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117  structures 940  species 0  interactions 1789  sequences 14  architectures

Family: VipB (PF05943)

Summary: EvpB/VC_A0108, tail sheath N-terminal domain

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EvpB/VC_A0108, tail sheath N-terminal domain Provide feedback

EvpB is a family of Gram-negative probable type VI secretion system components of the tail sheath. They have been known as COG:COG3517. These sheath-components, of which there are many copies in the sheath, are also variously referred to as VipA/VipB and TssB/TssC. On contact with another bacterial cell the sheath contracts and pushes the puncturing device and tube through the cell envelope and punches the target bacterial cell [1].

Literature references

  1. Filloux A;, F1000Prime Rep. 2013;5:52.: The rise of the Type VI secretion system. PUBMED:24381728 EPMC:24381728

This tab holds annotation information from the InterPro database.

InterPro entry IPR044031

The long cytoplasmic tubular structure of the T6SS system is wrapped by a sheath structure composed of two proteins, TssB and TssC. Contraction of the sheath causes the internal tube of the T6SS with associated effectors to be propelled out of the effector cell and across the membranes of bacterial or eukaryotic target cells [ PUBMED:24381728 , PUBMED:26370934 , PUBMED:29307484 ].

TssB and TssC assemble into tubular structures with cogwheel patterns resembling the bacteriophage contractile sheath [ PUBMED:24282569 ]. Several structures of T6SS sheath assemblies have been solved displaying a helical assembly [ PUBMED:29307484 , PUBMED:28947741 , PUBMED:25723168 ]. Interactions between TssB and TssC occur between the N-terminal region of TssC and the conserved a-helix of TssB [ PUBMED:24282569 ]. The two proteins of the F. novicida T6SS outer sheath, IglA (TssB) and IglB (TssC), are interdigitated into a single fold similar to that of the phage sheath. The F. novicida T6SS outer sheath has a highly interlaced two-dimensional array architecture with augmented beta sheets that is essential to secretory function [ PUBMED:25723168 ].

Three distinct T6SS subtypes exist, T6SSi, in which most proteobacterial T6SSs are found, including V. cholerae and P. aeruginosa; T6SSii for the Francisella T6SS; and T6SSiii for Bacteroidetes systems [ PUBMED:23341461 ].

TssB/TssC are also known as IglA/IglB and VipA/VipB.

This entry represents the N-terminal domain of TssC1, a type VI secretion system sheath protein.

Domain organisation

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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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Curation and family details

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Curation View help on the curation process

Seed source: Pfam-B_2566 (release 9.0)
Previous IDs: DUF877;
Type: Domain
Sequence Ontology: SO:0000417
Author: Moxon SJ
Number in seed: 95
Number in full: 1789
Average length of the domain: 295.4 aa
Average identity of full alignment: 43 %
Average coverage of the sequence by the domain: 58.65 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.3 27.0
Noise cut-off 24.9 26.6
Model length: 302
Family (HMM) version: 15
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Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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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 VipB domain has been found. There are 117 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
A0A0H3GSE9 View 3D Structure Click here
Q8ZRL7 View 3D Structure Click here
Q9I1B3 View 3D Structure Click here
Q9I367 View 3D Structure Click here
Q9I748 View 3D Structure Click here