Difference between revisions of "Sandbox"

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|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
−
|''abf2''
+
|''abfA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''xsa ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
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|style="background:#ABCDEF;" align="center"|'''Function''' || arabinan degradation
 
|style="background:#ABCDEF;" align="center"|'''Function''' || arabinan degradation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 56 kDa, 5.329  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 56 kDa, 5.344  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1485 bp, 495 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1500 bp, 500 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[trxA]]'', ''[[etfA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cstA]]'', ''[[araQ]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/xsa_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|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/xsa_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/abfA_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" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:xsa_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/xsa.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/araABDLMNPQ-abfA.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11985]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11900]
  
 
=== Additional information===
 
=== Additional information===
Line 90: Line 90:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[araA]]-[[araB]]-[[araD]]-[[araL]]-[[araM]]-[[araN]]-[[araP]]-[[araQ]]-[[abfA]]''
  
−
* '''Sigma factor:'''  
+
* '''Sigma factor:''' [[SigA]]
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
Line 98: Line 98:
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 120: Line 120:
 
=References=
 
=References=
  
−
# 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 17:55, 18 March 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
Gene sequence (+200bp) Protein sequence
Caution: The sequence for this gene in SubtiList contains errors
Genetic context
AbfA 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):

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:
  • 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

Your additional remarks

References

  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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