SII-SWORD/CoKE huggingface dataset:
VirG, insertion domain (VID)
Type: Domain

Outer membrane autotransporter VirG/IcsA is a virulence factor from Shigella flexneri that acts as an adhesin and actin-polymerising factor during infection . It mediates polar adhesion to host cells and their invasion. The bile salt deoxycholate activates adhesion and invasion of host cells, possibly by altering IcsA's conformation . VirG/IcsA consists of three major domains: an atypical signal peptide at the N terminus, followed by the passenger domain (presented on the cell surface) and a β-domain that anchors the protein to the bacterial outer membrane. This entry represents the insertion domain (VID) that appears to be inserted into a continuous sequence of β-helical coils .
Zona pellucida sperm-binding protein 1/4, Ig-like domain (ZP1/4_Ig-like)
Type: Domain

This entry represents an immunoglobulin-like domain found at the N-terminal of Zona pellucida sperm-binding proteins 1 and 4 (ZP1 and ZP4) . ZP1 and ZP4 are components of the zona pellucida, an extracellular matrix surrounding oocytes which mediates sperm binding, induction of the acrosome reaction and prevents post-fertilization polyspermy . This domain is also present in CIROZ proteins.
Type III secretion system effector HopBF1-like (T3SS_HopBF1-like)
Type: Domain

This entry includes HopBF1 family of bacterial type III secretion system (T3SS) effectors identified as eukaryotic-specific HSP90 protein kinases. HopBF1 (

) adopts a minimal and atypical protein kinase fold such that it is recognized by HSP90 as a host client. Utilizing this "betrayal-like" mechanism to achieve specificity, HopF1 phosphorylates and inactivates eukaryotic HSP90 by inhibiting the chaperone's ATPase activity. This prevents activation of immune receptors that trigger hypersensitive response in plants, thereby inducing severe disease symptoms in plants infected by certain plant pathogens .
T3SS, low calcium response E, C-terminal helical domain (T3SS_CopN_C)
Type: Domain

This domain is found at the C terminus of Low calcium response E from Chlamydia pneumoniae (CopN, also known as LcrE,

) and similar bacterial sequences. CopN is involved in the regulation of type III secretion systems (T3SSs). This protein contains three repetitions of a helical motif flanked by disordered N- and C-terminal extensions .
NACHT-associated inactive Restriction Endonuclease 1 sensor domain (NA-iREase1_dom)
Type: Domain

This entry represents a predicted sensor domain in bacterial NACHT conflict systems. It is likely to bind a ligand which could contribute to activation of enzymatic domains additionally fused to the N-terminal of the NACHT module .
TraI, helicase-associated ssDBD, N-terminal (TraI_hel_assoc_DBD_N)
Type: Domain

This entry represents the N-terminal fragment of the helicase-associated ssDNA binding domain of the conjugative transfer relaxase/helicase TraI. This domain adopts a globular structure that closely resembles that of the RecD N-terminal domain despite little sequence similarity. It is part of a larger domain, referred to as vestigial helicase domain, that functions as a ssDNA binding domain . This region doesn't have helicase activity or measurable DNA binding affinity itself but it may play a role in either DNA unwinding or regulation of ssDNA transfer from host to recipient cell. Members of this group are mainly found in proteobacteria.
PSMD12/CSN4-like, N-terminal (PSMD12-CSN4-like_N)
Type: Domain

The 26S proteasome consists of a 20S proteolytic core particle (CP) and a 19S regulatory particle (RP). The RP can be further divided into two subcomplexes, a base and a peripheral lid. The RP lid is structurally similar to the COP9 signalosome (CSN). The core CSN subunits (CSN4/5/7/6) show a remarkable one-to-one sequence correspondence with those of the RP lid (RPN5/11/9/8), suggesting a common ancestry and architecture . This entry represents the N-terminal region of PSMD12/RPN5 and CSN4 subunits, which consists of helical repeats .
Metapyrocatechase-like, N-terminal domain (XylE-like_N)
Type: Domain

This entry represents the N-terminal domain of a group of bacterial proteins that function as 2,3-dioxigenases, including Metapyrocatechase from Pseudomonas putida (XylE), which catalyses the incorporation of dioxygen into catechol and the extradiol ring cleavage to form 2-hydroxymuconate semialdehyde .
Ribonuclease R, first OB domain (RNR_OB1_N)
Type: Domain

This entry represents an N-terminal OB (oligonucleotide/oligosaccharide binding) domain found in a set of bacterial Ribonuclease R proteins.

