Difference between revisions of "Sandbox"

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−
* '''Description:''' general stress protein, similar to L25 <br/><br/>
+
* '''Description:''' similar to amino acid transporter <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'''
−
|''ctc''
+
|''yabM''
 
|-
 
|-
 
|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''' || ribosomal protein
+
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown  
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 21 kDa, 4.216  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 57 kDa, 9.623  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 612 bp, 204 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1596 bp, 532 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[prs]]'', ''[[spoVC]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[spoVT]]'', ''[[yabN]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ctc_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yabM_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ctc_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yabM_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ctc_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yabM_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 42: Line 42:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gcaD-prs-ctc.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yabMNOPQ-divIC-yabR.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10115]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10120]
  
 
=== Additional information===
 
=== Additional information===
Line 55: Line 55:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' Ctc subfamily
+
* '''Protein family:''' polysaccharide synthase family
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 71: Line 71:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' binds 5S rRNA [http://www.ncbi.nlm.nih.gov/sites/entrez/12432960 PubMed]
+
* '''Interactions:'''
  
−
* '''Localization:''' in the ribosome (large subunit) [http://www.ncbi.nlm.nih.gov/sites/entrez/12432960 PubMed]
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00520]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00570]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 87: Line 87:
 
=== 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=
  
−
* '''Operon:''' ''[[gcaD]]-[[prs]]-[[ctc]]'', ''[[ctc]]''
+
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' ''[[gcaD]]'': [[SigA]], ''[[ctc]]'': [[SigB]]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed], induced under stress conditions
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' alternative [[sigma factor]], [[SigB]]
+
* '''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 =
Line 112: Line 111:
 
* '''two-hybrid system:'''  
 
* '''two-hybrid system:'''  
  
−
* '''Antibody:''' available in [[Stülke]] lab
+
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
Line 120: Line 119:
 
=References=
 
=References=
  
−
# H&ouml;per et al. (2005) Comprehensive Characterization of the Contribution of Individual [[SigB]]-Dependent General Stress Genes to Stress Resistance of ''Bacillus subtilis''. J. Bact. '''187:''' 2810-2826  [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
 
−
# Gerth et al. (2008) Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis. J Bacteriol 190:321-331 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
 
−
# Schmalisch, M., Langbein, I. & Stülke, J. (2002) The general stress protein Ctc of ''Bacillus subtilis'' is a ribosomal protein. J. Mol. Microbiol. Biotechnol. 4: 495-501.  [http://www.ncbi.nlm.nih.gov/sites/entrez/12432960 PubMed]
 
−
# Ollington, J. F., Haldenwang, W. G., Huynh, T. V. and Losick, R. 1981. Developmentally regulated transcription in a cloned segment of the ''Bacillus subtilis'' chromosome. J. Bacteriol. 147: 432-442. [http://www.ncbi.nlm.nih.gov/sites/entrez/6790515 PubMed]
 
−
# Truitt, C. L., Weaver, E. A. and Haldenwang, W. G. 1988. Effects on growth and sporulation of inactivation of a ''Bacillus subtilis'' gene (''ctc'') transcribed in vitro by minor vegetative cell RNA polymerases (E-sigma(37), E-sigma(32)). Mol. Gen. Genet. 212: 166-171. [http://www.ncbi.nlm.nih.gov/sites/entrez/2836704 PubMed]
 
−
# Haldenwang, W. G. & Losick, R. (1979). A modified RNA polymerase transcribes a cloned gene under sporulation control in ''Bacillus subtilis''. Nature 282, 256-260 [http://www.ncbi.nlm.nih.gov/pubmed/116131 PubMed]
 
−
# Gongadze GM, Korepanov AP, Korobeinikova AV, Garber MB (2008) Bacterial 5S rRNA-binding proteins of the CTC family. ''Biochemistry (Moscow)'' '''73:''' 1405-1417. [http://www.ncbi.nlm.nih.gov/sites/entrez/19216708 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 02:54, 12 April 2009

  • Description: similar to amino acid transporter

Gene name yabM
Synonyms
Essential no
Product unknown
Function unknown
MW, pI 57 kDa, 9.623
Gene length, protein length 1596 bp, 532 aa
Immediate neighbours spoVT, yabN
Gene sequence (+200bp) Protein sequence
Genetic context
YabM 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: polysaccharide synthase 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: [3]
  • 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

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