# This file is the result of combining several RDB files, specifically # T0231.t04.dssp-ebghstl.rdb (weight 1.53986) # T0231.t04.stride-ebghtl.rdb (weight 1.24869) # T0231.t04.str2.rdb (weight 1.54758) # T0231.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 T0231.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0231 # 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 T0231.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 173.519 # # ============================================ # Comments from T0231.t04.stride-ebghtl.rdb # ============================================ # TARGET T0231 # 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 T0231.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 173.519 # # ============================================ # Comments from T0231.t04.str2.rdb # ============================================ # TARGET T0231 # 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 T0231.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 173.519 # # ============================================ # Comments from T0231.t04.alpha.rdb # ============================================ # TARGET T0231 # 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 T0231.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 173.519 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0742 0.0584 0.8674 2 S 0.1062 0.0718 0.8219 3 D 0.0824 0.1194 0.7982 4 S 0.0936 0.1928 0.7136 5 L 0.1968 0.1710 0.6322 6 V 0.3299 0.1263 0.5438 7 V 0.5350 0.0819 0.3830 8 C 0.5979 0.0571 0.3449 9 E 0.5561 0.0367 0.4072 10 V 0.2025 0.0439 0.7536 11 D 0.0727 0.0169 0.9104 12 P 0.0051 0.8866 0.1082 13 E 0.0049 0.9296 0.0655 14 L 0.0052 0.9469 0.0479 15 K 0.0047 0.9567 0.0386 16 E 0.0047 0.9562 0.0392 17 T 0.0048 0.9539 0.0413 18 L 0.0048 0.9497 0.0455 19 R 0.0052 0.9323 0.0625 20 K 0.0065 0.8848 0.1088 21 F 0.0277 0.7740 0.1984 22 R 0.0504 0.5433 0.4063 23 F 0.1036 0.3445 0.5519 24 R 0.1021 0.1596 0.7383 25 K 0.1043 0.1324 0.7634 26 E 0.1194 0.1487 0.7319 27 T 0.1165 0.1527 0.7308 28 N 0.1919 0.0881 0.7200 29 N 0.4025 0.0284 0.5691 30 A 0.6356 0.0112 0.3532 31 A 0.9101 0.0037 0.0862 32 I 0.9292 0.0034 0.0674 33 I 0.9331 0.0031 0.0638 34 M 0.9246 0.0038 0.0716 35 K 0.9246 0.0035 0.0719 36 V 0.8786 0.0061 0.1153 37 D 0.4907 0.0072 0.5022 38 K 0.0281 0.1238 0.8481 39 D 0.0399 0.1032 0.8570 40 R 0.1704 0.0463 0.7833 41 Q 0.4577 0.0117 0.5307 42 M 0.8947 0.0042 0.1011 43 V 0.8936 0.0037 0.1026 44 V 0.9024 0.0042 0.0934 45 L 0.8443 0.0080 0.1477 46 E 0.5934 0.0284 0.3783 47 D 0.3340 0.1077 0.5583 48 E 0.2636 0.1373 0.5991 49 L 0.2156 0.1092 0.6753 50 Q 0.1329 0.0940 0.7732 51 N 0.0972 0.0576 0.8452 52 I 0.1722 0.0191 0.8088 53 S 0.0852 0.0101 0.9047 54 P 0.0052 0.9103 0.0846 55 E 0.0048 0.9357 0.0595 56 E 0.0051 0.9442 0.0507 57 L 0.0054 0.9346 0.0601 58 K 0.0058 0.9109 0.0832 59 L 0.0072 0.7790 0.2138 60 E 0.0191 0.5230 0.4579 61 L 0.0662 0.0343 0.8995 62 P 0.0425 0.0367 0.9208 63 E 0.0150 0.1537 0.8313 64 R 0.0222 0.1229 0.8549 65 Q 0.0912 0.0288 0.8800 66 P 0.2542 0.0115 0.7343 67 R 0.6666 0.0164 0.3170 68 F 0.9124 0.0035 0.0841 69 V 0.9280 0.0035 0.0685 70 V 0.9321 0.0032 0.0647 71 Y 0.9179 0.0046 0.0775 72 S 0.8733 0.0048 0.1219 73 Y 0.6690 0.0155 0.3155 74 K 0.6125 0.0322 0.3553 75 Y 0.7408 0.0205 0.2387 76 V 0.7265 0.0231 0.2503 77 H 0.4025 0.0229 0.5746 78 D 0.0803 0.1151 0.8046 79 D 0.0536 0.0428 0.9036 80 G 0.0620 0.0533 0.8847 81 R 0.2615 0.0488 0.6898 82 V 0.6150 0.0302 0.3548 83 S 0.5479 0.0375 0.4147 84 Y 0.4187 0.0169 0.5644 85 P 0.4399 0.0131 0.5470 86 L 0.8541 0.0044 0.1416 87 C 0.9271 0.0034 0.0695 88 F 0.9301 0.0033 0.0666 89 I 0.9225 0.0042 0.0734 90 F 0.8891 0.0069 0.1040 91 S 0.7573 0.0172 0.2255 92 S 0.3493 0.0128 0.6379 93 P 0.1238 0.0700 0.8062 94 V 0.0447 0.0861 0.8691 95 G 0.0439 0.0595 0.8966 96 C 0.0782 0.0255 0.8963 97 K 0.0808 0.0244 0.8948 98 P 0.0137 0.8672 0.1191 99 E 0.0115 0.8932 0.0953 100 Q 0.0170 0.9055 0.0775 101 Q 0.0412 0.8630 0.0958 102 M 0.0938 0.7998 0.1063 103 M 0.1013 0.7774 0.1213 104 Y 0.0990 0.7399 0.1611 105 A 0.0740 0.6648 0.2612 106 G 0.0622 0.4977 0.4401 107 S 0.0528 0.4875 0.4597 108 K 0.0073 0.9382 0.0545 109 N 0.0057 0.9532 0.0411 110 R 0.0051 0.9546 0.0403 111 L 0.0056 0.9505 0.0438 112 V 0.0084 0.9368 0.0548 113 Q 0.0108 0.8935 0.0957 114 T 0.0201 0.7887 0.1911 115 A 0.0855 0.3428 0.5717 116 E 0.0708 0.0407 0.8884 117 L 0.2241 0.0131 0.7629 118 T 0.3706 0.0134 0.6160 119 K 0.8410 0.0041 0.1550 120 V 0.8979 0.0033 0.0987 121 F 0.9120 0.0036 0.0843 122 E 0.9030 0.0036 0.0934 123 I 0.7373 0.0082 0.2545 124 R 0.3594 0.0431 0.5974 125 T 0.1518 0.0225 0.8256 126 T 0.0157 0.5603 0.4240 127 D 0.0145 0.5861 0.3994 128 D 0.0429 0.5770 0.3800 129 L 0.1534 0.1730 0.6736 130 T 0.0745 0.1307 0.7947 131 E 0.0048 0.9526 0.0426 132 T 0.0047 0.9597 0.0357 133 W 0.0047 0.9589 0.0364 134 L 0.0047 0.9591 0.0363 135 K 0.0047 0.9586 0.0367 136 E 0.0051 0.9533 0.0417 137 K 0.0055 0.9347 0.0597 138 L 0.0094 0.8942 0.0964 139 A 0.0131 0.7621 0.2248 140 F 0.0224 0.4801 0.4975 141 F 0.0414 0.1308 0.8278 142 R 0.0560 0.0382 0.9058