CcpC - Revision history

134.76.70.252 at 14:04, 17 April 2014

2014-04-17T14:04:12Z

134.76.70.252 at 09:29, 17 April 2014

2014-04-17T09:29:03Z

134.76.38.147 at 13:35, 2 April 2014

2014-04-02T13:35:07Z

134.76.70.252 at 10:39, 7 January 2014

2014-01-07T10:39:45Z

134.76.70.252 at 13:09, 16 May 2013

2013-05-16T13:09:06Z

134.76.70.252 at 10:04, 14 May 2013

2013-05-14T10:04:55Z

134.76.70.252 at 12:42, 13 May 2013

2013-05-13T12:42:08Z

Jstuelk: /* References */

2012-11-10T11:08:55Z

‎References

Fmeyer: /* Biological materials */

2012-11-02T08:18:50Z

‎Biological materials

134.76.70.252 at 09:03, 7 August 2012

2012-08-07T09:03:42Z

← Older revision		Revision as of 14:04, 17 April 2014
Line 1:		Line 1:
−	* '''Description:~~''' transcriptional repressor of ''[[citZ]]'' and ''[[citB]]'' <br/><br/>~~	+	{{#bank: CcpC}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''ccpC''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''ykuM ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| transcriptional repressor ([[LysR family]])~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| regulation of tricarboxylic acid branch of the TCA cycle~~
−	\|-
−	\|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=BSU14140 ccpC]
−	\|-
−	\|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=ccpC ccpC]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 33 kDa, 5.932~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 879 bp, 293 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[ykuL]]'', ''[[ykuN]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU14140 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU14140 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU14140 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:ccpC_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=ccpC_1486045_1486926_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:ccpC_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU14140]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<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\|[[carbon core metabolism]]}},~~
−	~~{{SubtiWiki category\|[[transcription factors and their control]]}},~~
−	~~{{SubtiWiki category\|[[regulators of core metabolism]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[CcpA regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[CcpC regulon]]}}~~
−	~~=The CcpC regulon:=~~
−	* ''[[ccpC]]'', ''[[citB]]'', ''[[citZ]]-[[icd]]-[[mdh]]''
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU14140
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU14140&redirect=T BSU14140]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ykuJK-ykzF-ykuL-ccpC.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13297]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:''' [[LysR 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=BSU14140&redirect=T BSU14140]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O34827 O34827]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU14140]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:'''
−	** ''[[ykuJ]]-[[ykuK]]-[[abbA]]-[[ykuL]]-[[ccpC]]'' {{PubMed\|16395550}}
−	** ''[[ccpC]]'' {{PubMed\|16395550}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ccpC_1486045_1486926_1 ccpC] {{PubMed\|22383849}}
−
−	* '''Sigma factor:'''
−	** ''[[ccpC]]'': [[SigA]]
−
−	* '''Regulation:'''
−	** repressed in the presence of glucose and glutamate ([[CcpC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/11985717 PubMed]
−
−	* '''Regulatory mechanism:'''
−	** [[CcpC]]: transcription repression (molecular inducer: citrate) [http://www.ncbi.nlm.nih.gov/sites/entrez/11985717 PubMed]
−	** [[CcpA]]: transcription repression {{PubMed\|16395550}}
−
−	* '''Additional information:'''
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 79 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 101 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:''' GP206 (''aphA3'') & GP1442 (''aphA3'') , available in [[Stülke]] lab
−
−	* '''Expression vector:'''
−	** for expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP706, available in [[Stülke]] lab
−
−	* '''lacZ fusion:''' pGP707 (in [[pAC5]]), available in [[Stülke]] lab, pGP711 (in [[pAC6]]), available in [[Stülke]] lab
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~[[Linc Sonenshein\|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−
−	~~<pubmed>17994626,23139400,11985717,10656796 12591885 14636591, 16395550</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

← Older revision		Revision as of 09:29, 17 April 2014
Line 128:		Line 128:

	* '''Additional information:'''		* '''Additional information:'''
		+	** number of protein molecules per cell (minimal medium with glucose and ammonium): 79 {{PubMed\|24696501}}
		+	** number of protein molecules per cell (complex medium with amino acids, without glucose): 101 {{PubMed\|24696501}}

	=Biological materials =		=Biological materials =

@@ Line 62: / Line 62: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ykuJK-ykzF-ykuL-ccpC.html]
@@ Line 96: / Line 97: @@
 === Database entries ===
 * '''Structure:'''

@@ 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=BSU14140 ccpC]
 |-
-|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=ccpC ccpC]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 5.932

@@ 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=ccpC_1486045_1486926_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ccpC_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ccpC_1486045_1486926_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ccpC_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU14140]]
 |-
 |}

@@ Line 24: / Line 24: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykuL]]'', ''[[ykuN]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU14140 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU14140 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU14140 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU14140 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU14140 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU14140 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:ccpC_context.gif]]

@@ Line 150: / Line 150: @@
 =References=
-<pubmed>17994626,,11985717,10656796 12591885 14636591, 16395550</pubmed>
+<pubmed>17994626,23139400,11985717,10656796 12591885 14636591, 16395550</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 129: / Line 129: @@
 =Biological materials =
-* '''Mutant:''' GP206 (''aphA3''), available in [[Stülke]] lab
+* '''Mutant:''' GP206 (''aphA3'') & GP1442 (''aphA3'') , available in [[Stülke]] lab
 * '''Expression vector:'''

@@ Line 13: / Line 13: @@
 |-
 |style="background:#ABCDEF;" align="center"|'''Function''' || regulation of tricarboxylic acid branch of the TCA cycle
 |-
 |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]'''