# This file is the result of combining several RDB files, specifically # T0470.t04.dssp-ebghstl.rdb (weight 1.53986) # T0470.t04.stride-ebghtl.rdb (weight 1.24869) # T0470.t04.str2.rdb (weight 1.54758) # T0470.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 T0470.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0470 # 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 T0470.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 2110 # # ============================================ # Comments from T0470.t04.stride-ebghtl.rdb # ============================================ # TARGET T0470 # 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 T0470.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 2110 # # ============================================ # Comments from T0470.t04.str2.rdb # ============================================ # TARGET T0470 # 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 T0470.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 2110 # # ============================================ # Comments from T0470.t04.alpha.rdb # ============================================ # TARGET T0470 # 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 T0470.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 2110 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0607 0.0208 0.9185 2 T 0.0632 0.0578 0.8790 3 K 0.0279 0.5205 0.4515 4 Q 0.0139 0.7903 0.1958 5 E 0.0104 0.8837 0.1059 6 K 0.0089 0.8998 0.0913 7 I 0.0049 0.9471 0.0479 8 E 0.0049 0.9561 0.0390 9 K 0.0048 0.9525 0.0427 10 T 0.0048 0.9523 0.0428 11 I 0.0047 0.9587 0.0366 12 T 0.0047 0.9586 0.0367 13 F 0.0047 0.9572 0.0381 14 V 0.0048 0.9551 0.0401 15 K 0.0048 0.9553 0.0400 16 H 0.0052 0.9484 0.0464 17 I 0.0068 0.9244 0.0688 18 L 0.0162 0.8589 0.1249 19 E 0.0213 0.7350 0.2438 20 K 0.0255 0.5616 0.4129 21 D 0.0488 0.2795 0.6717 22 A 0.0613 0.1882 0.7506 23 S 0.0316 0.1875 0.7809 24 G 0.0431 0.1225 0.8344 25 H 0.1149 0.0870 0.7981 26 D 0.1236 0.0921 0.7843 27 W 0.0631 0.6957 0.2412 28 Y 0.0394 0.8248 0.1358 29 H 0.0279 0.8847 0.0874 30 I 0.0071 0.9470 0.0459 31 R 0.0047 0.9603 0.0350 32 R 0.0046 0.9613 0.0340 33 V 0.0047 0.9604 0.0350 34 H 0.0046 0.9612 0.0342 35 K 0.0046 0.9618 0.0336 36 M 0.0046 0.9617 0.0337 37 A 0.0047 0.9610 0.0343 38 I 0.0046 0.9614 0.0339 39 S 0.0046 0.9614 0.0340 40 L 0.0047 0.9607 0.0346 41 S 0.0047 0.9584 0.0369 42 E 0.0049 0.9495 0.0455 43 Q 0.0082 0.8813 0.1105 44 E 0.0436 0.4461 0.5103 45 G 0.0323 0.0503 0.9174 46 G 0.0431 0.0294 0.9275 47 N 0.0724 0.0430 0.8846 48 R 0.0067 0.9049 0.0884 49 F 0.0055 0.9444 0.0501 50 I 0.0056 0.9550 0.0394 51 I 0.0057 0.9586 0.0357 52 E 0.0057 0.9585 0.0358 53 M 0.0067 0.9546 0.0387 54 A 0.0066 0.9465 0.0469 55 A 0.0084 0.9184 0.0732 56 L 0.0093 0.8794 0.1113 57 L 0.0159 0.8402 0.1439 58 H 0.0229 0.7224 0.2548 59 D 0.0379 0.5019 0.4602 60 V 0.0661 0.3959 0.5379 61 A 0.1050 0.2300 0.6650 62 D 0.1167 0.1946 0.6887 63 E 0.0984 0.1839 0.7177 64 K 0.1129 0.1555 0.7316 65 L 0.1034 0.1899 0.7067 66 N 0.0667 0.2425 0.6908 67 E 0.0280 0.6136 0.3584 68 S 0.0250 0.7382 0.2368 69 E 0.0226 0.7790 0.1984 70 E 0.0245 0.7698 0.2056 71 A 0.0335 0.6777 0.2889 72 G 0.0268 0.5729 0.4003 73 M 0.0089 0.8398 0.1513 74 K 0.0065 0.9393 0.0542 75 K 0.0062 0.9497 0.0441 76 V 0.0053 0.9550 0.0397 77 S 0.0047 0.9591 0.0362 78 D 0.0047 0.9597 0.0356 79 W 0.0047 0.9599 0.0353 80 L 0.0048 0.9564 0.0389 81 E 0.0049 0.9454 0.0497 82 E 0.0064 0.8792 0.1143 83 L 0.0468 0.4424 0.5107 84 H 0.0434 0.0326 0.9240 85 V 0.0605 0.0176 0.9219 86 E 0.0539 0.0238 0.9224 87 E 0.0060 0.8892 0.1048 88 E 0.0056 0.9274 0.0670 89 E 0.0066 0.9190 0.0744 