Some metabolic pathways (e.g. glycolysis, the pathway which metabolises the sugar glucose) are almost identical in all organisms. We (S. Court, R. Allen, and myself) are interested in how these pathways might have evolved. In particular, we want to understand why biological evolution has selected specific chemical reactants and chemical reactions in those pathways. We have generated a network of feasible, enzyme-catalysed chemical reactions for organic molecules with up to 6 carbon atoms and investigated alternative pathways to glycolysis and gluconeogenesis (a glucose-making pathway, reverse to glycolysis) in hope to understand what makes the real pathway so universal. In this paper (Nature Communications) we show that, although there are potentially many alternative pathways, the real one performs best at typical physiological conditions. We have also found a few alternatives for which all the necessary enzymes are known to exist in contemporary organisms, albeit reactions that they catalyse have not been not associated with glycolysis.
We have generated a network of about 1000 chemical reactions for compounds with up to 4 carbon atoms. Some of these reactions are known to be utilized by biological organisms, but most are not, although in principle they could have been.
This picture shows a few of the hundreds of alternative pathways to glycolysis that we have found. The real pathway is no. 2.
Programs for generating networks of biochemical reactions
Here you can find computer programs that we used to generate the network of chemical reactions and to sample alternative pathways. If you are only interested in data files compounds + reactions) and do not want to generate your own, you can find some of them here.