Difference between revisions of "Sandbox"

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* '''Description:''' penicillin-binding protein PBP 2A <br/><br/>
+
* '''Description:''' penicillin-binding protein 2B <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'''
|''pbpA''
+
|''pbpB''
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqgF ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
|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''' || penicillin-binding protein PBP 2A
+
|style="background:#ABCDEF;" align="center"| '''Product''' || penicillin-binding protein 2B
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || spore outgrowth
+
|style="background:#ABCDEF;" align="center"|'''Function''' || septation
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 79 kDa, 9.571  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 79 kDa, 9.234  
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2148 bp, 716 aa  
 
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2148 bp, 716 aa  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pstS]]'', ''[[yqgE]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ftsL]]'', ''[[spoVD]]''
 
|-
 
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/pbpA_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/pbpB_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/pbpA_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/pbpB_protein.txt Protein sequence]'''
 
|-
 
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:pbpA_context.gif]]
+
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors
 +
|-
 +
|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 39: Line 41:
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yllB-ylxA-ftsL-pbpB.html]
  
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11678]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10221]
  
 
=== Additional information===
 
=== Additional information===
Line 73: Line 77:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
* '''Localization:''' extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
+
* '''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]
  
 
=== Database entries ===
 
=== Database entries ===
Line 81: Line 85:
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU25000]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU15160]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 93: Line 97:
 
* '''Sigma factor:'''  
 
* '''Sigma factor:'''  
  
* '''Regulation:'''  
+
* '''Regulation:''' constitutively expressed [http://www.ncbi.nlm.nih.gov/sites/entrez/15758244 Link to a summary]
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  

Revision as of 16:28, 6 April 2009

  • Description: penicillin-binding protein 2B

Gene name pbpB
Synonyms
Essential yes PubMed
Product penicillin-binding protein 2B
Function septation
MW, pI 79 kDa, 9.234
Gene length, protein length 2148 bp, 716 aa
Immediate neighbours ftsL, spoVD
Gene sequence (+200bp) Protein sequence
Caution: The sequence for this gene in SubtiList contains errors
Genetic context
PbpB 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: extracellular (signal peptide) PubMed, localizes to the sporulation septum during sporulation Link to a summary

Database entries

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

Additional information

Expression and regulation

  • Operon:
  • Sigma factor:
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Jeff Errington lab
  • Antibody:

Labs working on this gene/protein

Jeff Errington, Newcastle University, UK homepage

Your additional remarks

References

  1. Voigt et al. (2009) Cell physiology and protein secretion of Bacillus licheniformis compared to Bacillus subtilis. J Mol Microbiol Biotechnol. 16: 53-68 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed