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Remove unused files.

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mdehoon
2008-07-16 05:40:57 +00:00
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21
Tests/MetaTool/Example3.txt
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-ENZREV
3.5.1.38
-ENZIRREV
3.5.1.38
4.1.1.12
-METINT
L-Glutamine
H2O
L-glutamate
NH3
L-Aspartate
L-alanine
CO2
-METEXT
-CAT
3.5.1.38 : L-Glutamine + H2O = L-glutamate + NH3 .
4.1.1.12 : L-Aspartate = L-alanine + CO2 .

45
Tests/MetaTool/Example4.txt
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-ENZREV
2.6.1.19
3.5.1.6
3.5.2.2
-ENZIRREV
1.2.1.18
1.4.3.6
3.4.13.3
3.5.1.6
3.5.2.2
-METINT
3-Oxopropanoate
CoA
NAD(P)+
acetyl-CoA
CO2
NAD(P)H
RCH2NH2
O2
RCHO
NH3
H2O2
4-Aminobutanoate
2-oxoglutarate
succinate_semialdehyde
L-glutamate
Beta-alanyl-L-histidine
beta-alanine
L-histidine
N-Carbamoyl-beta-alanine
5,6-Dihydrouracil
3-ureidopropionate
-METEXT
H2O
-CAT
1.2.1.18 : 3-Oxopropanoate + CoA + NAD(P)+ = acetyl-CoA + CO2 + NAD(P)H .
1.4.3.6 : RCH2NH2 + H2O + O2 = RCHO + NH3 + H2O2 .
2.6.1.19 : 4-Aminobutanoate + 2-oxoglutarate = succinate_semialdehyde + L-glutamate .
3.4.13.3 : Beta-alanyl-L-histidine + H2O = beta-alanine + L-histidine .
3.5.1.6 : N-Carbamoyl-beta-alanine + H2O = beta-alanine + CO2 + NH3 .
3.5.2.2 : 5,6-Dihydrouracil + H2O = 3-ureidopropionate .

36
Tests/MetaTool/Example6.txt
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-ENZREV
1.2.1.5
-ENZIRREV
1.11.1.7
1.13.11.27
1.2.1.5
1.4.3.4
1.4.3.6
-METINT
Donor
oxidized_donor
4-Hydroxyphenylpyruvate
homogentisate
CO2
An_aldehyde
NAD(P)+
an_acid
NAD(P)H
H+
RCH2NH2
RCHO
NH3
-METEXT
H2O2
H2O
O2
-CAT
1.11.1.7 : Donor + H2O2 = oxidized_donor + 2 H2O .
1.13.11.27 : 4-Hydroxyphenylpyruvate + O2 = homogentisate + CO2 .
1.2.1.5 : An_aldehyde + NAD(P)+ + H2O = an_acid + NAD(P)H + H+ .
1.4.3.4 : RCH2NH2 + H2O + O2 = RCHO + NH3 + H2O2 .
1.4.3.6 : RCH2NH2 + H2O + O2 = RCHO + NH3 + H2O2 .

43
Tests/MetaTool/Example7.txt
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-ENZREV
5.3.3.2
-ENZIRREV
1.1.1.34
1.14.13.13
2.5.1.10
4.1.1.33
5.4.99.7
-METINT
(S)-3-Hydroxy-3-methylglutaryl-CoA
(R)-mevalonate
CoA
Calcidiol
O2
calcitriol
H2O
Geranyl_diphosphate
diphosphate
trans,trans-farnesyl_diphosphate
ATP
(R)-5-diphosphomevalonate
ADP
phosphate
CO2
Isopentenyl_diphosphate
dimethylallyl_diphosphate
(S)-2,3-Epoxysqualene
lanosterol
-METEXT
NADPH
NADP+
isopentenyl_diphosphate
-CAT
1.1.1.34 : (S)-3-Hydroxy-3-methylglutaryl-CoA + 2 NADPH = (R)-mevalonate + CoA + 2 NADP+ .
1.14.13.13 : Calcidiol + NADPH + O2 = calcitriol + NADP+ + H2O .
2.5.1.10 : Geranyl_diphosphate + isopentenyl_diphosphate = diphosphate + trans,trans-farnesyl_diphosphate .
4.1.1.33 : ATP + (R)-5-diphosphomevalonate = ADP + phosphate + isopentenyl_diphosphate + CO2 .
5.3.3.2 : Isopentenyl_diphosphate = dimethylallyl_diphosphate .
5.4.99.7 : (S)-2,3-Epoxysqualene = lanosterol .

40
Tests/MetaTool/Example8.txt
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-ENZREV
1.3.1.28
1.6.5.3
2.7.7.58
5.4.99.6
-ENZIRREV
2.1.1.64
6.2.1.26
-METINT
2,3-Dihydro-2,3-dihydroxybenzoate
ubiquinone
ubiquinol
S-Adenosyl-L-methionine
3-demethylubiquinone-9
S-adenosyl-L-homocysteine
ubiquinone-9
(2,3-dihydroxybenzoyl)adenylate
Chorismate
isochorismate
o-succinylbenzoate
CoA
AMP
o-succinylbenzoyl-CoA
-METEXT
NAD+
2,3-dihydroxybenzoate
NADH
ATP
diphosphate
-CAT
1.3.1.28 : 2,3-Dihydro-2,3-dihydroxybenzoate + NAD+ = 2,3-dihydroxybenzoate + NADH .
1.6.5.3 : NADH + ubiquinone = NAD+ + ubiquinol .
2.1.1.64 : S-Adenosyl-L-methionine + 3-demethylubiquinone-9 = S-adenosyl-L-homocysteine + ubiquinone-9 .
2.7.7.58 : ATP + 2,3-dihydroxybenzoate = diphosphate + (2,3-dihydroxybenzoyl)adenylate .
5.4.99.6 : Chorismate = isochorismate .
6.2.1.26 : ATP + o-succinylbenzoate + CoA = AMP + diphosphate + o-succinylbenzoyl-CoA .

