Difference between revisions of "Sandbox"

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* '''Description:''' glucosamine-specific phosphotransferase system, EIICBA <br/><br/>
+
* '''Description:''' glucosamine-6-phosphate deaminase <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'''
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|''gamP''
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|''gamA''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybfS, yzfA ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybfT ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || glucosamine-specific phosphotransferase system, EIICBA
+
|style="background:#ABCDEF;" align="center"| '''Product''' || glucosamine-6-phosphate deaminase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || glucosamine uptake and phosphorylation
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|style="background:#ABCDEF;" align="center"|'''Function''' || glucosamine utilization
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 67 kDa, 5.472  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 27 kDa, 5.793  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1893 bp, 631 aa  
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 747 bp, 249 aa  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gltP]]'', ''[[gamA]]''
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gamP]]'', ''[[ybgA]]''
 
|-
 
|-
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/gamP_nucleotide.txt    Gene sequence      (+200bp)  ]'''
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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:CAB12030&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/gamP_protein.txt Protein sequence]'''
 
 
|-
 
|-
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|colspan="2" | '''Genetic context''' <br/> [[Image:gamP_context.gif]]
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|colspan="2" | '''Genetic context''' <br/> [[Image:gamA_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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===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
delayed growth with glucosamine as the single carbon source [http://www.ncbi.nlm.nih.gov/sites/entrez/10627040 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
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* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11014]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12746]
  
 
=== Additional information===
 
=== Additional information===
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' protein EIIA N(pi)-phospho-L-histidine + protein EIIB = protein EIIA + protein EIIB N(pi)-phospho-L-histidine/cysteine (according to Swiss-Prot)  
+
* '''Catalyzed reaction/ biological activity:''' d-glucosamine 6-phosphate + H<sub>2</sub>O = D-fructose 6-phosphate + NH<sub>3</sub> (according to Swiss-Prot)  
  
−
* '''Protein family:''' PTS permease, glucose permease (Glc) family [http://www.ncbi.nlm.nih.gov/pubmed/10627040 PubMed]
+
* '''Protein family:''' NagB subfamily (according to Swiss-Prot)
  
−
* '''Paralogous protein(s):'''
+
* '''Paralogous protein(s):''' [[NagB]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' cell membrane (according to Swiss-Prot),  membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39816 P39816]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O31458 O31458]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU02350 BSU02350]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU02360 BSU02360]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.1.69 2.7.1.69]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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# Reizer et al. (1999) Novel phosphotransferase system genes revealed by genome analysis - the complete complement of PTS proteins encoded within the genome of ''Bacillus subtilis''. ''Microbiology'' '''145:''' 3419-3429 [http://www.ncbi.nlm.nih.gov/pubmed/10627040 PubMed]
 
# Reizer et al. (1999) Novel phosphotransferase system genes revealed by genome analysis - the complete complement of PTS proteins encoded within the genome of ''Bacillus subtilis''. ''Microbiology'' '''145:''' 3419-3429 [http://www.ncbi.nlm.nih.gov/pubmed/10627040 PubMed]
−
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics '''8:''' 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
 
−
# Reizer, J., Bachem, S., Reizer, A., Arnaud, M., Saier Jr., M. H. & Stülke, J. (1999) Novel phosphotransferase system genes revealed by genome analysis – the complete complement of PTS proteins encoded within the genome of Bacillus subtilis. Microbiology 145: 3419-3429. [http://www.ncbi.nlm.nih.gov/sites/entrez/10627040 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 12:21, 23 May 2009

  • Description: glucosamine-6-phosphate deaminase

Gene name gamA
Synonyms ybfT
Essential no
Product glucosamine-6-phosphate deaminase
Function glucosamine utilization
MW, pI 27 kDa, 5.793
Gene length, protein length 747 bp, 249 aa
Immediate neighbours gamP, ybgA
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
GamA 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: d-glucosamine 6-phosphate + H2O = D-fructose 6-phosphate + NH3 (according to Swiss-Prot)
  • Protein family: NagB subfamily (according to Swiss-Prot)
  • Paralogous protein(s): NagB

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. Reizer et al. (1999) Novel phosphotransferase system genes revealed by genome analysis - the complete complement of PTS proteins encoded within the genome of Bacillus subtilis. Microbiology 145: 3419-3429 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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