SII-SWORD/CoKE huggingface dataset:
Kinesin-like protein Kif23, Arf6-interacting domain (Kif23_Arf-bd)
Type: Domain

This entry represents a C-terminal region of kinesin-like protein Kif23 (also known as MKLP1) that is necessary for the interaction with the small GTPase Arf6. MKLP1 is a Flemming body-localising protein essential for cytokinesis. The Arf6-MKLP1 complex plays a crucial role in cytokinesis by connecting the microtubule bundle and membranes at the cleavage plane .
T-box transcription factor-associated (T-box_assoc)
Type: Domain

This domain lies downstream of the T-box in many eukaryotic T-box proteins. Transcription factors of the T-box family are required for early cell-fate decisions, and for differentiation and organogenesis . The exact function of this domain is not known.
Flagellar assembly protein T, middle domain (FlgT_M)
Type: Domain

This entry represents the middle region of a family of flagellar proteins that make up part of the basal body of the flagellum. The flagellum is a large macromolecular assembly composed of three major parts: the basal body, the hook, and the filament. The basal body has two unique ring structures, the T ring and the H ring. FlgT is required to form and stabilise both ring structures. FlgT is composed of three domains, the N-terminal domain (FlgT-N), the middle domain (FlgT-M), and the C-terminal domain (FlgT-C). FlgT-N and FlgT-M are thought to be involved in the H-ring and the T-ring formation, respectively, and FlgT-M is also required for the stable association of FlgT with the basal body .
Acetyl-coenzyme A synthetase, N-terminal domain (ACAS_N)
Type: Domain

This domain is found at the N terminus of many acetyl-coenzyme A synthetase enzymes. The function of this domain is not clear.
Flagellar assembly protein T, C-terminal (FlgT_C)
Type: Domain

This entry represents the C-terminal domain of a family of flagellar (FlgT) proteins that make up part of the basal body of the flagellum. FlgT is composed of three domains, the N-terminal domain (FlgT-N), the middle domain (FlgT-M), and the C-terminal domain (FlgT-C). The flagellum is a large macromolecular assembly composed of three major parts: the basal body, the hook, and the filament. The basal body has two unique ring structures, the T ring and the H ring. FlgT is required to form and stabilise both ring structures. FlgT-C is made up of seven β-strands and a helical segment, arranged in a core β-barrel structure and a β-hairpin. The C-terminal domain of FlgT is not essential but stabilises the H-ring structure .
Type II secretion system protein GspB, C-terminal (GspB_C)
Type: Domain

GspB is an accessory component of the type II secretion system (T2SS). Together with GspA, it contribute to GspD assembly and transport to the outer membrane possibly by increasing the pore size of the peptidoglycan or anchoring it to this structural meshwork .

This entry represents the C-terminal domain of these proteins (

).

The type II secretion system (T2SS) is one of several extracellular secretion systems in gram-negative bacteria. It delivers toxins and a range of hydrolytic enzymes including proteases, lipases and carbohydrate-active enzymes to the cell surface or extracellular space . T2SS systems are composed of 11 to 15 different proteins, which are generally called GspA to GspO and GspS. The T2SS spans the two bacterial membranes and ensures secretion of folded proteins across the outer membrane pore formed by GspD. The inner membrane complex contains GspC, GspL, GspM, and GspF. The cytoplasmic domains of GspL and GspF interact with an ATPase, GspE. GspE is thought to energize the formation of a short pseudopilus by several pilin-like proteins, GspG to GspK . GspD has been shown to interact with the inner membrane component GspC .
IpaB/BipB/SctE, N-terminal (IpaB/BipB/SctE_N)
Type: Domain

This entry represents the N-terminal coiled-coil region of the invasin IpaB, BipB and SipB. IpaB (also known as SctE) from Shigella sp., which forms a pore with IpaC and is inserted into the host cell membrane through the Mxi/Spa apparatus during cell contact .

