# This file is the result of combining several RDB files, specifically # T0407.t04.str2.rdb (weight 1.54425) # T0407.t04.str4.rdb (weight 0.924988) # T0407.t04.pb.rdb (weight 0.789901) # T0407.t04.bys.rdb (weight 0.748322) # T0407.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 T0407.t04.str2.rdb # ============================================ # TARGET T0407 # 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 T0407.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 1963 # # ============================================ # Comments from T0407.t04.str4.rdb # ============================================ # TARGET T0407 # 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 T0407.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 1963 # # ============================================ # Comments from T0407.t04.pb.rdb # ============================================ # TARGET T0407 # 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 T0407.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 1963 # # ============================================ # Comments from T0407.t04.bys.rdb # ============================================ # TARGET T0407 # 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 T0407.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 1963 # # ============================================ # Comments from T0407.t04.alpha.rdb # ============================================ # TARGET T0407 # 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 T0407.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 1963 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 P 0.1906 0.1399 0.6695 2 D 0.1854 0.1344 0.6802 3 L 0.1918 0.2099 0.5982 4 D 0.1411 0.2104 0.6485 5 G 0.0985 0.1719 0.7296 6 Y 0.2026 0.1469 0.6505 7 T 0.2811 0.1374 0.5814 8 T 0.3582 0.1249 0.5169 9 L 0.4848 0.0898 0.4254 10 K 0.6356 0.0499 0.3145 11 C 0.6896 0.0360 0.2744 12 D 0.6380 0.0463 0.3158 13 F 0.6537 0.0596 0.2867 14 H 0.6256 0.0544 0.3200 15 M 0.6101 0.0529 0.3370 16 H 0.4995 0.0766 0.4239 17 S 0.4601 0.0839 0.4560 18 V 0.3847 0.1388 0.4765 19 F 0.3244 0.1397 0.5360 20 S 0.2090 0.1585 0.6326 21 D 0.1217 0.2332 0.6451 22 G 0.1116 0.1805 0.7078 23 L 0.1876 0.1864 0.6260 24 V 0.2307 0.1046 0.6647 25 W 0.1739 0.0355 0.7907 26 P 0.0190 0.6863 0.2948 27 T 0.0102 0.8466 0.1432 28 V 0.0093 0.9086 0.0821 29 R 0.0090 0.9134 0.0776 30 V 0.0084 0.9150 0.0766 31 D 0.0083 0.9230 0.0687 32 E 0.0083 0.9231 0.0686 33 A 0.0084 0.9197 0.0720 34 Y 0.0088 0.9021 0.0891 35 R 0.0106 0.8346 0.1548 36 D 0.0509 0.2202 0.7289 37 G 0.0470 0.0638 0.8892 38 L 0.1954 