# This file is the result of combining several RDB files, specifically # T0407.t2k.str2.rdb (weight 1.54425) # T0407.t2k.str4.rdb (weight 0.924988) # T0407.t2k.pb.rdb (weight 0.789901) # T0407.t2k.bys.rdb (weight 0.748322) # T0407.t2k.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.t2k.str2.rdb # ============================================ # TARGET T0407 # Using neural net dunbrack-40pc-3157-t2k-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.t2k-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 419 # # ============================================ # Comments from T0407.t2k.str4.rdb # ============================================ # TARGET T0407 # Using neural net dunbrack-40pc-3157-t2k-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.t2k-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 419 # # ============================================ # Comments from T0407.t2k.pb.rdb # ============================================ # TARGET T0407 # Using neural net dunbrack-40pc-3157-t2k-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.t2k-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 419 # # ============================================ # Comments from T0407.t2k.bys.rdb # ============================================ # TARGET T0407 # Using neural net dunbrack-40pc-3157-t2k-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.t2k-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 419 # # ============================================ # Comments from T0407.t2k.alpha.rdb # ============================================ # TARGET T0407 # Using neural net dunbrack-40pc-3157-t2k-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.t2k-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 419 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.4504 0.1087 0.4409 2 E 0.5077 0.1337 0.3587 3 V 0.5079 0.2160 0.2761 4 K 0.4408 0.2883 0.2709 5 K 0.4427 0.2563 0.3010 6 V 0.3870 0.1897 0.4234 7 L 0.3275 0.1078 0.5647 8 V 0.3244 0.0737 0.6019 9 S 0.2885 0.1299 0.5816 10 A 0.2991 0.1493 0.5516 11 F 0.3317 0.0872 0.5811 12 L 0.2552 0.0927 0.6522 13 L 0.1965 0.2887 0.5148 14 T 0.2298 0.3141 0.4561 15 T 0.2815 0.2693 0.4493 16 C 0.2689 0.2414 0.4897 17 L 0.1327 0.4139 0.4535 18 M 0.1034 0.3376 0.5590 19 S 0.0899 0.2927 0.6173 20 G 0.0701 0.3553 0.5747 21 Q 0.1263 0.4097 0.4640 22 A 0.1294 0.5359 0.3348 23 Q 0.0873 0.6424 0.2703 24 R 0.0789 0.6395 0.2816 25 R 0.0778 0.5687 0.3535 26 N 0.0908 0.4179 0.4913 27 E 0.1397 0.3030 0.5573 28 I 0.2241 0.1864 0.5896 29 Q 0.2619 0.1235 0.6146 30 V 0.2759 0.0563 0.6678 31 P 0.2045 0.1399 0.6556 32 D 0.1952 0.1323 0.6725 33 L 0.1703 0.2074 0.6223 34 D 0.1283 0.2020 0.6696 35 G 0.1214 0.1447 0.7339 36 Y 0.2561 0.1112 0.6327 37 T 0.3693 0.0839 0.5468 38 T 0.5326 0.0576 0.4097 39 L 0.6271 0.0389 0.3339 40 K 0.6792 0.0287 0.2921 41 C 0.6762 0.0329 0.2908 42 D 0.6156 0.0462 0.3383 43 