METATOOL OUTPUT Version 3.5 (28.03.2001) C:\METATOOL\META35~1.EXE INPUT FILE: example2.txt INTERNAL METABOLITES: 15 REACTIONS: 19 6 int GAP 5 int F6P 3 external ATP 3 int FDP 3 external ADP 3 int Ru5P 3 int R5P 3 int X5P 2 external G6P 2 external Pi 2 int DHAP 2 int D13PG 2 external NADP 2 int GO6P 2 external NADPH 2 int GL6P 2 int S7P 2 int E4P 2 int P3G 2 int P2G 2 int PEP 1 external NAD 1 external NADH 1 external CO2 1 external PYR 1 external R5Pex 26 metabolites, 60 is the summarized frequency edges frequency of nodes 0 0 1 5 2 13 3 6 4 0 5 1 6 1 STOICHIOMETRIC MATRIX matrix dimension r15 x c19 0 0 0 0 0 0 -1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1 -1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 -1 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 0 0 0 -1 1 0 0 0 0 0 0 0 1 1 0 0 1 1 -1 0 0 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1 0 1 0 0 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 -1 0 0 0 0 0 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 -1 The following line indicates reversible (0) and irreversible reactions (1) 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 rows and columns are sorted as declared in the inputfile KERNEL matrix dimension r4 x c19 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 5 1 1 -2 -4 -2 -2 -2 0 0 -6 1 0 -6 -6 0 0 0 0 1 1 1 0 0 0 0 0 2 2 0 1 0 0 0 2 2 2 0 -5 -1 -1 -4 4 2 2 2 0 0 0 -1 0 0 0 0 0 0 -6 19 reactions (columns) are sorted in the same order as in the ENZREV ENZIRREV section. enzymes 1: Pfk Fbp irreversible 2: (5 Pgi) Ald Tpi (-2 Rpi) (-4 Rpe) (-2 TktI) (-2 TktII) (-2 Tal) (-6 Pgl) Pfk (-6 Zwf) (-6 Gnd) irreversible 3: Pgi Ald Tpi (2 Gpm) (2 Eno) Pfk (2 Pgk) (2 Pyk) (2 Gap) irreversible 4: (-5 Pgi) -Ald -Tpi (-4 Rpi) (4 Rpe) (2 TktI) (2 TktII) (2 Tal) -Pfk (-6 Prs_DeoB) irreversible overall reaction 1: ATP = ADP + Pi 2: 6 CO2 + ATP + 12 NADPH = ADP + 12 NADP + G6P 3: 3 ADP + 2 NAD + G6P + 2 Pi = 3 ATP + 2 NADH + 2 PYR 4: ADP + 6 R5Pex = ATP + 5 G6P SUBSETS OF REACTIONS matrix dimension r9 x c19 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 19 reactions (columns) are sorted in the same order as in the ENZREV ENZIRREV section. enzymes 1: Pgi reversible 2: Ald Tpi reversible 3: Rpi reversible 4: (2 Rpe) TktI TktII Tal reversible 5: Gpm Eno Pgk Pyk Gap irreversible 6: Pgl Zwf Gnd irreversible 7: Pfk irreversible 8: Fbp irreversible 9: Prs_DeoB irreversible overall reaction 1: G6P = F6P 2: FDP = 2 GAP 3: Ru5P = R5P 4: 2 Ru5P + R5P = 2 F6P + GAP 5: GAP + 2 ADP + NAD + Pi = 2 ATP + NADH + PYR 6: 2 NADP + G6P = Ru5P + CO2 + 2 NADPH 7: F6P + ATP = FDP + ADP 8: FDP = F6P + Pi 9: R5P = R5Pex REDUCED SYSTEM with 5 branch point metabolites in 9 reactions (columns) matrix dimension r5 x c9 0 0 -1 -2 0 1 0 0 0 0 -1 0 0 0 0 1 -1 0 1 0 0 2 0 0 -1 1 0 0 2 0 1 -1 0 0 0 0 0 0 1 -1 0 0 0 0 -1 The following line