diff --git a/ComplementaryData/modelCuration/Biolog_Substrate.tsv b/ComplementaryData/modelCuration/Biolog_Substrate.tsv
new file mode 100644
index 00000000..df385562
--- /dev/null
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+Substrate Name_in_Model Substrate_type Growth_Biolog Growth_Model
+L-Malic Acid (S)-malate C NG G
+L-Glutamic Acid L-glutamate C NG G
+Thymidine thymidine C NG NG
+D-Malic Acid C NG NG
+L-Alanine L-alanine C NG G
+Fumaric Acid fumarate C NG G
+L-Lactic Acid (S)-lactate C G G
+Butyric Acid butyrate C NG NG
+Methyl Pyruvate C NG NG
+α-Keto-Glutaric Acid 2-oxoglutarate C NG G
+D,L-Malic Acid C NG NG
+L-Alanyl-Glycine Ala-Gly C NG G
+Acetic Acid acetate C NG G
+Succinic Acid succinate C NG G
+L-Tartaric Acid C NG NG
+Propionic Acid C NG NG
+Pyruvic Acid pyruvate C G G
+Mono Methyl Succinate C NG NG
+L-Alaninamide C NG NG
+L-Serine L-serine C NG G
+Formic Acid formate C NG G
+γ-Amino Butyric Acid gamma-aminobutyrate C NG G
+Oxalo malicAcid 3-oxalomalate(3-) C G G
+Glycyl-L-Glutamic Acid C NG NG
+β-Hydroxy Butyric Acid C NG NG
+D-Mannitol Mannitol C NG NG
+D-Lactic Acid Methyl Ester C NG NG
+Adonitol (Ribitol) C NG NG
+D-Arabitol C NG NG
+L-Glutamine L-glutamine C NG G
+Succinamic Acid C NG NG
+Bromo Succinic Acid C NG NG
+L-L eucine L-leucine C NG NG
+D-Xylose D-xylose C G G
+L-Valine L-valine C NG NG
+D-Sorbitol D-glucitol C NG G
+L-Asparagine L-asparagine C NG G
+Glycyl-L-Proline C NG NG
+2-Aminoethanol (Ethanol amine) ethanolamine C NG NG
+D-Ribose D-ribose C G G
+Glycyl-L-Aspartic Acid C NG NG
+D-Galacturonic Acid D-galacturonate C NG NG
+Uridine uridine C NG NG
+L-Proline L-proline C NG G
+L-Galactonic Acid-γ-Lactone C NG NG
+D-Mannose D-mannose C G G
+δ-Amino Valeric Acid C NG NG
+α-Hydroxy GlutaricAcid-γ-Lactone C NG NG
+α-D-Glucose D-glucose C G G
+D-Psicose C NG NG
+D-Fructose D-fructose C G G
+L-Lyxose C G NG
+L-Lysine L-lysine C NG NG
+L-Isoleucine L-isoleucine C NG NG
+α-Keto-Butyric Acid 2-oxobutanoate C NG NG
+α-Hydroxy Butyric Acid C NG NG
+α-Keto Valeric Acid C NG NG
+3-0-β-D Galacto-pyranosyl-D-Arabinose C NG NG
+Acetoacetic Acid acetoacetate C G G
+Glyoxylic Acid glyoxylate C NG G
+Tween 20 C NG NG
+Palatinose 6-O-alpha-D-glucopyranosyl-D-fructofuranose C G G
+Dextrin Dextrin C NG NG
+3-Hydroxy 2-Butanone C NG NG
+5-Keto-D-Gluconic Acid 5-dehydro-D-gluconate C G G
+Tyramine C NG NG
+p-Hydroxy Phenyl Acetic Acid (4-Hydroxyphenylacetate) C NG NG
+Glucuronamide C G NG
+M-Tartaric Acid C NG NG
+Inosine inosine C NG G
+Citramalic Acid C NG NG
+Glycolic Acid glycolate C NG NG
+Melibionic Acid C NG NG
+D-Tartaric Acid C NG NG
+Glycerol glycerol C NG G
+Mucic Acid C NG NG
+3-Methyl Glucose C NG NG
+D-Fructose-6-Phosphate D-fructose 6-phosphate C NG NG
+D-Tagatose D-tagatose C G G
+N-Acetyl-L-Glutamic Acid N-acetyl-L-glutamate C NG G
+Turanose turanose C G G
+D-Glucose-6-Phosphate D-glucose 6-phosphate C NG G
+L-Sorbose L-sorbose C NG NG
+γ-Hydroxy Butyric Acid C NG NG
+N-Acetyl-D-Glucosamine N-Acetyl-D-glucosamine C NG NG
+β-Methyl-D-Glucuronic Acid C NG NG
+Dulcitol (Galactitol) C NG NG
+D-Arabinose D-arabinose C G G
+N-Acetyl-β-D-Mannosamine C NG NG
+D-Glucosaminic Acid C NG NG
+D-Melezitose C NG NG
+D-Cellobiose C NG NG
+Putrescine putrescine C NG NG
+Tween 80 C NG NG
+Quinic Acid C NG NG
+Tricarballylic Acid C NG NG
+β-D-Allose C NG NG
+Chondroitin Sulfate C C NG NG
+α-Methyl-D Galactoside C NG NG
+Maltotriose alpha-maltotriose C G G
+β-Methyl-D-Glucoside C NG NG
+Tween 40 C NG NG
+Glycogen glycogen C NG NG
+M-Inositol myo-inositol C NG NG
+Sucrose sucrose C G G
+D-Saccharic Acid D-Glucarate C NG NG
+Pectin pectin C NG NG
+D-Glucose-1-Phosphate D-glucose 1-phosphate C NG G
+Hydroxy-L Proline C NG NG
+D-Ribono-1,4-Lactone C NG NG
+L-Pyroglutamic Acid 5-oxo-L-proline C NG NG
+Lactulose C NG NG
+D-Raffinose raffinose C NG G
+Maltose maltose C G G
+L-Rhamnose C NG NG
+D-Galactose D-galactose C G G
+α-D-Lactose C NG NG
+N-Acetyl-D-Galactosamine C NG NG
+2,3-Butanediol C NG NG
+1,2-Propanediol C NG NG
+Amygdalin C NG NG
+Malonic Acid C NG NG
+D-Melibiose melibiose C NG NG
+D-Gluconic Acid D-gluconate C NG NG
+D.L-Octopamine C NG NG
+D-Aspartate C NG NG
+Gelatin C NG NG
+L-Aspartic Acid L-aspartate C NG G
+L-Ornithine C NG NG
+Salicin C NG NG
+L-Arabinose L-arabinose C G G
+L-Histidine L-histidine C NG NG
+D-Glucuronic Acid C NG NG
+L-Glucose C NG NG
+N-AcetylNeuraminic Acid C NG NG
+β-Methyl-D-Galactoside C NG NG
+Stachyose C NG NG
+Maltitol C NG NG
+Acetamide C NG NG
+I-Erythritol C NG NG
+Lactitol C NG NG
+N-Acetyl-D-Glucosaminitol C NG NG
+α-Methyl-D-Glucoside methyl alpha-D-glucopyranoside C G G
+D,L-Carnitine C NG NG
+D,L-α-Glycerol-Phosphate glycerol 3-phosphate C NG NG
+Sedoheptulosan C NG NG
+β-Methyl-D-Xyloside C NG NG
+β-Cyclodextrin C NG NG
+L-Arginine L-arginine C NG G
+α-Methyl-D-Mannoside C NG NG
+Gentiobiose C NG NG
+L-Fucose C NG NG
+L-T hreonine L-threonine C NG G
+L-Phenylalanine L-phenylalanine C NG NG
+Citric Acid citrate C NG G
+α-Cyclodextrin C NG NG
+Citraconic Acid C NG NG
+L-Arabitol L-arabinitol C NG G
+D-Trehalose trehalose C NG G
+γ-Cyclodextrin C NG NG
+L-Methionine L-methionine C NG NG
+Inulin C G NG
+D-Fucose C NG NG
+D-Galactonic Acid-γ-Lactone C NG NG
+L-Homoserine L-homoserine C NG G
+Oxalic Acid Oxalate C NG NG
+Arbutin C NG NG
+Laminarin C G NG
+Caproic Acid hexanoate C NG NG
+Phenylethyl-amine C NG NG
+Xylitol xylitol C NG G
+m-Hydroxy Phenyl Acetic Acid C NG NG
+Sec-Butylamine C NG NG
+D-Glucosamine D-Glucosamine C G G
+Sebacic Acid C NG NG
+Mannan mannan C NG NG
+Dihydroxy Acetone glycerone C G G
+2-Deoxy Adenosine 2'-deoxyadenosine C NG NG
+Adenosine adenosine C NG G
+D-Alanine C NG NG
+D-Serine D-Serine C NG NG
+2,3-Butanone H12 diacetyl C NG NG
+D-Threonine C NG NG
+Itaconic Acid itaconate C NG NG
+2-Deoxy-D-Ribose 2-deoxy-D-ribose C G NG
+4-Hydroxy Benzoic Acid 4-hydroxybenzoate C NG NG
+Capric Acid decanoate C NG G
+Sorbic Acid C G NG
+2-Hydroxy Benzoic Acid C NG NG
+Glycine L-glycine C NG G
+Uric Acid N NG NG
+Ala-Gln Ala-Gln N G G
+Ala-Leu Ala-Leu N G G
+Ala-Gly Ala-Gly N G G
+Xanthine 9H-xanthine N NG NG
+D,L-Lactamide N NG NG
+Cytosine cytosine N G G
+Gly-Gln Gly-Gln N G G
+Guanine guanine N NG G
+Ethylenediamine N NG NG
+Ala-His Ala-His N G G
+Allantoin allantoin N G G
+Parabanic Acid N G NG
+L-Alanine L-alanine N G G
+Guanosine guanosine N NG G
+L-Glutamine L-glutamine N G G
+L-Leucine L-leucine N G G
+Thymidine thymidine N NG NG
+Gly-Asn Gly-Asn N G G
+Ala-Glu Ala-Glu N G G
+Thymine N NG NG
+Cytidine cytidine N NG G
+Uracil uracil N NG NG
+L-Asparagine L-asparagine N G G
+Gly-Met Gly-Met N G G
+Ala-Asp Ala-Asp N G G
+γ-Amino-N-Butyric Acid gamma-aminobutyrate N G G
+D-Alanine N NG NG
+L-Serine L-serine N G G
+Urea urea N G G
+Gly-Glu Gly-Glu N G G
+Ala-Thr Ala-Thr N G G
+δ-Amino-N-Valeric Acid 5-Aminopentanoate N G NG
+Putrescine putrescine N NG NG
+Uridine uridine N NG NG
+Met-Ala Met-Ala N G G
+Glucuronamide N NG NG
+D-Serine D-Serine N NG NG
+L-Lysine L-lysine N NG NG
+L-Histidine L-histidine N G NG
+D-Glutamic Acid N NG NG
+Agmatine N NG NG
+Ammonia ammonium N G G
+Xanthosine xanthosine N NG NG
+Glycine L-glycine N G G
+L-Glutamic Acid L-glutamate N G G
+Ethanolamine ethanolamine N NG NG
+D-Lysine N NG NG
+L-Aspartic Acid L-aspartate N G G
+Alloxan N NG NG
+N-Acetyl-D-Glucosamine N-Acetyl-D-glucosamine N NG NG
+D-Aspartate N G NG
+L-Cysteine L-cysteine N G G
+L-Proline L-proline N G G
+L-Isoleucine L-isoleucine N G G
+ε-Amino-N-Caproic Acid N NG NG
+L-Tryptophan L-tryptophan N G G
+α-Amino-NValeric Acid N G NG
+D-Asparagine N NG NG
+L-Tyrosine L-tyrosine N G G
+Histamine N NG NG
+D-Mannosamine N NG NG
+D-Galactosamine N NG NG
+L-Arginine L-arginine N G G
+L-Pyroglutamic Acid 5-oxo-L-proline N NG NG
+L-Citrulline L-citrulline N G G
+Inosine inosine N NG NG
+Formamide N NG NG
+Ethylamine N NG NG
+Acetamide N NG NG
+L-Phenylalanine L-phenylalanine N G G
+Biuret N NG NG
+N-Butylamine N NG NG
+N-Acetyl-D-Galactosamine N NG NG
+N-Acetyl-D ,L-Glutamic Acid N-acetyl-L-glutamate N G G
+N-Acetyl-D-Mannosamine N NG NG
+L-Homoserine L-homoserine N G G
+Adenine adenine N NG G
+N-Amylamine N NG NG
+Tyramine N NG NG
+N-Phthaloyl-L-Glutamic Acid N NG NG
+Methylamine N NG NG
+L-Valine L-valine N G G
+Nitrate nitrate N NG NG
+L-Ornithine ornithine N G G
+L-Threonine L-threonine N G G
+β-Phenylethyl-amine N NG NG
+Nitrite Nitrite N NG NG
+L-Methionine L-methionine N G G
+D,L-α-Amino-Caprylic Acid N G NG
+D-Valine N NG NG
+D-Glucosamine D-Glucosamine N NG G
+D,L-α-Amino-N-Butyric Acid 2-aminobutanoate N G G
+Adenosine adenosine N NG G
+Hydroxylamine N NG NG
+Phosphoryl Choline choline phosphate P G G
+D,L-α-Glycerol Phosphate glycerol 1-phosphate P G G
+O-Phospho-D-Tyrosine P G NG
+D-2-Phospho-Glyceric Acid 2-phospho-D-glyceric acid P G G
+Guanosine-5’-monophosphate GMP P G G
+O-Phospho-L-Serine 3-phospho-serine P G G
+O-Phospho-D-Serine O-phosphonatooxy-D-serine(2-) P G G
+Phosphate phosphate P G G
+Pyrophosphate diphosphate P G G
+Thiophosphate P G NG
+Tripolyphosphate triphosphate P G G
+Uridine-5’-monophosphate UMP P G G
+Cytidine-5’-monophosphate CMP P G G
+Phosphoenol Pyruvate phosphoenolpyruvate P G G
+Trimetaphosphate P G NG
+Phospho-L-Arginine N(omega)-phospho-L-arginine P G G
+Carbamyl Phosphate carbamoyl phosphate P G G
+O-Phosphoryl-Ethanolamine O-phosphoethanolamine P G G
+D-Glucosamine-6-Phosphate alpha-D-glucosamine 6-phosphate P G G
+Phosphocreatine N-phosphocreatine P G NG
+Dithiophosphate P G NG
+Thymidine-5’-monophosphate thymidine 5'-monophosphate P G G
+Thymidine-3 ’-monophosphate thymidine 3'-monophosphate P G G
+Cysteamine-S-Phosphate cysteamine S-phosphate P G G
+2-Deoxy-D-Glucose 6-Phosphate 2-deoxy-D-glucose 6-phosphate P NG NG
+Guanosine-2’-monophosphate guanosine 2'-monophosphate P G G
+D-Glucose-6-Phosphate D-glucose 6-phosphate P G G
+β-Glycerol Phosphate glycerol 2-phosphate(2-) P G G
+Guanosine-3’-monophosphate 3'-GMP P G G
+Phospho-Glycolic Acid 2-phosphoglycolate P G G
+6-Phospho-Gluconic Acid 6-phospho-D-gluconate P G G
+D-Mannose-6-Phosphate D-mannose 6-phosphate P G G
+Cytidine-3’,5’-cyclic monophosphate 3',5'-cyclic CMP P NG NG
+Cytidine-2’-monophosphate cytidine 2'-phosphate P G G
+Inositol Hexaphosphate myo-inositol hexakisphosphate P G NG
+Guanosine-2’,3’-cyclic monophosphate 2',3'-cyclic GMP P G G
+O-Phospho-L-Tyrosine O(4)-phospho-L-tyrosine P G G
+O-Phospho-L-Threonine O-phospho-L-threonine P G G
+Cytidine-3’-monophosphate P NG NG
+D-3-Phospho-Glyceric Acid 3-phosphonato-D-glycerate(3-) P G G
+Triethyl Phosphate P NG NG
+Phosphono Acetic Acid P NG NG
+Uridine-2’-monophosphate uridine 2'-phosphate P G G
+D-Glucose-1-Phosphate D-glucose 1-phosphate P G G
+Uridine-3’-monophosphate 3'-UMP P G G
+Cytidine-2’ ,3’-cyclic monophosphate 2',3'-cyclic CMP P G G
+2-Aminoethyl Phosphonic Acid P NG NG
+Uridine-2’,3’-cyclic monophosphate 2',3'-cyclic UMP P G G
+Adenosine-2’-monophosphate adenosine 2'-phosphate P G G
+Adenosine-3’-monophosphate 3'-AMP P G G
+Adenosine-2’,3’-cyclic monophosphate 2',3'-cyclic AMP P G G
+Hypophosphite P NG NG
+Guanosine-3’,5’-cyclic monophosphate 3',5'-cyclic GMP P NG NG
+Thymidine 3’,5’-cyclic monophosphate P NG NG
+D-Mannose-1-Phosphate D-mannose 1-phosphate P G G
+Urid ine-3’,5’-cyclic monophosphate P NG NG
+Methylene Diphosphonic Acid P G NG
+Adenosine-3’,5’-cyclic monophosphate 3',5'-cyclic AMP P NG NG
+Adenosine-5’-monophosphate AMP P G G
+Sulfate sulphate S G G
+L-Cysteine L-cysteine S NG G
+Tetrathionate S NG NG
+Thiosulfate thiosulfate S G NG
+S-Methyl-L-Cysteine S G NG
+Hypotaurine S NG NG
+D-Methionine S NG NG
+L-Cysteinyl-Glycine L-cysteinylglycine S NG NG
+L-Methionine L-methionine S G G
+Glutathione glutathione S G G
+N-Acetyl-D,L-Methionine N(alpha)-acetyl-L-methionine S G G
+L-Methionine Sulfoxide L-Methionine S-oxide S NG G
+Glycyl-L-Methionine Gly-Met S G G
+Taurine tetrathionate S G NG
+D-Cysteine S NG NG
+Dithiophosphate S G NG
+Cystathionine S NG NG
+Cysteamine S NG NG
+L-Cysteine Sulfinic Acid 3-sulfino-L-alanine S G G
+Thiophosphate S G NG
+Lanthionine S NG NG
+N-Acetyl-L-Cysteine N-acetyl-L-cysteine S G G
+Thiourea S G NG
+1-Thio-β-D-Glucose S G NG
+Taurocholic Acid taurocholic acid S NG NG
+Butane Sulfonic Acid S G NG
+D,L-Lipoamide lipoamide S G NG
+L-Djenkolic Acid S NG NG
+Methane Sulfonic Acid S NG NG
+L-Cysteic Acid L-cysteate S G G
+p-Amino Benzene Sulfonic Acid S NG NG
+D,L-Ethionine S NG NG
+2-Hydroxyethane Sulfonic Acid 2-hydroxyethane-1-sulfonate S G G
+Tetramethylene Sulfone S NG NG
+L-Methionine Sulfone L-Methionine S-oxide S G G
+Ethanol ethanol C G G
+D-Raffinose raffinose C G G
+D-Cellobise C G NG
+sodium acetate acetate C G G
diff --git a/ComplementaryData/modelCuration/Biolog_newRxnMatrix.tsv b/ComplementaryData/modelCuration/Biolog_newRxnMatrix.tsv
new file mode 100644
index 00000000..f70f9f09
--- /dev/null
+++ b/ComplementaryData/modelCuration/Biolog_newRxnMatrix.tsv
@@ -0,0 +1,571 @@
+rxnID coefficient Metabolite standard name Metabolite_type compartment
+MNXR137087 1 Ala-Gln reactant extracellular
+MNXR137087 1 H+ reactant extracellular
+MNXR137087 1 H+ product cytoplasm
+MNXR137087 1 Ala-Gln product cytoplasm
+MNXR137087_cv 1 H+ reactant cytoplasm
+MNXR137087_cv 1 Ala-Gln reactant cytoplasm
+MNXR137087_cv 1 H+ product vacuole
+MNXR137087_cv 1 Ala-Gln product vacuole
+MNXR123345 1 Ala-Gln reactant vacuole
+MNXR123345 1 H2O reactant vacuole
+MNXR123345 1 L-glutamine product vacuole
+MNXR123345 1 L-alanine product vacuole
+MNXR101006 1 Ala-Glu reactant extracellular
+MNXR101006 1 H+ reactant extracellular
+MNXR101006 1 H+ product cytoplasm
+MNXR101006 1 Ala-Glu product cytoplasm
+MNXR101006_cv 1 H+ reactant cytoplasm
+MNXR101006_cv 1 Ala-Glu reactant cytoplasm
+MNXR101006_cv 1 H+ product vacuole
+MNXR101006_cv 1 Ala-Glu product vacuole
+MNXR101011 1 Ala-Glu reactant vacuole
+MNXR101011 1 H2O reactant vacuole
+MNXR101011 1 L-glutamate product vacuole
+MNXR101011 1 L-alanine product vacuole
+Ala-Thr transport via proton symport (extracellular to cytosol) 1 Ala-Thr reactant extracellular
+Ala-Thr transport via proton symport (extracellular to cytosol) 1 H+ reactant extracellular
