Table 1.
The sub-networks produced between different source and target molecules for a given size. These results were obtained on the graph constructed using reactions in the KEGG database.
| Source | Target | Size | Output sub-network | Comments |
|---|---|---|---|---|
| L-Arginine (C00062) | L-Citrulline (C00327) | 2 | R00551, R00665 | Matches with ATLAS and FMM |
| Pyruvate (C00022) | Itaconate (C00490) | 4 | R02491, R00209, R00237, R02405 | Matches with FMM, FMM does not report R00209 which produces C00024 – required by R02405† |
| Pyruvate (C00022) | Itaconate (C00490) | 5 | R00351, R02243, R00209, R00217, R01325 | Matches with FMM, FMM does not report R00351 which produces C00036 – required by R00351† |
| L-Tyrosine (C00082) | Naringenin (C00509) | 5 | R02446, R00737, R01616, R01613, R06641 | Matches with FMM, FMM does not report R06641† |
| L-Phenylalanine (C00079) | Resveratrol (C03582) | 5 | R01616, R00697, R02253, R06641, R01614 | Matches with FMM, FMM does not report R06641 which produces malonyl-CoA required by R01614† |
| Mevalonic acid (C00418) | Amorpha-4,11-diene (C16028) | 7 | R01658, R03245, R02245, R01121, R01123, R07630, R02003 | No paths found by FMM, ATLAS, however it is natively found in S. cerevisiae51. |
| D-Erythrose 4-phosphate (C00279) | 3-Amino-5-hydroxy-benzoate (C12107) | 7 | — | No paths reported by ATLAS, FMM and our algorithm |
We denote reactions and compounds using their respective KEGG IDs. It is interesting to note that our algorithm is able to recover the well-known pathway reported in S. cerevisiae, while the other algorithms fail to do so. Also, there exists no pathways of size 7 between C00279 and C12107, which is being consistently reported by all the methods. More details about the sub-networks can be found in Supplementary Results 5.3. Note that the source metabolites are included in the seed metabolite set. †Note that we did not find any pathways in ATLAS, when queried for pathways using no novel reactions. These novel reactions, integrate KEGG metabolites into novel enzymatic steps and are present only in the ATLAS database.