# This file is the result of combining several RDB files, specifically # T0328.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0328.t2k.stride-ebghtl.rdb (weight 1.24869) # T0328.t2k.str2.rdb (weight 1.54758) # T0328.t2k.alpha.rdb (weight 0.659012) # 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 T0328.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0328 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0328.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 140 # # ============================================ # Comments from T0328.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0328 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0328.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 140 # # ============================================ # Comments from T0328.t2k.str2.rdb # ============================================ # TARGET T0328 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0328.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 58.982 # # ============================================ # Comments from T0328.t2k.alpha.rdb # ============================================ # TARGET T0328 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0328.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 140 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1760 0.0280 0.7961 2 D 0.2504 0.0313 0.7183 3 I 0.2123 0.0282 0.7595 4 Q 0.1514 0.0459 0.8027 5 N 0.1357 0.0535 0.8108 6 M 0.1105 0.0481 0.8414 7 P 0.0855 0.0929 0.8217 8 R 0.0936 0.2832 0.6232 9 E 0.1214 0.3038 0.5748 10 Q 0.1729 0.2902 0.5369 11 L 0.1419 0.2881 0.5700 12 G 0.1883 0.2202 0.5915 13 V 0.3365 0.1909 0.4725 14 C 0.2597 0.1834 0.5569 15 A 0.1426 0.1398 0.7176 16 E 0.0986 0.1758 0.7256 17 G 0.0818 0.2508 0.6674 18 N 0.0993 0.2244 0.6763 19 L 0.1176 0.4433 0.4391 20 H 0.3047 0.3396 0.3557 21 S 0.5992 0.1704 0.2305 22 V 0.7945 0.0899 0.1156 23 Y 0.8635 0.0621 0.0744 24 L 0.8608 0.0615 0.0777 25 M 0.8578 0.0540 0.0883 26 F 0.7811 0.0601 0.1588 27 N 0.6353 0.0435 0.3211 28 A 0.2908 0.0772 0.6320 29 N 0.1409 0.0614 0.7977 30 D 0.0412 0.1997 0.7591 31 N 0.0269 0.1927 0.7804 32 V 0.0574 0.3068 0.6358 33 E 0.0091 0.8499 0.1410 34 S 0.0056 0.9038 0.0907 35 Q 0.0055 0.9116 0.0829 36 L 0.0061 0.9343 0.0596 37 R 0.0047 0.9520 0.0432 38 P 0.0048 0.9471 0.0482 39 C 0.0050 0.9448 0.0502 40 I 0.0049 0.9445 0.0506 41 A 0.0049 0.9281 0.0670 42 N 0.0054 0.9018 0.0928 43 V 