0.0303 0.7742 39 D 0.3314 0.0925 0.5761 40 A 0.7623 0.0183 0.2195 41 I 0.7664 0.0122 0.2214 42 S 0.7960 0.0068 0.1972 43 L 0.7499 0.0248 0.2253 44 T 0.5465 0.0394 0.4141 45 E 0.2407 0.1940 0.5653 46 H 0.1415 0.2301 0.6284 47 I 0.1428 0.2990 0.5582 48 E 0.1127 0.3137 0.5737 49 Y 0.1556 0.2293 0.6150 50 R 0.1769 0.1501 0.6729 51 P 0.0864 0.3975 0.5162 52 H 0.1013 0.3764 0.5223 53 K 0.1423 0.3079 0.5499 54 Q 0.1366 0.2813 0.5821 55 D 0.1660 0.2236 0.6104 56 V 0.1547 0.2882 0.5571 57 V 0.1521 0.3366 0.5113 58 S 0.1014 0.4781 0.4205 59 D 0.0864 0.4329 0.4806 60 H 0.0846 0.5181 0.3973 61 N 0.0631 0.6259 0.3111 62 R 0.0525 0.6611 0.2864 63 S 0.0531 0.6699 0.2771 64 F 0.0144 0.8443 0.1413 65 D 0.0095 0.8961 0.0944 66 L 0.0087 0.9106 0.0808 67 C 0.0086 0.9144 0.0770 68 R 0.0084 0.9143 0.0773 69 E 0.0083 0.9215 0.0702 70 Q 0.0084 0.9143 0.0773 71 A 0.0090 0.9053 0.0857 72 E 0.0091 0.8493 0.1416 73 K 0.0154 0.7882 0.1964 74 L 0.0588 0.2797 0.6615 75 G 0.0519 0.0664 0.8817 76 I 0.2497 0.0136 0.7367 77 L 0.4975 0.0182 0.4844 78 L 0.7165 0.0124 0.2712 79 I 0.6775 0.0211 0.3014 80 K 0.6457 0.0308 0.3235 81 G 0.6365 0.0257 0.3378 82 S 0.7072 0.0180 0.2748 83 E 0.7551 0.0147 0.2302 84 I 0.7404 0.0148 0.2448 85 T 0.6356 0.0261 0.3383 86 R 0.5492 0.0710 0.3798 87 A 0.3239 0.0915 0.5846 88 M 0.2009 0.1054 0.6938 89 A 0.1820 0.0723 0.7457 90 P 0.1458 0.2178 0.6365 91 G 0.1761 0.1880 0.6358 92 H 0.3839 0.1574 0.4587 93 F 0.5186 0.1574 0.3240 94 N 0.5073 0.2107 0.2820 95 A 0.4890 0.2557 0.2553 96 I 0.4420 0.2615 0.2965 97 F 0.3849 0.2216 0.3936 98 L 0.2692 0.1963 0.5345 99 S 0.1883 0.1434 0.6684 100 D 0.0760 0.3532 0.5708 101 S 0.0794 0.2655 0.6551 102 N 0.1667 0.1408 0.6924 103 P 0.0844 0.4284 0.4872 104 L 0.0730 0.6096 0.3174 105 E 0.0883 0.6150 0.2967 106 Q 0.0687 0.6730 0.2583 107 K 0.0649 0.7022 0.2329 108 D 0.0650 0.6873 0.2476 109 Y 0.0273 0.7639 0.2088 110 K 0.0120 0.8605 0.1275 111 D 0.0097 0.9077 0.0826 112 A 0.0093 0.9124 0.0783 113 F 0.0084 0.9201 0.0716 114 R 0.0085 0.9207 0.0708 115 E 0.0085 0.9190 0.0725 116 A 0.0090 0.9064 0.0845 117 K 0.0106 0.8550 0.1344 118 K 0.0148 0.7338 0.2514 119 Q 0.0619 0.2518 0.6863 120 G 0.0581 0.0852 0.8568 121 A 0.1918 0.0666 0.7415 122 F 0.5323 0.0450 0.4227 123 M 0.6834 0.0381 0.2785 124 F 0.6861 0.0500 0.2639 125 W 0.5330 0.1054 0.3616 126 N 0.3816 0.1110 0.5074 127 H 0.2185 0.0882 0.6932 128 P 0.0958 0.3829 0.5212 129 G 0.0771 0.2367 0.6861 130 W 0.1361 0.2518 0.6121 131 D 0.1399 0.2190 0.6411 132 S 0.1035 0.3470 0.5495 133 Q 0.1223 0.2403 0.6374 134 Q 0.1792 0.1278 0.6930 135 P 0.0922 0.3194 