# This file is the result of combining several RDB files, specifically # T0478.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0478.t2k.stride-ebghtl.rdb (weight 1.24869) # T0478.t2k.str2.rdb (weight 1.54758) # T0478.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 T0478.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0478 # 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 T0478.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 43 # # ============================================ # Comments from T0478.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0478 # 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 T0478.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 43 # # ============================================ # Comments from T0478.t2k.str2.rdb # ============================================ # TARGET T0478 # 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 T0478.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 43 # # ============================================ # Comments from T0478.t2k.alpha.rdb # ============================================ # TARGET T0478 # 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 T0478.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 43 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0925 0.0398 0.8677 2 S 0.1290 0.0503 0.8207 3 L 0.0984 0.1447 0.7569 4 D 0.0747 0.1611 0.7641 5 T 0.0742 0.2312 0.6947 6 G 0.0870 0.2350 0.6780 7 V 0.0931 0.2034 0.7035 8 T 0.0711 0.2579 0.6711 9 S 0.0335 0.5531 0.4133 10 V 0.0345 0.8004 0.1651 11 M 0.0313 0.8632 0.1056 12 F 0.0216 0.9013 0.0771 13 V 0.0192 0.9201 0.0607 14 E 0.0125 0.9318 0.0557 15 R 0.0111 0.9262 0.0627 16 S 0.0111 0.9274 0.0614 17 L 0.0064 0.9428 0.0507 18 N 0.0064 0.9436 0.0500 19 E 0.0065 0.9381 0.0554 20 I 0.0060 0.9425 0.0515 21 R 0.0050 0.9468 0.0481 22 F 0.0049 0.9546 0.0404 23 W 0.0048 0.9562 0.0390 24 S 0.0048 0.9569 0.0383 25 R 0.0048 0.9554 0.0398 26 I 0.0051 0.9462 0.0487 27 M 0.0056 0.9450 0.0494 28 K 0.0054 0.9444 0.0501 29 E 0.0056 0.9346 0.0598 30 H 0.0049 0.9386 0.0565 31 S 0.0050 0.9438 0.0513 32 F 0.0050 0.9474 0.0476 33 F 0.0053 0.9470 0.0477 34 L 0.0055 0.9388 0.0557 35 R 0.0065 0.9099 0.0836 36 L 0.0113 0.7935 0.1952 37 G 0.0212 0.5076 0.4711 38 F 0.0631 0.1023 0.8346 39 R 0.0513 0.0352 0.9135 40 C 0.0159 0.6420 0.3422 41 E 0.0110 0.6916 0.2974 42 D 0.0177 0.7255 0.2568 43 T 0.0150 0.7633 0.2217 44 Q 0.0138 0.7363 0.2499 45 L 0.0090 0.8382 0.1527 46 I 0.0060 0.9254 0.0686 47 E 0.0057 0.9367 0.0577 48 E 0.0052 0.9375 0.0573 49 A 0.0050 0.9485 0.0464 50 N 0.0049 0.9443 0.0508 51 Q 0.0049 0.9404 0.0547 52 F 0.0048 0.9457 0.0495 53 Y 0.0048 0.9502 0.0450 54 R 0.0049 0.9443 0.0507 55 L 0.0051 0.9374 0.0575 56 F 0.0052 0.9484 0.0463 57 E 0.0050 0.9492 0.0458 58 H 0.0051 0.9466 0.0483 59 I 0.0049 0.9477 0.0474 60 E 0.0050 0.9460 0.0490 61 Q 0.0054 0.9336 0.0610 62 I 0.0065 0.9135 0.0800 63 A 0.0162 0.8700 0.1138 64 H 0.0227 0.7815 0.1958 