# This file is the result of combining several RDB files, specifically # T0296.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0296.t2k.stride-ebghtl.rdb (weight 1.24869) # T0296.t2k.str2.rdb (weight 1.54758) # T0296.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 T0296.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0296 # 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 T0296.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 55 # # ============================================ # Comments from T0296.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0296 # 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 T0296.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 55 # # ============================================ # Comments from T0296.t2k.str2.rdb # ============================================ # TARGET T0296 # 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 T0296.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 11.8363 # # ============================================ # Comments from T0296.t2k.alpha.rdb # ============================================ # TARGET T0296 # 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 T0296.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 55 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0728 0.0512 0.8761 2 D 0.0790 0.0497 0.8713 3 I 0.0079 0.8897 0.1024 4 R 0.0055 0.9278 0.0668 5 Q 0.0052 0.9411 0.0537 6 V 0.0047 0.9560 0.0393 7 T 0.0047 0.9516 0.0436 8 E 0.0047 0.9367 0.0586 9 T 0.0050 0.9359 0.0591 10 I 0.0050 0.9350 0.0600 11 A 0.0047 0.9546 0.0408 12 M 0.0047 0.9549 0.0404 13 I 0.0060 0.9471 0.0469 14 E 0.0059 0.9300 0.0641 15 E 0.0067 0.8502 0.1431 16 Q 0.0233 0.5877 0.3890 17 N 0.0406 0.2759 0.6835 18 F 0.1073 0.1282 0.7646 19 D 0.2457 0.0928 0.6614 20 I 0.5406 0.1570 0.3024 21 R 0.5488 0.2033 0.2479 22 T 0.6814 0.1447 0.1739 23 I 0.6824 0.1338 0.1838 24 T 0.6320 0.1475 0.2205 25 M 0.5361 0.1673 0.2966 26 G 0.5806 0.0865 0.3329 27 I 0.5930 0.0667 0.3403 28 S 0.5207 0.0491 0.4302 29 L 0.1260 0.5397 0.3343 30 L 0.0654 0.6069 0.3277 31 D 0.0783 0.5745 0.3472 32 C 0.1155 0.3834 0.5011 33 I 0.1416 0.2202 0.6382 34 D 0.0796 0.1427 0.7777 35 P 0.0274 0.2803 0.6923 36 D 0.0841 0.2188 0.6971 37 I 0.0062 0.8642 0.1296 38 N 0.0055 0.9238 0.0708 39 R 0.0051 0.9358 0.0591 40 A 0.0051 0.9394 0.0555 41 A 0.0050 0.9364 0.0586 42 E 0.0050 0.9415 0.0535 43 K 0.0051 0.9404 0.0545 44 I 0.0048 0.9471 0.0481 45 Y 0.0048 0.9494 0.0458 46 Q 0.0049 0.9473 0.0478 47 K 0.0049 0.9397 0.0554 48 I 0.0051 0.9346 0.0603 49 T 0.0085 0.9077 0.0838 50 T 0.0052 0.9133 0.0815 51 K 0.0050 0.9254 0.0695 52 A 0.0048 0.9395 0.0556 53 A 