Difference between revisions of "Sandbox"

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Line 1: Line 1:
−
* '''Description:''' glucose 6-phosphate isomerase, glycolytic/ gluconeogenic enzyme<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'''
−
|''pgi''
+
|''yugO''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yugL ''
+
|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''' || glucose-6-phosphate isomerase
+
|style="background:#ABCDEF;" align="center"| '''Product''' ||  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis/ gluconeogenesis
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50.4 kDa, 4.85
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 49 kDa, 5.29 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1353 bp, 451 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1314 bp, 438 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yugM]]'', ''[[yugK]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yugP]]'', ''[[yugN]]''
 
|-
 
|-
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
Line 24: Line 24:
 
|-
 
|-
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:pgi_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yugO_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 37: Line 37:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:''' 3219772 - 3221124
+
* '''Coordinates:'''
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 43: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pgi-yugMN.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12366]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12369]
  
 
=== Additional information===
 
=== Additional information===
 +
  
 
=The protein=
 
=The protein=
Line 53: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' D-glucose 6-phosphate = D-fructose 6-phosphate
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' GPI family
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 65: Line 66:
 
* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylation on Thr-39 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
+
* '''Modification:'''
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
  
−
* '''Effectors of protein activity:''' inhibited by 6-phosphogluconate (in ''B.caldotenax, B.stearothermophilus'') [http://www.ncbi.nlm.nih.gov/pubmed/7400125 PubMed]
+
* '''Effectors of protein activity:'''
  
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' cytoplasm
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' ''Geobacillus stearothermophilus'' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=54052 NCBI], ''Geobacillus stearothermophilus'' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=11544 NCBI]
+
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P80860]
+
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU31350]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU31320]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/5.3.1.9 5.3.1.9]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
  
 +
=Expression and regulation=
  
−
=Expression and regulation=
+
* '''Operon:'''
  
−
* '''Operon:''' ''pgi'' [http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 PubMed]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Sigma factor:'''  
+
* '''Regulation:'''  
  
−
* '''Regulation:''' constitutively expressed [http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 PubMed]
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP508 (spc), available in [[Stülke]] lab
+
* '''Mutant:'''
  
−
* '''Expression vector:''' pGP762 (N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab
+
* '''Expression vector:'''
−
+
       
−
* '''lacZ fusion:''' pGP510 (in [[pAC6]]), available in [[Stülke]] lab
+
* '''lacZ fusion:'''
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
  
−
* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
+
* '''two-hybrid system:'''  
  
 
* '''Antibody:'''
 
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Stülke|Jörg Stülke]], University of Göttingen, Germany [http://wwwuser.gwdg.de/~genmibio/stuelke.html homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 120: Line 120:
 
=References=
 
=References=
  
−
# 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]
+
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
−
# Lee et al. (2008) Crystallization and preliminary crystallographic study of the phosphoglucose isomerase from Bacillus subtilis. Acta Cryst. Sect. F 64:1181-1183. [http://www.ncbi.nlm.nih.gov/sites/entrez/19052382 PubMed]
 
−
# Lin and Prasad (1975) Selection of a mutant of Bacillus subtilis deficient in glucose-6-phosphate dehydrogenase and phosphoglucoisomerase. J. Gen. Microbiol. 83:419-421. [http://www.ncbi.nlm.nih.gov/sites/entrez/4214896 PubMed]
 
−
# Ludwig, H., Homuth, G., Schmalisch, M., Dyka, F. M., Hecker, M., and Stülke, J. (2001) Transcription of glycolytic genes and operons in ''Bacillus subtilis'': evidence for the presence of multiple levels of control of the ''gapA'' operon. Mol Microbiol 41, 409-422.[http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 PubMed]
 
−
# Prasad and Freese (1974) Cell lysis of Bacillus subtilis caused by intracellular accumulation of glucose-1-phosphate. J. Bacteriol. 118:1111-1122. [http://www.ncbi.nlm.nih.gov/sites/entrez/4275311 PubMed]
 
−
# Stülke, J., Martin-Verstraete, I., Glaser, P. & Rapoport, G. (2001) Characterization of glucose repression resistant mutants of Bacillus subtilis: identification of the glcR gene. Arch. Microbiol. 175: 441-449. [http://www.ncbi.nlm.nih.gov/sites/entrez/11491085 PubMed]
 
−
# Macek et al. (2007) The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis. ''Mol Cell Proteomics'' '''6(4):''' 697-707. [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
 

Revision as of 15:02, 15 April 2009

  • Description: write here

Gene name yugO
Synonyms
Essential no
Product
Function unknown
MW, pI 49 kDa, 5.29
Gene length, protein length 1314 bp, 438 aa
Immediate neighbours yugP, yugN
Hier soll was neues rein
Genetic context
YugO context.gif
This image was kindly provided by SubtiList





The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

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):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [2]
  • E.C. number:

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

  1. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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