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

  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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