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Comparison: application of the big-Pi fungal predictor on the list created by Caro LH et al. , Yeast. 1997 Dec;13(15):1477-89

Contact:
Birgit Eisenhaber (IMP/Austria)
Georg Schneider (IMP/Austria)
Michael Wildpaner (IMP/Austria)
Frank Eisenhaber (IMP/Austria)

Summary Table:

  Prediction Quality Rate Percentage
1:P 48/58 82.76%
1:S 3/58 5.17%
1:S (Positive Total Score) 3/58 5.17%
1:S (Negative Total Score) - -
1:I 5/58 8.62%
1:N 2/58 3.45%
Not Predicted 7/58 12.07%
Predicted 51/58 87.93%

Reasons for not predicted proteins are detailed below

N   ID Length Prediction Quality Site Profile Score Function Score Total Score PValue
1 YAL063C 1322 1:P 1299 16.34 -5.97 10.37 3.562914e-05
2 YAR050W 1537 1:P 1514 16.34 -5.97 10.37 3.562914e-05
3 YBR067c 210 1:P 186 20.05 -0.43 19.62 7.750742e-07
4 YBR078w 468 1:I 444 -9.93 -50.53 -60.46 4.002212e-01
5 YCL048w 463 1:P 440 15.12 -1.24 13.88 9.585261e-06
6 YCR089w 1609 1:P 1588 14.61 -4.38 10.23 3.746978e-05
7 YDR055W 444 1:P 419 18.03 -3.65 14.38 7.870454e-06
8 YDR077W 338 1:P 318 19.28 -1.80 17.48 2.095550e-06
9 YDR144C 409 1:P 388 13.13 -5.18 7.95 8.059617e-05
10 YDR261C 562 1:I 539 3.07 -22.70 -19.63 2.424033e-02
11 YDR349C 596 1:N 573 5.62 -10.27 -4.65 2.154883e-03
12 YDR522C 502 1:P 475 14.12 -5.48 8.64 6.433754e-05
13 YDR534C 528 1:P 506 18.84 -0.29 18.55 1.286022e-06
14 YEL040W 467 1:P 445 16.55 -0.58 15.97 4.065408e-06
15 YER011W 254 1:P 233 17.71 -0.79 16.92 2.690687e-06
16 YER150W 148 1:P 127 20.06 -1.05 19.01 1.034709e-06
17 YGR189C 507 1:P 482 14.84 -2.56 12.28 1.779857e-05
18 YHR126C 159 1:P 137 17.08 -0.57 16.51 3.220714e-06
19 YHR211W 1075 1:P 1052 16.34 -5.97 10.37 3.562914e-05
20 YIL011W 269 1:P 245 19.43 -0.96 18.47 1.333957e-06
N   ID Length Prediction Quality Site Profile Score Function Score Total Score PValue
21 YIR019C 1367 1:P 1346 13.57 -3.00 10.57 3.324204e-05
22 YJL078C 881 1:P 853 15.07 -2.40 12.67 1.536207e-05
23 YJL171C 396 1:N 367 0.23 -16.77 -16.54 1.621107e-02
24 YJR004C 650 1:P 627 9.35 -6.18 3.17 3.330099e-04
25 YJR150C 298 1:P 275 20.07 -0.58 19.49 8.231140e-07
26 YJR151C 1161 1:P 1137 18.18 -1.34 16.84 2.781958e-06
27 YKL046C 449 1:P 428 12.98 -8.96 4.02 2.633158e-04
28 YKL096W 239 1:P 218 14.41 -0.06 14.35 7.943714e-06
29 YKL096W-A 92 1:P 71 18.86 -1.24 17.62 1.969735e-06
30 YKR102W 1169 1:I 1135 6.16 -21.09 -14.93 1.292145e-02
31 YLR040C 224 1:P 203 14.67 -1.39 13.28 1.213639e-05
32 YLR042C 161 1:P 139 8.07 -2.68 5.39 1.773594e-04
33 YLR110C 133 1:P 112 19.02 -1.27 17.75 1.855228e-06
34 YLR120C 569 1:S 548 8.90 -8.25 0.65 6.441821e-04
35 YLR121C 508 1:P 483 16.42 -1.63 14.79 6.638689e-06
36 YLR194CP 254 1:P 232 17.55 -0.25 17.30 2.270712e-06
37 YLR343WP 555 1:S 531 6.49 -4.97 1.52 5.167992e-04
38 YLR391W-AP 238 1:P 217 16.59 -1.95 14.64 7.055745e-06
39 YMR006C 706 1:P 681 16.44 -0.05 16.39 3.383570e-06
40 YMR008C 664 1:P 634 12.83 -2.99 9.84 4.279396e-05
N   ID Length Prediction Quality Site Profile Score Function Score Total Score PValue
41 YMR200W 218 1:P 197 12.41 -4.24 8.17 7.496052e-05
42 YMR215W 524 1:P 492 16.42 -0.28 16.14 3.768587e-06
43 YMR307W 559 1:P 528 17.09 -3.35 13.74 1.012428e-05
44 YNL190W 204 1:P 174 14.85 -1.44 13.41 1.153841e-05
45 YNL300W 102 1:P 80 15.37 -1.10 14.27 8.208180e-06
46 YNL322C 313 1:I 288 8.30 -10.69 -2.39 1.322547e-03
47 YNL327W 1041 1:P 1020 17.26 -0.98 16.28 3.554759e-06
48 YNR044W 725 1:P 700 12.82 -4.61 8.21 7.395845e-05
49 YOL030W 484 1:P 462 13.52 -2.02 11.50 2.375612e-05
50 YOL132W 471 1:S 447 10.07 -8.40 1.67 4.963281e-04
51 YOL155C 967 1:P 946 7.68 -5.02 2.66 3.832043e-04
52 YOR009W 487 1:P 465 18.83 -2.32 16.51 3.219705e-06
53 YOR010C 251 1:P 231 16.26 -0.94 15.32 5.346892e-06
54 YOR214C 236 1:P 213 13.19 -0.42 12.77 1.480982e-05
55 YOR382C 153 1:P 129 21.12 0.00 21.12 3.681945e-07
56 YOR383C 204 1:P 182 19.65 -0.36 19.29 9.063640e-07
57 YPL130W 223 1:P 198 13.42 -1.73 11.69 2.218126e-05
58 YPL261C 102 1:I 83 -4.93 -14.31 -19.24 2.310845e-02



7 proteins described in the paper have not been predicted as suitable candidates for GPI anchoring:

  1. We could not detect a suitable omega-site for 4 proteins:

    2. YDR261C
    YDR349C
    YNL322C
    YPL261C

  2. 1 protein lacks an appropriately constructed hydrophobic tail:

    3. YJL171C

  3. For 1 protein the GPI motif length is out of the interval [17..32] AAs:

    4. YKR102W

  4. 1 sequence is non-compatible with our prediction function at all:

    5. YBR078W (*) A corrected sequence for this ORF was given in Hamada et al., 1999, see entry EC33_YEAST in the learning set. After this correction the sequence would be predicted as suitable candidate for GPI anchoring.



Last modified: 18th September 2003