SrfAA - Revision history

Jstuelk: /* References */

2015-02-11T13:10:41Z

‎References

Jstuelk at 13:06, 11 February 2015

2015-02-11T13:06:39Z

Jstuelk at 17:55, 5 December 2014

2014-12-05T17:55:26Z

134.76.38.147 at 12:57, 2 April 2014

2014-04-02T12:57:59Z

Jstuelk at 12:18, 17 January 2014

2014-01-17T12:18:40Z

Atkovacs: /* Original publications */

2013-07-19T07:16:34Z

‎Original publications

Atkovacs: /* Phenotypes of a mutant */

2013-07-19T07:16:04Z

‎Phenotypes of a mutant

Jstuelk at 19:21, 18 June 2013

2013-06-18T19:21:41Z

134.76.70.252 at 12:31, 16 May 2013

2013-05-16T12:31:46Z

134.76.70.252 at 09:27, 14 May 2013

2013-05-14T09:27:26Z

← Older revision		Revision as of 13:10, 11 February 2015
Line 1:		Line 1:
−	* '''Description:~~''' surfactin synthetase / competence <br/><br/>~~	+	{{#bank: SrfAA}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''srfAA''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''comL''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| surfactin synthetase / competence~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| antibiotic synthesis~~
−	\|-
−	\|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=BSU03480 srfAA]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 401 kDa, 4.871~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 10764 bp, 3588 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[hxlR]]'', ''[[srfAB]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU03480 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU03480 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU03480 DNA_with_flanks]
−	\|-
−	\|-
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:srfAA_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=srfAA_376968_387731_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:srfAA_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU03480]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[miscellaneous metabolic pathways]]}},~~
−	~~{{SubtiWiki category\|[[biosynthesis of antibacterial compounds]]}},~~
−	~~{{SubtiWiki category\|[[membrane proteins]]}},~~
−	~~{{SubtiWiki category\|[[phosphoproteins]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[Abh regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[CodY regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[ComA regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[PerR regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[PhoP regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[Spx regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU03480
−
−	~~===Phenotypes of a mutant ===~~
−	* altered cell death pattern in colonies {{PubMed\|23012477}}
−	* reduced swarming of srfAA mutant of ''B. subtilis'' NCIB3610 {{PubMed\|15066026}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU03480&redirect=T BSU03480]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/srfAA-srfAB-comS-srfAC-srfAD.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10168]
−
−	~~=== Additional information===~~
−	* A mutation was found in this gene after evolution under relaxed selection for sporulation {{PubMed\|21821766}}
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:''' ATP-dependent AMP-binding enzyme family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:''' phosphorylation on Ser-1006 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:''' membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU03480&redirect=T BSU03480]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P27206 P27206]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU03480]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[srfAA]]-[[srfAB]]-[[comS]]-[[srfAC]]-[[srfAD]]'' {{PubMed\|1715856}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=srfAA_376968_387731_1 srfAA] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] {{PubMed\|1715856}}
−
−	* '''Regulation:'''
−	** repressed during growth in the presence of branched chain amino acids ([[CodY]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/8830686 PubMed]
−	** repressed during hydrogen peroxide stress ([[PerR]]) {{PubMed\|16166527}}
−	** expressed at high cell density ([[ComA]]) {{PubMed\|16091051}}
−	** induced under conditions of phosphate limitation ([[PhoP]]) {{PubMed\|25666134}}
−
−	* '''Regulatory mechanism:'''
−	** [[PhoP]]: transcription activation {{PubMed\|25666134}}
−	** [[CodY]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/8830686 PubMed]
−	** [[ComA]]: transcription activation {{PubMed\|1715856,16091051}}
−	** [[PerR]]: transcription activation {{PubMed\|16166527}}
−	** [[Spx]]: transcription repression {{PubMed\|12642660}}
−	** [[Abh]]: transcription repression{{PubMed\|20817675}}
−
−	* '''Additional information:'''
−	** A [[ncRNA]] is predicted between ''[[hxlR]]'' and ''[[srfAA]]'' {{PubMed\|20525796}}
−	** expressed in all cells in a population {{PubMed\|25448819}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed>20735481 </pubmed>~~
−	~~==Original publications==~~