0.0049 0.9397 0.0554 54 N 0.0053 0.9120 0.0827 55 L 0.0053 0.9391 0.0556 56 V 0.0048 0.9509 0.0442 57 A 0.0048 0.9425 0.0527 58 V 0.0047 0.9530 0.0423 59 G 0.0047 0.9556 0.0397 60 D 0.0048 0.9553 0.0400 61 E 0.0048 0.9551 0.0401 62 I 0.0049 0.9511 0.0439 63 A 0.0051 0.9457 0.0492 64 A 0.0062 0.9231 0.0708 65 E 0.0140 0.8489 0.1371 66 L 0.0488 0.4370 0.5142 67 G 0.0328 0.0237 0.9436 68 I 0.0835 0.0095 0.9070 69 P 0.4690 0.0085 0.5225 70 I 0.8356 0.0078 0.1567 71 V 0.8587 0.0108 0.1305 72 N 0.8133 0.0078 0.1788 73 K 0.7221 0.0083 0.2696 74 R 0.6445 0.0102 0.3453 75 V 0.6828 0.0154 0.3018 76 S 0.6285 0.0206 0.3509 77 V 0.4844 0.0234 0.4922 78 T 0.2386 0.0302 0.7312 79 P 0.1130 0.3318 0.5552 80 I 0.0535 0.6857 0.2608 81 S 0.0313 0.8099 0.1588 82 L 0.0278 0.8244 0.1478 83 I 0.0332 0.7641 0.2027 84 G 0.0259 0.6907 0.2835 85 A 0.0209 0.5855 0.3935 86 A 0.0263 0.4928 0.4809 87 T 0.0519 0.2890 0.6592 88 D 0.0466 0.2265 0.7268 89 A 0.0317 0.5876 0.3806 90 T 0.0117 0.7575 0.2308 91 D 0.0166 0.7713 0.2121 92 Y 0.0089 0.8853 0.1059 93 V 0.0080 0.9241 0.0679 94 V 0.0070 0.9381 0.0550 95 L 0.0051 0.9459 0.0489 96 A 0.0050 0.9466 0.0485 97 K 0.0051 0.9354 0.0595 98 A 0.0055 0.9227 0.0718 99 L 0.0052 0.9360 0.0589 100 D 0.0054 0.9505 0.0442 101 K 0.0048 0.9552 0.0400 102 A 0.0047 0.9570 0.0382 103 A 0.0048 0.9538 0.0414 104 K 0.0052 0.9428 0.0520 105 E 0.0062 0.9039 0.0899 106 I 0.0438 0.4931 0.4632 107 G 0.0438 0.0344 0.9219 108 V 0.1054 0.0225 0.8721 109 D 0.3461 0.0439 0.6100 110 F 0.6521 0.0580 0.2899 111 I 0.6007 0.0773 0.3220 112 G 0.4308 0.0771 0.4921 113 G 0.2106 0.2254 0.5640 114 F 0.2246 0.3335 0.4418 115 S 0.2788 0.4730 0.2482 116 A 0.3591 0.4652 0.1757 117 L 0.4606 0.3722 0.1672 118 V 0.4583 0.3382 0.2035 119 Q 0.3681 0.2614 0.3705 120 K 0.1125 0.2518 0.6356 121 G 0.0667 0.1303 0.8030 122 Y 0.1048 0.1097 0.7855 123 Q 0.1183 0.0814 0.8003 124 K 0.0290 0.3285 0.6425 125 G 0.0233 0.3099 0.6668 126 D 0.0257 0.5590 0.4153 127 E 0.0147 0.8567 0.1285 128 I 0.0212 0.8728 0.1060 129 L 0.0150 0.8902 0.0947 130 I 0.0169 0.8844 0.0987 131 N 0.0134 0.8484 0.1382 132 S 0.0142 0.7785 0.2073 133 I 0.0153 0.6565 0.3282 134 P 0.0065 0.8490 0.1445 135 R 0.0068 0.8497 0.1435 136 A 0.0152 0.8516 0.1332 137 L 0.0312 0.7644 0.2044 138 A 0.0373 0.6150 0.3477 139 E 0.0462 0.3486 0.6052 140 T 0.0834 0.0859 0.8307 141 D 0.0976 0.0848 0.8175 142 K 0.5411 0.0334 0.4255 143 V 0.7849 0.0181 0.1970 144 C 0.8191 0.0195 0.1614 145 S 0.8397 0.0122 0.1481 146 S 0.8191 0.0154 0.1655 147 V 0.8258 0.0133 0.1609 148 N 0.7665 0.0137 0.2198 149 I 0.5573 0.0601 0.3827 150 G 0.4201 0.0575 0.5224 151 S 0.3069 0.0621 0.6310 152 T 0.1507 0.1246 