# 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 23.1837 # # ============================================ # 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 23.1837 # # ============================================ # 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 23.1837 # # ============================================ # 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 23.1837 # # ============================================ # 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 23.1837 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3054 0.2701 0.4245 2 M 0.3223 0.2449 0.4328 3 F 0.3191 0.2111 0.4698 4 K 0.3005 0.1532 0.5462 5 W 0.2527 0.0955 0.6518 6 P 0.1560 0.2390 0.6050 7 W 0.1500 0.2937 0.5563 8 K 0.1621 0.2608 0.5771 9 A 0.1358 0.3323 0.5319 10 D 0.1253 0.3394 0.5353 11 D 0.0987 0.4585 0.4428 12 E 0.0720 0.5239 0.4041 13 S 0.0914 0.3803 0.5284 14 G 0.0907 0.2737 0.6356 15 N 0.1149 0.1983 0.6868 16 A 0.1888 0.1177 0.6934 17 E 0.1778 0.1168 0.7054 18 M 0.2245 0.0546 0.7209 19 P 0.1364 0.1722 0.6913 20 W 0.0341 0.7176 0.2483 21 E 0.0206 0.8274 0.1520 22 Q 0.0257 0.8263 0.1479 23 A 0.0445 0.7423 0.2131 24 L 0.0631 0.6144 0.3225 25 A 0.0859 0.4258 0.4883 26 I 0.1713 0.2344 0.5943 27 P 0.1200 0.4122 0.4679 28 V 0.0836 0.6402 0.2762 29 L 0.0675 0.6960 0.2365 30 A 0.0500 0.6083 0.3417 31 H 0.0748 0.3694 0.5558 32 L 0.1969 0.0910 0.7121 33 S 0.1573 0.0395 0.8032 34 S 0.0206 0.6536 0.3258 35 T 0.0115 0.8236 0.1649 36 E 0.0112 0.8871 0.1017 37 Q 0.0091 0.9143 0.0766 38 H 0.0084 0.9191 0.0725 39 K 0.0085 0.9210 0.0705 40 L 0.0083 0.9207 0.0709 41 T 0.0083 0.9215 0.0701 42 Q 0.0083 0.9242 0.0675 43 M 0.0083 0.9243 0.0674 44 A 0.0083 0.9240 0.0678 45 A 0.0083 0.9233 0.0684 46 R 0.0083 0.9227 0.0690 47 F 0.0084 0.9209 0.0707 48 L 0.0091 0.9072 0.0837 49 Q 0.0107 0.8755 0.1138 50 Q 0.0219 0.7973 0.1808 51 K 0.0740 0.6880 0.2380 52 R 0.1127 0.5918 0.2955 53 L 0.2315 0.4229 0.3457 54 V 0.2658 0.3596 0.3746 55 A 0.2941 0.2704 0.4356 56 L 0.2416 0.2318 0.5266 57 Q 0.1385 0.1656 0.6959 58 G 0.1054 0.1080 0.7865 59 L 0.3520 0.0316 0.6163 60 E 0.5165 0.0283 0.4553 61 L 0.4944 0.0393 0.4663 62 T 0.2458 0.0399 0.7143 63 P 0.0355 0.6515 0.3130 64 L 0.0346 0.7048 0.2606 65 H 0.0535 0.8085 0.1381 66 Q 0.0429 0.8512 0.1059 67 A 0.0333 0.8820 0.0848 68 R 0.0241 0.9006 0.0753 69 I 0.0202 0.9032 0.0766 70 A 0.0162 0.9102 0.0736 71 M 0.0138 0.9089 0.0773 72 L 0.0139 0.8948 0.0913 73 F 0.0235 0.8396 0.1370 74 C 0.0313 0.7963 0.1725 75 L 0.0484 0.7889 0.1627 76 P 0.0343 0.8123 0.1534 77 V 0.0380 0.8034 0.1587 78 L 0.0491 0.7531 0.1977 79 E 0.0978 0.5535 0.3487 80 L 0.1158 0.2726 0.6116 81 G 0.0942 0.1432 0.7625 82 I 0.1362 0.3184 0.5454 83 E 0.1296 0.4617 0.4087 84 W 0.1581 0.4666 0.3752 85 L 0.1854 0.3332 0.4814 86 D 0.0936 0.3932 0.5132 87 G 0.0710 0.2107 0.7183 88 F 0.3230 0.0718 0.6051 89 H 0.4754 0.0529 0.4717 90 E 0.7739 0.0124 0.2137 91 V 0.7679 0.0070 0.2251 92 L 0.8001 0.0060 0.1939 93 I 0.7556 0.0079 0.2365 94 Y 0.6180 0.0117 0.3703 95 P 0.3439 0.0378 0.6183