Difference between revisions of "Sandbox"

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Line 1: Line 1:
−
* '''Description:''' uricase <br/><br/>
+
* '''Description:''' anti-[[SigW]] <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'''
−
|''pucM''
+
|''rsiW''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yunM ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybbM''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || uricase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || anti-[[SigW]]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || purine utilization
+
|style="background:#ABCDEF;" align="center"|'''Function''' || control of [[SigW]] activity
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 13 kDa, 5.082  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 23 kDa, 6.646  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 363 bp, 121 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 624 bp, 208 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pucL]]'', ''[[pucE]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sigW]]'', ''[[ybbP]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15236&#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:CAB11950&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:pucM_context.gif]]
+
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:ybbM_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:''' BSU32460
+
* '''Locus tag:''' BSU01740
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pucRJKLM.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sigW-ybbM.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13987]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11574]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' 5-hydroxyisourate + H<sub>2</sub>O = 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate (according to Swiss-Prot)
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' 5-hydroxyisourate hydrolase subfamily (according to Swiss-Prot)
+
* '''Protein family:''' anti-sigma-W factor family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 70: Line 72:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''Interactions:''' [[PrsW]]-[[RsiW]],  [[RasP]]-[[RsiW]],  [[RsiW]]-[[SigW]]
  
−
* '''Localization:'''
+
* '''Localization:''' membrane (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2H0E 2H0E]
+
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O32142 O32142]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/Q45588 Q45588]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU32460]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU01740]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.5.2.17 3.5.2.17]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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* '''Regulation:'''  
 
* '''Regulation:'''  
 +
** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12076816 PubMed]
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
 +
** [[AbrB]]:  transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12076816 PubMed]
  
−
* '''Additional information:'''  
+
* '''Additional information:''' the mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]
  
 
=Biological materials =
 
=Biological materials =
Line 113: Line 117:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Thomas Wiegert]], University of Bayreuth, Germany [http://www.genetik.uni-bayreuth.de/LSGenetik1/Thomas%20Wiegert-Dateien/Thomas%20Wiegert.html Homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=

Revision as of 13:45, 11 June 2009

  • Description: anti-SigW

Gene name rsiW
Synonyms ybbM
Essential no
Product anti-SigW
Function control of SigW activity
MW, pI 23 kDa, 6.646
Gene length, protein length 624 bp, 208 aa
Immediate neighbours sigW, ybbP
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YbbM context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU01740

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: anti-sigma-W factor family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

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

Additional information

Expression and regulation

  • Operon:
  • Regulation:
  • Regulatory mechanism:
  • Additional information: the mRNA is very stable (half-life > 15 min) PubMed

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Thomas Wiegert, University of Bayreuth, Germany Homepage

Your additional remarks

References

  1. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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