# This file is the result of combining several RDB files, specifically # T0587.t06.str2.rdb (weight 1.54425) # T0587.t06.str4.rdb (weight 0.924988) # T0587.t06.pb.rdb (weight 0.789901) # T0587.t06.bys.rdb (weight 0.748322) # T0587.t06.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 T0587.t06.str2.rdb # ============================================ # TARGET T0587 # Using neural net dunbrack-40pc-3157-t06-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 T0587.t06-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 44.5879 # # ============================================ # Comments from T0587.t06.str4.rdb # ============================================ # TARGET T0587 # Using neural net dunbrack-40pc-3157-t06-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 T0587.t06-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 44.5879 # # ============================================ # Comments from T0587.t06.pb.rdb # ============================================ # TARGET T0587 # Using neural net dunbrack-40pc-3157-t06-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 T0587.t06-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 44.5879 # # ============================================ # Comments from T0587.t06.bys.rdb # ============================================ # TARGET T0587 # Using neural net dunbrack-40pc-3157-t06-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 T0587.t06-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 44.5879 # # ============================================ # Comments from T0587.t06.alpha.rdb # ============================================ # TARGET T0587 # Using neural net dunbrack-40pc-3157-t06-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 T0587.t06-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 44.5879 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 G 0.1809 0.0755 0.7436 2 P 0.1850 0.1547 0.6603 3 R 0.1933 0.2596 0.5471 4 A 0.1450 0.4835 0.3716 5 R 0.1009 0.5257 0.3734 6 D 0.1021 0.4523 0.4457 7 L 0.1100 0.2344 0.6556 8 G 0.0868 0.0913 0.8219 9 V 0.2320 0.0269 0.7411 10 P 0.2364 0.0506 0.7130 11 F 0.2165 0.1701 0.6134 12 E 0.1617 0.1795 0.6588 13 G 0.1668 0.1323 0.7009 14 T 0.2439 0.0474 0.7087 15 P 0.1833 0.1591 0.6576 16 G 0.1795 0.1339 0.6866 17 A 0.1646 0.2758 0.5596 18 L 0.1513 0.3440 0.5047 19 N 0.1994 0.2882 0.5124 20 A 0.3147 0.2647 0.4207 21 I 0.4618 0.2219 0.3163 22 T 0.4771 0.1915 0.3314 23 D 0.4489 0.1358 0.4154 24 V 0.3534 0.0973 0.5493 25 A 0.2177 0.1328 0.6495 26 G 0.2076 0.0822 0.7103 27 V 0.5139 0.0257 0.4604 28 E 0.6130 0.0229 0.3641 29 V 0.6309 0.0398 0.3293 30 G 0.5573 0.0475 0.3953 31 H 0.5902 0.0512 0.3586 32 T 0.6391 0.0430 0.3179 33 T 0.6458 0.0449 0.3092 34 V 0.5223 0.0748 0.4028 35 I 0.3823 0.1284 0.4893 36 S 0.2498 0.1239 0.6264 37 G 0.1488 0.1183 0.7330 38 D 0.1497 0.1480 0.7023 39 G 0.1594 0.1652 0.6754 40 A 0.2543 0.2336 0.5121 41 M 0.3811 0.2047 0.4142 42 V 0.4050 0.1724 0.4226 43 I 0.2728 0.1714 0.5558 