# This file is the result of combining several RDB files, specifically # T0427.t04.str2.rdb (weight 1.54425) # T0427.t04.str4.rdb (weight 0.924988) # T0427.t04.pb.rdb (weight 0.789901) # T0427.t04.bys.rdb (weight 0.748322) # T0427.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 T0427.t04.str2.rdb # ============================================ # TARGET T0427 # 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 T0427.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 2499 # # ============================================ # Comments from T0427.t04.str4.rdb # ============================================ # TARGET T0427 # 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 T0427.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 2499 # # ============================================ # Comments from T0427.t04.pb.rdb # ============================================ # TARGET T0427 # 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 T0427.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 2499 # # ============================================ # Comments from T0427.t04.bys.rdb # ============================================ # TARGET T0427 # 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 T0427.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 2499 # # ============================================ # Comments from T0427.t04.alpha.rdb # ============================================ # TARGET T0427 # 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 T0427.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 2499 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.5184 0.0188 0.4628 2 S 0.6463 0.0192 0.3345 3 V 0.7697 0.0094 0.2209 4 Q 0.7389 0.0117 0.2494 5 L 0.5550 0.0208 0.4243 6 V 0.3460 0.1002 0.5538 7 K 0.1654 0.0922 0.7424 8 G 0.1567 0.0576 0.7857 9 V 0.4672 0.0101 0.5227 10 N 0.7077 0.0070 0.2853 11 L 0.8092 0.0046 0.1863 12 H 0.8022 0.0068 0.1910 13 V 0.7759 0.0059 0.2182 14 I 0.6784 0.0129 0.3087 15 P 0.4621 0.0317 0.5062 16 T 0.2541 0.0646 0.6813 17 E 0.0554 0.3360 0.6086 18 K 0.0750 0.2449 0.6800 19 Y 0.2316 0.1193 0.6491 20 K 0.3220 0.1166 0.5614 21 T 0.6067 0.0542 0.3391 22 V 0.7296 0.0176 0.2528 23 R 0.7952 0.0100 0.1948 24 L 0.8241 0.0051 0.1708 25 L 0.8226 0.0045 0.1729 26 V 0.8263 0.0046 0.1691 27 R 0.8085 0.0054 0.1861 28 F 0.7380 0.0152 0.2468 29 N 0.4962 0.0368 0.4670 30 T 0.3020 0.1105 0.5874 31 R 0.1945 0.1188 0.6868 32 L 0.1902 0.1808 0.6290 33 N 0.1475 0.2779 0.5747 34 H 0.1398 0.2865 0.5737 35 E 0.1207 0.3710 0.5083 36 T 0.1030 0.3925 0.5044 37 I 0.0478 0.5997 0.3526 38 T 0.0414 0.7013 0.2572 