# This file is the result of combining several RDB files, specifically # T0389.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0389.t2k.stride-ebghtl.rdb (weight 1.24869) # T0389.t2k.str2.rdb (weight 1.54758) # T0389.t2k.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 T0389.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0389 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0389.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 510 # # ============================================ # Comments from T0389.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0389 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0389.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 510 # # ============================================ # Comments from T0389.t2k.str2.rdb # ============================================ # TARGET T0389 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0389.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 510 # # ============================================ # Comments from T0389.t2k.alpha.rdb # ============================================ # TARGET T0389 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0389.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 510 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0642 0.0391 0.8967 2 I 0.1491 0.0602 0.7907 3 G 0.0904 0.0950 0.8146 4 T 0.0450 0.5371 0.4179 5 Q 0.0668 0.6291 0.3041 6 I 0.0830 0.6777 0.2393 7 V 0.0661 0.6870 0.2469 8 T 0.0107 0.8931 0.0963 9 E 0.0082 0.9191 0.0728 10 R 0.0068 0.9233 0.0699 11 L 0.0073 0.9200 0.0726 12 V 0.0083 0.9124 0.0793 13 A 0.0092 0.8830 0.1078 14 L 0.0103 0.8667 0.1230 15 L 0.0153 0.8234 0.1613 16 E 0.0174 0.7635 0.2191 17 S 0.0346 0.5456 0.4198 18 G 0.0419 0.1961 0.7619 19 T 0.0620 0.1022 0.8358 20 E 0.0406 0.0959 0.8635 21 K 0.1377 0.0472 0.8151 22 V 0.7381 0.0052 0.2567 23 L 0.9120 0.0035 0.0845 24 L 0.9243 0.0032 0.0725 25 I 0.8980 0.0052 0.0968 26 D 0.8076 0.0056 0.1868 27 S 0.4214 0.0252 0.5534 28 R 0.1734 0.0211 0.8055 29 P 0.0950 0.0450 0.8601 30 F 0.0241 0.6658 0.3101 31 V 0.0184 0.7773 0.2043 32 E 0.0174 0.8161 0.1664 33 Y 0.0292 0.7746 0.1962 34 N 0.0350 0.6667 0.2983 35 T 0.0376 0.4733 0.4891 36 S 0.0617 0.2574 0.6809 37 H 0.1400 0.1421 0.7180 38 I 0.1203 0.1275 0.7523 39 L 0.0547 0.2318 0.7135 40 E 0.0756 0.1795 0.7449 41 A 0.2341 0.1490 0.6169 42 I 0.5057 0.0883 0.4060 43 N 0.5416 0.0540 0.4043 44 I 0.3570 0.0300 0.6129 45 N 0.1779 0.0278 0.7943 46 C 0.0203 0.5917 0.3880 47 S 0.0081 0.7868 0.2051 48 K 0.0071 0.8519 0.1410 49 L 0.0095 0.8771 0.1134 50 M 0.0152 0.8523 0.1325 51 K 0.0187 0.7965 0.1848 52 R 0.0237 0.7314 0.2449 53 R 0.0297 0.6785 0.2918 54 