# This file is the result of combining several RDB files, specifically # T0487.t06.str2.rdb (weight 1.54425) # T0487.t06.str4.rdb (weight 0.924988) # T0487.t06.pb.rdb (weight 0.789901) # T0487.t06.bys.rdb (weight 0.748322) # T0487.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 T0487.t06.str2.rdb # ============================================ # TARGET T0487 # 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 T0487.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 1 # # ============================================ # Comments from T0487.t06.str4.rdb # ============================================ # TARGET T0487 # 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 T0487.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 1 # # ============================================ # Comments from T0487.t06.pb.rdb # ============================================ # TARGET T0487 # 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 T0487.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 1 # # ============================================ # Comments from T0487.t06.bys.rdb # ============================================ # TARGET T0487 # 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 T0487.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 1 # # ============================================ # Comments from T0487.t06.alpha.rdb # ============================================ # TARGET T0487 # 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 T0487.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 1 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 G 0.1652 0.1553 0.6795 2 R 0.2647 0.1988 0.5365 3 R 0.3420 0.2148 0.4432 4 A 0.3300 0.2173 0.4527 5 V 0.3472 0.1647 0.4881 6 S 0.3020 0.1124 0.5855 7 K 0.2524 0.0538 0.6937 8 P 0.1763 0.1437 0.6800 9 A 0.0807 0.4935 0.4258 10 D 0.0768 0.5534 0.3698 11 A 0.1335 0.5478 0.3187 12 L 0.2230 0.4635 0.3135 13 R 0.2717 0.4027 0.3257 14 V 0.2928 0.3344 0.3728 15 G 0.2387 0.3335 0.4278 16 F 0.2522 0.4192 0.3285 17 Y 0.2239 0.4834 0.2927 18 R 0.1543 0.5663 0.2793 19 A 0.0836 0.6621 0.2543 20 Q 0.0558 0.7204 0.2238 21 E 0.0536 0.7480 0.1984 22 T 0.0535 0.7748 0.1716 23 A 0.0582 0.8058 0.1360 24 L 0.0769 0.8035 0.1195 25 A 0.1022 0.7831 0.1147 26 L 0.1618 0.6860 0.1522 27 L 0.2542 0.5127 0.2331 28 R 0.2867 0.3962 0.3172 29 L 0.2621 0.2916 0.4463 30 D 0.1370 0.2218 0.6411 31 G 0.0749 0.2191 0.7060 32 A 0.0936 0.3461 0.5604 33 Q 0.0923 0.2849 0.6228 34 G 0.0951 0.1978 0.7072 35 W 0.1339 0.2296 0.6365 36 P 0.0219 0.7467 0.2314 37 E 0.0102 0.8729 0.1170 38 F 0.0094 0.9064 0.0842 39 L 0.0086 0.9140 0.0774 40 R 0.0084 0.9190 0.0727 41 R 0.0084 0.9199 0.0718 42 A 0.0084 0.9194 0.0723 43 L 0.0087 0.9157 0.0756 44 L 0.0095 0.9084 0.0821 45 R 0.0135 0.8815 0.1050 46 A 0.0293 0.7544 0.2163 47 F 0.0634 0.4672 0.4694 48 G 0.0726 0.2649 0.6625 49 A 0.1218 0.2878 0.5903 50 S 0.1093 0.2436 0.6471 51 G 0.1079 0.1933 0.6988 52 A 0.1990 0.2445 0.5566 53 S 0.3481 0.2026 0.4493 54 L 0.4322 0.1909 0.3769 55 R 0.4815 0.1692 0.3494 56 L 0.4863 0.1894 0.3243 57 H 0.4490 0.1909 0.3601 58 T 0.4753 0.1745 0.3502 59 L 0.3673 0.2196 0.4130 60 H 0.3196 0.1904 0.4900 61 A 0.2927 0.1454 0.5619 62 H 0.2305 0.0520 0.7175 63 P 0.0837 0.3707 0.5456 64 S 0.0693 0.3858 0.5449 65 Q 0.0700 0.3988 0.5311 66 G 0.0698 0.4420 0.4882 67 L 0.0998 0.6076 0.2926 68 A 0.0850 0.7042 0.2109 69 F 0.0407 0.8266 0.1328 70 R 0.0131 0.8967 0.0902 71 E 0.0090 0.9121 0.0789 72 A 0.0094 0.9103 0.0803 73 L 0.0106 0.9031 0.0863 74 R 0.0098 0.9017 0.0885 75 K 0.0134 0.8700 0.1166 76 A 0.0276 0.8149 0.1576 77 K 0.0260 0.8072 0.1667 78 E 0.0382 0.6784 0.2834 79 E 0.0639 0.3314 0.6047 80 G 0.0646 0.1646 0.7708 81 V 0.2467 0.1179 0.6353 82 Q 0.4200 0.1101 0.4699 83 A 0.6654 0.0618 0.2728 84 V 0.7437 0.0306 0.2257 85 L 0.7568 0.0289 0.2143 86 V 0.7300 0.0295 0.2406 87 L 0.6103 0.0414 0.3483 88 T 0.3909 0.0208 0.5884 89 P 0.2176 0.0566 0.7258 90 P 0.1482 0.2416 0.6102 91 M 0.1550 0.3666 0.4784 92 A 0.1642 0.4077 0.4281 93 W 0.1182 0.5373 0.3445 94 E 0.0833 0.5834 0.3333 95 D 0.0759 0.5752 0.3489 96 R 0.0401 0.6749 0.2850 97 N 0.0323 0.7054 0.2623 98 R 0.0304 0.7816 0.1880 99 L 0.0321 0.8278 0.1400 100 K 0.0332 0.8465 0.1204 101 A 0.0406 0.8627 0.0967 102 L 0.0476 0.8453 0.1071 103 L 0.0809 0.7678 0.1513 104 L 0.0894 0.6991 0.2115 105 R 0.0826 0.5726 0.3448 106 E 0.0711 0.2901 0.6388 107 G 0.0526 0.1258 0.8216 108 L 0.1705 0.0383 0.7912 109 P 0.1444 0.2043 0.6513 110 S 0.1291 0.4546 0.4164 111 Q 0.1947 0.4278 0.3775 112 I 0.3254 0.2962 0.3784 113 L 0.4014 0.1587 0.4399 114 N 0.3187 0.1019 0.5794 115 V 0.3099 0.0312 0.6589 116 P 0.2438 0.0495 0.7067 117 L 0.2167 0.2202 0.5631 118 R 0.1587 0.3674 0.4738 119 E 0.0919 0.5848 0.3233 120 E 0.0704 0.6546 0.2750 121 E 0.0725 0.6758 0.2517 122 R 0.0806 0.6626 0.2568 123 H 0.0855 0.6422 0.2723 124 R 0.0648 0.6858 0.2493 125 W 0.0373 0.7903 0.1724 126 E 0.0186 0.8436 0.1378 127 N 0.0167 0.8603 0.1230 128 A 0.0148 0.8795 0.1057 129 L 0.0193 0.8759 0.1047 130 L 0.0157 0.8751 0.1092 131 G 0.0145 0.8836 0.1019 132 L 0.0163 0.8882 0.0955 133 L 0.0210 0.8686 0.1105 134 A 0.0240 0.8319 0.1441 135 K 0.0424 0.6743 0.2833 136 A 0.0750 0.3161 0.6089 137 G 0.0804 0.1517 0.7679 138 L 0.2706 0.0789 0.6505 139 Q 0.4578 0.0618 0.4804 140 V 0.5598 0.0489 0.3914 141 V 0.4404 0.0570 0.5025