65 S 0.0347 0.6720 0.2933 66 Y 0.0567 0.4970 0.4463 67 T 0.0648 0.2947 0.6405 68 N 0.0524 0.1598 0.7878 69 E 0.0526 0.1275 0.8200 70 T 0.0994 0.0975 0.8031 71 D 0.0883 0.1049 0.8068 72 P 0.0597 0.2774 0.6629 73 E 0.0347 0.5812 0.3841 74 Q 0.0534 0.6578 0.2888 75 I 0.0620 0.7877 0.1503 76 K 0.0661 0.8031 0.1308 77 R 0.0718 0.7985 0.1297 78 F 0.0392 0.8172 0.1437 79 N 0.0200 0.8274 0.1526 80 A 0.0051 0.9505 0.0444 81 E 0.0057 0.9498 0.0445 82 V 0.0048 0.9530 0.0422 83 Q 0.0047 0.9586 0.0367 84 Q 0.0047 0.9567 0.0386 85 A 0.0048 0.9563 0.0390 86 A 0.0047 0.9568 0.0385 87 T 0.0048 0.9549 0.0404 88 N 0.0049 0.9462 0.0490 89 I 0.0052 0.9390 0.0559 90 W 0.0056 0.9390 0.0554 91 G 0.0054 0.9228 0.0718 92 F 0.0061 0.9186 0.0752 93 K 0.0054 0.9336 0.0610 94 R 0.0052 0.9348 0.0600 95 K 0.0054 0.9370 0.0575 96 I 0.0051 0.9397 0.0551 97 L 0.0061 0.9388 0.0551 98 G 0.0074 0.9219 0.0708 99 L 0.0125 0.8705 0.1170 100 I 0.0311 0.8353 0.1336 101 L 0.0698 0.7151 0.2152 102 T 0.0817 0.5616 0.3567 103 C 0.1036 0.3344 0.5620 104 K 0.1728 0.2125 0.6148 105 L 0.2905 0.1701 0.5394 106 P 0.2833 0.1166 0.6001 107 G 0.1997 0.1272 0.6731 108 Q 0.0915 0.1068 0.8016 109 N 0.0667 0.1110 0.8223 110 N 0.1021 0.1572 0.7407 111 F 0.0701 0.2386 0.6913 112 P 0.0255 0.6770 0.2975 113 L 0.0419 0.7469 0.2112 114 L 0.0356 0.8296 0.1348 115 V 0.0105 0.9009 0.0886 116 D 0.0051 0.9493 0.0455 117 H 0.0048 0.9506 0.0445 118 T 0.0048 0.9526 0.0426 119 S 0.0049 0.9556 0.0395 120 R 0.0049 0.9539 0.0412 121 E 0.0047 0.9553 0.0399 122 A 0.0047 0.9582 0.0371 123 D 0.0047 0.9591 0.0362 124 Y 0.0047 0.9576 0.0376 125 F 0.0047 0.9583 0.0370 126 R 0.0047 0.9594 0.0359 127 K 0.0047 0.9578 0.0375 128 R 0.0047 0.9573 0.0380 129 L 0.0047 0.9552 0.0400 130 I 0.0047 0.9503 0.0449 131 Q 0.0048 0.9329 0.0623 132 L 0.0058 0.9038 0.0904 133 N 0.0068 0.8266 0.1666 134 E 0.0396 0.4202 0.5402 135 G 0.0318 0.0922 0.8761 136 K 0.0694 0.0612 0.8694 137 L 0.1507 0.0653 0.7841 138 D 0.0814 0.0769 0.8418 139 A 0.0931 0.1638 0.7431 140 L 0.0644 0.2577 0.6780 141 P 0.0383 0.4042 0.5575 142 D 0.0318 0.5568 0.4113 143 A 0.0323 0.6354 0.3323 144 I 0.0348 0.7523 0.2129 145 I 0.0302 0.7742 0.1956 146 K 0.0353 0.7753 0.1894 147 E 0.0375 0.8005 0.1620 148 N 0.0537 0.8151 0.1313 149 V 0.0793 0.8259 0.0948 150 F 0.0859 0.8060 0.1081 151 F 0.0511 0.8503 0.0985 152 L 0.0082 0.9284 0.0634 153 R 0.0056 0.9398 0.0547 154 I 0.0057 0.9356 0.0587 155 M 0.0059 0.9274 0.0667 156 A 0.0062 0.9214 0.0724 157 D 0.0072 0.8675 0.1253 158 H 0.0075 0.8639 0.1286 159 A 0.0104 0.8560 0.1336 160 K 0.0067 0.8111 0.1822 161 F 0.0103 0.8148 0.1749 162 I 0.0178 0.7936 0.1886 163 G 0.0184 0.7329 0.2487 164 H 0.0180 0.6610 0.3210 165 L 0.0344 0.5292 0.4364 166 L 0.0658 0.2453 0.6889 167 D 0.0783 0.1617 0.7599 168 P 0.0064 0.7986 0.1950 169 S 0.0072 0.8327 0.1601 170 E 0.0050 0.9330 0.0620 171 R 0.0049 0.9462 0.0489 172 K 0.0050 0.9511 0.0439 173 L 0.0048 0.9545 0.0408 174 V 0.0048 0.9556 0.0396 175 