+Ala-Thr transport via proton symport (extracellular to cytosol) 1 H+ product cytoplasm
+Ala-Thr transport via proton symport (extracellular to cytosol) 1 Ala-Thr product cytoplasm
+Ala-Thr transport via proton symport (cytosol to vacuole) 1 H+ reactant cytoplasm
+Ala-Thr transport via proton symport (cytosol to vacuole) 1 Ala-Thr reactant cytoplasm
+Ala-Thr transport via proton symport (cytosol to vacuole) 1 H+ product vacuole
+Ala-Thr transport via proton symport (cytosol to vacuole) 1 Ala-Thr product vacuole
+MNXR123349 1 Ala-Thr reactant vacuole
+MNXR123349 1 H2O reactant vacuole
+MNXR123349 1 L-threonine product vacuole
+L-threonine transport, vacuoluar 1 L-threonine reactant cytoplasm
+L-threonine transport, vacuoluar 1 L-threonine product vacuole
+MNXR123349 1 L-alanine product vacuole
+MNXR118741 1 thymidine 3'-monophosphate reactant cytoplasm
+MNXR118741 1 H2O reactant cytoplasm
+MNXR118741 1 thymidine product cytoplasm
+MNXR118741 1 phosphate product cytoplasm
+thymidine 3'-monophosphate transport 1 thymidine 3'-monophosphate reactant extracellular
+thymidine 3'-monophosphate transport 1 thymidine 3'-monophosphate product cytoplasm
+nucleotide-specific phosphatase (thymidine 5'-monophosphate) 1 thymidine 5'-monophosphate reactant cytoplasm
+nucleotide-specific phosphatase (thymidine 5'-monophosphate) 1 H2O reactant cytoplasm
+nucleotide-specific phosphatase (thymidine 5'-monophosphate) 1 thymidine product cytoplasm
+nucleotide-specific phosphatase (thymidine 5'-monophosphate) 1 phosphate product cytoplasm
+thymidine 5'-monophosphate transport 1 thymidine 5'-monophosphate reactant extracellular
+thymidine 5'-monophosphate transport 1 thymidine 5'-monophosphate product cytoplasm
+RHEA:11477 1 glycerol 1-phosphate reactant cytoplasm
+RHEA:11477 1 H2O reactant cytoplasm
+RHEA:11477 1 glycerol product cytoplasm
+RHEA:11477 1 phosphate product cytoplasm
+glycerol 1-phosphate transport 1 glycerol 1-phosphate reactant extracellular
+glycerol 1-phosphate transport 1 glycerol 1-phosphate product cytoplasm
+MNXR137107 1 Ala-His reactant extracellular
+MNXR137107 1 H+ reactant extracellular
+MNXR137107 1 H+ product cytoplasm
+MNXR137107 1 Ala-His product cytoplasm
+MNXR137107_cv 1 H+ reactant cytoplasm
+MNXR137107_cv 1 Ala-His reactant cytoplasm
+MNXR137107_cv 1 H+ product vacuole
+MNXR137107_cv 1 Ala-His product vacuole
+MNXR123347 1 Ala-His reactant vacuole
+MNXR123347 1 H2O reactant vacuole
+MNXR123347 1 L-histidine product vacuole
+MNXR123347 1 L-alanine product vacuole
+Gly-Asn transport via proton symport (extracellular to cytosol) 1 Gly-Asn reactant extracellular
+Gly-Asn transport via proton symport (extracellular to cytosol) 1 H+ reactant extracellular
+Gly-Asn transport via proton symport (extracellular to cytosol) 1 H+ product cytoplasm
+Gly-Asn transport via proton symport (extracellular to cytosol) 1 Gly-Asn product cytoplasm
+Gly-Asn transport via proton symport (cytosol to vacuole) 1 H+ reactant cytoplasm
+Gly-Asn transport via proton symport (cytosol to vacuole) 1 Gly-Asn reactant cytoplasm
+Gly-Asn transport via proton symport (cytosol to vacuole) 1 H+ product vacuole
+Gly-Asn transport via proton symport (cytosol to vacuole) 1 Gly-Asn product vacuole
+MNXR123350 1 Gly-Asn reactant vacuole
+MNXR123350 1 H2O reactant vacuole
+MNXR123350 1 L-glycine product vacuole
+MNXR123350 1 L-asparagine product vacuole
+MNXR137074 1 Gly-Gln reactant extracellular
+MNXR137074 1 H+ reactant extracellular
+MNXR137074 1 H+ product cytoplasm
+MNXR137074 1 Gly-Gln product cytoplasm
+MNXR137074_cv 1 H+ reactant cytoplasm
+MNXR137074_cv 1 Gly-Gln reactant cytoplasm
+MNXR137074_cv 1 H+ product vacuole
+MNXR137074_cv 1 Gly-Gln product vacuole
+MNXR123351 1 Gly-Gln reactant vacuole
+MNXR123351 1 H2O reactant vacuole
+MNXR123351 1 L-glycine product vacuole
+MNXR123351 1 L-glutamine product vacuole
+Gly-Glu transport via proton symport (extracellular to cytosol) 1 Gly-Glu reactant extracellular
+Gly-Glu transport via proton symport (extracellular to cytosol) 1 H+ reactant extracellular
+Gly-Glu transport via proton symport (extracellular to cytosol) 1 H+ product cytoplasm
+Gly-Glu transport via proton symport (extracellular to cytosol) 1 Gly-Glu product cytoplasm
+Gly-Glu transport via proton symport (cytosol to vacuole) 1 H+ reactant cytoplasm
+Gly-Glu transport via proton symport (cytosol to vacuole) 1 Gly-Glu reactant cytoplasm
+Gly-Glu transport via proton symport (cytosol to vacuole) 1 H+ product vacuole
+Gly-Glu transport via proton symport (cytosol to vacuole) 1 Gly-Glu product vacuole
+MNXR123352 1 Gly-Glu reactant vacuole
+MNXR123352 1 H2O reactant vacuole
+MNXR123352 1 L-glycine product vacuole
+MNXR123352 1 L-glutamate product vacuole
+MNXR99852 1 glycerol 2-phosphate(2-) reactant cytoplasm
+MNXR99852 1 H2O reactant cytoplasm
+MNXR99852 1 glycerol product cytoplasm
+MNXR99852 1 phosphate product cytoplasm
+MNXR98598 1 glycerol 2-phosphate(2-) reactant extracellular
+MNXR98598 1 glycerol 2-phosphate(2-) product cytoplasm
+MNXR103332 1 O-phospho-L-threonine reactant cytoplasm
+MNXR103332 1 H2O reactant cytoplasm
+MNXR103332 1 phosphate product cytoplasm
+MNXR103332 1 L-threonine product cytoplasm
+MNXR136678 1 H+ reactant extracellular
+MNXR136678 1 O-phospho-L-threonine reactant extracellular
+MNXR136678 1 O-phospho-L-threonine product cytoplasm
+MNXR136678 1 H+ product cytoplasm
+MNXR118732 1 guanosine 2'-monophosphate reactant cytoplasm
+MNXR118732 1 H2O reactant cytoplasm
+MNXR118732 1 guanosine product cytoplasm
+MNXR118732 1 phosphate product cytoplasm
+Guanosine transport via proton symport 1 H+ reactant extracellular
+Guanosine transport via proton symport 1 guanosine 2'-monophosphate reactant extracellular
+Guanosine transport via proton symport 1 guanosine 2'-monophosphate product cytoplasm
+Guanosine transport via proton symport 1 H+ product cytoplasm
+MNXR94936 1 3'-GMP reactant cytoplasm
+MNXR94936 1 H2O reactant cytoplasm
+MNXR94936 1 guanosine product cytoplasm
+MNXR94936 1 phosphate product cytoplasm
+Guanosine transport via proton symport(for 3'-GMP) 1 H+ reactant extracellular
+Guanosine transport via proton symport(for 3'-GMP) 1 3'-GMP reactant extracellular
+Guanosine transport via proton symport(for 3'-GMP) 1 3'-GMP product cytoplasm
+Guanosine transport via proton symport(for 3'-GMP) 1 H+ product cytoplasm
+MNXR94822 1 H+ reactant extracellular
+MNXR94822 1 2-phosphoglycolate reactant extracellular
+MNXR94822 1 2-phosphoglycolate product cytoplasm
+MNXR94822 1 H+ product cytoplasm
+MNXR102543 1 2-phosphoglycolate reactant cytoplasm
+MNXR102543 1 H2O reactant cytoplasm
+MNXR102543 1 phosphate product cytoplasm
+MNXR102543 1 glycolate product cytoplasm
+MNXR118734 1 cysteamine S-phosphate reactant cytoplasm
+MNXR118734 1 H2O reactant cytoplasm
+MNXR118734 1 cysteamine product cytoplasm
+MNXR137130 1 H+ reactant extracellular
+MNXR137130 1 cysteamine reactant extracellular
+MNXR137130 1 cysteamine product cytoplasm
+cysteamine exchange 1 cysteamine reactant extracellular
+MNXR137130 1 H+ product cytoplasm
+MNXR118734 1 phosphate product cytoplasm
+cysteamine S-phosphate transport via proton symport 1 cysteamine S-phosphate reactant extracellular
+cysteamine S-phosphate transport via proton symport 1 cysteamine S-phosphate product cytoplasm
+MNXR107528 1 cysteamine reactant cytoplasm
+MNXR107528 1 oxygen reactant cytoplasm
+MNXR107528 1 hypotaurine product cytoplasm
+MNXR107528 1 H+ product cytoplasm
+MNXR107116 1 hypotaurine reactant cytoplasm
+MNXR107116 1 H2O reactant cytoplasm
+MNXR107116 1 NAD reactant cytoplasm
+MNXR107116 1 taurine product cytoplasm
+MNXR107116 1 H+ product cytoplasm
+MNXR107116 1 NADH product cytoplasm
+MNXR103265 1 H2O reactant cytoplasm
+MNXR103265 1 O-phosphonatooxy-D-serine(2-) reactant cytoplasm
+MNXR103265 1 D-Serine product cytoplasm
+MNXR103265 1 phosphate product cytoplasm
+MNXR103244 1 O-phosphonatooxy-D-serine(2-) reactant extracellular
+MNXR103244 1 H+ reactant extracellular
+MNXR103244 1 H+ product cytoplasm
+MNXR103244 1 O-phosphonatooxy-D-serine(2-) product cytoplasm
+MNXR103594 1 2-oxobutanoate reactant cytoplasm
+MNXR103594 1 L-glutamate reactant cytoplasm
+MNXR103594 1 2-aminobutanoate product cytoplasm
+MNXR103594 1 2-oxoglutarate product cytoplasm
+2-aminobutyrate transport 1 H+ reactant extracellular
+2-aminobutyrate transport 1 2-aminobutanoate reactant extracellular
+2-aminobutyrate transport 1 2-aminobutanoate product cytoplasm
+2-aminobutyrate transport 1 H+ product cytoplasm
+MNXR118730 1 uridine 2'-phosphate reactant cytoplasm
+MNXR118730 1 H2O reactant cytoplasm
+MNXR118730 1 uridine product cytoplasm
+MNXR118730 1 phosphate product cytoplasm
+MNXR136675 1 H+ reactant extracellular
+MNXR136675 1 uridine 2'-phosphate reactant extracellular
+MNXR136675 1 uridine 2'-phosphate product cytoplasm
+MNXR136675 1 H+ product cytoplasm
+MNXR94932 1 3'-UMP reactant cytoplasm
+MNXR94932 1 H2O reactant cytoplasm
+MNXR94932 1 uridine product cytoplasm
+MNXR94932 1 phosphate product cytoplasm
+MNXR94982 1 H+ reactant extracellular
+MNXR94982 1 3'-UMP reactant extracellular
+MNXR94982 1 3'-UMP product cytoplasm
+MNXR94982 1 H+ product cytoplasm
+MNXR137072 1 Gly-Met reactant extracellular
+MNXR137072 1 H+ reactant extracellular
+MNXR137072 1 H+ product cytoplasm
+MNXR137072 1 Gly-Met product cytoplasm
+MNXR137072_cv 1 H+ reactant cytoplasm
+MNXR137072_cv 1 Gly-Met reactant cytoplasm
+MNXR137072_cv 1 H+ product vacuole
+MNXR137072_cv 1 Gly-Met product vacuole
+MNXR123343 1 Gly-Met reactant vacuole
+MNXR123343 1 H2O reactant vacuole
+MNXR123343 1 L-methionine product vacuole
+MNXR123343 1 L-glycine product vacuole
+MNXR111061 1 N-phosphocreatine reactant cytoplasm
+MNXR111061 1 creatinine product cytoplasm
+MNXR111061 1 phosphate product cytoplasm
+N-phosphocreatine transport 1 H+ reactant extracellular
+N-phosphocreatine transport 1 N-phosphocreatine reactant extracellular
+N-phosphocreatine transport 1 N-phosphocreatine product cytoplasm
+N-phosphocreatine transport 1 H+ product cytoplasm
+creatinine transport 1 H+ reactant extracellular
+creatinine transport 1 creatinine reactant extracellular
+creatinine transport 1 creatinine product cytoplasm
+creatinine transport 1 H+ product cytoplasm
+MNXR95943 1 H+ reactant cytoplasm
+MNXR95943 1 N(omega)-phospho-L-arginine reactant cytoplasm
+MNXR95943 1 ADP reactant cytoplasm
+MNXR95943 1 ATP product cytoplasm
+MNXR95943 1 L-arginine product cytoplasm
+MNXR95947 1 H+ reactant extracellular
+MNXR95947 1 N(omega)-phospho-L-arginine reactant extracellular
+MNXR95947 1 N(omega)-phospho-L-arginine product cytoplasm
+MNXR95947 1 H+ product cytoplasm
+MNXR117325 1 2',3'-cyclic GMP reactant cytoplasm
+MNXR117325 1 H2O reactant cytoplasm
+MNXR117325 1 H+ product cytoplasm
+MNXR117325 1 guanosine 2'-monophosphate product cytoplasm
+MNXR94721 1 2',3'-cyclic GMP reactant extracellular
+MNXR94721 1 2',3'-cyclic GMP product cytoplasm
+MNXR104998 1 H2O reactant cytoplasm
+MNXR104998 1 O(4)-phospho-L-tyrosine reactant cytoplasm
+MNXR104998 1 L-tyrosine product cytoplasm
+MNXR104998 1 phosphate product cytoplasm
+MNXR137095 1 H+ reactant extracellular
+MNXR137095 1 O(4)-phospho-L-tyrosine reactant extracellular
+MNXR137095 1 O(4)-phospho-L-tyrosine product cytoplasm
+MNXR137095 1 H+ product cytoplasm
+MNXR103069 1 triphosphate reactant cytoplasm
+MNXR103069 1 H2O reactant cytoplasm
+MNXR103069 1 phosphate product cytoplasm
+MNXR103069 1 diphosphate product cytoplasm
+MNXR135003 1 H+ reactant extracellular
+MNXR135003 1 triphosphate reactant extracellular
+MNXR135003 1 triphosphate product cytoplasm
+MNXR135003 1 H+ product cytoplasm
+MNXR118731 1 cytidine 2'-phosphate reactant cytoplasm
+MNXR118731 1 H2O reactant cytoplasm
+MNXR118731 1 cytidine product cytoplasm
+MNXR118731 1 phosphate product cytoplasm
+MNXR135010 1 H+ reactant extracellular
+MNXR135010 1 cytidine 2'-phosphate reactant extracellular
+MNXR135010 1 cytidine 2'-phosphate product cytoplasm
+MNXR135010 1 H+ product cytoplasm
+MNXR117327 1 2',3'-cyclic UMP reactant cytoplasm
+MNXR117327 1 H2O reactant cytoplasm
+MNXR117327 1 uridine 2'-phosphate product cytoplasm
+MNXR117327 1 H+ product cytoplasm
+MNXR136674 1 H+ reactant extracellular
+MNXR136674 1 2',3'-cyclic UMP reactant extracellular
+MNXR136674 1 2',3'-cyclic UMP product cytoplasm
+MNXR136674 1 H+ product cytoplasm
+MNXR123155 1 3-sulfino-L-alanine reactant cytoplasm
+MNXR123155 1 H2O reactant cytoplasm
+MNXR123155 1 L-alanine product cytoplasm
+MNXR123155 1 sulphite product cytoplasm
+MNXR137086 1 H+ reactant extracellular
+MNXR137086 1 3-sulfino-L-alanine reactant extracellular
+MNXR137086 1 3-sulfino-L-alanine product cytoplasm
+MNXR137086 1 H+ product cytoplasm
+MNXR94935 1 3'-AMP reactant cytoplasm
+MNXR94935 1 H2O reactant cytoplasm
+MNXR94935 1 adenosine product cytoplasm
+MNXR94935 1 phosphate product cytoplasm
+MNXR94857 1 3'-AMP reactant extracellular
+MNXR94857 1 3'-AMP product cytoplasm
+MNXR130717 1 6-O-alpha-D-glucopyranosyl-D-fructofuranose reactant cytoplasm
+MNXR130717 1 H2O reactant cytoplasm
+MNXR130717 1 D-fructose product cytoplasm
+MNXR130717 1 D-glucose product cytoplasm
+MNXR102339 1 H+ reactant extracellular
+MNXR102339 1 6-O-alpha-D-glucopyranosyl-D-fructofuranose reactant extracellular
+MNXR102339 1 6-O-alpha-D-glucopyranosyl-D-fructofuranose product cytoplasm
+MNXR102339 1 H+ product cytoplasm
+MNXR103637 1 N-acetyl-L-cysteine reactant cytoplasm
+MNXR103637 1 coenzyme A reactant cytoplasm
+MNXR103637 1 H+ reactant cytoplasm
+MNXR103637 1 acetyl-CoA product cytoplasm
+MNXR103637 1 L-cysteine product cytoplasm
+MNXR137052 1 H+ reactant extracellular
+MNXR137052 1 N-acetyl-L-cysteine reactant extracellular
+MNXR137052 1 N-acetyl-L-cysteine product cytoplasm
+MNXR137052 1 H+ product cytoplasm
+MNXR106345 1 tetrathionate reactant cytoplasm
+MNXR106345 2 ferricytochrome c reactant mitochondrion
+MNXR106345 2 thiosulfate product cytoplasm
+MNXR106345 2 ferrocytochrome c product mitochondrion
+MNXR104796 1 tetrathionate reactant extracellular
+MNXR104796 1 tetrathionate product cytoplasm
+L-methionine transport, vacuoluar 1 L-methionine reactant cytoplasm
