SII-SWORD/CoKE huggingface dataset:
Halocin C8-like, N-terminal domain (Hac8-like_N)
Type: Domain

This is a presumed domain found at the N-terminal of halocin C8 and similar sequences from archaea. Halocins are bacteriocin-like proteins or peptides produced by many species of the family Halobacteriaceae. Halocin C8 is derived from the C terminus of a 283 amino-acid prepro-protein (ProC8) . The N-terminal peptide of ProC8, known as Immunity protein HalI, acts as an immunity protein for halocin-C8. It is able to block the halocin-C8 activity by sequestering the activity of halocin-C8 through specific and direct binding .

Halocin C8, excreted by the Halobacterium, has a very wide activity spectrum. When a sensitive strain of Halorubrum saccharovorum was exposed to halocin C8, the treated cells swelled at the initial stage, the cell wall appeared to be nicked and the cytoplasm was then extruded out, and the whole cell was eventually completely lysed .
Colicin-A, N-terminal domain (ColA_N)
Type: Domain

This entry represents the N-terminal translocation domain of colicin A, an endonuclease active on both single- and double-stranded DNA but with undefined specificity . This domain interacts directly with TolAIII (C-terminal domain of TolA) which facilitates translocation through the cell envelope to reach their cytotoxic site of action . This group is specific to enterobacterales.
Endo-beta-N-acetylglucosaminidase EndoS, helical bundle (EndoS_helical)
Type: Domain

This entry represents a three-helical up-and-down bundle domain of EndoS from Streptococcus pyogenes and similar bacterial proteins. EndoS is involved in immune evasion mechanisms and possesses a specific endoglycosidase activity that targets IgG antibodies .
ToxT, N-terminal cupin-like domain (ToxT_N)
Type: Domain

This entry represents a cupin-like domain present in ToxT from Vibrio Cholerae (

,

) . ToxT serves as the culminating factor in the regulatory pathway, ensuring the coordinated production of two virulence factors: the toxin-coregulated pilus (TCP) and cholera toxin (CT), which are crucial for the pathogenicity of V.cholerae in causing cholera. ToxT possesses dimerisation and regulatory elements in its cupin-like N-terminal domain, while its C-terminal harbours two HTH AraC-like DNA binding domains .
AVR-Pik-like, HMA interaction domain (AVR-Pik_HID)
Type: Domain

This entry represents the HMA interaction domain of AVR-Pik {

), an effector protein from the rice blast fungus Pyricularia oryzae which binds and stabilizes rice HMA-domain containing NLR proteins to co-opt their function to suppress immunity . AVR-Pik adopts a six-stranded β-sandwich structure.
CRISPR-associated endonuclease Cas9, C-terminal domain (Cas9_C_2)
Type: Domain

This domain is found at the C-terminal end of CRISPR-associated endonuclease Cas9 from the gammaproteobacteria Francisella tularensis .
Methylated DNA-protein cysteine MeTransferase OGT, N-terminal domain (OGT_N)
Type: Domain

This entry represents the N-terminal of methylated DNA-protein cysteine methyltransferase (MGMT, also known as 6-O-methylguanine-DNA methyltransferase and MJ1529/OGT) from Methanocaldococcus jannaschii and similar sequences . This entry corresponds to the ribonuclease-like domain associated with 6-O-methylguanine DNA methyltransferase activity.
EhRGS-RhoGEF, PH domain-like (EhRGS-RhoGEF_PH-like)
Type: Domain

This entry represents the PH-like domain of a RGS-RhoGEF from Entamoeba histolytica (EhRGS-RhoGEF,

) which, like its mammalian homologues, serves as an EhGalpha1 effector and signals through Rho family GTPases playing important roles in its pathogenesis . This domain mediates activation of Rho family GTPases.
Carbohydrate binding module 74 (Cbm74)
Type: Domain

This entry represents a Carbohydrate binding module from Ruminococcus flavefaciens (Cbm74-rfgh5,

