# This file is the result of combining several RDB files, specifically # T0427.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0427.t2k.stride-ebghtl.rdb (weight 1.24869) # T0427.t2k.str2.rdb (weight 1.54758) # T0427.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 T0427.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0427 # 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 T0427.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 856 # # ============================================ # Comments from T0427.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0427 # 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 T0427.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 856 # # ============================================ # Comments from T0427.t2k.str2.rdb # ============================================ # TARGET T0427 # 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 T0427.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 856 # # ============================================ # Comments from T0427.t2k.alpha.rdb # ============================================ # TARGET T0427 # 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 T0427.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 856 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1410 0.0138 0.8452 2 S 0.4903 0.0127 0.4970 3 V 0.7604 0.0119 0.2277 4 Q 0.8204 0.0117 0.1679 5 L 0.4737 0.0201 0.5062 6 V 0.1036 0.1000 0.7964 7 K 0.0563 0.0332 0.9105 8 G 0.1643 0.0286 0.8071 9 V 0.6827 0.0054 0.3119 10 N 0.9109 0.0037 0.0854 11 L 0.9278 0.0031 0.0691 12 H 0.9221 0.0035 0.0744 13 V 0.9068 0.0036 0.0897 14 I 0.8473 0.0063 0.1463 15 P 0.6867 0.0181 0.2952 16 T 0.2213 0.0259 0.7527 17 E 0.0354 0.1011 0.8635 18 K 0.0406 0.0645 0.8949 19 Y 0.1648 0.0177 0.8175 20 K 0.2833 0.0202 0.6965 21 T 0.7692 0.0053 0.2256 22 V 0.8983 0.0037 0.0980 23 R 0.9245 0.0031 0.0724 24 L 0.9255 0.0034 0.0711 25 L 0.9288 0.0031 0.0681 26 V 0.9232 0.0034 0.0734 27 R 0.9103 0.0033 0.0864 28 F 0.8447 0.0051 0.1502 29 N 0.6081 0.0202 0.3717 30 T 0.2950 0.0448 0.6602 31 R 0.1028 0.0566 0.8406 32 L 0.1203 0.0983 0.7814 33 N 0.0835 0.2122 0.7043 34 H 0.0694 0.2112 0.7194 35 E 0.0523 0.1755 0.7722 36 T 0.0424 0.4651 0.4925 37 I 0.0309 0.5837 0.3855 38 T 0.0289 0.6139 0.3572 39 K 0.0123 0.8034 0.1843 40 R 0.0134 0.8183 0.1683 41 T 0.0189 0.8204 0.1607 42 L 0.0213 0.7887 0.1901 43 L 0.0178 0.8046 0.1776 44 S 0.0097 0.8569 0.1334 45 S 0.0091 0.8782 0.1128 46 L 0.0126 0.8636 0.1238 47 M 0.0193 0.7797 0.2010 48 E 0.0193 