Difference between revisions of "Easter egg"

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−
* '''Description:''' inhibitor of [[AbrB]] activity<br/><br/>
+
* '''Description:''' alpha-L-arabinofuranosidase <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'''
−
|''abbA ''
+
|''abf2''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ykzF''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''xsa ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || anti-repressor
+
|style="background:#ABCDEF;" align="center"| '''Product''' || alpha-L-arabinofuranosidase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || inhibition of [[AbrB]]
+
|style="background:#ABCDEF;" align="center"|'''Function''' || arabinan degradation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 7 kDa, 4.642  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 56 kDa, 5.329  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 195 bp, 65 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1485 bp, 495 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykuK]]'', ''[[ykuL]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[trxA]]'', ''[[etfA]]''
 
|-
 
|-
−
|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" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14811&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ykzF_context.gif]]
+
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:xsa_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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__TOC__
 
__TOC__
  
−
<br/><br/>
+
<br/><br/><br/><br/>
  
 
=The gene=
 
=The gene=
Line 35: Line 37:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU14120
+
* '''Locus tag:''' BSU28510
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ykuJK-ykzF-ykuL-ccpC.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/xsa.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13334]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11985]
  
 
=== Additional information===
 
=== Additional information===
Line 50: Line 52:
  
 
= Categories containing this gene/protein =
 
= Categories containing this gene/protein =
−
{{SubtiWiki category|[[transcription factors and their control]]}}
+
{{SubtiWiki category|[[utilization of specific carbon sources]]}}
 
=The protein=
 
=The protein=
  
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' inhibition of AbrB activity [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
+
* '''Catalyzed reaction/ biological activity:''' Hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides (according to Swiss-Prot)
  
−
* '''Protein family:'''
+
* '''Protein family:''' glycosyl hydrolase 51 family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 73: Line 75:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[AbbA]]-[[AbrB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/18840696 PubMed]
+
* '''Interactions:'''
  
 
* '''Localization:'''
 
* '''Localization:'''
Line 81: Line 83:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''UniProt:''' [http://www.uniprot.org/uniprot/O31697 O31697]
+
* '''UniProt:''' [http://www.uniprot.org/uniprot/P94552 P94552]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU14120]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU28510]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.2.1.55 3.2.1.55]
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[ykuJ]]-[[ykuK]]-[[abbA]]-[[ykuL]]-[[ccpC]]'' {{PubMed|16395550}}
+
* '''Operon:''' ''abf2'' [http://www.ncbi.nlm.nih.gov/sites/entrez/14973026 PubMed]
  
−
* '''Sigma factor:'''  
+
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/14973026 PubMed]
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
−
** repressed by glucose (4.3-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
+
** induced by arabinose ([[AraR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/14973026 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]  
+
** [[AraR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/14973026 PubMed]
−
** [[Spo0A]]: transcription activation by [[Spo0A]]~P {{PubMed|18840696,14651647}}
 
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP214 (deletion of ''[[ykuJ]]-[[ykuK]]-[[abbA]]-[[ykuL]]'', replaced by ''aphA3''), available in the [[Stülke]] lab
+
* '''Mutant:'''
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
 
          
 
          
−
* '''lacZ fusion:''' pGP708 (in [[pAC5]]), available in [[Stülke]] lab, pGP712 (in [[pAC6]]), available in [[Stülke]] lab
+
* '''lacZ fusion:'''
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
Line 120: 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=
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=References=
 
=References=
  
−
<pubmed>,18840696,14651647,12850135 18840696 12850135,16395550 </pubmed>
+
<pubmed>14973026,18757805,,14973026, </pubmed>
  
 
[[Category:Protein-coding genes]]
 
[[Category:Protein-coding genes]]

Revision as of 14:22, 30 November 2010

  • Description: alpha-L-arabinofuranosidase

Gene name abf2
Synonyms xsa
Essential no
Product alpha-L-arabinofuranosidase
Function arabinan degradation
MW, pI 56 kDa, 5.329
Gene length, protein length 1485 bp, 495 aa
Immediate neighbours trxA, etfA
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
Xsa context.gif
This image was kindly provided by SubtiList





The gene

Basic information

  • Locus tag: BSU28510

Phenotypes of a mutant

Database entries

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

Additional information

Categories containing this gene/protein

utilization of specific carbon sources

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: Hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides (according to Swiss-Prot)
  • Protein family: glycosyl hydrolase 51 family (according to Swiss-Prot)
  • 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]

Additional information

Expression and 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

José Manuel Inácio, Isabel Lopes Correia, Isabel de Sá-Nogueira
Two distinct arabinofuranosidases contribute to arabino-oligosaccharide degradation in Bacillus subtilis.
Microbiology (Reading): 2008, 154(Pt 9);2719-2729
[PubMed:18757805] [WorldCat.org] [DOI] (P p)

Maria Paiva Raposo, José Manuel Inácio, Luís Jaime Mota, Isabel de Sá-Nogueira
Transcriptional regulation of genes encoding arabinan-degrading enzymes in Bacillus subtilis.
J Bacteriol: 2004, 186(5);1287-96
[PubMed:14973026] [WorldCat.org] [DOI] (P p)

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