# This file is the result of combining several RDB files, specifically # T0462.t2k.str2.rdb (weight 1.54425) # T0462.t2k.str4.rdb (weight 0.924988) # T0462.t2k.pb.rdb (weight 0.789901) # T0462.t2k.bys.rdb (weight 0.748322) # T0462.t2k.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 T0462.t2k.str2.rdb # ============================================ # TARGET T0462 # Using neural net dunbrack-40pc-3157-t2k-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 T0462.t2k-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 46.7645 # # ============================================ # Comments from T0462.t2k.str4.rdb # ============================================ # TARGET T0462 # Using neural net dunbrack-40pc-3157-t2k-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 T0462.t2k-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 46.7645 # # ============================================ # Comments from T0462.t2k.pb.rdb # ============================================ # TARGET T0462 # Using neural net dunbrack-40pc-3157-t2k-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 T0462.t2k-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 46.7645 # # ============================================ # Comments from T0462.t2k.bys.rdb # ============================================ # TARGET T0462 # Using neural net dunbrack-40pc-3157-t2k-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 T0462.t2k-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 46.7645 # # ============================================ # Comments from T0462.t2k.alpha.rdb # ============================================ # TARGET T0462 # Using neural net dunbrack-40pc-3157-t2k-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 T0462.t2k-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 46.7645 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.4983 0.0382 0.4636 2 K 0.3781 0.0355 0.5865 3 L 0.2594 0.3778 0.3628 4 S 0.1717 0.4658 0.3625 5 R 0.2958 0.2411 0.4630 6 L 0.3472 0.0806 0.5722 7 V 0.2653 0.0405 0.6942 8 P 0.1530 0.1220 0.7250 9 G 0.0559 0.1043 0.8397 10 V 0.2714 0.0207 0.7079 11 P 0.5426 0.0156 0.4418 12 A 0.6682 0.0151 0.3167 13 R 0.7840 0.0071 0.2089 14 I 0.7355 0.0072 0.2572 15 K 0.6665 0.0234 0.3101 16 R 0.7286 0.0179 0.2535 17 L 0.6264 0.0335 0.3401 18 E 0.5162 0.0521 0.4317 19 V 0.2920 0.0924 0.6156 20 S 0.1320 0.1929 0.6751 21 G 0.0505 0.4795 0.4700 22 E 0.0369 0.7360 0.2271 23 L 0.0294 0.8392 0.1314 24 H 0.0176 0.8905 0.0919 25 E 0.0138 0.9060 0.0802 26 K 0.0165 0.8998 0.0837 27 L 0.0207 0.8727 0.1066 28 V 0.0258 0.8078 0.1664 29 G 0.0609 0.6335 0.3056 30 M 0.0768 0.2736 0.6496 31 G 0.1347 0.0900 0.7753 32 F 0.2921 0.0448 0.6631 33 V 0.2942 0.0230 0.6828 34 P 0.2214 0.1080 0.6706 35 G 0.1080 0.0976 0.7944 36 E 0.4072 0.0349 0.5579 37 E 0.6936 0.0121 0.2943 38 I 0.7833 0.0074 0.2092 39 E 0.8012 0.0062 0.1926 40 I 0.7930 0.0067 0.2003 41 V 0.7570 0.0178 0.2252 42 Q 0.7416 0.0200 0.2384 43 V 0.6213 0.0507 