Difference between revisions of "CPD-10792"

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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 2-AMINOMUCONATE_SEMIALDEHYDE == * common-name: ** (2z,4e)-2-amino-6-oxohexa-2,4-dienoate * smiles: ** c(c=c(c([o-])=o)n)=c[ch]=o * inchi-...")
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== SJAPGEM description ==
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[[Category:metabolite]]
 
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== Metabolite 2-AMINOMUCONATE_SEMIALDEHYDE ==
''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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** (2z,4e)-2-amino-6-oxohexa-2,4-dienoate
 
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* smiles:
== Automatic reconstruction with [http://aureme.genouest.org AuReMe] ==
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** c(c=c(c([o-])=o)n)=c[ch]=o
Model summary: [[MEDIA:summary.txt|summary]]
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* inchi-key:
 
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** qcgtzpzkjptaep-wftyeqlwsa-m
Download '''AuReMe''' Input/Output [LINK OR MEDIA data]
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* molecular-weight:
 
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** 140.118
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:
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== Reaction(s) known to consume the compound ==
* Based on annotation data:
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== Reaction(s) known to produce the compound ==
** Tool: [http://bioinformatics.ai.sri.com/ptools/ Pathway tools]
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* [[AMINO-CARBOXYMUCONATE-SEMIALDEHYDE-RXN]]
*** Creation of a metabolic network containing 2552 reactions
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== Reaction(s) of unknown directionality ==
* Based on orthology data:
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{{#set: common-name=(2z,4e)-2-amino-6-oxohexa-2,4-dienoate}}
** Tool: [http://pathtastic.gforge.inria.fr Pantograph]
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{{#set: inchi-key=inchikey=qcgtzpzkjptaep-wftyeqlwsa-m}}
*** 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
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{{#set: molecular-weight=140.118}}
*** 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 ''[https://gem-aureme.genouest.org/esilgem/ 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
 
 
 
[[FILE:venn.png|frameless|border]]
 
 
 
 
 
== 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 08:32, 15 March 2021

Metabolite 2-AMINOMUCONATE_SEMIALDEHYDE

  • common-name:
    • (2z,4e)-2-amino-6-oxohexa-2,4-dienoate
  • smiles:
    • c(c=c(c([o-])=o)n)=c[ch]=o
  • inchi-key:
    • qcgtzpzkjptaep-wftyeqlwsa-m
  • molecular-weight:
    • 140.118

Reaction(s) known to consume the compound

Reaction(s) known to produce the compound

Reaction(s) of unknown directionality