Table 3. Comparison of prenylation and cleavage prediction models with empirical observations.

			Prenylation					Cleavage
	yeast protein	CaaX	SVMa,b	PrePS	Freq	FPB	Observedc	SVMa	Freq	Observedd
similar sequences	Ras2	CIIS	+	+	+	+	+	+	+	+
	Hmg1	CIKS	-	-	-	-	-	NA	NA	NA
	Rho2	CIIL	+	+	+	-	+	+	+	+
	Ssp2	CIDL	-	-	-	-	-	NA	NA	NA
	Skt5, MiY1	CVIM	+	+	+	-	+	+	+	+
	Tbs1	CVKM	-	-	-	-	+	+	-	-
	YDL022C-A	CSII	+	+	+	+	+	+	+	+
	YBR096W	CSEI	-	-	-	-	-	NA	NA	NA
	YMR265C	CSNA	-	-	+	-	+	-	-	-
	Pet18	CYNA	-	-	-	+	+	-	-	-
	Lih1	CSGL	-	-	+	-	-	NA	NA	NA
	Cup1	CSGK	-	-	-	-	-	NA	NA	NA
other sequences	Nap1	CKQS	+	+	+	-	+	-	-	-
	Cst26	CFIF	+	+	-	-	+	+	-	-
	YIL134C-A	CAPY	+	+	-	-	+	-	-	-
	Atr1	CTVA	+	+	+	+	+	+	+	+
	Las21	CALD	+	-	+	+	+	-	+	-
	YDL009C	CAVS	+	+	+	+	+	-	+	+
	Sua5	CIQF	+	+	+	-	+	+	-	-
number observed/predicted			16/19	15/19	14/19	11/19		10/14	13/14

^aSigns represent predictions of prenylation and cleavage that were reported as positive (+) or negative (-) by the indicated model. NA—not applicable; the non-prenylated status of the sequence precludes it from being cleaved; CaaX cleavage is prenyl-dependent.

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

^cObserved by Ydj1p prenylation gel shift–see Fig 3A, S1 Fig.

^dObserved by a-factor mating–see Fig 3C.