Difference between revisions of "Sandbox"

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* '''Description:''' [[16S rRNA]]<br/><br/>
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* '''Description:''' glutamine-fructose-6-phosphate transaminase
  
{| align="right" border="1" cellpadding="2"  
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{| align="right" border="1" cellpadding="2" |- |style="background:#ABCDEF;" align="center"|'''Gene name''' |''glmS'' |- |style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''gcaA, ybxD '' |- |style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed] |- |style="background:#ABCDEF;" align="center"| '''Product''' || glutamine-fructose-6-phosphate transaminase |- |style="background:#ABCDEF;" align="center"|'''Function''' || cell wall synthesis |- |colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]:
|-
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[http://subtiwiki.uni-goettingen.de/pathways/murein/index.html Murein recycling]''' |- |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 65 kDa, 4.796 |- |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1800 bp, 600 aa |- |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[glmM]]'', ''[[ybbU]]'' |- |colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11954]+-newId sequences]
|style="background:#ABCDEF;" align="center"|'''Gene name'''
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(Barbe ''et al.'', 2009)''' |- |colspan="2" | '''Genetic context'''
|''rrnA-16S''
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[[Image:glmS_context.gif]]
|-
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This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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|- |colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=glmS_200277_202079_1 Expression at a glance]'''  {{PubMed|22383849}}
|-
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[[Image:glmS_expression.png|500px]] |- |} __TOC__
|style="background:#ABCDEF;" align="center"| '''Essential''' ||  
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Product''' || ribosomal RNA-16S
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || translation
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Gene length''' || 1553 bp
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[bofA]]'', ''[[trnA-Ile]]''
 
|-
 
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/rrnA-16S_nucleotide.txt    Gene sequence      (+200bp)   ]'''  
 
|-
 
|colspan="2" | '''Genetic context''' <br/> [[Image:rrnA-16S_context.gif]]
 
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
|-
 
|}
 
  
__TOC__
 
  
<br/><br/><br/><br/>
 
  
  
= [[Categories]] containing this gene/protein =
 
{{SubtiWiki category|[[translation]]}}
 
  
= This gene is a member of the following [[regulons]] =
 
  
  
=The gene=
 
  
=== Basic information ===
 
  
* '''Locus tag:'''
 
  
===Phenotypes of a mutant ===
 
  
=== Database entries ===
 
  
* '''DBTBS entry:''' no entry
 
  
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG00011]
 
  
* '''Structure:'''
 
  
=== Additional information===
 
  
  
  
  
=Expression and regulation=
 
  
* '''Operon:''' ''[[rrnA-16S]]-[[trnA-Ile]]-[[trnA-Ala]]-[[rrnA-23S]]-[[rrnA-5S]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/6312418 PubMed]
 
  
* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/6312418 PubMed]
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= [[Categories]] containing this gene/protein = {{SubtiWiki category|[[cell wall synthesis]]}}, {{SubtiWiki category|[[biosynthesis of cell wall components]]}}, {{SubtiWiki category|[[essential genes]]}} = This gene is a member of the following [[regulons]] = {{SubtiWiki regulon|[[glmS ribozyme]]}} =The gene= === Basic information === * '''Locus tag:''' BSU01780 ===Phenotypes of a mutant === essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed] === Database entries === * '''DBTBS entry:''' no entry * '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10948] === Additional information=== =The protein= === Basic information/ Evolution === * '''Catalyzed reaction/ biological activity:''' L-glutamine + D-fructose 6-phosphate = L-glutamate + D-glucosamine 6-phosphate (according to Swiss-Prot) * '''Protein family:''' * '''Paralogous protein(s):''' === Extended information on the protein === * '''Kinetic information:''' * '''Domains:''' * '''Modification:''' * '''Cofactor(s):''' * '''Effectors of protein activity:''' * '''[[SubtInteract|Interactions]]:''' * '''[[Localization]]:''' ** cytoplasm (according to Swiss-Prot) === Database entries === * '''Structure:'''[http://www.pdb.org/pdb/explore/explore.do?structureId=HIV HIV] (from ''Bacillus subtilis'', 100% identity) {{PubMed|13454352}}
 
