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gem
capsuledb
Commits
405e22e8
Commit
405e22e8
authored
Jan 21, 2016
by
Bertrand NÉRON
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provide new introduction text for the database
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405e22e8
<!DOCTYPE html>
<html>
<head>
<title>
Txss DB
</title>
<head>
<meta
charset=
"UTF-8"
>
<title>
MacSyDB/TXSSdb
</title>
<link
rel=
"stylesheet"
href=
"style/main.css"
type=
"text/css"
>
<link
rel=
"stylesheet"
href=
"style/tooltip.css"
type=
"text/css"
>
<link
rel=
"stylesheet"
href=
"style/smoothness/jquery-ui-1.8.17.custom.css"
type=
"text/css"
>
<script
src=
"/_utils/script/jquery.js"
></script>
<!-- <script src="/_utils/script/jquery-ui-1.8.11.custom.min.js"></script>-->
<script
src=
"script/jquery-ui-1.8.17.custom.min.js"
></script>
</head>
<body>
<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>
</head>
<body>
<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>
</div>
<div
id=
"request"
>
<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>
</div>
</body>
<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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