Difference between revisions of "CPD-4702"

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(Created page with "== ESUBGEM description == ''Ectocarpus subulatus'' is a small filamentous brown alga that is able to live in freshwater. Its full genome was published in 2020 ([https://doi.o...")
(Created page with "Category:metabolite == Metabolite CPD-13912 == * common-name: ** 2-carboxy-l-threo-pentonate * molecular-weight: ** 208.124 * inchi-key: ** cqirjdzgdxtxkf-uhfffaoysa-l * s...")
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== ESUBGEM description ==
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[[Category:metabolite]]
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== Metabolite CPD-13912 ==
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''Ectocarpus subulatus'' is a small filamentous brown alga that is able to live in freshwater. Its full genome was published in 2020 ([https://doi.org/10.1016/j.margen.2020.100740 Dittami et al., Marine Genomics]), alongside with a first version of a genome-scale metabolic network (still available at  http://gem-aureme.irisa.fr/sububftgem). In a follow-up study (Girard et al., ''in preparation'') we are now curating specifically the sterol biosynthesis pathways (PWY-8191, PWY-8238).
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* common-name:
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** 2-carboxy-l-threo-pentonate
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== Automatic reconstruction with [http://aureme.genouest.org AuReMe] ==
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* molecular-weight:
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Model summary: [[MEDIA:summary.txt|summary]]
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** 208.124
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* inchi-key:
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Download '''AuReMe''' Input/Output [LINK OR MEDIA data]
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** cqirjdzgdxtxkf-uhfffaoysa-l
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* smiles:
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The automatic reconstruction of ''Ectocarpus subulatus strain BFT'' results to a Genome scale [[MEDIA:model.xml|Model]] containing 2086 reactions, 2204 metabolites, 5052 genes and 1152 pathways. This GeM was obtained based on the following sources:
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** c(c(c(o)c(c([o-])=o)(c([o-])=o)o)o)o
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* Based on annotation data:
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== Reaction(s) known to consume the compound ==
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** Tool: [http://bioinformatics.ai.sri.com/ptools/ PathwayTools]
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== Reaction(s) known to produce the compound ==
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** Creation of a metabolic network containing 1459 reactions
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* [[RXN-12871]]
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* Based on expertise:
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== Reaction(s) of unknown directionality ==
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** 480 reaction(s) added
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{{#set: common-name=2-carboxy-l-threo-pentonate}}
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* Based on orthology data:
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{{#set: molecular-weight=208.124}}
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** Creation of a global metabolic network containing 417 reactions
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{{#set: inchi-key=inchikey=cqirjdzgdxtxkf-uhfffaoysa-l}}
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** Tool: [http://pathtastic.gforge.inria.fr Pantograph]
 
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*** From template ''a.taliana.aragem'' creation of a metabolic network containing: 417 reactions
 
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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[AT]inria.fr
 

Revision as of 15:14, 15 March 2021

Metabolite CPD-13912

  • common-name:
    • 2-carboxy-l-threo-pentonate
  • molecular-weight:
    • 208.124
  • inchi-key:
    • cqirjdzgdxtxkf-uhfffaoysa-l
  • smiles:
    • c(c(c(o)c(c([o-])=o)(c([o-])=o)o)o)o

Reaction(s) known to consume the compound

Reaction(s) known to produce the compound

Reaction(s) of unknown directionality

Retrieved from "http://gem-aureme.genouest.org//esubgem/index.php?title=CPD-4702&oldid=29439"