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Table 4 False negative (FN) predictions that could not be corrected by our network modifications.

From: Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis

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