# This file is the result of combining several RDB files, specifically # T0290.t04.dssp-ebghstl.rdb (weight 1.53986) # T0290.t04.stride-ebghtl.rdb (weight 1.24869) # T0290.t04.str2.rdb (weight 1.54758) # T0290.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 T0290.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0290 # 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 T0290.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 95.3807 # # ============================================ # Comments from T0290.t04.stride-ebghtl.rdb # ============================================ # TARGET T0290 # 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 T0290.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 95.3807 # # ============================================ # Comments from T0290.t04.str2.rdb # ============================================ # TARGET T0290 # 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 T0290.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 95.3807 # # ============================================ # Comments from T0290.t04.alpha.rdb # ============================================ # TARGET T0290 # 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 T0290.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 95.3807 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 R 0.0731 0.0117 0.9152 2 P 0.1007 0.0618 0.8376 3 R 0.2605 0.0791 0.6604 4 C 0.4863 0.0446 0.4691 5 F 0.5638 0.0524 0.3838 6 F 0.5589 0.0476 0.3935 7 D 0.6033 0.0553 0.3414 8 I 0.7353 0.0604 0.2043 9 A 0.7849 0.0567 0.1584 10 I 0.7538 0.0634 0.1827 11 N 0.5067 0.0485 0.4448 12 N 0.2874 0.0312 0.6814 13 Q 0.2790 0.0167 0.7043 14 P 0.2367 0.0480 0.7154 15 A 0.1647 0.0735 0.7618 16 G 0.3493 0.0319 0.6188 17 R 0.6522 0.0113 0.3365 18 V 0.9096 0.0034 0.0871 19 V 0.9274 0.0036 0.0690 20 F 0.9294 0.0035 0.0671 21 E 0.9137 0.0045 0.0817 22 L 0.7912 0.0121 0.1967 23 F 0.3281 0.0354 0.6364 24 S 0.0641 0.2649 0.6710 25 D 0.0304 0.3023 0.6673 26 V 0.0461 0.3451 0.6089 27 C 0.0573 0.1758 0.7668 28 P 0.0261 0.5784 0.3955 29 K 0.0270 0.8354 0.1376 30 T 0.0307 0.8695 0.0998 31 C 0.0163 0.9238 0.0598 32 E 0.0104 0.9252 0.0645 33 N 0.0092 0.9070 0.0838 34 F 0.0085 0.9255 0.0660 35 R 0.0095 0.9293 0.0612 36 C 0.0094 0.9302 0.0605 37 L 0.0101 0.9012 0.0887 38 C 0.0321 0.7355 0.2324 39 T 0.0773 0.3974 0.5252 40 G 0.0589 0.1485 0.7926 41 E 0.0842 0.1670 0.7489 42 K 0.0749 0.1709 0.7542 43 G 0.0895 0.1251 0.7855 44 T 0.1640 0.0922 0.7438 45 G 0.1951 0.0812 0.7237 46 K 0.1616 0.1432 0.6953 47 S 0.1387 0.1408 0.7205 48 T 0.1236 0.1184 0.7580 49 Q 0.1296 0.0728 0.7976 50 K 0.2028 0.0294 0.7678 51 P 0.3355 0.0416 0.6229 52 L 0.4630 0.1007 0.4362 53 H 0.5085 0.0943 0.3972 54 Y 0.4861 0.1055 0.4083 55 K 0.1794 0.1196 0.7010 56 S 0.1352 0.0500 0.8148 57 C 0.4368 0.0289 0.5343 58 L 0.7092 0.0406 0.2503 59 F 0.7289 0.0619 0.2091 60 H 0.7038 0.0766 0.2197 61 R 0.7231 0.0602 0.2167 62 V 0.7207 0.0539 0.2254 63 V 0.5564 0.0581 