# This file is the result of combining several RDB files, specifically # T0268.t04.dssp-ebghstl.rdb (weight 1.53986) # T0268.t04.stride-ebghtl.rdb (weight 1.24869) # T0268.t04.str2.rdb (weight 1.54758) # T0268.t04.alpha.rdb (weight 0.659012) # These files were combined by translating their predictions into EHL # predictions with tables generated by compare-real, and then combining # those predictions with weights proportional to their mutual information # with the EHL alphabet. The comments from the individual files follow. # # Comments from T0268.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0268 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0268.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 31.1622 # # ============================================ # Comments from T0268.t04.stride-ebghtl.rdb # ============================================ # TARGET T0268 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0268.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 31.1622 # # ============================================ # Comments from T0268.t04.str2.rdb # ============================================ # TARGET T0268 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0268.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 31.1622 # # ============================================ # Comments from T0268.t04.alpha.rdb # ============================================ # TARGET T0268 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0268.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 31.1622 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0708 0.0310 0.8983 2 R 0.0976 0.0263 0.8760 3 P 0.1055 0.0832 0.8113 4 M 0.1007 0.2220 0.6773 5 T 0.1269 0.2291 0.6439 6 H 0.1320 0.2652 0.6028 7 V 0.1006 0.4837 0.4157 8 P 0.0970 0.6848 0.2182 9 V 0.1192 0.7357 0.1452 10 L 0.1016 0.7828 0.1156 11 Y 0.0331 0.8832 0.0837 12 Q 0.0118 0.9224 0.0658 13 E 0.0187 0.9053 0.0760 14 A 0.0227 0.8916 0.0857 15 L 0.0384 0.8539 0.1076 16 D 0.0477 0.8030 0.1493 17 L 0.0388 0.7538 0.2074 18 L 0.1336 0.4878 0.3786 19 A 0.2696 0.2189 0.5114 20 V 0.3195 0.0870 0.5935 21 R 0.1321 0.0229 0.8449 22 P 0.0434 0.0689 0.8878 23 G 0.0332 0.0405 0.9262 24 G 0.2881 0.0226 0.6894 25 V 0.8394 0.0035 0.1571 26 Y 0.9267 0.0036 0.0697 27 V 0.9253 0.0034 0.0713 28 D 0.8861 0.0067 0.1072 29 A 0.6856 0.0174 0.2970 30 T 0.4673 0.0372 0.4954 31 L 0.2686 0.0840 0.6474 32 G 0.1275 0.0842 0.7883 33 G 0.0898 0.1282 0.7820 34 A 0.0788 0.2209 0.7004 35 G 0.0793 0.3228 0.5978 36 H 0.0737 0.5549 0.3714 37 A 0.0409 0.7733 0.1858 38 R 0.0561 0.7975 0.1464 39 G 0.1186 0.7402 0.1412 40 I 0.1634 0.7026 0.1341 41 L 0.1718 0.6117 0.2165 42 E 0.1186 0.4306 0.4508 43 R 0.0739 0.1933 0.7328 44 G 0.0606 0.0347 0.9047 45 G 0.2057 0.0119 0.7824 46 R 0.7794 0.0057 0.2150 47 V 0.9222 0.0031 0.0747 48 I 0.8973 0.0128 0.0898 49 G 0.9129 0.0045 0.0826 50 L 0.8207 0.0090 0.1702 51 D 0.4272 0.0187 0.5541 52 Q 0.1061 0.0338 0.8601 53 D 0.0928 0.0231 0.8841 54 P 0.0052 0.9020 0.0928 55 E 0.0051 0.9408 0.0541 56 A 0.0051 0.9502 0.0448 57 V 0.0052 0.9536 0.0412 