141
Tests/MetaTool/Example9.txt
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-ENZREV
1.1.1.205
2.1.2.2
2.1.2.3
2.4.2.1
2.4.2.22
2.4.2.4
2.4.2.7
2.4.2.8
2.7.1.25
2.7.4.11
2.7.4.3
2.7.4.6
2.7.4.8
2.7.6.1
2.7.7.6
2.7.7.7
2.7.7.8
3.1.3.5
-ENZIRREV
1.17.4.1
1.6.6.8
2.1.2.2
2.1.2.3
2.4.2.1
2.4.2.14
2.4.2.4
2.7.1.25
2.7.6.1
2.7.6.5
3.1.3.5
3.1.4.16
3.1.4.17
3.1.5.1
3.2.2.2
3.2.2.4
-METINT
Inosine_5`-phosphate
NAD+
xanthosine_5`-phosphate
NADH
Ribonucleoside_diphosphate
reduced_thioredoxin
2`-deoxyribonucleoside_diphosphate
oxidized_thioredoxin
NADPH
guanosine_5`-phosphate
NADP+
inosine_5`-phosphate
10-Formyltetrahydrofolate
5`-phosphoribosylglycinamide
tetrahydrofolate
5`-phosphoribosyl-N-formylglycinamide
5`-phosphoribosyl-5-amino-4-imidazolecarboxamide
5`-phosphoribosyl-5-formamido-4-imidazolecarboxamide
Purine_nucleoside
phosphate
purine
alpha-D-ribose_1-phosphate
5-Phospho-beta-D-ribosylamine
L-glutamate
L-glutamine
5-phospho-alpha-D-ribose_1-diphosphate
5-Phospho-alpha-D-ribose_1-diphosphate
xanthine
(9-D-ribosylxanthine)-5`-phosphate
Thymidine
thymine
2-deoxy-D-ribose_1-phosphate
Adenine
AMP
Hypoxanthine
IMP
adenylylsulfate
3`-phosphoadenylylsulfate
dAMP
dADP
nucleoside_diphosphate
nucleoside_triphosphate
GMP
GDP
D-ribose_5-phosphate
GTP
guanosine_3`-diphosphate_5`-triphosphate
Nucleoside_triphosphate
RNAn
RNAn+1
Deoxynucleoside_triphosphate
DNAn
DNAn+1
a_nucleoside_diphosphate
A_5`-ribonucleotide
a_ribonucleoside
Nucleoside_2`,3`-cyclic_phosphate
nucleoside_3`-phosphate
Nucleoside_3`,5`-cyclic_phosphate
nucleoside_5`-phosphate
dGTP
deoxyguanosine
triphosphate
Inosine
hypoxanthine
D-ribose
adenine
-METEXT
H2O
diphosphate
ATP
ADP
-CAT
1.1.1.205 : Inosine_5`-phosphate + NAD+ + H2O = xanthosine_5`-phosphate + NADH .
1.17.4.1 : Ribonucleoside_diphosphate + reduced_thioredoxin = 2`-deoxyribonucleoside_diphosphate + oxidized_thioredoxin + H2O .
1.6.6.8 : NADPH + guanosine_5`-phosphate = NADP+ + inosine_5`-phosphate .
2.1.2.2 : 10-Formyltetrahydrofolate + 5`-phosphoribosylglycinamide = tetrahydrofolate + 5`-phosphoribosyl-N-formylglycinamide .
2.1.2.3 : 10-Formyltetrahydrofolate + 5`-phosphoribosyl-5-amino-4-imidazolecarboxamide = tetrahydrofolate + 5`-phosphoribosyl-5-formamido-4-imidazolecarboxamide .
2.4.2.1 : Purine_nucleoside + phosphate = purine + alpha-D-ribose_1-phosphate .
2.4.2.14 : 5-Phospho-beta-D-ribosylamine + diphosphate + L-glutamate = L-glutamine + 5-phospho-alpha-D-ribose_1-diphosphate + H2O .
2.4.2.22 : 5-Phospho-alpha-D-ribose_1-diphosphate + xanthine = (9-D-ribosylxanthine)-5`-phosphate + diphosphate .
2.4.2.4 : Thymidine + phosphate = thymine + 2-deoxy-D-ribose_1-phosphate .
2.4.2.7 : Adenine + 5-phospho-alpha-D-ribose_1-diphosphate = AMP + diphosphate .
2.4.2.8 : Hypoxanthine + 5-phospho-alpha-D-ribose_1-diphosphate = IMP + diphosphate .
2.7.1.25 : ATP + adenylylsulfate = ADP + 3`-phosphoadenylylsulfate .
2.7.4.11 : ATP + dAMP = ADP + dADP .
2.7.4.3 : ATP + AMP = ADP + ADP .
2.7.4.6 : ATP + nucleoside_diphosphate = ADP + nucleoside_triphosphate .
2.7.4.8 : ATP + GMP = ADP + GDP .
2.7.6.1 : ATP + D-ribose_5-phosphate = AMP + 5-phospho-alpha-D-ribose_1-diphosphate .
2.7.6.5 : ATP + GTP = AMP + guanosine_3`-diphosphate_5`-triphosphate .
2.7.7.6 : Nucleoside_triphosphate + RNAn = diphosphate + RNAn+1 .
2.7.7.7 : Deoxynucleoside_triphosphate + DNAn = diphosphate + DNAn+1 .
2.7.7.8 : RNAn+1 + phosphate = RNAn + a_nucleoside_diphosphate .
3.1.3.5 : A_5`-ribonucleotide + H2O = a_ribonucleoside + phosphate .
3.1.4.16 : Nucleoside_2`,3`-cyclic_phosphate + H2O = nucleoside_3`-phosphate .
3.1.4.17 : Nucleoside_3`,5`-cyclic_phosphate + H2O = nucleoside_5`-phosphate .
3.1.5.1 : dGTP + H2O = deoxyguanosine + triphosphate .
3.2.2.2 : Inosine + H2O = hypoxanthine + D-ribose .
3.2.2.4 : AMP + H2O = adenine + D-ribose_5-phosphate .

