdhE_C)
Type: Domain

This is the C-terminal domain of FdhE from Escherichia coli and similar proteins necessary for formate dehydrogenase activity. This domain is found associated with

and

. It shows an α-β configuration (

).

This entry contains formate dehydrogenase accessory protein FdhE and its homologues, found largely in proteobacteria, where the fdhE genes are almost always genetically-linked to the structural genes for formate dehydrogenases . FdhE is required for the assembly of formate dehydrogenase although not present in the final complex. In E.coli, FdhE interacts with the catalytic subunits of the respiratory formate dehydrogenases. FdhE is an iron-binding rubredoxin that can adopt monomeric and homodimeric forms. E.coli FdhE interacts with the catalytic subunits, FdnG and FdoG, of the Tat-dependent respiratory formate dehydrogenases. Site-directed mutagenesis has shown that conserved cysteine motifs are essential for the physiological activity of the FdhE protein and are also involved in Fe(III) ligation. The iron likely is redox active, suggesting that the switch from aerobic to anaerobic conditions may be important in modulating FdhE function. Alternatively, FdhE may be involved in an electron transfer reaction, similar to other rubredoxins .
FdhE, central domain (FdhE_central)
Type: Domain

This is the central domain of FdhE from Escherichia coli and similar bacterial proteins necessary for formate dehydrogenase activity. This domain is found associated with

and

.

This entry contains formate dehydrogenase accessory protein FdhE and its homologues, found largely in proteobacteria, where the fdhE genes are almost always genetically-linked to the structural genes for formate dehydrogenases . FdhE is required for the assembly of formate dehydrogenase although not present in the final complex. In E.coli, FdhE interacts with the catalytic subunits of the respiratory formate dehydrogenases. FdhE is an iron-binding rubredoxin that can adopt monomeric and homodimeric forms. E.coli FdhE interacts with the catalytic subunits, FdnG and FdoG, of the Tat-dependent respiratory formate dehydrogenases. Site-directed mutagenesis has shown that conserved cysteine motifs are essential for the physiological activity of the FdhE protein and are also involved in Fe(III) ligation. The iron likely is redox active, suggesting that the switch from aerobic to anaerobic conditions may be important in modulating FdhE function. Alternatively, FdhE may be involved in an electron transfer reaction, similar to other rubredoxins .
Fe-containing alcohol dehydrogenase-like, C-terminal (ADH_Fe_C)
Type: Domain

This domain is found C-terminal in iron-containing alcohol dehydrogenases from all cellular organisms, mainly bacteria. It is usually found associated with

and

. It folds into an array of α-helices .
Aegyptin/gSG7 salivary protein-like, four-helix bundle (ALL3/gSG7_salivary-like_helix)
Type: Domain

This entry represents a four-helix bundle found at the C-terminal of Aegyptin and salivary IL-4-inducing protein from Aedes aegypti and as the only structural domain in gSG7 salivary protein from Anopheles sp.

Aegyptin modulates blood feeding of female mosquitoes on vertebrate hosts . This domain is predicted to adopt an all alpha configuration. Salivary IL-4-inducing protein induces expression of IL4 in host skin by diverting host CD4 cells away from Th1 and towards Th2 responsiveness . It induces expression of IL10 in host skin and it down-regulates expression of IL12B, IFN-gamma (IFNG) and TNF-alpha (TNF) in host skin . gSG7 salivary protein potently inhibits the alternative pathway of complement system activation in the host while having no inhibitory effect on the classical or lectin pathways . It binds and stabilises activated host C3-convertase complex C3bBb (C3-CFB) and inhibits its convertase activity . It enhances accumulation of C3bBb on immobilised properdin .

This domain is also found in Simplagrin from Simulium nigrimanum which inhibits host platelet aggregation induced by low concentrations of collagen via blocking the von Willebrand Factor (VWF) interaction with collagen .
RNA-binding protein RO60, vWA domain (vWA_Ro60)
Type: Domain

This entry represents the vWA domain of RNA-binding protein RO60 which is found after the TROVE domain at the N-terminal end . RO60 binds to misfolded non-coding RNAs, pre-5S rRNA, and several small cytoplasmic RNA molecules known as Y RNAs . This domain closes the ring from the TROVE domain.
SBSPON-like, C-terminal (SBSPON_C)
Type: Domain

This domain is found at the C-terminal end of human Somatomedin-B and thrombospondin type-1 domain-containing protein (SBSPON) and similar animal sequences. This domain is usually found associated with

.
Serine/threonine-protein kinase ATR-like, M-HEAT region (ATR-like_M-HEAT)
Type: Domain

This region of HEAT repeats is found in human Serine/threonine-protein kinase ATR and similar eukaryotic proteins. This entry represents the M-HEAT region.

This region is also found in Serine/threonine-protein kinase MEC1 from Saccharomyces cerevisiae, which activates checkpoint signalling upon genotoxic stresses such as ionizing radiation (IR), ultraviolet light (UV), or DNA replication stalling, thereby acting as a DNA damage sensor .

ATR acts as a DNA damage sensor and is associated with severe disorders such as Seckel syndrome 1. This protein is organised into a large N-terminal α-solenoid containing HEAT repeats, a FAT (FRAP, ATM, TRRAP) domain (

), a kinase domain (

), and a C-terminal short segment referred to as FATC (

). N-terminal part has two continuous HEAT repeat regions, the N-HEAT and the M-HEAT. The FAT domain contains TPR (tetratricopeptide) repeats followed by a HEAT repeat domain .
Serine/threonine-protein kinase ATR-like, N-HEAT region (ATR-like_N-HEAT)
Type: Domain

This region of HEAT repeats is found in human Serine/threonine-protein kinase ATR and similar proteins from vertebrates. This entry represents the N-HEAT region.

ATR acts as a DNA damage sensor and is associated with severe disorders such as Seckel syndrome 1. This protein is organised into a large N-terminal α-solenoid containing HEAT repeats, a FAT (FRAP, ATM, TRRAP) domain (

), a kinase domain (

), and a C-terminal short segment referred to as FATC (

). N-terminal part has two continuous HEAT repeat regions, the N-HEAT and the M-HEAT. The FAT domain contains TPR (tetratricopeptide) repeats followed by a HEAT repeat domain .