Difference between revisions of "Easter egg"

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−
* '''Description:''' amino acid permease <br/><br/>
+
* '''Description:''' inhibitor of [[AbrB]] activity<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'''
−
|''aapA''
+
|''abbA ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ykzF''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || amino acid permease
+
|style="background:#ABCDEF;" align="center"| '''Product''' || anti-repressor
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || amino acid uptake
+
|style="background:#ABCDEF;" align="center"|'''Function''' || inhibition of [[AbrB]]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 9.675  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 7 kDa, 4.642  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1377 bp, 459 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 195 bp, 65 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[levR]]'', ''[[yrhP]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykuK]]'', ''[[ykuL]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14651&#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:CAB13285&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|-
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ykzF_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:aapA_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>
 
|-
 
|-
Line 31: Line 29:
 
__TOC__
 
__TOC__
  
−
<br/><br/><br/><br/>
+
<br/><br/>
  
 
=The gene=
 
=The gene=
Line 37: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU27090
+
* '''Locus tag:''' BSU14120
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 43: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ykuJK-ykzF-ykuL-ccpC.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12556]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13334]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 50:
  
 
= Categories containing this gene/protein =
 
= Categories containing this gene/protein =
−
{{SubtiWiki category|[[transporters/ other]]}}
+
{{SubtiWiki category|[[transcription factors and their control]]}}
 
=The protein=
 
=The protein=
  
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' inhibition of AbrB activity [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
  
−
* '''Protein family:''' amino acid-polyamine-organocation (APC) superfamily (according to Swiss-Prot)
+
* '''Protein family:'''
  
−
* '''Paralogous protein(s):''' [[YtnA]], [[YbxG]], [[YdgF]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 75: Line 73:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''Interactions:''' [[AbbA]]-[[AbrB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
  
 
* '''Localization:'''
 
* '''Localization:'''
Line 83: Line 81:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''UniProt:''' [http://www.uniprot.org/uniprot/O06005 O06005]
+
* '''UniProt:''' [http://www.uniprot.org/uniprot/O31697 O31697]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU27090]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU14120]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 93: Line 91:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[ykuJ]]-[[ykuK]]-[[abbA]]-[[ykuL]]-[[ccpC]]'' {{PubMed|16395550}}
  
−
* '''[[Sigma factor]]:'''  
+
* '''Sigma factor:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
 +
** repressed by glucose (4.3-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
 +
** expressed under conditions that trigger sporulation ([[Spo0A]]) {{PubMed|18840696,14651647}}
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
 +
** [[CcpA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12850135 PubMed]
 +
** [[Spo0A]]: transcription activation by [[Spo0A]]~P {{PubMed|18840696,14651647}}
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:'''
+
* '''Mutant:''' GP214 (deletion of ''[[ykuJ]]-[[ykuK]]-[[abbA]]-[[ykuL]]'', replaced by ''aphA3''), available in the [[Stülke]] lab
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
 
          
 
          
−
* '''lacZ fusion:'''
+
* '''lacZ fusion:''' pGP708 (in [[pAC5]]), available in [[Stülke]] lab, pGP712 (in [[pAC6]]), available in [[Stülke]] lab
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
Line 118: Line 120:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Richard Losick]], Harvard Univ., Cambridge, USA [http://www.mcb.harvard.edu/Losick/ homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
  
 
=References=
 
=References=
 +
 +
<pubmed>,18840696,14651647,12850135 18840696 12850135,16395550 </pubmed>
  
 
[[Category:Protein-coding genes]]
 
[[Category:Protein-coding genes]]

Revision as of 15:22, 30 November 2010

  • Description: inhibitor of AbrB activity

Gene name abbA
Synonyms ykzF
Essential no
Product anti-repressor
Function inhibition of AbrB
MW, pI 7 kDa, 4.642
Gene length, protein length 195 bp, 65 aa
Immediate neighbours ykuK, ykuL
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YkzF context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU14120

Phenotypes of a mutant

Database entries

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

Additional information

Categories containing this gene/protein

transcription factors and their control

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: inhibition of AbrB activity PubMed
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Localization:

Database entries

  • Structure:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Sigma factor:
  • Regulation:
    • repressed by glucose (4.3-fold) (CcpA) PubMed
    • expressed under conditions that trigger sporulation (Spo0A) PubMed
  • Additional information:

Biological materials

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

Labs working on this gene/protein

Richard Losick, Harvard Univ., Cambridge, USA homepage

Your additional remarks

References

Allison V Banse, Arnaud Chastanet, Lilah Rahn-Lee, Errett C Hobbs, Richard Losick
Parallel pathways of repression and antirepression governing the transition to stationary phase in Bacillus subtilis.
Proc Natl Acad Sci U S A: 2008, 105(40);15547-52
[PubMed:18840696] [WorldCat.org] [DOI] (I p)

Hans-Matti Blencke, Irene Reif, Fabian M Commichau, Christian Detsch, Ingrid Wacker, Holger Ludwig, Jörg Stülke
Regulation of citB expression in Bacillus subtilis: integration of multiple metabolic signals in the citrate pool and by the general nitrogen regulatory system.
Arch Microbiol: 2006, 185(2);136-46
[PubMed:16395550] [WorldCat.org] [DOI] (P p)

Virginie Molle, Masaya Fujita, Shane T Jensen, Patrick Eichenberger, José E González-Pastor, Jun S Liu, Richard Losick
The Spo0A regulon of Bacillus subtilis.
Mol Microbiol: 2003, 50(5);1683-701
[PubMed:14651647] [WorldCat.org] [DOI] (P p)

Hans-Matti Blencke, Georg Homuth, Holger Ludwig, Ulrike Mäder, Michael Hecker, Jörg Stülke
Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways.
Metab Eng: 2003, 5(2);133-49
[PubMed:12850135] [WorldCat.org] [DOI] (P p)

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