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Comparison: application of the big-Pi plant predictor on the list created by Borner GHH et al. , Plant Physiol 2002 Jun;129(2):486-99

Contact:
Birgit Eisenhaber (IMP/Austria)
Michael Wildpaner (IMP/Austria)
Frank Eisenhaber (IMP/Austria)
Carolyn Schultz (University of Adelaide/Australia)
Paul Dupree and Georg Borner (University of Cambridge/UK)

Summary Table:

  Prediction Quality Rate Percentage
1:P 126/208 60.58%
1:S 15/208 7.21%
1:S (Positive Total Score) 11/208 5.29%
1:S (Negative Total Score) 4/208 1.92%
1:I 52/208 25.00%
1:N 15/208 7.21%
Not Predicted 71/208 34.13%
Predicted 137/208 65.87%

With a relaxed definition of prediction by big-Pi, all P and S cases, 141 out of 208 sequences (67.79%) would be suggested as suitable candidates for GPI anchoring.

Reasons for not predicted proteins are detailed below

N   ID Length Prediction Quality Site Profile Score Function Score Total Score PValue
1 AAC24384.1 350 1:I 331 -23.94 -47.37 -71.31 6.284886e-01
2 AAD10681.1 247 1:P 224 14.59 -0.40 14.19 1.250229e-06
3 AAF82207.1 252 1:I 226 -11.05 -56.20 -67.25 5.679897e-01
4 AAF79572.1 258 1:P 234 8.25 -2.66 5.59 7.155918e-05
5 AAG42922.1 492 1:P 466 11.97 -0.87 11.10 6.337929e-06
6 AAC32929.1 228 1:P 208 14.80 -5.10 9.70 1.240284e-05
7 AAB60732.1 361 1:P 336 18.80 -0.70 18.10 1.159778e-07
8 AAD50026.1 729 1:I 701 -9.79 -19.59 -29.38 8.201486e-02
9 AAF78376.1 180 1:P 158 20.09 -1.08 19.01 6.284218e-08
10 AAF98409.1 184 1:S 158 10.20 -9.69 0.51 4.242757e-04
11 AAF79910.1 316 1:S 286 10.38 -9.21 1.17 3.440482e-04
12 AAF18529.1 174 1:N 148 1.06 -4.99 -3.93 1.502548e-03
13 AAC00615.1 144 1:P 120 12.00 -1.04 10.96 6.810274e-06
14 AAC00572.1 377 1:N 352 7.65 -12.79 -5.14 2.032900e-03
15 AAF97962.1 125 1:P 95 12.48 -5.87 6.61 4.769818e-05
16 AAF98573.1 197 1:P 172 13.83 -0.56 13.27 2.076090e-06
17 AAF79851.1 304 1:I 272 -6.18 -27.19 -33.37 1.141246e-01
18 AAG12864.1 407 1:P 385 10.50 -5.09 5.41 7.660791e-05
19 AAD32933.1 239 1:P 216 17.73 -0.16 17.57 1.639646e-07
20 AAC77827.1 133 1:P 109 20.29 -1.03 19.26 5.297011e-08
N   ID Length Prediction Quality Site Profile Score Function Score Total Score PValue
21 AAF79800.1 219 1:I 192 -12.84 -39.00 -51.84 3.326408e-01
22 AAC64895.1 200 1:P 174 8.74 -0.70 8.04 2.609657e-05
23 AAG21543.1 58 1:P 36 15.61 -2.53 13.08 2.291733e-06
24 AAG50914.1 163 1:N 142 -4.10 -6.80 -10.90 7.085780e-03
25 AAD14473.1 360 1:P 335 8.35 -3.92 4.43 1.110509e-04
26 AAC28508.1 429 1:P 401 7.63 -2.46 5.17 8.406813e-05
27 AAF19714.1 299 1:N 268 6.90 -14.74 -7.84 3.798053e-03
28 AAF19686.1 174 1:I 149 16.77 -16.80 -0.03 5.002063e-04
29 AAF98209.1 747 1:P 726 10.83 -4.02 6.81 4.382232e-05
30 AAF98210.1 1109 1:I 1090 -22.43 -51.65 -74.08 6.678269e-01