39 K 0.0154 0.8439 0.1406 40 R 0.0092 0.9082 0.0825 41 T 0.0088 0.9173 0.0739 42 L 0.0085 0.9208 0.0708 43 L 0.0084 0.9190 0.0726 44 S 0.0084 0.9191 0.0725 45 S 0.0084 0.9164 0.0752 46 L 0.0097 0.8878 0.1024 47 M 0.0123 0.8561 0.1316 48 E 0.0228 0.7611 0.2161 49 T 0.0621 0.3714 0.5665 50 N 0.0641 0.1871 0.7488 51 S 0.1296 0.2279 0.6425 52 L 0.0867 0.3655 0.5478 53 N 0.1024 0.2226 0.6750 54 Y 0.1885 0.1195 0.6921 55 P 0.1209 0.2599 0.6192 56 N 0.1233 0.2779 0.5988 57 Q 0.0232 0.6933 0.2835 58 V 0.0128 0.8281 0.1590 59 K 0.0122 0.8939 0.0940 60 L 0.0099 0.8964 0.0937 61 S 0.0084 0.9173 0.0743 62 E 0.0083 0.9214 0.0702 63 R 0.0084 0.9194 0.0723 64 L 0.0086 0.9075 0.0839 65 A 0.0087 0.9019 0.0894 66 E 0.0099 0.8642 0.1258 67 L 0.0240 0.7049 0.2712 68 Y 0.0671 0.3547 0.5782 69 G 0.0688 0.2455 0.6857 70 A 0.1719 0.2536 0.5745 71 S 0.2463 0.2488 0.5049 72 F 0.3134 0.2062 0.4804 73 G 0.2876 0.1456 0.5668 74 I 0.3921 0.1222 0.4856 75 G 0.4061 0.1102 0.4837 76 V 0.4528 0.0730 0.4741 77 S 0.3196 0.0710 0.6094 78 K 0.1875 0.2490 0.5635 79 K 0.1337 0.1847 0.6816 80 G 0.0815 0.1228 0.7957 81 N 0.2095 0.0949 0.6956 82 Q 0.3412 0.0920 0.5668 83 H 0.4678 0.0740 0.4582 84 W 0.6413 0.0350 0.3237 85 F 0.7521 0.0171 0.2309 86 N 0.7909 0.0119 0.1972 87 I 0.8084 0.0083 0.1833 88 S 0.7897 0.0104 0.1999 89 M 0.7713 0.0168 0.2119 90 N 0.6979 0.0375 0.2646 91 I 0.6003 0.0596 0.3401 92 V 0.3827 0.1303 0.4869 93 N 0.2038 0.1838 0.6124 94 D 0.0635 0.4083 0.5282 95 H 0.0589 0.4113 0.5298 96 Y 0.1059 0.3841 0.5099 97 L 0.1344 0.3707 0.4949 98 Q 0.1328 0.3337 0.5335 99 D 0.1464 0.2754 0.5782 100 S 0.0202 0.6837 0.2962 101 Q 0.0154 0.7553 0.2293 102 V 0.0159 0.8401 0.1441 103 L 0.0093 0.8882 0.1025 104 A 0.0084 0.9133 0.0783 105 E 0.0084 0.9145 0.0771 106 A 0.0084 0.9215 0.0701 107 V 0.0083 0.9221 0.0696 108 D 0.0083 0.9194 0.0722 109 F 0.0083 0.9230 0.0687 110 L 0.0084 0.9184 0.0732 111 K 0.0084 0.9153 0.0763 112 E 0.0088 0.8967 0.0945 113 I 0.0113 0.8662 0.1225 114 I 0.0272 0.7567 0.2161 115 F 0.0559 0.5623 0.3817 116 A 0.1354 0.2850 0.5796 117 P 0.0562 0.4930 0.4508 118 N 0.0661 0.5130 0.4210 119 I 0.0868 0.5759 0.3373 120 Q 0.0915 0.5077 0.4009 121 A 0.0840 0.2993 0.6167 122 G 0.0496 0.1683 0.7820 123 Q 0.1767 0.1296 0.6938 124 F 0.2451 0.0772 0.6777 125 E 0.1854 0.0697 0.7448 126 A 0.0162 0.7309 0.2529 127 E 0.0107 0.8451 0.1442 128 T 0.0126 0.8871 0.1002 129 F 0.0128 0.8993 0.0879 130 Q 0.0099 0.9139 0.0762 131 R 0.0094 0.9178 0.0728 132 E 0.0096 0.9113 0.0790 133 K 0.0086 0.9168 0.0746 134 E 0.0087 0.9206 0.0707 135 N 0.0092 0.9204 0.0704 136 L 0.0085 