# This file is the result of combining several RDB files, specifically # T0197.t04.dssp-ebghstl.rdb (weight 1.53986) # T0197.t04.stride-ebghtl.rdb (weight 1.24869) # T0197.t04.str2.rdb (weight 1.54758) # T0197.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 T0197.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0197 # 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 T0197.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 147 # # ============================================ # Comments from T0197.t04.stride-ebghtl.rdb # ============================================ # TARGET T0197 # 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 T0197.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 147 # # ============================================ # Comments from T0197.t04.str2.rdb # ============================================ # TARGET T0197 # 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 T0197.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 147 # # ============================================ # Comments from T0197.t04.alpha.rdb # ============================================ # TARGET T0197 # 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 T0197.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 147 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.0999 0.0980 0.8021 2 H 0.1403 0.1436 0.7161 3 H 0.1386 0.1863 0.6751 4 H 0.1274 0.1753 0.6973 5 H 0.1219 0.2297 0.6484 6 H 0.1264 0.2234 0.6502 7 H 0.0895 0.2207 0.6898 8 G 0.1319 0.2541 0.6140 9 S 0.3031 0.2434 0.4535 10 E 0.6517 0.1516 0.1968 11 V 0.7892 0.0913 0.1195 12 E 0.8438 0.0640 0.0923 13 I 0.8160 0.0699 0.1141 14 K 0.7809 0.0785 0.1406 15 F 0.7410 0.0394 0.2196 16 K 0.6137 0.0224 0.3639 17 I 0.3731 0.0114 0.6155 18 K 0.1309 0.0092 0.8599 19 L 0.0055 0.9077 0.0868 20 E 0.0048 0.9453 0.0499 21 D 0.0048 0.9483 0.0469 22 F 0.0050 0.9539 0.0411 23 L 0.0050 0.9567 0.0383 24 H 0.0050 0.9548 0.0402 25 T 0.0049 0.9474 0.0477 26 L 0.0058 0.9259 0.0683 27 N 0.0058 0.8311 0.1630 28 T 0.0095 0.6295 0.3610 29 F 0.0603 0.2488 0.6909 30 N 0.0713 0.0373 0.8914 31 P 0.0141 0.6271 0.3588 32 E 0.0253 0.6390 0.3357 33 F 0.0708 0.6145 0.3147 34 V 0.1915 0.3021 0.5065 35 R 0.2591 0.2040 0.5368 36 Y 0.3166 0.3472 0.3362 37 E 0.4072 0.2586 0.3342 38 E 0.4418 0.1947 0.3634 39 Q 0.4390 0.1730 0.3879 40 E 0.3964 0.1386 0.4650 41 D 0.4686 0.0865 0.4449 42 V 0.6548 0.0798 0.2654 43 Y 0.7857 0.0440 0.1702 44 F 0.7608 0.0260 0.2132 45 E 0.5564 0.0244 0.4193 46 V 0.2642 0.0168 0.7189 47 P 0.1037 0.0599 0.8365 48 R 0.0898 0.0322 0.8780 49 P 0.0649 0.1166 0.8185 50 K 0.2391 0.0995 0.6614 51 L 0.8151 0.0140 0.1709 52 L 0.9061 0.0044 0.0895 53 R 0.9250 0.0043 0.0707 54 I 0.9151 0.0054 0.0795 55 R 0.8662 0.0126 0.1212 56 G 0.8163 0.0118 0.1719 57 V 0.6328 0.0498 0.3174 58 H 0.3012 0.0628 0.6360 59 N 0.1175 0.0783 0.8042 60 L 0.1340 0.1010 0.7650 61 K 0.1149 0.0849 0.8002 62 K 0.4399 0.0407 0.5195 63 Y 0.7679 0.0094 0.2227 64 Y 0.9140 0.0047 0.0813 65 L 0.9174 0.0037 0.0789 66 T 0.9123 0.0052 0.0826 67 