Conjugal transfer protein

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.

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.

External database links

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

There are various ways to view or download the sequence alignments that we store. You can use a sequence viewer to look at either the seed or full alignment for the family, or you can look at a plain text version of the sequence in a variety of different formats. More...

View options

Formatting options

Download options

Very large alignments can often cause problems for the formatting tool above. If you find that downloading or viewing a large alignment is problematic, you can also download a gzip-compressed, Stockholm-format file containing the seed or full alignment for this family.

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

The main seed and full alignments are generated using sequences from the UniProt sequence database. However, we also generate alignments using sequences from the NCBI sequence database and the "metaseq" metagenomics dataset.

You can view alignments from these two additional datasets using the form above, or you can download alignments of NCBI or metagenomics sequences, as gzip-compressed files.

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 HMMER2.

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...

This page displays the phylogenetic tree for this family. 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 or full alignments.

Note: You can also download the data files for the seed, full, NCBI or metagenomics trees.

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

HMM information

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the MSD 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.