Difference between revisions of "Sandbox"

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* '''Description:''' anti-anti-SigF <br/><br/>
+
* '''Description:''' penicillin-binding protein I, 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'''
−
|''spoIIAA''
+
|''dacF''
 
|-
 
|-
 
|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''' || anti-anti-SigF
+
|style="background:#ABCDEF;" align="center"| '''Product''' || penicillin-binding protein I, <br/>D-alanyl-D-alanine carboxypeptidase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || control of SigF activity
+
|style="background:#ABCDEF;" align="center"|'''Function''' || carboxypeptidase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 12 kDa, 5.855  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 43 kDa, 9.912  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 351 bp, 117 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1167 bp, 389 aa  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[spoIIAB]]'', ''[[dacF]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[spoIIAA]]'', ''[[punA]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/spoIIAA_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/dacF_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/spoIIAA_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/dacF_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:spoIIAA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:dacF_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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* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dacF-spoIIAAB-sigF.html]
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dacF-spoIIAAB-sigF.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10296]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10295]
  
 
=== Additional information===
 
=== Additional information===
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* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' STAS domain
+
* '''Protein family:''' peptidase S11 family
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylation on (Ser-58 OR Ser-59) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
+
* '''Modification:'''
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU23470]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU23480]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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* '''Operon:''' ''[[dacF]]-[[spoIIAA]]-[[spoIIAB]]-[[sigF]]''
 
* '''Operon:''' ''[[dacF]]-[[spoIIAA]]-[[spoIIAB]]-[[sigF]]''
−
''[[spoIIAA]]-[[spoIIAB]]-[[sigF]]''
 
  
−
* '''[[Sigma factor]]:''' ''[[dacF]]'': [[SigF]], [[SigG]]
+
* '''[[Sigma factor]]:''' [[SigF]], [[SigG]]
−
''[[spoIIA]]'': [[SigH]]
 
  
−
* '''Regulation:''' repressed by glucose (5.2-fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed],  ''[[dacF]]'': expressed during sporulation, ''[[spoIIAA]]'': expressed early during sporulation
+
* '''Regulation:''' repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed] ,  expressed during sporulation in the prespore [http://www.ncbi.nlm.nih.gov/sites/entrez/15758244 Link to a summary]
  
−
* '''Regulatory mechanism:''' ''[[spoIIAA]]'': activated by [[Spo0A]] and repressed by [[SinR]]
+
* '''Regulatory mechanism:'''  
  
 
* '''Additional information:'''
 
* '''Additional information:'''
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=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Tony Wilkinson]], York University, U.K. [http://www.york.ac.uk/depts/chem/staff/ajw.html homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
+
# M&#228;der et al. (2002) Transcriptome and Proteome Analysis of ''Bacillus subtilis'' Gene Expression Modulated by Amino Acid Availability. ''J. Bacteriol'' '''184:''' 1844288-4295 [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]
−
# L&#233;vine et al. (2006) Analysis of the dynamic ''Bacillus subtilis'' Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. ''Proteomics'' '''6:''' 2157-2173 [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
 
−
# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model  bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707  [http://www.ncbi.nlm.nih.gov/pubmed/17218307 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 05:24, 12 April 2009

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

Gene name dacF
Synonyms
Essential no
Product penicillin-binding protein I,
D-alanyl-D-alanine carboxypeptidase
Function carboxypeptidase
MW, pI 43 kDa, 9.912
Gene length, protein length 1167 bp, 389 aa
Immediate neighbours spoIIAA, punA
Gene sequence (+200bp) Protein sequence
Genetic context
DacF context.gif
This image was kindly provided by SubtiList




The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family: peptidase S11 family
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

  • Structure:
  • Swiss prot entry:
  • 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

  1. Mäder et al. (2002) Transcriptome and Proteome Analysis of Bacillus subtilis Gene Expression Modulated by Amino Acid Availability. J. Bacteriol 184: 1844288-4295 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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