# This file is the result of combining several RDB files, specifically # T0310.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0310.t2k.stride-ebghtl.rdb (weight 1.24869) # T0310.t2k.str2.rdb (weight 1.54758) # T0310.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 T0310.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0310 # 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 T0310.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 507 # # ============================================ # Comments from T0310.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0310 # 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 T0310.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 507 # # ============================================ # Comments from T0310.t2k.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.t2k-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 158.363 # # ============================================ # Comments from T0310.t2k.alpha.rdb # ============================================ # TARGET T0310 # 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 T0310.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 507 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 T 0.0530 0.5440 0.4030 2 V 0.0079 0.9114 0.0806 3 E 0.0062 0.9284 0.0654 4 Q 0.0058 0.9381 0.0561 5 Q 0.0050 0.9426 0.0524 6 G 0.0055 0.9489 0.0456 7 E 0.0056 0.9480 0.0464 8 M 0.0060 0.9468 0.0472 9 A 0.0053 0.9475 0.0471 10 R 0.0055 0.9438 0.0507 11 S 0.0054 0.9377 0.0569 12 G 0.0056 0.9206 0.0738 13 G 0.0067 0.9078 0.0855 14 R 0.0061 0.9004 0.0935 15 M 0.0070 0.8742 0.1188 16 L 0.0098 0.7663 0.2239 17 A 0.0102 0.5614 0.4284 18 T 0.0190 0.2997 0.6812 19 L 0.0603 0.0746 0.8651 20 E 0.0512 0.0252 0.9236 21 P 0.0057 0.9143 0.0800 22 E 0.0049 0.9405 0.0546 23 Q 0.0053 0.9481 0.0466 24 R 0.0047 0.9585 0.0368 25 A 0.0051 0.9549 0.0400 26 E 0.0049 0.9529 0.0422 27 I 0.0049 0.9536 0.0415 28 I 0.0048 0.9548 0.0404 29 H 0.0049 0.9557 0.0393 30 H 0.0050 0.9573 0.0377 31 L 0.0048 0.9559 0.0393 32 A 0.0047 0.9554 0.0399 33 D 0.0048 0.9441 0.0512 34 L 0.0050 0.9334 0.0616 35 L 0.0054 0.9257 0.0689 36 T 0.0057 0.8998 0.0945 37 D 0.0117 0.8289 0.1595 38 Q 0.0284 0.7420 0.2297 39 R 0.0095 0.8889 0.1016 40 D 0.0067 0.9371 0.0563 41 E 0.0050 0.9446 0.0503 42 I 0.0047 0.9548 0.0405 43 L 0.0047 0.9542 0.0411 44 L 0.0047 0.9489 0.0464 45 A 0.0051 0.9309 0.0640 46 N 0.0067 0.8853 0.1080 47 K 0.0065 0.8884 0.1051 48 K 0.0077 0.8829 0.1094 49 D 0.0081 0.8269 0.1650 50 L 0.0186 0.7785 0.2030 51 