Difference between revisions of "Sandbox"

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−
* '''Description:''' hypoxanthin/ guanine permease <br/><br/>
+
* '''Description:''' galactarate dehydratase <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'''
−
|''pbuG''
+
|''ycbH''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yebB ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''garD ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || hypoxanthin/ guanine permease
+
|style="background:#ABCDEF;" align="center"| '''Product''' || galactarate dehydratase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || hypoxanthine and guanine uptake
+
|style="background:#ABCDEF;" align="center"|'''Function''' || galactarate utilization
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46 kDa, 8.808  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 54 kDa, 5.705  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1320 bp, 440 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1530 bp, 510 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[guaA]]'', ''[[yebC]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ycbG]]'', ''[[ycbJ]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12456&#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:CAB12045&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:pbuG_context.gif]]
+
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:ycbH_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 37:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU06370
+
* '''Locus tag:''' BSU02510
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pbuG.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ycbCDEFGHJ.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12811]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11163]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' d-galactarate = 5-dehydro-4-deoxy-D-glucarate + H<sub>2</sub>O (according to Swiss-Prot)
  
−
* '''Protein family:'''
+
* '''Protein family:''' uxaA family (according to Swiss-Prot)
  
−
* '''Paralogous protein(s):''' [[PbuO]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 72: Line 74:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2EEW 2EEW] (the pbuG riboswitch, U47c mutant, bound to hypoxanthine)
+
* '''Structure:'''
  
−
* '''Swiss prot entry:'''
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P42240 P42240]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU06370]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU02510]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.1.42 4.2.1.42]
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''pbuG''
+
* '''Operon:''' ''[[ycbC]]-[[ycbD]]-[[ycbE]]-[[ycbF]]-[[ycbG]]-[[ycbH]]-[[ycbJ]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/12044674 PubMed]
  
 
* '''[[Sigma factor]]:'''  
 
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:'''  
+
* '''Regulation:''' induced by D-glucarate/galactarate ([[YcbG]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12044674 PubMed]
−
** repressed in the presence of purine nucleotides ([[PurR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/11591660 PubMed]
 
−
** repressed by hypoxanthine and guanine, [[PurR]]-independent, ([[G-box]])[http://www.ncbi.nlm.nih.gov/sites/entrez/12923093 PubMed]
 
−
** repressed in the presence of adenine or adenosine([[PurR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/2536750 PubMed]
 
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[YcbG]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12044674 PubMed]
−
** [[PurR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/11591660 PubMed]
 
−
** [[PurR]]: transcription repression (molecular inducer: PRPP) [http://www.ncbi.nlm.nih.gov/sites/entrez/2536750 PubMed]
 
−
**[[G-box]]: transcription termination/ antitermination ([[riboswitch]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12923093 PubMed]
 
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 124: Line 120:
 
=References=
 
=References=
  
−
<pubmed>11591660,18763711 12923093, </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]
 
−
# Johansen et al. (2003) Definition of a second ''Bacillus subtilis pur'' regulon comprising the ''pur'' and ''xpt-pbuX'' operons plus ''pbuG'', ''nupG'' (''yxjA''), and ''pbuE'' (''ydhL''). ''J. Bacteriol.'' '''185:''' 5200-5209. [http://www.ncbi.nlm.nih.gov/sites/entrez/12923093 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 20:05, 12 June 2009

  • Description: galactarate dehydratase

Gene name ycbH
Synonyms garD
Essential no
Product galactarate dehydratase
Function galactarate utilization
MW, pI 54 kDa, 5.705
Gene length, protein length 1530 bp, 510 aa
Immediate neighbours ycbG, ycbJ
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YcbH context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU02510

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: d-galactarate = 5-dehydro-4-deoxy-D-glucarate + H2O (according to Swiss-Prot)
  • Protein family: uxaA 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:

Database entries

  • Structure:
  • KEGG entry: [3]

Additional information

Expression and regulation

  • Regulation: induced by D-glucarate/galactarate (YcbG) PubMed
  • Regulatory mechanism: YcbG: transcription repression PubMed
  • 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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