# This file is the result of combining several RDB files, specifically # T0228.t04.dssp-ebghstl.rdb (weight 1.53986) # T0228.t04.stride-ebghtl.rdb (weight 1.24869) # T0228.t04.str2.rdb (weight 1.54758) # T0228.t04.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 T0228.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0228 # 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 T0228.t04-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 131.101 # # ============================================ # Comments from T0228.t04.stride-ebghtl.rdb # ============================================ # TARGET T0228 # 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 T0228.t04-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 131.101 # # ============================================ # Comments from T0228.t04.str2.rdb # ============================================ # TARGET T0228 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.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 T0228.t04-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 131.101 # # ============================================ # Comments from T0228.t04.alpha.rdb # ============================================ # TARGET T0228 # 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 T0228.t04-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 131.101 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0537 0.0445 0.9018 2 S 0.0595 0.0634 0.8772 3 E 0.0598 0.2569 0.6834 4 P 0.0287 0.5502 0.4212 5 V 0.0624 0.6198 0.3178 6 I 0.0830 0.6539 0.2631 7 K 0.0609 0.7121 0.2269 8 S 0.0511 0.7143 0.2346 9 L 0.0272 0.7482 0.2246 10 L 0.0305 0.7205 0.2490 11 D 0.0304 0.6384 0.3312 12 T 0.0304 0.5706 0.3990 13 D 0.0169 0.6457 0.3374 14 M 0.0406 0.8349 0.1244 15 Y 0.0326 0.8842 0.0832 16 K 0.0270 0.9069 0.0661 17 I 0.0208 0.9076 0.0716 18 T 0.0147 0.8953 0.0900 19 M 0.0071 0.9413 0.0516 20 H 0.0100 0.9390 0.0510 21 A 0.0124 0.9388 0.0488 22 A 0.0218 0.9204 0.0577 23 V 0.0387 0.8742 0.0871 24 F 0.0724 0.7661 0.1615 25 T 0.1027 0.4402 0.4572 26 N 0.0871 0.0891 0.8237 27 F 0.0825 0.0229 0.8946 28 P 0.0476 0.0768 0.8755 29 D 0.0784 0.0434 0.8782 30 V 0.3267 0.0211 0.6522 31 T 0.6645 0.0082 0.3274 32 V 0.9073 0.0035 0.0892 33 T 0.9223 0.0033 0.0743 34 Y 0.9215 0.0035 0.0750 35 K 0.9200 0.0034 0.0766 36 Y 0.9063 0.0035 0.0903 37 T 0.8595 0.0074 0.1331 38 N 0.7378 0.0118 0.2504 39 R 0.4558 0.0440 0.5003 40 S 0.2571 0.0573 0.6856 41 S 0.1374 0.0769 0.7857 42 Q 0.1063 0.1315 0.7622 43 L 0.1487 0.1418 0.7094 44 T 0.1291 0.1894 0.6815 