E 0.0167 0.7459 0.2374 52 E 0.0159 0.8039 0.1802 53 A 0.0254 0.7387 0.2360 54 E 0.0173 0.7847 0.1981 55 G 0.0129 0.7562 0.2309 56 R 0.0248 0.6460 0.3293 57 L 0.0272 0.5385 0.4343 58 A 0.0296 0.5375 0.4329 59 A 0.0202 0.6539 0.3259 60 P 0.0081 0.8464 0.1455 61 L 0.0071 0.8887 0.1041 62 L 0.0082 0.8983 0.0935 63 K 0.0078 0.9049 0.0873 64 R 0.0089 0.8726 0.1186 65 L 0.0075 0.8581 0.1344 66 S 0.0098 0.7412 0.2490 67 L 0.0131 0.5488 0.4381 68 S 0.0257 0.4066 0.5677 69 T 0.0375 0.3296 0.6329 70 S 0.0049 0.9231 0.0720 71 K 0.0050 0.9301 0.0649 72 L 0.0048 0.9423 0.0529 73 N 0.0047 0.9483 0.0470 74 S 0.0048 0.9482 0.0470 75 L 0.0049 0.9392 0.0559 76 A 0.0049 0.9404 0.0547 77 I 0.0051 0.9402 0.0547 78 G 0.0075 0.8992 0.0932 79 L 0.0097 0.8552 0.1352 80 R 0.0155 0.8534 0.1311 81 Q 0.0150 0.8708 0.1142 82 I 0.0137 0.8378 0.1485 83 A 0.0238 0.8023 0.1738 84 A 0.0284 0.7039 0.2677 85 S 0.0332 0.4389 0.5279 86 S 0.0513 0.1691 0.7795 87 Q 0.0582 0.1515 0.7903 88 D 0.0688 0.1056 0.8256 89 S 0.0611 0.1684 0.7705 90 V 0.0971 0.1496 0.7533 91 G 0.1463 0.1174 0.7363 92 R 0.3208 0.0891 0.5902 93 V 0.5891 0.0735 0.3374 94 L 0.5925 0.0972 0.3103 95 R 0.5358 0.0887 0.3755 96 R 0.5500 0.0832 0.3668 97 T 0.6003 0.0750 0.3247 98 R 0.6389 0.0560 0.3051 99 I 0.3886 0.0576 0.5538 100 A 0.1288 0.0988 0.7724 101 K 0.0516 0.0765 0.8719 102 N 0.0702 0.0595 0.8703 103 L 0.3498 0.0298 0.6204 104 E 0.6987 0.0142 0.2870 105 L 0.8048 0.0114 0.1837 106 E 0.8548 0.0112 0.1339 107 Q 0.8875 0.0052 0.1073 108 V 0.8612 0.0058 0.1330 109 T 0.8200 0.0077 0.1722 110 V 0.6460 0.0107 0.3433 111 P 0.3679 0.0213 0.6107 112 I 0.3437 0.0405 0.6158 113 G 0.6182 0.0189 0.3629 114 V 0.8331 0.0039 0.1630 115 L 0.9134 0.0053 0.0813 116 L 0.9202 0.0037 0.0761 117 V 0.8974 0.0043 0.0982 118 I 0.8065 0.0137 0.1799 119 F 0.5855 0.0180 0.3964 120 E 0.2590 0.0799 0.6611 121 S 0.1172 0.1066 0.7762 122 R 0.0692 0.1078 0.8230 123 P 0.0717 0.1725 0.7558 124 D 0.1443 0.3359 0.5198 125 C 0.1206 0.5587 0.3208 126 L 0.0411 0.7389 0.2200 127 P 0.0172 0.8898 0.0930 128 Q 0.0130 0.9264 0.0606 129 V 0.0077 0.9437 0.0486 130 A 0.0065 0.9502 0.0433 131 A 0.0062 0.9516 0.0422 132 L 0.0058 0.9528 0.0414 133 A 0.0061 0.9505 0.0435 134 I 0.0078 0.9355 0.0566 135 A 0.0098 0.8058 0.1844 136 S 0.0397 0.4977 0.4626 137 G 0.0330 0.0858 0.8813 138 N 0.0688 0.0461 0.8851 139 G 0.5098 0.0394 0.4507 140 L 0.8397 0.0166 0.1437 141 L 0.8848 0.0114 0.1039 142 L 0.8647 0.0110 0.1242 143 K 0.5647 0.0288 0.4065 144 G 0.1280 0.0681 0.8039 145 G 0.0507 0.2296 0.7197 146 K 