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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.
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