Table 1. Determination of S4TE 2.0 weightings according to the positive predictive value of each S4TE module in Legionella pneumophila Philadelphia 1.

Enumeration of effectors predicted by individual features implemented in S4TE 2.0: the number of true positives, false positives and the positive predictive value (PPV, expressed in %) is indicated.

S4TE2.0 features	Promoter motif	Homology	Euk-like domains	DUF	EPIYA	NLS	MLS	Prenylation domain	Coiled coil	C-ter basicity	C-ter charges	C-ter hydrophobicity	Global hydrophobicity	E-block
True positives	108	285	13	2	30	105	6	1	100	262	62	41	117	98
False positives	434	34	27	106	101	783	79	6	231	2376	863	339	156	232
PPV (%)	20	89	32	2	23	12	7	14	30	10	7	10	42	30