+L-methionine transport, vacuoluar 1 L-methionine product vacuole
+MNXR99485 1 2-hydroxyethane-1-sulfonate reactant cytoplasm
+MNXR99485 1 FMNH2 reactant cytoplasm
+MNXR99485 1 oxygen reactant cytoplasm
+MNXR99485 1 H+ product cytoplasm
+MNXR99485 1 sulphite product cytoplasm
+MNXR99485 1 H2O product cytoplasm
+MNXR99485 1 FMN product cytoplasm
+MNXR99485 1 glycolaldehyde product cytoplasm
+MNXR137058 1 H+ reactant extracellular
+MNXR137058 1 2-hydroxyethane-1-sulfonate reactant extracellular
+MNXR137058 1 2-hydroxyethane-1-sulfonate product cytoplasm
+MNXR137058 1 H+ product cytoplasm
+MNXR95065 1 H+ reactant cytoplasm
+MNXR95065 1 NADPH reactant cytoplasm
+MNXR95065 1 5-dehydro-D-gluconate reactant cytoplasm
+MNXR95065 1 D-gluconate product cytoplasm
+MNXR95065 1 NADP(+) product cytoplasm
+MNXR95066 1 H+ reactant extracellular
+MNXR95066 1 5-dehydro-D-gluconate reactant extracellular
+MNXR95066 1 5-dehydro-D-gluconate product cytoplasm
+MNXR95066 1 H+ product cytoplasm
+MNXR137135 1 Ala-Asp reactant extracellular
+MNXR137135 1 H+ reactant extracellular
+MNXR137135 1 H+ product cytoplasm
+MNXR137135 1 Ala-Asp product cytoplasm
+MNXR137135_cv 1 H+ reactant cytoplasm
+MNXR137135_cv 1 Ala-Asp reactant cytoplasm
+MNXR137135_cv 1 H+ product vacuole
+MNXR137135_cv 1 Ala-Asp product vacuole
+MNXR123344 1 Ala-Asp reactant vacuole
+MNXR123344 1 H2O reactant vacuole
+MNXR123344 1 L-alanine product vacuole
+MNXR123344 1 L-aspartate product vacuole
+MNXR96247 1 methyl alpha-D-glucopyranoside reactant cytoplasm
+MNXR96247 1 H2O reactant cytoplasm
+MNXR96247 1 D-glucose product cytoplasm
+MNXR96247 1 methanol product cytoplasm
+MNXR101464 1 methanol reactant cytoplasm
+MNXR101464 1 methanol product extracellular
+MNXR98748 1 methanol reactant extracellular
+MNXR137048 1 H+ reactant extracellular
+MNXR137048 1 methyl alpha-D-glucopyranoside reactant extracellular
+MNXR137048 1 methyl alpha-D-glucopyranoside product cytoplasm
+MNXR137048 1 H+ product cytoplasm
+MNXR117326 1 2',3'-cyclic CMP reactant cytoplasm
+MNXR117326 1 H2O reactant cytoplasm
+MNXR117326 1 cytidine 2'-phosphate product cytoplasm
+MNXR117326 1 H+ product cytoplasm
+MNXR136673 1 H+ reactant extracellular
+MNXR136673 1 2',3'-cyclic CMP reactant extracellular
+MNXR136673 1 2',3'-cyclic CMP product cytoplasm
+MNXR136673 1 H+ product cytoplasm
+MNXR107830 1 D-tagatose reactant cytoplasm
+MNXR107830 1 ATP reactant cytoplasm
+MNXR107830 1 ADP product cytoplasm
+MNXR107830 1 D-tagatofuranose 6-phosphate product cytoplasm
+MNXR107830 1 H+ product cytoplasm
+R11623 1 D-tagatofuranose 6-phosphate reactant cytoplasm
+R11623 1 D-fructose 6-phosphate product cytoplasm
+MNXR104707 1 D-tagatose reactant extracellular
+MNXR104707 1 D-tagatose product cytoplasm
+MNXR130716 1 turanose reactant extracellular
+MNXR130716 1 H2O reactant extracellular
+MNXR130716 1 D-fructose product extracellular
+MNXR130716 1 D-glucose product extracellular
+MNXR95136 1 acetoacetate reactant cytoplasm
+MNXR95136 1 ATP reactant cytoplasm
+MNXR95136 1 coenzyme A reactant cytoplasm
+MNXR95136 1 AMP product cytoplasm
+MNXR95136 1 diphosphate product cytoplasm
+MNXR95136 1 acetoacetyl-CoA product cytoplasm
+MNXR95208 1 acetoacetate reactant extracellular
+MNXR95208 1 acetoacetate product cytoplasm
+MNXR103709 1 N(alpha)-acetyl-L-methionine reactant cytoplasm
+MNXR103709 1 H2O reactant cytoplasm
+MNXR103709 1 acetate product cytoplasm
+MNXR103709 1 L-methionine product cytoplasm
+MNXR137089 1 H+ reactant extracellular
+MNXR137089 1 N(alpha)-acetyl-L-methionine reactant extracellular
+MNXR137089 1 N(alpha)-acetyl-L-methionine product cytoplasm
+MNXR137089 1 H+ product cytoplasm
+MNXR106549 1 3-oxalomalate(3-) reactant cytoplasm
+MNXR106549 1 oxaloacetate product cytoplasm
+MNXR106549 1 glyoxylate product cytoplasm
+MNXR137067 1 H+ reactant extracellular
+MNXR137067 1 3-oxalomalate(3-) reactant extracellular
+MNXR137067 1 3-oxalomalate(3-) product cytoplasm
+MNXR137067 1 H+ product cytoplasm
+MNXR111236 1 L-cysteate reactant cytoplasm
+MNXR111236 1 H2O reactant cytoplasm
+MNXR111236 1 pyruvate product cytoplasm
+MNXR111236 1 ammonium product cytoplasm
+MNXR111236 1 sulphite product cytoplasm
+MNXR124424 1 H+ reactant extracellular
+MNXR124424 1 L-cysteate reactant extracellular
+MNXR124424 1 L-cysteate product cytoplasm
+MNXR124424 1 H+ product cytoplasm
+MNXR101619 1 alpha-maltotriose reactant extracellular
+MNXR101619 1 H2O reactant extracellular
+MNXR101619 1 maltose product extracellular
+MNXR101619 1 D-glucose product extracellular
+MNXR94824 1 H+ reactant extracellular
+MNXR94824 1 2-phospho-D-glyceric acid reactant extracellular
+MNXR94824 1 2-phospho-D-glyceric acid product cytoplasm
+MNXR94824 1 H+ product cytoplasm
+MNXR94973 1 H+ reactant extracellular
+MNXR94973 1 3-phosphonato-D-glycerate(3-) reactant extracellular
+MNXR94973 1 3-phosphonato-D-glycerate(3-) product cytoplasm
+MNXR94973 1 H+ product cytoplasm
+Met-Ala transport via proton symport (extracellular to cytosol) 1 Met-Ala reactant extracellular
+Met-Ala transport via proton symport (extracellular to cytosol) 1 H+ reactant extracellular
+Met-Ala transport via proton symport (extracellular to cytosol) 1 H+ product cytoplasm
+Met-Ala transport via proton symport (extracellular to cytosol) 1 Met-Ala product cytoplasm
+Met-Ala transport via proton symport (cytosol to vacuole) 1 H+ reactant cytoplasm
+Met-Ala transport via proton symport (cytosol to vacuole) 1 Met-Ala reactant cytoplasm
+Met-Ala transport via proton symport (cytosol to vacuole) 1 H+ product vacuole
+Met-Ala transport via proton symport (cytosol to vacuole) 1 Met-Ala product vacuole
+MNXR99849 1 D-glucose 1-phosphate reactant extracellular
+MNXR99849 1 D-glucose 1-phosphate product cytoplasm
+MNXR96488 1 carbamoyl phosphate reactant extracellular
+MNXR96488 1 carbamoyl phosphate product cytoplasm
+MNXR103245 1 3-phospho-serine reactant extracellular
+MNXR103245 1 H+ reactant extracellular
+MNXR103245 1 H+ product cytoplasm
+MNXR103245 1 3-phospho-serine product cytoplasm
+MNXR100385 1 GMP reactant extracellular
+MNXR100385 1 H+ reactant extracellular
+MNXR100385 1 H+ product cytoplasm
+MNXR100385 1 GMP product cytoplasm
+MNXR101585 1 myo-inositol hexakisphosphate reactant extracellular
+MNXR101585 1 myo-inositol hexakisphosphate product cytoplasm
+MNXR98531 1 D-glucose 6-phosphate reactant extracellular
+MNXR98531 1 D-glucose 6-phosphate product cytoplasm
+MNXR105127 1 UMP reactant extracellular
+MNXR105127 1 UMP product cytoplasm
+MNXR102493 1 phosphoenolpyruvate reactant extracellular
+MNXR102493 1 H+ reactant extracellular
+MNXR102493 1 H+ product cytoplasm
+MNXR102493 1 phosphoenolpyruvate product cytoplasm
+MNXR101385 1 D-mannose 6-phosphate reactant extracellular
+MNXR101385 1 D-mannose 6-phosphate product cytoplasm
+MNXR135002 1 O-phosphoethanolamine reactant extracellular
+MNXR135002 1 H+ reactant extracellular
+MNXR135002 1 H+ product cytoplasm
+MNXR135002 1 O-phosphoethanolamine product cytoplasm
+MNXR95102 1 6-phospho-D-gluconate reactant extracellular
+MNXR95102 1 H+ reactant extracellular
+MNXR95102 1 H+ product cytoplasm
+MNXR95102 1 6-phospho-D-gluconate product cytoplasm
+MNXR101377 1 D-mannose 1-phosphate reactant extracellular
+MNXR101377 1 H+ reactant extracellular
+MNXR101377 1 H+ product cytoplasm
+MNXR101377 1 D-mannose 1-phosphate product cytoplasm
+MNXR136667 1 diphosphate reactant extracellular
+MNXR136667 2 H+ reactant extracellular
+MNXR136667 2 H+ product cytoplasm
+MNXR136667 1 diphosphate product cytoplasm
+MNXR96703 1 choline phosphate reactant extracellular
+MNXR96703 1 choline phosphate product cytoplasm
+MNXR104966 1 thiosulfate reactant extracellular
+MNXR104966 1 thiosulfate product cytoplasm
+MNXR95831 1 AMP reactant extracellular
+MNXR95831 1 H+ reactant extracellular
+MNXR95831 1 H+ product cytoplasm
+MNXR95831 1 AMP product cytoplasm
+MNXR94718 1 2',3'-cyclic AMP reactant extracellular
+MNXR94718 1 2',3'-cyclic AMP product cytoplasm
+MNXR135007 1 adenosine 2'-phosphate reactant extracellular
+MNXR135007 1 H+ reactant extracellular
+MNXR135007 1 H+ product cytoplasm
+MNXR135007 1 adenosine 2'-phosphate product cytoplasm
+MNXR96805 1 CMP reactant extracellular
+MNXR96805 1 H+ reactant extracellular
+MNXR96805 1 H+ product cytoplasm
+MNXR96805 1 CMP product cytoplasm
+MNXR100035 1 D-Glucosamine reactant extracellular
+MNXR100035 1 D-Glucosamine product cytoplasm
+2-deoxy-D-ribose transport 1 2-deoxy-D-ribose reactant extracellular
+2-deoxy-D-ribose transport 1 2-deoxy-D-ribose product cytoplasm
+MNXR96737 1 L-citrulline reactant extracellular
+MNXR96737 1 H+ reactant extracellular
+MNXR96737 1 H+ product cytoplasm
+MNXR96737 1 L-citrulline product cytoplasm
+MNXR97367 1 glycerone reactant extracellular
+MNXR97367 1 glycerone product cytoplasm
+Ala-Leu transport via proton symport (extracellular to cytosol) 1 Ala-Leu reactant extracellular
+Ala-Leu transport via proton symport (extracellular to cytosol) 1 H+ reactant extracellular
+Ala-Leu transport via proton symport (extracellular to cytosol) 1 H+ product cytoplasm
+Ala-Leu transport via proton symport (extracellular to cytosol) 1 Ala-Leu product cytoplasm
+Ala-Leu transport via proton symport (cytosol to vacuole) 1 H+ reactant cytoplasm
+Ala-Leu transport via proton symport (cytosol to vacuole) 1 Ala-Leu reactant cytoplasm
+Ala-Leu transport via proton symport (cytosol to vacuole) 1 H+ product vacuole
+Ala-Leu transport via proton symport (cytosol to vacuole) 1 Ala-Leu product vacuole
+MNXR137133 1 Ala-Gly reactant extracellular
+MNXR137133 1 H+ reactant extracellular
+MNXR137133 1 H+ product cytoplasm
+MNXR137133 1 Ala-Gly product cytoplasm
+MNXR137133_cv 1 H+ reactant cytoplasm
+MNXR137133_cv 1 Ala-Gly reactant cytoplasm
+MNXR137133_cv 1 H+ product vacuole
+MNXR137133_cv 1 Ala-Gly product vacuole
+N-acetyl-L-glutamate transport 1 N-acetyl-L-glutamate reactant extracellular
+N-acetyl-L-glutamate transport 1 N-acetyl-L-glutamate product cytoplasm
+N-acetyl-L-glutamate transport, mitochondrion 1 N-acetyl-L-glutamate reactant cytoplasm
+N-acetyl-L-glutamate transport, mitochondrion 1 N-acetyl-L-glutamate product mitochondrion
+MNXR137094 1 lipoamide reactant extracellular
+MNXR137094 1 H+ reactant extracellular
+MNXR137094 1 H+ product cytoplasm
+MNXR137094 1 lipoamide product cytoplasm
+MNXR101483 1 L-Methionine S-oxide reactant extracellular
+MNXR101483 1 L-Methionine S-oxide product cytoplasm
+Hydrogen sulfide oxidation 1 hydrogen sulfide reactant cytoplasm
+Hydrogen sulfide oxidation 2 oxygen reactant cytoplasm
+Hydrogen sulfide oxidation 1 H+ product cytoplasm
+Hydrogen sulfide oxidation 1 sulphate product cytoplasm
+MNXR95704 1 H+ reactant cytoplasm
+MNXR95704 1 L-alanine reactant cytoplasm
+MNXR95704 1 L-alanine product vacuole
+MNXR95704 1 H+ product vacuole
+MNXR100368 1 H+ reactant cytoplasm
+MNXR100368 1 L-glycine reactant cytoplasm
+MNXR100368 1 L-glycine product vacuole
+MNXR100368 1 H+ product vacuole
+MNXR104382 1 O-succinyl-L-homoserine reactant cytoplasm
+MNXR104382 1 hydrogen sulfide reactant cytoplasm
+MNXR104382 1 L-homocysteine product cytoplasm
+MNXR104382 1 succinate product cytoplasm
+MNXR94843 1 oxygen reactant cytoplasm
+MNXR94843 1 3-(4-hydroxyphenyl)pyruvate reactant cytoplasm
+MNXR94843 1 homogentisate product cytoplasm
+MNXR94843 1 carbon dioxide product cytoplasm
+MNXR100628 1 homogentisate reactant cytoplasm
+MNXR100628 1 oxygen reactant cytoplasm
+MNXR100628 1 4-maleylacetoacetate product cytoplasm
+MNXR100628 1 H+ product cytoplasm
+MNXR101325 1 4-maleylacetoacetate reactant cytoplasm
+MNXR101325 1 4-fumarylacetoacetate product cytoplasm
+MNXR99706 1 4-fumarylacetoacetate reactant cytoplasm
+MNXR99706 1 H2O reactant cytoplasm
+MNXR99706 1 fumarate product cytoplasm
+MNXR99706 1 acetoacetate product cytoplasm
+MNXR99706 1 H+ product cytoplasm
+MNXR95187 1 L-arabinitol reactant cytoplasm
+MNXR95187 1 NAD reactant cytoplasm
+MNXR95187 1 H+ product cytoplasm
+MNXR95187 1 NADH product cytoplasm
+MNXR95187 1 L-xylulose product cytoplasm
+MNXR105265 1 L-xylulose reactant cytoplasm
+MNXR105265 1 NADPH reactant cytoplasm
+MNXR105265 1 H+ reactant cytoplasm
+MNXR105265 1 xylitol product cytoplasm
+MNXR105265 1 NADP(+) product cytoplasm
+arabinose reductase (D-arabinose) 1 D-arabinose reactant cytoplasm
+arabinose reductase (D-arabinose) 1 NADPH reactant cytoplasm
+arabinose reductase (D-arabinose) 1 H+ reactant cytoplasm
+arabinose reductase (D-arabinose) 1 D-arabinitol product cytoplasm
+arabinose reductase (D-arabinose) 1 NADP(+) product cytoplasm
+MNXR95188 1 D-arabinitol reactant cytoplasm
+MNXR95188 1 NAD reactant cytoplasm
+MNXR95188 1 H+ product cytoplasm
+MNXR95188 1 NADH product cytoplasm
+MNXR95188 1 D-xylulose product cytoplasm
+MNXR118733 1 adenosine 2'-phosphate reactant cytoplasm
+MNXR118733 1 H2O reactant cytoplasm
+MNXR118733 1 adenosine product cytoplasm
+MNXR118733 1 phosphate product cytoplasm
diff --git a/ComplementaryData/modelCuration/Biolog_newRxnMetAnnotation.tsv b/ComplementaryData/modelCuration/Biolog_newRxnMetAnnotation.tsv
new file mode 100644
index 00000000..12926410
--- /dev/null
+++ b/ComplementaryData/modelCuration/Biolog_newRxnMetAnnotation.tsv
@@ -0,0 +1,152 @@
+NewMetName Charged formula Charge compartment KEGG ID CHEBI ID Remark
+Ala-Gln [extracellular] C8H15N3O4 0 extracellular CHEBI:73788 MNXM40495
+Ala-Gln [cytoplasm] C8H15N3O4 0 cytoplasm CHEBI:73788 MNXM40495
+Ala-Gln [vacuole] C8H15N3O4 0 vacuole CHEBI:73788 MNXM40495
+Ala-Glu [extracellular] C8H13N2O5 -1 extracellular C20958 CHEBI:61396 MNXM4026
+Ala-Glu [cytoplasm] C8H13N2O5 -1 cytoplasm C20958 CHEBI:61396 MNXM4026
+Ala-Glu [vacuole] C8H13N2O5 -1 vacuole C20958 CHEBI:61396 MNXM4026
+Ala-Thr [extracellular] C7H14N2O4 0 extracellular CHEBI:73762 MNXM40497
+Ala-Thr [cytoplasm] C7H14N2O4 0 cytoplasm CHEBI:73762 MNXM40497
+Ala-Thr [vacuole] C7H14N2O4 0 vacuole CHEBI:73762 MNXM40497
+L-threonine [vacuole] C4H9NO3 0 vacuole C00188 CHEBI:16857 MNXM142
+thymidine 3'-monophosphate [cytoplasm] C10H13N2O8P -2 cytoplasm CHEBI:77843 MNXM87165
