# This file is the result of combining several RDB files, specifically # T0493.t04.str2.rdb (weight 1.54425) # T0493.t04.str4.rdb (weight 0.924988) # T0493.t04.pb.rdb (weight 0.789901) # T0493.t04.bys.rdb (weight 0.748322) # T0493.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 T0493.t04.str2.rdb # ============================================ # TARGET T0493 # 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 T0493.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 1831 # # ============================================ # Comments from T0493.t04.str4.rdb # ============================================ # TARGET T0493 # 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 T0493.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 1831 # # ============================================ # Comments from T0493.t04.pb.rdb # ============================================ # TARGET T0493 # 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 T0493.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 1831 # # ============================================ # Comments from T0493.t04.bys.rdb # ============================================ # TARGET T0493 # 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 T0493.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 1831 # # ============================================ # Comments from T0493.t04.alpha.rdb # ============================================ # TARGET T0493 # 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 T0493.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 1831 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1850 0.1589 0.6562 2 N 0.1787 0.1704 0.6509 3 A 0.2166 0.2391 0.5442 4 S 0.2312 0.1992 0.5696 5 Y 0.2460 0.2055 0.5485 6 R 0.2480 0.1978 0.5541 7 S 0.1874 0.1600 0.6527 8 T 0.0507 0.5501 0.3992 9 Q 0.0145 0.7966 0.1889 10 Q 0.0124 0.8864 0.1011 11 I 0.0090 0.9101 0.0809 12 T 0.0084 0.9179 0.0737 13 D 0.0083 0.9222 0.0694 14 F 0.0084 0.9211 0.0705 15 T 0.0083 0.9203 0.0713 16 K 0.0084 0.9173 0.0743 17 E 0.0087 0.9083 0.0831 18 I 0.0110 0.8916 0.0974 19 L 0.0199 0.8149 0.1653 20 V 0.0378 0.6604 0.3018 21 N 0.0844 0.2217 0.6939 22 G 0.0732 0.1259 0.8009 23 E 0.1793 0.1209 0.6998 24 A 0.2864 0.1259 0.5877 25 V 0.3496 0.1454 0.5050 26 T 0.3959 0.1167 0.4874 27 A 0.4030 0.1416 0.4554 28 F 0.3355 0.1654 0.4991 29 D 0.2431 0.1533 0.6035 30 R 0.1623 0.2488 0.5889 31 Q 0.1221 0.1624 0.7155 32 G 0.1098 0.1045 0.7856 33 D 0.2113 0.0532 0.7355 34 L 0.3414 0.0239 0.6347 35 P 0.4328 0.0316 0.5356 36 N 0.6382 0.0254 0.3364 37 V 0.7170 0.0105 0.2726 38 V 0.7148 0.0166 0.2685 39 V 0.6594 0.0155 0.3252 40 T 0.3234 0.0174 0.6592 41 P 0.1960 0.1524 0.6515 42 N 0.1472 0.1128 0.7400 43 F 0.0299 0.6288 0.3414 44 E 0.0135 0.8008 0.1858 45 A 0.0110 0.8689 0.1200 46 G 0.0141 0.8792 0.1068 47 V 0.0088 0.9088 0.0824 48 D 0.0084 0.9188 0.0727 49 Q 0.0085 0.9202 0.0713 50 V 0.0084 0.9171 0.0744 51 V 0.0084 0.9170 0.0746 52 D 0.0085 0.9140 0.0775 53 Q 0.0097 0.8950 0.0954 54 L 0.0175 0.8529 0.1297 55 A 0.0336 0.7120 0.2543 56 M 0.0724 0.5275 0.4001 57 N 0.1077 0.3175 0.5748 58 D 0.1025 0.2670 