# This file is the result of combining several RDB files, specifically # T0271.t04.dssp-ebghstl.rdb (weight 1.53986) # T0271.t04.stride-ebghtl.rdb (weight 1.24869) # T0271.t04.str2.rdb (weight 1.54758) # T0271.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 T0271.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0271 # 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 T0271.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 3.81558 # # ============================================ # Comments from T0271.t04.stride-ebghtl.rdb # ============================================ # TARGET T0271 # 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 T0271.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 3.81558 # # ============================================ # Comments from T0271.t04.str2.rdb # ============================================ # TARGET T0271 # 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 T0271.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 3.81558 # # ============================================ # Comments from T0271.t04.alpha.rdb # ============================================ # TARGET T0271 # 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 T0271.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 3.81558 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2214 0.0111 0.7675 2 E 0.5839 0.0094 0.4067 3 L 0.7414 0.0147 0.2439 4 K 0.7598 0.0257 0.2145 5 L 0.8848 0.0064 0.1088 6 I 0.8619 0.0052 0.1329 7 P 0.8046 0.0044 0.1910 8 I 0.5357 0.0158 0.4485 9 E 0.3680 0.0532 0.5787 10 K 0.1972 0.0226 0.7802 11 P 0.0974 0.1151 0.7876 12 E 0.0647 0.2023 0.7330 13 N 0.1002 0.1591 0.7407 14 L 0.2832 0.0478 0.6691 15 N 0.4623 0.0472 0.4905 16 V 0.8746 0.0116 0.1137 17 I 0.9018 0.0122 0.0861 18 L 0.8247 0.0313 0.1440 19 G 0.5125 0.0509 0.4367 20 Q 0.2713 0.1770 0.5517 21 A 0.1928 0.2989 0.5083 22 H 0.1641 0.3175 0.5184 23 F 0.2608 0.3228 0.4163 24 I 0.3015 0.2970 0.4015 25 K 0.2616 0.3097 0.4287 26 T 0.2052 0.3618 0.4330 27 V 0.0151 0.9016 0.0832 28 E 0.0093 0.9144 0.0763 29 D 0.0108 0.9195 0.0697 30 L 0.0050 0.9518 0.0432 31 H 0.0051 0.9537 0.0412 32 E 0.0059 0.9523 0.0418 33 A 0.0082 0.9449 0.0469 34 L 0.0158 0.9127 0.0715 35 V 0.0214 0.8640 0.1146 36 T 0.0359 0.7572 0.2069 37 A 0.0597 0.5984 0.3419 38 V 0.0655 0.1138 0.8207 39 P 0.0308 0.1357 0.8335 40 G 0.0439 0.0858 0.8703 41 I 0.3047 0.0668 0.6284 42 R 0.5528 0.0777 0.3695 43 F 0.8225 0.0491 0.1285 44 G 0.8258 0.0686 0.1056 45 L 0.8210 0.0822 0.0968 46 A 0.7612 0.1118 0.1270 47 F 0.6133 0.1590 0.2277 48 S 0.4322 0.2094 0.3584 49 E 0.2294 0.2662 0.5044 50 A 0.1616 0.2080 0.6304 51 S 0.1098 0.1588 0.7314 52 G 0.0815 0.2227 0.6958 53 K 0.0996 0.3450 0.5554 54 R 0.2406 0.3563 0.4031 55 L 0.4948 0.2457 0.2594 56 V 0.6274 0.1733 0.1993 57 R 0.6433 