Ribonuclease R proteins are 3'-5' exoribonucleases that release 5'-nucleoside monophosphates and are involved in maturation of structured RNAs .
LysX/ArgX, preATP-grasp domain (LysX/ArgX_preATP_grasp)
Type: Domain

This entry represents the preATP-grasp domain found at the N-terminal of archaeal LysX and similar proteins. LysX catalyses the ATP-dependent formation of a covalent bond between the amino group of alpha-aminoadipate (AAA) and the gamma-carboxyl group of the C-terminal glutamate residue in LysW . ArgX catalyses the ATP-dependent formation of a covalent bond between the amino group of glutamate and the gamma-carboxyl group of the C-terminal glutamate residue in LysW .
Hyaluronate lyase-like, N-terminal (HylB-like_N)
Type: Domain

This entry represents the N-terminal domain of hyaluronate lyases (HylB) mainly found in Lactobacillales. These enzymes degrade hyaluronan and certain chondroitin sulfates at beta-1,4 glycosidic linkages and constitutes a virulence factor in Streptococcus agalactiae .

This domain is also found in accessory protein BppA and related proteins. Given the structural similarity to carbohydrate binding domains, it is likely that this domain is a carbohydrate binding module. BppA is a virion baseplate component. The precise role of this protein in absorption is elusive but the presence of a carbohydrate binding domain with an extended saccharide binding site suggests that this protein probably participates in receptor binding together with the bona fide receptor binding proteins .
Tail sheath protein Gp18-like, domain III N-terminal region (Gp18_domIII_N)
Type: Domain

This entry represents the N-terminal segment of domain III from the phage tail sheath protein Gp18 y similar sequences . Domain III is completed by

with an overall structure consisting of a β-sheet with five parallel and one anti-parallel β-strands plus six α-helices, which surround the β-sheet.
Tail sheath protein Gp18-like, domain I (Gp18-like_dom_I)
Type: Domain

This entry represents domain I from bacteriophage tail sheath protein Gp18, a protein that surrounds the central non-contractile tail tube of the tail sheath from bacteriophages, which contracts during infection . These proteins consist of three domains, domains I, II (

) and III (which consists of

and

). Domains I and II form the protease-resistant fragment .
MannoseP isomerase/GMP-like, beta-helix domain (ManC/GMP-like_b-helix)
Type: Domain

This entry represents a left-handed β-helix domain found at the C-terminal of Guanosine-diphospho-d-mannose Pyrophosphorylase (GMP) from Thermotoga maritima (

) and as a linker domain in mannose-1-phosphate guanylyltransferases (ManC), alginate biosynthesis protein AlgA and xanthan biosynthesis protein XanB, among others, located between the nucleotidyl transferase domain at the N-terminal (

) and the C-terminal isomerase cupin domain (

). This domain is composed of an α-helix followed by a short left-handed β-helix. GMP forms a dimer in which two molecules associate through a tail-to-tail arrangement of this domain .
NACHT N-terminal Helical domain 7 (NNH7)
Type: Domain

This entry represents an helical domain found at the N-terminal of bacterial NACHT conflict systems. This position is frequently occupied by an effector domain .
NACHT N-terminal Helical domain 3 (NNH3)
Type: Domain

This is an helical domain found at the N-terminal of bacterial NACHT conflict systems . This position is frequently occupied by an effector domain.
NACHT N-terminal Helical domain 2 (NNH2)
Type: Domain