58 A 0.0058 0.9463 0.0479 59 R 0.0068 0.9303 0.0629 60 A 0.0080 0.9048 0.0872 61 K 0.0119 0.7941 0.1940 62 G 0.0153 0.6267 0.3580 63 L 0.0337 0.5295 0.4368 64 H 0.0711 0.2412 0.6877 65 L 0.0622 0.0568 0.8809 66 P 0.0283 0.1087 0.8630 67 G 0.0689 0.0583 0.8727 68 L 0.5422 0.0166 0.4412 69 T 0.8382 0.0099 0.1520 70 V 0.8908 0.0099 0.0994 71 V 0.8105 0.0237 0.1658 72 Q 0.5269 0.0490 0.4241 73 G 0.1388 0.0721 0.7892 74 N 0.0969 0.0973 0.8057 75 F 0.0285 0.6511 0.3204 76 R 0.0090 0.8564 0.1346 77 H 0.0091 0.8902 0.1007 78 L 0.0069 0.9168 0.0763 79 K 0.0051 0.9501 0.0448 80 R 0.0048 0.9517 0.0435 81 H 0.0048 0.9558 0.0394 82 L 0.0049 0.9542 0.0410 83 A 0.0050 0.9452 0.0498 84 A 0.0068 0.9091 0.0841 85 L 0.0441 0.4779 0.4780 86 G 0.0400 0.0424 0.9176 87 V 0.0677 0.0503 0.8819 88 E 0.1061 0.1135 0.7804 89 R 0.3157 0.0983 0.5860 90 V 0.4373 0.0228 0.5399 91 D 0.4930 0.0499 0.4571 92 G 0.8737 0.0071 0.1192 93 I 0.9178 0.0055 0.0767 94 L 0.9216 0.0066 0.0718 95 A 0.8634 0.0229 0.1137 96 D 0.6296 0.0255 0.3448 97 L 0.2631 0.0662 0.6707 98 G 0.1173 0.0538 0.8289 99 V 0.2256 0.0501 0.7242 100 S 0.1682 0.0547 0.7771 101 S 0.1322 0.1872 0.6805 102 F 0.1320 0.2495 0.6185 103 H 0.2610 0.2393 0.4997 104 L 0.2879 0.0987 0.6134 105 D 0.1919 0.0634 0.7447 106 D 0.1081 0.0392 0.8527 107 P 0.0344 0.2274 0.7382 108 S 0.0482 0.2471 0.7047 109 R 0.1147 0.1901 0.6952 110 G 0.2131 0.1008 0.6860 111 F 0.3950 0.1017 0.5033 112 S 0.4963 0.1311 0.3726 113 Y 0.4230 0.2149 0.3621 114 Q 0.3310 0.2294 0.4395 115 K 0.2231 0.1870 0.5899 116 E 0.1180 0.1070 0.7751 117 G 0.0947 0.0373 0.8680 118 P 0.1448 0.1024 0.7528 119 L 0.2420 0.1660 0.5920 120 D 0.2889 0.2007 0.5104 121 M 0.3064 0.2301 0.4636 122 R 0.3559 0.1734 0.4707 123 M 0.3129 0.1138 0.5734 124 G 0.1376 0.0565 0.8058 125 L 0.0480 0.1158 0.8362 126 E 0.0397 0.0921 0.8682 127 G 0.0499 0.0660 0.8841 128 P 0.1025 0.1197 0.7777 129 T 0.2134 0.2370 0.5496 130 A 0.0140 0.9259 0.0601 131 K 0.0154 0.9357 0.0489 132 E 0.0173 0.9347 0.0481 133 V 0.0168 0.9293 0.0538 134 V 0.0239 0.8625 0.1135 135 N 0.0340 0.6094 0.3565 136 R 0.0424 0.2603 0.6973 137 L 0.0674 0.0260 0.9065 138 P 0.0625 0.0189 0.9186 139 L 0.0049 0.9391 0.0560 140 E 0.0047 0.9586 0.0368 141 A 0.0048 0.9590 0.0362 142 L 0.0047 0.9598 0.0355 143 A 0.0047 0.9602 0.0351 144 R 0.0047 0.9598 0.0356 145 L 0.0047 0.9591 0.0362 146 L 0.0047 0.9559 0.0394 147 R 0.0050 0.9449 0.0501 148 E 0.0073 0.8802 0.1126 149 L 0.0385 0.5887 0.3728 150 G 0.0323 0.0764 0.8913 151 E 0.0404 0.0968 0.8628 152 E 0.0445 0.1864 0.7691 153 P 0.0258 0.5300 0.4442 154 Q 0.0149 0.8135 0.1717 155 A 0.0053 0.9407 0.0540 156 Y 0.0048 0.9596 0.0356 157 R 0.0047 0.9614 0.0339 158 I 0.0047 0.9605 0.0348 159 A 0.0046 0.9612 0.0342 160 R 0.0046 0.9617 0.0337 161 A 0.0046 0.9617 0.0337 162 I 0.0047 0.9603 0.0350 163 V 0.0047 0.9596 0.0357 164 A 0.0048 0.9531 0.0421 165 A 0.0057 0.9275 0.0668 166 R 0.0134 0.8463 0.1403 167 E 0.0160 0.6408 0.3433 168 K 0.0310 0.4205 0.5484 169 A 0.0614 0.0825 0.8561 170 P 0.0605 0.1527 0.7869 171 I 0.1444 0.3312 0.5244 172 E 0.1989 0.4514 