45 F 0.0842 0.2755 0.6403 46 N 0.0526 0.4671 0.4803 47 K 0.0182 0.8858 0.0959 48 E 0.0217 0.9128 0.0655 49 A 0.0160 0.9270 0.0569 50 I 0.0065 0.9467 0.0468 51 N 0.0051 0.9474 0.0475 52 W 0.0048 0.9442 0.0510 53 L 0.0048 0.9516 0.0435 54 K 0.0047 0.9599 0.0354 55 E 0.0047 0.9602 0.0351 56 Q 0.0048 0.9568 0.0385 57 F 0.0048 0.9537 0.0415 58 S 0.0050 0.9414 0.0536 59 Y 0.0063 0.8992 0.0945 60 L 0.0189 0.7841 0.1970 61 G 0.0134 0.5156 0.4710 62 N 0.0200 0.2132 0.7668 63 L 0.1042 0.0824 0.8134 64 R 0.1676 0.0262 0.8062 65 F 0.1873 0.0104 0.8023 66 T 0.0681 0.0107 0.9212 67 E 0.0049 0.9461 0.0490 68 E 0.0047 0.9558 0.0395 69 E 0.0048 0.9568 0.0384 70 I 0.0050 0.9583 0.0367 71 E 0.0048 0.9549 0.0404 72 Y 0.0051 0.9457 0.0493 73 L 0.0054 0.9267 0.0679 74 K 0.0078 0.8846 0.1076 75 Q 0.0088 0.7567 0.2345 76 E 0.0158 0.5169 0.4673 77 I 0.0805 0.0817 0.8377 78 P 0.0248 0.1773 0.7979 79 Y 0.0475 0.1696 0.7829 80 L 0.0688 0.0380 0.8931 81 P 0.0537 0.1443 0.8020 82 S 0.0073 0.8403 0.1525 83 A 0.0083 0.8814 0.1103 84 Y 0.0057 0.9383 0.0559 85 I 0.0061 0.9455 0.0483 86 K 0.0055 0.9430 0.0515 87 Y 0.0055 0.9380 0.0565 88 I 0.0086 0.9062 0.0852 89 S 0.0150 0.8093 0.1757 90 S 0.0308 0.6680 0.3012 91 S 0.0324 0.3325 0.6351 92 N 0.0380 0.1195 0.8424 93 Y 0.0789 0.0770 0.8441 94 K 0.0953 0.0481 0.8566 95 L 0.1471 0.0241 0.8287 96 H 0.1056 0.0175 0.8770 97 P 0.1432 0.1829 0.6739 98 E 0.3328 0.1388 0.5284 99 E 0.6704 0.0703 0.2593 100 Q 0.8446 0.0235 0.1319 101 I 0.8302 0.0286 0.1412 102 S 0.8191 0.0152 0.1657 103 F 0.5410 0.0147 0.4443 104 T 0.2553 0.0254 0.7194 105 S 0.2066 0.1281 0.6652 106 E 0.1870 0.2090 0.6040 107 E 0.1750 0.2288 0.5962 108 I 0.2685 0.1485 0.5830 109 E 0.1666 0.0802 0.7532 110 G 0.1210 0.0391 0.8399 111 K 0.3128 0.0200 0.6673 112 P 0.5270 0.0236 0.4494 113 T 0.4160 0.0329 0.5512 114 H 0.3044 0.0467 0.6489 115 Y 0.1716 0.0990 0.7294 116 K 0.1778 0.0592 0.7631 117 L 0.4358 0.0149 0.5493 118 K 0.5871 0.0099 0.4030 119 I 0.8776 0.0058 0.1166 120 L 0.9090 0.0053 0.0857 121 V 0.8971 0.0063 0.0966 122 S 0.7629 0.0200 0.2171 123 G 0.3762 0.0137 0.6101 124 S 0.2260 0.0333 0.7406 125 W 0.0501 0.5619 0.3880 126 K 0.0478 0.6687 0.2835 127 D 0.0634 0.7017 0.2349 128 T 0.1267 0.7132 0.1601 129 I 0.1846 0.7230 0.0925 130 L 0.1881 0.7509 0.0610 131 Y 0.1662 0.7536 0.0802 132 E 0.1162 0.8002 0.0836 133 I 0.0646 0.8088 0.1266 134 P 0.0481 0.8164 0.1356 135 L 0.0554 0.8299 0.1147 136 L 0.0440 0.8568 0.0993 137 S 0.0409 0.8049 0.1542 138 L 0.0376 0.7247 0.2377 139 I 0.0666 0.5137 0.4197 140 S 0.0866 