# This file is the result of combining several RDB files, specifically # T0518.t04.str2.rdb (weight 1.54425) # T0518.t04.str4.rdb (weight 0.924988) # T0518.t04.pb.rdb (weight 0.789901) # T0518.t04.bys.rdb (weight 0.748322) # T0518.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 T0518.t04.str2.rdb # ============================================ # TARGET T0518 # 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 T0518.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 878 # # ============================================ # Comments from T0518.t04.str4.rdb # ============================================ # TARGET T0518 # 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 T0518.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 878 # # ============================================ # Comments from T0518.t04.pb.rdb # ============================================ # TARGET T0518 # 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 T0518.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 878 # # ============================================ # Comments from T0518.t04.bys.rdb # ============================================ # TARGET T0518 # 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 T0518.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 878 # # ============================================ # Comments from T0518.t04.alpha.rdb # ============================================ # TARGET T0518 # 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 T0518.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 878 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2470 0.1495 0.6035 2 K 0.2040 0.1703 0.6257 3 K 0.1665 0.3273 0.5062 4 V 0.1656 0.2934 0.5410 5 F 0.2509 0.1807 0.5684 6 Y 0.2574 0.1692 0.5734 7 P 0.2286 0.3678 0.4037 8 L 0.2476 0.4351 0.3174 9 A 0.2825 0.4394 0.2781 10 C 0.3220 0.4298 0.2482 11 C 0.3171 0.4728 0.2101 12 C 0.3042 0.4841 0.2117 13 L 0.2026 0.5599 0.2375 14 A 0.1602 0.5031 0.3367 15 A 0.1196 0.3692 0.5112 16 G 0.1063 0.3054 0.5883 17 V 0.2190 0.3467 0.4343 18 F 0.2639 0.4004 0.3357 19 A 0.2383 0.4408 0.3209 20 S 0.2139 0.3824 0.4037 21 C 0.1695 0.2749 0.5556 22 G 0.1189 0.1782 0.7029 23 G 0.1061 0.2069 0.6871 24 Q 0.1383 0.3399 0.5218 25 K 0.1656 0.4182 0.4162 26 K 0.1596 0.4768 0.3637 27 A 0.1306 0.5376 0.3318 28 N 0.1264 0.4537 0.4199 29 A 0.1173 0.4537 0.4290 30 Q 0.1430 0.3467 0.5103 31 E 0.1494 0.3177 0.5328 32 E 0.1651 0.2215 0.6134 33 P 0.0781 0.5160 0.4059 34 S 0.0641 0.6592 0.2767 35 K 0.0629 0.7611 0.1760 36 V 0.0818 0.7748 0.1434 37 A 0.0758 0.7983 0.1259 38 L 0.0885 0.7826 0.1288 39 S 0.0899 0.7654 0.1447 40 Y 0.1044 0.6971 0.1985 41 S 0.1038 0.6543 0.2418 42 K 0.1026 0.6056 0.2918 43 S 0.1339 0.4963 0.3699 44 L 0.1663 0.3795 0.4542 45 K 0.2004 0.2286 0.5710 46 A 0.2067 0.1084 0.6849 47 P 0.1467 0.2257 0.6277 48 E 0.1412 0.2993 0.5594 49 T 0.1504 0.3040 0.5456 50 D 0.1345 0.2941 0.5714 51 S 0.1389 0.3363 0.5248 52 L 0.1628 0.2490 0.5882 53 N 0.1872 0.1312 0.6816 54 L 0.2341 0.0958 0.6700 55 P 0.2127 0.1172 0.6701 56 V 0.2428 0.1736 0.5836 57 D 0.1767 0.1139 0.7094 58 E 0.0618 0.4090 