+thymidine 3'-monophosphate [extracellular] C10H13N2O8P -2 extracellular CHEBI:77843 MNXM87165
+thymidine 5'-monophosphate [cytoplasm] C10H13N2O8P -2 cytoplasm CHEBI:15245 MNXM87167
+thymidine 5'-monophosphate [extracellular] C10H13N2O8P -2 extracellular CHEBI:15245 MNXM87167
+glycerol 1-phosphate [cytoplasm] C3H7O6P -2 cytoplasm C03189 CHEBI:231935 MNXM682
+glycerol 1-phosphate [extracellular] C3H7O6P -2 extracellular C03189 CHEBI:231935 MNXM682
+Ala-His [extracellular] C9H14N4O3 0 extracellular CHEBI:73771 MNXM40496
+Ala-His [cytoplasm] C9H14N4O3 0 cytoplasm CHEBI:73771 MNXM40496
+Ala-His [vacuole] C9H14N4O3 0 vacuole CHEBI:73771 MNXM40496
+Gly-Asn [extracellular] C6H11N3O4 0 extracellular CHEBI:73888 MNXM55268
+Gly-Asn [cytoplasm] C6H11N3O4 0 cytoplasm CHEBI:73888 MNXM55268
+Gly-Asn [vacuole] C6H11N3O4 0 vacuole CHEBI:73888 MNXM55268
+Gly-Gln [extracellular] C7H13N3O4 0 extracellular CHEBI:73898 MNXM55276
+Gly-Gln [cytoplasm] C7H13N3O4 0 cytoplasm CHEBI:73898 MNXM55276
+Gly-Gln [vacuole] C7H13N3O4 0 vacuole CHEBI:73898 MNXM55276
+Gly-Glu [extracellular] C7H11N2O5 -1 extracellular CHEBI:73784 MNXM55454
+Gly-Glu [cytoplasm] C7H11N2O5 -1 cytoplasm CHEBI:73784 MNXM55454
+Gly-Glu [vacuole] C7H11N2O5 -1 vacuole CHEBI:73784 MNXM55454
+glycerol 2-phosphate(2-) [cytoplasm] C3H7O6P -2 cytoplasm C02979 CHEBI:58083 MNXM2527
+glycerol 2-phosphate(2-) [extracellular] C3H7O6P -2 extracellular C02979 CHEBI:58083 MNXM2527
+O-phospho-L-threonine [cytoplasm] C4H8NO6P -2 cytoplasm C12147 CHEBI:58675 MNXM1492
+O-phospho-L-threonine [extracellular] C4H8NO6P -2 extracellular C12147 CHEBI:58675 MNXM1492
+guanosine 2'-monophosphate [cytoplasm] C10H12N5O8P -2 cytoplasm CHEBI:74604 MNXM18285
+guanosine 2'-monophosphate [extracellular] C10H12N5O8P -2 extracellular CHEBI:74604 MNXM18285
+3'-GMP [cytoplasm] C10H12N5O8P -2 cytoplasm C06193 CHEBI:60732 MNXM2183
+3'-GMP [extracellular] C10H12N5O8P -2 extracellular C06193 CHEBI:60732 MNXM2183
+2-phosphoglycolate [extracellular] C2H2O6P -3 extracellular C00988 CHEBI:58033 MNXM2074
+2-phosphoglycolate [cytoplasm] C2H2O6P -3 cytoplasm C00988 CHEBI:58033 MNXM2074
+cysteamine S-phosphate [cytoplasm] C2H7NO3PS -1 cytoplasm CHEBI:74631 MNXM48297
+cysteamine [cytoplasm] C2H8NS 1 cytoplasm C01678 CHEBI:58029 MNXM1226
+cysteamine [extracellular] C2H8NS 1 extracellular C01678 CHEBI:58029 MNXM1226
+cysteamine S-phosphate [extracellular] C2H7NO3PS -1 extracellular CHEBI:74631 MNXM48297
+hypotaurine [cytoplasm] C2H7NO2S 0 cytoplasm C00519 CHEBI:16668 MNXM726
+O-phosphonatooxy-D-serine(2-) [cytoplasm] C3H6NO6P -2 cytoplasm C02532 CHEBI:58680 MNXM4752
+O-phosphonatooxy-D-serine(2-) [extracellular] C3H6NO6P -2 extracellular C02532 CHEBI:58680 MNXM4752
+2-aminobutanoate [cytoplasm] C4H9NO2 0 cytoplasm CHEBI:35621 MNXM15850
+2-aminobutanoate [extracellular] C4H9NO2 0 extracellular CHEBI:35621 MNXM15850
+uridine 2'-phosphate [cytoplasm] C9H11N2O9P -2 cytoplasm C03031 CHEBI:77802 MNXM13238
+uridine 2'-phosphate [extracellular] C9H11N2O9P -2 extracellular C03031 CHEBI:77802 MNXM13238
+3'-UMP [cytoplasm] C9H11N2O9P -2 cytoplasm C01368 CHEBI:60784 MNXM2184
+3'-UMP [extracellular] C9H11N2O9P -2 extracellular C01368 CHEBI:60784 MNXM2184
+Gly-Met [extracellular] C7H14N2O3S 0 extracellular CHEBI:74393 MNXM55287
+Gly-Met [cytoplasm] C7H14N2O3S 0 cytoplasm CHEBI:74393 MNXM55287
+Gly-Met [vacuole] C7H14N2O3S 0 vacuole CHEBI:74393 MNXM55287
+N-phosphocreatine [cytoplasm] C4H8N3O5P -2 cytoplasm CHEBI:58092 MNXM819
+creatinine [cytoplasm] C4H7N3O 0 cytoplasm C00791 CHEBI:16737 MNXM1470
+N-phosphocreatine [extracellular] C4H8N3O5P -2 extracellular CHEBI:58092 MNXM819
+creatinine [extracellular] C4H7N3O 0 extracellular C00791 CHEBI:16737 MNXM1470
+N(omega)-phospho-L-arginine [cytoplasm] C6H14N4O5P -1 cytoplasm C05945 CHEBI:58477 MNXM3663
+N(omega)-phospho-L-arginine [extracellular] C6H14N4O5P -1 extracellular C05945 CHEBI:58477 MNXM3663
+2',3'-cyclic GMP [cytoplasm] C10H11N5O7P -1 cytoplasm C06194 CHEBI:60837 MNXM3149
+2',3'-cyclic GMP [extracellular] C10H11N5O7P -1 extracellular C06194 CHEBI:60837 MNXM3149
+O(4)-phospho-L-tyrosine [cytoplasm] C9H10NO6P -2 cytoplasm C06501 CHEBI:62338 MNXM3323
+O(4)-phospho-L-tyrosine [extracellular] C9H10NO6P -2 extracellular C06501 CHEBI:62338 MNXM3323
+triphosphate [cytoplasm] O10P3 -5 cytoplasm C00536 CHEBI:18036 MNXM332
+triphosphate [extracellular] O10P3 -5 extracellular C00536 CHEBI:18036 MNXM332
+cytidine 2'-phosphate [cytoplasm] C9H12N3O8P -2 cytoplasm C03104 CHEBI:77766 MNXM11237
+cytidine 2'-phosphate [extracellular] C9H12N3O8P -2 extracellular C03104 CHEBI:77766 MNXM11237
+2',3'-cyclic UMP [cytoplasm] C9H10N2O8P -1 cytoplasm C02355 CHEBI:60873 MNXM3150
+2',3'-cyclic UMP [extracellular] C9H10N2O8P -1 extracellular C02355 CHEBI:60873 MNXM3150
+3-sulfino-L-alanine [cytoplasm] C3H6NO4S -1 cytoplasm C00606 CHEBI:61085 MNXM498
+3-sulfino-L-alanine [extracellular] C3H6NO4S -1 extracellular C00606 CHEBI:61085 MNXM498
+3'-AMP [cytoplasm] C10H12N5O7P -2 cytoplasm C01367 CHEBI:60880 MNXM1985
+3'-AMP [extracellular] C10H12N5O7P -2 extracellular C01367 CHEBI:60880 MNXM1985
+6-O-alpha-D-glucopyranosyl-D-fructofuranose [cytoplasm] C12H22O11 0 cytoplasm C01742 CHEBI:18394 MNXM3518
+6-O-alpha-D-glucopyranosyl-D-fructofuranose [extracellular] C12H22O11 0 extracellular C01742 CHEBI:18394 MNXM3518
+N-acetyl-L-cysteine [cytoplasm] C5H8NO3S -1 cytoplasm C06809 CHEBI:78236 MNXM98606
+N-acetyl-L-cysteine [extracellular] C5H8NO3S -1 extracellular C06809 CHEBI:78236 MNXM98606
+tetrathionate [cytoplasm] O6S4 -2 cytoplasm C02084 CHEBI:15226 MNXM1781
+thiosulfate [cytoplasm] HO3S2 -1 cytoplasm C00320 CHEBI:33542 MNXM323
+tetrathionate [extracellular] O6S4 -2 extracellular C02084 CHEBI:15226 MNXM1781
+glycyl-L-methionine [extracellular] C7H14N2O3S 0 extracellular CHEBI:74393 MNXM55287
+glycyl-L-methionine [cytoplasm] C7H14N2O3S 0 cytoplasm CHEBI:74393 MNXM55287
+glycyl-L-methionine [vacuole] C7H14N2O3S 0 vacuole CHEBI:74393 MNXM55287
+2-hydroxyethane-1-sulfonate [cytoplasm] C2H5O4S -1 cytoplasm C05123 CHEBI:61904 MNXM1630
+2-hydroxyethane-1-sulfonate [extracellular] C2H5O4S -1 extracellular C05123 CHEBI:61904 MNXM1630
+5-dehydro-D-gluconate [cytoplasm] C6H9O7 -1 cytoplasm C01062 CHEBI:58143 MNXM963
+5-dehydro-D-gluconate [extracellular] C6H9O7 -1 extracellular C01062 CHEBI:58143 MNXM963
+Ala-Asp [extracellular] C7H11N2O5 -1 extracellular CHEBI:74363 MNXM40494
+Ala-Asp [cytoplasm] C7H11N2O5 -1 cytoplasm CHEBI:74363 MNXM40494
+Ala-Asp [vacuole] C7H11N2O5 -1 vacuole CHEBI:74363 MNXM40494
+methyl alpha-D-glucopyranoside [cytoplasm] C7H14O6 0 cytoplasm CHEBI:320061 MNXM61741
+methanol [cytoplasm] CH4O 0 cytoplasm C00132 CHEBI:17790 MNXM157
+methanol [extracellular] CH4O 0 extracellular C00132 CHEBI:17790 MNXM157
+methyl alpha-D-glucopyranoside [extracellular] C7H14O6 0 extracellular CHEBI:320061 MNXM61741
+2',3'-cyclic CMP [cytoplasm] C9H11N3O7P -1 cytoplasm C02354 CHEBI:60877 MNXM3148
+2',3'-cyclic CMP [extracellular] C9H11N3O7P -1 extracellular C02354 CHEBI:60877 MNXM3148
+D-tagatose [cytoplasm] C6H12O6 0 cytoplasm C00795 CHEBI:4249 MNXM92401
+D-tagatofuranose 6-phosphate [cytoplasm] C6H11O9P -2 cytoplasm C01097 CHEBI:58695 MNXM795
+D-tagatose [extracellular] C6H12O6 0 extracellular C00795 CHEBI:4249 MNXM92401
+turanose [extracellular] C12H22O11 0 extracellular C19636 CHEBI:32528 MNXM161984
+acetoacetate [cytoplasm] C4H5O3 -1 cytoplasm C00164 CHEBI:13705 MNXM154
+acetoacetate [extracellular] C4H5O3 -1 extracellular C00164 CHEBI:13705 MNXM154
+N(alpha)-acetyl-L-methionine [cytoplasm] C7H12NO3S -1 cytoplasm C02712 CHEBI:132957 MNXM7576
+N(alpha)-acetyl-L-methionine [extracellular] C7H12NO3S -1 extracellular C02712 CHEBI:132957 MNXM7576
+3-oxalomalate(3-) [cytoplasm] C6H3O8 -3 cytoplasm C01990 CHEBI:15593 MNXM3850
+3-oxalomalate(3-) [extracellular] C6H3O8 -3 extracellular C01990 CHEBI:15593 MNXM3850
+L-cysteate [cytoplasm] C3H6NO5S -1 cytoplasm C00506 CHEBI:58090 MNXM713
+L-cysteate [extracellular] C3H6NO5S -1 extracellular C00506 CHEBI:58090 MNXM713
+alpha-maltotriose [extracellular] C18H32O16 0 extracellular C01835 CHEBI:61993 MNXM468
+2-phospho-D-glyceric acid [extracellular] C3H4O7P -3 extracellular C00631 CHEBI:58289 MNXM275
+3-phosphonato-D-glycerate(3-) [extracellular] C3H4O7P -3 extracellular C00197 CHEBI:58272 MNXM126
+Met-Ala [extracellular] C8H16N2O3S 0 extracellular CHEBI:73610 MNXM61647
+Met-Ala [cytoplasm] C8H16N2O3S 0 cytoplasm CHEBI:73610 MNXM61647
+D-glucose 1-phosphate [extracellular] C6H11O9P -2 extracellular C00103 CHEBI:57629 MNXM89588
+carbamoyl phosphate [extracellular] CH2NO5P -2 extracellular C00169 CHEBI:58228 MNXM138
+3-phospho-serine [extracellular] C3H6NO6P -2 extracellular C01005 CHEBI:57524 MNXM379
+GMP [extracellular] C10H12N5O8P -2 extracellular C00144 CHEBI:58115 MNXM113
+myo-inositol hexakisphosphate [extracellular] C6H6O24P6 -12 extracellular C01204 CHEBI:58130 MNXM491
+D-glucose 6-phosphate [extracellular] C6H11O9P -2 extracellular C00092 CHEBI:61548 MNXM160
+UMP [extracellular] C9H11N2O9P -2 extracellular C00105 CHEBI:57865 MNXM80
+phosphoenolpyruvate [extracellular] C3H2O6P -3 extracellular C00074 CHEBI:58702 MNXM73
+D-mannose 6-phosphate [extracellular] C6H11O9P -2 extracellular C00275 CHEBI:58735 MNXM427
+O-phosphoethanolamine [extracellular] C2H7NO4P -1 extracellular C00346 CHEBI:58190 MNXM187
+6-phospho-D-gluconate [extracellular] C6H10O10P -3 extracellular C00345 CHEBI:58759 MNXM325
+D-mannose 1-phosphate [extracellular] C6H11O9P -2 extracellular C00636 CHEBI:58409 MNXM721
+diphosphate [extracellular] HO7P2 -3 extracellular C00013 CHEBI:33019 MNXM11
+choline phosphate [extracellular] C5H13NO4P -1 extracellular C00588 CHEBI:295975 MNXM229
+thiosulfate [extracellular] HO3S2 -1 extracellular C00320 CHEBI:33542 MNXM323
+AMP [extracellular] C10H12N5O7P -2 extracellular C00020 CHEBI:456215 MNXM14
+2',3'-cyclic AMP [extracellular] C10H11N5O6P -1 extracellular C02353 CHEBI:60879 MNXM2598
+adenosine 2'-phosphate [extracellular] C10H12N5O7P -2 extracellular C00946 CHEBI:77740 MNXM7028
+CMP [extracellular] C9H12N3O8P -2 extracellular C00055 CHEBI:60377 MNXM31
+D-Glucosamine [extracellular] C6H14NO5 1 extracellular C00329 CHEBI:58723 MNXM533
+2-deoxy-D-ribose [extracellular] C5H10O4 0 extracellular C08347 CHEBI:28816 MNXM2474
+L-citrulline [extracellular] C6H13N3O3 0 extracellular C00327 CHEBI:16349 MNXM211
+glycerone [extracellular] C3H6O3 0 extracellular C00184 CHEBI:16016 MNXM460
+Ala-Leu [extracellular] C9H18N2O3 0 extracellular CHEBI:73770 MNXM15786
+Ala-Leu [cytoplasm] C9H18N2O3 0 cytoplasm CHEBI:73770 MNXM15786
+Ala-Gly [extracellular] C5H10N2O3 0 extracellular CHEBI:73757 MNXM15783
+Ala-Gly [cytoplasm] C5H10N2O3 0 cytoplasm CHEBI:73757 MNXM15783
+N-acetyl-L-glutamate [extracellular] C7H9NO5 -2 extracellular C00624 CHEBI:44337 MNXM730
+N-acetyl-L-glutamate [cytoplasm] C7H9NO5 -2 cytoplasm C00624 CHEBI:44337 MNXM730
+lipoamide [extracellular] C8H15NOS2 0 extracellular C00248 CHEBI:17460 MNXM1024
+lipoamide [cytoplasm] C8H15NOS2 0 cytoplasm C00248 CHEBI:17460 MNXM1024
+L-Methionine S-oxide [extracellular] C5H11NO3S 0 extracellular C02989 CHEBI:17016 MNXM2246
+homogentisate [cytoplasm] C8H7O4 -1 cytoplasm C00544 CHEBI:16169 MNXM345
+4-maleylacetoacetate [cytoplasm] C8H6O6 -2 cytoplasm C01036 CHEBI:17105 MNXM691
+4-fumarylacetoacetate [cytoplasm] C8H6O6 -2 cytoplasm C01061 CHEBI:18034 MNXM708
+L-xylulose [cytoplasm] C5H10O5 0 cytoplasm C00310 CHEBI:17140 MNXM597
+D-arabinitol [cytoplasm] C5H12O5 0 cytoplasm C01904 CHEBI:18333 MNXM1018
diff --git a/ComplementaryData/modelCuration/Biolog_newRxnProp.tsv b/ComplementaryData/modelCuration/Biolog_newRxnProp.tsv
new file mode 100644
index 00000000..931b7c29
--- /dev/null
+++ b/ComplementaryData/modelCuration/Biolog_newRxnProp.tsv
@@ -0,0 +1,156 @@
+rxnID rev GPR rxn_name_seed EC rxnID_kegg Source;reason
+MNXR98598 1 glycerol 2-phosphate(2-) transport bigg:EX_glyc2p_e;glycerol 2-phosphate(2-)_P Source
+MNXR99852 0 Glycerol-2-phosphate phosphohydrolase 3.1.3.19 R01043 rhea:13105;glycerol 2-phosphate(2-)_P Source
+MNXR136678 1 L-Threonine phosphate transport in via proton symport seed:rxn11407;O-phospho-L-threonine_P Source
+MNXR103332 0 acid phosphatase / phosphotransferase 3.1.3.- rhea:30579;O-phospho-L-threonine_P Source
+MNXR118732 0 alkaline phosphatase 3.1.3.- metacyc:RXN-14512;guanosine 2'-monophosphate_P Source
+Guanosine transport via proton symport 1 Guanosine transport via proton symport NA;guanosine 2'-monophosphate_P Source
+MNXR94936 0 Guanosine 3'-phosphate phosphohydrolase 3.1.3.6 R02148 rhea:27862;3'-GMP_P Source
+Guanosine transport via proton symport(for 3'-GMP) 1 Guanosine transport via proton symport(for 3'-GMP) NA;3'-GMP_P Source
+MNXR94822 1 2-Phosphoglycolate transport in/out via proton symport seed:rxn05473;2-phosphoglycolate_P Source
+MNXR102543 0 2-phosphoglycolate phosphohydrolase 3.1.3.18 R01334 rhea:14369;2-phosphoglycolate_P Source
+MNXR118734 0 alkaline phosphatase 3.1.3.- rhea:37251;cysteamine S-phosphate_P Source
+cysteamine S-phosphate transport via proton symport 1 cysteamine S-phosphate transport via proton symport NA;cysteamine S-phosphate_P Source
+MNXR107528 0 Cysteamine:oxygen oxidoreductase 1.13.11.19 R02467 rhea:14409;cysteamine S-phosphate_P Source
+MNXR107116 0 hypotaurine:NAD+ oxidoreductase 1.8.1.3 R01681 rhea:17385;cysteamine S-phosphate_P Source
+MNXR103594 1 2-aminobutanoate:2-oxoglutarate aminotransferase 2.6.1.42 R10991 bigg:RE2034C;2-aminobutanoate_N Source
+2-aminobutyrate transport 1 2-aminobutyrate transport NA;2-aminobutanoate_N Source
+MNXR118730 0 alkaline phosphatase 3.1.3.- rhea:37355;uridine 2'-phosphate_P Source
+MNXR136675 1 Uridine 2'-phosphate transport in via proton symport seed:rxn11403;uridine 2'-phosphate_P Source
+MNXR94932 0 Uridine 3'-monophosphate phosphohydrolase 3.1.3.6 R01877 rhea:27890;3'-UMP_P Source
+MNXR94982 1 3'-UMP transport in via proton symport seed:rxn05480;3'-UMP_P Source
+MNXR137072 1 Gly-Met transport via proton symport seed:rxn12552;Gly-Met_N Source
+MNXR123343 0 dipeptidase 3.4.13.18 rhea:37323;Gly-Met_N Source
+MNXR111061 0 R07420 R07420 seed:rxn05129;N-phosphocreatine_P Source
+N-phosphocreatine transport 1 N-phosphocreatine transport NA;N-phosphocreatine_P Source
