Difference between revisions of "Main Page"

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(Created page with "Category:Reaction == Reaction [http://metacyc.org/META/NEW-IMAGE?object=RXN-17782 RXN-17782] == * direction: ** LEFT-TO-RIGHT * common name: ** acetyl-_c-acetyltransferase...")
 
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[[Category:Reaction]]
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== TISOGEM description ==
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== Reaction [http://metacyc.org/META/NEW-IMAGE?object=RXN-17782 RXN-17782] ==
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== Automatic reconstruction with [http://aureme.genouest.org AuReMe] ==
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* direction:
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Model summary: [[MEDIA:summary.txt|summary]]
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** LEFT-TO-RIGHT
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* common name:
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** acetyl-_c-acetyltransferase
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** thiolase
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** 3-ketoacyl-_thiolase
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* ec number:
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** [http://enzyme.expasy.org/EC/2.3.1.16 EC-2.3.1.16]
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* Synonym(s):
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== Reaction Formula ==
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Download '''AuReMe''' Input/Output [LINK OR MEDIA data]
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* With identifiers:
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** 1 [[CPD-19167]][c] '''+''' 1 [[CO-A]][c] '''=>''' 1 [[CPD-15436]][c] '''+''' 1 [[ACETYL-COA]][c]
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* With common name(s):
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** 1 3-oxo-(7Z)-hexadecenoyl-CoA[c] '''+''' 1 coenzyme A[c] '''=>''' 1 (5Z)-tetradecenoyl-CoA[c] '''+''' 1 acetyl-CoA[c]
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== Genes associated with this reaction  ==
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The automatic reconstruction of ''Tisocrysis_lutea'' results to a Genome scale [[MEDIA:model.xml|Model]] containing 2799 reactions, 2747 metabolites, 2728 genes and 1212 pathways. This GeM was obtained based on the following sources:
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Genes have been associated with this reaction based on different elements listed below.
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* Based on annotation data:
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* Gene: [[Tiso_gene_3856]]
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** Tool: [http://bioinformatics.ai.sri.com/ptools/ Pathway tools]
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** Source: [[annotation-in-silico_annotation]]
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*** Creation of a metabolic network containing 2568 reactions
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*** Assignment: EC-NUMBER
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* Based on orthology data:
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* Gene: [[Tiso_gene_17451]]
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** Tool: [http://pathtastic.gforge.inria.fr Pantograph]
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** Source: [[annotation-in-silico_annotation]]
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*** From template ''CREINHARDTII'' creation of a metabolic network containing: 558 reactions
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*** Assignment: EC-NUMBER
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*** From template ''SYNECHOCYSTIS'' creation of a metabolic network containing: 260 reactions
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** Source: [[annotation-experimental_annotation]]
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*** From template ''ATHALIANA'' creation of a metabolic network containing: 419 reactions
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*** Assignment: EC-NUMBER
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*** From template ''ESILICULOSUS'' creation of a metabolic network containing: 1191 reactions
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* Gene: [[Tiso_gene_10116]]
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* Based on expertise:
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** Source: [[annotation-in-silico_annotation]]
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*** 317 reaction(s) added
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*** Assignment: EC-NUMBER
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* Based on gap-filling:
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** Source: [[annotation-experimental_annotation]]
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** Tool: [https://pypi.python.org/pypi/meneco meneco]
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*** Assignment: EC-NUMBER
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*** 17 reaction(s) added
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* Gene: [[Tiso_gene_3855]]
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** Source: [[annotation-in-silico_annotation]]
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[[FILE:venn.png|frameless|border]]
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*** Assignment: EC-NUMBER
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** Source: [[annotation-experimental_annotation]]
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== Collaborative curation ==  
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*** Assignment: EC-NUMBER
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* Suggest reactions to add or remove:
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* Gene: [[Tiso_gene_15327]]
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** Download this [[MEDIA:Add_delete_reaction.csv|form]]
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** Source: [[annotation-experimental_annotation]]
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* Suggest new reactions to create and add:
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*** Assignment: EC-NUMBER
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** Download this [[MEDIA:Reaction_creator.csv|form]]
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== Pathways  ==
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* '''Follow the examples given in the form(s) to correctly share your suggestions'''
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== Reconstruction information  ==
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* Send the filled form(s) to: gem-aureme@inria.fr
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* Category: [[annotation]]
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** Source: [[annotation-in-silico_annotation]]
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*** Tool: [[pathwaytools]]
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** Source: [[annotation-experimental_annotation]]
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*** Tool: [[pathwaytools]]
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== External links  ==
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{{#set: direction=LEFT-TO-RIGHT}}
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{{#set: common name=acetyl-_c-acetyltransferase}}
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{{#set: common name=thiolase}}
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{{#set: common name=3-ketoacyl-_thiolase}}
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{{#set: ec number=EC-2.3.1.16}}
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{{#set: gene associated=Tiso_gene_3856|Tiso_gene_17451|Tiso_gene_10116|Tiso_gene_3855|Tiso_gene_15327}}
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{{#set: in pathway=}}
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{{#set: reconstruction category=annotation}}
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{{#set: reconstruction source=annotation-in-silico_annotation|annotation-experimental_annotation}}
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{{#set: reconstruction tool=pathwaytools}}
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Latest revision as of 13:11, 16 November 2018

TISOGEM description

Automatic reconstruction with AuReMe

Model summary: summary

Download AuReMe Input/Output [LINK OR MEDIA data]

The automatic reconstruction of Tisocrysis_lutea results to a Genome scale Model containing 2799 reactions, 2747 metabolites, 2728 genes and 1212 pathways. This GeM was obtained based on the following sources:

  • Based on annotation data:
    • Tool: Pathway tools
      • Creation of a metabolic network containing 2568 reactions
  • Based on orthology data:
    • Tool: Pantograph
      • From template CREINHARDTII creation of a metabolic network containing: 558 reactions
      • From template SYNECHOCYSTIS creation of a metabolic network containing: 260 reactions
      • From template ATHALIANA creation of a metabolic network containing: 419 reactions
      • From template ESILICULOSUS creation of a metabolic network containing: 1191 reactions
  • Based on expertise:
      • 317 reaction(s) added
  • Based on gap-filling:
    • Tool: meneco
      • 17 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
Retrieved from "http://gem-aureme.irisa.fr/tisogem/index.php?title=Main_Page&oldid=48746"