ScoC - Revision history

Jstuelk at 11:52, 15 May 2015

2015-05-15T11:52:43Z

Jstuelk: /* References */

2015-04-03T14:45:07Z

‎References

134.76.70.252 at 09:37, 17 April 2014

2014-04-17T09:37:51Z

134.76.38.147 at 13:19, 2 April 2014

2014-04-02T13:19:47Z

134.76.70.252 at 10:26, 7 January 2014

2014-01-07T10:26:51Z

134.76.70.252 at 14:15, 18 November 2013

2013-11-18T14:15:10Z

Jstuelk at 16:07, 24 May 2013

2013-05-24T16:07:17Z

134.76.70.252 at 12:53, 16 May 2013

2013-05-16T12:53:56Z

134.76.70.252 at 09:49, 14 May 2013

2013-05-14T09:49:51Z

134.76.70.252 at 12:28, 13 May 2013

2013-05-13T12:28:12Z

← Older revision		Revision as of 11:52, 15 May 2015
Line 1:		Line 1:
−	* '''Description:''' transcriptional repressor of genes expressed in the transition phase<br/><br/>	+	{{#bank: ScoC}}
−	{~~\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''scoC''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''hpr, catA''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| transcriptional repressor (MarR family)~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| transition state regulator~~
−	\|-
−	\|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=BSU09990 scoC]
−	\|-
−	~~\|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=ScoC~~ ScoC]
−	\|-
−	\|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=scoC scoC]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 23 kDa, 5.188~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 609 bp, 203 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[yhaI]]'', ''[[yhaH]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU09990 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU09990 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU09990 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:hpr_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=scoC_1073106_1073717_-1 Expression at a glance]'''   {{PubMed\|22383849~~}~~}<br/>[[Image:scoC_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU09990]]~~
−	\|-
−	\|}

−	~~__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\|[[phosphoproteins]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[AbrB regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[SalA regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[SenS regulon]]}}~~
−
−	~~=The [[ScoC regulon]]=~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU09990
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU09990&redirect=T BSU09990]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/hpr.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10659]
−
−	~~=== 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:'''
−	** phosphorylated on Arg-3 {{PubMed\|22517742}}
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[SinR]]-[[ScoC]]
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU09990&redirect=T BSU09990]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2FXA 2FXA]
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P11065 P11065]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU09990]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''scoC'' {{PubMed\|3131303}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=scoC_1073106_1073717_-1 scoC] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−
−	* '''Regulation:'''
−	** expressed upon transition into the stationary phase ([[AbrB]]) {{PubMed\|2504584}}
−
−	* '''Regulatory mechanism:'''
−	** [[AbrB]]: transcription activation {{PubMed\|2504584}}
−	** [[SenS]]: positive regulation {{PubMed\|16321961}}
−	** [[SalA]]: negative regulation {{PubMed\|15126467}}
−
−	* '''Additional information:'''
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 217 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 495 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:''' Strain OM213 of Ogura MA, et al {{PubMed\|15126467}}, genotype ''trpC2 scoC::pMutin-scoC leuC7'', available as [http://bgsc.org BGSC] 1A918
−	** 1A918 ( ''scoC''::''erm''), {{PubMed\|15126467}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A918&Search=1A918 BGSC]
−
−	* '''Expression vector:''' for expression, purification in E. coli with N-terminal His-tag, pRSETA available in Gerth lab
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−
−	~~<pubmed>3131303,16923912,1906467,10383984,16321961,14629015,1907636,15126467,2504584, 15104138, 19118355 19801406 19898538 20382764 22517742 23660663 11717292</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 151: / Line 151: @@
 =References=
-<pubmed>3131303,16923912,1906467,10383984,16321961,14629015,1907636,15126467,2504584, 15104138,  19118355 19801406 19898538 20382764 22517742 23660663</pubmed>
+<pubmed>3131303,16923912,1906467,10383984,16321961,14629015,1907636,15126467,2504584, 15104138,  19118355 19801406 19898538 20382764 22517742 23660663 11717292</pubmed>
 [[Category:Protein-coding genes]]

← Older revision		Revision as of 09:37, 17 April 2014
Line 127:		Line 127:

	* '''Additional information:'''		* '''Additional information:'''
		+	** number of protein molecules per cell (minimal medium with glucose and ammonium): 217 {{PubMed\|24696501}}
		+	** number of protein molecules per cell (complex medium with amino acids, without glucose): 495 {{PubMed\|24696501}}

	=Biological materials =		=Biological materials =

@@ Line 61: / Line 61: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/hpr.html]
@@ Line 97: / Line 98: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2FXA 2FXA]

@@ Line 17: / Line 17: @@
 |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=ScoC ScoC]
 |-
-|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], [http://subtiwiki.uni-goettingen.de/pathways/other_nitrogen_sources/index.html Alternative nitrogen sources]'''
+|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=scoC scoC]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 23 kDa, 5.188

@@ Line 15: / Line 15: @@
 |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=BSU09990 scoC]
 |-
-|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/ScoC ScoC]
+|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=ScoC ScoC]
 |-
 |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], [http://subtiwiki.uni-goettingen.de/pathways/other_nitrogen_sources/index.html Alternative nitrogen sources]'''

@@ Line 38: / Line 38: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/>
+<br/><br/>
 = [[Categories]] containing this gene/protein =
@@ Line 118: / Line 114: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=scoC_1073106_1073717_-1 scoC] {{PubMed|22383849}}
-* '''Sigma factor:'''
+* '''[[Sigma factor]]:'''
 * '''Regulation:'''
@@ Line 151: / Line 147: @@
 =References=
-<pubmed>3131303,16923912,1906467,10383984,16321961,14629015,1907636,15126467,2504584, 15104138,  19118355 19801406 19898538 20382764 22517742</pubmed>
+<pubmed>3131303,16923912,1906467,10383984,16321961,14629015,1907636,15126467,2504584, 15104138,  19118355 19801406 19898538 20382764 22517742 23660663</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 30: / Line 30: @@
   <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=scoC_1073106_1073717_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:scoC_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=scoC_1073106_1073717_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:scoC_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU09990]]
 |-
 |}

@@ Line 25: / Line 25: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yhaI]]'', ''[[yhaH]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU09990 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU09990 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU09990 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU09990 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU09990 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU09990 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:hpr_context.gif]]