) and similar sequences. This domain adopts a β-sandwich fold typical of carbohydrate binding modules (CBMs) (

) .
Colicin S4, translocation domain (Csa_translocation_dom)
Type: Domain

This entry represents the N-terminal translocation domain of Colicin S4 from Escherichia coli (Csa,

), a polypeptide toxin produced and active against E.coli. This protein consists of four distinct domains, this domain, two receptor-binding domains and the C-terminal pore-forming domain (

). This domain shows an antiparallel β-sheet formed by three strands, an extended, glycine-rich loop structure and a short helix .
Class 2 C-terminal docking domain (Class_2_docking_dom)
Type: Domain

This short domain is found at the C-terminal end of the polyketide synthase module CurG from the cyanobacteria Moorena producens (

). It consists of two α-helices connected by a sharp bend (

) .
Mu Gam/Sipho_Gp157-like domain of the TOTE conflict systems (Mu_Gam-Sipho_Gp157-TOTE)
Type: Domain

This entry represents a DNA/RNA hybrid duplex binding domain found in the TOTE (TPR, OB, TBP, Effector) conflict systems . This domain occasionally displaces the more widely observed TOTE-TPR domain .
DNA transposase THAP9, C-terminal domain (THAP9_C)
Type: Domain

This domain is found at the C-terminal of human DNA transposase THAP9 and similar proteins mainly from vertebrates. This domain is predicted to be mainly formed by α-helices.
Short NACHT-associated C-terminal domain, family 5 (SNaCT5)
Type: Domain

The SNaCT domains are a rapidly evolving, monophyletic assemblage of domains found C-terminal to the NACHT module in several bacterial NACHT conflict systems. They contain a well-conserved aspartate near the N-terminal of the domain. SNaCT domains are thought to occlude the NTP-binding region, potentially until they interact with phage-encoded bNACHT inhibitors .
Short NACHT-associated C-terminal domain, family 13 (SNaCT13)
Type: Domain

The SNaCT domains are a rapidly evolving, monophyletic assemblage of domains found C-terminal to the NACHT module in several bacterial NACHT conflict systems. They contain a well-conserved aspartate near the N-terminal of the domain. SNaCT domains are thought to occlude the NTP-binding region, potentially until they interact with phage-encoded bNACHT inhibitors .
Short NACHT-associated C-terminal domain, family 8 (SNaCT8)
Type: Domain

The SNaCT domains are a rapidly evolving, monophyletic assemblage of domains found C-terminal to the NACHT module in several bacterial NACHT conflict systems. They contain a well-conserved aspartate near the N-terminal of the domain. SNaCT domains are thought to occlude the NTP-binding region, potentially until they interact with phage-encoded bNACHT inhibitors .
Short NACHT-associated C-terminal domain, family 9 (SNaCT9)
Type: Domain

The SNaCT domains are a rapidly evolving, monophyletic assemblage of domains found C-terminal to the NACHT module in several bacterial NACHT conflict systems. They contain a well-conserved aspartate near the N-terminal of the domain. SNaCT domains are thought to occlude the NTP-binding region, potentially until they interact with phage-encoded bNACHT inhibitors .
Protelomerase TelK, N-terminal domain (TelK_N)
Type: Domain

This entry represents the N-terminal domain of protelomerase TelK from Klebsiella phage phiKO2 and similar proteins from tailed bacteriophages and bacterial prophages.

TelK is a hairpin telomere resolvase with DNA cleavage-rejoining activity that resolves the catenated circular dimer produced from the bidirectional replication of a chromosome. The core of the TelK monomer consists of an N-terminal domain and a catalytic domain connected by a long α-helical linker. However, there are two extensions of the protein: a C-terminal DNA binding domain named the stirrup (

) and an N-terminal domain containing an insertion, called the muzzle domain (

) .
Peptidoglycan O-acetylesterase, N-terminal (Ape1_N)
Type: Domain

This domain is found at the N-terminal end of peptidoglycan O-acetylesterases Ape1 from Neisseria meningitidis and similar sequences mainly found in proteobacteria. Ape1, which occurs in bacteria that O-acetylate their peptidoglycan, has an SGNH catalytic domain (

