# This file is the result of combining several RDB files, specifically # T0586.t06.str2.rdb (weight 1.54425) # T0586.t06.str4.rdb (weight 0.924988) # T0586.t06.pb.rdb (weight 0.789901) # T0586.t06.bys.rdb (weight 0.748322) # T0586.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 T0586.t06.str2.rdb # ============================================ # TARGET T0586 # 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 T0586.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 9555 # # ============================================ # Comments from T0586.t06.str4.rdb # ============================================ # TARGET T0586 # 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 T0586.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 9555 # # ============================================ # Comments from T0586.t06.pb.rdb # ============================================ # TARGET T0586 # 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 T0586.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 9555 # # ============================================ # Comments from T0586.t06.bys.rdb # ============================================ # TARGET T0586 # 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 T0586.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 9555 # # ============================================ # Comments from T0586.t06.alpha.rdb # ============================================ # TARGET T0586 # 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 T0586.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 9555 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1515 0.2095 0.6390 2 N 0.1423 0.2252 0.6325 3 A 0.2050 0.1908 0.6042 4 M 0.2801 0.1042 0.6157 5 N 0.2670 0.0484 0.6846 6 P 0.1911 0.1906 0.6183 7 T 0.1923 0.1883 0.6194 8 F 0.1389 0.2940 0.5671 9 H 0.1170 0.2407 0.6422 10 A 0.1026 0.2570 0.6404 11 D 0.0845 0.1774 0.7381 12 K 0.1836 0.1578 0.6586 13 P 0.1212 0.3895 0.4893 14 I 0.0379 0.7528 0.2094 15 Y 0.0114 0.8786 0.1101 16 S 0.0084 0.9194 0.0722 17 Q 0.0083 0.9231 0.0686 18 I 0.0083 0.9206 0.0711 19 S 0.0084 0.9200 0.0716 20 D 0.0083 0.9233 0.0685 21 W 0.0083 0.9222 0.0695 22 M 0.0083 0.9226 0.0691 23 K 0.0084 0.9195 0.0721 24 K 0.0083 0.9178 0.0739 25 Q 0.0087 0.9040 0.0873 26 M 0.0105 0.8930 0.0964 27 I 0.0179 0.7746 0.2075 28 T 0.0575 0.2249 0.7177 29 G 0.0534 0.0909 0.8557 30 E 0.2303 0.0598 0.7099 31 W 0.3596 0.0481 0.5923 32 K 0.2074 0.0462 0.7464 33 G 0.0926 0.2796 0.6278 34 E 0.0589 0.2462 0.6949 35 D 0.1499 0.2110 0.6391 36 K 0.2161 0.1281 0.6558 37 L 0.2070 0.0620 0.7310 38 P 0.1564 0.1591 0.6845 39 S 0.1307 0.2753 0.5940 40 V 0.0136 0.7753 0.2111 41 R 0.0096 0.8771 0.1133 42 E 0.0090 0.9195 0.0715 43 M 0.0086 0.9187 0.0727 44 G 0.0091 0.9099 0.0811 45 V 0.0111 0.8981 0.0907 46 K 0.0252 0.7710 0.2038 47 L 0.0734 0.3758 0.5507 48 A 0.0781 0.1726 0.7493 49 V 0.2183 0.0835 0.6981 50 N 0.1871 0.0388 0.7741 51 P 0.0168 0.6442 0.3390 52 N 0.0121 0.7797 0.2082 53 T 0.0110 0.8895 0.0995 54 V 0.0086 0.9077 0.0837 55 S 0.0084 0.9173 0.0743 56 R 0.0083 0.9236 0.0682 57 A 0.0083 0.9234 0.0684 58 Y 0.0083 0.9200 0.0717 59 Q 0.0083 0.9242 0.0676 60 E 0.0083 0.9233 0.0684 61 L 0.0084 0.9195 0.0721 62 E 0.0087 0.9045 0.0867 63 R 0.0129 0.8095 0.1776 64 A 0.0580 0.2552 0.6868 65 G 0.0638 0.0776 0.8587 66 Y 0.3967 0.0389 0.5644 67 I 0.6974 0.0222 0.2804 68 Y 0.7508 0.0210 0.2282 69 A 0.7331 0.0185 0.2485 70 K 0.6440 0.0322 0.3238 71 R 0.3763 0.0634 0.5603 72 G 0.2357 0.0728 0.6915 73 M 0.3887 0.0557 0.5556 74 G 0.5037 0.0389 0.4574 75 S 0.6840 0.0289 0.2871 76 F 0.7402 0.0195 0.2403 77 V 0.7041 0.0254 0.2704 78 T 0.5893 0.0315 0.3792 79 S 0.3254 0.1090 0.5656 80 D 0.1752 0.2013 0.6235 81 K 0.1194 0.4049 0.4757 82 A 0.0985 0.4988 0.4027 83 L 0.0916 0.5370 0.3714 84 F 0.0961 0.5612 0.3428 85 D 0.0714 0.6167 0.3118 86 Q 0.1014 0.5517 0.3468 87 L 0.1022 0.5116 0.3862 88 K 0.0601 0.6973 0.2425 89 K 0.0211 0.8308 0.1481 90 E 0.0193 0.8493 0.1313 91 L 0.0236 0.8438 0.1326 92 A 0.0158 0.8691 0.1151 93 D 0.0135 0.8742 0.1122 94 A 0.0144 0.8653 0.1203 95 I 0.0211 0.8388 0.1402 96 T 0.0226 0.8326 0.1447 97 E 0.0221 0.8183 0.1596 98 R 0.0301 0.7801 0.1898 99 F 0.0478 0.7289 0.2233 100 L 0.0515 0.7304 0.2181 101 E 0.0359 0.7573 0.2068 102 E 0.0433 0.7109 0.2458 103 A 0.0601 0.6479 0.2919 104 K 0.0771 0.5756 0.3474 105 S 0.1007 0.4442 0.4551 106 I 0.1139 0.3173 0.5688 107 G 0.1010 0.2328 0.6662 108 L 0.1298 0.2973 0.5729 109 D 0.1216 0.3420 0.5364 110 D 0.0689 0.5671 0.3640 111 Q 0.0403 0.7339 0.2258 112 T 0.0360 0.7999 0.1641 113 A 0.0255 0.8486 0.1259 114 I 0.0154 0.8858 0.0988 115 E 0.0121 0.8955 0.0924 116 L 0.0150 0.8815 0.1035 117 L 0.0273 0.8252 0.1474 118 I 0.0361 0.7985 0.1654 119 K 0.0303 0.7620 0.2076 120 R 0.0422 0.6440 0.3138 121 S 0.0697 0.4815 0.4488 122 R 0.0811 0.3736 0.5453 123 N 0.1036 0.2725 0.6239 124 H 0.1228 0.2314 0.6458 125 E 0.1244 0.2428 0.6328