Difference between revisions of "Sandbox"

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* '''Description:''' penicillin-binding protein I, D-alanyl-D-alanine carboxypeptidase <br/><br/>
+
* '''Description:''' RNA polymerase forespore-specific (early) sigma factor SigF <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'''
−
|''dacF''
+
|''sigF''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''spoIIAC ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || penicillin-binding protein I, <br/>D-alanyl-D-alanine carboxypeptidase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || RNA polymerase forespore-specific (early) sigma factor SigF
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || carboxypeptidase
+
|style="background:#ABCDEF;" align="center"|'''Function''' || transcription of sporulation genes (late mother cell)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 43 kDa, 9.912  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 5.078  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1167 bp, 389 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 765 bp, 255 aa  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[spoIIAA]]'', ''[[punA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[spoVAA]]'', ''[[spoIIAB]]''
 
|-
 
|-
−
|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/sigF_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/dacF_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/sigF_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:dacF_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:sigF_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+BG10295]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10298]
  
 
=== Additional information===
 
=== Additional information===
Line 58: Line 58:
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
 +
 +
=== Genes controlled by SigF ===
 +
 +
''[[dacF]]-[[spoIIAA]]-[[spoIIAB]]-[[sigF]]'', ''[[sigG]]'','' [[pbpF]]'', ''[[yphA]]-[[seaA]]''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU23480]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU23450]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 90: Line 94:
  
 
* '''Operon:''' ''[[dacF]]-[[spoIIAA]]-[[spoIIAB]]-[[sigF]]''
 
* '''Operon:''' ''[[dacF]]-[[spoIIAA]]-[[spoIIAB]]-[[sigF]]''
 +
''[[spoIIAA]]-[[spoIIAB]]-[[sigF]]''
  
−
* '''Sigma factor:''' [[SigF]], [[SigG]]
+
* '''Sigma factor:''' ''[[dacF]]'': [[SigF]], [[SigG]]
 +
''[[spoIIA]]'': [[SigH]]
  
−
* '''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]
+
* '''Regulation:''' repressed by Casamino Acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed] ,  ''[[dacF]]'': expressed during sporulation, ''[[spoIIAA]]'': expressed early during sporulation
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' ''[[spoIIAA]]'': activated by [[Spo0A]] and repressed by [[SinR]]
  
 
* '''Additional information:'''
 
* '''Additional information:'''

Revision as of 11:11, 31 March 2009

  • Description: RNA polymerase forespore-specific (early) sigma factor SigF

Gene name sigF
Synonyms spoIIAC
Essential no
Product RNA polymerase forespore-specific (early) sigma factor SigF
Function transcription of sporulation genes (late mother cell)
MW, pI 29 kDa, 5.078
Gene length, protein length 765 bp, 255 aa
Immediate neighbours spoVAA, spoIIAB
Gene sequence (+200bp) Protein sequence
Genetic context
SigF 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:
  • Paralogous protein(s):

Genes controlled by SigF

dacF-spoIIAA-spoIIAB-sigF, sigG, pbpF, yphA-seaA

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

spoIIAA-spoIIAB-sigF

spoIIA: SigH

  • Regulation: repressed by Casamino Acids PubMed , dacF: expressed during sporulation, spoIIAA: expressed early during sporulation
  • 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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