Difference between revisions of "Sandbox"

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* '''Description:''' small regulatory RNA controlling [[AhrC]] expression<br/><br/>
+
* '''Description:''' surfactin synthetase / competence <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'''
−
|''sr1''
+
|''srfAC''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ykzW ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''comL ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || small regulatory RNA/ regulatory peptide
+
|style="background:#ABCDEF;" align="center"| '''Product''' || surfactin synthetase / competence
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || control of arginine metabolism
+
|style="background:#ABCDEF;" align="center"|'''Function''' || antibiotic synthesis
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 4.4 kDa, 3.89
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 143 kDa, 4.97 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 205 bp (RNA), 120 bp (ORF), 39 aa
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 3822 bp, 1274 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[slp]]'', ''[[speA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[comS]]'', ''[[srfAD]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/sr1_nucleotide.txt    Gene sequence        ]'''  
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12145&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
−
|style="background:#FAF8CC;" align="center"|
 
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:sr1_context.gif]]
+
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:srfAC_context.gif]]
 +
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
|-
 
|-
 
|}
 
|}
Line 29: Line 31:
 
__TOC__
 
__TOC__
  
−
<br/><br/><br/>
+
<br/><br/><br/><br/>
  
−
 
 
=The gene=
 
=The gene=
  
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:'''
+
* '''Locus tag:''' BSU03510
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 42: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/srfAA-srfAB-comS-srfAC-srfAD.html]
−
 
 
−
=== Additional information===
 
−
Located between the ''[[slp]]'' and ''[[speA]]'' genes.
 
−
 
 
−
 
 
−
=The RNA=
 
  
−
=== Basic information/ Evolution ===
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10170]
−
 
 
−
* '''Catalyzed reaction/ biological activity:''' hybridizes to ''[[ahrC]]'' mRNA and inhibits [[AhrC]] translation. [http://www.ncbi.nlm.nih.gov/sites/entrez/17020585 PubMed]
 
−
 
 
−
=== Extended information on the RNA===
 
−
 
 
−
* '''Kinetic information'''
 
−
 
 
−
* '''Interactions:''' Binds ''[[ahrC]]'' mRNA [http://www.ncbi.nlm.nih.gov/sites/entrez/17020585 PubMed]
 
−
 
 
−
* '''Localization'''
 
−
 
 
−
=== Database entries ===
 
−
 
 
−
* '''Structure''':
 
  
 
=== Additional information===
 
=== Additional information===
  
−
Information on the structure of the RNA can be found in [http://www.ncbi.nlm.nih.gov/pubmed/17020585?ordinalpos=8&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum Heidrich ''et al''., 2006 ]
 
  
−
=The peptide=
+
=The protein=
  
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
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* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' the peptide is conserved in bacilli
+
* '''Protein family:''' acyl carrier domain (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:'''
+
* '''Modification:''' phosphorylation on Ser-1003 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
Line 98: Line 78:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2VSQ 2VSQ]
  
−
* '''Swiss prot entry:'''
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/Q08787 Q08787]
  
−
* '''KEGG entry:'''
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU03510]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' sr1 [http://www.ncbi.nlm.nih.gov/sites/entrez/16164558 PubMed]
+
* '''Operon:'''  
  
−
* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16164558 PubMed]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' Repressed in the presence of glucose by [[CcpN]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16164558 PubMed]
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/16164558 PubMed]
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' 168 sr1::cat, available in [[Brantl]] lab
+
* '''Mutant:'''
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
−
+
       
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
 +
 +
* '''GFP fusion:'''
 +
 +
* '''two-hybrid system:'''
 +
 +
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Sabine Brantl |Sabine Brantl]], Bacterial Genetics, Friedrich-Schiller-University of Jena, Germany [http://www.uni-jena.de/AG_Bakteriengenetik_(_Doz__Dr__Sabine_Brantl_).html homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
<pubmed>16164558 17020585 17576690, </pubmed>
+
<pubmed>17218307, </pubmed>
−
# Licht et al. (2005) Implication of CcpN in the regulation of a novel untranslated RNA (SR1) in Bacillus subtilis. Mol. Microbiol. 58: 189-206. [http://www.ncbi.nlm.nih.gov/sites/entrez/16164558 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]
−
# Heidrich et al. (2006) The small untranslated RNA SR1 from the Bacillus subtilis genome is involved in the regulation of arginine catabolism. Mol. Microbiol. 62: 520-536. [http://www.ncbi.nlm.nih.gov/sites/entrez/17020585 PubMed]
+
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
−
# Heidrich et al. (2007) In vitro analysis of the interaction between the small RNA SR1 and its primary target ahrC mRNA. Nucl. Acids Res. 35: 4331-4346. [http://www.ncbi.nlm.nih.gov/sites/entrez/17576690 PubMed]
 

Revision as of 13:37, 8 June 2009

  • Description: surfactin synthetase / competence

Gene name srfAC
Synonyms comL
Essential no
Product surfactin synthetase / competence
Function antibiotic synthesis
MW, pI 143 kDa, 4.97
Gene length, protein length 3822 bp, 1274 aa
Immediate neighbours comS, srfAD
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
SrfAC context.gif
This image was kindly provided by SubtiList





The gene

Basic information

  • Locus tag: BSU03510

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: acyl carrier domain (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification: phosphorylation on Ser-1003 PubMed
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

  • KEGG entry: [3]
  • 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

Boris Macek, Ivan Mijakovic, Jesper V Olsen, Florian Gnad, Chanchal Kumar, Peter R Jensen, Matthias Mann
The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis.
Mol Cell Proteomics: 2007, 6(4);697-707
[PubMed:17218307] [WorldCat.org] [DOI] (P p)

  1. Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol. Cell. Proteomics 6: 697-707 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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