# This file is the result of combining several RDB files, specifically # T0310.t06.dssp-ebghstl.rdb (weight 1.53986) # T0310.t06.stride-ebghtl.rdb (weight 1.24869) # T0310.t06.str2.rdb (weight 1.54758) # T0310.t06.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 T0310.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0310 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0310.t06-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 3999 # # ============================================ # Comments from T0310.t06.stride-ebghtl.rdb # ============================================ # TARGET T0310 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0310.t06-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 3999 # # ============================================ # Comments from T0310.t06.str2.rdb # ============================================ # TARGET T0310 # 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 T0310.t06-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 3999 # # ============================================ # Comments from T0310.t06.alpha.rdb # ============================================ # TARGET T0310 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0310.t06-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 3999 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 T 0.0784 0.0633 0.8583 2 V 0.0049 0.9413 0.0538 3 E 0.0047 0.9549 0.0404 4 Q 0.0050 0.9547 0.0404 5 Q 0.0057 0.9533 0.0409 6 G 0.0047 0.9593 0.0360 7 E 0.0047 0.9607 0.0346 8 M 0.0047 0.9591 0.0361 9 A 0.0047 0.9591 0.0362 10 R 0.0048 0.9504 0.0448 11 S 0.0050 0.8994 0.0956 12 G 0.0098 0.8356 0.1547 13 G 0.0082 0.7973 0.1945 14 R 0.0095 0.8466 0.1438 15 M 0.0155 0.8347 0.1498 16 L 0.0188 0.7696 0.2116 17 A 0.0179 0.5598 0.4223 18 T 0.0299 0.2567 0.7134 19 L 0.0785 0.0474 0.8741 20 E 0.0555 0.0180 0.9265 21 P 0.0049 0.9471 0.0480 22 E 0.0047 0.9593 0.0360 23 Q 0.0047 0.9603 0.0350 24 R 0.0047 0.9603 0.0350 25 A 0.0047 0.9603 0.0351 26 E 0.0047 0.9600 0.0353 27 I 0.0047 0.9584 0.0368 28 I 0.0047 0.9591 0.0362 29 H 0.0047 0.9591 0.0362 30 H 0.0047 0.9497 0.0456 31 L 0.0049 0.9533 0.0418 32 A 0.0047 0.9578 0.0375 33 D 0.0047 0.9565 0.0388 34 L 0.0048 0.9502 0.0449 35 L 0.0049 0.9372 0.0580 36 T 0.0053 0.9035 0.0912 37 D 0.0089 0.7934 0.1977 38 Q 0.0113 0.7434 0.2454 39 R 0.0062 0.9175 0.0763 40 D 0.0049 0.9511 0.0441 41 E 0.0047 0.9568 0.0385 42 I 0.0047 0.9593 0.0360 43 L 0.0047 0.9578 0.0375 44 L 0.0048 0.9538 0.0414 45 A 0.0054 0.9389 0.0557 46 N 0.0063 0.8932 0.1004 47 K 0.0078 0.8626 0.1296 48 K 