# This file is the result of combining several RDB files, specifically # T0337.t04.dssp-ebghstl.rdb (weight 1.53986) # T0337.t04.stride-ebghtl.rdb (weight 1.24869) # T0337.t04.str2.rdb (weight 1.54758) # T0337.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 T0337.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0337 # 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 T0337.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 1386 # # ============================================ # Comments from T0337.t04.stride-ebghtl.rdb # ============================================ # TARGET T0337 # 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 T0337.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 1386 # # ============================================ # Comments from T0337.t04.str2.rdb # ============================================ # TARGET T0337 # 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 T0337.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 1386 # # ============================================ # Comments from T0337.t04.alpha.rdb # ============================================ # TARGET T0337 # 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 T0337.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 1386 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0679 0.0377 0.8943 2 D 0.0668 0.1466 0.7866 3 C 0.0627 0.2580 0.6793 4 M 0.0572 0.3173 0.6255 5 R 0.0697 0.3223 0.6080 6 K 0.1092 0.2246 0.6661 7 L 0.0775 0.1504 0.7720 8 D 0.0500 0.1424 0.8076 9 R 0.0048 0.9518 0.0434 10 V 0.0047 0.9585 0.0368 11 D 0.0048 0.9583 0.0369 12 M 0.0047 0.9608 0.0346 13 Q 0.0046 0.9610 0.0344 14 L 0.0046 0.9604 0.0349 15 V 0.0047 0.9604 0.0350 16 K 0.0047 0.9600 0.0353 17 I 0.0048 0.9570 0.0382 18 L 0.0051 0.9440 0.0509 19 S 0.0066 0.8916 0.1018 20 E 0.0140 0.6841 0.3019 21 N 0.0499 0.2465 0.7035 22 S 0.0461 0.1655 0.7884 23 R 0.0514 0.1337 0.8149 24 L 0.1063 0.0492 0.8445 25 T 0.0869 0.0508 0.8623 26 Y 0.0048 0.9512 0.0440 27 R 0.0049 0.9581 0.0370 28 E 0.0049 0.9570 0.0381 29 L 0.0047 0.9594 0.0360 30 A 0.0047 0.9556 0.0397 31 D 0.0054 0.9357 0.0589 32 I 0.0080 0.8847 0.1073 33 L 0.0492 0.4939 0.4569 34 N 0.0386 0.1064 0.8551 35 T 0.0678 0.0479 0.8843 36 T 0.0727 0.0449 0.8824 37 R 0.0063 0.8799 0.1138 38 Q 0.0047 0.9567 0.0386 39 R 0.0047 0.9598 0.0355 40 I 0.0047 0.9603 0.0350 41 A 0.0047 0.9608 0.0345 42 R 0.0046 0.9592 0.0362 43 R 0.0047 0.9575 0.0379 44 I 0.0047 0.9609 0.0344 45 D 0.0046 0.9612 0.0342 46 K 0.0046 0.9614 0.0340 47 L 0.0047 0.9606 0.0347 48 K 0.0048 0.9541 0.0411 49 K 0.0058 0.9184 0.0757 50 L 0.0430 0.4264 0.5306 51 G 0.0351 0.0344 0.9306 52 I 0.1274 