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Tests/MetaTool/Meta10.out
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METATOOL OUTPUT Version 3.5 (28.03.2001) C:\METATOOL\META35~1.EXE
INPUT FILE: EXAMPLE10.TXT
INTERNAL METABOLITES: 5
REACTIONS: 2
2 external L-Glutamate
2 external NAD+
2 external NADH
1 int L-glutamine
1 int oxoglutarate
1 int H2O
1 int 2-oxoglutarate
1 int NH3
8 metabolites, 11 is the summarized frequency
edges frequency of nodes
0 0
1 5
2 3
STOICHIOMETRIC MATRIX
matrix dimension r5 x c2
0 1
0 2
-1 0
1 0
1 0
The following line indicates reversible (0) and irreversible reactions (1)
0 1
rows and columns are sorted as declared in the inputfile
NOT BALANCED INTERNAL METABOLITES
L-glutamine oxoglutarate H2O 2-oxoglutarate NH3
KERNEL
matrix dimension r0 x c2
2 reactions (columns) are sorted in the same order as in the ENZREV ENZIRREV section.
enzymes
- not found -
overall reaction
- not found -
The remaining overall reactions perform no net transformation of external metabolites.
SUBSETS OF REACTIONS
matrix dimension r0 x c2
2 reactions (columns) are sorted in the same order as in the ENZREV ENZIRREV section.
enzymes
- not found -
overall reaction
- not found -
The remaining overall reactions perform no net transformation of external metabolites.
REDUCED SYSTEM with 5 branch point metabolites in 2 reactions (columns)
matrix dimension r0 x c2
The following line indicates reversible (0) and irreversible reactions (1)
0 0
-> Branch metabolites are :
met cons built reactions
-> No branch metabolites are :
met cons built reactions
L-glutamine 0 1 1 i
oxoglutarate 0 1 1 i
H2O 1 0 1 r
2-oxoglutarate 0 1 1 r
NH3 0 1 1 r
CONVEX BASIS
matrix dimension r0 x c2
enzymes
- not found -
overall reaction
- not found -
The remaining overall reactions perform no net transformation of external metabolites.
CONSERVATION RELATIONS
matrix dimension r3 x c5
-2 1 0 0 0
0 0 1 1 0
0 0 1 0 1
1 : L-glutamine + oxoglutarate = const
2 : H2O + 2-oxoglutarate = const
3 : H2O + NH3 = const
ELEMENTARY MODES
matrix dimension r0 x c2
2 reactions (columns) are sorted in the same order as in the ENZREV ENZIRREV section.
enzymes
- not found -
overall reaction
- not found -
The remaining overall reactions perform no net transformation of external metabolites.
The elementary modes ARE EQUAL to convex basis.