90 S 0.0048 0.9499 0.0453 91 K 0.0048 0.9565 0.0387 92 H 0.0047 0.9584 0.0369 93 V 0.0047 0.9594 0.0359 94 L 0.0047 0.9612 0.0342 95 H 0.0046 0.9617 0.0337 96 I 0.0047 0.9607 0.0346 97 I 0.0047 0.9568 0.0384 98 A 0.0054 0.9419 0.0527 99 N 0.0094 0.8620 0.1286 100 M 0.0522 0.6324 0.3155 101 S 0.0629 0.2526 0.6844 102 Y 0.0733 0.1196 0.8071 103 K 0.0501 0.1320 0.8180 104 G 0.0511 0.0951 0.8538 105 G 0.0623 0.0875 0.8502 106 H 0.0864 0.0961 0.8175 107 G 0.0756 0.0872 0.8373 108 G 0.0614 0.0628 0.8759 109 K 0.1060 0.0576 0.8364 110 V 0.2080 0.0849 0.7071 111 E 0.1638 0.0842 0.7520 112 S 0.1302 0.1232 0.7466 113 I 0.0500 0.7451 0.2049 114 E 0.0459 0.8210 0.1331 115 G 0.0430 0.8300 0.1270 116 K 0.0530 0.8402 0.1068 117 L 0.0623 0.8463 0.0914 118 V 0.0372 0.8676 0.0952 119 Q 0.0266 0.8627 0.1107 120 D 0.0451 0.7811 0.1738 121 A 0.0199 0.7872 0.1929 122 D 0.0176 0.7008 0.2815 123 R 0.0177 0.8225 0.1599 124 L 0.0314 0.8104 0.1582 125 D 0.0363 0.7423 0.2214 126 A 0.0395 0.7351 0.2253 127 L 0.0758 0.5421 0.3821 128 G 0.0568 0.2519 0.6913 129 A 0.0671 0.2522 0.6807 130 I 0.0786 0.2850 0.6364 131 G 0.0700 0.3317 0.5983 132 I 0.0762 0.5543 0.3695 133 A 0.1104 0.6307 0.2589 134 R 0.1513 0.6453 0.2034 135 T 0.2099 0.5959 0.1943 136 F 0.2220 0.5797 0.1983 137 A 0.2587 0.5373 0.2040 138 Y 0.2574 0.4921 0.2506 139 G 0.1790 0.3108 0.5102 140 G 0.0931 0.1843 0.7226 141 A 0.1637 0.2231 0.6132 142 K 0.1232 0.2177 0.6591 143 G 0.0920 0.1360 0.7720 144 R 0.1779 0.1426 0.6795 145 L 0.3627 0.1309 0.5064 146 M 0.3566 0.1106 0.5328 147 Y 0.3040 0.0793 0.6166 148 D 0.1223 0.0217 0.8559 149 P 0.0135 0.1397 0.8468 150 T 0.0222 0.0992 0.8785 151 I 0.0904 0.0314 0.8782 152 P 0.0720 0.0165 0.9114 153 P 0.0916 0.4848 0.4236 154 R 0.0818 0.6368 0.2814 155 E 0.1314 0.6505 0.2182 156 V 0.2322 0.4889 0.2789 157 M 0.2353 0.3496 0.4151 158 T 0.2015 0.3003 0.4982 159 K 0.0604 0.6329 0.3067 160 D 0.0425 0.6777 0.2798 161 E 0.0375 0.6974 0.2652 162 Y 0.0713 0.6539 0.2748 163 R 0.0936 0.5321 0.3743 164 K 0.0848 0.3760 0.5392 165 N 0.0776 0.1540 0.7684 166 N 0.0459 0.0998 0.8543 167 D 0.0776 0.0954 0.8270 168 P 0.0338 0.3902 0.5761 169 S 0.0432 0.5291 0.4277 170 L 0.0244 0.7492 0.2264 171 N 0.0127 0.8161 0.1712 172 H 0.0089 0.8940 0.0971 173 F 0.0054 0.9405 0.0541 174 Y 0.0047 0.9577 0.0375 175 E 0.0047 0.9600 0.0353 176 K 0.0048 0.9563 0.0389 177 L 0.0048 0.9392 0.0560 178 L 0.0054 0.8737 0.1208 179 K 0.0069 0.7648 0.2284 180 L 0.0157 0.6862 0.2981 181 K 0.0124 0.7476 0.2400 182 D 0.0140 0.7312 0.2548 183 L 0.0134 0.7272 0.2594 184 M 0.0318 0.5785 0.3896 185 N 0.0489 0.4928 0.4582 186 T 0.0453 0.5336 0.4211 187 N 0.0139 0.8141 0.1721 188 A 0.0078 0.9091 0.0832 189 A 0.0067 0.9335 0.0599 190 K 0.0068 0.9464 0.0468 191 Q 0.0075 0.9466 0.0460 192 E 0.0057 0.9516 0.0427 193 A 0.0050 0.9568 0.0382 194 E 0.0050 0.9577 0.0373 195 V 0.0050 0.9560 0.0390 196 R 0.0047 0.9504 0.0449 197 H 0.0048 0.9446 0.0506 198 R 0.0048 0.9418 0.0534 199 Y 0.0047 0.9410 0.0543 200 M 0.0047 0.9558 0.0395 201 E 0.0046 0.9614 0.0340 202 Q 0.0046 0.9610 0.0343 203 F 0.0047 0.9600 0.0353 204 I 0.0047 0.9605 0.0349 205 E 0.0047 0.9613 0.0341 206 Q 0.0048 0.9589 0.0363 207 F 0.0049 0.9509 0.0442 208 M 0.0048 0.9434 0.0518 209 K 0.0050 0.9071 0.0879 210 E 0.0061 0.8577 0.1362 211 W 0.0183 0.7581 0.2236 212 N 0.0132 0.6433 0.3435 213 A 0.0116 0.7805 0.2079 214 Q 0.0186 0.8262 0.1551 215 I 0.0366 0.8402 0.1233 216 L 0.0695 0.7818 0.1487 217 E 0.0817 0.7020 0.2163 218 H 0.0735 0.6081 0.3184 219 H 0.0708 0.5393 0.3899 220 H 0.0651 0.4009 0.5341 221 H 0.0650 0.3040 0.6310 222 H 0.0623 0.1524 0.7853 223 H 0.0483 0.0474 0.9043