# This file is the result of combining several RDB files, specifically # T0315.t04.dssp-ebghstl.rdb (weight 1.53986) # T0315.t04.stride-ebghtl.rdb (weight 1.24869) # T0315.t04.str2.rdb (weight 1.54758) # T0315.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 T0315.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0315 # Using neural net t06-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 T0315.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 1154 # # ============================================ # Comments from T0315.t04.stride-ebghtl.rdb # ============================================ # TARGET T0315 # 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 T0315.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 1154 # # ============================================ # Comments from T0315.t04.str2.rdb # ============================================ # TARGET T0315 # Using neural net t06-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 T0315.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 1154 # # ============================================ # Comments from T0315.t04.alpha.rdb # ============================================ # TARGET T0315 # 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 T0315.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 1154 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1391 0.0128 0.8481 2 L 0.5318 0.0167 0.4515 3 I 0.6603 0.0168 0.3229 4 D 0.5968 0.0233 0.3800 5 T 0.5061 0.0823 0.4116 6 H 0.5447 0.0590 0.3963 7 V 0.5550 0.0569 0.3881 8 H 0.4665 0.0365 0.4970 9 L 0.2248 0.0628 0.7123 10 N 0.1524 0.0445 0.8031 11 D 0.0554 0.2662 0.6784 12 E 0.0124 0.4525 0.5351 13 Q 0.0179 0.4738 0.5083 14 Y 0.0451 0.2628 0.6921 15 D 0.0538 0.2222 0.7240 16 D 0.0315 0.3058 0.6627 17 D 0.0524 0.2966 0.6510 18 L 0.0049 0.9431 0.0521 19 S 0.0047 0.9590 0.0363 20 E 0.0047 0.9602 0.0351 21 V 0.0047 0.9602 0.0351 22 I 0.0047 0.9604 0.0350 23 T 0.0046 0.9604 0.0350 24 R 0.0046 0.9606 0.0347 25 A 0.0047 0.9596 0.0357 26 R 0.0048 0.9527 0.0425 27 E 0.0053 0.9242 0.0706 28 A 0.0401 0.3946 0.5652 29 G 0.0492 0.0115 0.9394 30 V 0.0968 0.0067 0.8964 31 D 0.2350 0.0358 0.7292 32 R 0.9092 0.0040 0.0867 33 M 0.9304 0.0033 0.0663 34 F 0.9306 0.0033 0.0661 35 V 0.8947 0.0038 0.1015 36 V 0.5911 0.0228 0.3861 37 G 0.2325 0.0229 0.7445 38 F 0.1280 0.0338 0.8381 39 N 0.1053 0.0185 0.8762 40 K 0.0142 0.6800 0.3059 41 S 0.0121 0.7134 0.2745 42 T 0.0190 0.7778 0.2031 43 I 0.0051 0.9480 0.0469 44 E 0.0047 0.9591 0.0362 45 R 0.0047 0.9596 0.0358 46 A 0.0047 0.9603 0.0351 47 M 0.0047 0.9598 0.0356 48 K 0.0047 0.9581 0.0372 49 L 0.0050 0.9493 0.0457 50 I 0.0055 0.9353 0.0592 51 D 0.0058 0.8678 0.1264 52 E 0.0120 0.6889 0.2992 53 Y 0.0700 0.1577 0.7723 54 D 