Difference between revisions of "Sandbox"

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−
* '''Description:''' glucosamine-6-phosphate deaminase <br/><br/>
+
* '''Description:''' aminomethyltransferase (glycine cleavage system protein T) <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'''
−
|''gamA''
+
|''gcvT''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybfT ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqhI ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || glucosamine-6-phosphate deaminase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || aminomethyltransferase <br/>(glycine cleavage system protein T)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || glucosamine utilization
+
|style="background:#ABCDEF;" align="center"|'''Function''' || glycine utilization  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 27 kDa, 5.793  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 39 kDa, 5.734  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 747 bp, 249 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1086 bp, 362 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gamP]]'', ''[[ybgA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gcvPA]]'', ''[[yqhH]]''
 
|-
 
|-
−
|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)'''
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14388&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:gamA_context.gif]]
+
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:gcvT_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/><br/>
  
 
=The gene=
 
=The gene=
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU02360
+
* '''Locus tag:''' BSU24570
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gcvT-gcvPA-gcvPB.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12746]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11509]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''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)  
+
* '''Catalyzed reaction/ biological activity:''' [Protein]-S(8)-aminomethyldihydrolipoyllysine + tetrahydrofolate = [protein]-dihydrolipoyllysine + 5,10-methylenetetrahydrofolate + NH<sub>3</sub> (according to Swiss-Prot)  
  
−
* '''Protein family:''' NagB subfamily (according to Swiss-Prot)
+
* '''Protein family:''' gcvT family (according to Swiss-Prot)
  
−
* '''Paralogous protein(s):''' [[NagB]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1YX2 1YX2]
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O31458 O31458]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P54378 P54378]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU02360]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU24570]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.1.2.10 2.1.2.10]
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[gamA]]-[[gamP]]''
+
* '''Operon:''''' [[gcvT]]-[[gcvPA]]-[[gcvPB]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/15472076 PubMed]
  
 
* '''[[Sigma factor]]:'''  
 
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:'''  
+
* '''Regulation:''' induced by glycine [http://www.ncbi.nlm.nih.gov/sites/entrez/15472076 PubMed]
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' induction requires a co-operatively acting riboswitch [http://www.ncbi.nlm.nih.gov/sites/entrez/15472076 PubMed]
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 118: Line 120:
 
=References=
 
=References=
  
−
<pubmed>10627040, </pubmed>
+
<pubmed>15472076, </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]
+
# Mandal M, Lee M, Barrick JE, Weinberg Z, Emilsson GM, Ruzzo WL, Breaker RR (2004) A glycine-dependent riboswitch that uses cooperative binding to control gene expression. ''Science'' '''306:''' 275-279. [http://www.ncbi.nlm.nih.gov/sites/entrez/15472076 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 14:04, 8 June 2009

  • Description: aminomethyltransferase (glycine cleavage system protein T)

Gene name gcvT
Synonyms yqhI
Essential no
Product aminomethyltransferase
(glycine cleavage system protein T)
Function glycine utilization
MW, pI 39 kDa, 5.734
Gene length, protein length 1086 bp, 362 aa
Immediate neighbours gcvPA, yqhH
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
GcvT context.gif
This image was kindly provided by SubtiList






The gene

Basic information

  • Locus tag: BSU24570

Phenotypes of a mutant

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: [Protein]-S(8)-aminomethyldihydrolipoyllysine + tetrahydrofolate = [protein]-dihydrolipoyllysine + 5,10-methylenetetrahydrofolate + NH3 (according to Swiss-Prot)
  • Protein family: gcvT 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

  • KEGG entry: [3]

Additional information

Expression and regulation

  • Regulation: induced by glycine PubMed
  • Regulatory mechanism: induction requires a co-operatively acting riboswitch PubMed
  • 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

Maumita Mandal, Mark Lee, Jeffrey E Barrick, Zasha Weinberg, Gail Mitchell Emilsson, Walter L Ruzzo, Ronald R Breaker
A glycine-dependent riboswitch that uses cooperative binding to control gene expression.
Science: 2004, 306(5694);275-9
[PubMed:15472076] [WorldCat.org] [DOI] (I p)

  1. Mandal M, Lee M, Barrick JE, Weinberg Z, Emilsson GM, Ruzzo WL, Breaker RR (2004) A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science 306: 275-279. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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