METATOOL OUTPUT Version 3.5 (28.03.2001) C:\METATOOL\META35~1.EXE INPUT FILE: example.txt INTERNAL METABOLITES: 16 REACTIONS: 24 6 int CoA 5 int PEP 5 external CO2 5 int OAA 5 int OG 4 int Pyr 4 external ATP 4 int Glu 3 external ADP 3 external NAD 3 int AcCoA 3 external NADH 3 int IsoCit 3 int SucCoA 3 int Succ 3 int Fum 3 int Mal 3 int Asp 2 int Cit 2 external NADP 2 external NADPH 2 int Gly 2 external NH3 2 int Ala 1 external PG 1 external FAD 1 external FADH2 1 external Aspex 1 external AMP 1 external Gluex 1 external Alaex 1 external Sucex 32 metabolites, 88 is the summarized frequency edges frequency of nodes 0 0 1 8 2 6 3 10 4 3 5 4 6 1 STOICHIOMETRIC MATRIX matrix dimension r16 x c24 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 -1 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 0 0 0 0 0 0 -1 1 -1 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 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 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 -1 0 0 0 0 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 1 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 -1 0 -1 0 0 0 0 0 0 0 0 0 0 -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 0 1 -1 0 0 0 0 -1 0 0 0 0 0 0 -1 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 0 0 0 0 0 0 1 0 0 0 0 0 0 0 -1 1 0 -1 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 -1 1 -1 0 0 0 0 0 0 0 0 0 -1 0 0 0 1 0 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 0 0 1 -1 1 0 0 0 The following line indicates reversible (0) and irreversible reactions (1) 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 rows and columns are sorted as declared in the inputfile KERNEL matrix dimension r9 x c24 1 1 1 1 1 1 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 2 1 0 1 1 2 1 1 0 2 2 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 0 1 1 2 0 0 0 2 2 1 0 0 1 1 0 0 1 0 0 0 0 0 1 1 0 1 1 2 0 0 0 2 2 1 0 0 1 1 0 0 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 3 2 0 1 1 2 0 1 0 3 3 2 1 0 1 1 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 2 1 -1 0 0 1 0 0 0 2 2 1 0 0 1 1 0 0 0 0 0 0 0 1 24 reactions (columns) are sorted in the same order as in the ENZREV ENZIRREV section. enzymes 1: Eno Acn SucCD Sdh Fum Mdh Pyk AceEF GltA Icd SucAB irreversible 2: (2 Eno) Acn Sdh Fum (2 Mdh) AspC Gdh (2 Pyk) (2 AceEF) GltA Icl Mas AspCon irreversible 3: Fum Mdh AspC Gdh AspA irreversible 4: Eno Acn Sdh Fum (2 Mdh) (2 Pyk) (2 AceEF) GltA Icl Mas Pck irreversible 5: Eno Acn Sdh Fum (2 Mdh) (2 Pyk) (2 AceEF) GltA Icl Mas -Ppc irreversible 6: Pyk Pps irreversible 7: (3 Eno) (2 Acn) Sdh Fum (2 Mdh) Gdh (3 Pyk) (3 AceEF) (2 GltA) Icd Icl Mas GluCon irreversible 8: Eno Gdh IlvEAvtA Pyk AlaCon irreversible 9: (2 Eno) Acn -SucCD Mdh (2 Pyk) (2 AceEF) GltA Icl Mas SucCoACon irreversible overall reaction 1: 2 ADP + FAD + NADP + 3 NAD + PG = 2 ATP + FADH2 + NADPH + 3 NADH + 3 CO2 2: 2 ADP + NH3 + FAD + NADPH + 4 NAD + 2 PG = 2 ATP + Aspex + FADH2 + NADP + 4 NADH + 2 CO2 3: NADPH + NAD = NADP + NADH 4: ADP + FAD + 4 NAD + PG = ATP + FADH2 + 4 NADH + 3 CO2 5: 2 ADP + FAD + 4 NAD + PG = 2 ATP + FADH2 + 4 NADH + 3 CO2 6: ADP = AMP 7: 3 ADP + NH3 + FAD + 5 NAD + 3 PG = Gluex + 3 ATP + FADH2 + 5 NADH + 4 CO2 8: ADP + NH3 + NADPH + PG = Alaex + ATP + NADP 9: ADP + 3 NAD + 2 PG = Sucex + ATP + 3 NADH + 2 CO2 SUBSETS OF REACTIONS matrix dimension r21 x c24 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 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 0 0 0 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 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 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 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 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 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 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 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 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 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 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 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 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 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 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 0 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 24 reactions (columns) are sorted in the same order as in the ENZREV ENZIRREV section. enzymes 1: Eno reversible 2: Acn GltA irreversible 3: SucCD reversible 4: Sdh reversible 5: Fum reversible 6: Mdh reversible 7: AspC reversible 8: Gdh reversible 9: IlvEAvtA AlaCon irreversible 10: Pyk irreversible 11: AceEF irreversible 12: Icd irreversible 13: SucAB irreversible 14: Icl Mas irreversible 15: AspCon irreversible 16: AspA irreversible 17: Pck irreversible 18: Ppc irreversible 19: Pps irreversible 20: GluCon irreversible 21: SucCoACon irreversible overall reaction 1: PG = PEP 2: OAA + AcCoA = IsoCit + CoA 3: SucCoA + ADP = Succ + CoA + ATP 4: Succ + FAD = Fum + FADH2 5: Fum = Mal 6: Mal + NAD = OAA + NADH 7: Glu + OAA = Asp + OG 8: OG + NH3 + NADPH = Glu + NADP 9: Glu + Pyr = OG + Alaex 10: PEP + ADP = Pyr + ATP 11: CoA + Pyr + NAD = AcCoA + NADH + CO2 12: IsoCit + NADP = OG + NADPH + CO2 13: OG + CoA + NAD = SucCoA + NADH + CO2 14: IsoCit + AcCoA = Mal + Succ + CoA 15: Asp = Aspex 16: Asp = Fum + NH3 17: OAA + ATP = PEP + ADP + CO2 18: PEP + CO2 = OAA 19: Pyr + ATP = PEP + AMP 20: Glu = Gluex 21: SucCoA = CoA + Sucex REDUCED SYSTEM with 13 branch point metabolites in 21 reactions (columns) matrix dimension r13 x c21 0 0 0 0 0 0 1 0 0 0 0 0 0 0 -1 -1 0 0 0 0 0 0 0 0 0 0 0 -1 1 -1 0 0 0 0 0 0 0 0 0 0 -1 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 1 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 -1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 1 -1 