Difference between revisions of "Sandbox"

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* '''Description:''' glutamate-1-semialdehyde aminotransferase <br/><br/>
+
* '''Description:''' transcriptional repressor of the peroxide regulon <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'''
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|''gsaB''
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|''perR''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ygaG ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || glutamate-1-semialdehyde aminotransferase
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|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional repressor
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of porphyrins
+
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of the response to peroxide
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46 kDa, 5.644  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 16 kDa, 5.888  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1287 bp, 429 aa  
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 435 bp, 145 aa  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ygaE]]'', ''[[ygaF]]''
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ygaF]]'', ''[[ygzB]]''
 
|-
 
|-
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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:CAB12699&#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:CAB12701&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|-
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|colspan="2" | '''Genetic context''' <br/> [[Image:perR_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:gsaB_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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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/perR.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11943]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12227]
  
 
=== Additional information===
 
=== Additional information===
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* '''Protein family:'''
 
* '''Protein family:'''
  
−
* '''Paralogous protein(s):'''
+
* '''Paralogous protein(s):''' [[Zur]], [[Fur]]
 +
 
 +
=== Genes repressed by PerR ===
  
 +
''[[zosA]]''
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
  
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
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* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU08710]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU08730]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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* '''[[Sigma factor]]:'''  
 
* '''[[Sigma factor]]:'''  
  
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* '''Regulation:'''  
+
* '''Regulation:''' negative autoregulation [http://www.ncbi.nlm.nih.gov/sites/entrez/12029044 PubMed]
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' repressed by '''PerR''' [http://www.ncbi.nlm.nih.gov/sites/entrez/12029044 PubMed]
  
−
* '''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=
  
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
# Herbig AF, Helmann JD. (2001) Roles of metal ions and hydrogen peroxide in modulating the interaction of the Bacillus subtilis PerR peroxide regulon repressor with operator DNA. ''Mol Microbiol.'' '''Aug;41(4):''' 849-59. [http://www.ncbi.nlm.nih.gov/sites/entrez/11532148 PubMed]
 +
# Fuangthong M, Herbig AF, Bsat N, Helmann JD. (2002) Regulation of the Bacillus subtilis fur and perR genes by PerR: not all members of the PerR regulon are peroxide inducible. ''J Bacteriol.'' '''Jun;184(12):''' 3276-86.[http://www.ncbi.nlm.nih.gov/sites/entrez/12029044 PubMed]

Revision as of 01:46, 30 April 2009

  • Description: transcriptional repressor of the peroxide regulon

Gene name perR
Synonyms ygaG
Essential no
Product transcriptional repressor
Function regulation of the response to peroxide
MW, pI 16 kDa, 5.888
Gene length, protein length 435 bp, 145 aa
Immediate neighbours ygaF, ygzB
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
PerR 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): Zur, Fur

Genes repressed by PerR

zosA

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: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Regulation: negative autoregulation PubMed
  • Regulatory mechanism: repressed by PerR PubMed
  • 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. Herbig AF, Helmann JD. (2001) Roles of metal ions and hydrogen peroxide in modulating the interaction of the Bacillus subtilis PerR peroxide regulon repressor with operator DNA. Mol Microbiol. Aug;41(4): 849-59. PubMed
  2. Fuangthong M, Herbig AF, Bsat N, Helmann JD. (2002) Regulation of the Bacillus subtilis fur and perR genes by PerR: not all members of the PerR regulon are peroxide inducible. J Bacteriol. Jun;184(12): 3276-86.PubMed
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