Difference between revisions of "Manual-4 newreactions"

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(Created page with "Category:Reaction == Reaction [http://bigg.ucsd.edu/universal/reactions/ExchangeSeed_pan4p ExchangeSeed_pan4p] == * direction: ** REVERSIBLE * Synonym(s): == Reaction For...")
 
(Created page with "== EFAEV583GEM description == == Automatic reconstruction with [http://aureme.genouest.org AuReMe] == The automatic reconstruction of ''Enterococcus_faecalis_str_v583'' result...")
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[[Category:Reaction]]
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== EFAEV583GEM description ==
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== Reaction [http://bigg.ucsd.edu/universal/reactions/ExchangeSeed_pan4p ExchangeSeed_pan4p] ==
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== Automatic reconstruction with [http://aureme.genouest.org AuReMe] ==
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* direction:
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The automatic reconstruction of ''Enterococcus_faecalis_str_v583'' results to a Genome scale Model containing 1117 reactions, 911 metabolites, 610 genes and 106 pathways. This GeM was obtained based on the following sources:
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** REVERSIBLE
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* Based on orthology data:
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* Synonym(s):
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** Tool: [http://pathtastic.gforge.inria.fr Pantograph]
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*** From template ''E_COLI_SSTR_K12_SUBSTR_MG1655'' creation of a metabolic network containing: 528 reactions
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*** From template ''L_PLANTARUM_WCFS1'' creation of a metabolic network containing: 385 reactions
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*** From template ''B_SUBTILIS_SUBSP_SUBTILIS_STR168'' creation of a metabolic network containing: 463 reactions
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* Based on expertise:
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*** 221 reaction(s) added
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* Based on gap-filling:
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** Tool: [https://pypi.python.org/pypi/meneco meneco]
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*** 50 reaction(s) added
  
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== Reaction Formula ==
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[[FILE:venn.png|frameless|border]]
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* With identifiers:
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** 1.0 [[pan4p]][C-BOUNDARY] '''<=>''' 1.0 [[pan4p]][e]
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* With common name(s):
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** 1.0 Pantetheine 4'-phosphate[C-BOUNDARY] '''<=>''' 1.0 Pantetheine 4'-phosphate[e]
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== Genes associated with this reaction  ==
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== Collaborative curation ==  
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== Pathways  ==
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* Suggest reactions to add or remove:
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== Reconstruction information  ==
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** Download this [[MEDIA:Add_delete_reaction.csv|from]]
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* [[manual]]:
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* Suggest new reactions to create and add:
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** [[added to manage seeds from boundary to extracellular compartment]]
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** Download this [[MEDIA:Reaction_creator.csv|form]]
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== External links  ==
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* '''Follow the examples given in the form to correctly share your suggestions'''
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{{#set: direction=REVERSIBLE}}
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* Send the completed form(s) to: CONTACT_MAIL
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{{#set: in pathway=}}
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{{#set: reconstruction category=manual}}
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{{#set: reconstruction source=added to manage seeds from boundary to extracellular compartment}}
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Revision as of 17:19, 10 January 2018

EFAEV583GEM description

Automatic reconstruction with AuReMe

The automatic reconstruction of Enterococcus_faecalis_str_v583 results to a Genome scale Model containing 1117 reactions, 911 metabolites, 610 genes and 106 pathways. This GeM was obtained based on the following sources:

  • Based on orthology data:
    • Tool: Pantograph
      • From template E_COLI_SSTR_K12_SUBSTR_MG1655 creation of a metabolic network containing: 528 reactions
      • From template L_PLANTARUM_WCFS1 creation of a metabolic network containing: 385 reactions
      • From template B_SUBTILIS_SUBSP_SUBTILIS_STR168 creation of a metabolic network containing: 463 reactions
  • Based on expertise:
      • 221 reaction(s) added
  • Based on gap-filling:
    • Tool: meneco
      • 50 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 to correctly share your suggestions
  • Send the completed form(s) to: CONTACT_MAIL
Retrieved from "http://gem-aureme.irisa.fr/efaecV583/index.php?title=Manual-4_newreactions&oldid=5590"