This is an helical domain found at the N-terminal of bacterial NACHT conflict systems . This position is frequently occupied by an effector domain.
NACHT, C-terminal Cysteine and Histidine-containing domain (NCC-H_dom)
Type: Domain

This is a domain discovered C-terminal to HEAT repeat modules, observed in some bacterial NACHT conflict systems. These domains feature highly conserved cysteine and histidine residues .
NACHT-associated inactive Restriction Endonuclease 2 sensor domain (NA-iREase3_dom)
Type: Domain

This entry represents a predicted sensor domain in bacterial NACHT conflict systems. It is likely to bind a ligand which could contribute to activation of enzymatic domains additionally fused to the N terminus of the NACHT module .
TATA-binding-like protein domain of the TOTE conflict systems (TBP-TOTE)
Type: Domain

This entry represents the principal predicted hybrid duplex-binding domain of the TOTE (TPR, OB, TBP, Effector) conflict systems described as TATA-binding-like protein (TBP) domain of the TOTE (TBP-TOTE) in .
Phosphatase PP2A regulatory subunit A/Splicing factor 3B subunit 1-like, HEAT repeat (PP2A/SF3B1-like_HEAT)
Type: Domain

This entry represents HEAT repeats found in serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A (PP2ARA) and Splicing factor 3B subunit 1 .

PP2AR serves as a scaffolding molecule to coordinate the assembly of the catalytic subunit and a variable regulatory B subunit. It is required for proper chromosome segregation and for centromeric localisation of SGO1 in mitosis .

SF3B1 is a component of the splicing factor SF3B complex, which is important for anchoring the spliceosome to precursor mRNA. SF3B1 binds to pre-mRNA on both sides of the intron branch site region . This subunit is required for 'A' splicing complex assembly (formed by the stable binding of U2 snRNP to the branchpoint sequence in pre-mRNA) and 'E' splicing complex assembly .
Cgl0159-like domain (Cgl0159_dom)
Type: Domain

This domain is found in the uncharacterised protein Cgl0159 from Corynebacterium glutamicum (

) and its homologues mainly from actinomycetes. It adopts a classical (β/α)8 barrel. Members of this entry share significant similarity with Deoxyribose-phosphate aldolase.
Glyoxalase At5g48480-like, C-terminal (At5g48480-like_C)
Type: Domain

This entry includes plant sequences that belong to the Lactoylglutathione lyase/glyoxalase I family. They are poorly characterised and contain two characteristic VOC domains. Members of this entry contain conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping. This entry represents the C-terminal domain.
Glyoxalase At5g48480-like, N-terminal (At5g48480-like_N)
Type: Domain

This entry includes, mainly, plant sequences that belong to the Lactoylglutathione lyase/glyoxalase I family. They are poorly characterised and contain two characteristic VOC domains. Members of this entry contain conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping. This entry represents the N-terminal domain.
OBP47-like domain (OBP47-like_dom)
Type: Domain

This domain is found in the Anopheles gambiae odorant-binding protein AgamOBP47 (

) and related insect proteins. OBP47 belongs a C-plus class OBP and possesses 13 cysteine residues. It folds into a eight helical structure instead of six as observed in the classical OBPs and no internal cavity .
SpoU L30e-like, N-terminal (SpoU_sub_bind-like_N)
Type: Domain

This domain is found in a group of rRNA methyltransferases that belong to SpoU family, including 23S rRNA (uridine(2479)-2'-O)-methyltransferase from Streptomyces viridochromogenes. They are composed of two domains: N-terminal, represented by this entry, and the RNA-binding domain and C-terminal domain responsible for AdoMet-binding, catalysis and dimerisation (

) .
4-O-methyl-glucuronoyl methylesterase-like domain (GCE-like_dom)
Type: Domain

