About
Protein secretion systems are key virulence factors of all major bacterial pathogens with an LPS-containing outer membrane: Shigella, Escherichia coli, Yersinia pestis, Salmonella, Pseudomonas aeruginosa, Helicobacter pylori, Vibrio cholerae, etc. Protein secretion systems are also involved in complex antagonistic ecological interactions between bacteria, as recently exemplified by the ability of bacteria to use type 6 and type 5 secretion systems to respond to aggressive behaviour by other bacteria.
We designed models and protein profiles to detect an unprecedented number and diversity (∼10000) of bacterial protein secretion systems and evolutionarily related appendages in partial and complete genomic data. The tools developped in the study are freely available for systematic searches in large datasets (standalone version) and or in a webserver.
To use the webserver version go to https://galaxy.pasteur.fr/root?tool_id=toolshed.pasteur.fr/repos/odoppelt/txsscan/TXSScan/1.0.2.
To download the protein profiles and the MacSyFinder models : https://github.com/gem-pasteur/Macsyfinder_models/tree/master/models/TXSS.
The models and profiles are to be used in conjunction with MacSyFinder and MacSyView. The documentation on these programs can be found at http://macsyfinder.readthedocs.org/.
Contact: Sophie Abby (sophie.abbyATuniv-grenoble-alpes.fr)
