Difference between revisions of "ThiU"

From SubtiWiki
Jump to: navigation, search
(Undo revision 120326 by Adr (Talk))
 
(19 intermediate revisions by 5 users not shown)
Line 13: Line 13:
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || thiamine uptake
 
|style="background:#ABCDEF;" align="center"|'''Function''' || thiamine 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=BSU13240 thiU]
 +
|-
 +
|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=ThiU ThiU]
 +
|-
 +
|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=thiU thiU]'''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 21 kDa, 6.046   
 
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 21 kDa, 6.046   
Line 20: Line 26:
 
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[thiV]]'', ''[[ykoG]]''
 
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[thiV]]'', ''[[ykoG]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13181&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU13240 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU13240 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU13240 DNA_with_flanks]
 
|-
 
|-
 
|colspan="2" | '''Genetic context''' <br/> [[Image:ykoF_context.gif]]
 
|colspan="2" | '''Genetic context''' <br/> [[Image:ykoF_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>
 +
|-
 +
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=thiU_1391040_1391642_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:thiU_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU13240]]
 
|-
 
|-
 
|}
 
|}
  
 
__TOC__
 
__TOC__
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
 +
 +
<br/><br/><br/><br/><br/><br/>
 +
 +
= [[Categories]] containing this gene/protein =
 +
{{SubtiWiki category|[[ABC transporters]]}},
 +
{{SubtiWiki category|[[biosynthesis of cofactors]]}},
 +
{{SubtiWiki category|[[membrane proteins]]}}
  
−
<br/><br/>
+
= This gene is a member of the following [[regulons]] =
 +
{{SubtiWiki regulon|[[Thi-box]]}}
  
 
=The gene=
 
=The gene=
Line 40: Line 62:
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU13240&redirect=T BSU13240]
  
 
* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
Line 46: Line 69:
  
 
=== Additional information===
 
=== Additional information===
 +
 +
  
  
Line 70: Line 95:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[ThiW]]-([[ThiV]]-[[ThiX]])-[[ThiU]] {{PubMed|16291685}}
+
* '''[[SubtInteract|Interactions]]:'''
 +
** [[ThiW]]-([[ThiV]]-[[ThiX]])-[[ThiU]] {{PubMed|16291685}}
  
−
* '''Localization:''' membrane associated (via [[ThiV]]-[[ThiX]]) {{PubMed|16291685}}
+
* '''[[Localization]]:''' membrane associated (via [[ThiV]]-[[ThiX]]) {{PubMed|16291685}}
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU13240&redirect=T BSU13240]
  
 
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1SBR 1SBR] (complex with thiamine),  [http://www.rcsb.org/pdb/explore.do?structureId=1S99 1S99]
 
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1SBR 1SBR] (complex with thiamine),  [http://www.rcsb.org/pdb/explore.do?structureId=1S99 1S99]
Line 87: Line 114:
  
 
=Expression and regulation=
 
=Expression and regulation=
 +
* '''Operon:''' ''[[thiU]]-[[thiV]]-[[thiW]]-[[thiX]]'' {{PubMed|16291685}}
  
−
* '''Operon:''' ''[[thiU]]-[[thiV]]-[[thiW]]-[[thiX]]'' {{PubMed|16291685}}
+
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=thiU_1391040_1391642_-1 thiU] {{PubMed|22383849}}
  
−
* '''[[Sigma factor]]:'''  
+
* '''Sigma factor:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
 +
** repressed by thiamine ([[Thi-box]]) {{PubMed|12376536}}
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
 +
** [[Thi-box]]: [[RNA switch]] {{PubMed|12376536}}
  
 
* '''Additional information:'''
 
* '''Additional information:'''
 +
** number of protein molecules per cell (minimal medium with glucose and ammonium): 257 {{PubMed|24696501}}
 +
** number of protein molecules per cell (complex medium with amino acids, without glucose): 745 {{PubMed|24696501}}
 +
** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 1463 {{PubMed|21395229}}
 +
** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 433 {{PubMed|21395229}}
 +
** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 540 {{PubMed|21395229}}
  
 
=Biological materials =
 
=Biological materials =
−
 
 
* '''Mutant:'''
 
* '''Mutant:'''
  
Line 118: Line 152:
 
=References=
 
=References=
  
−
<pubmed>16291685,,15451668, </pubmed>
+
<pubmed>16291685,12376536 ,15451668, </pubmed>
  
 
[[Category:Protein-coding genes]]
 
[[Category:Protein-coding genes]]

Latest revision as of 14:18, 17 April 2014

Gene name thiU
Synonyms ykoF
Essential no
Product thiamine ABC transporter (binding protein)
Function thiamine uptake
Gene expression levels in SubtiExpress: thiU
Interactions involving this protein in SubtInteract: ThiU
Metabolic function and regulation of this protein in SubtiPathways:
thiU
MW, pI 21 kDa, 6.046
Gene length, protein length 600 bp, 200 aa
Immediate neighbours thiV, ykoG
Sequences Protein DNA DNA_with_flanks
Genetic context
YkoF context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
ThiU expression.png




























Categories containing this gene/protein

ABC transporters, biosynthesis of cofactors, membrane proteins

This gene is a member of the following regulons

Thi-box

The gene

Basic information

  • Locus tag: BSU13240

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:

Database entries

  • Structure: 1SBR (complex with thiamine), 1S99
  • KEGG entry: [2]
  • E.C. number:

Additional information

Expression and regulation

  • Sigma factor:
  • Additional information:
    • number of protein molecules per cell (minimal medium with glucose and ammonium): 257 PubMed
    • number of protein molecules per cell (complex medium with amino acids, without glucose): 745 PubMed
    • number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 1463 PubMed
    • number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 433 PubMed
    • number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 540 PubMed

Biological materials

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

Labs working on this gene/protein

Your additional remarks

References

Ghislain Schyns, Sébastien Potot, Yi Geng, Teresa M Barbosa, Adriano Henriques, John B Perkins
Isolation and characterization of new thiamine-deregulated mutants of Bacillus subtilis.
J Bacteriol: 2005, 187(23);8127-36
[PubMed:16291685] [WorldCat.org] [DOI] (P p)

Yancho Devedjiev, Yogesh Surendranath, Urszula Derewenda, Alexandra Gabrys, David R Cooper, Rong-guang Zhang, Lour Lezondra, Andrzej Joachimiak, Zygmunt S Derewenda
The structure and ligand binding properties of the B. subtilis YkoF gene product, a member of a novel family of thiamin/HMP-binding proteins.
J Mol Biol: 2004, 343(2);395-406
[PubMed:15451668] [WorldCat.org] [DOI] (P p)

Dmitry A Rodionov, Alexey G Vitreschak, Andrey A Mironov, Mikhail S Gelfand
Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms.
J Biol Chem: 2002, 277(50);48949-59
[PubMed:12376536] [WorldCat.org] [DOI] (P p)

Retrieved from "http://subtiwiki-test.uni-goettingen.de/wiki//index.php?title=ThiU&oldid=204834"