# This file is the result of combining several RDB files, specifically # T0443.t06.str2.rdb (weight 1.54425) # T0443.t06.str4.rdb (weight 0.924988) # T0443.t06.pb.rdb (weight 0.789901) # T0443.t06.bys.rdb (weight 0.748322) # T0443.t06.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 T0443.t06.str2.rdb # ============================================ # TARGET T0443 # Using neural net dunbrack-40pc-3157-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 T0443.t06-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 T0443.t06.str4.rdb # ============================================ # TARGET T0443 # Using neural net dunbrack-40pc-3157-t06-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 T0443.t06-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 T0443.t06.pb.rdb # ============================================ # TARGET T0443 # Using neural net dunbrack-40pc-3157-t06-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 T0443.t06-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 T0443.t06.bys.rdb # ============================================ # TARGET T0443 # Using neural net dunbrack-40pc-3157-t06-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 T0443.t06-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 T0443.t06.alpha.rdb # ============================================ # TARGET T0443 # Using neural net dunbrack-40pc-3157-t06-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 T0443.t06-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 D 0.1808 0.1276 0.6916 2 I 0.2441 0.0671 0.6888 3 P 0.1954 0.1894 0.6152 4 D 0.2740 0.1631 0.5630 5 I 0.3905 0.1310 0.4785 6 H 0.4625 0.0992 0.4384 7 Y 0.4488 0.0996 0.4517 8 S 0.2672 0.1453 0.5875 9 N 0.1733 0.1681 0.6585 10 D 0.1460 0.2036 0.6504 11 S 0.1456 0.2555 0.5990 12 K 0.1650 0.2404 0.5945 13 Y 0.2374 0.1361 0.6264 14 T 0.2694 0.0538 0.6769 15 P 0.2149 0.1095 0.6756 16 S 0.2042 0.0746 0.7211 17 P 0.0654 0.5263 0.4083 18 A 0.0416 0.7194 0.2390 19 A 0.0654 0.7820 0.1526 20 F 0.1030 0.7473 0.1497 21 I 0.1291 0.7180 0.1529 22 R 0.1313 0.6762 0.1924 23 Q 0.1848 0.5434 0.2718 24 Y 0.2348 0.3991 0.3662 25 R 0.2440 0.3288 0.4272 26 Y 0.2825 0.2639 0.4537 27 D 0.2514 0.2222 0.5264 28 V 0.2365 0.3075 0.4561 29 T 0.1905 0.3369 0.4726 30 H 0.1680 0.3741 0.4579 31 D 0.1320 0.4131 0.4550 32 L 0.0524 0.6997 0.2479 33 Q 0.0431 0.7522 0.2047 34 E 0.0456 0.7557 0.1987 35 A 0.0472 0.7613 0.1915 36 E 0.0498 0.7424 0.2078 37 T 0.1037 0.6926 0.2037 38 A 0.1793 0.6353 0.1854 39 L 0.2986 0.5243 0.1770 40 L 0.4082 0.4007 0.1912 41 I 0.4237 0.3490 0.2273 42 W 0.3647 0.3150 0.3203 43 R 0.2875 0.2591 0.4534 44 N 0.1875 0.1811 0.6315 45 A 0.1009 0.3642 0.5349 46 E 0.0720 0.4646 0.4634 47 D 0.0775 0.5053 0.4171 48 D 0.1133 0.4915 0.3952 49 V 0.2365 0.4675 0.2960 50 M 0.2824 0.4496 0.2681 51 Y 0.3175 0.4232 0.2593 52 Q 0.2928 0.3976 0.3097 53 T 0.2758 0.3227 0.4016 54 L 0.2077 0.3051 0.4872 55 D 0.1186 0.2771 0.6043 56 G 0.0806 0.2764 0.6430 57 F 0.1406 0.3882 0.4712 58 D 0.1459 0.4839 0.3702 59 M 0.1919 0.6028 0.2053 60 M 0.1957 0.6503 0.1539 61 L 0.2326 0.6338 0.1336 62 L 0.1716 0.6905 0.1379 63 E 0.1499 0.6858 0.1642 64 I 0.1573 0.5596 0.2831 65 M 0.1340 0.3632 0.5028 66 G 0.1111 0.2245 0.6645 67 S 0.1198 0.2992 0.5810 68 S 0.1159 0.3757 0.5084 69 A 0.1390 0.4316 0.4294 70 L 0.2186 0.3454 0.4360 71 S 0.2125 0.3165 0.4710 72 F 0.0910 0.5944 0.3146 73 D 0.0469 0.7239 0.2291 74 T 0.0362 0.8052 0.1587 75 L 0.0265 0.8427 0.1308 76 A 0.0195 0.8669 0.1137 77 Q 0.0228 0.8644 0.1128 78 T 0.0413 0.8253 0.1334 79 L 0.0683 0.7692 0.1625 80 V 0.0851 0.7278 0.1871 81 E 0.1004 0.6314 0.2682 82 F 0.1564 0.4357 0.4079 83 M 0.2296 0.1509 0.6195 84 P 0.1565 0.2271 0.6164 85 K 0.1006 0.3416 0.5578 86 A 0.0899 0.4213 0.4888 87 D 0.0645 0.4307 0.5048 88 N 0.0756 0.3507 0.5737 89 W 0.0876 0.5398 0.3726 90 K 0.0885 0.5994 0.3121 91 N 0.1598 0.5482 0.2920 92 I 0.2677 0.4792 0.2531 93 L 0.3111 0.4130 0.2759 94 L 0.2562 0.3283 0.4155 95 G 0.1865 0.2432 0.5703 96 K 0.2006 0.2904 0.5090 97 W 0.1939 0.3424 0.4637 98 S 0.1395 0.3734 0.4871 99 G 0.1394 0.3670 0.4936 100 W 0.2307 0.4162 0.3531 101 I 0.2608 0.4499 0.2892 102 E 0.2589 0.4200 0.3211 103 Q 0.3341 0.3322 0.3337 104 R 0.4422 0.2134 0.3444 105 I 0.5788 0.1102 0.3111 106 I 0.5259 0.0946 0.3795 107 I 0.3808 0.0582 0.5609 108 P 0.2258 0.1749 0.5993 109 S 0.1987 0.2432 0.5581 110 L 0.1211 0.4784 0.4005 111 S 0.1077 0.5725 0.3198 112 A 0.1319 0.5774 0.2907 113 I 0.1682 0.5054 0.3264 114 S 0.1489 0.4945 0.3566 115 E 0.0846 0.5185 0.3969 116 N 0.0978 0.3942 0.5080 117 M 0.1334 0.2969 0.5696 118 E 0.1237 0.2393 0.6370 119 G 0.1034 0.1554 0.7412 120 N 0.1481 0.1085 0.7434 121 S 0.2076 0.0575 0.7348 122 P 0.1170 0.2797 0.6033 123 S 0.1217 0.2987 0.5796 124 Q 0.1050 0.4165 0.4786 125 N 0.1242 0.3599 0.5159 126 H 0.1880 0.3323 0.4796 127 L 0.2390 0.2448 0.5162 128 S 0.2348 0.1996 0.5656 129 A 0.1837 0.2521 0.5642