Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
* '''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''' || '' ''
Line 10: Line 10:
 
|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>
 
|-
 
|-
Line 35: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
* '''Locus tag:''' BSU07100
+
* '''Locus tag:''' BSU23190
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 41:
 
=== 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 ===
Line 78: Line 78:
 
* '''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:'''
Line 88: Line 88:
 
=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 =
Line 118: Line 118:
 
=References=
 
=References=
  
<pubmed>7921237,10092453, </pubmed>
+
<pubmed>10498740,9864321,1548223,7642500,14731276,19542328 , </pubmed>

Revision as of 15:48, 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