Difference between revisions of "Sandbox"

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−
* '''Description:''' alpha-phosphoglucomutase, required for UDP-glucose synthesis <br/><br/>
+
* '''Description:''' glycerol-3-phosphate dehydrogenase (menaquinone 7) <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'''
−
|''pgcA''
+
|''glpD''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yhxB''
+
|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''' || alpha-phosphoglucomutase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || glycerol-3-phosphate dehydrogenase (menaquinone 7)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || interconversion of glucose 6-phosphate and alpha-glucose 1-phosphate
+
|style="background:#ABCDEF;" align="center"|'''Function''' ||  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 62 kDa, 4.913  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 62 kDa, 8.002  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1695 bp, 565 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1665 bp, 555 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[glpD]]'', ''[[yhcY]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[glpK]]'', ''[[pgcA]]''
 
|-
 
|-
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
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|-
 
|-
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yhxB_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:glpD_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=
Line 43: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/glpD.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10189]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10188]
  
 
=== Additional information===
 
=== Additional information===
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* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylated on ser/ thr/ tyr [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed] 
+
* '''Modification:'''
  
−
* '''Cofactor(s):'''
+
* '''Cofactor(s):''' FAD
  
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU09310]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU09300]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[glpD]]''
  
−
* '''[[Sigma factor]]:'''  
+
* '''[[Sigma factor]]:''' [[SigA]]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' repressed by glucose ([[CcpA]]) 
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 120: Line 120:
 
=References=
 
=References=
  
−
# Eymann et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in ''Bacillus subtilis''. ''Proteomics'' '''7:''' 3509-3526. [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
+
 
−
# L&#233;vine et al. (2006) Analysis of the dynamic ''Bacillus subtilis'' Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. ''Proteomics'' '''6:''' 2157-2173 [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
+
# Glatz E, Nilsson RP, Rutberg L, Rutberg B (1996) A dual role of the ''Bacillus subtilis glpD'' leader and the GlpP protein in the regulated expression of glpD: antitermination and control of mRNA stability. Mol Microbiol 19:319-328. [http://www.ncbi.nlm.nih.gov/sites/entrez/8825777 PubMed]
 +
# Holmberg C, Rutberg L (1992) An inverted repeat preceding the ''Bacillus subtilis glpD'' gene is a conditional terminator of transcription. Mol Microbiol 6:2931-2938. [http://www.ncbi.nlm.nih.gov/sites/entrez/1479885 PubMed]
 +
# Glatz E, Farewell A, Rutberg B: The ''Bacillus subtilis glpD'' leader and antiterminator protein GlpP provide a target for glucose repression in ''Escherichia coli''. FEMS Microbiol Lett 1998;162:93-96. [http://www.ncbi.nlm.nih.gov/sites/entrez/9595668 PubMed]
 +
# Glatz E, Persson M, Rutberg B: Antiterminator protein GlpP of ''Bacillus subtilis'' binds to ''glpD'' leader mRNA. Microbiology 1998;144:449-456. [http://www.ncbi.nlm.nih.gov/sites/entrez/9493382 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 15:33, 15 April 2009

  • Description: glycerol-3-phosphate dehydrogenase (menaquinone 7)

Gene name glpD
Synonyms
Essential no
Product glycerol-3-phosphate dehydrogenase (menaquinone 7)
Function
MW, pI 62 kDa, 8.002
Gene length, protein length 1665 bp, 555 aa
Immediate neighbours glpK, pgcA
Hier soll was neues rein
Genetic context
GlpD 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:
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s): FAD
  • 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)
  • Regulatory mechanism: CcpA: transcription repression
  • 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. Glatz E, Nilsson RP, Rutberg L, Rutberg B (1996) A dual role of the Bacillus subtilis glpD leader and the GlpP protein in the regulated expression of glpD: antitermination and control of mRNA stability. Mol Microbiol 19:319-328. PubMed
  2. Holmberg C, Rutberg L (1992) An inverted repeat preceding the Bacillus subtilis glpD gene is a conditional terminator of transcription. Mol Microbiol 6:2931-2938. PubMed
  3. Glatz E, Farewell A, Rutberg B: The Bacillus subtilis glpD leader and antiterminator protein GlpP provide a target for glucose repression in Escherichia coli. FEMS Microbiol Lett 1998;162:93-96. PubMed
  4. Glatz E, Persson M, Rutberg B: Antiterminator protein GlpP of Bacillus subtilis binds to glpD leader mRNA. Microbiology 1998;144:449-456. PubMed
  5. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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