Metabolic model of Sulfolobus solfataricus
SulfoSys - Biotec

Genome scale metabolic model of Sulfolobus solfataricus
specific scenario: modelling of L-fucose degradation pathways

Contributor: Jacqueline Wolf

Biological problem addressed: Metabolic Network

Snapshots: No snapshots

iKS1317.xml
INBioPharm

The new GEM of S. coelicolor developed by Tjasa Kumelj, Snorre Sulheim, Alexander Wentzel and Eivind Almaas in 2017/2018

Creators: Snorre Sulheim, Tjasa Kumelj

Contributor: Snorre Sulheim

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Metabolic model of Sulfolobus solfataricus
SulfoSys - Biotec

Metabolic model of Sulfolobus solfataricus P2 in the SBML (xml) and metano (txt, sce, fba) format. Scenarios are specific for growth on D-glucose or L-fucose as sole carbon source. Different theoretical routes of L-fucose degradation were modeled (E. coli-like, Xanthomonas-like and lactaldehyde-forming). Highest overall agreement between the model and experimental data was observed for the lactaldehyde-forming route.

Creators: Jacqueline Wolf, Helge Stark, Dietmar Schomburg

Contributor: Jacqueline Wolf

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Reconstruction of Danio rerio metabolic model accounting for subcellular compartmentalisation
GenoSysFat

Abstract (Expand)

Plant and microbial metabolic engineering is commonly used in the production of functional foods and quality trait improvement. Computational model-based approaches have been used in this important … endeavour. However, to date, fish metabolic models have only been scarcely and partially developed, in marked contrast to their prominent success in metabolic engineering. In this study we present the reconstruction of fully compartmentalised models of the Danio rerio (zebrafish) on a global scale. This reconstruction involves extraction of known biochemical reactions in D. rerio for both primary and secondary metabolism and the implementation of methods for determining subcellular localisation and assignment of enzymes. The reconstructed model (ZebraGEM) is amenable for constraint-based modelling analysis, and accounts for 4,988 genes coding for 2,406 gene-associated reactions and only 418 non-gene-associated reactions. A set of computational validations (i.e., simulations of known metabolic functionalities and experimental data) strongly testifies to the predictive ability of the model. Overall, the reconstructed model is expected to lay down the foundations for computational-based rational design of fish metabolic engineering in aquaculture.

Author: M. Bekaert

Date Published: 14th Nov 2012

Journal: PLoS One

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