# This file is the result of combining several RDB files, specifically # T0279.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0279.t2k.stride-ebghtl.rdb (weight 1.24869) # T0279.t2k.str2.rdb (weight 1.54758) # T0279.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 T0279.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0279 # 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 T0279.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 70 # # ============================================ # Comments from T0279.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0279 # 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 T0279.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 70 # # ============================================ # Comments from T0279.t2k.str2.rdb # ============================================ # TARGET T0279 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0279.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 70 # # ============================================ # Comments from T0279.t2k.alpha.rdb # ============================================ # TARGET T0279 # 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 T0279.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 70 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1286 0.1549 0.7164 2 R 0.1587 0.1685 0.6728 3 R 0.1457 0.1397 0.7147 4 L 0.1349 0.1005 0.7646 5 E 0.1139 0.1100 0.7760 6 E 0.1137 0.1431 0.7432 7 D 0.0957 0.1134 0.7910 8 A 0.1253 0.0572 0.8175 9 V 0.4416 0.0239 0.5345 10 R 0.8390 0.0044 0.1566 11 V 0.9119 0.0036 0.0845 12 A 0.9100 0.0039 0.0861 13 Y 0.8766 0.0054 0.1180 14 A 0.5941 0.0229 0.3830 15 G 0.1447 0.0139 0.8414 16 L 0.0498 0.1425 0.8077 17 R 0.0318 0.2798 0.6884 18 R 0.0387 0.3111 0.6502 19 K 0.0155 0.6478 0.3367 20 E 0.0120 0.8064 0.1816 21 A 0.0064 0.9124 0.0812 22 F 0.0055 0.9474 0.0471 23 K 0.0049 0.9566 0.0386 24 A 0.0047 0.9585 0.0368 25 L 0.0047 0.9598 0.0355 26 A 0.0047 0.9584 0.0369 27 E 0.0048 0.9493 0.0459 28 K 0.0051 0.9171 0.0778 29 L 0.0383 0.4038 0.5579 30 G 0.0352 0.0261 0.9387 31 F 0.0833 0.0113 0.9055 32 T 0.4466 0.0071 0.5463 33 P 0.8312 0.0057 0.1631 34 L 0.8472 0.0163 0.1365 35 L 0.8553 0.0054 0.1393 36 F 0.6286 0.0071 0.3643 37 P 0.4683 0.0107 0.5210 38 V 0.6802 0.0142 0.3056 39 Q 0.8146 0.0115 0.1739 40 A 0.8608 0.0059 0.1333 41 T 0.8004 0.0099 0.1896 42 E 0.6149 0.0111 0.3740 43 K 0.3732 0.0129 0.6139 44 V 0.1190 0.0357 0.8453 45 P 0.0610 0.0765 0.8625 46 V 0.0646 0.1005 0.8349 47 P 0.0198 0.3881 0.5921 48 E 0.0324 0.4677 0.4999 49 Y 0.0298 0.6393 0.3310 50 R 0.0183 0.7648 0.2169 51 D 0.0165 0.8116 0.1719 52 Q 0.0195 0.8273 0.1533 53 V 0.0246 0.8292 0.1463 54 R 0.0276 0.8054 0.1669 55 A 0.0232 0.7768 0.2001 56 L 0.0309 0.7198 0.2493 57 A 0.0440 