Metabolic Route Explorer (MRE) is an open-access online tool for heterologous biosynthesis pathway design. Given the starting material, the desired product, and the heterologous host, MRE explores biosynthesis routes and ranks them. To be useful for the design purpose, MRE only considers verified metabolic parts with known activities. Because of this constraint, for any non-native enzymatic reactions in heterologous biosynthesis pathways, MRE is able to suggest real foreign genes that can be introduced into the host organism. To rank biosynthesis routes, MRE considers the competition for the utilization of each metabolic precursor with endogenous reactions using thermodynamics data and gives information about which reactions are competing with non-native reactions in each heterologous biosynthesis pathway.
| Examples | From | To | Max number of reactions | Organism code | KEGG RPAIR constraints | Other excluded compounds |
| example 1 | L-tyrosine (C00082) | naringenin (C00509) | 8 | E. coli (ECO) | Main + Cofac + Trans | None |
| example 2 | alpha-D-Glucose (C00267) | pyruvate (C00022) | 5 | E. coli (ECO) | Main + Cofac + Trans | None |
| example 3 | UDP-glucose (C00029) | methanol (C00132) | 15 | Yeast (SCE) | Main + Cofac + Trans | None |
| example 4 | pyruvate (C00022) | 3-Hydroxypropanoate (C01013) | 5 | E. coli (ECO) | Main + Cofac + Trans | CO2 (C00011) |