Regarding model handling, OptFlux makes available a number of operations to visualize, import and export stoichiometric metabolic models, including reactions, metabolites, equations and, if available, gene-reaction associations.
All metabolic models, including an explicit listing of the reactions and metabolites, can be found in the additional file 1: Supplement.
The annotated genes of the R. ferrireducens genome as well as genes from several high-quality genome-scale metabolic models, including previously published Escherichia coli [ 56], Geobacter sulfurreducens [ 22], and Bacillus subtilis [ 57] models, were utilized for BLASTP sequence similarity search to generate a draft network as a starting point for model reconstruction.
Other recent and related strategies that exploit modern advances in 'omics and network biology to limit the search space in constraint-based metabolic modelling include references [137,151,298 306].
Our photosynthetic metabolic model includes all of the central metabolic pathways that previous works [ 23- 25] considered.
Energy parameters of the metabolic model including GAM, NGAM and proton translocation stoichiometry were estimated as follows.
The genome-scale P. propionicus metabolic model included 661 genes among the 3831 genes in the P. propionicus genome.
Upon completion, the genome-scale P. carbinolicus metabolic model included 741 genes of the 3389 genes in the P. carbinolicus genome.
Energy parameters of the P. carbinolicus metabolic model including growth-associated maintenance (GAM) energy and non-growth associated maintenance (nGAM) energy were determined using four sets of experimental data obtained in chemostats of P. carbinolicus during acetoin fermentation at dilution rates of 0.03 to 0.06 h-1.
The development of metabolic networks models includes several steps which must interconnect with each other, related to biological knowledge, experimental data acquirement, mathematical modeling, parameters estimation, and model evaluation.
