Difference between revisions of "Sandbox"

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|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''gcaD''
+
|''dacB''
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''tms, tms26 ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || UDP-N-acetylglucosamine pyrophosphorylase (EC 2.7.7.23)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || D-alanyl-D-alanine carboxypeptidase (penicillin-binding  5*) (EC 3.4.16.4)
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Function''' ||  
+
|style="background:#ABCDEF;" align="center"|'''Function''' || required for spore cortex synthesis
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 49 kDa, 5.65  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 42 kDa, 9.725  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Gene length,  length''' || 1368 bp, 456 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length,  length''' || 1146 bp, 382 aa  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[spoVG]]'', ''[[prs]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[spmA]]'', ''[[ypuI]]''
 
|-
 
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/gcaD_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/dacB_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/gcaD_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/dacB_protein.txt Protein sequence]'''
 
|-
 
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:gcaD_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:dacB_context.gif]]
 
|-
 
|-
 
|}
 
|}
Line 38: Line 38:
  
 
===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/gcaD-prs-ctc.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dacB-spmAB.html]
  
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10113]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10527]
  
 
=== Additional information===
 
=== Additional information===
Line 90: Line 88:
 
=Expression and regulation=
 
=Expression and regulation=
  
* '''Operon:''' ''[[gcaD]]-[[prs]]-[[ctc]]''
+
* '''Operon:''' ''[[dacB]]-[[spmA]]-[[spmB]]''
  
* '''Sigma factor:''' [[SigA]]
+
* '''Sigma factor:''' [[SigE]] [http://www.ncbi.nlm.nih.gov/sites/entrez/15758244 Link to a summary]
  
* '''Regulation:'''  
+
* '''Regulation:''' expressed during sporulation in the mother cell [http://www.ncbi.nlm.nih.gov/sites/entrez/15758244 Link to a summary]
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  

Revision as of 13:07, 17 March 2009

  • Description: write here

Gene name dacB
Synonyms
Essential no
Product D-alanyl-D-alanine carboxypeptidase (penicillin-binding 5*) (EC 3.4.16.4)
Function required for spore cortex synthesis
MW, pI 42 kDa, 9.725
Gene length, length 1146 bp, 382 aa
Immediate neighbours spmA, ypuI
Gene sequence (+200bp) Protein sequence
Genetic context
DacB context.gif



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

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

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry:
  • E.C. number:

Additional information

Expression and 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