# This file is the result of combining several RDB files, specifically # T0489.t04.str2.rdb (weight 1.54425) # T0489.t04.str4.rdb (weight 0.924988) # T0489.t04.pb.rdb (weight 0.789901) # T0489.t04.bys.rdb (weight 0.748322) # T0489.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 T0489.t04.str2.rdb # ============================================ # TARGET T0489 # 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 T0489.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 53.4163 # # ============================================ # Comments from T0489.t04.str4.rdb # ============================================ # TARGET T0489 # 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 T0489.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 53.4163 # # ============================================ # Comments from T0489.t04.pb.rdb # ============================================ # TARGET T0489 # 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 T0489.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 53.4163 # # ============================================ # Comments from T0489.t04.bys.rdb # ============================================ # TARGET T0489 # 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 T0489.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 53.4163 # # ============================================ # Comments from T0489.t04.alpha.rdb # ============================================ # TARGET T0489 # 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 T0489.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 53.4163 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3292 0.1695 0.5013 2 M 0.3741 0.1515 0.4743 3 F 0.4035 0.1238 0.4728 4 K 0.3543 0.1140 0.5317 5 W 0.2831 0.0832 0.6336 6 P 0.1787 0.2976 0.5238 7 W 0.1738 0.3970 0.4291 8 K 0.2122 0.3339 0.4539 9 A 0.2250 0.2887 0.4863 10 D 0.1730 0.3026 0.5244 11 D 0.1023 0.4791 0.4187 12 E 0.0767 0.5250 0.3983 13 S 0.1002 0.3809 0.5189 14 G 0.1230 0.1782 0.6988 15 N 0.1417 0.1437 0.7147 16 A 0.1927 0.0918 0.7155 17 E 0.1689 0.1097 0.7214 18 M 0.1673 0.2961 0.5366 19 P 0.0843 0.5102 0.4055 20 W 0.0170 0.7957 0.1873 21 E 0.0122 0.8622 0.1256 22 Q 0.0116 0.8844 0.1039 23 A 0.0166 0.8370 0.1464 24 L 0.0303 0.7447 0.2250 25 A 0.0422 0.6374 0.3205 26 I 0.1198 0.4668 0.4134 27 P 0.0813 0.5153 0.4034 28 V 0.0551 0.7315 0.2134 29 L 0.0571 0.7300 0.2129 30 A 0.0544 0.6711 0.2745 31 H 0.0835 0.3487 0.5678 32 L 0.1779 0.1299 0.6921 33 S 0.1554 0.0425 0.8021 34 S 0.0165 0.6914 0.2921 35 T 0.0104 0.8243 0.1653 36 E 0.0099 0.8902 0.0999 37 Q 0.0089 0.9135 0.0776 38 H 0.0090 0.9165 0.0745 39 K 0.0089 0.9167 0.0744 40 L 0.0084 0.9197 0.0718 41 T 0.0083 0.9229 0.0688 42 Q 0.0083 0.9243 0.0674 43 M 0.0083 0.9245 0.0673 44 A 0.0083 0.9235 0.0682 45 A 0.0083 0.9247 0.0671 46 R 0.0094 0.9201 0.0705 47 F 0.0084 0.9135 0.0781 48 L 0.0102 0.8975 0.0923 49 Q 0.0127 0.8638 0.1235 50 Q 0.0337 0.7021 0.2642 51 K 0.0950 0.5008 0.4043 52 R 0.1892 0.3579 0.4529 53 L 0.3439 0.2349 0.4212 54 V 0.4232 0.1675 0.4093 55 A 0.4355 0.1362 0.4283 56 L 0.3328 0.1669 0.5003 57 Q 0.1618 0.1431 0.6951 58 G 0.1079 0.0874 0.8047 59 L 0.3669 0.0297 0.6034 60 E 0.5508 0.0282 0.4210 61 L 0.4644 0.0518 0.4838 62 T 0.2324 0.0496 0.7180 63 P 0.0223 0.6910 0.2867 64 L 0.0131 0.8123 0.1746 65 H 0.0212 0.8711 0.1078 66 Q 0.0222 0.8921 0.0857 67 A 0.0242 0.8982 0.0777 68 R 0.0248 0.9018 0.0735 69 I 0.0239 0.9039 0.0723 70 A 0.0158 0.9125 0.0717 71 M 0.0276 0.8931 0.0793 72 L 0.0322 0.8762 0.0916 73 F 0.0554 0.8130 0.1316 74 C 0.0648 0.7423 0.1929 75 L 0.0899 0.7262 0.1839 76 P 0.0423 0.7871 0.1707 77 V 0.0847 0.7136 0.2017 78 L 0.0882 0.6727 0.2392 79 E 0.0967 0.5419 0.3614 80 L 0.1121 0.3306 0.5573 81 G 0.1041 0.2356 0.6603 82 I 0.1009 0.4337 0.4654 83 E 0.1113 0.5223 0.3664 84 W 0.1471 0.4950 0.3579 85 L 0.1803 0.3410 0.4787 86 D 0.1213 0.2380 0.6407 87 G 0.0785 0.1361 0.7853 88 F 0.2907 0.0539 0.6554 89 H 0.4292 0.0657 0.5051 90 E 0.7478 0.0099 0.2423 91 V 0.7639 0.0069 0.2291 92 L 0.8027 0.0051 0.1921 93 I 0.7907 0.0072 0.2021 94 Y 0.6117 0.0097 0.3786 95 P 0.3584 0.0410 0.6006 96 A 0.2364 0.0410 0.7226 97 P 0.2304 0.1683 0.6013 98 F 0.3847 0.1052 0.5101 99 I 0.4987 0.0612 0.4401 100 V 0.4552 0.0504 0.4944 101 D 0.3003 0.0924 0.6073 102 D 0.2037 0.2354 0.5609 103 E 0.2553 0.2585 0.4862 104 W 0.3141 0.2604 0.4255 105 E 0.3254 0.2372 0.4374 106 D 0.2560 0.2374 0.5066 107 D 0.1668 0.3043 0.5289 108 I 0.1913 0.1643 0.6444 109 G 0.2947 0.0846 0.6207 110 L 0.5596 0.0447 0.3957 111 V 0.6402 0.0475 0.3123 112 H 0.5877 0.0613 0.3510 113 N 0.4535 0.1312 0.4153 114 Q 0.3167 0.2642 0.4190 115 R 0.3262 0.3096 0.3643 116 V 0.3589 0.3302 0.3109 117 V 0.3179 0.3908 0.2913 118 Q 0.2900 0.3708 0.3391 119 S 0.2414 0.2751 0.4835 120 G 0.1979 0.2329 0.5692 121 Q 0.3046 0.2861 0.4093 122 S 0.3659 0.2680 0.3661 123 W 0.2889 0.2889 0.4222 124 Q 0.2037 0.2773 0.5189 125 Q 0.1981 0.1208 0.6811 126 G 0.2468 0.0419 0.7113 127 P 0.4011 0.0409 0.5580 128 V 0.7497 0.0117 0.2386 129 V 0.7476 0.0090 0.2434 130 L 0.6691 0.0213 0.3096 131 N 0.3566 0.0332 0.6102