0.5292 59 N 0.0773 0.2089 0.7138 60 G 0.1304 0.1170 0.7526 61 Y 0.4271 0.0641 0.5088 62 I 0.6144 0.0565 0.3292 63 T 0.6289 0.0617 0.3094 64 I 0.5476 0.1199 0.3325 65 F 0.4827 0.1171 0.4001 66 D 0.2827 0.1005 0.6168 67 G 0.1332 0.1415 0.7253 68 E 0.2820 0.1447 0.5733 69 T 0.3229 0.1117 0.5654 70 F 0.1986 0.2553 0.5461 71 N 0.1639 0.1940 0.6422 72 G 0.1874 0.1480 0.6646 73 W 0.3532 0.1424 0.5044 74 R 0.4932 0.1042 0.4026 75 G 0.4294 0.1027 0.4680 76 Y 0.3386 0.1185 0.5429 77 G 0.2117 0.0933 0.6950 78 K 0.1715 0.1659 0.6625 79 D 0.1798 0.1622 0.6580 80 R 0.2272 0.1057 0.6671 81 V 0.3100 0.0398 0.6501 82 P 0.2915 0.0630 0.6455 83 T 0.3639 0.0870 0.5491 84 K 0.5504 0.0387 0.4109 85 W 0.7018 0.0146 0.2836 86 T 0.7419 0.0093 0.2488 87 I 0.7047 0.0138 0.2815 88 E 0.5910 0.0464 0.3626 89 D 0.3202 0.0463 0.6335 90 G 0.3913 0.0355 0.5732 91 C 0.6952 0.0093 0.2956 92 I 0.7697 0.0061 0.2242 93 K 0.8096 0.0059 0.1845 94 F 0.7977 0.0072 0.1951 95 N 0.6985 0.0258 0.2757 96 G 0.5348 0.0340 0.4312 97 S 0.3243 0.0799 0.5958 98 G 0.1704 0.1018 0.7278 99 G 0.1379 0.1092 0.7528 100 G 0.1670 0.1053 0.7277 101 E 0.2540 0.1276 0.6184 102 A 0.2795 0.1195 0.6010 103 Q 0.2534 0.1524 0.5942 104 D 0.2116 0.1203 0.6681 105 G 0.1710 0.1245 0.7045 106 D 0.1767 0.1470 0.6763 107 G 0.2263 0.1013 0.6723 108 G 0.3830 0.0731 0.5439 109 D 0.6004 0.0624 0.3371 110 L 0.7171 0.0431 0.2397 111 I 0.7146 0.0457 0.2397 112 F 0.6392 0.0473 0.3136 113 A 0.4666 0.1687 0.3648 114 H 0.4012 0.1683 0.4306 115 K 0.3899 0.1394 0.4707 116 F 0.3509 0.1076 0.5415 117 K 0.2905 0.1260 0.5835 118 N 0.3676 0.0766 0.5558 119 F 0.6609 0.0147 0.3244 120 E 0.7685 0.0070 0.2245 121 L 0.8081 0.0048 0.1871 122 E 0.8193 0.0054 0.1753 123 L 0.8193 0.0044 0.1763 124 E 0.8088 0.0072 0.1839 125 W 0.7989 0.0061 0.1951 126 K 0.7759 0.0095 0.2146 127 V 0.6987 0.0141 0.2872 128 A 0.4770 0.0609 0.4621 129 K 0.2097 0.1490 0.6413 130 G 0.1586 0.1031 0.7384 131 S 0.1774 0.1610 0.6617 132 N 0.1938 0.1593 0.6469 133 S 0.2749 0.1239 0.6013 134 G 0.4759 0.0679 0.4562 135 I 0.6779 0.0436 0.2785 136 L 0.7183 0.0327 0.2491 137 Y 0.7169 0.0466 0.2365 138 L 0.6400 0.0821 0.2779 139 A 0.5598 0.1026 0.3376 140 Q 0.4185 0.1611 0.4204 141 E 0.3677 0.1574 0.4749 142 V 0.2751 0.1612 0.5637 143 T 0.1993 0.1870 0.6137 144 S 0.1803 0.1748 0.6449 145 K 0.1644 0.2044 0.6312 146 D 0.1706 0.1569 0.6725 147 K 0.1427 0.2483 0.6090 148 D 0.1248 0.1683 0.7069 149 G 0.1047 0.1376 0.7577 150 N 0.1669 0.1325 0.7006 151 D 0.1950 0.1717 0.6332 152 V 0.2508 0.2016 0.5476 153 L 0.3242 0.1572 0.5187 154 E 0.4238 0.1112 0.4651 155 P 0.3896 0.1708 0.4396 156 I 0.4155 0.1456 0.4389 157 Y 0.4038 0.0951 0.5011 158 I 0.2771 0.1628 0.5600 159 S 0.2109 0.1234 0.6658 160 A 0.2724 0.0664 0.6612 161 P 0.2644 0.1747 0.5609 162 E 0.4623 0.1838 0.3539 163 Y 0.6630 0.0635 0.2735 164 Q 0.6746 0.0492 0.2761 165 I 0.6472 0.0844 0.2684 166 L 0.4823 0.1719 0.3458 167 D 0.2781 0.2174 0.5045 168 N 0.1742 0.2371 0.5887 169 A 0.1176 0.2430 0.6394 170 N 0.1137 0.1515 0.7348 171 H 0.2207 0.0603 0.7190 172 P 0.1586 0.2536 0.5879 173 D 0.1815 0.2117 0.6069 174 A 0.2152 0.2566 