# This file is the result of combining several RDB files, specifically # T0379.t04.dssp-ebghstl.rdb (weight 1.53986) # T0379.t04.stride-ebghtl.rdb (weight 1.24869) # T0379.t04.str2.rdb (weight 1.54758) # T0379.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 T0379.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0379 # 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 T0379.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 2240 # # ============================================ # Comments from T0379.t04.stride-ebghtl.rdb # ============================================ # TARGET T0379 # 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 T0379.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 2240 # # ============================================ # Comments from T0379.t04.str2.rdb # ============================================ # TARGET T0379 # 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 T0379.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 2240 # # ============================================ # Comments from T0379.t04.alpha.rdb # ============================================ # TARGET T0379 # 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 T0379.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 2240 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0848 0.0408 0.8744 2 I 0.2381 0.0093 0.7527 3 R 0.3425 0.0364 0.6211 4 N 0.8893 0.0049 0.1058 5 I 0.9283 0.0032 0.0684 6 V 0.9312 0.0032 0.0655 7 F 0.9151 0.0046 0.0802 8 D 0.6933 0.0067 0.3000 9 L 0.2302 0.0556 0.7142 10 G 0.0569 0.0489 0.8942 11 G 0.1044 0.0493 0.8463 12 V 0.4073 0.0428 0.5498 13 L 0.7645 0.0337 0.2018 14 I 0.6707 0.0531 0.2762 15 H 0.4701 0.0541 0.4758 16 L 0.1276 0.1247 0.7477 17 N 0.0680 0.2007 0.7313 18 R 0.0152 0.7419 0.2428 19 E 0.0101 0.8681 0.1218 20 E 0.0113 0.9127 0.0760 21 S 0.0070 0.9414 0.0516 22 I 0.0064 0.9486 0.0451 23 R 0.0054 0.9535 0.0411 24 R 0.0054 0.9551 0.0395 25 F 0.0054 0.9540 0.0406 26 K 0.0057 0.9476 0.0468 27 A 0.0060 0.9426 0.0514 28 I 0.0145 0.9134 0.0722 29 G 0.0100 0.8922 0.0978 30 V 0.0130 0.8436 0.1433 31 A 0.0481 0.5304 0.4215 32 D 0.0404 0.0724 0.8872 33 I 0.0613 0.0500 0.8888 34 E 0.0869 0.1276 0.7854 35 E 0.0868 0.2434 0.6698 36 M 0.0869 0.2516 0.6615 37 L 0.0406 0.6159 0.3434 38 D 0.0252 0.8119 0.1629 39 P 0.0098 0.8916 0.0986 40 Y 0.0124 0.9014 0.0862 41 L 0.0190 0.8804 0.1006 42 Q 0.0209 0.8309 0.1482 43 K 0.0305 0.6878 0.2817 44 G 0.0445 0.4375 0.5180 45 L 0.0712 0.3066 0.6222 46 F 0.0989 0.3038 0.5973 47 L 0.0856 0.3295 0.5849 48 D 0.0875 0.3656 0.5468 49 L 0.0320 0.7135 0.2545 50 E 0.0270 0.7277 0.2453 51 S 0.0329 0.7133 0.2539 52 G 0.0395 0.6537 0.3067 53 R 0.0400 0.6882 0.2717 54 K 0.0480 0.7001 0.2519 55 S 0.0358 0.6765 0.2877 56 E 0.0188 0.7806 0.2006 57 E 0.0077 0.8686 0.1237 58 E 0.0095 0.8632 0.1273 59 F 0.0180 0.8138 0.1682 60 R 0.0151 0.8031 0.1818 61 T 0.0149 0.7868 0.1984 62 E 0.0202 0.7993 0.1805 63 L 0.0190 0.8333 0.1476 64 S 0.0179 0.8227 0.1595 65 R 0.0200 0.8070 0.1730 66 Y 0.0204 0.8073 0.1722 67 I 0.0225 0.7482 0.2293 68 G 0.0232 0.6488 0.3280 69 K 0.0280 0.7014 0.2706 70 E 0.0231 0.8016 0.1753 71 L 0.0153 0.8592 0.1256 72 T 0.0147 0.8779 0.1075 73 Y 0.0068 0.9363 0.0569 74 Q 0.0061 0.9486 0.0454 75 Q 0.0053 0.9522 0.0425 76 V 0.0050 0.9537 0.0413 77 Y 0.0048 0.9549 0.0404 78 D 0.0052 0.9501 0.0447 79 A 0.0058 0.9276 0.0666 80 L 0.0079 0.8797 0.1125 81 L 0.0191 0.7775 0.2034 82 