SII-SWORD/CoKE huggingface dataset:
Nonstructural protein 13, stalk domain, coronavirus (NSP13_stalk_CoV)
Type: Domain

This entry represents the stalk domain, which lies between the ZBD domain and the 1B domain; a short loop connects the ZBD to the stalk domain. It comprises three tightly-interacting α-helices connected to the 1B domain, transferring the effect from the ZBD domain onto the helicase core domains. The ZBD and stalk domains are critical for the helicase activity of SARS-CoV NSP13 .

Nonstructural protein 13 (NSP13) is encoded by the replicase polyprotein 1a/ab of coronaviruses and released after a proteolytic process. It plays a critical role catalysing the unwinding of duplex oligonucleotides into single strands in an NTP-dependent manner. It In SARS-CoV, it has been shown that NSP12 directly interacts with NSP13 and enhances its helicase activity.

NSP13 is a multidomain protein consisting of a N-terminal zinc-binding domain (ZBD), a stalk domain that connects the ZBD with the 1B domain and the helicase domain (that contains two RecA1 and RecA2 domains). ZBD, stalk and 1B domains are unique to nidovirus helicases . NSP13 adopts a triangular pyramid shape in which the two RecA1 and A2 and 1B domains form the triangular base while N-terminal ZBD and stalk domains are arranged at the apex of the pyramid . Recently, it has been reported that SARS-CoV-2 NSP13 acts as an interferon antagonist. It is involved in type I interferon (IFN-I) response as it binds and blocks TBK1 phosphorylation to inhibit interferon regulatory factor 3 (IRF3) which results in decreased IRF3 activation .
Ubiquinone biosynthesis protein COQ9, HTH domain (COQ9_HTH)
Type: Domain

This domain is found towards the N-terminal of ubiquinone biosynthesis protein COQ9 from humans and similar proteins predominantly from vertebrates. COQ9 is a lipid-binding protein involved in the biosynthesis of coenzyme Q, also named ubiquinone, an essential lipid-soluble electron transporter for aerobic cellular respiration. This protein has structural homology to the TFR family of bacterial transcriptional regulators. This domain contains an a helix-turn- helix (HTH) motif that largely lacks the positive charges required for DNA binding .
IcmR, middle region (IcmR_middle)
Type: Domain

IcmR plays a role in the Dot/Icm translocase from Legionella pneumophila. This Type IVb secretion system (T4bSS) is responsible for the delivery of protein effectors to the host cell cytoplasm. The middle region of IcmR (this entry) binds to the N-terminal domain of IcmQ, which is essential for IcmQ (

) to function correctly. The interacting domains form helical hairpins within a four-helix bundle that is stabilised by hydrophobic packing .
COMMD9, N-terminal domain (COMMD9_N)
Type: Domain

This domain is found at the N-terminal of COMM domain-containing protein 9 from humans and similar proteins from vertebrates. COMMD9 contains a conserved and unique motif termed the COMM (copper metabolism gene MURR1,

) domain at the C-terminal, which functions as an interface for protein-protein interactions. This domain shows a globular structure that consists of a six-helix bundle with a meander topology .
Type VI secretion system component TssM1, helical domain (TssM1_hel)
Type: Domain

This entry represents the α-helical domain from homologues of the Type VI secretion component TssM1 from Pseudomonas aeruginosa (

), which plays a role in the release of toxins targeting both eukaryotic and prokaryotic species, plays an essential role in stabilization of assembled TssK1 structure at a fixed perimembrane site and forms part of the tip complex . This domain is also found in bacterial IcmF (intracellular multiplication and human macrophage-killing) proteins .
Intercellular adhesion molecule 1/3/5, D2 domain (ICAM1_3_5_D2)
Type: Domain

Intercellular adhesion moleculea (ICAMs) promote intercellular adhesion and are important in inflammation, immune responses and in intracellular signalling events . They belong to the Ig-like superfamily and differ in their cell expression patterns and numbers of Ig-like domains (ICAM-2 and ICAM-4 have two, ICAM-1 and ICAM-3 have five and ICAM-5 has nine ). Domain 2 (D2), represented in this entry, is most similar between ICAM-1, 3 and 5 .
Conserved oligomeric Golgi complex subunit 4, N-terminal (COG4_N)
Type: Domain

This is the N-terminal coiled-coil of COG4.

