# 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 2671 # # ============================================ # 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 2671 # # ============================================ # 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 2671 # # ============================================ # 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 2671 # # ============================================ # 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 2671 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.4787 0.0212 0.5001 2 S 0.6319 0.0213 0.3469 3 V 0.7624 0.0100 0.2276 4 Q 0.7366 0.0130 0.2503 5 L 0.5708 0.0218 0.4073 6 V 0.3557 0.0999 0.5444 7 K 0.1707 0.0887 0.7406 8 G 0.1529 0.0594 0.7877 9 V 0.4660 0.0104 0.5236 10 N 0.7050 0.0071 0.2879 11 L 0.8072 0.0046 0.1881 12 H 0.8000 0.0071 0.1929 13 V 0.7738 0.0060 0.2203 14 I 0.6772 0.0131 0.3098 15 P 0.4696 0.0315 0.4989 16 T 0.2580 0.0653 0.6767 17 E 0.0572 0.3321 0.6108 18 K 0.0763 0.2440 0.6797 19 Y 0.2298 0.1181 0.6521 20 K 0.3215 0.1126 0.5659 21 T 0.6096 0.0489 0.3415 22 V 0.7352 0.0151 0.2497 23 R 0.7992 0.0088 0.1920 24 L 0.8253 0.0049 0.1699 25 L 0.8229 0.0045 0.1726 26 V 0.8262 0.0046 0.1692 27 R 0.8080 0.0052 0.1868 28 F 0.7334 0.0155 0.2511 29 N 0.4873 0.0375 0.4752 30 T 0.2954 0.1134 0.5912 31 R 0.1913 0.1230 0.6856 32 L 0.1879 0.1839 0.6282 33 N 0.1483 0.2768 0.5748 34 H 0.1385 0.2922 0.5693 35 E 0.1195 0.3752 0.5054 36 T 0.1048 0.3841 0.5112 37 I 0.0488 0.5907 0.3605 38 T 0.0435 0.6889 0.2677 39 K 0.0161 0.8398 0.1441 40 R 0.0095 0.9068 0.0836 41 T 0.0089 0.9169 0.0742 42 L 0.0085 0.9208 0.0708 43 L 0.0084 0.9189 0.0727 44 S 0.0084 0.9191 0.0725 45 S 0.0085 0.9162 0.0753 46 L 0.0099 0.8874 0.1026 47 M 0.0129 0.8563 0.1308 48 E 0.0234 0.7578 0.2188 49 T 0.0629 0.3695 0.5676 50 N 0.0649 0.1857 0.7494 51 S 0.1290 0.2301 0.6409 52 L 0.0882 0.3613 0.5505 53 N 0.1042 0.2208 0.6750 54 Y 0.1884 0.1195 0.6921 55 P 0.1199 0.2683 0.6118 56 N 0.1222 0.2894 0.5885 57 Q 0.0226 0.6987 0.2787 58 V 0.0127 0.8322 0.1550 59 K 0.0121 0.8963 0.0916 60 L 0.0098 0.8981 0.0920 61 S 0.0084 0.9177 0.0739 62 E 0.0083 0.9218 0.0699 63 R 0.0083 0.9198 0.0719 64 L 0.0086 0.9080 0.0834 65 A 0.0086 0.9020 0.0894 66 E 0.0099 0.8638 0.1263 67 L 0.0241 0.6999 0.2760 68 Y 0.0671 0.3470 0.5860 69 G 0.0684 0.2336 0.6980 70 A 