Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' alanine racemase <br/><br/>
+
* '''Description:''' acetolactate synthase <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'''
−
|''alr''
+
|''alsS''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''dal, alrA ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || alanine racemase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || acetolactate synthase)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || peptidoglycan biosynthesis
+
|style="background:#ABCDEF;" align="center"|'''Function''' || overflow metabolism
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 43 kDa, 8.431  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 61 kDa, 5.164  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1167 bp, 389 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1713 bp, 571 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ydcC]]'', ''[[ndoAI]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[alsD]]'', ''[[alsR]]''
 
|-
 
|-
−
|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" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15618&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:alr_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:alsS_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>
 
|-
 
|-
Line 35: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU04640
+
* '''Locus tag:''' BSU36010
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/alsSD.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10950]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10471]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' L-alanine = D-alanine (according to Swiss-Prot)  
+
* '''Catalyzed reaction/ biological activity:''' 2 pyruvate = 2-acetolactate + CO<sub>2</sub> (according to Swiss-Prot)  
  
−
* '''Protein family:''' alanine racemase family (according to Swiss-Prot)
+
* '''Protein family:''' TPP enzyme family (according to Swiss-Prot)
  
−
* '''Paralogous protein(s):''' [[YncD]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 78: Line 76:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''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)
+
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P10725 P10725]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/Q04789 Q04789]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU04640]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU36010]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/5.1.1.1 5.1.1.1]
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.2.1.6 2.2.1.6]
  
 
=== Additional information===
 
=== Additional information===
Line 90: Line 88:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[alsS]]-[[alsD]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/7685336 PubMed]
  
−
* '''[[Sigma factor]]:'''  
+
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/7685336 PubMed]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' induction by acetate ([[AlsR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/7685336 PubMed], repressed as long as terminal electron acceptors are available for respiration ([[Rex]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/16428414 PubMed]
 +
Note: since acetate formation requires ''[[ackA]]'' activation by [[CcpA]] there is an indirect effect of [[CcpA]] on the ''alsSD'' operon: the operon is not expressed in ''[[ccpA]]'' mutants
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[AlsR]]: transcription activation in the presence of acetate [http://www.ncbi.nlm.nih.gov/sites/entrez/7685336 PubMed], [[Rex]]: transcription repression if the ratio NADH2/NAD is high [http://www.ncbi.nlm.nih.gov/sites/entrez/16428414 PubMed]
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 119: Line 118:
  
 
=References=
 
=References=
 +
 +
<pubmed> 19383131, 7685336, 16428414  </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: acetolactate synthase

Gene name alsS
Synonyms
Essential no
Product acetolactate synthase)
Function overflow metabolism
MW, pI 61 kDa, 5.164
Gene length, protein length 1713 bp, 571 aa
Immediate neighbours alsD, alsR
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
AlsS context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU36010

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: 2 pyruvate = 2-acetolactate + CO2 (according to Swiss-Prot)
  • Protein family: TPP enzyme 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:

Database entries

  • Structure:
  • KEGG entry: [3]

Additional information

Expression and regulation

  • Regulation: induction by acetate (AlsR) PubMed, repressed as long as terminal electron acceptors are available for respiration (Rex) PubMed

Note: since acetate formation requires ackA activation by CcpA there is an indirect effect of CcpA on the alsSD operon: the operon is not expressed in ccpA mutants

  • Regulatory mechanism: AlsR: transcription activation in the presence of acetate PubMed, Rex: transcription repression if the ratio NADH2/NAD is high PubMed
  • 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
Retrieved from "http://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=84099"