Difference between revisions of "Sandbox"

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* '''Description:''' ATP-dependent Clp protease, ATPase subunit <br/><br/>
+
* '''Description:''' phosphatase (RapI) regulator <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'''
−
|''clpC''
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|''phrI''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''mecB ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || ATP-dependent Clp protease, ATPase subunit
+
|style="background:#ABCDEF;" align="center"| '''Product''' || phosphatase (RapI) regulator
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || protein degradation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || control of sporulation initiation
−
positive regulator of autolysin ([[LytC]] and [[LytD]]) synthesis
 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 89 kDa, 5.746  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 4 kDa, 8.907  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2430 bp, 810 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 117 bp, 39 aa  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[mcsB]]'', ''[[radA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rapI]]'', ''[[yddM]]''
 
|-
 
|-
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|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14213&#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:CAB12309&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:clpC_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:phrI_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/><br/>
  
 
=The gene=
 
=The gene=
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ctsR-mcsAB-clpC-radA-yacK.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rapI-phrI.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10148]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12645]
  
 
=== Additional information===
 
=== Additional information===
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' ATPase/chaperone
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' mecA family (according to Swiss-Prot) clpA/clpB family. ClpC subfamily (according to Swiss-Prot), AAA+ -type ATPase (IPR013093) [http://www.ebi.ac.uk/interpro/IEntry?ac=IPR013093 InterPro] (PF07724) [http://pfam.sanger.ac.uk/family?acc=PF07724 PFAM]
+
* '''Protein family:''' phr family (according to Swiss-Prot)
  
−
* '''Paralogous protein(s):''' [[ClpE]], [[ClpX]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Kinetic information:'''
 
* '''Kinetic information:'''
  
−
* '''Domains:''' AAA-ATPase [http://pfam.sanger.ac.uk/family?acc=PF07724 PFAM]
+
* '''Domains:'''  
  
 
* '''Modification:'''
 
* '''Modification:'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[YpbH]]-[[ClpC]],  [[McsB]]-[[ClpC]],  [[ClpC]]-[[MecA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/10447896 PubMed],  [[ClpC]]-[[ClpP]]
+
* '''Interactions:'''
  
−
* '''Localization:''' cytoplasmic polar clusters, excluded from the nucleoid, induced clustering upon heatshock, colocalization with [[ClpP]] [http://www.ncbi.nlm.nih.gov/pubmed/18786145 Pubmed]
+
* '''Localization:'''
−
[[File:ClpC.jpg‎ ]]
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2K77 2K77] (N-terminal domain)
+
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P37571 P37571]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O31492 O31492]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00860 BSU00860]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU05020 BSU05020]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=== Additional information===
 
=== Additional information===
  
−
:* subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
 
 
=Expression and regulation=
 
=Expression and regulation=
  
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* '''Operon:''' ''[[ctsR]]-[[mcsA]]-[[mcsB]]-[[clpC]]-[[radA]]-[[disA]]'' [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed]
+
* '''Operon:''' ''[[rapI]]-[[phrI]]''
  
−
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed], [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed1] [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed2]  
+
* '''[[Sigma factor]]:''' [[SigA]], [[SigH]] [http://www.ncbi.nlm.nih.gov/sites/entrez/11466295 Pubmed]
  
−
* '''Regulation:''' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed], induced by heat ([[CtsR]]) [http://www.ncbi.nlm.nih.gov/pubmed/9987115 PubMed]
+
* '''Regulation:'''  
  
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* '''Regulatory mechanism:''' [[CtsR]]: transcription repression [http://www.ncbi.nlm.nih.gov/pubmed/9987115 PubMed1], [http://www.ncbi.nlm.nih.gov/pubmed/11179229 PubMed2], [http://www.ncbi.nlm.nih.gov/pubmed/16163393 PubMed3], [http://www.ncbi.nlm.nih.gov/pubmed/17380125 PubMed4]
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:''' subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' ''clpC::tet'' available from the [http://subtiwiki.uni-goettingen.de/wiki/index.php/Leendert_Hamoen Hamoen]] Lab
+
* '''Mutant:'''
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
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* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
−
* '''GFP fusion:''' C-terminal GFP fusions (single copy, also as CFP and YFP variants) available from the [http://subtiwiki.uni-goettingen.de/wiki/index.php/Leendert_Hamoen Hamoen]] Lab
+
* '''GFP fusion:'''
  
 
* '''two-hybrid system:'''  
 
* '''two-hybrid system:'''  
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=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
[[Leendert Hamoen]], Newcastle University, UK [http://www.ncl.ac.uk/camb/staff/profile/l.hamoen homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
  
 
=References=
 
=References=
−
 
−
<pubmed> 11544224, 17981983, 14763982, 18786145, 19361434 </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 16:17, 25 May 2009

  • Description: phosphatase (RapI) regulator

Gene name phrI
Synonyms
Essential no
Product phosphatase (RapI) regulator
Function control of sporulation initiation
MW, pI 4 kDa, 8.907
Gene length, protein length 117 bp, 39 aa
Immediate neighbours rapI, yddM
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
PhrI 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: phr 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:
  • E.C. number:

Additional information

Expression and regulation

  • 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

  1. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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