+creatinine transport 1 creatinine transport NA;N-phosphocreatine_P Source
+MNXR95943 1 ATP:L-arginine Nomega-phosphotransferase 2.7.3.3 R00554 rhea:22940;N(omega)-phospho-L-arginine_P Source
+MNXR95947 1 L-arginine phosphate transport in/out via proton symport seed:rxn05502;N(omega)-phospho-L-arginine_P Source
+MNXR104998 0 acid phosphatase / phosphotransferase rhea:30863;O(4)-phospho-L-tyrosine_P Source
+MNXR135003 1 Tripolyphosphate transport in via proton symport seed:rxn05717;triphosphate_P Source
+MNXR118731 0 alkaline phosphatase 3.1.3.- rhea:37351;cytidine 2'-phosphate_P Source
+MNXR135010 1 Cytidine- 2'- Monophosphate transport in via proton symport seed:rxn05724;cytidine 2'-phosphate_P Source
+MNXR117327 0 cyclic phosphodiesterase 3.1.4.37 rhea:37239;2',3'-cyclic UMP_P Source
+MNXR136674 1 2',3'-Cyclic UMP transport in via proton symport seed:rxn11402;2',3'-cyclic UMP_P Source
+MNXR123155 0 3-Sulfino-L-alanine 4-carboxy-lyase 3.13.1.- R00863 rhea:28278;3-sulfino-L-alanine_S Source
+MNXR137086 1 3-Sulfino-L-alanine transport via proton antiport seed:rxn12567;3-sulfino-L-alanine_S Source
+MNXR94935 0 adenosine 3'-phosphate phosphohydrolase 3.1.3.6 R01562 rhea:27898;3'-AMP_P Source
+MNXR94857 1 3AMP transport via diffusion (extracellular to periplasm) seed:rxn07973;3'-AMP_P Source
+MNXR130717 0 alpha-glucosidase 3.2.1.20 sabiork:11700;6-O-alpha-D-glucopyranosyl-D-fructofuranose_C Source
+MNXR102339 1 Palatinose transport in via proton symport seed:rxn05629;6-O-alpha-D-glucopyranosyl-D-fructofuranose_C Source
+MNXR103637 1 Amino-Acid N-Acetyltransferase bigg:RE2223M;N-acetyl-L-cysteine_S Source
+MNXR137052 1 Acetylcysteine transport via proton symport seed:rxn12528;N-acetyl-L-cysteine_S Source
+MNXR106345 1 thiosulfate:ferricytochrome-c oxidoreductase 1.8.2.2 R00029;tetrathionate_S Source
+MNXR104796 1 etrathionate transport via diffusion bigg:TETtex;tetrathionate_S Source
+MNXR95065 0 D-Gluconate:NADP+ 5-oxidoreductase 1.1.1.-;1.1.1.69 R01740 rhea:23936;5-dehydro-D-gluconate_C Source
+MNXR95066 1 5-Dehydro-D-gluconate transport via proton symport rhea:28819;5-dehydro-D-gluconate_C Source
+MNXR123344 0 dipeptidase 3.4.13.18 rhea:37267;Ala-Asp_N Source
+MNXR137135 1 ala-L-asp-L transport via proton symport seed:rxn12628;Ala-Asp_N Source
+MNXR117326 0 cyclic phosphodiesterase 3.1.4.37 rhea:41956;cytidine 2'-phosphate_P Source
+MNXR136673 1 2',3'-Cyclic CMP transport in via proton symport seed:rxn11401;2',3'-cyclic CMP_P Source
+MNXR96247 1 beta-glucosidase (methyl-alpha-D-glucoside) 3.2.1.21 seed:rxn09978;methyl alpha-D-glucopyranoside_C Source
+MNXR101464 0 Methanol diffusion rhea:34871;methyl alpha-D-glucopyranoside_C Source
+MNXR137048 1 alpha-Methyl-D-glucoside transport via proton symport seed:rxn12524;methyl alpha-D-glucopyranoside_C Source
+MNXR107830 0 ATP:D-tagatose 6-phosphotransferase 2.7.1.101 seed:rxn02094;D-tagatose_C Source
+R11623 1 D-tagatose 6-phosphate 4-epimerase NA;D-tagatose_C Source
+MNXR104707 1 D-tagatose uptake via diffusion bigg:TAGAT_Dt;D-tagatose_C Source
+MNXR95136 0 Acetoacetate:CoA ligase (AMP-forming) 6.2.1.16 R01357 rhea:16117;acetoacetate_C Source
+MNXR103709 1 N-Acyl-Aliphatic-L-Amino Acid Amidohydrolase 3.5.1.14 bigg:RE2640C;N(alpha)-acetyl-L-methionine_S Source
+MNXR137087 1 Ala-Gln transport via proton symport seed:rxn12568;Ala-Gln_N Source
+MNXR101006_cv 1 L-alanyl-L-glutamate transport in via proton symport rhea:35131;Ala-Glu_N Source
+MNXR101619 0 Maltodextrin glucosidase (maltotriose) 3.2.1.20 seed:rxn05746;alpha-maltotriose_C Source
+Ala-Thr transport via proton symport (cytosol to vacuole) 1 Ala-Thr transport via proton symport NA;Ala-Thr_N Source
+Ala-Thr transport via proton symport (extracellular to cytosol) 1 Ala-Thr transport via proton symport (extracellular to cytosol) NA;Ala-Thr_N Source
+MNXR103069 0 ( YHR201C or YDR452W ) Triphosphate phosphohydrolase 3.6.1.25 R00138 rhea:14157;triphosphate_P Source
+Gly-Asn transport via proton symport (extracellular to cytosol) 1 Gly-Asn transport via proton symport (extracellular to cytosol) NA;Gly-Asn_N Source
+glycerol 1-phosphate transport 1 glycerol 1-phosphate transport NA;glycerol 1-phosphate_P Source
+MNXR103244 1 D-O-Phosphoserine transport in/out via proton symport seed:rxn05639;O-phosphonatooxy-D-serine(2-)_P Source
+MNXR103265 1 D-O-Phosphoserine phosphohydrolase 3.1.3.3 R02853 rhea:24873;O-phosphonatooxy-D-serine(2-)_P Source
+MNXR101006 1 L-alanyl-L-glutamate transport in via proton symport rhea:35131;Ala-Glu_N Source
+MNXR101011 0 L-alanyl-gamma-L-glutamate peptidase 3.4.13.18 rhea:29335;Ala-Glu_N Source
+MNXR106549 1 3-oxalomalate glyoxylate-lyase (oxaloacetate-forming) 4.1.3.13 R00477 rhea:22032;3-oxalomalate(3-)_C Source
+MNXR111236 0 L-cysteate bisulfite-lyase (deaminating) 4.4.1.25 R07634 rhea:13441;L-cysteate_S Source
+MNXR117325 0 cyclic phosphodiesterase 3.1.4.37 rhea:37211;guanosine 2'-monophosphate_P Source
+MNXR118741 0 deoxynucleotide 3'-phosphatase 3.1.3.34 rhea:37247;thymidine 3'-monophosphate_P Source
+MNXR123345 0 cytosol nonspecific dipeptidase 3.4.13.18 rhea:37275;Ala-Gln_N Source
+MNXR123347 0 Cytosol non-specific dipeptidase 3.4.13.18 rhea:37283;Ala-His_N Source
+MNXR123349 0 Cytosol non-specific dipeptidase 3.4.13.18 rhea:37299;Ala-Thr_N Source
+MNXR123350 0 Cytosol non-specific dipeptidase 3.4.13.18 rhea:37307;Gly-Asn_N Source
+MNXR123351 0 Cytosol non-specific dipeptidase 3.4.13.18 rhea:37315;Gly-Gln_N Source
+MNXR124424 1 L-Cysteate transport via proton symport seed:rxn12602;L-cysteate_S Source
+MNXR130716 1 alpha-glucosidase 3.2.1.20 sabiork:11699;turanose_C Source
+MNXR137058 1 2-Hydroxyethanesulfonate transport via proton symport seed:rxn12535;2-hydroxyethane-1-sulfonate_S Source
+MNXR137067 1 3-Oxalomalate transport via proton symport seed:rxn12545;3-oxalomalate(3-)_C Source
+MNXR137072_cv 1 Gly-Met transport via proton symport seed:rxn12552;Gly-Met_N Source
+MNXR137074 1 Gly-Gln transport via proton symport seed:rxn12555;Gly-Gln_N Source
+MNXR137074_cv 1 Gly-Gln transport via proton symport seed:rxn12555;Gly-Gln_N Source
+MNXR137087_cv 1 Ala-Gln transport via proton symport seed:rxn12568;Ala-Gln_N Source
+MNXR137089 1 N-Acetylmethionine transport via proton symport seed:rxn12570;N(alpha)-acetyl-L-methionine_S Source
+MNXR137095 1 Phosphotyrosine transport via proton symport seed:rxn12580;O(4)-phospho-L-tyrosine_P Source
+MNXR137107 1 Ala-His transport via proton symport seed:rxn12594;Ala-His_N Source
+MNXR137107_cv 1 Ala-His transport via proton symport seed:rxn12594;Ala-His_N Source
+MNXR137135_cv 1 ala-L-asp-L transport via proton symport seed:rxn12628;Ala-Asp_N Source
+MNXR99485 0 FMNH2-dependent alkanesulfonate monooxygenase 1.14.14.5 rhea:29715;2-hydroxyethane-1-sulfonate_S Source
+thymidine 3'-monophosphate transport 1 thymidine 3-monophosphate transport NA;thymidine 3'-monophosphate_P Source
+thymidine 5'-monophosphate transport 1 thymidine 5-monophosphate transport NA;thymidine 5'-monophosphate_P Source
+RHEA:11477 0 ( YIL053W or YER062C ) glycerol-1-phosphate phosphohydrolase R08658 NA;glycerol 1-phosphate_P Source
+nucleotide-specific phosphatase (thymidine 5'-monophosphate) 0 nucleotide-specific phosphatase (thymidine 5'-monophosphate) NA;thymidine 5'-monophosphate_P Source
+Gly-Glu transport via proton symport (extracellular to cytosol) 1 Gly-Glu transport via proton symport (extracellular to cytosol) NA;Gly-Glu_N Source
+Gly-Glu transport via proton symport (cytosol to vacuole) 1 Gly-Glu transport via proton symport (cytosol to vacuole) NA;Gly-Glu_N Source
+MNXR123352 0 cytosol nonspecific dipeptidase 3.4.13.18 rhea:36463;Gly-Glu_N Source
+L-methionine transport, vacuoluar 1 L-methionine transport, vacuoluar NA;L-methionine_N Source
+L-threonine transport, vacuoluar 1 L-threonine transport, vacuoluar NA;L-threonine_N Source
+cysteamine exchange 1 cysteamine exchange NA;cysteamine S-phosphate_P Source
+MNXR94721 1 23cGMP transport via diffusion (extracellular to periplasm) seed:rxn07927;2',3'-cyclic GMP_P Source
+MNXR94824 1 D-Glycerate 2-phosphate transport in/out via proton symport seed:rxn05474;2-phospho-D-glyceric acid_P Source
+MNXR94973 1 3-Phospho-D-glycerate transport in/out via proton symport seed:rxn05479;3-phosphonato-D-glycerate(3-)_P Source
+MNXR99849 1 D-glucose 1-phosphate transport via diffusion seed:rxn08545;D-glucose 1-phosphate_P Source
+MNXR96488 1 carbamoyl phosphate nuclear transport via diffusion seed:rxn09823;carbamoyl phosphate_P Source
+Met-Ala transport via proton symport (extracellular to cytosol) 1 Met-Ala transport via proton symport (extracellular to cytosol) NA;Met-Ala_N Source
+Met-Ala transport via proton symport (cytosol to vacuole) 1 Met-Ala transport via proton symport (cytosol to vacuole) NA;Met-Ala_N Source
+MNXR103245 1 O-Phospho-L-serine transport in via proton symport seed:rxn05640;3-phospho-serine_P Source
+MNXR100385 1 GMP transport via proton symport seed:rxn05471;GMP_P Source
+MNXR101585 1 myo-inositol phosphate transport via diffusion (extracellular to periplasm) seed:rxn08925;myo-inositol hexakisphosphate_P Source
+MNXR98531 1 D-glucose 6-phosphate transport bigg:EX_g6p_e;D-glucose 6-phosphate_P Source
+MNXR105127 1 UMP transport rhea:27926;UMP_P Source
+MNXR102493 1 Phosphoenolpyruvate transport in via proton symport seed:rxn05630;phosphoenolpyruvate_P Source
+MNXR101385 1 Mannose 6-phosphate transport via diffusion (extracellular to periplasm) seed:rxn08880;D-mannose 6-phosphate_P Source
+MNXR135002 1 O-Phosphoryl-Ethanolamine transport in via proton symport seed:rxn05716;O-phosphoethanolamine_P Source
+MNXR95102 1 6-Phospho-D-gluconate transport in/out via proton symport seed:rxn05482;6-phospho-D-gluconate_P Source
+MNXR101377 1 MAN1P transport in/out via proton symport seed:rxn05609;D-mannose 1-phosphate_P Source
+MNXR136667 1 Pyrophosphate transport in via proton symport seed:rxn11395;diphosphate_P Source
+MNXR96703 1 Choline phosphate intracellular transport bigg:CHOLPtg;choline phosphate_P Source
+MNXR104966 1 thiosulfate transport rhea:32807;thiosulfate_S Source
+MNXR95831 1 AMP transport in/out via proton symport seed:rxn05497;AMP_P Source
+MNXR94718 1 23cAMP transport via diffusion (extracellular to periplasm) seed:rxn07925;2',3'-cyclic AMP_P Source
+MNXR135007 1 Adenosine- 2'-Monophosphate transport in via proton symport seed:rxn05721;CMP_P Source
+MNXR96805 1 CMP transport in/out via proton symport seed:rxn05525;CMP_P Source
+MNXR100035 1 D-glucosamine transport via diffusion (extracellular to periplasm) seed:rxn08593;D-Glucosamine_C Source
+2-deoxy-D-ribose transport 1 2-deoxy-D-ribose transport NA;2-deoxy-D-ribose_C Source
+MNXR96737 1 L-Citrulline transport in via proton symport seed:rxn05674;L-citrulline_N Source
+MNXR97367 1 Dihydroxyacetone transport via facilitated diffusion seed:rxn05532;glycerone_C Source
+Ala-Leu transport via proton symport (extracellular to cytosol) 1 Ala-Leu transport via proton symport (extracellular to cytosol) NA;Ala-Leu_N Source
+Ala-Leu transport via proton symport (cytosol to vacuole) 1 Ala-Leu transport via proton symport (cytosol to vacuole) NA;Ala-Leu_N Source
+MNXR137133 1 L-alanylglycine transport via proton antiport seed:rxn12625;Ala-Gly_N Source
+MNXR137133_cv 1 L-alanylglycine transport via proton antiport seed:rxn12625;Ala-Gly_N Source
+N-acetyl-L-glutamate transport 1 N-acetyl-L-glutamate transport NA;N-acetyl-L-glutamate_N Source
+N-acetyl-L-glutamate transport, mitochondrion 1 N-acetyl-L-glutamate transport NA;N-acetyl-L-glutamate_N Source
+MNXR137094 1 Lipoamide transport via proton symport seed:rxn12577;lipoamide_S Source
+MNXR101483 1 L-methionine S-oxide transport via diffusion (extracellular) seed:rxn08915;L-Methionine S-oxide_S Source
+Gly-Asn transport via proton symport (cytosol to vacuole) 1 Gly-Asn transport via proton symport NA;Gly-Asn_N Source
+MNXR137130 1 Cysteamine transport via proton antiport seed:rxn12622;cysteamine S-phosphate_P Source
+Hydrogen sulfide oxidation 0 Hydrogen sulfide oxidation NA;general sulfur metabolism_S Source
+MNXR95704 1 L-alanine transport in via proton symport rhea:29443;L-alanine_N Source
+MNXR100368 1 Glycine transport (vacuole) rhea:28899;L-glycine_N Source
+MNXR104382 1 ( YJR130C or YLL058W or YML082W ) O4-succinyl-L-homoserine:hydrogen sulfide S-(3-amino-3-carboxypropyl)transferase; O-succinyl-L-homoserine succinate-lyase (adding hydrogen sulfide) 2.5.1.-;2.5.1.48 R01288 rhea:27826;L-methionine_N Source
+MNXR94843 0 4-Hydroxyphenylpyruvate:oxygen oxidoreductase (hydroxylating,decarboxylating) 1.13.11.27 R02521 rhea:16189;L-tyrosine_N Source
+MNXR100628 0 Homogentisate:oxygen 1,2-oxidoreductase (decyclizing) 1.13.11.5 R02519 rhea:15449;L-tyrosine_N Source
+MNXR101325 0 4-Maleylacetoacetate cis-trans-isomerase 5.2.1.2 R03181 rhea:14817;L-tyrosine_N Source
+MNXR99706 0 4-fumarylacetoacetate fumarylhydrolase 3.7.1.2 R01364 rhea:10244;L-tyrosine_N Source
+MNXR95187 0 L-arabinitol:NAD+ 4-oxidoreductase (L-xylulose-forming) 1.1.1.12 R01903 rhea:16381;D-arabinose_C Source
+MNXR105265 1 Xylitol:NADP+ 4-oxidoreductase (L-xylulose-forming) 1.1.1.10 R01904 rhea:17025;D-arabinose_C Source
+arabinose reductase (D-arabinose) 0 arabinose reductase (D-arabinose) NA;D-arabinose_C Source
+MNXR95188 0 D-arabinitol:NAT 4-oxidoreductase 1.1.1.11 R05604 rhea:17921;D-arabinose_C Source
+MNXR95208 1 Acetoacetate transport via diffusion rhea:29751;acetoacetate_C Source
+MNXR98748 1 methanol exchange bigg:EX_meoh_e;methyl alpha-D-glucopyranoside_C Source
+MNXR118733 0 alkaline phosphatase 3.1.3.- rhea:37343;adenosine 2'-phosphate_P Source
diff --git a/ComplementaryScripts/modelCuration/SubstrateUsage.m b/ComplementaryScripts/modelCuration/SubstrateUsage.m
new file mode 100644
index 00000000..f373a820
--- /dev/null
+++ b/ComplementaryScripts/modelCuration/SubstrateUsage.m
@@ -0,0 +1,153 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% SubstrateUsage
+%
+% Automatically adds exchange reactions for every metabolite in
+% ComplementaryData/modelCuration/Biolog_substrate.tsv and checks whether
+% it can be used as a "solo" substrate.
