Difference between revisions of "Sandbox"

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* '''Description:''' transcriptional repressor of the peroxide regulon <br/><br/>
+
* '''Description:''' vegetative catalase 1 <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'''
|''perR''
+
|''katA''
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ygaG ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''kat-19 ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional repressor
+
|style="background:#ABCDEF;" align="center"| '''Product''' || vegetative catalase 1
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of the response to peroxide
+
|style="background:#ABCDEF;" align="center"|'''Function''' || detoxification (degradation) of hydrogen peroxide
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 16 kDa, 5.888  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 54 kDa, 6.151  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 435 bp, 145 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1449 bp, 483 aa  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ygaF]]'', ''[[ygzB]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[senS]]'', ''[[ssuB]]''
 
|-
 
|-
|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)'''
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12710&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:perR_context.gif]]
+
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:katA_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 43:
 
=== Database entries ===
 
=== Database entries ===
  
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/perR.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/katA.html]
  
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12227]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10849]
  
 
=== Additional information===
 
=== Additional information===
Line 56: Line 58:
 
* '''Protein family:'''
 
* '''Protein family:'''
  
* '''Paralogous protein(s):''' [[Zur]], [[Fur]]
+
* '''Paralogous protein(s):'''
 
 
=== 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:'''
  
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU08730]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU08820]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 95: Line 94:
 
* '''[[Sigma factor]]:'''  
 
* '''[[Sigma factor]]:'''  
  
* '''Regulation:''' negative autoregulation [http://www.ncbi.nlm.nih.gov/sites/entrez/12029044 PubMed]
+
* '''Regulation:'''  
  
* '''Regulatory mechanism:''' repressed by '''PerR''' [http://www.ncbi.nlm.nih.gov/sites/entrez/12029044 PubMed]
+
* '''Regulatory mechanism:'''  
  
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 116: Line 115:
  
 
=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=
Line 122: Line 120:
 
=References=
 
=References=
  
# 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]
+
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID 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: vegetative catalase 1

Gene name katA
Synonyms kat-19
Essential no
Product vegetative catalase 1
Function detoxification (degradation) of hydrogen peroxide
MW, pI 54 kDa, 6.151
Gene length, protein length 1449 bp, 483 aa
Immediate neighbours senS, ssuB
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
KatA 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:
  • 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:
  • 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