131
Tests/MetaTool/Meta12.out
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METATOOL OUTPUT Version 3.5 (28.03.2001) C:\METATOOL\META35~1.EXE
INPUT FILE: EXAMPLE12.TXT
INTERNAL METABOLITES: 6
REACTIONS: 3
2 external dehydroascorbate
1 int L-Ascorbate
1 int H2O2
1 int H2O
1 int Glutathione
1 int oxidized_glutathione
1 int ascorbate
7 metabolites, 8 is the summarized frequency
edges frequency of nodes
0 0
1 6
2 1
STOICHIOMETRIC MATRIX
matrix dimension r6 x c3
0 -1 0
0 -1 0
0 2 0
-2 0 0
1 0 0
1 0 0
The following line indicates reversible (0) and irreversible reactions (1)
0 1 1
rows and columns are sorted as declared in the inputfile
NOT BALANCED INTERNAL METABOLITES
L-Ascorbate H2O2 H2O Glutathione oxidized_glutathione ascorbate
KERNEL
matrix dimension r1 x c3
0 0 1
3 reactions (columns) are sorted in the same order as in the ENZREV ENZIRREV section.
enzymes
1: 1.8.5.1 irreversible
overall reaction
- not found -
The remaining overall reactions perform no net transformation of external metabolites.
SUBSETS OF REACTIONS
matrix dimension r1 x c3
0 0 1
3 reactions (columns) are sorted in the same order as in the ENZREV ENZIRREV section.
enzymes
1: 1.8.5.1 irreversible
overall reaction
- not found -
The remaining overall reactions perform no net transformation of external metabolites.
REDUCED SYSTEM with 6 branch point metabolites in 1 reactions (columns)
matrix dimension r0 x c1
The following line indicates reversible (0) and irreversible reactions (1)
1
-> Branch metabolites are :
met cons built reactions
-> No branch metabolites are :
met cons built reactions
L-Ascorbate 1 0 1 i
H2O2 1 0 1 i
H2O 0 1 1 i
Glutathione 1 0 1 r
oxidized_glutathione 0 1 1 r
ascorbate 0 1 1 r
CONVEX BASIS
matrix dimension r1 x c3
0 0 1
enzymes
1: 1.8.5.1 irreversible
overall reaction
- not found -
The remaining overall reactions perform no net transformation of external metabolites.
CONSERVATION RELATIONS
matrix dimension r4 x c6
1 -1 0 0 0 0
2 0 1 0 0 0
0 0 0 1 2 0
0 0 0 1 0 2
1 : L-Ascorbate + H2O2 = const
2 : L-Ascorbate + H2O = const
3 : Glutathione + oxidized_glutathione = const
4 : Glutathione + ascorbate = const
ELEMENTARY MODES
matrix dimension r1 x c3
0 0 1
3 reactions (columns) are sorted in the same order as in the ENZREV ENZIRREV section.
enzymes
1: 1.8.5.1 irreversible
overall reaction
- not found -
The remaining overall reactions perform no net transformation of external metabolites.
The elementary modes ARE EQUAL to convex basis.

191
Tests/MetaTool/Meta13.out
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METATOOL OUTPUT Version 3.5 (28.03.2001) C:\METATOOL\META35~1.EXE
INPUT FILE: EXAMPLE13.TXT
INTERNAL METABOLITES: 19
REACTIONS: 6
3 external H2O
1 int 5,10-Methylenetetrahydrofolate
1 int glycine
1 int tetrahydrofolate
1 int L-serine
1 int (5-L-Glutamyl)-peptide
1 int an_amino_acid
1 int peptide
1 int 5-L-glutamyl_amino_acid
1 int beta-D-oligosaccarides
1 int n_D-glucose
1 int L-Asparagine
1 int L-aspartate
1 int NH3
1 int ATP
1 int L-Asp
1 int NH4+
1 int AMP
1 int diphosphate
1 int L-Asn
20 metabolites, 22 is the summarized frequency
edges frequency of nodes
0 0
1 19
2 0
3 1
STOICHIOMETRIC MATRIX
matrix dimension r19 x c6
-1 0 0 0 0 0
-1 0 0 0 0 0
1 0 0 0 0 0
1 0 0 0 0 0
0 0 -1 0 0 0
0 0 -1 0 0 0
0 0 1 0 0 0
0 0 1 0 0 0
0 0 0 -1 0 0
0 0 0 1 0 0
0 0 0 0 -1 0
0 0 0 0 1 0
0 0 0 0 1 0
0 0 0 0 0 -1
0 0 0 0 0 -1
0 0 0 0 0 -1
0 0 0 0 0 1
0 0 0 0 0 1
0 0 0 0 0 1
The following line indicates reversible (0) and irreversible reactions (1)
0 1 1 1 1 1
rows and columns are sorted as declared in the inputfile
NOT BALANCED INTERNAL METABOLITES
5,10-Methylenetetrahydrofolate glycine tetrahydrofolate L-serine (5-L-Glutamyl)-peptide an_amino_acid peptide 5-L-glutamyl_amino_acid beta-D-oligosaccarides n_D-glucose L-Asparagine L-aspartate NH3 ATP L-Asp NH4+ AMP diphosphate L-Asn
KERNEL
matrix dimension r1 x c6
0 1 0 0 0 0
6 reactions (columns) are sorted in the same order as in the ENZREV ENZIRREV section.
enzymes
1: 2.1.2.1 irreversible
overall reaction
- not found -
The remaining overall reactions perform no net transformation of external metabolites.
SUBSETS OF REACTIONS
matrix dimension r1 x c6
0 1 0 0 0 0
6 reactions (columns) are sorted in the same order as in the ENZREV ENZIRREV section.
enzymes
1: 2.1.2.1 irreversible
overall reaction
- not found -
The remaining overall reactions perform no net transformation of external metabolites.
REDUCED SYSTEM with 19 branch point metabolites in 1 reactions (columns)
matrix dimension r0 x c1
The following line indicates reversible (0) and irreversible reactions (1)
1
-> Branch metabolites are :
met cons built reactions
-> No branch metabolites are :
met cons built reactions
5,10-Methylenetetrahydrofolate 1 0 1 r
glycine 1 0 1 r
tetrahydrofolate 0 1 1 r
L-serine 0 1 1 r
(5-L-Glutamyl)-peptide 1 0 1 i
an_amino_acid 1 0 1 i
peptide 0 1 1 i
5-L-glutamyl_amino_acid 0 1 1 i
beta-D-oligosaccarides 1 0 1 i
n_D-glucose 0 1 1 i
L-Asparagine 1 0 1 i
L-aspartate 0 1 1 i
NH3 0 1 1 i
ATP 1 0 1 i
L-Asp 1 0 1 i
NH4+ 1 0 1 i
AMP 0 1 1 i
diphosphate 0 1 1 i
L-Asn 0 1 1 i
CONVEX BASIS
matrix dimension r1 x c6
0 1 0 0 0 0
enzymes
1: 2.1.2.1 irreversible
overall reaction
- not found -
The remaining overall reactions perform no net transformation of external metabolites.
CONSERVATION RELATIONS
matrix dimension r14 x c19
1 -1 0 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 0 0 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 1 0 1 0 0 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 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 1 0 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 0 0 0 1 -1 0 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 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 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1
1 : 5,10-Methylenetetrahydrofolate + glycine = const
2 : 5,10-Methylenetetrahydrofolate + tetrahydrofolate = const
3 : 5,10-Methylenetetrahydrofolate + L-serine = const
4 : (5-L-Glutamyl)-peptide + an_amino_acid = const
5 : (5-L-Glutamyl)-peptide + peptide = const
6 : (5-L-Glutamyl)-peptide + 5-L-glutamyl_amino_acid = const
7 : beta-D-oligosaccarides + n_D-glucose = const
8 : L-Asparagine + L-aspartate = const
9 : L-Asparagine + NH3 = const
10 : ATP + L-Asp = const
11 : ATP + NH4+ = const
12 : ATP + AMP = const
13 : ATP + diphosphate = const
14 : ATP + L-Asn = const
ELEMENTARY MODES
matrix dimension r1 x c6
0 1 0 0 0 0
6 reactions (columns) are sorted in the same order as in the ENZREV ENZIRREV section.
enzymes
1: 2.1.2.1 irreversible
overall reaction
- not found -
The remaining overall reactions perform no net transformation of external metabolites.
The elementary modes ARE EQUAL to convex basis.

