Difference between revisions of "Sandbox"

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|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
−
|''abn2''
+
|''abnA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yxiA ''
+
|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''' || endo-1,5-alpha-L-arabinosidase  
+
|style="background:#ABCDEF;" align="center"| '''Product''' || endo-1,5-alpha-L-arabinosidase
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || arabinan degradation
 
|style="background:#ABCDEF;" align="center"|'''Function''' || arabinan degradation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52 kDa, 7.371  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 34 kDa, 8.618  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1407 bp, 469 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 939 bp, 313 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yxiB]]'', ''[[hutP]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[araA]]'', ''[[ysdC]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yxiA_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/abnA_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yxiA_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/abnA_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:yxiA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:abnA_context.gif]]
 
|-
 
|-
 
|}
 
|}
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yxiA.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/abnA.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11130]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11901]
  
 
=== Additional information===
 
=== Additional information===
Line 62: Line 62:
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
  
−
* '''Kinetic information:''' With linear-alpha-1,5-l-arabinan as the preferred substrate, the enzyme exhibited an apparent K(m) of 2.0 mg ml(-1) and V(max) of 0.25 mmol min(-1) mg(-1) at pH 7.0 and 50°C. [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]
+
* '''Kinetic information:'''
  
 
* '''Domains:'''  
 
* '''Domains:'''  
Line 74: Line 74:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' extracellular [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
Line 84: Line 84:
 
* '''KEGG entry:'''
 
* '''KEGG entry:'''
  
−
* '''E.C. number:''' 3.2.1.99
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
Line 90: Line 90:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''abn2'' [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]
+
* '''Operon:'''  
  
−
* '''Sigma factor:''' [[SigA]], [[SigH]] [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]
+
* '''Sigma factor:'''  
  
−
* '''Regulation:''' expression is stimulated by arabinose and pectin and repressed by glucose [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' unknown [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]
+
* '''Regulatory mechanism:'''  
  
 
* '''Additional information:'''  
 
* '''Additional information:'''  
Line 115: Line 115:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Isabel de Sa-Nogueira]], Lisboa, Portugal [http://www.itqb.unl.pt/research/biology/microbial-genetics homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
−
 
  
 
=References=
 
=References=
  
−
# Inácio JM, and de Sá-Nogueira I(2008) Characterization of ''abn2'' (''yxiA''), encoding a ''Bacillus subtilis'' GH43 arabinanase, Abn2, and its role in arabino-polysaccharide degradation.''J. Bacteriol.'' '''190:''' 4272-4280. [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]
 
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 17:55, 18 March 2009

  • Description: endo-1,5-alpha-L-arabinosidase

Gene name abnA
Synonyms
Essential no
Product endo-1,5-alpha-L-arabinosidase
Function arabinan degradation
MW, pI 34 kDa, 8.618
Gene length, protein length 939 bp, 313 aa
Immediate neighbours araA, ysdC
Gene sequence (+200bp) Protein sequence
Caution: The sequence for this gene in SubtiList contains errors
Genetic context
AbnA 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

  • Operon:
  • Sigma factor:
  • 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. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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