0.3497 173 T 0.1711 0.5600 0.2690 174 T 0.0311 0.8505 0.1184 175 T 0.0071 0.9446 0.0483 176 Q 0.0066 0.9509 0.0425 177 L 0.0047 0.9572 0.0381 178 A 0.0047 0.9610 0.0343 179 E 0.0047 0.9612 0.0341 180 I 0.0047 0.9602 0.0351 181 V 0.0048 0.9549 0.0403 182 R 0.0051 0.9463 0.0486 183 K 0.0067 0.9002 0.0931 184 A 0.0126 0.8144 0.1729 185 V 0.0562 0.4423 0.5015 186 G 0.0461 0.2179 0.7360 187 F 0.0730 0.2216 0.7054 188 R 0.0972 0.1947 0.7081 189 R 0.0817 0.1883 0.7300 190 A 0.0475 0.1590 0.7935 191 G 0.0432 0.0741 0.8827 192 H 0.0919 0.0814 0.8267 193 P 0.0677 0.4963 0.4360 194 A 0.0436 0.7661 0.1902 195 R 0.0507 0.7604 0.1890 196 K 0.0516 0.8585 0.0899 197 T 0.0580 0.8615 0.0806 198 F 0.0563 0.8744 0.0693 199 Q 0.0508 0.8740 0.0753 200 A 0.0449 0.8802 0.0749 201 L 0.0395 0.8923 0.0681 202 R 0.0848 0.8523 0.0629 203 I 0.1951 0.7431 0.0618 204 Y 0.1472 0.7445 0.1083 205 V 0.0721 0.7261 0.2018 206 N 0.0131 0.7697 0.2171 207 D 0.0066 0.7667 0.2268 208 E 0.0059 0.8660 0.1281 209 L 0.0060 0.9195 0.0745 210 N 0.0047 0.9412 0.0541 211 A 0.0047 0.9365 0.0587 212 L 0.0048 0.9474 0.0478 213 K 0.0047 0.9569 0.0384 214 E 0.0047 0.9551 0.0402 215 F 0.0048 0.9517 0.0435 216 L 0.0047 0.9541 0.0412 217 E 0.0047 0.9545 0.0408 218 Q 0.0049 0.9474 0.0477 219 A 0.0051 0.9378 0.0571 220 A 0.0054 0.9270 0.0676 221 E 0.0063 0.8970 0.0967 222 V 0.0116 0.8288 0.1597 223 L 0.0669 0.5277 0.4054 224 A 0.0518 0.0704 0.8777 225 P 0.0223 0.1167 0.8610 226 G 0.0307 0.0512 0.9181 227 G 0.2796 0.0204 0.7000 228 R 0.7037 0.0052 0.2911 229 L 0.9199 0.0031 0.0770 230 V 0.9303 0.0034 0.0663 231 V 0.9329 0.0031 0.0639 232 I 0.9191 0.0035 0.0775 233 A 0.8469 0.0040 0.1490 234 F 0.5141 0.0182 0.4678 235 H 0.2454 0.0297 0.7249 236 S 0.1204 0.0440 0.8356 237 L 0.0077 0.8584 0.1339 238 E 0.0081 0.9030 0.0888 239 D 0.0112 0.9159 0.0729 240 R 0.0073 0.9514 0.0413 241 V 0.0055 0.9566 0.0379 242 V 0.0052 0.9561 0.0387 243 K 0.0056 0.9548 0.0396 244 R 0.0069 0.9390 0.0541 245 F 0.0073 0.9216 0.0711 246 L 0.0171 0.8656 0.1173 247 R 0.0283 0.7707 0.2010 248 E 0.0403 0.5057 0.4540 249 S 0.0435 0.2065 0.7499 250 G 0.0407 0.0784 0.8809 251 L 0.2924 0.0555 0.6520 252 K 0.6074 0.0426 0.3499 253 V 0.7643 0.0384 0.1973 254 L 0.6861 0.0466 0.2674 255 T 0.5488 0.0408 0.4104 256 K 0.2928 0.0484 0.6589 257 K 0.1703 0.0159 0.8138 258 P 0.1753 0.0205 0.8041 259 L 0.1940 0.0279 0.7781 260 V 0.1349 0.0120 0.8531 261 P 0.1043 0.0243 0.8714 262 S 0.0734 0.0493 0.8773 263 E 0.0049 0.9486 0.0464 264 K 0.0048 0.9548 0.0404 265 E 0.0048 0.9541 0.0411 266 A 0.0048 0.9444 0.0508 267 A 0.0058 0.8333 0.1608 268 Q 0.0128 0.5987 0.3885 269 N 0.0833 0.0788 0.8379 270 P 0.0122 0.3043 0.6835 271 R 0.0216 0.3137 0.6647 272 A 0.1088 0.3644 0.5267 273 R 0.1627 0.3840 0.4533 274 S 0.1797 0.4123 0.4080 275 A 0.1897 0.5616 0.2487 276 K 0.2525 0.5782 0.1692 277 L 0.4026 0.4311 0.1663 278 R 0.4866 0.3649 0.1485 279 A 0.5231 0.3311 0.1458 280 A 0.5352 0.2922 0.1726 281 E 0.5441 0.2146 0.2413 282 K 0.3629 0.1327 0.5045 283 E 0.1153 0.0546 0.8302 284 A 0.0644 0.0139 0.9217 285 P 0.0473 0.0332 0.9196