G 0.0172 0.6124 0.3705 83 F 0.0278 0.5328 0.4393 84 L 0.0623 0.4309 0.5068 85 E 0.0782 0.3345 0.5873 86 E 0.1083 0.2647 0.6270 87 I 0.1020 0.1529 0.7451 88 S 0.0704 0.1154 0.8142 89 A 0.0121 0.6642 0.3237 90 E 0.0135 0.5789 0.4076 91 K 0.0189 0.8100 0.1711 92 F 0.0176 0.8605 0.1219 93 D 0.0147 0.8772 0.1081 94 Y 0.0063 0.9231 0.0705 95 I 0.0081 0.9118 0.0800 96 D 0.0071 0.8561 0.1368 97 S 0.0106 0.7166 0.2729 98 L 0.0423 0.4732 0.4845 99 R 0.0499 0.0823 0.8678 100 P 0.0140 0.1785 0.8075 101 D 0.0196 0.0527 0.9277 102 Y 0.2913 0.0135 0.6952 103 R 0.6876 0.0147 0.2977 104 L 0.9299 0.0034 0.0667 105 F 0.9327 0.0033 0.0641 106 L 0.9323 0.0032 0.0644 107 L 0.9006 0.0050 0.0944 108 S 0.5321 0.0124 0.4554 109 N 0.1007 0.0397 0.8596 110 T 0.0515 0.0502 0.8983 111 N 0.0841 0.0642 0.8517 112 P 0.0142 0.7481 0.2377 113 Y 0.0152 0.8505 0.1343 114 V 0.0278 0.8701 0.1021 115 L 0.0425 0.8597 0.0977 116 D 0.0501 0.8406 0.1093 117 L 0.0530 0.8295 0.1175 118 A 0.0510 0.7833 0.1657 119 M 0.0754 0.6364 0.2882 120 S 0.0855 0.3797 0.5347 121 P 0.0405 0.4673 0.4922 122 R 0.0659 0.3174 0.6167 123 F 0.0792 0.1234 0.7974 124 L 0.0689 0.0774 0.8538 125 P 0.0501 0.1382 0.8117 126 S 0.0468 0.1434 0.8098 127 G 0.0576 0.1588 0.7836 128 R 0.1083 0.1718 0.7199 129 T 0.1800 0.2294 0.5906 130 L 0.0717 0.5834 0.3449 131 D 0.0403 0.6837 0.2760 132 S 0.0295 0.6632 0.3073 133 F 0.0509 0.5815 0.3676 134 F 0.2183 0.2223 0.5594 135 D 0.1161 0.2481 0.6358 136 K 0.6613 0.1527 0.1860 137 V 0.8298 0.0870 0.0832 138 Y 0.8490 0.0528 0.0981 139 A 0.6750 0.0451 0.2799 140 S 0.2730 0.1524 0.5745 141 C 0.1011 0.2718 0.6271 142 Q 0.1200 0.3270 0.5530 143 M 0.1026 0.2814 0.6160 144 G 0.0689 0.2220 0.7091 145 K 0.0705 0.1788 0.7507 146 Y 0.1098 0.0926 0.7976 147 K 0.1003 0.0237 0.8760 148 P 0.0925 0.0220 0.8855 149 N 0.0818 0.0193 0.8989 150 E 0.0064 0.9179 0.0757 151 D 0.0054 0.9467 0.0479 152 I 0.0048 0.9556 0.0395 153 F 0.0047 0.9590 0.0363 154 L 0.0046 0.9610 0.0343 155 E 0.0047 0.9613 0.0341 156 M 0.0046 0.9615 0.0339 157 I 0.0047 0.9607 0.0346 158 A 0.0048 0.9538 0.0414 159 D 0.0060 0.8985 0.0955 160 S 0.0447 0.4072 0.5481 161 G 0.0378 0.0176 0.9446 162 M 0.0610 0.0077 0.9314 163 K 0.0775 0.0089 0.9135 164 P 0.0385 0.6503 0.3112 165 E 0.0758 0.6120 0.3122 166 E 0.2613 0.4056 0.3332 167 T 0.8706 0.0149 0.1145 168 L 0.8983 0.0135 0.0882 169 F 0.9160 0.0063 0.0778 170 I 0.8570 0.0197 0.1233 171 D 0.5462 0.0219 0.4319 172 D 0.2005 0.0203 0.7792 173 G 0.0668 0.0436 0.8896 174 P 0.0124 0.6734 0.3142 175 A 0.0107 0.8321 0.1572 176 N 0.0113 0.8364 0.1523 177 V 0.0049 0.9523 0.0428 178 A 0.0049 0.9572 0.0379 179 T 0.0047 0.9602 0.0351 180 A 0.0047 0.9595 0.0358 181 E 0.0048 0.9543 0.0409 182 R 0.0057 0.9283 0.0659 183 L 0.0442 0.3779 0.5779 184 G 0.0455 0.0184 0.9361 185 F 0.0886 0.0079 0.9035 186 H 0.3192 0.0316 0.6492 187 T 0.8258 0.0106 0.1636 188 Y 0.8666 0.0069 0.1265 189 C 0.7975 0.0063 0.1962 190 P 0.5062 0.0125 0.4813 191 D 0.1975 0.0327 0.7698 192 N 0.0817 0.0679 0.8504 193 G 0.0490 0.1227 0.8283 194 E 0.0649 0.2089 0.7262 195 N 0.0964 0.1916 0.7120 196 W 0.1008 0.2449 0.6543 197 I 0.0794 0.3174 0.6031 198 P 0.0586 0.4933 0.4480 199 A 0.0588 0.5989 0.3423 200 I 0.0509 0.6966 0.2525 201 T 0.0385 0.7317 0.2298 202 R 0.0338 0.7522 0.2140 203 L 0.0340 0.8179 0.1481 204 L 0.0367 0.8064 0.1569 205 R 0.0380 0.7611 0.2009 206 E 0.0392 0.6873 0.2735 207 Q 0.0504 0.4123 0.5374 208 K 0.0320 0.1027 0.8653