D 0.0049 0.9528 0.0423 176 T 0.0051 0.9386 0.0563 177 A 0.0054 0.9413 0.0533 178 R 0.0054 0.9390 0.0557 179 N 0.0056 0.9298 0.0646 180 F 0.0060 0.9207 0.0733 181 S 0.0060 0.9347 0.0593 182 N 0.0059 0.9222 0.0719 183 D 0.0063 0.9127 0.0809 184 F 0.0058 0.9355 0.0586 185 D 0.0050 0.9442 0.0507 186 E 0.0050 0.9480 0.0470 187 L 0.0048 0.9542 0.0411 188 M 0.0047 0.9567 0.0386 189 Y 0.0048 0.9545 0.0408 190 Q 0.0048 0.9513 0.0439 191 A 0.0051 0.9509 0.0440 192 I 0.0054 0.9414 0.0532 193 D 0.0073 0.9159 0.0768 194 L 0.0079 0.8954 0.0967 195 E 0.0136 0.8474 0.1390 196 S 0.0131 0.7230 0.2639 197 M 0.0246 0.6445 0.3309 198 K 0.0528 0.4730 0.4742 199 P 0.0238 0.4052 0.5710 200 Q 0.0328 0.3121 0.6551 201 S 0.0438 0.2843 0.6719 202 Q 0.0401 0.2186 0.7413 203 T 0.0558 0.2161 0.7281 204 A 0.0514 0.4042 0.5444 205 P 0.0356 0.5700 0.3943 206 L 0.0386 0.6806 0.2808 207 L 0.0137 0.8207 0.1656 208 D 0.0140 0.8233 0.1628 209 Q 0.0130 0.8149 0.1721 210 F 0.0209 0.8135 0.1656 211 L 0.0184 0.8321 0.1495 212 D 0.0075 0.9020 0.0905 213 Q 0.0094 0.9074 0.0831 214 N 0.0062 0.9326 0.0612 215 R 0.0050 0.9518 0.0431 216 V 0.0048 0.9537 0.0416 217 S 0.0048 0.9540 0.0412 218 V 0.0049 0.9546 0.0405 219 A 0.0052 0.9526 0.0422 220 S 0.0060 0.9410 0.0530 221 L 0.0063 0.9441 0.0496 222 R 0.0059 0.9479 0.0462 223 D 0.0059 0.9399 0.0543 224 F 0.0051 0.9448 0.0500 225 K 0.0051 0.9525 0.0424 226 K 0.0049 0.9490 0.0461 227 T 0.0056 0.9396 0.0548 228 A 0.0085 0.9230 0.0685 229 R 0.0072 0.9040 0.0888 230 D 0.0109 0.8683 0.1209 231 L 0.0135 0.8306 0.1560 232 I 0.0281 0.8072 0.1647 233 E 0.0296 0.7861 0.1843 234 Q 0.0326 0.6720 0.2954 235 C 0.0491 0.6023 0.3486 236 K 0.1342 0.5962 0.2696 237 I 0.2847 0.5890 0.1264 238 K 0.3038 0.5848 0.1114 239 S 0.2280 0.6345 0.1375 240 I 0.1942 0.6743 0.1316 241 I 0.1296 0.7039 0.1665 242 H 0.0750 0.6934 0.2315 243 P 0.0264 0.7651 0.2085 244 L 0.0405 0.6995 0.2601 245 L 0.0381 0.6556 0.3063 246 A 0.0193 0.7196 0.2611 247 D 0.0141 0.7097 0.2762 248 H 0.0325 0.6884 0.2791 249 V 0.0676 0.7294 0.2030 250 F 0.0919 0.7738 0.1342 251 R 0.0496 0.8061 0.1443 252 E 0.0388 0.8397 0.1215 253 A 0.0130 0.9042 0.0829 254 D 0.0078 0.9238 0.0684 255 R 0.0069 0.9370 0.0561 256 F 0.0054 0.9516 0.0430 257 L 0.0049 0.9555 0.0395 258 E 0.0048 0.9561 0.0390 259 I 0.0049 0.9525 0.0426 260 I 0.0058 0.9421 0.0520 261 D 0.0060 0.9064 0.0876 262 M 0.0079 0.8456 0.1465 263 Y 0.0279 0.7442 0.2279 264 D 0.0284 0.6460 0.3256 265 V 0.0342 0.4493 0.5165 266 H 0.0640 0.2850 0.6510 267 L 0.0884 0.1260 0.7857 268 T 0.0729 0.0760 0.8511 269 N 0.0592 0.1867 0.7541 270 I 0.0643 0.1718 0.7639 271 Q 0.0985 0.1122 0.7894 272 S 0.1143 0.0532 0.8325 273 Q 0.0600 0.1357 0.8043 274 P 0.0708 0.1240 0.8052 275 R 0.0773 0.0793 0.8435 276 E 0.0879 0.0719 0.8402 277 G 0.0748 0.1637 0.7616 278 H 0.0842 0.2032 0.7125 279 H 0.0746 0.2975 0.6279 280 H 0.0933 0.2754 0.6313 281 H 0.1087 0.1760 0.7154 282 H 0.0844 0.0945 0.8210 283 H 0.0443 0.0361 0.9196