Table 1 Examples of anNET applications
From: anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data
Application | Ranges estimated | Notes |
|---|---|---|
Check thermodynamic consistency | none | Check only once feasibility. For non-feasible systems, use the troubleshooting routine. |
Estimate unmeasured concentrations | concentrations | |
Resolve concentrations in different compartments | concentrations | |
Find minimum/maximum feasible NADH/NAD ratio or adenylate energy charge | Non-linear terms | Define the ratio of interest as input with very loose (wide) bounds |
Infer reaction direction | Δ r G' | Find reactions that have a Δ r G' with a unique sign |
Verify reversibility in model | Δ r G' | Infer reaction directions from NET analysis and compare with reversibility in model or literature |
Spot putative control sites | Δ r G' | Find reactions that are known to be active and operate far from equilibrium |
Exclude activity of transporters | Δ r G' | Transporters with non-zero, positive Δ r G' are either not active or have reversed flux. |