# This file is the result of combining several RDB files, specifically # T0518.t2k.str2.rdb (weight 1.54425) # T0518.t2k.str4.rdb (weight 0.924988) # T0518.t2k.pb.rdb (weight 0.789901) # T0518.t2k.bys.rdb (weight 0.748322) # T0518.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 T0518.t2k.str2.rdb # ============================================ # TARGET T0518 # 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 T0518.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 347 # # ============================================ # Comments from T0518.t2k.str4.rdb # ============================================ # TARGET T0518 # 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 T0518.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 347 # # ============================================ # Comments from T0518.t2k.pb.rdb # ============================================ # TARGET T0518 # 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 T0518.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 347 # # ============================================ # Comments from T0518.t2k.bys.rdb # ============================================ # TARGET T0518 # 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 T0518.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 347 # # ============================================ # Comments from T0518.t2k.alpha.rdb # ============================================ # TARGET T0518 # 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 T0518.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 347 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1702 0.2779 0.5519 2 K 0.1538 0.2055 0.6407 3 K 0.1549 0.1857 0.6593 4 V 0.1702 0.2252 0.6046 5 F 0.1781 0.2811 0.5408 6 Y 0.2221 0.3329 0.4449 7 P 0.1576 0.5493 0.2932 8 L 0.1770 0.6087 0.2143 9 A 0.2030 0.6126 0.1844 10 C 0.2644 0.5406 0.1950 11 C 0.2804 0.4873 0.2323 12 C 0.2664 0.4711 0.2626 13 L 0.1525 0.5208 0.3267 14 A 0.1199 0.5043 0.3759 15 A 0.0863 0.2011 0.7125 16 G 0.0648 0.0914 0.8438 17 V 0.2437 0.0695 0.6868 18 F 0.4239 0.1053 0.4708 19 A 0.4100 0.1502 0.4399 20 S 0.3612 0.1608 0.4780 21 C 0.2490 0.1757 0.5753 22 G 0.1695 0.1445 0.6860 23 G 0.1653 0.1524 0.6823 24 Q 0.3063 0.1692 0.5245 25 K 0.4466 0.1705 0.3829 26 K 0.5045 0.1718 0.3237 27 A 0.4916 0.2160 0.2924 28 N 0.3809 0.2568 0.3623 29 A 0.2880 0.2826 0.4294 30 Q 0.1759 0.2483 0.5758 31 E 0.1459 0.2245 0.6296 32 E 0.1805 0.1781 0.6413 33 P 0.0997 0.5048 0.3954 34 S 0.0584 0.7164 0.2252 35 K 0.0556 0.7876 0.1569 36 V 0.0565 0.8101 0.1334 37 A 0.0446 0.8327 0.1227 38 L 0.0375 0.8397 0.1228 39 S 0.0356 0.8179 0.1465 40 Y 0.0474 0.7563 0.1963 41 S 0.0523 0.7151 0.2326 42 K 0.0511 0.6680 0.2809 43 S 0.0719 0.5686 0.3595 44 L 0.1019 0.4901 0.4080 45 K 0.1389 0.3384 0.5227 46 A 0.1819 0.1879 0.6302 47 P 0.1044 0.3714 0.5242 48 E 0.1159 0.3335 0.5506 49 T 0.1132 0.3694 0.5174 50 D 0.1063 0.3087 0.5850 51 S 0.1413 0.3023 0.5564 52 L 0.1688 0.2512 0.5801 53 N 0.2051 0.1690 0.6259 54 L 0.2473 0.1456 0.6071 55 P 0.2166 0.1974 0.5860 56 V 0.2651 0.2220 0.5129 57 D 0.1760 0.2199 0.6042 58 E 0.0601 0.4966 