0.0050 0.9284 0.0666 44 A 0.0049 0.9411 0.0540 45 Q 0.0049 0.9392 0.0559 46 Y 0.0049 0.9437 0.0515 47 I 0.0049 0.9365 0.0586 48 Y 0.0051 0.9202 0.0747 49 E 0.0055 0.8987 0.0957 50 L 0.0117 0.8287 0.1597 51 T 0.0234 0.6579 0.3186 52 D 0.0338 0.3647 0.6015 53 Q 0.0403 0.1404 0.8193 54 Y 0.0661 0.0515 0.8824 55 S 0.0696 0.0648 0.8656 56 D 0.0308 0.3750 0.5942 57 S 0.0391 0.4271 0.5339 58 A 0.1287 0.2521 0.6192 59 F 0.5324 0.0309 0.4367 60 N 0.7215 0.0284 0.2501 61 G 0.8896 0.0107 0.0997 62 F 0.9053 0.0114 0.0833 63 V 0.8857 0.0155 0.0988 64 A 0.8161 0.0207 0.1633 65 I 0.5714 0.0380 0.3906 66 G 0.2104 0.0581 0.7314 67 A 0.0221 0.5764 0.4015 68 N 0.0164 0.7139 0.2697 69 Y 0.0122 0.8266 0.1612 70 W 0.0107 0.8503 0.1390 71 D 0.0089 0.8178 0.1733 72 S 0.0158 0.7133 0.2709 73 L 0.0604 0.3929 0.5467 74 Y 0.0610 0.1257 0.8133 75 P 0.0384 0.1723 0.7892 76 E 0.0438 0.1451 0.8111 77 S 0.0666 0.0944 0.8390 78 R 0.0903 0.0495 0.8602 79 P 0.0728 0.2609 0.6664 80 E 0.0265 0.5416 0.4319 81 M 0.0495 0.5063 0.4442 82 L 0.1066 0.2977 0.5957 83 K 0.0981 0.1409 0.7610 84 P 0.1129 0.1114 0.7758 85 F 0.1273 0.0680 0.8048 86 P 0.1182 0.0788 0.8030 87 A 0.1740 0.1001 0.7259 88 M 0.1497 0.0908 0.7595 89 Q 0.0901 0.1048 0.8052 90 E 0.0597 0.1367 0.8036 91 G 0.0475 0.1453 0.8072 92 N 0.0829 0.1632 0.7539 93 R 0.1818 0.1384 0.6798 94 E 0.2182 0.0913 0.6905 95 A 0.1235 0.0837 0.7928 96 P 0.0912 0.1166 0.7921 97 A 0.1313 0.0996 0.7691 98 I 0.1415 0.0443 0.8142 99 E 0.0985 0.1432 0.7584 100 Y 0.1492 0.0772 0.7736 101 D 0.3567 0.0344 0.6088 102 L 0.8443 0.0086 0.1471 103 F 0.9167 0.0049 0.0784 104 V 0.9270 0.0043 0.0687 105 H 0.9206 0.0042 0.0753 106 L 0.8547 0.0109 0.1344 107 R 0.6633 0.0187 0.3180 108 C 0.2257 0.0791 0.6951 109 D 0.0587 0.0786 0.8627 110 R 0.0817 0.1451 0.7731 111 Y 0.0120 0.7462 0.2418 112 D 0.0107 0.8453 0.1440 113 I 0.0060 0.9454 0.0486 114 L 0.0047 0.9590 0.0363 115 H 0.0047 0.9598 0.0355 116 L 0.0047 0.9607 0.0346 117 V 0.0047 0.9603 0.0350 118 A 0.0047 0.9601 0.0352 119 N 0.0047 0.9594 0.0359 120 E 0.0047 0.9588 0.0364 121 I 0.0048 0.9555 0.0398 122 S 0.0050 0.9459 0.0490 123 Q 0.0062 0.8921 0.1017 124 M 0.0119 0.7578 0.2303 125 F 0.0376 0.5337 0.4287 126 E 0.0245 0.4523 0.5232 127 D 0.0219 0.4053 0.5728 128 L 0.1089 0.3757 0.5155 129 V 0.4118 0.1085 0.4797 130 E 0.6815 0.0669 0.2516 131 L 0.7913 0.0635 0.1452 132 V 0.7786 0.0930 0.1285 133 E 0.7004 0.1162 0.1834 134 E 