Supplementary Table S2. Gap filled reactions without an associated gene remaining in the model.

Reaction No.	Reaction							Action
rxn10447	calcium transport via ABC system				None
rxn10821	Ca ATPase							None
rxn09657	Thiamine transport in via proton symport			None	
rxn05166	Cobalt-ABC transport					None
rxn05149	Manganese-ABC transport					None
rxn05039	pyrimidine phosphatase					None
rxn03167	2-Amino-4-hydroxy-6-(erythro-1,2,3-trihydroxypropyl) dihydropteridine triphosphate phosphohydrolase			None
rxn01538	ATP thiamine phosphotransferase				None
rxn00979	glycolaldehydeNAD+ oxidoreductase			None
rxn03919	D-glycero-D-manno-heptose 1,7-bisphosphate phosphatase		None
        

Initial Gap filled reactions for which gene association has been made, or which have been replaced by an alternative reaction , or which are true gaps in the model and for which the reaction has been removed.

rxn02304	Protoporphyrinogen-IXoxygen oxidoreductase		BP2372 assigned

rxn03087	N-Succinyl-L-2,6-diaminoheptanedioate:2-oxoglutarate aminotransferase								BP0451 assigned

rxn06022	Apo-ACP biosynthesis	reaction removed/replaced with Rcure023

rxn05144	PLP biosynthesis by PdxT/S.	Reaction removed/replaced by Rcure002

rxn03087	N-Succinyl-L-2,6-diaminoheptanedioate:2-oxoglutarate amino-transferase									BP0451 assigned

rxn02988	quinolinate synthase			Reaction removed/true gap

rxn00338	quinolinate synthase			Reaction removed/true gap

rxn06848	Endotoxin Synthesis (myristoyl transferase)		BP3073 assigned

rxn09225	rhamnosyltransferase I (LPS core biosynthesis)		removed*

rxn08954	3-deoxy-D-manno-octulosonic acid transferase III (LPS core biosynthesis)								removed*

rxn08713	heptosyltransferase IV (LPS core synthesis)	removed*


rxn08712	heptosyltransferase III (LPS core synthesis)	removed*


rxn08709	LPS heptose kinase II (LPS core synthesis)		removed*


rxn08620	glucosyltransferase III (LPS core synthesis)	removed*


rxn08708	LPS heptose kinase I (LPS core synthesis)		removed*


rxn08620	glucosyltransferase III (LPS core synthesis)	removed*


rxn08619	glucosyltransferase II (LPS core synthesis)	removed*


rxn08618	glucosyltransferase I (LPS core synthesis)		removed*


rxn08583	galactosyltransferase I (LPS core synthesis)	removed*