0.0113 0.8350 0.1537 49 D 0.0292 0.7316 0.2391 50 L 0.0426 0.5912 0.3662 51 E 0.0400 0.4400 0.5200 52 E 0.0689 0.3850 0.5461 53 A 0.0396 0.3026 0.6578 54 E 0.0296 0.3637 0.6068 55 G 0.0331 0.2189 0.7479 56 R 0.0479 0.2709 0.6812 57 L 0.0714 0.2148 0.7138 58 A 0.0618 0.2533 0.6849 59 A 0.0156 0.7565 0.2279 60 P 0.0069 0.8781 0.1150 61 L 0.0060 0.9089 0.0852 62 L 0.0067 0.9257 0.0676 63 K 0.0065 0.9185 0.0750 64 R 0.0069 0.8822 0.1109 65 L 0.0097 0.8315 0.1588 66 S 0.0083 0.8170 0.1746 67 L 0.0107 0.7870 0.2023 68 S 0.0175 0.7419 0.2406 69 T 0.0095 0.8231 0.1674 70 S 0.0069 0.8422 0.1508 71 K 0.0137 0.8675 0.1188 72 L 0.0057 0.9534 0.0409 73 N 0.0047 0.9581 0.0372 74 S 0.0047 0.9583 0.0371 75 L 0.0047 0.9597 0.0356 76 A 0.0047 0.9585 0.0368 77 I 0.0047 0.9422 0.0531 78 G 0.0047 0.9406 0.0546 79 L 0.0047 0.9573 0.0380 80 R 0.0047 0.9598 0.0355 81 Q 0.0047 0.9586 0.0367 82 I 0.0048 0.9539 0.0413 83 A 0.0049 0.9345 0.0606 84 A 0.0052 0.8816 0.1132 85 S 0.0082 0.7919 0.1999 86 S 0.0297 0.5857 0.3846 87 Q 0.0282 0.5048 0.4670 88 D 0.0440 0.3813 0.5747 89 S 0.0446 0.3587 0.5967 90 V 0.0663 0.2425 0.6913 91 G 0.0773 0.1331 0.7896 92 R 0.2604 0.1094 0.6302 93 V 0.5578 0.0792 0.3630 94 L 0.5028 0.0773 0.4199 95 R 0.3815 0.0894 0.5291 96 R 0.3063 0.1490 0.5447 97 T 0.4125 0.1555 0.4320 98 R 0.5154 0.1465 0.3382 99 I 0.4287 0.1623 0.4090 100 A 0.2022 0.1416 0.6562 101 K 0.0715 0.1585 0.7700 102 N 0.0640 0.0778 0.8583 103 L 0.2695 0.0435 0.6870 104 E 0.5239 0.0303 0.4458 105 L 0.7844 0.0188 0.1968 106 E 0.8396 0.0138 0.1467 107 Q 0.8938 0.0073 0.0989 108 V 0.8674 0.0070 0.1257 109 T 0.7847 0.0096 0.2057 110 V 0.5425 0.0136 0.4439 111 P 0.3294 0.0288 0.6418 112 I 0.3371 0.0454 0.6175 113 G 0.6037 0.0137 0.3826 114 V 0.8412 0.0060 0.1528 115 L 0.9212 0.0038 0.0749 116 L 0.9296 0.0035 0.0669 117 V 0.9304 0.0032 0.0664 118 I 0.8945 0.0055 0.1000 119 F 0.6437 0.0100 0.3462 120 E 0.1702 0.0801 0.7497 121 S 0.0710 0.1079 0.8211 122 R 0.0700 0.1140 0.8160 123 P 0.0367 0.3873 0.5760 124 D 0.0416 0.4787 0.4797 125 C 0.0349 0.6175 0.3476 126 L 0.0175 0.7819 0.2005 127 P 0.0063 0.9027 0.0910 128 Q 0.0064 0.9253 0.0682 129 V 0.0062 0.9409 0.0530 130 A 0.0047 0.9544 0.0409 131 A 0.0048 0.9587 0.0365 132 L 0.0048 0.9559 0.0393 133 A 0.0048 0.9521 0.0431 134 I 0.0054 0.9331 0.0615 135 A 0.0086 0.7945 0.1969 136 S 0.0531 0.3411 0.6059 137 G 0.0402 0.0743 0.8856 138 N 0.0812 0.0295 0.8894 139 G 0.5453 0.0235 0.4312 140 L 0.9033 0.0053 0.0914 141 L 0.9206 0.0048 0.0747 142 L 0.8551 0.0257 0.1192 143 K 0.6316 0.0341 0.3343 