) at the C-terminal end. This entry represents the N-terminal canonical β-sandwich that consists of two antiparallel β-sheets. It is likely to interact with a specific carbohydrate moiety .
ADP-ribosylating toxin CARDS, C-terminal beta-trefoil domain (CARDS_D3)
Type: Domain

This domain is found at the C-terminal end of ADP-ribosylating toxin CARDS from Mycoplasma pneumoniae, the main virulence factor for this bacteria. CARDS (for Community-Acquired Respiratory Distress Syndrome Toxin) is organised into three domains, an N-terminal

and tandem C-terminal β-trefoil domain. This entry represents the last domain (named D3) .
CARDS D2, beta trefoil domain (CARDS-D2)
Type: Domain

This domain is found at the C-terminal end of ADP-ribosylating toxin CARDS from Mycoplasma pneumoniae, the main virulence factor for this bacteria. CARDS (for Community-Acquired Respiratory Distress Syndrome Toxin) is organised into three domains, an N-terminal

and tandem C-terminal β-trefoil domain. This entry represents the second domain (named D2) .
Dicer, dsRNA-binding domain (Dcr1_dsRNA-bd_dom)
Type: Domain

This domain is found at the C-terminal end of Protein Dicer from Schizosaccharomyces pombe (Dcr1) and similar sequences from Schizosaccharomyces species. Dcr1 processes double-stranded RNA (dsRNA) precursors endonucleolytically. This domain adopts an extended dsRNA binding domain fold that embeds a zinc-binding motif (

) .
Turkey Adenovirus 3 Fibre protein-like, head domain (TAdV_Fibre-like_head)
Type: Domain

This entry represents the C-terminal Head Domain of the Fibre protein from Turkey Adenovirus 3, also known as turkey hemorrhagic enteritis virus (THEV) (

) .
Nab2-like, CCCH zinc finger (Nab2-like_Znf-CCCH)
Type: Domain

This entry represents the C-terminal zinc CCCH finger of Nab2-like proteins from fungi . Nab2 is a nuclear polyadenylated RNA-binding protein.
Testis-expressed protein 13B, C-terminal (TEX13B_C)
Type: Domain

This domain is found at the C-terminal end of human Testis-expressed protein 13B and similar sequences from mammals.
Short NACHT-associated C-terminal domain 14 (SNaCT14)
Type: Domain

The SNaCT domains are a rapidly evolving, monophyletic assemblage of domains found C-terminal to the NACHT module in several bacterial NACHT conflict systems. They contain a well-conserved aspartate near the N terminus of the domain. SNaCT domains are thought to occlude the NTP-binding region, potentially until they interact with phage-encoded bNACHT inhibitors .
Short NACHT-associated C-terminal domain 7 (SNaCT7)
Type: Domain

The SNaCT domains are a rapidly evolving, monophyletic assemblage of domains found C-terminal to the NACHT module in several bacterial NACHT conflict systems. They contain a well-conserved aspartate near the N terminus of the domain. SNaCT domains are thought to occlude the NTP-binding region, potentially until they interact with phage-encoded bNACHT inhibitors .
WsaF, C-terminal domain (WsaF_C)
Type: Domain

This entry represents a domain found at the C-terminal of WsaF (

) from Geobacillus stearothermophilus and related bacterial proteins. WsaF catalyses the formation of beta-1-2-linkage of rhamnose sugars in the carbohydrate polymer. It consists of two domains, the N-terminal which binds the acceptor (the growing rhamnan chain), and a C-terminal which binds the substrate (dTDP-beta-l-rhamnose) .

