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15  structures 797  species 0  interactions 1580  sequences 10  architectures

Family: CagX (PF03524)

Summary: Conjugal transfer protein

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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Conjugal transfer protein Provide feedback

This family includes type IV secretion system CagX conjugation protein. Other members of this family are involved in conjugal transfer to plant cells of T-DNA.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR010258

Several bacterial pathogens utilise conjugation machines to export effector molecules during infection. Such systems are members of the type IV or 'adapted conjugation' secretion family. The prototypical type IV system is the Agrobacterium tumefaciens T-DNA transfer machine, which delivers oncogenic nucleoprotein particles to plant cells. Other pathogens, including Bordetella pertussis, Legionella pneumophila, Brucella spp. and Helicobacter pylori (Campylobacter pylori), use type IV machines to export effector proteins to the extracellular milieu or the mammalian cell cytosol.

Conjugation machines of Gram-negative bacteria consist of two surface structures, the mating channel through which the DNA transfer intermediate and proteins are translocated and the conjugal pilus for contacting recipient cells. Various conjugative pili have been visualised, but to date there is no ultrastructural information about the mating channel. Recent work on the A. tumefaciens T-DNA transfer system has focused on identifying interactions among the VirB protein subunits and defining steps in the transporter assembly pathway. There are three functional groups of VirB proteins: proteins localised exocellularly forming the T-pilus or other adhesive structures; mating-channel components; and cytoplasmic membrane ATPases. Although all of these proteins probably assemble as a supramolecular complex, as yet there is no direct evidence for a physical association between the conjugative pilus and the mating channel.

Several lines of evidence suggest that VirB6-VirB10 are probable channel subunits. VirB6, a highly hydrophobic protein, is thought to span the cytoplasmic membrane several times and presently is the best candidate for a channel-forming protein. VirB7, an outer membrane lipoprotein, interacts with itself and with VirB9 via disulphide bonds between unique reactive cysteines present in each protein. The VirB7-VirB9 heterodimer localises at the outer membrane and plays a critical role in stabilising other VirB proteins during assembly of the transfer machine. VirB9 is also required for formation of chemically crosslinked VirB10 oligomers probably corresponding to homotrimers [PUBMED:10920394].

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
(150)
Full
(1580)
Representative proteomes NCBI
(1390)
Meta
(79)
RP15
(62)
RP35
(186)
RP55
(252)
RP75
(335)
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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
(150)
Full
(1580)
Representative proteomes NCBI
(1390)
Meta
(79)
RP15
(62)
RP35
(186)
RP55
(252)
RP75
(335)
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
(150)
Full
(1580)
Representative proteomes NCBI
(1390)
Meta
(79)
RP15
(62)
RP35
(186)
RP55
(252)
RP75
(335)
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: PRINTS & Pfam-B_5812 (Release 7.5)
Previous IDs: cagX;
Type: Family
Author: Bateman A
Number in seed: 150
Number in full: 1580
Average length of the domain: 205.60 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 75.21 %

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 25.2 25.2
Trusted cut-off 25.5 26.7
Noise cut-off 24.8 25.1
Model length: 215
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Structures

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 CagX domain has been found. There are 15 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 seqence.

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