# This file is the result of combining several RDB files, specifically # T0465.t04.str2.rdb (weight 1.54425) # T0465.t04.str4.rdb (weight 0.924988) # T0465.t04.pb.rdb (weight 0.789901) # T0465.t04.bys.rdb (weight 0.748322) # T0465.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 T0465.t04.str2.rdb # ============================================ # TARGET T0465 # 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 T0465.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 35.4237 # # ============================================ # Comments from T0465.t04.str4.rdb # ============================================ # TARGET T0465 # 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 T0465.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 35.4237 # # ============================================ # Comments from T0465.t04.pb.rdb # ============================================ # TARGET T0465 # 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 T0465.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 35.4237 # # ============================================ # Comments from T0465.t04.bys.rdb # ============================================ # TARGET T0465 # 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 T0465.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 35.4237 # # ============================================ # Comments from T0465.t04.alpha.rdb # ============================================ # TARGET T0465 # 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 T0465.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 35.4237 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2482 0.2516 0.5003 2 S 0.2101 0.2773 0.5125 3 E 0.1680 0.4112 0.4208 4 N 0.1605 0.3144 0.5251 5 Q 0.1363 0.3301 0.5336 6 N 0.1396 0.3817 0.4788 7 E 0.1881 0.4094 0.4025 8 K 0.2084 0.4024 0.3892 9 V 0.2074 0.4215 0.3711 10 Y 0.2580 0.3202 0.4218 11 D 0.2497 0.2302 0.5201 12 L 0.0449 0.6390 0.3162 13 S 0.0270 0.7495 0.2235 14 F 0.0205 0.7893 0.1902 15 F 0.0598 0.5666 0.3736 16 M 0.1330 0.3159 0.5511 17 P 0.0959 0.2916 0.6125 18 G 0.0488 0.2480 0.7033 19 Q 0.1125 0.2336 0.6539 20 T 0.2031 0.2691 0.5278 21 I 0.2757 0.2763 0.4479 22 D 0.2862 0.2207 0.4931 23 A 0.2258 0.3581 0.4160 24 E 0.2134 0.3630 0.4236 25 E 0.3371 0.1958 0.4671 26 V 0.4125 0.0949 0.4926 27 E 0.4088 0.0595 0.5317 28 V 0.4315 0.0301 0.5384 29 P 0.3573 0.0437 0.5990 30 I 0.3865 0.1413 0.4722 31 S 0.3626 0.1606 0.4768 32 K 0.4377 0.1718 0.3905 33 R 0.5902 0.0996 0.3101 34 F 0.6500 0.0700 0.2799 35 V 0.6726 0.0575 0.2699 36 D 0.4563 0.0626 0.4811 37 K 0.2116 0.2897 0.4987 38 E 0.1019 0.1570 0.7411 39 G 0.0945 0.0974 0.8081 40 N 0.3241 0.0291 0.6469 41 V 0.5452 0.0238 0.4310 42 V 0.6025 0.0179 0.3796 43 P 0.6459 0.0224 0.3317 44 F 0.7340 0.0123 0.2537 45 I 0.7413 0.0112 0.2475 46 F 0.7070 0.0125 0.2805 47 K 0.6444 0.0279 0.3277 48 A 0.5219 0.0407 0.4373 49 I 0.3512 0.0692 