Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
 
(209 intermediate revisions by 6 users not shown)
Line 1: Line 1:
−
'''All genes are grouped in one or more categories. These categories help to identify genes/proteins with common function, regulation or properties.
+
* '''Description:''' glutamine-fructose-6-phosphate transaminase <br/><br/>
  
−
To see additional subcategories, please go to the pages for the six top-level categories.
+
{| align="right" border="1" cellpadding="2"
 +
|-
 +
|style="background:#ABCDEF;" align="center"|'''Gene name''' glaube ich oder nicht
 +
|''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]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=sandbox sandbox]'''
 +
|-
 +
|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+&#91;EMBLCDS:CAB11954&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:quintos.gif]]
 +
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 +
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:test.gif]]
 +
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 +
|-
 +
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=glmS_200277_202079_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:glmS_expression.png|500px]]
 +
|-
 +
|}
  
−
'''
+
__TOC__
−
==1. [[Cellular processes]]==
+
<br/><br/><br/><br/>
−
* 1.1. Cell envelope and cell division
+
<br/><br/><br/><br/>
−
** 1.1.1. [[Cell wall synthesis]]
+
<br/><br/><br/><br/>
−
** 1.1.2. [[Cell shape]]
+
<br/><br/><br/><br/>
−
** 1.1.3. [[Cell wall degradation/ turnover]]
+
<br/><br/><br/><br/>
−
** 1.1.4. [[Capsule biosynthesis and degradation]]
 
−
** 1.1.5. [[Cell wall/ other]]
 
−
** 1.1.6. [[Membrane dynamics]]
 
−
** 1.1.7. [[Cell division]]
 
−
* 1.2. Transporters
 
−
** 1.2.1. [[ABC transporters]]
 
−
** 1.2.2. [[Phosphotransferase systems]]
 
−
** 1.2.3. [[Transporters/ other]]
 
−
* 1.3. Homeostasis
 
−
** 1.3.1. [[Metal ion homeostasis (K, Na, Ca, Mg)]]
 
−
** 1.3.2. [[Trace metal homeostasis (Cu, Zn, Ni, Mn, Mo)]]
 
−
** 1.3.3. [[Acquisition of iron]]
 
−
** 1.3.4. [[pH homeostasis]]
 
  
−
==2. [[Metabolism]]==
 
−
* 2.1. Electron transport and ATP synthesis
 
−
** 2.1.1. [[Regulators of electron transport]]
 
−
** 2.1.2. [[Respiration]]
 
−
** 2.1.3. [[Electron transport/ other]]
 
−
** 2.1.4. [[ATP synthesis]]
 
−
* 2.2. Carbon metabolism
 
−
** 2.2.1. [[Carbon core metabolism]]
 
−
** 2.2.2. [[Utilization of specific carbon sources]]
 
−
* 2.3. Amino acid/ nitrogen metabolism
 
−
** 2.3.1. [[Biosynthesis/ acquisition of amino acids]]
 
−
** 2.3.2. [[Utilization of amino acids]]
 
−
** 2.3.3. [[Utilization of nitrogen sources other than amino acids]]
 
−
** 2.3.4. [[Putative amino acid transporter]]
 
−
* 2.4. Lipid metabolism
 
−
** 2.4.1. [[Utilization of lipids]]
 
−
** 2.4.2. [[Biosynthesis of lipids]]
 
−
** 2.4.3. [[Lipid metabolism/ other]]
 
−
* 2.5. Nucleotide metabolism
 
−
** 2.5.1. [[Utilization of nucleotides]]
 
−
** 2.5.2. [[Biosynthesis/ acquisition of nucleotides]]
 
−
** 2.5.3. [[Metabolism of signalling nucleotides]]
 
−
** 2.5.4. [[Nucleotide metabolism/ other]]
 
−
* 2.6. Additional metabolic pathways
 
−
** 2.6.1. [[Biosynthesis of cell wall components]]
 
−
** 2.6.2. [[Biosynthesis of cofactors]]
 
−
** 2.6.3. [[Phosphate metabolism]]
 
−
** 2.6.4. [[Sulfur metabolism]]
 
−
** 2.6.5. [[Iron metabolism]]
 
