Difference between revisions of "Sandbox"

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−
* '''Description:''' 3-hydroxy-1-pyrroline-5-carboxylate dehydrogenase <br/><br/>
+
* '''Description:''' ornithine transaminase <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'''
−
|''rocA''
+
|''rocD''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ipa-76d ''
+
|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''' || 3-hydroxy-1-pyrroline-5-carboxylate dehydrogenase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || ornithine transaminase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || arginine, ornithine and citrulline utilization  
+
|style="background:#ABCDEF;" align="center"|'''Function''' || arginine, ornithine and citrulline utilization
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 56 kDa, 5.58  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 43 kDa, 4.894  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1545 bp, 515 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1203 bp, 401 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rocB]]'', ''[[rocG]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rocE]]'', ''[[rocR]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15805&#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:CAB16071&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:rocA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:rocD_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:''' BSU37780
+
* '''Locus tag:''' BSU40340
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rocABC.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rocDEF.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10622]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10722]
  
 
=== Additional information===
 
=== Additional information===
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' (S)-1-pyrroline-5-carboxylate + NAD(P)<sup>+</sup> + 2 H<sub>2</sub>O = L-glutamate + NAD(P)H (according to Swiss-Prot)  
+
* '''Catalyzed reaction/ biological activity:''' L-ornithine + a 2-oxo acid = L-glutamate 5-semialdehyde + an L-amino acid (according to Swiss-Prot)  
  
−
* '''Protein family:''' RocA subfamily (according to Swiss-Prot)
+
* '''Protein family:''' OAT subfamily (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylation on (Thr-2 OR Thr-4 OR Tyr-5) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
+
* '''Modification:'''
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39634 P39634]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P38021 P38021]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU37780]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU40340]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.5.1.12 1.5.1.12]
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.6.1.13 2.6.1.13]
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[rocA]]-[[rocB]]-[[rocC]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/8113162 PubMed]
+
* '''Operon:''' ''[[rocD]]-[[rocE]]-[[rocF]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/7540694 PubMed]  
  
−
* '''[[Sigma factor]]:''' [[SigL]] [http://www.ncbi.nlm.nih.gov/sites/entrez/8113162 PubMed]
+
* '''[[Sigma factor]]:''' [[SigL]] [http://www.ncbi.nlm.nih.gov/sites/entrez/7540694 PubMed]  
  
−
* '''Regulation:''' induction by arginine ([[RocR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/8113162 PubMed], repressed by [[CodY]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]
+
* '''Regulation:''' induced by arginine ([[RocR]], [[AhrC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/7540694 PubMed], repressed by [[CodY]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]
  
−
* '''Regulatory mechanism:''' [[CodY]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed], [[RocR]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/8113162 PubMed]
+
* '''Regulatory mechanism:''' [[RocR]], [[AhrC]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/7540694 PubMed], [[CodY]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]
  
 
* '''Additional information:'''
 
* '''Additional information:'''
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=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:'''
+
* '''Mutant:''' GP656, aphA3, available in the [[Stülke]] lab
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
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=References=
 
=References=
  
−
<pubmed>8113162 17218307, </pubmed>
+
<pubmed>7540694, </pubmed>
−
# Calogero S, Gardan R, Glaser P, Schweizer J, Rapoport G, Debarbouille M. (1994) RocR, a novel regulatory protein controlling arginine utilization in ''Bacillus subtilis'', belongs to the NtrC/NifA family of transcriptional activators. ''J. Bacteriol.'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/8113162 PubMed]
+
# Gardan R, Rapoport G, Débarbouillé M. (1995) Expression of the rocDEF operon involved in arginine catabolism in Bacillus subtilis. ''J Mol Biol. '' '''Jun 23;249(5):''' 843-56. [http://www.ncbi.nlm.nih.gov/sites/entrez/7540694 PubMed]  
−
# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model  bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707  [http://www.ncbi.nlm.nih.gov/pubmed/17218307 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 13:33, 8 June 2009

  • Description: ornithine transaminase

Gene name rocD
Synonyms
Essential no
Product ornithine transaminase
Function arginine, ornithine and citrulline utilization
MW, pI 43 kDa, 4.894
Gene length, protein length 1203 bp, 401 aa
Immediate neighbours rocE, rocR
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
RocD context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU40340

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: L-ornithine + a 2-oxo acid = L-glutamate 5-semialdehyde + an L-amino acid (according to Swiss-Prot)
  • Protein family: OAT subfamily (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

  • Additional information:

Biological materials

  • Mutant: GP656, aphA3, available in the Stülke lab
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

  1. Gardan R, Rapoport G, Débarbouillé M. (1995) Expression of the rocDEF operon involved in arginine catabolism in Bacillus subtilis. J Mol Biol. Jun 23;249(5): 843-56. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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