Difference between revisions of "Sandbox"

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−
* '''Description:''' cytochrome bd2, menaquinol oxidase (7:1 protons) <br/><br/>
+
* '''Description:''' subtilosin A <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'''
−
|''ythB''
+
|''sboA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''sbo ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || cytochrome bd2, menaquinol oxidase (7:1 protons)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || subtilosin A
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || respiration
+
|style="background:#ABCDEF;" align="center"|'''Function''' || antimicrobial peptide
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 38 kDa, 9.18  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 4 kDa, 4.569  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1038 bp, 346 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 129 bp, 43 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ythA]]'', ''[[ythC]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywiB]]'', ''[[sboX]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15050&#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:CAB15763&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ythB_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:sboA_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:''' BSU30720
+
* '''Locus tag:''' BSU37350
  
 
===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/sboAX-albABCDEFG.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13858]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12671]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 54:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:'''
+
* '''Protein family:''' bacteriocin class V family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 72: Line 72:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:'''
+
* '''Localization:''' secreted (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1PXQ 1PXQ]
  
−
* '''Swiss prot entry:'''
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O07623 O07623]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU30720]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU37350]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 88: Line 88:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[sboA]]-[[sboX]]-[[albA]]-[[albB]]-[[albC]]-[[albD]]-[[albE]]-[[albF]]-[[albG]]''
  
−
* '''[[Sigma factor]]:'''  
+
* '''[[Sigma factor]]:''' [[SigA]]
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
 +
** repressed by [[Rok]] [http://www.ncbi.nlm.nih.gov/sites/entrez/15743949 PubMed]
 +
** expressed under anaerobic conditions ([[ResD]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10809710 PubMed]
 +
** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10572140,17720793 PubMed]
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
 +
** [[Rok]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/15743949 PubMed]
 +
** [[ResD]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/10809710 PubMed]
 +
** [[AbrB]]:  transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/10572140,17720793 PubMed]
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 118: Line 124:
 
=References=
 
=References=
  
 +
<pubmed>15743949,10809710,10572140,17720793, </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 20:38, 12 June 2009

  • Description: subtilosin A

Gene name sboA
Synonyms sbo
Essential no
Product subtilosin A
Function antimicrobial peptide
MW, pI 4 kDa, 4.569
Gene length, protein length 129 bp, 43 aa
Immediate neighbours ywiB, sboX
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
SboA context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU37350

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: bacteriocin class V 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)

Database entries

  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • 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

Mark A Strauch, Benjamin G Bobay, John Cavanagh, Fude Yao, Angelo Wilson, Yoann Le Breton
Abh and AbrB control of Bacillus subtilis antimicrobial gene expression.
J Bacteriol: 2007, 189(21);7720-32
[PubMed:17720793] [WorldCat.org] [DOI] (P p)

Mark Albano, Wiep Klaas Smits, Linh T Y Ho, Barbara Kraigher, Ines Mandic-Mulec, Oscar P Kuipers, David Dubnau
The Rok protein of Bacillus subtilis represses genes for cell surface and extracellular functions.
J Bacteriol: 2005, 187(6);2010-9
[PubMed:15743949] [WorldCat.org] [DOI] (P p)

M M Nakano, G Zheng, P Zuber
Dual control of sbo-alb operon expression by the Spo0 and ResDE systems of signal transduction under anaerobic conditions in Bacillus subtilis.
J Bacteriol: 2000, 182(11);3274-7
[PubMed:10809710] [WorldCat.org] [DOI] (P p)

G Zheng, L Z Yan, J C Vederas, P Zuber
Genes of the sbo-alb locus of Bacillus subtilis are required for production of the antilisterial bacteriocin subtilosin.
J Bacteriol: 1999, 181(23);7346-55
[PubMed:10572140] [WorldCat.org] [DOI] (P p)

  1. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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