44 G 0.1773 0.1352 0.6875 45 K 0.1878 0.1135 0.6987 46 G 0.2211 0.0622 0.7167 47 P 0.2916 0.1042 0.6042 48 Y 0.3889 0.1145 0.4966 49 R 0.4542 0.0918 0.4540 50 T 0.4690 0.0643 0.4666 51 G 0.4921 0.0388 0.4691 52 V 0.6738 0.0165 0.3097 53 T 0.7328 0.0131 0.2541 54 I 0.7908 0.0084 0.2008 55 I 0.7522 0.0108 0.2370 56 H 0.6119 0.0135 0.3746 57 P 0.4099 0.0361 0.5540 58 L 0.1752 0.1420 0.6828 59 G 0.1162 0.1055 0.7783 60 K 0.1767 0.1355 0.6878 61 T 0.2204 0.1956 0.5841 62 S 0.2264 0.1583 0.6152 63 L 0.1326 0.3039 0.5635 64 D 0.1191 0.1840 0.6969 65 G 0.1211 0.1233 0.7556 66 V 0.3829 0.0484 0.5687 67 A 0.5563 0.0500 0.3937 68 A 0.6893 0.0564 0.2543 69 G 0.7283 0.0549 0.2169 70 R 0.7461 0.0521 0.2018 71 A 0.6836 0.0644 0.2520 72 V 0.5812 0.0970 0.3218 73 I 0.3336 0.1350 0.5315 74 N 0.1762 0.1154 0.7085 75 G 0.1500 0.1003 0.7497 76 T 0.1851 0.1287 0.6862 77 G 0.1557 0.1983 0.6460 78 E 0.1892 0.2457 0.5651 79 W 0.2449 0.2325 0.5226 80 T 0.2098 0.2221 0.5680 81 G 0.2049 0.2014 0.5936 82 M 0.2722 0.3037 0.4241 83 H 0.2968 0.3527 0.3505 84 L 0.3415 0.3353 0.3232 85 V 0.3241 0.3114 0.3645 86 D 0.2369 0.2610 0.5021 87 E 0.0804 0.5661 0.3535 88 V 0.0645 0.2299 0.7055 89 G 0.0689 0.0985 0.8326 90 Q 0.2576 0.0706 0.6718 91 F 0.4081 0.0534 0.5385 92 L 0.3489 0.0595 0.5916 93 G 0.3503 0.0561 0.5936 94 P 0.5229 0.0992 0.3779 95 I 0.7169 0.0563 0.2268 96 A 0.7220 0.0509 0.2270 97 L 0.6444 0.0652 0.2903 98 T 0.3667 0.0809 0.5524 99 G 0.1562 0.0796 0.7642 100 T 0.1873 0.1335 0.6792 101 G 0.1505 0.2883 0.5612 102 N 0.1369 0.4879 0.3753 103 V 0.1148 0.5977 0.2874 104 G 0.0782 0.7042 0.2176 105 L 0.0436 0.8076 0.1488 106 V 0.0324 0.8527 0.1149 107 H 0.0139 0.8856 0.1005 108 Q 0.0091 0.9069 0.0840 109 S 0.0093 0.9167 0.0740 110 M 0.0091 0.9192 0.0717 111 M 0.0086 0.9184 0.0730 112 D 0.0089 0.9106 0.0805 113 W 0.0100 0.8942 0.0958 114 S 0.0142 0.8620 0.1238 115 V 0.0201 0.7809 0.1990 116 G 0.0333 0.5350 0.4317 117 K 0.0888 0.3349 0.5763 118 V 0.1674 0.0890 0.7437 119 P 0.0667 0.3683 0.5650 120 E 0.0764 0.2974 0.6262 121 E 0.1686 0.3005 0.5309 122 A 0.2346 0.2151 0.5503 123 L 0.3227 0.1763 0.5010 124 F 0.3502 0.1363 0.5134 125 S 0.3834 0.1454 0.4712 126 R 0.5155 0.0983 0.3861 127 L 0.5502 0.0683 0.3815 128 L 0.5262 0.0344 0.4394 129 P 0.5188 0.0447 0.4364 130 V 0.6273 0.0585 0.3142 131 V 0.7047 0.0527 0.2426 132 A 0.7245 0.0466 0.2289 133 E 0.6909 0.0725 0.2365 134 T 0.6022 0.1093 0.2885 135 L 0.4121 0.1674 0.4205 136 D 0.2555 0.2029 0.5415 137 N 0.1081 0.3695 0.5225 138 R 0.1299 0.3906 0.4795 139 L 0.1307 0.2741 0.5953 140 N 0.1129 0.1883 0.6988 141 D 0.1823 0.1682 0.6495 142 V 0.1581 0.3249 0.5170 143 F 0.1701 0.2442 0.5856 144 G 0.1849 0.2122 0.6029 145 H 0.2187 0.1324 0.6489 146 G 0.2145 0.0973 0.6882 147 L 0.2287 0.1122 0.6590 148 T 0.1818 0.0641 0.7541 149 R 0.0147 0.7430 0.2423 150 D 0.0106 0.8338 0.1556 151 H 0.0103 0.8983 0.0914 152 V 0.0090 0.9119 0.0792 153 F 0.0084 0.9189 0.0727 154 A 0.0084 0.9168 0.0747 155 A 