# This file is the result of combining several RDB files, specifically # T0267.t04.dssp-ebghstl.rdb (weight 1.53986) # T0267.t04.stride-ebghtl.rdb (weight 1.24869) # T0267.t04.str2.rdb (weight 1.54758) # T0267.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 T0267.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0267 # 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 T0267.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 2336 # # ============================================ # Comments from T0267.t04.stride-ebghtl.rdb # ============================================ # TARGET T0267 # 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 T0267.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 2336 # # ============================================ # Comments from T0267.t04.str2.rdb # ============================================ # TARGET T0267 # 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 T0267.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 2336 # # ============================================ # Comments from T0267.t04.alpha.rdb # ============================================ # TARGET T0267 # 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 T0267.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 2336 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1945 0.0201 0.7854 2 V 0.5563 0.0141 0.4296 3 R 0.7642 0.0119 0.2239 4 I 0.8136 0.0116 0.1748 5 R 0.7220 0.0195 0.2586 6 R 0.5311 0.0203 0.4485 7 A 0.1843 0.0285 0.7872 8 G 0.1001 0.0221 0.8778 9 L 0.0069 0.7709 0.2222 10 E 0.0103 0.7179 0.2718 11 D 0.0125 0.6703 0.3173 12 L 0.0077 0.8846 0.1077 13 P 0.0049 0.9495 0.0456 14 G 0.0048 0.9557 0.0395 15 V 0.0048 0.9569 0.0383 16 A 0.0047 0.9581 0.0372 17 R 0.0047 0.9581 0.0372 18 V 0.0050 0.9543 0.0407 19 L 0.0050 0.9486 0.0464 20 V 0.0055 0.9414 0.0532 21 D 0.0060 0.9345 0.0594 22 T 0.0068 0.9224 0.0708 23 W 0.0106 0.8999 0.0895 24 R 0.0162 0.8870 0.0968 25 A 0.0226 0.8326 0.1448 26 T 0.0359 0.7322 0.2320 27 Y 0.0624 0.5463 0.3913 28 R 0.0628 0.3996 0.5376 29 G 0.0660 0.2506 0.6834 30 V 0.1042 0.1694 0.7265 31 V 0.0909 0.0834 0.8257 32 P 0.0577 0.3165 0.6258 33 E 0.0217 0.7440 0.2344 34 A 0.0287 0.7650 0.2063 35 F 0.0370 0.7474 0.2156 36 L 0.0495 0.6914 0.2591 37 E 0.0355 0.6096 0.3549 38 G 0.0320 0.4433 0.5246 39 L 0.0679 0.3618 0.5703 40 S 0.0673 0.3007 0.6320 41 Y 0.0436 0.3352 0.6212 42 E 0.0279 0.5674 0.4047 43 G 0.0322 0.5417 0.4261 44 Q 0.0243 0.6953 0.2804 45 A 0.0051 0.9458 0.0492 46 E 0.0049 0.9553 0.0397 47 R 0.0050 0.9558 0.0392 48 W 0.0047 0.9568 0.0384 49 A 0.0048 0.9545 0.0408 50 Q 0.0052 0.9408 0.0540 51 R 0.0068 0.8940 0.0992 52 L 0.0235 0.7673 0.2092 53 K 0.0378 0.4091 0.5531 54 T 0.0644 0.0373 0.8983 55 P 0.0270 0.1042 0.8688 56 T 0.0454 0.0759 0.8787 57 W 0.0743 0.0514 0.8743 58 P 0.0701 0.0933 0.8366 59 G 0.2077 0.0639 0.7284 60 R 0.5742 0.0214 0.4044 61 L 0.8445 0.0052 0.1503 62 F 0.9145 0.0036 0.0820 63 V 0.9244 0.0037 0.0719 64 A 0.9169 0.0042 0.0789 