|
|
| Line 1: |
Line 1: |
| − | == SJAPGEM description ==
| + | [[Category:metabolite]] |
| − | | + | == Metabolite [http://metacyc.org/META/NEW-IMAGE?object=CPD0-1108 CPD0-1108] == |
| − | ''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]).
| + | * common-name: |
| − | 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 carotenoid biosynthesis pathway (CAROTENOID-PWY) and on the first cycle of xanthophylls (PWY-5945).
| + | ** β-d-ribofuranose |
| − | | + | * smiles: |
| − | == Automatic reconstruction with [http://aureme.genouest.org AuReMe] ==
| + | ** c(c1(c(o)c(o)c(o)o1))o |
| − | Model summary: [[MEDIA:summary.txt|summary]]
| + | * inchi-key: |
| − | | + | ** hmfhbzshggewlo-txicztdvsa-n |
| − | Download '''AuReMe''' Input/Output [LINK OR MEDIA data]
| + | * molecular-weight: |
| − | | + | ** 150.131 |
| − | 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:
| + | == Reaction(s) known to consume the compound == |
| − | * Based on annotation data: | + | * [[RXN-4315-CPD-4207/WATER//CPD0-1108/CPD-4209.35.]] |
| − | ** Tool: [http://bioinformatics.ai.sri.com/ptools/ Pathway tools] | + | == Reaction(s) known to produce the compound == |
| − | *** Creation of a metabolic network containing 2568 reactions
| + | * [[RXN-4315-CPD-4207/WATER//CPD0-1108/CPD-4209.35.]] |
| − | * Based on orthology data: | + | == Reaction(s) of unknown directionality == |
| − | ** Tool: [http://pathtastic.gforge.inria.fr Pantograph] | + | {{#set: common-name=β-d-ribofuranose}} |
| − | *** 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: inchi-key=inchikey=hmfhbzshggewlo-txicztdvsa-n}} |
| − | *** 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
| + | {{#set: molecular-weight=150.131}} |
| − | *** From template ''[http://gem-aureme.irisa.fr/ectogem/ ECTOCARPUS_SILICULOSUS]'' creation of a metabolic network containing: 1498 reactions | |
| − | * Based on expertise: | |
| − | *** 17 reaction(s) added | |
| − | * Based on gap-filling: | |
| − | ** Tool: [https://pypi.python.org/pypi/meneco meneco] | |
| − | *** 91 reaction(s) added
| |
| − | | |
| − | == Collaborative curation ==
| |
| − | * Suggest reactions to add or remove: | |
| − | ** Download this [[MEDIA:Add_delete_reaction.csv|form]]
| |
| − | * 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: gabriel.markov@sb-roscoff.fr
| |
