Difference between revisions of "Sandbox"

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−
* '''Description:''' class I heat-shock protein (molecular chaperone) <br/><br/>
+
* '''Description:''' write here <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'''
−
|''dnaK''
+
|''drm''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqkN ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || class I heat-shock protein (molecular chaperone)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || phosphopentomutase (EC 5.4.2.7)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || protein quality control
+
|style="background:#ABCDEF;" align="center"|'''Function''' || conversion of ribose-1-P/deoxyribose-1-P to ribose-5-P/deoxyribose-5-P
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 65 kDa, 4.571  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 43 kDa, 4.974  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1833 bp, 611 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1182 bp, 394 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[surC]]'', ''[[grpE]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[punA]]'', ''[[ripX]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/dnaK_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/drm_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/dnaK_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/drm_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:dnaK_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:drm_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>
 
|-
 
|-
Line 42: Line 44:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/lepA-hemN-hrcA-grpE-dnaKJ-yqeTUV.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/drm-punA.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10664]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11331]
  
 
=== Additional information===
 
=== Additional information===
Line 65: Line 67:
 
* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylated on ser/ thr/ tyr [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]  
+
* '''Modification:''' phosphorylation on (Thr-87 OR Thr-89) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
Line 73: Line 75:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' Membrane-proximal (Spotty) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU25470]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU23500]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 89: Line 91:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[hrcA]]-[[grpE]]-[[dnaK]]-[[dnaJ]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/1339421 PubMed]
+
* '''Operon:'''  
  
−
* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/1339421 PubMed]
+
* '''Sigma factor:'''  
  
−
* '''Regulation:''' induced by heat shock [http://www.ncbi.nlm.nih.gov/sites/entrez/1339421 PubMed]
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' repressed at normal temperature by [[HrcA]]
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 114: Line 116:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Wolfgang Schumann]], Bayreuth University, Germany [http://www.genetik.uni-bayreuth.de/LSGenetik1/schumann_research.htm Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 122: Line 122:
  
 
# 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]
 
# 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]
−
# Meile et al. (2006) Systematic localisation of proteins fused to the green fluorescent protein in ''Bacillus subtilis'': identification of new proteins at the DNA replication factory ''Proteomics'' '''6:''' 2135-2146. [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 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]
−
# Wetzstein, M., U. Völker, J. Dedio, S. Löbau, U. Zuber, M. Schiesswohl, C. Herget, M. Hecker, and W. Schumann. 1992. Cloning, sequencing, and molecular analysis of the ''dnaK'' locus from ''Bacillus subtilis''. J. Bacteriol. 174:3300-3310. [http://www.ncbi.nlm.nih.gov/sites/entrez/1339421 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 16:08, 31 March 2009

  • Description: write here

Gene name drm
Synonyms yqkN
Essential no
Product phosphopentomutase (EC 5.4.2.7)
Function conversion of ribose-1-P/deoxyribose-1-P to ribose-5-P/deoxyribose-5-P
MW, pI 43 kDa, 4.974
Gene length, protein length 1182 bp, 394 aa
Immediate neighbours punA, ripX
Gene sequence (+200bp) Protein sequence
Caution: The sequence for this gene in SubtiList contains errors
Genetic context
Drm 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: phosphorylation on (Thr-87 OR Thr-89) PubMed, PubMed
  • 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

  • Operon:
  • Sigma factor:
  • 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

  1. Eymann et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in Bacillus subtilis. Proteomics 7: 3509-3526. PubMed
  2. Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol. Cell. Proteomics 6: 697-707 PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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