indicates reversible (0) and irreversible reactions (1) 0 0 0 0 1 1 1 1 1 -> Branch metabolites are : met cons built reactions Ru5P 2 1 3 irr FDP 2 1 3 iir F6P 1 4 5 riirr GAP 2 4 6 rrirrr R5P 2 1 3 rri -> No branch metabolites are : met cons built reactions E4P 1 1 2 rr S7P 1 1 2 rr X5P 2 1 3 rrr GO6P 1 1 2 ir GL6P 1 1 2 ri DHAP 1 1 2 rr D13PG 1 1 2 ii P3G 1 1 2 ir P2G 1 1 2 rr PEP 1 1 2 ri CONVEX BASIS matrix dimension r6 x c19 0 0 0 1 0 0 0 0 0 0 1 0 0 1 1 0 0 0 1 -2 0 0 1 2 1 1 1 1 1 3 0 0 3 3 1 1 1 0 -5 -1 -1 2 4 2 2 2 0 0 6 0 1 6 6 0 0 0 0 5 1 1 4 -4 -2 -2 -2 0 0 0 1 0 0 0 0 0 0 6 1 1 1 0 0 0 0 0 2 2 0 1 0 0 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 enzymes 1: Rpi Pgl Zwf Gnd Prs_DeoB irreversible 2: (-2 Pgi) Rpi (2 Rpe) TktI TktII Tal Gpm Eno (3 Pgl) (3 Zwf) (3 Gnd) Pgk Pyk Gap irreversible 3: (-5 Pgi) -Ald -Tpi (2 Rpi) (4 Rpe) (2 TktI) (2 TktII) (2 Tal) (6 Pgl) Fbp (6 Zwf) (6 Gnd) irreversible 4: (5 Pgi) Ald Tpi (4 Rpi) (-4 Rpe) (-2 TktI) (-2 TktII) (-2 Tal) Pfk (6 Prs_DeoB) irreversible 5: Pgi Ald Tpi (2 Gpm) (2 Eno) Pfk (2 Pgk) (2 Pyk) (2 Gap) irreversible 6: Pfk Fbp irreversible overall reaction 1: 2 NADP + G6P = CO2 + 2 NADPH + R5Pex 2: 2 ADP + NAD + 6 NADP + G6P + Pi = 3 CO2 + 2 ATP + NADH + 6 NADPH + PYR 3: 12 NADP + G6P = 6 CO2 + 12 NADPH + Pi 4: ATP + 5 G6P = ADP + 6 R5Pex 5: 3 ADP + 2 NAD + G6P + 2 Pi = 3 ATP + 2 NADH + 2 PYR 6: ATP = ADP + Pi CONSERVATION RELATIONS matrix dimension r0 x c15 ELEMENTARY MODES matrix dimension r7 x c19 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 1 1 0 0 0 0 0 2 2 0 1 0 0 0 2 2 2 0 0 0 0 1 0 0 0 0 0 0 1 0 0 1 1 0 0 0 1 -2 0 0 1 2 1 1 1 1 1 3 0 0 3 3 1 1 1 0 -5 -1 -1 2 4 2 2 2 0 0 6 0 1 6 6 0 0 0 0 0 2 2 1 2 1 1 1 5 5 3 2 0 3 3 5 5 5 0 5 1 1 4 -4 -2 -2 -2 0 0 0 1 0 0 0 0 0 0 6 19 reactions (columns) are sorted in the same order as in the ENZREV ENZIRREV section. enzymes 1: Pfk Fbp irreversible 2: Pgi Ald Tpi (2 Gpm) (2 Eno) Pfk (2 Pgk) (2 Pyk) (2 Gap) irreversible 3: Rpi Pgl Zwf Gnd Prs_DeoB irreversible 4: (-2 Pgi) Rpi (2 Rpe) TktI TktII Tal Gpm Eno (3 Pgl) (3 Zwf) (3 Gnd) Pgk Pyk Gap irreversible 5: (-5 Pgi) -Ald -Tpi (2 Rpi) (4 Rpe) (2 TktI) (2 TktII) (2 Tal) (6 Pgl) Fbp (6 Zwf) (6 Gnd) irreversible 6: (2 Ald) (2 Tpi) Rpi (2 Rpe) TktI TktII Tal (5 Gpm) (5 Eno) (3 Pgl) (2 Pfk) (3 Zwf) (3 Gnd) (5 Pgk) (5 Pyk) (5 Gap) irreversible 7: (5 Pgi) Ald Tpi (4 Rpi) (-4 Rpe) (-2 TktI) (-2 TktII) (-2 Tal) Pfk (6 Prs_DeoB) irreversible overall reaction 1: ATP = ADP + Pi 2: 3 ADP + 2 NAD + G6P + 2 Pi = 3 ATP + 2 NADH + 2 PYR 3: 2 NADP + G6P = CO2 + 2 NADPH + R5Pex 4: 2 ADP + NAD + 6 NADP + G6P + Pi = 3 CO2 + 2 ATP + NADH + 6 NADPH + PYR 5: 12 NADP + G6P = 6 CO2 + 12 NADPH + Pi 6: 8 ADP + 5 NAD + 6 NADP + 3 G6P + 5 Pi = 3 CO2 + 8 ATP + 5 NADH + 6 NADPH + 5 PYR 7: ATP + 5 G6P = ADP + 6 R5Pex The elementary mode 6 is additional to the convex basis.