Difference between revisions of "Category:Pathway"

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(Created page with "{{#ask: Category:Pathway | ?common name | ?reaction found | ?total reaction | ?completion rate }}")
 
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== EFAEV583GEM description ==
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{{#ask: [[Category:Pathway]]
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== Automatic reconstruction with [http://aureme.genouest.org AuReMe] ==
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| ?common name
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Model summary: [[MEDIA:summary.txt|summary]]
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| ?reaction found
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| ?total reaction
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Download '''AuReMe''' Input/Output [LINK OR MEDIA data]
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| ?completion rate
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}}
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The automatic reconstruction of ''Enterococcus_faecalis_str_v583'' results to a Genome scale [[MEDIA:model.xml|Model]] containing 1117 reactions, 911 metabolites, 610 genes and 106 pathways. This GeM was obtained based on the following sources:
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* Based on orthology data:
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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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[[FILE:venn.png|frameless|border]]
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== Collaborative curation ==
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* Suggest reactions to add or remove:
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** Download this [[MEDIA:Add_delete_reaction.csv|form]]
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* Suggest new reactions to create and add:
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** Download this [[MEDIA:Reaction_creator.csv|form]]
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* '''Follow the examples given in the form(s) to correctly share your suggestions'''
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* Send the filled form(s) to: gem-aureme@inria.fr
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Latest revision as of 15:46, 21 March 2018

 Common nameReaction foundTotal reactionCompletion rate
Map00010Glycolysis / Gluconeogenesis2414916.0
Map00020Citrate cycle (TCA cycle)4706.0
Map00030Pentose phosphate pathway266938.0
Map00040Pentose and glucuronate interconversions155428.0
Map00051Fructose and mannose metabolism226335.0
Map00052Galactose metabolism176725.0
Map00053Ascorbate and aldarate metabolism75014.0
Map00061Fatty acid biosynthesis6516041.0
Map00071Fatty acid degradation31672.0
Map00072Synthesis and degradation of ketone bodies2375.0
Map00130Ubiquinone and other terpenoid-quinone biosynthesis94023.0
Map00190Oxidative phosphorylation1353.0
Map00220Arginine biosynthesis96514.0
Map00230Purine metabolism9729833.0
Map00240Pyrimidine metabolism8224434.0
Map00250Alanine, aspartate and glutamate metabolism229324.0
Map00254Aflatoxin biosynthesis1425.0
Map00260Glycine, serine and threonine metabolism2313317.0
Map00261Monobactam biosynthesis3838.0
Map00270Cysteine and methionine metabolism2513519.0
Map00280Valine, leucine and isoleucine degradation91556.0
Map00290Valine, leucine and isoleucine biosynthesis94918.0
Map00300Lysine biosynthesis133438.0
Map00310Lysine degradation61384.0
Map00330Arginine and proline metabolism2214915.0
Map00332Carbapenem biosynthesis21414.0
Map00340Histidine metabolism6907.0
Map00350Tyrosine metabolism91029.0
Map00360Phenylalanine metabolism71096.0
Map00362Benzoate degradation21142.0
Map00380Tryptophan metabolism71634.0
Map00400Phenylalanine, tyrosine and tryptophan biosynthesis135922.0
Map00401Novobiocin biosynthesis21712.0
Map00405Phenazine biosynthesis2
Map00410Beta-Alanine metabolism8919.0
Map00430Taurine and hypotaurine metabolism52421.0
Map00450Selenocompound metabolism63517.0
Map00460Cyanoamino acid metabolism1147.0
Map00471D-Glutamine and D-glutamate metabolism41040.0
Map00473D-Alanine metabolism2367.0
Map00480Glutathione metabolism103926.0
Map00500Starch and sucrose metabolism158119.0
Map00511Other glycan degradation1617.0
Map00520Amino sugar and nucleotide sugar metabolism248030.0
Map00521Streptomycin biosynthesis71450.0
Map00523Polyketide sugar unit biosynthesis44100.0
Map00524Neomycin, kanamycin and gentamicin biosynthesis1333.0
Map00525Acarbose and validamycin biosynthesis22100.0
Map00531Glycosaminoglycan degradation1714.0
Map00540Lipopolysaccharide biosynthesis1166.0
... further results
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