0.5282 175 K 0.2698 0.2289 0.5012 176 L 0.2790 0.1533 0.5677 177 G 0.2101 0.0978 0.6921 178 K 0.2605 0.1203 0.6192 179 D 0.2140 0.1560 0.6300 180 N 0.1452 0.2002 0.6546 181 N 0.1364 0.2294 0.6343 182 R 0.1893 0.2129 0.5977 183 Q 0.2436 0.1987 0.5577 184 S 0.2575 0.2018 0.5406 185 A 0.2636 0.2489 0.4875 186 S 0.3197 0.2759 0.4044 187 L 0.3056 0.3190 0.3754 188 Y 0.3182 0.2502 0.4316 189 D 0.2406 0.2184 0.5410 190 M 0.2370 0.1660 0.5969 191 I 0.2530 0.0650 0.6820 192 P 0.2058 0.1113 0.6829 193 A 0.2088 0.1300 0.6612 194 V 0.2142 0.0724 0.7134 195 P 0.1508 0.2273 0.6219 196 Q 0.1393 0.2728 0.5879 197 N 0.2047 0.1826 0.6127 198 S 0.2460 0.1032 0.6508 199 K 0.2677 0.0336 0.6987 200 P 0.1980 0.0593 0.7427 201 F 0.1305 0.1932 0.6763 202 G 0.0881 0.1373 0.7746 203 E 0.3351 0.0769 0.5879 204 W 0.5910 0.0356 0.3734 205 N 0.6562 0.0320 0.3118 206 K 0.7750 0.0110 0.2139 207 A 0.8006 0.0067 0.1927 208 K 0.8206 0.0047 0.1747 209 I 0.8246 0.0044 0.1710 210 M 0.8148 0.0065 0.1787 211 V 0.7643 0.0077 0.2280 212 Y 0.6689 0.0257 0.3054 213 K 0.3294 0.0406 0.6300 214 G 0.2163 0.0685 0.7152 215 T 0.6258 0.0167 0.3575 216 V 0.7423 0.0080 0.2497 217 V 0.7923 0.0090 0.1988 218 H 0.8083 0.0081 0.1836 219 G 0.7444 0.0135 0.2421 220 Q 0.7066 0.0336 0.2598 221 N 0.4772 0.0390 0.4838 222 D 0.2168 0.0615 0.7217 223 E 0.5272 0.0426 0.4302 224 N 0.6199 0.0390 0.3411 225 V 0.6836 0.0363 0.2802 226 L 0.6907 0.0431 0.2662 227 E 0.6930 0.0412 0.2658 228 Y 0.6246 0.0630 0.3124 229 H 0.5188 0.0812 0.4000 230 L 0.3491 0.1445 0.5064 231 W 0.2486 0.1798 0.5716 232 T 0.2342 0.1755 0.5903 233 K 0.1219 0.4233 0.4549 234 Q 0.1123 0.4530 0.4347 235 W 0.1168 0.4493 0.4339 236 T 0.0898 0.4424 0.4678 237 D 0.0879 0.4804 0.4318 238 M 0.1549 0.4832 0.3619 239 L 0.2097 0.4510 0.3393 240 Q 0.1641 0.4703 0.3656 241 A 0.1721 0.3578 0.4701 242 S 0.1687 0.2660 0.5653 243 K 0.0985 0.4251 0.4764 244 F 0.1584 0.3246 0.5170 245 S 0.1704 0.3107 0.5189 246 E 0.1511 0.3376 0.5113 247 D 0.1357 0.2617 0.6026 248 K 0.1235 0.2196 0.6570 249 W 0.1832 0.1570 0.6598 250 P 0.1882 0.2859 0.5259 251 L 0.2040 0.3643 0.4317 252 A 0.1902 0.3964 0.4134 253 F 0.1731 0.4336 0.3933 254 E 0.1622 0.4365 0.4013 255 L 0.1762 0.3973 0.4265 256 L 0.1631 0.3407 0.4962 257 N 0.1367 0.2847 0.5787 258 N 0.1366 0.2618 0.6016 259 C 0.1157 0.1827 0.7016 260 G 0.0955 0.1079 0.7966 261 G 0.1662 0.0890 0.7448 262 E 0.2471 0.1141 0.6388 263 N 0.2371 0.1092 0.6537 264 H 0.1965 0.1937 0.6098 265 E 0.2188 0.1665 0.6147 266 G 0.2956 0.0849 0.6195 267 F 0.5452 0.0622 0.3925 268 I 0.7054 0.0396 0.2550 269 G 0.7259 0.0345 0.2396 270 L 0.7084 0.0499 0.2417 271 Q 0.6084 0.0688 0.3228 272 D 0.3822 0.1389 0.4788 273 H 0.1655 0.1197 0.7149 274 G 0.1233 0.0813 0.7954 275 D 0.2045 0.0702 0.7253 276 D 0.4205 0.0834 0.4961 277 V 0.6462 0.0404 0.3134 278 W 0.7153 0.0259 0.2589 279 F 0.7378 0.0152 0.2470 280 R 0.6540 0.0415 0.3045 281 N 0.6886 0.0144 0.2970 282 I 0.6908 0.0078 0.3014 283 R 0.7119 0.0110 0.2771 284 V 0.7136 0.0090 0.2774 285 K 0.6988 0.0183 0.2828 286 V 0.6603 0.0157 0.3240 287 L 0.3635 0.0389 0.5976 288 D 0.2181 0.0677 0.7142