Difference between revisions of "Sandbox"

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−
* '''Description:''' lipoprotein, putative ABC transporter (solute binding protein) <br/><br/>
+
* '''Description:''' penicillin-binding protein 5, D-alanyl-D-alanine carboxypeptidase <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'''
−
|''lplA''
+
|''dacB''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
+
|style="background:#ABCDEF;" align="center"| '''Product''' || penicillin-binding protein 5, D-alanyl-D-alanine carboxypeptidase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+
|style="background:#ABCDEF;" align="center"|'''Function''' || carboxypeptidase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 56 kDa, 5.607  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 42 kDa, 9.725  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1506 bp, 502 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1146 bp, 382 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yetA]]'', ''[[lplB]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[spmA]]'', ''[[ypuI]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12529&#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:CAB14251&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:lplA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:dacB_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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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU07100
+
* '''Locus tag:''' BSU23190
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dacB-spmAB.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10434]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10527]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala (according to Swiss-Prot)
  
−
* '''Protein family:'''
+
* '''Protein family:''' peptidase S11 family (according to Swiss-Prot)
  
−
* '''Paralogous protein(s):''' [[YtcQ]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P37966 P37966]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P35150 P35150]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU07100]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU23190]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[dacB]]-[[spmA]]-[[spmB]]''
  
−
* '''[[Sigma factor]]:'''  
+
* '''[[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:'''  
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
  
−
<pubmed>7921237,10092453, </pubmed>
+
<pubmed>10498740,9864321,1548223,7642500,14731276,19542328 , </pubmed>

Revision as of 16:48, 2 July 2009

  • Description: penicillin-binding protein 5, D-alanyl-D-alanine carboxypeptidase

Gene name dacB
Synonyms
Essential no
Product penicillin-binding protein 5, D-alanyl-D-alanine carboxypeptidase
Function carboxypeptidase
MW, pI 42 kDa, 9.725
Gene length, protein length 1146 bp, 382 aa
Immediate neighbours spmA, ypuI
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
DacB context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU23190

Phenotypes of a mutant

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala (according to Swiss-Prot)
  • Protein family: peptidase S11 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)

Database entries

  • Structure:
  • KEGG entry: [3]
  • 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

Ralf Moeller, Peter Setlow, Günther Reitz, Wayne L Nicholson
Roles of small, acid-soluble spore proteins and core water content in survival of Bacillus subtilis spores exposed to environmental solar UV radiation.
Appl Environ Microbiol: 2009, 75(16);5202-8
[PubMed:19542328] [WorldCat.org] [DOI] (I p)

Dirk-Jan Scheffers, Laura J F Jones, Jeffery Errington
Several distinct localization patterns for penicillin-binding proteins in Bacillus subtilis.
Mol Microbiol: 2004, 51(3);749-64
[PubMed:14731276] [WorldCat.org] [DOI] (P p)

D L Popham, J Meador-Parton, C E Costello, P Setlow
Spore peptidoglycan structure in a cwlD dacB double mutant of Bacillus subtilis.
J Bacteriol: 1999, 181(19);6205-9
[PubMed:10498740] [WorldCat.org] [DOI] (P p)

D L Popham, M E Gilmore, P Setlow
Roles of low-molecular-weight penicillin-binding proteins in Bacillus subtilis spore peptidoglycan synthesis and spore properties.
J Bacteriol: 1999, 181(1);126-32
[PubMed:9864321] [WorldCat.org] [DOI] (P p)

D L Popham, B Illades-Aguiar, P Setlow
The Bacillus subtilis dacB gene, encoding penicillin-binding protein 5*, is part of a three-gene operon required for proper spore cortex synthesis and spore core dehydration.
J Bacteriol: 1995, 177(16);4721-9
[PubMed:7642500] [WorldCat.org] [DOI] (P p)

C E Buchanan, M L Ling
Isolation and sequence analysis of dacB, which encodes a sporulation-specific penicillin-binding protein in Bacillus subtilis.
J Bacteriol: 1992, 174(6);1717-25
[PubMed:1548223] [WorldCat.org] [DOI] (P p)

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