0.6305 59 S 0.1089 0.2284 0.6627 60 E 0.1449 0.1201 0.7350 61 R 0.1523 0.1668 0.6810 62 D 0.1930 0.1399 0.6671 63 T 0.3947 0.0766 0.5288 64 T 0.6563 0.0320 0.3117 65 A 0.7825 0.0092 0.2083 66 I 0.8129 0.0070 0.1802 67 I 0.7655 0.0175 0.2170 68 G 0.6077 0.0514 0.3409 69 K 0.3644 0.1692 0.4664 70 S 0.1929 0.2719 0.5353 71 L 0.0453 0.5954 0.3593 72 A 0.0205 0.7234 0.2561 73 E 0.0237 0.8037 0.1726 74 C 0.0096 0.8917 0.0987 75 E 0.0086 0.9140 0.0774 76 A 0.0084 0.9194 0.0721 77 L 0.0084 0.9213 0.0703 78 T 0.0083 0.9229 0.0688 79 K 0.0083 0.9243 0.0674 80 A 0.0083 0.9224 0.0693 81 L 0.0085 0.9130 0.0785 82 K 0.0089 0.8858 0.1052 83 A 0.0123 0.8135 0.1741 84 R 0.0550 0.2977 0.6473 85 G 0.0492 0.0685 0.8822 86 E 0.1833 0.0193 0.7974 87 Q 0.3272 0.0318 0.6410 88 V 0.6428 0.0288 0.3284 89 T 0.7117 0.0194 0.2690 90 L 0.6730 0.0220 0.3051 91 I 0.5211 0.0540 0.4249 92 Q 0.3111 0.0781 0.6108 93 T 0.2059 0.1191 0.6750 94 E 0.1349 0.2976 0.5675 95 N 0.1464 0.3064 0.5472 96 Q 0.1906 0.3472 0.4622 97 R 0.2356 0.2538 0.5107 98 L 0.2392 0.1791 0.5817 99 A 0.2372 0.0693 0.6936 100 P 0.1836 0.1497 0.6666 101 G 0.2469 0.0921 0.6610 102 V 0.5027 0.0174 0.4799 103 I 0.6776 0.0185 0.3039 104 V 0.7072 0.0192 0.2736 105 V 0.5879 0.0406 0.3714 106 P 0.4547 0.0950 0.4503 107 S 0.2388 0.4527 0.3085 108 F 0.1726 0.5276 0.2998 109 L 0.1548 0.5239 0.3213 110 A 0.1470 0.4701 0.3829 111 K 0.1165 0.2321 0.6514 112 G 0.1098 0.1277 0.7624 113 L 0.2658 0.0840 0.6502 114 E 0.4453 0.0719 0.4828 115 F 0.4865 0.0262 0.4873 116 D 0.4399 0.0630 0.4971 117 A 0.7729 0.0102 0.2170 118 V 0.7604 0.0095 0.2301 119 I 0.7944 0.0056 0.2000 120 V 0.7488 0.0080 0.2432 121 W 0.5961 0.0335 0.3704 122 N 0.3246 0.0337 0.6417 123 A 0.1777 0.2518 0.5705 124 N 0.1488 0.2403 0.6109 125 Q 0.0969 0.3977 0.5054 126 E 0.1000 0.3344 0.5656 127 N 0.1623 0.2322 0.6055 128 Y 0.2456 0.1391 0.6153 129 Q 0.1999 0.1524 0.6476 130 R 0.1622 0.2047 0.6331 131 E 0.0701 0.4275 0.5023 132 D 0.0636 0.4610 0.4754 133 E 0.0875 0.5201 0.3924 134 R 0.1405 0.5373 0.3222 135 Q 0.1725 0.5927 0.2348 136 L 0.2690 0.4975 0.2335 137 L 0.3701 0.4629 0.1669 138 Y 0.4011 0.4669 0.1320 139 T 0.4096 0.4803 0.1101 140 I 0.3472 0.5163 0.1366 141 C 0.2216 0.6345 0.1438 142 S 0.0764 0.7649 0.1587 143 R 0.0529 0.7918 0.1553 144 A 0.0323 0.8253 0.1424 145 M 0.0556 0.7511 0.1933 146 H 0.0782 0.6496 0.2722 147 E 0.2543 0.4063 0.3394 148 L 0.5821 0.1409 0.2770 149 T 0.7040 0.0681 0.2279 150 L 0.7459 0.0389 0.2152 151 V 0.7033 0.0463 0.2504 152 A 0.5604 0.0544 0.3852 153 V 0.2709 0.1335 0.5955 154 G 0.1466 0.1297 0.7237 155 S 0.1700 0.1107 0.7193 156 L 0.1343 0.2395 0.6262 157 S 0.1299 0.2719 0.5982 158 P 0.0197 0.7281 0.2523 159 L 0.0164 0.8005 0.1831 160 L 0.0164 0.8503 0.1333 161 A 0.0165 0.8350 0.1485 162 R 0.0300 0.7362 0.2338 163 V 0.1010 0.5689 0.3300 164 N 0.0973 0.4971 0.4056 165 H 0.0328 0.6659 0.3012 166 A 0.0458 0.6243 0.3299 167 L 0.1027 0.5099 0.3874 168 Y 0.2353 0.3560 0.4087 169 T 0.3073 0.2657 0.4271 170 L 0.2701 0.2757 0.4542 171 N 0.2331 0.2205 0.5464 172 E 0.2230 0.1593 0.6177 173 A 0.1930 0.1586 0.6484 174 K 0.1720 0.1621 0.6659