0.4681 0.4878 58 Q 0.0477 0.1934 0.7589 59 G 0.0728 0.0908 0.8364 60 V 0.1329 0.0152 0.8518 61 D 0.1872 0.0461 0.7668 62 L 0.9127 0.0042 0.0831 63 F 0.9317 0.0033 0.0650 64 L 0.9295 0.0036 0.0669 65 A 0.9076 0.0051 0.0873 66 T 0.5849 0.0151 0.4001 67 T 0.1230 0.0266 0.8504 68 G 0.0099 0.7545 0.2356 69 V 0.0086 0.8700 0.1214 70 G 0.0054 0.9304 0.0641 71 V 0.0051 0.9529 0.0420 72 R 0.0054 0.9519 0.0427 73 D 0.0047 0.9512 0.0441 74 L 0.0047 0.9495 0.0457 75 L 0.0048 0.9509 0.0443 76 E 0.0050 0.9463 0.0487 77 A 0.0051 0.9380 0.0568 78 G 0.0056 0.9217 0.0727 79 K 0.0055 0.8958 0.0987 80 A 0.0079 0.8220 0.1701 81 L 0.0379 0.4837 0.4784 82 G 0.0412 0.2163 0.7425 83 L 0.0380 0.4171 0.5449 84 D 0.0306 0.6348 0.3346 85 L 0.0147 0.7422 0.2431 86 E 0.0144 0.7972 0.1884 87 G 0.0189 0.7793 0.2018 88 P 0.0176 0.7827 0.1997 89 L 0.0265 0.6901 0.2835 90 A 0.0267 0.3854 0.5879 91 K 0.0344 0.1297 0.8359 92 A 0.1332 0.0280 0.8388 93 F 0.3671 0.0252 0.6077 94 R 0.8407 0.0138 0.1455 95 L 0.8711 0.0134 0.1155 96 A 0.8630 0.0100 0.1270 97 R 0.5427 0.0303 0.4270 98 G 0.1173 0.0502 0.8325 99 A 0.0163 0.7463 0.2374 100 K 0.0104 0.8535 0.1361 101 A 0.0074 0.9292 0.0634 102 A 0.0048 0.9539 0.0413 103 R 0.0048 0.9561 0.0390 104 A 0.0047 0.9577 0.0376 105 L 0.0048 0.9571 0.0381 106 K 0.0050 0.9468 0.0482 107 E 0.0051 0.9210 0.0739 108 A 0.0391 0.4826 0.4784 109 G 0.0333 0.0438 0.9229 110 L 0.0814 0.0251 0.8935 111 P 0.1685 0.0209 0.8106 112 P 0.2235 0.1491 0.6274 113 H 0.2375 0.1836 0.5789 114 A 0.2721 0.1177 0.6102 115 V 0.1606 0.0463 0.7931 116 G 0.0740 0.0555 0.8705 117 D 0.0723 0.1121 0.8156 118 G 0.0703 0.1856 0.7441 119 T 0.1067 0.2829 0.6104 120 S 0.0103 0.8850 0.1047 121 K 0.0067 0.9316 0.0616 122 S 0.0056 0.9381 0.0564 123 L 0.0056 0.9391 0.0553 124 L 0.0063 0.9276 0.0661 125 P 0.0066 0.8619 0.1314 126 L 0.0092 0.7832 0.2076 127 L 0.0409 0.5897 0.3694 128 P 0.0222 0.5020 0.4758 129 Q 0.0223 0.4142 0.5635 130 G 0.0554 0.2427 0.7019 131 R 0.1063 0.0823 0.8114 132 G 0.1880 0.0653 0.7468 133 V 0.6953 0.0295 0.2752 134 A 0.8310 0.0202 0.1488 135 A 0.8656 0.0146 0.1198 136 L 0.8263 0.0152 0.1585 137 Q 0.6067 0.0284 0.3650 138 L 0.2124 0.0761 0.7115 139 Y 0.0853 0.1236 0.7911 140 G 0.0462 0.2325 0.7213 141 K 0.0467 0.2994 0.6538 142 P 0.0441 0.3573 0.5987 143 L 0.0374 0.5408 0.4218 144 P 0.0134 0.8323 0.1543 145 L 0.0114 0.8879 0.1007 146 L 0.0068 0.9275 0.0657 147 E 0.0051 0.9508 0.0441 148 N 0.0052 0.9555 0.0392 149 A 0.0047 0.9575 0.0378 150 L 0.0050 0.9560 0.0390 151 A 0.0052 0.9426 0.0522 152 E 0.0058 0.8633 0.1309 153 R 0.0394 0.2763 0.6843 154 G 0.0390 0.0197 0.9414 155 Y 0.1155 0.0117 0.8728 156 R 0.7382 0.0079 0.2539 157 V 0.8979 0.0035 0.0986 158 L 0.8840 0.0127 0.1033 159 P 0.9032 0.0043 0.0925 160 L 0.8050 