0.5884 136 D 0.0907 0.3028 0.6064 137 T 0.1245 0.2624 0.6131 138 T 0.1079 0.4170 0.4750 139 K 0.0608 0.5153 0.4239 140 W 0.0807 0.4287 0.4906 141 W 0.0776 0.4664 0.4561 142 P 0.0151 0.8002 0.1848 143 E 0.0118 0.8690 0.1193 144 H 0.0106 0.8917 0.0977 145 T 0.0089 0.9082 0.0828 146 A 0.0088 0.9145 0.0767 147 L 0.0098 0.9016 0.0886 148 Y 0.0126 0.8820 0.1054 149 Q 0.0153 0.8339 0.1508 150 E 0.0321 0.6557 0.3122 151 G 0.0886 0.3587 0.5526 152 C 0.1446 0.1764 0.6791 153 M 0.2410 0.1397 0.6194 154 H 0.3851 0.0968 0.5181 155 G 0.6790 0.0404 0.2807 156 I 0.7773 0.0190 0.2037 157 E 0.7901 0.0155 0.1945 158 V 0.7431 0.0414 0.2155 159 A 0.5060 0.1186 0.3754 160 N 0.2548 0.1338 0.6114 161 G 0.1297 0.1768 0.6935 162 H 0.1197 0.2310 0.6494 163 L 0.1127 0.2679 0.6194 164 Y 0.1089 0.2479 0.6431 165 M 0.0965 0.3186 0.5849 166 P 0.0121 0.8256 0.1622 167 E 0.0094 0.8872 0.1034 168 A 0.0084 0.9203 0.0713 169 I 0.0083 0.9230 0.0687 170 Q 0.0083 0.9243 0.0675 171 W 0.0083 0.9217 0.0700 172 C 0.0086 0.9132 0.0782 173 L 0.0093 0.8890 0.1017 174 D 0.0157 0.7759 0.2084 175 K 0.0584 0.2440 0.6975 176 N 0.0557 0.0664 0.8778 177 L 0.2252 0.0161 0.7587 178 T 0.5135 0.0318 0.4547 179 M 0.7675 0.0122 0.2203 180 I 0.7579 0.0163 0.2258 181 G 0.6921 0.0214 0.2865 182 T 0.5042 0.0649 0.4310 183 S 0.2853 0.1248 0.5899 184 D 0.2146 0.1891 0.5963 185 I 0.1482 0.2643 0.5875 186 H 0.1643 0.1710 0.6647 187 Q 0.2122 0.1174 0.6704 188 P 0.1611 0.2438 0.5951 189 I 0.1734 0.2700 0.5566 190 Q 0.1959 0.2613 0.5427 191 T 0.1909 0.2607 0.5484 192 D 0.1880 0.2079 0.6041 193 Y 0.1920 0.2880 0.5200 194 D 0.2127 0.2240 0.5633 195 F 0.2407 0.1972 0.5621 196 E 0.1980 0.1832 0.6188 197 K 0.1397 0.2602 0.6001 198 G 0.1206 0.1980 0.6814 199 E 0.1343 0.3074 0.5584 200 H 0.1667 0.3350 0.4983 201 R 0.1890 0.4562 0.3548 202 T 0.2274 0.4911 0.2816 203 M 0.2061 0.5741 0.2198 204 T 0.2160 0.5986 0.1854 205 F 0.1992 0.6355 0.1653 206 V 0.1742 0.6583 0.1674 207 F 0.1285 0.6625 0.2090 208 A 0.0761 0.6832 0.2407 209 K 0.0638 0.6059 0.3304 210 E 0.0759 0.5003 0.4238 211 R 0.1340 0.3489 0.5170 212 S 0.1494 0.2605 0.5900 213 L 0.0464 0.6411 0.3126 214 Q 0.0269 0.7570 0.2161 215 G 0.0283 0.8072 0.1645 216 I 0.0196 0.8694 0.1110 217 R 0.0157 0.8863 0.0980 218 E 0.0165 0.8853 0.0983 219 A 0.0185 0.8641 0.1175 220 L 0.0298 0.7890 0.1812 221 D 0.0366 0.6481 0.3153 222 N 0.0622 0.4606 0.4772 223 R 0.0972 0.3502 0.5526 224 R 0.1282 0.2831 0.5887 225 T 0.2042 0.1924 0.6034 226 A 0.2234 0.1934 0.5833 227 A 0.2405 0.2376 0.5219 228 Y 0.2644 0.2100 0.5256 229 F 0.2481 0.1375 0.6144 230 H 0.2046 0.1282 0.6671