Difference between revisions of "Sandbox"

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* '''Description:''' heme O synthase (major enzyme) <br/><br/>
+
* '''Description:''' cytochrome-c oxidase (subunit II) <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'''
|''ctaB''
+
|''ctaC''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
Line 10: Line 10:
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || heme O synthase (major enzyme)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || cytochrome-c oxidase (subunit II)
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || heme biosynthesis
+
|style="background:#ABCDEF;" align="center"|'''Function''' || respiration
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 9.566  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 39 kDa, 8.635  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 915 bp, 305 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1068 bp, 356 aa  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ctaA]]'', ''[[ctaC]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ctaB]]'', ''[[ctaD]]''
 
|-
 
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13361&#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:CAB13362&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:ctaB_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ctaC_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>
 
|-
 
|-
Line 43: Line 43:
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ctaBCDEFG.html]
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ctaBCDEFG.html]
  
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10214]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10215]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 54:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
* '''Protein family:''' Protoheme IX farnesyltransferase subfamily (according to Swiss-Prot) ubiA prenyltransferase family, Protoheme IX farnesyltransferase subfamily (according to Swiss-Prot)
+
* '''Protein family:''' cytochrome c oxidase subunit 2 family (according to Swiss-Prot) cytochrome c oxidase subunit 2 family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 78: Line 78:
 
* '''Structure:'''
 
* '''Structure:'''
  
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P24009 P24009]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P24011 P24011]
  
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU14880 BSU14880]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU14890 BSU14890]
  
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.9.3.1 1.9.3.1]
  
 
=== Additional information===
 
=== Additional information===
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* '''[[Sigma factor]]:'''  
 
* '''[[Sigma factor]]:'''  
  
* '''Regulation:'''  
+
* '''Regulation:''' repressed by glucose (11-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed] 
  
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression
  
 
* '''Additional information:'''  
 
* '''Additional information:'''  
Line 118: Line 118:
 
=References=
 
=References=
  
 +
# 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]
 
# 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 22:22, 19 May 2009

  • Description: cytochrome-c oxidase (subunit II)

Gene name ctaC
Synonyms
Essential no
Product cytochrome-c oxidase (subunit II)
Function respiration
MW, pI 39 kDa, 8.635
Gene length, protein length 1068 bp, 356 aa
Immediate neighbours ctaB, ctaD
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
CtaC context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

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: cytochrome c oxidase subunit 2 family (according to Swiss-Prot) cytochrome c oxidase subunit 2 family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: cell membrane (according to Swiss-Prot)

Database entries

  • Structure:

Additional information

Expression and regulation

  • Operon:
  • Regulation: repressed by glucose (11-fold) (CcpA) PubMed
  • Regulatory mechanism: CcpA: transcription repression
  • 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. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed