# This file is the result of combining several RDB files, specifically # T0287.t04.dssp-ebghstl.rdb (weight 1.53986) # T0287.t04.stride-ebghtl.rdb (weight 1.24869) # T0287.t04.str2.rdb (weight 1.54758) # T0287.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 T0287.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0287 # 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 T0287.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 1 # # ============================================ # Comments from T0287.t04.stride-ebghtl.rdb # ============================================ # TARGET T0287 # 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 T0287.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 1 # # ============================================ # Comments from T0287.t04.str2.rdb # ============================================ # TARGET T0287 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0287.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 1 # # ============================================ # Comments from T0287.t04.alpha.rdb # ============================================ # TARGET T0287 # 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 T0287.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 1 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0647 0.2256 0.7097 2 S 0.0546 0.3366 0.6088 3 N 0.0270 0.4733 0.4997 4 N 0.0340 0.4757 0.4904 5 M 0.0274 0.7666 0.2061 6 R 0.0231 0.8373 0.1396 7 K 0.0388 0.8422 0.1190 8 L 0.0560 0.8630 0.0810 9 F 0.0723 0.8302 0.0975 10 S 0.0489 0.8568 0.0943 11 M 0.0482 0.8445 0.1073 12 I 0.0644 0.7721 0.1634 13 A 0.0692 0.6219 0.3089 14 D 0.0667 0.3777 0.5557 15 S 0.0437 0.4014 0.5550 16 K 0.0159 0.5487 0.4354 17 D 0.0293 0.5805 0.3902 18 K 0.0147 0.7856 0.1996 19 K 0.0115 0.8535 0.1351 20 E 0.0120 0.9117 0.0763 21 K 0.0159 0.9134 0.0708 22 L 0.0177 0.9186 0.0637 23 I 0.0165 0.9200 0.0634 24 E 0.0149 0.9132 0.0719 25 S 0.0112 0.8971 0.0917 26 L 0.0177 0.8041 0.1782 27 Q 0.0277 0.6811 0.2913 28 E 0.0229 0.7409 0.2362 29 N 0.0338 0.5758 0.3905 30 E 0.0585 0.5455 0.3959 31 L 0.1104 0.5201 0.3694 32 L 0.0979 0.4189 0.4832 33 N 0.1145 0.2343 0.6512 34 T 0.0560 0.3131 0.6308 35 D 0.0239 0.5639 0.4122 36 E 0.0125 0.7938 0.1937 37 K 0.0140 0.8426 0.1434 38 K 0.0197 0.8376 0.1426 39 K 0.0535 0.8053 0.1412 40 I 0.0341 0.8715 0.0944 41 I 0.0213 0.8964 0.0823 42 D 0.0100 0.9208 0.0691 43 Q 0.0078 0.9289 0.0633 44 I 0.0105 0.9071 0.0824 45 K 0.0164 0.8749 0.1087 46 T 0.0214 0.8398 0.1388 47 M 0.0088 0.8932 0.0980 48 H 0.0073 0.9115 0.0812 49 D 0.0052 0.9370 0.0578 50 F 0.0053 0.9446 0.0501 51 F 0.0059 0.9368 0.0573 52 K 0.0063 0.9327 0.0609 53 Q 0.0078 0.9113 0.0810 54 M 0.0191 0.8473 0.1337 55 H 0.0396 0.6842 0.2762 56 T 0.0368 0.5454 0.4178 57 N 0.0317 0.3997 0.5686 58 K 0.0432 0.5212 0.4356 59 G 0.0274 0.5997 0.3729 60 A 0.0269 0.7864 0.1867 61 L 0.0134 0.9012 0.0854 62 D 0.0083 0.9329 0.0587 63 K 0.0056 0.9531 0.0413 64 V 0.0054 0.9529 0.0417 65 L 0.0061 0.9465 0.0473 66 R 0.0062 0.9333 0.0605 67 N 0.0073 0.8764 0.1163 68 Y 0.0099 0.8259 0.1642 69 M 0.0189 0.8047 0.1764 70 K 0.0111 0.8790 0.1098 71 D 0.0188 0.8466 0.1345 72 Y 0.0178 0.8817 0.1006 73 R 0.0176 0.8997 0.0827 74 A 0.0327 0.8984 0.0689 75 V 0.0567 0.8805 0.0628 76 I 0.0671 0.8616 0.0713 77 K 0.0605 0.8416 