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Elim2_model.txt
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Elim2_model.txt
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#-------------------------------------------------------------------------------
# Name: Adapted E. limosum Model
# Model definition file for E. limosum of mfapy
#
# Author: Katie Hoyt Christian Byrd Fumio_Matsuda
#
"# Created: 12/06/2018, revised December 2022"
# Copyright: (c) Fumio_Matsuda 2021
# Licence: MIT license
#-------------------------------------------------------------------------------
//Reactions
r1 SubsGlc --> G6P SubsGlc --> G6P ABCDEF --> ABCDEF (kegg:R02848) 0 1000
r2 G6P --> F6P G6P --> F6P ABCDEF --> ABCDEF (kegg:R00771f) 0 1000
r3 F6P --> G6P F6P --> G6P ABCDEF --> ABCDEF (kegg:R00771r) 0 1000
r4 F6P --> FBP F6P --> FBP ABCDEF --> ABCDEF (kegg:R00756) 0 1000
r5 FBP --> F6P FBP --> F6P ABCDEF --> ABCDEF (kegg:R01068f) 0 1000
r6 FBP --> DHAP + GAP FBP --> DHAP + GAP ABCDEF --> CBA + DEF (kegg:R01068r) 0 1000
r7 DHAP + GAP --> FBP DHAP + GAP --> FBP CBA + DEF --> ABCDEF (kegg:R01015f) 0 1000
r8 DHAP --> GAP DHAP --> GAP ABC --> ABC (kegg:R01015r) 0 1000
r9 GAP --> DHAP GAP --> DHAP ABC --> ABC (kegg:R01061f) 0 1000
r10 GAP --> PGA GAP --> PGA ABC --> ABC (kegg:R01061r) 0 1000
r11 PGA --> GAP PGA --> GAP ABC --> ABC (kegg:R01512f) 0 1000
r12 PGA --> PEP PGA --> PEP ABC --> ABC (kegg:R01512r) 0 1000
r13 PEP --> PGA PEP --> PGA ABC --> ABC (kegg:R00200) 0 1000
r14 PEP --> Pyr PEP --> Pyr ABC --> ABC (kegg:R01196) 0 1000
r15 Pyr --> PEP Pyr --> PEP ABC --> ABC (kegg:R00351) 0 1000
r16 Pyr --> AcCOA + CO2in Pyr --> AcCOA + CO2in ABC --> BC + A (kegg:R00709f) 0 1000
r17 AcCOA + Oxa --> IsoCit AcCOA + Oxa --> IsoCit AB + CDEF --> FEDBAC (kegg:R00709r) 0 1000
r18 IsoCit --> aKG + CO2in IsoCit --> aKG + CO2in ABCDEF --> ABCDE + F (kegg:R01197) 0 1000
r19 aKG --> Suc + CO2in aKG --> Suc + CO2in ABCDE --> BCDE + A (kegg:R02164f) 0 1000
r20 Suc --> Fum Suc --> Fum ABCD --> ABCD (kegg:R02164r) 0 1000
r21 Fum --> Suc Fum --> Suc ABCD --> ABCD (kegg:R01082f) 0 1000
r22 Fum --> Mal Fum --> Mal ABCD --> ABCD (kegg:R01082r) 0 1000
r23 Mal --> Fum Mal --> Fum ABCD --> ABCD (kegg:R00343f) 0 1000
r24 Mal --> Oxa Mal --> Oxa ABCD --> ABCD (kegg:R00343r) 0 1000
r25 Oxa --> Mal Oxa --> Mal ABCD --> ABCD (kegg:R00344) 0 1000
r26 IsoCit + AcCOA --> Mal + Suc IsoCit + AcCOA --> Mal + Suc ABCDEF + GH --> ABHG + FCDE (kegg:R00216) 0 1000
