Table 2. Top-ranked pathways identified by MRE for various biosynthesis specifications.
| Biosynthesis specification | Results of top-ranked pathway identified by MRE | Comparison with existing tools | |||||
|---|---|---|---|---|---|---|---|
| Source | Target | Host | Steps | Necessary foreign enzymes | Remark | Found a patha | Match with MREb |
| L-tyrosine | naringenin | E. coli | 4 | 4.3.1.23, 6.2.1.12, 2.3.1.74, | Recovered a known route (29) | FMM, XTMS | FMM |
| (C00082) | (C00509) | (ECO) | 5.5.1.6 | as the top route | |||
| glycerol | 1,3-PDO | E. coli | 2 | 4.2.1.30, 1.1.1.202 | Recovered a known route (30) | FMM, PHT | FMM, PHT |
| (C00116) | (C02457) | (ECO) | as the top route | ||||
| glycerol | R-1,2-PDO | yeast | 5 | 4.2.3.3, 1.1.1.79, 1.1.1.77 | Recovered a known route (31) | MT | MT |
| (C00116) | (C02912) | (SCE) | as the top route | ||||
| acetyl-CoA | artemisinic acid | yeast | 10 | 2.5.1.92, 4.2.3.50, 4.2.3.82, | Recovered a known route (32), | none | none |
| (C00024) | (C20309) | (SCE) | 4.2.3.24, 1.14.13.158 | and predicted better ones | |||
| L-tyrosine | resveratrol | E. coli | 3 | 4.3.1.23, 6.2.1.12, 2.3.1.95 | Recovered a known route (33) | FMM | FMM |
| (C00082) | (C03582) | (ECO) | as the top route | ||||
| D-xylose | xylitol | E. coli | 2 | 1.1.1.21, 1.1.1.307 | Recovered two known routes (34) | FMM, PHT | FMM, PHT |
| (C00181) | (C00379) | (ECO) | as the top routes | ||||
| PRPP | histidine | E. coli | 8 | 2.6.1.27 | Predicted | ||
| better and shorter routes | FMM, MT | none | |||||
| (C00119) | (C00135) | (ECO) | than a known native route (35) | ||||
| chorismate | tryptophan | yeast | 5 | none | Predicted the native route (36) as | FMM, MT, | FMM |
| (C00251) | (C00078) | (SCE) | the best, and found shorter routes | PHT | |||
For each biosynthesis specification, the source and target compounds are specified in KEGG ID, and the host organism is in KEGG organism code. For each pathway, the number of reaction steps and the necessary foreign enzymes(in EC number) are specified. Comparison with FMM (13), Metabolic tinker (MT) (8), PHT (14) and XTMS (9) is also shown. For each tool, its default setting was used, except for the configuration of a pathway length, which was set to accommodate known pathways.
aTools that have identified at least one path for a given biosynthesis specification.
bTools whose top-ranked pathway is the same as the top-ranked one from MRE.