Difference between revisions of "Sandbox"

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−
* '''Description:''' malate dehydrogenase <br/><br/>
+
* '''Description:''' two-component sensor kinase, regulation of phosphate metabolism <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'''
−
|''mdh''
+
|''phoR''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citH ''
+
|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''' || malate dehydrogenase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || two-component sensor kinase (OmpR family)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
+
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of phosphate metabolism
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 4.727  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 64 kDa, 5.957  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 936 bp, 312 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1737 bp, 579 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[icd]], [[phoP]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[polA]]'', ''[[phoP]]''
 
|-
 
|-
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:mdh_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:phoR_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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__TOC__
 
__TOC__
  
−
<br/><br/><br/><br/>
+
<br/><br/>
  
 
=The gene=
 
=The gene=
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/phoPR.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11386]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10364]
  
 
=== Additional information===
 
=== Additional information===
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* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:'''
+
* '''Modification:''' two transmembrane segments, C-terminal histidine phosphotransferase domain
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
  
−
* '''Effectors of protein activity:'''
+
* '''Effectors of protein activity:'''  
  
−
* '''Interactions:'''
+
* '''Interactions:''' [[PhoP]]-[[PhoR]]
  
−
* '''Localization:''' membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1EMD 1EMD] (''E.coli'')
+
* '''Structure:'''
  
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29120]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29100]
  
−
* '''E.C. number:''' 1.1.1.37
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
  
−
* '''Operon:'''
+
=Expression and regulation=
−
**''[[citZ]]-[[icd]]-[[mdh]]''
 
−
**''[[icd]]-[[mdh]]''
 
  
−
* '''Sigma factor:''' [[SigA]]
+
* '''Operon:''' ''[[phoP]]-[[phoR]]''
  
−
* '''Regulation:''' ''[[citZ]]'': catabolite repression ([[CcpA]]), repression by glucose + glutamate ([[CcpC]])
+
* '''[[Sigma factor]]:''' [[SigA]]
−
''[[mdh]]'': constitutive
 
−
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression, [[CcpC]]: transcription repression
 
  
 +
* '''Regulation:''' induced by phosphate limitation ([[PhoP]]), carbon catabolite repression ([[CcpA]])
  
 +
* '''Regulatory mechanism:''' [[PhoP]]: transcription activation, [[CcpA]]: transcription repression
  
 
* '''Additional information:'''
 
* '''Additional information:'''
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=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP719 (spc), available in [[Stülke]] lab
+
* '''Mutant:'''
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
Line 120: Line 118:
 
=References=
 
=References=
  
−
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics '''8:''' 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 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 18:19, 15 April 2009

  • Description: two-component sensor kinase, regulation of phosphate metabolism

Gene name phoR
Synonyms
Essential no
Product two-component sensor kinase (OmpR family)
Function regulation of phosphate metabolism
MW, pI 64 kDa, 5.957
Gene length, protein length 1737 bp, 579 aa
Immediate neighbours polA, phoP
Hier soll was neues rein
Genetic context
PhoR 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: two transmembrane segments, C-terminal histidine phosphotransferase domain
  • Cofactor(s):
  • Effectors of protein activity:
  • Localization:

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Regulation: induced by phosphate limitation (PhoP), carbon catabolite repression (CcpA)
  • Regulatory mechanism: PhoP: transcription activation, 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. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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