0.9228 0.0688 137 K 0.0085 0.9218 0.0697 138 A 0.0084 0.9234 0.0683 139 Y 0.0085 0.9192 0.0722 140 L 0.0090 0.9095 0.0816 141 E 0.0095 0.8988 0.0917 142 S 0.0135 0.8462 0.1402 143 I 0.0379 0.7209 0.2412 144 V 0.0527 0.5792 0.3681 145 E 0.0646 0.4398 0.4956 146 D 0.1318 0.2367 0.6315 147 K 0.0172 0.7090 0.2738 148 Q 0.0123 0.8248 0.1629 149 T 0.0123 0.8941 0.0936 150 Y 0.0114 0.9070 0.0816 151 A 0.0096 0.9130 0.0774 152 S 0.0085 0.9201 0.0714 153 L 0.0083 0.9214 0.0703 154 A 0.0084 0.9193 0.0723 155 L 0.0087 0.9091 0.0822 156 Q 0.0089 0.9017 0.0894 157 S 0.0096 0.8855 0.1050 158 V 0.0149 0.8384 0.1468 159 Y 0.0370 0.6759 0.2871 160 F 0.0685 0.5119 0.4196 161 N 0.0662 0.3970 0.5367 162 Q 0.0852 0.2632 0.6515 163 S 0.1636 0.1376 0.6988 164 E 0.0517 0.4691 0.4792 165 D 0.0644 0.3694 0.5661 166 Q 0.1456 0.2583 0.5961 167 K 0.2048 0.1465 0.6486 168 I 0.3069 0.0685 0.6246 169 P 0.2343 0.1175 0.6482 170 S 0.1955 0.2749 0.5296 171 F 0.1591 0.2278 0.6131 172 G 0.1769 0.1129 0.7102 173 T 0.1829 0.1099 0.7072 174 V 0.0273 0.7012 0.2716 175 A 0.0168 0.8186 0.1646 176 A 0.0171 0.8568 0.1261 177 L 0.0180 0.8251 0.1568 178 A 0.0187 0.7661 0.2151 179 E 0.0320 0.6254 0.3427 180 E 0.1023 0.4197 0.4780 181 T 0.1474 0.1599 0.6928 182 A 0.0113 0.7501 0.2386 183 A 0.0091 0.8712 0.1197 184 S 0.0085 0.9203 0.0712 185 L 0.0084 0.9219 0.0697 186 A 0.0083 0.9233 0.0684 187 A 0.0083 0.9242 0.0675 188 Y 0.0083 0.9224 0.0692 189 Y 0.0085 0.9172 0.0743 190 Q 0.0089 0.9093 0.0818 191 K 0.0119 0.8668 0.1212 192 M 0.0334 0.7160 0.2505 193 L 0.0981 0.4193 0.4826 194 A 0.1514 0.1585 0.6901 195 E 0.0582 0.3788 0.5630 196 D 0.0610 0.2265 0.7125 197 Q 0.1688 0.0872 0.7441 198 V 0.5084 0.0125 0.4791 199 D 0.7233 0.0086 0.2681 200 I 0.8188 0.0043 0.1770 201 F 0.8146 0.0055 0.1799 202 V 0.7956 0.0055 0.1989 203 L 0.6851 0.0220 0.2929 204 G 0.4595 0.0367 0.5038 205 D 0.2427 0.0449 0.7124 206 V 0.2366 0.0816 0.6818 207 N 0.1789 0.0240 0.7972 208 E 0.0137 0.7279 0.2584 209 A 0.0097 0.8490 0.1413 210 E 0.0091 0.8953 0.0956 211 L 0.0097 0.8865 0.1038 212 V 0.0092 0.9072 0.0836 213 P 0.0085 0.9068 0.0846 214 L 0.0088 0.9016 0.0895 215 F 0.0102 0.8848 0.1050 216 K 0.0110 0.8054 0.1837 217 Q 0.0285 0.6076 0.3639 218 L 0.1094 0.2828 0.6079 219 P 0.0899 0.3353 0.5747 220 F 0.1387 0.2246 0.6366 221 T 0.1842 0.1082 0.7077 222 P 0.1562 0.2485 0.5953 223 R 0.1852 0.2568 0.5581 224 E 0.1364 0.3201 0.5435 225 E 0.1150 0.3044 0.5806 226 G 0.1041 0.1865 0.7094 227 K 0.1778 0.1608 0.6613 228 A 0.2620 0.1480 0.5900 229 A 0.2709 0.1823 0.5469 230 I 0.2964 0.1802 0.5234 231 F 0.2725 0.1600 0.5675 