# This file is the result of combining several RDB files, specifically # T0257.t04.dssp-ebghstl.rdb (weight 1.53986) # T0257.t04.stride-ebghtl.rdb (weight 1.24869) # T0257.t04.str2.rdb (weight 1.54758) # T0257.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 T0257.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0257 # 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 T0257.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 37.1229 # # ============================================ # Comments from T0257.t04.stride-ebghtl.rdb # ============================================ # TARGET T0257 # 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 T0257.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 37.1229 # # ============================================ # Comments from T0257.t04.str2.rdb # ============================================ # TARGET T0257 # 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 T0257.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 37.1229 # # ============================================ # Comments from T0257.t04.alpha.rdb # ============================================ # TARGET T0257 # 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 T0257.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 37.1229 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0884 0.0574 0.8543 2 A 0.1938 0.0585 0.7477 3 V 0.2632 0.0575 0.6793 4 D 0.4166 0.0565 0.5269 5 M 0.7696 0.0300 0.2004 6 F 0.8897 0.0103 0.0999 7 I 0.9025 0.0058 0.0917 8 K 0.8717 0.0055 0.1227 9 I 0.6203 0.0405 0.3392 10 G 0.1450 0.0712 0.7837 11 D 0.1335 0.0435 0.8230 12 V 0.3215 0.0261 0.6524 13 K 0.2717 0.0353 0.6930 14 G 0.1706 0.0627 0.7667 15 E 0.1927 0.1538 0.6535 16 S 0.1930 0.2960 0.5109 17 K 0.1396 0.3648 0.4956 18 D 0.1481 0.4000 0.4519 19 K 0.1148 0.4101 0.4751 20 T 0.1287 0.2506 0.6207 21 H 0.2164 0.2380 0.5456 22 A 0.1260 0.3758 0.4982 23 E 0.1395 0.3202 0.5403 24 E 0.4965 0.1767 0.3268 25 I 0.7442 0.0434 0.2124 26 D 0.8602 0.0252 0.1146 27 V 0.8921 0.0162 0.0918 28 L 0.8367 0.0383 0.1250 29 A 0.8426 0.0167 0.1408 30 W 0.7685 0.0355 0.1959 31 S 0.6596 0.0521 0.2883 32 W 0.4468 0.1105 0.4427 33 G 0.3625 0.0795 0.5580 34 M 0.4404 0.0752 0.4844 35 S 0.4255 0.0666 0.5079 36 Q 0.3224 0.0453 0.6323 37 S 0.2340 0.0603 0.7056 38 G 0.2014 0.0639 0.7347 39 S 0.2326 0.0431 0.7243 40 M 0.1778 0.1434 0.6788 41 H 0.2001 0.1576 0.6423 42 M 0.2030 0.1408 0.6561 43 G 0.1522 0.0786 0.7692 44 G 0.1605 0.0513 0.7882 45 G 0.1231 0.0578 0.8190 46 G 0.1143 0.0739 0.8117 47 G 0.1364 0.0885 0.7751 48 A 0.1891 0.0794 0.7314 49 G 0.2414 0.0607 0.6979 50 K 0.5039 0.0336 0.4625 51 V 0.6743 0.0116 0.3140 52 N 0.7481 0.0087 0.2431 53 V 0.7330 0.0175 0.2495 54 Q 0.4877 0.0446 0.4677 55 D 0.5728 0.0287 0.3985 56 L 0.7090 0.0085 0.2826 57 S 0.8863 0.0053 0.1084 