SII-SWORD/CoKE huggingface dataset:
Effector-associated domain 2 (EAD2)
Type: Domain

This entry represents the effector-associated domain 2 (EAD2). This domain is one of the most prevalent EADs, predominantly found in actinobacteria and to a lesser extent in cyanobacteria and Chloroflexi. EAD2 occurs fused to the signalling peptidases and nucleotide-utilizing domains fused to the VMAP component of those ternary systems and it has been suggested that it recruits the signalling components of the system . It is predicted to be an all α-helical domain.

Effector-associated domains (EADs) are predicted to function as adaptor domains mediating protein-protein interactions. The EADs show a characteristic architectural pattern. One copy is always fused, typically to the N- or C-terminal, of a core component of a biological conflict system; examples include VMAP (vWA-MoxR associated protein), iSTAND (inactive STAND (iSTAND) NTPase system), or GAP1 (GTPase-associated protein 1). Further copies of the same EAD are fused to either effector or signal-transducing domains, or additional EADs. EAD pairs are frequently observed together on the genome in conserved gene neighborhoods, but can also be severed from such neighborhoods and located in distant regions, indicating EAD-EAD protein domain coupling approximates the advantages of collinear transcription . EADs are all small domains with no enzymatic features.
Effector-associated domain 5 (EAD5)
Type: Domain

This entry represents the effector-associated domain 5 (EAD5) that appears to primarily recruit other effectors to the systems, similar to EAD1. This domain has a predicted mixed α+β arrangement .

Effector-associated domains (EADs) are predicted to function as adaptor domains mediating protein-protein interactions. The EADs show a characteristic architectural pattern. One copy is always fused, typically to the N- or C-terminal, of a core component of a biological conflict system; examples include VMAP (vWA-MoxR associated protein), iSTAND (inactive STAND (iSTAND) NTPase system), or GAP1 (GTPase-associated protein 1). Further copies of the same EAD are fused to either effector or signal-transducing domains, or additional EADs. EAD pairs are frequently observed together on the genome in conserved gene neighborhoods, but can also be severed from such neighborhoods and located in distant regions, indicating EAD-EAD protein domain coupling approximates the advantages of collinear transcription . EADs are all small domains with no enzymatic features.
Effector-associated domain 6 (EAD6)
Type: Domain

This entry represents the effector-associated domain 6 (EAD6) found in cyanobacteria. Similar to EAD2, it has been suggested to recruit the signalling components of the system . It is predicted to be an all α-helical domain.

Effector-associated domains (EADs) are predicted to function as adaptor domains mediating protein-protein interactions. The EADs show a characteristic architectural pattern. One copy is always fused, typically to the N- or C-terminal, of a core component of a biological conflict system; examples include VMAP (vWA-MoxR associated protein), iSTAND (inactive STAND (iSTAND) NTPase system), or GAP1 (GTPase-associated protein 1). Further copies of the same EAD are fused to either effector or signal-transducing domains, or additional EADs. EAD pairs are frequently observed together on the genome in conserved gene neighborhoods, but can also be severed from such neighborhoods and located in distant regions, indicating EAD-EAD protein domain coupling approximates the advantages of collinear transcription . EADs are all small domains with no enzymatic features.
Effector-associated domain 4 (EAD4)
Type: Domain

This entry represents the effector-associated domain 4 (EAD4) found in cyanobacteria that appears to primarily recruit other effectors to the systems, similar to EAD1. This domain has a predicted mixed α-β arrangement .

Effector-associated domains (EADs) are predicted to function as adaptor domains mediating protein-protein interactions. The EADs show a characteristic architectural pattern. One copy is always fused, typically to the N- or C-terminal, of a core component of a biological conflict system; examples include VMAP (vWA-MoxR associated protein), iSTAND (inactive STAND (iSTAND) NTPase system), or GAP1 (GTPase-associated protein 1). Further copies of the same EAD are fused to either effector or signal-transducing domains, or additional EADs. EAD pairs are frequently observed together on the genome in conserved gene neighborhoods, but can also be severed from such neighborhoods and located in distant regions, indicating EAD-EAD protein domain coupling approximates the advantages of collinear transcription . EADs are all small domains with no enzymatic features.
Effector-associated domain 7 (EAD7)
Type: Domain

This entry represents the effector-associated domain 7 (EAD7). Similarly to EAD1, it may primarily recruit other effectors to the systems . It is predicted to be an all α-helical domain.

