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| − | == sjapGEM description ==
| + | [[Category:pathway]] |
| − | | + | == Pathway PWY-3861 == |
| − | ''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]).
| + | * taxonomic-range: |
| − | 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).
| + | ** tax-58023 |
| − | | + | * common-name: |
| − | == Automatic reconstruction with [http://aureme.genouest.org AuReMe] == | + | ** mannitol degradation ii |
| − | Model summary: [[MEDIA:summary.txt|summary]]
| + | == Reaction(s) found == |
| − | | + | * [[MANNKIN-RXN]] |
| − | Download '''AuReMe''' Input/Output [LINK OR MEDIA data]
| + | * [[MANNPISOM-RXN]] |
| − | | + | == Reaction(s) not found == |
| − | 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:
| + | * [None1.1.1.255-RXN 1.1.1.255-RXN] |
| − | * Based on annotation data: | + | * [NoneRXN-14500 RXN-14500] |
| − | ** Tool: [http://bioinformatics.ai.sri.com/ptools/ Pathway tools] | + | {{#set: taxonomic-range=tax-58023}} |
| − | *** Creation of a metabolic network containing 2568 reactions | + | {{#set: common-name=mannitol degradation ii}} |
| − | * Based on orthology data:
| + | {{#set: nb reaction found=2}} |
| − | ** Tool: [http://pathtastic.gforge.inria.fr Pantograph] | + | {{#set: completion rate=0.5}} |
| − | *** 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 | + | {{#set: nb total reaction=4}} |
| − | *** 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 | |
| − | *** From template ''[http://gem-aureme.irisa.fr/ectogem/ ECTOCARPUS_SILICULOSUS]'' creation of a metabolic network containing: 1498 reactions | |
| − | * 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
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