r27 G6P --> m6PG G6P --> m6PG ABCDEF --> ABCDEF (kegg:R00835) 0 1000
r28 m6PG --> Ru5P + CO2in m6PG --> Ru5P + CO2in ABCDEF --> BCDEF + A (kegg:R01528) 0 1000
r29 Ru5P --> R5P Ru5P --> R5P ABCDE --> ABCDE (kegg:R01056f) 0 1000
r30 R5P --> Ru5P R5P --> Ru5P ABCDE --> ABCDE (kegg:R01056r) 0 1000
r31 Ru5P --> Xu5P Ru5P --> Xu5P ABCDE --> ABCDE (kegg:R01529f) 0 1000
r32 Xu5P --> Ru5P Xu5P --> Ru5P ABCDE --> ABCDE (kegg:R01529r) 0 1000
r33 R5P + Xu5P --> S7P + GAP R5P + Xu5P --> S7P + GAP ABCDE + FGHIJ --> FGABCDE + HIJ (kegg:R01641f) 0 1000
r34 GAP + S7P --> Xu5P + R5P GAP + S7P --> Xu5P + R5P HIJ + FGABCDE --> FGHIJ + ABCDE (kegg:R01641r) 0 1000
r35 GAP + S7P --> F6P + E4P GAP + S7P --> F6P + E4P ABC + DEFGHIJ --> DEFABC + GHIJ (kegg:R08575f) 0 1000
r36 E4P + F6P --> S7P + GAP E4P + F6P --> S7P + GAP GHIJ + DEFABC --> DEFGHIJ + ABC (kegg:R08575r) 0 1000
r37 E4P + Xu5P --> F6P + GAP E4P + Xu5P --> F6P + GAP ABCD + EFGHI --> EFABCD + GHI (kegg:R01067f) 0 1000
r38 GAP + F6P --> Xu5P + E4P GAP + F6P --> Xu5P + E4P GHI + EFABCD --> EFGHI + ABCD (kegg:R01067r) 0 1000
r39 m6PG --> Pyr + GAP m6PG --> Pyr + GAP ABCDEF --> ABC + DEF (kegg:R00703) 0 1000
r40 PEP + CO2in --> Oxa PEP + CO2in --> Oxa ABC + D --> ABCD (kegg:Lacex) 0 1000
r41 Oxa --> PEP + CO2in Oxa --> PEP + CO2in ABCD --> ABC + D (kegg:SubsGln) 0 1000
r42 Mal --> Pyr + CO2in Mal --> Pyr + CO2in ABCD --> ABC + D (kegg:R00253) 0 1000
r49 AcCOA --> Acetate AcCOA --> Acetate AB --> AB (kegg:Aspex) 0 1000
r50 Acetate --> Acetateex nd nd (kegg:R00483) 0 1000
r56 SubsCO2 --> CO2in SubsCO2 --> CO2in A --> A (kegg:SubsVal) 0 1000
r57 CO2in --> CO2ex nd nd (kegg:Glu) 0 1000
r58 Pyr --> Ala Pyr --> Ala ABC --> ABC (kegg:Arg) 0 1000
r59 Oxa --> Asp Oxa --> Asp ABCD --> ABCD (kegg:R00352) 0 1000
r60 Oxa --> Thr Oxa --> Thr ABCD --> ABCD (kegg:BiomassAcCoA) 0 1000
r61 aKG --> Glu aKG --> Glu ABCDE --> ABCDE (kegg:BiomassG6P) 0 1000
r62 E4P + PEP + PEP --> Phe E4P + PEP + PEP --> Phe ABCD + EFG + HIJ --> EFGIJABCD (kegg:BiomassR5P) 0 1000
r63 E4P + PEP + PEP --> Tyr E4P + PEP + PEP --> Tyr ABCD + EFG + HIJ --> EFGIJABCD (kegg:BiomassDHAP) 0 1000
r64 Oxa + Pyr --> Ile Oxa + Pyr --> Ile ABCD + EFG --> ABFGCD (kegg:R01513) 0 1000
r65 AcCOA + Pyr + Pyr --> Leu AcCOA + Pyr + Pyr --> Leu AB + CDE + FGH --> ABDEGH (kegg:BiomassAla) 0 1000
r66 Pyr + Pyr --> Val Pyr + Pyr --> Val ABC + DEF --> ABECF (kegg:BiomassAsp) 0 1000