0.4433 59 N 0.0741 0.2056 0.7203 60 G 0.0858 0.0821 0.8320 61 Y 0.4415 0.0341 0.5243 62 I 0.6442 0.0241 0.3317 63 T 0.6764 0.0251 0.2985 64 I 0.6538 0.0562 0.2900 65 F 0.5628 0.0618 0.3754 66 D 0.3403 0.0684 0.5913 67 G 0.1795 0.0956 0.7249 68 E 0.3237 0.1099 0.5664 69 T 0.3975 0.0858 0.5167 70 F 0.2911 0.1992 0.5097 71 N 0.2355 0.1939 0.5706 72 G 0.2443 0.1390 0.6167 73 W 0.4806 0.0968 0.4226 74 R 0.5121 0.1038 0.3840 75 G 0.4223 0.1140 0.4637 76 Y 0.2890 0.1242 0.5869 77 G 0.1567 0.0936 0.7497 78 K 0.1885 0.1666 0.6450 79 D 0.1691 0.1496 0.6812 80 R 0.2199 0.1080 0.6721 81 V 0.2898 0.0337 0.6765 82 P 0.2647 0.0793 0.6560 83 T 0.2851 0.1305 0.5845 84 K 0.4675 0.0625 0.4700 85 W 0.6337 0.0167 0.3496 86 T 0.7279 0.0111 0.2610 87 I 0.6882 0.0156 0.2962 88 E 0.5872 0.0551 0.3577 89 D 0.4016 0.0512 0.5472 90 G 0.4019 0.0444 0.5536 91 C 0.6826 0.0111 0.3063 92 I 0.7533 0.0071 0.2397 93 K 0.7906 0.0082 0.2012 94 F 0.7382 0.0148 0.2470 95 N 0.5892 0.0337 0.3771 96 G 0.3729 0.0758 0.5513 97 S 0.2200 0.1058 0.6742 98 G 0.1445 0.1243 0.7312 99 G 0.1522 0.1106 0.7372 100 G 0.2301 0.1230 0.6468 101 E 0.3266 0.1839 0.4895 102 A 0.3436 0.1837 0.4727 103 Q 0.2878 0.1753 0.5370 104 D 0.1944 0.1176 0.6880 105 G 0.1447 0.1106 0.7446 106 D 0.1663 0.1268 0.7069 107 G 0.1675 0.0990 0.7336 108 G 0.2997 0.0973 0.6031 109 D 0.5318 0.0705 0.3977 110 L 0.6535 0.0747 0.2718 111 I 0.6628 0.0666 0.2706 112 F 0.5798 0.0619 0.3583 113 A 0.4068 0.2107 0.3825 114 H 0.3939 0.2189 0.3872 115 K 0.3540 0.1966 0.4494 116 F 0.3508 0.1222 0.5269 117 K 0.2996 0.1029 0.5975 118 N 0.4492 0.0550 0.4958 119 F 0.6464 0.0170 0.3366 120 E 0.7634 0.0071 0.2296 121 L 0.8130 0.0053 0.1817 122 E 0.8088 0.0049 0.1863 123 L 0.8178 0.0050 0.1772 124 E 0.8061 0.0063 0.1876 125 W 0.8059 0.0075 0.1866 126 K 0.7697 0.0099 0.2205 127 V 0.6911 0.0151 0.2939 128 A 0.4261 0.0309 0.5430 129 K 0.2082 0.1229 0.6689 130 G 0.1273 0.0891 0.7836 131 S 0.2040 0.1230 0.6730 132 N 0.2950 0.0987 0.6063 133 S 0.4133 0.0894 0.4973 134 G 0.5755 0.0426 0.3820 135 I 0.7491 0.0110 0.2399 136 L 0.7817 0.0087 0.2095 137 Y 0.7931 0.0084 0.1985 138 L 0.7562 0.0134 0.2304 139 A 0.6860 0.0247 0.2893 140 Q 0.5528 0.0683 0.3789 141 E 0.4312 0.0978 0.4710 142 V 0.3019 0.1491 0.5490 143 T 0.2232 0.1837 0.5931 144 S 0.1941 0.1626 0.6433 145 K 0.1715 0.3104 0.5181 146 D 0.1732 0.2493 0.5776 147 K 0.0910 0.4482 0.4607 148 D 0.0979 0.2596 0.6425 149 G 0.0961 0.2039 0.7001 150 N 0.1461 0.2020 0.6520 151 D 0.1716 0.1884 0.6400 152 V 0.2034 0.2248 0.5718 153 L 0.2483 0.1772 0.5745 154 E 0.2680 0.1051 0.6269 155 P 0.2346 0.1797 0.5857 156 I 0.3005 0.1736 0.5259 157 Y 0.3369 0.1422 0.5209 158 I 0.3094 0.1473 0.5433 159 S 0.2802 0.0977 0.6221 160 A 0.3029 0.0475 0.6496 161 P 0.3204 0.1078 0.5718 162 E 0.5583 0.0785 0.3632 163 Y 0.7121 0.0357 0.2521 164 Q 0.7403 0.0251 0.2346 165 I 0.6884 0.0489 0.2626 166 L 0.5564 0.0837 0.3598 167 D 0.3049 0.1331 0.5620 168 N 0.1648 0.1776 0.6577 169 A 0.0704 0.3366 0.5929 170 N 0.1036 0.2153 0.6811 171 H 0.1859 0.1292 0.6849 172 P 0.0930 0.3398 0.5672 173 D 0.1162 0.3298 0.5540 174 A 0.0919 0.5413 