# This file is the result of combining several RDB files, specifically # T0472.t04.str2.rdb (weight 1.54425) # T0472.t04.str4.rdb (weight 0.924988) # T0472.t04.pb.rdb (weight 0.789901) # T0472.t04.bys.rdb (weight 0.748322) # T0472.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 T0472.t04.str2.rdb # ============================================ # TARGET T0472 # 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 T0472.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 26.1173 # # ============================================ # Comments from T0472.t04.str4.rdb # ============================================ # TARGET T0472 # 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 T0472.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 26.1173 # # ============================================ # Comments from T0472.t04.pb.rdb # ============================================ # TARGET T0472 # 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 T0472.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 26.1173 # # ============================================ # Comments from T0472.t04.bys.rdb # ============================================ # TARGET T0472 # 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 T0472.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 26.1173 # # ============================================ # Comments from T0472.t04.alpha.rdb # ============================================ # TARGET T0472 # 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 T0472.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 26.1173 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2108 0.1848 0.6044 2 S 0.2519 0.1277 0.6204 3 G 0.3180 0.0904 0.5916 4 W 0.5809 0.0772 0.3419 5 Y 0.7429 0.0176 0.2395 6 E 0.7653 0.0150 0.2197 7 L 0.7525 0.0186 0.2289 8 S 0.6989 0.0420 0.2591 9 K 0.6344 0.0781 0.2875 10 S 0.4107 0.0931 0.4962 11 S 0.1491 0.2350 0.6159 12 N 0.1076 0.1462 0.7462 13 D 0.1371 0.0988 0.7641 14 Q 0.4698 0.0369 0.4934 15 F 0.7022 0.0153 0.2825 16 K 0.7897 0.0083 0.2020 17 F 0.8199 0.0055 0.1745 18 V 0.8152 0.0056 0.1792 19 L 0.8001 0.0066 0.1933 20 K 0.7572 0.0142 0.2286 21 A 0.5164 0.0555 0.4280 22 G 0.2655 0.1062 0.6283 23 N 0.1474 0.1098 0.7428 24 G 0.2028 0.0654 0.7318 25 E 0.5639 0.0309 0.4052 26 V 0.7273 0.0143 0.2584 27 I 0.7548 0.0220 0.2232 28 L 0.7413 0.0267 0.2320 29 T 0.6239 0.0523 0.3238 30 S 0.4460 0.0942 0.4597 31 E 0.2716 0.2644 0.4640 32 L 0.2419 0.2578 0.5004 33 Y 0.2254 0.2498 0.5249 34 T 0.1748 0.2633 0.5619 35 G 0.1255 0.2464 0.6281 36 K 0.0475 0.6087 0.3438 37 S 0.0242 0.7340 0.2419 38 G 0.0223 0.8120 0.1656 39 A 0.0174 0.8700 0.1126 40 M 0.0129 0.8809 0.1062 41 N 0.0150 0.8659 0.1191 42 G 0.0174 0.8747 0.1080 43 I 0.0153 0.8835 0.1012 44 E 0.0136 0.8912 0.0952 45 S 0.0281 0.8507 0.1212 46 V 0.0527 0.7817 0.1655 47 Q 0.0566 0.7431 0.2004 48 T 0.0630 0.6247 0.3123 49 N 0.0855 0.3069 0.6076 50 S 0.1667 0.1041 0.7292 51 P 0.1211 0.2146 0.6643 52 I 0.0997 0.3650 0.5354 53 E 0.0843 0.5303 0.3854 54 A 0.1073 0.6062 0.2865 55 R 0.1787 0.5763 0.2450 56 Y 0.2705 0.4836 0.2460 57 A 0.2932 0.4623 0.2445 58 K 0.3516 0.4010 0.2475 59 E 0.4046 0.3181 0.2773 60 V 0.3956 0.2898 0.3147 61 A 0.2518 0.2968 0.4514 62 K 0.1261 0.2915 0.5824 63 N 0.0994 0.1315 0.7691 64 D 0.1200 0.0858 0.7942 65 K 0.3752 0.0241 0.6007 66 P 0.5101 0.0279 0.4620 67 Y 0.6677 0.0249 0.3073 68 F 0.7689 0.0119 0.2192 69 N 0.7548 0.0110 0.2342 70 L 0.7569 0.0215 0.2216 71 K 0.6872 0.0467 0.2660 72 A 0.5032 0.1276 0.3692 73 A 0.2600 0.1735 0.5664 74 N 0.1263 0.1164 0.7573 75 H 0.1985 0.0827 0.7187 76 Q 0.4874 0.0359 0.4767 77 I 0.6343 0.0230 0.3427 78 I 0.6189 0.0455 0.3355 79 G 0.5736 0.0440 0.3824 80 T 0.4813 0.1079 0.4108 81 S 0.3665 0.2004 0.4331 82 Q 0.2779 0.3424 0.3797 83 M 0.2549 0.3722 0.3729 84 Y 0.2118 0.4304 0.3578 85 S 0.1699 0.4449 0.3853 86 S 0.1131 0.5276 0.3593 87 T 0.0283 0.7515 0.2202 88 A 0.0203 0.8289 0.1507 89 A 0.0224 0.8332 0.1444 90 R 0.0198 0.8365 0.1437 91 D 0.0206 0.7921 0.1873 92 N 0.0541 0.5563 0.3896 93 G 0.0485 0.5505 0.4010 94 I 0.0369 0.7958 0.1673 95 K 0.0284 0.8420 0.1296 96 S 0.0419 0.8414 0.1166 97 V 0.0289 0.8632 0.1078 98 M 0.0332 0.8278 0.1390 99 E 0.0387 0.7141 0.2471 100 N 0.0640 0.3567 0.5793 101 G 0.1279 0.1802 0.6920 102 K 0.1152 0.1969 0.6879 103 T 0.1616 0.1608 0.6776 104 T 0.2615 0.1298 0.6088 105 T 0.3728 0.1361 0.4911 106 I 0.3694 0.2275 0.4031 107 K 0.3576 0.2242 0.4183 108 D 0.3272 0.1766 0.4962 109 L 0.1948 0.2311 0.5741 110 T 0.1646 0.1733 0.6621