0.2564 0.6570 141 E 0.0401 0.6425 0.3174 142 A 0.0945 0.5555 0.3500 143 Y 0.1856 0.4713 0.3430 144 F 0.3093 0.2758 0.4149 145 K 0.3163 0.2474 0.4364 146 F 0.4088 0.1926 0.3986 147 V 0.3431 0.1680 0.4889 148 D 0.2152 0.1374 0.6475 149 I 0.0901 0.2391 0.6708 150 D 0.1089 0.1664 0.7247 151 W 0.1039 0.2036 0.6925 152 D 0.0951 0.2320 0.6730 153 Y 0.0117 0.8847 0.1036 154 E 0.0078 0.9178 0.0743 155 N 0.0090 0.9183 0.0727 156 Q 0.0068 0.9390 0.0543 157 L 0.0050 0.9577 0.0374 158 E 0.0047 0.9592 0.0361 159 Q 0.0048 0.9568 0.0384 160 A 0.0048 0.9539 0.0412 161 E 0.0053 0.9534 0.0413 162 K 0.0056 0.9477 0.0467 163 K 0.0064 0.9365 0.0571 164 A 0.0077 0.9365 0.0558 165 E 0.0067 0.9374 0.0558 166 T 0.0077 0.9274 0.0649 167 L 0.0090 0.9099 0.0811 168 F 0.0117 0.8561 0.1322 169 D 0.0155 0.6920 0.2925 170 N 0.0451 0.2539 0.7010 171 G 0.0419 0.0290 0.9291 172 I 0.1779 0.0131 0.8089 173 R 0.5643 0.0149 0.4208 174 F 0.7327 0.0621 0.2052 175 S 0.6723 0.1059 0.2217 176 E 0.6656 0.1253 0.2091 177 F 0.4898 0.1151 0.3952 178 G 0.3000 0.1184 0.5816 179 T 0.3111 0.1842 0.5047 180 R 0.2930 0.2592 0.4478 181 R 0.2142 0.2849 0.5009 182 R 0.1496 0.3322 0.5182 183 R 0.1204 0.2695 0.6102 184 S 0.0973 0.2454 0.6573 185 L 0.0229 0.7165 0.2606 186 K 0.0241 0.7408 0.2352 187 A 0.0149 0.8328 0.1523 188 Q 0.0071 0.9175 0.0755 189 D 0.0056 0.9466 0.0478 190 L 0.0067 0.9489 0.0444 191 I 0.0062 0.9535 0.0403 192 M 0.0056 0.9538 0.0406 193 Q 0.0047 0.9536 0.0417 194 G 0.0056 0.9403 0.0540 195 I 0.0075 0.9227 0.0697 196 M 0.0058 0.9382 0.0560 197 K 0.0078 0.9257 0.0664 198 A 0.0129 0.8614 0.1258 199 V 0.0418 0.7106 0.2476 200 N 0.0473 0.4269 0.5258 201 G 0.0511 0.1676 0.7813 202 N 0.0670 0.0457 0.8873 203 P 0.0325 0.1917 0.7758 204 D 0.0530 0.2058 0.7412 205 R 0.0934 0.1795 0.7271 206 N 0.0916 0.0953 0.8131 207 K 0.0631 0.1861 0.7508 208 S 0.0744 0.1554 0.7703 209 L 0.2048 0.1427 0.6525 210 L 0.3277 0.0817 0.5906 211 L 0.3316 0.0915 0.5770 212 G 0.2619 0.1389 0.5992 213 T 0.1398 0.4110 0.4492 214 S 0.0479 0.7424 0.2097 215 N 0.0298 0.8601 0.1102 216 I 0.0145 0.9384 0.0471 217 L 0.0091 0.9463 0.0446 218 F 0.0069 0.9514 0.0417 219 A 0.0079 0.9484 0.0438 220 K 0.0073 0.9378 0.0549 221 K 0.0092 0.8872 0.1037 222 Y 0.0455 0.4613 0.4932 223 G 0.0409 0.0218 0.9373 224 V 0.0668 0.0083 0.9250 225 K 0.1405 0.0097 0.8497 226 P 0.3222 0.0454 0.6324 227 I 0.3357 0.0715 0.5928 228 G 0.2929 0.0577 0.6494 229 T 0.2184 0.0896 0.6921 230 V 0.1361 0.3206 0.5434 231 A 0.0456 0.6521 0.3024 232 H 0.0163 0.8356 0.1482 233 E 0.0121 0.9108 0.0771 