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<h1>MacSyDB/TXSSdb</h1>
<div id="head">
<p>Protein secretion systems are key virulence factors of all major bacterial pathogens with an
LPS-containing outer membrane:
<span class="species">Shigella</span>
<span class="species">Escherichia coli</span>,
<span class="species">Yersinia pestis</span>
<span class="species">Salmonella</span>
<span class="species">Pseudomonas aeruginosa</span>
<span class="species">Helicobacter pylori</span>
<span class="species">Vibrio cholerae</span>,
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.
</p>
<img src="images/txss_mb_named.png" title="Secretion Systems schema"
alt="Secretion Systems schema">
<p>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 (<a href="#txsscan">TXSScan)</a>.</p>
<h1>MacSyDB/TXSSdb</h1>
<p>This database contains the results of the prediction of the most studied secretion systems in 1528 diderm bacteria:
<ul>
<li>T1SS</li>
<li>T2SS, and the related type IV pilus and Tad pilus</li>
<li>T3SS, and the related bacterial flagellum</li>
<li>T4SS </li>
<li>T5aSS, T5bSS and T5cSS</li>
<li>T6SS<span>i</span>, T6SS<span>ii</span> and T6SS<span>iii</span></li>
<li>T9SS</li>
</ul>
</p>
<div>
<p>References:</p>
<div class="citation">
<span class="citation_author">Abby SS,</span>
<span class="citation_author">Cury J,</span>
<span class="citation_author">Guglielmini J,</span>
<span class="citation_author">Néron B,</span>
<span class="citation_author">Touchon M,</span>
<span class="citation_author">Rocha EPC.</span>
<span class="citation_date">(2015)</span>
<span class="citation_article_title">Identification of protein secretion systems in bacterial genomes. Submitted.</span>
<a href="http://biorxiv.org/content/early/2015/11/09/031039">
<span class="citation_journal_title">(preprint available at http://biorxiv.org/content/early/2015/11/09/031039)</span>
</a>
</div>
<p>For T3SS and Flagellar profiles:</p>
<div class="citation">
<span class="citation_author">Abby SS</span>,
<span class="citation_author">Rocha EPC </span>
<span class="citation_date">(2012)</span>
<a href="http://www.plosgenetics.org/doi/pgen.1002983" target="_blank">
<span class="citation_article_title">The Non-Flagellar Type III Secretion System Evolved from the Bacterial
Flagellum and Diversified into Host-Cell Adapted Systems.</span></a>
<span class="citation_journal_title">PLoS Genet</span>
<span class="citation_issue"> 8(9):</span>
<span class="citation_start_page">e1002983.</span>
</div>
<p>For T4SS profiles:</p>
<div class="citation">
<span class="citation_author">Guglielmini, J.</span>,
<span class="citation_author">Quintais, L.</span>,
<span class="citation_author">Garcillan-Barcia, M. P.,</span>
<span class="citation_author">de la Cruz,F.</span>
<span class="citation_author">Rocha, E. P.</span>
<span class="citation_date">(2011)</span>
<span class="citation_article_title">The Repertoire of ICE in Prokaryotes Underscores the Unity, Diversity, and Ubiquity of Conjugation.</span></a>
<span class="citation_journal_title">PLoS Genet.</span>
<span class="citation_issue">7,</span>
<span class="citation_start_page">e1002222,</span>
<a href="https://dx.doi.org/10.1371/journal.pgen.1002222">doi:10.1371/journal.pgen.1002222</a>
</div>
<div class="citation">
<span class="citation_author">Guglielmini, J. et al.</span>,
<span class="citation_article_title">Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion.</span>
<span class="citation_date">(2014)</span>.
<span class="citation_journal_title"> Nucleic Acids Res.</span>,
<a href="https://dx.doi.org/10.1093/nar/gku194">doi:10.1093/nar/gku194</a>.
</div>
</div>
<div>
<p id="txsscan">The tool “TXSScan” developed and used in our study is freely available for systematic searches in large datasets (standalone version) or in a webserver.
</p>
<ul>
<li>You can use the <a href="http://mobyle.pasteur.fr/cgi-bin/portal.py#forms::txsscan">webserver version.</a></li>
<li>Or <a href="https://researchpullzone-yhello.netdna-ssl.com/wp-content/uploads/2015/10/research.pasteur.fr_txsscan-models-and-profiles-for-protein-secretion-systems.gz">
download the protein profiles and the MacSyFinder models click here: FileS1_TXSScan.tar</a>.</li>
</ul>
The models and profiles are to be used in conjunction with MacSyFinder and MacSyView
(<a href="https://github.com/gem-pasteur/macsyfinder">MacSyFinder</a> and 
<a href="https://github.com/gem-pasteur/macsyview">MacSyView</a> are freely available).