0.0255 0.1409 0.8336 55 F 0.1177 0.0897 0.7926 56 L 0.6924 0.0204 0.2872 57 Y 0.8531 0.0134 0.1334 58 G 0.8753 0.0108 0.1140 59 I 0.8554 0.0131 0.1315 60 I 0.7540 0.0348 0.2112 61 G 0.6135 0.0224 0.3641 62 W 0.4838 0.0316 0.4846 63 H 0.3105 0.0210 0.6684 64 P 0.1316 0.1959 0.6725 65 V 0.0899 0.2701 0.6400 66 D 0.1148 0.2702 0.6150 67 A 0.0468 0.5338 0.4194 68 I 0.0408 0.4845 0.4746 69 D 0.0510 0.4178 0.5312 70 F 0.0652 0.2249 0.7099 71 T 0.0511 0.2000 0.7489 72 E 0.0051 0.9241 0.0708 73 E 0.0050 0.9273 0.0677 74 H 0.0051 0.9427 0.0522 75 L 0.0047 0.9578 0.0375 76 E 0.0047 0.9576 0.0378 77 W 0.0048 0.9547 0.0406 78 I 0.0047 0.9565 0.0388 79 E 0.0048 0.9561 0.0391 80 S 0.0050 0.9473 0.0477 81 L 0.0061 0.9088 0.0851 82 A 0.0076 0.7856 0.2069 83 Q 0.0137 0.4765 0.5097 84 H 0.0694 0.0449 0.8857 85 P 0.0381 0.1281 0.8338 86 K 0.1266 0.0891 0.7843 87 V 0.6693 0.0180 0.3126 88 I 0.8335 0.0273 0.1392 89 G 0.8931 0.0088 0.0981 90 I 0.8473 0.0255 0.1272 91 G 0.7937 0.0241 0.1823 92 E 0.7076 0.0403 0.2521 93 M 0.5253 0.0680 0.4067 94 G 0.3958 0.0725 0.5316 95 L 0.3762 0.0997 0.5241 96 D 0.3962 0.1285 0.4753 97 Y 0.3563 0.1671 0.4766 98 H 0.2896 0.1069 0.6036 99 W 0.1738 0.1272 0.6990 100 D 0.1226 0.0884 0.7890 101 K 0.0703 0.0914 0.8383 102 S 0.0655 0.0362 0.8983 103 P 0.0475 0.1882 0.7642 104 A 0.0320 0.4461 0.5220 105 D 0.0275 0.7318 0.2407 106 V 0.0140 0.8686 0.1174 107 Q 0.0104 0.8813 0.1083 108 K 0.0064 0.9324 0.0612 109 E 0.0047 0.9478 0.0475 110 V 0.0047 0.9511 0.0442 111 F 0.0047 0.9578 0.0375 112 R 0.0046 0.9608 0.0345 113 K 0.0046 0.9614 0.0339 114 Q 0.0047 0.9608 0.0345 115 I 0.0046 0.9613 0.0340 116 A 0.0046 0.9611 0.0343 117 L 0.0046 0.9603 0.0350 118 A 0.0047 0.9585 0.0368 119 K 0.0048 0.9506 0.0446 120 R 0.0058 0.9018 0.0924 121 L 0.0462 0.3940 0.5598 122 K 0.0305 0.0296 0.9399 123 L 0.0646 0.0081 0.9273 124 P 0.2651 0.0053 0.7296 125 I 0.8846 0.0042 0.1112 126 I 0.9249 0.0034 0.0717 127 I 0.9105 0.0067 0.0828 128 H 0.7782 0.0118 0.2100 129 N 0.3085 0.0249 0.6666 130 R 0.0689 0.1718 0.7593 131 E 0.0586 0.2360 0.7055 132 A 0.0569 0.3151 0.6280 133 T 0.0403 0.4233 0.5364 134 Q 0.0057 0.9097 0.0846 135 D 0.0049 0.9304 0.0647 136 C 0.0048 0.9499 0.0453 137 I 0.0047 0.9599 0.0354 138 D 0.0046 0.9615 0.0339 139 I 0.0047 0.9607 0.0347 140 L 0.0048 0.9561 0.0391 141 L 0.0051 0.9433 0.0516 142 E 0.0064 0.8888 0.1048 143 E 0.0171 0.7063 0.2765 144 H 0.0586 0.3445 0.5969 145 A 0.0310 0.3459 0.6231 146 E 0.0448 0.2695 0.6856 147 E 0.1476 0.1505 0.7019 148 V 0.2592 0.0805 0.6602 149 G 0.5780 0.0325 0.3895 150 G 0.8575 0.0109 0.1316 151 I 0.8947 0.0076 0.0977 152 M 0.8207 0.0162 0.1631 153 H 0.5763 0.0282 0.3955 154 S 0.2532 0.0529 0.6939 155 F 0.1158 0.0714 0.8129 156 S 0.0864 0.0505 0.8631 