Difference between revisions of "Sandbox"

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* '''Description:''' regulation of a large regulon in response to branched-chain amino acid limitation <br/><br/>
+
* '''Description:''' flagellar-specific ATP synthase <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'''
−
|''codY''
+
|''fliI''
 
|-
 
|-
 
|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''' || transcriptional pleiotropic repressor
+
|style="background:#ABCDEF;" align="center"| '''Product''' || flagellar-specific ATP synthase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of a large regulon in response to branched-chain amino acid limitation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || movement and chemotaxis
−
 
+
|-
−
to the presence of branched-chain amino acids
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 47 kDa, 5.598 
 +
|-
 +
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1320 bp, 440 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 4.75 
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[fliH]]'', ''[[fliJ]]''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 777 bp, 259 aa
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13497&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[clpY]]'', ''[[flgB]]''
 
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13490&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:codY_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:fliI_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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===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
No swarming motility on B medium. [http://www.ncbi.nlm.nih.gov/sites/entrez/19202088 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/codV-clpQY-codY.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/fla-che.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10968]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10243]
  
 
=== Additional information===
 
=== Additional information===
Line 61: Line 59:
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
−
 
−
=== Genes/ operons controlled by CodY ===
 
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylation on Ser-215 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
+
* '''Modification:'''
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
Line 86: Line 82:
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU16170]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU16240]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 119: Line 115:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]
 
−
 
−
[[Tony Wilkinson]], York University, U.K. [http://www.york.ac.uk/depts/chem/staff/ajw.html homepage]
 
−
 
−
[[Oscar Kuipers]], University of Groningen, The Netherlands
 
−
[http://molgen.biol.rug.nl/molgen/index.php Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 131: Line 120:
 
=References=
 
=References=
  
−
# 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]
 
−
# Kim, H. J., S. I. Kim, M. Ratnayake-Lecamwasam, K. Tachikawa, A. L. Sonenshein, and M. Strauch. (2003) Complex regulation of the Bacillus subtilis aconitase gene. J. Bacteriol. 185:1672-1680. [http://www.ncbi.nlm.nih.gov/sites/entrez/12591885 PubMed]
 
−
# Hamze et al. (2009) Identification of genes required for different stages of dendritic swarming in ''Bacillus subtilis'', with a novel role for ''phrC''.  ''Microbiology'' '''155:''' 398-412. [http://www.ncbi.nlm.nih.gov/sites/entrez/19202088 PubMed]
 
−
# Molle V, Nakura Y, Shivers RP, Yamaguchi H, Losick R, Fujita Y, Sonenshein AL: Additional targets of the Bacillus subtilis global regulator CodY identified by chromatin immunoprecipitation and genome-wide transcript analysis. J Bacteriol 2003, 185:1911-1922. [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]
 
−
# Sonenshein AL: CodY, a global regulator of stationary phase and virulence in Gram-positive bacteria. Curr Opin Microbiol 2005, 8:203-207. [http://www.ncbi.nlm.nih.gov/sites/entrez/15802253 PubMed]
 
−
# Ratnayake-Lecamwasam M, Serror P, Wong KW, Sonenshein AL: Bacillus subtilis CodY represses early-stationary-phase genes by sensing GTP levels. Genes Dev 2001, 15:1093-1103.[http://www.ncbi.nlm.nih.gov/sites/entrez/11331605 PubMed]
 
−
# Shivers RP, Sonenshein AL: Activation of the Bacillus subtilis global regulator CodY by direct interaction with branched-chain amino acids. Mol Microbiol 2004, 53:599-611. [http://www.ncbi.nlm.nih.gov/sites/entrez/15228537 PubMed]
 
−
# Serror P, Sonenshein AL: Interaction of CodY, the novel Bacillus subtilis DNA-binding protein, with the dpp promoter region. Mol Microbiol 1996, 20:843-852. [http://www.ncbi.nlm.nih.gov/sites/entrez/8793880 PubMed]
 
−
# Joseph P, Ratnayake-Lecamwasam M, Sonenshein AL: A region of Bacillus subtilis CodY protein required for interaction with DNA. J Bacteriol 2005, 187:4127-4139. [http://www.ncbi.nlm.nih.gov/sites/entrez/15937175 PubMed]
 
−
# Shivers RP, Sonenshein AL: Bacillus subtilis ilvB operon: an intersection of global regulons. Mol Microbiol 2005, 56:1549-1559. [http://www.ncbi.nlm.nih.gov/sites/entrez/15916605 PubMed]
 
−
# Tojo S, Satomura T, Morisaki K, Deutscher J, Hirooka K, Fujita Y: Elaborate transcription regulation of the Bacillus subtilis ilv-leu operon involved in the biosynthesis of branched-chain amino acids through global regulators of CcpA, CodY and TnrA. Mol Microbiol 2005, 56:1560-1573. [http://www.ncbi.nlm.nih.gov/sites/entrez/15916606 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 02:17, 30 April 2009

  • Description: flagellar-specific ATP synthase

Gene name fliI
Synonyms
Essential no
Product flagellar-specific ATP synthase
Function movement and chemotaxis
MW, pI 47 kDa, 5.598
Gene length, protein length 1320 bp, 440 aa
Immediate neighbours fliH, fliJ
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
FliI 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):

Extended information on the protein

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

Database entries

  • Structure:
  • Swiss prot entry:
  • 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

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