Difference between revisions of "Sandbox"

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* '''Description:''' extracellular 2',3' cyclic nucleotide phosphodiesterase, 2' (or 3') nucleotidase and 5' nucleotidase <br/><br/>
+
* '''Description:''' component of the cytochrome bc complex, cytochrome-c reductase <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'''
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|''yfkN''
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|''qcrA''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''bfcA, petC ''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/sites/entrez/17114254 PubMed]
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || 2',3' cyclic nucleotide phosphodiesterase, 2' (or 3') nucleotidase and 5' nucleotidase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || cytochrome-c reductase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || probably phosphate acquisition
+
|style="background:#ABCDEF;" align="center"|'''Function''' || respiration
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 159 kDa, 5.021  
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 18 kDa, 6.078  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 4386 bp, 1462 aa  
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 501 bp, 167 aa  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yfkO]]'', ''[[yfkM]]''
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[qcrB]]'', ''[[ypiF]]''
 
|-
 
|-
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yfkN_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/qcrA_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yfkN_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/qcrA_protein.txt Protein sequence]'''
 
|-
 
|-
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|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors
+
|colspan="2" | '''Genetic context''' <br/> [[Image:qcrA_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yfkN_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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===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
essential [http://www.ncbi.nlm.nih.gov/sites/entrez/17114254 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yfkN.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/qcrABC.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12930]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11325]
  
 
=== Additional information===
 
=== Additional information===
Line 61: Line 57:
 
* '''Protein family:'''
 
* '''Protein family:'''
  
−
* '''Paralogous protein(s):''' [[YhcR]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 85: Line 81:
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU07840]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU22560]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 97: Line 93:
 
* '''Sigma factor:'''  
 
* '''Sigma factor:'''  
  
−
* '''Regulation:''' repressed by glucose (5.2-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]   
+
* '''Regulation:''' repressed by glucose (5.5-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed],  repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]   
  
 
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression  
 
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression  
Line 124: Line 120:
  
 
# 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]
 
# 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]
+
# 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]
 
# 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 10:03, 6 April 2009

  • Description: component of the cytochrome bc complex, cytochrome-c reductase

Gene name qcrA
Synonyms bfcA, petC
Essential no
Product cytochrome-c reductase
Function respiration
MW, pI 18 kDa, 6.078
Gene length, protein length 501 bp, 167 aa
Immediate neighbours qcrB, ypiF
Gene sequence (+200bp) Protein sequence
Genetic context
QcrA 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:
  • 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: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Sigma factor:
  • Regulation: repressed by glucose (5.5-fold) (CcpA) PubMed, repressed by casamino acids 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. Mäder et al. (2002) Transcriptome and Proteome Analysis of Bacillus subtilis Gene Expression Modulated by Amino Acid Availability. J. Bacteriol 184: 1844288-4295 PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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