Difference between revisions of "Sandbox"

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−
* '''Description:''' serine protease Do (heat-shock protein) <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'''
−
|''htrA''
+
|''abfA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ykdA ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || serine protease Do (heat-shock protein)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || alpha-L-arabinofuranosidase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || probably involved in processing, maturation, or secretion of extracellular enzymes
+
|style="background:#ABCDEF;" align="center"|'''Function''' || arabinan degradation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 47 kDa, 4.699  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 56 kDa, 5.344  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1347 bp, 449 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1500 bp, 500 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykcC]]'', ''[[proG]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cstA]]'', ''[[araQ]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13147&#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:CAB14832&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
 
|-
 
|-
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:htrA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:abfA_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 37: Line 37:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU12900
+
* '''Locus tag:''' BSU28720
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 43: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/htrA.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/araABDLMNPQ-abfA.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12608]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11900]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' Hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides (according to Swiss-Prot)
  
−
* '''Protein family:''' PDZ (DHR) domain (according to Swiss-Prot)
+
* '''Protein family:''' glycosyl hydrolase 51 family (according to Swiss-Prot)
  
−
* '''Paralogous protein(s):''' [[YyxA]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' cell membrane (according to Swiss-Prot),  extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
+
* '''Localization:''' cell membrane (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1QW8 1QW8] (complex with Ara-alpha-Xyl, Geobacillus stearothermophilus),  [http://www.rcsb.org/pdb/explore.do?structureId=1PZ3 1PZ3] (Geobacillus stearothermophilus)
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O34358 O34358]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P94531 P94531]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU12900]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28720]
  
−
* '''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:'''  
+
* '''Operon:''' ''[[araA]]-[[araB]]-[[araD]]-[[araL]]-[[araM]]-[[araN]]-[[araP]]-[[araQ]]-[[abfA]]''
  
−
* '''[[Sigma factor]]:'''  
+
* '''[[Sigma factor]]:''' [[SigA]]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' repressed by glucose ([[CcpA]])
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
  
−
<pubmed>12850135, </pubmed>
+
<pubmed>12949161 9084180, </pubmed>
−
# Voigt et al. (2009) Cell physiology and protein secretion of ''Bacillus licheniformis'' compared to ''Bacillus subtilis''. ''J Mol Microbiol Biotechnol.'' '''16:''' 53-68 [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
+
 
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID 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]
 +
# 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]

Revision as of 13:06, 8 June 2009

  • Description: alpha-L-arabinofuranosidase

Gene name abfA
Synonyms
Essential no
Product alpha-L-arabinofuranosidase
Function arabinan degradation
MW, pI 56 kDa, 5.344
Gene length, protein length 1500 bp, 500 aa
Immediate neighbours cstA, araQ
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
AbfA context.gif
This image was kindly provided by SubtiList





The gene

Basic information

  • Locus tag: BSU28720

Phenotypes of a mutant

Database entries

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

Additional information

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: cell membrane (according to Swiss-Prot)

Database entries

  • Structure: 1QW8 (complex with Ara-alpha-Xyl, Geobacillus stearothermophilus), 1PZ3 (Geobacillus stearothermophilus)
  • KEGG entry: [3]

Additional information

Expression and regulation

  • Regulation: repressed by glucose (CcpA)
  • Regulatory mechanism: CcpA: transcription repression
  • 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, Carla Costa, Isabel de Sá-Nogueira
Distinct molecular mechanisms involved in carbon catabolite repression of the arabinose regulon in Bacillus subtilis.
Microbiology (Reading): 2003, 149(Pt 9);2345-2355
[PubMed:12949161] [WorldCat.org] [DOI] (P p)

Isabel S-Nogueira, Teresa V Nogueira, Snia Soares, Hermnia de Lencastre
The Bacillus subtilis L-arabinose (ara) operon: nucleotide sequence, genetic organization and expression.
Microbiology (Reading): 1997, 143 ( Pt 3);957-969
[PubMed:9084180] [WorldCat.org] [DOI] (P p)


  1. 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. PubMed# Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
  2. 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. PubMed
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