# This file is the result of combining several RDB files, specifically # T0449.t06.str2.rdb (weight 1.54425) # T0449.t06.str4.rdb (weight 0.924988) # T0449.t06.pb.rdb (weight 0.789901) # T0449.t06.bys.rdb (weight 0.748322) # T0449.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 T0449.t06.str2.rdb # ============================================ # TARGET T0449 # 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 T0449.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 1151 # # ============================================ # Comments from T0449.t06.str4.rdb # ============================================ # TARGET T0449 # 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 T0449.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 1151 # # ============================================ # Comments from T0449.t06.pb.rdb # ============================================ # TARGET T0449 # 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 T0449.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 1151 # # ============================================ # Comments from T0449.t06.bys.rdb # ============================================ # TARGET T0449 # 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 T0449.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 1151 # # ============================================ # Comments from T0449.t06.alpha.rdb # ============================================ # TARGET T0449 # 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 T0449.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 1151 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.5716 0.0202 0.4082 2 D 0.6832 0.0103 0.3065 3 Y 0.7871 0.0066 0.2063 4 T 0.7941 0.0063 0.1996 5 I 0.7424 0.0090 0.2486 6 E 0.6616 0.0331 0.3053 7 N 0.3966 0.0431 0.5603 8 N 0.2440 0.0913 0.6647 9 M 0.4395 0.0452 0.5153 10 I 0.7040 0.0100 0.2859 11 K 0.7899 0.0069 0.2031 12 V 0.8214 0.0047 0.1739 13 V 0.8102 0.0049 0.1849 14 I 0.7594 0.0063 0.2344 15 S 0.5468 0.0330 0.4203 16 D 0.3097 0.1411 0.5492 17 H 0.2032 0.1410 0.6558 18 G 0.3060 0.0751 0.6189 19 A 0.6266 0.0230 0.3505 20 E 0.7404 0.0174 0.2422 21 I 0.7356 0.0146 0.2497 22 Q 0.6807 0.0269 0.2924 23 S 0.7870 0.0112 0.2018 24 V 0.7285 0.0147 0.2568 25 K 0.6973 0.0194 0.2832 26 S 0.4610 0.0371 0.5019 27 A 0.1405 0.1986 0.6609 28 H 0.0931 0.1304 0.7765 29 T 0.2338 0.0922 0.6740 30 D 0.3165 0.0883 0.5952 31 E 0.4510 0.1431 0.4060 32 E 0.5358 0.1395 0.3246 33 F 0.5725 0.1136 