BipB from Burkholderia sp., which plays a role in the bacterium-induced formation of multinucleated giant cell (MNGC), which is formed after host cell fusion, as well as in the intercellular spreading of bacteria and in the induction of apoptosis in macrophages. BipB may act in concert with other effector proteins to induce fusion of host cell membranes .

SipB (also known as SPI-1 type 3 secretion system translocon protein SctE) from Salmonella sp., which is required for entry into the host cell through presentation or delivery of SipC at the host cell plasma membrane .

This domain is homologous in activity to the pore-forming toxins of other Gram-negative pathogens, such as colicin Ia .
SATB, ubiquitin-like oligomerisation domain (ULD)
Type: Domain

This entry represents the N-terminal oligomerisation domain, also known as ULD domain, of the SATB (special AT-rich sequence-binding) protein. SATBs are global chromatin organisers and regulators of gene expression that are essential for T-cell development, breast cancer tumour growth and metastasis. SATBs assemble into a tetramer via the ULD (ubiquitin-like) domain, and the tetramerisation of SATBs is essential for recognising specific DNA sequences (such as multiple AT-rich DNA fragments). Thus, SATBs may regulate gene expression directly by binding to various promoters and upstream regions and thereby influencing promoter activity .
STIM1/2, Orai1-activating region (SOAR_STIM1/2)
Type: Domain

This domain, also known as SOAR, is the Orai1-activating region of STIM1 (stromal interaction molecule 1) and related proteins. The SOAR region forms a dimer, and is essential for oligomerisation of the whole of STIM1 .

STIM1 (Stromal Interaction Molecule 1) is a key Ca2+ sensor located in the membrane of the endoplasmic reticulum (ER). Upon depletion of ER Ca2+ stores, STIM1 undergoes a conformational change and oligomerises, migrating to ER-plasma membrane junctions to activate Orai1, a Ca2+-release-activated Ca2+ (CRAC) channel, in the plasma membrane. STIM1 contains a single SAM (sterile alpha motif) domain (

) and an unpaired EF-hand domain (

) in the conserved luminal region, which together serve as a Ca2+-sensing module. These domains form a stable intramolecular complex when Ca2+ is bound. During Ca2+ depletion, destabilisation of the EF-SAM interaction leads to partial unfolding and promotes homooligomerisation, an essential step for CRAC channel activation . The cytoplasmic region includes coiled-coil domains that are conserved in structure and position and are necessary for interaction with Orai1 . In human cells, STIM1 and its homologue STIM2 regulate store-operated calcium entry (SOCE) as well as basal cytoplasmic Ca2+ levels .
Anoctamin, dimerisation domain (Anoct_dimer)
Type: Domain

This appears to be the cytoplasmic domain of the calcium-activated chloride-channel anoctamin . It is responsible for creating the homodimeric architecture of the chloride-channel proteins .
Sf6-type phage tail needle knob (Phage_tail_NK)
Type: Domain

This entry represents the globular tip protein of some tailed bacteriophages, including Tail needle protein from Shigella phage Sf6. Tailed bacteriophage virions deliver DNA to susceptible cells after adsorbing to specific receptors on the surface of the bacteria. In the Gram-negative bacteria these receptors are surface proteins or polysaccharides. In the phage Sf6-type needle, this distal tip folds into a knob with a TNF-like fold, similar to the fibre knobs of bacteriophage PRD1 and Adenovirus. It contains three bound L-glutamate molecules that are bind tightly in the crevices between the trimers of this trimeric tip .
Spindle assembly abnormal protein 6, N-terminal (SAS-6_N)
Type: Domain

Spindle assembly abnormal protein 6 (SAS-6) is the centre of the cartwheel assembly that scaffolds centrioles early in their biogenesis. Structural studies have shown that SAS-6 self-associates in vitro into assemblies that resemble cartwheel centres through the formation of a parallel coiled-coil dimer .

