Difference between revisions of "Sandbox"

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−
* '''Description:''' flagellar hook-associated protein 2 (HAP2) <br/><br/>
+
* '''Description:''' regulatory RNA<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'''
−
|''fliD''
+
|''fsrA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''mrgC''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || flagellar hook-associated protein 2 (HAP2)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || sRNA FsrA
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || movement and chemotaxis
+
|style="background:#ABCDEF;" align="center"|'''Function''' || inhibition of ''[[sdhC]]'' translation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 54 kDa, 4.804 
+
|style="background:#ABCDEF;" align="center"| '''Gene length''' || aaa bp
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1494 bp, 498 aa
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykuI]]'', ''[[ykuJ]]''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[fliS]]'', ''[[yvyC]]''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15551&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|colspan="2" | '''Genetic context''' <br/> [[Image:FsrA_context.jpg]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:fliD_context.gif]]
 
−
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
 
|-
 
|-
 
|}
 
|}
Line 35: Line 32:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU35340
+
* '''Locus tag:'''
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 38:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yvyC-fliDST.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10921]
+
* '''SubtiList entry:''' no entry
 +
 
 +
* '''Structure:'''
  
 
=== Additional information===
 
=== Additional information===
  
 +
* '''Swiss prot entry:'''
  
−
=The protein=
+
* '''KEGG entry:''' no entry
 +
 
 +
* '''E.C. number:'''
  
−
=== Basic information/ Evolution ===
+
=== Additional information===
  
−
* '''Catalyzed reaction/ biological activity:'''
+
=The RNA=
  
−
* '''Protein family:''' fliD family (according to Swiss-Prot)
+
=== Basic information/ Evolution ===
−
 
 
−
* '''Paralogous protein(s):'''
 
−
 
 
−
=== Extended information on the protein ===
 
−
 
 
−
* '''Kinetic information:'''
 
  
−
* '''Domains:'''  
+
* '''Catalyzed reaction/ biological activity:''' hybridizes to ''[[sdhC]], [[citB]], [[lutB]], and [[leuC]]-[[leuD]]'' mRNAs and inhibits their translation. [http://www.ncbi.nlm.nih.gov/sites/entrez/18697947 PubMed]
  
−
* '''Modification:'''
+
=== Extended information on the RNA===
  
−
* '''Cofactor(s):'''
+
* '''Kinetic information'''
  
−
* '''Effectors of protein activity:'''
+
* '''Interactions:''' Binds ''[[sdhC]], [[citB]], [[lutB]], and [[leuC]]-[[leuD]]'' mRNAs [http://www.ncbi.nlm.nih.gov/sites/entrez/18697947 PubMed]
  
−
* '''Interactions:'''
+
* '''Localization'''
−
 
 
−
* '''Localization:''' secreted (according to Swiss-Prot),  extracellular (no signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure''':  
−
 
 
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39738 P39738]
 
−
 
 
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU35340]
 
−
 
 
−
* '''E.C. number:'''
 
  
 
=== Additional information===
 
=== Additional information===
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* '''[[Sigma factor]]:'''  
 
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:'''  
+
* '''Regulation:''' induced by iron starvation ([[Fur]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/18697947 PubMed]
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[Fur]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/18697947 PubMed]
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 103: Line 91:
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
−
       
+
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
−
* '''GFP fusion:'''
+
=Labs working on this gene/RNA=
−
 
 
−
* '''two-hybrid system:'''
 
−
 
 
−
* '''Antibody:'''
 
  
−
=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 118: Line 102:
 
=References=
 
=References=
  
−
<pubmed>18957862, </pubmed>
+
<pubmed>18697947, </pubmed>
−
# Voigt et al. (2009) Cell physiology and protein secretion of ''Bacillus licheniformis'' compared to ''Bacillus subtilis''. ''J Mol Microbiol Biotechnol.'' '''16:''' 53-68 [http://www.ncbi.nlm.nih.gov/pubmed/18957862 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/18697947 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 14:03, 8 June 2009

  • Description: regulatory RNA

Gene name fsrA
Synonyms mrgC
Essential no
Product sRNA FsrA
Function inhibition of sdhC translation
Gene length aaa bp
Immediate neighbours ykuI, ykuJ
Gene sequence (+200bp)
Genetic context
FsrA context.jpg



The gene

Basic information

  • Locus tag:

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: no entry
  • Structure:

Additional information

  • Swiss prot entry:
  • KEGG entry: no entry
  • E.C. number:

Additional information

The RNA

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: hybridizes to sdhC, citB, lutB, and leuC-leuD mRNAs and inhibits their translation. PubMed

Extended information on the RNA

  • Kinetic information
  • Localization

Database entries

  • Structure:

Additional information

Expression and regulation

  • Operon:
  • Regulation: induced by iron starvation (Fur) PubMed
  • Regulatory mechanism: Fur: transcription repression PubMed
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:

Labs working on this gene/RNA

John Helmann, Cornell University, USA Homepage

Your additional remarks

References

Ahmed Gaballa, Haike Antelmann, Claudio Aguilar, Sukhjit K Khakh, Kyung-Bok Song, Gregory T Smaldone, John D Helmann
The Bacillus subtilis iron-sparing response is mediated by a Fur-regulated small RNA and three small, basic proteins.
Proc Natl Acad Sci U S A: 2008, 105(33);11927-32
[PubMed:18697947] [WorldCat.org] [DOI] (I p)

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