Difference between revisions of "Sandbox"

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* '''Description:''' write here <br/><br/>
+
* '''Description:''' transcription regulator of iron homoeostasis <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'''
−
|''ripX''
+
|''fur''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ykqM ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqkL ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || site-specific integrase/recombinase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional repressor
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || involved in the resolution of chromosome dimers
+
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of iron homoeostasis
 +
and transcription of ferri-siderophore uptake genes
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 10  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 17 kDa, 5.374  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 888 bp, 296 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 447 bp, 149 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[drm]]'', ''[[fur]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ripX]]'', ''[[spoIIM]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14283&#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:CAB14284&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
 
|-
 
|-
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ripX_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:fur_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/><br/>
  
 
=The gene=
 
=The gene=
Line 43: Line 44:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/fur.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11332]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11766]
  
 
=== Additional information===
 
=== Additional information===
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* '''Protein family:'''
 
* '''Protein family:'''
  
−
* '''Paralogous protein(s):'''
+
* '''Paralogous protein(s):''' [[PerR]], [[Zur]]
 +
 
 +
=== Genes controlled by Fur ===
 +
 
 +
''[[fsrA]]''
  
 
=== 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+BSU23510]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU23520]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''fur''
  
−
* '''[[Sigma factor]]:'''  
+
* '''[[Sigma factor]]:''' [[SigA]]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' repressed by [[PerR]]
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[PerR]]: transcription repression
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
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=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
[[John Helmann]], Cornell University, USA [http://www.micro.cornell.edu/research/labs/helmann-lab/index.cfm Homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 120: Line 126:
 
=References=
 
=References=
  
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
# Baichoo N, Wang T, Ye R, Helmann JD. (2002) Global analysis of the Bacillus subtilis Fur regulon and the iron starvation stimulon. ''Mol Microbiol.'' '''Sep;45(6):''' 1613-29. [http://www.ncbi.nlm.nih.gov/sites/entrez/12354229  PubMed]
 +
# Ollinger J, Song KB, Antelmann H, Hecker M, Helmann JD. (2006) Role of the Fur regulon in iron transport in Bacillus subtilis. ''J Bacteriol.'' '''May;188(10):''' 3664-73. [http://www.ncbi.nlm.nih.gov/sites/entrez/16672620  PubMed]
 +
# Gaballa A, Antelmann H, Aguilar C, Khakh SK, Song KB, Smaldone GT, Helmann JD (2008) The ''Bacillus subtilis'' iron-sparing response is mediated by a Fur-regulated small RNA and three small, basic proteins. PNAS 105: 11927-11932. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 02:47, 30 April 2009

  • Description: transcription regulator of iron homoeostasis

Gene name fur
Synonyms yqkL
Essential no
Product transcriptional repressor
Function regulation of iron homoeostasis

and transcription of ferri-siderophore uptake genes

MW, pI 17 kDa, 5.374
Gene length, protein length 447 bp, 149 aa
Immediate neighbours ripX, spoIIM
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
Fur 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:

Genes controlled by Fur

fsrA

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: fur
  • Regulation: repressed by PerR
  • Regulatory mechanism: PerR: transcription repression
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

John Helmann, Cornell University, USA Homepage

Your additional remarks

References

  1. Baichoo N, Wang T, Ye R, Helmann JD. (2002) Global analysis of the Bacillus subtilis Fur regulon and the iron starvation stimulon. Mol Microbiol. Sep;45(6): 1613-29. PubMed
  2. Ollinger J, Song KB, Antelmann H, Hecker M, Helmann JD. (2006) Role of the Fur regulon in iron transport in Bacillus subtilis. J Bacteriol. May;188(10): 3664-73. PubMed
  3. Gaballa A, Antelmann H, Aguilar C, Khakh SK, Song KB, Smaldone GT, Helmann JD (2008) The Bacillus subtilis iron-sparing response is mediated by a Fur-regulated small RNA and three small, basic proteins. PNAS 105: 11927-11932. PubMed
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