SlrA - Revision history

134.76.38.147 at 15:07, 2 April 2014

2014-04-02T15:07:56Z

134.76.70.252 at 11:57, 7 January 2014

2014-01-07T11:57:14Z

134.76.70.252 at 14:22, 18 November 2013

2013-11-18T14:22:53Z

134.76.70.252 at 14:54, 16 May 2013

2013-05-16T14:54:14Z

134.76.70.252 at 11:35, 14 May 2013

2013-05-14T11:35:58Z

134.76.70.252 at 14:10, 13 May 2013

2013-05-13T14:10:30Z

Jstuelk at 16:07, 24 February 2013

2013-02-24T16:07:18Z

Jstuelk at 17:57, 4 January 2013

2013-01-04T17:57:34Z

Jstuelk: /* References */

2013-01-04T17:31:25Z

‎References

Awiechert at 13:23, 22 November 2012

2012-11-22T13:23:29Z

← Older revision		Revision as of 15:07, 2 April 2014
Line 1:		Line 1:
−	* '''Description:~~''' anti-repressor, antagonist of [[SinR]] and [[SlrR]], involved in control of flagellar genes and ''[[epsA\|eps]]'' and ''[[tapA]]-[[sipW]]-[[tasA]]'' operons <br/><br/>~~	+	{{#bank: SlrA}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''slrA''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| antagonist of [[SinR]] and [[SlrR]]~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| control of [[biofilm formation]]~~
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU38229 slrA]
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=SlrA SlrA]
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Regulation of this protein in [[SubtiPathways\|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=slrA slrA]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 6.1 kDa, 9.992~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 156 bp, 52 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[ywcC]]'', ''[[ywcB]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU38229 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU38229 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU38229 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:ywcC_context.gif]]~~
−	~~<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>~~
−	\|-
−	\|colspan="2" \|'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=slrA_3923319_3923477_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:slrA_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU38229]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[transcription factors and their control]]}},~~
−	~~{{SubtiWiki category\|[[transition state regulators]]}},~~
−	~~{{SubtiWiki category\|[[biofilm formation]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[YwcC regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU38229
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−
−	* '''DBTBS entry:''' no entry
−
−	* '''SubtiList entry:'''
−
−	~~=== Additional information===~~
−
−	* This gene was only recently identified. [http://www.ncbi.nlm.nih.gov/sites/entrez/18647168 PubMed]
−	* SlrA overexpression results in reduced expression of the [[SigD regulon]] and in enhanced expression of the [[SinR regulon]], this can be suppressed by inactivation of either ''[[remA]]'', ''[[remB]]'', ''[[slrR]]'', or ''[[sinR]]'' {{PubMed\|22329926}}
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' binding of [[SinR]] resulting in induction of [[SinR]]-repressed genes and operons {{PubMed\|19788541}}
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):''' [[SinI]]
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:''' [[SlrR]] inhibits activity of [[SlrA]] (i. e. binding to [[SinR]]) {{PubMed\|19788541}}
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[SlrA]]-[[SinR]] {{PubMed\|19788541}}, K(D) 10.6 nM {{PubMed\|23430750}}
−	** [[SlrA]]-[[SlrR]] {{PubMed\|19788541}}
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P0C8M5 P0C8M5]
−
−	* '''KEGG entry:''' no entry
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−	* '''Operon:'''
−	** ''[[slrA]]-[[ywcB]]-[[ywcA]]''
−	** ''[[slrA]]-[[ywcB]]''
−	** ''[[slrA]]''
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=slrA_3923319_3923477_1 slrA] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−
−	* '''Regulation:'''
−
−	* '''Regulatory mechanism:'''
−	** [[YwcC]]: transcription repression {{PubMed\|18647168,19788541}}
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~'''Additional publications:''' {{PubMed\|22329926}}~~
−	~~<pubmed>18647168, 19788541, 23430750</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 18: / Line 18: @@
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=SlrA SlrA]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/biofilm.html Biofilm]'''
+|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=slrA slrA]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 6.1 kDa, 9.992

@@ Line 16: / Line 16: @@
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU38229 slrA]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/SlrA SlrA]
+|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=SlrA SlrA]
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/biofilm.html Biofilm]'''

@@ Line 31: / Line 31: @@
   <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 |-
-|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=slrA_3923319_3923477_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:slrA_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=slrA_3923319_3923477_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:slrA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU38229]]
 |-
 |}

@@ Line 26: / Line 26: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywcC]]'', ''[[ywcB]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU38229 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU38229 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU38229 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU38229 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU38229 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU38229 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:ywcC_context.gif]]

@@ Line 91: / Line 91: @@
 * '''[[SubtInteract|Interactions]]:'''
-** [[SlrA]]-[[SinR]] {{PubMed|19788541}}, [[SlrA]]-[[SlrR]] {{PubMed|19788541}}
+** [[SlrA]]-[[SinR]] {{PubMed|19788541}}, K(D) 10.6 nM  {{PubMed|23430750}}
 * '''[[Localization]]:'''
@@ Line 115: / Line 116: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=slrA_3923319_3923477_1 slrA] {{PubMed|22383849}}
-* '''Sigma factor:'''
+* '''[[Sigma factor]]:'''
 * '''Regulation:'''
@@ Line 144: / Line 145: @@
 =References=
 '''Additional publications:''' {{PubMed|22329926}}
-<pubmed>18647168, 19788541, </pubmed>
+<pubmed>18647168, 19788541, 23430750</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 39: / Line 39: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/>
+<br/><br/>
 = [[Categories]] containing this gene/protein =
@@ Line 69: / Line 65: @@
 === Additional information===
-This gene was only recently identified. [http://www.ncbi.nlm.nih.gov/sites/entrez/18647168 PubMed]
+* This gene was only recently identified. [http://www.ncbi.nlm.nih.gov/sites/entrez/18647168 PubMed]
+* SlrA overexpression results in reduced expression of the [[SigD regulon]] and in enhanced expression of the [[SinR regulon]], this can be suppressed by inactivation of either ''[[remA]]'', ''[[remB]]'', ''[[slrR]]'', or ''[[sinR]]'' {{PubMed|22329926}}
 =The protein=

@@ Line 20: / Line 20: @@
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/biofilm.html Biofilm]'''
 |-
-|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 6 kDa, 9.992
+|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 6.1 kDa, 9.992
 |-
 |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 156 bp, 52 aa