Fig 1.
redGEM uses as inputs a GEM and the part of the metabolism of interest, along with the defined medium.
With a 3 steps procedure that uses a set of methods, it generates core models for different purposes, such as FBA, TFA, kinetic modelling and metabolic flux analysis (MFA).
Table 1.
Statistics on starting subsystems with intra-expansion reactions, RT.
Table 2.
The statistics of different Core Networks CND.
Fig 2.
Pairwise connections between 6 intracellular starting subsystems.
i/j/k represents the number of connecting reactions with respect to degree of connections D = 1, D = 2 and D = 3 respectively. The numbers are not cumulative, and represent the unique reactions for degree of connection. GLY: Glycolysis/ Gluconeogenesis, PPP: Pentose phosphate pathway, PYR: Pyruvate metabolism, ETC: Electron transport chain/Oxidative Phosphorylation, GLX: Glyoxylate metabolism, TCA: Tricarboxylic acid cycle.
Table 3.
Metabolites that connect subsystems and the number of pairwise connections they achieve with different degrees of connection parameter D. (According to postulate 1, see Material and Methods).
Table 4.
The subsystems that can be reached from starting subsystems in 6 steps.
Table 5.
The subsystems that are connecting 6 starting subsystems.
Fig 3.
The synthesis of histidine from core carbon network.
Histidine synthesis starts from ribose-5-phosphate (R5P) from Pentose Phosphate Pathway, and consists of 10 reaction steps. Not all reactions of core network are shown. Orange reactions form the linear pathways for histidine as defined in databases. Metabolites colored with green are core metabolites, whereas orange and purple metabolites are non-core. The non-core metabolites along the linear pathway for histidine synthesis are balanced by the purple reactions.
Table 6.
The specific growth rates (/hr) with 10 mmol/gDWhr uptake for each carbon source.
Fig 4.
Flux variability of reactions in starting subsystems in D = 1 model compared to corresponding reactions in GEM.
The red lines represents FVA for redGEM, black lines represents FVA for GEM. There cannot be any reaction in rGEM that has a wider range than corresponding GEM reaction. Thus, for the reactions that do not have the black line have the same range for rGEM and GEM. Maximum flux bounds are between -60 to 60 mmol/gDWhr, since the uptake of glucose is fixed to 10 mmol/gDWhr, and the maximum allowable flux in the network cannot exceed 10 mmol/gDWhr times 6, which is the number of carbon in glucose.