# This file is the result of combining several RDB files, specifically # T0278.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0278.t2k.stride-ebghtl.rdb (weight 1.24869) # T0278.t2k.str2.rdb (weight 1.54758) # T0278.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 T0278.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0278 # 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 T0278.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 2860 # # ============================================ # Comments from T0278.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0278 # 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 T0278.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 2860 # # ============================================ # Comments from T0278.t2k.str2.rdb # ============================================ # TARGET T0278 # 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 T0278.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 2860 # # ============================================ # Comments from T0278.t2k.alpha.rdb # ============================================ # TARGET T0278 # 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 T0278.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 2860 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0514 0.0268 0.9218 2 K 0.0931 0.0297 0.8772 3 R 0.1061 0.0400 0.8540 4 L 0.0752 0.0583 0.8665 5 S 0.0868 0.0783 0.8349 6 L 0.1409 0.1033 0.7557 7 R 0.1407 0.0709 0.7884 8 E 0.2099 0.1136 0.6765 9 A 0.3128 0.1784 0.5088 10 W 0.3098 0.1919 0.4983 11 P 0.2063 0.2153 0.5783 12 Y 0.1660 0.2784 0.5557 13 L 0.0853 0.5767 0.3380 14 K 0.0730 0.6030 0.3240 15 D 0.0681 0.5476 0.3843 16 L 0.0810 0.3920 0.5270 17 Q 0.0621 0.2555 0.6824 18 Q 0.0359 0.2212 0.7429 19 D 0.0585 0.1918 0.7497 20 P 0.0336 0.6712 0.2951 21 L 0.0180 0.8498 0.1322 22 A 0.0060 0.9283 0.0657 23 V 0.0054 0.9428 0.0519 24 L 0.0051 0.9471 0.0478 25 L 0.0048 0.9494 0.0458 26 E 0.0049 0.9523 0.0429 27 W 0.0049 0.9467 0.0484 28 G 0.0056 0.9231 0.0714 29 R 0.0068 0.8687 0.1245 30 A 0.0147 0.7375 0.2478 31 H 0.0617 0.2744 0.6639 32 P 0.0508 0.0541 0.8951 33 R 0.1295 0.0664 0.8042 34 L 0.5267 0.0617 0.4117 35 F 0.7163 0.0368 0.2470 36 L 0.7333 0.0328 0.2340 37 P 0.6209 0.0359 0.3432 38 L 0.3286 0.0610 0.6104 39 P 0.1539 0.0524 0.7936 40 R 0.1263 0.0405 0.8333 41 F 0.1693 0.0193 0.8113 42 P 0.3718 0.0165 0.6117 43 L 0.8415 0.0049 0.1536 44 A 0.9172 0.0035 0.0794 45 L 0.9199 0.0036 0.0765 46 I 0.8700 0.0066 0.1235 47 F 0.4827 0.0183 0.4991 48 D 0.1382 0.0098 0.8520 49 P 0.0064 0.8490 0.1446 50 E 0.0050 0.9370 0.0579 51 G 0.0052 0.9444 0.0504 52 V 0.0048 0.9535 0.0417 53 E 0.0049 0.9547 0.0403 54 G 0.0053 0.9489 0.0458 55 A 0.0063 0.9345 0.0593 56 L 0.0127 0.8818 0.1055 57 L 0.0204 0.7569 0.2227 58 A 0.0503 0.4782 0.4714 59 E 0.0357 0.3087 0.6557 60 G 0.0503 0.2806 0.6691 61 T 0.0815 0.3198 0.5987 62 T 0.1126 0.2662 0.6212 63 K 0.1105 0.2364 0.6531 