# This file is the result of combining several RDB files, specifically # T0354.t06.dssp-ebghstl.rdb (weight 1.53986) # T0354.t06.stride-ebghtl.rdb (weight 1.24869) # T0354.t06.str2.rdb (weight 1.54758) # T0354.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 T0354.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0354 # 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 T0354.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 85.0152 # # ============================================ # Comments from T0354.t06.stride-ebghtl.rdb # ============================================ # TARGET T0354 # 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 T0354.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 85.0152 # # ============================================ # Comments from T0354.t06.str2.rdb # ============================================ # TARGET T0354 # Using neural net 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 T0354.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 85.0152 # # ============================================ # Comments from T0354.t06.alpha.rdb # ============================================ # TARGET T0354 # 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 T0354.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 85.0152 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0433 0.0578 0.8989 2 E 0.0647 0.1666 0.7688 3 I 0.0118 0.7894 0.1989 4 Q 0.0060 0.9132 0.0809 5 E 0.0052 0.9412 0.0536 6 I 0.0047 0.9551 0.0402 7 S 0.0047 0.9605 0.0348 8 K 0.0046 0.9611 0.0342 9 L 0.0047 0.9605 0.0348 10 A 0.0047 0.9586 0.0367 11 I 0.0047 0.9589 0.0364 12 E 0.0050 0.9534 0.0416 13 A 0.0051 0.9395 0.0553 14 L 0.0060 0.9178 0.0762 15 E 0.0079 0.8549 0.1372 16 D 0.0119 0.6867 0.3014 17 I 0.0613 0.4822 0.4565 18 K 0.0658 0.1557 0.7785 19 G 0.1169 0.1511 0.7320 20 K 0.1457 0.1894 0.6649 21 D 0.3750 0.0951 0.5298 22 I 0.7235 0.0312 0.2454 23 I 0.8555 0.0180 0.1266 24 E 0.9020 0.0101 0.0879 25 L 0.8221 0.0092 0.1687 26 D 0.6350 0.0091 0.3558 27 T 0.1814 0.1893 0.6292 28 S 0.0470 0.2465 0.7065 29 K 0.0468 0.2850 0.6682 30 L 0.1107 0.2964 0.5929 31 T 0.1470 0.3043 0.5487 32 S 0.1865 0.3574 0.4562 33 L 0.3101 0.3195 0.3704 34 F 0.4777 0.1124 0.4099 35 Q 0.4325 0.1052 0.4622 36 R 0.8622 0.0236 0.1142 37 M 0.9126 0.0135 0.0739 38 I 0.9198 0.0131 0.0671 39 V 0.9054 0.0110 0.0836 40 A 0.7866 0.0207 0.1927 41 T 0.4535 0.0213 0.5253 42 G 0.1233 0.0587 0.8180 43 D 0.0942 0.0664 0.8394 44 S 0.0577 0.3623 0.5800 45 N 0.0074 0.8194 0.1732 46 R 0.0111 0.9228 0.0661 47 Q 0.0077 0.9481 0.0443 48 V 0.0050 0.9565 0.0385 49 K 0.0047 0.9595 0.0359 50 A 0.0047 0.9591 0.0362 51 L 0.0048 0.9555 0.0397 52 A 0.0047 0.9573 0.0380 53 N 0.0051 0.9543 0.0406 54 S 0.0049 0.9504 0.0447 55 V 0.0048 0.9539 0.0413 56 Q 0.0047 0.9587 0.0366 57 V 0.0047 0.9604 0.0349 58 K 0.0047 0.9599 0.0354 59 L 0.0047 0.9588 0.0365 60 K 0.0048 0.9515 0.0437 61 E 0.0056 0.9248 0.0696 62 A 0.0421 0.4519 0.5060 63 G 0.0365 0.0231 0.9403 64 V 0.1016 0.0128 0.8856 65 D 0.3818 0.0177 0.6005 66 I 0.5645 0.0401 0.3954 67 V 0.5334 0.0749 0.3917 68 G 0.4745 0.0763 0.4492 69 S 0.5758 0.0711 0.3531 70 E 0.5882 0.0503 0.3614 71 G 0.4050 0.0397 0.5552 72 H 0.2852 0.0648 0.6500 73 E 0.1983 0.1006 0.7010 74 S 0.0830 0.0724 0.8446 75 G 0.1135 0.0394 0.8471 76 E 0.4302 0.0127 0.5571 77 W 0.8990 0.0033 0.0976 78 V 0.9292 0.0034 0.0674 79 L 0.9326 0.0031 0.0643 80 V 0.9116 0.0045 0.0840 81 D 0.7754 0.0064 0.2182 82 A 0.2367 0.0659 0.6974 83 G 0.0842 0.0557 0.8602 84 D 0.2283 0.0602 0.7115 85 V 0.8062 0.0180 0.1758 86 V 0.9174 0.0095 0.0731 87 V 0.9047 0.0212 0.0742 88 H 0.8451 0.0515 0.1034 89 V 0.7241 0.0616 0.2143 90 M 0.5148 0.0811 0.4042 91 L 0.2474 0.0528 0.6998 92 P 0.0447 0.6116 0.3437 93 A 0.0354 0.6123 0.3523 94 V 0.0568 0.6776 0.2656 95 R 0.0747 0.6228 0.3025 96 D 0.0674 0.5608 0.3718 97 Y 0.1087 0.5719 0.3194 98 Y 0.1510 0.4803 0.3687 99 D 0.1220 0.4475 0.4305 100 I 0.0075 0.9178 0.0746 101 E 0.0073 0.9077 0.0850 102 A 0.0111 0.8780 0.1108 103 L 0.0181 0.7989 0.1829 104 W 0.0320 0.5856 0.3824 105 G 0.0436 0.2842 0.6722 106 G 0.0373 0.1232 0.8395 107 Q 0.0573 0.0682 0.8745 108 K 0.0692 0.0310 0.8998 109 P 0.1093 0.0645 0.8262 110 S 0.2714 0.1334 0.5952 111 F 0.4422 0.1146 0.4432 112 A 0.4732 0.0908 0.4360 113 V 0.3008 0.1355 0.5637 114 G 0.1699 0.1072 0.7229 115 A 0.1152 0.1219 0.7629 116 A 0.1199 0.1059 0.7741 117 K 0.1062 0.0534 0.8405 118 P 0.1027 0.0914 0.8059 119 W 0.0535 0.4956 0.4509 120 S 0.0428 0.6736 0.2835 121 A 0.0433 0.7512 0.2055 122 V 0.0595 0.7498 0.1906 123 L 0.1023 0.6480 0.2497 124 E 0.0828 0.5812 0.3360 125 H 0.0598 0.4848 0.4553 126 H 0.0573 0.3457 0.5969 127 H 0.0538 0.2204 0.7258 128 H 0.0551 0.1544 0.7906 129 H 0.0451 0.1049 0.8500 130 H 0.0434 0.0493 0.9073