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(Created page with "Category:reaction == Reaction GLURS-RXN == * direction: ** left-to-right * common-name: ** glutamate-trna ligase * ec-number: ** [http://enzyme.expasy.org/EC/6.1.1.17 ec-6...")
(Created page with "== ESILGEM description == ''Ectocarpus siliculosus'' is a model filamentous brown alga. It was the first brown alga to be sequenced ([doi:10.1038/nature09016 Cock et al., Na...")
 
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[[Category:reaction]]
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== ESILGEM description ==
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== Reaction GLURS-RXN ==
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* direction:
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''Ectocarpus siliculosus'' is a model filamentous brown alga. It was the first brown alga to be sequenced ([doi:10.1038/nature09016 Cock et al., Nature 2010]), and the genome sequence was used to build the first brown algal genome-scale metabolic network ([doi:10.1111/tpj.12627 Prigent et al., The Plant Journal, 2014]), using a preliminary version of the AuReMe pipeline. A second version of the genome-scale metabolic network, based on an improved version of the genome assembly and annotation ([https://doi.org/10.1111/nph.14321, Cormier et al., New Phytol 2017 ] was published in 2018 ([https://doi.org/10.1371/journal.pcbi.1006146 Aite et al., Plos Comp. Biol]). Now, in a more focussed follow-up study (Girard et al., ''in preparation''), we are curating specifically the sterol biosynthesis pathways (PWY-8191, PWY-8238).  
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** left-to-right
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* common-name:
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** glutamate-trna ligase
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== Automatic reconstruction with [http://aureme.genouest.org AuReMe] ==
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* ec-number:
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Model summary: [[MEDIA:summary.txt|summary]]
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** [http://enzyme.expasy.org/EC/6.1.1.17 ec-6.1.1.17]
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== Reaction formula ==
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Download '''AuReMe''' Input/Output [LINK OR MEDIA data]
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* 1 [[ATP]][c] '''+''' 1 [[GLT]][c] '''+''' 1 [[GLT-tRNAs]][c] '''+''' 1 [[PROTON]][c] '''=>''' 1 [[AMP]][c] '''+''' 1 [[Charged-GLT-tRNAs]][c] '''+''' 1 [[PPI]][c]
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== Gene(s) associated with this reaction  ==
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The automatic reconstruction of ''Ectocarpus siliculosus'' results to a Genome scale [[MEDIA:model.xml|Model]] containing 1987 reactions, 2140 metabolites, 2288 genes and 1103 pathways. This GeM was obtained based on the following sources:
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* Gene: [[Ec-06_008480]]
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* Based on annotation data:
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** Category: [[annotation]]
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** Tool: [http://bioinformatics.ai.sri.com/ptools/ PathwayTools]
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*** Source: [[esiliculosus_genome]], Tool: [[pathwaytools]], Assignment: go-term, Comment: n.a
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** Creation of a metabolic network containing 1661 reactions
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== Pathway(s) ==
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* Based on orthology data:
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* [[TRNA-CHARGING-PWY]], tRNA charging:
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** Tool: [http://pathtastic.gforge.inria.fr Pantograph]
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** '''21''' reactions found over '''21''' reactions in the full pathway
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** Creation of a global metabolic network containing 440 reactions
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* [[PWY-5188]], tetrapyrrole biosynthesis I (from glutamate):
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*** From template ''aragem'' creation of a metabolic network containing: 440 reactions
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** '''6''' reactions found over '''6''' reactions in the full pathway
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* Based on gap-filling:
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== Reconstruction information  ==
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** Tool: [https://pypi.python.org/pypi/meneco Meneco]
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* category: [[annotation]]; source: [[esiliculosus_genome]]; tool: [[pathwaytools]]; comment: n.a
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*** 85 reaction(s) added
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== External links  ==
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* Based on expertise:
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<div class="toccolours mw-collapsible mw-collapsed" style="width:100%; overflow:auto;">
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** 80 reaction(s) added
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* RHEA:
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** [http://www.ebi.ac.uk/rhea/reaction.xhtml?id=23541 23541]
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[[FILE:venn.png|frameless|border]]
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* LIGAND-RXN:
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** [http://www.genome.jp/dbget-bin/www_bget?R05578 R05578]
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* UNIPROT:
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== Collaborative curation ==
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** [http://www.uniprot.org/uniprot/P47700 P47700]
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* Suggest reactions to add or remove:
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** [http://www.uniprot.org/uniprot/O52914 O52914]
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** Download this [[MEDIA:Add_delete_reaction.csv|form]]
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** [http://www.uniprot.org/uniprot/P43818 P43818]
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* Suggest new reactions to create and add:
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** [http://www.uniprot.org/uniprot/O26157 O26157]
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** Download this [[MEDIA:Reaction_creator.csv|form]]
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** [http://www.uniprot.org/uniprot/Q9ZLJ1 Q9ZLJ1]
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* '''Follow the examples given in the form(s) to correctly share your suggestions'''
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** [http://www.uniprot.org/uniprot/O25360 O25360]
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* Send the filled form(s) to: gem-aureme[at]inria.fr
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** [http://www.uniprot.org/uniprot/O51345 O51345]
 