232 Y 0.2516 0.1462 0.6023 233 N 0.2334 0.0999 0.6668 234 Q 0.2521 0.0569 0.6910 235 P 0.2439 0.0767 0.6794 236 I 0.2452 0.1442 0.6106 237 R 0.2227 0.1679 0.6094 238 N 0.2424 0.1502 0.6074 239 V 0.2875 0.1349 0.5775 240 I 0.3179 0.1733 0.5088 241 E 0.3974 0.1724 0.4302 242 E 0.5471 0.1197 0.3332 243 R 0.6185 0.0832 0.2983 244 T 0.6259 0.0754 0.2987 245 E 0.5657 0.1022 0.3321 246 R 0.4418 0.1508 0.4074 247 E 0.3701 0.1409 0.4889 248 V 0.2803 0.2093 0.5104 249 L 0.2238 0.2931 0.4831 250 A 0.1657 0.4014 0.4330 251 Q 0.1950 0.4038 0.4013 252 S 0.2933 0.3276 0.3791 253 K 0.5326 0.1829 0.2845 254 L 0.6942 0.0685 0.2372 255 N 0.7082 0.0619 0.2299 256 L 0.7507 0.0447 0.2046 257 A 0.6708 0.0565 0.2727 258 Y 0.6064 0.0461 0.3474 259 N 0.3839 0.0712 0.5449 260 T 0.3084 0.1058 0.5858 261 D 0.2266 0.1205 0.6529 262 I 0.1725 0.2769 0.5506 263 Y 0.1665 0.2373 0.5963 264 Y 0.1634 0.2085 0.6281 265 G 0.1263 0.1462 0.7275 266 D 0.1629 0.1965 0.6406 267 S 0.0267 0.5948 0.3786 268 Y 0.0212 0.6966 0.2823 269 Y 0.0232 0.8155 0.1613 270 F 0.0202 0.8684 0.1115 271 A 0.0155 0.8917 0.0928 272 L 0.0106 0.9135 0.0759 273 Q 0.0093 0.9192 0.0715 274 V 0.0090 0.9186 0.0723 275 F 0.0108 0.8985 0.0907 276 N 0.0122 0.8860 0.1018 277 G 0.0174 0.8258 0.1568 278 I 0.0355 0.7060 0.2585 279 F 0.0754 0.4377 0.4869 280 G 0.0805 0.2314 0.6881 281 G 0.0851 0.1537 0.7612 282 F 0.1511 0.1237 0.7252 283 P 0.0904 0.3197 0.5900 284 H 0.0858 0.4131 0.5011 285 S 0.0622 0.6061 0.3317 286 K 0.0306 0.7759 0.1934 287 L 0.0245 0.8409 0.1345 288 F 0.0269 0.8663 0.1068 289 M 0.0273 0.8704 0.1022 290 N 0.0475 0.8222 0.1303 291 V 0.0708 0.7914 0.1378 292 R 0.1005 0.7395 0.1600 293 E 0.0991 0.6998 0.2011 294 K 0.0975 0.5718 0.3307 295 E 0.0961 0.3732 0.5307 296 H 0.1323 0.2574 0.6103 297 L 0.2748 0.2452 0.4801 298 A 0.4393 0.1982 0.3625 299 Y 0.5505 0.1453 0.3042 300 Y 0.5629 0.1234 0.3137 301 A 0.5010 0.1604 0.3386 302 S 0.4122 0.1752 0.4126 303 S 0.3462 0.2072 0.4466 304 S 0.2962 0.2247 0.4792 305 I 0.2823 0.2407 0.4770 306 D 0.2401 0.2176 0.5423 307 T 0.1751 0.2913 0.5336 308 F 0.1802 0.2163 0.6035 309 R 0.2088 0.1340 0.6573 310 G 0.3001 0.0697 0.6302 311 F 0.5755 0.0476 0.3769 312 M 0.7641 0.0168 0.2191 313 T 0.8023 0.0076 0.1901 314 V 0.8006 0.0102 0.1892 315 Q 0.7487 0.0179 0.2334 316 T 0.6636 0.0327 0.3036 317 G 0.4554 0.0467 0.4979 318 I 0.3418 0.0788 0.5793 319 D 0.1877 0.0565 0.7558 320 G 0.0551 0.3574 0.5875 321 K 0.0516 0.4055 0.5430 322 N 0.1153 0.3580 0.5267 323 R 0.0141 0.7633 0.2226 324 N 0.0093 0.8754 0.1153 325 Q 0.0083 0.9222 0.0694 326 V 0.0083 0.9238 0.0679 327 L 0.0083 