0.0056 0.1893 161 M 0.6997 0.0063 0.2940 162 P 0.6441 0.0172 0.3387 163 Y 0.6876 0.0308 0.2816 164 R 0.6606 0.0447 0.2947 165 H 0.4629 0.0551 0.4821 166 L 0.2944 0.0390 0.6666 167 P 0.1469 0.0366 0.8165 168 D 0.0657 0.1383 0.7960 169 P 0.0433 0.2271 0.7296 170 E 0.0405 0.2563 0.7033 171 G 0.0526 0.2321 0.7153 172 I 0.0118 0.7939 0.1943 173 L 0.0066 0.9053 0.0881 174 R 0.0053 0.9351 0.0597 175 L 0.0048 0.9473 0.0479 176 E 0.0047 0.9526 0.0427 177 E 0.0050 0.9520 0.0430 178 A 0.0048 0.9497 0.0455 179 L 0.0057 0.9382 0.0560 180 L 0.0054 0.8932 0.1013 181 R 0.0300 0.4882 0.4819 182 G 0.0289 0.1126 0.8585 183 E 0.0664 0.0321 0.9015 184 V 0.1500 0.0070 0.8430 185 D 0.2984 0.0347 0.6669 186 A 0.9204 0.0041 0.0755 187 L 0.9312 0.0035 0.0653 188 A 0.9283 0.0040 0.0677 189 F 0.8953 0.0058 0.0989 190 V 0.4171 0.0223 0.5606 191 A 0.0873 0.0128 0.9000 192 A 0.0085 0.8323 0.1592 193 I 0.0052 0.9394 0.0553 194 Q 0.0049 0.9486 0.0465 195 V 0.0047 0.9560 0.0392 196 E 0.0047 0.9570 0.0383 197 F 0.0047 0.9552 0.0400 198 L 0.0048 0.9510 0.0441 199 F 0.0049 0.9440 0.0511 200 E 0.0051 0.9266 0.0683 201 G 0.0059 0.8873 0.1068 202 A 0.0164 0.7983 0.1854 203 K 0.0165 0.6882 0.2953 204 D 0.0287 0.5558 0.4155 205 P 0.0353 0.4253 0.5395 206 K 0.0393 0.3192 0.6415 207 A 0.0429 0.4524 0.5047 208 L 0.0372 0.5713 0.3916 209 R 0.0182 0.7457 0.2362 210 E 0.0147 0.7776 0.2077 211 A 0.0169 0.7644 0.2187 212 L 0.0237 0.7290 0.2473 213 N 0.0446 0.5625 0.3929 214 T 0.0311 0.3475 0.6214 215 R 0.0741 0.1329 0.7930 216 V 0.2132 0.0223 0.7645 217 K 0.5832 0.0128 0.4040 218 A 0.9035 0.0056 0.0909 219 L 0.9084 0.0062 0.0854 220 A 0.8842 0.0067 0.1091 221 V 0.5832 0.0268 0.3899 222 G 0.1411 0.0392 0.8197 223 R 0.0295 0.5933 0.3772 224 V 0.0193 0.7809 0.1997 225 T 0.0117 0.8745 0.1139 226 A 0.0050 0.9410 0.0540 227 D 0.0051 0.9518 0.0431 228 A 0.0047 0.9573 0.0380 229 L 0.0047 0.9571 0.0382 230 R 0.0049 0.9467 0.0484 231 E 0.0053 0.9150 0.0797 232 W 0.0383 0.4365 0.5252 233 G 0.0371 0.0352 0.9277 234 V 0.0859 0.0175 0.8966 235 K 0.2606 0.0221 0.7173 236 P 0.5847 0.0390 0.3762 237 F 0.7207 0.0348 0.2445 238 Y 0.7378 0.0232 0.2390 239 V 0.5464 0.0229 0.4307 240 D 0.2179 0.0546 0.7274 241 E 0.0883 0.1140 0.7976 242 T 0.0982 0.0872 0.8146 243 E 0.0968 0.0655 0.8377 244 R 0.0835 0.0423 0.8742 245 L 0.0078 0.8816 0.1106 246 G 0.0050 0.9429 0.0521 247 S 0.0052 0.9493 0.0455 248 L 0.0047 0.9563 0.0389 249 L 0.0047 0.9592 0.0361 250 Q 0.0047 0.9580 0.0373 251 G 0.0047 0.9580 0.0374 252 F 0.0047 0.9569 0.0384 253 K 0.0047 0.9539 0.0413 254 R 0.0049 0.9383 0.0568 255 A 0.0059 0.9103 0.0838 256 L 0.0111 0.8439 0.1450 257 Q 0.0099 0.7598 0.2303 258 K 0.0149 0.6938 0.2913 259 E 0.0176 0.5308 0.4517 260 V 0.0382 0.3470 0.6148 261 A 0.0252 0.0873 0.8875