Table 4. Confusion matrices for gene essentiality prediction.

‘All genes’ denotes agreement/disagreement between the model prediction and the transposon mutagenesis experiment considering all genes in the metabolic reconstruction (excluding the two ‘technical non-essential’ genes). ‘Excluding AA’ repeats the same comparison as ‘All genes’, with genes for amino acid utilization (uptake and peptidase genes) excluded. See Table 2 for individual gene essentialities in silico and in vivo.

	All genes		Excluding AA
Exp. / Model	Essential	Non-essential	Essential	Non-essential
Essential	101	4	101	4
Quasi-essential	22	14	22	4
Non-essential	0	12	0	10