Difference between revisions of "Sandbox"

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* '''Description:''' required for activity of PurR <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'''
−
|''yabJ''
+
|''gcaD''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''tms, tms26 ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
+
|style="background:#ABCDEF;" align="center"| '''Product''' || UDP-N-acetylglucosamine pyrophosphorylase (EC 2.7.7.23)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of purine biosynthesis
+
|style="background:#ABCDEF;" align="center"|'''Function''' ||  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 13 kDa, 5.134  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 49 kDa, 5.65  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 375 bp, 125 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1368 bp, 456 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[purR]]'', ''[[spoVG]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[spoVG]]'', ''[[prs]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11824&#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:CAB11826&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yabJ_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:gcaD_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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===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/purR-yabJ.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gcaD-prs-ctc.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10111]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10113]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 56:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' YjgF family
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 70: Line 72:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' forms a trimer [http://www.ncbi.nlm.nih.gov/sites/entrez/10557275 PubMed]
+
* '''Interactions:'''
  
 
* '''Localization:''' Cytoplasm
 
* '''Localization:''' Cytoplasm
Line 76: Line 78:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' 1QD9 [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=11484 NCBI] [http://www.ncbi.nlm.nih.gov/sites/entrez/10557275 PubMed]
+
* '''Structure:'''
  
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00480]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00500]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 88: Line 90:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[purR]]-[[yabJ]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/7638212 PubMed]
+
* '''Operon:''' ''[[gcaD]]-[[prs]]-[[ctc]]''
  
−
* '''[[Sigma factor]]:'''  
+
* '''[[Sigma factor]]:''' [[SigA]]
  
−
* '''Regulation:''' negative autoregulation [http://www.ncbi.nlm.nih.gov/sites/entrez/7638212 PubMed]
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' repression by [[PurR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/7638212 PubMed]
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 118: Line 120:
 
=References=
 
=References=
  
−
# Weng et al. (1995) Identification of the ''Bacillus subtilis pur'' operon repressor. ''Proc. Natl. Acad. Sci. USA'' '''92:''' 7455-7459. [http://www.ncbi.nlm.nih.gov/sites/entrez/7638212 PubMed]
 
−
# Sinha et al. (1999) Crystal structure of Bacillus subtilis YabJ, a purine regulatory protein and member of the highly conserved YjgF family.''Proc. Natl. Acad. Sci. USA'' '''96:''' 13074-13079. [http://www.ncbi.nlm.nih.gov/sites/entrez/10557275 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 01:11, 30 April 2009

  • Description: write here

Gene name gcaD
Synonyms tms, tms26
Essential yes PubMed
Product UDP-N-acetylglucosamine pyrophosphorylase (EC 2.7.7.23)
Function
MW, pI 49 kDa, 5.65
Gene length, protein length 1368 bp, 456 aa
Immediate neighbours spoVG, prs
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
GcaD context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

essential PubMed

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

Database entries

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

Additional information

Expression and regulation

  • 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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