F 0.6015 0.0984 0.3000 44 H 0.5797 0.0982 0.3221 45 M 0.5743 0.1041 0.3216 46 H 0.5034 0.0951 0.4014 47 S 0.4579 0.1211 0.4211 48 V 0.3747 0.1840 0.4414 49 F 0.3246 0.1685 0.5068 50 S 0.2377 0.1836 0.5787 51 D 0.1213 0.1998 0.6789 52 G 0.0855 0.1410 0.7735 53 L 0.1777 0.1304 0.6920 54 V 0.2198 0.1254 0.6547 55 W 0.1672 0.0837 0.7491 56 P 0.0224 0.6899 0.2877 57 T 0.0121 0.8299 0.1580 58 V 0.0092 0.9090 0.0818 59 R 0.0087 0.9190 0.0723 60 V 0.0084 0.9170 0.0746 61 D 0.0083 0.9238 0.0679 62 E 0.0083 0.9245 0.0673 63 A 0.0083 0.9231 0.0687 64 Y 0.0085 0.9057 0.0858 65 R 0.0107 0.8349 0.1543 66 D 0.0520 0.2387 0.7092 67 G 0.0491 0.0671 0.8838 68 L 0.2091 0.0418 0.7491 69 D 0.3709 0.0847 0.5444 70 A 0.7340 0.0412 0.2248 71 I 0.7470 0.0248 0.2282 72 S 0.7723 0.0199 0.2078 73 L 0.7341 0.0358 0.2301 74 T 0.6051 0.0387 0.3561 75 E 0.3139 0.1448 0.5413 76 H 0.2304 0.1921 0.5775 77 I 0.1618 0.3296 0.5086 78 E 0.1655 0.3094 0.5250 79 Y 0.1959 0.2099 0.5942 80 R 0.1961 0.1525 0.6514 81 P 0.1546 0.2893 0.5561 82 H 0.1706 0.2676 0.5617 83 K 0.1340 0.4180 0.4479 84 Q 0.0981 0.4452 0.4567 85 D 0.1200 0.3258 0.5542 86 V 0.2005 0.2268 0.5727 87 V 0.1862 0.1597 0.6541 88 S 0.0535 0.5738 0.3727 89 D 0.0367 0.6257 0.3376 90 H 0.0467 0.6809 0.2724 91 N 0.0392 0.7384 0.2224 92 R 0.0274 0.8037 0.1689 93 S 0.0244 0.8278 0.1479 94 F 0.0162 0.8819 0.1018 95 D 0.0092 0.9100 0.0808 96 L 0.0087 0.9152 0.0761 97 C 0.0089 0.9155 0.0756 98 R 0.0085 0.9134 0.0781 99 E 0.0087 0.9106 0.0807 100 Q 0.0109 0.8849 0.1042 101 A 0.0142 0.8596 0.1262 102 E 0.0185 0.7920 0.1895 103 K 0.0391 0.6669 0.2940 104 L 0.0716 0.2294 0.6990 105 G 0.0707 0.0714 0.8580 106 I 0.3333 0.0183 0.6484 107 L 0.6068 0.0194 0.3738 108 L 0.7206 0.0128 0.2666 109 I 0.6263 0.0165 0.3572 110 K 0.4946 0.0371 0.4683 111 G 0.3725 0.0533 0.5742 112 S 0.5221 0.0629 0.4150 113 E 0.6634 0.0320 0.3046 114 I 0.6826 0.0328 0.2846 115 T 0.5602 0.0466 0.3932 116 R 0.4145 0.1450 0.4405 117 A 0.2986 0.1453 0.5561 118 M 0.2324 0.1281 0.6395 119 A 0.1949 0.0945 0.7106 120 P 0.1267 0.1912 0.6822 121 G 0.1394 0.1360 0.7246 122 H 0.3293 0.1194 0.5512 123 F 0.4719 0.1050 0.4231 124 N 0.5198 0.0896 0.3906 125 A 0.4596 0.1932 0.3472 126 I 0.4102 0.2093 0.3806 127 F 0.3792 0.1812 0.4396 128 L 0.2767 0.1912 0.5321 129 S 0.1965 0.1780 0.6255 130 D 0.1183 0.2728 0.6088 131 S 0.1238 0.2142 0.6620 132 N 0.1633 0.1561 0.6806 133 P 0.1093 0.2617 0.6290 134 L 0.1310 0.3353 0.5337 135 E 0.1299 0.3873 0.4828 136 Q 0.1295 0.3936 0.4769 137 K 0.1269 0.3644 0.5087 138 D 0.1245 0.2873 0.5882 139 Y 0.0461 0.6204 0.3335 140 K 0.0134 0.8449 0.1417 141 D 0.0101 0.9034 0.0866 142 A 0.0097 0.9163 0.0741 143 F 0.0083 0.9208 0.0709 144 R 0.0083 0.9237 0.0680 145 E 0.0083 0.9234 0.0683 146 A 0.0084 0.9169 0.0746 147 K 0.0087 0.8935 0.0977 148 K 0.0155 0.8046 0.1798 149 Q 0.0589 0.3164 0.6247 150 G 0.0569 0.0684 0.8747 151 A 0.2306 