0.3280 44 A 0.5469 0.0335 0.4196 45 P 0.3943 0.1304 0.4754 46 L 0.1579 0.1556 0.6865 47 G 0.1107 0.1213 0.7680 48 D 0.2263 0.0342 0.7395 49 P 0.3371 0.0589 0.6039 50 I 0.6297 0.0280 0.3423 51 V 0.7914 0.0078 0.2009 52 C 0.8010 0.0068 0.1922 53 K 0.7628 0.0069 0.2303 54 I 0.6560 0.0260 0.3179 55 G 0.4001 0.0467 0.5531 56 N 0.2532 0.0635 0.6833 57 R 0.4910 0.0466 0.4624 58 N 0.6821 0.0244 0.2935 59 I 0.7602 0.0180 0.2219 60 T 0.7458 0.0250 0.2292 61 L 0.7004 0.0517 0.2479 62 R 0.4993 0.1065 0.3942 63 K 0.2303 0.4279 0.3418 64 R 0.1052 0.5531 0.3417 65 E 0.1725 0.4178 0.4096 66 A 0.2756 0.3604 0.3640 67 D 0.3556 0.2343 0.4101 68 L 0.6074 0.0830 0.3096 69 I 0.7220 0.0192 0.2588 70 E 0.7507 0.0100 0.2393 71 V 0.7830 0.0079 0.2091 72 E 0.7434 0.0103 0.2463 73 V 0.6462 0.0217 0.3321 74 V 0.4170 0.0634 0.5195 75 G 0.2199 0.0949 0.6852 76 G 0.1657 0.1148 0.7195 77 E 0.2931 0.1015 0.6053 78 L 0.3573 0.0469 0.5958 79 P 0.3506 0.0838 0.5656 80 L 0.4631 0.1354 0.4016 81 I 0.5316 0.1242 0.3442 82 L 0.5138 0.1227 0.3636 83 A 0.3621 0.1679 0.4701 84 D 0.2179 0.2026 0.5795 85 D 0.1114 0.1649 0.7238 86 G 0.0945 0.1193 0.7863 87 T 0.2628 0.1019 0.6353 88 Y 0.3662 0.0802 0.5536 89 E 0.4563 0.1311 0.4126 90 I 0.4979 0.1556 0.3465 91 T 0.4738 0.1728 0.3534 92 K 0.3919 0.2016 0.4065 93 L 0.2608 0.2476 0.4916 94 N 0.1648 0.1816 0.6536 95 G 0.1128 0.1431 0.7441 96 G 0.1343 0.2045 0.6613 97 R 0.2087 0.3023 0.4890 98 R 0.2175 0.4626 0.3198 99 F 0.1718 0.6038 0.2244 100 L 0.1214 0.7017 0.1769 101 F 0.1023 0.7341 0.1636 102 R 0.0965 0.7108 0.1927 103 M 0.0924 0.6839 0.2237 104 K 0.1046 0.6363 0.2591 105 N 0.1339 0.5083 0.3578 106 L 0.1355 0.2908 0.5737 107 G 0.1277 0.1695 0.7029 108 I 0.1462 0.2754 0.5784 109 E 0.1893 0.2317 0.5789 110 S 0.1847 0.1337 0.6815 111 G 0.1817 0.0701 0.7482 112 K 0.3990 0.0252 0.5758 113 K 0.6883 0.0117 0.3000 114 I 0.7900 0.0076 0.2024 115 Q 0.7850 0.0087 0.2064 116 V 0.7517 0.0134 0.2349 117 S 0.5890 0.0334 0.3775 118 G 0.3435 0.0450 0.6114 119 R 0.2781 0.0759 0.6460 120 R 0.2438 0.2186 0.5376 121 Y 0.2420 0.2262 0.5318 122 Y 0.2698 0.1824 0.5478 123 I 0.2722 0.1357 0.5921 124 E 0.2254 0.1540 0.6206 125 G 0.2135 0.1375 0.6490 126 R 0.2906 0.1898 0.5196 127 E 0.4320 0.2184 0.3496 128 I 0.5133 0.2034 0.2833 129 D 0.4210 0.2243 0.3547 130 L 0.2445 0.3951 0.3604 131 G 0.2024 0.3541 0.4435 132 Y 0.1755 0.2471 0.5774 133 G 0.1403 0.1705 0.6892 134 E 0.1592 0.2800 0.5608 135 A 0.1920 0.2689 0.5392 136 T 0.2780 0.1606 0.5614 137 K 0.3731 0.0672 0.5597 138 I 0.4964 0.0634 0.4402 139 W 0.5403 0.0627 0.3970 140 V 0.4869 0.0572 0.4559 141 R 0.4145 0.0412 0.5442 142 R 0.3433 0.0955 0.5612 143 V 0.3835 0.0858 0.5308 144 S 0.4021 0.0676 0.5303 145 D 0.3617 0.0737 0.5645 146 A 0.2357 0.2282 0.5361 147 G 0.1645 0.1536 0.6819 148 E 0.1809 0.2862 0.5329 149 E 0.1743 0.3098 0.5159 150 S 0.1997 0.1780 0.6223 151 H 0.2248 0.0928 0.6825 152 P 0.1769 0.2026 0.6205 153 Q 0.2263 0.1665 0.6071 154 K 0.2183 0.1539 0.6279