Difference between revisions of "Sandbox"

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* '''Description:''' penicillin-binding protein 2B <br/><br/>
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* '''Description:''' mother-cell specific penicillin-binding protein (spore cortex) <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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|''pbpB''
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|''spoVD''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || penicillin-binding protein 2B
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|style="background:#ABCDEF;" align="center"| '''Product''' || penicillin-binding protein (spore cortex)
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Function''' || septation
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|style="background:#ABCDEF;" align="center"|'''Function''' || spore morphogenesis
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 79 kDa, 9.234  
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 71 kDa, 8.85  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2148 bp, 716 aa  
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1935 bp, 645 aa  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ftsL]]'', ''[[spoVD]]''
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pbpB]]'', ''[[murE]]''
 
|-
 
|-
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/pbpB_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/spoVD_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/pbpB_protein.txt Protein sequence]'''
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/spoVD_protein.txt Protein sequence]'''
 
|-
 
|-
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|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:spoVD_context.gif]]
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|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:pbpB_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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__TOC__
 
__TOC__
  
−
<br/><br/><br/><br/>
+
<br/><br/>
  
 
=The gene=
 
=The gene=
Line 41: Line 39:
  
 
===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/yllB-ylxA-ftsL-pbpB.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/spoVD.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10221]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10222]
  
 
=== Additional information===
 
=== Additional information===
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* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' transpeptidase family
+
* '''Protein family:''' PASTA domain
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Interactions:'''
 
* '''Interactions:'''
  
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* '''Localization:''' extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed],  localizes to the sporulation septum during sporulation [http://www.ncbi.nlm.nih.gov/sites/entrez/15758244 Link to a summary]
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
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* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU15160]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU15170]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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* '''Operon:'''  
 
* '''Operon:'''  
  
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* '''[[Sigma factor]]:'''  
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* '''[[Sigma factor]]:''' [[SigE]] [http://www.ncbi.nlm.nih.gov/sites/entrez/15758244 Link to a summary]
  
−
* '''Regulation:''' constitutively expressed [http://www.ncbi.nlm.nih.gov/sites/entrez/15758244 Link to a summary]
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* '''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:'''  
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* '''GFP fusion:'''
 
* '''GFP fusion:'''
  
−
* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jeff Errington]] lab
+
* '''two-hybrid system:'''  
  
 
* '''Antibody:'''
 
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Jeff Errington]], Newcastle University, UK [http://www.ncl.ac.uk/camb/staff/profile/jeff.errington homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
# Voigt et al. (2009) Cell physiology and protein secretion of ''Bacillus licheniformis'' compared to ''Bacillus subtilis''. ''J Mol Microbiol Biotechnol.'' '''16:''' 53-68 [http://www.ncbi.nlm.nih.gov/pubmed/18957862 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 04:32, 12 April 2009

  • Description: mother-cell specific penicillin-binding protein (spore cortex)

Gene name spoVD
Synonyms
Essential no
Product penicillin-binding protein (spore cortex)
Function spore morphogenesis
MW, pI 71 kDa, 8.85
Gene length, protein length 1935 bp, 645 aa
Immediate neighbours pbpB, murE
Gene sequence (+200bp) Protein sequence
Genetic context
SpoVD 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: PASTA domain
  • 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: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • 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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