YtrA - Revision history

Jstuelk at 17:54, 11 June 2014

2014-06-11T17:54:03Z

134.76.38.147 at 14:34, 2 April 2014

2014-04-02T14:34:25Z

134.76.70.252 at 11:30, 7 January 2014

2014-01-07T11:30:45Z

134.76.70.252 at 14:22, 16 May 2013

2013-05-16T14:22:23Z

134.76.70.252 at 11:04, 14 May 2013

2013-05-14T11:04:37Z

134.76.70.252 at 13:40, 13 May 2013

2013-05-13T13:40:07Z

134.76.70.252 at 15:11, 7 August 2012

2012-08-07T15:11:41Z

134.76.70.252 at 11:32, 20 April 2012

2012-04-20T11:32:21Z

134.76.70.252 at 15:49, 16 April 2012

2012-04-16T15:49:51Z

Jstuelk at 15:41, 24 August 2011

2011-08-24T15:41:44Z

← Older revision		Revision as of 17:54, 11 June 2014
Line 1:		Line 1:
−	* '''Description:~~''' [[transcription factors\|transcriptional repressor]], [[GntR family]], control of cell envelope stress responses in response to ramoplanin <br/><br/>~~	+	{{#bank: YtrA}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''ytrA''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	~~\|-a~~
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| [[transcription factors\|transcriptional repressor]] ([[GntR family]])~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| control of cell envelope stress responses~~
−	\|-
−	\|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=BSU30460 ytrA]
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Metabolic function and regulation of this protein in [[SubtiPathways\|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=ytrA ytrA]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 14 kDa, 8.094~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 390 bp, 130 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[ytrB]]'', ''[[ytrG]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU30460 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU30460 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU30460 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:ytrA_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=ytrA_3118847_3119239_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:ytrA_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU30460]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<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\|[[cold stress proteins]]}},~~
−	~~{{SubtiWiki category\|[[resistance against toxins/ antibiotics]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[YtrA regulon]]}}~~
−	~~=The [[YtrA regulon]]=~~
−
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU30460
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU30460&redirect=T BSU30460]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ytrABCDEF.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13911]
−
−	~~=== Additional information===~~
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU30460&redirect=T BSU30460]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/explore/explore.do?pdbId=3NEU 3NEU] (similar protein from ''Listeria innocua'', 41% identity)
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O34712 O34712]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU30460]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[ytrG]]-[[ytrA]]-[[ytrB]]-[[ytrC]]-[[ytrD]]-[[ytrE]]-[[ytrF]]'' {{PubMed\|10986249,21856850}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ytrA_3118847_3119239_-1 ytrA] {{PubMed\|22383849}}
−
−	* '''Sigma factor:''' [[SigA]] {{PubMed\|10986249}}
−
−	* '''Regulation:'''
−	** induced by ramoplanin ([[YtrA]]) {{PubMed\|21856850}}
−	** expressed early in the stationary phase {{PubMed\|10986249}}
−	** induced by cold shock (5-fold) {{PubMed\|12399512}}
−
−	* '''Regulatory mechanism:'''
−	** [[YtrA]]: transcription repression {{PubMed\|10986249,21856850}}
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~'''Additional publications:''' {{PubMed\|21856850}}~~
−	~~<pubmed>10986249,12399512, </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 62: / Line 62: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ytrABCDEF.html]
@@ Line 97: / Line 98: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/explore/explore.do?pdbId=3NEU 3NEU] (similar protein from ''Listeria innocua'', 41% identity)

@@ 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=BSU30460 ytrA]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
+|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=ytrA ytrA]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 14 kDa, 8.094

@@ 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=ytrA_3118847_3119239_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ytrA_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ytrA_3118847_3119239_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ytrA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU30460]]
 |-
 |}

@@ Line 24: / Line 24: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ytrB]]'', ''[[ytrG]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU30460 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU30460 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU30460 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU30460 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU30460 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU30460 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:ytrA_context.gif]]

@@ Line 13: / Line 13: @@
 |-
 |style="background:#ABCDEF;" align="center"|'''Function''' || control of cell envelope stress responses
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''

@@ Line 102: / Line 102: @@
 * '''Operon:''' ''[[ytrG]]-[[ytrA]]-[[ytrB]]-[[ytrC]]-[[ytrD]]-[[ytrE]]-[[ytrF]]''  {{PubMed|10986249,21856850}}
-* '''[[Sigma factor]]:''' [[SigA]]  {{PubMed|10986249}}
+* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ytrA_3118847_3119239_-1 ytrA] {{PubMed|22383849}}
 * '''Regulation:'''

@@ Line 34: / Line 34: @@
 = [[Categories]] containing this gene/protein =
 {{SubtiWiki category|[[transcription factors and their control]]}},
-{{SubtiWiki category|[[cold stress proteins]]}}
+{{SubtiWiki category|[[cold stress proteins]]}},
 = This gene is a member of the following [[regulons]] =