F 0.8437 0.0081 0.1481 68 K 0.6237 0.0449 0.3314 69 E 0.4708 0.0296 0.4996 70 I 0.3319 0.0566 0.6115 71 L 0.2427 0.0807 0.6766 72 D 0.1417 0.0984 0.7599 73 E 0.0697 0.1967 0.7335 74 N 0.0879 0.1255 0.7866 75 N 0.1214 0.1084 0.7702 76 E 0.1937 0.1303 0.6759 77 E 0.4054 0.1044 0.4902 78 F 0.5892 0.0652 0.3456 79 Y 0.7456 0.0298 0.2247 80 E 0.8484 0.0202 0.1314 81 V 0.8559 0.0191 0.1251 82 E 0.8124 0.0169 0.1707 83 F 0.6761 0.0136 0.3103 84 E 0.5096 0.0172 0.4733 85 I 0.1304 0.2670 0.6026 86 G 0.0521 0.3024 0.6455 87 D 0.0785 0.2864 0.6351 88 F 0.0089 0.8830 0.1081 89 E 0.0064 0.9413 0.0522 90 K 0.0051 0.9526 0.0424 91 A 0.0056 0.9496 0.0447 92 V 0.0047 0.9581 0.0372 93 E 0.0048 0.9552 0.0400 94 V 0.0048 0.9565 0.0387 95 F 0.0048 0.9511 0.0441 96 K 0.0050 0.9375 0.0576 97 R 0.0059 0.8749 0.1192 98 L 0.0398 0.3646 0.5956 99 G 0.0353 0.0259 0.9388 100 F 0.0881 0.0132 0.8987 101 K 0.3725 0.0126 0.6150 102 I 0.6960 0.0108 0.2932 103 Q 0.7576 0.0240 0.2184 104 A 0.8199 0.0086 0.1716 105 T 0.8854 0.0063 0.1084 106 I 0.8851 0.0064 0.1085 107 K 0.8575 0.0103 0.1322 108 K 0.8949 0.0091 0.0960 109 K 0.8866 0.0142 0.0992 110 R 0.9029 0.0058 0.0913 111 W 0.9063 0.0066 0.0870 112 V 0.9124 0.0084 0.0793 113 Y 0.9100 0.0076 0.0824 114 K 0.8874 0.0128 0.0998 115 L 0.6884 0.0345 0.2771 116 N 0.0940 0.0324 0.8735 117 G 0.0595 0.0308 0.9097 118 V 0.7258 0.0088 0.2654 119 T 0.9176 0.0043 0.0781 120 L 0.9233 0.0035 0.0732 121 E 0.9278 0.0036 0.0686 122 V 0.9090 0.0041 0.0869 123 N 0.7708 0.0228 0.2064 124 R 0.6956 0.0303 0.2742 125 V 0.5648 0.0722 0.3630 126 E 0.2952 0.1610 0.5438 127 G 0.1452 0.1141 0.7407 128 I 0.1478 0.0839 0.7683 129 G 0.1250 0.0583 0.8167 130 D 0.1953 0.0574 0.7473 131 F 0.6649 0.0218 0.3133 132 V 0.8663 0.0068 0.1269 133 D 0.9225 0.0039 0.0737 134 I 0.9187 0.0041 0.0771 135 E 0.9095 0.0048 0.0857 136 V 0.8849 0.0055 0.1095 137 I 0.7896 0.0109 0.1995 138 S 0.4266 0.0209 0.5526 139 D 0.0745 0.0533 0.8721 140 S 0.0814 0.0136 0.9050 141 P 0.0072 0.8935 0.0993 142 E 0.0049 0.9460 0.0490 143 E 0.0049 0.9510 0.0441 144 A 0.0048 0.9522 0.0429 145 K 0.0047 0.9562 0.0390 146 E 0.0048 0.9560 0.0392 147 K 0.0049 0.9548 0.0403 148 I 0.0047 0.9548 0.0404 149 W 0.0047 0.9572 0.0381 150 E 0.0047 0.9581 0.0371 151 V 0.0047 0.9594 0.0359 152 A 0.0048 0.9589 0.0363 153 K 0.0051 0.9503 0.0446 154 M 0.0074 0.9162 0.0764 155 L 0.0461 0.4721 0.4818 156 G 0.0395 0.0286 0.9319 157 L 0.0643 0.0097 0.9260 158 K 0.1001 0.0176 0.8824 159 E 0.1103 0.3902 0.4995 160 E 0.0745 0.3906 0.5349 161 D 0.0561 0.3303 0.6136 162 V 0.0962 0.2214 0.6824 163 E 0.0741 0.1957 0.7303 164 P 0.0365 0.6980 0.2656 165 R 0.0294 0.7890 0.1816 166 L 0.0335 0.8136 0.1530 167 Y 0.0173 0.8966 0.0861 168 L 0.0123 0.9316 0.0562 169 E 0.0125 0.9374 0.0501 170 L 0.0084 0.9355 0.0562 171 I 0.0090 0.9204 0.0707 172 N 0.0119 0.8526 0.1355 173 E 0.0259 0.7011 0.2730 174 L 0.0380 0.5237 0.4383 175 S 0.0475 0.3167 0.6358 176 G 0.0338 0.2265 0.7396 177 R 0.0554 0.1492 0.7955 178 S 0.0602 0.0931 0.8467 179 S 0.0447 0.0578 0.8975