64 A 0.0894 0.1998 0.7108 65 T 0.0851 0.1568 0.7582 66 F 0.0974 0.1121 0.7906 67 Q 0.1105 0.1172 0.7723 68 Y 0.1492 0.1565 0.6944 69 R 0.1634 0.2100 0.6266 70 A 0.2053 0.2605 0.5342 71 L 0.2337 0.2713 0.4950 72 S 0.2382 0.2351 0.5267 73 R 0.2154 0.2525 0.5321 74 L 0.1952 0.2014 0.6034 75 T 0.1766 0.1331 0.6903 76 G 0.1315 0.0931 0.7754 77 R 0.1760 0.0814 0.7426 78 G 0.4702 0.0523 0.4775 79 L 0.6917 0.0383 0.2700 80 L 0.6875 0.0368 0.2757 81 T 0.4363 0.0408 0.5229 82 D 0.1375 0.0699 0.7926 83 W 0.0564 0.0510 0.8926 84 G 0.0391 0.1955 0.7654 85 K 0.0123 0.8228 0.1649 86 S 0.0079 0.8990 0.0930 87 W 0.0057 0.9365 0.0578 88 K 0.0053 0.9463 0.0485 89 E 0.0066 0.9451 0.0483 90 A 0.0051 0.9449 0.0499 91 R 0.0065 0.9436 0.0499 92 K 0.0071 0.9286 0.0642 93 A 0.0091 0.8712 0.1198 94 L 0.0212 0.7906 0.1882 95 K 0.0273 0.6713 0.3014 96 D 0.0129 0.6911 0.2961 97 P 0.0210 0.5498 0.4293 98 F 0.0759 0.3024 0.6217 99 L 0.0640 0.1542 0.7818 100 P 0.0115 0.8040 0.1845 101 K 0.0078 0.8326 0.1597 102 S 0.0103 0.8476 0.1422 103 V 0.0122 0.8726 0.1152 104 R 0.0081 0.8789 0.1130 105 G 0.0097 0.8158 0.1745 106 Y 0.0110 0.8445 0.1445 107 R 0.0081 0.9145 0.0774 108 E 0.0050 0.9469 0.0481 109 A 0.0050 0.9516 0.0434 110 M 0.0048 0.9537 0.0415 111 E 0.0048 0.9576 0.0376 112 E 0.0048 0.9574 0.0377 113 E 0.0048 0.9569 0.0384 114 A 0.0047 0.9568 0.0385 115 W 0.0047 0.9569 0.0384 116 A 0.0048 0.9529 0.0424 117 F 0.0049 0.9464 0.0487 118 F 0.0057 0.9260 0.0684 119 G 0.0059 0.8608 0.1333 120 E 0.0111 0.7172 0.2716 121 W 0.0517 0.2865 0.6618 122 R 0.0260 0.1415 0.8324 123 G 0.0252 0.0756 0.8992 124 E 0.0933 0.0417 0.8650 125 E 0.3424 0.0269 0.6307 126 R 0.5862 0.0188 0.3950 127 D 0.3668 0.0155 0.6177 128 L 0.0181 0.7949 0.1870 129 D 0.0066 0.8890 0.1044 130 H 0.0053 0.9157 0.0790 131 E 0.0057 0.9193 0.0750 132 M 0.0076 0.8946 0.0979 133 L 0.0060 0.8925 0.1015 134 A 0.0067 0.8708 0.1224 135 L 0.0080 0.8597 0.1323 136 S 0.0102 0.8857 0.1041 137 L 0.0048 0.9422 0.0531 138 R 0.0048 0.9519 0.0434 139 L 0.0047 0.9583 0.0370 140 L 0.0047 0.9588 0.0365 141 G 0.0048 0.9568 0.0385 142 R 0.0058 0.9477 0.0464 143 A 0.0066 0.9336 0.0598 144 L 0.0102 0.8878 0.1019 145 F 0.0430 0.5820 0.3749 146 G 0.0369 0.1216 0.8415 147 K 0.0776 0.0721 0.8503 148 P 0.1233 0.0835 0.7932 149 L 0.0470 0.3225 0.6304 150 S 0.0399 0.2928 0.6672 151 P 0.0447 0.3481 0.6072 152 S 0.0383 0.4196 0.5420 153 L 0.0435 0.4508 0.5058 154 A 0.0281 0.6517 0.3202 155 E 0.0122 0.8543 0.1335 156 H 0.0086 0.8945 0.0969 157 A 0.0062 0.9282 0.0655 158 L 0.0056 0.9442 0.0503 159 K 0.0053 0.9473 0.0474 160 A 0.0051 0.9477 0.0472 161 L 0.0054 0.9432 0.0514 162 D 0.0057 0.9326 0.0617 163 R 0.0068 0.9034 0.0898 164 I 0.0098 0.8559 0.1343 165 M 0.0206 0.7786 0.2008 166 A 0.0204 0.7184 0.2613 167 Q 0.0268 0.6567 0.3165 168 T 0.0404 0.5574 0.4022 169 R 0.0502 0.4699 0.4798 170 S 0.0513 0.4699 0.4787 171 P 0.0564 0.4715 0.4721 172 L 0.0672 0.4357 0.4971 173 A 0.0645 