Difference between revisions of "RXN-12056"

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(Created page with "Category:reaction == Reaction 1.14.11.2-RXN == * common-name: ** prolyl 4-hydroxylase * ec-number: ** [http://enzyme.expasy.org/EC/1.14.11.2 ec-1.14.11.2] * direction: **...")
(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...")
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[[Category:reaction]]
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== ESUBGEM description ==
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== Reaction 1.14.11.2-RXN ==
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* common-name:
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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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** prolyl 4-hydroxylase
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* ec-number:
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== Automatic reconstruction with [http://aureme.genouest.org AuReMe] ==
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** [http://enzyme.expasy.org/EC/1.14.11.2 ec-1.14.11.2]
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Model summary: [[MEDIA:summary.txt|summary]]
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* direction:
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** left-to-right
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Download '''AuReMe''' Input/Output [LINK OR MEDIA data]
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== Reaction formula ==
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* 1 [[2-KETOGLUTARATE]][c] '''+''' 1 [[OXYGEN-MOLECULE]][c] '''+''' 1 [[PROCOLLAGEN-L-PROLINE]][c] '''=>''' 1 [[CARBON-DIOXIDE]][c] '''+''' 1 [[CPD-6321]][c] '''+''' 1 [[SUC]][c]
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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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== Gene(s) associated with this reaction  ==
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* Based on annotation data:
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* Gene: [[E_subulatus_16981]]
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** Tool: [http://bioinformatics.ai.sri.com/ptools/ PathwayTools]
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** Category: [[annotation]]
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** Creation of a metabolic network containing 1459 reactions
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*** Source: [[ectocarpus_subulatus]], Tool: [[pathwaytools]], Assignment: ec-number, Comment: n.a
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* Based on expertise:
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* Gene: [[E_subulatus_17536]]
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** 480 reaction(s) added
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** Category: [[annotation]]
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* Based on orthology data:
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*** Source: [[ectocarpus_subulatus]], Tool: [[pathwaytools]], Assignment: ec-number, Comment: n.a
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** Creation of a global metabolic network containing 417 reactions
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* Gene: [[E_subulatus_16982]]
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** Tool: [http://pathtastic.gforge.inria.fr Pantograph]
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** Category: [[annotation]]
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*** From template ''a.taliana.aragem'' creation of a metabolic network containing: 417 reactions
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*** Source: [[ectocarpus_subulatus]], Tool: [[pathwaytools]], Assignment: ec-number, Comment: n.a
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* Gene: [[E_subulatus_16980]]
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** Category: [[annotation]]
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== Collaborative curation ==
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*** Source: [[ectocarpus_subulatus]], Tool: [[pathwaytools]], Assignment: ec-number, Comment: n.a
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* Suggest reactions to add or remove:
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* Gene: [[E_subulatus_02339]]
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** Download this [[MEDIA:Add_delete_reaction.csv|form]]
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** Category: [[annotation]]
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* Suggest new reactions to create and add:
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*** Source: [[ectocarpus_subulatus]], Tool: [[pathwaytools]], Assignment: ec-number, Comment: n.a
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** Download this [[MEDIA:Reaction_creator.csv|form]]
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* Gene: [[E_subulatus_17537]]
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* '''Follow the examples given in the form(s) to correctly share your suggestions'''
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** Category: [[annotation]]
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* Send the filled form(s) to: gem-aureme[AT]inria.fr
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*** Source: [[ectocarpus_subulatus]], Tool: [[pathwaytools]], Assignment: ec-number, Comment: n.a
 
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== Pathway(s)  ==
 
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* [[PWY-7894]]:
 
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** '''1''' reactions found over '''n.a''' reactions in the full pathway
 
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== Reconstruction information  ==
 
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* category: [[annotation]]; source: [[ectocarpus_subulatus]]; tool: [[pathwaytools]]; comment: n.a
 
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== External links  ==
 
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* DB : UNIPROT
 
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* ID : P21195
 
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{{#set: common-name=prolyl 4-hydroxylase}}
 
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{{#set: ec-number=ec-1.14.11.2}}
 
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{{#set: direction=left-to-right}}
 
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{{#set: nb gene associated=6}}
 
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{{#set: nb pathway associated=1}}
 
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{{#set: reconstruction category=annotation}}
 
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{{#set: reconstruction tool=pathwaytools}}
 
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{{#set: reconstruction comment=n.a}}
 
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{{#set: reconstruction source=ectocarpus_subulatus}}
 

Revision as of 15:14, 15 March 2021

ESUBGEM description

Ectocarpus subulatus is a small filamentous brown alga that is able to live in freshwater. Its full genome was published in 2020 (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).

Automatic reconstruction with AuReMe

Model summary: summary

Download AuReMe Input/Output [LINK OR MEDIA data]

The automatic reconstruction of Ectocarpus subulatus strain BFT results to a Genome scale Model containing 2086 reactions, 2204 metabolites, 5052 genes and 1152 pathways. This GeM was obtained based on the following sources:

  • Based on annotation data:
    • Tool: PathwayTools
    • Creation of a metabolic network containing 1459 reactions
  • Based on expertise:
    • 480 reaction(s) added
  • Based on orthology data:
    • Creation of a global metabolic network containing 417 reactions
    • Tool: Pantograph
      • From template a.taliana.aragem creation of a metabolic network containing: 417 reactions


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[AT]inria.fr
Retrieved from "http://gem-aureme.genouest.org//esubgem/index.php?title=RXN-12056&oldid=29457"