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(Created page with "Category:Reaction == Reaction [http://metacyc.org/META/NEW-IMAGE?object=AICARSYN-RXN AICARSYN-RXN] == * direction: ** REVERSIBLE * ec number: ** [http://enzyme.expasy.org/...")
 
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[[Category:Reaction]]
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== TISOGEM description ==
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== Reaction [http://metacyc.org/META/NEW-IMAGE?object=AICARSYN-RXN AICARSYN-RXN] ==
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== Automatic reconstruction with [http://aureme.genouest.org AuReMe] ==
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* direction:
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Model summary: [[MEDIA:summary.txt|summary]]
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** REVERSIBLE
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* ec number:
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** [http://enzyme.expasy.org/EC/4.3.2.2 EC-4.3.2.2]
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* Synonym(s):
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== Reaction Formula ==
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Download '''AuReMe''' Input/Output [LINK OR MEDIA data]
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* With identifiers:
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** 1 [[P-RIBOSYL-4-SUCCCARB-AMINOIMIDAZOLE]][c] '''<=>''' 1 [[FUM]][c] '''+''' 1 [[AICAR]][c]
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* With common name(s):
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** 1 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole[c] '''<=>''' 1 fumarate[c] '''+''' 1 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide[c]
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== Genes associated with this reaction  ==
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The automatic reconstruction of ''Tisocrysis_lutea'' results to a Genome scale [[MEDIA:model.xml|Model]] containing 2799 reactions, 2747 metabolites, 2728 genes and 1212 pathways. This GeM was obtained based on the following sources:
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== Pathways  ==
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* Based on annotation data:
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* [[PWY-6123]], inosine-5'-phosphate biosynthesis I: [http://metacyc.org/META/NEW-IMAGE?object=PWY-6123 PWY-6123]
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** Tool: [http://bioinformatics.ai.sri.com/ptools/ Pathway tools]
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** '''5''' reactions found over '''6''' reactions in the full pathway
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*** Creation of a metabolic network containing 2568 reactions
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* [[PWY-6124]], inosine-5'-phosphate biosynthesis II: [http://metacyc.org/META/NEW-IMAGE?object=PWY-6124 PWY-6124]
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* Based on orthology data:
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** '''5''' reactions found over '''5''' reactions in the full pathway
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** Tool: [http://pathtastic.gforge.inria.fr Pantograph]
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* [[PWY-7234]], inosine-5'-phosphate biosynthesis III: [http://metacyc.org/META/NEW-IMAGE?object=PWY-7234 PWY-7234]
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*** From template ''CREINHARDTII'' creation of a metabolic network containing: 558 reactions
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** '''4''' reactions found over '''6''' 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: [[manual]]
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*** From template ''ESILICULOSUS'' creation of a metabolic network containing: 1191 reactions
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** Source: [[manual-primary_network]]
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* Based on expertise:
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* Category: [[annotation]]
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*** 317 reaction(s) added
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** Source: [[annotation-in-silico_annotation]]
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* Based on gap-filling:
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*** Tool: [[pathwaytools]]
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** Tool: [https://pypi.python.org/pypi/meneco meneco]
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== External links  ==
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*** 17 reaction(s) added
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* RHEA:
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** [http://www.ebi.ac.uk/rhea/reaction.xhtml?id=23920 23920]
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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?R04559 R04559]
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== Collaborative curation ==
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* UNIPROT:
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* Suggest reactions to add or remove:
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** [http://www.uniprot.org/uniprot/P21265 P21265]
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** Download this [[MEDIA:Add_delete_reaction.csv|form]]
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** [http://www.uniprot.org/uniprot/Q58339 Q58339]
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* Suggest new reactions to create and add:
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** [http://www.uniprot.org/uniprot/Q9CF40 Q9CF40]
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** Download this [[MEDIA:Reaction_creator.csv|form]]
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** [http://www.uniprot.org/uniprot/Q9PJ88 Q9PJ88]
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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/Q9JSP3 Q9JSP3]
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* Send the filled form(s) to: gem-aureme@inria.fr
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** [http://www.uniprot.org/uniprot/P0AB89 P0AB89]
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** [http://www.uniprot.org/uniprot/O65180 O65180]
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** [http://www.uniprot.org/uniprot/P12047 P12047]
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{{#set: direction=REVERSIBLE}}
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{{#set: ec number=EC-4.3.2.2}}
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{{#set: in pathway=PWY-6123|PWY-6124|PWY-7234}}
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{{#set: reconstruction category=manual|annotation}}
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{{#set: reconstruction source=manual-primary_network|annotation-in-silico_annotation}}
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{{#set: reconstruction tool=pathwaytools}}
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Latest revision as of 14:11, 16 November 2018

TISOGEM description

Automatic reconstruction with AuReMe

Model summary: summary

Download AuReMe Input/Output [LINK OR MEDIA data]

The automatic reconstruction of Tisocrysis_lutea results to a Genome scale Model containing 2799 reactions, 2747 metabolites, 2728 genes and 1212 pathways. This GeM was obtained based on the following sources:

  • Based on annotation data:
    • Tool: Pathway tools
      • Creation of a metabolic network containing 2568 reactions
  • Based on orthology data:
    • Tool: Pantograph
      • From template CREINHARDTII creation of a metabolic network containing: 558 reactions
      • From template SYNECHOCYSTIS creation of a metabolic network containing: 260 reactions
      • From template ATHALIANA creation of a metabolic network containing: 419 reactions
      • From template ESILICULOSUS creation of a metabolic network containing: 1191 reactions
  • Based on expertise:
      • 317 reaction(s) added
  • Based on gap-filling:
    • Tool: meneco
      • 17 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@inria.fr
Retrieved from "http://gem-aureme.irisa.fr/tisogem/index.php?title=Main_Page&oldid=48746"