# This file is the result of combining several RDB files, specifically # T0489.t06.str2.rdb (weight 1.54425) # T0489.t06.str4.rdb (weight 0.924988) # T0489.t06.pb.rdb (weight 0.789901) # T0489.t06.bys.rdb (weight 0.748322) # T0489.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 T0489.t06.str2.rdb # ============================================ # TARGET T0489 # 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 T0489.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 53.6898 # # ============================================ # Comments from T0489.t06.str4.rdb # ============================================ # TARGET T0489 # 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 T0489.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 53.6898 # # ============================================ # Comments from T0489.t06.pb.rdb # ============================================ # TARGET T0489 # 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 T0489.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 53.6898 # # ============================================ # Comments from T0489.t06.bys.rdb # ============================================ # TARGET T0489 # 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 T0489.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 53.6898 # # ============================================ # Comments from T0489.t06.alpha.rdb # ============================================ # TARGET T0489 # 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 T0489.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 53.6898 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2870 0.1917 0.5214 2 M 0.2948 0.1876 0.5175 3 F 0.2948 0.1906 0.5147 4 K 0.2752 0.1705 0.5543 5 W 0.2458 0.1240 0.6302 6 P 0.1465 0.3485 0.5050 7 W 0.1134 0.5070 0.3796 8 K 0.1364 0.4695 0.3941 9 A 0.1399 0.4295 0.4306 10 D 0.1368 0.3596 0.5037 11 D 0.0893 0.4608 0.4500 12 E 0.0675 0.4799 0.4526 13 S 0.0986 0.3036 0.5977 14 G 0.1120 0.1870 0.7010 15 N 0.1363 0.1457 0.7180 16 A 0.1983 0.0975 0.7042 17 E 0.1819 0.1005 0.7176 18 M 0.1863 0.1241 0.6896 19 P 0.0816 0.4273 0.4911 20 W 0.0248 0.7815 0.1938 21 E 0.0157 0.8548 0.1295 22 Q 0.0147 0.8722 0.1131 23 A 0.0207 0.8323 0.1469 24 L 0.0326 0.7254 0.2420 25 A 0.0464 0.5838 0.3699 26 I 0.1074 0.4217 0.4709 27 P 0.0587 0.5634 0.3779 28 V 0.0428 0.7453 0.2119 29 L 0.0353 0.7806 0.1842 30 A 0.0302 0.6685 0.3014 31 H 0.0550 0.3814 0.5636 32 L 0.1954 0.0841 0.7205 33 S 0.1567 0.0333 0.8100 34 S 0.0159 0.6952 0.2889 35 T 0.0108 0.8366 0.1527 36 E 0.0113 0.8907 0.0980 37 Q 0.0089 0.9165 0.0746 38 H 0.0084 0.9202 0.0714 39 K 0.0084 0.9213 0.0703 40 L 0.0083 0.9218 0.0698 41 T 0.0083 0.9222 0.0695 42 Q 0.0083 0.9242 0.0675 43 M 0.0083 0.9244 0.0673 44 A 0.0083 0.9240 0.0677 45 A 0.0083 0.9230 0.0687 46 R 0.0083 0.9226 0.0691 47 F 0.0085 0.9194 0.0721 48 L 0.0098 0.9020 0.0882 49 Q 0.0127 0.8525 0.1347 50 Q 0.0303 0.7366 0.2331 51 K 0.1193 0.5595 0.3212 52 R 0.1895 0.4436 0.3669 53 L 0.3620 0.2556 0.3824 54 V 0.4222 0.2130 0.3647 55 A 0.4250 0.1726 0.4024 56 L 0.3067 0.1971 0.4962 57 Q 0.1505 0.1385 0.7110 58 G 0.0982 0.0990 0.8028 59 L 0.3351 0.0299 0.6350 60 E 0.5220 0.0265 0.4515 61 L 0.5180 0.0341 0.4479 62 T 0.2570 0.0321 0.7109 63 P 0.0405 0.6465 0.3131 64 L 0.0368 0.6922 0.2710 65 H 0.0631 0.7917 0.1452 66 Q 0.0594 0.8238 0.1168 67 A 0.0513 0.8570 0.0917 68 R 0.0389 0.8812 0.0799 69 I 0.0341 0.8839 0.0820 70 A 0.0340 0.8864 0.0796 71 M 0.0229 0.8972 0.0799 72 L 0.0267 0.8759 0.0974 73 F 0.0451 0.8168 0.1381 74 C 0.0526 0.7694 0.1781 75 L 0.1052 0.7000 0.1948 76 P 0.0675 0.7325 0.2000 77 V 0.0666 0.7127 0.2207 78 L 0.0785 0.6449 0.2765 79 E 0.1318 0.4277 0.4406 80 L 0.1390 0.2254 0.6355 81 G 0.1136 0.1549 0.7315 82 I 0.1179 0.4132 0.4689 83 E 0.1199 0.4979 0.3822 84 W 0.1612 0.4683 0.3704 85 L 0.1913 0.3126 0.4962 86 D 0.0899 0.3726 0.5375 87 G 0.0636 0.2022 0.7342 88 F 0.2877 0.0681 0.6442 89 H 0.4127 0.0631 0.5242 90 E 0.7694 0.0133 0.2173 91 V 0.7675 0.0071 0.2254 92 L 0.7945 0.0064 0.1991 93 I 0.7550 0.0083 0.2368 94 Y 0.6347 0.0116 0.3536 95 P 0.3413 0.0388 0.6200 96 A 0.2640 0.0538 0.6822 97 P 0.2444 0.1801 0.5755 98 F 0.4268 0.1154 0.4577 99 I 0.5591 0.0542 0.3867 100 V 0.4471 0.0439 0.5090 101 D 0.3178 0.0814 0.6008 102 D 0.2273 0.2077 0.5650 103 E 0.2964 0.2411 0.4625 104 W 0.3359 0.2263 0.4378 105 E 0.2914 0.2415 0.4671 106 D 0.2232 0.2343 0.5425 107 D 0.1530 0.3187 0.5283 108 I 0.1610 0.1870 0.6520 109 G 0.2220 0.0831 0.6949 110 L 0.4841 0.0359 0.4800 111 V 0.6156 0.0357 0.3487 112 H 0.5723 0.0553 0.3723 113 N 0.4441 0.1259 0.4300 114 Q 0.3216 0.2761 0.4022 115 R 0.3614 0.2833 0.3553 116 V 0.3727 0.3238 0.3035 117 V 0.3022 0.3978 0.2999 118 Q 0.2903 0.3544 0.3553 119 S 0.2223 0.2525 0.5252 120 G 0.1803 0.1547 0.6650 121 Q 0.3312 0.1642 0.5046 122 S 0.3651 0.1913 0.4437 123 W 0.2175 0.2854 0.4970 124 Q 0.1677 0.2351 0.5972 125 Q 0.1584 0.1429 0.6987 126 G 0.2595 0.0455 0.6950 127 P 0.4165 0.0256 0.5579 128 V 0.7567 0.0118 0.2315 129 V 0.7296 0.0141 0.2564 130 L 0.6285 0.0294 0.3421 131 N 0.3878 0.0354 0.5768