Difference between revisions of "Main Page"

From metabolic_network
Jump to: navigation, search
(Created page with "Category:Reaction == Reaction [http://bigg.ucsd.edu/universal/reactions/ALR4x ALR4x] == * direction: ** LEFT-TO-RIGHT * common name: ** Aldose reductase (acetol) * Synonym...")
 
 
(3 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Category:Reaction]]
+
== EFAEV583GEM description ==
== Reaction [http://bigg.ucsd.edu/universal/reactions/ALR4x ALR4x] ==
+
== Automatic reconstruction with [http://aureme.genouest.org AuReMe] ==
* direction:
+
Model summary: [[MEDIA:summary.txt|summary]]
** LEFT-TO-RIGHT
+
* common name:
+
** Aldose reductase (acetol)
+
* Synonym(s):
+
  
== Reaction Formula ==
+
Download '''AuReMe''' Input/Output [LINK OR MEDIA data]
* With identifiers:
+
** 1.0 [[nadh]][c] '''+''' 1.0 [[acetol]][c] '''+''' 1.0 [[h]][c] '''=>''' 1.0 [[nad]][c] '''+''' 1.0 [[12ppd__R]][c]
+
* With common name(s):
+
** 1.0 Nicotinamide adenine dinucleotide - reduced[c] '''+''' 1.0 Acetol cytosol[c] '''+''' 1.0 H+[c] '''=>''' 1.0 Nicotinamide adenine dinucleotide[c] '''+''' 1.0 (R)-Propane-1,2-diol[c]
+
  
== Genes associated with this reaction  ==
+
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:
Genes have been associated with this reaction based on different elements listed below.
+
* Based on orthology data:
* [[EF1358]]
+
** Tool: [http://pathtastic.gforge.inria.fr Pantograph]
** [[pantograph]]-[[e_coli_sstr_k12_substr_mg1655]]
+
*** From template ''E_COLI_SSTR_K12_SUBSTR_MG1655'' creation of a metabolic network containing: 528 reactions
== Pathways  ==
+
*** From template ''L_PLANTARUM_WCFS1'' creation of a metabolic network containing: 385 reactions
== Reconstruction information  ==
+
*** From template ''B_SUBTILIS_SUBSP_SUBTILIS_STR168'' creation of a metabolic network containing: 463 reactions
* [[orthology]]:
+
* Based on expertise:
** [[pantograph]]:
+
*** 221 reaction(s) added
*** [[e_coli_sstr_k12_substr_mg1655]]
+
* Based on gap-filling:
== External links  ==
+
** Tool: [https://pypi.python.org/pypi/meneco meneco]
* MetaNetX (MNX) Equation : MNXR95790
+
*** 50 reaction(s) added
{{#set: direction=LEFT-TO-RIGHT}}
+
 
{{#set: common name=Aldose reductase (acetol)}}
+
[[FILE:venn.png|frameless|border]]
{{#set: gene associated=EF1358}}
+
 
{{#set: in pathway=}}
+
== Collaborative curation ==  
{{#set: reconstruction category=orthology}}
+
* Suggest reactions to add or remove:
{{#set: reconstruction tool=pantograph}}
+
** Download this [[MEDIA:Add_delete_reaction.csv|form]]
{{#set: reconstruction source=e_coli_sstr_k12_substr_mg1655}}
+
* Suggest new reactions to create and add:
 +
** Download this [[MEDIA:Reaction_creator.csv|form]]
 +
* '''Follow the examples given in the form(s) to correctly share your suggestions'''
 +
* Send the filled form(s) to: gem-aureme@inria.fr

Latest revision as of 15:59, 21 March 2018

EFAEV583GEM description

Automatic reconstruction with AuReMe

Model summary: summary

Download AuReMe Input/Output [LINK OR MEDIA data]

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(s) to correctly share your suggestions
  • Send the filled form(s) to: gem-aureme@inria.fr