Difference between revisions of "Sandbox"

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−
* '''Description:''' response regulator aspartate phosphatase <br/><br/>
+
* '''Description:''' uricase <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'''
−
|''rapA''
+
|''pucM''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''gsiAA, spo0L ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yunM ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || response regulator aspartate phosphatase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || uricase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || control of sporulation initiation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || purine utilization
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 44 kDa, 4.848  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 13 kDa, 5.082  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1134 bp, 378 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 363 bp, 121 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yjoB]]'', ''[[phrA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pucL]]'', ''[[pucE]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13100&#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:CAB15236&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:rapA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:pucM_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:''' BSU12430
+
* '''Locus tag:''' BSU32460
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rapA-phrA.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pucRJKLM.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10652]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13987]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''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)
  
−
* '''Protein family:''' RAP family (according to Swiss-Prot)
+
* '''Protein family:''' 5-hydroxyisourate hydrolase subfamily (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[RapA]]-[[PhrA]],  [[RapA]]-[[Spo0F]]
+
* '''Interactions:'''
  
 
* '''Localization:'''
 
* '''Localization:'''
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=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2H0E 2H0E]
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/Q00828 Q00828]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O32142 O32142]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU12430]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU32460]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.5.2.17 3.5.2.17]
  
 
=== Additional information===
 
=== Additional information===
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* '''[[Sigma factor]]:'''  
 
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' repressed by glucose (4.2-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed],  repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed] 
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression
+
* '''Regulatory mechanism:'''  
  
 
* '''Additional information:'''  
 
* '''Additional information:'''  
Line 117: Line 117:
  
 
=References=
 
=References=
−
 
−
<pubmed> 12107147, 19380751, 12850135  </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 13:17, 11 June 2009

  • Description: uricase

Gene name pucM
Synonyms yunM
Essential no
Product uricase
Function purine utilization
MW, pI 13 kDa, 5.082
Gene length, protein length 363 bp, 121 aa
Immediate neighbours pucL, pucE
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
PucM context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU32460

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: 5-hydroxyisourate + H2O = 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate (according to Swiss-Prot)
  • Protein family: 5-hydroxyisourate hydrolase subfamily (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

  • KEGG entry: [3]

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
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