Difference between revisions of "Sandbox"

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* '''Description:''' glycerol facilitator <br/><br/>
+
* '''Description:''' glycerol kinase <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'''
−
|''glpF''
+
|''glpK''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || glycerol facilitator
+
|style="background:#ABCDEF;" align="center"| '''Product''' || glycerol kinase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || glycerol uptake
+
|style="background:#ABCDEF;" align="center"|'''Function''' || glycerol utilization
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 9.506  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 54 kDa, 4.985  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 822 bp, 274 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1488 bp, 496 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[glpP]]'', ''[[glpK]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[glpF]]'', ''[[glpD]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/glpF_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/glpK_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/glpF_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/glpK_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:glpF_context.gif]]
+
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:glpK_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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* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/glpFK.html]
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/glpFK.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10186]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10187]
  
 
=== Additional information===
 
=== Additional information===
Line 55: Line 57:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' View classification
+
* '''Protein family:''' FGGY kinase family
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 81: Line 83:
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU09280]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU09290]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
−
 
  
 
=Expression and regulation=
 
=Expression and regulation=
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* '''[[Sigma factor]]:''' [[SigA]]
 
* '''[[Sigma factor]]:''' [[SigA]]
  
−
* '''Regulation:''' repressed by glucose (8-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed],  carbon catabolite repression, induction by glycerol
+
* '''Regulation:''' repressed by glucose ([[CcpA]]) ,  carbon catabolite repression, induction by glycerol
  
 
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression,  catabolite repression: repression by [[CcpA]], induction: [[GlpP]]-dependent RNA switch (transcriptional antitermination)
 
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression,  catabolite repression: repression by [[CcpA]], induction: [[GlpP]]-dependent RNA switch (transcriptional antitermination)
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=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
  
 +
[[Josef Deutscher]], Paris-Grignon, France
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 121: Line 123:
 
=References=
 
=References=
  
−
# 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]
+
 
−
# Beijer L, Nilsson RP, Holmberg C, Rutberg L: The ''glpP'' and ''glpF'' genes of the glycerol regulon in ''Bacillus subtilis''. J Gen Microbiol 1993;139:349-359. [http://www.ncbi.nlm.nih.gov/sites/entrez/8436953 PubMed]
+
# Beijer L, Rutberg L (1992) Utilisation of glycerol and glycerol-3-phosphate is differently affected by the phosphotransferase system in ''Bacillus subtilis''. FEMS Microbiol Lett 100:217-220. [http://www.ncbi.nlm.nih.gov/sites/entrez/1335945 PubMed]
 +
# Charrier V, Buckley E, Parsonage D, Galinier A, Darbon E, Jaquinod M, Forest E, Deutscher J, Claiborne A (1997) Cloning and sequencing of two enterococcal ''glpK'' genes and regulation of the encoded glycerol kinases by phosphoenolpyruvate-dependent, phosphotransferase system-catalyzed phosphorylation of a single histidyl residue. J Biol Chem 272:14166-14174. [http://www.ncbi.nlm.nih.gov/sites/entrez/9162046 PubMed]
 
# Darbon E, Servant P, Poncet S, Deutscher J (2002) Antitermination by GlpP, catabolite repression via CcpA and inducer exclusion triggered by P~GlpK dephosphorylation control ''Bacillus subtilis glpFK'' expression. Mol Microbiol 43:1039-1052. [http://www.ncbi.nlm.nih.gov/sites/entrez/11929549 PubMed]
 
# Darbon E, Servant P, Poncet S, Deutscher J (2002) Antitermination by GlpP, catabolite repression via CcpA and inducer exclusion triggered by P~GlpK dephosphorylation control ''Bacillus subtilis glpFK'' expression. Mol Microbiol 43:1039-1052. [http://www.ncbi.nlm.nih.gov/sites/entrez/11929549 PubMed]
 +
# Wehtje C, Beijer L, Nilsson RP, Rutberg B (1995) Mutations in the glycerol kinase gene restore the ability of a ''ptsGHI'' mutant of ''Bacillus subtilis'' to grow on glycerol. Microbiology 141:1193-1198. [http://www.ncbi.nlm.nih.gov/sites/entrez/7773413 PubMed]
 +
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 03:55, 12 April 2009

  • Description: glycerol kinase

Gene name glpK
Synonyms
Essential no
Product glycerol kinase
Function glycerol utilization
MW, pI 54 kDa, 4.985
Gene length, protein length 1488 bp, 496 aa
Immediate neighbours glpF, glpD
Gene sequence (+200bp) Protein sequence
Caution: The sequence for this gene in SubtiList contains errors
Genetic context
GlpK context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family: FGGY kinase family
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

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

Additional information

Expression and regulation

  • Regulation: repressed by glucose (CcpA) , carbon catabolite repression, induction by glycerol
  • Regulatory mechanism: CcpA: transcription repression, catabolite repression: repression by CcpA, induction: GlpP-dependent RNA switch (transcriptional antitermination)
  • Additional information:

Biological materials

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

Labs working on this gene/protein

Josef Deutscher, Paris-Grignon, France

Your additional remarks

References

  1. Beijer L, Rutberg L (1992) Utilisation of glycerol and glycerol-3-phosphate is differently affected by the phosphotransferase system in Bacillus subtilis. FEMS Microbiol Lett 100:217-220. PubMed
  2. Charrier V, Buckley E, Parsonage D, Galinier A, Darbon E, Jaquinod M, Forest E, Deutscher J, Claiborne A (1997) Cloning and sequencing of two enterococcal glpK genes and regulation of the encoded glycerol kinases by phosphoenolpyruvate-dependent, phosphotransferase system-catalyzed phosphorylation of a single histidyl residue. J Biol Chem 272:14166-14174. PubMed
  3. Darbon E, Servant P, Poncet S, Deutscher J (2002) Antitermination by GlpP, catabolite repression via CcpA and inducer exclusion triggered by P~GlpK dephosphorylation control Bacillus subtilis glpFK expression. Mol Microbiol 43:1039-1052. PubMed
  4. Wehtje C, Beijer L, Nilsson RP, Rutberg B (1995) Mutations in the glycerol kinase gene restore the ability of a ptsGHI mutant of Bacillus subtilis to grow on glycerol. Microbiology 141:1193-1198. PubMed
  5. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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