0.1389 0.2179 58 R 0.4809 0.1401 0.3789 59 S 0.1792 0.0791 0.7416 60 G 0.0872 0.0426 0.8703 61 T 0.0864 0.0422 0.8715 62 D 0.0368 0.5616 0.4016 63 E 0.0048 0.9510 0.0442 64 A 0.0047 0.9599 0.0354 65 L 0.0047 0.9610 0.0344 66 V 0.0047 0.9610 0.0343 67 E 0.0047 0.9604 0.0349 68 L 0.0047 0.9578 0.0376 69 A 0.0047 0.9539 0.0414 70 V 0.0050 0.9505 0.0446 71 K 0.0054 0.9402 0.0544 72 N 0.0060 0.8935 0.1005 73 L 0.0069 0.8795 0.1136 74 L 0.0123 0.8009 0.1868 75 N 0.0301 0.7365 0.2334 76 L 0.0676 0.5831 0.3493 77 A 0.0840 0.3273 0.5888 78 C 0.1026 0.2611 0.6362 79 G 0.1273 0.1133 0.7594 80 H 0.4046 0.0383 0.5571 81 V 0.7274 0.0207 0.2520 82 F 0.9031 0.0096 0.0873 83 L 0.9223 0.0107 0.0671 84 I 0.9158 0.0121 0.0721 85 V 0.8426 0.0197 0.1377 86 L 0.5326 0.0605 0.4069 87 G 0.1449 0.1022 0.7529 88 E 0.0516 0.1585 0.7900 89 G 0.0701 0.1694 0.7604 90 F 0.2137 0.1539 0.6323 91 Y 0.2598 0.1799 0.5603 92 P 0.2203 0.3824 0.3974 93 I 0.1892 0.5956 0.2152 94 N 0.1567 0.6168 0.2266 95 V 0.0760 0.8207 0.1033 96 L 0.0342 0.8753 0.0905 97 H 0.0229 0.8646 0.1124 98 A 0.0243 0.8447 0.1309 99 V 0.0436 0.7661 0.1903 100 K 0.0439 0.6445 0.3116 101 A 0.0416 0.4403 0.5181 102 C 0.0566 0.1702 0.7732 103 P 0.0230 0.5725 0.4046 104 E 0.0845 0.5826 0.3328 105 V 0.3020 0.4921 0.2059 106 V 0.5069 0.3636 0.1295 107 R 0.6726 0.2400 0.0873 108 I 0.6828 0.2345 0.0827 109 Y 0.6324 0.2740 0.0936 110 A 0.6249 0.2291 0.1460 111 A 0.5234 0.2158 0.2608 112 T 0.3639 0.1520 0.4841 113 A 0.1816 0.1268 0.6916 114 N 0.1499 0.0365 0.8136 115 P 0.1061 0.1858 0.7081 116 L 0.2814 0.1325 0.5861 117 K 0.6568 0.0610 0.2822 118 V 0.9016 0.0101 0.0882 119 V 0.9192 0.0080 0.0728 120 V 0.9111 0.0080 0.0809 121 A 0.8458 0.0120 0.1422 122 E 0.7190 0.0226 0.2584 123 E 0.3792 0.0488 0.5720 124 G 0.1099 0.0660 0.8241 125 E 0.1379 0.0934 0.7687 126 Q 0.2331 0.0633 0.7036 127 R 0.4967 0.0231 0.4803 128 A 0.8439 0.0057 0.1503 129 I 0.9148 0.0038 0.0815 130 L 0.9005 0.0100 0.0896 131 G 0.8798 0.0079 0.1124 132 V 0.8130 0.0129 0.1741 133 M 0.6561 0.0251 0.3188 134 D 0.3966 0.0269 0.5765 135 G 0.1486 0.0499 0.8015 136 F 0.1499 0.0429 0.8072 137 T 0.1451 0.0362 0.8188 138 P 0.1130 0.1379 0.7491 139 L 0.1113 0.1613 0.7274 140 G 0.1538 0.1226 0.7236 141 V 0.2769 0.0861 0.6370 142 E 0.2838 0.0530 0.6632 143 D 0.1370 0.0451 0.8178 144 E 0.0066 0.9055 0.0879 145 A 0.0052 0.9311 0.0638 146 E 0.0054 0.9319 0.0626 147 V 0.0051 0.9400 0.0550 148 A 0.0048 0.9296 0.0657 149 W 0.0051 0.9117 0.0832 150 R 0.0048 0.9318 0.0634 151 K 0.0047 0.9575 0.0378 152 D 0.0047 0.9587 0.0366 153 L 0.0047 0.9590 0.0363 154 L 0.0047 0.9559 0.0394 155 R 0.0049 0.9466 0.0485 156 R 0.0062 0.9130 0.0808 157 L 0.0383 0.6201 0.3417 158 G 0.0420 0.1112 0.8468 159 Y 0.1118 0.0638 0.8244 160 K 0.1658 0.0537 0.7805 161 L 0.0840 0.0433 0.8727