0.1738 0.2401 0.5861 71 S 0.2511 0.2359 0.5130 72 F 0.3223 0.1960 0.4816 73 G 0.2950 0.1402 0.5648 74 I 0.3986 0.1193 0.4821 75 G 0.4045 0.1081 0.4874 76 V 0.4464 0.0746 0.4790 77 S 0.3109 0.0725 0.6165 78 K 0.1812 0.2547 0.5641 79 K 0.1378 0.1888 0.6733 80 G 0.0864 0.1266 0.7870 81 N 0.2061 0.1024 0.6915 82 Q 0.3250 0.0985 0.5766 83 H 0.4491 0.0773 0.4736 84 W 0.6305 0.0345 0.3350 85 F 0.7496 0.0163 0.2341 86 N 0.7913 0.0110 0.1977 87 I 0.8094 0.0079 0.1828 88 S 0.7910 0.0099 0.1991 89 M 0.7729 0.0153 0.2117 90 N 0.6995 0.0359 0.2646 91 I 0.6017 0.0579 0.3404 92 V 0.3863 0.1267 0.4871 93 N 0.2056 0.1796 0.6149 94 D 0.0621 0.4126 0.5253 95 H 0.0570 0.4132 0.5298 96 Y 0.1050 0.3868 0.5082 97 L 0.1343 0.3708 0.4949 98 Q 0.1330 0.3355 0.5315 99 D 0.1450 0.2755 0.5796 100 S 0.0200 0.6877 0.2923 101 Q 0.0150 0.7619 0.2231 102 V 0.0152 0.8450 0.1399 103 L 0.0092 0.8901 0.1007 104 A 0.0084 0.9144 0.0773 105 E 0.0083 0.9158 0.0759 106 A 0.0084 0.9216 0.0700 107 V 0.0083 0.9222 0.0695 108 D 0.0083 0.9199 0.0718 109 F 0.0083 0.9229 0.0688 110 L 0.0084 0.9186 0.0730 111 K 0.0084 0.9154 0.0762 112 E 0.0088 0.8971 0.0940 113 I 0.0114 0.8648 0.1238 114 I 0.0275 0.7531 0.2193 115 F 0.0571 0.5550 0.3879 116 A 0.1378 0.2772 0.5850 117 P 0.0595 0.4838 0.4568 118 N 0.0676 0.5134 0.4190 119 I 0.0792 0.5892 0.3316 120 Q 0.0838 0.5221 0.3941 121 A 0.0840 0.2954 0.6206 122 G 0.0524 0.1665 0.7811 123 Q 0.1815 0.1247 0.6938 124 F 0.2468 0.0770 0.6761 125 E 0.1858 0.0706 0.7436 126 A 0.0163 0.7315 0.2522 127 E 0.0107 0.8447 0.1446 128 T 0.0128 0.8864 0.1008 129 F 0.0128 0.9000 0.0872 130 Q 0.0098 0.9146 0.0756 131 R 0.0092 0.9190 0.0718 132 E 0.0094 0.9138 0.0769 133 K 0.0085 0.9175 0.0740 134 E 0.0085 0.9218 0.0698 135 N 0.0089 0.9208 0.0702 136 L 0.0083 0.9231 0.0686 137 K 0.0085 0.9221 0.0694 138 A 0.0084 0.9235 0.0682 139 Y 0.0085 0.9190 0.0725 140 L 0.0090 0.9090 0.0819 141 E 0.0095 0.8980 0.0926 142 S 0.0139 0.8426 0.1435 143 I 0.0388 0.7119 0.2493 144 V 0.0542 0.5705 0.3752 145 E 0.0655 0.4372 0.4973 146 D 0.1301 0.2440 0.6259 147 K 0.0179 0.7067 0.2754 148 Q 0.0127 0.8241 0.1632 149 T 0.0126 0.8944 0.0931 150 Y 0.0113 0.9078 0.0809 151 A 0.0094 0.9137 0.0769 152 S 0.0085 0.9203 0.0712 153 L 0.0083 0.9215 0.0702 154 A 0.0084 0.9194 0.0722 155 L 0.0087 0.9089 0.0824 156 Q 0.0089 0.9013 0.0898 157 S 0.0096 0.8837 0.1067 