0.0979 78 S 0.0584 0.7481 0.1935 79 I 0.0672 0.4980 0.4348 80 G 0.0725 0.1362 0.7913 81 V 0.0761 0.3124 0.6115 82 D 0.0544 0.4896 0.4560 83 K 0.0290 0.7194 0.2516 84 F 0.0273 0.8092 0.1635 85 K 0.0268 0.8713 0.1019 86 K 0.0496 0.8600 0.0904 87 V 0.0582 0.8653 0.0765 88 Y 0.0433 0.8826 0.0741 89 R 0.0353 0.8847 0.0800 90 L 0.0219 0.8891 0.0890 91 L 0.0298 0.8056 0.1646 92 E 0.0372 0.6683 0.2945 93 S 0.0281 0.7143 0.2576 94 E 0.0182 0.7574 0.2244 95 T 0.0188 0.8243 0.1569 96 M 0.0137 0.9036 0.0827 97 E 0.0183 0.9073 0.0743 98 L 0.0131 0.9357 0.0511 99 L 0.0107 0.9427 0.0466 100 H 0.0086 0.9454 0.0459 101 A 0.0100 0.9362 0.0539 102 I 0.0178 0.8885 0.0937 103 A 0.0286 0.8022 0.1692 104 E 0.0413 0.5825 0.3761 105 N 0.0908 0.0836 0.8255 106 P 0.0129 0.2981 0.6890 107 N 0.0228 0.2800 0.6972 108 F 0.1181 0.3702 0.5117 109 L 0.2097 0.3298 0.4605 110 F 0.2428 0.3376 0.4196 111 S 0.1567 0.3614 0.4818 112 K 0.0968 0.4300 0.4732 113 F 0.1055 0.3201 0.5744 114 D 0.1103 0.3162 0.5735 115 R 0.0584 0.5443 0.3973 116 S 0.1117 0.4989 0.3894 117 I 0.1580 0.5635 0.2785 118 L 0.2111 0.4912 0.2978 119 G 0.3005 0.3769 0.3226 120 I 0.4306 0.2877 0.2817 121 F 0.4338 0.2337 0.3325 122 L 0.2818 0.2123 0.5059 123 P 0.1554 0.2790 0.5656 124 F 0.1463 0.2752 0.5785 125 F 0.2036 0.1552 0.6412 126 S 0.1171 0.1086 0.7743 127 K 0.1067 0.0733 0.8201 128 P 0.2077 0.1489 0.6434 129 I 0.5873 0.1224 0.2903 130 M 0.6939 0.1054 0.2007 131 F 0.7058 0.0999 0.1943 132 K 0.6791 0.0811 0.2398 133 M 0.6232 0.0527 0.3241 134 S 0.5591 0.0511 0.3898 135 I 0.3333 0.3634 0.3033 136 R 0.2732 0.4386 0.2882 137 E 0.2653 0.4058 0.3289 138 M 0.2284 0.3409 0.4306 139 D 0.1398 0.3362 0.5240 140 S 0.1171 0.4012 0.4816 141 Q 0.2356 0.3928 0.3716 142 I 0.4826 0.2486 0.2688 143 E 0.5382 0.2356 0.2262 144 L 0.4940 0.2476 0.2584 145 Y 0.2504 0.1854 0.5642 146 G 0.1457 0.0861 0.7681 147 T 0.1272 0.0945 0.7783 148 N 0.1370 0.0784 0.7846 149 L 0.1188 0.0985 0.7826 150 P 0.1461 0.1605 0.6934 151 L 0.2989 0.2840 0.4170 152 L 0.5617 0.1799 0.2584 153 K 0.6711 0.1530 0.1759 154 L 0.7520 0.1124 0.1356 155 F 0.8004 0.0779 0.1217 156 V 0.8055 0.0529 0.1416 157 M 0.6702 0.0384 0.2914 158 T 0.3523 0.0425 0.6052 159 D 0.0847 0.2393 0.6759 160 E 0.0530 0.4520 0.4950 161 E 0.1155 0.5211 0.3633 162 V 0.2710 0.4066 0.3223 163 N 0.2892 0.3717 0.3391 164 F 0.2462 0.5149 0.2388 165 Y 0.2392 0.5169 0.2440 166 A 0.2025 0.4634 0.3341 167 N 0.1686 0.3505 0.4810 168 L 0.1477 0.4681 0.3842 169 K 0.1418 0.5165 0.3416 170 T 0.1235 0.6193 0.2571 171 I 0.0451 0.8084 0.1465 172 E 0.0313 0.8406 0.1281 173 Q 0.0313 0.8166 0.1520 174 Y 0.0264 0.7850 0.1887 175 N 0.0237 0.7453 0.2310 176 D 0.0094 0.8924 0.0982 177 Y 0.0088 0.9156 0.0756 178 V 0.0091 0.9353 0.0556 179 R 0.0069 0.9451 0.0480 180 D 0.0066 0.9427 0.0507 181 L 0.0077 0.9363 0.0560 182 L 0.0150 0.8950 0.0900 183 M 0.0256 0.8278 0.1466 184 K 0.0553 0.6567 0.2880 185 F 0.1179 0.3125 0.5696 186 D 0.1238 0.1660 0.7101 187 L 0.0091 0.8986 0.0923 188 E 0.0064 0.9345 0.0591 189 K 0.0058 0.9511 0.0431 190 Y 0.0068 0.9493 0.0439 191 M 0.0091 0.9381 0.0528 192 K 0.0103 0.9252 0.0645 193 E 0.0129 0.8954 0.0917 194 K 0.0393 0.6542 0.3065 195 G 0.0362 0.1591 0.8047 196 V 0.1047 0.1526 0.7427 197 Q 0.1521 0.1624 0.6855 198 N 0.1224 0.1080 0.7696 199 A 0.0538 0.1105 0.8356