This entry represents the N-terminal domain of the SAS-6 , both in C.elegans and in humans. The N-terminal domain is the region through which the 9 rod-shaped homodimers that SAS-6 forms on oligomerisation interact with each other. Proper functioning of the centriole requires this correct oligomerisation .
Rel homology dimerisation domain (RHD_dimer)
Type: Domain

The Rel homology domain (RHD) is composed of two structural domains, an N-terminal DNA-binding domain (

) and a C-terminal dimerisation domain. This is the dimerisation domain .

This domain can be found in both nuclear factor of activated T cells (NFAT) and nuclear factor kappa-B (NFkB), which are RHD-containing transcription factors .
Infectious hypodermal and haematopoietic necrosis virus, capsid protein (IHHNV_capsid)
Type: Family

This entry represents the single capsid protein of infectious hypodermal and haematopoietic necrosis virus (IHHNV), found particularly in shrimp densovirus. Densoviruses are a subfamily of the parvoviruses. The capsid protein has an eight-stranded anti-parallel β-barrel 'jelly roll' motif similar to that found in many icosahedral viruses, including other parvoviruses. The N-terminal portion of the IHHNV coat protein adopts a 'domain-swappe' conformation relative to its twofold-related neighbour. The loops connecting the strands of the structurally conserved jelly roll motif differ considerably in structure and length from those of other parvoviruses. IHHNV was first reported as a highly lethal disease of juvenile shrimp in 1983, and has only one type of capsid protein that lacks the phospholipase A2 activity that has been implicated as a requirement during parvoviral host cell infection. The structure of recombinant virus-like particles, composed of 60 copies of the 37.5kDa coat protein is the smallest parvoviral capsid protein reported thus far. The small size of the PstDNV capsid protein makes the system attractive as a model for studying assembly mechanisms of icosahedral virus capsids .
RelB leucine zipper (RelB_leu_zip)
Type: Domain

This domain is a leucine zipper found in RelB transcription factors .
RelB transactivation domain (RelB_transact)
Type: Domain

This domain is the transactivation domain of the transcription factor RelB .
Enhancer of mRNA-decapping protein 4, WD40 repeat region (EDC4_WD40)
Type: Domain

This entry represents the N-terminal region of Ge-1, also known as EDC4 (enhancer of mRNA-decapping protein 4). This WD40-repeat region is involved in protein-protein interactions .
Putative adherens-junction anchoring domain (AbLIM_anchor)
Type: Domain

This is a domain lying between the LIM actin-binding and the vilin-head domains of actin-binding LIM proteins (abLIMs). It is likely that this domain is involved in anchoring abLIMs to circumferential actin bundles in specific cell types . It is also found in Dematin, an actin-binding protein originally identified in the junctional complex of the erythrocyte plasma membrane .
Exocyst component Exo84, C-terminal (Exo84_C)
Type: Domain

The exocyst is a large complex that is required for tethering vesicles at the final stages of the exocytic pathway in all eukaryotes. Exocyst subunits are composed of mostly helical modules strung together into long rods .

This entry represents the C-terminal helical region of the exocyst component Exo84. This region resembles a cullin-repeat, a multi-helical bundle.
Two-component sensor protein CpxA, periplasmic domain (CpxA_peri)
Type: Domain

This entry represents the periplasmic domain (also known as the VpCpxA-peri domain) of CpxA from Vibrio parahaemolyticus , Klebsiella pneumoniae , and similar proteins from gammaproteobacteria. The VpCpxA-peri domain possesses a PAS fold that play a role in sensing envelope stress signals . It recognises KCl and RbCl .

