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(Created page with "Category:Reaction == Reaction [http://metacyc.org/META/NEW-IMAGE?object=6PGLUCONDEHYDROG-RXN 6PGLUCONDEHYDROG-RXN] == * direction: ** LEFT-TO-RIGHT * common name: ** phosp...")
 
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[[Category:Reaction]]
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== TISOGEM description ==
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== Reaction [http://metacyc.org/META/NEW-IMAGE?object=6PGLUCONDEHYDROG-RXN 6PGLUCONDEHYDROG-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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** LEFT-TO-RIGHT
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* common name:
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** phosphogluconate dehydrogenase [NAD(P)+-dependent, decarboxylating]
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* ec number:
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** [http://enzyme.expasy.org/EC/1.1.1.351 EC-1.1.1.351]
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* Synonym(s):
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** 6PGD
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** 6-phosphogluconic carboxylase
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** 6-phosphogluconic dehydrogenase
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** Phosphogluconic acid dehydrogenase
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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 [[CPD-2961]][c] '''+''' 1 [[NAD-P-OR-NOP]][c] '''=>''' 1 [[CARBON-DIOXIDE]][c] '''+''' 1 [[RIBULOSE-5P]][c] '''+''' 1 [[NADH-P-OR-NOP]][c]
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* With common name(s):
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** 1 D-gluconate 6-phosphate[c] '''+''' 1 NAD(P)+[c] '''=>''' 1 CO2[c] '''+''' 1 D-ribulose 5-phosphate[c] '''+''' 1 NAD(P)H[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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Genes have been associated with this reaction based on different elements listed below.
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* Based on annotation data:
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* [[Tiso_gene_20238]]
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** Tool: [http://bioinformatics.ai.sri.com/ptools/ Pathway tools]
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** [[pantograph]]-[[athaliana]]
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*** Creation of a metabolic network containing 2568 reactions
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** [[pantograph]]-[[athaliana]]
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* Based on orthology data:
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** [[pantograph]]-[[synechocystis]]
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** Tool: [http://pathtastic.gforge.inria.fr Pantograph]
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** [[pantograph]]-[[creinhardtii]]
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*** From template ''CREINHARDTII'' creation of a metabolic network containing: 558 reactions
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* [[Tiso_gene_7157]]
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*** From template ''SYNECHOCYSTIS'' creation of a metabolic network containing: 260 reactions
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** [[pantograph]]-[[synechocystis]]
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*** From template ''ATHALIANA'' creation of a metabolic network containing: 419 reactions
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** [[pantograph]]-[[creinhardtii]]
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*** From template ''ESILICULOSUS'' creation of a metabolic network containing: 1191 reactions
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* [[Tiso_gene_91]]
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* Based on expertise:
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** [[pantograph]]-[[esiliculosus]]
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*** 317 reaction(s) added
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== Pathways  ==
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* Based on gap-filling:
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* [[P122-PWY]], heterolactic fermentation: [http://metacyc.org/META/NEW-IMAGE?object=P122-PWY P122-PWY]
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** Tool: [https://pypi.python.org/pypi/meneco meneco]
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** '''14''' reactions found over '''18''' reactions in the full pathway
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*** 17 reaction(s) added
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== Reconstruction information  ==
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* [[orthology]]:
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[[FILE:venn.png|frameless|border]]
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** [[pantograph]]:
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*** [[creinhardtii]]
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== Collaborative curation ==
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*** [[synechocystis]]
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* Suggest reactions to add or remove:
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*** [[athaliana]]
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** Download this [[MEDIA:Add_delete_reaction.csv|form]]
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*** [[esiliculosus]]
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* Suggest new reactions to create and add:
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== External links  ==
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** Download this [[MEDIA:Reaction_creator.csv|form]]
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* RHEA:
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* '''Follow the examples given in the form(s) to correctly share your suggestions'''
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** [http://www.ebi.ac.uk/rhea/reaction.xhtml?id=10116 10116]
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* Send the filled form(s) to: gem-aureme@inria.fr
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* UNIPROT:
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** [http://www.uniprot.org/uniprot/P14332 P14332]
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** [http://www.uniprot.org/uniprot/P31072 P31072]
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** [http://www.uniprot.org/uniprot/Q9CDN4 Q9CDN4]
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** [http://www.uniprot.org/uniprot/P47506 P47506]
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** [http://www.uniprot.org/uniprot/Q9JWS3 Q9JWS3]
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** [http://www.uniprot.org/uniprot/P43774 P43774]
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** [http://www.uniprot.org/uniprot/P12013 P12013]
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** [http://www.uniprot.org/uniprot/P41576 P41576]
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** [http://www.uniprot.org/uniprot/P00350 P00350]
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** [http://www.uniprot.org/uniprot/P00349 P00349]
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** [http://www.uniprot.org/uniprot/P52209 P52209]
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** [http://www.uniprot.org/uniprot/P41581 P41581]
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** [http://www.uniprot.org/uniprot/P41582 P41582]
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** [http://www.uniprot.org/uniprot/Q59275 Q59275]
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** [http://www.uniprot.org/uniprot/P41583 P41583]
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** [http://www.uniprot.org/uniprot/Q60254 Q60254]
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** [http://www.uniprot.org/uniprot/P37754 P37754]
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** [http://www.uniprot.org/uniprot/Q59410 Q59410]
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** [http://www.uniprot.org/uniprot/P52207 P52207]
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** [http://www.uniprot.org/uniprot/P70718 P70718]
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** [http://www.uniprot.org/uniprot/Q7M451 Q7M451]
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** [http://www.uniprot.org/uniprot/P41572 P41572]
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** [http://www.uniprot.org/uniprot/P14062 P14062]
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** [http://www.uniprot.org/uniprot/P21577 P21577]
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** [http://www.uniprot.org/uniprot/P38720 P38720]
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** [http://www.uniprot.org/uniprot/Q40311 Q40311]
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** [http://www.uniprot.org/uniprot/P53319 P53319]
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** [http://www.uniprot.org/uniprot/O81237 O81237]
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** [http://www.uniprot.org/uniprot/O81238 O81238]
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** [http://www.uniprot.org/uniprot/O81239 O81239]
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** [http://www.uniprot.org/uniprot/O22111 O22111]
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** [http://www.uniprot.org/uniprot/Q17761 Q17761]
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** [http://www.uniprot.org/uniprot/O32911 O32911]
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{{#set: direction=LEFT-TO-RIGHT}}
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{{#set: common name=phosphogluconate dehydrogenase [NAD(P)+-dependent, decarboxylating]}}
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{{#set: ec number=EC-1.1.1.351}}
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{{#set: common name=6PGD|6-phosphogluconic carboxylase|6-phosphogluconic dehydrogenase|Phosphogluconic acid dehydrogenase}}
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{{#set: gene associated=Tiso_gene_20238|Tiso_gene_7157|Tiso_gene_91}}
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{{#set: in pathway=P122-PWY}}
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{{#set: reconstruction category=orthology}}
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{{#set: reconstruction tool=pantograph}}
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{{#set: reconstruction source=creinhardtii|synechocystis|athaliana|esiliculosus}}
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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"