58 F 0.8762 0.0063 0.1174 59 T 0.8172 0.0176 0.1652 60 K 0.7755 0.0276 0.1969 61 Y 0.6497 0.0606 0.2896 62 I 0.4078 0.1200 0.4721 63 D 0.2121 0.1599 0.6281 64 K 0.0456 0.3761 0.5783 65 S 0.0487 0.3610 0.5903 66 T 0.0240 0.4319 0.5442 67 P 0.0053 0.9373 0.0574 68 N 0.0048 0.9482 0.0470 69 L 0.0047 0.9543 0.0410 70 M 0.0047 0.9533 0.0420 71 M 0.0047 0.9475 0.0478 72 A 0.0058 0.9252 0.0691 73 C 0.0082 0.8645 0.1273 74 S 0.0226 0.6469 0.3305 75 S 0.0416 0.1859 0.7726 76 G 0.0281 0.0480 0.9239 77 K 0.1240 0.0453 0.8307 78 H 0.3330 0.0401 0.6269 79 Y 0.2783 0.0325 0.6892 80 P 0.1593 0.1197 0.7209 81 Q 0.4979 0.0633 0.4388 82 A 0.8210 0.0056 0.1734 83 K 0.9214 0.0035 0.0751 84 L 0.9298 0.0031 0.0670 85 T 0.9259 0.0035 0.0705 86 I 0.9237 0.0032 0.0731 87 R 0.9053 0.0047 0.0900 88 K 0.8774 0.0050 0.1176 89 A 0.4997 0.0312 0.4691 90 G 0.1518 0.0257 0.8225 91 G 0.0765 0.0414 0.8821 92 E 0.1094 0.0721 0.8185 93 N 0.3227 0.0584 0.6189 94 Q 0.5906 0.0566 0.3528 95 V 0.7435 0.0260 0.2305 96 E 0.8231 0.0125 0.1644 97 Y 0.9070 0.0042 0.0888 98 L 0.9196 0.0037 0.0768 99 I 0.9263 0.0036 0.0701 100 I 0.9229 0.0043 0.0728 101 T 0.9003 0.0049 0.0948 102 L 0.8071 0.0092 0.1837 103 K 0.4878 0.0538 0.4584 104 E 0.5137 0.0284 0.4579 105 V 0.7877 0.0060 0.2064 106 L 0.9137 0.0035 0.0828 107 V 0.9064 0.0033 0.0903 108 S 0.8346 0.0288 0.1366 109 S 0.8022 0.0056 0.1922 110 V 0.7716 0.0096 0.2188 111 S 0.7016 0.0119 0.2864 112 T 0.5319 0.0386 0.4296 113 G 0.2754 0.0409 0.6838 114 G 0.1723 0.0325 0.7952 115 S 0.1090 0.0482 0.8428 116 G 0.0576 0.0646 0.8778 117 G 0.0645 0.0731 0.8624 118 E 0.0821 0.1406 0.7773 119 D 0.1526 0.0970 0.7505 120 R 0.2945 0.0432 0.6623 121 L 0.4475 0.0229 0.5295 122 T 0.6748 0.0195 0.3057 123 E 0.8305 0.0074 0.1621 124 N 0.8848 0.0036 0.1116 125 V 0.9087 0.0036 0.0877 126 T 0.9194 0.0033 0.0774 127 L 0.8969 0.0037 0.0994 128 N 0.8572 0.0046 0.1382 129 F 0.8126 0.0199 0.1675 130 A 0.7163 0.0411 0.2426 131 Q 0.8639 0.0107 0.1254 132 V 0.9040 0.0040 0.0919 133 Q 0.9139 0.0039 0.0823 134 V 0.9045 0.0042 0.0913 135 D 0.8807 0.0066 0.1127 136 Y 0.8631 0.0052 0.1317 137 Q 0.7346 0.0079 0.2575 138 P 0.6423 0.0180 0.3397 139 Q 0.4485 0.0506 0.5009 140 K 0.3104 0.0537 0.6359 141 A 0.1959 0.1094 0.6948 142 D 0.1665 0.0680 0.7655 143 G 0.1465 0.0631 0.7904 144 A 0.1754 0.0986 0.7261 145 K 0.1800 0.1553 0.6647 146 D 0.1294 0.1127 0.7579 147 G 0.1108 0.0609 0.8283 148 G 0.2012 0.0297 0.7691 149 P 0.4401 0.0325 0.5274 150 V 0.5519 0.0279 0.4202 151 K 0.6180 0.0480 0.3340 152 Y 0.6093 0.0603 0.3304 153 G 0.4990 0.0470 0.4540 154 W 0.5257 0.0282 0.4461 155 N 0.4501 0.0254 0.5244 156 I 0.0984 0.5883 0.3133 157 R 0.0768 0.6051 0.3182 158 Q 0.0747 0.5350 0.3902 159 N 0.1156 0.3063 0.5781 160 V 0.1589 0.2386 0.6025 161 Q 0.1659 0.1382 0.6959 162 A 0.0679 0.0583 0.8738