0.6099 0.3708 49 T 0.0342 0.3887 0.5771 50 N 0.0443 0.2672 0.6884 51 S 0.0272 0.3438 0.6290 52 L 0.0333 0.3970 0.5697 53 N 0.0414 0.4552 0.5034 54 Y 0.0465 0.5441 0.4094 55 P 0.0470 0.5630 0.3900 56 N 0.0235 0.8441 0.1324 57 Q 0.0103 0.9258 0.0639 58 V 0.0074 0.9472 0.0453 59 K 0.0069 0.9520 0.0411 60 L 0.0051 0.9551 0.0399 61 S 0.0051 0.9547 0.0402 62 E 0.0049 0.9514 0.0437 63 R 0.0058 0.9330 0.0612 64 L 0.0093 0.8824 0.1083 65 A 0.0176 0.7491 0.2333 66 E 0.0308 0.4473 0.5218 67 L 0.0360 0.2196 0.7443 68 Y 0.0593 0.1562 0.7845 69 G 0.0507 0.2040 0.7453 70 A 0.0638 0.1629 0.7733 71 S 0.0909 0.0890 0.8201 72 F 0.0718 0.0778 0.8504 73 G 0.0056 0.9063 0.0882 74 I 0.0049 0.9369 0.0582 75 G 0.0048 0.9484 0.0468 76 V 0.0047 0.9556 0.0397 77 S 0.0047 0.9544 0.0409 78 K 0.0048 0.9486 0.0466 79 K 0.0048 0.9403 0.0549 80 G 0.0059 0.9305 0.0636 81 N 0.0063 0.9009 0.0928 82 Q 0.0111 0.7782 0.2107 83 H 0.0517 0.4918 0.4565 84 W 0.0979 0.1545 0.7476 85 F 0.3225 0.1139 0.5636 86 N 0.6682 0.0803 0.2515 87 I 0.7272 0.0636 0.2091 88 S 0.7095 0.0394 0.2511 89 M 0.6094 0.0741 0.3164 90 N 0.5176 0.0765 0.4060 91 I 0.4496 0.0612 0.4892 92 V 0.2957 0.0616 0.6427 93 N 0.1565 0.1223 0.7212 94 D 0.1948 0.1412 0.6640 95 H 0.4408 0.1022 0.4570 96 Y 0.7222 0.0513 0.2266 97 L 0.8092 0.0527 0.1381 98 Q 0.8097 0.0618 0.1286 99 D 0.7662 0.0715 0.1622 100 S 0.5748 0.1676 0.2577 101 Q 0.4718 0.1871 0.3411 102 V 0.3180 0.1638 0.5183 103 L 0.1408 0.2135 0.6458 104 A 0.0240 0.6648 0.3112 105 E 0.0121 0.6964 0.2915 106 A 0.0171 0.6832 0.2997 107 V 0.0091 0.8651 0.1258 108 D 0.0049 0.9345 0.0606 109 F 0.0050 0.9388 0.0561 110 L 0.0048 0.9477 0.0475 111 K 0.0053 0.9462 0.0484 112 E 0.0053 0.9341 0.0606 113 I 0.0056 0.9219 0.0725 114 I 0.0094 0.8984 0.0922 115 F 0.0073 0.8857 0.1069 116 A 0.0077 0.9024 0.0899 117 P 0.0058 0.8789 0.1153 118 N 0.0102 0.8587 0.1311 119 I 0.0151 0.7648 0.2201 120 Q 0.0311 0.5676 0.4013 121 A 0.0734 0.1556 0.7711 122 G 0.0358 0.1888 0.7754 123 Q 0.0634 0.1693 0.7674 124 F 0.0990 0.0425 0.8585 125 E 0.0611 0.0320 0.9069 126 A 0.0053 0.8992 0.0955 127 E 0.0048 0.9225 0.0726 128 T 0.0050 0.9394 0.0556 129 F 0.0047 0.9521 0.0432 130 Q 0.0047 0.9492 0.0461 131 R 0.0048 0.9484 0.0468 132 E 0.0048 0.9510 0.0442 133 K 0.0048 0.9547 0.0405 134 E 0.0049 0.9547 0.0404 135 N 0.0048 0.9558 0.0394 136 L 0.0047 0.9562 0.0391 137 K 0.0047 0.9579 0.0374 138 A 0.0047 0.9561 0.0392 139 Y 0.0047 0.9546 0.0406 140 L 0.0048 0.9520 0.0433 141 E 0.0053 0.9322 0.0625 142 S 0.0069 0.8651 0.1280 143 I 0.0167 