Table 1. BioMog proposed de novo biomass equations for E. coli and S. oneidensis.

E. coli Biomass		S. oneidensis Biomass
Unique	Contains Alternatives	Unique	Contains Alternatives
2,3-dihydroxybenzoylserine; 5-Formyltetrahydrofolate; L-Glutamate 5-phosphate; L-Histidine; L-Isoleucine; KDO(2)-lipid IV(A); protoheme; L-Proline	2omhmbl; [2Fe-1S] desulfurated iron-sulfur cluster; 4c2me; L-Arginine; adenosine thiamine triphosphate; Biotin; cardiolipin (tetraoctadec-11-enoyl, n-C18:1); Coenzyme A; Flavin adenine dinucleotide oxidized; L-Leucine; L-Lysine; Murein5p3p_p; nadp; pe181; L-Phenylalanine; O-Phospho-L-serine; Pyridoxamine; Siroheme; Selenite; L-Tryptophan; uagmda	L-Arginine; gdptp; L-Histidine; O-Phospho-L-homoserine	Reduced glutathione; DNA; L-Leucine; L-Methionine; 2-Oxo-3-hydroxy-4-phosphobutanoate; L-Phenylalanine; L-Proline; O-Phospho-L-serine; L-Tryptophan; L-Tyrosine

Unique metabolites were those compounds for which there was no alternative that would have maximized the objective function. Conversely, metabolites which possessed alternatives could be replaced with another compound without adversely impacting the objective function. Abbreviations used were as follows: 2omhmbl, 2-octaprenyl-3-methyl-5-hydroxy-6-methoxy-1,4-benzoquinol, 4c2me, 4-(cytidine 5′-diphospho)-2-C-methyl-D-erythritol, murein5p3p_p, two linked disacharide pentapeptide and tripeptide murein units (uncrosslinked, middle of chain), nadp, nicotinamide adenine dinucleotide phosphate, pe181, phosphatidylethanolamine (dioctadec-11-enoyl, n-C18:1), uagmda, undecaprenyl-diphospho-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine, gdptp, guanosine 3′-diphosphate 5′-triphosphate.