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'''
−
|''mntD''
+
|''nrgA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ytgD ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''amtB ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || manganese ABC transporter
+
|style="background:#ABCDEF;" align="center"| '''Product''' || ammonium transporter
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || manganese uptake
+
|style="background:#ABCDEF;" align="center"|'''Function''' || ammonium uptake
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 30 kDa, 6.308  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 42 kDa, 5.727  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 885 bp, 295 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1212 bp, 404 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ythC]]'', ''[[mntC]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywoB]]'', ''[[nrgB]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/mntD_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|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/mntD_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/nrgA_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:mntD_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:nrgA_context.gif]]
 
|-
 
|-
 
|}
 
|}
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/mntABCD.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/nrgAB.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13854]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10869]
  
 
=== Additional information===
 
=== Additional information===
Line 70: Line 70:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''Interactions:''' [[NrgA]]-[[NrgB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/14600241 PubMed]
  
−
* '''Localization:'''
+
* '''Localization:''' membrane
  
 
=== Database entries ===
 
=== Database entries ===
Line 88: Line 88:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[nrgA]]-[[nrgB]]''
  
−
* '''Sigma factor:'''  
+
* '''Sigma factor:''' [[SigA]]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' induced by ammonium limitation
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' transcription activation by [[TnrA]]
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
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 118: Line 120:
 
=References=
 
=References=
  
−
# Que Q, Helmann JD. (2000) Manganese homeostasis in Bacillus subtilis is regulated by MntR, a bifunctional regulator related to the diphtheria toxin repressor family of proteins. ''Mol Microbiol. '' '''Mar;35(6):''' 1454-68. [http://www.ncbi.nlm.nih.gov/sites/entrez/10760146 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 nrgA
Synonyms amtB
Essential no
Product ammonium transporter
Function ammonium uptake
MW, pI 42 kDa, 5.727
Gene length, protein length 1212 bp, 404 aa
Immediate neighbours ywoB, nrgB
Gene sequence (+200bp) Protein sequence
Genetic context
NrgA 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:
  • Localization: membrane

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry:
  • E.C. number:

Additional information

Expression and regulation

  • Regulation: induced by ammonium limitation
  • Regulatory mechanism: transcription activation by TnrA
  • Additional information:

Biological materials

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

Labs working on this gene/protein

Susan Fisher, Boston, USA homepage

Your additional remarks

References

  1. 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. PubMed
  2. 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. PubMed
  3. Detsch, C. & Stülke, J. (2003) Ammonium utilization in Bacillus subtilis: transport and regulatory functions of NrgA and NrgB. Microbiology 149: 3289-3297. PubMed
  4. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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