Difference between revisions of "Sandbox"

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−
* '''Description:''' fatty acid degradation, similar to proline dehydrogenase <br/><br/>
+
* '''Description:''' Fur-regulated basic protein, acts as RNA chaperone for fsrA, response to iron limitation <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'''
−
|''fadM''
+
|''fbpB''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yusM''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ydbN''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown 
+
|style="background:#ABCDEF;" align="center"| '''Product''' || Fur-regulated basic protein, acts as RNA chaperone<br/> for fsrA, response to iron limitation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || fatty acid degradation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA chaperone
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 34 kDa, 9.377  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 6 kDa, 9.9  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 906 bp, 302 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 177 bp, 59 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[fadN]]'', ''[[yusN]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ydbM]]'', ''[[fbpA]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15274&#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:CAB12260&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yusM_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:FbpA_fbpB_context.jpeg]]
−
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
 
|-
 
|-
 
|}
 
|}
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU32850
+
* '''Locus tag:''' BSU04530
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 40:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yusMLKJ.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ydbN.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14025]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12081]
  
 
=== Additional information===
 
=== Additional information===
  
 +
 +
The sequence of the former ydbN gene was corrected, and does now contain two genes, [[fbpA]] and [[fbpB]]. [http://www.ncbi.nlm.nih.gov/sites/entrez/18697947 PubMed]
  
 
=The protein=
 
=The protein=
Line 52: Line 53:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' L-proline + acceptor = (S)-1-pyrroline-5-carboxylate + reduced acceptor (according to Swiss-Prot)
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' proline dehydrogenase family (according to Swiss-Prot)
+
* '''Protein family:'''
  
−
* '''Paralogous protein(s):''' [[YcgM]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O32179 O32179]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P96609 P96609]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU32850]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU04530]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 118: Line 119:
 
=References=
 
=References=
  
−
<pubmed>17189250, </pubmed>
+
<pubmed>18697947, </pubmed>
−
# Matsuoka H, Hirooka K, Fujita Y. (2007) Organization and function of the YsiA regulon of Bacillus subtilis involved in fatty acid degradation. ''J Biol Chem. '' '''Feb 23;282(8):''' 5180-94. [http://www.ncbi.nlm.nih.gov/sites/entrez/17189250 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. ''Proc Natl Acad Sci U S A.'' '''Aug 19;105(33):''' 11927-32. [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 14:02, 8 June 2009

  • Description: Fur-regulated basic protein, acts as RNA chaperone for fsrA, response to iron limitation

Gene name fbpB
Synonyms ydbN
Essential no
Product Fur-regulated basic protein, acts as RNA chaperone
for fsrA, response to iron limitation
Function RNA chaperone
MW, pI 6 kDa, 9.9
Gene length, protein length 177 bp, 59 aa
Immediate neighbours ydbM, fbpA
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
FbpA fbpB context.jpeg



The gene

Basic information

  • Locus tag: BSU04530

Phenotypes of a mutant

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The sequence of the former ydbN gene was corrected, and does now contain two genes, fbpA and fbpB. PubMed

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:

Database entries

  • Structure:
  • 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

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. Proc Natl Acad Sci U S A. Aug 19;105(33): 11927-32. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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