# This file is the result of combining several RDB files, specifically # T0285.t04.dssp-ebghstl.rdb (weight 1.53986) # T0285.t04.stride-ebghtl.rdb (weight 1.24869) # T0285.t04.str2.rdb (weight 1.54758) # T0285.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 T0285.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0285 # 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 T0285.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 1 # # ============================================ # Comments from T0285.t04.stride-ebghtl.rdb # ============================================ # TARGET T0285 # 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 T0285.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 1 # # ============================================ # Comments from T0285.t04.str2.rdb # ============================================ # TARGET T0285 # Using neural net t06-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 T0285.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 1 # # ============================================ # Comments from T0285.t04.alpha.rdb # ============================================ # TARGET T0285 # 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 T0285.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 1 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.1329 0.1192 0.7479 2 Y 0.2061 0.0896 0.7043 3 L 0.1327 0.0287 0.8386 4 P 0.0731 0.0563 0.8706 5 D 0.0451 0.0970 0.8579 6 D 0.0426 0.0801 0.8773 7 S 0.0589 0.0632 0.8779 8 P 0.0233 0.6194 0.3572 9 A 0.0179 0.7937 0.1884 10 K 0.0244 0.8327 0.1429 11 R 0.0489 0.8433 0.1078 12 L 0.0709 0.8360 0.0931 13 L 0.0721 0.8458 0.0822 14 F 0.0913 0.8280 0.0808 15 Q 0.0926 0.8199 0.0875 16 M 0.0990 0.7793 0.1217 17 V 0.0904 0.6920 0.2176 18 G 0.0737 0.5471 0.3792 19 N 0.0729 0.5425 0.3846 20 A 0.0905 0.6035 0.3060 21 I 0.1310 0.5146 0.3544 22 N 0.1176 0.3891 0.4933 23 R 0.0431 0.5107 0.4462 24 N 0.0542 0.4114 0.5344 25 T 0.0541 0.5666 0.3793 26 Q 0.0683 0.6830 0.2488 27 Q 0.1302 0.6640 0.2057 28 L 0.1336 0.6616 0.2048 29 T 0.1164 0.6343 0.2493 30 Q 0.0840 0.6742 0.2419 31 D 0.0767 0.6513 0.2720 32 L 0.0595 0.6824 0.2580 33 R 0.0702 0.5211 0.4087 34 A 0.0905 0.3788 0.5307 35 M 0.0981 0.0605 0.8414 36 P 0.0479 0.1406 0.8115 37 N 0.0706 0.1087 0.8207 38 W 0.2148 0.0858 0.6995 39 S 0.4297 0.0500 0.5204 40 L 0.7119 0.0244 0.2637 41 R 0.7856 0.0199 0.1946 42 F 0.8987 0.0069 0.0944 43 V 0.9122 0.0066 0.0813 44 Y 0.9163 0.0063 0.0775 45 I 0.9043 0.0077 0.0880 46 V 0.8326 0.0143 0.1531 47 D 0.5955 0.0188 0.3857 48 R 0.1023 0.1615 0.7362 49 N 0.0642 0.1189 0.8170 50 N 0.0827 0.1774 0.7400 51 Q 0.0706 0.3692 0.5602 52 D 0.1798 0.4193 0.4009 53 L 0.1850 0.5413 0.2736 54 L 0.2764 0.3945 0.3291 55 K 0.2548 0.2843 0.4609 56 R 0.1681 0.0686 0.7633 57 P 0.1475 0.0410 0.8115 58 L 0.0999 0.0154 0.8847 59 P 0.0701 0.0163 0.9136 60 P 0.0473 0.1387 0.8140 61 G 0.1174 0.1192 0.7634 62 I 0.5769 0.0885 0.3346 63 M 0.8006 0.0399 0.1595 64 V 0.8220 0.0315 0.1465 65 L 0.6672 0.0515 0.2813 66 A 0.3134 0.0590 0.6276 67 P 0.1614 0.2225 0.6161 68 R 0.1808 0.2785 0.5408 69 L 0.2315 0.2380 0.5305 70 T 0.2089 0.2007 0.5904 71 A 0.1720 0.1715 0.6565 72 K 0.1364 0.1237 0.7399 73 H 0.1015 0.0294 0.8691 74 P 0.0746 0.1300 0.7953 75 Y 0.0663 0.2974 0.6363 76 D 0.0725 0.3915 0.5360 77 K 0.1163 0.4727 0.4110 78 V 0.1886 0.4739 0.3376 79 Q 0.2125 0.4355 0.3520 80 D 0.1344 0.4611 0.4046 81 R 0.0911 0.4529 0.4559 82 N 0.0915 0.3252 0.5834 83 R 0.1458 0.3139 0.5402 84 K 0.2865 0.2887 0.4248 85 L 0.4098 0.2284 0.3618 86 Y 0.3685 0.1118 0.5198 87 G 0.3090 0.0707 0.6202 88 R 0.4560 0.0536 0.4904 89 H 0.6809 0.0292 0.2898 90 I 0.7716 0.0133 0.2151 91 T 0.7738 0.0104 0.2157 92 L 0.5835 0.0426 0.3739 93 N 0.2810 0.0510 0.6680 94 D 0.1071 0.0584 0.8344 95 G 0.0752 0.0637 0.8611 96 N 0.1755 0.0455 0.7790 97 S 0.5286 0.0184 0.4530 98 V 0.7562 0.0053 0.2385 99 K 0.8638 0.0042 0.1320 100 V 0.9054 0.0035 0.0912 101 V 0.9010 0.0046 0.0944 102 T 0.8951 0.0041 0.1008 103 I 0.8036 0.0128 0.1836 104 S 0.5908 0.0240 0.3852 105 A 0.2971 0.0836 0.6193 106 G 0.1430 0.0737 0.7833 107 R 0.1585 0.0951 0.7464 108 D 0.1217 0.1047 0.7735 109 E 0.0913 0.0949 0.8138 110 G 0.0596 0.0309 0.9096 111 P 0.0548 0.1144 0.8308 112 D 0.0654 0.2393 0.6953 113 R 0.0409 0.6406 0.3185 114 D 0.0382 0.8099 0.1519 115 I 0.0422 0.8840 0.0738 116 I 0.0256 0.9233 0.0511 117 W 0.0210 0.9333 0.0457 118 E 0.0180 0.9377 0.0442 119 M 0.0202 0.9271 0.0528 120 F 0.0218 0.9103 0.0680 121 L 0.0203 0.8946 0.0851 122 E 0.0209 0.8286 0.1505 123 N 0.0292 0.6129 0.3579 124 L 0.0450 0.4148 0.5402 125 E 0.0323 0.1647 0.8030