Effector-associated domains (EADs) are predicted to function as adaptor domains mediating protein-protein interactions. The EADs show a characteristic architectural pattern. One copy is always fused, typically to the N- or C-terminal, of a core component of a biological conflict system; examples include VMAP (vWA-MoxR associated protein), iSTAND (inactive STAND (iSTAND) NTPase system), or GAP1 (GTPase-associated protein 1). Further copies of the same EAD are fused to either effector or signal-transducing domains, or additional EADs. EAD pairs are frequently observed together on the genome in conserved gene neighborhoods, but can also be severed from such neighborhoods and located in distant regions, indicating EAD-EAD protein domain coupling approximates the advantages of collinear transcription . EADs are all small domains with no enzymatic features.
Protein of unknown function DUF6507 (DUF6507)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria.
Effector-associated domain 8 (EAD8)
Type: Domain

This entry represents the effector-associated domain 8 (EAD8). Similarly to EAD1, it may primarily recruit other effectors to the systems . It is predicted to be an all α-helical domain.

Effector-associated domains (EADs) are predicted to function as adaptor domains mediating protein-protein interactions. The EADs show a characteristic architectural pattern. One copy is always fused, typically to the N- or C-terminal, of a core component of a biological conflict system; examples include VMAP (vWA-MoxR associated protein), iSTAND (inactive STAND (iSTAND) NTPase system), or GAP1 (GTPase-associated protein 1). Further copies of the same EAD are fused to either effector or signal-transducing domains, or additional EADs. EAD pairs are frequently observed together on the genome in conserved gene neighborhoods, but can also be severed from such neighborhoods and located in distant regions, indicating EAD-EAD protein domain coupling approximates the advantages of collinear transcription . EADs are all small domains with no enzymatic features.
Effector-associated domain 9 (EAD9)
Type: Domain

This entry represents the effector-associated domain 9 (EAD9). Similarly to EAD2, it may primarily recruit the signalling components of the system . It is predicted to be an all α-helical domain.

Effector-associated domains (EADs) are predicted to function as adaptor domains mediating protein-protein interactions. The EADs show a characteristic architectural pattern. One copy is always fused, typically to the N- or C-terminal, of a core component of a biological conflict system; examples include VMAP (vWA-MoxR associated protein), iSTAND (inactive STAND (iSTAND) NTPase system), or GAP1 (GTPase-associated protein 1). Further copies of the same EAD are fused to either effector or signal-transducing domains, or additional EADs. EAD pairs are frequently observed together on the genome in conserved gene neighborhoods, but can also be severed from such neighborhoods and located in distant regions, indicating EAD-EAD protein domain coupling approximates the advantages of collinear transcription . EADs are all small domains with no enzymatic features.
Effector-associated domain 11 (EAD11)
Type: Domain

This entry represents the effector-associated domain 11 (EAD11). It is predicted to be an all α-helical domain . This domain is found in Roc-COR-CHAT protease, a recently characterised protease for substrate gasdermin bGSDM. It cleaves the bGSDM precursor, releasing the pore-forming moiety, which integrates into the membrane and triggers cell death .

Effector-associated domains (EADs) are predicted to function as adaptor domains mediating protein-protein interactions. The EADs show a characteristic architectural pattern. One copy is always fused, typically to the N- or C-terminal, of a core component of a biological conflict system; examples include VMAP (vWA-MoxR associated protein), iSTAND (inactive STAND (iSTAND) NTPase system), or GAP1 (GTPase-associated protein 1). Further copies of the same EAD are fused to either effector or signal-transducing domains, or additional EADs. EAD pairs are frequently observed together on the genome in conserved gene neighborhoods, but can also be severed from such neighborhoods and located in distant regions, indicating EAD-EAD protein domain coupling approximates the advantages of collinear transcription . EADs are all small domains with no enzymatic features.
vWA-MoxR associated protein middle region 1 (VMAP-M1)
Type: Domain

This domain represents VMAP-M1, predominantly found in cyanobacteria.

This domain represents a highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. Using sequence similarity-based clustering it has been possible to identify 29 distinct versions named VMAP-M0-28, that may be involved in sensing of invasive entities . It is predicted to adopt an all-α-helical secondary structure.
Protein of unknown function DUF6506 (DUF6506)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea.
Protein of unknown function DUF6505 (DUF6505)
Type: Family

DUF6505 is a group of uncharacterised proteins from bacteria.
Domain of unknown function DUF6504 (DUF6504)
Type: Domain

This is a presumed domain found at the C-terminal of functionally uncharacterised proteins found in bacteria. In some sequences, it covers the full length.
Protein of unknown function DUF6503 (DUF6503)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria.
Protein of unknown function DUF6502 (DUF6502)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria.
vWA-MoxR associated protein middle region 2 (VMAP-M2)
Type: Domain

This domain is known as VMAP-M2, found in actinobacteria.

