# This file is the result of combining several RDB files, specifically # T0364.t06.dssp-ebghstl.rdb (weight 1.53986) # T0364.t06.stride-ebghtl.rdb (weight 1.24869) # T0364.t06.str2.rdb (weight 1.54758) # T0364.t06.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 T0364.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0364 # 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 T0364.t06-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 1402 # # ============================================ # Comments from T0364.t06.stride-ebghtl.rdb # ============================================ # TARGET T0364 # Using neural net t06-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 T0364.t06-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 1402 # # ============================================ # Comments from T0364.t06.str2.rdb # ============================================ # TARGET T0364 # 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 T0364.t06-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 1402 # # ============================================ # Comments from T0364.t06.alpha.rdb # ============================================ # TARGET T0364 # Using neural net t06-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 T0364.t06-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 1402 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0606 0.0097 0.9297 2 P 0.0899 0.0364 0.8737 3 A 0.1742 0.0562 0.7696 4 L 0.4517 0.0404 0.5080 5 I 0.7408 0.0133 0.2458 6 T 0.8524 0.0071 0.1405 7 Y 0.8464 0.0061 0.1476 8 R 0.7933 0.0088 0.1979 9 T 0.7935 0.0055 0.2010 10 T 0.7846 0.0062 0.2092 11 V 0.5985 0.0078 0.3936 12 Q 0.3241 0.0120 0.6639 13 E 0.0323 0.6081 0.3596 14 D 0.0241 0.5853 0.3906 15 W 0.0693 0.5840 0.3467 16 V 0.3538 0.1386 0.5076 17 D 0.1598 0.0664 0.7738 18 Y 0.0260 0.3113 0.6627 19 N 0.0490 0.1365 0.8145 20 G 0.0618 0.1374 0.8008 21 H 0.2260 0.1772 0.5968 22 L 0.4573 0.1558 0.3869 23 R 0.1734 0.2306 0.5960 24 D 0.0966 0.3592 0.5442 25 A 0.0512 0.7979 0.1509 26 F 0.0520 0.8816 0.0664 27 Y 0.0230 0.9305 0.0465 28 L 0.0151 0.9396 0.0453 29 L 0.0100 0.9430 0.0470 30 I 0.0083 0.9417 0.0501 31 F 0.0062 0.9497 0.0441 32 S 0.0056 0.9506 0.0438 33 Y 0.0054 0.9485 0.0461 34 A 0.0049 0.9402 0.0549 35 T 0.0049 0.9484 0.0467 36 D 0.0047 0.9537 0.0416 37 A 0.0047 0.9555 0.0397 38 L 0.0047 0.9550 0.0403 39 M 0.0047 0.9529 0.0424 40 D 0.0049 0.9419 0.0532 41 R 0.0059 0.8994 0.0947 42 I 0.0450 0.4483 0.5067 43 G 0.0432 0.0290 0.9278 44 L 0.0722 0.0141 0.9137 45 D 0.0930 0.0197 0.8873 46 A 0.0116 0.7712 0.2172 47 D 0.0100 0.7956 0.1944 48 S 0.0123 0.7968 0.1909 49 R 0.0380 0.6865 0.2755 50 G 0.0425 0.5111 0.4464 51 Q 0.0500 0.4554 0.4945 52 S 0.0566 0.1840 0.7594 53 G 0.0500 0.0517 0.8983 