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0  structures 797  species 0  interactions 1506  sequences 9  architectures

Family: CagE_TrbE_VirB (PF03135)

Summary: CagE, TrbE, VirB family, component of type IV transporter system

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CagE, TrbE, VirB family, component of type IV transporter system Provide feedback

This family includes the Helicobacter pylori protein CagE Q48252 which together with other proteins from the cag pathogenicity island (PAI), encodes a type IV transporter secretion system. The precise role of CagE is not known, but studies in animal models have shown that it is essential for pathogenesis in Helicobacter pylori induced gastritis and peptic ulceration [1]. Indeed, the expression of the cag PAI has been shown to be essential for stimulating human gastric epithelial cell apoptosis in vitro [2]. Similar type IV transport systems are also found in other bacteria. This family includes the TrbE P54910 and VirB P05353 proteins from the respective trb and Vir conjugal transfer systems in Agrobacterium tumefaciens. Homologues of VirB proteins from other species are also members of this family, e.g. VirB from Brucella suis Q9RPY1.

Literature references

  1. Ogura K, Maeda S, Nakao M, Watanabe T, Tada M, Kyutoku T, Yoshida H, Shiratori Y, Omata M; , J Exp Med 2000;192:1601-1610.: Virulence factors of Helicobacter pylori responsible for gastric diseases in Mongolian gerbil. PUBMED:11104802 EPMC:11104802

  2. Le'Negrate G, Ricci V, Hofman V, Mograbi B, Hofman P, Rossi B; , Infect Immun 2001;69:5001-5009.: Epithelial Intestinal Cell Apoptosis Induced by Helicobacter pylori Depends on Expression of the cag Pathogenicity Island Phenotype. PUBMED:11447179 EPMC:11447179

  3. Li PL, Hwang I, Miyagi H, True H, Farrand SK; , J Bacteriol 1999;181:5033-5041.: Essential components of the Ti plasmid trb system, a type IV macromolecular transporter. PUBMED:10438776 EPMC:10438776


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR018145

This domain is found in (amongst others): the Helicobacter pylori protein CagE (see examples), which together with other proteins from the cag pathogenicity island (PAI), encodes a type IV transporter secretion system. The precise role of CagE is not known, but studies in animal models have shown that it is essential for pathogenesis in Helicobacter pylori induced gastritis and peptic ulceration [PUBMED:11104802]. Indeed, the expression of the cag PAI has been shown to be essential for stimulating human gastric epithelial cell apoptosis in vitro [PUBMED:11447179].

Similar type IV transport systems are also found in other bacteria. This domain is also found in proteins from the trb and Vir conjugal transfer systems in Agrobacterium tumefaciens and homologues of VirB proteins from other species.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(15)
Full
(1506)
Representative proteomes NCBI
(1404)
Meta
(70)
RP15
(58)
RP35
(171)
RP55
(237)
RP75
(316)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(15)
Full
(1506)
Representative proteomes NCBI
(1404)
Meta
(70)
RP15
(58)
RP35
(171)
RP55
(237)
RP75
(316)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(15)
Full
(1506)
Representative proteomes NCBI
(1404)
Meta
(70)
RP15
(58)
RP35
(171)
RP55
(237)
RP75
(316)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

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

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_843 (release 6.5)
Previous IDs: none
Type: Family
Author: Mifsud W
Number in seed: 15
Number in full: 1506
Average length of the domain: 190.30 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 25.11 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.5 20.5
Trusted cut-off 20.6 20.5
Noise cut-off 20.3 20.4
Model length: 205
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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