31 AAK43968.1 222 1:P 197 11.98 -1.62 10.36 9.094143e-06
32 AAB61099.1 378 1:P 356 9.79 -0.37 9.42 1.413705e-05
33 AAD55511.1 138 1:S 111 4.30 -5.47 -1.17 7.034085e-04
34 AAG21490.1 181 1:P 153 13.61 -2.67 10.94 6.863952e-06
35 AAF36746.1 193 1:P 169 13.15 -2.27 10.88 7.058630e-06
36 AAD55298.1 709 1:I 671 17.92 -32.93 -15.01 1.453600e-02
37 AAF07793.1 409 1:I 374 8.01 -16.21 -8.20 4.108550e-03
38 AAF08558.1 363 1:I 342 0.91 -29.32 -28.41 7.504540e-02
39 AAF68112.1 192 1:P 166 18.73 -4.00 14.73 9.214194e-07
40 AAD55468.1 496 1:P 469 8.61 -3.77 4.84 9.542634e-05
N   ID Length Prediction Quality Site Profile Score Function Score Total Score PValue
41 AAD12705.1 288 1:I 249 -1.01 -45.14 -46.15 2.545321e-01
42 AAD22328.1 254 1:S 232 12.19 -10.76 1.43 3.152760e-04
43 AAG40020.2 191 1:P 172 12.83 -2.62 10.21 9.768812e-06
44 AAB81674.1 350 1:P 318 11.33 -0.76 10.57 8.223500e-06
45 AAD10143.1 478 1:P 451 5.92 -1.76 4.16 1.226344e-04
46 AAK20859.1 247 1:I 220 13.55 -15.42 -1.87 8.591675e-04
47 AAD20925.1 181 1:P 153 13.96 -1.17 12.79 2.672529e-06
48 AAC77824.1 131 1:P 107 20.93 -1.04 19.89 3.425805e-08
49 AAB87117.1 185 1:P 159 11.66 -1.76 9.90 1.128687e-05
50 AAC63667.1 207 1:P 182 15.08 -4.01 11.07 6.444261e-06
51 AAD18116.1 280 1:P 256 20.10 -1.52 18.58 8.451990e-08
52 AAD23007.1 176 1:P 154 13.07 -3.79 9.28 1.504901e-05
53 AAB95306.1 206 1:P 178 10.56 -2.21 8.35 2.278833e-05
54 AAC77871.1 176 1:P 149 14.11 -3.03 11.08 6.411561e-06
55 AAD20685.1 115 1:I 90 0.37 -10.03 -9.66 5.555518e-03
56 AAC63847.1 200 1:P 177 16.68 -2.33 14.35 1.145833e-06
57 AAC32038.1 261 1:P 232 7.00 -2.84 4.16 1.226142e-04
58 AAC26689.1 401 1:P 382 12.73 -1.28 11.45 5.332528e-06
59 AAD21471.1 475 1:I 455 -18.70 -52.74 -71.44 6.304566e-01
60 AAB97119.1 549 1:N 528 -2.46 -7.44 -9.90 5.831289e-03
N   ID Length Prediction Quality Site Profile Score Function Score Total Score PValue
61 AAC78534.1 99 1:I 67 2.94 -22.20 -19.26 2.706428e-02
62 AAD21728.1 462 1:I 432 7.43 -16.71 -9.28 5.151579e-03
63 AAB64040.1 134 1:I 103 -4.09 -22.72 -26.81 6.442684e-02
64 AAC16079.1 205 1:I 179 -0.26 -13.19 -13.45 1.123253e-02
65 AAC16080.1 204 1:I 178 -1.69 -15.90 -17.59 2.148846e-02
66 AAB47973.1 202 1:P 178 17.68 -0.84 16.84 2.596617e-07
67 AAC31167.1 342 1:S 317 5.21 -5.84 -0.63 6.007296e-04
68 AAB82617.1 420 1:P 392 16.56 -1.34 15.22 6.940608e-07
69 AAG24284.1 73 1:I 37 12.65 -21.25 -8.60 4.472549e-03
70 AAC63647.1 136 1:P 108 19.68 -4.07 15.61 5.511601e-07
71 AAD48513.1 183 1:P 157 13.79 -2.39 11.40 5.483314e-06
72 AAF26167.1 167 1:S 138 12.01 -11.74 0.27 4.560764e-04
73 AAF01553.1 136 1:P 112 15.76 -3.48 12.28 3.494692e-06
74 AAF01556.1 87 1:P 64 14.68 -1.30 13.38 1.956909e-06
75 AAF14841.1 70 1:N 38 -6.74 -10.49 -17.23 2.039811e-02
