Difference between revisions of "CPD-10792"

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(Created page with "Category:reaction == Reaction [http://metacyc.org/META/NEW-IMAGE?object=ARGDECARBOX-RXN ARGDECARBOX-RXN] == * direction: ** reversible * common-name: ** arginine decarboxy...")
(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:reaction]]
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== SJAPGEM description ==
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== Reaction [http://metacyc.org/META/NEW-IMAGE?object=ARGDECARBOX-RXN ARGDECARBOX-RXN] ==
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* direction:
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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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** reversible
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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 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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* common-name:
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** arginine decarboxylase, biosynthetic
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== Automatic reconstruction with [http://aureme.genouest.org AuReMe] ==
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* ec-number:
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Model summary: [[MEDIA:summary.txt|summary]]
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** [http://enzyme.expasy.org/EC/4.1.1.19 ec-4.1.1.19]
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== Reaction formula ==
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Download '''AuReMe''' Input/Output [LINK OR MEDIA data]
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* 1 [[ARG]][c] '''+''' 1 [[PROTON]][c] '''<=>''' 1 [[AGMATHINE]][c] '''+''' 1 [[CARBON-DIOXIDE]][c]
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== Gene(s) associated with this reaction  ==
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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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* Gene: [[SJ12405]]
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* Based on annotation data:
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** Category: [[annotation]]
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** Tool: [http://bioinformatics.ai.sri.com/ptools/ Pathway tools]
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*** Source: [[saccharina_japonica_genome]], Tool: [[pathwaytools]], Assignment: ec-number, Comment: n.a
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*** Creation of a metabolic network containing 2552 reactions
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== Pathway(s)  ==
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* Based on orthology data:
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* [[PWY-6305]], putrescine biosynthesis IV: [http://metacyc.org/META/NEW-IMAGE?object=PWY-6305 PWY-6305]
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** Tool: [http://pathtastic.gforge.inria.fr Pantograph]
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** '''4''' reactions found over '''4''' reactions in the full pathway
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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: 589 reactions
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* [[PWY0-1299]], arginine dependent acid resistance: [http://metacyc.org/META/NEW-IMAGE?object=PWY0-1299 PWY0-1299]
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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: 419 reactions
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** '''1''' reactions found over '''1''' reactions in the full pathway
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*** From template ''[https://gem-aureme.genouest.org/esilgem/ ECTOCARPUS_SILICULOSUS]'' creation of a metabolic network containing: 1492 reactions
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* [[PWY-40]], putrescine biosynthesis I: [http://metacyc.org/META/NEW-IMAGE?object=PWY-40 PWY-40]
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* Based on expertise:
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** '''2''' reactions found over '''2''' reactions in the full pathway
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** 64 reaction(s) added
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* [[PWY-6834]], spermidine biosynthesis III: [http://metacyc.org/META/NEW-IMAGE?object=PWY-6834 PWY-6834]
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* Based on gap-filling:
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** '''2''' reactions found over '''4''' reactions in the full pathway
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** Tool: [https://pypi.python.org/pypi/meneco meneco]
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* [[ARGDEG-III-PWY]], L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway): [http://metacyc.org/META/NEW-IMAGE?object=ARGDEG-III-PWY ARGDEG-III-PWY]
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*** 106 reaction(s) added
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** '''3''' reactions found over '''3''' reactions in the full pathway
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* [[PWY0-823]], L-arginine degradation III (arginine decarboxylase/agmatinase pathway): [http://metacyc.org/META/NEW-IMAGE?object=PWY0-823 PWY0-823]
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[[FILE:venn.png|frameless|border]]
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** '''2''' reactions found over '''2''' reactions in the full pathway
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* [[PWY-43]], putrescine biosynthesis II: [http://metacyc.org/META/NEW-IMAGE?object=PWY-43 PWY-43]
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** '''3''' reactions found over '''3''' reactions in the full pathway
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== Collaborative curation ==
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== Reconstruction information  ==
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* Suggest reactions to add or remove:
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* category: [[annotation]]; source: [[saccharina_japonica_genome]]; tool: [[pathwaytools]]; comment: n.a
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** Download this [[MEDIA:Add_delete_reaction.csv|form]]
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== External links  ==
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* Suggest new reactions to create and add:
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<div class="toccolours mw-collapsible mw-collapsed" style="width:100%; overflow:auto;">
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** Download this [[MEDIA:Reaction_creator.csv|form]]
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* RHEA:
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* '''Follow the examples given in the form(s) to correctly share your suggestions'''
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** [http://www.ebi.ac.uk/rhea/reaction.xhtml?id=17644 17644]
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* Send the filled form(s) to: gabriel.markov@sb-roscoff.fr
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* LIGAND-RXN:
 
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** [http://www.genome.jp/dbget-bin/www_bget?R00566 R00566]
 
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* UNIPROT:
 
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** [http://www.uniprot.org/uniprot/P21170 P21170]
 
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** [http://www.uniprot.org/uniprot/Q9PPF5 Q9PPF5]
 
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** [http://www.uniprot.org/uniprot/Q9JT25 Q9JT25]
 
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** [http://www.uniprot.org/uniprot/P49726 P49726]
 
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** [http://www.uniprot.org/uniprot/P22220 P22220]
 
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** [http://www.uniprot.org/uniprot/P28629 P28629]
 
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** [http://www.uniprot.org/uniprot/Q43075 Q43075]
 
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** [http://www.uniprot.org/uniprot/Q9SI64 Q9SI64]
 
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** [http://www.uniprot.org/uniprot/P72587 P72587]
 
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** [http://www.uniprot.org/uniprot/P74576 P74576]
 
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** [http://www.uniprot.org/uniprot/O24128 O24128]
 
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** [http://www.uniprot.org/uniprot/O23141 O23141]
 
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** [http://www.uniprot.org/uniprot/Q39827 Q39827]
 
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** [http://www.uniprot.org/uniprot/O81161 O81161]
 
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** [http://www.uniprot.org/uniprot/O04429 O04429]
 
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** [http://www.uniprot.org/uniprot/Q96412 Q96412]
 
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** [http://www.uniprot.org/uniprot/O81177 O81177]
 
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** [http://www.uniprot.org/uniprot/O64453 O64453]
 
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</div>
 
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{{#set: direction=reversible}}
 
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{{#set: common-name=arginine decarboxylase, biosynthetic}}
 
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{{#set: ec-number=ec-4.1.1.19}}
 
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{{#set: nb gene associated=1}}
 
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{{#set: nb pathway associated=7}}
 
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{{#set: reconstruction category=annotation}}
 
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{{#set: reconstruction tool=pathwaytools}}
 
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{{#set: reconstruction comment=n.a}}
 
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{{#set: reconstruction source=saccharina_japonica_genome}}
 

Revision as of 11:20, 15 January 2021

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 was published in 2019 (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).

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 3345 reactions, 2211 metabolites, 5021 genes and 1389 pathways. This GeM was obtained based on the following sources:

  • Based on annotation data:
    • Tool: Pathway tools
      • Creation of a metabolic network containing 2552 reactions
  • Based on orthology data:
  • Based on expertise:
    • 64 reaction(s) added
  • Based on gap-filling:
    • Tool: meneco
      • 106 reaction(s) added

Venn.png


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=CPD-10792&oldid=113810"