0.3855 64 K 0.2392 0.1701 0.5907 65 D 0.2215 0.1292 0.6493 66 F 0.5688 0.0836 0.3476 67 M 0.8130 0.0258 0.1611 68 V 0.8342 0.0174 0.1483 69 Q 0.7058 0.0264 0.2677 70 G 0.3688 0.0431 0.5881 71 G 0.2119 0.0426 0.7455 72 D 0.2749 0.0440 0.6811 73 F 0.1793 0.0718 0.7488 74 S 0.1485 0.0844 0.7672 75 E 0.1180 0.0783 0.8037 76 G 0.0971 0.0525 0.8504 77 N 0.1314 0.0414 0.8271 78 G 0.1268 0.0573 0.8160 79 R 0.2076 0.0504 0.7420 80 G 0.1672 0.0478 0.7850 81 G 0.1868 0.0457 0.7675 82 E 0.3550 0.0655 0.5795 83 S 0.3698 0.0719 0.5583 84 I 0.3186 0.1219 0.5595 85 Y 0.1880 0.0905 0.7215 86 G 0.0896 0.0601 0.8503 87 G 0.1448 0.0460 0.8092 88 F 0.2966 0.0589 0.6444 89 F 0.2017 0.0989 0.6994 90 E 0.1404 0.1843 0.6753 91 D 0.0993 0.2202 0.6805 92 E 0.1106 0.2902 0.5992 93 S 0.1368 0.2465 0.6168 94 F 0.1870 0.1783 0.6347 95 A 0.2247 0.1542 0.6211 96 V 0.2828 0.1270 0.5902 97 K 0.2357 0.1415 0.6228 98 H 0.1855 0.1510 0.6634 99 N 0.1273 0.0977 0.7750 100 A 0.1372 0.1451 0.7177 101 A 0.2665 0.1482 0.5853 102 F 0.5327 0.1237 0.3436 103 L 0.7293 0.1242 0.1465 104 L 0.7596 0.1271 0.1133 105 S 0.6920 0.1654 0.1427 106 M 0.6203 0.1776 0.2021 107 A 0.5027 0.1982 0.2992 108 N 0.3039 0.1831 0.5130 109 R 0.1515 0.1236 0.7249 110 G 0.0702 0.0297 0.9001 111 K 0.0518 0.0685 0.8798 112 D 0.0603 0.0567 0.8830 113 T 0.0929 0.0806 0.8265 114 N 0.1006 0.0900 0.8094 115 G 0.1130 0.0841 0.8029 116 S 0.2861 0.0536 0.6603 117 Q 0.6133 0.0385 0.3482 118 F 0.8349 0.0186 0.1465 119 F 0.8916 0.0168 0.0916 120 I 0.8883 0.0167 0.0949 121 T 0.8114 0.0190 0.1696 122 T 0.5608 0.0242 0.4150 123 K 0.2678 0.0282 0.7039 124 P 0.1850 0.0402 0.7748 125 T 0.1121 0.0565 0.8314 126 P 0.0562 0.2398 0.7041 127 H 0.0670 0.2383 0.6947 128 L 0.1411 0.1383 0.7206 129 D 0.0752 0.0653 0.8595 130 G 0.0479 0.0688 0.8833 131 H 0.1576 0.0536 0.7888 132 H 0.6076 0.0154 0.3771 133 V 0.7538 0.0104 0.2358 134 V 0.8423 0.0107 0.1470 135 F 0.7124 0.0343 0.2533 136 G 0.6223 0.0347 0.3430 137 Q 0.7700 0.0278 0.2022 138 V 0.8054 0.0349 0.1598 139 I 0.5852 0.0953 0.3195 140 S 0.2483 0.1667 0.5851 141 G 0.0521 0.3692 0.5787 142 Q 0.0185 0.8399 0.1416 143 E 0.0156 0.9053 0.0791 144 V 0.0112 0.9322 0.0566 145 V 0.0117 0.9387 0.0496 146 R 0.0112 0.9346 0.0542 147 E 0.0119 0.9231 0.0650 148 I 0.0134 0.8774 0.1092 149 E 0.0164 0.7458 0.2378 150 N 0.0230 0.4890 0.4880 151 Q 0.0779 0.1399 0.7822 152 K 0.1073 0.0642 0.8285 153 T 0.2094 0.0578 0.7328 154 D 0.1168 0.0723 0.8109 155 A 0.0409 0.2624 0.6967 156 A 0.0483 0.1416 0.8101 157 S 0.0546 0.0746 0.8707 158 K 0.1617 0.0134 0.8249 159 P 0.3130 0.0105 0.6765 160 F 0.3593 0.0493 0.5914 161 A 0.5198 0.0400 0.4402 162 E 0.6323 0.0199 0.3478 163 V 0.7547 0.0069 0.2384 164 R 0.8703 0.0054 0.1244 165 I 0.8874 0.0053 0.1072 166 L 0.8147 0.0277 0.1575 167 S 0.7470 0.0144 0.2386 168 C 0.6300 0.0452 0.3248 169 G 0.5849 0.0498 0.3653 170 E 0.6644 0.0396 0.2960 171 L 0.5135 0.0314 0.4551 172 I 0.1706 0.0167 0.8127 173 P 0.0476 0.0373 0.9151