COG4 is a component of the conserved oligomeric Golgi (COG) complex which mediates the proper glycosylation of proteins trafficking through the Golgi apparatus. It is a member of the CATCHR (complexes associated with tethering containing helical rods) family, which includes components of the exocyst, COG, GARP, and Dsl1 complexes, sharing structural and functional features: the α-helical bundles at the middle/C-terminal and a N-terminal coiled-coil region .
Intron-encoded endonuclease 1, DNA-binding domain (I-TevI_DNA-bd)
Type: Domain

This entry represents a domain found at the C-terminal end of in Intron-encoded endonuclease 1 (I-TevI) from Bacteriophage T4 (

). I-TevI is a site-specific endonuclease that belongs to the GIY-YIG family that shows a catalytic domain (

) and a DNA-binding domain (this entry), which is organised into three DNA recognition subdomains: a Zn finger, an elongated subdomain that includes a minor groove-binding α-helix and a helix-turn-helix subdomain .
Conserved oligomeric Golgi complex subunit 4 (COG4)
Type: Family

COG4 is a component of the conserved oligomeric Golgi (COG) complex which mediates the proper glycosylation of proteins trafficking through the Golgi apparatus. It is a member of the CATCHR (complexes associated with tethering containing helical rods) family, which includes components of the exocyst, COG, GARP, and Dsl1 complexes, sharing structural and functional features: the α-helical bundles at the middle/C-terminal and a N-terminal coiled-coil region .
Bacteriophage Sf6, terminase small subunit-like (Sf6_terminase)
Type: Family

In many tailed double-stranded DNA (dsDNA) virus such as Bacteriophage Sf6 (

), the DNA newly synthesized is packaged into a preformed procapsid. The small subunit of the terminase is the component responsible for concatemeric viral DNA-recognition in the molecular machine that carries out this process. The small subunit of the terminase from phage Sf6, also known as gp1, consists of an N-terminal domain, a central α-helical domain and a C- terminal domain forming a β-barrel, and adopts a ring-like octameric structure composed of monomers .
Conserved oligomeric Golgi complex subunit 4, C-terminal (COG4_C)
Type: Domain

This is the C-terminal domain of COG4, which contains the key Arginine residue that stabilises this domain and it is required for the proper glycosylation of cell surface proteins .

COG4 is a component of the conserved oligomeric Golgi (COG) complex which mediates the proper glycosylation of proteins trafficking through the Golgi apparatus. It is a member of the CATCHR (complexes associated with tethering containing helical rods) family, which includes components of the exocyst, COG, GARP, and Dsl1 complexes, sharing structural and functional features: the α-helical bundles at the middle/C-terminal and a N-terminal coiled-coil region .
Conserved oligomeric Golgi complex subunit 3, C-terminal (COG3_C)
Type: Domain

This entry represents the α-helical bundles of COG3.

This entry includes the Conserved oligomeric Golgi complex subunit 3 (COG3, also known as Sec34) which is a component of the peripheral membrane COG complex, involved in intra-Golgi protein trafficking . COG is a member of the complexes associated with tethering containing helical rods (CATCHR) family which also includes the exocyst, GARP and Dsl1 complexes, which are evolutionarily related and share structural features consisting of α-helical bundles towards the C-terminal and an N-terminal coiled-coil region .
E3 ubiquitin-protein ligase SHPRH, first helical domain (SHPRH_helical_1st)
Type: Domain

This entry represents the first helical domain found in the central region of the E3 ubiquitin-protein ligase SHPRH, a protein involved in DNA repair . Helices in this domain adopt an arrangement similar to TPRs.
Uncharacterized motility-related protein HVO_2248-like (HVO_2248-like)
Type: Family

This family represents a group of uncharacterised proteins from archaea, including the Uncharacterized motility-related protein HVO_2248 from Haloferax (

), which is related to hypermotility and predicted as a cytoplasmic protein . Homologues of HVO_2248 are only found in Halobacteria.
CofB-like, pilin domain (CofB-like_pilin_dom)
Type: Domain

This domain is found in CofB from Escherichia coli and in similar proteins predominantly from gammaproteobacteria. CofB is a minor pilin, required for assembly of Type IV pili. This entry represents the pilin domain, which is located in the N-terminal region of the protein. It shows a canonical T4b pilin fold seen in the major pilins, with an α-helical backbone and a five-stranded antiparallel β-sheet .
Envelope glycoprotein GP350, N-terminal, B domain, herpervirus (GP350_N_B_dom_herpes)
Type: Domain

This entry represents domain B of the N-terminal region of GP350 .

This entry includes Envelope glycoprotein GP350 from Epstein-Barr virus (also known as BLLF1 viral late glycoprotein), the most abundantly expressed glycoprotein in the viral envelope of Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies
in vivo
. It is a 907 residues long gp350 polypeptide containing an 18-residue peptide at the C terminus that is located inside the viral membrane, a membrane-spanning domain and a large N-terminal segment (860 residues) predicted to extend outside the viral membrane. The extreme N-terminal region (1-470) is sufficient to bind receptor CR2 (also known as CD21) and fold into three distinct domains (denoted as A (

), B (

) and C (

)) that organise into an "L-shape" structure.

