Difference between revisions of "Sandbox"

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* '''Description:''' IMP dehydrogenase <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'''
−
|''guaB''
+
|''dacA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''guaA ''
+
|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''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || IMP dehydrogenase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || penicillin-binding protein 5*, <br/>D-alanyl-D-alanine carboxypeptidase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of GMP
+
|style="background:#ABCDEF;" align="center"|'''Function''' || carboxypeptidase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52 kDa, 6.168  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 5.668  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1464 bp, 488 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1329 bp, 443 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaC]]'', ''[[dacA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[guaB]]'', ''[[pdxS]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11785&#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:CAB11786&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:guaB_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:dacA_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/>
  
 
=The gene=
 
=The gene=
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU00090
+
* '''Locus tag:''' BSU00100
  
 
===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/guaB.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10073]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10074]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' Inosine 5'-phosphate + NAD<sup>+</sup> + H<sub>2</sub>O = xanthosine 5'-phosphate + NADH (according to Swiss-Prot)  
+
* '''Catalyzed reaction/ biological activity:''' Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala (according to Swiss-Prot)  
  
−
* '''Protein family:''' IMPDH/GMPR family (according to Swiss-Prot)
+
* '''Protein family:''' peptidase S11 family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylated (STY) [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed], S-cysteinlyation after diamide stress (Cys-308) [http://www.ncbi.nlm.nih.gov/pubmed/17611193 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
+
* '''Modification:'''
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:'''
+
* '''Localization:''' secreted (according to Swiss-Prot),  membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
Line 80: Line 78:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P21879 P21879]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P08750 P08750]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00090]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00100]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.205 1.1.1.205]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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* '''Regulation:'''  
 
* '''Regulation:'''  
−
** activated during growth in the presence of branched chain amino acids ([[CodY]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]
 
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
−
** [[CodY]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]
 
  
−
* '''Additional information:''' the mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
  
−
<pubmed>17611193,12884008,1722815,,12618455,17726680 17726680 17611193, </pubmed>
+
<pubmed>,9864321,18763711, </pubmed>
−
 
+
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics '''8:''' 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
−
[http://www.ncbi.nlm.nih.gov/pubmed/PMID PubMed]
 

Revision as of 12:51, 14 June 2009

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

Gene name dacA
Synonyms
Essential no
Product penicillin-binding protein 5*,
D-alanyl-D-alanine carboxypeptidase
Function carboxypeptidase
MW, pI 48 kDa, 5.668
Gene length, protein length 1329 bp, 443 aa
Immediate neighbours guaB, pdxS
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
DacA context.gif
This image was kindly provided by SubtiList




The gene

Basic information

  • Locus tag: BSU00100

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

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: secreted (according to Swiss-Prot), membrane associated PubMed

Database entries

  • Structure:
  • KEGG entry: [2]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • 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

Hannes Hahne, Susanne Wolff, Michael Hecker, Dörte Becher
From complementarity to comprehensiveness--targeting the membrane proteome of growing Bacillus subtilis by divergent approaches.
Proteomics: 2008, 8(19);4123-36
[PubMed:18763711] [WorldCat.org] [DOI] (I 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)

  1. Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing Bacillus subtilis by divergent approaches. Proteomics 8: 4123-4136 PubMed
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