Difference between revisions of "Sandbox"

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* '''Description:''' glyoxal reductase, general stress protein <br/><br/>
+
* '''Description:''' cadmium transporting ATPase, resistance to cadmium <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'''
−
|''yvgN''
+
|''cadA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvsB ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvgW ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || glyoxal reductase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || cadmium transporting ATPase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+
|style="background:#ABCDEF;" align="center"|'''Function''' || cadmium export
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 31 kDa, 5.066  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 75 kDa, 5.998  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 828 bp, 276 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2106 bp, 702 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvgM]]'', ''[[yvgO]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[bdbD]]'', ''[[copA]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15345&#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:CAB15354&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yvgN_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yvgW_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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* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14096]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14105]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' Lactaldehyde + NADP<sup>+</sup> = methylglyoxal + NADPH
+
* '''Catalyzed reaction/ biological activity:''' ATP + H<sub>2</sub>O + Cd<sup>2+</sup>(In) = ADP + phosphate + Cd<sup>2+</sup>(Out)
  
−
* '''Protein family:''' aldo/keto reductase family (according to Swiss-Prot)
+
* '''Protein family:''' Type IB subfamily (according to Swiss-Prot)
  
−
* '''Paralogous protein(s):''' [[YtbE]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 72: Line 72:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:'''
+
* '''Localization:''' cell membrane (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=3B3E 3B3E]
+
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O32210 O32210]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O32219 O32219]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33400 BSU33400]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33490 BSU33490]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.283 1.1.1.283]
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.6.3.3 3.6.3.3]
  
 
=== Additional information===
 
=== Additional information===
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* '''Operon:'''  
 
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed], repressed by [[SinR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16430695 PubMed]
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' [[SinR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/16430695 PubMed]
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 118: Line 118:
 
=References=
 
=References=
  
−
# H&ouml;per et al. (2005) Comprehensive Characterization of the Contribution of Individual [[SigB]]-Dependent General Stress Genes to Stress Resistance of ''Bacillus subtilis''. J. Bact. '''187:''' 2810-2826  [http://www.ncbi.nlm.nih.gov/pubmed/15805528 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 02:46, 23 May 2009

  • Description: cadmium transporting ATPase, resistance to cadmium

Gene name cadA
Synonyms yvgW
Essential no
Product cadmium transporting ATPase
Function cadmium export
MW, pI 75 kDa, 5.998
Gene length, protein length 2106 bp, 702 aa
Immediate neighbours bdbD, copA
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YvgW 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: ATP + H2O + Cd2+(In) = ADP + phosphate + Cd2+(Out)
  • Protein family: Type IB subfamily (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:
  • 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. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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