Difference between revisions of "Annotation"

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(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...")
(Created page with "Category:metabolite == Metabolite 23S-rRNA-2-methyladenine2503 == * common-name: ** a 2-methyladenine2503 in 23s rrna == Reaction(s) known to consume the compound == == Re...")
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== SJAPGEM description ==
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[[Category:metabolite]]
 
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== Metabolite 23S-rRNA-2-methyladenine2503 ==
''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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* 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 was published in 2019 ([https://doi.org/10.3390/antiox8110564 Nègre et al., Antioxidants]). In this study, extensive manual curation was performed on the carotenoid biosynthesis pathway (CAROTENOID-PWY) and on the first cycle of xanthophylls (PWY-5945). In a follow-up study (Girard et al., in preparation) we are now curating the sterol biosynthesis pathways (PWY-8191, PWY-8238).
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** a 2-methyladenine2503 in 23s rrna
 
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== Reaction(s) known to consume the compound ==
== Automatic reconstruction with [http://aureme.genouest.org AuReMe] ==
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== Reaction(s) known to produce the compound ==
Model summary: [[MEDIA:summary.txt|summary]]
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* [[RXN-11586]]
 
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== Reaction(s) of unknown directionality ==
Download '''AuReMe''' Input/Output [LINK OR MEDIA data]
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{{#set: common-name=a 2-methyladenine2503 in 23s rrna}}
 
 
The automatic reconstruction of ''Saccharina japonica'' results to a Genome scale [[MEDIA:S.japonica carotenoid curated.sbml|Model]] containing 3345 reactions, 2211 metabolites, 5021 genes and 1389 pathways. This GeM was obtained based on the following sources:
 
* Based on annotation data:
 
** Tool: [http://bioinformatics.ai.sri.com/ptools/ Pathway tools]
 
*** Creation of a metabolic network containing 2552 reactions
 
* Based on orthology data:
 
** Tool: [http://pathtastic.gforge.inria.fr Pantograph]
 
*** From template ''NANNOCHLOROPSIS_SALINA'' ([https://doi.org/10.1186/s12918-017-0441-1 Loira et al., 2017]) creation of a metabolic network containing: 589 reactions
 
*** 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: 419 reactions
 
*** From template ''[http://gem-aureme.irisa.fr/ectogem/ ECTOCARPUS_SILICULOSUS]'' creation of a metabolic network containing: 1492 reactions
 
* Based on expertise:
 
** 64 reaction(s) added
 
* Based on gap-filling:
 
** Tool: [https://pypi.python.org/pypi/meneco meneco]
 
*** 106 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
 

Revision as of 13:13, 14 January 2021

Metabolite 23S-rRNA-2-methyladenine2503

  • common-name:
    • a 2-methyladenine2503 in 23s rrna

Reaction(s) known to consume the compound

Reaction(s) known to produce the compound

Reaction(s) of unknown directionality