# This file is the result of combining several RDB files, specifically # T0466.t04.str2.rdb (weight 1.54425) # T0466.t04.str4.rdb (weight 0.924988) # T0466.t04.pb.rdb (weight 0.789901) # T0466.t04.bys.rdb (weight 0.748322) # T0466.t04.alpha.rdb (weight 0.678173) # 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 T0466.t04.str2.rdb # ============================================ # TARGET T0466 # Using neural net dunbrack-40pc-3157-t04-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 T0466.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 16.3137 # # ============================================ # Comments from T0466.t04.str4.rdb # ============================================ # TARGET T0466 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-str4-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 21 (1 str4 ) # The input amino acid frequencies were determined from # alignment T0466.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 16.3137 # # ============================================ # Comments from T0466.t04.pb.rdb # ============================================ # TARGET T0466 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-pb-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 16 (1 pb ) # The input amino acid frequencies were determined from # alignment T0466.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 16.3137 # # ============================================ # Comments from T0466.t04.bys.rdb # ============================================ # TARGET T0466 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-bys-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 Bystroff ) # The input amino acid frequencies were determined from # alignment T0466.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 16.3137 # # ============================================ # Comments from T0466.t04.alpha.rdb # ============================================ # TARGET T0466 # Using neural net dunbrack-40pc-3157-t04-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 T0466.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 16.3137 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2212 0.4222 0.3566 2 M 0.3328 0.3439 0.3233 3 R 0.3422 0.3287 0.3290 4 L 0.2086 0.3888 0.4026 5 A 0.1511 0.3443 0.5046 6 N 0.1172 0.1722 0.7106 7 G 0.1771 0.0821 0.7408 8 I 0.4926 0.0277 0.4797 9 V 0.5790 0.0219 0.3991 10 L 0.5214 0.0333 0.4453 11 D 0.2907 0.0289 0.6804 12 K 0.0906 0.4576 0.4517 13 D 0.0985 0.3933 0.5082 14 T 0.2441 0.2477 0.5082 15 T 0.2834 0.2098 0.5068 16 F 0.2585 0.2510 0.4906 17 G 0.2596 0.2632 0.4773 18 E 0.4078 0.2734 0.3189 19 L 0.5214 0.2097 0.2689 20 K 0.4491 0.2561 0.2948 21 F 0.3408 0.3531 0.3061 22 S 0.2436 0.4725 0.2839 23 A 0.3033 0.4198 0.2769 24 L 0.2967 0.4175 0.2858 25 R 0.2992 0.3911 0.3097 26 R 0.3045 0.3594 0.3362 27 E 0.3940 0.2828 0.3233 28 V 0.5648 0.1523 0.2829 29 R 0.6071 0.1208 0.2721 30 I 0.6541 0.0893 0.2567 31 Q 0.5655 0.1107 0.3238 32 N 0.3450 0.0694 0.5855 33 E 0.0919 0.3348 0.5732 34 D 0.0711 0.1677 0.7612 35 G 0.0862 0.0859 0.8280 36 S 0.2687 0.0347 0.6967 37 V 0.4174 0.0603 0.5223 38 S 0.3287 0.0979 0.5735 39 D 0.1971 0.3881 0.4148 40 E 0.3038 0.3899 0.3063 41 I 0.4045 0.3597 0.2357 42 K 0.4027 0.3378 0.2595 43 E 0.4849 0.2402 0.2749 44 R 0.5423 0.1418 0.3159 45 T 0.6147 0.0789 0.3064 46 Y 0.6260 0.0710 0.3030 47 D 0.5494 0.0726 0.3780 48 L 0.4629 0.1970 0.3401 49 K 0.3533 0.1979 0.4488 50 S 0.3073 0.1755 0.5172 51 K 0.1410 0.3255 0.5335 52 G 0.1436 0.2569 0.5995 53 Q 0.1765 0.1374 0.6861 54 G 0.1802 0.0789 0.7409 55 R 0.3240 0.0671 0.6089 56 M 0.6074 0.0203 0.3723 57 I 0.7305 0.0085 0.2610 58 Q 0.7654 0.0065 0.2281 59 V 0.7890 0.0058 0.2052 60 S 0.7563 0.0093 0.2344 61 I 0.6309 0.0117 0.3575 62 P 0.3548 0.0162 0.6289 63 A 0.2751 0.2150 0.5099 64 S 0.2350 0.1163 0.6487 65 V 0.3404 0.0485 0.6110 66 P 0.2208 0.0409 0.7383 67 L 0.1985 0.3531 0.4484 68 K 0.1828 0.3802 0.4370 69 E 0.2781 0.2994 0.4225 70 F 0.3394 0.0974 0.5632 71 D 0.2629 0.0698 0.6674 72 Y 0.1161 0.3502 0.5337 73 N 0.1235 0.2857 0.5908 74 A 0.2390 0.2402 0.5208 75 R 0.4897 0.1381 0.3722 76 V 0.6471 0.0443 0.3086 77 E 0.6563 0.0536 0.2901 78 L 0.6521 0.0530 0.2949 79 I 0.5083 0.1229 0.3688 80 N 0.3619 0.0822 0.5559 81 P 0.1569 0.3992 0.4439 82 I 0.1480 0.5285 0.3236 83 A 0.1895 0.5201 0.2904 84 D 0.1588 0.5900 0.2512 85 T 0.2018 0.6053 0.1930 86 V 0.2285 0.5885 0.1830 87 A 0.2863 0.5242 0.1895 88 T 0.2599 0.5237 0.2164 89 A 0.3190 0.4247 0.2564 90 T 0.3231 0.2999 0.3770 91 Y 0.2750 0.2314 0.4936 92 Q 0.1719 0.1656 0.6624 93 G 0.1195 0.1068 0.7737 94 A 0.3004 0.0641 0.6355 95 D 0.4240 0.0466 0.5294 96 V 0.5562 0.0356 0.4083 97 D 0.5913 0.0300 0.3787 98 W 0.7722 0.0100 0.2178 99 Y 0.7831 0.0079 0.2091 100 I 0.7804 0.0077 0.2119 101 K 0.6504 0.0130 0.3366 102 A 0.4777 0.0822 0.4401 103 D 0.3004 0.1377 0.5619 104 D 0.3490 0.1200 0.5310 105 I 0.5540 0.0520 0.3940 106 V 0.6370 0.0466 0.3164 107 L 0.6096 0.0515 0.3390 108 T 0.4440 0.0921 0.4639 109 K 0.2995 0.1598 0.5406 110 D 0.1956 0.1881 0.6163 111 S 0.1716 0.2013 0.6271 112 S 0.1676 0.2662 0.5662 113 S 0.1912 0.2758 0.5330 114 F 0.2246 0.2371 0.5383 115 K 0.2152 0.2242 0.5606 116 A 0.2314 0.1687 0.5999 117 Q 0.2562 0.0668 0.6769 118 P 0.1925 0.2274 0.5801 119 Q 0.1617 0.2905 0.5479 120 A 0.1509 0.2762 0.5729 121 K 0.1408 0.2194 0.6398 122 K 0.1936 0.1350 0.6714 123 E 0.2297 0.0586 0.7117 124 P 0.2075 0.1950 0.5975 125 T 0.2281 0.1872 0.5848 126 Q 0.2261 0.1590 0.6149 127 D 0.1698 0.1594 0.6709 128 K 0.1683 0.2038 0.6278