This entry also includes O-antigen biosynthesis protein from Myxococcus xanthus (RfbC).
Short NACHT-associated C-terminal domain 1 (SNaCT1)
Type: Domain

The SNaCT domains are a rapidly evolving, monophyletic assemblage of domains found C-terminal to the NACHT module in several bacterial NACHT conflict systems. They contain a well-conserved aspartate near the N terminus of the domain. SNaCT domains are thought to occlude the NTP-binding region, potentially until they interact with phage-encoded bNACHT inhibitors .
Short NACHT-associated C-terminal domain 6 (SNaCT6)
Type: Domain

The SNaCT domains are a rapidly evolving, monophyletic assemblage of domains found C-terminal to the NACHT module in several bacterial NACHT conflict systems. They contain a well-conserved aspartate near the N terminus of the domain. SNaCT domains are thought to occlude the NTP-binding region, potentially until they interact with phage-encoded bNACHT inhibitors .
Short NACHT-associated C-terminal domain 11 (SNaCT11)
Type: Domain

The SNaCT domains are a rapidly evolving, monophyletic assemblage of domains found C-terminal to the NACHT module in several bacterial NACHT conflict systems. They contain a well-conserved aspartate near the N terminus of the domain. SNaCT domains are thought to occlude the NTP-binding region, potentially until they interact with phage-encoded bNACHT inhibitors .
Short NACHT-associated C-terminal domain 10 (SNaCT10)
Type: Domain

The SNaCT domains are a rapidly evolving, monophyletic assemblage of domains found C-terminal to the NACHT module in several bacterial NACHT conflict systems. They contain a well-conserved aspartate near the N terminus of the domain. SNaCT domains are thought to occlude the NTP-binding region, potentially until they interact with phage-encoded bNACHT inhibitors .
Short NACHT-associated C-terminal domain 12 (SNaCT12)
Type: Domain

The SNaCT domains are a rapidly evolving, monophyletic assemblage of domains found C-terminal to the NACHT module in several bacterial NACHT conflict systems. They contain a well-conserved aspartate near the N terminus of the domain. SNaCT domains are thought to occlude the NTP-binding region, potentially until they interact with phage-encoded bNACHT inhibitors .
ArgL-like (ArgL-like)
Type: Family

This protein family includes the putative translational regulatory protein ArgL from Escherichia coli, the product of a small open reading frame (smORF), which may serve a regulatory role in the expression of its downstream gene .
PilJ-like, pilin-like domain (PilJ_N)
Type: Domain

This entry represents a N-terminal Pilin-like domain of PilJ from Clostridium difficile .
Fim1F, C-terminal domain (Fim1F_C)
Type: Domain

This domain is found at the C-terminal end of the putative fimbrium tip subunit Fim1F from Parabacteroides distasonis, which contain an N-terminal domain (

) and a slightly larger C-terminal domain (this entry) with a transthyretin-like fold that contains seven core β-strands arranged in two β-sheets an extra conserved 'appendage' of two amphipathic β-strands .
RavJ, peptidase domain (RavJ_pept_dom)
Type: Domain

This entry represents the N-terminal cysteine proteinase domain of RavJ from Legionella pneumophila (

, ).
Acyl-CoA oxidase, C-alpha1 domain (ACOX_C_alpha1)
Type: Domain

This entry represents the C-alpha1 domain from acyl-CoA oxidases which has an all-α helical structure that a forms a four α-helical bundle . This domain includes the FAD-binding and substrate-binding sites.
Cmr1, C-terminal domain (Cmr1_C)
Type: Domain

This entry represents the C-terminal RRM domain of CRISPR system Cmr subunit Cmr1 from Archaeoglobus fulgidus .
PsV, capsid protein, C-terminal domain (PsV_CP_C)
Type: Domain

This domain is found at the C-terminal end of the putative capsid protein from Penicillium stoloniferum virus F (CP,

). This protein has a disordered N-terminal end that interacts with the dsRNA genome and probably participates in its packaging or transcription, and a C-terminal domain (this entry) that shows a helix-loop-helix motif involved in the formation flexible channels thought to be involved in RNA synthesis activity .
Small ribosomal subunit protein mS39, PPR (Rib_mS39_PPR)
Type: Repeat