0.0425 0.8301 53 I 0.5562 0.0306 0.4132 54 R 0.5664 0.0648 0.3689 55 K 0.6434 0.0416 0.3150 56 F 0.7536 0.0148 0.2316 57 T 0.8264 0.0101 0.1636 58 I 0.8459 0.0085 0.1457 59 I 0.7228 0.0099 0.2673 60 P 0.3406 0.0319 0.6275 61 D 0.1597 0.0196 0.8207 62 I 0.0094 0.8019 0.1887 63 D 0.0072 0.8445 0.1483 64 K 0.0105 0.8285 0.1610 65 L 0.0787 0.3772 0.5441 66 G 0.0614 0.0862 0.8523 67 Y 0.3141 0.0431 0.6427 68 M 0.6763 0.0100 0.3137 69 Y 0.8212 0.0085 0.1702 70 A 0.9181 0.0035 0.0784 71 I 0.9303 0.0032 0.0665 72 V 0.9300 0.0032 0.0668 73 L 0.9235 0.0036 0.0730 74 I 0.9019 0.0045 0.0936 75 K 0.8558 0.0051 0.1391 76 S 0.5534 0.0159 0.4308 77 K 0.1951 0.0345 0.7705 78 V 0.0864 0.0191 0.8945 79 P 0.0234 0.3788 0.5978 80 S 0.0152 0.5091 0.4756 81 D 0.0200 0.6437 0.3363 82 A 0.0057 0.9027 0.0915 83 D 0.0049 0.9456 0.0495 84 K 0.0047 0.9542 0.0411 85 V 0.0048 0.9568 0.0384 86 I 0.0048 0.9567 0.0385 87 S 0.0048 0.9543 0.0409 88 E 0.0054 0.9380 0.0566 89 I 0.0061 0.8912 0.1028 90 S 0.0075 0.6948 0.2977 91 D 0.0135 0.3705 0.6160 92 I 0.0647 0.1079 0.8274 93 E 0.0223 0.3418 0.6358 94 Y 0.1465 0.4156 0.4379 95 V 0.3241 0.4413 0.2346 96 K 0.3728 0.4576 0.1696 97 S 0.4273 0.4054 0.1672 98 V 0.4048 0.4061 0.1891 99 E 0.4264 0.3189 0.2547 100 K 0.3126 0.2847 0.4027 101 G 0.2109 0.1624 0.6266 102 V 0.1401 0.0843 0.7756 103 G 0.1188 0.0576 0.8236 104 R 0.1763 0.0928 0.7309 105 Y 0.2744 0.0648 0.6609 106 N 0.3608 0.0605 0.5788 107 I 0.8835 0.0060 0.1104 108 I 0.9257 0.0034 0.0709 109 V 0.9257 0.0037 0.0706 110 R 0.9237 0.0050 0.0714 111 L 0.8985 0.0061 0.0954 112 L 0.7808 0.0100 0.2092 113 L 0.3784 0.0148 0.6068 114 P 0.1291 0.0543 0.8166 115 K 0.0543 0.1000 0.8457 116 D 0.0860 0.0484 0.8656 117 I 0.0063 0.9157 0.0780 118 K 0.0050 0.9502 0.0448 119 D 0.0052 0.9463 0.0485 120 A 0.0048 0.9549 0.0403 121 E 0.0047 0.9582 0.0371 122 N 0.0047 0.9578 0.0375 123 L 0.0047 0.9560 0.0393 124 I 0.0047 0.9558 0.0394 125 S 0.0047 0.9577 0.0376 126 E 0.0050 0.9515 0.0435 127 F 0.0051 0.9414 0.0535 128 L 0.0055 0.9209 0.0736 129 Q 0.0061 0.8185 0.1754 130 R 0.0128 0.6192 0.3680 131 I 0.0704 0.1836 0.7460 132 K 0.0224 0.2279 0.7496 133 N 0.0312 0.1066 0.8622 134 A 0.1453 0.1175 0.7372 135 E 0.2884 0.1290 0.5827 136 N 0.5019 0.0638 0.4343 137 V 0.6592 0.0231 0.3176 138 E 0.7942 0.0159 0.1899 139 V 0.8883 0.0073 0.1044 140 I 0.8958 0.0092 0.0949 141 L 0.9087 0.0077 0.0836 142 I 0.8779 0.0155 0.1067 143 S 0.8208 0.0189 0.1603 144 E 0.7786 0.0262 0.1952 145 V 0.7867 0.0288 0.1845 146 R 0.7837 0.0341 0.1821 147 K 0.7184 0.0611 0.2204 148 F 0.5915 0.0761 0.3324 149 E 0.3902 0.0835 0.5264 150 I 0.2034 0.0645 0.7320 151 I 0.0870 0.0411 0.8719