158 V 0.0147 0.8357 0.1497 159 Y 0.0375 0.6691 0.2934 160 F 0.0693 0.5004 0.4303 161 N 0.0671 0.3896 0.5434 162 Q 0.0865 0.2576 0.6559 163 S 0.1643 0.1366 0.6991 164 E 0.0510 0.4732 0.4758 165 D 0.0630 0.3780 0.5590 166 Q 0.1439 0.2648 0.5912 167 K 0.2033 0.1497 0.6469 168 I 0.3038 0.0667 0.6295 169 P 0.2284 0.1166 0.6550 170 S 0.1860 0.2816 0.5324 171 F 0.1498 0.2362 0.6139 172 G 0.1673 0.1183 0.7145 173 T 0.1798 0.1253 0.6949 174 V 0.0278 0.7045 0.2677 175 A 0.0174 0.8223 0.1603 176 A 0.0162 0.8642 0.1196 177 L 0.0175 0.8328 0.1498 178 A 0.0182 0.7764 0.2054 179 E 0.0307 0.6441 0.3253 180 E 0.0984 0.4433 0.4583 181 T 0.1448 0.1741 0.6811 182 A 0.0114 0.7512 0.2374 183 A 0.0091 0.8710 0.1199 184 S 0.0085 0.9203 0.0713 185 L 0.0084 0.9218 0.0698 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 0.8677 0.1204 192 M 0.0326 0.7219 0.2455 193 L 0.0946 0.4293 0.4761 194 A 0.1479 0.1663 0.6858 195 E 0.0591 0.3773 0.5636 196 D 0.0617 0.2294 0.7089 197 Q 0.1709 0.0893 0.7399 198 V 0.5111 0.0127 0.4762 199 D 0.7225 0.0089 0.2686 200 I 0.8192 0.0043 0.1765 201 F 0.8144 0.0056 0.1800 202 V 0.7960 0.0055 0.1985 203 L 0.6830 0.0224 0.2946 204 G 0.4555 0.0377 0.5067 205 D 0.2425 0.0456 0.7119 206 V 0.2375 0.0811 0.6813 207 N 0.1793 0.0238 0.7969 208 E 0.0138 0.7275 0.2587 209 A 0.0097 0.8478 0.1425 210 E 0.0091 0.8937 0.0971 211 L 0.0098 0.8847 0.1055 212 V 0.0094 0.9054 0.0852 213 P 0.0086 0.9068 0.0845 214 L 0.0090 0.9010 0.0900 215 F 0.0107 0.8795 0.1098 216 K 0.0119 0.8018 0.1863 217 Q 0.0318 0.5934 0.3749 218 L 0.1185 0.2695 0.6120 219 P 0.1080 0.2949 0.5971 220 F 0.1564 0.1997 0.6439 221 T 0.1951 0.0932 0.7117 222 P 0.1707 0.2255 0.6039 223 R 0.1945 0.2424 0.5631 224 E 0.1420 0.3120 0.5460 225 E 0.1183 0.2985 0.5832 226 G 0.1079 0.1820 0.7101 227 K 0.1783 0.1595 0.6622 228 A 0.2640 0.1410 0.5951 229 A 0.2706 0.1820 0.5474 230 I 0.3007 0.1859 0.5133 231 F 0.2808 0.1693 0.5499 232 Y 0.2586 0.1491 0.5923 233 N 0.2316 0.1013 0.6671 234 Q 0.2491 0.0649 0.6861 235 P 0.2430 0.0852 0.6718 236 I 0.2618 0.1265 0.6117 237 R 0.2268 0.1561 0.6171 238 N 0.2488 0.1336 0.6175 239 V 0.2763 0.1125 0.6112 240 I 0.3009 0.1432 0.5559 241 E 0.3458 0.1719 0.4823 242 E 0.4837 0.1301 0.3862 243 R 0.5621 0.0949 0.3430 244 T 0.6013 0.0673 0.3313 245 E 0.5413 0.0773 0.3814 246 R 0.3771 0.0912 0.5317 247 E 0.2154 0.2604 0.5242 248 