Commit 405e22e8 authored by Bertrand  NÉRON's avatar Bertrand NÉRON

provide new introduction text for the database

parent 74e868eb
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<title>Txss DB</title>
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<title>MacSyDB/TXSSdb</title>
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<h1>Txss DB</h1>
<h2>Non-Flagellar Type III Secretion Systems in sequenced genomes</h2>
<div id="head">
<img src="images/systeme_complet.png" title="Non-Flagellar Type III Secretion System schema"
alt="Non-Flagellar Type III Secretion System schema">
<p>Non-Flagellar Type III Secretion Systems (NF-T3SS, or injectisomes)
are bacterial machineries partially homologous to the bacterial flagellum,
which allow direct injection of bacterial effectors from bacterial cytoplasm
to eukaryotic cells via a molecular needle (cf. schema above).
NF-T3SS are found in animal and plant pathogens
(<span class="gene_name">Yersinia pestis</span>,
<span class="gene_name">Escherichia coli</span>,
<span class="gene_name">Burkholderia</span>,...),
but also in plant and insect symbionts (e.g., Rhizobiales).</p>
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<p>This website allows to query a dataset of 216 NF-T3SS retrieved from 1385 complete genome sequences.
These systems were detected with proteic profiles of NF-T3SS core genes
(<span class="gene_name">sctC</span>, <span class="gene_name">sctN</span>,
<span class="gene_name">sctJ</span>, <span class="gene_name">sctQ</span>,
<span class="gene_name">sctR</span>, <span class="gene_name">sctS</span>, <span class="gene_name">sctT</span>,
<span class="gene_name">sctU</span>, <span class="gene_name">sctV</span>),
and with an analysis of the genomic context of the hits obtained.
This dataset along with the methodology is described in
<a href="http://www.plosgenetics.org/doi/pgen.1002983">Abby and Rocha 2012</a>.</p>
<p>Proteic profiles used for this study are available to analyze user data on the
Mobyle web server:
<a href="http://mobyle.pasteur.fr/cgi-bin/portal.py#forms::T3SSscan-FLAGscan"
target="_blank">http://mobyle.pasteur.fr/cgi-bin/portal.py#forms::T3SSscan-FLAGscan</a>.
These profiles allow to detect both NF-T3SS and flagella.</p>
<div class="citation">
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">
<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 (TXSScan, link to the bottom of the page that introduces TXSScan).</p>
<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>
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<form>
<fieldset>
<legend>Detected NF-T3SS can be queried: </legend>
<label for="taxidSearch">by replicon taxon id (ex:400667)
<input type="text" name="taxidSearch" id="taxidInput" class="ui-widget ui-corner-all" />
<button type="button" id="taxidButton">search by taxid</button>
</label>
<label for="ncbiidSearch">by replicon NCBI id (ex:NC_009085)
<input type="text" name="ncbiidSearch" id="ncbiidInput" class="ui-widget ui-corner-all" />
<button type="button" id="ncbiidButton">search by NCBI ID</button>
</label>
<label for="strainSearch">by strain <span style="font-size:smaller; font-style:italic;">(enter at least 3 characters)</span>
<input type="text" name="strainSearch" id="strainInput" size="100" class="ui-widget ui-corner-all" />
</label>
<label for="taxonomySearch">by taxonomy <span style="font-size:smaller; font-style:italic;">(enter at least 3 characters)</span>
<input type="text" name="taxonomySearch" id="taxonomyInput" size="50" class="ui-widget ui-corner-all" />
</label>
<label for="predictedSystemSearch">by Predicted system
<select name="predictedSystemSearch" id="predictedSystemList" class="ui-widget ui-corner-all ui-state-default"> </select>
</label>
<label for="nameSearch">by replicon name (ex:HADE001c01a)
<input type="text" name="nameSearch" id="nameInput"class="ui-widget ui-corner-all" />
<select name="queryType" id="nameQueryType"class="ui-widget ui-corner-all ui-state-default">
<option value="is" selected="selected" class="ui-widget ui-corner-all ">is</option>
<option value="start_with" class="ui-widget ui-corner-all ">start_with</option>
</select>
<button type="button" id="nameButton">search by name</button>
</label>
</fieldset>
</form>
</div>
<div id="results"></div>
<div id="footer">
Visit our website:
<a href="http://www.pasteur.fr/ip/easysite/pasteur/en/research/scientific-departments/genomes-and-genetics/units-and-groups/evolutionary-microbial-genomics/index">Microbial evolutionary genomics group</a>
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<script type="text/javascript">
<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="request">
<form>
<fieldset>
<legend>Detected systems can be queried: </legend>
<label for="taxidSearch">by replicon taxon id (ex:400667)
<input type="text" name="taxidSearch" id="taxidInput" class="ui-widget ui-corner-all" />
<button type="button" id="taxidButton">search by taxid</button>
</label>
<label for="strainSearch">by strain <span style="font-size:smaller; font-style:italic;">(enter at least 3 characters)</span>
<input type="text" name="strainSearch" id="strainInput" size="100" class="ui-widget ui-corner-all" />
</label>
<label for="taxonomySearch">by taxonomy <span style="font-size:smaller; font-style:italic;">(enter at least 3 characters)</span>
<input type="text" name="taxonomySearch" id="taxonomyInput" size="50" class="ui-widget ui-corner-all" />
</label>
<label for="predictedSystemSearch">by type of system
<select name="predictedSystemSearch" id="predictedSystemList" class="ui-widget ui-corner-all ui-state-default"> </select>
</label>
<label for="ncbiidSearch">by replicon NCBI id (ex:NC_009085)
<input type="text" name="ncbiidSearch" id="ncbiidInput" class="ui-widget ui-corner-all" />
<button type="button" id="ncbiidButton">search by NCBI ID</button>
</label>
<label for="nameSearch">by replicon name (ex:HADE001c01a)
<input type="text" name="nameSearch" id="nameInput"class="ui-widget ui-corner-all" />
<select name="queryType" id="nameQueryType"class="ui-widget ui-corner-all ui-state-default">
<option value="is" selected="selected" class="ui-widget ui-corner-all ">is</option>
<option value="start_with" class="ui-widget ui-corner-all ">start_with</option>
</select>
<button type="button" id="nameButton">search by name</button>
</label>
</fieldset>
</form>
</div>
<div id="results"></div>
<div id="footer">
Visit our website:
<a href="https://research.pasteur.fr/en/team/microbial-evolutionary-genomics/">Microbial evolutionary genomics group</a>
</div>
</body>
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