The binding of the viral major glycoprotein BLLF1 to the CD21 cellular receptor is responsible for viral attachment to the cell surface during infection of B lymphocytes by the Epstein-Barr virus (strain GD1) (HHV-4) (Human herpesvirus 4) .
CRISPR RNA silencing complex Cmr2 subunit, Zn-binding domain (Cmr2_Zn-bd)
Type: Domain

The prokaryotic CRISPR RNA-Cas protein (Cmr) complex provides protection against mobile genetic elements by cleaving foreign RNA. Its largest subunit is Cmr2. This protein shows a N-terminal HD (histidine-aspartate) domain, two RRM domains resembling adenylate cyclase and two α-helical domains. This entry represents the conserved Zn binding subdomain included in the first RMM domain (D1 domain) of Cmr2 . This region shows two α-helices.
Envelope glycoprotein GP350, N-terminal, C domain, herpesvirus (GP350_C_dom_herpes)
Type: Domain

This entry represents domain C of the N-terminal region of GP350 .

This entry includes Envelope glycoprotein GP350 from Epstein-Barr virus (also known as BLLF1 viral late glycoprotein), the most abundantly expressed glycoprotein in the viral envelope of Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies
in vivo
. It is a 907 residues long gp350 polypeptide containing an 18-residue peptide at the C terminus that is located inside the viral membrane, a membrane-spanning domain and a large N-terminal segment (860 residues) predicted to extend outside the viral membrane. The extreme N-terminal region (1-470) is sufficient to bind receptor CR2 (also known as CD21) and fold into three distinct domains (denoted as A (

), B (

) and C (

)) that organise into an "L-shape" structure.

The binding of the viral major glycoprotein BLLF1 to the CD21 cellular receptor is responsible for viral attachment to the cell surface during infection of B lymphocytes by the Epstein-Barr virus (strain GD1) (HHV-4) (Human herpesvirus 4) .
CRISPR RNA silencing complex Cmr2-like, C-terminal domain (Cmr2-like_C)
Type: Domain

The prokaryotic CRISPR RNA-Cas protein (Cmr) complex provides protection against mobile genetic elements by cleaving foreign RNA. Its largest subunit is Cmr2. This protein shows a N-terminal HD (histidine-aspartate) domain, two RRM domains resembling adenylate cyclase and two α-helical domains. This entry represents the second α-helical domain, found at its N-terminal. It is similar to the small subunit Cmr5, which contains six α-helices and two helical insertions that fold into a single globular structure . This domain is also found in Cas10 proteins from bacteria .
CRISPR RNA silencing complex Cmr2 subunit, first helical domain (Cmr2_hel_dom1)
Type: Domain

The prokaryotic CRISPR RNA-Cas protein (Cmr) complex provides protection against mobile genetic elements by cleaving foreign RNA. Its largest subunit is Cmr2. This protein shows a N-terminal HD (histidine-aspartate) domain, two RRM domains resembling adenylate cyclase and two α-helical domains. This entry represents the first α-helical domain, which is similar to the thumb of DNA polymerases .
E3 ubiquitin-protein ligase SHPRH, second helical domain (SHPRH_helical_2nd)
Type: Domain

This entry represents the second helical domain found after the first helical domain (

) and before the zinc finger (

), towards the C-terminal of the E3 ubiquitin-protein ligase SHPRH, a protein involved in DNA repair .
SHQ1-like, CS domain (SHQ1-like_CS)
Type: Domain

This domain is found at the N-terminal of SHQ1 from yeast and its homologue from animals, including human SHQ1.

SHQ1 is a factor required for the biogenesis and assembly of H/ACA small nucleolar ribonucleoparticle (snoRNP), which are essential for ribosomal RNA and telomerase RNA processing and metabolism. This protein contains two domains: an N-terminal CS (named after CHORD-containing proteins and SGT1) or HSP20-like domain and a C-terminal region called the Shq1 domain (

). This entry represents the CS domain, which folds into a compact antiparallel β-sandwich made of two β-sheets with four and three β-strands, respectively, and a short α-helix .
SidC, C-terminal domain (SidC_C)
Type: Domain

This entry represents the C-terminal domain of SidC, which shows an α-helical fold. Its function is unknown

SidC is one of the effectors delivered by Legionella pneumophila into the host cell. Like its paralogue SdcA, SidC anchors on the Legionella-containing vacuole (LCV) to facilitate the recruitment of endoplasmic reticulum (ER) proteins. This protein is organised into four domains that are packed into an arch-like shape: the N- terminal SNL domain (

), the INS domain (which is inserted within the SNL domain), the P4C domain, and a C-terminal domain .
Envelope glycoprotein GP350, N-terminal, C domain, herpesvirus superfamily (GP350_C_dom_herpes_sf)
Type: Homologous_superfamily

This entry represents domain C of the N-terminal region of GP350 .

