Click here for new version of METATOOL (4.9) with improved performance/algorithms and bug fixes!
METATOOL is a C program developed from 1998 to 2000 by Thomas Pfeiffer (Berlin) in cooperationwith Juan Carlos Nuno (Madrid) Stefan Schuster and Ferdinand Moldenhauer (Berlin) . It serves to derive conclusionsabout the pathway structure of metabolic networks from the stoichiometric reaction equations and information aboutreversibility and irreversibility of enzymes. It is based on an algorithm described in the file algorithm.pdf.
The latest version 25/October/2002 meta4.3_int.cpp implementsbetter performance and internal memory management than the older versions. The stoichiometric coefficients areintegers and intermediate results are calculated with integer numbers. For Win32 (Windows 95,NT 4.0 or XP) operating system please use meta4.3_int.exe.
Sometimes intermediate results cause integer overflows. If meta4.3_int.exe breaks off the calculations by such an error, please restart the calculations employing meta4.3_double.exe (C++ sourcecode meta4.3_double.cpp). That program uses double real numbers. The results of metaX.x_double.exe and metaX.x_int.exe for "small" systems have to be the same. Meta4.x_double is able to read non-integer stoichiometric coefficients (see below). WARNING: The double version of METATOOL 4.3 contains many errors and should not be used! Please use version 4.9 or higher instead.
New: since 04/Aug/2000
METATOOL (meta*.c) should preferably be compiled with the GNU compiler.
For DOS and Win32 console applications,comment out the two lines
#include <conio.h>
and
#include <malloc.h>
The program requires the two file names. First the input file and second the output file in the command line.If they are not specified, the program will ask for them.
To explain the format of the input file, we give an example file (Example.dat), which codifies a reaction scheme comprising the tricarboxylic acid cycle, glyoxylate shunt and adjacent reactions of amino acid synthesis in E. coli (cf. Ref. 1).
If you download the ASCII-files (*.dat, *.c) please check the correct newline-character-transfer to your operatingsystem. For an easy transfer at Win32 platforms use (10to1310.exe).
Explanation:
-ENZREV, -ENZIRREV
After the key words -ENZREV and -ENZIRREV, names or abbreviations
of the reversible and irreversible enzymes, respectively, have to be written.
-METINT, -METEXT
After the key word -METINT, names or abbreviations of the internal
metabolites have to be written. Theseare the substances which have to fulfil
a steady-state condition (production = consumption). After the key word -METEXT
names or abbreviations of the external metabolites have to be written. External
metabolites (sourcesand sinks) need not be balanced in the scheme under
consideration. The order of these four fields is important.All internal
and external metabolites must have an underscore or a letter (no number)
as the first character andmust not include a white space in the old version.
This restriction are not further required.
-CAT
After the key word -CAT, the reaction equations are listed in any
order. The raction name is written firstjust as after the key words -ENZREV
and -ENZREV. The reaction name is followed by a white space(space
or tab), a colon and a white space. Then the stoichiometric reaction equation
follows. Stoichiometric coefficientsare integers separated by a white space
from the metabolites. After the metabolites, a white space and a plus oran
equal sign and a white space follow. The end of each reaction equation is
formed by a white space and a fullstop. Metabolites are written in the same
way as after the key words -METINT and -METEXT. Theorder
of metabolites in the reaction equations makes no difference. However, the
sides of the reaction equationsare exchangeable only in the reversible reactions.
The metabolites that are formed by the irreversible reactionshave to be
written on the right side of the reaction equations.
The program writes the results in an output file. For our example, this file reads as follows:
METATOOL OUTPUT Version 3.0 [your path to]\meta3_int.exeINPUT
FILE: Example.datINTERNAL METABOLITES: 16REACTIONS: 24
STOICHIOMETRIC MATRIX:
matrix dimension 16 x 24
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
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
Explanation:
The program gives the numbers of internal metabolites and reactions. It also parses the reactionequations and translates them into a stoichiometric matrix. This matrix includes the stoichiometric coefficients(molecularities) of the internal metabolites in all the reaction equations, with the rows corresponding to internalmetabolites and the columns corresponding to reactions. The line following the stoichiometric matrix indicatesthe reversible and irreversible reactions in the same order as after the key words -ENZREV and -ENZIRREV.
KERNEL matrix dimension 9 x 24
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
Explanation:
The kernel or nullspace is the subspace of all flux vectors V that satisfy the equation Stoich. matrix times V = 0 (see Ref. 2). The rows of the above matrix span this subspace.
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
Explanation:
This list contains the enzymes that correspond to the rows of the kernel matrix. The coefficientsindicate relative fluxes carried by the enzymes. A minus sign before an enzyme name stands for -1. The followingnine lines contain the sum of metabolites which are involved in these enzyme reactions. E.g. in reaction 6, Pykand Pps catalyse PEP + ADP = Pyr + ATP and Pyr + ATP = PEP + AMP, respectively, which gives, as the overall reaction:ADP = AMP.
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 (21 rows) matrix dimension 21 x 24
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
Explanation:
Enzyme subsets are sets of enzymes that always operate together in fixed flux ratios. For example,if aconitase (Acn) is operative, then also citrate synthase (GltA) is operative. This information can be writtenin the form of a matrix (see above). For example, the second row contains ones at positions 2 and 12, which correspondto Acn and GltA. Below, this information is given in more detailed form, together with the overall reactions of the subsets.
