Difference between revisions of "Sandbox"

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* '''Description:''' copper-transporting ATPase, resistance to copper <br/><br/>
+
* '''Description:''' general stress protein, similar to carboxylesterase <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'''
|''copA''
+
|''yvaK''
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvgX ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || copper transporting ATPase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || copper export
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 85 kDa, 5.484  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 4.992  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2409 bp, 803 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 744 bp, 248 aa  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cadA]]'', ''[[copZ]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rnr]]'', ''[[secG]]''
 
|-
 
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15355&#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:CAB15367&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:yvgX_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yvaK_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:''' no entry
 
* '''DBTBS entry:''' no entry
  
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14106]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14066]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
* '''Catalyzed reaction/ biological activity:''' ATP + H<sub>2</sub>O + Cu<sup>1+</sup>(In) = ADP + phosphate + Cu<sup>1+</sup>(Out)
+
* '''Catalyzed reaction/ biological activity:''' A carboxylic ester + H<sub>2</sub>O = an alcohol + a carboxylate
  
* '''Protein family:''' Type IB subfamily (according to Swiss-Prot)
+
* '''Protein family:''' lipase/esterase LIP3/bchO family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 70: Line 70:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
* '''Interactions:''' [[CopA]]-[[CopZ]]
+
* '''Interactions:'''
  
* '''Localization:''' cell membrane (according to Swiss-Prot)
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
  
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2RML 2RML] ( N-terminal soluble domain)
+
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1TQH 1TQH] (Geobacillus stearothermophilus)
  
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O32220 O32220]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O32232 O32232]
  
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33500 BSU33500]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33620 BSU33620]
  
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.1.1.1 3.1.1.1]
  
 
=== Additional information===
 
=== Additional information===
Line 90: Line 90:
 
* '''Operon:'''  
 
* '''Operon:'''  
  
* '''[[Sigma factor]]:'''  
+
* '''[[Sigma factor]]:''' [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]
  
* '''Regulation:'''  
+
* '''Regulation:''' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
Line 118: Line 118:
 
=References=
 
=References=
  
<pubmed> 19378562  </pubmed>
+
# Petersohn et al. (2001) Global Analysis of the General Stress Response of ''Bacillus subtilis''. ''J Bacteriol.'' '''183:''' 5617-5631 [http://www.ncbi.nlm.nih.gov/pubmed/11544224 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 01:49, 23 May 2009

  • Description: general stress protein, similar to carboxylesterase

Gene name yvaK
Synonyms
Essential no
Product unknown
Function unknown
MW, pI 28 kDa, 4.992
Gene length, protein length 744 bp, 248 aa
Immediate neighbours rnr, secG
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YvaK 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: A carboxylic ester + H2O = an alcohol + a carboxylate
  • Protein family: lipase/esterase LIP3/bchO 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:

Database entries

  • Structure: 1TQH (Geobacillus stearothermophilus)

Additional information

Expression and regulation

  • Operon:
  • 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. Petersohn et al. (2001) Global Analysis of the General Stress Response of Bacillus subtilis. J Bacteriol. 183: 5617-5631 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed