# This file is the result of combining several RDB files, specifically # T0283.t06.dssp-ebghstl.rdb (weight 1.53986) # T0283.t06.stride-ebghtl.rdb (weight 1.24869) # T0283.t06.str2.rdb (weight 1.54758) # T0283.t06.alpha.rdb (weight 0.659012) # 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 T0283.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0283 # Using neural net t06-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0283.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 7.00874 # # ============================================ # Comments from T0283.t06.stride-ebghtl.rdb # ============================================ # TARGET T0283 # Using neural net t06-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0283.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 7.00874 # # ============================================ # Comments from T0283.t06.str2.rdb # ============================================ # TARGET T0283 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0283.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 7.00874 # # ============================================ # Comments from T0283.t06.alpha.rdb # ============================================ # TARGET T0283 # Using neural net 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 T0283.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 7.00874 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0395 0.1958 0.7648 2 S 0.0375 0.4588 0.5037 3 F 0.0128 0.8281 0.1591 4 I 0.0083 0.8941 0.0976 5 E 0.0054 0.9461 0.0484 6 K 0.0068 0.9412 0.0520 7 M 0.0089 0.9349 0.0562 8 I 0.0158 0.9024 0.0818 9 G 0.0146 0.7904 0.1950 10 S 0.0195 0.7470 0.2335 11 L 0.0214 0.7677 0.2109 12 N 0.0183 0.6675 0.3142 13 D 0.0235 0.6830 0.2935 14 K 0.0112 0.8850 0.1039 15 R 0.0083 0.9155 0.0761 16 E 0.0085 0.9228 0.0686 17 W 0.0051 0.9430 0.0519 18 K 0.0050 0.9523 0.0428 19 A 0.0047 0.9501 0.0452 20 M 0.0047 0.9481 0.0471 21 E 0.0047 0.9560 0.0394 22 A 0.0047 0.9538 0.0416 23 R 0.0048 0.9414 0.0538 24 A 0.0049 0.9209 0.0743 25 K 0.0092 0.7940 0.1968 26 A 0.0097 0.5112 0.4791 27 L 0.0297 0.1843 0.7860 28 P 0.0269 0.2250 0.7481 29 K 0.0070 0.8412 0.1518 30 E 0.0063 0.8705 0.1232 31 Y 0.0055 0.9321 0.0624 32 H 0.0048 0.9544 0.0408 33 H 0.0047 0.9573 0.0380 34 A 0.0048 0.9568 0.0384 35 Y 0.0047 0.9588 0.0365 36 K 0.0047 0.9595 0.0358 37 A 0.0047 0.9590 0.0363 38 I 0.0048 0.9547 0.0405 39 Q 0.0050 0.9517 0.0433 40 K 0.0067 0.9351 0.0581 41 Y 0.0113 0.8988 0.0899 42 M 0.0293 0.8326 0.1381 43 W 0.0638 0.7104 0.2258 44 T 0.0601 0.6315 0.3084 45 S 0.0761 0.4173 0.5066 46 G 0.0688 0.1602 0.7710 47 G 0.0654 0.0572 0.8774 48 P 0.0914 0.1112 0.7975 49 T 0.1068 0.1257 0.7675 50 D 0.1026 0.1882 0.7092 51 W 0.0311 0.6989 0.2700 52 Q 0.0175 0.7660 0.2166 53 D 0.0271 0.7331 0.2398 54 T 0.0129 0.8742 0.1129 55 K 0.0087 0.9152 0.0761 56 R 0.0073 0.9156 0.0771 57 I 0.0064 0.9273 0.0663 58 F 0.0052 0.9342 0.0607 59 G 0.0048 0.9138 0.0813 60 G 0.0053 0.9127 0.0821 61 I 0.0051 0.9436 0.0513 62 L 0.0056 0.9401 0.0543 63 D 0.0048 0.9537 0.0416 64 L 0.0048 0.9567 0.0385 65 F 0.0050 0.9530 0.0420 66 E 0.0059 0.9488 0.0453 67 E 0.0075 0.9402 0.0524 68 G 0.0122 0.9017 0.0861 69 A 0.0124 0.8577 0.1299 70 A 0.0185 0.7133 0.2682 71 E 0.0422 0.2276 0.7302 72 G 0.0321 0.0324 0.9355 73 K 0.1467 0.0187 0.8346 74 K 0.3902 0.0156 0.5942 75 V 0.3337 0.2704 0.3960 76 T 0.2691 0.4210 0.3099 77 D 0.2339 0.4589 0.3072 78 L 0.2281 0.2900 0.4819 79 T 0.1406 0.2057 0.6536 80 G 0.0674 0.3652 0.5674 81 E 0.0212 0.6149 0.3640 82 D 0.0275 0.7142 0.2583 83 V 0.0053 0.9359 0.0588 84 A 0.0047 0.9370 0.0583 85 A 0.0047 0.9141 0.0812 86 F 0.0097 0.9188 0.0716 87 C 0.0048 0.9512 0.0441 88 D 0.0047 0.9561 0.0392 89 E 0.0050 0.9494 0.0456 90 L 0.0057 0.9257 0.0686 91 M 0.0068 0.8185 0.1747 92 K 0.0094 0.6251 0.3654 93 D 0.0282 0.4183 0.5535 94 T 0.0420 0.3758 0.5822 95 K 0.0217 0.3298 0.6486 96 T 0.0412 0.4990 0.4599 97 W 0.0272 0.7815 0.1912 98 M 0.0178 0.8679 0.1143 99 D 0.0073 0.9454 0.0473 100 K 0.0054 0.9526 0.0421 101 Y 0.0055 0.9515 0.0430 102 R 0.0054 0.9540 0.0405 103 T 0.0059 0.9512 0.0429 104 K 0.0064 0.9376 0.0561 105 L 0.0068 0.9183 0.0749 106 N 0.0123 0.8660 0.1217 107 D 0.0093 0.8304 0.1602 108 S 0.0143 0.7635 0.2222 109 I 0.0510 0.5461 0.4028 110 G 0.0567 0.2567 0.6867 111 R 0.0658 0.1322 0.8021 112 D 0.0582 0.0439 0.8979