Table 1. Explanation of metabolic differences between the iJR904 and iAF1260 models of E. coli.

Metabolic Difference	Description of Metabolic Difference	Functional Effect
1,2-Propanediol Synthesis	The iAF1260 model has the ability to secrete 1,2-propanediol; the iJR904 model does not.	The ability to convert glucose to 1,2-propanediol gives the iAF1260 model greater flexibility in choosing fermentation products under some conditions.
Aldehyde Dehydrogenase	The iAF1260 model has a unique aldehyde dehydrogenase which the iJR904 model lacks.	This reaction grants the iAF1260 model the ability to convert acetaldehyde to acetate using NADP. This reaction was selected for deletion by CONGA in iJR dominant strategies, but was never directly implicated in a solution.
Ethanol Synthesis	The iAF1260 model has unique reactions to convert acetyl-CoA to acetaldehyde which the iJR904 model lacks.	Deletions are possible in which the iJR904 model produces no ethanol while the iAF1260 model produces ethanol at high levels.
Hexokinase	The iAF1260 model has a unique hexokinase that it can use as an alternative to phosphoglucose isomerase (PGI).	The iAF1260 model has the ability to recover from multiple-reaction deletions containing PGI, while the iJR904 model does not.
Hydrogen Transport	The iAF1260 model has the ability to secrete hydrogen gas; the iJR904 model does not.	The ability to secrete hydrogen gas allows the iAF1260 model to convert formate to and , consuming a proton in the process. This provides the iAF1260 model an additional way to consume cytoplasmic , and changes the preferred fermentation products under some conditions.
Succinate Transport	The iAF1260 model employs a hydrogen antiporter for succinate; the iJR904 model employs a hydrogen symporter.	Production of succinate becomes less energetically favorable in the iAF1260 model, as the synthesis route consumes fewer cytoplasmic protons.

Six metabolic differences accounted for the majority of the model-dominant strategies identified by CONGA.