0.4712 0.4642 174 L 0.0672 0.5079 0.4249 175 L 0.0436 0.5953 0.3611 176 D 0.0408 0.5889 0.3704 177 L 0.0507 0.5417 0.4076 178 A 0.0839 0.4196 0.4965 179 A 0.0486 0.4895 0.4619 180 E 0.0499 0.5557 0.3943 181 A 0.0405 0.5634 0.3961 182 R 0.0470 0.5782 0.3747 183 F 0.0534 0.5395 0.4071 184 R 0.0549 0.4471 0.4980 185 K 0.0446 0.3625 0.5930 186 D 0.0470 0.1823 0.7707 187 R 0.0529 0.1533 0.7938 188 G 0.0498 0.2807 0.6695 189 A 0.0390 0.3468 0.6142 190 L 0.0680 0.3840 0.5480 191 Y 0.0100 0.8987 0.0913 192 R 0.0069 0.9436 0.0496 193 E 0.0069 0.9509 0.0423 194 A 0.0069 0.9534 0.0397 195 E 0.0063 0.9530 0.0408 196 A 0.0068 0.9381 0.0551 197 L 0.0082 0.8994 0.0924 198 I 0.0135 0.8156 0.1709 199 V 0.0443 0.6774 0.2783 200 H 0.0420 0.5433 0.4147 201 P 0.0344 0.3827 0.5829 202 P 0.0411 0.1608 0.7981 203 L 0.0301 0.0774 0.8924 204 S 0.0702 0.0648 0.8650 205 H 0.1483 0.0421 0.8097 206 L 0.1789 0.0230 0.7981 207 P 0.0791 0.0218 0.8991 208 R 0.0055 0.9248 0.0697 209 E 0.0048 0.9400 0.0552 210 R 0.0048 0.9503 0.0449 211 A 0.0047 0.9572 0.0381 212 L 0.0047 0.9575 0.0378 213 S 0.0047 0.9565 0.0387 214 E 0.0048 0.9553 0.0400 215 A 0.0047 0.9572 0.0381 216 V 0.0048 0.9578 0.0374 217 T 0.0051 0.9534 0.0415 218 L 0.0052 0.9528 0.0420 219 L 0.0056 0.9455 0.0489 220 V 0.0067 0.9191 0.0743 221 A 0.0144 0.8174 0.1682 222 G 0.0207 0.5951 0.3842 223 H 0.0135 0.6872 0.2993 224 E 0.0113 0.7393 0.2494 225 T 0.0100 0.7811 0.2089 226 V 0.0058 0.8968 0.0974 227 A 0.0047 0.9519 0.0434 228 S 0.0047 0.9559 0.0394 229 A 0.0047 0.9580 0.0373 230 L 0.0047 0.9598 0.0355 231 T 0.0047 0.9606 0.0348 232 W 0.0046 0.9609 0.0344 233 S 0.0046 0.9612 0.0342 234 F 0.0047 0.9603 0.0351 235 L 0.0047 0.9596 0.0357 236 L 0.0049 0.9555 0.0396 237 L 0.0051 0.9408 0.0541 238 S 0.0060 0.8815 0.1126 239 H 0.0166 0.6411 0.3423 240 R 0.0823 0.1315 0.7862 241 P 0.0076 0.8927 0.0997 242 D 0.0056 0.9274 0.0670 243 W 0.0052 0.9438 0.0510 244 Q 0.0048 0.9564 0.0388 245 K 0.0051 0.9543 0.0406 246 R 0.0049 0.9512 0.0439 247 V 0.0049 0.9507 0.0444 248 A 0.0049 0.9501 0.0451 249 E 0.0053 0.9349 0.0599 250 S 0.0055 0.9278 0.0667 251 E 0.0054 0.9132 0.0814 252 E 0.0056 0.8988 0.0956 253 A 0.0066 0.8212 0.1723 254 A 0.0079 0.7946 0.1975 255 L 0.0081 0.8828 0.1090 256 A 0.0114 0.9119 0.0767 257 A 0.0131 0.9246 0.0623 258 F 0.0262 0.9170 0.0568 259 Q 0.0263 0.9150 0.0587 260 E 0.0316 0.8973 0.0711 261 A 0.0278 0.8830 0.0892 262 L 0.0423 0.8210 0.1367 263 R 0.0650 0.6895 0.2455 264 L 0.1039 0.4595 0.4366 265 Y 0.1171 0.0901 0.7928 266 P 0.0918 0.0508 0.8574 267 P 0.1083 0.0817 0.8100 268 A 0.1288 0.0722 0.7990 269 W 0.1304 0.0865 0.7831 270 I 0.1823 0.0818 0.7359 271 L 0.2533 0.0578 0.6889 272 T 0.3367 0.0696 0.5937 273 R 0.5373 0.0735 0.3891 274 R 0.6633 0.0455 0.2912 275 L 0.5832 0.0474 0.3694 276 E 0.3913 0.0781 0.5306 277 R 0.3386 0.0578 0.6036 278 P 0.4617 0.0397 0.4987 279 L 0.7719 0.0129 0.2152 280 L 0.8380 0.0123 0.1497 281 L 0.7218 0.0281 