Table 1.
Required and accessible reactions and metabolites for alternate penalty implementations and metabolomics constraints
| Medium | Rich |
Virulence |
||||||
|---|---|---|---|---|---|---|---|---|
| Omics constraints | None | Transcriptomics | Metabolomics | Transcriptomics, metabolomics | None | Transcriptomics | Metabolomics | Transcriptomics, metabolomics |
| Reactions considereda | 2201 | |||||||
| Accessible reactions | 1517 | 1517 | 1517 | 1517 | 1483 | 1483 | 1483 | 1483 |
| Required reactions | 343 | 374 | 355 | 386 | 344 | 377 | 356 | 389 |
| Metabolites consideredb | 1461 | |||||||
| Accessible metabolites | 985 | 985 | 985 | 985 | 971 | 971 | 971 | 971 |
| Required metabolites | 420 | 429 | 447 | 456 | 427 | 443 | 456 | 472 |
aAll network (cellular, non-demand) reactions were included.
bAll model cellular metabolites were included.