Table 3.
A comprehensive overview of prenylation prediction using in-house and published models.
| Proteina | Motif (n = 48) | Observedb | %b | PrePSc | SVMd | RRS EFe | YDJ1 HM |
|---|---|---|---|---|---|---|---|
| Ras2 | CIIS | + | 100 | 1.281 | 1 | 9.011500 | 4.07 |
| Hmg1 | CIKS | − | 41 | −3.588 | 0 | 0.034717 | 1.93 |
| Rho2 | CIIL | + | 100 | 0.817 | 1 | 10.313800 | 3.65 |
| Ssp2 | CIDL | − | 0 | −4.893 | 0 | 0.254070 | 1.82 |
| Skt5, Miy1 | CVIM | + | 100 | 2.200 | 1 | 3.371400 | 3.66 |
| Tbs1 | CVKM | + | 100 | −2.909 | 0 | 0.066541 | 2.47 |
| YDL022C-A | CSII | + | 100 | 0.987 | 1 | 11.350000 | 3.34 |
| YBR096W | CSEI | − | 0 | −5.759 | 0 | 0.149720 | 1.88 |
| YMR265C | CSNA | + | 100 | −4.848 | 0 | 0.039925 | 3.84 |
| Pet18 | CYNA | + | 100 | −5.843 | 0 | 0.079849 | 4.95 |
| Lih1 | CSGL f | − | 0 | −4.577 | 0 | 0.041301 | 2.79 |
| Cup1 | CSGK f | − | 0 | −6.461 | 0 | 0.099811 | 1.75 |
| Nap1 | CKQS | + | 100 | −0.975 | 1 | 0.066541 | 4.97 |
| Cst26 | CFIF | + | 100 | −1.924 | 1 | 3.194000 | 4.81 |
| YIL134C-A | CAPY | + | 100 | −2.164 | 1 | 0.199620 | 4.73 |
| Atr1 | CTVA | + | 100 | 0.273 | 1 | 7.775800 | 4.55 |
| Las21 | CALD | + | 100 | −2.887 | 1 | 0.028518 | 4.20 |
| YDL009C | CAVS | + | 100 | 0.237 | 1 | 6.607500 | 4.69 |
| Sua5 | CIQF | + | 100 | −0.601 | 1 | 0.199620 | 5.49 |
| NA | CAAQ | + | 100 | −3.280 | 1 | 0.399250 | 4.82 |
| NA | CAHQ | + | 100 | −3.599 | 1 | 0.399250 | 4.74 |
| NA | CASA | + | 100 | −2.693 | 1 | 0.243980 | 3.91 |
| NA | CKQH | + | 70 | −2.442 | 1 | 0.399250 | 4.37 |
| NA | CNLI | + | 95 | −3.804 | 1 | 0.133080 | 3.84 |
| NA | CSFL | + | 68 | −4.425 | 1 | 0.108890 | 4.28 |
| NA | CVAA | + | 100 | −2.789 | 1 | 0.079849 | 4.81 |
| NA | CVFM | + | 100 | −2.939 | 1 | 2.395500 | 4.76 |
| NA | CKQG | + | 73 | −1.876 | 0 | 0.099811 | 4.06 |
| NA | CKQL | + | 50 | −1.680 | 0 | 0.057035 | 3.84 |
| NA | CQTS | + | 100 | −0.922 | 0 | 0.057035 | 5.44 |
| NA | CQSQ | + | 100 | −1.624 | 1 | 0.159700 | 5.27 |
| NA | CKQA | + | 95 | −1.149 | 1 | 0.133080 | 4.57 |
| NA | CKQC | + | 100 | −0.745 | 1 | 0.099811 | 4.12 |
| NA | CKQD | + | 67 | −4.103 | 0 | 0.066541 | 3.51 |
| NA | CKQE | − | 19 | −3.745 | 0 | 0.066541 | 3.36 |
| NA | CKQF | − | 28 | −2.345 | 0 | 0.057035 | 4.62 |
| NA | CKQH | + | 73 | −2.442 | 1 | 0.399250 | 4.37 |
| NA | CKQI | + | 70 | −1.700 | 1 | 0.099811 | 3.90 |
| NA | CKQK | − | 0 | −4.010 | 0 | 0.036295 | 2.22 |
| NA | CKQM | + | 100 | −1.045 | 1 | 0.133080 | 4.50 |
| NA | CKQN | + | 88 | −5.046 | 0 | 0.199620 | 4.48 |
| NA | CKQP | − | 13 | −2.887 | 0 | 0.399250 | 1.97 |
| NA | CKQQ | + | 100 | −0.747 | 1 | 0.399250 | 5.35 |
| NA | CKQR f | − | 0 | −4.533 | 0 | 0.399250 | 1.77 |
| NA | CKQT | + | 96 | −1.874 | 1 | 0.079849 | 4.68 |
| NA | CKQV | + | 100 | −1.744 | 1 | 0.133080 | 4.50 |
| NA | CKQW | + | 71 | −5.184 | 0 | 0.199620 | 3.57 |
| NA | CKQY | + | 100 | −3.326 | 0 | 0.399250 | 4.50 |
| # Predicted correctly | 30 | 38 | 17 | 45 | |||
| # False positive | 0 | 0 | 0 | 2 | |||
| # False negative | 18 | 10 | 31 | 1 | |||
| % Predicted correctly | 62.5% | 79.2% | 35.4% | 93.8% | |||
| % False positive | 0.0% | 0.0% | 0.0% | 5.1% | |||
| % False negative | 64.3% | 50.0% | 75.6% | 11.1% | |||
Protein or gene name as reported in the Saccharomyces Genome Database.
Prenylation status and % gel-shift observed in context of Ydj1.
Values reported from Maurer-Stroh and Eisenhaber (2005); positive cutoff > −2.
Values reported from Berger, Yeung et al. (2022); positive cutoff > 0.
Values reported from Stein, Kubala et al. (2015); positive cutoff > 3.
The Ydj1 gel-shift patterns of these sequences revealed a doublet in both the presence and absence of FTase, so they were deemed as having 0% prenylation; the reason for the doublet pattern is unknown.