1 0 0 1 -1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 -1 0 -1 0 0 0 0 0 0 0 0 -1 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 -1 1 0 0 0 0 -1 0 0 0 0 0 0 0 0 1 0 0 -1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 -1 0 -1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 -1 1 -1 0 0 0 0 0 0 0 -1 0 0 1 0 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 1 -1 1 0 0 The following line indicates reversible (0) and irreversible reactions (1) 0 1 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 -> Branch metabolites are : met cons built reactions Asp 2 1 3 rii Glu 3 1 4 rrir Mal 1 2 3 rri Fum 1 2 3 rri Succ 1 2 3 rri SucCoA 2 1 3 iri OG 2 3 5 iirrr IsoCit 2 1 3 rii OAA 3 2 5 irrii AcCoA 2 1 3 iii CoA 2 4 6 iiirii Pyr 3 1 4 iiir PEP 2 3 5 riiii -> No branch metabolites are : met cons built reactions Ala 1 1 2 ri Gly 1 1 2 ii Cit 1 1 2 ir CONVEX BASIS matrix dimension r12 x c24 0 0 0 0 1 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 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 1 0 0 1 0 0 0 0 1 0 -1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 1 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 1 1 1 1 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 2 1 0 0 0 0 0 1 0 1 1 1 1 0 0 0 0 0 0 1 0 1 0 0 1 1 0 1 1 2 0 0 0 2 2 1 0 0 1 1 0 0 1 0 0 0 0 0 2 1 0 1 1 2 1 1 0 2 2 1 0 0 1 1 1 0 0 0 0 0 0 0 2 1 -1 0 0 1 0 0 0 2 2 1 0 0 1 1 0 0 0 0 0 0 0 1 3 2 0 1 1 2 0 1 0 3 3 2 1 0 1 1 0 0 0 0 0 1 0 0 enzymes 1: Fum Mdh AspC Gdh AspA irreversible 2: Pck Ppc irreversible 3: Pyk Pps irreversible 4: Eno AspC Gdh AspCon Ppc irreversible 5: Eno -SucCD -Sdh -Fum -Mdh Ppc SucCoACon irreversible 6: Eno Gdh IlvEAvtA Pyk AlaCon irreversible 7: Eno Acn SucCD Sdh Fum Mdh Pyk AceEF GltA Icd SucAB irreversible 8: (2 Eno) Acn Gdh Pyk AceEF GltA Icd Ppc GluCon irreversible 9: Eno Acn Sdh Fum (2 Mdh) (2 Pyk) (2 AceEF) GltA Icl Mas Pck irreversible 10: (2 Eno) Acn Sdh Fum (2 Mdh) AspC Gdh (2 Pyk) (2 AceEF) GltA Icl Mas AspCon irreversible 11: (2 Eno) Acn -SucCD Mdh (2 Pyk) (2 AceEF) GltA Icl Mas SucCoACon irreversible 12: (3 Eno) (2 Acn) Sdh Fum (2 Mdh) Gdh (3 Pyk) (3 AceEF) (2 GltA) Icd Icl Mas GluCon irreversible overall reaction 1: NADPH + NAD = NADP + NADH 2: ATP = ADP 3: ADP = AMP 4: NH3 + NADPH + CO2 + PG = Aspex + NADP 5: ATP + FADH2 + NADH + CO2 + PG = Sucex + ADP + FAD + NAD 6: ADP + NH3 + NADPH + PG = Alaex + ATP + NADP 7: 2 ADP + FAD + NADP + 3 NAD + PG = 2 ATP + FADH2 + NADPH + 3 NADH + 3 CO2 8: ADP + NH3 + NAD + 2 PG = Gluex + ATP + NADH + CO2 9: ADP + FAD + 4 NAD + PG = ATP + FADH2 + 4 NADH + 3 CO2 10: 2 ADP + NH3 + FAD + NADPH + 4 NAD + 2 PG = 2 ATP + Aspex + FADH2 + NADP + 4 NADH + 2 CO2 11: ADP + 3 NAD + 2 PG = Sucex + ATP + 3 NADH + 2 CO2 12: 3 ADP + NH3 + FAD + 5 NAD + 3 PG = Gluex + 3 ATP + FADH2 + 5 NADH + 4 CO2 CONSERVATION RELATIONS matrix dimension r1 x c16 0 0 0 0 0 0 0 1 0 0 0 0 1 1 0 0 1 : SucCoA + AcCoA + CoA = const