Difference between revisions of "Sandbox"

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* '''Description:''' cytochrome-c oxidase (subunit II) <br/><br/>
+
* '''Description:''' cytochrome-c oxidase (subunit I) <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'''
|''ctaC''
+
|''ctaD''
 
|-
 
|-
 
|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''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/17114254 PubMed]
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || cytochrome-c oxidase (subunit II)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || cytochrome-c oxidase (subunit I)
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || respiration  
 
|style="background:#ABCDEF;" align="center"|'''Function''' || respiration  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 39 kDa, 8.635  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 68 kDa, 6.985  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1068 bp, 356 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1866 bp, 622 aa  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ctaB]]'', ''[[ctaD]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ctaC]]'', ''[[ctaE]]''
 
|-
 
|-
|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" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13363&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:ctaC_context.gif]]
+
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:ctaD_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 38: Line 40:
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
essential [http://www.ncbi.nlm.nih.gov/pubmed/17114254 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
Line 43: Line 47:
 
* '''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+BG10215]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10216]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 58:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''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)
+
* '''Protein family:''' heme-copper respiratory oxidase family (according to Swiss-Prot) heme-copper respiratory oxidase family (according to Swiss-Prot)
  
* '''Paralogous protein(s):'''
+
* '''Paralogous protein(s):''' [[QoxB]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 78: Line 82:
 
* '''Structure:'''
 
* '''Structure:'''
  
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P24011 P24011]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P24010 P24010]
  
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU14890 BSU14890]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU14900 BSU14900]
  
 
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.9.3.1 1.9.3.1]
 
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.9.3.1 1.9.3.1]
Line 92: Line 96:
 
* '''[[Sigma factor]]:'''  
 
* '''[[Sigma factor]]:'''  
  
* '''Regulation:''' repressed by glucose (11-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed] 
+
* '''Regulation:'''  
  
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression
+
* '''Regulatory mechanism:'''  
  
 
* '''Additional information:'''  
 
* '''Additional information:'''  
Line 118: Line 122:
 
=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]
+
# Thomaides, H. B., Davison, E. J., Burston, L., Johnson, H., Brown, D. R., Hunt, A. C., Errington, J., and Czaplewski, L. (2007) Essential bacterial functions encoded by gene pairs. J Bacteriol 189, 591-602. [http://www.ncbi.nlm.nih.gov/sites/entrez/17114254 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 22:23, 19 May 2009

  • Description: cytochrome-c oxidase (subunit I)

Gene name ctaD
Synonyms
Essential yes PubMed
Product cytochrome-c oxidase (subunit I)
Function respiration
MW, pI 68 kDa, 6.985
Gene length, protein length 1866 bp, 622 aa
Immediate neighbours ctaC, ctaE
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
CtaD context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

essential PubMed

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family: heme-copper respiratory oxidase family (according to Swiss-Prot) heme-copper respiratory oxidase family (according to Swiss-Prot)
  • Paralogous protein(s): QoxB

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:
  • 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

  1. Thomaides, H. B., Davison, E. J., Burston, L., Johnson, H., Brown, D. R., Hunt, A. C., Errington, J., and Czaplewski, L. (2007) Essential bacterial functions encoded by gene pairs. J Bacteriol 189, 591-602. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed