Difference between revisions of "Sandbox"

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−
* '''Description:''' aldehyde dehydrogenase (NAD), general stress protein <br/><br/>
+
* '''Description:''' alanine racemase <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'''
−
|''aldY''
+
|''alr''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yxkE ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''dal, alrA ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || aldehyde dehydrogenase (NAD)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || alanine racemase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || stress resistance
+
|style="background:#ABCDEF;" align="center"|'''Function''' || peptidoglycan biosynthesis
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52 kDa, 5.021  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 43 kDa, 8.431  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1455 bp, 485 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1167 bp, 389 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yxkF]]'', ''[[yxkD]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ydcC]]'', ''[[ndoAI]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15909&#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:CAB12271&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:aldY_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:alr_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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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU38830
+
* '''Locus tag:''' BSU04640
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/aldY.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11903]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10950]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' L-alanine = D-alanine (according to Swiss-Prot)
  
−
* '''Protein family:''' aldehyde dehydrogenase family (according to Swiss-Prot)
+
* '''Protein family:''' alanine racemase family (according to Swiss-Prot)
  
−
* '''Paralogous protein(s):'''
+
* '''Paralogous protein(s):''' [[YncD]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 76: Line 78:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1L6G 1L6G] (with N-[5�-phosphopyridoxyl]-D-alanine, Geobacillus stearothermophilus),  [http://www.rcsb.org/pdb/explore.do?structureId=1SFT 1SFT] (Geobacillus stearothermophilus)
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P94358 P94358]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P10725 P10725]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU38830]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU04640]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/5.1.1.1 5.1.1.1]
  
 
=== Additional information===
 
=== Additional information===
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* '''Operon:'''  
 
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
+
* '''Regulation:'''  
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 118: Line 120:
 
=References=
 
=References=
  
−
# H&ouml;per et al. (2005) Comprehensive Characterization of the Contribution of Individual [[SigB]]-Dependent General Stress Genes to Stress Resistance of ''Bacillus subtilis''. J. Bact. '''187:''' 2810-2826  [http://www.ncbi.nlm.nih.gov/pubmed/15805528 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 09:53, 3 June 2009

  • Description: alanine racemase

Gene name alr
Synonyms dal, alrA
Essential yes PubMed
Product alanine racemase
Function peptidoglycan biosynthesis
MW, pI 43 kDa, 8.431
Gene length, protein length 1167 bp, 389 aa
Immediate neighbours ydcC, ndoAI
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
Alr context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU04640

Phenotypes of a mutant

essential PubMed

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: L-alanine = D-alanine (according to Swiss-Prot)
  • Protein family: alanine racemase family (according to Swiss-Prot)
  • Paralogous protein(s): YncD

Extended information on the protein

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

Database entries

  • Structure: 1L6G (with N-[5�-phosphopyridoxyl]-D-alanine, Geobacillus stearothermophilus), 1SFT (Geobacillus stearothermophilus)
  • KEGG entry: [2]

Additional information

Expression and regulation

  • Operon:
  • 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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