0.7788 0.2045 144 V 0.0200 0.6156 0.3645 145 E 0.0250 0.3355 0.6395 146 D 0.0798 0.0632 0.8570 147 K 0.0083 0.7355 0.2563 148 Q 0.0068 0.8375 0.1557 149 T 0.0067 0.9066 0.0867 150 Y 0.0074 0.9334 0.0592 151 A 0.0076 0.9236 0.0688 152 S 0.0056 0.9303 0.0641 153 L 0.0064 0.9373 0.0562 154 A 0.0055 0.9411 0.0535 155 L 0.0059 0.9385 0.0556 156 Q 0.0061 0.9282 0.0657 157 S 0.0076 0.9045 0.0879 158 V 0.0106 0.8350 0.1544 159 Y 0.0294 0.6146 0.3561 160 F 0.0826 0.1829 0.7345 161 N 0.0495 0.1326 0.8179 162 Q 0.0266 0.1452 0.8282 163 S 0.0416 0.1014 0.8570 164 E 0.1095 0.0504 0.8401 165 D 0.1137 0.1120 0.7743 166 Q 0.1238 0.1305 0.7457 167 K 0.1599 0.0949 0.7452 168 I 0.1973 0.0520 0.7507 169 P 0.1677 0.0529 0.7794 170 S 0.1546 0.1026 0.7427 171 F 0.1233 0.0831 0.7936 172 G 0.1036 0.0383 0.8580 173 T 0.0959 0.0788 0.8252 174 V 0.0116 0.8649 0.1235 175 A 0.0081 0.8675 0.1244 176 A 0.0142 0.8427 0.1431 177 L 0.0240 0.8292 0.1468 178 A 0.0114 0.6828 0.3059 179 E 0.0226 0.3801 0.5973 180 E 0.1194 0.0932 0.7874 181 T 0.0734 0.0430 0.8835 182 A 0.0051 0.9333 0.0617 183 A 0.0048 0.9436 0.0515 184 S 0.0048 0.9521 0.0431 185 L 0.0047 0.9566 0.0387 186 A 0.0047 0.9583 0.0370 187 A 0.0047 0.9523 0.0429 188 Y 0.0049 0.9473 0.0478 189 Y 0.0053 0.9378 0.0569 190 Q 0.0058 0.9097 0.0845 191 K 0.0113 0.8353 0.1534 192 M 0.0236 0.7038 0.2725 193 L 0.0993 0.2963 0.6044 194 A 0.1154 0.0699 0.8147 195 E 0.0443 0.1728 0.7829 196 D 0.0368 0.1171 0.8460 197 Q 0.2244 0.0525 0.7231 198 V 0.7415 0.0043 0.2542 199 D 0.9127 0.0034 0.0839 200 I 0.9316 0.0031 0.0654 201 F 0.9258 0.0035 0.0708 202 V 0.9162 0.0034 0.0805 203 L 0.7291 0.0234 0.2474 204 G 0.3685 0.0182 0.6133 205 D 0.2085 0.0200 0.7716 206 V 0.2232 0.0218 0.7550 207 N 0.0946 0.0173 0.8881 208 E 0.0052 0.8949 0.0998 209 A 0.0050 0.9358 0.0592 210 E 0.0049 0.9456 0.0494 211 L 0.0048 0.9526 0.0426 212 V 0.0047 0.9574 0.0380 213 P 0.0047 0.9569 0.0384 214 L 0.0048 0.9572 0.0380 215 F 0.0048 0.9548 0.0405 216 K 0.0048 0.9493 0.0458 217 Q 0.0060 0.9228 0.0712 218 L 0.0098 0.8595 0.1307 219 P 0.0412 0.6809 0.2779 220 F 0.0264 0.3768 0.5968 221 T 0.0334 0.2969 0.6697 222 P 0.0652 0.1656 0.7693 223 R 0.0563 0.1587 0.7850 224 E 0.0602 0.2114 0.7284 225 E 0.0584 0.1807 0.7608 226 G 0.0733 0.1611 0.7656 227 K 0.0947 0.1225 0.7828 228 A 0.1042 0.1071 0.7887 229 A 0.0978 0.0979 0.8043 230 I 0.1059 0.0918 0.8022 231 F 0.1187 0.0874 0.7939 232 Y 0.1198 0.0782 0.8019 233 N 0.1227 0.0729 0.8044 234 Q 0.1232 0.0721 0.8047 235 P 0.1163 0.0648 0.8189 236 I 0.1245 0.0707 