# This file is the result of combining several RDB files, specifically # T0391.t06.str2.rdb (weight 1.54425) # T0391.t06.str4.rdb (weight 0.924988) # T0391.t06.pb.rdb (weight 0.789901) # T0391.t06.bys.rdb (weight 0.748322) # T0391.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 T0391.t06.str2.rdb # ============================================ # TARGET T0391 # 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 T0391.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 2619 # # ============================================ # Comments from T0391.t06.str4.rdb # ============================================ # TARGET T0391 # 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 T0391.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 2619 # # ============================================ # Comments from T0391.t06.pb.rdb # ============================================ # TARGET T0391 # 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 T0391.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 2619 # # ============================================ # Comments from T0391.t06.bys.rdb # ============================================ # TARGET T0391 # 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 T0391.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 2619 # # ============================================ # Comments from T0391.t06.alpha.rdb # ============================================ # TARGET T0391 # 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 T0391.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 2619 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1986 0.1176 0.6838 2 D 0.1671 0.0973 0.7356 3 P 0.0165 0.6902 0.2932 4 E 0.0216 0.7188 0.2596 5 I 0.0340 0.7484 0.2176 6 S 0.0424 0.7108 0.2468 7 E 0.0415 0.7050 0.2535 8 Q 0.0651 0.6481 0.2868 9 D 0.0513 0.6455 0.3032 10 E 0.0341 0.7152 0.2507 11 E 0.0406 0.6813 0.2782 12 K 0.0848 0.5586 0.3567 13 K 0.1361 0.4168 0.4471 14 K 0.1454 0.2939 0.5607 15 Y 0.1742 0.2041 0.6217 16 T 0.2478 0.1244 0.6278 17 S 0.4182 0.0699 0.5119 18 V 0.6200 0.0315 0.3485 19 C 0.6293 0.0376 0.3332 20 V 0.5609 0.0485 0.3906 21 G 0.4801 0.0377 0.4823 22 R 0.3110 0.0698 0.6192 23 E 0.0858 0.5374 0.3768 24 E 0.0566 0.5929 0.3506 25 D 0.0816 0.4150 0.5035 26 I 0.2316 0.1288 0.6396 27 R 0.1654 0.0808 0.7538 28 K 0.0570 0.3226 0.6204 29 S 0.0635 0.1944 0.7421 30 E 0.2406 0.0970 0.6624 31 R 0.5010 0.0422 0.4569 32 M 0.6629 0.0262 0.3109 33 T 0.7560 0.0111 0.2329 34 A 0.7737 0.0100 0.2163 35 V 0.7475 0.0106 0.2420 36 V 0.6386 0.0289 0.3325 37 H 0.2853 0.0772 0.6375 38 D 0.1315 0.0800 0.7885 39 R 0.4495 0.0201 0.5304 40 E 0.6722 0.0146 0.3132 41 V 0.8078 0.0053 0.1869 42 V 0.8224 0.0047 0.1729 43 I 0.8222 0.0047 0.1732 44 F 0.8111 0.0053 0.1836 45 Y 0.7295 0.0110 0.2595 46 H 0.5485 0.0721 0.3794 47 K 0.1891 0.0841 0.7268 48 G 0.1077 0.0789 0.8133 49 E 0.4745 0.0217 0.5038 