This entry represents a domain found in 4-O-methyl-glucuronoyl methylesterase from Schizophyllum commune (GCE) and similar glucuronyl esterases from fungi and bacteria. This protein seems to play a significant role in biomass degradation, as they can disconnect hemicellulose from lignin through the hydrolysis of the ester bond between 4-O-methyl-D-glucuronic acid residues of glucuronoxylans and aromatic alcohols of lignin . Members of this group belong to the carbohydrate esterase family 15 (CE15) .
Nucleoid occlusion factor SlmA-like, C-terminal (SlmA-like_C)
Type: Domain

This domain is found at the C-terminal end of Nucleoid occlusion factor SlmA from Escherichia coli and similar transcriptional repressors from proteobacteria. SlmA is required for the nucleoid occlusion (NO) phenomenon, which prevents Z-ring formation and cell division over the nucleoid. It is organised into two domains, a small N-terminal

and a C-terminal domain (this entry). This domain adopts an all-α globular structure. This region mediates dimerisation .
Encapsulated ferritin-like (EncFtn-like)
Type: Family

This protein family includes Encapsulated ferritin-like protein from Rhodospirillum rubrum (EncFtn) and similar prokaryotic sequences. This encapsulated ferritin that acts as a ferroxidase adopts an open decameric structure. Each monomer has an N-terminal 3-10-helix, two long antiparallel α-helices and a shorter helix at the end

.
Dimethylamine monooxygenase subunit DmmA-like, N-terminal domain (DmmA-like_N)
Type: Domain

This entry represents the N-terminal domain of the dimethylamine monooxygenase subunit DmmA from Methylocella silvestris (Msil_3607,

) and similar sequences, mainly found in proteobacteria and actinomycetes. Dimethylamine (DMA) monooxygenase is required for metabolism of trimethylamine N-oxide (TMAO) . This domain may adopt a Rossmann-like fold similar to Ferredoxin/Ferric reductase-like NAD binding domain.

This domain is also found in a central position in Carnitine monooxygenase reductase subunit from Escherichia coli , Heme-dependent oxidative N-demethylase delta subunit from Ectopseudomonas mendocina , Vanillate O-demethylase oxidoreductase from Pseudomonas putida and closely related species.
Aldos-2-ulose dehydratase, beta-propeller domain (Beta-prop_AUDH)
Type: Domain

This domain is found in Aldos-2-ulose dehydratase from Phanerodontia chrysosporium (AUDH) and similar sequences from invertebrates, fungi and bacteria. AUDH is a bifunctional enzyme which catalyses the dehydration of anhydrofructose into ascopyrone M, and the isomerisation of ascopyrone M into microthecin. It is organised into three domains: an N-terminal domain with a β-propeller fold (this entry), a middle domain containing two cupin folds (

) and a C-terminal lectin domain. This domain folds into a seven-bladed β-propeller, where each blade is made up of a four-stranded, antiparallel β-sheet .
Envelope glycoprotein GP2-like, HR1-HR2 (Ebola-like_HR1-HR2)
Type: Domain

This entry spans heptad repeats 1 and 2 of the glycoprotein (GP) from Ebola and Marburg viruses . Viral infection involves the formation of a trimer-of-hairpins structure (three HR1s helices, buttressed by three HR2 helices lying in antiparallel orientation). This domain may have been acquired via horizontal transfer from retroviruses.
External alternative NADH-ubiquinone oxidoreductase-like, C-terminal domain (NDH2-like_C)
Type: Domain

This entry represent the C-terminal domain of alternative NADH:quinone oxidoreductases known as NDH2 and related proteins. NDH2 delivers electrons to the respiratory chain by oxidation of NADH and reduction of quinones but does not pump protons. NDH2 have a particular relevance in yeasts like Saccharomyces cerevisiae and in several prokaryotes, whose respiratory chains are devoid of complex I, in which NDH2 keep the balance and are the main entry point of electrons into the respiratory chains . NDH2 proteins are found in bacteria, certain plant, fungal and protozoan mitochondria, they have been used as a drug target for Mycoplasma tuberculosis, Plasmodium falciparum and Toxoplasma gondii .