0.6419 0.1500 0.2082 135 E 0.5630 0.1554 0.2816 136 R 0.4443 0.1047 0.4510 137 G 0.4196 0.0558 0.5245 138 F 0.5554 0.0370 0.4076 139 R 0.6167 0.0386 0.3447 140 F 0.4513 0.0384 0.5103 141 M 0.1881 0.0495 0.7624 142 D 0.0977 0.0346 0.8676 143 S 0.0503 0.4078 0.5419 144 R 0.0854 0.4648 0.4497 145 D 0.1419 0.4993 0.3588 146 L 0.1419 0.4506 0.4075 147 T 0.1225 0.2346 0.6429 148 G 0.1618 0.1383 0.6999 149 F 0.2452 0.0898 0.6650 150 V 0.3432 0.0849 0.5719 151 D 0.2229 0.0733 0.7038 152 G 0.1429 0.1314 0.7257 153 T 0.1613 0.1102 0.7285 154 E 0.1576 0.0857 0.7567 155 N 0.0887 0.0386 0.8726 156 P 0.0406 0.1300 0.8294 157 K 0.0476 0.1695 0.7830 158 G 0.0529 0.2094 0.7378 159 R 0.0340 0.3455 0.6204 160 H 0.0653 0.4016 0.5331 161 R 0.1240 0.4664 0.4096 162 Q 0.2381 0.4552 0.3067 163 E 0.3566 0.4464 0.1970 164 V 0.4294 0.4289 0.1417 165 A 0.4603 0.3935 0.1462 166 L 0.4943 0.3446 0.1611 167 V 0.4516 0.2514 0.2970 168 G 0.2596 0.1366 0.6037 169 S 0.0959 0.0959 0.8082 170 E 0.0625 0.0808 0.8567 171 D 0.0668 0.0755 0.8577 172 P 0.0289 0.3259 0.6451 173 E 0.0327 0.3336 0.6337 174 F 0.0835 0.3383 0.5782 175 K 0.0729 0.2418 0.6853 176 G 0.0755 0.1425 0.7820 177 G 0.1205 0.2524 0.6271 178 S 0.1906 0.5036 0.3057 179 Y 0.2473 0.6473 0.1054 180 I 0.2643 0.6625 0.0732 181 H 0.2536 0.6875 0.0589 182 V 0.2241 0.7186 0.0573 183 Q 0.1828 0.7481 0.0691 184 K 0.1275 0.7940 0.0785 185 Y 0.0948 0.8198 0.0854 186 A 0.0661 0.8189 0.1150 187 H 0.0422 0.6949 0.2629 188 N 0.0498 0.4442 0.5060 189 L 0.0185 0.6516 0.3299 190 S 0.0093 0.7754 0.2153 191 K 0.0103 0.7681 0.2215 192 W 0.0191 0.7945 0.1864 193 H 0.0232 0.6176 0.3592 194 R 0.0346 0.4550 0.5104 195 L 0.0727 0.0859 0.8414 196 P 0.0684 0.0670 0.8646 197 L 0.0068 0.8332 0.1599 198 K 0.0053 0.8799 0.1148 199 K 0.0067 0.8784 0.1149 200 Q 0.0173 0.8930 0.0897 201 E 0.0397 0.8362 0.1241 202 D 0.0734 0.7207 0.2059 203 I 0.1102 0.5771 0.3128 204 I 0.1737 0.3709 0.4555 205 G 0.2034 0.1518 0.6448 206 R 0.2796 0.0882 0.6322 207 T 0.3728 0.0701 0.5570 208 K 0.2245 0.1287 0.6468 209 Q 0.1196 0.1257 0.7547 210 D 0.0607 0.0748 0.8645 211 N 0.0539 0.0458 0.9003 212 I 0.2706 0.0236 0.7059 213 E 0.4605 0.0243 0.5151 214 Y 0.2987 0.0722 0.6291 215 E 0.1416 0.1022 0.7562 216 S 0.0719 0.0995 0.8286 217 E 0.0992 0.0737 0.8270 218 D 0.1033 0.0678 0.8289 219 K 0.0996 0.0942 0.8063 220 P 0.0932 0.1347 0.7721 221 L 0.1037 0.1711 0.7252 222 T 0.1594 0.1695 0.6711 223 