+%
+% NOTE: requires COBRA
+%
+% Feiran Li 2018-08-25
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+% Load model:
+cd ..
+model = loadYeastModel;
+
+% Load data:
+fid2 = fopen('../ComplementaryData/modelCuration/Biolog_substrate.tsv');
+substrate = textscan(fid2,'%s %s %s %s %s %s','Delimiter','\t','HeaderLines',1);
+SubBiologName = substrate{1};
+SubModelName = substrate{2};
+Subtype = substrate{3};
+BiologUsage = substrate{4};
+fclose(fid2);
+
+% Main loop:
+cd otherChanges
+ExchRxn = '';
+TransRxn = '';
+GapfillMets = '';
+TransEotherfillMets = '';
+TransECfillMets = '';
+FBAresult = '';
+for i = 1:length(SubBiologName)
+ newModel = model;
+ if ~isequal(SubModelName{i},'')
+ metE = strcat(SubModelName{i},' [extracellular]');
+ metC = strcat(SubModelName{i},' [cytoplasm]');
+ [~,metEOrd] = ismember(metE,newModel.metNames);
+ [~,metCOrd] = ismember(metC,newModel.metNames);
+ %check whther exchange reaction for this met exists
+ duplicateE = find(sum(newModel.S ~= 0, 1) == 1 & any(newModel.S == -1, 1) & any(newModel.S(metEOrd(metEOrd~=0), :), 1));
+ if ~isempty(duplicateE)
+ warning(['Model already has the same exchange reaction you tried to add: ', newModel.rxns{duplicateE}]);
+ ExchRxn = newModel.rxns{duplicateE};
+ ExchLB = newModel.lb(duplicateE);
+ else
+ if metEOrd == 0
+ newID = getNewIndex(newModel.mets);
+ metE_ID = strcat('s_',newID,'[e]');
+ newModel = addMetabolite(newModel,metE_ID,'metName',metE);
+ [~,metEOrd] = ismember(metE,newModel.metNames);
+ end
+ %adding exchange rxn for this metE
+ newID = getNewIndex(newModel.rxns);
+ ExchRxn = ['r_' newID];
+ ExchLB = 0;
+ end
+ metE_ID = newModel.mets{metEOrd};
+ [newModel,rxnIDexists] = addReaction(newModel,ExchRxn, ...
+ 'reactionName', [SubModelName{i}, ' exchange'], ...
+ 'metaboliteList', cellstr(metE_ID), 'stoichCoeffList', -1, ...
+ 'lowerBound', ExchLB, 'upperBound', 1000, 'subSystem', '', ...
+ 'checkDuplicate', false);
+ newModel = rmfield(newModel,'grRules');
+
+ % Fix confidence score:
+ SubRxnIndex = findRxnIDs(newModel,ExchRxn);
+ newModel.rxnConfidenceScores(SubRxnIndex) = NaN; %exchange rxns
+
+ % Change media:
+ newModel_test = newModel;
+ exchangeRxns = findExcRxns(newModel_test);
+ newModel_test.lb(exchangeRxns) = 0;
+ newModel_test.ub(exchangeRxns) = 1000;
+ commonExchanges = {...
+ 'r_1992'; ... % oxygen exchange
+ 'r_1861'; ... % iron exchange
+ 'r_1832'; ... % hydrogen exchange
+ };
+ glcExchange = {'r_1714'}; % D-glucose exchange
+ amoExchange = {'r_1654'}; % ammonium exchange
+ phoExchange = {'r_2005'}; % phosphate exchange
+ sulExchange = {'r_2060'}; % phosphate exchange
+ uptakeRxnIndexes = findRxnIDs(newModel_test,commonExchanges);
+ amoExchangeIndex = findRxnIDs(newModel_test,amoExchange);
+ phoExchangeIndex = findRxnIDs(newModel_test,phoExchange);
+ glcExchangeIndex = findRxnIDs(newModel_test,glcExchange);
+ sulExchangeIndex = findRxnIDs(newModel_test,sulExchange);
+ if length(uptakeRxnIndexes) ~= 3
+ error('Not all exchange reactions were found.')
+ end
+ newModel_test.lb(uptakeRxnIndexes) = -1000;
+ newModel_test.lb(glcExchangeIndex) = -10;
+ newModel_test.lb(amoExchangeIndex) = -1000;
+ newModel_test.lb(phoExchangeIndex) = -1000;
+ newModel_test.lb(sulExchangeIndex) = -1000;
+ if Subtype{i} == 'C'
+ newModel_test.lb(glcExchangeIndex) = 0;
+ elseif Subtype{i} == 'N'
+ newModel_test.lb(amoExchangeIndex) = 0;
+ elseif Subtype{i} == 'P'
+ newModel_test.lb(phoExchangeIndex) = 0;
+ elseif Subtype{i} == 'S'
+ newModel_test.lb(sulExchangeIndex) = 0;
+ end
+ newModel_test.lb(SubRxnIndex) = -10;
+
+ % Simulate model:
+ sol = optimizeCbModel(newModel_test);
+ if sol.obj > 0.000001
+ model = newModel;
+ fprintf(metE,'can be used as solo substrate\n');
+ FBAresult = [FBAresult;SubBiologName(i,1),SubModelName(i,1),Subtype(i,1),BiologUsage(i,1),'G'];
+ else
+ FBAresult = [FBAresult;SubBiologName(i,1),SubModelName(i,1),Subtype(i,1),BiologUsage(i,1),'NG'];
+ if strcmp(BiologUsage(i,1),'G')
+ fprintf(metE,'cannot be used as solo substrate, pathways need to be manually checked\n');
+ if numel(find(newModel_test.S(metEOrd,:))) < 2 && metCOrd~=0 %metE appear only once without metC
+ warning(['Transport reaction should be added for:', newModel_test.metNames{metEOrd}])
+ TransECfillMets = [TransECfillMets;newModel_test.metNames(metEOrd)];
+ elseif numel(find(newModel_test.S(metEOrd,:))) < 2 && metCOrd ==0 %metE appear only once without metC
+ S = regexp(newModel_test.metNames{metEOrd}, ' [', 'split');
+ met_temp = char(S(1));
+ metEMapping = find(strncmp(met_temp,model.metNames,length(met_temp)));
+ if isempty(metEMapping)
+ warning(['mets only appear once, fill the gap for mets:', newModel_test.metNames{metEOrd}])
+ GapfillMets = [GapfillMets;newModel_test.metNames(metEOrd)];
+ else
+ TransEotherfillMets = [TransEotherfillMets;newModel_test.metNames(metEOrd);model.metNames(metEMapping)];
+ end
+ end
+ end
+ end
+ else
+ FBAresult = [FBAresult;SubBiologName(i,1),SubModelName(i,1),Subtype(i,1),BiologUsage(i,1),'NG'];
+ end
+end
+
+% Update results from model:
+cd ..
+fid2 = fopen('../ComplementaryData/modelCuration/Biolog_substrate.tsv','w');
+formatSpec = '%s\t%s\t%s\t%s\t%s\n';
+fprintf(fid2,formatSpec,'Substrate','Name_in_Model','Substrate_type','Growth_Biolog','Growth_Model');
+for i = 1:length(FBAresult)
+ fprintf(fid2,formatSpec,char(FBAresult(i,1)),char(FBAresult(i,2)),char(FBAresult(i,3)),char(FBAresult(i,4)),char(FBAresult(i,5)));
+end
+
+% Save model:
+saveYeastModel(model)
+cd modelCuration
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
diff --git a/ComplementaryScripts/modelCuration/addBiologRxnToGEM.m b/ComplementaryScripts/modelCuration/addBiologRxnToGEM.m
new file mode 100644
index 00000000..185ff13f
--- /dev/null
+++ b/ComplementaryScripts/modelCuration/addBiologRxnToGEM.m
@@ -0,0 +1,151 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% addBiologRxnToGEM
+% Adds rxns and metabolites based on Biolog results, see
+% Biolog_substrate_type.tsv for substrates that can be utilized.
+% Input: model, Biolog_substrate_type.tsv, Biolog_newRxnProp.tsv,
+% Biolog_newRxnMet.tsv.
+%
+% NOTE: changeGeneAssociation.m is a function from COBRA
+%
+% Feiran Li 2018-08-25
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+% Load model:
+cd ..
+model = loadYeastModel;
+
+% Load stoichiometry data:
+fid = fopen('../ComplementaryData/modelCuration/Biolog_newRxnMatrix.tsv');
+newreaction = textscan(fid,'%s %s %s %s %s','Delimiter','\t','HeaderLines',1);
+matrix.rxnIDs = newreaction{1};
+matrix.metcoef = cellfun(@str2num, newreaction{2});
+matrix.metIDs = newreaction{3};
+matrix.mettype = newreaction{4};
+matrix.metcompartments = newreaction{5};
+fclose(fid);
+
+% Load rxn properties data:
+fid = fopen('../ComplementaryData/modelCuration/Biolog_newRxnProp.tsv','r');
+rev = textscan(fid,'%s %s %s %s %s %s %s','Delimiter','\t','HeaderLines',1);
+newrxn.ID = rev{1};
+newrxn.Rev = cellfun(@str2num, rev{2});
+newrxn.GPR = rev{3};
+newrxn.rxnNames = rev{4};
+newrxn.rxnECNumbers = rev{5};
+newrxn.rxnKEGGID = rev{6};
+newrxn.rxnNotes = rev{7};
+newrxn.rxnMetaNetXID = newrxn.ID;
+for i = 1:length(newrxn.rxnMetaNetXID)
+ if ~startsWith(newrxn.rxnMetaNetXID{i},'MNXR')
+ newrxn.rxnMetaNetXID{i} = '';
+ end
+end
+newrxn.rxnMetaNetXID = regexprep(newrxn.rxnMetaNetXID,'_cv','');
+fclose(fid);
+
+% Change coefficients for reactants:
+for i=1:length(matrix.rxnIDs)
+ if strcmp(matrix.mettype(i),'reactant')
+ matrix.metcoef(i) = matrix.metcoef(i)*-1;
+ end
+end
+
+% Change compartments:
+CONValldata = cat(2,model.compNames,model.comps);
+lbracket = ' [' ;
+llbracket = '[';
+rbrackets = ']';
+space = ' ';
+[m, n] = size(CONValldata);
+for i = 1:m
+ aa = CONValldata(i,1);
+ aa = char(aa);
+ for j=1:length(matrix.rxnIDs)
+ bb = matrix.metcompartments(j,1);
+ bb = char(bb);
+ if strcmp(bb,aa)
+ matrix.Newcomps(j,1) = CONValldata(i,2);
+ end
+ end
+end
+for i=1:length(matrix.rxnIDs)
+ matrix.metnames(i) = strcat(matrix.metIDs(i),lbracket,matrix.metcompartments(i),rbrackets);
+ matrix.Newcomps(i) = strcat(llbracket,matrix.Newcomps(i),rbrackets);
+end
+
+% Map mets to model.metnames, get s_index for new mets:
+cd otherChanges
+for j = 1:length(matrix.metnames)
+ [~,metindex] = ismember(matrix.metnames(j),model.metNames);
+ if metindex ~= 0
+ matrix.mets(j) = model.mets(metindex);
+ elseif metindex == 0
+ newID = getNewIndex(model.mets);
+ matrix.mets(j) = strcat('s_',newID,matrix.Newcomps(j));
+ model = addMetabolite(model,char(matrix.mets(j)), ...
+ 'metName',matrix.metnames(j));
+ end
+end
+
+% Add metabolite data:
+fid = fopen('../../ComplementaryData/modelCuration/Biolog_newRxnMetAnnotation.tsv');
+newmet_annot = textscan(fid,'%s %s %s %s %s %s %s','Delimiter','\t','HeaderLines',1);
+newmet.metNames = newmet_annot{1};
+newmet.metFormulas = newmet_annot{2};
+newmet.metCharges = cellfun(@str2num, newmet_annot{3});
+newmet.metKEGGID = newmet_annot{5};
+newmet.metChEBIID = newmet_annot{6};
+newmet.metMetaNetXID = newmet_annot{7};
+
+fclose(fid);
+for i = 1:length(newmet.metNames)
+ [~,metID] = ismember(newmet.metNames(i),model.metNames);
+ if metID ~= 0
+ model.metFormulas{metID} = newmet.metFormulas{i};
+ model.metCharges(metID) = newmet.metCharges(i);
+ model.metKEGGID{metID} = newmet.metKEGGID{i};
+ model.metChEBIID{metID} = newmet.metChEBIID{i};
+ model.metMetaNetXID{metID} = newmet.metMetaNetXID{i};
+ model.metNotes{metID} = '';
+ end
+end
+
+% Add new reactions according to rev ID: Met Coef needs to be a column, not
+% a row. Coef should be a double, which was converted at the import section
+EnergyResults = {};
+MassChargeresults = {};
+RedoxResults = {};
+if ~isfield(model,'rxnMetaNetXID')
+ model.rxnMetaNetXID = cell(size(model.rxns));
+end
+for i = 1:length(newrxn.ID)
+ newID = getNewIndex(model.rxns);
+ j = find(strcmp(matrix.rxnIDs,newrxn.ID{i}));
+ Met = matrix.mets(j);
+ Coef = transpose(matrix.metcoef(j));
+ [model,rxnIndex] = addReaction(model, ['r_' newID],...
+ 'reactionName', newrxn.ID{i},...
+ 'metaboliteList',Met,...
+ 'stoichCoeffList',Coef,...
+ 'reversible',newrxn.Rev(i,1),...
+ 'geneRule',newrxn.GPR{i},...
+ 'checkDuplicate',1);
+ [EnergyResults,RedoxResults] = CheckEnergyProduction(model,{['r_' newID]},EnergyResults,RedoxResults);
+ [MassChargeresults] = CheckBalanceforSce(model,{['r_' newID]},MassChargeresults);
+ if isempty(rxnIndex)
+ rxnIndex = strcmp(model.rxns,['r_' newID]);
+ end
+ % Add rxn annotation:
+ model.rxnNames{rxnIndex} = newrxn.rxnNames{i};
+ model.rxnECNumbers(rxnIndex) = newrxn.rxnECNumbers(i);
+ model.rxnKEGGID(rxnIndex) = newrxn.rxnKEGGID(i);
+ model.rxnMetaNetXID(rxnIndex) = newrxn.rxnMetaNetXID(i);
+ model.rxnConfidenceScores(rxnIndex) = 1; %reactions without gene but needed for modelling
+end
+
+% Save model:
+cd ..
+saveYeastModel(model)
+cd modelCuration
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
diff --git a/ComplementaryScripts/modelCuration/minimal_Y6.m b/ComplementaryScripts/modelCuration/minimal_Y6.m
index 75150349..1a226b66 100755
--- a/ComplementaryScripts/modelCuration/minimal_Y6.m
+++ b/ComplementaryScripts/modelCuration/minimal_Y6.m
@@ -1,30 +1,45 @@
function model = minimal_Y6(model)
% change Y6 model media to minimal - ammonium, glucose, oxygen,
% phosphate, sulphate
+% Bicarbonate production is blocked to get rid of conflict due to bicarbonate and carbon dioxide
+% are regarded as equivalent
% the function is from:https://doi.org/10.1371/journal.pcbi.1004530
% start with a clean slate: set all exchange reactions to upper bound = 1000
% and lower bound = 0 (ie, unconstrained excretion, no uptake)
+
+%Feiran Li 2018.09.05
+
exchangeRxns = findExcRxns(model);
model.lb(exchangeRxns) = 0;
model.ub(exchangeRxns) = 1000;
-desiredExchanges = {'r_1654'; ... % 'ammonium exchange';
- 'r_1992'; ... % 'oxygen exchange';
- 'r_2005'; ... % 'phosphate exchange';
- 'r_2060'; ... % 'sulphate exchange';
- 'r_1861'; ... % iron for test of expanded biomass def;
- 'r_1832'}; % hydrogen exchange;
-
-glucoseExchange = {'r_1714'}; % D-glucose exchange'
-
-uptakeRxnIndexes = findRxnIDs(model,desiredExchanges);
+
+desiredExchanges = {'r_1654'; ... % ammonium exchange
+ 'r_1992'; ... % oxygen exchange
+ 'r_2005'; ... % phosphate exchange
+ 'r_2060'; ... % sulphate exchange
+ 'r_1861'; ... % iron exchange, for test of expanded biomass def
+ 'r_1832'; ... % hydrogen exchange
+ 'r_2100'}; % water exchange
+
+blockedExchanges = {'r_1663'; ... % bicarbonate exchange
+ 'r_4062'; ... % lipid backbone exchange
+ 'r_4064'}; % lipid chain exchange
+
+glucoseExchange = {'r_1714'}; % D-glucose exchange
+
+uptakeRxnIndexes = findRxnIDs(model,desiredExchanges);
glucoseExchangeIndex = findRxnIDs(model,glucoseExchange);
+BlockedRxnIndex = findRxnIDs(model,blockedExchanges);
-if length(uptakeRxnIndexes) ~= 6 %5;
+if length(uptakeRxnIndexes) ~= 7
error('Not all exchange reactions were found.')
end
-model.lb(uptakeRxnIndexes)=-1000;
-model.lb(glucoseExchangeIndex)=-10;
+model.lb(uptakeRxnIndexes) = -1000;
+model.lb(glucoseExchangeIndex) = -1;
+
+model.lb(BlockedRxnIndex) = 0;
+model.ub(BlockedRxnIndex) = 0;
end
diff --git a/ComplementaryScripts/saveYeastModel.m b/ComplementaryScripts/saveYeastModel.m
index 6c7f121c..c872e2cc 100644
--- a/ComplementaryScripts/saveYeastModel.m
+++ b/ComplementaryScripts/saveYeastModel.m
@@ -3,7 +3,11 @@
% Saves model as a .xml, .txt and .yml file. Also updates complementary
% files (boundaryMets.txt, README.md and dependencies.txt).
%
-% Benjamín J. Sánchez
+% model model structure to save (note: must be in COBRA format)
+% upDATE logical =true if updating the date in the README file is needed
+% (opt, default true)
+%
+% Benjamin J. Sanchez
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function saveYeastModel(model,upDATE)
@@ -12,14 +16,21 @@ function saveYeastModel(model,upDATE)
upDATE = true;
end
-%Remove any space in rxnECNumbers:
-model.rxnECNumbers = strrep(model.rxnECNumbers,' ','');
-
%Get and change to the script folder, as all folders are relative to this
%folder
scriptFolder = fileparts(which(mfilename));
currentDir = cd(scriptFolder);
+%Set minimal media
+cd modelCuration
+model = minimal_Y6(model);
+cd ..