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METATOOL OUTPUT Version 3.5 (28.03.2001) C:\METATOOL\META35~1.EXE
INPUT FILE: EXAMPLE14.TXT
INTERNAL METABOLITES: 13
REACTIONS: 5
2 external H2O
1 int 5,6,7,8-Tetrahydrofolate
1 int NADP+
1 int 7,8-dihydrofolate
1 int NADPH
1 int An_orthophosphoric_monoester
1 int an_alcohol
1 int phosphate
1 int GTP
1 int formate
1 int 2-amino-4-hydroxy-6-(erythro-1,2,3-trihydroxypropyl)dihydropteridine_triphosphate
1 int 6-(L-erythro-1,2-Dihydroxypropyl_3-triphosphate)-7,8-dihydropterin
1 int 6-(1,2-dioxopropyl)-5,6,7,8-tetrahydropterin
1 int triphosphate
14 metabolites, 15 is the summarized frequency
edges frequency of nodes
0 0
1 13
2 1
STOICHIOMETRIC MATRIX
matrix dimension r13 x c5
-1 0 0 0 0
-1 0 0 0 0
1 0 0 0 0
1 0 0 0 0
0 0 -1 0 0
0 0 1 0 0
0 0 1 0 0
0 0 0 -1 0
0 0 0 1 0
0 0 0 1 0
0 0 0 0 -1
0 0 0 0 1
0 0 0 0 1
The following line indicates reversible (0) and irreversible reactions (1)
0 1 1 1 1
rows and columns are sorted as declared in the inputfile
NOT BALANCED INTERNAL METABOLITES
5,6,7,8-Tetrahydrofolate NADP+ 7,8-dihydrofolate NADPH An_orthophosphoric_monoester an_alcohol phosphate GTP formate 2-amino-4-hydroxy-6-(erythro-1,2,3-trihydroxypropyl)dihydropteridine_triphosphate 6-(L-erythro-1,2-Dihydroxypropyl_3-triphosphate)-7,8-dihydropterin 6-(1,2-dioxopropyl)-5,6,7,8-tetrahydropterin triphosphate
KERNEL
matrix dimension r1 x c5
0 1 0 0 0
5 reactions (columns) are sorted in the same order as in the ENZREV ENZIRREV section.
enzymes
1: 1.5.1.3 irreversible
overall reaction
- not found -
The remaining overall reactions perform no net transformation of external metabolites.
SUBSETS OF REACTIONS
matrix dimension r1 x c5
0 1 0 0 0
5 reactions (columns) are sorted in the same order as in the ENZREV ENZIRREV section.
enzymes
1: 1.5.1.3 irreversible
overall reaction
- not found -
The remaining overall reactions perform no net transformation of external metabolites.
REDUCED SYSTEM with 13 branch point metabolites in 1 reactions (columns)
matrix dimension r0 x c1
The following line indicates reversible (0) and irreversible reactions (1)
1
-> Branch metabolites are :
met cons built reactions
-> No branch metabolites are :
met cons built reactions
5,6,7,8-Tetrahydrofolate 1 0 1 r
NADP+ 1 0 1 r
7,8-dihydrofolate 0 1 1 r
NADPH 0 1 1 r
An_orthophosphoric_monoester 1 0 1 i
an_alcohol 0 1 1 i
phosphate 0 1 1 i
GTP 1 0 1 i
formate 0 1 1 i
2-amino-4-hydroxy-6-(erythro-1,2,3-trihydroxypropyl)dihydropteridine_triphosphate 0 1 1 i
6-(L-erythro-1,2-Dihydroxypropyl_3-triphosphate)-7,8-dihydropterin 1 0 1 i
6-(1,2-dioxopropyl)-5,6,7,8-tetrahydropterin 0 1 1 i
triphosphate 0 1 1 i
CONVEX BASIS
matrix dimension r1 x c5
0 1 0 0 0
enzymes
1: 1.5.1.3 irreversible
overall reaction
- not found -
The remaining overall reactions perform no net transformation of external metabolites.
CONSERVATION RELATIONS
matrix dimension r9 x c13
1 -1 0 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 1 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 1 0 1 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 1 0 1 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 1 0 1
1 : 5,6,7,8-Tetrahydrofolate + NADP+ = const
2 : 5,6,7,8-Tetrahydrofolate + 7,8-dihydrofolate = const
3 : 5,6,7,8-Tetrahydrofolate + NADPH = const
4 : An_orthophosphoric_monoester + an_alcohol = const
5 : An_orthophosphoric_monoester + phosphate = const
6 : GTP + formate = const
7 : GTP + 2-amino-4-hydroxy-6-(erythro-1,2,3-trihydroxypropyl)dihydropteridine_triphosphate = const
8 : 6-(L-erythro-1,2-Dihydroxypropyl_3-triphosphate)-7,8-dihydropterin + 6-(1,2-dioxopropyl)-5,6,7,8-tetrahydropterin = const
9 : 6-(L-erythro-1,2-Dihydroxypropyl_3-triphosphate)-7,8-dihydropterin + triphosphate = const
ELEMENTARY MODES
matrix dimension r1 x c5
0 1 0 0 0
5 reactions (columns) are sorted in the same order as in the ENZREV ENZIRREV section.
enzymes
1: 1.5.1.3 irreversible
overall reaction
- not found -
The remaining overall reactions perform no net transformation of external metabolites.
The elementary modes ARE EQUAL to convex basis.