This domain represents a highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. Using sequence similarity-based clustering it has been possible to identify 29 distinct versions named VMAP-M0-28, that may be involved in sensing of invasive entities . It is predicted to adopt an all-α-helical secondary structure.
Protein of unknown function DUF6501 (DUF6501)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria.
Protein of unknown function DUF6500 (DUF6500)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria.
vWA-MoxR associated protein middle region 4 (VMAP-M4)
Type: Domain

This domain is known as VMAP-M4, found in alpha and betaprotobacteria.

This domain represents a highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. Using sequence similarity-based clustering it has been possible to identify 29 distinct versions named VMAP-M0-28, that may be involved in sensing of invasive entities . It is predicted to adopt an all-α-helical secondary structure.
vWA-MoxR associated protein, C-terminal domain (VMAP_C)
Type: Domain

This domain represents the C-terminal region of the VMAP protein of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems, which is the most conserved part. It is predicted to adopt a mixed α+β domain with no apparent structural similarity to known protein folds. It contains several, nearly universally polar residues, suggesting a conserved interaction interface. Even though VMAP-C is possible to have enzymatic function, but it appears unlikely. Sensing of invasive elements by VMAP-Ms are predicted to trigger a sequence of conformational changes, which is communicated to the switch-component (MoxR) of the system via the more constant VMAP-C .
vWA-MoxR associated protein middle region 5 (VMAP-M5)
Type: Domain

This domain is known as VMAP-M5.

This domain represents a highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. Using sequence similarity-based clustering it has been possible to identify 29 distinct versions named VMAP-M0-28, that may be involved in sensing of invasive entities . It is predicted to adopt an all-α-helical secondary structure.
vWA-MoxR associated protein middle region 7 (VMAP-M7)
Type: Domain

This domain is known as VMAP-M7, found in actinobacteria.

This domain represents a highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. Using sequence similarity-based clustering it has been possible to identify 29 distinct versions named VMAP-M0-28, that may be involved in sensing of invasive entities . It is predicted to adopt an all-α-helical secondary structure.
vWA-MoxR associated protein middle region 8 (VMAP-M8)
Type: Domain

This domain is known as VMAP-M8, found in actinobacteria.

This domain represents a highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. Using sequence similarity-based clustering it has been possible to identify 29 distinct versions named VMAP-M0-28, that may be involved in sensing of invasive entities . It is predicted to adopt an all-α-helical secondary structure.
vWA-MoxR associated protein middle region 9 (VMAP-M9)
Type: Domain

This domain is known as VMAP-M9, found in cyanobacteria.

This domain represents a highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. Using sequence similarity-based clustering it has been possible to identify 29 distinct versions named VMAP-M0-28, that may be involved in sensing of invasive entities . It is predicted to adopt an all-α-helical secondary structure.
NrS-1 polymerase-like, helicase domain (NrS-1_pol-like_helicase)
Type: Domain

This entry represents a helicase domain predominantly found in bacteria, but spread over all domains of life. This domain is found in putative P4-specific DNA primase from the Bacteriophage P4, a protein that acts as a DNA primase and DNA helicase and it has been characterised in NrS-1 polymerase (

) from Nitratiruptor phage NrS-1 , the first known phage that can infect Epsilonproteobacteria, one of the predominant primary producers in the deep-sea hydrothermal vent ecosystems. NrS-1 polymerase is a multidomain enzyme and is a key component of the phage replisome.
vWA-MoxR associated protein middle region 14 (VMAP-M14)
Type: Domain

This domain is known as VMAP-M14.

This domain represents a highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. Using sequence similarity-based clustering it has been possible to identify 29 distinct versions named VMAP-M0-28, that may be involved in sensing of invasive entities . It is predicted to adopt an all-α-helical secondary structure.
vWA-MoxR associated protein middle region 19 (VMAP-M19)
Type: Domain

This domain is known as VMAP-M19.

This domain represents a highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. Using sequence similarity-based clustering it has been possible to identify 29 distinct versions named VMAP-M0-28, that may be involved in sensing of invasive entities . It is predicted to adopt an all-α-helical secondary structure.
Wolframin, Sel1-like repeat (Wolframin_Sel1-like_rpt)
Type: Repeat

This entry represents the N-terminal Sel1-like repeats found in the wolframin protein. This region has been linked to calmodulin-binding, suggesting these repeats may mediate a protein interaction .