54 N 0.1404 0.0401 0.8196 55 S 0.4843 0.0231 0.4926 56 L 0.7413 0.0185 0.2402 57 F 0.8161 0.0144 0.1695 58 T 0.8713 0.0146 0.1140 59 L 0.8505 0.0328 0.1167 60 E 0.8885 0.0126 0.0988 61 A 0.8867 0.0105 0.1028 62 H 0.8511 0.0160 0.1329 63 I 0.8557 0.0104 0.1339 64 N 0.8626 0.0126 0.1248 65 Y 0.8540 0.0106 0.1354 66 L 0.6951 0.0312 0.2737 67 H 0.6082 0.0161 0.3756 68 E 0.5746 0.0163 0.4092 69 V 0.4536 0.0115 0.5349 70 K 0.2223 0.0161 0.7615 71 L 0.0713 0.0647 0.8640 72 G 0.0458 0.0418 0.9125 73 T 0.2740 0.0144 0.7116 74 E 0.7314 0.0037 0.2649 75 V 0.9049 0.0036 0.0916 76 W 0.9287 0.0032 0.0681 77 V 0.9274 0.0034 0.0691 78 Q 0.9222 0.0035 0.0742 79 T 0.9172 0.0038 0.0790 80 Q 0.9137 0.0041 0.0822 81 I 0.9153 0.0042 0.0805 82 L 0.8207 0.0241 0.1552 83 G 0.7668 0.0128 0.2204 84 F 0.6721 0.0264 0.3015 85 D 0.4431 0.0339 0.5230 86 R 0.1710 0.0734 0.7556 87 K 0.3846 0.0641 0.5513 88 R 0.8210 0.0108 0.1682 89 L 0.9087 0.0037 0.0876 90 H 0.9269 0.0039 0.0691 91 V 0.9309 0.0033 0.0658 92 Y 0.9263 0.0043 0.0694 93 H 0.9261 0.0036 0.0703 94 S 0.9251 0.0039 0.0710 95 L 0.9202 0.0059 0.0738 96 H 0.8941 0.0099 0.0960 97 R 0.7822 0.0140 0.2038 98 A 0.1161 0.0772 0.8067 99 G 0.0627 0.0571 0.8802 100 F 0.0885 0.0359 0.8756 101 D 0.1457 0.0341 0.8202 102 E 0.7282 0.0097 0.2620 103 V 0.9056 0.0050 0.0894 104 L 0.9041 0.0063 0.0896 105 A 0.9155 0.0052 0.0794 106 A 0.9164 0.0049 0.0786 107 S 0.9118 0.0041 0.0841 108 E 0.9090 0.0058 0.0852 109 Q 0.9211 0.0036 0.0752 110 M 0.9227 0.0045 0.0728 111 L 0.9288 0.0036 0.0676 112 L 0.9239 0.0045 0.0716 113 H 0.9161 0.0044 0.0795 114 V 0.8499 0.0079 0.1423 115 D 0.5413 0.0084 0.4503 116 L 0.0813 0.1231 0.7956 117 A 0.0399 0.0916 0.8685 118 G 0.0678 0.0430 0.8892 119 P 0.0748 0.0416 0.8835 120 Q 0.2367 0.0245 0.7389 121 S 0.3408 0.0273 0.6319 122 A 0.2382 0.0236 0.7382 123 P 0.1787 0.0290 0.7923 124 F 0.1145 0.0549 0.8305 125 G 0.0698 0.0907 0.8395 126 H 0.0157 0.7485 0.2358 127 T 0.0205 0.8462 0.1333 128 T 0.0158 0.8985 0.0857 129 V 0.0137 0.9233 0.0630 130 C 0.0111 0.9250 0.0639 131 R 0.0085 0.9203 0.0711 132 L 0.0075 0.9150 0.0775 133 N 0.0063 0.9263 0.0674 134 H 0.0060 0.9195 0.0745 135 L 0.0073 0.9085 0.0842 136 V 0.0162 0.8694 0.1144 137 E 0.0195 0.8105 0.1700 138 Q 0.0249 0.7077 0.2675 139 Q 0.0408 0.5476 0.4116 140 E 0.0313 0.4430 0.5258 141 G 0.0346 0.3003 0.6651 142 A 0.0579 0.1523 0.7898 143 Q 0.0787 0.1438 0.7775 144 A 0.0690 0.0804 0.8506 145 P 0.0682 0.3595 0.5723 146 Q 0.0448 0.5869 0.3683 147 Y 0.0563 0.6134 0.3303 148 M 0.0882 0.4388 0.4730 149 G 0.0729 0.1850 0.7422 150 R 0.1861 0.1179 0.6961 151 T 0.4230 0.1285 0.4485 152 I 0.3793 0.0842 0.5365 153 K 0.2862 0.0471 0.6667 154 L 0.1179 0.0233 0.8588 155 P 0.0623 0.0147 0.9230 156 A 0.0275 0.0689 0.9037