227
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METATOOL OUTPUT Version 3.5 (28.03.2001) C:\METATOOL\META35~1.EXE
INPUT FILE: EXAMPLE15.TXT
INTERNAL METABOLITES: 26
REACTIONS: 11
4 external H2O
2 int NH3
2 int S-Adenosyl-L-methionine
2 int S-adenosyl-L-homocysteine
2 int N-formimino-L-glutamate
1 int RCH2NH2
1 int O2
1 int RCHO
1 int H2O2
1 int carnosine
1 int anserine
1 int histamine
1 int Ntau-methylhistamine
1 int 5-Formiminotetrahydrofolate
1 int L-glutamate
1 int tetrahydrofolate
1 int N-Acetyl-L-aspartate
1 int a_fatty_acid_anion
1 int L-aspartate
1 int 4-Imidazolone-5-propanoate
1 int L-Tryptophan
1 int tryptamine
1 int CO2
1 int Urocanate
1 int 4,5-dihydro-4-oxo-5-imidazolepropanoate
1 int L-Histidine
1 int urocanate
27 metabolites, 34 is the summarized frequency
edges frequency of nodes
0 0
1 22
2 4
3 0
4 1
STOICHIOMETRIC MATRIX
matrix dimension r26 x c11
0 0 -1 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 1 0 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 -1 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 0 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
-1 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 1 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 1 0 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 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 -1 0 0 0 0 0 0 0 0 0
0 1 0 0 0 0 0 0 0 0 0
The following line indicates reversible (0) and irreversible reactions (1)
0 0 1 1 1 1 1 1 1 1 1
rows and columns are sorted as declared in the inputfile
NOT BALANCED INTERNAL METABOLITES
RCH2NH2 O2 RCHO H2O2 carnosine anserine histamine Ntau-methylhistamine 5-Formiminotetrahydrofolate L-glutamate tetrahydrofolate N-Acetyl-L-aspartate a_fatty_acid_anion L-aspartate 4-Imidazolone-5-propanoate L-Tryptophan tryptamine CO2 Urocanate 4,5-dihydro-4-oxo-5-imidazolepropanoate L-Histidine urocanate
KERNEL
matrix dimension r2 x c11
0 0 0 0 0 1 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 1
11 reactions (columns) are sorted in the same order as in the ENZREV ENZIRREV section.
enzymes
1: 2.1.2.5 irreversible
2: 4.3.1.3 irreversible
overall reaction
- not found -
The remaining overall reactions perform no net transformation of external metabolites.
SUBSETS OF REACTIONS
matrix dimension r2 x c11
0 0 0 0 0 1 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 1
11 reactions (columns) are sorted in the same order as in the ENZREV ENZIRREV section.
enzymes
1: 2.1.2.5 irreversible
2: 4.3.1.3 irreversible
overall reaction
- not found -
The remaining overall reactions perform no net transformation of external metabolites.
REDUCED SYSTEM with 26 branch point metabolites in 2 reactions (columns)
matrix dimension r0 x c2
The following line indicates reversible (0) and irreversible reactions (1)
1 1
-> Branch metabolites are :
met cons built reactions
-> No branch metabolites are :
met cons built reactions
RCH2NH2 1 0 1 i
O2 1 0 1 i
RCHO 0 1 1 i
NH3 0 2 2 ir
H2O2 0 1 1 i
S-Adenosyl-L-methionine 2 0 2 ii
carnosine 1 0 1 i
S-adenosyl-L-homocysteine 0 2 2 ii
anserine 0 1 1 i
histamine 1 0 1 i
Ntau-methylhistamine 0 1 1 i
5-Formiminotetrahydrofolate 1 0 1 r
L-glutamate 1 0 1 r
tetrahydrofolate 0 1 1 r
N-formimino-L-glutamate 0 2 2 ri
N-Acetyl-L-aspartate 1 0 1 i
a_fatty_acid_anion 0 1 1 i
L-aspartate 0 1 1 i
4-Imidazolone-5-propanoate 1 0 1 i
L-Tryptophan 1 0 1 i
tryptamine 0 1 1 i
CO2 0 1 1 i
Urocanate 1 0 1 i
4,5-dihydro-4-oxo-5-imidazolepropanoate 0 1 1 i
L-Histidine 1 0 1 r
urocanate 0 1 1 r
CONVEX BASIS
matrix dimension r2 x c11
0 0 0 0 0 1 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 1
enzymes
1: 2.1.2.5 irreversible
2: 4.3.1.3 irreversible
overall reaction
- not found -
The remaining overall reactions perform no net transformation of external metabolites.
CONSERVATION RELATIONS
matrix dimension r17 x c26
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 1 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 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 0 1 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 1 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 -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 -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 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 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 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 1 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 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 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 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 0 1 1 0 0
1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
1 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 : RCH2NH2 + O2 = const
2 : RCH2NH2 + RCHO = const
3 : RCH2NH2 + H2O2 = const
4 : S-Adenosyl-L-methionine + S-adenosyl-L-homocysteine = const
5 : carnosine + anserine = const
6 : S-Adenosyl-L-methionine + carnosine + histamine = const
7 : S-Adenosyl-L-methionine + carnosine + Ntau-methylhistamine = const
8 : 5-Formiminotetrahydrofolate + L-glutamate = const
9 : 5-Formiminotetrahydrofolate + tetrahydrofolate = const
10 : N-Acetyl-L-aspartate + a_fatty_acid_anion = const
11 : N-Acetyl-L-aspartate + L-aspartate = const
12 : 5-Formiminotetrahydrofolate + N-formimino-L-glutamate + 4-Imidazolone-5-propanoate = const
13 : L-Tryptophan + tryptamine = const
14 : L-Tryptophan + CO2 = const
15 : Urocanate + 4,5-dihydro-4-oxo-5-imidazolepropanoate = const
16 : RCH2NH2 + NH3 + L-Histidine = const
17 : RCH2NH2 + NH3 + urocanate = const
ELEMENTARY MODES
matrix dimension r2 x c11
0 0 0 0 0 1 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 1
11 reactions (columns) are sorted in the same order as in the ENZREV ENZIRREV section.
enzymes
1: 2.1.2.5 irreversible
2: 4.3.1.3 irreversible
overall reaction
- not found -
The remaining overall reactions perform no net transformation of external metabolites.
The elementary modes ARE EQUAL to convex basis.