r67 PGA --> Ser PGA --> Ser ABC --> ABC (kegg:BiomassAsn) 0 1000
r68 Ser --> Gly + MEETHF Ser --> Gly + MEETHF ABC --> AB + C (kegg:Glu2) 0 1000
r69 Gly + MEETHF --> Ser Gly + MEETHF --> Ser AB + C --> ABC (kegg:BiomassGln) 0 1000
r72 G6P --> Biomass nd nd (kegg:BiomassLeu) 0 1000
r73 F6P --> Biomass nd nd (kegg:BiomassIle) 0 1000
r74 DHAP --> Biomass nd nd (kegg:BiomassVal) 0 1000
r75 PGA --> Biomass nd nd (kegg:CO2ex) 0 1000
r76 Ser --> Biomass nd nd (kegg:SubsCO2) 0 1000
r77 Gly --> Biomass nd nd (keggPGAex) 0 1000
r78 MEETHF --> Biomass nd nd (kegg:FAex) 0 1000
r79 PEP --> Biomass nd nd (kegg:MAL_cyt) 0 1000
r80 Pyr --> Biomass nd nd (kegg:MAL_cyt) 0 1000
r81 AcCOA --> Biomass nd nd (kegg:OXA_cyt) 0 1000
r82 aKG --> Biomass nd nd (kegg:OXA_cyt) 0 1000
r83 Oxa --> Biomass nd nd (kegg:ATP) 0 1000
r84 R5P --> Biomass nd nd (kegg:NADH) 0 1000
r85 E4P --> Biomass nd nd (kegg:NADPH) 0 1000
r86 Ala --> Alaex nd nd (kegg:Arg) 0 1000
r87 Asp --> Aspex nd nd (kegg:R00352) 0 1000
r88 Thr --> Threx nd nd (kegg:BiomassAcCoA) 0 1000
r89 Glu --> Gluex nd nd (kegg:BiomassG6P) 0 1000
r90 Phe --> Pheex nd nd (kegg:BiomassR5P) 0 1000
r91 Tyr --> Tyrex nd nd (kegg:BiomassDHAP) 0 1000
r92 Ile --> Ileex nd nd (kegg:R01513) 0 1000
r93 Leu --> Leuex nd nd (kegg:BiomassAla) 0 1000
r94 Val --> Valex nd nd (kegg:BiomassAsp) 0 1000
r104 Subsmeoh --> meoh Subsmeoh --> meoh A --> A (kegg:MTI/MTII) 0 1000
r105 meoh --> METHF meoh --> METHF A --> A (kegg:TBD) 0 1000
r106 METHF --> MEETHF METHF --> MEETHF A --> A (kegg:TBD) 0 1000
r107 MEETHF --> METHF MEETHF --> METHF A --> A (kegg:TBD) 0 1000
r108 CO2in + METHF --> AcCOA CO2in + METHF --> AcCOA A + B --> AB (kegg:TBD) 0 1000
r109 AcCOA + CO2in --> Pyr AcCOA + CO2in --> Pyr BC + A --> ABC (kegg:R00709f) 0 1000
//Reversible_reactions
PGI r2 r3 (kegg:R00771) -1000 1000
FBA r4 r5 (kegg:R01068) -1000 1000
TPI r8 r9 (kegg:R01015) -1000 1000
GAPDH r10 r11 (kegg:R01061) -1000 1000
PEPH r12 r13 (kegg:R01512) -1000 1000
SDH r20 r21 (kegg:R02164) -1000 1000
MDH r24 r25 (kegg:R00342) -1000 1000
RPI r29 r30 (kegg:R01056) -1000 1000
RBE r31 r32 (kegg:R01529) -1000 1000
TKT1 r33 r34 (kegg:R01641) -1000 1000
TAL r35 r36 (kegg:R08575) -1000 1000
TKT2 r37 r38 (kegg:R01067) -1000 1000
FH r22 r23 (kegg:R01082) -1000 1000
THF r106 r107 (kegg:TBD) -1000 1000
PFOR r16 r109 (kegg:R00709f) -1000 1000
#
#Name_ofintermediate{\t}carbon_number