0.9242 0.0675 328 R 0.0083 0.9251 0.0666 329 L 0.0083 0.9242 0.0675 330 I 0.0083 0.9225 0.0692 331 S 0.0083 0.9224 0.0693 332 T 0.0083 0.9230 0.0687 333 E 0.0083 0.9227 0.0690 334 L 0.0084 0.9194 0.0722 335 E 0.0083 0.9202 0.0715 336 N 0.0087 0.9069 0.0845 337 I 0.0108 0.8916 0.0976 338 R 0.0159 0.8188 0.1653 339 L 0.0475 0.4962 0.4563 340 G 0.0430 0.1731 0.7839 341 K 0.0994 0.1043 0.7963 342 I 0.1823 0.0844 0.7332 343 R 0.1538 0.0902 0.7559 344 E 0.0144 0.7433 0.2422 345 L 0.0096 0.8655 0.1248 346 E 0.0094 0.9173 0.0733 347 I 0.0083 0.9216 0.0701 348 E 0.0083 0.9233 0.0684 349 Q 0.0083 0.9237 0.0680 350 T 0.0083 0.9229 0.0688 351 K 0.0083 0.9229 0.0689 352 A 0.0083 0.9228 0.0689 353 M 0.0084 0.9211 0.0705 354 L 0.0087 0.9168 0.0745 355 K 0.0086 0.9103 0.0811 356 N 0.0105 0.8742 0.1153 357 Q 0.0166 0.8412 0.1422 358 Y 0.0278 0.8248 0.1475 359 I 0.0334 0.8210 0.1457 360 L 0.0591 0.7328 0.2081 361 A 0.0994 0.5593 0.3413 362 L 0.0736 0.5279 0.3985 363 D 0.0828 0.3947 0.5225 364 N 0.1179 0.2794 0.6026 365 A 0.0377 0.5958 0.3665 366 G 0.0215 0.7549 0.2236 367 A 0.0164 0.8681 0.1154 368 W 0.0134 0.8878 0.0988 369 L 0.0116 0.9016 0.0868 370 E 0.0098 0.9086 0.0816 371 K 0.0092 0.9083 0.0825 372 E 0.0105 0.9037 0.0858 373 Y 0.0120 0.8890 0.0990 374 L 0.0129 0.8651 0.1221 375 N 0.0166 0.8344 0.1490 376 E 0.0307 0.7550 0.2143 377 L 0.0760 0.5005 0.4236 378 M 0.1477 0.2337 0.6186 379 P 0.1056 0.2760 0.6184 380 Q 0.1322 0.1980 0.6698 381 T 0.1628 0.1606 0.6765 382 M 0.0624 0.5602 0.3774 383 L 0.0538 0.6380 0.3082 384 T 0.0893 0.6098 0.3008 385 A 0.0126 0.8125 0.1749 386 E 0.0092 0.8812 0.1096 387 E 0.0085 0.9216 0.0699 388 W 0.0084 0.9219 0.0697 389 I 0.0083 0.9199 0.0717 390 A 0.0084 0.9189 0.0727 391 R 0.0088 0.9126 0.0786 392 I 0.0108 0.8647 0.1245 393 N 0.0139 0.6807 0.3054 394 A 0.0468 0.4160 0.5371 395 V 0.1737 0.1398 0.6865 396 T 0.1653 0.0296 0.8051 397 I 0.0264 0.6526 0.3210 398 P 0.0095 0.8625 0.1280 399 E 0.0088 0.9145 0.0767 400 I 0.0084 0.9227 0.0689 401 Q 0.0083 0.9229 0.0687 402 E 0.0083 0.9248 0.0670 403 V 0.0083 0.9243 0.0674 404 A 0.0083 0.9206 0.0710 405 K 0.0085 0.9103 0.0812 406 R 0.0105 0.8679 0.1216 407 L 0.0331 0.7193 0.2476 408 E 0.0528 0.4795 0.4678 409 L 0.0644 0.4287 0.5070 410 Q 0.0967 0.2820 0.6212 411 A 0.2248 0.1395 0.6357 412 I 0.5003 0.0526 0.4471 413 F 0.7092 0.0155 0.2753 414 F 0.7790 0.0085 0.2124 415 L 0.7696 0.0095 0.2209 416 E 0.6615 0.0314 0.3071 417 G 0.4133 0.0256 0.5611 418 E 0.2483 0.1366 0.6152 419 T 0.2427 0.1283 0.6291 420 E 0.2033 0.1860 0.6107 421 N 0.1677 0.1728 0.6595 422 D 0.1516 0.2014 0.6471