0.0185 0.5065 0.4751 147 E 0.0255 0.5394 0.4351 148 A 0.0227 0.5570 0.4203 149 A 0.0081 0.7994 0.1925 150 H 0.0077 0.8572 0.1350 151 S 0.0066 0.9175 0.0759 152 N 0.0051 0.9451 0.0499 153 R 0.0047 0.9563 0.0390 154 I 0.0047 0.9595 0.0359 155 L 0.0047 0.9601 0.0353 156 H 0.0047 0.9598 0.0355 157 L 0.0047 0.9579 0.0374 158 L 0.0047 0.9581 0.0372 159 T 0.0048 0.9515 0.0437 160 Q 0.0051 0.9394 0.0556 161 E 0.0058 0.9151 0.0791 162 A 0.0128 0.8415 0.1458 163 L 0.0186 0.6927 0.2887 164 S 0.0256 0.6245 0.3499 165 I 0.0361 0.5418 0.4220 166 H 0.0405 0.3099 0.6496 167 G 0.0355 0.0519 0.9126 168 V 0.0946 0.0711 0.8343 169 K 0.1860 0.1684 0.6457 170 E 0.1993 0.4648 0.3360 171 A 0.2599 0.5024 0.2377 172 V 0.3295 0.4760 0.1946 173 Q 0.3484 0.4643 0.1874 174 L 0.3381 0.4298 0.2322 175 V 0.3050 0.4100 0.2850 176 N 0.2596 0.3945 0.3460 177 T 0.1449 0.5184 0.3366 178 R 0.0354 0.7836 0.1811 179 E 0.0349 0.8111 0.1540 180 E 0.0305 0.8410 0.1285 181 V 0.0487 0.7516 0.1996 182 E 0.0571 0.5865 0.3564 183 L 0.0520 0.4097 0.5383 184 D 0.0676 0.1041 0.8282 185 K 0.0312 0.1854 0.7834 186 M 0.1356 0.1210 0.7434 187 I 0.4256 0.0171 0.5573 188 D 0.6044 0.0449 0.3507 189 L 0.9111 0.0059 0.0830 190 I 0.9211 0.0045 0.0745 191 I 0.8817 0.0064 0.1120 192 P 0.5909 0.0117 0.3973 193 R 0.1358 0.0497 0.8145 194 G 0.0496 0.0405 0.9099 195 S 0.0430 0.2606 0.6964 196 S 0.0078 0.9084 0.0838 197 Q 0.0059 0.9443 0.0498 198 L 0.0048 0.9564 0.0388 199 V 0.0047 0.9582 0.0371 200 R 0.0060 0.9564 0.0376 201 D 0.0053 0.9560 0.0387 202 I 0.0076 0.9506 0.0418 203 Q 0.0079 0.9363 0.0559 204 K 0.0087 0.8406 0.1507 205 A 0.0277 0.5604 0.4119 206 A 0.0297 0.2777 0.6927 207 K 0.0553 0.1122 0.8325 208 G 0.0968 0.0459 0.8572 209 I 0.2980 0.0122 0.6898 210 P 0.5635 0.0083 0.4282 211 V 0.8514 0.0155 0.1330 212 M 0.8739 0.0174 0.1086 213 G 0.8169 0.0258 0.1574 214 H 0.6905 0.0346 0.2749 215 S 0.4104 0.0454 0.5442 216 E 0.1835 0.0508 0.7657 217 G 0.2103 0.0418 0.7479 218 I 0.4502 0.0457 0.5041 219 C 0.4771 0.0240 0.4988 220 H 0.6537 0.0363 0.3100 221 M 0.8278 0.0139 0.1583 222 Y 0.8603 0.0118 0.1279 223 V 0.7914 0.0136 0.1950 224 D 0.2800 0.0301 0.6899 225 S 0.0278 0.1660 0.8062 226 E 0.0284 0.1124 0.8592 227 A 0.0866 0.0643 0.8491 228 S 0.0996 0.0282 0.8721 229 V 0.0060 0.9158 0.0782 230 D 0.0050 0.9429 0.0521 231 K 0.0050 0.9476 0.0474 232 V 0.0048 0.9514 0.0438 233 T 0.0051 0.9527 0.0422 234 R 0.0053 0.9524 0.0424 235 L 0.0054 0.9502 0.0444 236 V 0.0099 0.9376 0.0524 237 R 0.0096 0.8930 0.0975 238 D 0.0196 0.7414 0.2389 239 S 0.0202 