Difference between revisions of "RXN-17824"

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(Created page with "Category:reaction == Reaction RXN0-4261 == * ec-number: ** [http://enzyme.expasy.org/EC/5.6.2.c ec-5.6.2.c] * direction: ** left-to-right * common-name: ** replicative dna...")
(Created page with "== description == == Automatic reconstruction with [http://aureme.genouest.org AuReMe] == Model summary: summary Download '''AuReMe''' Input/Output [LI...")
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[[Category:reaction]]
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== description ==
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== Reaction RXN0-4261 ==
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== Automatic reconstruction with [http://aureme.genouest.org AuReMe] ==
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* ec-number:
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Model summary: [[MEDIA:summary.txt|summary]]
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** [http://enzyme.expasy.org/EC/5.6.2.c ec-5.6.2.c]
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* direction:
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Download '''AuReMe''' Input/Output [LINK OR MEDIA data]
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** left-to-right
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* common-name:
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The automatic reconstruction of ''Fibrobacter succinogenes'' results to a Genome scale [[MEDIA:model.xml|Model]] containing 1567 reactions, 1588 metabolites, 1314 genes and 931 pathways. This GeM was obtained based on the following sources:
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** replicative dna helicase
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* Based on annotation data:
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** uvrd-helicase domain-containing protein
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** Creation of a metabolic network containing 826 reactions
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** helicase
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* Based on orthology data:
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== Reaction formula ==
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** Creation of a global metabolic network containing 377 reactions
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* 1 [[ATP]][c] '''+''' 1 [[Supercoiled-Duplex-DNAs]][c] '''+''' 1 [[WATER]][c] '''=>''' 1 [[ADP]][c] '''+''' 1 [[Pi]][c] '''+''' 2 [[Single-Stranded-DNAs]][c]
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* Based on expertise:
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== Gene(s) associated with this reaction  ==
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** 568 reaction(s) added
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<div class="toccolours mw-collapsible mw-collapsed" style="width:100%; overflow:auto;">
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* Gene: [[FISUC_RS03735]]
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*List of tools used:
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** Category: [[annotation]]
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** Tool: [http://bioinformatics.ai.sri.com/ptools/ PathwayTools]
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*** Source: [[genome]], Tool: [[pathwaytools]], Assignment: automated-name-match, Comment: n.a
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** Tool: [https://github.com/davidemms/OrthoFinder Orthofinder]
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* Gene: [[FISUC_RS01385]]
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** Tool: [https://pypi.python.org/pypi/meneco meneco]
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** Category: [[annotation]]
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*** Source: [[genome]], Tool: [[pathwaytools]], Assignment: automated-name-match, Comment: n.a
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[[FILE:venn.png|frameless|border]]
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* Gene: [[FISUC_RS12830]]
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** Category: [[annotation]]
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== Collaborative curation ==
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*** Source: [[genome]], Tool: [[pathwaytools]], Assignment: automated-name-match, Comment: n.a
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* Suggest reactions to add or remove:
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* Gene: [[FISUC_RS12770]]
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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: [[genome]], Tool: [[pathwaytools]], Assignment: automated-name-match, Comment: n.a
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** Download this [[MEDIA:Reaction_creator.csv|form]]
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* Gene: [[FSU_RS03265]]
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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: [[genome]], Tool: [[pathwaytools]], Assignment: automated-name-match, Comment: n.a
 
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* Gene: [[FSU_RS07800]]
 
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** Category: [[annotation]]
 
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*** Source: [[genome]], Tool: [[pathwaytools]], Assignment: automated-name-match, Comment: n.a
 
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* Gene: [[FSU_RS14805]]
 
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** Category: [[annotation]]
 
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*** Source: [[genome]], Tool: [[pathwaytools]], Assignment: automated-name-match, Comment: n.a
 
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* Gene: [[FSU_RS14745]]
 
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** Category: [[annotation]]
 
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*** Source: [[genome]], Tool: [[pathwaytools]], Assignment: automated-name-match, Comment: n.a
 
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* Gene: [[FSU_RS05625]]
 
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** Category: [[annotation]]
 
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*** Source: [[genome]], Tool: [[pathwaytools]], Assignment: automated-name-match, Comment: n.a
 
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* Gene: [[FSU_RS10840]]
 
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** Category: [[annotation]]
 
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*** Source: [[genome]], Tool: [[pathwaytools]], Assignment: automated-name-match, Comment: n.a
 
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* Gene: [[FISUC_RS08900]]
 
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** Category: [[annotation]]
 
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*** Source: [[genome]], Tool: [[pathwaytools]], Assignment: automated-name-match, Comment: n.a
 
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* Gene: [[FISUC_RS05900]]
 
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** Category: [[annotation]]
 
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*** Source: [[genome]], Tool: [[pathwaytools]], Assignment: automated-name-match, Comment: n.a
 
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</div>
 
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== Pathway(s) ==
 
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== Reconstruction information  ==
 
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* category: [[annotation]]; source: [[genome]]; tool: [[pathwaytools]]; comment: n.a
 
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== External links  ==
 
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{{#set: ec-number=ec-5.6.2.c}}
 
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{{#set: direction=left-to-right}}
 
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{{#set: common-name=replicative dna helicase|helicase|uvrd-helicase domain-containing protein}}
 
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{{#set: nb gene associated=12}}
 
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{{#set: nb pathway associated=0}}
 
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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=genome}}
 

Revision as of 15:57, 18 March 2021

description

Automatic reconstruction with AuReMe

Model summary: summary

Download AuReMe Input/Output [LINK OR MEDIA data]

The automatic reconstruction of Fibrobacter succinogenes results to a Genome scale Model containing 1567 reactions, 1588 metabolites, 1314 genes and 931 pathways. This GeM was obtained based on the following sources:

  • Based on annotation data:
    • Creation of a metabolic network containing 826 reactions
  • Based on orthology data:
    • Creation of a global metabolic network containing 377 reactions
  • Based on expertise:
    • 568 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[at]inria.fr
Retrieved from "http://gem-aureme.genouest.org//fsucgem/index.php?title=RXN-17824&oldid=71561"