234 W 0.0123 0.9246 0.0631 235 V 0.0145 0.9257 0.0597 236 M 0.0186 0.9111 0.0703 237 G 0.0118 0.8925 0.0956 238 V 0.0194 0.8499 0.1306 239 A 0.0203 0.7947 0.1849 240 S 0.0297 0.7260 0.2444 241 I 0.0525 0.5961 0.3513 242 S 0.0548 0.3447 0.6005 243 E 0.0070 0.7085 0.2845 244 D 0.0154 0.6643 0.3203 245 Y 0.0150 0.6769 0.3081 246 L 0.0173 0.6714 0.3112 247 H 0.0137 0.6509 0.3353 248 A 0.0151 0.6342 0.3506 249 N 0.0077 0.8758 0.1165 250 K 0.0053 0.9474 0.0473 251 N 0.0048 0.9544 0.0408 252 A 0.0047 0.9573 0.0380 253 M 0.0047 0.9595 0.0358 254 D 0.0047 0.9602 0.0351 255 C 0.0048 0.9589 0.0363 256 W 0.0050 0.9513 0.0437 257 I 0.0054 0.9452 0.0494 258 N 0.0061 0.9131 0.0807 259 T 0.0144 0.8020 0.1836 260 F 0.0678 0.3449 0.5873 261 G 0.0399 0.0952 0.8649 262 A 0.0382 0.1228 0.8391 263 K 0.0486 0.1223 0.8291 264 N 0.1802 0.0583 0.7614 265 A 0.3866 0.0271 0.5863 266 G 0.8545 0.0089 0.1366 267 L 0.9227 0.0037 0.0736 268 A 0.9232 0.0040 0.0728 269 L 0.8963 0.0060 0.0978 270 T 0.7342 0.0148 0.2510 271 D 0.4666 0.0383 0.4950 272 T 0.1848 0.1030 0.7122 273 F 0.1049 0.1163 0.7789 274 G 0.0750 0.0882 0.8368 275 T 0.0473 0.5307 0.4220 276 D 0.0072 0.9030 0.0898 277 D 0.0061 0.9287 0.0652 278 F 0.0065 0.9314 0.0621 279 L 0.0074 0.9226 0.0700 280 K 0.0079 0.8752 0.1169 281 S 0.0113 0.7213 0.2674 282 F 0.0384 0.4331 0.5285 283 R 0.0457 0.1097 0.8446 284 P 0.0300 0.2527 0.7173 285 P 0.0237 0.4574 0.5189 286 Y 0.0245 0.5612 0.4143 287 S 0.0401 0.5161 0.4438 288 D 0.0274 0.4841 0.4885 289 A 0.0856 0.3824 0.5320 290 Y 0.2330 0.2070 0.5600 291 V 0.2714 0.1567 0.5719 292 G 0.4510 0.0646 0.4844 293 V 0.5893 0.0331 0.3776 294 R 0.5663 0.0227 0.4110 295 Q 0.2925 0.0645 0.6431 296 D 0.1185 0.0573 0.8242 297 S 0.0877 0.0590 0.8532 298 G 0.0599 0.0513 0.8888 299 D 0.0964 0.0527 0.8510 300 P 0.0070 0.9067 0.0862 301 V 0.0050 0.9525 0.0425 302 E 0.0049 0.9578 0.0373 303 Y 0.0048 0.9570 0.0383 304 T 0.0047 0.9595 0.0358 305 K 0.0046 0.9615 0.0339 306 K 0.0047 0.9611 0.0342 307 I 0.0047 0.9584 0.0368 308 S 0.0047 0.9595 0.0358 309 H 0.0048 0.9519 0.0433 310 H 0.0050 0.9366 0.0584 311 Y 0.0050 0.9324 0.0627 312 H 0.0057 0.9186 0.0757 313 D 0.0063 0.8753 0.1183 314 V 0.0119 0.7950 0.1931 315 L 0.0574 0.4412 0.5015 316 K 0.0471 0.0532 0.8997 317 L 0.0686 0.0126 0.9187 318 P 0.0671 0.0406 0.8923 319 K 0.0640 0.2439 0.6921 320 F 0.1256 0.1748 0.6997 321 S 0.3010 0.0442 0.6548 322 K 0.7926 0.0072 0.2002 323 I 0.9073 0.0039 0.0888 324 I 0.9293 0.0036 0.0671 325 C 0.9222 0.0039 0.0739 326 Y 0.8507 0.0094 0.1399 327 S 0.5321 