Difference between revisions of "Sandbox"

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−
* '''Description:''' phospho-beta-mannosidase <br/><br/>
+
* '''Description:''' gluconokinase <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'''
−
|''gmuD''
+
|''gntK''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ydhP''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || phospho-beta-mannosidase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || gluconokinase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || glucomannan utilization
+
|style="background:#ABCDEF;" align="center"|'''Function''' || gluconate utilization
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 54 kDa, 5.732  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 56 kDa, 5.517  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1395 bp, 465 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1539 bp, 513 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gmuC]]'', ''[[gmuR]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gntR]]'', ''[[gntP]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12403&#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:CAB16043&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ydhP_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:gntK_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:''' BSU05840
+
* '''Locus tag:''' BSU40060
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gmuBACDREFG.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gntRKPZ.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12193]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10649]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' ATP + D-gluconate = ADP + 6-phospho-D-gluconate (according to Swiss-Prot)
  
−
* '''Protein family:'''
+
* '''Protein family:''' FGGY kinase family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 78: Line 78:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:'''
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P12011 P12011]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU05840]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU40060]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.1.12 2.7.1.12]
  
 
=== Additional information===
 
=== Additional information===
Line 88: Line 88:
 
=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:''' ''[[gntR]]-[[gntK]]-[[gntP]]-[[gntZ]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/10746760 PubMed1][http://www.ncbi.nlm.nih.gov/sites/entrez/3020045 PubMed2]
  
−
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/18177310 PubMed]
+
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/3020045 PubMed]
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
−
** induced by conjac glucomannan (requires [[GmuG]]) ([[GmuR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/18177310 PubMed]
+
** induced by gluconate ([[GntR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/3020045 PubMed]
−
** induced by cellobiose ([[GmuR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/18177310 PubMed]
+
** repressed by glucose ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/8370661 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]
+
** [[GntR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/3020045 PubMed]
−
** [[CcpA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/18177310 PubMed]
+
** [[CcpA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/10666464 PubMed]
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 123: Line 122:
 
=References=
 
=References=
  
−
<pubmed>10627040 18177310, </pubmed>
+
<pubmed>3020045 1659648, </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]
+
 
−
# 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]
+
# Fujita Y, Fujita T, Miwa Y, Nihashi J, Aratani Y. (1986) Organization and transcription of the gluconate operon, gnt, of Bacillus subtilis. ''J Biol Chem.'' '''Oct 15;261(29):''' 13744-53. [http://www.ncbi.nlm.nih.gov/sites/entrez/3020045 PubMed]
 +
# Reizer A., Deutscher J., Saier M.H. Jr., Reizer J. (1991) Analysis of the gluconate (gnt) operon of Bacillus subtilis. ''Mol. Microbiol.'' '''5:''' 1081-1089. [http://www.ncbi.nlm.nih.gov/sites/entrez/1659648 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 14:05, 8 June 2009

  • Description: gluconokinase

Gene name gntK
Synonyms
Essential no
Product gluconokinase
Function gluconate utilization
MW, pI 56 kDa, 5.517
Gene length, protein length 1539 bp, 513 aa
Immediate neighbours gntR, gntP
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
GntK context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU40060

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: ATP + D-gluconate = ADP + 6-phospho-D-gluconate (according to Swiss-Prot)
  • Protein family: FGGY kinase 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

  • 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

A Reizer, J Deutscher, M H Saier, J Reizer
Analysis of the gluconate (gnt) operon of Bacillus subtilis.
Mol Microbiol: 1991, 5(5);1081-9
[PubMed:1659648] [WorldCat.org] [DOI] (P p)

Y Fujita, T Fujita, Y Miwa, J Nihashi, Y Aratani
Organization and transcription of the gluconate operon, gnt, of Bacillus subtilis.
J Biol Chem: 1986, 261(29);13744-53
[PubMed:3020045] [WorldCat.org] (P p)


  1. Fujita Y, Fujita T, Miwa Y, Nihashi J, Aratani Y. (1986) Organization and transcription of the gluconate operon, gnt, of Bacillus subtilis. J Biol Chem. Oct 15;261(29): 13744-53. PubMed
  2. Reizer A., Deutscher J., Saier M.H. Jr., Reizer J. (1991) Analysis of the gluconate (gnt) operon of Bacillus subtilis. Mol. Microbiol. 5: 1081-1089. PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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