Difference between revisions of "Sandbox"

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* '''Description:''' alpha-L-arabinofuranosidase <br/><br/>
+
* '''Description:''' transcriptional regulator of transition state genes <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'''
−
|''abfA''
+
|''abh''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ylxT, yzaA ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || alpha-L-arabinofuranosidase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || arabinan degradation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of gene expression during the transition from growth to stationary phase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 56 kDa, 5.344  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 10 kDa, 5.753  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1500 bp, 500 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 276 bp, 92 aa  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cstA]]'', ''[[araQ]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[mreBH]]'', ''[[kinC]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/abfA_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/abh_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/abfA_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/abh_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors
+
|colspan="2" | '''Genetic context''' <br/> [[Image:abh_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:abfA_context.gif]]
 
 
|-
 
|-
 
|}
 
|}
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/araABDLMNPQ-abfA.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/abh.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11900]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10988]
  
 
=== Additional information===
 
=== Additional information===
Line 58: Line 56:
 
* '''Protein family:'''
 
* '''Protein family:'''
  
−
* '''Paralogous protein(s):'''
+
* '''Paralogous protein(s):''' [[AbrB]], [[SpoVT]] (only N-terminal domain)
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28720]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU14480]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[araA]]-[[araB]]-[[araD]]-[[araL]]-[[araM]]-[[araN]]-[[araP]]-[[araQ]]-[[abfA]]''
+
* '''Operon:''' ''[[abh]]''
  
−
* '''Sigma factor:''' [[SigA]]
+
* '''Sigma factor:''' [[SigW]], [[SigX]]
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
Line 115: Line 113:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Mark Strauch]], Baltimore, USA [http://lifesciences.umaryland.edu/Pages/faculty_profile.aspx?ID=212 homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 120: Line 120:
 
=References=
 
=References=
  
−
 
+
# Yao, F and M.A. Strauch (2005) Independent and Interchangeable Multimerization Domains of the AbrB, Abh and SpoVT Global Regulatory Proteins. J. Bacteriol. 187:6354-6362 [http://www.ncbi.nlm.nih.gov/sites/entrez/16159768 PubMed]
−
# Inácio JM, Costa C, de Sá-Nogueira I. (2003) Distinct molecular mechanisms involved in carbon catabolite repression of the arabinose regulon in Bacillus subtilis. ''Microbiology. '' '''Sep;149(Pt 9):''' 2345-55. [http://www.ncbi.nlm.nih.gov/sites/entrez/12949161 PubMed]# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
# Bobay, B.G., Mueller, G.A., Thompson, R.J., Venters, R.A., Murzin, A.G., Strauch, M.A. & J. Cavanagh (2006) NMR structure of AbhN and comparison with AbrBN: First Insights into the DNA-binding Promiscuity and Specificity of AbrB-like Transition-state Regulator Proteins. J. Biol. Chem. 281:21399-21409  [http://www.ncbi.nlm.nih.gov/sites/entrez/16702211 PubMed]
−
# Sa-Nogueira I.M.G., Nogueira T.V., Soares S., de Lencastre H. (1997) The Bacillus subtilis L-arabinose (ara) operon: nucleotide sequence, genetic organization and expression. ''Microbiology.'' '''Mar;143(Pt 3):''' 957-69. [http://www.ncbi.nlm.nih.gov/sites/entrez/9084180 PubMed]
+
# Strauch MA. Bobay BG. Cavanagh J. Yao F. Wilson A. Le Breton Y. (2007) Abh and AbrB control of Bacillus subtilis antimicrobial gene expression. J. of Bacteriol. 189:7720-7732. [http://www.ncbi.nlm.nih.gov/sites/entrez/17720793 PubMed]

Revision as of 14:46, 19 March 2009

  • Description: transcriptional regulator of transition state genes

Gene name abh
Synonyms ylxT, yzaA
Essential no
Product transcriptional regulator
Function regulation of gene expression during the transition from growth to stationary phase
MW, pI 10 kDa, 5.753
Gene length, protein length 276 bp, 92 aa
Immediate neighbours mreBH, kinC
Gene sequence (+200bp) Protein sequence
Genetic context
Abh context.gif



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family:
  • Paralogous protein(s): AbrB, SpoVT (only N-terminal domain)

Extended information on the protein

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

Database entries

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

Additional information

Expression and regulation

  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

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

Labs working on this gene/protein

Mark Strauch, Baltimore, USA homepage

Your additional remarks

References

  1. Yao, F and M.A. Strauch (2005) Independent and Interchangeable Multimerization Domains of the AbrB, Abh and SpoVT Global Regulatory Proteins. J. Bacteriol. 187:6354-6362 PubMed
  2. Bobay, B.G., Mueller, G.A., Thompson, R.J., Venters, R.A., Murzin, A.G., Strauch, M.A. & J. Cavanagh (2006) NMR structure of AbhN and comparison with AbrBN: First Insights into the DNA-binding Promiscuity and Specificity of AbrB-like Transition-state Regulator Proteins. J. Biol. Chem. 281:21399-21409 PubMed
  3. Strauch MA. Bobay BG. Cavanagh J. Yao F. Wilson A. Le Breton Y. (2007) Abh and AbrB control of Bacillus subtilis antimicrobial gene expression. J. of Bacteriol. 189:7720-7732. PubMed
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