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** [http://www.uniprot.org/uniprot/Q9Z7Z3 Q9Z7Z3]
 
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** [http://www.uniprot.org/uniprot/P96551 P96551]
 
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** [http://www.uniprot.org/uniprot/O67271 O67271]
 
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** [http://www.uniprot.org/uniprot/O83679 O83679]
 
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** [http://www.uniprot.org/uniprot/Q9ZLZ7 Q9ZLZ7]
 
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** [http://www.uniprot.org/uniprot/Q9PP78 Q9PP78]
 
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** [http://www.uniprot.org/uniprot/Q9CDZ7 Q9CDZ7]
 
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** [http://www.uniprot.org/uniprot/O84451 O84451]
 
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** [http://www.uniprot.org/uniprot/Q9X2I8 Q9X2I8]
 
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** [http://www.uniprot.org/uniprot/Q9JWT4 Q9JWT4]
 
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** [http://www.uniprot.org/uniprot/Q9ZDK3 Q9ZDK3]
 
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** [http://www.uniprot.org/uniprot/Q9X172 Q9X172]
 
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** [http://www.uniprot.org/uniprot/Q58772 Q58772]
 
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** [http://www.uniprot.org/uniprot/Q9ZCT8 Q9ZCT8]
 
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** [http://www.uniprot.org/uniprot/P59690 P59690]
 
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** [http://www.uniprot.org/uniprot/Q43768 Q43768]
 
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** [http://www.uniprot.org/uniprot/Q43794 Q43794]
 
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** [http://www.uniprot.org/uniprot/P46655 P46655]
 
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** [http://www.uniprot.org/uniprot/P48525 P48525]
 
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** [http://www.uniprot.org/uniprot/P75114 P75114]
 
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** [http://www.uniprot.org/uniprot/Q49061 Q49061]
 
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** [http://www.uniprot.org/uniprot/P22249 P22249]
 
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** [http://www.uniprot.org/uniprot/P22250 P22250]
 
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** [http://www.uniprot.org/uniprot/P04805 P04805]
 
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** [http://www.uniprot.org/uniprot/P07814 P07814]
 
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** [http://www.uniprot.org/uniprot/P15189 P15189]
 
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** [http://www.uniprot.org/uniprot/O65253 O65253]
 
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** [http://www.uniprot.org/uniprot/O68055 O68055]
 
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** [http://www.uniprot.org/uniprot/O68142 O68142]
 
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** [http://www.uniprot.org/uniprot/O86528 O86528]
 
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** [http://www.uniprot.org/uniprot/O13775 O13775]
 
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** [http://www.uniprot.org/uniprot/Q9ZFA3 Q9ZFA3]
 
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** [http://www.uniprot.org/uniprot/O82462 O82462]
 
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</div>
 
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{{#set: direction=left-to-right}}
 
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{{#set: common-name=glutamate-trna ligase}}
 
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{{#set: ec-number=ec-6.1.1.17}}
 
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{{#set: nb gene associated=1}}
 
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{{#set: nb pathway associated=2}}
 
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{{#set: reconstruction category=annotation}}
 
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{{#set: reconstruction tool=pathwaytools}}
 
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{{#set: reconstruction comment=n.a}}
 
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{{#set: reconstruction source=esiliculosus_genome}}
 

Latest revision as of 09:01, 18 March 2021

ESILGEM description

Ectocarpus siliculosus is a model filamentous brown alga. It was the first brown alga to be sequenced ([doi:10.1038/nature09016 Cock et al., Nature 2010]), and the genome sequence was used to build the first brown algal genome-scale metabolic network ([doi:10.1111/tpj.12627 Prigent et al., The Plant Journal, 2014]), using a preliminary version of the AuReMe pipeline. A second version of the genome-scale metabolic network, based on an improved version of the genome assembly and annotation (Cormier et al., New Phytol 2017 was published in 2018 (Aite et al., Plos Comp. Biol). Now, in a more focussed follow-up study (Girard et al., in preparation), we are curating specifically the sterol biosynthesis pathways (PWY-8191, PWY-8238).


Automatic reconstruction with AuReMe

Model summary: summary

Download AuReMe Input/Output [LINK OR MEDIA data]

The automatic reconstruction of Ectocarpus siliculosus results to a Genome scale Model containing 1987 reactions, 2140 metabolites, 2288 genes and 1103 pathways. This GeM was obtained based on the following sources:

  • Based on annotation data:
    • Tool: PathwayTools
    • Creation of a metabolic network containing 1661 reactions
  • Based on orthology data:
    • Tool: Pantograph
    • Creation of a global metabolic network containing 440 reactions
      • From template aragem creation of a metabolic network containing: 440 reactions
  • Based on gap-filling:
    • Tool: Meneco
      • 85 reaction(s) added
  • Based on expertise:
    • 80 reaction(s) added

Venn.png


Collaborative curation

  • Suggest reactions to add or remove:
  • Suggest new reactions to create and add:
  • Follow the examples given in the form(s) to correctly share your suggestions
  • Send the filled form(s) to: gem-aureme[at]inria.fr
Retrieved from "http://gem-aureme.genouest.org//esilgem/index.php?title=Main_Page&oldid=88554"