Difference between revisions of "Sandbox"

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* '''Description:''' cell-division protein (septum formation), controls together with EzrA dynamics of the FtsZ ring <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'''
|''ftsL''
+
|''pbpB''
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ylxB, yllD ''
+
|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''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || cell-division protein
+
|style="background:#ABCDEF;" align="center"| '''Product''' || penicillin-binding protein 2B
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || septum formation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || septation
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 12 kDa, 10.083  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 79 kDa, 9.234  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 351 bp, 117 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2148 bp, 716 aa  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[mraW]]'', ''[[pbpB]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ftsL]]'', ''[[spoVD]]''
 
|-
 
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13388&#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:CAB13389&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:ftsL_context.gif]]
+
|-
 +
|-
 +
|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>
 
|-
 
|-
Line 29: Line 31:
 
__TOC__
 
__TOC__
  
<br/><br/>
+
<br/><br/><br/><br/>
  
 
=The gene=
 
=The gene=
Line 45: Line 47:
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yllB-ylxA-ftsL-pbpB.html]
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yllB-ylxA-ftsL-pbpB.html]
  
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10220]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10221]
  
 
=== Additional information===
 
=== Additional information===
Line 56: Line 58:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
* '''Protein family:''' ftsL family (according to Swiss-Prot) ftsL family (according to Swiss-Prot)
+
* '''Protein family:''' transpeptidase family (according to Swiss-Prot) transpeptidase family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 72: Line 74:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
* '''Interactions:''' [[RasP]]-[[FtsL]],  [[DivIC]]-[[FtsL]]
+
* '''Interactions:'''
  
* '''Localization:''' cell membrane (according to Swiss-Prot)
+
* '''Localization:''' cell membrane (according to Swiss-Prot),  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 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
Line 80: Line 82:
 
* '''Structure:'''
 
* '''Structure:'''
  
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/Q07867 Q07867]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/Q07868 Q07868]
  
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU15150 BSU15150]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU15160 BSU15160]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 94: Line 96:
 
* '''[[Sigma factor]]:'''  
 
* '''[[Sigma factor]]:'''  
  
* '''Regulation:'''  
+
* '''Regulation:''' constitutively expressed [http://www.ncbi.nlm.nih.gov/sites/entrez/15758244 PubMed]
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
Line 110: Line 112:
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
  
* '''two-hybrid system:'''  
+
* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jeff Errington]] lab
  
 
* '''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=
Line 120: Line 124:
 
=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 23:28, 19 May 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
Get the DNA and protein sequences
(Barbe et al., 2009)
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: transpeptidase family (according to Swiss-Prot) transpeptidase family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: cell membrane (according to Swiss-Prot), extracellular (signal peptide) PubMed, localizes to the sporulation septum during sporulation PubMed

Database entries

  • Structure:
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Regulation: constitutively expressed PubMed
  • 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