Difference between revisions of "Sandbox"

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* '''Description:''' small RNA <br/><br/>
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* '''Description:''' membrane-embedded thiol-disulfide oxidoreductase <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'''
−
|''bsrH''
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|''ccdA''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || small RNA
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|style="background:#ABCDEF;" align="center"| '''Product''' || thiol-disulfide oxidoreductase
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+
|style="background:#ABCDEF;" align="center"|'''Function''' || cytochrome c synthesis
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Gene length''' ||  bp
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 25 kDa, 9.667  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ratA]]'', ''[[yqbM]]''
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 705 bp, 235 aa
 
|-
 
|-
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE.txt    Gene sequence      (+200bp)  ]'''  
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ynzD]]'', ''[[yneI]]''
 
|-
 
|-
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|colspan="2" | '''Genetic context''' <br/> [[Image:genE_context.gif]]
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|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13677&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:ccdA_context.gif]]
 +
<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/>
  
−
<br/><br/><br/><br/><br/>
 
 
=The gene=
 
=The gene=
  
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:'''
+
* '''Locus tag:''' BSU17930
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
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=== Database entries ===
 
=== Database entries ===
  
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* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ccdA-yneIJ.html]
  
−
* '''SubtiList entry:''' no entry
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11240]
−
 
−
* '''Structure:'''
 
  
 
=== Additional information===
 
=== Additional information===
  
 +
 +
=The protein=
 +
 +
=== Basic information/ Evolution ===
 +
 +
* '''Catalyzed reaction/ biological activity:'''
 +
 +
* '''Protein family:''' dsbD 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:'''
 +
 +
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P45706 P45706]
 +
 +
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU17930]
 +
 +
* '''E.C. number:'''
 +
 +
=== Additional information===
  
 
=Expression and regulation=
 
=Expression and regulation=
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* '''Operon:'''  
 
* '''Operon:'''  
  
−
* '''Sigma factor:'''  
+
* '''[[Sigma factor]]:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
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* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
 +
* '''GFP fusion:'''
 +
 +
* '''two-hybrid system:'''
  
−
=Labs working on this gene/RNA=
+
* '''Antibody:'''
  
−
Kouji Nakamura, Tsukuba, University, Japan
+
=Labs working on this gene/protein=
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
<pubmed>18948176, </pubmed>
+
<pubmed>9068642, </pubmed>
−
# Saito S, Kakeshita H, Nakamura K (2009) Novel small RNA-encoding genes in the intergenic regions of ''Bacillus subtilis''. ''Gene'' '''428:''' 2-8. [http://www.ncbi.nlm.nih.gov/sites/entrez/18948176 PubMed]
+
# Schiött T, von Wachenfeldt C, Hederstedt L. (1997) Identification and characterization of the ccdA gene, required for cytochrome c synthesis in Bacillus subtilis. ''J Bacteriol.'' '''Mar;179(6):''' 1962-73. [http://www.ncbi.nlm.nih.gov/sites/entrez/9068642 PubMed]
 +
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 13:59, 8 June 2009

  • Description: membrane-embedded thiol-disulfide oxidoreductase

Gene name ccdA
Synonyms
Essential no
Product thiol-disulfide oxidoreductase
Function cytochrome c synthesis
MW, pI 25 kDa, 9.667
Gene length, protein length 705 bp, 235 aa
Immediate neighbours ynzD, yneI
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
CcdA context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU17930

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: dsbD 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:
  • 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

T Schiött, C von Wachenfeldt, L Hederstedt
Identification and characterization of the ccdA gene, required for cytochrome c synthesis in Bacillus subtilis.
J Bacteriol: 1997, 179(6);1962-73
[PubMed:9068642] [WorldCat.org] [DOI] (P p)

  1. Schiött T, von Wachenfeldt C, Hederstedt L. (1997) Identification and characterization of the ccdA gene, required for cytochrome c synthesis in Bacillus subtilis. J Bacteriol. Mar;179(6): 1962-73. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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