Difference between revisions of "Sandbox"

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* '''Description:''' DNA polymerase  III (beta subunit), beta clamp <br/><br/>
+
* '''Description:''' 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase <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'''
−
|''dnaN''
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|''mtnX ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''dnaG, dnaK ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ykrX''
 
|-
 
|-
−
|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''' || DNA polymerase  III <br/>(beta subunit), beta clamp
+
|style="background:#ABCDEF;" align="center"| '''Product''' || 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || DNA replication
+
|style="background:#ABCDEF;" align="center"|'''Function''' || methionine salvage
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 4.718  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 26 kDa, 4.658  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1134 bp, 378 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 705 bp, 235 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dnaA]]'', ''[[yaaA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[mtnW]]'', ''[[mtnB]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11778&#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:CAB13233&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:DnaA_dnaN_yaaA_recF_yaaB_gyrB_context.png]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ykrX_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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__TOC__
 
__TOC__
  
−
<br/><br/><br/>
+
<br/><br/>
  
 
=The gene=
 
=The gene=
Line 38: Line 38:
  
 
===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/dnaAN.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/mtnWXBD.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10066]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13283]
  
 
=== Additional information===
 
=== Additional information===
Line 72: Line 70:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[DnaA]]-[[YabA]]-[[DnaN]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12060778 PubMed]
+
* '''Interactions:'''
  
−
* '''Localization:''' cytoplasm (according to Swiss-Prot),  Nucleoid (Mid-cell) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed] nucleoid (mid-cell spot) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P05649 P05649]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O31667 O31667]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00020]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU13600]
  
−
* '''E.C. number:''' 2.7.7.7
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[dnaA]]-[[dnaN]]''  [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
+
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' [[SigA]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' negatively controlled by [[DnaA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2168872 PubMed] and [[Spo0A]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
+
* '''Regulation:''' repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]   
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
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=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
[[Philippe Noirot]], Jouy-en-Josas, France [http://locus.jouy.inra.fr/cms/index.php?id=18 homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 121: Line 118:
 
=References=
 
=References=
  
−
# Meile et al. (2006) Systematic localisation of proteins fused to the green fluorescent protein in ''Bacillus subtilis'': identification of new proteins at the DNA replication factory ''Proteomics'' '''6:''' 2135-2146. [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
+
# M&#228;der et al. (2002) Transcriptome and Proteome Analysis of ''Bacillus subtilis'' Gene Expression Modulated by Amino Acid Availability. ''J. Bacteriol'' '''184:''' 1844288-4295 [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]
−
# Ogasawara et al. (1985) Structure and function of the region of the replication origin of the ''Bacillus subtilis'' chromosome. IV. Transcription of the oriC region and expression of DNA gyrase genes and other open reading frames.''Nucl. Acids Res.'' '''11:''' 2267-2279. [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
 
−
# Fukuoka et al.  (1990) Purification and characterization of an initiation protein for chromosomal replication, DnaA, in ''Bacillus subtilis''. ''J. Biochem.'' '''107:''' 732-739. [http://www.ncbi.nlm.nih.gov/sites/entrez/2168872 PubMed]
 
−
# Meile et al. (2006) Systematic localisation of proteins fused to the green fluorescent protein in Bacillus subtilis: identification of new proteins at the DNA replication factory ''Proteomics'' '''6:''' 2135-2146. [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
 
−
# Molle et al. (2003) The Spo0A regulon of ''Bacillus subtilis''.''Mol. Microbiol.'' '''50:''' 1683-1701. [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
 
−
# Noirot-Gros et al. (2002) An expanded view of bacterial DNA replication. ''Proc. Natl. Acad. Sci. USA'' '''99:''' 8342-8347. [http://www.ncbi.nlm.nih.gov/sites/entrez/12060778 PubMed]
 
−
# Noirot-Gros et al. (2002) Functional dissection of YabA, a negative regulator of DNA replication initiation in Bacillus Title ''Proc. Natl. Acad. Sci. USA'' '''103:''' 2368-2373. [http://www.ncbi.nlm.nih.gov/sites/entrez/16461910 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 22:56, 4 May 2009

  • Description: 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase

Gene name mtnX
Synonyms ykrX
Essential no
Product 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase
Function methionine salvage
MW, pI 26 kDa, 4.658
Gene length, protein length 705 bp, 235 aa
Immediate neighbours mtnW, mtnB
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YkrX context.gif
This image was kindly provided by SubtiList



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

Database entries

  • Structure:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Regulation: repressed by casamino acids PubMed
  • 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. Mäder et al. (2002) Transcriptome and Proteome Analysis of Bacillus subtilis Gene Expression Modulated by Amino Acid Availability. J. Bacteriol 184: 1844288-4295 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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