# This file is the result of combining several RDB files, specifically # T0495.t04.dssp-ebghstl.rdb (weight 1.53986) # T0495.t04.stride-ebghtl.rdb (weight 1.24869) # T0495.t04.str2.rdb (weight 1.54758) # T0495.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 T0495.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0495 # 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 T0495.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 128 # # ============================================ # Comments from T0495.t04.stride-ebghtl.rdb # ============================================ # TARGET T0495 # 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 T0495.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 128 # # ============================================ # Comments from T0495.t04.str2.rdb # ============================================ # TARGET T0495 # 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 T0495.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 128 # # ============================================ # Comments from T0495.t04.alpha.rdb # ============================================ # TARGET T0495 # 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 T0495.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 128 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0599 0.0249 0.9152 2 P 0.0683 0.0820 0.8496 3 M 0.0612 0.1933 0.7455 4 T 0.0618 0.2978 0.6404 5 L 0.0767 0.2480 0.6753 6 D 0.0828 0.1846 0.7326 7 L 0.0654 0.2616 0.6730 8 Q 0.0535 0.2936 0.6530 9 P 0.0146 0.7273 0.2581 10 G 0.0048 0.9366 0.0586 11 Q 0.0047 0.9571 0.0383 12 R 0.0047 0.9596 0.0357 13 L 0.0047 0.9598 0.0355 14 A 0.0047 0.9600 0.0353 15 R 0.0047 0.9585 0.0369 16 G 0.0047 0.9550 0.0403 17 V 0.0047 0.9568 0.0384 18 A 0.0047 0.9597 0.0356 19 R 0.0047 0.9595 0.0359 20 H 0.0047 0.9580 0.0372 21 L 0.0048 0.9498 0.0454 22 R 0.0050 0.9134 0.0816 23 A 0.0074 0.7944 0.1983 24 H 0.0449 0.2863 0.6689 25 G 0.0342 0.0254 0.9404 26 F 0.2269 0.0152 0.7580 27 V 0.7246 0.0106 0.2648 28 S 0.7631 0.0100 0.2268 29 V 0.6167 0.0407 0.3426 30 E 0.4761 0.1048 0.4190 31 E 0.4497 0.0945 0.4558 32 F 0.4921 0.0664 0.4415 33 V 0.4607 0.0417 0.4976 34 P 0.1894 0.0702 0.7404 35 A 0.0529 0.1269 0.8202 36 R 0.0445 0.0664 0.8891 37 G 0.0454 0.0478 0.9068 38 L 0.1867 0.0226 0.7907 39 R 0.5321 0.0222 0.4457 40 V 0.5570 0.0108 0.4323 41 D 0.6131 0.0156 0.3713 42 V 0.8945 0.0115 0.0940 43 M 0.8926 0.0124 0.0950 44 G 0.9060 0.0065 0.0875 45 L 0.8439 0.0120 0.1440 46 G 0.3080 0.0139 0.6781 47 P 0.0508 0.0873 0.8619 48 K 0.0348 0.0592 0.9059 49 G 0.1008 0.0454 0.8537 50 E 0.3997 0.0155 0.5847 51 I 0.8340 0.0038 0.1622 52 