Difference between revisions of "Sandbox"

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−
* '''Description:''' toxic peptide <br/><br/>
+
* '''Description:''' urease (gamma subunit) <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'''
−
|''txpA ''
+
|''ureA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqcR, yqdB''
+
|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''' || toxic peptide
+
|style="background:#ABCDEF;" align="center"| '''Product''' || urease (gamma subunit)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || toxin
+
|style="background:#ABCDEF;" align="center"|'''Function''' || utilization of urea as alternative nitrogen source
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 6 kDa, 8.139  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 11 kDa, 4.98  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 177 bp, 59 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 315 bp, 105 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqbN]]'', ''[[ratA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ureB]]'', ''[[csbD]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14546&#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:CAB15683&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yqdB_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ureA_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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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU26050
+
* '''Locus tag:''' BSU36660
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/txpA.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ureABC.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11512]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11981]
  
 
=== Additional information===
 
=== Additional information===
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' Urea + H<sub>2</sub>O = CO<sub>2</sub> + 2 NH<sub>3</sub> (according to Swiss-Prot)
  
−
* '''Protein family:'''
+
* '''Protein family:''' urease gamma subunit family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:'''
+
* '''Localization:''' cytoplasm (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P54373 P54373]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P75030 P75030]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU26050]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU36660]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.5.1.5 3.5.1.5]
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''txpA'' [http://www.ncbi.nlm.nih.gov/sites/entrez/16166525 PubMed]
+
* '''Operon:''' ''[[ureA]]-[[ureB]]-[[ureC]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/9287005 PubMed]
  
−
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16166525 PubMed]
+
* '''[[Sigma factor]]:''' [[SigA]], [[SigH]] [http://www.ncbi.nlm.nih.gov/sites/entrez/9287005 PubMed]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' induced by nitrogen limitation ([[GlnR]], [[TnrA]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/9287005 PubMed], repressed by [[CodY]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]
  
−
* '''Regulatory mechanism:''' expression is prevented by the ''[[ratA]]'' antisense RNA [http://www.ncbi.nlm.nih.gov/sites/entrez/16166525 PubMed]
+
* '''Regulatory mechanism:''' [[GlnR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/9287005 PubMed], [[TnrA]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/9287005 PubMed], [[CodY]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed1]  [http://www.ncbi.nlm.nih.gov/sites/entrez/18083814 PubMed2]
  
 
* '''Additional information:'''
 
* '''Additional information:'''
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=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Richard Losick]], Harvard University, Cambridge, USA [http://www.mcb.harvard.edu/Losick/ Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
<pubmed>16166525, </pubmed>
+
<pubmed>1670935, </pubmed>
−
# Silvaggi JM, Perkins JB, Losick R (2005) Small untranslated RNA antitoxin in ''Bacillus subtilis''.''J. Bacteriol.'' '''187:''' 6641-6650. [http://www.ncbi.nlm.nih.gov/sites/entrez/16166525 PubMed]
+
# Atkinson MR, Fisher SH (1991) Identification of genes and gene products whose expression is activated during nitrogen-limited growth in Bacillus subtilis. J Bacteriol 173:23-27. [http://www.ncbi.nlm.nih.gov/sites/entrez/1670935 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 13:41, 8 June 2009

  • Description: urease (gamma subunit)

Gene name ureA
Synonyms
Essential no
Product urease (gamma subunit)
Function utilization of urea as alternative nitrogen source
MW, pI 11 kDa, 4.98
Gene length, protein length 315 bp, 105 aa
Immediate neighbours ureB, csbD
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
UreA context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU36660

Phenotypes of a mutant

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: Urea + H2O = CO2 + 2 NH3 (according to Swiss-Prot)
  • Protein family: urease gamma subunit family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: cytoplasm (according to Swiss-Prot)

Database entries

  • Structure:
  • KEGG entry: [3]

Additional information

Expression and regulation

  • 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

M R Atkinson, S H Fisher
Identification of genes and gene products whose expression is activated during nitrogen-limited growth in Bacillus subtilis.
J Bacteriol: 1991, 173(1);23-7
[PubMed:1670935] [WorldCat.org] [DOI] (P p)

  1. Atkinson MR, Fisher SH (1991) Identification of genes and gene products whose expression is activated during nitrogen-limited growth in Bacillus subtilis. J Bacteriol 173:23-27. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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