# This file is the result of combining several RDB files, specifically # T0316.t04.dssp-ebghstl.rdb (weight 1.53986) # T0316.t04.stride-ebghtl.rdb (weight 1.24869) # T0316.t04.str2.rdb (weight 1.54758) # T0316.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 T0316.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0316 # 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 T0316.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 1903 # # ============================================ # Comments from T0316.t04.stride-ebghtl.rdb # ============================================ # TARGET T0316 # 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 T0316.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 1903 # # ============================================ # Comments from T0316.t04.str2.rdb # ============================================ # TARGET T0316 # 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 T0316.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 1903 # # ============================================ # Comments from T0316.t04.alpha.rdb # ============================================ # TARGET T0316 # 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 T0316.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 1903 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0913 0.0343 0.8743 2 S 0.1351 0.0524 0.8125 3 D 0.1158 0.0974 0.7868 4 N 0.0964 0.1298 0.7738 5 S 0.0688 0.1253 0.8059 6 K 0.0550 0.0868 0.8582 7 T 0.1510 0.0267 0.8223 8 R 0.6905 0.0047 0.3048 9 V 0.9201 0.0034 0.0765 10 V 0.9328 0.0032 0.0640 11 V 0.9317 0.0034 0.0649 12 G 0.9190 0.0054 0.0756 13 M 0.8643 0.0082 0.1275 14 S 0.5708 0.0150 0.4143 15 G 0.1679 0.0303 0.8018 16 G 0.0864 0.0625 0.8512 17 V 0.0562 0.3402 0.6036 18 D 0.0291 0.5954 0.3755 19 S 0.0052 0.9314 0.0634 20 S 0.0047 0.9569 0.0384 21 V 0.0047 0.9602 0.0351 22 T 0.0047 0.9608 0.0346 23 A 0.0046 0.9615 0.0339 24 L 0.0046 0.9617 0.0337 25 L 0.0046 0.9615 0.0339 26 L 0.0047 0.9607 0.0346 27 K 0.0048 0.9565 0.0387 28 E 0.0058 0.9190 0.0751 29 Q 0.0414 0.3805 0.5781 30 G 0.0383 0.0204 0.9413 31 Y 0.0637 0.0120 0.9244 32 D 0.3415 0.0169 0.6416 33 V 0.7647 0.0054 0.2299 34 I 0.8512 0.0099 0.1388 35 G 0.9136 0.0038 0.0826 36 I 0.9153 0.0038 0.0809 37 F 0.9139 0.0041 0.0820 38 M 0.8765 0.0058 0.1177 39 K 0.7963 0.0175 0.1862 40 N 0.6918 0.0152 0.2930 41 W 0.4597 0.0367 0.5036 42 D 0.3321 0.0450 0.6229 43 D 0.2182 0.1074 0.6744 44 T 0.1577 0.0906 0.7516 45 D 0.0822 0.1450 0.7728 46 E 0.0586 0.1825 0.7590 47 N 0.0975 0.1210 0.7814 48 G 0.0866 0.0793 0.8342 49 V 0.1962 0.0859 0.7180 50 C 0.2077 0.0746 0.7177 51 T 0.1119 0.0703 0.8177 52 A 0.0672 0.1429 0.7899 53 T 0.0409 0.4759 0.4832 54 E 0.0409 0.5895 0.3695 55 D 0.0460 0.5902 0.3639 56 Y 0.0055 0.9381 0.0564 57 K 0.0048 0.9562 0.0390 58 D 0.0047 0.9588 0.0365 59 V 0.0047 0.9598 0.0355 60 V 0.0046 0.9614 0.0340 61 A 0.0046 0.9615 0.0338 62 V 0.0046 0.9614 0.0339 63 A 0.0047 0.9605 0.0349 64 D 0.0048 0.9533 0.0418 65 Q 0.0056 0.9249 0.0696 66 I 0.0448 0.4666 0.4886 67 G 0.0447 0.0144 0.9409 68 I 0.0642 0.0079 0.9279 69 P 0.2294 0.0098 0.7608 70 Y 0.8407 0.0064 0.1529 71 Y 0.9048 0.0049 0.0903 72 S 0.9221 0.0037 0.0742 73 V 0.8432 0.0115 0.1453 74 N 0.4902 0.0068 0.5030 75 F 0.0843 0.4064 0.5093 76 E 0.0353 0.5920 0.3727 77 K 0.0124 0.8125 0.1751 78 E 0.0175 0.8504 0.1321 79 Y 0.0147 0.8686 0.1167 80 W 0.0083 