# This file is the result of combining several RDB files, specifically # T0134.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0134.t2k.stride-ebghtl.rdb (weight 1.24869) # T0134.t2k.str.rdb (weight 1.53983) # T0134.t2k.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 T0134.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0134 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0134.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 4 # # ============================================ # Comments from T0134.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0134 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0134.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 4 # # ============================================ # Comments from T0134.t2k.str.rdb # ============================================ # TARGET T0134 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0134.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 4 # # ============================================ # Comments from T0134.t2k.alpha.rdb # ============================================ # TARGET T0134 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0134.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 4 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 G 0.0489 0.0329 0.9181 2 E 0.1048 0.0527 0.8425 3 P 0.1308 0.1320 0.7372 4 V 0.0975 0.2241 0.6784 5 Q 0.0892 0.2280 0.6827 6 N 0.0648 0.2971 0.6381 7 G 0.0601 0.2459 0.6940 8 A 0.0697 0.2185 0.7118 9 P 0.0781 0.2924 0.6295 10 E 0.0672 0.2836 0.6492 11 E 0.0702 0.1980 0.7318 12 E 0.0847 0.1242 0.7911 13 Q 0.1000 0.0806 0.8194 14 L 0.1006 0.0416 0.8578 15 P 0.0740 0.0394 0.8866 16 P 0.0471 0.1675 0.7855 17 E 0.0360 0.1743 0.7897 18 S 0.0813 0.1720 0.7467 19 S 0.0560 0.5104 0.4336 20 Y 0.0853 0.5911 0.3237 21 S 0.1234 0.6162 0.2604 22 L 0.1204 0.6222 0.2574 23 L 0.1455 0.5451 0.3094 24 A 0.1667 0.4409 0.3923 25 E 0.1507 0.3020 0.5473 26 N 0.1364 0.1295 0.7341 27 S 0.1593 0.1286 0.7121 28 Y 0.4847 0.0452 0.4701 29 V 0.6997 0.0150 0.2853 30 K 0.8128 0.0166 0.1706 31 M 0.8769 0.0101 0.1130 32 T 0.8536 0.0146 0.1318 33 C 0.7862 0.0164 0.1974 34 D 0.5312 0.0169 0.4519 35 I 0.2365 0.0884 0.6750 36 R 0.1402 0.0743 0.7855 37 G 0.1908 0.0518 0.7574 38 S 0.1595 0.0339 0.8067 39 L 0.0868 0.3321 0.5811 40 Q 0.0598 0.3504 0.5899 41 E 0.0654 0.3193 0.6153 42 D 0.0698 0.1194 0.8108 43 S 0.1665 0.0450 0.7884 44 Q 0.4952 0.0154 0.4894 45 V 0.8111 0.0045 0.1843 46 T 0.8855 0.0039 0.1107 47 V 0.9135 0.0041 0.0824 48 A 0.9228 0.0035 0.0737 49 I 0.9219 0.0036 0.0745 50 V 0.9178 0.0038 0.0784 51 L 0.8552 0.0065 0.1384 52 E 0.6016 0.0355 0.3629 53 N 0.3124 0.0415 0.6461 54 R 