0.3139 34 M 0.4930 0.1270 0.3800 35 W 0.3808 0.1483 0.4709 36 Q 0.2619 0.1543 0.5838 37 A 0.1830 0.1464 0.6707 38 N 0.1835 0.1040 0.7125 39 P 0.0476 0.5732 0.3792 40 E 0.0616 0.5940 0.3444 41 I 0.1092 0.5114 0.3794 42 W 0.1262 0.4296 0.4442 43 G 0.1051 0.3699 0.5250 44 R 0.1124 0.2606 0.6270 45 H 0.1690 0.1284 0.7026 46 A 0.2799 0.0745 0.6455 47 P 0.3355 0.0964 0.5681 48 V 0.5400 0.1058 0.3542 49 L 0.5875 0.1040 0.3085 50 F 0.4908 0.1146 0.3946 51 P 0.3313 0.2422 0.4265 52 I 0.2641 0.3251 0.4108 53 V 0.1743 0.2473 0.5784 54 G 0.1152 0.1447 0.7400 55 R 0.2789 0.1360 0.5851 56 L 0.3216 0.1337 0.5447 57 K 0.1924 0.2195 0.5881 58 N 0.1299 0.1375 0.7326 59 D 0.2111 0.0933 0.6956 60 E 0.4837 0.0639 0.4524 61 Y 0.6401 0.0298 0.3301 62 T 0.6264 0.0343 0.3393 63 Y 0.5403 0.0716 0.3881 64 K 0.2560 0.0838 0.6602 65 G 0.1440 0.0634 0.7925 66 K 0.5323 0.0263 0.4414 67 T 0.6725 0.0190 0.3085 68 Y 0.6938 0.0242 0.2819 69 H 0.6379 0.0266 0.3355 70 L 0.4464 0.0632 0.4904 71 G 0.2795 0.1117 0.6088 72 Q 0.2033 0.2457 0.5510 73 H 0.2218 0.2283 0.5498 74 G 0.2276 0.2406 0.5318 75 F 0.2665 0.2669 0.4666 76 A 0.2740 0.3112 0.4148 77 R 0.2410 0.2712 0.4878 78 N 0.2579 0.1433 0.5988 79 A 0.3121 0.0907 0.5972 80 D 0.3417 0.0848 0.5735 81 F 0.5228 0.0424 0.4347 82 E 0.6278 0.0343 0.3379 83 V 0.6500 0.0372 0.3128 84 E 0.5681 0.0719 0.3600 85 N 0.5580 0.0543 0.3877 86 H 0.4444 0.0571 0.4985 87 T 0.3408 0.0346 0.6246 88 K 0.1974 0.1972 0.6053 89 E 0.2773 0.1345 0.5883 90 S 0.6416 0.0305 0.3279 91 I 0.7624 0.0068 0.2308 92 T 0.8217 0.0048 0.1735 93 F 0.8255 0.0045 0.1700 94 L 0.8133 0.0050 0.1817 95 L 0.7549 0.0075 0.2375 96 K 0.6780 0.0178 0.3043 97 D 0.4370 0.0252 0.5378 98 N 0.1632 0.1891 0.6477 99 E 0.0554 0.4412 0.5033 100 E 0.0746 0.4652 0.4602 101 T 0.1441 0.4328 0.4231 102 R 0.1720 0.4424 0.3856 103 K 0.2554 0.3178 0.4268 104 V 0.3573 0.1632 0.4795 105 Y 0.4508 0.0519 0.4972 106 P 0.4152 0.0742 0.5106 107 F 0.5563 0.0680 0.3758 108 K 0.6668 0.0223 0.3110 109 F 0.7860 0.0082 0.2057 110 E 0.8088 0.0057 0.1855 111 F 0.8187 0.0049 0.1763 112 R 0.8263 0.0044 0.1693 113 V 0.8254 0.0045 0.1701 114 N 0.8116 0.0057 0.1827 115 Y 0.8168 0.0055 0.1778 116 N 0.7894 0.0067 0.2039 117 L 0.6931 0.0191 0.2877 118 M 0.4867 0.0734 0.4399 119 N 0.2195 0.0940 0.6865 120 N 0.2304 0.0896 0.6800 121 L 0.5647 0.0469 0.3884 122 L 0.6988 0.0226 0.2786 123 E 0.7642 0.0155 0.2203 124 E 0.7872 0.0143 0.1985 125 N 0.7743 0.0156 0.2102 126 F 0.7972 0.0081 