157 G 0.0447 0.0396 0.9158 158 S 0.0679 0.0414 0.8907 159 P 0.0056 0.9385 0.0558 160 E 0.0048 0.9533 0.0418 161 I 0.0050 0.9531 0.0419 162 A 0.0047 0.9580 0.0373 163 D 0.0047 0.9543 0.0410 164 I 0.0048 0.9413 0.0540 165 V 0.0070 0.9214 0.0717 166 T 0.0115 0.8540 0.1344 167 N 0.0098 0.7199 0.2703 168 K 0.0247 0.3998 0.5755 169 L 0.0667 0.0798 0.8535 170 N 0.1189 0.0334 0.8476 171 F 0.6401 0.0091 0.3508 172 Y 0.9118 0.0038 0.0844 173 I 0.9211 0.0038 0.0751 174 S 0.8937 0.0062 0.1000 175 L 0.7249 0.0107 0.2644 176 G 0.3102 0.0219 0.6679 177 G 0.1995 0.0232 0.7773 178 P 0.2267 0.0461 0.7272 179 V 0.2653 0.0601 0.6746 180 T 0.2358 0.0674 0.6968 181 F 0.1257 0.1889 0.6854 182 K 0.0835 0.2321 0.6845 183 N 0.0794 0.1770 0.7436 184 A 0.0372 0.3764 0.5863 185 K 0.0397 0.3895 0.5708 186 Q 0.0637 0.3482 0.5881 187 P 0.0167 0.8606 0.1226 188 K 0.0070 0.9349 0.0581 189 E 0.0077 0.9426 0.0497 190 V 0.0072 0.9378 0.0550 191 A 0.0124 0.9047 0.0829 192 K 0.0143 0.7810 0.2047 193 H 0.0208 0.5335 0.4458 194 V 0.0767 0.1101 0.8132 195 S 0.0850 0.0475 0.8676 196 M 0.0412 0.4984 0.4604 197 E 0.0730 0.4601 0.4670 198 R 0.3960 0.3286 0.2754 199 L 0.7666 0.0899 0.1435 200 L 0.8549 0.0549 0.0902 201 V 0.8145 0.0701 0.1153 202 E 0.7054 0.0655 0.2291 203 T 0.4076 0.0595 0.5329 204 D 0.1814 0.0513 0.7673 205 A 0.1010 0.0905 0.8085 206 P 0.0695 0.1625 0.7680 207 Y 0.1073 0.1481 0.7446 208 L 0.1241 0.0762 0.7997 209 S 0.1080 0.0365 0.8555 210 P 0.1097 0.0584 0.8319 211 H 0.1371 0.0577 0.8052 212 P 0.1155 0.1420 0.7425 213 Y 0.1132 0.1681 0.7187 214 R 0.0917 0.1428 0.7656 215 G 0.0569 0.0741 0.8690 216 K 0.1051 0.0640 0.8309 217 R 0.1447 0.0956 0.7598 218 N 0.0915 0.0986 0.8100 219 E 0.0954 0.1006 0.8040 220 P 0.0673 0.3916 0.5411 221 A 0.0446 0.6165 0.3388 222 R 0.0401 0.7143 0.2456 223 V 0.0154 0.8893 0.0953 224 T 0.0083 0.9374 0.0543 225 L 0.0075 0.9498 0.0427 226 V 0.0056 0.9513 0.0431 227 A 0.0047 0.9569 0.0384 228 E 0.0047 0.9610 0.0343 229 Q 0.0047 0.9601 0.0352 230 I 0.0048 0.9566 0.0385 231 A 0.0051 0.9529 0.0420 232 E 0.0058 0.9342 0.0600 233 L 0.0168 0.8577 0.1255 234 K 0.0425 0.4291 0.5284 235 G 0.0335 0.0286 0.9379 236 L 0.0768 0.0108 0.9124 237 S 0.0696 0.0084 0.9220 238 Y 0.0049 0.9448 0.0504 239 E 0.0047 0.9611 0.0343 240 E 0.0047 0.9612 0.0341 241 V 0.0046 0.9614 0.0340 242 C 0.0047 0.9600 0.0354 243 E 0.0047 0.9567 0.0387 244 Q 0.0047 0.9475 0.0478 245 T 0.0048 0.9338 0.0614 246 T 0.0054 0.9143 0.0803 247 K 0.0068 0.8810 0.1122 248 N 0.0076 0.8345 0.1579 249 A 0.0048 0.9487 0.0464 250 E 0.0051 0.9511 0.0438 251 K 0.0051 0.9451 0.0498 252 L 0.0066 0.9039 0.0895 253 F 0.0214 0.6523 0.3262 254 N 0.0274 0.2630 0.7095 255 L 0.0565 0.0720 0.8716 256 N 0.0520 0.0445 0.9035 257 S 0.0633 0.0393 0.8974