0.8048 237 R 0.1467 0.0915 0.7618 238 N 0.1490 0.0883 0.7627 239 V 0.1742 0.0752 0.7507 240 I 0.2547 0.0615 0.6838 241 E 0.5031 0.0373 0.4596 242 E 0.7621 0.0192 0.2187 243 R 0.8355 0.0156 0.1489 244 T 0.8311 0.0152 0.1537 245 E 0.7325 0.0225 0.2450 246 R 0.4637 0.0307 0.5057 247 E 0.1698 0.0722 0.7580 248 V 0.1135 0.0768 0.8097 249 L 0.1257 0.1917 0.6826 250 A 0.1492 0.2571 0.5937 251 Q 0.2725 0.2660 0.4615 252 S 0.4244 0.1849 0.3906 253 K 0.6486 0.1501 0.2013 254 L 0.8035 0.0883 0.1081 255 N 0.7990 0.0934 0.1076 256 L 0.7684 0.0841 0.1475 257 A 0.6472 0.0883 0.2646 258 Y 0.4627 0.0756 0.4616 259 N 0.2958 0.1020 0.6022 260 T 0.1507 0.0987 0.7506 261 D 0.1105 0.0924 0.7971 262 I 0.0962 0.0812 0.8226 263 Y 0.1046 0.0987 0.7967 264 Y 0.0570 0.1606 0.7824 265 G 0.0445 0.1139 0.8417 266 D 0.0838 0.1075 0.8088 267 S 0.0092 0.5265 0.4643 268 Y 0.0120 0.5632 0.4248 269 Y 0.0171 0.7683 0.2146 270 F 0.0212 0.8581 0.1208 271 A 0.0054 0.9441 0.0505 272 L 0.0054 0.9521 0.0425 273 Q 0.0047 0.9559 0.0394 274 V 0.0047 0.9574 0.0378 275 F 0.0051 0.9551 0.0398 276 N 0.0055 0.9467 0.0479 277 G 0.0072 0.9194 0.0734 278 I 0.0126 0.8673 0.1201 279 F 0.0339 0.5888 0.3773 280 G 0.0360 0.2024 0.7616 281 G 0.0361 0.1342 0.8297 282 F 0.0406 0.2131 0.7462 283 P 0.0304 0.4685 0.5012 284 H 0.0272 0.6099 0.3629 285 S 0.0151 0.8202 0.1646 286 K 0.0075 0.9290 0.0636 287 L 0.0059 0.9332 0.0609 288 F 0.0066 0.9391 0.0543 289 M 0.0074 0.9439 0.0487 290 N 0.0077 0.9435 0.0488 291 V 0.0099 0.9422 0.0479 292 R 0.0122 0.9311 0.0567 293 E 0.0100 0.9037 0.0863 294 K 0.0143 0.8129 0.1728 295 E 0.0466 0.4226 0.5308 296 H 0.0482 0.1077 0.8441 297 L 0.2258 0.1213 0.6529 298 A 0.5465 0.0862 0.3673 299 Y 0.6509 0.0994 0.2498 300 Y 0.7226 0.0742 0.2032 301 A 0.6857 0.1169 0.1974 302 S 0.6793 0.1084 0.2124 303 S 0.5929 0.1211 0.2861 304 S 0.5246 0.1179 0.3576 305 I 0.4538 0.1130 0.4332 306 D 0.3480 0.0858 0.5662 307 T 0.1895 0.1188 0.6917 308 F 0.1707 0.0875 0.7418 309 R 0.1724 0.0679 0.7597 310 G 0.3011 0.0429 0.6560 311 F 0.6537 0.0185 0.3278 312 M 0.8635 0.0079 0.1287 313 T 0.9072 0.0048 0.0880 314 V 0.9084 0.0057 0.0860 315 Q 0.8746 0.0095 0.1159 316 T 0.7612 0.0235 0.2152 317 G 0.5242 0.0301 0.4457 318 I 0.2559 0.0284 0.7158 319 D 0.1115 0.0259 0.8626 320 G 0.0201 0.4573 0.5226 321 K 0.0144 0.4838 0.5018 322 N 0.0248 0.5740 0.4012 323 R 0.0063 0.9078 0.0858 324 N 0.0050 0.9472 0.0478 325 Q 0.0049 0.9548 0.0404 326 V 0.0050 0.9576 0.0374 327 L 0.0047 0.9596 0.0357 328 R 0.0047 0.9591 0.0362 329 L 0.0047 0.9579 