Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' RNA polymerase sigma factor SigI <br/><br/>
+
* '''Description:''' superoxide dismutase, general stress protein <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'''
−
|''sigI''
+
|''sodA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ykoZ ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqgD ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || RNA polymerase sigma factor SigI
+
|style="background:#ABCDEF;" align="center"| '''Product''' || superoxide dismutase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || control of a class of heat shock genes
+
|style="background:#ABCDEF;" align="center"|'''Function''' || detoxification of oxygen radicals
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 8.306  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 5.203  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 753 bp, 251 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 606 bp, 202 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykoY]]'', ''[[rsgI]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqgE]]'', ''[[yqgC]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13218&#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:CAB14432&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:sigI_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:sodA_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 35: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU13450
+
* '''Locus tag:''' BSU25020
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
temperature-sensitive growth on agar plates [http://www.ncbi.nlm.nih.gov/sites/entrez/11157964 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sigI-rsgI.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13269]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11676]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' 2 superoxide + 2 H<sup>+</sup> = O<sub>2</sub> + H<sub>2</sub>O<sub>2</sub> (according to Swiss-Prot)  
−
 
 
−
* '''Protein family:'''
 
−
 
 
−
* '''Paralogous protein(s):'''
 
  
−
=== Members of the SigI regulon ===
+
* '''Protein family:''' iron/manganese superoxide dismutase family (according to Swiss-Prot)
  
−
''[[gsiB]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/11157964 PubMed], ''[[mreBH]], [[bcrC]]''  [http://www.ncbi.nlm.nih.gov/sites/entrez/18156261 PubMed]
+
* '''Paralogous protein(s):''' [[SodF]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 70: Line 64:
 
* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:'''
+
* '''Modification:''' phosphorylation on Thr-34 AND Thr-70 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
Line 76: Line 70:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[RsgI]]-[[SigI]],  [[RsgI]]-[[SigI]], the interaction inhibits SigI activity [http://www.ncbi.nlm.nih.gov/sites/entrez/17185538 PubMed]
+
* '''Interactions:'''
  
−
* '''Localization:'''
+
* '''Localization:''' cell membrane (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2RCV 2RCV]
  
−
* '''Swiss prot entry:'''
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P54375 P54375]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU13450]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU25020]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 95: Line 89:
  
 
* '''Operon:'''  
 
* '''Operon:'''  
−
* '''Operon:''' ''[[sigI]]-[[rsgI]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/17185538 PubMed]
 
  
−
* '''Sigma factor:''' [[SigI]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17185538 PubMed]
+
* '''[[Sigma factor]]:''' [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]  
  
−
* '''Regulation:''' induced by heat [http://www.ncbi.nlm.nih.gov/sites/entrez/17185538 PubMed]
+
* '''Regulation:''' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 125: Line 118:
 
=References=
 
=References=
  
−
<pubmed>17185538 11157964 18156261, </pubmed>
+
<pubmed>15805528 17218307, </pubmed>
−
# Asai K, Ootsuji T, Obata K, Matsumoto T, Fujita Y, Sadaie Y. (2007) Regulatory role of RsgI in ''sigI'' expression in ''Bacillus subtilis''. ''Microbiology'' '''153:''' 92-101. [http://www.ncbi.nlm.nih.gov/sites/entrez/17185538 PubMed]
+
# H&ouml;per et al. (2005) Comprehensive Characterization of the Contribution of Individual [[SigB]]-Dependent General Stress Genes to Stress Resistance of ''Bacillus subtilis''. J. Bact. '''187:''' 2810-2826  [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
−
# Zuber, U., K. Drzewiecki, and M. Hecker (2001) Putative sigma factor SigI (YkoZ) of ''Bacillus subtilis'' is induced by heat shock ''J. Bacteriol.'' '''183:''' 1472-1475. [http://www.ncbi.nlm.nih.gov/sites/entrez/11157964 PubMed]
+
# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model  bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707  [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
−
# Tseng, C. L., and Shaw, G. C. (2008) Genetic evidence for the actin homolog gene ''mreBH'' and the bacitracin resistance gene ''bcrC'' as targets of the alternative sigma factor SigI of ''Bacillus subtilis''. ''J. Bacteriol.'' '''190:''' 1561-1567. [http://www.ncbi.nlm.nih.gov/sites/entrez/18156261 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 13:37, 8 June 2009

  • Description: superoxide dismutase, general stress protein

Gene name sodA
Synonyms yqgD
Essential no
Product superoxide dismutase
Function detoxification of oxygen radicals
MW, pI 22 kDa, 5.203
Gene length, protein length 606 bp, 202 aa
Immediate neighbours yqgE, yqgC
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
SodA context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU25020

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: 2 superoxide + 2 H+ = O2 + H2O2 (according to Swiss-Prot)
  • Protein family: iron/manganese superoxide dismutase family (according to Swiss-Prot)
  • Paralogous protein(s): SodF

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification: phosphorylation on Thr-34 AND Thr-70 PubMed
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: cell membrane (according to Swiss-Prot)

Database entries

  • KEGG entry: [2]
  • E.C. number:

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. Höper et al. (2005) Comprehensive Characterization of the Contribution of Individual SigB-Dependent General Stress Genes to Stress Resistance of Bacillus subtilis. J. Bact. 187: 2810-2826 PubMed
  2. Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol. Cell. Proteomics 6: 697-707 PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
Retrieved from "https://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=88949"