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
Explanation:
Enzymes belonging to the same subset can be lumped. This gives rise to the following reduced reaction system.
REDUCED SYSTEM with 13 branch point
metabolites in 21 reactions (columns) matrix dimension 13 x 21
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
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
Explanation:
"The simplified system is a kind of skeleton model of the original system. It contains onlymetabolites at branch points. Skeleton models are often used in metabolic modeling to reduce the number of variables"(see Refs. 5, 6, 7).
CONVEX BASIS matrix dimension 12 x 21
0 0 0 0 1 1 1 1 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 1 1 0 0 0 0 0 0 0 0 0
0 0 0 1 0 0 0 0 0 0 0 0
1 0 0 1 0 0 0 0 0 1 1 0
0 0 0 0 0 1 0 0 1 0 0 0
1 0 -1 -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 1 1 1 0 0 0 0 0
0 0 0 0 0 0 1 1 1 1 1 1
0 0 0 1 1 1 1 0 0 0 0 0
0 0 0 2 1 0 0 0 0 0 1 0
1 1 1 0 0 0 0 0 1 0 1 0
1 1 0 1 1 2 0 0 0 2 2 0
0 1 0 0 1 0 0 0 0 2 1 0
1 1 2 1 1 0 2 2 0 0 1 1
0 0 0 0 0 0 2 1 -1 0 0 1
0 0 0 2 2 0 0 1 0 0 0 0
0 0 1 3 2 0 1 1 2 0 1 0
3 3 1 0 1 0 0 0 0 0 1 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
Explanation:
The convex basis is the minimum number of elementary modes to reconstruct the whole reaction system.Any admissible flux distribution in the system (i.e. any distribution that is compatible with the steady-statecondition and the directionality of the irreversible reactions) can be written as a non-negative linear combinationof the vectors forming the convex basis (Ref. 5). These vectors form the rows of the abovematrix. These rows are then translated into lists of enzymes in the same way as have been translated above therows of the null-space matrix. A basis vector is reversible if its negative is an admissible flux distributionas well, otherwise it is irreversible.
CONSERVATON RELATIONS
matrix dimension 1 x 16
0 0 0 0 0 0 0 1 0 0 0 0 1 1 0 0
Explanation:
Conservation relations indicate that linear combinations (e.g. the sum) of several internal metabolitesare constant. The metabolites are in the same order as after the keyword -METINT. The above row meansthat SucCoA + AcCoA + CoA = const. (Minus signs in the above row is irrelevant because we can multiply the equationby -1).
ELEMENTARY MODES
matrix dimension 16 x 21
0 0 0 0 1 1 1 1 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 1 1 0 0 0 0 0 0 0 0 0
0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 1
0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0
1 0 0 0 1 0 -1 -1 -1 -1 0 0 0 0 0 0
0 0 0 0 0 1 0 0 1 1 0 -1 -1 0 0 1
1 0 0 0 0 0 0 0 1 0 1 0 0 1 1 0
0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0
0 0 0 2 1 -1 0 0 1 0 0 0 2 2 0 0
1 0 0 0 0 0 0 1 1 1 1 1 1 1 0 0
0 1 1 1 1 0 0 0 0 0 0 0 0 3 1 -2
-1 -1 0 0 0 0 2 2 0 0 1 0 0 0 1 0
0 2 2 1 0 0 0 0 0 1 0 1 1 1 0 0
0 0 0 1 0 1 0 2 1 0 0 0 0 0 0 0
1 1 1 1 0 0 0 0 1 0 0 1 1 1 0 1
1 2 0 0 0 2 2 0 0 1 0 0 1 0 0 0
0 2 1 0 1 1 2 1 1 0 2 2 0 0 1 1
0 0 0 0 0 0 3 2 0 1 1 2 0 1 0 3
3 1 0 1 0 0 0 0 0 1 0 3 2 0 1 1
2 0 0 0 3 3 1 1 1 0 0 0 0 0 0 1
Explanation:
The choice of the basis vectors of the kernel (or nullspace) is not unique. Therefore, it wasproposed (Refs. 1, 3, 4, 5, 7) to take a complete set of the simplest basis vectors compatible with the directionality ofthe irreversible reactions. These are called elementary modes. There may be more of them then actually needed tospan the admissible region in flux space, but they have the favourable property to be uniquely determined (up toscalar multiples). These modes can be brought in relation with the biochemical pathways in the system. The rowsof the elementary modes matrix give the elementary modes for our example system.
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 6 10 12 16 are additional to the convex basis.
Explanation:
Above is the verbal listing of the elementary modes and of the overall reactions in terms ofthe external metabolites.
Page of Thomas Pfeifer: http://www.eco.ethz.ch/portrai ts/pfeiffer/.
Metatool forms the calculation background to the internet application phpMETATOOL http://www-bm.ipk-gatersleben.de/tools/phpMetatool/ prepared by the bioinfomatics group of magdeburg. It uses the internet databases KEGG and WIT for collecting biochemicalreaction equations belonging to special organisms.