The Cpx system is one of extracytoplasmic stress response systems (ESR) found in Gram-negative bacteria. ESRs are operated by a two-component signalling system which consists of a sensory histidine kinase (HK) and a response regulator (RR) as basal elements. In the Cpx system, CpxA is the inner membrane-spanning, sensory HK .
Kinesin-associated (Kinesin_assoc)
Type: Domain

This short domain is found in some kinesin-like proteins (KIF1, KIF13, KIF14). It is found between the motor domain (

) and the forkhead-associated (FHA) domain (

). Its function is unknown.
Cyclic nucleotide-gated channel, C-terminal leucine zipper domain (CLZ_dom)
Type: Domain

This entry represents the C-terminal leucine-zipper domain (also known as CLZ domain) of of cyclic nucleotide-gated channel proteins. This domain forms homotypic trimers in solution thus constraining the channel of the CNGs to contain three cyclic nucleotide-gated subunits, CNGA. The CLZ domains formed homotypic parallel 3-helix coiled-coil domains, consistent with their proposed role in regulating subunit assembly .
Haemophore, haem-binding (MHB)
Type: Domain

This entry represents a coiled-coil domain that binds free haem in mycobacterial cytoplasm to deliver it to membrane proteins for shuttling through the membrane .
Sensor histidine kinase RisS, periplasmic domain (RisS_PPD)
Type: Domain

This entry represents the periplasmic domain of the sensor histidine kinases such as RisS. It is purported to be the region of the kinase that senses the pH of the environs.
Rho guanine nucleotide exchange factor 6/7, coiled-coil domain (GEF6/7_CC)
Type: Domain

This entry represents the C-terminal coiled-coil (CC) region found in Rho guanine nucleotide exchange factors (GEFs) 6 and 7 (also known as alpha and betaPIX, respectively) . This domain is upstream of the PDZ binding motif and is important for the multimerization of betaPIX .
ATP-binding cassette sub-family B member 6, N-terminal five TM domain (ABCB6_N)
Type: Domain

This is the N-terminal five transmembrane (TM) helices domain found in ATP-binding cassette sub-family B member 6 (ABCB6), which has a crucial role in lysosomal targeting .
Flagellar FLiS export co-chaperone, HP1076 (FliS_cochap)
Type: Family

HP1076 is a co-chaperone for FliS, one of the type III secretion system flagellar chaperones. The HP1076 and FliS complex together prevents premature polymerisation of flagellins and is critical for flagellar assembly and bacterial colonisation. The HP1076 shows co-chaperone activity that promotes protein folding of FliS with mutations in the flagellin binding pocket and enhances the chaperone activity of FliS .
Myosin VI, cargo binding domain (Myosin-VI_CBD)
Type: Domain

This entry represents the C-terminal cargo binding domain (CBD) of myosin-VI. Several adaptor proteins have been reported to interact specifically with the CBD, thus defining the specific subcellular functions of myosin VI. The crystal structure determination of the myosin VI CBD/Dab2 (an endocytic adaptor protein Disabled-2 that is a cargo) complex shows that the CBD forms a cargo-induced dimer, suggesting that the motor undergoes monomer-to-dimer conversion that is dependent upon cargo binding. In the absence of cargo, myosin VI exists as a stable monomer. This cargo binding-mediated monomer-to-dimer conversion mechanism adopted by myosin VI may be shared by other unconventional myosins, such as myosin VII and myosin X .
Atypical Arm repeat (Arm_3)
Type: Repeat

This atypical Arm repeat appears at the very C terminus of eukaryotic proteins such as importin subunit alpha, as the last of the repeating units.
Matrix protein, Bornaviridae (BDV_M)
Type: Family

This entry represents the matrix protein M from negative-strand Bornaviridae viruses (BDV-M). Its most stable oligomeric form is a tetramer, and it lies beneath the viral envelope where it associates with the inner layer of the viral membrane. It bridges the gap between the nucleocapsid and the viral envelope thereby imparting structural integrity and individual form to the virus particle. Borna disease virus (BDV) is a neurotropic enveloped RNA virus causing a noncytolytic, persistent infection of the central nervous system in mammals. The order to which this virus belongs, Mononegavirales, also contains the Ebola, mumps, rabies and measles viruses, amongst other highly infectious agents .