0.9136 0.0781 81 D 0.0068 0.9188 0.0744 82 R 0.0080 0.9133 0.0787 83 V 0.0117 0.8986 0.0898 84 F 0.0155 0.8870 0.0976 85 E 0.0177 0.8803 0.1020 86 Y 0.0221 0.8619 0.1160 87 F 0.0242 0.8467 0.1291 88 L 0.0199 0.8749 0.1052 89 A 0.0082 0.9239 0.0679 90 E 0.0079 0.9230 0.0692 91 Y 0.0171 0.8918 0.0911 92 R 0.0231 0.8164 0.1605 93 A 0.0370 0.4755 0.4874 94 G 0.0275 0.0928 0.8797 95 R 0.0796 0.0365 0.8839 96 T 0.1218 0.0146 0.8636 97 P 0.1117 0.0324 0.8559 98 N 0.1127 0.0340 0.8533 99 P 0.0519 0.2198 0.7283 100 D 0.0721 0.3206 0.6073 101 V 0.1066 0.4577 0.4357 102 M 0.1072 0.4064 0.4864 103 C 0.0714 0.4471 0.4816 104 N 0.0306 0.5382 0.4312 105 K 0.0105 0.8408 0.1487 106 E 0.0117 0.8943 0.0940 107 I 0.0201 0.9034 0.0765 108 K 0.0163 0.9011 0.0826 109 F 0.0079 0.9371 0.0550 110 K 0.0066 0.9440 0.0494 111 A 0.0051 0.9551 0.0398 112 F 0.0048 0.9569 0.0383 113 L 0.0047 0.9603 0.0350 114 D 0.0047 0.9608 0.0345 115 Y 0.0047 0.9612 0.0342 116 A 0.0047 0.9608 0.0345 117 I 0.0048 0.9546 0.0406 118 T 0.0052 0.9365 0.0583 119 L 0.0405 0.4564 0.5031 120 G 0.0614 0.0122 0.9265 121 A 0.0843 0.0194 0.8963 122 D 0.0705 0.0591 0.8703 123 Y 0.8681 0.0140 0.1180 124 V 0.9183 0.0088 0.0729 125 A 0.9082 0.0119 0.0799 126 T 0.7916 0.0372 0.1712 127 G 0.4384 0.0437 0.5179 128 H 0.2520 0.0831 0.6649 129 Y 0.2154 0.1330 0.6516 130 A 0.1277 0.3556 0.5167 131 R 0.0975 0.4571 0.4454 132 V 0.0939 0.5228 0.3833 133 A 0.1102 0.5161 0.3737 134 R 0.1030 0.4289 0.4680 135 D 0.0940 0.3118 0.5943 136 E 0.0974 0.1854 0.7172 137 D 0.0571 0.2289 0.7141 138 G 0.0660 0.2124 0.7216 139 T 0.2113 0.3001 0.4887 140 V 0.2955 0.3540 0.3505 141 H 0.3015 0.3940 0.3045 142 M 0.3096 0.4003 0.2901 143 L 0.2588 0.3784 0.3628 144 R 0.1465 0.2798 0.5737 145 G 0.1031 0.1961 0.7008 146 V 0.1017 0.3250 0.5734 147 D 0.0881 0.3666 0.5453 148 N 0.0540 0.3665 0.5795 149 G 0.0464 0.2785 0.6751 150 K 0.0538 0.3772 0.5690 151 D 0.0442 0.4479 0.5079 152 Q 0.0624 0.4928 0.4447 153 T 0.1356 0.4292 0.4352 154 Y 0.1813 0.3952 0.4235 155 F 0.2117 0.3860 0.4022 156 L 0.1802 0.4021 0.4177 157 S 0.1428 0.3678 0.4895 158 Q 0.0954 0.2887 0.6159 159 L 0.0984 0.1206 0.7810 160 S 0.0735 0.1047 0.8218 161 Q 0.0080 0.7811 0.2109 162 E 0.0089 0.7799 0.2112 163 Q 0.0170 0.7614 0.2216 164 L 0.0443 0.6906 0.2651 165 Q 0.1012 0.5521 0.3467 166 K 0.2033 0.4776 0.3191 167 T 0.3237 0.4085 0.2677 168 M 0.4202 0.2676 0.3122 169 F 0.3379 0.2040 0.4581 170 P 0.2098 0.2324 0.5578 171 L 0.0805 0.3844 0.5352 172 G 0.0610 0.3123 0.6267 173 H 0.0693 0.2278 0.7029 174 L 0.1204 0.0419 0.8377 175 E 0.0634 0.0252 0.9114 176 K 0.0087 0.9381 0.0532 177 P 0.0047 0.9598 0.0356 178 E 0.0047 0.9610 0.0343 179 V 0.0047 0.9609 0.0345 180 R 0.0046 0.9611 0.0342 181 R 0.0046 0.9616 0.0338 182 L 0.0046 0.9618 0.0336 183 A 0.0046 0.9613 0.0341 184 E 0.0048 0.9561 0.0391 185 E 0.0054 0.9385 0.0561 186 A 0.0424 0.4663 0.4912 187 G 0.0441 0.0171 0.9388 188 L 0.0634 0.0088 0.9278 189 S 0.1076 0.0453 0.8470 190 T 0.3073 0.1229 0.5698 191 A 0.3477 0.1470 0.5053 192 K 0.4049 0.1223 0.4728 193 K 0.2923 0.0570 0.6507 194 K 0.1652 0.0800 0.7549 195 D 0.1310 0.0477 0.8214 196 S 0.0953 0.1111 0.7937 197 T 0.1164 0.0935 0.7901 198 G 0.1815 0.0901 0.7284 199 I 0.2920 0.0978 0.6101 200 C 0.4438 0.0966 0.4597 201 F 0.4163 0.0996 0.4841 202 I 0.2969 0.0969 0.6062 203 G 0.1418 0.0712 0.7870 204 E 0.0958 0.0835 0.8207 205 K 0.0916 0.0448 0.8636