L 0.0287 0.6053 0.3660 55 Q 0.0292 0.5325 0.4382 56 Q 0.0487 0.3731 0.5782 57 D 0.0565 0.3084 0.6351 58 K 0.0474 0.4488 0.5039 59 V 0.0768 0.4712 0.4520 60 L 0.1000 0.5051 0.3949 61 I 0.1198 0.5753 0.3049 62 T 0.1382 0.5791 0.2827 63 E 0.1849 0.5247 0.2904 64 L 0.1916 0.4484 0.3600 65 I 0.1741 0.3306 0.4953 66 Q 0.0993 0.2910 0.6097 67 H 0.0456 0.4719 0.4825 68 S 0.0375 0.5414 0.4211 69 A 0.0390 0.5866 0.3745 70 K 0.0551 0.5873 0.3576 71 H 0.0772 0.5485 0.3744 72 K 0.0915 0.5261 0.3824 73 V 0.1064 0.4802 0.4134 74 D 0.1111 0.3342 0.5547 75 I 0.0960 0.2639 0.6401 76 D 0.0880 0.1766 0.7354 77 C 0.0620 0.1487 0.7892 78 S 0.0811 0.0637 0.8552 79 Q 0.2126 0.0177 0.7697 80 K 0.6126 0.0048 0.3827 81 V 0.8951 0.0039 0.1011 82 V 0.9228 0.0033 0.0739 83 V 0.9140 0.0035 0.0825 84 Y 0.8478 0.0057 0.1464 85 D 0.4263 0.0175 0.5562 86 Q 0.0671 0.0950 0.8379 87 S 0.0568 0.0719 0.8713 88 S 0.0601 0.1213 0.8186 89 Q 0.0748 0.1925 0.7327 90 D 0.1404 0.2732 0.5864 91 V 0.0769 0.3772 0.5459 92 A 0.0561 0.4158 0.5280 93 S 0.0400 0.5338 0.4262 94 L 0.0402 0.5542 0.4056 95 S 0.0326 0.5957 0.3717 96 S 0.0172 0.7182 0.2646 97 D 0.0143 0.7567 0.2290 98 C 0.0140 0.8178 0.1682 99 F 0.0085 0.9006 0.0909 100 L 0.0075 0.9186 0.0740 101 T 0.0064 0.9358 0.0578 102 V 0.0062 0.9417 0.0521 103 L 0.0062 0.9385 0.0552 104 L 0.0061 0.9372 0.0567 105 G 0.0065 0.9273 0.0662 106 K 0.0068 0.9158 0.0775 107 L 0.0088 0.8686 0.1226 108 E 0.0161 0.7595 0.2244 109 K 0.0419 0.3729 0.5852 110 S 0.0439 0.0807 0.8754 111 F 0.0935 0.0406 0.8660 112 N 0.1502 0.0574 0.7924 113 S 0.3640 0.0499 0.5861 114 V 0.7956 0.0207 0.1837 115 H 0.8795 0.0145 0.1061 116 L 0.8892 0.0128 0.0979 117 L 0.7665 0.0417 0.1917 118 A 0.3639 0.1020 0.5341 119 G 0.1082 0.1287 0.7632 120 G 0.0752 0.2672 0.6575 121 F 0.0130 0.8341 0.1529 122 A 0.0056 0.9232 0.0712 123 E 0.0055 0.9379 0.0566 124 F 0.0053 0.9366 0.0581 125 S 0.0064 0.9235 0.0701 126 R 0.0080 0.8547 0.1373 127 C 0.0162 0.7133 0.2706 128 F 0.0665 0.2752 0.6583 129 P 0.0304 0.3972 0.5724 130 G 0.0217 0.5055 0.4728 131 L 0.0496 0.5152 0.4352 132 C 0.1567 0.2270 0.6163 133 E 0.1616 0.1305 0.7079 134 G 0.1121 0.0948 0.7931 135 K 0.1098 0.0801 0.8100 136 S 0.1418 0.0722 0.7860 137 T 0.1736 0.0684 0.7580 138 L 0.1591 0.0683 0.7726 139 V 0.1445 0.0848 0.7708 140 P 0.1303 0.0840 0.7857 141 T 0.1236 0.0906 0.7858 142 C 0.1074 0.1142 0.7785 143 I 0.0891 0.1461 0.7647 144 S 0.1009 0.1145 0.7846 145 Q 0.0927 0.0826 0.8248 146 P 0.0901 0.0821 0.8278 147 A 0.0632 0.1662 0.7706 148 H 0.0677 0.1690 0.7633 149 H 0.1030 0.1420 0.7550 150 H 0.1459 0.1271 0.7270 151 H 0.1491 0.1003 0.7506 152 H 0.0975 0.0983 0.8042 153 H 0.0463 0.0475 0.9062