Structural studies on this protein have shown that heterologously expressed BDV-M co-purifies with and protects ssRNA oligonucleotides taken up from the expression host. This has revealed the ability of BDV-M to bind RNA and lipid membranes simultaneously, thus expanding the repertoire of M-protein functionalities .
TRPM, tetramerisation domain (TRPM_tetra)
Type: Domain

This entry represents a short anti-parallel coiled-coil tetramerisation domain of the transient receptor potential cation channel subfamily M member proteins 1/3/6/7. It is held together by extensive core packing and interstrand polar interactions. Transient receptor potential (TRP) channels comprise a large family of tetrameric cation-selective ion channels that respond to diverse forms of sensory input. The presence of cytoplasmic domains that direct channel assembly appears to be a feature of many voltage-gated ion channel superfamily members .
Peptidase M24, C-terminal domain (Peptidase_M24_C)
Type: Domain

This is a short region at the C terminus of a number of metallo-peptidases of the M24 family.
T3SS negative regulator GrlR (GrlR)
Type: Family

This entry represents a small family of bacterial proteins with structural similarity to GrlR.

GrlR is a family of protobacterial type III secretion system negative regulators. Structurally, GrlR consists of a typical β-barrel fold with eight β-strands containing an internal hydrophobic cavity and a plug-like loop on one side of the barrel. Strong hydrophobic interactions between the two β-barrels maintain its dimeric architecture. A unique surface-exposed EDED (Glu-Asp-Glu-Asp) motif is identified to be critical for GrlA-GrlR interaction and for the repressive activity of GrlR . The locus of enterocyte effacement (LEE) is essential for virulence of enterohaemorrhagic Escherichia coli (EHEC) and enteropathogenic E. coli (EPEC). It encodes some 20 genes including an overall regulator ler and two others, GrlR and GrlA, that form the type three secretion system for infection. GrlR comlexes with GrlA to repress expression of ler .
Ubiquitin-activating enzyme E1, FCCH domain (E1_FCCH)
Type: Domain

This domain is found in the ubiquitin-activating E1 (Ub-E1) family enzymes. It is one of the catalytic cysteine half-domains of Ub-E1. The catalytic cysteine half-domains contain the E1 active site cysteine, and are known as FCCH and SCCH, for 'first' and 'second' catalytic cysteine half-domain, respectively .
NF-kappa-B essential modulator NEMO, CC2-LZ domain (CC2-LZ_dom)
Type: Domain

NF-kappa-B essential modulator NEMO comprises two coiled-coil regions, denoted as CC1 and CC2, a leucine zipper (LZ), and a zinc finger (ZF). This entry represents the CC2-LZ domain that plays a regulatory role. It contains a ubiquitin-binding domain (UBD) and represents one region that contributes to NEMO oligomerisation. NEMO itself is an integral part of the IkappaB kinase complex and serves as a molecular switch via which the NF-kappaB signalling pathway is regulated .
Ubiquitin-activating enzyme E1, four-helix bundle (E1_4HB)
Type: Domain

This domain is found in the ubiquitin-activating E1 family enzymes and is C-terminal to the FCCH domain .
Protein O-mannosyl-transferase, C-terminal four TM domain (PMT_4TMC)
Type: Domain

This is the C-terminal four membrane-pass region of protein-O-mannosyltransferases, including yeast Dolichyl-phosphate-mannose--protein mannosyltransferase 1 and similar enzymes from bacteria and eukaryotes.

Dolichyl-phosphate-mannose-protein mannosyltransferase proteins

belong to the glycosyltransferase family 39 (

) and are responsible for O-linked glycosylation of proteins. They catalyse the reaction:
Dolichyl phosphate D-mannose + protein ->dolichyl phosphate + O-D-mannosyl-protein.

The transfer of mannose to seryl and threonyl residues of secretory proteins is catalysed by a family of protein mannosyltransferases in Saccharomyces cerevisiae coded for by seven genes (PMT1-7). Protein O-glycosylation is essential for cell wall rigidity and cell integrity and this protein modification is vital for S. cerevisiae .