0.5983 0.3815 240 K 0.0518 0.4433 0.5049 241 C 0.0741 0.3001 0.6258 242 E 0.0846 0.1571 0.7583 243 Y 0.0961 0.1080 0.7959 244 P 0.0725 0.1552 0.7723 245 A 0.2365 0.2501 0.5134 246 A 0.3531 0.2389 0.4080 247 C 0.2723 0.2414 0.4863 248 N 0.2553 0.2020 0.5427 249 A 0.2132 0.4251 0.3617 250 L 0.1316 0.5756 0.2928 251 E 0.0936 0.6166 0.2898 252 T 0.2562 0.5511 0.1927 253 L 0.4250 0.4408 0.1342 254 L 0.5694 0.2847 0.1459 255 I 0.5107 0.2360 0.2533 256 H 0.1772 0.3236 0.4992 257 R 0.0124 0.7590 0.2286 258 D 0.0095 0.7779 0.2126 259 L 0.0106 0.7772 0.2123 260 L 0.0122 0.6799 0.3079 261 R 0.0072 0.6306 0.3621 262 T 0.0089 0.5892 0.4019 263 P 0.0143 0.6435 0.3422 264 L 0.0108 0.8285 0.1607 265 F 0.0050 0.9348 0.0602 266 D 0.0048 0.9450 0.0502 267 Q 0.0049 0.9524 0.0427 268 I 0.0048 0.9573 0.0379 269 I 0.0048 0.9580 0.0372 270 D 0.0047 0.9559 0.0393 271 M 0.0050 0.9495 0.0455 272 L 0.0051 0.9327 0.0622 273 R 0.0070 0.8698 0.1232 274 V 0.0421 0.6490 0.3090 275 E 0.0698 0.3116 0.6186 276 Q 0.1251 0.1706 0.7043 277 V 0.1978 0.1720 0.6302 278 K 0.3134 0.1635 0.5231 279 I 0.3085 0.1690 0.5226 280 H 0.2913 0.1256 0.5831 281 A 0.2237 0.0803 0.6960 282 G 0.1719 0.1258 0.7023 283 P 0.1848 0.1376 0.6775 284 K 0.2858 0.2049 0.5093 285 F 0.2441 0.2560 0.4999 286 A 0.2074 0.2511 0.5415 287 S 0.2038 0.1552 0.6410 288 Y 0.1453 0.0808 0.7740 289 L 0.1121 0.0785 0.8094 290 T 0.0549 0.2168 0.7283 291 F 0.0540 0.1928 0.7532 292 V 0.0323 0.5987 0.3690 293 K 0.0228 0.6632 0.3140 294 S 0.0267 0.7049 0.2684 295 L 0.0416 0.7275 0.2308 296 R 0.0407 0.7154 0.2439 297 T 0.0804 0.6517 0.2679 298 E 0.1288 0.5349 0.3363 299 Y 0.1674 0.4176 0.4150 300 G 0.2051 0.2277 0.5671 301 D 0.1837 0.1395 0.6768 302 L 0.3953 0.1236 0.4811 303 E 0.6880 0.0649 0.2471 304 L 0.7902 0.0169 0.1928 305 C 0.8640 0.0084 0.1276 306 I 0.8941 0.0047 0.1012 307 E 0.8841 0.0056 0.1103 308 V 0.8445 0.0091 0.1464 309 V 0.6105 0.0191 0.3704 310 D 0.1402 0.0689 0.7909 311 N 0.0999 0.0326 0.8674 312 V 0.0055 0.9292 0.0653 313 Q 0.0047 0.9570 0.0382 314 D 0.0048 0.9573 0.0379 315 A 0.0047 0.9596 0.0357 316 I 0.0047 0.9575 0.0377 317 D 0.0048 0.9549 0.0403 318 H 0.0052 0.9472 0.0477 319 I 0.0084 0.9328 0.0587 320 H 0.0119 0.8720 0.1161 321 K 0.0223 0.6584 0.3193 322 Y 0.0555 0.2724 0.6721 323 G 0.0537 0.0874 0.8590 324 S 0.0553 0.0779 0.8668 325 S 0.0759 0.1686 0.7555 326 H 0.2240 0.1938 0.5823 327 T 0.3211 0.1694 0.5095 328 D 0.5303 0.1455 0.3242 329 V 0.7348 0.0914 0.1738 330 I 0.8103 0.0544 0.1353 331 V 0.8025 0.0326 0.1650 332 T 0.5421 0.0389 