Difference between revisions of "Sandbox"

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−
* '''Description:''' acetolactate decarboxylase <br/><br/>
+
* '''Description:''' amino acid carrier protein <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'''
−
|''alsD''
+
|''alsT''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || acetolactate decarboxylase)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || amino acid carrier protein
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || overflow metabolism
+
|style="background:#ABCDEF;" align="center"|'''Function''' || amino acid uptake
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 4.603  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 9.39  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 765 bp, 255 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1395 bp, 465 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywrO]]'', ''[[alsS]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ynfC]]'', ''[[bglC]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15617&#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:CAB13695&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:alsD_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:alsT_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:''' BSU36000
+
* '''Locus tag:''' BSU18120
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/alsSD.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10472]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11798]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' (2S)-2-hydroxy-2-methyl-3-oxobutanoate = (3R)-3-hydroxybutan-2-one + CO<sub>2</sub> (according to Swiss-Prot)
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' alpha-acetolactate decarboxylase family (according to Swiss-Prot)
+
* '''Protein family:''' sodium:alanine (SAF) symporter family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 64: Line 64:
 
* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylated on ser/ thr/ tyr [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
+
* '''Modification:'''
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:'''
+
* '''Localization:''' cell membrane (according to Swiss-Prot),  membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/Q04777 Q04777]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/Q45068 Q45068]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU36000]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU18120]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/4.1.1.5 4.1.1.5]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[alsS]]-[[alsD]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/7685336 PubMed]
+
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/7685336 PubMed]
+
* '''[[Sigma factor]]:'''  
  
−
* '''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]
+
* '''Regulation:'''  
−
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 [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]
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
  
−
<pubmed>16493705 7685336 16428414, </pubmed>
+
<pubmed>18763711, </pubmed>
−
# L&#233;vine et al. (2006) Analysis of the dynamic ''Bacillus subtilis'' Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. ''Proteomics'' '''6:''' 2157-2173 [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
+
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics '''8:''' 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
−
# Renna, M. C., Najimudin, N., Winik, L. R., and Zahler, S. A. (1993). Regulation of the ''Bacillus subtilis alsS'', ''alsD'', and ''alsR'' genes involved in post-exponential-phase production of acetoin. J. Bacteriol. 175, 3863-3875. [http://www.ncbi.nlm.nih.gov/sites/entrez/7685336 PubMed]
 
−
# Reents, H., R. Münch, T. Dammeyer, D. Jahn, and E. Härtig. 2006. The Fnr regulon of ''Bacillus subtilis''. J. Bacteriol. 188: 1103-1112. [http://www.ncbi.nlm.nih.gov/sites/entrez/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 13:56, 8 June 2009

  • Description: amino acid carrier protein

Gene name alsT
Synonyms
Essential no
Product amino acid carrier protein
Function amino acid uptake
MW, pI 50 kDa, 9.39
Gene length, protein length 1395 bp, 465 aa
Immediate neighbours ynfC, bglC
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
AlsT context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU18120

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family: sodium:alanine (SAF) symporter 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: cell membrane (according to Swiss-Prot), membrane PubMed

Database entries

  • Structure:
  • KEGG entry: [2]
  • E.C. number:

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

Hannes Hahne, Susanne Wolff, Michael Hecker, Dörte Becher
From complementarity to comprehensiveness--targeting the membrane proteome of growing Bacillus subtilis by divergent approaches.
Proteomics: 2008, 8(19);4123-36
[PubMed:18763711] [WorldCat.org] [DOI] (I p)

  1. Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing Bacillus subtilis by divergent approaches. Proteomics 8: 4123-4136 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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