Summary: Type II secretion system protein B
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Type II secretion system protein B Provide feedback
This is the B protein from some operons of bacterial secretion systems of type II. The exact function of the B protein is not known, though in the case of Vibrio cholerae there is a fusion protein between proteins A and B that includes an AAA domain, a PG_binding domains well as this domain at the C-terminus . Many of the other species have no A or B domain genes in this operon. The type II secretion pathway is conserved in Gram-negative bacteria that are prevalent in bacterial pathogens of plants (Pseudomonas fluorescens, Erwinia or Xanthomonas species), animals (Aeromonas hydrophila) and humans (Klebsiella oxytoca, Pseudomonas aeruginosa, Vibrio cholerae or Legionella pneumophila). Typical type II secretion systems (T2SSs) are encoded by a set of 12 to 16 gsp (general secretion pathway) genes organised into large operons including the conserved 'core' genes denoted C to O and in some bacterial species, as indicated above, extra gsp genes such as gspAB, gspN or gspS. A different nomenclature is used for Pseudomonas T2SSs, so the B gene is referred to as the P protein .
Korotkov KV, Sandkvist M, Hol WG;, Nat Rev Microbiol. 2012;10:336-351.: The type II secretion system: biogenesis, molecular architecture and mechanism. PUBMED:22466878 EPMC:22466878
Martynowski D, Grochulski P, Howard PS;, Acta Crystallogr D Biol Crystallogr. 2013;69:142-149.: Structure of a periplasmic domain of the EpsAB fusion protein of the Vibrio vulnificus type II secretion system. PUBMED:23385451 EPMC:23385451
Internal database links
|Similarity to PfamA using HHSearch:||T2SSC|
This tab holds annotation information from the InterPro database.
InterPro entry IPR032389
GspB is an accessory component of the type II secretion system (T2SS). Together with GspA, it contribute to GspD assembly and transport to the outer membrane possibly by increasing the pore size of the peptidoglycan or anchoring it to this structural meshwork [ PUBMED:30767847 ].
The type II secretion system (T2SS) is one of several extracellular secretion systems in gram-negative bacteria. It delivers toxins and a range of hydrolytic enzymes including proteases, lipases and carbohydrate-active enzymes to the cell surface or extracellular space [ PUBMED:30767847 ]. T2SS systems are composed of 11 to 15 different proteins, which are generally called GspA to GspO and GspS. The T2SS spans the two bacterial membranes and ensures secretion of folded proteins across the outer membrane pore formed by GspD. The inner membrane complex contains GspC, GspL, GspM, and GspF. The cytoplasmic domains of GspL and GspF interact with an ATPase, GspE. GspE is thought to energize the formation of a short pseudopilus by several pilin-like proteins, GspG to GspK [ PUBMED:22523076 ]. GspD has been shown to interact with the inner membrane component GspC [ PUBMED:19217396 ].
The T2SS pseudopilus is a periplasmic filament composed of the major pseudopilin, EpsG, and four minor pseudopilins, EpsH, EpsI, EpsJ and EpsK. Pseudopilus is assembled by the polymerization of GspG (also known as PulG) subunits. Pseudopilin proteins have a conserved N-terminal hydrophobic segment followed by a more variable C-terminal periplasmic and globular domain [ PUBMED:28258547 ].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||type II protein secretion system complex (GO:0015627)|
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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|Number in seed:||42|
|Number in full:||563|
|Average length of the domain:||59 aa|
|Average identity of full alignment:||29 %|
|Average coverage of the sequence by the domain:||21.9 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||8|
|Download:||download the raw HMM for this family|
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The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
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Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
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Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
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For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the T2SSB domain has been found. There are 1 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.
|Protein||Predicted structure||External Information|
|A0A0H3GMT1||View 3D Structure||Click here|
|Q01563||View 3D Structure||Click here|