This entry represents a pentatricopeptide repeat (PPR) section found at the N-terminal of animal Small ribosomal subunit protein mS39 (also known as PPR domain protein 3 (PTCD3)), a mitochondrial RNA-binding protein that has a role in mitochondrial translation .
BRISC complex subunit FAM175B, helical domain (BRISC_FAM175B_helical)
Type: Domain

This domain is found in BRISC complex subunit FAM175B from Camponotus floridanus and similar proteins mainly found in arthropods. This protein is an homologue of human Abraxas 2 or KIAA0157, a component of the BRISC complex, a multiprotein complex that specifically cleaves 'Lys-63'-linked polyubiquitin, leaving the last ubiquitin chain attached to its substrates . This domain, which shows an α-helical configuration, is normally found C-terminal to

.
MCM10, OB-fold (MCM10_OB)
Type: Domain

MCM10 is an essential eukaryotic DNA replication protein required for assembly and progression of the replication fork. This entry represents the OB fold domain from the internal domain (ID) which also contains a C3H-type zinc finger (

).
4'-phosphopantetheinyl transferase, N-terminal (AASDHPPT_N)
Type: Domain

This domain is found at the N-terminal end of human 4'-phosphopantetheinyl transferase (also known as L-aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase, AASDHPPT), which catalyses the post-translational modification of target proteins by phosphopantetheine. This protein consists of two nearly identical domains (this entry and

) connected by a short linker region. Both domains fold into a pair of β-sheets connected by a loop region .
Alpha-amylase-like, C-terminal (AmyB-like_C)
Type: Domain

This domain is found at the C-terminal end of Alpha-amylase from Thermotoga neapolitana (AmyB), which belongs to glycoside hydrolase family 13 (GH13) and liberates maltose from multiple substrates, including starch, amylopectin and glycogen . This domain shows an all-β structure.
Coat protein, P (projecting) domain (Coat_P)
Type: Domain

This entry represents the P (projecting) domain found at the C terminus of ssRNA positive-strand viruses coat proteins, such as that in tomato bushy stunt virus .
Flagellar hook protein FlgE, third domain (FlgE_third)
Type: Domain

This domain is found in Flagellar hook protein FlgE from Caulobacter vibrioides and similar sequences from Caulobacter. Multiple copies of FlgE form part of the hook, a highly flexible universal joint that connects the filament to the motor of flagella. This protein consists of an N-terminal domain

, followed by

, then a third domain which is represented in this entry,

and a C-terminal domain

. This domain shows β-strands organised like a rugby ball, that is completed with some long loops .
Epidermin leader peptide-processing serine protease EpiP, N-terminal propeptide (EpiP_N)
Type: Domain

This entry represents the propeptide domain found at the N-terminal of peptidases belonging to MEROPS family S8A, subtilisins, including Epidermin leader peptide-processing serine protease EpiP from Staphylococcus epidermidis (EpiP). This propeptide is removed by proteolytic cleavage, which activates the enzyme.
PHLPP-like, RA domain (RA_PHLPP-like)
Type: Domain

This entry represents the N-terminal RA domain found in the PHLPP family proteins which are are serine/threonine phosphatases that play a crucial role in the regulation of cellular signalling pathways. They are involved in the dephosphorylation of the AGC kinase family members, including AKT1, AKT2, AKT3, PRKCA, and PRKCB, which are key regulators of cell survival, apoptosis, and proliferation . These proteins act as tumour suppressors by triggering apoptosis through the dephosphorylation of specific serine residues on these kinases . They also regulate cap-dependent translation by dephosphorylating RPS6KB1 and control the activity of STK4 and RAF1 kinases, influencing apoptosis and kinase activity, respectively. Additionally, they have roles in long-term memory formation, circadian rhythm consolidation, and T-cell development and function. PHLPP2 contains a Ras-associating (RA) domain followed by a PH domain, leucine-rich repeats and protein phosphatase 2C (PP2C) domain. The presence of a PH domain is important for interaction with some of their substrates.