0.7247 153 K 0.0789 0.2068 0.7143 154 S 0.0475 0.1405 0.8120 155 G 0.0695 0.0606 0.8699 156 I 0.2545 0.0257 0.7198 157 N 0.2218 0.0296 0.7485 158 M 0.0050 0.9399 0.0551 159 T 0.0047 0.9533 0.0420 160 A 0.0048 0.9552 0.0400 161 V 0.0047 0.9588 0.0365 162 A 0.0048 0.9513 0.0439 163 D 0.0048 0.9387 0.0565 164 M 0.0050 0.9262 0.0688 165 G 0.0051 0.9290 0.0659 166 R 0.0058 0.9431 0.0511 167 I 0.0055 0.9443 0.0502 168 I 0.0075 0.9393 0.0532 169 K 0.0080 0.9315 0.0605 170 E 0.0095 0.8976 0.0930 171 T 0.0133 0.8365 0.1502 172 A 0.0254 0.6309 0.3437 173 N 0.0259 0.4556 0.5185 174 L 0.0390 0.3211 0.6399 175 S 0.0562 0.1100 0.8338 176 D 0.0377 0.2041 0.7582 177 M 0.0552 0.2221 0.7226 178 G 0.0804 0.1990 0.7205 179 V 0.1702 0.2597 0.5702 180 A 0.3601 0.2494 0.3904 181 K 0.5282 0.2523 0.2196 182 L 0.6712 0.2154 0.1134 183 V 0.7293 0.1648 0.1059 184 V 0.7094 0.1812 0.1094 185 F 0.6825 0.1734 0.1441 186 A 0.5682 0.1744 0.2574 187 N 0.4700 0.1000 0.4300 188 A 0.3057 0.0767 0.6177 189 V 0.1892 0.0788 0.7321 190 E 0.0943 0.1406 0.7651 191 D 0.0565 0.0874 0.8561 192 N 0.0691 0.0409 0.8900 193 P 0.0701 0.1415 0.7884 194 F 0.1851 0.1302 0.6847 195 M 0.2831 0.1179 0.5990 196 A 0.2659 0.1115 0.6226 197 G 0.1801 0.1199 0.7001 198 A 0.1280 0.2176 0.6543 199 F 0.1923 0.2082 0.5995 200 H 0.2036 0.1318 0.6646 201 G 0.1586 0.1013 0.7401 202 V 0.1725 0.1101 0.7173 203 G 0.1281 0.0819 0.7901 204 E 0.1452 0.0923 0.7625 205 A 0.1504 0.1027 0.7469 206 D 0.1955 0.0716 0.7329 207 V 0.6494 0.0310 0.3196 208 I 0.8746 0.0112 0.1142 209 I 0.8684 0.0156 0.1159 210 N 0.8130 0.0172 0.1698 211 V 0.6750 0.0390 0.2860 212 G 0.4995 0.0425 0.4579 213 V 0.4076 0.0545 0.5378 214 S 0.2038 0.0629 0.7333 215 G 0.0908 0.0911 0.8180 216 P 0.0241 0.4025 0.5735 217 G 0.0189 0.5832 0.3979 218 V 0.0312 0.8668 0.1020 219 V 0.0199 0.9237 0.0565 220 K 0.0073 0.9499 0.0428 221 R 0.0058 0.9528 0.0414 222 A 0.0049 0.9498 0.0453 223 L 0.0054 0.9347 0.0599 224 E 0.0056 0.8933 0.1011 225 K 0.0099 0.7870 0.2030 226 V 0.0404 0.4738 0.4858 227 R 0.0210 0.2636 0.7154 228 G 0.0311 0.1418 0.8270 229 Q 0.0532 0.1329 0.8139 230 S 0.0888 0.1541 0.7571 231 F 0.0781 0.6466 0.2753 232 D 0.0486 0.7596 0.1917 233 V 0.0947 0.7511 0.1542 234 V 0.0171 0.8573 0.1257 235 A 0.0058 0.9197 0.0745 236 E 0.0049 0.9422 0.0529 237 T 0.0049 0.9453 0.0498 238 V 0.0051 0.9439 0.0510 239 K 0.0050 0.9440 0.0510 240 K 0.0053 0.9381 0.0567 241 T 0.0052 0.9330 0.0618 242 A 0.0048 0.9391 0.0560 243 F 0.0048 0.9412 0.0540 244 K 0.0051 0.9336 0.0613 245 I 0.0073 0.9343 0.0584 246 T 0.0083 0.9093 0.0823 247 R 0.0074 0.8688 0.1238 248 I 0.0052 0.9236 0.0712 249 G 0.0048 0.9263 0.0689 250 Q 0.0048 