0.0435 0.7259 152 F 0.5501 0.0277 0.4222 153 M 0.7660 0.0171 0.2169 154 F 0.7682 0.0235 0.2083 155 W 0.7052 0.0488 0.2460 156 N 0.5444 0.0676 0.3880 157 H 0.2794 0.0391 0.6815 158 P 0.1307 0.2277 0.6417 159 G 0.1155 0.1915 0.6930 160 W 0.1626 0.2459 0.5915 161 D 0.1522 0.2667 0.5811 162 S 0.1403 0.2633 0.5964 163 Q 0.1713 0.1476 0.6810 164 Q 0.1914 0.0742 0.7345 165 P 0.0975 0.3330 0.5695 166 D 0.0858 0.3599 0.5543 167 T 0.1168 0.3143 0.5690 168 T 0.1271 0.3137 0.5592 169 K 0.1396 0.3276 0.5328 170 W 0.1806 0.2455 0.5739 171 W 0.2006 0.1432 0.6562 172 P 0.1037 0.3756 0.5206 173 E 0.0404 0.7224 0.2371 174 H 0.0340 0.8008 0.1651 175 T 0.0453 0.8207 0.1340 176 A 0.0447 0.8292 0.1261 177 L 0.0690 0.7499 0.1811 178 Y 0.0929 0.5575 0.3495 179 Q 0.1114 0.3417 0.5469 180 E 0.1095 0.2044 0.6861 181 G 0.1194 0.1449 0.7357 182 C 0.3165 0.1194 0.5641 183 M 0.4791 0.0986 0.4224 184 H 0.5335 0.0929 0.3735 185 G 0.5225 0.1023 0.3752 186 I 0.4642 0.1090 0.4268 187 E 0.3775 0.1269 0.4955 188 V 0.2631 0.1705 0.5664 189 A 0.1538 0.2604 0.5858 190 N 0.1161 0.1993 0.6846 191 G 0.0915 0.2125 0.6960 192 H 0.0936 0.3575 0.5489 193 L 0.0955 0.3936 0.5109 194 Y 0.1088 0.3528 0.5384 195 M 0.0936 0.3826 0.5238 196 P 0.0114 0.8231 0.1655 197 E 0.0091 0.8850 0.1059 198 A 0.0083 0.9212 0.0705 199 I 0.0083 0.9233 0.0684 200 Q 0.0083 0.9233 0.0684 201 W 0.0084 0.9189 0.0727 202 C 0.0094 0.8987 0.0919 203 L 0.0115 0.8231 0.1654 204 D 0.0228 0.7077 0.2695 205 K 0.0599 0.2103 0.7298 206 N 0.0659 0.0758 0.8582 207 L 0.2776 0.0272 0.6952 208 T 0.5855 0.0248 0.3897 209 M 0.7427 0.0160 0.2414 210 I 0.7278 0.0231 0.2491 211 G 0.6382 0.0339 0.3279 212 T 0.4428 0.0652 0.4920 213 S 0.2493 0.1391 0.6116 214 D 0.1704 0.2357 0.5939 215 I 0.1439 0.2963 0.5598 216 H 0.1624 0.1968 0.6408 217 Q 0.1867 0.1356 0.6777 218 P 0.1605 0.2645 0.5750 219 I 0.1894 0.2393 0.5713 220 Q 0.1964 0.2230 0.5806 221 T 0.1738 0.2414 0.5848 222 D 0.1648 0.2400 0.5952 223 Y 0.1669 0.3234 0.5097 224 D 0.1751 0.3007 0.5242 225 F 0.1444 0.3831 0.4725 226 E 0.1441 0.3230 0.5329 227 K 0.1571 0.1792 0.6636 228 G 0.1513 0.1217 0.7270 229 E 0.1956 0.1947 0.6097 230 H 0.2345 0.1367 0.6288 231 R 0.3195 0.0964 0.5841 232 T 0.3761 0.0991 0.5248 233 M 0.4960 0.0675 0.4365 234 T 0.6443 0.0387 0.3170 235 F 0.7152 0.0273 0.2575 236 V 0.7330 0.0268 0.2403 237 F 0.6452 0.0426 0.3122 238 A 0.3979 0.1832 0.4189 239 K 0.1776 0.4172 0.4052 240 E 0.1153 0.4072 0.4775 241 R 0.1459 0.3134 0.5407 242 S 0.1345 0.2385 0.6270 243 L 0.0148 0.7687 0.2165 244 Q 0.0097 0.8661 0.1242 245 G 0.0087 0.9152 0.0761 246 I 0.0084 0.9142 0.0773 247 R 0.0083 0.9212 0.0705 248 E 0.0083 0.9239 0.0679 249 A 0.0084 0.9190 0.0726 250 L 0.0089 0.8979 0.0932 251 D 0.0134 0.7878 0.1988 252 N 0.0476 0.3716 0.5807 253 R 0.0517 0.1186 0.8298 254 R 0.2035 0.1059 0.6906 255 T 0.4599 0.0916 0.4485 256 A 0.6513 0.0753 0.2734 257 A 0.6805 0.0732 