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* '''Description:''' write here <br/><br/>
* '''Description:''' riboflavin [[ECF transporter]], S protein <br/><br/>


{| align="right" border="1" cellpadding="2"  
{| align="right" border="1" cellpadding="2"  
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ypaA''
|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''' ||  
|style="background:#ABCDEF;" align="center"| '''Product''' || S protein of riboflavin [[ECF transporter]]
|-
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|style="background:#ABCDEF;" align="center"|'''Function''' || riboflavin uptake
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU23050 ribU]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=RibU RibU]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=ribU ribU]'''
|-
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 20 kDa, 10.12   
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 20 kDa, 10.12   
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 570 bp, 190 aa  
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 570 bp, 190 aa  
|-
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' ||  
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[fer]]'', ''[[ypzE]]''
|-
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ypaA_nucleotide.txt    Gene sequence     (+200bp)  ]'''
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU23050 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU23050 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU23050 DNA_with_flanks]
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ypaA_protein.txt Protein sequence]'''
|-
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:ypaA_context.gif]]
|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>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=fmnP_2410017_2410589_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ribU_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU23050]]
|-
|-
|}
|}


__TOC__
__TOC__
<br/><br/><br/><br/>
<br/><br/><br/><br/>
<br/><br/><br/><br/>
<br/><br/>


<br/><br/>
= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[ECF transporter]]}},
{{SubtiWiki category|[[biosynthesis of cofactors]]}},
{{SubtiWiki category|[[membrane proteins]]}}
 
= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[FMN-box]]}}


=The gene=
=The gene=
Line 35: Line 53:
=== Basic information ===
=== Basic information ===


* '''Coordinates:'''
* '''Locus tag:''' BSU23050


===Phenotypes of a mutant ===
===Phenotypes of a mutant ===


=== Database entries ===
=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU23050&redirect=T BSU23050]


* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ypaA.html]
* '''DBTBS entry:''' no entry


* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11428]
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11428]


=== Additional information===
=== Additional information===


=The protein=
=The protein=
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* '''Kinetic information:'''
* '''Kinetic information:'''


* '''Domains:'''  
* '''[[Domains]]:'''  


* '''Modification:'''
* '''Modification:'''


* '''Cofactor(s):'''
* '''[[Cofactors]]:'''


* '''Effectors of protein activity:'''
* '''Effectors of protein activity:'''


* '''Interactions:'''
* '''[[SubtInteract|Interactions]]:'''
** [[YbaF]]-[[RibU]] {{PubMed|20497229}}


* '''Localization:'''
* '''[[Localization]]:''' membrane


=== Database entries ===
=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU23050&redirect=T BSU23050]


* '''Structure:'''
* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=3P5N 3P5N] (RibU from ''Staphylococcus aureus'')


* '''Swiss prot entry:'''
* '''UniProt:''' [http://www.uniprot.org/uniprot/P50726 P50726]


* '''KEGG entry:'''
* '''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:'''  
* '''Operon:''' ''[[ribU]]'' {{PubMed|21815947}}
** there is a promoter directly in front of ''[[ribU]]'' {{PubMed|17693491}}
 
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=fmnP_2410017_2410589_-1 ribU] {{PubMed|22383849}}


* '''Sigma factor:'''  
* '''[[Sigma factor]]:'''  


* '''Regulation:'''  
* '''Regulation:''' expressed in the absence of FMN ([[FMN-box]]) {{PubMed|17693491}}


* '''Regulatory mechanism:'''  
* '''Regulatory mechanism:''' [[FMN-box]]: [[riboswitch]], controls access of the ribosome to the Shine-Dalgarno sequence {{PubMed|12456892}}


* '''Additional information:'''  
* '''Additional information:'''
** the mRNA is substantially stabilized upon depletion of [[Rny|RNase Y]] {{PubMed|21815947}}


=Biological materials =
=Biological materials =


* '''Mutant:'''
* '''Mutant:'''  


* '''Expression vector:'''
* '''Expression vector:'''
Line 117: Line 141:


=References=
=References=
==Reviews==
<pubmed> 20497229 22574898 24362466 </pubmed>
==Original publications==
<pubmed>12456892, 20972419,17693491,21815947  24356467 24755604 25438558 </pubmed>


# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
[[Category:Protein-coding genes]]

Latest revision as of 18:10, 5 December 2014

Gene name ribU
Synonyms ypaA
Essential no
Product S protein of riboflavin ECF transporter
Function riboflavin uptake
Gene expression levels in SubtiExpress: ribU
Interactions involving this protein in SubtInteract: RibU
Metabolic function and regulation of this protein in SubtiPathways:
ribU
MW, pI 20 kDa, 10.12
Gene length, protein length 570 bp, 190 aa
Immediate neighbours fer, ypzE
Sequences Protein DNA DNA_with_flanks
Genetic context
This image was kindly provided by SubtiList
Expression at a glance   PubMed
File:RibU expression.png















Categories containing this gene/protein

ECF transporter, biosynthesis of cofactors, membrane proteins

This gene is a member of the following regulons

FMN-box

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:
  • Modification:
  • Effectors of protein activity:

Database entries

  • Structure: 3P5N (RibU from Staphylococcus aureus)
  • KEGG entry: [2]
  • E.C. number:

Additional information

Expression and regulation

  • Additional information:
    • the mRNA is substantially stabilized upon depletion of RNase Y PubMed

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

Reviews

<pubmed> 20497229 22574898 24362466 </pubmed>

Original publications

<pubmed>12456892, 20972419,17693491,21815947 24356467 24755604 25438558 </pubmed>

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