76 AAF14840.1 70 1:S 41 6.76 -6.86 -0.10 5.118038e-04
77 AAF02128.1 452 1:P 426 11.20 -5.08 6.12 5.793040e-05
78 AAF26986.1 488 1:I 466 -1.03 -13.89 -14.92 1.433200e-02
79 AAF26777.1 332 1:I 315 -0.96 -47.61 -48.57 2.867206e-01
80 AAF04894.1 159 1:P 137 16.24 0.00 16.24 3.770785e-07
N   ID Length Prediction Quality Site Profile Score Function Score Total Score PValue
81 AAF63823.1 147 1:P 127 15.63 -1.22 14.41 1.106196e-06
82 AAF02148.1 128 1:I 110 -27.16 -76.13 -103.29 9.175929e-01
83 AAF02137.1 462 1:I 429 -6.70 -46.66 -53.36 3.548030e-01
84 BAB00834.1 255 1:S 225 9.95 -8.47 1.48 3.102655e-04
85 BAB01759.1 60 1:P 33 9.61 -7.02 2.59 2.144392e-04
86 BAB00585.1 653 1:P 628 11.66 -3.67 7.99 2.666751e-05
87 BAB02017.1 335 1:N 306 3.80 -13.51 -9.71 5.616297e-03
88 BAB02217.1 188 1:P 171 12.96 -2.87 10.09 1.032879e-05
89 BAB01165.1 203 1:P 179 20.10 -1.39 18.71 7.724964e-08
90 BAB01166.1 633 1:P 607 13.78 -8.38 5.40 7.711078e-05
91 BAB01475.1 170 1:P 146 12.77 -4.19 8.58 2.062659e-05
92 BAB02092.1 595 1:N 576 -7.36 -10.24 -17.60 2.152685e-02
93 BAB02115.1 174 1:P 148 16.93 -1.10 15.83 4.820164e-07
94 BAA95716.1 132 1:P 108 19.61 -1.35 18.26 1.041891e-07
95 AAG12670.1 441 1:P 417 17.15 -0.73 16.42 3.370452e-07
96 CAB83144.1 193 1:P 166 12.13 -2.43 9.70 1.242207e-05
97 CAB62325.1 420 1:I 395 7.63 -15.00 -7.37 3.428513e-03
98 CAB62355.1 89 1:I 69 -19.30 -47.46 -66.76 5.605047e-01
99 CAB62655.1 529 1:P 504 9.30 -1.81 7.49 3.304501e-05
100 CAB62657.2 475 1:P 449 10.83 0.00 10.83 7.247040e-06
N   ID Length Prediction Quality Site Profile Score Function Score Total Score PValue
101 CAC07928.1 436 1:I 410 -27.77 -61.88 -89.65 8.397609e-01
102 CAB88347.1 154 1:I 129 -3.51 -25.96 -29.47 8.267168e-02
103 CAB81604.1 103 1:P 81 4.84 -0.97 3.87 1.362560e-04
104 CAB41186.1 61 1:P 35 17.04 -4.17 12.87 2.574044e-06
105 CAB68193.1 177 1:P 152 10.73 -8.48 2.25 2.409041e-04
106 CAB88306.1 293 1:I 275 -12.58 -13.61 -26.19 6.055774e-02
107 CAB87864.1 187 1:P 164 9.03 -2.06 6.97 4.109705e-05
108 AAB07009.1 222 1:P 198 15.97 -3.89 12.08 3.875946e-06
109 CAB82694.1 422 1:P 398 15.40 -4.96 10.44 8.730674e-06
110 CAB71905.1 117 1:P 86 14.98 -0.08 14.90 8.362888e-07
111 CAB77890.1 766 1:I 743 -1.66 -24.55 -26.21 6.068374e-02
112 CAB77992.1 194 1:P 164 16.89 -5.83 11.06 6.490063e-06
113 CAB78027.1 127 1:P 107 15.92 -2.50 13.42 1.913372e-06
114 CAB45983.1 161 1:P 139 9.76 -3.16 6.60 4.777802e-05
115 CAB41712.1 587 1:P 562 16.93 -6.79 10.14 1.009186e-05
116 AAK20858.1 403 1:N 378 3.00 -5.83 -2.83 1.122288e-03
117 CAB45494.1 176 1:P 154 10.92 -3.82 7.10 3.887082e-05
118 CAB78588.1 148 1:S 123 8.20 -7.47 0.73 3.949825e-04
119 CAA74765.1 661 1:I 637 6.02 -21.17 -15.15 1.486889e-02
120 CAB78656.1 164 1:P 141 11.63 -5.87 5.76 6.680693e-05