0.1947 127 S 0.7997 0.0077 0.1926 128 V 0.7793 0.0096 0.2111 129 V 0.6880 0.0222 0.2898 130 N 0.4351 0.0226 0.5423 131 K 0.1674 0.1993 0.6333 132 S 0.1683 0.1593 0.6725 133 D 0.1442 0.1558 0.7000 134 E 0.1879 0.2017 0.6103 135 T 0.3032 0.1552 0.5415 136 M 0.4514 0.0852 0.4634 137 I 0.4924 0.1240 0.3836 138 F 0.4790 0.1357 0.3854 139 G 0.4340 0.1462 0.4198 140 V 0.3874 0.1959 0.4167 141 G 0.3232 0.1819 0.4948 142 G 0.3058 0.1274 0.5668 143 H 0.2921 0.0604 0.6475 144 P 0.1555 0.2546 0.5899 145 G 0.1876 0.2192 0.5932 146 F 0.3525 0.1077 0.5398 147 N 0.4004 0.0632 0.5364 148 L 0.3577 0.0375 0.6048 149 P 0.2337 0.0937 0.6726 150 T 0.1475 0.1832 0.6693 151 D 0.1217 0.2328 0.6455 152 H 0.1065 0.1695 0.7240 153 G 0.1027 0.1216 0.7757 154 E 0.2301 0.0944 0.6754 155 N 0.3127 0.0737 0.6136 156 K 0.2717 0.1768 0.5515 157 E 0.2313 0.2099 0.5589 158 D 0.2877 0.1252 0.5871 159 F 0.5172 0.0521 0.4307 160 Y 0.6878 0.0227 0.2895 161 F 0.7315 0.0172 0.2513 162 D 0.6804 0.0170 0.3026 163 M 0.5489 0.0197 0.4314 164 H 0.2646 0.0156 0.7198 165 P 0.0779 0.3668 0.5554 166 S 0.0912 0.3704 0.5384 167 V 0.2297 0.3209 0.4493 168 T 0.3853 0.1805 0.4341 169 R 0.4369 0.1379 0.4252 170 V 0.3925 0.1348 0.4728 171 R 0.3783 0.1249 0.4968 172 I 0.2936 0.0630 0.6434 173 P 0.1971 0.2003 0.6026 174 L 0.2179 0.1329 0.6492 175 K 0.1479 0.2155 0.6366 176 D 0.1416 0.1605 0.6979 177 A 0.1477 0.1870 0.6653 178 S 0.2574 0.1656 0.5770 179 L 0.3501 0.1320 0.5179 180 D 0.3131 0.1160 0.5709 181 W 0.2465 0.2475 0.5060 182 N 0.1844 0.2417 0.5739 183 N 0.1750 0.1724 0.6526 184 R 0.1800 0.1223 0.6977 185 S 0.2486 0.0763 0.6751 186 L 0.2562 0.1286 0.6152 187 A 0.3175 0.0600 0.6225 188 P 0.2386 0.0963 0.6652 189 T 0.1523 0.2251 0.6227 190 D 0.1374 0.2274 0.6352 191 S 0.2493 0.1824 0.5683 192 L 0.3472 0.1626 0.4901 193 I 0.4892 0.0916 0.4192 194 A 0.4464 0.0840 0.4697 195 L 0.3110 0.1380 0.5510 196 S 0.2018 0.1383 0.6600 197 D 0.0928 0.4247 0.4824 198 D 0.0982 0.4234 0.4784 199 L 0.1445 0.3522 0.5032 200 F 0.2451 0.1889 0.5660 201 K 0.1915 0.1930 0.6155 202 D 0.1717 0.2277 0.6006 203 D 0.2600 0.1903 0.5497 204 A 0.5662 0.1006 0.3332 205 L 0.6766 0.0593 0.2641 206 I 0.6714 0.0639 0.2647 207 Y 0.5823 0.0876 0.3301 208 E 0.4308 0.1071 0.4621 209 L 0.2692 0.1536 0.5772 210 R 0.1814 0.1604 0.6582 211 G 0.1324 0.1366 0.7311 212 N 0.1505 0.1302 0.7193 213 D 0.2363 0.0824 0.6813 214 N 0.4057 0.0595 0.5348 215 K 0.6850 0.0187 0.2963 216 V 0.7835 0.0064 0.2100 217 S 0.8013 