−
** 2.6.6. [[Miscellaneous metabolic pathways]]
 
  
−
==3. [[Information processing]]==
+
<br/><br/>
−
* 3.1. Genetics
 
−
** 3.1.1. [[DNA replication]]
 
−
** 3.1.2. [[DNA condensation/ segregation]]
 
−
** 3.1.3. [[DNA restriction/ modification]]
 
−
** 3.1.4. [[DNA repair/ recombination]]
 
−
** 3.1.5. [[Genetic competence]]
 
−
** 3.1.6. [[Genetics/ other]]
 
−
* 3.2. RNA synthesis and degradation
 
−
** 3.2.1. [[Transcription]]
 
−
** 3.2.2. [[RNA chaperones]]
 
−
** 3.2.3. [[DEAD-box RNA helicases]]
 
−
** 3.2.4. [[RNases]]
 
−
* 3.3. Protein synthesis, modification and degradation
 
−
** 3.3.1. [[Translation]]
 
−
** 3.3.2. [[Chaperones/ protein folding]]
 
−
** 3.3.3. [[Protein modification]]
 
−
** 3.3.4. [[Protein secretion]]
 
−
** 3.3.5. [[Proteolysis]]
 
−
* 3.4. Regulation of gene expression
 
−
** 3.4.1. [[Sigma factors and their control]]
 
−
**''' 3.4.2. [[Two-component regulatory systems and their control]]'''
 
−
**''' 3.4.3. [[DNA binding transcription factors and their control]]'''
 
−
** 3.4.4. [[Trigger enzymes]]
 
−
**''' 3.4.5. [[PRD-type regulators]]'''
 
−
** 3.4.6. [[RNA binding regulators]]
 
  
 +
= [[Categories]] containing this gene/protein =
 +
{{SubtiWiki category|[[cell wall synthesis]]}},
 +
{{SubtiWiki category|[[biosynthesis of cell wall components]]}},
 +
{{SubtiWiki category|[[essential genes]]}}
  
−
==4. [[Lifestyles]]==
+
= This gene is a member of the following [[regulons]] =
−
* 4.1. Exponential and early post-exponential lifestyles
+
{{SubtiWiki regulon|[[glmS ribozyme]]}}
−
** 4.1.1. [[Motility and chemotaxis]]
 
−
** 4.1.2. [[Biofilm formation]]
 
−
** 4.1.3. [[Genetic competence]]
 
−
'''** 4.1.4. [[Transition state regulators]]'''
 
−
'''** 4.1.5. [[Quorum sensing]]'''
 
−
* 4.2. Sporulation and Germination
 
−
** 4.2.1. [[Sporulation proteins]]
 
−
** 4.2.2. [[Phosphorelay]]
 
−
** 4.2.3. [[Sporulation/ other]]
 
−
** 4.2.4. [[Germination]]
 
−
* 4.3. Coping with stress
 
−
** 4.3.1. [[General stress proteins (controlled by SigB)]]
 
−
** 4.3.2. [[Cell envelope stress proteins (controlled by SigM, W, X, Y)]]
 
−
** 4.3.3. [[Acid stress proteins (controlled by YvrI-YvrHa)]]
 
−
** 4.3.4. [[Heat shock proteins]]
 
−
** 4.3.5. [[Cold stress proteins]]
 
−
** 4.3.6. [[Coping with hyper-osmotic stress]]
 
−
** 4.3.7. [[Coping with hypo-osmotic stress]]
 
−
** 4.3.8. [[Resistance against oxidative and electrophile stress]]
 
−
** 4.3.9. [[Resistance against other toxic compounds (nitric oxide, phenolic acids, flavonoids, oxalate)]]
 
−
** 4.3.10.[[ Resistance against toxic metals]]
 
−
** 4.3.11.[[ Resistance against toxins/ antibiotics]]
 
−
** 4.3.12.[[ Biosynthesis of antibacterial compounds]]
 
−
** 4.3.13.[[ Toxins, antitoxins and immunity against toxins]]
 
−
* 4.4. [[Lifestyles/ miscellaneous]]
 
  
−
==5. [[Prophages and mobile genetic elements]]==
+
=The gene=
−
* 5.1. Prophages
 
