Table 4. Comparison of SVM-ESM-1b and PrePS prenylation predictions with empirical observations.

Reporter	Prenylation
Ydj1-Cxxx	SVMa,b	PrePS	Freq	FPB	Observedc
CAAQ	+	-	+	-	+
CAHQ	+	-	+	-	+
CASA	+	-	+	-	+
CKQH	+	-	+	-	+
CNLI	+	-	+	-	+
CSFL	+	-	+	-	+
CVAA	+	-	+	-	+
CVFM	+	-	+	-	+
CKQG	-	+	+	-	+
CKQL	-	+	+	-	+
CQTS	-	+	-	-	+
CQSQd	+	+	-	-	+
number observed/predicted	9/12	4/12	10/12	0/12

^aSigns represent predictions of prenylation and cleavage that were reported as positive (+) or negative (-) by the indicated model.

^bSVM–SVM-ESM-1b; PrePS–Prenylation Prediction Suite; Freq–in-house, frequency-based; FPB–FlexPepBind.

^cObserved by Ydj1p prenylation gel shift–see Fig 3B.

^dObservation previously reported [22].