V 0.1732 0.3558 0.4710 249 L 0.2126 0.3309 0.4565 250 A 0.1655 0.4111 0.4233 251 Q 0.2001 0.4126 0.3873 252 S 0.2934 0.3438 0.3628 253 K 0.5190 0.1993 0.2817 254 L 0.6843 0.0795 0.2362 255 N 0.6987 0.0692 0.2320 256 L 0.7474 0.0479 0.2047 257 A 0.6692 0.0582 0.2725 258 Y 0.6055 0.0464 0.3481 259 N 0.3854 0.0709 0.5437 260 T 0.3099 0.1050 0.5851 261 D 0.2272 0.1205 0.6523 262 I 0.1723 0.2781 0.5496 263 Y 0.1661 0.2387 0.5951 264 Y 0.1625 0.2093 0.6282 265 G 0.1257 0.1478 0.7265 266 D 0.1618 0.2032 0.6351 267 S 0.0283 0.5947 0.3770 268 Y 0.0217 0.6970 0.2813 269 Y 0.0233 0.8134 0.1634 270 F 0.0211 0.8652 0.1138 271 A 0.0161 0.8889 0.0950 272 L 0.0106 0.9130 0.0764 273 Q 0.0094 0.9190 0.0716 274 V 0.0091 0.9182 0.0727 275 F 0.0108 0.8980 0.0913 276 N 0.0123 0.8845 0.1032 277 G 0.0179 0.8228 0.1593 278 I 0.0363 0.7037 0.2600 279 F 0.0770 0.4359 0.4871 280 G 0.0809 0.2293 0.6898 281 G 0.0849 0.1519 0.7632 282 F 0.1516 0.1208 0.7276 283 P 0.0916 0.3155 0.5929 284 H 0.0867 0.4055 0.5078 285 S 0.0655 0.5929 0.3416 286 K 0.0317 0.7699 0.1984 287 L 0.0246 0.8389 0.1365 288 F 0.0264 0.8666 0.1070 289 M 0.0267 0.8711 0.1022 290 N 0.0459 0.8229 0.1312 291 V 0.0703 0.7905 0.1392 292 R 0.1013 0.7354 0.1633 293 E 0.1019 0.6917 0.2064 294 K 0.0998 0.5600 0.3401 295 E 0.0983 0.3608 0.5409 296 H 0.1335 0.2469 0.6196 297 L 0.2779 0.2325 0.4896 298 A 0.4395 0.1849 0.3756 299 Y 0.5459 0.1366 0.3174 300 Y 0.5520 0.1172 0.3307 301 A 0.4842 0.1603 0.3555 302 S 0.4012 0.1694 0.4294 303 S 0.3427 0.2010 0.4563 304 S 0.2984 0.2152 0.4864 305 I 0.2874 0.2320 0.4805 306 D 0.2452 0.2088 0.5460 307 T 0.1766 0.2878 0.5356 308 F 0.1803 0.2149 0.6049 309 R 0.2092 0.1308 0.6600 310 G 0.3009 0.0680 0.6311 311 F 0.5801 0.0447 0.3752 312 M 0.7652 0.0160 0.2188 313 T 0.8029 0.0074 0.1898 314 V 0.8009 0.0100 0.1891 315 Q 0.7490 0.0175 0.2335 316 T 0.6640 0.0325 0.3035 317 G 0.4565 0.0457 0.4978 318 I 0.3440 0.0764 0.5795 319 D 0.1876 0.0555 0.7569 320 G 0.0545 0.3590 0.5865 321 K 0.0513 0.4042 0.5445 322 N 0.1153 0.3556 0.5291 323 R 0.0142 0.7621 0.2238 324 N 0.0093 0.8749 0.1157 325 Q 0.0083 0.9222 0.0695 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 0.9245 0.0672 330 I 0.0083 0.9226 0.0691 331 S 0.0083 0.9225 0.0692 332 T 0.0083 0.9231 0.0686 333 E 0.0083 0.9229 0.0688 334 L 0.0084 0.9196 0.0721 335 E 0.0083 0.9203 0.0713 336 N 