Difference between revisions of "Sandbox"

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−
* '''Description:''' glucomannan-specific phosphotransferase system, EIIC component <br/><br/>
+
* '''Description:''' NADP-dependent phosphogluconate dehydrogenase <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'''
−
|''gmuC''
+
|''gndA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ydhO''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqjI''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || glucomannan-specific phosphotransferase system, <br/>EIIC component
+
|style="background:#ABCDEF;" align="center"| '''Product''' || NADP-dependent phosphogluconate dehydrogenase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || glucomannan uptake and phosphorylation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || pentose phosphate pathway
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 9.803  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 51 kDa, 5.076  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1326 bp, 442 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1407 bp, 469 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gmuA]]'', ''[[gmuD]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[zwf]]'', ''[[polY1]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12402&#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:CAB14318&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ydhO_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yqjI_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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__TOC__
 
__TOC__
  
−
<br/><br/><br/><br/>
+
<br/><br/>
  
 
=The gene=
 
=The gene=
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU05830
+
* '''Locus tag:''' BSU23860
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yqjHI.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12192]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11738]
  
 
=== Additional information===
 
=== Additional information===
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' 6-phospho-D-gluconate + NADP<sup>+</sup> = D-ribulose 5-phosphate + CO<sub>2</sub> + NADPH (according to Swiss-Prot)
  
−
* '''Protein family:''' PTS permease, lactose permease (Lac) family [http://www.ncbi.nlm.nih.gov/pubmed/10627040 PubMed]
+
* '''Protein family:''' 6-phosphogluconate dehydrogenase family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:'''
+
* '''Modification:''' phosphorylation on (Thr-15 OR Thr-17) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:'''
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P80859 P80859]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU05830]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU23860]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.44 1.1.1.44]
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[gmuB]]-[[gmuA]]-[[gmuC]]-[[gmuD]]-[[gmuR]]-[[gmuE]]-[[gmuF]]-[[gmuG]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/18177310 PubMed]
+
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/18177310 PubMed]
+
* '''[[Sigma factor]]:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
−
** induced by conjac glucomannan (requires [[GmuG]]) ([[GmuR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/18177310 PubMed]
 
−
** induced by cellobiose ([[GmuR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/18177310 PubMed]
 
−
** subject to carbon catabolite repression ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/18177310 PubMed]
 
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
−
** [[GmuR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/18177310 PubMed]
 
−
** [[CcpA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/18177310 PubMed]
 
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
  
−
<pubmed>10627040 18177310, </pubmed>
+
<pubmed>17218307, </pubmed>
−
# Reizer et al. (1999) Novel phosphotransferase system genes revealed by genome analysis - the complete complement of PTS proteins encoded within the genome of ''Bacillus subtilis''. ''Microbiology'' '''145:''' 3419-3429 [http://www.ncbi.nlm.nih.gov/pubmed/10627040 PubMed]
+
# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model  bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707  [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
−
# Sadaie Y, Nakadate H, Fukui R, Yee LM, Asai K. (2008) Glucomannan utilization operon of Bacillus subtilis. ''FEMS Microbiol Lett.'' '''Feb;279(1):''' 103-9. [http://www.ncbi.nlm.nih.gov/sites/entrez/18177310 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 13:19, 8 June 2009

  • Description: NADP-dependent phosphogluconate dehydrogenase

Gene name gndA
Synonyms yqjI
Essential no
Product NADP-dependent phosphogluconate dehydrogenase
Function pentose phosphate pathway
MW, pI 51 kDa, 5.076
Gene length, protein length 1407 bp, 469 aa
Immediate neighbours zwf, polY1
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YqjI context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU23860

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: 6-phospho-D-gluconate + NADP+ = D-ribulose 5-phosphate + CO2 + NADPH (according to Swiss-Prot)
  • Protein family: 6-phosphogluconate dehydrogenase family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification: phosphorylation on (Thr-15 OR Thr-17) PubMed
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

  • Structure:
  • 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

Boris Macek, Ivan Mijakovic, Jesper V Olsen, Florian Gnad, Chanchal Kumar, Peter R Jensen, Matthias Mann
The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis.
Mol Cell Proteomics: 2007, 6(4);697-707
[PubMed:17218307] [WorldCat.org] [DOI] (P p)

  1. Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol. Cell. Proteomics 6: 697-707 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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