0.0374 330 I 0.0047 0.9586 0.0367 331 S 0.0047 0.9600 0.0353 332 T 0.0047 0.9599 0.0355 333 E 0.0047 0.9586 0.0367 334 L 0.0047 0.9579 0.0374 335 E 0.0047 0.9578 0.0375 336 N 0.0048 0.9527 0.0425 337 I 0.0057 0.9407 0.0536 338 R 0.0063 0.9180 0.0756 339 L 0.0150 0.6920 0.2930 340 G 0.0441 0.2362 0.7197 341 K 0.0512 0.0272 0.9216 342 I 0.0664 0.0106 0.9230 343 R 0.0505 0.0114 0.9381 344 E 0.0052 0.9265 0.0682 345 L 0.0048 0.9442 0.0510 346 E 0.0048 0.9540 0.0413 347 I 0.0047 0.9598 0.0355 348 E 0.0047 0.9582 0.0371 349 Q 0.0047 0.9562 0.0391 350 T 0.0048 0.9562 0.0391 351 K 0.0048 0.9574 0.0378 352 A 0.0049 0.9540 0.0411 353 M 0.0050 0.9455 0.0495 354 L 0.0057 0.9362 0.0581 355 K 0.0059 0.9166 0.0775 356 N 0.0096 0.8451 0.1454 357 Q 0.0144 0.7598 0.2258 358 Y 0.0296 0.7535 0.2169 359 I 0.0419 0.7247 0.2334 360 L 0.0414 0.6553 0.3032 361 A 0.0487 0.5232 0.4280 362 L 0.0636 0.3926 0.5438 363 D 0.0579 0.2644 0.6777 364 N 0.0720 0.1425 0.7855 365 A 0.0107 0.7951 0.1942 366 G 0.0075 0.8946 0.0979 367 A 0.0067 0.9335 0.0598 368 W 0.0050 0.9503 0.0448 369 L 0.0048 0.9518 0.0434 370 E 0.0048 0.9513 0.0439 371 K 0.0048 0.9497 0.0455 372 E 0.0048 0.9492 0.0460 373 Y 0.0053 0.9426 0.0520 374 L 0.0059 0.9363 0.0579 375 N 0.0072 0.9293 0.0635 376 E 0.0096 0.9157 0.0746 377 L 0.0122 0.8535 0.1343 378 M 0.0221 0.6442 0.3337 379 P 0.0345 0.2320 0.7335 380 Q 0.0447 0.0758 0.8795 381 T 0.0675 0.0873 0.8452 382 M 0.0632 0.2195 0.7174 383 L 0.0600 0.2170 0.7230 384 T 0.0597 0.2302 0.7100 385 A 0.0067 0.9072 0.0861 386 E 0.0055 0.9269 0.0675 387 E 0.0055 0.9349 0.0596 388 W 0.0051 0.9444 0.0504 389 I 0.0048 0.9477 0.0475 390 A 0.0049 0.9415 0.0535 391 R 0.0057 0.9157 0.0786 392 I 0.0144 0.8555 0.1301 393 N 0.0088 0.7365 0.2548 394 A 0.0197 0.4570 0.5233 395 V 0.0872 0.1291 0.7837 396 T 0.0577 0.0430 0.8993 397 I 0.0050 0.9335 0.0615 398 P 0.0049 0.9448 0.0503 399 E 0.0049 0.9515 0.0436 400 I 0.0048 0.9563 0.0390 401 Q 0.0047 0.9586 0.0367 402 E 0.0047 0.9553 0.0400 403 V 0.0049 0.9526 0.0425 404 A 0.0057 0.9428 0.0515 405 K 0.0060 0.9225 0.0715 406 R 0.0101 0.8723 0.1177 407 L 0.0158 0.7943 0.1899 408 E 0.0460 0.4628 0.4912 409 L 0.0610 0.2021 0.7369 410 Q 0.0466 0.1623 0.7911 411 A 0.0512 0.1215 0.8273 412 I 0.1821 0.0394 0.7785 413 F 0.7401 0.0057 0.2542 414 F 0.9067 0.0035 0.0898 415 L 0.9264 0.0032 0.0704 416 E 0.9184 0.0034 0.0782 417 G 0.8930 0.0035 0.1035 418 E 0.6408 0.0141 0.3451 419 T 0.2853 0.0156 0.6992 420 E 0.1298 0.0399 0.8304 421 N 0.0613 0.0808 0.8579 422 D 0.0376 0.0443 0.9181