METATOOL OUTPUT (double) Version 4.3 (25 October 2002) ./meta INPUT FILE: ../krebs-ex.dat INTERNAL METABOLITES: 13 EXTERNAL METABOLITES: 16 REACTIONS: 16 5 int Mal 4 external CO2 4 int Pi 4 external NAD 4 external CoA 4 external NADH2 3 int Pyr 3 int OAA 3 int Cit 3 int Akg 3 external Mal_ext 2 external ATP 2 external ADP 2 int ACoA 2 external H2O 2 int Isocit 2 int SucCoA 2 int Succ 2 int Fum 2 external Pi_ext 1 external FAD 1 external FADH2 1 external Cit_ext 1 external AKG_ext 1 external Pyr_ext 1 int Asp 1 external Glu_ext 1 external Asp_ext 1 int Glu 29 metabolites, 67 is the summarized frequency edges frequency of nodes 1 9 2 9 3 5 4 5 5 1 freq_of_nodes = 13.0688 * edges^(-1.0941) Linear correlation coefficient r = -0.772108 The dependency is significant (p<0.05). STOICHIOMETRIC MATRIX matrix dimension r13 x c16 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 0 0 1 -1 0 0 0 -1 0 0 0 0 -1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 -1 0 0 -1 0 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 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 1 -1 0 -1 0 0 0 0 0 0 0 1 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 1 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 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1 -1 0 0 0 1 The following line indicates reversible (0) and irreversible reactions (1) 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 rows and columns are sorted as declared in the inputfile NOT BALANCED INTERNAL METABOLITES Glu Asp KERNEL matrix dimension r4 x c16 0 0 0 0 2 1 0 2 -1 0 -1 1 1 0 0 0 -1 0 0 0 0 1 1 0 0 0 0 0 0 -1 0 0 0 1 1 1 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 -1 0 0 -2 1 0 1 0 0 0 0 1 16 reactions (columns) are sorted in the same order as in the ENZREV ENZIRREV section. enzymes 1: (2 R15) T1 (2 T5) -T7 -R6i R7i R8i irreversible 2: -R9 T1 T2 -R10i irreversible 3: R12 R13 R14 T2 T5 R11i irreversible 4: -R15 (-2 T5) T7 R6i T6 irreversible T12 1 enzyme is not involved in reactions. overall reaction 1: 3 NAD + ADP + H2O + 2 Mal_ext + Pi_ext = 3 NADH2 + ATP + 2 CO2 + Cit_ext 2: NADH2 + CO2 + AKG_ext = NAD + Cit_ext 3: NAD + FAD + ADP + H2O + AKG_ext + Pi_ext = NADH2 + FADH2 + ATP + CO2 + Mal_ext 4: Pyr_ext + NADH2 + ATP + CO2 = NAD + ADP + Mal_ext + Pi_ext SUBSETS OF REACTIONS matrix dimension r9 x c16 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 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 1 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 1 0 1 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 1 16 reactions (columns) are sorted in the same