Difference between revisions of "RXN0-4261"

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(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...")
(Created page with "Category:reaction == Reaction RXN0-4261 == * direction: ** left-to-right * common-name: ** helicase ** helicase domain == Reaction formula == * 1 ATP[c] '''+''' 1 Su...")
 
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== ESILGEM description ==
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[[Category:reaction]]
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== Reaction RXN0-4261 ==
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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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* direction:
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** left-to-right
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* common-name:
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== Automatic reconstruction with [http://aureme.genouest.org AuReMe] ==
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** helicase
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Model summary: [[MEDIA:summary.txt|summary]]
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** helicase domain
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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 [[Supercoiled-Duplex-DNAs]][c] '''+''' 1 [[WATER]][c] '''=>''' 1 [[ADP]][c] '''+''' 1 [[Pi]][c] '''+''' 1 [[Single-Stranded-DNAs]][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 1992 reactions, 2146 metabolites, 2290 genes and 1103 pathways. This GeM was obtained based on the following sources:
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* Gene: [[Ec-18_003980]]
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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: automated-name-match, Comment: n.a
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** Creation of a metabolic network containing 1661 reactions
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* Gene: [[Ec-02_002310]]
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* Based on orthology data:
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** Category: [[annotation]]
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** Tool: [http://pathtastic.gforge.inria.fr Pantograph]
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*** Source: [[esiliculosus_genome]], Tool: [[pathwaytools]], Assignment: automated-name-match, Comment: n.a
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** Creation of a global metabolic network containing 440 reactions
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== Pathway(s)  ==
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*** From template ''aragem'' creation of a metabolic network containing: 440 reactions
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== Reconstruction information  ==
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* Based on gap-filling:
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* category: [[annotation]]; source: [[esiliculosus_genome]]; tool: [[pathwaytools]]; comment: n.a
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** Tool: [https://pypi.python.org/pypi/meneco Meneco]
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== External links  ==
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*** 85 reaction(s) added
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* METANETX-RXN : MNXR123180
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* Based on expertise:
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{{#set: direction=left-to-right}}
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** 80 reaction(s) added
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{{#set: common-name=helicase domain|helicase}}
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{{#set: nb gene associated=2}}
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[[FILE:venn.png|frameless|border]]
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{{#set: nb pathway associated=0}}
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{{#set: reconstruction category=annotation}}
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{{#set: reconstruction tool=pathwaytools}}
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== Collaborative curation ==  
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{{#set: reconstruction comment=n.a}}
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* Suggest reactions to add or remove:
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{{#set: reconstruction source=esiliculosus_genome}}
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** Download this [[MEDIA:Add_delete_reaction.csv|form]]
 
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* Suggest new reactions to create and add:
 
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** Download this [[MEDIA:Reaction_creator.csv|form]]
 
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* '''Follow the examples given in the form(s) to correctly share your suggestions'''
 
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* Send the filled form(s) to: gem-aureme@inria.fr
 

Latest revision as of 09:01, 18 March 2021

Reaction RXN0-4261

  • direction:
    • left-to-right
  • common-name:
    • helicase
    • helicase domain

Reaction formula

Gene(s) associated with this reaction

Pathway(s)

Reconstruction information

External links

  • METANETX-RXN : MNXR123180





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