0.9441 0.0511 251 L 0.0048 0.9540 0.0412 252 V 0.0047 0.9577 0.0376 253 G 0.0047 0.9595 0.0359 254 Q 0.0047 0.9607 0.0346 255 M 0.0047 0.9603 0.0350 256 A 0.0047 0.9592 0.0361 257 S 0.0047 0.9575 0.0378 258 E 0.0055 0.9449 0.0496 259 R 0.0075 0.9071 0.0854 260 L 0.0502 0.5846 0.3651 261 G 0.0443 0.0393 0.9164 262 V 0.0743 0.0158 0.9098 263 E 0.1946 0.0306 0.7747 264 F 0.5659 0.0345 0.3996 265 G 0.7665 0.0188 0.2146 266 I 0.8643 0.0113 0.1244 267 V 0.8523 0.0120 0.1357 268 D 0.7450 0.0184 0.2366 269 L 0.5187 0.0809 0.4003 270 S 0.4068 0.0805 0.5127 271 L 0.2738 0.1167 0.6095 272 A 0.2149 0.0590 0.7261 273 P 0.1785 0.0588 0.7626 274 T 0.1002 0.0590 0.8409 275 P 0.0363 0.3097 0.6540 276 A 0.0326 0.2652 0.7022 277 V 0.0467 0.3166 0.6367 278 G 0.0465 0.1904 0.7631 279 D 0.0664 0.3440 0.5897 280 S 0.1646 0.5172 0.3182 281 V 0.0069 0.9406 0.0525 282 A 0.0050 0.9567 0.0382 283 R 0.0047 0.9593 0.0360 284 V 0.0047 0.9602 0.0352 285 L 0.0048 0.9579 0.0373 286 E 0.0053 0.9467 0.0480 287 E 0.0073 0.8916 0.1011 288 M 0.0389 0.5410 0.4201 289 G 0.0505 0.1142 0.8354 290 L 0.0768 0.1131 0.8101 291 E 0.1525 0.2043 0.6431 292 T 0.2506 0.2131 0.5363 293 V 0.2022 0.1594 0.6385 294 G 0.0860 0.0740 0.8400 295 T 0.0682 0.1587 0.7731 296 H 0.0494 0.3464 0.6042 297 G 0.0283 0.6164 0.3552 298 T 0.0067 0.9175 0.0759 299 T 0.0047 0.9575 0.0378 300 A 0.0047 0.9601 0.0352 301 A 0.0047 0.9603 0.0350 302 L 0.0047 0.9597 0.0356 303 A 0.0047 0.9596 0.0357 304 L 0.0048 0.9571 0.0381 305 L 0.0052 0.9528 0.0420 306 N 0.0091 0.9447 0.0462 307 D 0.0053 0.9508 0.0438 308 Q 0.0052 0.9486 0.0462 309 V 0.0059 0.9366 0.0576 310 K 0.0092 0.9154 0.0754 311 K 0.0144 0.8571 0.1286 312 G 0.0346 0.7788 0.1866 313 G 0.0281 0.7729 0.1990 314 V 0.0362 0.8054 0.1585 315 M 0.0391 0.8105 0.1504 316 A 0.0907 0.6881 0.2212 317 C 0.1220 0.4592 0.4187 318 N 0.1054 0.2695 0.6251 319 Q 0.1453 0.1482 0.7064 320 V 0.2900 0.1144 0.5956 321 G 0.2542 0.0967 0.6491 322 G 0.2605 0.0806 0.6589 323 L 0.3057 0.1246 0.5697 324 S 0.2562 0.1305 0.6133 325 G 0.2628 0.1545 0.5827 326 A 0.4311 0.1098 0.4591 327 F 0.5212 0.0576 0.4212 328 I 0.4816 0.0359 0.4825 329 P 0.3304 0.0714 0.5982 330 V 0.1341 0.5202 0.3457 331 S 0.0696 0.5306 0.3998 332 E 0.0295 0.5762 0.3942 333 D 0.0190 0.5946 0.3864 334 E 0.0085 0.9182 0.0733 335 G 0.0066 0.9404 0.0530 336 M 0.0048 0.9540 0.0412 337 I 0.0049 0.9583 0.0368 338 A 0.0049 0.9595 0.0356 339 A 0.0048 0.9591 0.0361 340 V 0.0051 0.9515 0.0434 341 Q 0.0053 0.9341 0.0606 342 N 0.0424 0.5633 0.3943 343 G 0.0248 0.1610 0.8142 344 S 0.0726 0.0681 0.8593 345 L 0.2966 0.0360 0.6673 346 N 0.2348 0.0343 0.7309 347 L 0.0097 0.8738 0.1165 348 E 