−
** 5.1.1. [[PBSX prophage]]
 
−
** 5.1.2. [[SPß prophage]]
 
−
** 5.1.3. [[Skin element]]
 
−
** 5.1.4. [[Phage-related functions]]
 
−
* 5.2. [[Mobile genetic elements]]
 
  
−
==6. [[Groups of genes]]==
+
=== Basic information ===
−
* 6.1. [[Essential genes]]
+
 
−
* 6.2. [[Membrane proteins]]
+
* '''Locus tag:''' BSU01780
−
* 6.3. [[GTP-binding proteins]]
+
 
−
* 6.4. [[Phosphoproteins]]
+
===Phenotypes of a mutant ===
−
* 6.5. [[Universally conserved proteins]]
+
 
−
* 6.6. [[Poorly characterized/ putative enzymes]]
+
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
−
* 6.7. [[Proteins of unknown function]]
+
 
−
* 6.8. [[Short peptides]]
+
=== Database entries ===
−
* 6.9. [[ncRNA]]
+
* '''BsubCyc:''' [HELLO BSU00100]
−
* 6.10. [[Pseudogenes]]
+
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00240&redirect=T"]
−
*''' 6.11. [[Regulators of core metabolism]]'''
+
 
 +
* '''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 ===
 +
* '''BsubCyc:''' [HELLO BSU00100]
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00240&redirect=T BSU00240]
 +
 
 +
* '''Structure:'''
 +
**[http://www.pdb.org/pdb/explore/explore.do?structureId=HIV2 HIV2] (from ''Bacillus subtilis'', 100% identity) {{PubMed|13454352}}
 +
** [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}}
 +
** number of protein molecules per cell (minimal medium with glucose and ammonium): 2000 {{PubMed|24696501}}
 +
** number of protein molecules per cell (complex medium with amino acids, without glucose): 4000 {{PubMed|24696501}}
 +
 
 +
=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==
 +
<pubmed> 18279655 </pubmed>
 +
 
 +
==The ''glmS'' Ribozyme==
 +
<pubmed>18079181 ,16484375, 16784238 ,15096624 , 16990543 ,17114942 ,16484375 , 15029187, 17283212 , 16298301, 19228039 21317896 21395279 </pubmed>
 +
 
 +
==Other Original Publications==
 +
'''Additional publications:''' {{PubMed|22211522}}
 +
<pubmed> 14343123 17981983 ,11160890, 18295797 20525796  </pubmed>
 +
[[Category:Protein-coding genes]]

Latest revision as of 13:22, 29 July 2014

  • Description: glutamine-fructose-6-phosphate transaminase

Gene name glaube ich oder nicht glmS
Synonyms gcaA, ybxD
Essential yes PubMed
Product glutamine-fructose-6-phosphate transaminase
Function cell wall synthesis
Metabolic function and regulation of this protein in SubtiPathways:
sandbox
MW, pI 65 kDa, 4.796
Gene length, protein length 1800 bp, 600 aa
Immediate neighbours glmM, ybbU
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
File:Quintos.gif
This image was kindly provided by SubtiList
Genetic context
Test.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
GlmS 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

  • BsubCyc: [HELLO BSU00100]
  • BsubCyc: "
  • 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:

Database entries

  • BsubCyc: [HELLO BSU00100]
  • BsubCyc: BSU00240
  • Structure:
    • HIV2 (from Bacillus subtilis, 100% identity) PubMed
    • 2VF4 (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)
  • KEGG entry: [2]

Additional information

  • subject to Clp-dependent proteolysis upon glucose starvation PubMed

Expression and regulation

  • Regulation:
    • repressed by glucosamine, N-acetylglucosamine, N-propionylglucosamine or N-formylglucosamine PubMed
    • 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 PubMed
    • A ncRNA is predicted between glmM and glmS PubMed
    • number of protein molecules per cell (minimal medium with glucose and ammonium): 2000 PubMed
    • number of protein molecules per cell (complex medium with amino acids, without glucose): 4000 PubMed

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


The glmS Ribozyme


Other Original Publications

Additional publications: PubMed

Retrieved from "https://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=206021"