0.0086 0.9148 0.0766 156 L 0.0096 0.9021 0.0883 157 D 0.0109 0.8266 0.1626 158 G 0.0186 0.6186 0.3627 159 A 0.0658 0.4310 0.5032 160 K 0.0804 0.3062 0.6134 161 G 0.0881 0.1489 0.7630 162 G 0.1641 0.0663 0.7696 163 P 0.2244 0.1216 0.6540 164 V 0.2671 0.1548 0.5780 165 A 0.2268 0.2441 0.5290 166 E 0.2128 0.1995 0.5877 167 G 0.2028 0.1056 0.6915 168 N 0.2782 0.0987 0.6231 169 V 0.2503 0.1385 0.6112 170 G 0.2067 0.1249 0.6684 171 G 0.2193 0.1616 0.6192 172 G 0.2292 0.1690 0.6018 173 T 0.1820 0.2437 0.5743 174 G 0.2236 0.1936 0.5828 175 M 0.4360 0.1734 0.3906 176 I 0.5501 0.1464 0.3036 177 A 0.5832 0.1336 0.2832 178 Y 0.5151 0.1162 0.3687 179 T 0.5212 0.1007 0.3780 180 F 0.4143 0.0934 0.4923 181 K 0.3029 0.1210 0.5761 182 G 0.2301 0.1051 0.6647 183 G 0.2227 0.1123 0.6650 184 I 0.2585 0.1729 0.5686 185 G 0.3019 0.1274 0.5707 186 T 0.3386 0.1565 0.5049 187 S 0.3543 0.2058 0.4399 188 S 0.4481 0.1816 0.3704 189 R 0.6105 0.1041 0.2854 190 V 0.6561 0.0588 0.2851 191 V 0.6393 0.0360 0.3248 192 S 0.4601 0.0457 0.4942 193 A 0.2098 0.1812 0.6090 194 G 0.1275 0.1445 0.7280 195 D 0.1374 0.1355 0.7271 196 T 0.1654 0.1219 0.7126 197 R 0.3462 0.0696 0.5842 198 Y 0.6345 0.0212 0.3442 199 T 0.7033 0.0236 0.2732 200 V 0.7469 0.0515 0.2016 201 G 0.6912 0.1186 0.1901 202 V 0.7456 0.0868 0.1676 203 L 0.7389 0.0863 0.1747 204 V 0.6905 0.1255 0.1840 205 Q 0.5387 0.1745 0.2869 206 A 0.4830 0.1924 0.3246 207 N 0.2843 0.1413 0.5744 208 H 0.1378 0.1607 0.7014 209 G 0.1262 0.1308 0.7430 210 D 0.1830 0.1398 0.6771 211 R 0.1597 0.3107 0.5297 212 N 0.1596 0.3414 0.4990 213 D 0.2220 0.2627 0.5153 214 L 0.1760 0.4503 0.3737 215 R 0.2215 0.4382 0.3403 216 I 0.2339 0.4155 0.3506 217 A 0.1480 0.2352 0.6168 218 G 0.1352 0.1293 0.7355 219 V 0.3930 0.0381 0.5689 220 Q 0.4403 0.0617 0.4981 221 I 0.2746 0.1739 0.5515 222 G 0.2008 0.1696 0.6295 223 K 0.2086 0.3738 0.4176 224 E 0.2486 0.3846 0.3669 225 I 0.1996 0.3114 0.4890 226 K 0.1031 0.2771 0.6198 227 G 0.0703 0.1951 0.7345 228 A 0.1683 0.1522 0.6795 229 W 0.2126 0.0781 0.7093 230 P 0.1510 0.2417 0.6073 231 E 0.1267 0.3086 0.5647 232 V 0.1068 0.4776 0.4156 233 N 0.0757 0.5396 0.3847 234 G 0.0749 0.5331 0.3920 235 I 0.1127 0.5691 0.3182 236 V 0.1254 0.5613 0.3134 237 A 0.1130 0.4515 0.4355 238 A 0.1357 0.2888 0.5755 239 G 0.1426 0.1014 0.7560 240 P 0.1299 0.2432 0.6269 241 D 0.1347 0.2564 0.6088 242 A 0.1192 0.2779 0.6029 243 G 0.1425 0.1382 0.7193 244 K 0.2126 0.0492 0.7383 245 P 0.2095 0.1038 0.6868 246 Q 0.1581 0.1997 0.6422 247 D 0.1305 0.2010 0.6685 248 K 0.1031 0.1952 0.7017 249 N 0.1144 0.1020 0.7835 250 S 0.4035 0.0178 0.5788 251 L 0.7543 0.0063 0.2394 252 L 0.8177 0.0050 0.1774 253 I 0.8222 0.0043 0.1735 254 V 0.8141 0.0047 0.1811 255 I 0.7803 0.0077 0.2121 256 A 0.6872 0.0257 0.2870 257 T 0.4056 0.0843 0.5102 258 D 0.2006 0.0868 0.7126 259 A 0.1752 0.1368 0.6879 260 P 0.1516 0.2216 0.6268 261 L 0.1726 0.1593 0.6681 262 M 0.1700 0.0626 0.7674 263 P 0.0135 0.7350 0.2515 264 H 0.0096 0.8307 