Difference between revisions of "Sandbox"

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* '''Description:''' transcription regulator of iron homoeostasis <br/><br/>
+
* '''Description:''' required for dissolution of the septal cell wall <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'''
−
|''fur''
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|''spoIIM''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqkL ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional repressor
+
|style="background:#ABCDEF;" align="center"| '''Product''' || sporulation protein
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of iron homoeostasis
+
|style="background:#ABCDEF;" align="center"|'''Function''' || dissolution of the septal cell wall
−
and transcription of ferri-siderophore uptake genes
 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 17 kDa, 5.374  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 24 kDa, 9.84  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 447 bp, 149 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 642 bp, 214 aa  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ripX]]'', ''[[spoIIM]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[fur]]'', ''[[yqkK]]''
 
|-
 
|-
−
|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" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14285&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|-
+
|colspan="2" | '''Genetic context''' <br/> [[Image:spoIIM_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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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/fur.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/spoIIM.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11766]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10768]
  
 
=== Additional information===
 
=== Additional information===
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* '''Protein family:'''
 
* '''Protein family:'''
  
−
* '''Paralogous protein(s):''' [[PerR]], [[Zur]]
+
* '''Paralogous protein(s):'''
−
 
 
−
=== 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+BSU23520]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU23530]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 95: Line 88:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''fur''
+
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' [[SigA]]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' repressed by [[PerR]]
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' [[PerR]]: transcription repression
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 120: Line 113:
  
 
=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 126: Line 118:
 
=References=
 
=References=
  
−
# 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]
+
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID 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: required for dissolution of the septal cell wall

Gene name spoIIM
Synonyms
Essential no
Product sporulation protein
Function dissolution of the septal cell wall
MW, pI 24 kDa, 9.84
Gene length, protein length 642 bp, 214 aa
Immediate neighbours fur, yqkK
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
SpoIIM 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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