Difference between revisions of "Sandbox"

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−
* '''Description:''' glucose 6-phosphate dehydrogenase, pentose-phosphate pathway <br/><br/>
+
* '''Description:''' inhibitor of AbrB activity<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'''
−
|''zwf''
+
|''abbA ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqjJ ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ykzF''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || glucose 6-phosphate dehydrogenase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || anti-repressor
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || initiation of the pentose phosphate pathway
+
|style="background:#ABCDEF;" align="center"|'''Function''' || inhibition of AbrB
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 55 kDa, 5.28  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 7 kDa, 4.642  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1467 bp, 489 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 195 bp, 65 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rnz]]'', ''[[gndA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykuK]]'', ''[[ykuL]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14317&#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:CAB13285&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|-
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ykzF_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:zwf_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:''' BSU23850
+
* '''Locus tag:''' BSU14120
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 43: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/zwf.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ykuJK-ykzF-ykuL-ccpC.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11739]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13334]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' D-glucose 6-phosphate + NADP<sup>+</sup> = D-glucono-1,5-lactone 6-phosphate + NADPH (according to Swiss-Prot)
+
* '''Catalyzed reaction/ biological activity:''' inhibition of AbrB activity [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
  
−
* '''Protein family:''' glucose-6-phosphate dehydrogenase family (according to Swiss-Prot)
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''Interactions:''' [[AbbA]]-[[AbrB]],  AbbA-[[AbrB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
  
 
* '''Localization:'''
 
* '''Localization:'''
Line 80: Line 78:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P54547 P54547]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O31697 O31697]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU23850]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU14120]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.49 1.1.1.49]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''zwf'' [http://www.ncbi.nlm.nih.gov/sites/entrez/12850135 PubMed]
+
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:'''  
+
* '''Sigma factor:'''  
  
−
* '''Regulation:''' constitutive [http://www.ncbi.nlm.nih.gov/sites/entrez/12850135 PubMed]
+
* '''Regulation:''' repressed by glucose (4.3-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed],  subject to carbon catabolite repression (4-fold: [[CcpA]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12850135 PubMed], expressed at onset of stationary phase ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression,  [[CcpA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12850135 PubMed], [[Spo0A]]: transcription activation by Spo0A~P [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
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=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Richard Losick]], Harvard Univ., Cambridge, USA [http://www.mcb.harvard.edu/Losick/ homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 120: Line 120:
 
=References=
 
=References=
  
−
<pubmed>12850135, </pubmed>
+
<pubmed>12850135 18840696 12850135, </pubmed>
 +
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
 +
# Banse et al. (2008) Parallel pathways of repression and antirepression governing the transition to stationary phase in ''Bacillus subtilis''.''Proc. Natl. Acad. Sci. USA'' '''105:''' 15547-15552. [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
 
# Blencke, H.-M., Homuth, G., Ludwig, H., Mäder, U., Hecker, M. & Stülke, J. (2003) Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metab. Engn. 5: 133-149. [http://www.ncbi.nlm.nih.gov/sites/entrez/12850135 PubMed]
 
# Blencke, H.-M., Homuth, G., Ludwig, H., Mäder, U., Hecker, M. & Stülke, J. (2003) Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metab. Engn. 5: 133-149. [http://www.ncbi.nlm.nih.gov/sites/entrez/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 13:55, 8 June 2009

  • Description: inhibitor of AbrB activity

Gene name abbA
Synonyms ykzF
Essential no
Product anti-repressor
Function inhibition of AbrB
MW, pI 7 kDa, 4.642
Gene length, protein length 195 bp, 65 aa
Immediate neighbours ykuK, ykuL
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YkzF context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU14120

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: inhibition of AbrB activity PubMed
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

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

Additional information

Expression and regulation

  • Operon:
  • Sigma factor:
  • Regulation: repressed by glucose (4.3-fold) (CcpA) PubMed, subject to carbon catabolite repression (4-fold: CcpA) PubMed, expressed at onset of stationary phase (Spo0A) PubMed
  • Regulatory mechanism: CcpA: transcription repression, CcpA: transcription repression PubMed, Spo0A: transcription activation by Spo0A~P PubMed
  • Additional information:

Biological materials

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

Labs working on this gene/protein

Richard Losick, Harvard Univ., Cambridge, USA homepage

Your additional remarks

References

Allison V Banse, Arnaud Chastanet, Lilah Rahn-Lee, Errett C Hobbs, Richard Losick
Parallel pathways of repression and antirepression governing the transition to stationary phase in Bacillus subtilis.
Proc Natl Acad Sci U S A: 2008, 105(40);15547-52
[PubMed:18840696] [WorldCat.org] [DOI] (I p)

Hans-Matti Blencke, Georg Homuth, Holger Ludwig, Ulrike Mäder, Michael Hecker, Jörg Stülke
Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways.
Metab Eng: 2003, 5(2);133-49
[PubMed:12850135] [WorldCat.org] [DOI] (P p)

  1. Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metab Eng. 5: 133-149 PubMed
  2. Banse et al. (2008) Parallel pathways of repression and antirepression governing the transition to stationary phase in Bacillus subtilis.Proc. Natl. Acad. Sci. USA 105: 15547-15552. PubMed
  3. Blencke, H.-M., Homuth, G., Ludwig, H., Mäder, U., Hecker, M. & Stülke, J. (2003) Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metab. Engn. 5: 133-149. PubMed
  4. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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