0.1597 265 Q 0.0087 0.9081 0.0832 266 L 0.0085 0.9152 0.0764 267 E 0.0083 0.9203 0.0714 268 R 0.0083 0.9234 0.0684 269 M 0.0084 0.9202 0.0714 270 A 0.0084 0.9200 0.0716 271 R 0.0084 0.9158 0.0758 272 R 0.0105 0.8865 0.1030 273 A 0.0176 0.8434 0.1390 274 A 0.0288 0.7585 0.2127 275 L 0.0508 0.6026 0.3465 276 G 0.0835 0.4541 0.4624 277 V 0.1708 0.3882 0.4410 278 G 0.2583 0.2718 0.4700 279 R 0.2808 0.2024 0.5167 280 N 0.2502 0.1147 0.6351 281 G 0.2155 0.0770 0.7075 282 S 0.2301 0.1311 0.6388 283 T 0.2390 0.1763 0.5847 284 A 0.2935 0.1377 0.5688 285 G 0.2613 0.1195 0.6192 286 A 0.2126 0.1542 0.6331 287 L 0.1660 0.2002 0.6339 288 S 0.1139 0.1641 0.7221 289 G 0.0938 0.1158 0.7903 290 E 0.2847 0.1411 0.5743 291 F 0.6237 0.1015 0.2748 292 A 0.7264 0.0645 0.2091 293 L 0.7625 0.0505 0.1869 294 A 0.7285 0.0661 0.2054 295 F 0.6863 0.0821 0.2315 296 S 0.5828 0.0823 0.3349 297 T 0.3214 0.1303 0.5482 298 S 0.1923 0.1969 0.6108 299 H 0.2285 0.1607 0.6108 300 V 0.3265 0.1018 0.5717 301 I 0.3125 0.0492 0.6383 302 P 0.2615 0.0999 0.6386 303 L 0.1626 0.1915 0.6458 304 G 0.1097 0.1519 0.7384 305 G 0.0991 0.1213 0.7796 306 K 0.1895 0.0736 0.7369 307 P 0.1771 0.1631 0.6598 308 R 0.2062 0.1321 0.6616 309 L 0.2145 0.1156 0.6699 310 P 0.1543 0.3663 0.4793 311 A 0.1797 0.4884 0.3319 312 I 0.2019 0.4771 0.3210 313 I 0.1935 0.4444 0.3622 314 N 0.1628 0.4138 0.4233 315 D 0.1312 0.3359 0.5329 316 T 0.1211 0.3446 0.5343 317 D 0.0745 0.4544 0.4711 318 S 0.0216 0.7271 0.2512 319 E 0.0128 0.8149 0.1723 320 T 0.0153 0.8543 0.1304 321 M 0.0116 0.8879 0.1005 322 N 0.0084 0.9104 0.0812 323 A 0.0084 0.9190 0.0726 324 L 0.0083 0.9211 0.0706 325 F 0.0083 0.9211 0.0705 326 R 0.0084 0.9213 0.0704 327 G 0.0085 0.9219 0.0697 328 V 0.0085 0.9206 0.0709 329 V 0.0085 0.9201 0.0714 330 Q 0.0087 0.9119 0.0794 331 A 0.0094 0.9094 0.0812 332 T 0.0092 0.9175 0.0732 333 E 0.0086 0.9195 0.0719 334 E 0.0096 0.9116 0.0789 335 A 0.0128 0.9036 0.0836 336 L 0.0139 0.8996 0.0865 337 V 0.0130 0.8952 0.0918 338 N 0.0132 0.8643 0.1225 339 Q 0.0205 0.8549 0.1246 340 L 0.0308 0.8349 0.1343 341 V 0.0624 0.7671 0.1705 342 A 0.0893 0.6710 0.2397 343 S 0.1261 0.5410 0.3329 344 E 0.1425 0.4328 0.4247 345 T 0.1757 0.3477 0.4766 346 M 0.2132 0.2526 0.5342 347 T 0.2405 0.1695 0.5901 348 G 0.1954 0.1086 0.6960 349 A 0.1753 0.1805 0.6442 350 N 0.1267 0.1620 0.7113 351 N 0.1383 0.1127 0.7490 352 A 0.3868 0.0667 0.5465 353 K 0.5764 0.0455 0.3781 354 V 0.6008 0.0532 0.3460 355 Y 0.5088 0.0842 0.4070 356 G 0.4175 0.0797 0.5029 357 I 0.3428 0.0339 0.6232 358 P 0.1909 0.0565 0.7526 359 H 0.0300 0.6747 0.2953 360 D 0.0117 0.8393 0.1490 361 Q 0.0105 0.8960 0.0935 362 L 0.0089 0.9154 0.0756 363 A 0.0084 0.9194 0.0723 364 R 0.0083 0.9213 0.0704 365 I 0.0088 0.9143 0.0769 366 M 0.0108 0.8922 0.0970 367 K 0.0126 0.8494 0.1381 368 A 0.0251 0.7050 0.2698 369 R 0.0740 0.4004 0.5256 370 F 0.1556 0.1634 0.6810 371 P 0.1465 0.1880 0.6654 372 R 0.1709 0.1841 0.6450 373 R 0.1772 0.1674 0.6554