50 Y 0.7050 0.0120 0.2831 51 H 0.7497 0.0220 0.2282 52 A 0.7808 0.0207 0.1985 53 M 0.7226 0.0503 0.2272 54 D 0.6085 0.1005 0.2910 55 I 0.3990 0.1722 0.4288 56 R 0.3194 0.1716 0.5090 57 C 0.2899 0.1159 0.5942 58 Y 0.1585 0.2766 0.5649 59 H 0.1546 0.2476 0.5977 60 S 0.1151 0.2116 0.6732 61 G 0.1019 0.1115 0.7866 62 G 0.2496 0.0359 0.7145 63 P 0.3871 0.0566 0.5563 64 L 0.3876 0.0931 0.5193 65 H 0.3628 0.0941 0.5431 66 L 0.2585 0.1410 0.6005 67 G 0.2795 0.0875 0.6330 68 E 0.4746 0.0790 0.4464 69 I 0.5480 0.0966 0.3554 70 E 0.4498 0.1511 0.3990 71 D 0.3653 0.1903 0.4443 72 F 0.2033 0.2523 0.5444 73 N 0.0998 0.1395 0.7607 74 G 0.0923 0.0836 0.8241 75 Q 0.2923 0.0386 0.6691 76 S 0.4609 0.0452 0.4939 77 C 0.6951 0.0231 0.2817 78 I 0.7402 0.0165 0.2432 79 V 0.7043 0.0166 0.2792 80 C 0.5003 0.0156 0.4841 81 P 0.2495 0.1960 0.5544 82 W 0.1814 0.2130 0.6056 83 H 0.2176 0.1708 0.6116 84 K 0.2861 0.1344 0.5795 85 Y 0.5267 0.0752 0.3982 86 K 0.6655 0.0418 0.2927 87 I 0.7451 0.0178 0.2371 88 T 0.5974 0.0247 0.3779 89 L 0.3862 0.2003 0.4135 90 A 0.2299 0.2715 0.4987 91 T 0.1952 0.1294 0.6754 92 G 0.1494 0.0814 0.7692 93 E 0.4066 0.0460 0.5474 94 G 0.5558 0.0551 0.3891 95 L 0.5439 0.0750 0.3811 96 Y 0.5419 0.0555 0.4026 97 Q 0.4551 0.0599 0.4850 98 S 0.3363 0.1109 0.5529 99 I 0.2756 0.1295 0.5949 100 N 0.2167 0.0607 0.7226 101 P 0.0926 0.2738 0.6337 102 K 0.0999 0.2431 0.6570 103 D 0.1834 0.1050 0.7116 104 P 0.1000 0.2915 0.6085 105 S 0.1438 0.2491 0.6072 106 A 0.1699 0.1947 0.6353 107 K 0.1969 0.1295 0.6736 108 P 0.1229 0.3834 0.4936 109 K 0.1357 0.3567 0.5076 110 W 0.1868 0.3043 0.5090 111 C 0.1843 0.2025 0.6132 112 S 0.1027 0.3753 0.5219 113 K 0.0692 0.3301 0.6006 114 G 0.0721 0.1950 0.7330 115 V 0.2709 0.0697 0.6594 116 K 0.3910 0.0440 0.5650 117 Q 0.5354 0.0255 0.4391 118 R 0.6219 0.0224 0.3557 119 I 0.7010 0.0116 0.2874 120 H 0.7254 0.0138 0.2608 121 T 0.7162 0.0090 0.2748 122 V 0.7528 0.0100 0.2372 123 K 0.7717 0.0087 0.2197 124 V 0.7123 0.0159 0.2718 125 D 0.5515 0.0913 0.3571 126 N 0.2540 0.0469 0.6991 127 G 0.2954 0.0412 0.6633 128 N 0.6523 0.0116 0.3362 129 I 0.7770 0.0059 0.2171 130 Y 0.8063 0.0059 0.1877 131 V 0.8094 0.0054 0.1852 132 T 0.7574 0.0083 0.2344 133 L 0.6288 0.0324 0.3388 134 S 0.3172 0.0382 0.6446 135 K 0.1204 0.2552 0.6244 136 E 0.1669 0.1410 0.6921 137 P 0.1641 0.1999 0.6359 138 F 0.2001 0.1764 0.6235 139 K 0.1827 0.1742 0.6431 140 C 0.1961 0.1612 0.6427 141 D 0.1339 0.2600 0.6060 142 S 0.1070 0.4367 0.4563 143 D 0.1053 0.4246 0.4700 144 Y 0.1337 0.4212 0.4451 145 Y 0.1931 0.2943 0.5126 146 A 0.1763 0.2284 0.5953 147 T 0.1416 0.2356 0.6228 148 G 0.0829 0.3049 0.6121 149 E 0.1343 0.3523 0.5134 150 F 0.2585 0.2778 0.4637 151 K 0.3220 0.2699 0.4080 152 V 0.3973 0.2461 0.3566 153 I 0.3418 0.2644 0.3938 154 Q 0.2839 0.2573 0.4588 155 S 0.2267 0.2009 0.5723 156 S 0.1464 0.2437 0.6098 157 S 0.1554 0.2020 0.6425