N   ID Length Prediction Quality Site Profile Score Function Score Total Score PValue
121 CAB78706.1 364 1:N 338 4.69 -7.23 -2.54 1.037086e-03
122 CAB37461.1 431 1:I 401 1.15 -20.38 -19.23 2.697327e-02
123 CAA16548.1 162 1:P 137 10.27 -5.76 4.51 1.078469e-04
124 CAA16549.1 116 1:I 88 -2.23 -21.51 -23.74 4.673572e-02
125 CAB38961.1 59 1:P 38 15.31 -4.72 10.59 8.140760e-06
126 CAB36515.1 759 1:P 735 13.91 -3.10 10.81 7.309804e-06
127 CAB38841.1 668 1:P 636 10.74 -4.19 6.55 4.870229e-05
128 CAB38264.1 349 1:P 326 14.52 -0.28 14.24 1.212966e-06
129 CAB36779.1 304 1:P 282 17.51 -6.50 11.01 6.639663e-06
130 CAB79630.1 160 1:P 135 12.74 -1.62 11.12 6.292866e-06
131 CAB79777.1 190 1:P 163 13.09 -1.42 11.67 4.779703e-06
132 CAB79832.1 484 1:P 460 9.07 -2.15 6.92 4.190108e-05
133 CAA16540.1 278 1:P 255 17.44 -1.08 16.36 3.501847e-07
134 CAB40754.1 177 1:P 154 17.82 -1.55 16.27 3.697304e-07
135 CAA22576.1 216 1:P 187 12.33 -3.05 9.28 1.507796e-05
136 CAA21474.1 455 1:N 431 2.14 -6.58 -4.44 1.708298e-03
137 CAA18495.1 301 1:P 276 12.22 -5.65 6.57 4.831037e-05
138 AAG41964.1 209 1:P 183 16.19 -2.13 14.06 1.346535e-06
139 CAB81444.1 450 1:I 426 7.60 -27.20 -19.60 2.831801e-02
140 BAB08377.1 246 1:P 219 11.44 -2.78 8.66 1.989181e-05
N   ID Length Prediction Quality Site Profile Score Function Score Total Score PValue
141 BAB08961.1 465 1:I 449 -16.29 -52.33 -68.62 5.887269e-01
142 CAB87275.1 213 1:P 184 19.96 -6.46 13.50 1.830506e-06
143 CAB62612.1 194 1:N 171 7.59 -14.90 -7.31 3.381889e-03
144 CAB93722.1 67 1:P 46 5.47 -0.91 4.56 1.059625e-04
145 CAC05463.1 129 1:I 110 -1.87 -28.36 -30.23 8.834439e-02
146 CAB92049.1 528 1:P 503 16.07 -0.58 15.49 5.919264e-07
147 CAB89400.1 135 1:P 111 22.16 -2.16 20.00 3.160536e-08
148 CAB87692.1 61 1:P 35 21.13 -1.75 19.38 4.898819e-08
149 CAB87672.1 181 1:P 154 11.34 -3.48 7.86 2.822303e-05
150 BAB11118.1 151 1:I 120 8.02 -15.74 -7.72 3.700852e-03
151 BAB08290.1 70 1:P 41 11.06 -3.82 7.24 3.669818e-05
152 BAB08294.1 383 1:S 362 3.74 -2.65 1.09 3.527080e-04
153 BAB08298.1 119 1:S 92 5.14 -5.65 -0.51 5.793993e-04
154 CAB42531.1 150 1:P 126 16.40 -6.60 9.80 1.185559e-05
155 CAB89342.1 75 1:I 57 1.12 -21.62 -20.50 3.183354e-02
156 CAC01762.1 395 1:P 373 16.48 -1.03 15.45 6.062885e-07
157 BAB09480.1 488 1:N 465 0.39 -7.23 -6.84 3.037574e-03
158 CAA77089.1 196 1:P 174 19.11 -1.50 17.61 1.596242e-07
159 BAB08342.1 172 1:N 151 8.08 -14.61 -6.53 2.829823e-03
160 AAC26242.1 187 1:I 155 9.27 -14.25 -4.98 1.958295e-03
N   ID Length Prediction Quality Site Profile Score Function Score Total Score PValue
161 BAB09930.1 287 1:I 263 -2.03 -23.40 -25.43 5.603864e-02
162 BAB09366.1 478 1:S 452 12.12 -10.76 1.36 3.233221e-04
163 BAB10221.1 703 1:I 668 -18.81 -61.18 -79.99 7.439493e-01
