# This file is the result of combining several RDB files, specifically # T0487.t04.str2.rdb (weight 1.54425) # T0487.t04.str4.rdb (weight 0.924988) # T0487.t04.pb.rdb (weight 0.789901) # T0487.t04.bys.rdb (weight 0.748322) # T0487.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 T0487.t04.str2.rdb # ============================================ # TARGET T0487 # 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 T0487.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 1 # # ============================================ # Comments from T0487.t04.str4.rdb # ============================================ # TARGET T0487 # 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 T0487.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 1 # # ============================================ # Comments from T0487.t04.pb.rdb # ============================================ # TARGET T0487 # 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 T0487.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 1 # # ============================================ # Comments from T0487.t04.bys.rdb # ============================================ # TARGET T0487 # 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 T0487.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 1 # # ============================================ # Comments from T0487.t04.alpha.rdb # ============================================ # TARGET T0487 # 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 T0487.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 1 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 I 0.4540 0.2185 0.3275 2 L 0.4601 0.2241 0.3159 3 C 0.4035 0.2779 0.3187 4 E 0.2850 0.4008 0.3142 5 M 0.2817 0.3786 0.3397 6 S 0.2150 0.3931 0.3919 7 L 0.0495 0.7303 0.2202 8 E 0.0299 0.8408 0.1293 9 A 0.0306 0.8732 0.0961 10 W 0.0330 0.8543 0.1127 11 L 0.0363 0.8184 0.1453 12 A 0.0540 0.7000 0.2460 13 Q 0.0791 0.3219 0.5989 14 G 0.0631 0.1270 0.8099 15 H 0.1759 0.0465 0.7776 16 P 0.1930 0.0896 0.7173 17 L 0.2172 0.0655 0.7173 18 P 0.1543 0.2081 0.6376 19 K 0.1103 0.4349 0.4548 20 R 0.1644 0.4525 0.3831 21 V 0.1913 0.4815 0.3273 22 R 0.1433 0.5319 0.3248 23 N 0.1452 0.4941 0.3607 24 A 0.0920 0.5552 0.3528 25 Y 0.1222 0.4602 0.4176 26 D 0.1171 0.3958 0.4871 27 R 0.0878 0.4841 0.4281 28 R 0.1198 0.4649 0.4153 29 T 0.1692 0.4939 0.3369 30 W 0.1642 0.5946 0.2412 31 E 0.1862 0.6316 0.1822 32 L 0.2174 0.5695 0.2130 33 L 0.2909 0.4453 0.2638 34 R 0.2883 0.3431 0.3686 35 L 0.1701 0.2658 0.5641 36 G 0.1413 0.1347 0.7239 37 E 0.1735 0.1923 0.6342 38 E 0.2326 0.1591 0.6084 39 D 0.2130 0.0428 0.7442 40 P 0.0427 0.4799 0.4773 41 K 0.0678 0.4194 0.5128 42 E 0.1609 0.2505 0.5887 43 L 0.2729 0.0558 0.6714 44 P 0.2470 0.0631 0.6899 45 L 0.2363 0.0557 0.7081 46 P 0.1467 0.1699 0.6834 47 G 0.1052 0.1643 0.7304 48 G 0.1627 0.1488 0.6885 49 L 0.3028 0.1829 0.5144 50 S 0.3521 0.2451 0.4029 51 L 0.2731 0.4031 0.3238 52 L 0.2831 0.3960 0.3209 53 D 0.2361 0.4097 0.3542 54 Y 0.1802 0.4773 0.3425 55 H 0.1869 0.3994 0.4136 56 A 0.1609 0.4211 0.4180 57 S 0.1358 0.3636 0.5007 58 K 0.1153 0.2511 0.6337 59 G 0.1301 0.1627 0.7072 60 R 0.2869 0.1611 0.5520 61 L 0.4006 0.1486 0.4509 62 Q 0.3444 0.1251 0.5305 63 G 0.2508 0.0955 0.6537 64 R 0.2900 0.1411 0.5689 65 E 0.2219 0.1568 0.6213 66 G 0.1520 0.0959 0.7521 67 G 0.2564 0.0629 0.6807 68 R 0.5556 0.0456 0.3988 69 V 0.6869 0.0300 0.2831 70 A 0.7086 0.0359 0.2555 71 W 0.7348 0.0334 0.2319 72 V 0.6753 0.0431 0.2816 73 A 0.5348 0.0494 0.4158 74 D 0.2814 0.0202 0.6984 75 P 0.0622 0.3620 0.5759 76 K 0.0745 0.2820 0.6435 77 D 0.1723 0.1445 0.6832 78 P 0.0839 0.3350 0.5811 79 R 0.1137 0.2214 0.6649 80 K 0.2176 0.0606 0.7218 81 P 0.2320 0.0640 0.7039 82 I 0.2872 0.0634 0.6495 83 P 0.2421 0.1932 0.5647 84 H 0.2833 0.2385 0.4783 85 L 0.3158 0.2259 0.4583 86 T 0.2757 0.1743 0.5500 87 G 0.3144 0.1186 0.5670 88 L 0.4508 0.0814 0.4677 89 L 0.4823 0.0540 0.4637 90 V 0.3744 0.0302 0.5954 91 P 0.2345 0.0537 0.7118