This entry includes Envelope glycoprotein GP350 from Epstein-Barr virus (also known as BLLF1 viral late glycoprotein), the most abundantly expressed glycoprotein in the viral envelope of Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies
in vivo
. It is a 907 residues long gp350 polypeptide containing an 18-residue peptide at the C terminus that is located inside the viral membrane, a membrane-spanning domain and a large N-terminal segment (860 residues) predicted to extend outside the viral membrane. The extreme N-terminal region (1-470) is sufficient to bind receptor CR2 (also known as CD21) and fold into three distinct domains (denoted as A (

), B (

) and C (

)) that organise into an "L-shape" structure.
SidC, lipid-binding domain (SidC_lipid-bd)
Type: Domain

This entry represents the lipid-binding domain, which shows a four α-helix bundle with one end sealed by a C-terminal short β-hairpin and a highly positively charged pocket at the other end formed by two loops connecting the α-helices. This pocket is thought to be the binding site, responsible for the stimulation of the E3 ligase activity of the SNL domain .

SidC is one of the effectors delivered by Legionella pneumophila into the host cell. Like its paralogue SdcA, SidC anchors on the Legionella-containing vacuole (LCV) to facilitate the recruitment of endoplasmic reticulum (ER) proteins. This protein is organised into four domains that are packed into an arch-like shape: the N- terminal SNL domain (

), the INS domain (which is inserted within the SNL domain), the P4C domain, and a C-terminal domain .
Envelope glycoprotein GP350, N-terminal, A domain, herpervirus superfamily (GP350_N_A_dom_herpes_sf)
Type: Homologous_superfamily

This entry represents domain A of the N-terminal region of GP350. This domain is located in the middle of the "L-shape" structure adopted by the N-terminal, bridging domain B on one side and domain C on the other .

This entry includes Envelope glycoprotein GP350 from Epstein-Barr virus (also known as BLLF1 viral late glycoprotein), the most abundantly expressed glycoprotein in the viral envelope of Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies
in vivo
. It is a 907 residues long gp350 polypeptide containing an 18-residue peptide at the C terminus that is located inside the viral membrane, a membrane-spanning domain and a large N-terminal segment (860 residues) predicted to extend outside the viral membrane. The extreme N-terminal region (1-470) is sufficient to bind receptor CR2 (also known as CD21) and fold into three distinct domains (denoted as A (

), B (

) and C (

)) that organise into an "L-shape" structure.

The binding of the viral major glycoprotein BLLF1 to the CD21 cellular receptor is responsible for viral attachment to the cell surface during infection of B lymphocytes by the Epstein-Barr virus (strain GD1) (HHV-4) (Human herpesvirus 4) .
CIP2A, N-terminal (CIP2A_N)
Type: Domain

Cancerous inhibitor of PP2A (CIP2A) functions via protein binding through interactions with many other proteins including MYC, polo like kinase (PLK1) and NIMA protein. It is an inhibitor of PP2A, a tumour suppressor. CIP2A binds to PP2A and inhibits its phosphatase functions resulting in tumourigenesis transformation of cells .

This is the N-terminal HEAT repeats domain, which can be subdivided into tip, stem and C-dimerisation subdomains; the latter is responsible for CIP2A dimerisation .
SidD, C-terminal domain (SidD_C)
Type: Domain

SidD from Legionella pneumophila is a virulence effector that plays a role in hijacking the host vesicular trafficking by recruiting the small guanosine triphosphatase (GTPase) Rab1 to the cytosolic face of the Legionella-containing vacuole (LCVs).

