Difference between revisions of "Sandbox"

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* '''Description:''' write here <br/><br/>
+
* '''Description:''' endo-1,5-alpha-L-arabinosidase <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'''
−
|''pelC''
+
|''abn2''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvpA ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yxiA ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' ||  
+
|style="background:#ABCDEF;" align="center"| '''Product''' || endo-1,5-alpha-L-arabinosidase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+
|style="background:#ABCDEF;" align="center"|'''Function''' || arabinan degradation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 24 kDa, 9.14  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52 kDa, 7.371  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 663 bp, 221 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1407 bp, 469 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvpB]]'', ''[[yvoF]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yxiB]]'', ''[[hutP]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yvpA_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|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/yvpA_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yxiA_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yvpA_context.gif]]
+
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors
−
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
+
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:yxiA_context.gif]]
 
|-
 
|-
 
|}
 
|}
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yxiA.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14129]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11130]
  
 
=== Additional information===
 
=== Additional information===
Line 61: Line 62:
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
  
−
* '''Kinetic information:'''
+
* '''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]
  
 
* '''Domains:'''  
 
* '''Domains:'''  
Line 73: Line 74:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
+
* '''Localization:''' extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed],  extracellular [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU34950]
+
* '''KEGG entry:'''
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' 3.2.1.99
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''abn2'' [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]
  
−
* '''Sigma factor:'''  
+
* '''Sigma factor:''' [[SigA]], [[SigH]] [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' repressed by glucose (4.3-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed],  expression is stimulated by arabinose and pectin and repressed by glucose [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression,  unknown [http://www.ncbi.nlm.nih.gov/sites/entrez/18408032 PubMed]
  
 
* '''Additional information:'''  
 
* '''Additional information:'''  
Line 114: 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=
  
 
# 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]
 
# 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]
 +
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
 +
# 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 16:26, 6 April 2009

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

Gene name abn2
Synonyms yxiA
Essential no
Product endo-1,5-alpha-L-arabinosidase
Function arabinan degradation
MW, pI 52 kDa, 7.371
Gene length, protein length 1407 bp, 469 aa
Immediate neighbours yxiB, hutP
Gene sequence (+200bp) Protein sequence
Caution: The sequence for this gene in SubtiList contains errors
Genetic context
YxiA 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: 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. PubMed
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: extracellular (signal peptide) PubMed, extracellular PubMed

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry:
  • E.C. number: 3.2.1.99

Additional information

Expression and regulation

  • Regulation: repressed by glucose (4.3-fold) (CcpA) PubMed, expression is stimulated by arabinose and pectin and repressed by glucose PubMed
  • Regulatory mechanism: CcpA: transcription repression, unknown PubMed
  • Additional information:

Biological materials

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

Labs working on this gene/protein

Isabel de Sa-Nogueira, Lisboa, Portugal homepage

Your additional remarks

References

  1. Voigt et al. (2009) Cell physiology and protein secretion of Bacillus licheniformis compared to Bacillus subtilis. J Mol Microbiol Biotechnol. 16: 53-68 PubMed
  2. Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metab Eng. 5: 133-149 PubMed
  3. 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. PubMed
  4. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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