#
//Metabolites
m6PG 6 no no no (kegg:C00345) 0 300
AcCOA 2 no no no (kegg:C00024) 0 300
Acetate 2 no no no (dummy) 0 300
Acetateex 2 no no excreted (dummy) 0 300
aKG 5 no no no (kegg:C00026) 0 300
Ala 3 no no no (kegg:C00041) 0 300
Asp 4 no no no (kegg:C00049) 0 300
Biomass 1 no no excreted (dummy) 0 300
CO2ex 1 no no excreted (dummy) 0 300
CO2in 1 no no no (dummy) 0 300
DHAP 3 no no no (kegg:C00111) 0 300
E4P 4 no no no (kegg:C00279) 0 300
F6P 6 no no no (kegg:C00085) 0 300
FBP 6 no no no (kegg:C00354) 0 300
Formate 1 no no no (dummy) 0 300
G6P 6 no no no (kegg:C00092) 0 300
GAP 3 no no no (kegg:C00118) 0 300
Glu 5 no no no (kegg:C00025) 0 300
Gly 2 no no no (kegg:C00037) 0 300
Ile 6 no no no (kegg:C00407) 0 300
IsoCit 6 no no no (dummy) 0 300
Leu 6 no no no (kegg:C00123) 0 300
Mal 4 no no no (kegg:C00149) 0 300
MEETHF 1 no no no (dummy) 0 300
METHF 1 no no no (dummy) 0 300
Subsmeoh 1 no carbonsource no (dummy) 0 300
meoh 1 no no no (dummy) 0 300
Oxa 4 no no no (kegg:C00036) 0 300
PEP 3 no no no (kegg:C00074) 0 300
PGA 3 no no no (kegg:C00631)(kegg:C00197) 0 300
Phe 9 no no no (dummy) 0 300
Pyr 3 no no no (kegg:C00022) 0 300
R5P 5 no no no (kegg:C00117) 0 300
Ru5P 5 no no no (kegg:C00199) 0 300
S7P 7 no no no (kegg:C05382) 0 300
Ser 3 no no no (kegg:C00065) 0 300
SubsCO2 1 no carbonsource no (dummy) 0 300
SubsGlc 6 no carbonsource no (dummy) 0 300
Fum 4 symmetry no no (kegg:C00122) 0 300
Suc 4 symmetry no no (kegg:C00042) 0 300
Thr 4 no no no (dummy) 0 300
Tyr 9 no no no (dummy) 0 300
Val 5 no no no (kegg:C00183) 0 300
Xu5P 5 no no no (kegg:C00231) 0 300
Alaex 3 no no excreted (dummy) 0 300
Aspex 4 no no excreted (dummy) 0 300
Threx 4 no no excreted (dummy) 0 300
Gluex 5 no no excreted (dummy) 0 300
Pheex 9 no no excreted (dummy) 0 300
Tyrex 9 no no excreted (dummy) 0 300
Ileex 6 no no excreted (dummy) 0 300
Leuex 6 no no excreted (dummy) 0 300
Valex 5 no no excreted (dummy) 0 300
//Target_fragments
AlaMes intermediate Ala_1:2:3 use C3H7NO2
AspMes intermediate Asp_1:2:3:4 use C4H7NO4
GluMes intermediate Glu_1:2:3:4:5 use C5H9NO4
PheMes intermediate Phe_1:2:3:4:5:6:7:8:9 use C9H11NO2
GlyMes intermediate Gly_1:2 use C2H5NO2
IleMes intermediate Ile_1:2:3:4:5:6 use C6H13NO2
SerMes intermediate Ser_1:2:3 use C3H7NO3
ValMes intermediate Val_1:2:3:4:5 use C5H11NO2
TyrMes intermediate Tyr_1:2:3:4:5:6:7:8:9 use C9H11NO3
ThrMes intermediate Thr_1:2:3:4 use C4H9NO3