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- W2116538067 abstract "choosing which components are to be parts of a detailed BOF and the core BOF. In order to obtain a universal core prokaryotic BOF, we integrated BOFs of 71 genome-scale manually curated prokaryotic models, the ModelSEED framework for biomass composition (5) and data from the literature. We used a semi-automatic process to standardize the nomenclature of metabolites in the 71 BOFs, as there is still not a norm for the terminology of metabolites in GS- CBM. We found that the clustering of these 71 models based on their BOFs fails to represent the phylogenetic relationship of the modelled prokaryotes. No cofactor was present in all the BOFs analysed, including the important redox cofactors nicotinamide adenine dinucleotide (NAD) or NADPhosphate. Both the ModelSEED framework and other literature indicate some cofactors and many ions as universally essential. We conclude that not only the redox cofactors but also others as coenzyme A, flavins and thiamin might need to be added to the BOFs for improving future essentiality studies. We present a proposal of a set of cofactors for a universal core prokaryotic BOF." @default.
- W2116538067 created "2016-06-24" @default.
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- W2116538067 date "2014-01-01" @default.
- W2116538067 modified "2023-09-25" @default.
- W2116538067 title "Standardization and comparison of the biomass objective functions of manually curated genome-scale metabolic models" @default.
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