Difference between revisions of "Category:Organism"

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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:metabolite == Metabolite CPD-7414 == * smiles: ** cc(=cc=cc=c(c)c=cc=c(c)c=cc1(c(c)(c)ccc=c(c)1))c=cc=c(c)c=cc2(c(c)=cccc(c)(c)2) * common-name: ** ε-caro...")
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== ESILGEM description ==
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[[Category:metabolite]]
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== Metabolite CPD-7414 ==
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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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* smiles:
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** cc(=cc=cc=c(c)c=cc=c(c)c=cc1(c(c)(c)ccc=c(c)1))c=cc=c(c)c=cc2(c(c)=cccc(c)(c)2)
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* common-name:
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== Automatic reconstruction with [http://aureme.genouest.org AuReMe] ==
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** ε-carotene
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Model summary: [[MEDIA:summary.txt|summary]]
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* inchi-key:
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** qabfxomooywzlz-gdbzimipsa-n
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Download '''AuReMe''' Input/Output [LINK OR MEDIA data]
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* molecular-weight:
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** 536.882
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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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== Reaction(s) known to consume the compound ==
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* Based on annotation data:
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== Reaction(s) known to produce the compound ==
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** Tool: [http://bioinformatics.ai.sri.com/ptools/ PathwayTools]
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* [[RXN-8028]]
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** Creation of a metabolic network containing 1661 reactions
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== Reaction(s) of unknown directionality ==
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* Based on orthology data:
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{{#set: common-name=ε-carotene}}
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** Tool: [http://pathtastic.gforge.inria.fr Pantograph]
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{{#set: inchi-key=inchikey=qabfxomooywzlz-gdbzimipsa-n}}
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** Creation of a global metabolic network containing 440 reactions
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{{#set: molecular-weight=536.882}}
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*** From template ''aragem'' creation of a metabolic network containing: 440 reactions
 
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* Based on gap-filling:
 
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** Tool: [https://pypi.python.org/pypi/meneco Meneco]
 
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*** 85 reaction(s) added
 
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* Based on expertise:
 
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** 80 reaction(s) added
 
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[[FILE:venn.png|frameless|border]]
 
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== Collaborative curation ==  
 
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* Suggest reactions to add or remove:
 
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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
 

Revision as of 13:45, 14 January 2021

Metabolite CPD-7414

  • smiles:
    • cc(=cc=cc=c(c)c=cc=c(c)c=cc1(c(c)(c)ccc=c(c)1))c=cc=c(c)c=cc2(c(c)=cccc(c)(c)2)
  • common-name:
    • ε-carotene
  • inchi-key:
    • qabfxomooywzlz-gdbzimipsa-n
  • molecular-weight:
    • 536.882

Reaction(s) known to consume the compound

Reaction(s) known to produce the compound

Reaction(s) of unknown directionality

Pages in category "Organism"

This category contains only the following page.

E

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