Difference between revisions of "Sandbox"

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−
* '''Description:''' urease (gamma subunit) <br/><br/>
+
* '''Description:''' cell wall-associated protein precursor <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'''
−
|''ureA''
+
|''wprA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yisM ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || urease (gamma subunit)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || cell wall-associated protein precursor
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || utilization of urea as alternative nitrogen source
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 11 kDa, 4.98  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 96 kDa, 9.58  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 315 bp, 105 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2682 bp, 894 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ureB]]'', ''[[csbD]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yisL]]'', ''[[yisN]]''
 
|-
 
|-
−
|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" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12917&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ureA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:wprA_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:''' BSU36660
+
* '''Locus tag:''' BSU10770
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ureABC.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/wprA.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11981]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11846]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' Urea + H<sub>2</sub>O = CO<sub>2</sub> + 2 NH<sub>3</sub> (according to Swiss-Prot)
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' urease gamma subunit family (according to Swiss-Prot)
+
* '''Protein family:''' peptidase S8 family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 72: Line 72:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' cytoplasm (according to Swiss-Prot)
+
* '''Localization:''' secreted (according to Swiss-Prot),  extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed],  membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
Line 78: Line 78:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P75030 P75030]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P54423 P54423]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU36660]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU10770]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.5.1.5 3.5.1.5]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[ureA]]-[[ureB]]-[[ureC]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/9287005 PubMed]
+
* '''Operon:''' ''[[wprA]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/16306698 PubMed]
  
−
* '''[[Sigma factor]]:''' [[SigA]], [[SigH]] [http://www.ncbi.nlm.nih.gov/sites/entrez/9287005 PubMed]
+
* '''[[Sigma factor]]:'''  
  
−
* '''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]
+
* '''Regulation:'''  
  
−
* '''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]
+
* '''Regulatory mechanism:''' activated by [[YvrHb]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16306698 PubMed]
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 118: Line 118:
 
=References=
 
=References=
  
−
<pubmed>1670935, </pubmed>
+
<pubmed>18957862 18763711 16306698, </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]
+
# Voigt et al. (2009) Cell physiology and protein secretion of ''Bacillus licheniformis'' compared to ''Bacillus subtilis''. ''J Mol Microbiol Biotechnol.'' '''16:''' 53-68 [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
 +
# 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]
 +
# Serizawa M, Kodama K, Yamamoto H, Kobayashi K, Ogasawara N, Sekiguchi J. (2005) Functional analysis of the YvrGHb two-component system of ''Bacillus subtilis'': identification of the regulated genes by DNA microarray and northern blot analyses. ''Biosci. Biotechnol. Biochem.'' '''69:''' 2155-2169. [http://www.ncbi.nlm.nih.gov/sites/entrez/16306698 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: cell wall-associated protein precursor

Gene name wprA
Synonyms yisM
Essential no
Product cell wall-associated protein precursor
Function unknown
MW, pI 96 kDa, 9.58
Gene length, protein length 2682 bp, 894 aa
Immediate neighbours yisL, yisN
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
WprA context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU10770

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: peptidase S8 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: secreted (according to Swiss-Prot), extracellular (signal peptide) PubMed, membrane PubMed

Database entries

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

Additional information

Expression and regulation

  • 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

  1. Voigt et al. (2009) Cell physiology and protein secretion of Bacillus licheniformis compared to Bacillus subtilis. J Mol Microbiol Biotechnol. 16: 53-68 PubMed
  2. Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing Bacillus subtilis by divergent approaches. Proteomics 8: 4123-4136 PubMed
  3. Serizawa M, Kodama K, Yamamoto H, Kobayashi K, Ogasawara N, Sekiguchi J. (2005) Functional analysis of the YvrGHb two-component system of Bacillus subtilis: identification of the regulated genes by DNA microarray and northern blot analyses. Biosci. Biotechnol. Biochem. 69: 2155-2169. PubMed
  4. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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