Difference between revisions of "Sandbox"

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−
* '''Description:''' germination (cortex hydrolysis) and sporulation <br/><br/>
+
* '''Description:''' RNase PH<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'''
−
|''gerM''
+
|''rph''
 
|-
 
|-
 
|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''' || unknown
+
|style="background:#ABCDEF;" align="center"| '''Product''' || exoribonuclease PH (EC 2.7.7.56)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || germination (cortex hydrolysis) and sporulation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || 3'-5' exoribonuclease
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 39 kDa, 4.683  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 26 kDa, 4.888  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1098 bp, 366 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 735 bp, 245 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rph]]'', ''[[racE]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ysnA]]'', ''[[gerM]]''
 
|-
 
|-
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:gerM_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:rph_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 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gerM.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10356]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10357]
  
 
=== Additional information===
 
=== Additional information===
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' 3'-5' exoribonuclease
  
 
* '''Protein family:'''
 
* '''Protein family:'''
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28380]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28370]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 90: Line 90:
 
* '''Operon:'''  
 
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:'''  
+
* '''Sigma factor:'''  
  
−
* '''Regulation:''' repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed] 
+
* '''Regulation:'''  
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
Line 113: Line 113:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[David Bechhofer]], Mount Sinai School, New York, USA [http://www.mountsinai.org/Research/Centers%20Laboratories%20and%20Programs/Bechhofer%20Laboratory?citype=Physician&ciid=Bechhofer%20David%20H%201255565 Homepage]
 +
 +
[[Ciaran Condon]], IBPC, Paris, France [http://www.ibpc.fr/UPR9073/condon/index_en.html Homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 118: Line 122:
 
=References=
 
=References=
  
−
# 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]
+
# Yao, S., Blaustein, J. B. & Bechhofer, D. H. (2007). Processing of ''Bacillus subtilis'' small cytoplasmic RNA: evidence for an additional endonuclease cleavage site. Nucleic Acids Res. 35:4464-4473. [http://www.ncbi.nlm.nih.gov/sites/entrez/17576666 PubMed]
 +
# Oussenko, I. A., Abe, T., Ujiie, H., Muto, A. & Bechhofer, D. H. (2005). Participation of 3'-to-5' exoribonucleases in the turnover of ''Bacillus subtilis'' mRNA. J Bacteriol 187:2758-2767. [http://www.ncbi.nlm.nih.gov/sites/entrez/15805522 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 18:24, 15 April 2009

  • Description: RNase PH

Gene name rph
Synonyms
Essential no
Product exoribonuclease PH (EC 2.7.7.56)
Function 3'-5' exoribonuclease
MW, pI 26 kDa, 4.888
Gene length, protein length 735 bp, 245 aa
Immediate neighbours ysnA, gerM
Hier soll was neues rein
Genetic context
Rph context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: 3'-5' exoribonuclease
  • 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:
  • Swiss prot entry:
  • KEGG entry: [2]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Sigma factor:
  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

David Bechhofer, Mount Sinai School, New York, USA Homepage

Ciaran Condon, IBPC, Paris, France Homepage

Your additional remarks

References

  1. Yao, S., Blaustein, J. B. & Bechhofer, D. H. (2007). Processing of Bacillus subtilis small cytoplasmic RNA: evidence for an additional endonuclease cleavage site. Nucleic Acids Res. 35:4464-4473. PubMed
  2. Oussenko, I. A., Abe, T., Ujiie, H., Muto, A. & Bechhofer, D. H. (2005). Participation of 3'-to-5' exoribonucleases in the turnover of Bacillus subtilis mRNA. J Bacteriol 187:2758-2767. PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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