0.2502 282 G 0.1335 0.0344 0.8320 283 E 0.1151 0.0502 0.8346 284 D 0.7335 0.0099 0.2565 285 R 0.8237 0.0046 0.1717 286 L 0.6585 0.0067 0.3348 287 P 0.1562 0.0146 0.8292 288 Q 0.0320 0.0593 0.9087 289 G 0.0413 0.0371 0.9216 290 T 0.2819 0.0168 0.7012 291 T 0.7521 0.0089 0.2391 292 L 0.8790 0.0116 0.1094 293 V 0.8806 0.0145 0.1049 294 L 0.8013 0.0303 0.1683 295 S 0.5598 0.0669 0.3733 296 P 0.1705 0.5247 0.3048 297 Y 0.1003 0.6337 0.2660 298 V 0.0933 0.6671 0.2396 299 T 0.0932 0.5773 0.3295 300 Q 0.0955 0.3007 0.6038 301 R 0.0888 0.1932 0.7180 302 L 0.1203 0.1149 0.7648 303 Y 0.1243 0.1516 0.7241 304 F 0.1122 0.0733 0.8145 305 P 0.0782 0.0617 0.8602 306 E 0.1034 0.0479 0.8488 307 G 0.0224 0.4599 0.5177 308 E 0.0261 0.4185 0.5554 309 A 0.0996 0.4431 0.4573 310 F 0.2241 0.1030 0.6729 311 Q 0.1296 0.0503 0.8201 312 P 0.0209 0.5687 0.4104 313 E 0.0172 0.6390 0.3437 314 R 0.0390 0.6573 0.3036 315 F 0.0943 0.4072 0.4985 316 L 0.0994 0.2959 0.6047 317 A 0.0576 0.2972 0.6452 318 E 0.0477 0.2869 0.6654 319 R 0.0577 0.2103 0.7320 320 G 0.0670 0.1867 0.7462 321 T 0.0811 0.1408 0.7780 322 P 0.0876 0.1137 0.7987 323 S 0.0880 0.2302 0.6819 324 G 0.1022 0.3093 0.5885 325 R 0.1521 0.2682 0.5797 326 Y 0.3163 0.1566 0.5272 327 F 0.3332 0.0532 0.6136 328 P 0.2369 0.0716 0.6915 329 F 0.1544 0.0691 0.7765 330 G 0.1487 0.0675 0.7838 331 L 0.1001 0.0756 0.8243 332 G 0.0825 0.0613 0.8561 333 Q 0.0883 0.1381 0.7735 334 R 0.1209 0.1524 0.7267 335 L 0.1875 0.0991 0.7134 336 C 0.1051 0.0815 0.8133 337 L 0.0219 0.3895 0.5886 338 G 0.0155 0.5759 0.4086 339 R 0.0087 0.8670 0.1242 340 D 0.0054 0.9322 0.0624 341 F 0.0048 0.9494 0.0458 342 A 0.0047 0.9557 0.0396 343 L 0.0047 0.9586 0.0367 344 L 0.0047 0.9595 0.0358 345 E 0.0047 0.9591 0.0362 346 G 0.0047 0.9602 0.0351 347 P 0.0047 0.9605 0.0348 348 I 0.0047 0.9610 0.0344 349 V 0.0046 0.9612 0.0342 350 L 0.0047 0.9602 0.0351 351 R 0.0047 0.9602 0.0352 352 A 0.0048 0.9567 0.0385 353 F 0.0048 0.9495 0.0457 354 F 0.0055 0.9124 0.0822 355 R 0.0081 0.7519 0.2400 356 R 0.0188 0.5346 0.4466 357 F 0.1108 0.1233 0.7659 358 R 0.1959 0.0465 0.7576 359 L 0.4458 0.0336 0.5206 360 D 0.5277 0.0274 0.4449 361 P 0.4217 0.0250 0.5533 362 L 0.2046 0.0382 0.7572 363 P 0.0899 0.0890 0.8211 364 F 0.0662 0.0841 0.8497 365 P 0.0787 0.0896 0.8317 366 R 0.0941 0.1067 0.7992 367 V 0.0896 0.1142 0.7962 368 L 0.0908 0.1601 0.7491 369 A 0.1035 0.1820 0.7145 370 Q 0.1546 0.1271 0.7183 371 V 0.1969 0.0918 0.7113 372 T 0.1645 0.0520 0.7834 373 L 0.1896 0.1775 0.6329 374 R 0.2297 0.1843 0.5859 375 P 0.2770 0.1767 0.5463 376 E 0.3338 0.0838 0.5823 377 G 0.3391 0.0684 0.5925 378 G 0.4863 0.0410 0.4727 379 L 0.7414 0.0157 0.2429 380 P 0.8026 0.0124 0.1849 381 A 0.7690 0.0116 0.2194 382 R 0.5172 0.0173 0.4656 383 P 0.2769 0.0520 0.6710 384 R 0.1548 0.0996 0.7456 385 E 0.0835 0.0542 0.8623 386 G 0.1122 0.0438 0.8440 387 V 0.4157 0.0190 0.5653 388 R 0.3201 0.0169 0.6630 389 A 0.0740 0.0164 0.9096