0.0087 0.9077 0.0836 337 I 0.0108 0.8929 0.0963 338 R 0.0160 0.8215 0.1625 339 L 0.0468 0.5076 0.4456 340 G 0.0435 0.1781 0.7784 341 K 0.0971 0.1072 0.7957 342 I 0.1807 0.0869 0.7324 343 R 0.1532 0.0959 0.7509 344 E 0.0144 0.7443 0.2413 345 L 0.0096 0.8657 0.1247 346 E 0.0094 0.9172 0.0734 347 I 0.0083 0.9218 0.0699 348 E 0.0083 0.9236 0.0681 349 Q 0.0083 0.9242 0.0675 350 T 0.0083 0.9229 0.0688 351 K 0.0083 0.9229 0.0688 352 A 0.0083 0.9228 0.0689 353 M 0.0084 0.9216 0.0699 354 L 0.0087 0.9178 0.0735 355 K 0.0086 0.9120 0.0794 356 N 0.0100 0.8800 0.1100 357 Q 0.0157 0.8495 0.1348 358 Y 0.0254 0.8352 0.1394 359 I 0.0299 0.8324 0.1377 360 L 0.0548 0.7479 0.1973 361 A 0.0944 0.5774 0.3282 362 L 0.0710 0.5366 0.3924 363 D 0.0807 0.3985 0.5208 364 N 0.1173 0.2804 0.6023 365 A 0.0404 0.5810 0.3786 366 G 0.0229 0.7422 0.2349 367 A 0.0179 0.8597 0.1224 368 W 0.0143 0.8838 0.1019 369 L 0.0120 0.8999 0.0881 370 E 0.0101 0.9069 0.0830 371 K 0.0093 0.9073 0.0834 372 E 0.0107 0.9027 0.0867 373 Y 0.0123 0.8868 0.1009 374 L 0.0140 0.8616 0.1245 375 N 0.0171 0.8299 0.1530 376 E 0.0326 0.7478 0.2197 377 L 0.0790 0.4893 0.4317 378 M 0.1497 0.2267 0.6237 379 P 0.1055 0.2768 0.6177 380 Q 0.1312 0.1977 0.6711 381 T 0.1633 0.1562 0.6805 382 M 0.0622 0.5599 0.3779 383 L 0.0531 0.6430 0.3039 384 T 0.0877 0.6154 0.2969 385 A 0.0127 0.8135 0.1738 386 E 0.0092 0.8812 0.1095 387 E 0.0085 0.9215 0.0701 388 W 0.0084 0.9218 0.0698 389 I 0.0084 0.9198 0.0718 390 A 0.0084 0.9189 0.0727 391 R 0.0088 0.9122 0.0790 392 I 0.0109 0.8626 0.1266 393 N 0.0141 0.6778 0.3081 394 A 0.0460 0.4144 0.5396 395 V 0.1736 0.1384 0.6880 396 T 0.1650 0.0288 0.8062 397 I 0.0266 0.6490 0.3244 398 P 0.0095 0.8625 0.1280 399 E 0.0088 0.9147 0.0765 400 I 0.0084 0.9228 0.0688 401 Q 0.0083 0.9230 0.0687 402 E 0.0083 0.9248 0.0670 403 V 0.0083 0.9243 0.0674 404 A 0.0083 0.9205 0.0711 405 K 0.0085 0.9101 0.0814 406 R 0.0105 0.8678 0.1218 407 L 0.0331 0.7155 0.2514 408 E 0.0531 0.4716 0.4753 409 L 0.0654 0.4175 0.5171 410 Q 0.0997 0.2718 0.6285 411 A 0.2300 0.1328 0.6372 412 I 0.5156 0.0478 0.4367 413 F 0.7158 0.0144 0.2698 414 F 0.7821 0.0082 0.2098 415 L 0.7711 0.0091 0.2198 416 E 0.6590 0.0311 0.3099 417 G 0.4085 0.0250 0.5665 418 E 0.2493 0.1368 0.6140 419 T 0.2485 0.1275 0.6240 420 E 0.2075 0.1848 0.6076 421 N 0.1694 0.1720 0.6587 422 D 0.1545 0.1983 0.6473