This entry represents the C-terminal α-helical domain, which targets SidD to the Golgi and critical for membrane localisation within host cells . A two-helix bundle at the very C terminus determines SidD specificity .
Transposable element Tc3 transposase-like, DNA-binding HTH domain (Tnp_Tc3-like_HTH)
Type: Domain

This entry represents the specific DNA-binding HTH domain found in Transposable element Tc3 transposase from Caenorhabditis elegans and similar sequences mainly from nematodes and arthropods. This protein binds specifically to the terminal nucleotides of the TC3 inverted repeat and acts by making double strand breaks at the ends of TC3 element. It has two DNA-binding domains at the N terminus, the first one represented in

and the second one in this entry . They both bind to the major groove on a single DNA oligomer, separated by a linker that interacts closely with the minor groove .
SidD, catalytic domain (SidD_cat)
Type: Domain

SidD from Legionella pneumophila is a virulence effector that plays a role in hijacking the host vesicular trafficking by recruiting the small guanosine triphosphatase (GTPase) Rab1 to the cytosolic face of the Legionella-containing vacuole (LCVs). This entry represents the catalytic domain .
Phosphoinositide phosphatase SidF-like (SidF)
Type: Family

Legionella pneumophila modulates the host metabolism of phosphoinositides (PIs) to impair membrane trafficking and establish the Legionella-containing vacuole (LCV) for its own replication. The virulence factor SidF (

) is a unique PI phosphatase that specifically hydrolyses PI(3,4)P2 and PI(3,4,5)P3. This protein shows a large single domain that resembles a cowboy hat, which consists of 19 α-helices located around a 10-stranded twisted β-sheet core (

) .
Cellophane-induced 1 repeat (Cin1_rpt)
Type: Repeat

Venturia inaequalis is a hemi-biotrophic fungus that causes scab disease of apple. A recently-identified gene from this fungus, cin1 (cellophane-induced 1), is up-regulated over 1000-fold in planta and considerably on cellophane membranes, and encodes a cysteine-rich secreted protein of 523 residues with eight imperfect tandem repeats of ~60 amino acids .
Cellophane-induced 1 repeat superfamily (Cin1_rpt_sf)
Type: Homologous_superfamily

Venturia inaequalis is a hemi-biotrophic fungus that causes scab disease of apple. A recently-identified gene from this fungus, cin1 (cellophane-induced 1), is up-regulated over 1000-fold in planta and considerably on cellophane membranes, and encodes a cysteine-rich secreted protein of 523 residues with eight imperfect tandem repeats of ~60 amino acids .
Putative antitoxin VapB45-like, DNA-binding HTH domain (VapB45-like_HTH)
Type: Domain

This entry represents a domain found at the N-terminal of the VapB45 protein from Mycobacterium tuberculosis (

) and similar bacterial sequences. VapB45 is thought to be part the antitoxin component of a Toxin-Antitoxin system . This domain adopts a helix-turn-helix structure that is likely to be a DNA-binding domain.
Chop1, PIN domain (Chp1_PIN)
Type: Domain

This domain is found at the C-terminal of Chromo domain- containing protein 1 from Schizosaccharomyces pombe (Chp1) and similar proteins predominantly found in Glomeromycetes and Schizosaccharomycetes. Chp1 is a component of the RNA-induced initiation of Transcriptional Gene Silencing (RITS) complex, a central player RNA interference (RNAi) pathway which is important for heterochromatin formation and accurate chromosome segregation. This entry represents the PIN domain of Chp1, which shows an α/β fold .
Tail knob protein gp9, C-terminal domain (Gp9_C)
Type: Domain

This domain is found at the C-terminal end of Tail knob protein gp9 from Bacillus phage phi29 and similar proteins from tailed bacteriophages and prokaryotic prophages. This protein blocks the end of the tube before DNA ejection while forming a channel perforating the host membrane in the process by adopting a hexameric tube structure with six flexible hydrophobic loops. This entry represents the region of the protein that forms the central part of the tube. It is organised into an α/β subdomain, a long loop that protrudes from the inner wall covering about two-thirds of the tube, and a β-domain in which the β-strands are almost parallel with the tube axis .
S-adenosylmethionine-dependent methyltransferase Rv2258c-like, winged HTH domain (Rv2258c-like_HTH)
Type: Domain

The Mycobacterium tuberculosis Rv2258c protein (

) is an S-adenosyl-L-methionine (SAM)-dependent methyltransferase (MTase) . The monomeric structure of Rv2258c consists of two domains which are linked by a long α-helix. The N-terminal domain, found in this entry, is essential for dimerisation and the C-terminal domain has the Class I MTase fold. This domain has a winged Helix-Turn-Helix (HTH) fold.
Tail sheath protein gp29, gp29PR (Gp29_gp29PR)
Type: Domain

This domain is found in the Tail sheath protein gp29 from the giant Bacteriophage phiKZ and similar proteins mainly found in tailed bacteriophages. This entry represents a protease resistant fragment of this protein, gp29PR, which consists of a single domain showing a seven-stranded β-sandwich with long insertions connecting adjacent β-strands, including a long α-helix .
Choline-binding repeat (Choline_bind_rpt)
Type: Repeat

This entry represents probable choline-binding cell wall repeats.