Difference between revisions of "Sandbox"

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−
* '''Description:''' carbamoyl-phosphate transferase-arginine subunit B) <br/><br/>
+
* '''Description:''' transcriptional regulator (LacI family) <br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
−
|''carB''
+
|''ccpB''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''cpa ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yyaG ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || carbamoyl-phosphate transferase-arginine subunit B)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator (LacI family)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of arginine
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 +
and sucrose of gluconate (gnt) and xylose (xyl) operons,
 +
in parallel to CcpA
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 112 kDa, 4.712  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 34 kDa, 6.327  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 3090 bp, 1030 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 933 bp, 311 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[carA]]'', ''[[argF]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yyaH]]'', ''[[exoA]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12965&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB16124&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|-
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ccpB_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:carB_context.gif]]
 
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
|-
 
|-
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU11240
+
* '''Locus tag:''' BSU40870
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/argCJBD-carAB-argF.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/exoA-ccpB.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10196]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10045]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' 2 ATP + L-glutamine + HCO<sub>3</sub><sup>-</sup> + H<sub>2</sub>O = 2 ADP + phosphate + L-glutamate + carbamoyl phosphate (according to Swiss-Prot)
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' carB family (according to Swiss-Prot)
+
* '''Protein family:'''
  
−
* '''Paralogous protein(s):''' [[PyrAB]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P18185 P18185]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P37517 P37517]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU11240]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU40870]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/6.3.5.5 6.3.5.5]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
  
−
:* subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
 
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[argC]]-[[argJ]]-[[argB]]-[[argD]]-[[carA]]-[[carB]]-[[argF]]''
+
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' [[SigA]]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed], repressed by arginine ([[AhrC]])
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' [[AhrC]]: transcription repression
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:''' subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
  
−
<pubmed>12107147, </pubmed>
+
<pubmed>9457849, </pubmed>
−
# M&#228;der et al. (2002) Transcriptome and Proteome Analysis of ''Bacillus subtilis'' Gene Expression Modulated by Amino Acid Availability. ''J. Bacteriol'' '''184:''' 1844288-4295 [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]
+
# Chauvaux S, Paulsen IT, Saier MH Jr. 1998. CcpB, a novel transcription factor implicated in catabolite repression in Bacillus subtilis. J Bacteriol 180:491-497. [http://www.ncbi.nlm.nih.gov/sites/entrez/9457849 PubMed]
−
# Gerth et al. (2008) Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis. J Bacteriol 190:321-331 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
 
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 13:11, 8 June 2009

  • Description: transcriptional regulator (LacI family)

Gene name ccpB
Synonyms yyaG
Essential no
Product transcriptional regulator (LacI family)
Function unknown

and sucrose of gluconate (gnt) and xylose (xyl) operons, in parallel to CcpA

MW, pI 34 kDa, 6.327
Gene length, protein length 933 bp, 311 aa
Immediate neighbours yyaH, exoA
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
CcpB context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU40870

Phenotypes of a mutant

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

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:
  • Interactions:
  • Localization:

Database entries

  • Structure:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Regulation:
  • Regulatory mechanism:
  • 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

S Chauvaux, I T Paulsen, M H Saier
CcpB, a novel transcription factor implicated in catabolite repression in Bacillus subtilis.
J Bacteriol: 1998, 180(3);491-7
[PubMed:9457849] [WorldCat.org] [DOI] (P p)

  1. Chauvaux S, Paulsen IT, Saier MH Jr. 1998. CcpB, a novel transcription factor implicated in catabolite repression in Bacillus subtilis. J Bacteriol 180:491-497. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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