+
+%Delete model.grRules (redundant and possibly conflicting with model.rules):
+if isfield(model,'grRules')
+ model = rmfield(model,'grRules');
+end
+
%Update SBO terms in model:
cd missingFields
model = addSBOterms(model);
diff --git a/ModelFiles/boundaryMets.txt b/ModelFiles/boundaryMets.txt
index e1ac8e68..4c031f7b 100644
--- a/ModelFiles/boundaryMets.txt
+++ b/ModelFiles/boundaryMets.txt
@@ -166,3 +166,75 @@ s_3715[e] raffinose [extracellular]
s_3716[e] melibiose [extracellular]
s_3746[c] lipid backbone [cytoplasm]
s_3747[c] lipid chain [cytoplasm]
+s_4074[e] cysteamine [extracellular]
+s_4124[e] methanol [extracellular]
+s_4170[e] Ala-Gly [extracellular]
+s_4137[e] 3-oxalomalate(3-) [extracellular]
+s_4109[e] 6-O-alpha-D-glucopyranosyl-D-fructofuranose [extracellular]
+s_4118[e] 5-dehydro-D-gluconate [extracellular]
+s_4130[e] D-tagatose [extracellular]
+s_4131[e] turanose [extracellular]
+s_4150[e] D-glucose 6-phosphate [extracellular]
+s_4140[e] alpha-maltotriose [extracellular]
+s_4145[e] D-glucose 1-phosphate [extracellular]
+s_4125[e] methyl alpha-D-glucopyranoside [extracellular]
+s_4164[e] D-Glucosamine [extracellular]
+s_4167[e] glycerone [extracellular]
+s_4034[e] Ala-Gln [extracellular]
+s_4168[e] Ala-Leu [extracellular]
+s_4056[e] Gly-Gln [extracellular]
+s_4050[e] Ala-His [extracellular]
+s_4053[e] Gly-Asn [extracellular]
+s_4037[e] Ala-Glu [extracellular]
+s_4085[e] Gly-Met [extracellular]
+s_4119[e] Ala-Asp [extracellular]
+s_4059[e] Gly-Glu [extracellular]
+s_4040[e] Ala-Thr [extracellular]
+s_4143[e] Met-Ala [extracellular]
+s_4166[e] L-citrulline [extracellular]
+s_4080[e] 2-aminobutanoate [extracellular]
+s_4158[e] choline phosphate [extracellular]
+s_4049[e] glycerol 1-phosphate [extracellular]
+s_4141[e] 2-phospho-D-glyceric acid [extracellular]
+s_4148[e] GMP [extracellular]
+s_4147[e] 3-phospho-serine [extracellular]
+s_4078[e] O-phosphonatooxy-D-serine(2-) [extracellular]
+s_4157[e] diphosphate [extracellular]
+s_4099[e] triphosphate [extracellular]
+s_4152[e] phosphoenolpyruvate [extracellular]
+s_4093[e] N(omega)-phospho-L-arginine [extracellular]
+s_4146[e] carbamoyl phosphate [extracellular]
+s_4154[e] O-phosphoethanolamine [extracellular]
+s_4075[e] cysteamine S-phosphate [extracellular]
+s_4067[e] guanosine 2'-monophosphate [extracellular]
+s_4063[e] glycerol 2-phosphate(2-) [extracellular]
+s_4069[e] 3'-GMP [extracellular]
+s_4070[e] 2-phosphoglycolate [extracellular]
+s_4155[e] 6-phospho-D-gluconate [extracellular]
+s_4153[e] D-mannose 6-phosphate [extracellular]
+s_4095[e] 2',3'-cyclic GMP [extracellular]
+s_4097[e] O(4)-phospho-L-tyrosine [extracellular]
+s_4065[e] O-phospho-L-threonine [extracellular]
+s_4142[e] 3-phosphonato-D-glycerate(3-) [extracellular]
+s_4162[e] adenosine 2'-phosphate [extracellular]
+s_4107[e] 3'-AMP [extracellular]
+s_4161[e] 2',3'-cyclic AMP [extracellular]
+s_4156[e] D-mannose 1-phosphate [extracellular]
+s_4160[e] AMP [extracellular]
+s_4135[e] N(alpha)-acetyl-L-methionine [extracellular]
+s_4176[e] L-Methionine S-oxide [extracellular]
+s_4105[e] 3-sulfino-L-alanine [extracellular]
+s_4111[e] N-acetyl-L-cysteine [extracellular]
+s_4139[e] L-cysteate [extracellular]
+s_4116[e] 2-hydroxyethane-1-sulfonate [extracellular]
+s_4133[e] acetoacetate [extracellular]
+s_4172[e] N-acetyl-L-glutamate [extracellular]
+s_4151[e] UMP [extracellular]
+s_4163[e] CMP [extracellular]
+s_4047[e] thymidine 5'-monophosphate [extracellular]
+s_4045[e] thymidine 3'-monophosphate [extracellular]
+s_4101[e] cytidine 2'-phosphate [extracellular]
+s_4082[e] uridine 2'-phosphate [extracellular]
+s_4084[e] 3'-UMP [extracellular]
+s_4127[e] 2',3'-cyclic CMP [extracellular]
+s_4103[e] 2',3'-cyclic UMP [extracellular]
diff --git a/ModelFiles/dependencies.txt b/ModelFiles/dependencies.txt
index 92ff2a9b..341091c9 100644
--- a/ModelFiles/dependencies.txt
+++ b/ModelFiles/dependencies.txt
@@ -1,7 +1,7 @@
MATLAB 9.4.0.813654 (R2018a)
libSBML 5.17.0
-RAVEN_toolbox 2.0.0
-COBRA_toolbox commit 6a4b12e
+RAVEN_toolbox 2.0.2
+COBRA_toolbox commit 75d530c
SBML_level 3
SBML_version 1
fbc_version 2
diff --git a/ModelFiles/txt/yeastGEM.txt b/ModelFiles/txt/yeastGEM.txt
index 54463b54..70ebd3a2 100644
--- a/ModelFiles/txt/yeastGEM.txt
+++ b/ModelFiles/txt/yeastGEM.txt
@@ -83,8 +83,8 @@ r_0099 s_0376[m] + s_1845[m] <=> s_0372[m] + s_0532[m] YKL192C -1000.00 1000.0
r_0100 s_0250[p] + s_0534[p] -> s_0378[p] + s_1305[p] YIL160C 0.00 1000.00 0.00
r_0101 s_0243[p] + s_0534[p] -> s_0378[p] + s_1482[p] YIL160C 0.00 1000.00 0.00
r_0102 s_0253[p] + s_0534[p] -> s_0378[p] + s_1179[p] YIL160C 0.00 1000.00 0.00
-r_0103 2 s_0373[c] -> s_0367[c] + s_0529[c] YPL028W 0.00 1000.00 0.00
-r_0104 2 s_0376[m] -> s_0370[m] + s_0532[m] YPL028W 0.00 1000.00 0.00
+r_0103 2 s_0373[c] <=> s_0367[c] + s_0529[c] YPL028W -1000.00 1000.00 0.00
+r_0104 2 s_0376[m] <=> s_0370[m] + s_0532[m] YPL028W -1000.00 1000.00 0.00
r_0105 s_0257[p] + s_0534[p] -> s_0378[p] + s_1076[p] YIL160C 0.00 1000.00 0.00
r_0106 s_0239[p] + s_0534[p] -> s_0378[p] + s_1258[p] YIL160C 0.00 1000.00 0.00
r_0107 s_0247[p] + s_0534[p] -> s_0378[p] + s_0605[p] YIL160C 0.00 1000.00 0.00
@@ -609,7 +609,7 @@ r_0757 s_0126[c] + s_0803[c] -> s_1153[c] + s_1322[c] ( YDR287W or YHR046C )
r_0758 s_0568[c] -> s_0126[c] YJL153C 0.00 1000.00 0.00
r_0759 s_0799[m] + s_1191[m] + s_1214[m] -> s_0145[m] + s_1210[m] + s_1326[m] YER069W 0.00 1000.00 0.00
r_0760 s_0373[c] + s_0412[c] <=> s_0529[c] + s_0794[c] + s_1190[c] YFL017C -1000.00 1000.00 0.00
-r_0761 s_0376[m] + s_0993[m] -> s_0532[m] + s_0799[m] + s_1192[m] ( YJL071W or YMR062C ) 0.00 1000.00 0.00
+r_0761 s_0376[m] + s_0993[m] <=> s_0532[m] + s_0799[m] + s_1192[m] ( YJL071W or YMR062C ) -1000.00 1000.00 0.00
r_0762 s_0803[c] + s_1195[c] -> s_0722[c] + s_0794[c] + s_1020[c] YDR428C 0.00 1000.00 0.00
r_0763 s_0794[c] + 2 s_1196[c] + s_1212[c] -> s_1185[c] + s_1207[c] ( YDR402C and YDR403W ) 0.00 1000.00 0.00
r_0764 s_0809[p] + s_1202[p] -> s_0426[p] + 2 s_0801[p] + s_1228[p] YGL067W 0.00 1000.00 0.00
@@ -2540,7 +2540,7 @@ r_1658 s_0969[c] -> s_0971[m] 0.00 1000.00 0.00
r_1659 s_0973[c] + s_0995[p] <=> s_0976[p] + s_0991[c] -1000.00 1000.00 0.00
r_1660 s_0434[c] <=> s_0438[n] -1000.00 1000.00 0.00
r_1661 s_0434[c] <=> s_0435[er] -1000.00 1000.00 0.00
-r_1663 s_0446[e] -> 0.00 1000.00 0.00
+r_1663 s_0446[e] -> 0.00 0.00 0.00
r_1664 s_0460[m] + s_0807[m] <=> s_0447[m] + s_0799[m] -1000.00 1000.00 0.00
r_1665 s_0461[n] + s_0808[n] <=> s_0448[n] + s_0800[n] -1000.00 1000.00 0.00
r_1667 s_0456[c] + s_0803[c] <=> s_0445[c] + s_0794[c] YNL036W -1000.00 1000.00 0.00
@@ -2829,7 +2829,7 @@ r_2003 s_1318[c] <=> s_1320[m] -1000.00 1000.00 0.00
r_2004 s_1032[c] -> s_1034[m] 0.00 1000.00 0.00
r_2005 s_1324[e] <=> -1000.00 1000.00 0.00
r_2008 s_1322[c] <=> s_1329[v] -1000.00 1000.00 0.00
-r_2020 s_1374[e] <=> -1000.00 1000.00 0.00
+r_2020 s_1374[e] -> 0.00 1000.00 0.00
r_2022 s_1384[c] <=> s_1385[m] -1000.00 1000.00 0.00
r_2023 s_1386[c] <=> s_1387[m] -1000.00 1000.00 0.00
r_2024 s_1390[e] -> 0.00 1000.00 0.00
@@ -2852,7 +2852,7 @@ r_2043 s_1418[e] -> 0.00 1000.00 0.00
r_2044 s_1425[e] -> 0.00 1000.00 0.00
r_2045 s_1039[c] <=> s_1042[m] -1000.00 1000.00 0.00
r_2046 s_1435[e] -> 0.00 1000.00 0.00
-r_2049 s_1438[e] <=> -1000.00 1000.00 0.00
+r_2049 s_1438[e] -> 0.00 1000.00 0.00
r_2050 s_0373[c] + s_1439[c] -> s_0529[c] + s_0794[c] + s_1180[c] 0.00 1000.00 0.00
r_2051 s_1440[e] -> 0.00 1000.00 0.00
r_2052 s_1443[e] -> 0.00 1000.00 0.00
@@ -2877,7 +2877,7 @@ r_2071 s_0581[c] + s_0794[c] + s_0981[c] + s_1003[c] + s_1233[c] -> s_0293[c] +
r_2072 s_1045[c] -> s_1047[m] 0.00 1000.00 0.00
r_2073 s_1494[e] -> 0.00 1000.00 0.00
r_2074 s_0434[c] + s_1493[c] -> s_0394[c] + s_0649[c] + s_0794[c] 0.00 1000.00 0.00
-r_2075 s_1494[e] -> s_1493[c] 0.00 1000.00 0.00
+r_2075 s_1494[e] <=> s_1493[c] -1000.00 1000.00 0.00
r_2080 s_1520[c] <=> s_1522[v] -1000.00 1000.00 0.00
r_2082 s_1048[c] -> s_1050[m] 0.00 1000.00 0.00
r_2083 s_1530[e] -> 0.00 1000.00 0.00
@@ -3702,3 +3702,228 @@ r_4337 s_0437[m] + s_0807[m] + s_4022[m] <=> s_0397[m] + s_0799[m] + s_1326[m]
r_4338 s_0803[c] + s_4024[c] <=> 2 s_3951[c] YOL157C -1000.00 1000.00 0.00
r_4339 s_3764[er] <=> s_4025[g] YEL004W -1000.00 1000.00 0.00
r_4340 s_0373[c] + s_4032[c] <=> s_0529[c] + s_0794[c] + s_4033[c] YEL066W -1000.00 1000.00 0.00
+r_4341 s_4063[e] <=> s_4062[c] -1000.00 1000.00 0.00
+r_4342 s_0803[c] + s_4062[c] -> s_0765[c] + s_1322[c] 0.00 1000.00 0.00
+r_4343 s_0796[e] + s_4065[e] <=> s_0794[c] + s_4064[c] -1000.00 1000.00 0.00
+r_4344 s_0803[c] + s_4064[c] -> s_1045[c] + s_1322[c] 0.00 1000.00 0.00
+r_4345 s_0803[c] + s_4066[c] -> s_0790[c] + s_1322[c] 0.00 1000.00 0.00
+r_4346 s_0796[e] + s_4067[e] <=> s_0794[c] + s_4066[c] -1000.00 1000.00 0.00
+r_4347 s_0803[c] + s_4068[c] -> s_0790[c] + s_1322[c] 0.00 1000.00 0.00
+r_4348 s_0796[e] + s_4069[e] <=> s_0794[c] + s_4068[c] -1000.00 1000.00 0.00
+r_4349 s_0796[e] + s_4070[e] <=> s_0794[c] + s_4071[c] -1000.00 1000.00 0.00
+r_4350 s_0803[c] + s_4071[c] -> s_1322[c] + s_3997[c] 0.00 1000.00 0.00
+r_4351 s_0803[c] + s_4072[c] -> s_1322[c] + s_4073[c] 0.00 1000.00 0.00
+r_4352 s_4075[e] <=> s_4072[c] -1000.00 1000.00 0.00
+r_4353 s_1275[c] + s_4073[c] -> s_0794[c] + s_4076[c] 0.00 1000.00 0.00
+r_4354 s_0803[c] + s_1198[c] + s_4076[c] -> s_0794[c] + s_1203[c] + s_1471[c] 0.00 1000.00 0.00
+r_4355 s_0178[c] + s_0991[c] <=> s_0180[c] + s_4079[c] -1000.00 1000.00 0.00
+r_4356 s_0796[e] + s_4080[e] <=> s_0794[c] + s_4079[c] -1000.00 1000.00 0.00
+r_4357 s_0803[c] + s_4081[c] -> s_1322[c] + s_1556[c] 0.00 1000.00 0.00
+r_4358 s_0796[e] + s_4082[e] <=> s_0794[c] + s_4081[c] -1000.00 1000.00 0.00
+r_4359 s_0803[c] + s_4083[c] -> s_1322[c] + s_1556[c] 0.00 1000.00 0.00
+r_4360 s_0796[e] + s_4084[e] <=> s_0794[c] + s_4083[c] -1000.00 1000.00 0.00
+r_4361 s_0796[e] + s_4085[e] <=> s_0794[c] + s_4086[c] -1000.00 1000.00 0.00
+r_4362 s_0810[v] + s_4087[v] -> s_3758[v] + s_3839[v] 0.00 1000.00 0.00
+r_4363 s_4088[c] -> s_1322[c] + s_4089[c] 0.00 1000.00 0.00
+r_4364 s_0796[e] + s_4090[e] <=> s_0794[c] + s_4088[c] -1000.00 1000.00 0.00
+r_4365 s_0796[e] + s_4091[e] <=> s_0794[c] + s_4089[c] -1000.00 1000.00 0.00
+r_4366 s_0394[c] + s_0794[c] + s_4092[c] <=> s_0434[c] + s_0965[c] -1000.00 1000.00 0.00
+r_4367 s_0796[e] + s_4093[e] <=> s_0794[c] + s_4092[c] -1000.00 1000.00 0.00
+r_4368 s_0803[c] + s_4096[c] -> s_1051[c] + s_1322[c] 0.00 1000.00 0.00
+r_4369 s_0796[e] + s_4099[e] <=> s_0794[c] + s_4098[c] -1000.00 1000.00 0.00
+r_4370 s_0803[c] + s_4100[c] -> s_0543[c] + s_1322[c] 0.00 1000.00 0.00
+r_4371 s_0796[e] + s_4101[e] <=> s_0794[c] + s_4100[c] -1000.00 1000.00 0.00
+r_4372 s_0803[c] + s_4102[c] -> s_0794[c] + s_4081[c] 0.00 1000.00 0.00
+r_4373 s_0796[e] + s_4103[e] <=> s_0794[c] + s_4102[c] -1000.00 1000.00 0.00
+r_4374 s_0803[c] + s_4104[c] -> s_0955[c] + s_1469[c] 0.00 1000.00 0.00
+r_4375 s_0796[e] + s_4105[e] <=> s_0794[c] + s_4104[c] -1000.00 1000.00 0.00
+r_4376 s_0803[c] + s_4106[c] -> s_0386[c] + s_1322[c] 0.00 1000.00 0.00
+r_4377 s_4107[e] <=> s_4106[c] -1000.00 1000.00 0.00
+r_4378 s_0803[c] + s_4108[c] -> s_0553[c] + s_0563[c] 0.00 1000.00 0.00
+r_4379 s_0796[e] + s_4109[e] <=> s_0794[c] + s_4108[c] -1000.00 1000.00 0.00
+r_4380 s_0529[c] + s_0794[c] + s_4110[c] <=> s_0373[c] + s_0981[c] -1000.00 1000.00 0.00
+r_4381 s_0796[e] + s_4111[e] <=> s_0794[c] + s_4110[c] -1000.00 1000.00 0.00
+r_4382 2 s_0709[m] + s_4112[c] <=> 2 s_0710[m] + 2 s_4113[c] -1000.00 1000.00 0.00
+r_4383 s_4114[e] <=> s_4112[c] -1000.00 1000.00 0.00
+r_4384 s_0794[c] + s_1212[c] + s_4117[c] -> s_1207[c] + s_3875[c] 0.00 1000.00 0.00
+r_4385 s_0796[e] + s_4118[e] <=> s_0794[c] + s_4117[c] -1000.00 1000.00 0.00
+r_4386 s_0810[v] + s_4121[v] -> s_0977[v] + s_3759[v] 0.00 1000.00 0.00
+r_4387 s_0796[e] + s_4119[e] <=> s_0794[c] + s_4120[c] -1000.00 1000.00 0.00
+r_4388 s_0803[c] + s_4126[c] -> s_0794[c] + s_4100[c] 0.00 1000.00 0.00
+r_4389 s_0796[e] + s_4127[e] <=> s_0794[c] + s_4126[c] -1000.00 1000.00 0.00
+r_4390 s_0803[c] + s_4122[c] <=> s_0563[c] + s_4123[c] -1000.00 1000.00 0.00
+r_4391 s_4123[c] -> s_4124[e] 0.00 1000.00 0.00
+r_4392 s_0796[e] + s_4125[e] <=> s_0794[c] + s_4122[c] -1000.00 1000.00 0.00
+r_4393 s_0434[c] + s_4128[c] -> s_0394[c] + s_0794[c] + s_4129[c] 0.00 1000.00 0.00
+r_4394 s_4129[c] <=> s_0557[c] -1000.00 1000.00 0.00
+r_4395 s_4130[e] <=> s_4128[c] -1000.00 1000.00 0.00
+r_4396 s_0434[c] + s_0529[c] + s_4132[c] -> s_0367[c] + s_0423[c] + s_0633[c] 0.00 1000.00 0.00
+r_4397 s_0803[c] + s_4134[c] <=> s_0362[c] + s_1029[c] -1000.00 1000.00 0.00
+r_4398 s_0796[e] + s_4034[e] <=> s_0794[c] + s_4035[c] -1000.00 1000.00 0.00
+r_4399 s_0794[c] + s_4038[c] <=> s_0802[v] + s_4039[v] -1000.00 1000.00 0.00
+r_4400 s_0805[e] + s_4140[e] -> s_0565[e] + s_1106[e] 0.00 1000.00 0.00
+r_4401 s_0794[c] + s_4041[c] <=> s_0802[v] + s_4042[v] -1000.00 1000.00 0.00
+r_4402 s_0796[e] + s_4040[e] <=> s_0794[c] + s_4041[c] -1000.00 1000.00 0.00
+r_4403 s_0803[c] + s_4098[c] -> s_0633[c] + s_1322[c] ( YHR201C or YDR452W ) 0.00 1000.00 0.00
+r_4404 s_0796[e] + s_4053[e] <=> s_0794[c] + s_4054[c] -1000.00 1000.00 0.00
+r_4405 s_4049[e] <=> s_4048[c] -1000.00 1000.00 0.00
+r_4406 s_0796[e] + s_4078[e] <=> s_0794[c] + s_4077[c] -1000.00 1000.00 0.00
+r_4407 s_0803[c] + s_4077[c] <=> s_1322[c] + s_3904[c] -1000.00 1000.00 0.00