−	<pubmed>8288534,8387999,1938922,16166527,17227471,8825779, 8830686,18763711 17218307, 17190806 1715856 19605685 19826092 12642660 20148996 16091051 20797616 20525796 21821766 23012477 22511326,20817675,15066026 24425772 25448819 25666134</pubmed>
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 50: / Line 50: @@
 {{SubtiWiki regulon|[[ComA regulon]]}},
 {{SubtiWiki regulon|[[PerR regulon]]}},
 {{SubtiWiki regulon|[[Spx regulon]]}}
@@ Line 123: / Line 124: @@
 ** repressed during hydrogen peroxide stress ([[PerR]]) {{PubMed|16166527}}
 ** expressed at high cell density ([[ComA]]) {{PubMed|16091051}}
 * '''Regulatory mechanism:'''
 ** [[CodY]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/8830686 PubMed]
 ** [[ComA]]: transcription activation {{PubMed|1715856,16091051}}
@@ Line 157: / Line 160: @@
 <pubmed>20735481 </pubmed>
 ==Original publications==
-<pubmed>8288534,8387999,1938922,16166527,17227471,8825779, 8830686,18763711 17218307, 17190806 1715856 19605685 19826092 12642660 20148996 16091051 20797616 20525796 21821766 23012477 22511326,20817675,15066026 24425772 25448819 </pubmed>
+<pubmed>8288534,8387999,1938922,16166527,17227471,8825779, 8830686,18763711 17218307, 17190806 1715856 19605685 19826092 12642660 20148996 16091051 20797616 20525796 21821766 23012477 22511326,20817675,15066026 24425772 25448819 25666134</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 133: / Line 133: @@
 * '''Additional information:'''
 ** A [[ncRNA]] is predicted between ''[[hxlR]]'' and ''[[srfAA]]'' {{PubMed|20525796}}
 =Biological materials =
@@ Line 156: / Line 157: @@
 <pubmed>20735481 </pubmed>
 ==Original publications==
-<pubmed>8288534,8387999,1938922,16166527,17227471,8825779, 8830686,18763711 17218307, 17190806 1715856 19605685 19826092 12642660 20148996 16091051 20797616 20525796 21821766 23012477 22511326,20817675,15066026 24425772 </pubmed>
+<pubmed>8288534,8387999,1938922,16166527,17227471,8825779, 8830686,18763711 17218307, 17190806 1715856 19605685 19826092 12642660 20148996 16091051 20797616 20525796 21821766 23012477 22511326,20817675,15066026 24425772 25448819 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 63: / Line 63: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/srfAA-srfAB-comS-srfAC-srfAD.html]
@@ Line 98: / Line 99: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 70: / Line 70: @@
 === Additional information===
 * A mutation was found in this gene after evolution under relaxed selection for sporulation  {{PubMed|21821766}}
 =The protein=
@@ Line 86: / Line 85: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:''' phosphorylation on Ser-1006 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 155: / Line 154: @@
 <pubmed>20735481 </pubmed>
 ==Original publications==
-<pubmed>8288534,8387999,1938922,16166527,17227471,8825779, 8830686,18763711 17218307, 17190806 1715856 19605685 19826092 12642660 20148996 16091051 20797616 20525796 21821766 23012477 22511326,20817675,15066026</pubmed>
+<pubmed>8288534,8387999,1938922,16166527,17227471,8825779, 8830686,18763711 17218307, 17190806 1715856 19605685 19826092 12642660 20148996 16091051 20797616 20525796 21821766 23012477 22511326,20817675,15066026 24425772 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 60: / Line 60: @@
 ===Phenotypes of a mutant ===
 * altered cell death pattern in colonies {{PubMed|23012477}}
 === Database entries ===

@@ Line 37: / Line 37: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/>
+<br/><br/>
 = [[Categories]] containing this gene/protein =
@@ Line 115: / Line 115: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=srfAA_376968_387731_1 srfAA] {{PubMed|22383849}}
-* '''Sigma factor:''' [[SigA]] {{PubMed|1715856}}
+* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|1715856}}
 * '''Regulation:'''
@@ Line 154: / Line 154: @@
 <pubmed>20735481 </pubmed>
 ==Original publications==
-'''Additional publications:''' {{PubMed|22511326,20817675}}
+<pubmed>8288534,8387999,1938922,16166527,17227471,8825779, 8830686,18763711 17218307, 17190806 1715856 19605685 19826092 12642660 20148996 16091051 20797616 20525796 21821766 23012477 22511326,20817675</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 29: / Line 29: @@
   <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=srfAA_376968_387731_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:srfAA_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=srfAA_376968_387731_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:srfAA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU03480]]
 |-
 |}

@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[hxlR]]'', ''[[srfAB]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU03480 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU03480 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU03480 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU03480 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU03480 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU03480 DNA_with_flanks]
 |-
 |-