0.1797 0.0849 0.7354 55 S 0.1272 0.1078 0.7650 56 S 0.0665 0.3681 0.5654 57 S 0.1002 0.4155 0.4842 58 I 0.2377 0.4056 0.3566 59 L 0.3409 0.3055 0.3536 60 K 0.3438 0.3207 0.3355 61 G 0.4306 0.2990 0.2704 62 M 0.4521 0.2786 0.2693 63 E 0.4973 0.2845 0.2182 64 L 0.3895 0.3792 0.2313 65 S 0.3115 0.3808 0.3077 66 V 0.1914 0.5723 0.2363 67 L 0.1628 0.6119 0.2253 68 D 0.1423 0.6143 0.2434 69 S 0.1491 0.5932 0.2577 70 L 0.1513 0.5799 0.2688 71 N 0.1618 0.5069 0.3313 72 A 0.1789 0.4938 0.3273 73 R 0.2171 0.4810 0.3019 74 M 0.2882 0.3698 0.3419 75 A 0.2836 0.2633 0.4531 76 R 0.1660 0.0828 0.7512 77 P 0.0863 0.0965 0.8171 78 Q 0.0384 0.0988 0.8629 79 G 0.0484 0.0805 0.8711 80 S 0.1141 0.0574 0.8284 81 S 0.2089 0.1014 0.6897 82 V 0.1596 0.1381 0.7023 83 H 0.1328 0.1256 0.7416 84 D 0.1323 0.0743 0.7934 85 G 0.1326 0.0822 0.7852 86 V 0.3622 0.0337 0.6041 87 P 0.4305 0.0273 0.5422 88 V 0.3194 0.0432 0.6374 89 P 0.2069 0.1595 0.6336 90 F 0.1718 0.2236 0.6046 91 Q 0.1820 0.1584 0.6595 92 L 0.1402 0.0474 0.8124 93 P 0.0695 0.0266 0.9039 94 P 0.0391 0.1305 0.8303 95 G 0.0433 0.0778 0.8788 96 V 0.1174 0.0719 0.8107 97 S 0.1072 0.0588 0.8340 98 N 0.0927 0.1378 0.7695 99 E 0.1969 0.1356 0.6675 100 A 0.3882 0.0606 0.5513 101 Q 0.5905 0.0289 0.3805 102 Y 0.7988 0.0238 0.1774 103 V 0.8685 0.0265 0.1050 104 F 0.8539 0.0352 0.1109 105 T 0.8484 0.0609 0.0907 106 I 0.7819 0.1066 0.1115 107 Q 0.6761 0.1765 0.1475 108 S 0.5468 0.2872 0.1661 109 I 0.3836 0.4680 0.1484 110 V 0.2842 0.5881 0.1277 111 M 0.1468 0.7016 0.1515 112 A 0.1001 0.7165 0.1834 113 Q 0.1184 0.6281 0.2535 114 K 0.1256 0.5345 0.3399 115 L 0.2345 0.2976 0.4678 116 K 0.2035 0.1949 0.6016 117 G 0.3876 0.1214 0.4911 118 T 0.6779 0.0679 0.2542 119 L 0.7923 0.0515 0.1563 120 S 0.8256 0.0366 0.1378 121 F 0.8339 0.0282 0.1379 122 I 0.8308 0.0262 0.1430 123 A 0.6905 0.0213 0.2882 124 K 0.4608 0.0414 0.4977 125 N 0.2522 0.0513 0.6966 126 D 0.1300 0.0922 0.7777 127 E 0.0863 0.1038 0.8099 128 G 0.0732 0.0876 0.8392 129 A 0.1057 0.0834 0.8109 130 T 0.1216 0.1216 0.7569 131 H 0.1159 0.2333 0.6508 132 E 0.1620 0.3131 0.5249 133 K 0.2340 0.3190 0.4469 134 L 0.4282 0.1750 0.3968 135 D 0.4601 0.1279 0.4120 136 F 0.5939 0.0983 0.3078 137 R 0.5912 0.0847 0.3240 138 L 0.4757 0.0500 0.4742 139 H 0.4467 0.0292 0.5241 140 F 0.4323 0.0301 0.5377 141 S 0.4266 0.0302 0.5431 142 C 0.5599 0.0409 0.3992 143 S 0.5998 0.0393 0.3608 144 S 0.7575 0.0306 0.2119 145 Y 0.8409 0.0117 0.1473 146 L 0.8444 0.0099 0.1457 147 I 0.6426 0.0106 0.3468 148 T 0.3062 0.0213 0.6725 149 T 0.1504 0.0337 0.8159 150 P 0.1137 0.0743 0.8121 151 C 0.1384 0.0865 0.7751 152 Y 0.1441 0.1154 0.7405 153 S 0.0583 0.3305 0.6112 