S 0.2403 0.2227 0.5370 224 H 0.3021 0.2378 0.4600 225 I 0.3605 0.2687 0.3708 226 K 0.4331 0.2296 0.3373 227 R 0.4796 0.1998 0.3206 228 V 0.5126 0.1194 0.3680 229 N 0.5395 0.0849 0.3755 230 L 0.4238 0.1622 0.4141 231 K 0.2960 0.1654 0.5386 232 D 0.1237 0.2094 0.6669 233 E 0.0412 0.1902 0.7685 234 N 0.0436 0.0951 0.8613 235 G 0.0475 0.0803 0.8722 236 K 0.0861 0.1297 0.7841 237 S 0.2242 0.1991 0.5766 238 I 0.3500 0.2505 0.3995 239 E 0.5197 0.2772 0.2031 240 I 0.5739 0.2929 0.1332 241 L 0.5440 0.3119 0.1440 242 R 0.5078 0.2701 0.2221 243 Q 0.4051 0.2241 0.3708 244 S 0.2949 0.1024 0.6027 245 M 0.2141 0.0271 0.7588 246 P 0.1416 0.0417 0.8167 247 Y 0.1152 0.1012 0.7836 248 G 0.0748 0.0966 0.8286 249 S 0.0955 0.0907 0.8139 250 L 0.0649 0.2686 0.6665 251 K 0.0673 0.2649 0.6678 252 E 0.1296 0.2879 0.5825 253 Q 0.2681 0.1526 0.5793 254 G 0.4751 0.0550 0.4699 255 L 0.7986 0.0205 0.1809 256 M 0.8938 0.0139 0.0923 257 F 0.9142 0.0118 0.0740 258 I 0.8938 0.0187 0.0874 259 S 0.8483 0.0267 0.1250 260 T 0.7458 0.0546 0.1995 261 C 0.5095 0.0897 0.4007 262 R 0.1345 0.1021 0.7634 263 T 0.0933 0.0371 0.8696 264 P 0.0100 0.8442 0.1457 265 D 0.0092 0.8973 0.0935 266 H 0.0081 0.9249 0.0669 267 F 0.0050 0.9457 0.0493 268 E 0.0051 0.9504 0.0445 269 K 0.0056 0.9542 0.0402 270 M 0.0050 0.9550 0.0400 271 L 0.0057 0.9524 0.0419 272 H 0.0056 0.9450 0.0494 273 S 0.0085 0.9090 0.0824 274 M 0.0145 0.8598 0.1257 275 V 0.0386 0.7280 0.2334 276 F 0.0426 0.4796 0.4778 277 G 0.0616 0.1801 0.7583 278 D 0.0527 0.0643 0.8829 279 G 0.0283 0.1111 0.8606 280 A 0.0441 0.1031 0.8529 281 G 0.0399 0.1237 0.8364 282 N 0.0681 0.2876 0.6444 283 H 0.1029 0.3846 0.5124 284 D 0.0812 0.5076 0.4112 285 H 0.0835 0.6436 0.2730 286 L 0.0685 0.7222 0.2093 287 M 0.0671 0.7061 0.2268 288 H 0.0769 0.6408 0.2824 289 F 0.1297 0.5321 0.3382 290 T 0.2263 0.2962 0.4775 291 S 0.2596 0.1574 0.5830 292 A 0.2336 0.1972 0.5692 293 L 0.2281 0.1870 0.5850 294 T 0.1863 0.1323 0.6814 295 G 0.1775 0.1386 0.6839 296 S 0.3049 0.1885 0.5066 297 S 0.5523 0.1617 0.2860 298 F 0.6550 0.1353 0.2096 299 F 0.6552 0.0964 0.2484 300 A 0.4707 0.0460 0.4833 301 P 0.1998 0.0401 0.7601 302 S 0.0830 0.1080 0.8090 303 L 0.0067 0.8837 0.1097 304 D 0.0051 0.9075 0.0874 305 F 0.0055 0.9137 0.0808 306 L 0.0069 0.8940 0.0992 307 M 0.0095 0.7959 0.1947 308 Q 0.0118 0.6363 0.3519 309 F 0.0470 0.4021 0.5509 310 D 0.0438 0.2905 0.6657 311 N 0.0522 0.0731 0.8747