0.0065 0.1922 218 L 0.7751 0.0066 0.2184 219 R 0.7598 0.0138 0.2264 220 T 0.5632 0.0117 0.4251 221 D 0.1989 0.2397 0.5614 222 K 0.0863 0.2779 0.6358 223 N 0.1136 0.1397 0.7467 224 K 0.2142 0.0744 0.7114 225 F 0.5738 0.0190 0.4072 226 H 0.7518 0.0079 0.2403 227 V 0.8072 0.0060 0.1868 228 N 0.7963 0.0056 0.1981 229 V 0.7940 0.0066 0.1994 230 W 0.7263 0.0160 0.2576 231 T 0.5268 0.0518 0.4214 232 R 0.2209 0.1590 0.6202 233 D 0.1714 0.1322 0.6965 234 A 0.2652 0.0462 0.6886 235 P 0.2869 0.1226 0.5905 236 F 0.5932 0.0589 0.3479 237 V 0.7641 0.0134 0.2225 238 G 0.7928 0.0091 0.1981 239 I 0.7990 0.0078 0.1932 240 W 0.7432 0.0172 0.2396 241 S 0.5850 0.0197 0.3953 242 Q 0.3208 0.1079 0.5713 243 Y 0.2523 0.0577 0.6900 244 P 0.1297 0.1877 0.6825 245 K 0.1102 0.2138 0.6759 246 T 0.1643 0.1606 0.6751 247 D 0.2025 0.1473 0.6502 248 N 0.3208 0.1007 0.5785 249 Y 0.6303 0.0244 0.3453 250 V 0.7407 0.0151 0.2442 251 C 0.7603 0.0124 0.2274 252 I 0.7301 0.0231 0.2469 253 E 0.6444 0.0188 0.3368 254 P 0.4495 0.0796 0.4709 255 W 0.3239 0.1662 0.5099 256 W 0.2917 0.1381 0.5703 257 G 0.2278 0.1209 0.6513 258 I 0.2592 0.1027 0.6382 259 A 0.2076 0.1874 0.6050 260 D 0.1821 0.1483 0.6696 261 R 0.1023 0.3463 0.5514 262 D 0.0786 0.4095 0.5120 263 D 0.1018 0.3088 0.5894 264 A 0.1024 0.3550 0.5426 265 D 0.0823 0.3243 0.5933 266 G 0.0648 0.3695 0.5657 267 D 0.1053 0.4512 0.4435 268 L 0.1256 0.5265 0.3479 269 E 0.1251 0.5004 0.3745 270 H 0.1221 0.4417 0.4362 271 K 0.1176 0.3215 0.5609 272 Y 0.1392 0.1454 0.7154 273 G 0.1361 0.0904 0.7735 274 M 0.3716 0.0471 0.5814 275 N 0.6239 0.0286 0.3475 276 H 0.6918 0.0219 0.2863 277 L 0.5655 0.0269 0.4076 278 K 0.2918 0.0196 0.6886 279 P 0.1234 0.1529 0.7237 280 G 0.0461 0.1069 0.8470 281 K 0.3317 0.0313 0.6370 282 E 0.6418 0.0223 0.3359 283 F 0.6964 0.0276 0.2760 284 Q 0.7271 0.0165 0.2564 285 A 0.7372 0.0179 0.2449 286 G 0.7687 0.0099 0.2214 287 F 0.8109 0.0059 0.1833 288 S 0.8187 0.0051 0.1762 289 M 0.8219 0.0047 0.1734 290 T 0.8168 0.0055 0.1778 291 Y 0.7792 0.0083 0.2125 292 H 0.6969 0.0214 0.2817 293 S 0.5401 0.0497 0.4102 294 T 0.2920 0.1122 0.5958 295 T 0.2053 0.1960 0.5987 296 D 0.1665 0.2782 0.5553 297 E 0.2250 0.3420 0.4330 298 V 0.2842 0.2734 0.4423 299 K 0.2801 0.2545 0.4654 300 L 0.1882 0.4790 0.3328 301 E 0.1330 0.5502 0.3167 302 H 0.1580 0.5089 0.3331 303 H 0.1520 0.4634 0.3847 304 H 0.1666 0.3630 0.4704 305 H 0.1569 0.2981 0.5450 306 H 0.1511 0.2294 0.6195 307 H 0.1704 0.1580 0.6715