144 G 0.2276 0.0353 0.7371 145 G 0.0880 0.0753 0.8366 146 K 0.0332 0.2937 0.6731 147 E 0.0336 0.3191 0.6473 148 A 0.0341 0.2768 0.6891 149 A 0.0156 0.7151 0.2693 150 H 0.0121 0.8424 0.1454 151 S 0.0055 0.9368 0.0577 152 N 0.0047 0.9575 0.0377 153 R 0.0046 0.9614 0.0340 154 I 0.0046 0.9615 0.0339 155 L 0.0047 0.9610 0.0344 156 H 0.0046 0.9613 0.0341 157 L 0.0046 0.9605 0.0349 158 L 0.0046 0.9572 0.0381 159 T 0.0047 0.9580 0.0374 160 Q 0.0047 0.9601 0.0353 161 E 0.0047 0.9600 0.0353 162 A 0.0047 0.9603 0.0350 163 L 0.0047 0.9589 0.0364 164 S 0.0050 0.9488 0.0461 165 I 0.0096 0.8785 0.1119 166 H 0.0452 0.4445 0.5103 167 G 0.0380 0.0358 0.9262 168 V 0.0607 0.0244 0.9149 169 K 0.0469 0.1474 0.8057 170 E 0.3418 0.1601 0.4981 171 A 0.6605 0.0956 0.2438 172 V 0.7986 0.0488 0.1526 173 Q 0.8671 0.0321 0.1008 174 L 0.8793 0.0272 0.0935 175 V 0.8092 0.0227 0.1681 176 N 0.4940 0.0339 0.4722 177 T 0.1403 0.0503 0.8094 178 R 0.0644 0.2384 0.6972 179 E 0.0855 0.3614 0.5531 180 E 0.1462 0.3881 0.4657 181 V 0.1555 0.3210 0.5236 182 E 0.1360 0.2376 0.6264 183 L 0.0850 0.2344 0.6806 184 D 0.1030 0.1642 0.7328 185 K 0.0350 0.3158 0.6493 186 M 0.0993 0.2007 0.7000 187 I 0.3698 0.0663 0.5639 188 D 0.3699 0.0622 0.5679 189 L 0.8644 0.0118 0.1238 190 I 0.8972 0.0085 0.0943 191 I 0.8676 0.0105 0.1219 192 P 0.5877 0.0406 0.3717 193 R 0.2579 0.0363 0.7058 194 G 0.0734 0.0479 0.8787 195 S 0.0484 0.1836 0.7680 196 S 0.0056 0.9093 0.0851 197 Q 0.0048 0.9561 0.0392 198 L 0.0047 0.9578 0.0374 199 V 0.0047 0.9610 0.0344 200 R 0.0046 0.9617 0.0336 201 D 0.0046 0.9614 0.0340 202 I 0.0047 0.9584 0.0369 203 Q 0.0048 0.9535 0.0417 204 K 0.0057 0.9270 0.0672 205 A 0.0099 0.8173 0.1728 206 A 0.0489 0.5199 0.4312 207 K 0.0296 0.1952 0.7753 208 G 0.0516 0.0655 0.8829 209 I 0.1492 0.0243 0.8265 210 P 0.3183 0.0312 0.6505 211 V 0.4548 0.1221 0.4231 212 M 0.4646 0.1320 0.4034 213 G 0.3481 0.1341 0.5178 214 H 0.2147 0.0886 0.6966 215 S 0.0931 0.0584 0.8485 216 E 0.0777 0.1256 0.7967 217 G 0.0821 0.0837 0.8342 218 I 0.1890 0.0407 0.7703 219 C 0.2144 0.0210 0.7646 220 H 0.4056 0.0349 0.5596 221 M 0.7240 0.0206 0.2554 222 Y 0.8721 0.0100 0.1179 223 V 0.8111 0.0175 0.1714 224 D 0.2324 0.0197 0.7478 225 S 0.0154 0.1325 0.8521 226 E 0.0304 0.0759 0.8937 227 A 0.1064 0.0385 0.8551 228 S 0.1047 0.0260 0.8693 229 V 0.0054 0.9368 0.0578 230 D 0.0047 0.9572 0.0381 231 K 0.0047 0.9586 0.0366 232 V 0.0052 0.9582 0.0366 233 T 0.0047 0.9587 0.0366 234 R 0.0052 0.9569 0.0379 235 L 0.0053 0.9520 0.0427 236 V 0.0064 0.9387 0.0548 237 R 0.0081 0.8937 0.0982 