Difference between revisions of "Sandbox"

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−
* '''Description:''' repair, recombination <br/><br/>
+
* '''Description:''' riboflavin transporter <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'''
−
|''recF''
+
|''ribU ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ypaA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' ||  
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
+
|style="background:#ABCDEF;" align="center"| '''Product''' || riboflavin transporter
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || repair, recombination
+
|style="background:#ABCDEF;" align="center"|'''Function''' || riboflavin uptake
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 42 kDa, 7.015  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 20 kDa, 10.12  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1110 bp, 370 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 570 bp, 190 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaA]]'', ''[[yaaB]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[fer]]'', ''[[ypzE]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11780&#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:CAB14237&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:DnaA_dnaN_yaaA_recF_yaaB_gyrB_context.png]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ypaA_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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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU00040
+
* '''Locus tag:''' BSU23050
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yaaA-recF-yaaB-gyrB.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10068]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11428]
  
 
=== Additional information===
 
=== Additional information===
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* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' recF family (according to Swiss-Prot)
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' cytoplasm (according to Swiss-Prot)
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P05651 P05651]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P50726 P50726]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00040]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU23050]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[yaaA]]-[[recF]]-[[yaaB]]-[[gyrB]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
+
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:'''  
+
* '''Regulation:''' expressed in the absence of FMN ([[FMN-box]])
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[FMN-box]]: [[riboswitch]], controls access of the ribosome to the Shine-Dalgarno sequence
  
 
* '''Additional information:'''
 
* '''Additional information:'''
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=References=
 
=References=
  
−
<pubmed>2987848, </pubmed>
+
<pubmed>17693491, </pubmed>
−
# Ogasawara et al. (1985) Structure and function of the region of the replication origin of the ''Bacillus subtilis'' chromosome. IV. Transcription of the oriC region and expression of DNA gyrase genes and other open reading frames.''Nucl. Acids Res.'' '''11:''' 2267-2279. [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
+
# Vogl, C., Grill, S., Schilling, O., Stülke, J., Mack, M. & Stolz, J. (2007) Characterization of riboflavin (vitamin B2) transport proteins from Bacillus subtilis and Corynebacterium glutamicum. J. Bacteriol. 189: 7367-7375. [http://www.ncbi.nlm.nih.gov/sites/entrez/17693491 PubMed]
 +
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 13:32, 8 June 2009

  • Description: riboflavin transporter

Gene name ribU
Synonyms ypaA
Essential no
Product riboflavin transporter
Function riboflavin uptake
MW, pI 20 kDa, 10.12
Gene length, protein length 570 bp, 190 aa
Immediate neighbours fer, ypzE
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YpaA context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU23050

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

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:

Database entries

  • Structure:
  • KEGG entry: [2]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Regulation: expressed in the absence of FMN (FMN-box)
  • Regulatory mechanism: FMN-box: riboswitch, controls access of the ribosome to the Shine-Dalgarno sequence
  • 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

Christian Vogl, Simon Grill, Oliver Schilling, Jörg Stülke, Matthias Mack, Jürgen Stolz
Characterization of riboflavin (vitamin B2) transport proteins from Bacillus subtilis and Corynebacterium glutamicum.
J Bacteriol: 2007, 189(20);7367-75
[PubMed:17693491] [WorldCat.org] [DOI] (P p)

  1. Vogl, C., Grill, S., Schilling, O., Stülke, J., Mack, M. & Stolz, J. (2007) Characterization of riboflavin (vitamin B2) transport proteins from Bacillus subtilis and Corynebacterium glutamicum. J. Bacteriol. 189: 7367-7375. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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