0.0061 0.9071 0.0867 349 K 0.0081 0.8976 0.0943 350 L 0.0167 0.8892 0.0941 351 E 0.0281 0.8376 0.1343 352 A 0.0384 0.8029 0.1587 353 M 0.0532 0.7221 0.2248 354 T 0.1043 0.6131 0.2825 355 A 0.1934 0.4900 0.3166 356 I 0.3267 0.4007 0.2726 357 C 0.3689 0.3211 0.3099 358 S 0.3515 0.2215 0.4270 359 V 0.2430 0.2211 0.5359 360 G 0.2427 0.1341 0.6232 361 L 0.2950 0.1546 0.5504 362 D 0.3387 0.1631 0.4982 363 M 0.5517 0.0844 0.3639 364 I 0.6056 0.0338 0.3607 365 A 0.6415 0.0184 0.3401 366 I 0.4366 0.0193 0.5440 367 P 0.1561 0.1217 0.7222 368 E 0.0482 0.1281 0.8237 369 D 0.0544 0.1762 0.7694 370 T 0.0860 0.0483 0.8657 371 P 0.0612 0.1065 0.8323 372 A 0.0051 0.9351 0.0599 373 E 0.0048 0.9524 0.0428 374 T 0.0048 0.9561 0.0391 375 I 0.0047 0.9586 0.0367 376 A 0.0047 0.9578 0.0374 377 A 0.0047 0.9549 0.0404 378 M 0.0047 0.9541 0.0412 379 I 0.0048 0.9484 0.0469 380 A 0.0048 0.9371 0.0582 381 D 0.0054 0.9076 0.0870 382 E 0.0053 0.9325 0.0622 383 A 0.0056 0.9376 0.0568 384 A 0.0084 0.9352 0.0563 385 I 0.0125 0.9325 0.0549 386 G 0.0333 0.8999 0.0667 387 V 0.0341 0.8721 0.0938 388 I 0.0413 0.7444 0.2143 389 N 0.0338 0.3234 0.6428 390 M 0.0302 0.0826 0.8872 391 K 0.1580 0.0206 0.8214 392 T 0.3125 0.0095 0.6780 393 T 0.6324 0.0274 0.3403 394 A 0.8795 0.0068 0.1137 395 V 0.9190 0.0036 0.0774 396 R 0.9223 0.0036 0.0741 397 I 0.8843 0.0051 0.1106 398 I 0.7903 0.0058 0.2040 399 P 0.5881 0.0098 0.4021 400 K 0.2746 0.0296 0.6958 401 G 0.0858 0.0613 0.8529 402 K 0.0473 0.0630 0.8898 403 E 0.0630 0.0549 0.8821 404 G 0.0999 0.0664 0.8337 405 D 0.2853 0.1010 0.6137 406 M 0.6654 0.0852 0.2495 407 I 0.7637 0.0673 0.1690 408 E 0.7279 0.0842 0.1879 409 F 0.5514 0.0951 0.3534 410 G 0.3209 0.1000 0.5791 411 G 0.2654 0.1296 0.6050 412 L 0.3438 0.1760 0.4801 413 L 0.3219 0.1538 0.5244 414 G 0.1985 0.0855 0.7160 415 T 0.2564 0.0424 0.7012 416 A 0.3320 0.0115 0.6566 417 P 0.4068 0.0123 0.5809 418 V 0.7806 0.0146 0.2048 419 M 0.8219 0.0120 0.1661 420 K 0.7983 0.0103 0.1915 421 V 0.5466 0.0310 0.4224 422 N 0.2376 0.0513 0.7111 423 G 0.0865 0.0985 0.8150 424 A 0.1034 0.0732 0.8234 425 S 0.1214 0.0492 0.8295 426 S 0.0407 0.5421 0.4172 427 V 0.0312 0.8014 0.1674 428 D 0.0494 0.8430 0.1076 429 F 0.0957 0.7930 0.1113 430 I 0.1137 0.7294 0.1570 431 S 0.0907 0.6530 0.2563 432 R 0.0566 0.4739 0.4695 433 G 0.0551 0.1465 0.7984 434 G 0.1015 0.0579 0.8405 435 Q 0.2549 0.0365 0.7086 436 I 0.2602 0.0378 0.7021 437 P 0.2561 0.0426 0.7013 438 A 0.2318 0.1311 0.6371 439 P 0.2219 0.1927 0.5854 440 I 0.2065 0.3609 0.4326 441 H 0.1986 0.3888 0.4127 442 S 0.1891 0.3370 0.4739 443 F 0.2240 0.1954 0.5806 444 K 0.1564 0.1120 0.7317 445 N 0.0767 0.0307 0.8926