164 BAB08533.1 130 1:P 109 15.70 -0.05 15.65 5.364610e-07
165 BAB09698.1 68 1:N 41 -3.48 -11.45 -14.93 1.435971e-02
166 BAB09700.1 69 1:I 42 -4.41 -16.34 -20.75 3.284112e-02
167 BAB11104.1 286 1:P 261 11.40 -3.46 7.94 2.731906e-05
168 BAB11105.1 287 1:P 259 11.72 -3.45 8.27 2.360888e-05
169 BAB11106.1 287 1:P 263 6.63 -0.74 5.89 6.345912e-05
170 BAB08443.1 425 1:P 401 13.69 -0.14 13.55 1.784927e-06
171 BAB10980.1 247 1:P 224 15.69 -0.01 15.68 5.278481e-07
172 BAB09219.1 425 1:I 393 7.59 -15.97 -8.38 4.263376e-03
173 BAB10345.1 663 1:P 638 10.00 -4.70 5.30 8.002897e-05
174 BAB10346.1 162 1:P 139 15.97 -0.37 15.60 5.539111e-07
175 BAB10290.1 175 1:I 147 0.86 -22.92 -22.06 3.852724e-02
176 BAB08664.1 592 1:P 564 13.78 -4.19 9.59 1.302712e-05
177 BAB09787.1 63 1:P 38 12.46 -1.55 10.91 6.962598e-06
178 BAB10717.1 370 1:P 345 14.87 -8.71 6.16 5.699746e-05
179 BAB08565.1 766 1:P 742 12.01 -4.49 7.52 3.267140e-05
180 BAB09240.1 424 1:P 398 9.96 -1.81 8.15 2.494549e-05
N   ID Length Prediction Quality Site Profile Score Function Score Total Score PValue
181 BAB09299.1 168 1:P 144 13.85 -1.65 12.20 3.645513e-06
182 BAA97180.1 60 1:P 38 16.69 -6.90 9.79 1.187008e-05
183 BAB10996.1 747 1:S 722 11.20 -9.85 1.35 3.236966e-04
184 BAB11001.1 518 1:I 494 -0.13 -21.86 -21.99 3.822081e-02
185 BAA96908.1 750 1:P 728 15.54 -0.44 15.10 7.444868e-07
186 BAB10263.1 465 1:P 442 12.65 -3.81 8.84 1.838499e-05
187 BAB08232.1 249 1:S 220 7.60 -5.82 1.78 2.811136e-04
188 AAK56072.1 456 1:P 431 19.08 -0.78 18.30 1.019147e-07
189 BAB10644.1 204 1:I 181 -18.24 -46.14 -64.38 5.237022e-01
190 BAB10375.1 171 1:I 142 11.69 -13.47 -1.78 8.393127e-04
191 BAA97185.1 223 1:P 196 24.41 -0.71 23.70 1.858257e-09
192 BAA97210.1 696 1:P 672 20.16 -1.86 18.30 1.016945e-07
193 BAB08815.1 69 1:P 40 9.98 -6.95 3.03 1.841470e-04
194 BAB10276.1 182 1:P 153 16.52 -2.86 13.66 1.676305e-06
195 BAB09862.1 131 1:P 108 11.81 -0.06 11.75 4.588110e-06
196 BAA97291.1 485 1:P 457 8.94 -4.80 4.14 1.235603e-04
197 BAB11561.1 130 1:P 106 19.68 -1.05 18.63 8.158456e-08
198 AAC77825.1 139 1:P 116 13.57 -0.86 12.71 2.799657e-06
199 AAC17632.1 477 1:I 449 2.14 -24.63 -22.49 4.052852e-02
200 BAB00758.1 456 1:I 430 -6.46 -19.04 -25.50 5.647970e-02
N   ID Length Prediction Quality Site Profile Score Function Score Total Score PValue
201 CAB88124.1 376 1:P 350 16.49 -2.32 14.17 1.262525e-06
202 BAB01476.1 203 1:P 181 19.11 -0.84 18.27 1.036879e-07
203 AAD15432.1 169 1:P 147 14.92 -8.35 6.57 4.831245e-05
204 BAA96979.1 67 1:I 39 -4.67 -12.93 -17.60 2.153183e-02
205 AAF99747.1 229 1:I 212 1.21 -29.02 -27.81 7.096424e-02
206 AAC24095.1 150 1:P 120 11.13 -2.26 8.87 1.812560e-05
207 CAC01831.1 104 1:S 84 7.22 -6.12 1.10 3.518288e-04
208 BAB02002.1 510 1:I 488 7.99 -8.68 -0.69 6.109457e-04