+r_4408 s_0796[e] + s_4037[e] <=> s_0794[c] + s_4038[c] -1000.00 1000.00 0.00
+r_4409 s_0810[v] + s_4039[v] -> s_0996[v] + s_3759[v] 0.00 1000.00 0.00
+r_4410 s_4136[c] <=> s_0779[c] + s_1271[c] -1000.00 1000.00 0.00
+r_4411 s_0803[c] + s_4138[c] -> s_0419[c] + s_1399[c] + s_1469[c] 0.00 1000.00 0.00
+r_4412 s_0803[c] + s_4094[c] -> s_0794[c] + s_4066[c] 0.00 1000.00 0.00
+r_4413 s_0803[c] + s_4044[c] -> s_1322[c] + s_1493[c] 0.00 1000.00 0.00
+r_4414 s_0810[v] + s_4036[v] -> s_1002[v] + s_3759[v] 0.00 1000.00 0.00
+r_4415 s_0810[v] + s_4052[v] -> s_1009[v] + s_3759[v] 0.00 1000.00 0.00
+r_4416 s_0810[v] + s_4042[v] -> s_3759[v] + s_4043[v] 0.00 1000.00 0.00
+r_4417 s_0810[v] + s_4055[v] -> s_0972[v] + s_3839[v] 0.00 1000.00 0.00
+r_4418 s_0810[v] + s_4058[v] -> s_1002[v] + s_3839[v] 0.00 1000.00 0.00
+r_4419 s_0796[e] + s_4139[e] <=> s_0794[c] + s_4138[c] -1000.00 1000.00 0.00
+r_4420 s_0805[e] + s_4131[e] <=> s_0554[e] + s_0565[e] -1000.00 1000.00 0.00
+r_4421 s_0796[e] + s_4116[e] <=> s_0794[c] + s_4115[c] -1000.00 1000.00 0.00
+r_4422 s_0796[e] + s_4137[e] <=> s_0794[c] + s_4136[c] -1000.00 1000.00 0.00
+r_4423 s_0794[c] + s_4086[c] <=> s_0802[v] + s_4087[v] -1000.00 1000.00 0.00
+r_4424 s_0796[e] + s_4056[e] <=> s_0794[c] + s_4057[c] -1000.00 1000.00 0.00
+r_4425 s_0794[c] + s_4057[c] <=> s_0802[v] + s_4058[v] -1000.00 1000.00 0.00
+r_4426 s_0794[c] + s_4035[c] <=> s_0802[v] + s_4036[v] -1000.00 1000.00 0.00
+r_4427 s_0796[e] + s_4135[e] <=> s_0794[c] + s_4134[c] -1000.00 1000.00 0.00
+r_4428 s_0796[e] + s_4097[e] <=> s_0794[c] + s_4096[c] -1000.00 1000.00 0.00
+r_4429 s_0796[e] + s_4050[e] <=> s_0794[c] + s_4051[c] -1000.00 1000.00 0.00
+r_4430 s_0794[c] + s_4051[c] <=> s_0802[v] + s_4052[v] -1000.00 1000.00 0.00
+r_4431 s_0794[c] + s_4120[c] <=> s_0802[v] + s_4121[v] -1000.00 1000.00 0.00
+r_4432 s_0717[c] + s_1275[c] + s_4115[c] -> s_0714[c] + s_0775[c] + s_0794[c] + s_0803[c] + s_1469[c] 0.00 1000.00 0.00
+r_4433 s_4045[e] <=> s_4044[c] -1000.00 1000.00 0.00
+r_4434 s_4047[e] <=> s_4046[c] -1000.00 1000.00 0.00
+r_4435 s_0803[c] + s_4048[c] -> s_0765[c] + s_1322[c] ( YIL053W or YER062C ) 0.00 1000.00 0.00
+r_4436 s_0803[c] + s_4046[c] -> s_1322[c] + s_1493[c] 0.00 1000.00 0.00
+r_4437 s_0796[e] + s_4059[e] <=> s_0794[c] + s_4060[c] -1000.00 1000.00 0.00
+r_4438 s_0794[c] + s_4060[c] <=> s_0802[v] + s_4061[v] -1000.00 1000.00 0.00
+r_4439 s_0810[v] + s_4061[v] -> s_0996[v] + s_3839[v] 0.00 1000.00 0.00
+r_4440 s_1029[c] <=> s_3758[v] -1000.00 1000.00 0.00
+r_4441 s_1045[c] <=> s_4043[v] -1000.00 1000.00 0.00
+r_4442 s_4074[e] -> 0.00 1000.00 0.00
+r_4443 s_4095[e] <=> s_4094[c] -1000.00 1000.00 0.00
+r_4444 s_0796[e] + s_4141[e] <=> s_0188[c] + s_0794[c] -1000.00 1000.00 0.00
+r_4445 s_0796[e] + s_4142[e] <=> s_0260[c] + s_0794[c] -1000.00 1000.00 0.00
+r_4446 s_4145[e] <=> s_0567[c] -1000.00 1000.00 0.00
+r_4447 s_4146[e] <=> s_0455[c] -1000.00 1000.00 0.00
+r_4448 s_0796[e] + s_4143[e] <=> s_0794[c] + s_4144[c] -1000.00 1000.00 0.00
+r_4449 s_0794[c] + s_4144[c] <=> s_0802[v] + s_3757[v] -1000.00 1000.00 0.00
+r_4450 s_0796[e] + s_4147[e] <=> s_0259[c] + s_0794[c] -1000.00 1000.00 0.00
+r_4451 s_0796[e] + s_4148[e] <=> s_0782[c] + s_0794[c] -1000.00 1000.00 0.00
+r_4452 s_4149[e] <=> s_1158[c] -1000.00 1000.00 0.00
+r_4453 s_4150[e] <=> s_0568[c] -1000.00 1000.00 0.00
+r_4454 s_4151[e] <=> s_1545[c] -1000.00 1000.00 0.00
+r_4455 s_0796[e] + s_4152[e] <=> s_0794[c] + s_1360[c] -1000.00 1000.00 0.00
+r_4456 s_4153[e] <=> s_0574[c] -1000.00 1000.00 0.00
+r_4457 s_0796[e] + s_4154[e] <=> s_0794[c] + s_1239[c] -1000.00 1000.00 0.00
+r_4458 s_0796[e] + s_4155[e] <=> s_0340[c] + s_0794[c] -1000.00 1000.00 0.00
+r_4459 s_0796[e] + s_4156[e] <=> s_0573[c] + s_0794[c] -1000.00 1000.00 0.00
+r_4460 2 s_0796[e] + s_4157[e] <=> s_0633[c] + 2 s_0794[c] -1000.00 1000.00 0.00
+r_4461 s_4158[e] <=> s_0514[c] -1000.00 1000.00 0.00
+r_4462 s_4159[e] <=> s_4113[c] -1000.00 1000.00 0.00
+r_4463 s_0796[e] + s_4160[e] <=> s_0423[c] + s_0794[c] -1000.00 1000.00 0.00
+r_4464 s_4161[e] <=> s_0131[c] -1000.00 1000.00 0.00
+r_4465 s_0796[e] + s_4162[e] <=> s_0389[c] + s_0794[c] -1000.00 1000.00 0.00
+r_4466 s_0796[e] + s_4163[e] <=> s_0526[c] + s_0794[c] -1000.00 1000.00 0.00
+r_4467 s_4164[e] <=> s_3953[c] -1000.00 1000.00 0.00
+r_4468 s_4165[e] <=> s_0152[c] -1000.00 1000.00 0.00
+r_4469 s_0796[e] + s_4166[e] <=> s_0794[c] + s_0979[c] -1000.00 1000.00 0.00
+r_4470 s_4167[e] <=> s_0771[c] -1000.00 1000.00 0.00
+r_4471 s_0796[e] + s_4168[e] <=> s_0794[c] + s_4169[c] -1000.00 1000.00 0.00
+r_4472 s_0794[c] + s_4169[c] <=> s_0802[v] + s_3840[v] -1000.00 1000.00 0.00
+r_4473 s_0796[e] + s_4170[e] <=> s_0794[c] + s_4171[c] -1000.00 1000.00 0.00
+r_4474 s_0794[c] + s_4171[c] <=> s_0802[v] + s_3838[v] -1000.00 1000.00 0.00
+r_4475 s_4172[e] <=> s_4173[c] -1000.00 1000.00 0.00
+r_4476 s_4173[c] <=> s_1192[m] -1000.00 1000.00 0.00
+r_4477 s_0796[e] + s_4174[e] <=> s_0794[c] + s_4175[c] -1000.00 1000.00 0.00
+r_4478 s_4176[e] <=> s_3837[c] -1000.00 1000.00 0.00
+r_4479 s_0794[c] + s_4054[c] <=> s_0802[v] + s_4055[v] -1000.00 1000.00 0.00
+r_4480 s_0796[e] + s_4074[e] <=> s_0794[c] + s_4073[c] -1000.00 1000.00 0.00
+r_4481 s_0841[c] + 2 s_1275[c] -> s_0794[c] + s_1467[c] 0.00 1000.00 0.00
+r_4482 s_0794[c] + s_0955[c] <=> s_0802[v] + s_3759[v] -1000.00 1000.00 0.00
+r_4483 s_0794[c] + s_1003[c] <=> s_0802[v] + s_3839[v] -1000.00 1000.00 0.00
+r_4484 s_0841[c] + s_1241[c] <=> s_1012[c] + s_1458[c] ( YJR130C or YLL058W or YML082W ) -1000.00 1000.00 0.00
+r_4485 s_0204[c] + s_1275[c] -> s_0456[c] + s_4177[c] 0.00 1000.00 0.00
+r_4486 s_1275[c] + s_4177[c] -> s_0794[c] + s_4178[c] 0.00 1000.00 0.00
+r_4487 s_4178[c] -> s_4179[c] 0.00 1000.00 0.00
+r_4488 s_0803[c] + s_4179[c] -> s_0725[c] + s_0794[c] + s_4132[c] 0.00 1000.00 0.00
+r_4489 s_0961[c] + s_1198[c] -> s_0794[c] + s_1203[c] + s_4180[c] 0.00 1000.00 0.00
+r_4490 s_0794[c] + s_1212[c] + s_4180[c] <=> s_1207[c] + s_1566[c] -1000.00 1000.00 0.00
+r_4491 s_0548[c] + s_0794[c] + s_1212[c] -> s_1207[c] + s_4181[c] 0.00 1000.00 0.00
+r_4492 s_1198[c] + s_4181[c] -> s_0580[c] + s_0794[c] + s_1203[c] 0.00 1000.00 0.00
+r_4493 s_4133[e] <=> s_4132[c] -1000.00 1000.00 0.00
+r_4494 s_4124[e] -> 0.00 1000.00 0.00
+r_4495 s_0389[c] + s_0803[c] -> s_0386[c] + s_1322[c] 0.00 1000.00 0.00
+r_4496 s_4170[e] -> 0.00 1000.00 0.00
+r_4497 s_4137[e] -> 0.00 1000.00 0.00
+r_4498 s_4109[e] -> 0.00 1000.00 0.00
+r_4499 s_4118[e] -> 0.00 1000.00 0.00
+r_4500 s_4130[e] -> 0.00 1000.00 0.00
+r_4501 s_4131[e] -> 0.00 1000.00 0.00
+r_4502 s_4150[e] -> 0.00 1000.00 0.00
+r_4503 s_4140[e] -> 0.00 1000.00 0.00
+r_4504 s_4145[e] -> 0.00 1000.00 0.00
+r_4505 s_4125[e] -> 0.00 1000.00 0.00
+r_4506 s_4164[e] -> 0.00 1000.00 0.00
+r_4507 s_4167[e] -> 0.00 1000.00 0.00
+r_4508 s_4034[e] -> 0.00 1000.00 0.00
+r_4509 s_4168[e] -> 0.00 1000.00 0.00
+r_4510 s_4056[e] -> 0.00 1000.00 0.00
+r_4511 s_4050[e] -> 0.00 1000.00 0.00
+r_4512 s_4053[e] -> 0.00 1000.00 0.00
+r_4513 s_4037[e] -> 0.00 1000.00 0.00
+r_4514 s_4085[e] -> 0.00 1000.00 0.00
+r_4515 s_4119[e] -> 0.00 1000.00 0.00
+r_4516 s_4059[e] -> 0.00 1000.00 0.00
+r_4517 s_4040[e] -> 0.00 1000.00 0.00
+r_4518 s_4143[e] -> 0.00 1000.00 0.00
+r_4519 s_4166[e] -> 0.00 1000.00 0.00
+r_4520 s_4080[e] -> 0.00 1000.00 0.00
+r_4521 s_4158[e] -> 0.00 1000.00 0.00
+r_4522 s_4049[e] -> 0.00 1000.00 0.00
+r_4523 s_4141[e] -> 0.00 1000.00 0.00
+r_4524 s_4148[e] -> 0.00 1000.00 0.00
+r_4525 s_4147[e] -> 0.00 1000.00 0.00
+r_4526 s_4078[e] -> 0.00 1000.00 0.00
+r_4527 s_4157[e] -> 0.00 1000.00 0.00
+r_4528 s_4099[e] -> 0.00 1000.00 0.00
+r_4529 s_4152[e] -> 0.00 1000.00 0.00
+r_4530 s_4093[e] -> 0.00 1000.00 0.00
+r_4531 s_4146[e] -> 0.00 1000.00 0.00
+r_4532 s_4154[e] -> 0.00 1000.00 0.00
+r_4533 s_4075[e] -> 0.00 1000.00 0.00
+r_4534 s_4067[e] -> 0.00 1000.00 0.00
+r_4535 s_4063[e] -> 0.00 1000.00 0.00
+r_4536 s_4069[e] -> 0.00 1000.00 0.00
+r_4537 s_4070[e] -> 0.00 1000.00 0.00
+r_4538 s_4155[e] -> 0.00 1000.00 0.00
+r_4539 s_4153[e] -> 0.00 1000.00 0.00
+r_4540 s_4095[e] -> 0.00 1000.00 0.00
+r_4541 s_4097[e] -> 0.00 1000.00 0.00
+r_4542 s_4065[e] -> 0.00 1000.00 0.00
+r_4543 s_4142[e] -> 0.00 1000.00 0.00
+r_4544 s_4162[e] -> 0.00 1000.00 0.00
+r_4545 s_4107[e] -> 0.00 1000.00 0.00
+r_4546 s_4161[e] -> 0.00 1000.00 0.00
+r_4547 s_4156[e] -> 0.00 1000.00 0.00
+r_4548 s_4160[e] -> 0.00 1000.00 0.00
+r_4549 s_4135[e] -> 0.00 1000.00 0.00
+r_4550 s_4176[e] -> 0.00 1000.00 0.00
+r_4551 s_4105[e] -> 0.00 1000.00 0.00
+r_4552 s_4111[e] -> 0.00 1000.00 0.00
+r_4553 s_4139[e] -> 0.00 1000.00 0.00
+r_4554 s_4116[e] -> 0.00 1000.00 0.00
+r_4555 s_4133[e] -> 0.00 1000.00 0.00
+r_4556 s_4172[e] -> 0.00 1000.00 0.00
+r_4557 s_4151[e] -> 0.00 1000.00 0.00
+r_4558 s_4163[e] -> 0.00 1000.00 0.00
+r_4559 s_4047[e] -> 0.00 1000.00 0.00
+r_4560 s_4045[e] -> 0.00 1000.00 0.00
+r_4561 s_4101[e] -> 0.00 1000.00 0.00
+r_4562 s_4082[e] -> 0.00 1000.00 0.00
+r_4563 s_4084[e] -> 0.00 1000.00 0.00
+r_4564 s_4127[e] -> 0.00 1000.00 0.00
+r_4565 s_4103[e] -> 0.00 1000.00 0.00
diff --git a/ModelFiles/xml/yeastGEM.xml b/ModelFiles/xml/yeastGEM.xml
index da908964..5ec34031 100644
--- a/ModelFiles/xml/yeastGEM.xml
+++ b/ModelFiles/xml/yeastGEM.xml
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@@ -46226,12 +49142,8580 @@
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+ Confidence Level: 2
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+ Confidence Level: 2
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+ Confidence Level: 2
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+ Confidence Level: 3
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+ Confidence Level: 3
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+ Confidence Level: 2
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+ Confidence Level: 3
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+ Confidence Level: 3
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+ Confidence Level: 3
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+ Confidence Level: 3
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+ Confidence Level: 3
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+ Confidence Level: 2
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+ Confidence Level: 3
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+ Confidence Level: 2
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Confidence Level: 2
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Confidence Level: 2
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Confidence Level: 2
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Confidence Level: 3
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Confidence Level: 3
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Confidence Level: 2
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Confidence Level: 3
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Confidence Level: 3
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Confidence Level: 3
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Confidence Level: 3
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Confidence Level: 3
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Confidence Level: 3
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Confidence Level: 3
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Confidence Level: 3
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Confidence Level: 3
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Confidence Level: 3
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Confidence Level: 3
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Confidence Level: 3
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Confidence Level: 3
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Confidence Level: 3
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Confidence Level: 3
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Confidence Level: 3
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Confidence Level: 3
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Confidence Level: 3
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Confidence Level: 3
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Confidence Level: 3
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Confidence Level: 3
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Confidence Level: 3
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Confidence Level: 3
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Confidence Level: 3
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Confidence Level: 3
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Confidence Level: 3
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Confidence Level: 2
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Confidence Level: 3
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Confidence Level: 3
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Confidence Level: 3
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Confidence Level: 3
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Confidence Level: 3
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Confidence Level: 3
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