Figure 1.
Flowchart for GAFBA algorithm.
A schematic depiction of the GAFBA algorithm used to determine the genome-scale metabolic model for M. galliscepticum.
Table 1.
Summary of reactions added to the metabolic model based on experimental data in the literature.
Table 2.
Summary of reactions added based on BLASTP analysis.
Table 3.
Reactions added based on Pathway Tools analysis.
Table 4.
Reactions removed based on experimental studies.
Table 5.
Initial model modifications.
Table 6.
Remaining changes made to model.
Figure 2.
The purple circle shows the unconstrained metabolite. The thin blue arrows are the standard fluxes, while the thick blue arrows are the exchange fluxes. The orange arrow represents the proposed solution. The solid blue line is the plasma membrane and the dashed blue line is the system boundary. The red circle is an abstraction of the biomass pool.
Figure 3.
Predicted growth rate over the course of model evolution.
40 simulations were carried out for 2,000 generations each. The columns represent the growth rate values. Result 41 is the average value of the experimentally measured M. gallisepticum growth rate. The dashed line running the length of the graph also indicates the average experimentally measured growth rate and is shown as a reference to facilitate comparison with the simulation results.
Figure 4.
Metabolic constraints relaxed over the course of model evolution.
40 simulations were carried out for 2,000 generations each. The columns represent the number of mass balances for which the constraints were relaxed.
Table 7.
Comparison of the Mycoplasma gentialium model (iPS189) [49] and the model presented in this paper for Mycoplasma gallisepticum.
Table 8.
Result of the analysis of relaxed mass balances constraints for select simulations.