This entry also includes yeast Rotenone-insensitive NADH-ubiquinone oxidoreductase and plant Internal alternative NAD(P)H-ubiquinone oxidoreductase A1/2 .
MACPF-like domain, fungal (MACPF_1_fungal)
Type: Domain

This entry represents a MACPF-like domain in uncharacterised proteins primarily found in Fungi.
Complement C4A/B, CUB C-terminal domain (CO4A-B_CUB_C)
Type: Domain

Complement C4 is organised in 12 structural domains, with eight macroglobulin (MG) domains forming the core of the molecule . They have a thioester domain (TED,

), a large α-helical domain inserted in the CUB (complement C1r/C1s, Uegf, Bmp1) domain which consists of two antiparallel β-sheets. This entry covers a fraction of the CUB domain corresponding to the C-terminal part (residues 1323-1389 in human C4A/B) as this domain is made up of residues located apart in these sequences . Members of this entry are specific to vertebrates.
Csa3, N-terminal (Csa3_N)
Type: Domain

This domain is found at the N-terminal in CRISPR-associated protein Csa3 and related proteins.

Csa3 proteins consist of two domains that intertwine to form a homodimer. The N-terminal domain (also known as CARF domain) is a unique variation on the nucleotide-binding domain, and it is essential for dimer formation. It is composed of a mixed β-sheet flanked on both sides with α-helices . This domain contains two conserved sequence motifs [(D/N)-X-(S/T)-X3-(R/K) and L-X(2)-G-h-R] that map to a 2-fold symmetric pocket on the dimer axis. It has been shown that this pocket binds cyclic tetra-adenylate (cA4). The C-terminal domain is structurally similar to MarR-like winged helix-turn-helix domains and is involved in DNA recognition.
NACHT C-terminal Helical domain 4 (NCH4)
Type: Domain

This is an helical domain found at the C terminus of bacterial NACHT conflict systems .
Ephrin receptor 1, SAM domain-like (EPH_SAM)
Type: Domain

This entry represents the SAM-like domain found in the Ephrin receptor 1 from nematodes.

The Ephrin receptor 1 family comprises tyrosine kinase receptors that interact with ephrins and major sperm proteins (MSPs). They play a crucial role in various biological processes including the inhibition of oocyte meiotic maturation and ovulation in the absence of sperm, regulation of somatic cell contraction rates, and modulation of insulin-like signaling pathways through phosphorylation and subsequent degradation of daf-18/PTEN. Additionally, they are involved in morphogenetic events such as head epidermis development, gastrulation, ventral epidermis closure, spermatheca morphogenesis, and axon guidance during neurogenesis.
PL28 ulvan lyase (PL28)
Type: Domain

This entry includes sequences from the PL28 family of ulvan lyases. These enzymes degrade ulvan next to either epimer of uronic acid. They adopt a β-sandwich structure with a jelly-roll topology containing a deep positively charged cleft that defines the substrate binding site .

This domain is found as standalone or in combination with other domains.
Inactive Receiver domain (iREC)
Type: Domain

This entry represents the inactive Receiver domain (iREC). iREC is predicted to dimerize with active counterparts as part of signal transduction relays in a subset of TOTE (TPR, OB, TBP, Effector) biological conflict systems .
Beta-mannosidase-like, galactose-binding domain-like (Beta-mannosidase-like_N2)
Type: Domain

This domain is found in a group of proteins belonging to glycosyl hydrolase 2 family (GH2) including beta-mannosidases, beta-glucuronidases and similar sequences .
Lon protease, AAA+ ATPase lid domain (Lon_lid)
Type: Domain

This entry represents the AAA+ ATPase lid domain of Lon proteases .

Lon protease belongs to the S16 peptidase family and is an ATP-dependent serine protease that mediates the selective degradation of mutant and abnormal proteins, as well as certain short-lived regulatory proteins. It is required for cellular homeostasis and for survival from DNA damage and developmental changes induced by stress . In pathogenic bacteria, it is required for the expression of virulence genes that promote cell infection .