0.4190 333 E 0.1259 0.0469 0.8272 334 D 0.0907 0.0421 0.8671 335 E 0.0050 0.9275 0.0675 336 N 0.0049 0.9523 0.0428 337 T 0.0048 0.9545 0.0407 338 A 0.0047 0.9576 0.0377 339 E 0.0047 0.9577 0.0375 340 F 0.0051 0.9487 0.0462 341 F 0.0053 0.9430 0.0517 342 L 0.0059 0.9245 0.0696 343 Q 0.0069 0.8062 0.1869 344 H 0.0176 0.6828 0.2996 345 V 0.1114 0.2658 0.6228 346 D 0.1221 0.1519 0.7259 347 S 0.3861 0.1642 0.4498 348 A 0.5052 0.1377 0.3571 349 C 0.7170 0.1008 0.1822 350 V 0.8434 0.0485 0.1081 351 F 0.8480 0.0504 0.1015 352 W 0.7724 0.0709 0.1567 353 N 0.5339 0.0855 0.3806 354 A 0.3030 0.1216 0.5755 355 S 0.2380 0.1456 0.6164 356 T 0.2463 0.1910 0.5627 357 R 0.2221 0.2131 0.5648 358 F 0.2291 0.1846 0.5863 359 S 0.2344 0.1272 0.6383 360 D 0.1572 0.1212 0.7217 361 G 0.1155 0.1712 0.7133 362 Y 0.1615 0.1704 0.6681 363 R 0.2350 0.1767 0.5883 364 F 0.2308 0.1243 0.6449 365 G 0.1658 0.1114 0.7228 366 L 0.1654 0.1399 0.6947 367 G 0.2440 0.0855 0.6705 368 A 0.4675 0.0853 0.4472 369 E 0.6531 0.0808 0.2661 370 V 0.5711 0.1085 0.3204 371 G 0.4545 0.0874 0.4582 372 I 0.3071 0.1103 0.5826 373 S 0.2306 0.0978 0.6716 374 T 0.1665 0.1166 0.7169 375 S 0.1345 0.1477 0.7179 376 R 0.1449 0.2853 0.5698 377 I 0.1342 0.3027 0.5630 378 H 0.1099 0.3087 0.5814 379 A 0.0886 0.2202 0.6913 380 R 0.0708 0.1357 0.7935 381 G 0.0749 0.0707 0.8545 382 P 0.0880 0.2006 0.7114 383 V 0.1649 0.2398 0.5953 384 G 0.1973 0.2488 0.5539 385 L 0.0943 0.6395 0.2662 386 E 0.1017 0.6666 0.2317 387 G 0.1433 0.5938 0.2629 388 L 0.2532 0.4335 0.3133 389 L 0.3447 0.2638 0.3916 390 T 0.4912 0.1214 0.3874 391 T 0.6096 0.0611 0.3293 392 K 0.7487 0.0350 0.2163 393 W 0.8670 0.0183 0.1147 394 L 0.8876 0.0129 0.0995 395 L 0.8829 0.0106 0.1065 396 R 0.6306 0.0281 0.3413 397 G 0.2425 0.0342 0.7233 398 K 0.0921 0.0642 0.8437 399 D 0.1812 0.0457 0.7731 400 H 0.7081 0.0161 0.2758 401 V 0.8509 0.0102 0.1389 402 V 0.7283 0.0350 0.2367 403 S 0.5214 0.0968 0.3819 404 D 0.2915 0.1849 0.5236 405 F 0.2393 0.2030 0.5577 406 S 0.1785 0.1854 0.6361 407 E 0.1275 0.1329 0.7396 408 H 0.0679 0.1397 0.7925 409 G 0.0579 0.1585 0.7836 410 S 0.0857 0.1922 0.7221 411 L 0.1264 0.2282 0.6454 412 K 0.1496 0.3558 0.4946 413 Y 0.1795 0.4197 0.4008 414 L 0.1344 0.4822 0.3835 415 H 0.1528 0.4816 0.3656 416 E 0.1192 0.4350 0.4458 417 N 0.0927 0.2585 0.6488 418 L 0.0935 0.0387 0.8678 419 P 0.0969 0.0348 0.8683 420 I 0.1202 0.0463 0.8335 421 P 0.0767 0.1101 0.8133 422 Q 0.1051 0.1484 0.7465 423 R 0.1075 0.1266 0.7659 424 N 0.0920 0.0603 0.8477 425 T 0.0464 0.0412 0.9124