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Table 2 Flux comparison between EcoCyc–18.0–GEM and iJO1366: ATP maximization objective under aerobic conditions

From: A genome-scale metabolic flux model of Escherichia coli K–12 derived from the EcoCyc database

EcoCyc   iJO1366  
Reaction Flux Reaction Flux
ATP maximization objective 216 ATPM 235
Glucose uptake 10 EX_glc(e) 10
O 2 uptake 60 EX_o2(e) 60
H 2O production 60 EX_h2o(e) 60
CO 2 production 60 EX_co2(e) 60
ATP synthase* 176 ATPS4rpp 195
NADH-DEHYDROG-A-RXN 100 NADH16pp 100
Cytochrome bo oxidase* 60 CYTBO3_4pp 120
PYRNUTRANSHYDROGEN-RXN 20 NADTRHD 20
GAPOXNPHOSPHN-RXN 20 GAPD 20
ISOCITDEH-RXN 20 ICDHyr 20
3PGAREARR-RXN 20 ENO 20
ACONITATEDEHYDR-RXN 20 ACONTa/b 20
PHOSGLYPHOS-RXN 20 PGK 20
CITSYN-RXN 20 CS 20
2OXOGLUTARATEDEH-RXN 20 AKGDH 20
2PGADEHYDRAT-RXN 20 ENO 20
Succinate dehydrogenase* 20 SUCDi 20
MALATE-DEH-RXN 20 MDH 20
FUMHYDR-RXN 20 FUM 20
PYRUVDEH-RXN 20 PDH 20
SUCCOASYN-RXN 20 SUCOAS 20
PGLUCISOM-RXN 10 PGI 10
Glucose PTS uptake* 10 GLCptspp 10
TRIOSEPISOMERIZATION-RXN 10 TPI 10
RXN0-313 10 F6PA 10
2.7.1.121-RXN 10 DHAPT 10
  1. Glucose uptake is set to 10 mmol/gCDW/hr. Other nutrient and secretion fluxes are unbounded. Flux rates are reported as absolute values for clarity. True iJO1366 fluxes for EX_glc(e), EX_o2(e), PGK, PGM, and SUCOAS are negative because of reaction directionality convention. Most EcoCyc reactions are identifed by their EcoCyc frame IDs. The remainder are marked with asterisks, and their frame IDs are as follows: ATP synthase EcoCyc frame ID: TRANS-RXN-249; cytochrome bo oxidase EcoCyc frame ID: RXN0-5268; succinate dehydrogenase EcoCyc frame ID: SUCCINATE-DEHYDROGENASE-UBIQUINONE-RXN; glucose PTS uptake EcoCyc frame ID: TRANS-RXN-157/RXN0-6717/RXN0-6718; fructose 6-phosphate aldolase EcoCyc frame ID: RXN0-313; dihydroxyacetone kinase EcoCyc frame ID: 2.7.1.121-RXN.