Another trend is that many cyclical EFMs involve transport reactions across membranes. In particular, 221,576 of the 226,014 cyclical EFMs (>98%) found in module # 143,830 (Figure 2B) include at least one reaction involved in the transport of TCA cycle intermediates such as citrate, malate, and succinate across the mitochondrial membrane (Additional file 1: TCA_Transport_Reactions). Depending on the cycling direction, the function of such substrate cycles could be to transfer protons or phosphate ions across the mitochondrial membrane without bringing about a net change in other metabolite concentrations across the membrane. These cyclical EFMs are part of a module that also contains several TCA cycle carbon backbone reactions, underscoring the coupling between energy production reactions and membrane charge transfer reactions required to mediate the proton gradient for oxidative phosphorylation.