W 0.8797 0.0038 0.1165 53 V 0.9259 0.0031 0.0710 54 I 0.9254 0.0035 0.0711 55 E 0.9224 0.0034 0.0743 56 C 0.8603 0.0051 0.1346 57 K 0.5960 0.0108 0.3932 58 S 0.3182 0.0187 0.6631 59 S 0.1449 0.0444 0.8106 60 R 0.0099 0.8249 0.1652 61 A 0.0147 0.8296 0.1557 62 D 0.0177 0.8075 0.1748 63 F 0.0191 0.8320 0.1488 64 Q 0.0196 0.7417 0.2387 65 A 0.0212 0.6826 0.2962 66 D 0.0363 0.4806 0.4831 67 A 0.0351 0.3392 0.6257 68 K 0.0455 0.2685 0.6861 69 W 0.0537 0.4245 0.5219 70 Q 0.0276 0.6138 0.3586 71 G 0.0341 0.5884 0.3776 72 Y 0.0422 0.6413 0.3165 73 L 0.0354 0.6629 0.3018 74 E 0.0344 0.5945 0.3711 75 W 0.0600 0.5576 0.3824 76 C 0.1723 0.2460 0.5817 77 D 0.1464 0.1797 0.6739 78 R 0.4427 0.0858 0.4715 79 Y 0.8603 0.0157 0.1240 80 F 0.9221 0.0055 0.0724 81 W 0.9147 0.0048 0.0805 82 A 0.8555 0.0080 0.1364 83 V 0.4877 0.0162 0.4960 84 D 0.1436 0.0717 0.7847 85 M 0.0233 0.2207 0.7561 86 E 0.0333 0.1728 0.7939 87 F 0.0816 0.0294 0.8890 88 P 0.0794 0.0283 0.8923 89 A 0.0110 0.8130 0.1760 90 E 0.0115 0.7680 0.2205 91 L 0.0256 0.6935 0.2809 92 L 0.1224 0.0635 0.8142 93 P 0.0689 0.0788 0.8523 94 A 0.0229 0.2546 0.7225 95 E 0.0490 0.1857 0.7653 96 S 0.2913 0.0546 0.6541 97 G 0.6992 0.0127 0.2882 98 L 0.8977 0.0045 0.0978 99 L 0.9189 0.0040 0.0772 100 I 0.9088 0.0041 0.0871 101 A 0.8405 0.0094 0.1501 102 D 0.4828 0.0117 0.5055 103 A 0.0813 0.1863 0.7324 104 Y 0.0689 0.1378 0.7933 105 D 0.1256 0.1274 0.7470 106 A 0.4025 0.0853 0.5122 107 E 0.7326 0.0824 0.1850 108 I 0.8443 0.0615 0.0942 109 V 0.7946 0.0785 0.1269 110 R 0.7609 0.0660 0.1732 111 M 0.4850 0.0848 0.4302 112 A 0.1408 0.0361 0.8231 113 P 0.0887 0.1187 0.7926 114 E 0.0874 0.2374 0.6752 115 Q 0.1231 0.1756 0.7013 116 K 0.1070 0.1673 0.7256 117 L 0.0807 0.0762 0.8431 118 A 0.0533 0.0608 0.8858 119 P 0.0411 0.3385 0.6204 120 A 0.0386 0.5440 0.4174 121 R 0.0343 0.6465 0.3191 122 R 0.0057 0.9284 0.0659 123 K 0.0049 0.9531 0.0420 124 V 0.0047 0.9591 0.0363 125 L 0.0047 0.9603 0.0350 126 I 0.0047 0.9593 0.0360 127 Q 0.0047 0.9583 0.0370 128 K 0.0047 0.9516 0.0437 129 F 0.0048 0.9444 0.0507 130 A 0.0047 0.9486 0.0467 131 T 0.0047 0.9475 0.0478 132 H 0.0048 0.9450 0.0502 133 A 0.0047 0.9511 0.0442 134 A 0.0047 0.9542 0.0411 135 R 0.0047 0.9550 0.0403 136 R 0.0048 0.9512 0.0440 137 L 0.0048 0.9417 0.0534 138 Q 0.0053 0.9048 0.0899 139 A 0.0077 0.8406 0.1518 140 L 0.0176 0.6921 0.2903 141 R 0.0468 0.4810 0.4723 142 D 0.0841 0.0364 0.8795 143 P 0.0104 0.1998 0.7898 144 E 0.0183 0.1581 0.8236 145 G 0.0562 0.2359 0.7080 146 H 0.0943 0.1753 0.7304 147 G 0.1307 0.1860 0.6832 148 I 0.1535 0.1859 0.6606 149 F 0.1278 0.1026 0.7696 150 E 0.0789 0.0663 0.8548