Table 4.

False negative (FN) predictions that could not be corrected by our network modifications.

Gene Locus	Gene Name	Pathway	Function/Reaction	Reasons Why Network Modification Could Not Be Made
Rv1304	atpB	Purine metabolism	Synthesis of ATP	The product of this gene catalyzes the reaction together with that of the TN gene atpH
Rv2391	nirA	Vitamin and cofactor metabolism	Reduction of nitrite	The product of this gene catalyzes the reaction together with that of the TN gene nirB
Rv3758c	proV	Transport	Transport of choline, L-carnitine, glycine betaine, and proline	The product of this gene catalyzes the transport of choline, L-carnitine, glycine betaine, and proline together with the TN genes proZ, proW, and proX
Rv2502c	accD1	Sugar metabolism	Convert propionyl-CoA into S-methylmalonyl-CoA	The product of this gene catalyzes the reaction together with the TN gene accA2
Rv2072c	cobL	Porphyrin metabolism	Production of S-adenosyl-L-homocysteine	The product of this gene catalyzes the synthesis of cobalamin together with the TN genes cobK, cobM, cobH, cobN, cobI, and cobG
Rv3534c	Rv3534c	Pyruvate metabolism	Convert 4-hydroxy-2-oxopentanoate into pyruvate	In a pathway without any synthesis or uptake reaction for the metabolite 4-hydroxy-2-oxopentanoate
Rv2241	aceE	Glycolysis/gluconeogenesis	Convert pyruvate into acetyl-CoA	Unable to determine the reason

A false negative (FN) prediction refers to a gene incorrectly predicted to be non-essential.