238 D 0.0137 0.7636 0.2227 239 S 0.0166 0.5672 0.4161 240 K 0.0425 0.2721 0.6854 241 C 0.1115 0.1903 0.6982 242 E 0.1093 0.1355 0.7553 243 Y 0.1141 0.1217 0.7642 244 P 0.1153 0.2046 0.6800 245 A 0.2467 0.2178 0.5355 246 A 0.3665 0.1775 0.4560 247 C 0.3501 0.1586 0.4913 248 N 0.3134 0.1089 0.5776 249 A 0.3212 0.1475 0.5312 250 L 0.3824 0.2161 0.4015 251 E 0.4103 0.2341 0.3556 252 T 0.6120 0.2159 0.1721 253 L 0.7518 0.1417 0.1065 254 L 0.7969 0.0967 0.1063 255 I 0.6395 0.1093 0.2512 256 H 0.3389 0.1654 0.4957 257 R 0.0689 0.4884 0.4426 258 D 0.0391 0.5024 0.4585 259 L 0.0273 0.5719 0.4008 260 L 0.0455 0.3800 0.5745 261 R 0.0371 0.2988 0.6641 262 T 0.0363 0.5757 0.3880 263 P 0.0081 0.7783 0.2136 264 L 0.0073 0.9123 0.0804 265 F 0.0047 0.9568 0.0385 266 D 0.0047 0.9596 0.0357 267 Q 0.0047 0.9587 0.0366 268 I 0.0047 0.9587 0.0366 269 I 0.0047 0.9594 0.0360 270 D 0.0048 0.9525 0.0427 271 M 0.0050 0.9389 0.0561 272 L 0.0054 0.9241 0.0705 273 R 0.0063 0.9003 0.0935 274 V 0.0112 0.8577 0.1312 275 E 0.0612 0.7351 0.2037 276 Q 0.0814 0.5390 0.3796 277 V 0.1038 0.3994 0.4968 278 K 0.0861 0.2487 0.6651 279 I 0.0977 0.1707 0.7316 280 H 0.0607 0.2100 0.7293 281 A 0.0673 0.1622 0.7705 282 G 0.0627 0.0597 0.8776 283 P 0.0189 0.3154 0.6657 284 K 0.0284 0.2795 0.6920 285 F 0.0904 0.3565 0.5532 286 A 0.1491 0.2314 0.6195 287 S 0.2060 0.3249 0.4691 288 Y 0.2018 0.3872 0.4111 289 L 0.2225 0.2821 0.4954 290 T 0.1110 0.2256 0.6635 291 F 0.0534 0.3769 0.5697 292 V 0.0648 0.3984 0.5368 293 K 0.0524 0.5044 0.4432 294 S 0.0855 0.5591 0.3554 295 L 0.0918 0.6791 0.2291 296 R 0.1221 0.6567 0.2212 297 T 0.2108 0.5616 0.2276 298 E 0.2532 0.4927 0.2541 299 Y 0.2457 0.3834 0.3709 300 G 0.1581 0.1805 0.6614 301 D 0.2246 0.0918 0.6835 302 L 0.4409 0.0600 0.4992 303 E 0.6923 0.0410 0.2667 304 L 0.7697 0.0232 0.2071 305 C 0.8056 0.0133 0.1812 306 I 0.8737 0.0066 0.1196 307 E 0.8662 0.0064 0.1274 308 V 0.7912 0.0129 0.1959 309 V 0.4153 0.0377 0.5470 310 D 0.1036 0.0702 0.8262 311 N 0.0871 0.0521 0.8608 312 V 0.0048 0.9372 0.0579 313 Q 0.0047 0.9562 0.0391 314 D 0.0047 0.9562 0.0390 315 A 0.0049 0.9581 0.0370 316 I 0.0047 0.9597 0.0356 317 D 0.0047 0.9598 0.0356 318 H 0.0048 0.9547 0.0406 319 I 0.0049 0.9451 0.0500 320 H 0.0062 0.8546 0.1393 321 K 0.0106 0.6530 0.3364 322 Y 0.0504 0.2430 0.7065 323 G 0.0445 0.0861 0.8694 324 S 0.0722 0.1012 0.8267 325 S 0.1068 0.1286 0.7646 326 H 0.2606 0.1259 0.6136 327 T 0.4310 0.0888 0.4802 328 D 0.6037 0.0840 0.3123 329 V 0.8536 0.0304 0.1160 330 I 0.8806 0.0204 0.0990 331 V 0.8469 0.0238 0.1294 