29
Tests/MetaTool/example11.txt
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-ENZREV
2.6.1.1
-ENZIRREV
1.14.18.1
2.6.1.1
-METINT
o-Diphenol
o-quinone
L-Tyrosine
dopaquinone
Monophenol
o-diphenol
L-Aspartate
2-oxoglutarate
oxaloacetate
L-glutamate
-METEXT
O2
H2O
L-dopa
-CAT
1.14.18.1 : 2 o-Diphenol + O2 = 2 o-quinone + 2 H2O .
1.14.18.1 : L-Tyrosine + L-dopa + O2 = L-dopa + dopaquinone + H2O .
1.14.18.1 : Monophenol + O2 = o-diphenol + H2O .
2.6.1.1 : L-Aspartate + 2-oxoglutarate = oxaloacetate + L-glutamate

21
Tests/MetaTool/example12.txt
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-ENZREV
1.8.5.1
-ENZIRREV
1.11.1.11
1.8.5.1
-METINT
L-Ascorbate
H2O2
H2O
Glutathione
oxidized_glutathione
ascorbate
-METEXT
dehydroascorbate
-CAT
1.11.1.11 : L-Ascorbate + H2O2 = dehydroascorbate + 2 H2O .
1.8.5.1 : 2 Glutathione + dehydroascorbate = oxidized_glutathione + ascorbate .

40
Tests/MetaTool/example13.txt
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-ENZREV
2.1.2.1
-ENZIRREV
2.1.2.1
2.3.2.2
3.2.1.21
3.5.1.1
6.3.1.1
-METINT
5,10-Methylenetetrahydrofolate
glycine
tetrahydrofolate
L-serine
(5-L-Glutamyl)-peptide
an_amino_acid
peptide
5-L-glutamyl_amino_acid
beta-D-oligosaccarides
n_D-glucose
L-Asparagine
L-aspartate
NH3
ATP
L-Asp
NH4+
AMP
diphosphate
L-Asn
-METEXT
H2O
-CAT
2.1.2.1 : 5,10-Methylenetetrahydrofolate + glycine + H2O = tetrahydrofolate + L-serine .
2.3.2.2 : (5-L-Glutamyl)-peptide + an_amino_acid = peptide + 5-L-glutamyl_amino_acid .
3.2.1.21 : beta-D-oligosaccarides + H2O = n_D-glucose .
3.5.1.1 : L-Asparagine + H2O = L-aspartate + NH3 .
6.3.1.1 : ATP + L-Asp + NH4+ = AMP + diphosphate + L-Asn .