Undecaprenyl phosphate-alpha-4-amino-4-deoxy-L-arabinose arabinosyl transferase proteins

belong to the glycosyltransferase family 83 (

). They catalyse the reaction:
4-amino-4-deoxy-alpha-L-arabinopyranosyl di-trans,octa-cis-undecaprenyl phosphate + lipid IV(A) = lipid II(A) + di-trans,octa-cis-undecaprenyl phosphate.
Huntingtin-interacting protein 1, clathrin-binding domain (HIP1_clath-bd)
Type: Domain

This entry represents the coiled-coil region of Huntingtin-interacting protein 1 (HIP1). It carries a highly conserved HADLLRKN sequence motif at its N terminus which effects the binding of HIP1R to clathrin light-chain EED regulatory site. This binding then stimulates clathrin lattice assembly. HIP1 is an obligate binding partner for Huntingtin, and loss of this interaction triggers the cascade of events that results in the apoptosis of neuronal cells and the onset of Huntington's disease . Clathrin light-chain binds to a flexible coiled-coil domain in HIP1 and induces a compact state that is refractory to actin binding .
AAA C-terminal domain (AAA_assoc_2)
Type: Domain

This domain is C-terminal to the AAA domains and is found in a subset of AAA ATPase proteins ranging from archaeal to fungi, plants and mammals.
Putative NADH-ubiquinone oxidoreductase chain E (NADH-UOR_E)
Type: Family

This putative NADH-ubiquinone oxidoreductase chain E family is found in Epsilonproteobacteria, chiefly in Helicobacter pylori. All proteins in the family are less than 100 residues in length.
Talin, N-terminal F0 domain (FERM_f0)
Type: Domain

This domain (F0), found in the talin head, forms a stable globular structure. The fold is an ubiquitin-like fold joined to the F1 domain in a novel fixed orientation by an extensive charged interface. It is required for maximal integrin-activation .
SUMO-activating enzyme subunit 2, C-terminal domain (UBA2_C)
Type: Domain

This is the C-terminal domain found in SUMO-activating enzyme subunit 2 (Uba2) . Uba2 forms a heterodimer with Aos1 which acts as a E1 ligase for SUMO (small ubiquitin-like modifier) proteins .
Phage P22-like portal protein (P22_portal)
Type: Family

The portal protein of P22 and similar Podoviridae tail phages is a dodecameric structure consisting of a hip (2), a leg(1) and a barrel(3). DNA viruses such as bacteriophages and herpesviruses deliver their genome into and out of the capsid through large proteinaceous assemblies, known as portal proteins. Domains 1 and 3 are mostly helical and form the majority of the DNA-translocating channel. Domain 2 adopts an α-β-fold characterised by two sheets of eight β-strands, which cross each other to form a β-barrel-like structure .
TrfB transcriptional repressor protein (TrfB)
Type: Domain

TrfB (also known as KORA) is a Gram-negative bacterial protein that acts as global repressors of genes involved in plasmid replication, conjugative transfer and stable inheritance in the IncP group of plasmids. KORA operates as a symmetric dimer, and contacts the DNA via the helix-turn-helix region at the N terminus .
Nibrin, second BRCT domain (Nibrin_BRCT2)
Type: Domain

This entry represents the second BRCT domain of Nibrin (or Nbs1), a component of the MRN (Mre11-Rad50-Nbs1) complex that is involved in the DNA damage response. This domain (BRCT2) is identified through nuclear magnetic resonance (NMR) spectroscopy structure determination. It is downstream from BRCT1 domain and has no significant amino acid sequence homology to other BRCT domains. However, it has the α/β topology characteristic of BRCT domains in other proteins, but differs markedly in having a disordered long loop inserted between α β strand and an α helix. BRCT2 is essential for an MDC1-dependent relocalisation of Nbs1 to DNA damage sites .