332 T 0.5453 0.0269 0.4279 333 E 0.0993 0.0665 0.8342 334 D 0.0956 0.0318 0.8726 335 E 0.0062 0.9065 0.0873 336 N 0.0054 0.9396 0.0550 337 T 0.0052 0.9484 0.0464 338 A 0.0047 0.9593 0.0360 339 E 0.0047 0.9600 0.0354 340 F 0.0047 0.9581 0.0372 341 F 0.0048 0.9537 0.0415 342 L 0.0054 0.9382 0.0564 343 Q 0.0062 0.8498 0.1440 344 H 0.0133 0.7277 0.2590 345 V 0.0795 0.3368 0.5837 346 D 0.0903 0.2193 0.6904 347 S 0.2800 0.1874 0.5326 348 A 0.4461 0.1151 0.4387 349 C 0.7226 0.0447 0.2328 350 V 0.8564 0.0215 0.1221 351 F 0.8909 0.0164 0.0927 352 W 0.8318 0.0187 0.1495 353 N 0.3648 0.0221 0.6131 354 A 0.1750 0.0584 0.7666 355 S 0.1560 0.0540 0.7900 356 T 0.1419 0.0395 0.8186 357 R 0.1109 0.0878 0.8013 358 F 0.1543 0.0935 0.7522 359 S 0.1514 0.0780 0.7706 360 D 0.1522 0.0619 0.7858 361 G 0.1928 0.0941 0.7131 362 Y 0.2176 0.1252 0.6572 363 R 0.2891 0.1254 0.5855 364 F 0.1967 0.1125 0.6908 365 G 0.1423 0.0924 0.7653 366 L 0.1717 0.1473 0.6810 367 G 0.1291 0.2013 0.6696 368 A 0.0949 0.4158 0.4894 369 E 0.1260 0.4541 0.4199 370 V 0.1056 0.4580 0.4364 371 G 0.1047 0.3893 0.5060 372 I 0.1135 0.4640 0.4224 373 S 0.1122 0.5604 0.3274 374 T 0.0470 0.8244 0.1286 375 S 0.0443 0.8381 0.1176 376 R 0.0462 0.8429 0.1109 377 I 0.0697 0.7863 0.1440 378 H 0.0901 0.6664 0.2435 379 A 0.1056 0.4805 0.4138 380 R 0.0993 0.2922 0.6085 381 G 0.1065 0.0420 0.8515 382 P 0.1907 0.0585 0.7508 383 V 0.4885 0.0717 0.4398 384 G 0.5787 0.0622 0.3592 385 L 0.4701 0.1418 0.3881 386 E 0.3127 0.1649 0.5223 387 G 0.1868 0.1508 0.6624 388 L 0.2164 0.1428 0.6409 389 L 0.2655 0.1281 0.6064 390 T 0.2882 0.1018 0.6100 391 T 0.3547 0.1106 0.5347 392 K 0.4645 0.1375 0.3980 393 W 0.6591 0.1054 0.2354 394 L 0.6825 0.1026 0.2148 395 L 0.6167 0.0683 0.3150 396 R 0.2923 0.0682 0.6395 397 G 0.1148 0.0521 0.8331 398 K 0.1012 0.0923 0.8065 399 D 0.1088 0.1344 0.7568 400 H 0.2147 0.1499 0.6354 401 V 0.3110 0.1642 0.5248 402 V 0.2655 0.2286 0.5060 403 S 0.1530 0.3618 0.4852 404 D 0.0958 0.4105 0.4937 405 F 0.0644 0.5149 0.4207 406 S 0.0730 0.4208 0.5062 407 E 0.0739 0.3479 0.5783 408 H 0.0858 0.2532 0.6610 409 G 0.0747 0.2202 0.7050 410 S 0.1109 0.2952 0.5939 411 L 0.1918 0.4059 0.4023 412 K 0.2815 0.3781 0.3404 413 Y 0.3210 0.3714 0.3076 414 L 0.3079 0.3414 0.3506 415 H 0.2787 0.2764 0.4449 416 E 0.1444 0.2422 0.6134 417 N 0.0804 0.1146 0.8050 418 L 0.1004 0.0315 0.8681 419 P 0.1240 0.0387 0.8374 420 I 0.1118 0.1002 0.7880 421 P 0.0765 0.2733 0.6503 422 Q 0.0667 0.4101 0.5232 423 R 0.0623 0.3189 0.6189 424 N 0.0805 0.1065 0.8130 425 T 0.0507 0.0531 0.8962