Difference between revisions of "PWY-6614"

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(Created page with "Category:metabolite == Metabolite [http://metacyc.org/META/NEW-IMAGE?object=tRNA-Dihydrouridines tRNA-Dihydrouridines] == * common-name: ** a 5,6-dihydrouridine in trna ==...")
 
(Created page with "== sjapGEM description == ''Saccharina japonica'' is the most cultivated alga worldwide, with nearly 8 millions tons of dry weight harvested in 2014, representing more than U...")
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[[Category:metabolite]]
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== sjapGEM description ==
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== Metabolite [http://metacyc.org/META/NEW-IMAGE?object=tRNA-Dihydrouridines tRNA-Dihydrouridines] ==
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* common-name:
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''Saccharina japonica'' is the most cultivated alga worldwide, with nearly 8 millions tons of dry weight harvested in 2014, representing more than US $1.3 billion value ([http://www.fao.org/fishery/culturedspecies/Laminaria_japonica/en#tcNA008C Chen J., FAO website, accessed on january 10th, 2019]).
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** a 5,6-dihydrouridine in trna
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Its draft genome sequence was published in 2015 ([http://doi.org/10.1038/ncomms7986 Ye et al., Nature Communications]). The genome version used here underwent an additional round of cleaning for bacterial contaminants using Taxoblast ([https://doi.org/10.7717/peerj.4073 Dittami and Corre, 2017]). The paper describing this GEM reconstruction in more detail is in preparation. Manual curation is ongoing on the abscisic acid synthesis pathway (PWY-695).
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== Reaction(s) known to consume the compound ==
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== Reaction(s) known to produce the compound ==
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== Automatic reconstruction with [http://aureme.genouest.org AuReMe] ==
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* [[RXN0-1281]]
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Model summary: [[MEDIA:summary.txt|summary]]
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== Reaction(s) of unknown directionality ==
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{{#set: common-name=a 5,6-dihydrouridine in trna}}
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Download '''AuReMe''' Input/Output [LINK OR MEDIA data]
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The automatic reconstruction of ''Saccharina japonica'' results to a Genome scale [[MEDIA:model.xml|Model]] containing 3344 reactions, 3242 metabolites, 5022 genes and 1388 pathways. This GeM was obtained based on the following sources:
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* Based on annotation data:
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** Tool: [http://bioinformatics.ai.sri.com/ptools/ Pathway tools]
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*** Creation of a metabolic network containing 2568 reactions
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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 ''NANNOCHLOROPSIS_SALINA'' ([https://doi.org/10.1186/s12918-017-0441-1 Loira et al., 2017]) creation of a metabolic network containing: 1337 reactions
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*** From template ''ARABIDOPSIS_THALIANA'' ([https://doi.org/10.1104/pp.109.148817 De Oliveira dal'Molin et al., 2010]) creation of a metabolic network containing: 901 reactions
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*** From template ''[http://gem-aureme.irisa.fr/ectogem/ ECTOCARPUS_SILICULOSUS]'' creation of a metabolic network containing: 1498 reactions
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* Based on expertise:
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*** 17 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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*** 91 reaction(s) added
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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: gabriel.markov@sb-roscoff.fr

Revision as of 14:18, 26 August 2019

sjapGEM description

Saccharina japonica is the most cultivated alga worldwide, with nearly 8 millions tons of dry weight harvested in 2014, representing more than US $1.3 billion value (Chen J., FAO website, accessed on january 10th, 2019). Its draft genome sequence was published in 2015 (Ye et al., Nature Communications). The genome version used here underwent an additional round of cleaning for bacterial contaminants using Taxoblast (Dittami and Corre, 2017). The paper describing this GEM reconstruction in more detail is in preparation. Manual curation is ongoing on the abscisic acid synthesis pathway (PWY-695).

Automatic reconstruction with AuReMe

Model summary: summary

Download AuReMe Input/Output [LINK OR MEDIA data]

The automatic reconstruction of Saccharina japonica results to a Genome scale Model containing 3344 reactions, 3242 metabolites, 5022 genes and 1388 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:
  • Based on expertise:
      • 17 reaction(s) added
  • Based on gap-filling:
    • Tool: meneco
      • 91 reaction(s) added

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: gabriel.markov@sb-roscoff.fr
Retrieved from "https://gem-aureme.genouest.org/sjapgem/index.php?title=PWY-6614&oldid=13104"