0.3668 175 K 0.1175 0.4785 0.4040 176 L 0.1487 0.2364 0.6149 177 G 0.1241 0.1092 0.7667 178 K 0.2243 0.1203 0.6555 179 D 0.2007 0.1072 0.6921 180 N 0.1222 0.2779 0.5999 181 N 0.1359 0.2258 0.6382 182 R 0.2646 0.1855 0.5499 183 Q 0.3552 0.1703 0.4745 184 S 0.3745 0.1738 0.4517 185 A 0.3696 0.1788 0.4516 186 S 0.4114 0.1964 0.3921 187 L 0.3676 0.2820 0.3503 188 Y 0.3157 0.2566 0.4277 189 D 0.2427 0.2362 0.5212 190 M 0.2206 0.1699 0.6094 191 I 0.2558 0.0593 0.6849 192 P 0.2085 0.1013 0.6901 193 A 0.2160 0.1486 0.6353 194 V 0.2194 0.0750 0.7056 195 P 0.1308 0.3591 0.5101 196 Q 0.1265 0.3469 0.5266 197 N 0.1600 0.2958 0.5442 198 S 0.2249 0.1458 0.6293 199 K 0.2627 0.0418 0.6955 200 P 0.2016 0.1067 0.6917 201 F 0.1500 0.1826 0.6673 202 G 0.1283 0.1147 0.7570 203 E 0.3324 0.0979 0.5697 204 W 0.5319 0.0927 0.3754 205 N 0.5434 0.0676 0.3890 206 K 0.6765 0.0353 0.2882 207 A 0.7585 0.0122 0.2293 208 K 0.8094 0.0056 0.1849 209 I 0.8229 0.0046 0.1725 210 M 0.8029 0.0050 0.1922 211 V 0.7532 0.0082 0.2387 212 Y 0.6166 0.0233 0.3601 213 K 0.2834 0.0413 0.6753 214 G 0.2336 0.0595 0.7068 215 T 0.5925 0.0187 0.3888 216 V 0.7352 0.0082 0.2566 217 V 0.7944 0.0067 0.1989 218 H 0.8019 0.0059 0.1922 219 G 0.7619 0.0095 0.2286 220 Q 0.6782 0.0313 0.2904 221 N 0.3892 0.0537 0.5571 222 D 0.2122 0.0733 0.7145 223 E 0.4250 0.0413 0.5337 224 N 0.5927 0.0381 0.3693 225 V 0.6752 0.0431 0.2817 226 L 0.6847 0.0444 0.2709 227 E 0.6721 0.0522 0.2757 228 Y 0.5786 0.0784 0.3430 229 H 0.4414 0.1036 0.4551 230 L 0.2427 0.2387 0.5187 231 W 0.1868 0.2541 0.5591 232 T 0.1561 0.2202 0.6237 233 K 0.0468 0.5633 0.3899 234 Q 0.0520 0.5965 0.3515 235 W 0.0414 0.7259 0.2327 236 T 0.0240 0.8194 0.1566 237 D 0.0215 0.8437 0.1348 238 M 0.0226 0.8497 0.1278 239 L 0.0277 0.8326 0.1397 240 Q 0.0363 0.7537 0.2100 241 A 0.0598 0.5827 0.3574 242 S 0.0930 0.4430 0.4640 243 K 0.0744 0.4092 0.5165 244 F 0.1226 0.3041 0.5733 245 S 0.1088 0.3496 0.5416 246 E 0.1030 0.3027 0.5944 247 D 0.1523 0.2014 0.6463 248 K 0.1309 0.2363 0.6328 249 W 0.1903 0.1342 0.6755 250 P 0.1305 0.3279 0.5416 251 L 0.1628 0.3927 0.4444 252 A 0.1587 0.5201 0.3212 253 F 0.1238 0.6203 0.2558 254 E 0.1121 0.6217 0.2662 255 L 0.1162 0.5491 0.3347 256 L 0.1153 0.4516 0.4332 257 N 0.0979 0.3332 0.5689 258 N 0.1125 0.2491 0.6384 259 C 0.1257 0.2128 0.6615 260 G 0.1100 0.1375 0.7526 261 G 0.1315 0.1360 0.7325 262 E 0.2090 0.1331 0.6579 263 N 0.2352 0.1160 0.6488 264 H 0.2008 0.2111 0.5881 265 E 0.2226 0.1631 0.6143 266 G 0.3187 0.0719 0.6094 267 F 0.5661 0.0376 0.3963 268 I 0.7086 0.0379 0.2535 269 G 0.7285 0.0296 0.2419 270 L 0.7123 0.0419 0.2458 271 Q 0.5623 0.0666 0.3711 272 D 0.4020 0.1260 0.4720 273 H 0.2211 0.1348 0.6441 274 G 0.1490 0.1013 0.7497 275 D 0.2187 0.1072 0.6740 276 D 0.3641 0.0707 0.5652 277 V 0.5926 0.0278 0.3795 278 W 0.7058 0.0185 0.2757 279 F 0.7082 0.0185 0.2733 280 R 0.6062 0.0489 0.3449 281 N 0.5744 0.0280 0.3976 282 I 0.6141 0.0192 0.3667 283 R 0.7127 0.0157 0.2715 284 V 0.7333 0.0174 0.2493 285 K 0.6773 0.0236 0.2991 286 V 0.5470 0.0335 0.4195 287 L 0.3298 0.0286 0.6415 288 D 0.1770 0.0629 0.7601