Wolframin, a multi-pass membrane protein found in the endoplasmic reticulum, is expressed by the Wolfram syndrome 1 gene (WFS1) . The detailed molecular function of the protein is not known, but it is believed to participate, at least in part, in the regulation of cellular calcium homeostasis by modulating the filling state of the endoplasmic reticulum calcium store.

Defects in WFS1 cause Wolfram Syndrome (WFS), also referred to as DIDMOAD - this syndrome is characterised by diabetes insipidus, childhood-onset diabetes mellitus, gradual loss of vision owing to optic atrophy, and deafness . It is a rare autosomal recessive disorder, and may give rise to other complications affecting the bladder and nervous system.

Wolframin homologues have been identified in a range of species, from mammals and amphibia to insects. Notwithstanding regions of high similarity, vertebrate and invertebrate wolframins exhibit characteristic lineage- specific differences. This entry represents the Wolframin family, and includes homologues from invertebrates.
Protein of unknown function DUF5908 (DUF5908)
Type: Family

This entry represents a group of short proteins of unknown function found in bacteria. A member of this family is though to be part of a contractile injection system in Photorhabdus asymbiotica .
Wolframin, EF-hand domain (Wolframin_EF-hand)
Type: Domain

This domain contains two characteristic copies of the bihelical repeat forming the basic EF-hand unit. The absence of the characteristic calcium-binding motif DxDxDG suggests that it could self-dimerize or dimerize with other EF-hand-containing proteins .

Wolframin, a multi-pass membrane protein found in the endoplasmic reticulum, is expressed by the Wolfram syndrome 1 gene (WFS1) . The detailed molecular function of the protein is not known, but it is believed to participate, at least in part, in the regulation of cellular calcium homeostasis by modulating the filling state of the endoplasmic reticulum calcium store.

Defects in WFS1 cause Wolfram Syndrome (WFS), also referred to as DIDMOAD - this syndrome is characterised by diabetes insipidus, childhood-onset diabetes mellitus, gradual loss of vision owing to optic atrophy, and deafness . It is a rare autosomal recessive disorder, and may give rise to other complications affecting the bladder and nervous system.

Wolframin homologues have been identified in a range of species, from mammals and amphibia to insects. Notwithstanding regions of high similarity, vertebrate and invertebrate wolframins exhibit characteristic lineage- specific differences. This entry represents the Wolframin family, and includes homologues from invertebrates.
Wolframin, OB-fold domain (Wolframin_OB_fold)
Type: Domain

This is the OB-fold domain found at the C terminus of the wolframin protein. It localizes to the ER lumen and lacks the conserved polar residues typical of OB-fold domain-mediated nucleic acid-binding. It has been predicted to mediate protein-protein interactions .

Wolframin, a multi-pass membrane protein found in the endoplasmic reticulum, is expressed by the Wolfram syndrome 1 gene (WFS1) . The detailed molecular function of the protein is not known, but it is believed to participate, at least in part, in the regulation of cellular calcium homeostasis by modulating the filling state of the endoplasmic reticulum calcium store.

Defects in WFS1 cause Wolfram Syndrome (WFS), also referred to as DIDMOAD - this syndrome is characterised by diabetes insipidus, childhood-onset diabetes mellitus, gradual loss of vision owing to optic atrophy, and deafness . It is a rare autosomal recessive disorder, and may give rise to other complications affecting the bladder and nervous system.

Wolframin homologues have been identified in a range of species, from mammals and amphibia to insects. Notwithstanding regions of high similarity, vertebrate and invertebrate wolframins exhibit characteristic lineage- specific differences. This entry represents the Wolframin family, and includes homologues from invertebrates.
Aminoacyl-tRNA synthetase, class I, anticodon-binding (aa-tRNA-synth_I_cd-bd)
Type: Domain

This entry represents the anticodon binding domain found at the C terminus of class I aminoacyl-tRNA synthetases (such as Glutamate-tRNA ligase) predominately in bacteria . Glutamate-tRNA ligase catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction: glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu) .

The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction . These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel β-sheet fold flanked by α-helices , and are mostly dimeric or multimeric, containing at least three conserved regions . However, tRNA binding involves an α-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c .

Structurally, an α-helix-bundle anticodon-binding domain characterises the class Ia synthetases, whereas the class Ib synthetases, GlnRS and GluRS have distinct anticodon-binding domains. The anticodon-binding domain has a multi-helical structure, consisting of two all-alpha subdomains. The Rossmann-fold, made up of alternate α-helices and β-sheets involved in ATP binding in the extended conformation, and the anticodon-binding domains are connected by a β-α-α-β-α topology ('SC fold') domain that contains the class I specific KMSKS motif .