ELEMENTARY MODES matrix dimension r16 x c24 0 0 0 0 1 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 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 1 0 0 1 0 0 0 0 1 0 -1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 1 0 -1 -1 0 0 1 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 1 1 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 2 1 -1 0 0 1 0 0 0 2 2 1 0 0 1 1 0 0 0 0 0 0 0 1 1 1 1 1 1 1 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 3 1 -2 -1 -1 0 0 0 0 2 2 1 0 0 1 1 0 0 0 1 0 0 0 2 2 1 0 0 0 0 0 1 0 1 1 1 1 0 0 0 0 0 0 1 0 1 0 0 2 1 0 0 0 0 0 0 0 1 1 1 1 1 0 0 0 0 0 1 0 0 0 1 1 1 0 1 1 2 0 0 0 2 2 1 0 0 1 1 0 0 1 0 0 0 0 0 2 1 0 1 1 2 1 1 0 2 2 1 0 0 1 1 1 0 0 0 0 0 0 0 3 2 0 1 1 2 0 1 0 3 3 2 1 0 1 1 0 0 0 0 0 1 0 0 3 2 0 1 1 2 0 0 0 3 3 2 1 1 1 1 0 0 0 0 0 0 0 1 24 reactions (columns) are sorted in the same order as in the ENZREV ENZIRREV section. enzymes 1: Fum Mdh AspC Gdh AspA irreversible 2: Pck Ppc irreversible 3: Pyk Pps irreversible 4: Eno AspC Gdh AspCon Ppc irreversible 5: Eno -SucCD -Sdh -Fum -Mdh Ppc SucCoACon irreversible 6: Eno -SucCD -Sdh AspC Gdh AspA Ppc SucCoACon irreversible 7: Eno Gdh IlvEAvtA Pyk AlaCon irreversible 8: (2 Eno) Acn -SucCD Mdh (2 Pyk) (2 AceEF) GltA Icl Mas SucCoACon irreversible 9: Eno Acn SucCD Sdh Fum Mdh Pyk AceEF GltA Icd SucAB irreversible 10: (3 Eno) Acn (-2 SucCD) -Sdh -Fum (2 Pyk) (2 AceEF) GltA Icl Mas Ppc (2 SucCoACon) irreversible 11: (2 Eno) Acn Gdh Pyk AceEF GltA Icd Ppc GluCon irreversible 12: (2 Eno) Acn Pyk AceEF GltA Icd SucAB Ppc SucCoACon irreversible 13: Eno Acn Sdh Fum (2 Mdh) (2 Pyk) (2 AceEF) GltA Icl Mas Pck irreversible 14: (2 Eno) Acn Sdh Fum (2 Mdh) AspC Gdh (2 Pyk) (2 AceEF) GltA Icl Mas AspCon irreversible 15: (3 Eno) (2 Acn) Sdh Fum (2 Mdh) Gdh (3 Pyk) (3 AceEF) (2 GltA) Icd Icl Mas GluCon irreversible 16: (3 Eno) (2 Acn) Sdh Fum (2 Mdh) (3 Pyk) (3 AceEF) (2 GltA) Icd SucAB Icl Mas SucCoACon irreversible overall reaction 1: NADPH + NAD = NADP + NADH 2: ATP = ADP 3: ADP = AMP 4: NH3 + NADPH + CO2 + PG = Aspex + NADP 5: ATP + FADH2 + NADH + CO2 + PG = Sucex + ADP + FAD + NAD 6: ATP + FADH2 + NADPH + CO2 + PG = Sucex + ADP + FAD + NADP 7: ADP + NH3 + NADPH + PG = Alaex + ATP + NADP 8: ADP + 3 NAD + 2 PG = Sucex + ATP + 3 NADH + 2 CO2 9: 2 ADP + FAD + NADP + 3 NAD + PG = 2 ATP + FADH2 + NADPH + 3 NADH + 3 CO2 10: FADH2 + 2 NAD + 3 PG = 2 Sucex + FAD + 2 NADH + CO2 11: ADP + NH3 + NAD + 2 PG = Gluex + ATP + NADH + CO2 12: ADP + NADP + 2 NAD + 2 PG = Sucex + ATP + NADPH + 2 NADH + 2 CO2 13: ADP + FAD + 4 NAD + PG = ATP + FADH2 + 4 NADH + 3 CO2 14: 2 ADP + NH3 + FAD + NADPH + 4 NAD + 2 PG = 2 ATP + Aspex + FADH2 + NADP + 4 NADH + 2 CO2 15: 3 ADP + NH3 + FAD + 5 NAD + 3 PG = Gluex + 3 ATP + FADH2 + 5 NADH + 4 CO2 16: 3 ADP + FAD + NADP + 6 NAD + 3 PG = Sucex + 3 ATP + FADH2 + NADPH + 6 NADH + 5 CO2 The elementary modes (4) 6 10 12 16 are additional to the convex basis.