Difference between revisions of "Sandbox"

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Line 4: Line 4:
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
−
|''nrgA''
+
|''rbsC''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''amtB ''
+
|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''' || ammonium transporter
+
|style="background:#ABCDEF;" align="center"| '''Product''' || ribose ABC transporter (permease)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || ammonium uptake
+
|style="background:#ABCDEF;" align="center"|'''Function''' || ribose transport
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 42 kDa, 5.727  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 10.309  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1212 bp, 404 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 966 bp, 322 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywoB]]'', ''[[nrgB]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rbsA]]'', ''[[rbsB]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/nrgA_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/rbsC_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/nrgA_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/rbsC_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:nrgA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:rbsC_context.gif]]
 
|-
 
|-
 
|}
 
|}
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/nrgAB.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rbsRKDACB.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10869]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10880]
  
 
=== Additional information===
 
=== Additional information===
Line 70: Line 70:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[NrgA]]-[[NrgB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/14600241 PubMed]
+
* '''Interactions:'''
  
−
* '''Localization:''' membrane
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
Line 88: Line 88:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[nrgA]]-[[nrgB]]''
+
* '''Operon:''' ''[[rbsR]]-[[rbsK]]-[[rbsD]]-[[rbsA]]-[[rbsC]]-[[rbsB]]''
  
 
* '''Sigma factor:''' [[SigA]]
 
* '''Sigma factor:''' [[SigA]]
  
−
* '''Regulation:''' induced by ammonium limitation
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' transcription activation by [[TnrA]]
+
* '''Regulatory mechanism:'''  
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 113: Line 113:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Susan Fisher]], Boston, USA [http://www.bumc.bu.edu/microbiology/research/susan-h-fisher-phd/ homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 120: Line 118:
 
=References=
 
=References=
  
−
 
+
# Woodson K, Devine KM. (1994) Analysis of a ribose transport operon from Bacillus subtilis. ''Microbiology. '' '''Aug;140 ( Pt 8):''' 1829-38. [http://www.ncbi.nlm.nih.gov/sites/entrez/7921236 PubMed]
−
# Atkinson MR, Fisher SH (1991) Identification of genes and gene products whose expression is activated during nitrogen-limited growth in Bacillus subtilis. J Bacteriol 173:23-27. [http://www.ncbi.nlm.nih.gov/sites/entrez/1670935 PubMed]
 
−
# Wray, L. V., Atkinson, M. R. & Fisher, S. H. (1994). The nitrogen-regulated Bacillus subtilis nrgAB operon encodes a membrane protein and a protein highly similar to the Escherichia coli glnB-encoded PII protein. J Bacteriol 176, 108-114. [http://www.ncbi.nlm.nih.gov/sites/entrez/8282685 PubMed]
 
−
# Detsch, C. & Stülke, J. (2003) Ammonium utilization in Bacillus subtilis: transport and regulatory functions of NrgA and NrgB. Microbiology 149: 3289-3297. [http://www.ncbi.nlm.nih.gov/sites/entrez/14600241 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 16:52, 9 March 2009

  • Description: write here

Gene name rbsC
Synonyms
Essential no
Product ribose ABC transporter (permease)
Function ribose transport
MW, pI 33 kDa, 10.309
Gene length, protein length 966 bp, 322 aa
Immediate neighbours rbsA, rbsB
Gene sequence (+200bp) Protein sequence
Genetic context
RbsC context.gif



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:
  • Swiss prot entry:
  • KEGG entry:
  • 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. Woodson K, Devine KM. (1994) Analysis of a ribose transport operon from Bacillus subtilis. Microbiology. Aug;140 ( Pt 8): 1829-38. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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