| Metabolic Task | In vitro | iPfal17 | Hypothesis for in vitro/in silico discrepancies |
---|---|---|---|---|
1a | Growth in the presence of antimetabolite, riboflavin? | no [68] | no | - |
1b | Growth in the presence of antimetabolite, thiamine? | no [68] | yes | Unknown antimetabolite mechanism; Off target effects of antimetabolite |
1c | Growth in the presence of antimetabolite, nicotinamide? | no [68] | yes | Unknown antimetabolite mechanism; Off target effects of antimetabolite |
1d | Growth in the presence of antimetabolite, pyridoxine? | no [68] | yes | Unknown antimetabolite mechanism; Off target effects of antimetabolite |
2a | Grows without loops? | no | no | - |
2b | ATP production if no exchange is allowed? | no | no | - |
3a | Can produce purines? | yes | yes | - |
3b | Growth with hypoxanthine as the only purine source? | yes [65] | yes | - |
3c | No growth if guanine, guanosine, inosine, adenine, or adenosine are only purine sources? | yes [65] | 60% | - |
4 | Growth with IPP supplementation and no apicoplast? | yes [139] | no | Nuclear encoded proteins that function within the apicoplast may be expressed in the cytoplasm if the organelle is not present. |
5a | Growth with glucose? | yes [66] | yes | - |
5b | Growth with alternative sugar source (no glucose, with ribose, mannose, fructose, galactose, or maltose)? | no [66] | yes | Central carbon metabolism contains many reversible reactions. Carbon sources that support growth are debated [140]. |
6a | Can produce all amino acids except isoleucine? | yes [66] | yes | - |
6b | Is growth reduced without methionine, proline, tyrosine, cystine, glutamate, or glutamine supplementation? | yes [63] | no | Model is not designed for growth reduction experiments. |
6c | Growth without isoleucine supplementation? | no | - | |
7 | Growth without calcium pantothenate? | no [93] | no | - |
8 | Growth without p-aminobenzoic acid? | no [141] | no | - |
9 | Cannot produce any metabolites if no exchange is allowed? | no | no | - |
10 | Accuracy of experimental essentiality predictions | - | 79.5%a | |
11 | Accuracy of P. berghei essentiality predictions | - | 61.4%a | See Additional file 3: Table S6 |