order as in the ENZREV ENZIRREV section. enzymes 1: R9 R10i irreversible 2: R12 R13 R14 R11i irreversible 3: R15 reversible 4: T1 reversible 5: T2 reversible 6: T5 reversible 7: T7 R6i irreversible 8: R7i R8i irreversible 9: T6 irreversible overall reaction 1: Cit + NAD = Akg + NADH2 + CO2 2: Akg + Pi + NAD + FAD + ADP + H2O = Mal + NADH2 + FADH2 + ATP + CO2 3: Mal + NAD = OAA + NADH2 4: Cit + Mal_ext = Mal + Cit_ext 5: Mal + AKG_ext = Akg + Mal_ext 6: Pi_ext = Pi 7: Mal + Pyr + ATP + CO2 + Pi_ext = OAA + 2 Pi + ADP + Mal_ext 8: OAA + Pyr + NAD + H2O = Cit + NADH2 + CO2 9: Pyr_ext = Pyr REDUCED SYSTEM with 6 branch point metabolites in 9 reactions (columns) matrix dimension r6 x c9 0 0 1 0 0 0 1 -1 0 -1 0 0 -1 0 0 0 1 0 1 -1 0 0 1 0 0 0 0 0 1 -1 1 -1 0 -1 0 0 0 -1 0 0 0 1 2 0 0 0 0 0 0 0 0 -1 -1 1 The following line indicates reversible (0) and irreversible reactions (1) 1 1 0 0 0 0 1 1 1 -> Branch metabolites are : met cons built reactions OAA 1 2 3 iir Cit 2 1 3 irr Akg 1 2 3 iir Mal 3 2 5 rrrrr Pi 1 3 4 irrr Pyr 2 1 3 iii -> No branch metabolites are : met cons built reactions ACoA 1 1 2 ii SucCoA 1 1 2 ir Succ 1 1 2 rr Fum 1 1 2 rr Isocit 1 1 2 ri Glu 0 1 1 r Asp 1 0 1 r CONVEX BASIS matrix dimension r4 x c16 1 0 0 0 0 -1 -1 0 0 0 0 0 0 1 0 0 0 1 1 1 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 0 0 0 0 0 1 1 0 0 1 0 0 0 0 -1 0 0 -2 1 0 1 0 0 0 0 1 enzymes 1: R9 -T1 -T2 R10i irreversible 2: R12 R13 R14 T2 T5 R11i irreversible 3: R15 T1 R7i R8i T6 irreversible 4: -R15 (-2 T5) T7 R6i T6 irreversible overall reaction 1: NAD + Cit_ext = NADH2 + CO2 + AKG_ext 2: NAD + FAD + ADP + H2O + AKG_ext + Pi_ext = NADH2 + FADH2 + ATP + CO2 + Mal_ext 3: Pyr_ext + 2 NAD + H2O + Mal_ext = 2 NADH2 + CO2 + Cit_ext 4: Pyr_ext + NADH2 + ATP + CO2 = NAD + ADP + Mal_ext + Pi_ext CONSERVATION RELATIONS matrix dimension r1 x c13 0 0 0 0 0 0 0 0 0 0 1 1 0 1 : Glu + Asp = const ELEMENTARY MODES matrix dimension r16 x c16 1 0 0 0 0 -1 -1 0 0 0 0 0 0 1 0 0 0 1 1 1 0 0 1 1 0 0 0 0 0 0 1 0 1 1 1 1 0 -1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 1 1 0 0 0 0 0 1 1 0 0 1 1 0 0 0 1 0 -1 0 0 0 0 1 1 1 0 1 0 0 0 0 -1 0 0 -2 1 0 1 0 0 0 0 1 0 0 0 0 0 1 0 -2 1 0 1 1 1 0 0 2 1 0 0 0 0 0 -1 -2 1 0 1 1 1 1 0 2 1 1 1 1 1 0 0 1 0 0 0 1 1 1 1 1 1 1 1 1 0 0 0 -1 1 0 1 1 1 1 1 2 0 2 2 2 -1 0 2 0 1 0 1 0 0 0 2 1 2 2 2 2 -1 -2 0 0 1 0 1 0 0 2 2 1 2 2 2 2 1 0 0 0 1 0 1 2 2 2 2 3 0 2 2 2 0 1 2 0 1 0 1 1 1 0 2 2 2 2 2 2 0 -1 0 0 1 0 1 1 1 2 2 2 1 2 2 2 0 0 1 0 1 0 1 1 1 1 2 2 16 reactions (columns) are sorted in the same order as in the ENZREV ENZIRREV section. enzymes # in () indicates # of enzymes used by the elementary mode 1: ( 4) R9 -T1 -T2 R10i irreversible 2: ( 6) R12 R13 R14 T2 T5 R11i irreversible 3: ( 8) R9 R12 R13 R14 -T1 T5 R10i R11i irreversible 4: ( 5) R15 T1 R7i R8i T6 irreversible 5: ( 7) R9 R15 -T2 R7i R8i R10i T6 irreversible 6: ( 5) -R15 (-2 T5) T7 R6i T6 irreversible 7: ( 7) T1 (-2 T5) T7 R6i R7i R8i (2 T6) irreversible 8: ( 9) R9 -T2 (-2 T5) T7 R6i R7i R8i R10i (2 T6) irreversible 9: (11) R9 R12 R13 R14 R15 T5 R7i R8i R10i R11i T6 irreversible 10: (12) R9 R12 R13 R14 -T5 T7 R6i R7i R8i R10i R11i (2 T6) irreversible 11: ( 9) (2 R12) (2 R13) (2 R14) -R15 (2 T2) T7 R6i (2 R11i) T6 irreversible 12: (11) (2 R9) (2 R12) (2 R13) (2 R14) -R15 (-2 T1) T7 R6i (2 R10i) (2 R11i) T6 irreversible 13: (12) (2 R9) (2 R12) (2 R13) (2 R14) R15 T7 R6i (2 R7i) (2 R8i) (2 R10i) (2 R11i) (3 T6) irreversible 14: (11) (2 R12) (2 R13) (2 R14) T1 (2 T2) T7 R6i R7i R8i (2 R11i) (2 T6) irreversible 15: (12) (2 R9) (2 R12) (2 R13) (2 R14) -T1 T7 R6i R7i R8i (2 R10i) (2 R11i) (2 T6) irreversible 16: (12) R9 (2 R12) (2 R13) (2 R14) T2 T7 R6i R7i R8i R10i (2 R11i) (2 T6) irreversible overall reaction 1: NAD + Cit_ext = NADH2 + CO2 + AKG_ext 2: NAD + FAD + ADP + H2O + AKG_ext + Pi_ext = NADH2 + FADH2 + ATP + CO2 + Mal_ext 3: 2 NAD + FAD + ADP + H2O + Cit_ext + Pi_ext = 2 NADH2 + FADH2 + ATP + 2 CO2 + Mal_ext 4: Pyr_ext + 2 NAD + H2O + Mal_ext = 2 NADH2 + CO2 + Cit_ext 5: Pyr_ext + 3 NAD + H2O + Mal_ext = 3 NADH2 + 2 CO2 + AKG_ext 6: Pyr_ext + NADH2 + ATP + CO2 = NAD + ADP + Mal_ext + Pi_ext 7: 2 Pyr_ext + NAD + ATP + H2O = NADH2 + ADP + Cit_ext + Pi_ext 8: 2 Pyr_ext + 2 NAD + ATP + H2O = 2 NADH2 + ADP + CO2 + AKG_ext + Pi_ext 9: Pyr_ext + 4 NAD + FAD + ADP + 2 H2O + Pi_ext = 4 NADH2 + FADH2 + ATP + 3 CO2 10: 2 Pyr_ext + 3 NAD + FAD + 2 H2O = 3 NADH2 + FADH2 + 2 CO2 + Mal_ext 11: Pyr_ext + NAD + 2 FAD + ADP + 2 H2O + 2 AKG_ext + Pi_ext = NADH2 + 2 FADH2 + ATP + CO2 + 3 Mal_ext 12: Pyr_ext + 3 NAD + 2 FAD + ADP + 2 H2O + 2 Cit_ext + Pi_ext = 3 NADH2 + 2 FADH2 + ATP + 3 CO2 + 3 Mal_ext 13: 3 Pyr_ext + 7 NAD + 2 FAD + ADP + 4 H2O + Pi_ext = 7 NADH2 + 2 FADH2 + ATP + 5 CO2 + Mal_ext 14: 2 Pyr_ext + 3 NAD + 2 FAD + ADP + 3 H2O + 2 AKG_ext + Pi_ext = 3 NADH2 + 2 FADH2 + ATP + 2 CO2 + 2 Mal_ext + Cit_ext 15: 2 Pyr_ext + 5 NAD + 2 FAD + ADP + 3 H2O + Cit_ext + Pi_ext = 5 NADH2 + 2 FADH2 + ATP + 4 CO2 + 2 Mal_ext 16: 2 Pyr_ext + 4 NAD + 2 FAD + ADP + 3 H2O + AKG_ext + Pi_ext = 4 NADH2 + 2 FADH2 + ATP + 3 CO2 + 2 Mal_ext T12 1 enzyme is not involved in reactions. The elementary modes (12) 3 5 7 8 9 10 11 12 13 14 15 16 are additional to the convex basis.