The documentation on these programs can be found at <a href="http://macsyfinder.readthedocs.org/">http://macsyfinder.readthedocs.org/</a>.</p>
<p>Reference:</p>
<div class="citation">
<span class="citation_author">Abby SS</span>,
<span class="citation_author">Rocha EPC </span>
<span class="citation_date">(2012)</span>
<a href="http://www.plosgenetics.org/doi/pgen.1002983" target="_blank">
<span class="citation_article_title">The Non-Flagellar Type III Secretion System Evolved from the Bacterial
Flagellum and Diversified into Host-Cell Adapted Systems.</span></a>
<span class="citation_journal_title">PLoS Genet</span>
<span class="citation_issue"> 8(9):</span>
<span class="citation_start_page">e1002983.</span>
</div>
</div>
<p>Protein secretion systems are key virulence factors of all major bacterial pathogens with an
LPS-containing outer membrane. They are also involved in complex antagonistic ecological interactions between
bacteria. We designed models and protein profiles to detect an unprecedented number and diversity (∼10000)
of bacterial protein secretion systems (T1SS, T2SS, T3SS, T4SS, T5SS, T6SS<sup>i-iii</sup>, T9SS) and evolutionarily related appendages
(T4P, Tad, Flagellum) in 1528 genomes of diderm bacteria.
<a href="http://macsydb.web.pasteur.fr/txssdb/_design/txssdb/index.html#txsscan">The TXSScan tool is also now available</a>.
</p>
</div>
<div id="request">
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</form>
</div>
<div id="results"></div>
<div id="links">
<p>TXSScan is freely available for systematic searches in large datasets (standalone version) or in a webserver.</p>
<ul>
<li>You can use the <a href="http://mobyle.pasteur.fr/cgi-bin/portal.py#forms::txsscan">webserver version.</a></li>
<li>Or <a href="https://researchpullzone-yhello.netdna-ssl.com/wp-content/uploads/2015/10/research.pasteur.fr_txsscan-models-and-profiles-for-protein-secretion-systems.gz">
download the protein profiles and the MacSyFinder models click here: FileS1_TXSScan.tar</a>.</li>
</ul>
The models and profiles are to be used in conjunction with MacSyFinder and MacSyView
(<a href="https://github.com/gem-pasteur/macsyfinder">MacSyFinder</a> and 
<a href="https://github.com/gem-pasteur/macsyview">MacSyView</a> are freely available).
The documentation on these programs can be found at <a href="http://macsyfinder.readthedocs.org/">http://macsyfinder.readthedocs.org/</a>.</p>
</div>
<div id="references">
<h2>References:</h2>
<div class="citation">
<span class="citation_author">Abby SS,</span>
<span class="citation_author">Cury J,</span>
<span class="citation_author">Guglielmini J,</span>
<span class="citation_author">Néron B,</span>
<span class="citation_author">Touchon M,</span>
<span class="citation_author">Rocha EPC.</span>
<span class="citation_date">(2015)</span>
<span class="citation_article_title">Identification of protein secretion systems in bacterial genomes. Submitted.</span>
<a href="http://biorxiv.org/content/early/2015/11/09/031039">
<span class="citation_journal_title">(preprint available at http://biorxiv.org/content/early/2015/11/09/031039)</span>
</a>
</div>
<p>For T3SS and Flagellar profiles:</p>
<div class="citation">
<span class="citation_author">Abby SS</span>,
<span class="citation_author">Rocha EPC </span>
<span class="citation_date">(2012)</span>
<a href="http://www.plosgenetics.org/doi/pgen.1002983" target="_blank">
<span class="citation_article_title">The Non-Flagellar Type III Secretion System Evolved from the Bacterial
Flagellum and Diversified into Host-Cell Adapted Systems.</span></a>
<span class="citation_journal_title">PLoS Genet</span>
<span class="citation_issue"> 8(9):</span>
<span class="citation_start_page">e1002983.</span>
</div>
<p>For T4SS profiles:</p>
<div class="citation">
<span class="citation_author">Guglielmini, J.</span>,
<span class="citation_author">Quintais, L.</span>,
<span class="citation_author">Garcillan-Barcia, M. P.,</span>
<span class="citation_author">de la Cruz,F.</span>
<span class="citation_author">Rocha, E. P.</span>
<span class="citation_date">(2011)</span>
<span class="citation_article_title">The Repertoire of ICE in Prokaryotes Underscores the Unity, Diversity, and Ubiquity of Conjugation.</span></a>
<span class="citation_journal_title">PLoS Genet.</span>
<span class="citation_issue">7,</span>
<span class="citation_start_page">e1002222,</span>
<a href="https://dx.doi.org/10.1371/journal.pgen.1002222">doi:10.1371/journal.pgen.1002222</a>
</div>
<div class="citation">
<span class="citation_author">Guglielmini, J. et al.</span>,
<span class="citation_article_title">Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion.</span>
<span class="citation_date">(2014)</span>.
<span class="citation_journal_title"> Nucleic Acids Res.</span>,
<a href="https://dx.doi.org/10.1093/nar/gku194">doi:10.1093/nar/gku194</a>.
</div>
</div>
</div>
<div id="footer">
Visit our website:
<a href="https://research.pasteur.fr/en/team/microbial-evolutionary-genomics/">Microbial evolutionary genomics group</a>
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