Lon (La) protease was the first ATP-dependent protease to be purified from
E. coli . The enzyme is a homotetramer of 87kDa subunits, with one proteolytic and one ATP-binding site per monomer, making it structurally less complex than other known ATP-dependent proteases . Despite this relative structural simplicity, Lon recognises its substrates directly, without delegating the task of substrate recognition to other enzymes .
Duffy-binding-like domain, C-terminal subdomain (DBL_C)
Type: Domain

This entry represents a domain found C-terminally to Duffy binding-like (DBL,

) domains of PfEMP1 (

), the adhesin of Plasmodium falciparum which is an important target for protective immunity and is implicated in the pathology of malaria through its ability to adhere to host endothelial receptors . This domain consists of an helical bundle.
Mono-ADP-ribosyltransferase PARP14, WWE domain (PARP14_WWE)
Type: Domain

This entry represents the WWE domain of protein mono-ADP-ribosyltransferase PARP14 from mouse and similar proteins from vertebrates. PARP14 is an ADP-ribosyltransferase that mediates mono-ADP-ribosylation of glutamate residues on target proteins . It is related to inhibition of STAT1 phosphorylation, however it has been suggested that this may be the result of sumoylation of STAT1 'Lys-703' .

WWE domains are characterised by the presence of a Trp-Trp-Glu region, which is important for the structure stabilisation of PARP14. WWE domains can bind to ADP-Ribose derivatives, including iso-ADP-ribose, a molecule specifically found in PAR and promote interactions with ubiquitinated proteins. The PARP14 WWE domain, however, is unable to bind to any ADP-ribose derivatives and whether it interacts with iso-ADP ribose or ubiquitinated targets is unknown.
N-acyl amino acid synthase FeeM, catalytic core (FeeM_cat)
Type: Domain

This entry represents the catalytic core of the N-acyl amino acid synthase FeeM (

,

). This domain folds into a central antiparallel β-sheet packed on both sides with α-helices and closely resembles the conserved core of members of the GNAT superfamily.
Single-stranded-DNA-specific exonuclease RecJ, C-terminal domain, thermales (RecJ_C_thermales)
Type: Domain

This entry represents the C-terminal domain present in a set of RecJ proteins from thermales, such as RecJ from Thermus thermophilus, a single-stranded-DNA-specific exonuclease acting in a 5' to 3' direction that has no detectable activity on ssRNA .
Transcription factor IIIA, beta-beta-alpha zinc finger (TFIIIA_Zfn-C2H2)
Type: Domain

This entry represents a beta-beta-alpha (C2H2-type) zinc finger from TFIIIA, a transcription factor involved in ribosomal large subunit biogenesis. It binds the approximately 50 base pairs internal control region (ICR) of 5S ribosomal RNA genes. It is required for their RNA polymerase III-dependent transcription and may also maintain the transcription of other genes . This group of proteins is specific to animals.

This entry also includes P43 5S RNA-binding protein, a 5S RNA binding protein which is a major constituent of oocytes and comprises part of a 42S ribonucleoprotein storage particle .
Transcription initiation factor IIE subunit beta, E-tether (TFA2_E-tether)
Type: Domain

The small TFIIE subunit Tfa2 (yeast Transcription initiation factor IIE subunit beta) contains two WH domains and two conserved α-helices called the E-tether (represented by this entry) that bind the E-linker . Consistent with the structure, the E-tether is essential for TFIIE function and subunit dimerisation. Members of this group are specific to fungi.
C2185-like, N-terminal (C2185-like_N)
Type: Domain

This domain is found at the N-terminal of a group of uncharacterised proteins mainly from Clostridia, including C2185 from Clostridium acetobutylicum (

). This domain is found associated with

and shows a NAD(P) binding Rossmann fold.
Testis-expressed protein 13A/B, middle region (TEX13A/B_middle)
Type: Domain

This entry represents the middle region of human Testis-expressed protein 13A/B, which is predicted to show a disordered structure.