Difference between revisions of "Gap-filling-gapfilling solution with meneco draft medium"

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(Created page with "Category:Reaction == Reaction [http://metacyc.org/META/NEW-IMAGE?object=RXN-11056 RXN-11056] == * direction: ** LEFT-TO-RIGHT * ec number: ** [http://enzyme.expasy.org/EC/...")
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== TISOGEM description ==
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[[Category:Reaction]]
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== Automatic reconstruction with [http://aureme.genouest.org AuReMe] ==
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== Reaction [http://metacyc.org/META/NEW-IMAGE?object=RXN-11056 RXN-11056] ==
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Model summary: [[MEDIA:Tlutea_final.txt|summary]]
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* direction:
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** LEFT-TO-RIGHT
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* ec number:
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** [http://enzyme.expasy.org/EC/1.14.14.1 EC-1.14.14.1]
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* Synonym(s):
  
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Download '''AuReMe''' Input/Output [https://mybox.inria.fr/f/d90e3f0a37/?raw=1 data]
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== Reaction Formula ==
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* With identifiers:
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** 1 [[Red-NADPH-Hemoprotein-Reductases]][c] '''+''' 1 [[N-ACETYL-5-METHOXY-TRYPTAMINE]][c] '''+''' 1 [[OXYGEN-MOLECULE]][c] '''=>''' 1 [[WATER]][c] '''+''' 1 [[Ox-NADPH-Hemoprotein-Reductases]][c] '''+''' 1 [[CPD-12014]][c]
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* With common name(s):
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** 1 a reduced [NADPH-hemoprotein reductase][c] '''+''' 1 melatonin[c] '''+''' 1 oxygen[c] '''=>''' 1 H2O[c] '''+''' 1 an oxidized [NADPH-hemoprotein reductase][c] '''+''' 1 6-hydroxymelatonin[c]
  
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The automatic reconstruction of ''Tisocrysis_lutea'' results to a Genome scale [[MEDIA:Tlutea_lvl3.xml|Model]] containing 2796 reactions, 2745 metabolites, 2728 genes and 1212 pathways. This GeM was obtained based on the following sources:
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== Genes associated with this reaction  ==
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* Based on annotation data:
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Genes have been associated with this reaction based on different elements listed below.
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** Tool: [http://bioinformatics.ai.sri.com/ptools/ Pathway tools]
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* [[Tiso_gene_1035]]
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*** Creation of a metabolic network containing 2568 reactions
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** [[pantograph]]-[[esiliculosus]]
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* Based on orthology data:
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== Pathways  ==
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** Tool: [http://pathtastic.gforge.inria.fr Pantograph]
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* [[PWY-6398]], melatonin degradation I: [http://metacyc.org/META/NEW-IMAGE?object=PWY-6398 PWY-6398]
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*** From template ''CREINHARDTII'' creation of a metabolic network containing: 558 reactions
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** '''5''' reactions found over '''5''' reactions in the full pathway
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*** From template ''SYNECHOCYSTIS'' creation of a metabolic network containing: 260 reactions
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== Reconstruction information  ==
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*** From template ''ATHALIANA'' creation of a metabolic network containing: 419 reactions
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* Category: [[orthology]]
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*** From template ''ESILICULOSUS'' creation of a metabolic network containing: 1191 reactions
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** Source: [[orthology-esiliculosus]]
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* Based on expertise:
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*** Tool: [[pantograph]]
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*** 314 reaction(s) added
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== External links  ==
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* Based on gap-filling:
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{{#set: direction=LEFT-TO-RIGHT}}
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** Tool: [https://pypi.python.org/pypi/meneco meneco]
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{{#set: ec number=EC-1.14.14.1}}
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*** 17 reaction(s) added
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{{#set: gene associated=Tiso_gene_1035}}
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{{#set: in pathway=PWY-6398}}
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[[FILE:venn.png|frameless|border]]
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{{#set: reconstruction category=orthology}}
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{{#set: reconstruction source=orthology-esiliculosus}}
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== Collaborative curation ==  
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{{#set: reconstruction tool=pantograph}}
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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
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Revision as of 00:18, 19 March 2018

Reaction RXN-11056

  • direction:
    • LEFT-TO-RIGHT
  • ec number:
  • Synonym(s):

Reaction Formula

Genes associated with this reaction

Genes have been associated with this reaction based on different elements listed below.

Pathways

  • PWY-6398, melatonin degradation I: PWY-6398
    • 5 reactions found over 5 reactions in the full pathway

Reconstruction information

External links

Retrieved from "http://gem-aureme.irisa.fr/tisogem/index.php?title=Gap-filling-gapfilling_solution_with_meneco_draft_medium&oldid=29684"