Difference between revisions of "Sandbox"

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* '''Description:''' sensor kinase of the YvrG-YvrHb two-component system <br/><br/>
+
* '''Description:''' oxalate decarboxylase <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'''
−
|''yvrG''
+
|''oxdC''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvrK ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || two-component sensor histidine kinase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || oxalate decarboxylase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation cell surface maintenance
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 66 kDa, 9.518  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 43 kDa, 5.101  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1719 bp, 573 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1155 bp, 385 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvrE]]'', ''[[yvrHb]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvrJ]]'', ''[[yvrL]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15311&#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:CAB15314&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|-
+
|colspan="2" | '''Genetic context''' <br/> [[Image:oxdC_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yvrG_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 ===
−
 
−
unusual autolysis and higher susceptibility to cell envelope antibiotics (bacitracin, aztreonam, cefepime, fosfomycin)  [http://www.ncbi.nlm.nih.gov/sites/entrez/16306698 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
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* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14146]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14148]
  
 
=== Additional information===
 
=== Additional information===
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' phosphorylation of the [[YvrHb]] response regulator  [http://www.ncbi.nlm.nih.gov/sites/entrez/16306698 PubMed]
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:'''  
+
* '''Protein family:'''
  
−
* '''Paralogous protein(s):''' [[CssS]], [[YkoH]], [[KinE]], [[YclK]]
+
* '''Paralogous protein(s):''' [[OxdD]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Kinetic information:'''
 
* '''Kinetic information:'''
  
−
* '''Domains:''' two transmembrane segments, C-terminal histidine phosphotransferase domain
+
* '''Domains:'''  
  
 
* '''Modification:'''
 
* '''Modification:'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' YvrG-[[YvrHb]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/16306698 PubMed]
+
* '''Interactions:'''
  
 
* '''Localization:''' Cytoplasm
 
* '''Localization:''' Cytoplasm
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33210]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33240]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[oxdC]]-[[yvrL]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/19047353 PubMed]
  
−
* '''Sigma factor:'''  
+
* '''[[Sigma factor]]:''' [[YvrI]]-[[YvrH]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19047353 PubMed]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' induced by acidic growth conditions [http://www.ncbi.nlm.nih.gov/sites/entrez/19047353 PubMed]
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
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=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
[[John Helmann]], Cornell University, USA [http://www.micro.cornell.edu/research/labs/helmann-lab/index.cfm Homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
# Serizawa M, Kodama K, Yamamoto H, Kobayashi K, Ogasawara N, Sekiguchi J. (2005) Functional analysis of the YvrGHb two-component system of ''Bacillus subtilis'': identification of the regulated genes by DNA microarray and northern blot analyses. ''Biosci. Biotechnol. Biochem.'' '''69:''' 2155-2169. [http://www.ncbi.nlm.nih.gov/sites/entrez/16306698 PubMed]
+
# MacLellan et al. (2009) The YvrI alternative [[sigma factor]] is essential for acid stress induction of oxalate decarboxylase in ''Bacillus subtilis''. ''J. Bacteriol.'' '''191:''' 931-939. [http://www.ncbi.nlm.nih.gov/sites/entrez/19047353 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 03:29, 30 April 2009

  • Description: oxalate decarboxylase

Gene name oxdC
Synonyms yvrK
Essential no
Product oxalate decarboxylase
Function unknown
MW, pI 43 kDa, 5.101
Gene length, protein length 1155 bp, 385 aa
Immediate neighbours yvrJ, yvrL
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
OxdC 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:
  • Protein family:
  • Paralogous protein(s): OxdD

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: Cytoplasm

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [2]
  • E.C. number:

Additional information

Expression and regulation

  • Regulation: induced by acidic growth conditions PubMed
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

John Helmann, Cornell University, USA Homepage

Your additional remarks

References

  1. MacLellan et al. (2009) The YvrI alternative sigma factor is essential for acid stress induction of oxalate decarboxylase in Bacillus subtilis. J. Bacteriol. 191: 931-939. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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