154 D 0.0447 0.6049 0.3504 155 A 0.0146 0.8117 0.1737 156 F 0.0165 0.8696 0.1139 157 A 0.0156 0.8972 0.0871 158 K 0.0184 0.8945 0.0871 159 L 0.0236 0.8790 0.0974 160 L 0.0452 0.7951 0.1597 161 E 0.0574 0.5916 0.3511 162 S 0.0706 0.2686 0.6608 163 G 0.0512 0.0910 0.8578 164 D 0.1244 0.0804 0.7951 165 L 0.3354 0.0823 0.5823 166 S 0.3261 0.0584 0.6154 167 M 0.2527 0.1635 0.5838 168 S 0.2329 0.1134 0.6537 169 S 0.4065 0.0651 0.5284 170 I 0.6558 0.0366 0.3076 171 K 0.7548 0.0167 0.2285 172 V 0.6485 0.0294 0.3221 173 D 0.2528 0.0832 0.6640 174 G 0.2791 0.0794 0.6414 175 I 0.6278 0.0809 0.2913 176 R 0.7398 0.1086 0.1516 177 M 0.7664 0.0962 0.1374 178 S 0.7207 0.0811 0.1982 179 F 0.1797 0.6805 0.1398 180 Q 0.0300 0.8725 0.0975 181 N 0.0209 0.8827 0.0964 182 L 0.0120 0.9254 0.0627 183 L 0.0095 0.9327 0.0578 184 A 0.0078 0.9398 0.0524 185 K 0.0101 0.9311 0.0588 186 I 0.0153 0.9124 0.0723 187 C 0.0242 0.8679 0.1079 188 F 0.0280 0.7719 0.2001 189 H 0.0409 0.5780 0.3811 190 H 0.0977 0.3055 0.5968 191 H 0.1753 0.0899 0.7348 192 F 0.3997 0.0460 0.5543 193 S 0.5983 0.0361 0.3656 194 V 0.7050 0.0544 0.2405 195 V 0.7244 0.0672 0.2084 196 E 0.6699 0.0664 0.2637 197 R 0.5410 0.0797 0.3793 198 V 0.3722 0.0616 0.5662 199 D 0.0991 0.2437 0.6572 200 S 0.0588 0.4582 0.4830 201 C 0.1425 0.5232 0.3344 202 A 0.1983 0.4343 0.3674 203 S 0.2413 0.3619 0.3969 204 M 0.1959 0.4380 0.3661 205 Y 0.2834 0.2784 0.4383 206 S 0.2738 0.2258 0.5004 207 R 0.3838 0.1821 0.4341 208 S 0.3334 0.1659 0.5007 209 I 0.1976 0.1202 0.6822 210 Q 0.0728 0.0576 0.8696 211 G 0.0805 0.0389 0.8806 212 H 0.2977 0.0229 0.6794 213 H 0.6927 0.0079 0.2994 214 V 0.8394 0.0065 0.1541 215 C 0.8869 0.0078 0.1053 216 L 0.8982 0.0066 0.0952 217 L 0.9024 0.0066 0.0910 218 V 0.8726 0.0076 0.1198 219 K 0.8148 0.0090 0.1761 220 K 0.5611 0.0679 0.3710 221 G 0.2024 0.0639 0.7337 222 E 0.1056 0.0918 0.8025 223 N 0.0975 0.0753 0.8272 224 S 0.3595 0.0340 0.6066 225 V 0.7053 0.0087 0.2860 226 S 0.7927 0.0086 0.1987 227 V 0.7146 0.0168 0.2686 228 D 0.2802 0.0416 0.6782 229 G 0.1239 0.0529 0.8232 230 K 0.1798 0.0670 0.7532 231 C 0.1607 0.0795 0.7598 232 S 0.0768 0.0644 0.8588 233 D 0.0628 0.1472 0.7900 234 S 0.0053 0.8146 0.1801 235 T 0.0060 0.8714 0.1226 236 L 0.0057 0.9138 0.0805 237 L 0.0046 0.9390 0.0564 238 S 0.0046 0.9422 0.0533 239 N 0.0046 0.9397 0.0557 240 L 0.0046 0.9448 0.0507 241 L 0.0045 0.9501 0.0454 242 E 0.0046 0.9451 0.0503 243 E 0.0053 0.9249 0.0698 244 M 0.0066 0.9307 0.0628 245 K 0.0055 0.9386 0.0559 246 A 0.0068 0.9282 0.0651 247 T 0.0093 0.9063 0.0844 248 L 0.0209 0.8374 0.1417 249 A 0.0298 0.6843 0.2860 250 K 0.0429 0.4273 0.5299 251 C 0.0366 0.0528 0.9106