Table 3. BioMog Modified Predefined Biomass for S. oneidensis using Growth Phenotype and Experimentally Measured Biomass.

Added			Unmodified	Removed
L-Alanine	L-Leucine	gdptp	amp	1,2-Diacyl-sn-glycerol 3-phosphate	Phosphatidylglycerol
L-Arginine	L-Lysine	Reduced Glutathione	dna_son	1,2-Diacylglycerol	protein_son_aerobic
L-Asparagine	L-Methionine	2-Oxo-3-hydroxy-4-phosphobutanoate	Glycogen	5-Methyltetrahydrofolate	Spermidine
L-Aspartate	L-Phenylalanine	O-Phospho-L-homoserine	nad	Acetyl-CoA	Succinyl-CoA
L-Cystine	L-Proline	O-Phospho-L-serine	nadh	acyl-glycerophosphoethanolamine	UDP-glucose
L-Glutamine	L-Serine		nadp	acyl-glycerophosphoglycerol
L-Glutamate	L-Threonine		nadph	Coenzyme-A
Glycine	L-Tryptophan		peptx_e	Flavin adenine dinucleotide
L-Histidine	L-Tyrosine		Putrescine	lipopolysaccharide
L-Isoleucine	L-Valine		rna_son	Phosphatidylethanolamine

While BioMog is now able to capture amino acid essentiality, it will still propose the removal of certain metabolites from the predefined biomass equation based on the present model structure and results from the growth phenotype experiments. These removals may not indicate that these metabolites are non-essential but may instead indicate an experimental or network structural issue. Abbreviations match those in Table 1 and 2 with the addition of protein_son_aerobic which represents an average protein macromolecule.