65 E 0.8972 0.0049 0.0979 66 S 0.5832 0.0166 0.4002 67 E 0.1185 0.0835 0.7980 68 S 0.0499 0.0196 0.9304 69 G 0.0738 0.0264 0.8998 70 E 0.5538 0.0071 0.4392 71 V 0.9172 0.0029 0.0799 72 V 0.8764 0.0158 0.1078 73 G 0.9224 0.0038 0.0738 74 F 0.9272 0.0033 0.0695 75 A 0.9176 0.0040 0.0784 76 A 0.8932 0.0042 0.1026 77 F 0.8079 0.0139 0.1782 78 G 0.6115 0.0139 0.3745 79 P 0.3478 0.0683 0.5840 80 D 0.1970 0.0989 0.7041 81 R 0.1323 0.1870 0.6807 82 A 0.0790 0.1923 0.7287 83 S 0.0778 0.1183 0.8039 84 G 0.0647 0.0739 0.8614 85 F 0.0983 0.0360 0.8657 86 P 0.0783 0.0792 0.8426 87 G 0.0823 0.0717 0.8460 88 Y 0.2074 0.0631 0.7295 89 T 0.5353 0.0462 0.4185 90 A 0.7854 0.0154 0.1992 91 E 0.8859 0.0100 0.1041 92 L 0.8953 0.0112 0.0935 93 W 0.8063 0.0421 0.1516 94 A 0.8567 0.0210 0.1224 95 I 0.8780 0.0221 0.0999 96 Y 0.8713 0.0192 0.1096 97 V 0.7423 0.0274 0.2302 98 L 0.2689 0.0463 0.6847 99 P 0.0194 0.6254 0.3552 100 T 0.0112 0.7023 0.2865 101 W 0.0216 0.7353 0.2431 102 Q 0.0191 0.5771 0.4038 103 R 0.0209 0.3734 0.6056 104 K 0.0505 0.2752 0.6743 105 G 0.0468 0.4668 0.4864 106 L 0.0170 0.8429 0.1401 107 G 0.0052 0.9486 0.0461 108 R 0.0047 0.9595 0.0358 109 A 0.0047 0.9608 0.0345 110 L 0.0047 0.9603 0.0351 111 F 0.0047 0.9603 0.0350 112 H 0.0046 0.9610 0.0343 113 E 0.0046 0.9593 0.0361 114 G 0.0047 0.9583 0.0370 115 A 0.0047 0.9604 0.0350 116 R 0.0047 0.9609 0.0344 117 L 0.0047 0.9610 0.0343 118 L 0.0047 0.9598 0.0355 119 Q 0.0049 0.9474 0.0477 120 A 0.0063 0.8795 0.1142 121 E 0.0416 0.3562 0.6021 122 G 0.0381 0.0196 0.9422 123 Y 0.0802 0.0117 0.9081 124 G 0.1696 0.0502 0.7802 125 R 0.8395 0.0097 0.1508 126 M 0.9186 0.0038 0.0776 127 L 0.9297 0.0039 0.0664 128 V 0.9180 0.0046 0.0774 129 W 0.8759 0.0066 0.1175 130 V 0.7254 0.0232 0.2514 131 L 0.3817 0.0564 0.5620 132 K 0.1117 0.2357 0.6526 133 E 0.0488 0.1909 0.7602 134 N 0.0854 0.0780 0.8367 135 P 0.0111 0.6292 0.3597 136 K 0.0107 0.7509 0.2383 137 G 0.0114 0.8415 0.1471 138 R 0.0064 0.9257 0.0680 139 G 0.0080 0.9269 0.0651 140 F 0.0095 0.9363 0.0542 141 Y 0.0100 0.9384 0.0516 142 E 0.0095 0.9312 0.0593 143 H 0.0134 0.8710 0.1155 144 L 0.0520 0.4739 0.4741 145 G 0.0582 0.0639 0.8779 146 G 0.2238 0.0341 0.7422 147 V 0.7190 0.0201 0.2609 148 L 0.8344 0.0151 0.1505 149 L 0.6793 0.0426 0.2781 150 G 0.4511 0.0231 0.5258 151 E 0.6571 0.0278 0.3151 152 R 0.7598 0.0232 0.2170 153 E 0.7680 0.0307 0.2012 154 I 0.7427 0.0365 0.2208 155 E 0.6336 0.0588 0.3077 156 L 0.3628 0.0886 0.5486 157 G 0.0923 0.0484 0.8593 158 G 0.0977 0.0486 0.8537 159 A 0.3197 0.0529 0.6274 160 K 0.5787 0.0662 0.3551 161 L 0.5815 0.1228 0.2957 162 W 0.6106 0.1483 0.2411 163 E 0.7559 0.1068 0.1374 164 V 0.7843 0.1111 0.1046 165 A 0.7797 0.1021 0.1182 166 Y 0.7160 0.1014 0.1827 167 G 0.6474 0.0900 0.2626 168 F 0.5080 0.1031 0.3889 169 D 0.3032 0.1054 0.5914 170 L 0.1195 0.2083 0.6722 171 G 0.0504 0.1330 0.8167 172 G 0.0449 0.1197 0.8354 173 H 0.0830 0.0903 0.8267 174 K 0.1200 0.0617 0.8183 175 W 0.0833 0.0362 0.8805