0.5796 50 T 0.1884 0.0373 0.7743 51 T 0.0262 0.6507 0.3231 52 D 0.0179 0.7954 0.1867 53 R 0.0215 0.8556 0.1229 54 I 0.0112 0.8943 0.0945 55 D 0.0094 0.9124 0.0782 56 E 0.0103 0.9148 0.0749 57 L 0.0120 0.9102 0.0778 58 E 0.0151 0.8954 0.0895 59 K 0.0201 0.8402 0.1397 60 E 0.0541 0.5828 0.3632 61 N 0.1186 0.3186 0.5628 62 T 0.2206 0.2067 0.5727 63 T 0.3807 0.1404 0.4789 64 Y 0.4874 0.1060 0.4066 65 K 0.5029 0.1133 0.3838 66 N 0.4838 0.0990 0.4171 67 V 0.4023 0.1020 0.4957 68 K 0.2059 0.1354 0.6587 69 G 0.1056 0.1435 0.7509 70 R 0.1364 0.1531 0.7105 71 G 0.1942 0.1088 0.6971 72 R 0.3442 0.0860 0.5699 73 V 0.3702 0.1721 0.4577 74 K 0.3417 0.2668 0.3916 75 E 0.3161 0.2604 0.4235 76 L 0.2725 0.2064 0.5210 77 D 0.1925 0.1671 0.6404 78 S 0.0358 0.6037 0.3604 79 Q 0.0173 0.7852 0.1974 80 R 0.0161 0.8606 0.1233 81 F 0.0170 0.8912 0.0918 82 Y 0.0205 0.8944 0.0851 83 A 0.0194 0.8996 0.0810 84 R 0.0352 0.8824 0.0824 85 I 0.0807 0.8234 0.0959 86 A 0.1762 0.7026 0.1212 87 V 0.1743 0.6588 0.1669 88 E 0.2275 0.5172 0.2553 89 T 0.3810 0.2748 0.3442 90 T 0.4187 0.1437 0.4375 91 V 0.3687 0.0967 0.5346 92 Y 0.2669 0.0690 0.6641 93 P 0.1214 0.3674 0.5112 94 T 0.1019 0.3037 0.5945 95 F 0.0957 0.3964 0.5078 96 K 0.0981 0.3082 0.5937 97 A 0.0850 0.5071 0.4079 98 K 0.0115 0.7843 0.2042 99 E 0.0108 0.8642 0.1250 100 L 0.0102 0.9031 0.0867 101 R 0.0114 0.8979 0.0908 102 E 0.0136 0.8687 0.1178 103 A 0.0243 0.7390 0.2367 104 Y 0.0653 0.3460 0.5887 105 K 0.0570 0.1552 0.7879 106 T 0.1600 0.1136 0.7264 107 E 0.1524 0.1236 0.7240 108 D 0.1754 0.0322 0.7924 109 P 0.0167 0.7092 0.2741 110 V 0.0093 0.8569 0.1338 111 E 0.0085 0.9173 0.0742 112 V 0.0088 0.9168 0.0744 113 A 0.0091 0.9087 0.0822 114 K 0.0096 0.8866 0.1038 115 R 0.0162 0.8561 0.1278 116 V 0.0518 0.7391 0.2092 117 L 0.0744 0.5970 0.3287 118 S 0.0997 0.4385 0.4618 119 V 0.0810 0.3939 0.5251 120 G 0.0684 0.3795 0.5521 121 G 0.0627 0.4111 0.5261 122 E 0.0917 0.6281 0.2803 123 Y 0.0664 0.7601 0.1735 124 A 0.0262 0.8549 0.1190 125 N 0.0172 0.8732 0.1096 126 W 0.0124 0.8822 0.1053 127 L 0.0123 0.8830 0.1047 128 N 0.0132 0.8708 0.1160 129 K 0.0222 0.8488 0.1290 130 A 0.0370 0.7911 0.1719 131 I 0.0619 0.7738 0.1642 132 E 0.1213 0.6848 0.1939 133 I 0.2085 0.4512 0.3403 134 N 0.1804 0.2434 0.5762 135 G 0.1194 0.1867 0.6940 136 F 0.1628 0.1813 0.6559 137 D 0.1546 0.1585 0.6869 138 D 0.0644 0.3549 0.5807 139 D 0.0933 0.3687 0.5379 140 L 0.0229 0.6958 0.2814 141 E 0.0138 0.8042 0.1820 142 D 0.0190 0.8472 0.1338 143 L 0.0176 0.8844 0.0980 144 E 0.0101 0.9109 0.0790 145 E 0.0117 0.9161 0.0722 146 A 0.0116 0.9124 0.0760 147 A 0.0184 0.8773 0.1043 148 K 0.0225 0.8065 0.1710 149 N 0.0546 0.5818 0.3637 150 L 0.0702 0.5576 0.3722 151 E 0.0925 0.4356 0.4719 152 H 0.1119 0.3170 0.5712 153 H 0.1042 0.2697 0.6261 154 H 0.1238 0.2355 0.6407 155 H 0.1475 0.2011 0.6514 156 H 0.1536 0.1980 0.6483 157 H 0.1776 0.1698 0.6526