32
Tests/MetaTool/example14.txt
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-ENZREV
1.5.1.3
-ENZIRREV
1.5.1.3
3.1.3.1
3.5.4.16
4.6.1.10
-METINT
5,6,7,8-Tetrahydrofolate
NADP+
7,8-dihydrofolate
NADPH
An_orthophosphoric_monoester
an_alcohol
phosphate
GTP
formate
2-amino-4-hydroxy-6-(erythro-1,2,3-trihydroxypropyl)dihydropteridine_triphosphate
6-(L-erythro-1,2-Dihydroxypropyl_3-triphosphate)-7,8-dihydropterin
6-(1,2-dioxopropyl)-5,6,7,8-tetrahydropterin
triphosphate
-METEXT
H2O
-CAT
1.5.1.3 : 5,6,7,8-Tetrahydrofolate + NADP+ = 7,8-dihydrofolate + NADPH .
3.1.3.1 : An_orthophosphoric_monoester + H2O = an_alcohol + phosphate .
3.5.4.16 : GTP + 2 H2O = formate + 2-amino-4-hydroxy-6-(erythro-1,2,3-trihydroxypropyl)dihydropteridine_triphosphate .
4.6.1.10 : 6-(L-erythro-1,2-Dihydroxypropyl_3-triphosphate)-7,8-dihydropterin = 6-(1,2-dioxopropyl)-5,6,7,8-tetrahydropterin + triphosphate .

56
Tests/MetaTool/example15.txt
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-ENZREV
2.1.2.5
4.3.1.3
-ENZIRREV
1.4.3.6
2.1.1.22
2.1.1.8
2.1.2.5
3.5.1.15
3.5.2.7
4.1.1.28
4.2.1.49
4.3.1.3
-METINT
RCH2NH2
O2
RCHO
NH3
H2O2
S-Adenosyl-L-methionine
carnosine
S-adenosyl-L-homocysteine
anserine
histamine
Ntau-methylhistamine
5-Formiminotetrahydrofolate
L-glutamate
tetrahydrofolate
N-formimino-L-glutamate
N-Acetyl-L-aspartate
a_fatty_acid_anion
L-aspartate
4-Imidazolone-5-propanoate
L-Tryptophan
tryptamine
CO2
Urocanate
4,5-dihydro-4-oxo-5-imidazolepropanoate
L-Histidine
urocanate
-METEXT
H2O
-CAT
1.4.3.6 : RCH2NH2 + H2O + O2 = RCHO + NH3 + H2O2 .
2.1.1.22 : S-Adenosyl-L-methionine + carnosine = S-adenosyl-L-homocysteine + anserine .
2.1.1.8 : S-Adenosyl-L-methionine + histamine = S-adenosyl-L-homocysteine + Ntau-methylhistamine .
2.1.2.5 : 5-Formiminotetrahydrofolate + L-glutamate = tetrahydrofolate + N-formimino-L-glutamate .
3.5.1.15 : N-Acetyl-L-aspartate + H2O = a_fatty_acid_anion + L-aspartate .
3.5.2.7 : 4-Imidazolone-5-propanoate + H2O = N-formimino-L-glutamate .
4.1.1.28 : L-Tryptophan = tryptamine + CO2 .
4.2.1.49 : Urocanate + H2O = 4,5-dihydro-4-oxo-5-imidazolepropanoate .
4.3.1.3 : L-Histidine = urocanate + NH3 .

30
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-ENZREV
Pgi Ald Tpi Rpi Rpe TktI TktII Tal Gpm Eno Pgl
-ENZIRREV
Pfk Fbp Zwf Gnd Pgk Pyk Gap Prs_DeoB
-METINT
E4P S7P X5P Ru5P GO6P GL6P
DHAP FDP F6P GAP D13PG P3G P2G PEP R5P
-METEXT
CO2 ATP ADP NAD NADH NADP NADPH
G6P PYR R5Pex Pi
-CAT
Pgi : G6P = F6P .
Pfk : F6P + ATP = FDP + ADP .
Fbp : FDP = F6P + Pi .
Ald : FDP = DHAP + GAP .
Tpi : DHAP = GAP .
Gap : GAP + NAD + Pi = D13PG + NADH .
Zwf : G6P + NADP = GO6P + NADPH .
Pgl : GO6P = GL6P .
Gnd : GL6P + NADP = Ru5P + NADPH + CO2 .
Rpi : Ru5P = R5P .
Rpe : Ru5P = X5P .
TktI : X5P + R5P = GAP + S7P .
TktII : E4P + X5P = F6P + GAP .
Tal : S7P + GAP = E4P + F6P .
Pgk : D13PG + ADP = P3G + ATP .
Gpm : P3G = P2G .
Eno : P2G = PEP .
Pyk : PEP + ADP = PYR + ATP .
Prs_DeoB : R5P = R5Pex .