Difference between revisions of "Sandbox"

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−
* '''Description:''' Modulator of CcpN activity<br/><br/>
+
* '''Description:''' cytochrome c550 <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'''
−
|''yqfL''
+
|''cccA''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || modulator of [[CcpN]] activity
+
|style="background:#ABCDEF;" align="center"| '''Product''' || cytochrome c550
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || inhibits [[CcpN]] activity
+
|style="background:#ABCDEF;" align="center"|'''Function''' || respiration
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 30,4 kDa, 5.78
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 12 kDa, 5.276 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 810 bp, 270 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 360 bp, 120 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqxD]]'', ''[[ccpN]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqfN]]'', ''[[sigA]]''
 
|-
 
|-
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yqfL_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:cccA_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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<br/><br/>
 
<br/><br/>
−
 
  
 
=The gene=
 
=The gene=
Line 36: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:''' 2603357 - 2604166
+
* '''Coordinates:'''
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 42: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ccpN-yqfL.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:'''[http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11659]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10315]
  
 
=== Additional information===
 
=== Additional information===
 +
  
 
=The protein=
 
=The protein=
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' negative effector of [[CcpN]] activity [http://www.ncbi.nlm.nih.gov/sites/entrez/15720552 PubMed]
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' pyruvate, phosphate dikinase regulatory protein family
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 62: Line 62:
 
* '''Kinetic information:'''
 
* '''Kinetic information:'''
  
−
* '''Domains:''' nucleotide binding domain (ATP) (151–158)
+
* '''Domains:'''  
  
 
* '''Modification:'''
 
* '''Modification:'''
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P54470]
+
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU25240]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU25190]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.-.- 2.7.-.-]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
−
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[ccpN]]''-''[[yqfL]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/15720552 PubMed]
+
* '''Operon:'''  
  
 
* '''[[Sigma factor]]:'''  
 
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' constitutive [http://www.ncbi.nlm.nih.gov/sites/entrez/15720552 PubMed]
+
* '''Regulation:''' repressed by glucose (4.8-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed],  carbon catabolite repression ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/11361075 PubMed]
 +
 
 +
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression,  [[CcpA]]: transcription repression, cre site overlaps -35 region of the promoter [http://www.ncbi.nlm.nih.gov/sites/entrez/11361075 PubMed]
  
 
* '''Additional information:'''
 
* '''Additional information:'''
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* '''Expression vector:'''
 
* '''Expression vector:'''
−
+
       
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
 +
 +
* '''two-hybrid system:'''
  
 
* '''Antibody:'''
 
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
[[Stephane Aymerich |Stephane Aymerich]], Microbiology and Molecular Genetics, INRA Paris-Grignon, France
 
−
 
−
 
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
# Servant et al. (2005) CcpN (YqzB), a novel regulator for CcpA-independent catabolite repression of ''Bacillus subtilis'' gluconeogenic genes. Mol. Microbiol. 55: 1435-1451. [http://www.ncbi.nlm.nih.gov/sites/entrez/15720552 PubMed]
+
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
 +
# Monedero, V., Boël, G., and Deutscher, J. (2001). Catabolite regulation of the cytochrome c550-encoding Bacillus subtilis cccA gene. J. Mol. Microbiol. Biotechnol. 3, 433-438. [http://www.ncbi.nlm.nih.gov/sites/entrez/11361075 PubMed]
 +
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 18:45, 15 April 2009

  • Description: cytochrome c550

Gene name cccA
Synonyms
Essential no
Product cytochrome c550
Function respiration
MW, pI 12 kDa, 5.276
Gene length, protein length 360 bp, 120 aa
Immediate neighbours yqfN, sigA
Hier soll was neues rein
Genetic context
CccA context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

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:
  • Swiss prot entry:
  • KEGG entry: [2]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Regulation: repressed by glucose (4.8-fold) (CcpA) PubMed, carbon catabolite repression (CcpA) PubMed
  • Regulatory mechanism: CcpA: transcription repression, CcpA: transcription repression, cre site overlaps -35 region of the promoter PubMed
  • 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

  1. Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metab Eng. 5: 133-149 PubMed
  2. Monedero, V., Boël, G., and Deutscher, J. (2001). Catabolite regulation of the cytochrome c550-encoding Bacillus subtilis cccA gene. J. Mol. Microbiol. Biotechnol. 3, 433-438. PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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