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. Author manuscript; available in PMC: 2012 Sep 1.
Published in final edited form as: Nat Protoc. 2011 Aug 4;6(9):1290–1307. doi: 10.1038/nprot.2011.308

Table 3.

growthExpMatch gap filling solutions

# KEGG ID Reaction Name Reaction Formula
1 ‘R01512_b’ phosphoglycerate kinase ATP + 3-Phospho-D-glycerate <=> ADP + 3-Phospho-D-glyceroyl phosphate
2 ‘R02188_f’ 3-Phospho-D-glyceroyl-phosphate:polyphosphate phosphotransferase 3-Phospho-D-glyceroyl phosphate + (Phosphate)n <=> 3-Phospho-D-glycerate + (Phosphate)n
3 ‘R01515_f’ acylphosphatase 3-Phospho-D-glyceroyl phosphate + H2O <=> 3-Phospho-D-glycerate + Orthophosphate
4 ‘R00761_f’ fructose-6-phosphate phosphoketolase D-Fructose 6-phosphate + Orthophosphate <=> Acetyl phosphate + D-Erythrose 4-phosphate + H2O
5 ‘R00024_f’ ribulose-bisphosphate carboxylase D-Ribulose 1,5-bisphosphate + CO2 + H2O <=> 2 3-Phospho-D-glycerate
‘R01523_f’ phosphoribulokinase ATP + D-Ribulose 5-phosphate <=> ADP + D-Ribulose 1,5-bisphosphate

Solutions from five iterations of growthExpMatch on a PGK knockout growing on glucose using the E. coli core model. The first solution returned is the knocked out reaction. Solutions from iterations 2, 3, and 5 are reactions to utilize 3-Phospho-D-glycerol phosphate while the solution from iteration 4 bypasses the gap by converting D-Fructose 6-phosphate to D-Erythrose 4-phosphate and Acetyl phosphate.