This domain is also found in fungal adenylate cyclases (also known as ATP pyrophosphate-lyase), which regulate developmental processes such as hyphal growth, biofilm formation, and phenotypic switching. It plays an essential role in regulation of cellular metabolism by catalysing the synthesis of a second messenger, cAMP. Fungal adenylate cyclase has at least four domains, including an N-terminal adenylate cyclase G-alpha binding domain, a Ras-associating (RA) domain, a middle leucine-rich repeat region, and a catalytic domain. The RA domain of adenylate cyclase post-translationally modifies a small GTPase called Ras, which is involved in cellular signal transduction. The activity of adenylate cyclase is stimulated directly by regulatory proteins (Ras1 and Gpa2), peptidoglycan fragments and carbon dioxide .
Ferlin, dsRNA-binding domain-like domain (Ferlin_DSRM)
Type: Domain

This entry represents a domain which structurally resembles double stranded RNA binding domains, which is found in ferlin proteins .

Ferlins are involved in vesicle fusion events . Ferlins and other proteins, such as synaptotagmins, are implicated in facilitating the fusion process when cell membranes fuse together. There are six known human Ferlins: Dysferlin (Fer1L1), Otoferlin (Fer1L2), Myoferlin (Fer1L3), Fer1L4, Fer1L5, and Fer1L6. Defects in these genes can lead to a wide range of diseases including muscular dystrophy (dysferlin), deafness (otoferlin), and infertility (fer-1, fertilization factor-1).

Structurally they have 6 tandem C2 domains, designated as (C2A-C2F) and a single C-terminal transmembrane domain, though there is a new study that disputes this and claims that there are actually 7 tandem C2 domains with another C2 domain inserted between C2D and C2E. In a subset of them (Dysferlin, Myoferlin, and Fer1) there is an additional conserved domain called DysF .
NOMO-like, ninth beta-sandwich domain (NOMO1-like_9th)
Type: Domain

This domain is found in human BOS complex subunit NOMO1 and similar sequences, mainly from animals and plants. This domain is predicted to adopt a seven stranded β-sandwich fold.

This domain is also found in Nicotinic receptor-associated protein 4 from Caenorhabditis elegans.

NOMO family of proteins includes NOMO1, NOMO2, NOMO3. These proteins are components of the multi-pass translocon (MPT) complex that mediates insertion of multi-pass membrane proteins into the lipid bilayer of membranes . They play an important role in the protein topogenesis and cells lacking these components show reduced multipass protein stability . NOMO proteins are multidomain proteins.
NOMO, second beta-sandwich domain (NOMO1-3_2nd)
Type: Domain

This domain is found at the N-terminal end of human BOS complex subunit NOMO1-3 and similar sequences mainly from animals and plants. This domain is predicted to adopt a seven stranded β-sandwich fold.

NOMO family of proteins includes NOMO1, NOMO2, NOMO3. These proteins are components of the multi-pass translocon (MPT) complex that mediates insertion of multi-pass membrane proteins into the lipid bilayer of membranes . They play an important role in the protein topogenesis and cells lacking these components show reduced multipass protein stability . NOMO proteins are multidomain proteins.
NOMO-like, N-terminal beta-sandwich domain (NOMO-like_N)
Type: Domain

This domain is found at the N-terminal end of human BOS complex subunit NOMO1 and similar sequences mainly from animals and plants. This domain is predicted to adopt a seven stranded β-sandwich fold.

This domain is also found in Nicotinic receptor-associated protein 4 from Caenorhabditis elegans.

NOMO family of proteins includes NOMO1, NOMO2, NOMO3. These proteins are components of the multi-pass translocon (MPT) complex that mediates insertion of multi-pass membrane proteins into the lipid bilayer of membranes . They play an important role in the protein topogenesis and cells lacking these components show reduced multipass protein stability . NOMO proteins are multidomain proteins.