Difference between revisions of "Manual-4 newreactions"

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(Collaborative curation)
(Created page with "{{#ask: Category:Reaction reconstruction source::manual-2_reaction_to_add_delete | ?COMMON NAME | ?ec number | ?reconstruction category | ?reconstruction tool | ?recon...")
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== EFAEV583GEM description ==
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{{#ask: [[Category:Reaction]] [[reconstruction source::manual-2_reaction_to_add_delete]]
== Automatic reconstruction with [http://aureme.genouest.org AuReMe] ==
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| ?COMMON NAME
Model summary: [[MEDIA:efaecalisV583_final.txt|summary]]
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| ?ec number
 
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| ?reconstruction category
Download '''AuReMe''' Input/Output [https://mybox.inria.fr/f/6e73f7ad41/?raw=1 data]
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| ?reconstruction tool
 
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| ?reconstruction source
The automatic reconstruction of ''Enterococcus_faecalis_str_v583'' results to a Genome scale [[MEDIA:efaecalisV583_final_lvl3.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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| ?reconstruction comment
* Based on orthology data:
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| ?gene associated
** Tool: [http://pathtastic.gforge.inria.fr Pantograph]
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| ?in pathway
*** 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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Revision as of 18:51, 18 March 2018

 COMMON NAMEEc numberReconstruction categoryReconstruction toolReconstruction sourceReconstruction commentGene associatedIn pathway
CLPNS140ManualManual-2 reaction to add deleteThis was a reaction occurring in the perisplasm of e. coliEF1608
EF0631
CLPNS161ManualManual-2 reaction to add deleteThis was a reaction occurring in the perisplasm of e. coliEF0631
EF1608
CLPNS180ManualManual-2 reaction to add deleteThis was a reaction occurring in the perisplasm of e. coliEF0631
EF1608
CO2tManualManual-2 reaction to add deleteReaction added for biomass
CYTBDManualManual-2 reaction to add deleteThis was a reaction occurring in the perisplasm of e. coliEF2061
EF2060
FRUpts2ManualManual-2 reaction to add deleteThis was a reaction occurring in the perisplasm of e. coliEF0021
EF0710
EF0022
EF0020
EF0709
FUMt2 2ManualManual-2 reaction to add deleteThis was a reaction occurring in the perisplasm of e. coliEF0387
FUMt2 3ManualManual-2 reaction to add deleteThis was a reaction occurring in the perisplasm of e. coliEF1920
GLUNManualManual-2 reaction to add deleteThis was a reaction occurring in the perisplasm of e. coliEF1163Map00240
Map01100
Map00250
HISt2rManualManual-2 reaction to add deleteThis was a reaction occurring in the perisplasm of e. coliEF1103
Kt3rManualManual-2 reaction to add deleteThis was a reaction occurring in the perisplasm of e. coliEF0296
L LACt2rManualManual-2 reaction to add deleteReaction added for biomass
LACZManualManual-2 reaction to add deleteThis was a reaction occurring in the perisplasm of e. coliEF1238Map01100
Map00600
Map00604
Map00052
Map00511
Map00531
MALt2 2ManualManual-2 reaction to add deleteThis was a reaction occurring in the perisplasm of e. coliEF0387
METSManualManual-2 reaction to add deleteReaction added for biomassMap01100
Map00450
Map01110
Map00270
Map01230
Map00670
MG2abcManualManual-2 reaction to add deleteThis was a reaction occurring in the perisplasm of e. coliEF1352
EF1304
MOGDSOrthology
Manual
PantographOrthology-e coli sstr k12 substr mg1655
Manual-2 reaction to add delete
Reaction added for biomassEF1385
MTHFR3ManualManual-2 reaction to add deleteReaction added for biomassMap01100
Map00720
Map00670
Map01120
NIabcManualManual-2 reaction to add deleteThis was a reaction occurring in the perisplasm of e. coliEF1352
PHEt2rManualManual-2 reaction to add deleteThis was a reaction occurring in the perisplasm of e. coliEF1103
PHPYROXManualManual-2 reaction to add deleteReaction added for biomass, from model l.plantarum
SERt4ManualManual-2 reaction to add deleteThis was a reaction occurring in the perisplasm of e. coliEF3015
SUCFUMtManualManual-2 reaction to add deleteThis was a reaction occurring in the perisplasm of e. coliEF1920