Difference between revisions of "Sandbox"

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* '''Description:''' write here <br/><br/>
+
* '''Description:''' gamma-DL-glutamyl hydrolase <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'''
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|''dltE''
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|''pgdS''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ipa-1r ''
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ywtD''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' ||  
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|style="background:#ABCDEF;" align="center"| '''Product''' || gamma-DL-glutamyl hydrolase
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Function''' || involved in lipoteichoic acid biosynthesis
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|style="background:#ABCDEF;" align="center"|'''Function''' || polyglutamic acid degradation
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 5.095  
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 45 kDa, 8.52  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 756 bp, 252 aa  
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1239 bp, 413 aa  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dltD]]'', ''[[ywaA]]''
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywtE]]'', ''[[capE]]''
 
|-
 
|-
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/dltE_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ywtD_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/dltE_protein.txt Protein sequence]'''
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ywtD_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors
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|colspan="2" | '''Genetic context''' <br/> [[Image:ywtD_context.gif]]
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|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:dltE_context.gif]]
 
 
|-
 
|-
 
|}
 
|}
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=== Database entries ===
 
=== Database entries ===
  
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* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dltABCDE.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ywtD.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10547]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12535]
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
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* '''Operon:''' ''[[dltA]]-[[dltB]]-[[dltC]]-[[dltD]]-[[dltE]]''
+
* '''Operon:'''  
  
−
* '''Sigma factor:''' [[SigD]], [[SigX]]
+
* '''Sigma factor:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' activated by [[YvrHb]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/16306698 PubMed]
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
  
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# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
# Suzuki & Tahara (2003) Characterization of the ''Bacillus subtilis ywtD'' gene, whose product is involved in gamma-polyglutamic acid degradation. ''J. Bacteriol.'' '''185:''' 2379-2382. [http://www.ncbi.nlm.nih.gov/sites/entrez/12644511 PubMed]

Revision as of 16:46, 9 March 2009

  • Description: gamma-DL-glutamyl hydrolase

Gene name pgdS
Synonyms ywtD
Essential no
Product gamma-DL-glutamyl hydrolase
Function polyglutamic acid degradation
MW, pI 45 kDa, 8.52
Gene length, protein length 1239 bp, 413 aa
Immediate neighbours ywtE, capE
Gene sequence (+200bp) Protein sequence
Genetic context
YwtD 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 protein

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

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry:
  • 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. Suzuki & Tahara (2003) Characterization of the Bacillus subtilis ywtD gene, whose product is involved in gamma-polyglutamic acid degradation. J. Bacteriol. 185: 2379-2382. PubMed
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