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[http://www.pdb.org/pdb/explore/explore.do?structureId=2VF4 2VF4] (GlmS from ''E. coli'', 39% identity, 58% similarity) {{PubMed|18295797}} ** the ribozyme: [http://www.rcsb.org/pdb/explore.do?structureId=3g8s 3G8S], [http://www.rcsb.org/pdb/explore.do?structureId=3G9C 3G9C], [http://www.rcsb.org/pdb/explore.do?structureId=3g8t 3G8T], [http://www.rcsb.org/pdb/explore.do?structureId=3g95 3G95], [http://www.rcsb.org/pdb/explore.do?structureId=3g96 3G96] (all for the ribozyme from ''Bacillus anthracis''), [http://www.rcsb.org/pdb/explore.do?structureId=2HO7 2HO7] (the ribozyme from ''Thermonanaerobacter tengcongensis'') * '''UniProt:''' [http://www.uniprot.org/uniprot/P39754 P39754] * '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01780] * '''E.C. number:''' [http://www.expasy.org/enzyme/2.6.1.16 2.6.1.16] === 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= * '''Operon:''' ''[[ybbP]]-[[ybbR]]-[[glmM]]-[[glmS]]'' * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=glmS_200277_202079_1 glmS] {{PubMed|22383849}} * '''Sigma factor:''' [[SigA]] {{PubMed|22211522}} * '''Regulation:''' ** repressed by glucosamine, N-acetylglucosamine, N-propionylglucosamine or N-formylglucosamine {{PubMed|14343123}} ** ''glmS'' is only expressed in the absence of glucosamine 6-phosphate ([[glmS]] [[ribozyme]]) * '''Regulatory mechanism:''' ''glmS'' [[ribozyme]]: glucosamine 6-phosphate binds the leader mRNA, and a [[riboswitch]] with [[ribozyme]] activity cleaves off the ''[[glmS]]'' section from the mRNA, resulting in stopp of transcript elongation * '''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] ** A [[ncRNA]] is predicted between ''[[glmM]]'' and ''[[glmS]]'' {{PubMed|20525796}} =Biological materials = * '''Mutant:''' * '''Expression vector:''' * '''lacZ fusion:''' * '''GFP fusion:''' * '''two-hybrid system:''' * '''Antibody:''' =Labs working on this gene/protein= [[Wade Winkler]], University of Texas, USA, [http://www.utsouthwestern.edu/findfac/professional/0,,68018,00.html Homepage] =Your additional remarks= =References= ==Reviews== 18279655 ==The ''glmS'' Ribozyme== 18079181 ,16484375, 16784238 ,15096624 , 16990543 ,17114942 ,16484375 , 15029187, 17283212 , 16298301, 19228039 21317896 21395279 ==Other Original Publications== '''Additional publications:''' {{PubMed|22211522}} 14343123 17981983 ,11160890, 18295797 20525796 [[Category:Protein-coding genes]]
* '''Regulation:'''  
 
 
 
* '''Regulatory mechanism:'''  
 
 
 
* '''Additional information:'''
 
 
 
=Biological materials =
 
 
 
* '''Mutant:'''
 
 
 
* '''Expression vector:'''
 
       
 
* '''lacZ fusion:'''
 
 
 
* '''two-hybrid system:'''  
 
 
 
* '''Antibody:'''
 
 
 
=Labs working on this gene/RNA=
 
 
 
=Your additional remarks=
 
 
 
=References=
 
'''Additional publications:''' {{PubMed|21303765}}
 
<pubmed> 6312418, 19447912 20634236 </pubmed>
 
 
 
[[Category:Ribosomal RNA]]
 

Revision as of 13:54, 25 November 2013

  • Description: glutamine-fructose-6-phosphate transaminase
Murein recycling |- |style="background:#ABCDEF;" align="center"| MW, pI || 65 kDa, 4.796 |- |style="background:#ABCDEF;" align="center"| Gene length, protein length || 1800 bp, 600 aa |- |style="background:#ABCDEF;" align="center"|Immediate neighbours || glmM, ybbU |- |colspan="2" style="background:#FAF8CC;" align="center"|Get the DNA and protein [EMBLCDS:CAB11954+-newId sequences] (Barbe et al., 2009) |- |colspan="2" | Genetic context GlmS context.gif This image was kindly provided by SubtiListGlmS expression.png |- |} = Categories containing this gene/protein = cell wall synthesis, biosynthesis of cell wall components, essential genes = This gene is a member of the following regulons = glmS ribozyme =The gene= === Basic information === * Locus tag: BSU01780 ===Phenotypes of a mutant === essential PubMed === Database entries === * DBTBS entry: no entry * SubtiList entry:[1] === Additional information=== =The protein= === Basic information/ Evolution === * Catalyzed reaction/ biological activity: L-glutamine + D-fructose 6-phosphate = L-glutamate + D-glucosamine 6-phosphate (according to Swiss-Prot) * Protein family: * Paralogous protein(s): === Extended information on the protein === * Kinetic information: * Domains: * Modification: * Cofactor(s): * Effectors of protein activity: * Interactions: * Localization: ** cytoplasm (according to Swiss-Prot) === Database entries === * Structure:HIV (from Bacillus subtilis, 100% identity) PubMed2VF4 (GlmS from E. coli, 39% identity, 58% similarity) PubMed ** the ribozyme: 3G8S, 3G9C, 3G8T, 3G95, 3G96 (all for the ribozyme from Bacillus anthracis), 2HO7 (the ribozyme from Thermonanaerobacter tengcongensis) * UniProt:P39754 * KEGG entry:[2] * E.C. number:2.6.1.16 === Additional information=== :* subject to Clp-dependent proteolysis upon glucose starvation PubMed =Expression and regulation= * Operon:ybbP-ybbR-glmM-glmS * Expression browser:glmSPubMed * Sigma factor:SigAPubMed * Regulation: ** repressed by glucosamine, N-acetylglucosamine, N-propionylglucosamine or N-formylglucosamine PubMed ** glmS is only expressed in the absence of glucosamine 6-phosphate (glmSribozyme) * Regulatory mechanism:glmSribozyme: glucosamine 6-phosphate binds the leader mRNA, and a riboswitch with ribozyme activity cleaves off the glmS section from the mRNA, resulting in stopp of transcript elongation * Additional information: ** subject to Clp-dependent proteolysis upon glucose starvation PubMed ** A ncRNA is predicted between glmM and glmSPubMed =Biological materials = * Mutant: * Expression vector: * lacZ fusion: * GFP fusion: * two-hybrid system: * Antibody: =Labs working on this gene/protein= Wade Winkler, University of Texas, USA, Homepage =Your additional remarks= =References= ==Reviews== 18279655 ==The glmS Ribozyme== 18079181 ,16484375, 16784238 ,15096624 , 16990543 ,17114942 ,16484375 , 15029187, 17283212 , 16298301, 19228039 21317896 21395279 ==Other Original Publications== Additional publications:PubMed 14343123 17981983 ,11160890, 18295797 20525796