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

  1. 3 proteins have an untypical N-terminal region [-11..-1] (relative to the omega-site):

    2. AAC31167.1
    BAB09219.1
    BAB02002.1

  2. We could not detect a suitable omega-site for 22 proteins:

    3. AAD50026.1
    AAG50914.1
    AAD55298.1
    AAF07793.1
    AAD12705.1
    AAD20685.1
    AAD21728.1
    AAC16079.1
    AAC16080.1
    AAG24284.1
    AAF14841.1
    AAF14840.1
    CAB88306.1
    CAA74765.1
    CAB78706.1
    CAB37461.1
    BAB09480.1
    AAC26242.1
    BAB09698.1
    BAB00758.1
    AAF18529.1
    AAK20858.1

  3. In further 4 proteins a typical spacer region is missing:

    4. AAF26986.1
    AAF26777.1
    CAA21474.1
    BAB09700.1

  4. 24 proteins lack an appropriately constructed hydrophobic tail:

    5. AAF82207.1
    AAF79851.1
    AAF19686.1
    AAD55511.1
    AAF08558.1
    AAK20859.1
    AAB97119.1
    AAC78534.1
    AAB64040.1
    CAB62325.1
    CAB77890.1
    CAA16549.1
    BAB11118.1
    BAB08298.1
    CAB89342.1
    BAB08342.1
    BAB10290.1
    BAB11001.1
    BAB10375.1
    AAC17632.1
    AAC00572.1
    AAF19714.1
    BAB02017.1
    CAB62612.1

  5. 18 sequences are non-compatible with our prediction function at all:

    6. AAC24384.1
    AAF79800.1
    AAF98210.1
    AAD21471.1
    CAB62355.1
    AAF02148.1
    AAF02137.1
    CAC07928.1
    CAB81444.1
    BAB08961.1
    CAC05463.1
    BAB09930.1
    BAB10221.1
    BAB10644.1
    BAA96979.1
    AAF99747.1
    BAB02092.1
    CAB88347.1



Last modified: 30th October 2002