0.2462 258 Y 0.6063 0.0923 0.3014 259 F 0.4949 0.0957 0.4094 260 H 0.3461 0.1038 0.5501 261 E 0.1768 0.3454 0.4778 262 L 0.2220 0.3100 0.4681 263 L 0.3767 0.2313 0.3920 264 I 0.4025 0.1942 0.4033 265 G 0.3857 0.1758 0.4385 266 R 0.3262 0.2784 0.3954 267 E 0.1935 0.4904 0.3161 268 D 0.1444 0.4964 0.3591 269 L 0.1258 0.4739 0.4003 270 L 0.1262 0.3579 0.5159 271 R 0.1384 0.3202 0.5414 272 P 0.0379 0.6693 0.2928 273 F 0.0479 0.6601 0.2920 274 F 0.0777 0.7109 0.2115 275 E 0.0843 0.7010 0.2146 276 K 0.1631 0.5553 0.2816 277 C 0.2844 0.3451 0.3705 278 V 0.4394 0.1626 0.3979 279 K 0.4061 0.1119 0.4820 280 I 0.3118 0.1719 0.5163 281 E 0.3124 0.1953 0.4923 282 E 0.4621 0.1337 0.4042 283 V 0.5587 0.0579 0.3833 284 S 0.5121 0.0517 0.4362 285 R 0.3959 0.1437 0.4603 286 N 0.2347 0.1457 0.6196 287 E 0.1387 0.2412 0.6201 288 Q 0.1383 0.1435 0.7182 289 G 0.3081 0.0751 0.6168 290 V 0.5554 0.0296 0.4150 291 T 0.6998 0.0201 0.2801 292 L 0.7668 0.0166 0.2166 293 S 0.7586 0.0179 0.2235 294 I 0.7312 0.0283 0.2404 295 T 0.6501 0.0503 0.2996 296 N 0.5219 0.0633 0.4148 297 V 0.3186 0.1235 0.5579 298 T 0.2586 0.1305 0.6109 299 D 0.2151 0.1753 0.6096 300 L 0.2052 0.3197 0.4750 301 V 0.2775 0.3513 0.3712 302 L 0.3609 0.3690 0.2700 303 K 0.4361 0.3226 0.2413 304 L 0.4802 0.2572 0.2626 305 K 0.4421 0.2089 0.3490 306 K 0.3152 0.2266 0.4582 307 T 0.2285 0.2037 0.5678 308 A 0.2027 0.1661 0.6312 309 H 0.1756 0.2089 0.6155 310 D 0.1654 0.2136 0.6211 311 T 0.2380 0.2112 0.5508 312 L 0.3994 0.1431 0.4575 313 L 0.4776 0.0913 0.4311 314 V 0.4502 0.1124 0.4374 315 Y 0.3963 0.1016 0.5020 316 F 0.3068 0.1325 0.5607 317 R 0.2652 0.1589 0.5759 318 D 0.3347 0.1316 0.5337 319 M 0.4370 0.0756 0.4874 320 T 0.4684 0.0482 0.4834 321 L 0.3892 0.0499 0.5609 322 K 0.2320 0.0439 0.7241 323 P 0.1702 0.2199 0.6099 324 H 0.2217 0.1561 0.6221 325 T 0.4618 0.0661 0.4721 326 R 0.6675 0.0264 0.3061 327 Y 0.7771 0.0113 0.2116 328 T 0.8006 0.0066 0.1927 329 V 0.8011 0.0081 0.1908 330 R 0.7618 0.0112 0.2270 331 I 0.6842 0.0330 0.2828 332 G 0.5307 0.0378 0.4314 333 F 0.4249 0.1151 0.4601 334 K 0.3138 0.1973 0.4889 335 Q 0.2558 0.1408 0.6034 336 G 0.2031 0.1149 0.6820 337 I 0.3560 0.0567 0.5873 338 K 0.3698 0.0720 0.5582 339 G 0.3722 0.0886 0.5392 340 G 0.3897 0.0773 0.5330 341 D 0.4654 0.0638 0.4708 342 V 0.5050 0.0657 0.4293 343 N 0.5078 0.0947 0.3975 344 F 0.5722 0.1040 0.3238 345 E 0.6596 0.0820 0.2584 346 V 0.6814 0.0701 0.2485 347 T 0.5722 0.1263 0.3016 348 N 0.6928 0.0692 0.2380 349 F 0.6821 0.0484 0.2695 350 I 0.7195 0.0306 0.2499 351 V 0.6629 0.0366 0.3006 352 A 0.4174 0.0251 0.5575 353 P 0.1994 0.1602 0.6404 354 D 0.1317 0.2147 0.6536 355 K 0.1456 0.1355 0.7189 356 G 0.2199 0.0687 0.7114 357 L 0.3350 0.0419 0.6231 358 K 0.5160 0.0273 0.4567 359 Y 0.6503 0.0199 0.3298 360 T 0.6480 0.0130 0.3391 361 I 0.6574 0.0336 0.3090 362 S 0.5453 0.0298 0.4249 363 L 0.4018 0.0616 0.5366