0.0193 0.4486 328 D 0.1571 0.0706 0.7724 329 S 0.1289 0.0569 0.8143 330 L 0.1661 0.0256 0.8083 331 N 0.0951 0.0190 0.8859 332 V 0.0052 0.9413 0.0535 333 E 0.0047 0.9596 0.0357 334 K 0.0048 0.9571 0.0381 335 A 0.0047 0.9603 0.0351 336 I 0.0047 0.9595 0.0358 337 T 0.0047 0.9574 0.0379 338 Y 0.0048 0.9546 0.0406 339 S 0.0047 0.9575 0.0378 340 H 0.0047 0.9582 0.0371 341 A 0.0047 0.9560 0.0393 342 A 0.0050 0.9413 0.0536 343 K 0.0054 0.8853 0.1093 344 E 0.0176 0.5997 0.3827 345 N 0.0360 0.1381 0.8259 346 G 0.0518 0.0465 0.9017 347 M 0.3022 0.0384 0.6594 348 L 0.6603 0.0376 0.3021 349 A 0.6884 0.0359 0.2758 350 T 0.8262 0.0194 0.1544 351 F 0.7950 0.0297 0.1753 352 G 0.7246 0.0271 0.2483 353 I 0.5153 0.0647 0.4200 354 G 0.3356 0.1078 0.5565 355 T 0.1771 0.2922 0.5307 356 N 0.1522 0.4196 0.4281 357 F 0.1321 0.5071 0.3609 358 T 0.1550 0.4574 0.3876 359 N 0.1412 0.3096 0.5491 360 D 0.1199 0.2215 0.6586 361 F 0.0756 0.2241 0.7003 362 R 0.0651 0.3042 0.6307 363 K 0.0702 0.2758 0.6540 364 K 0.1204 0.2026 0.6770 365 S 0.1253 0.0994 0.7753 366 E 0.0701 0.1012 0.8288 367 P 0.0467 0.2118 0.7415 368 Q 0.0681 0.2414 0.6906 369 V 0.1154 0.1881 0.6966 370 K 0.1054 0.1073 0.7872 371 S 0.1022 0.1069 0.7909 372 E 0.1072 0.1323 0.7605 373 P 0.0879 0.4026 0.5095 374 L 0.1883 0.4083 0.4034 375 N 0.3094 0.4017 0.2889 376 I 0.5936 0.2690 0.1374 377 V 0.7794 0.1348 0.0858 378 I 0.8328 0.0875 0.0797 379 K 0.8410 0.0850 0.0740 380 L 0.7734 0.1274 0.0991 381 L 0.7645 0.1212 0.1143 382 E 0.7731 0.1047 0.1222 383 V 0.6233 0.1263 0.2504 384 N 0.1651 0.0422 0.7927 385 G 0.0657 0.0332 0.9011 386 N 0.4162 0.0173 0.5665 387 H 0.6363 0.0160 0.3477 388 A 0.7223 0.0173 0.2604 389 I 0.8091 0.0086 0.1823 390 K 0.7794 0.0093 0.2113 391 I 0.6005 0.0146 0.3850 392 S 0.3270 0.0290 0.6440 393 D 0.1232 0.0962 0.7807 394 N 0.1115 0.0743 0.8142 395 L 0.0699 0.1783 0.7517 396 G 0.0894 0.1350 0.7756 397 K 0.1622 0.0943 0.7436 398 N 0.1328 0.0604 0.8068 399 M 0.0756 0.0633 0.8611 400 G 0.0653 0.0406 0.8941 401 D 0.0695 0.0302 0.9003 402 P 0.0204 0.7925 0.1871 403 A 0.0200 0.8661 0.1140 404 T 0.0445 0.8620 0.0935 405 V 0.0767 0.8432 0.0800 406 K 0.0839 0.8394 0.0767 407 R 0.1386 0.7801 0.0813 408 V 0.1029 0.8101 0.0870 409 K 0.0959 0.7914 0.1128 410 E 0.0531 0.8094 0.1375 411 E 0.0576 0.7302 0.2123 412 L 0.0562 0.3236 0.6201 413 G 0.0570 0.0460 0.8969 414 Y 0.2040 0.0269 0.7691 415 T 0.4093 0.0341 0.5566 416 E 0.3941 0.1363 0.4696 417 R 0.3262 0.1752 0.4986 418 S 0.2867 0.1959 0.5174 419 W 0.2481 0.2239 0.5280 420 S 0.1896 0.1796 0.6308 421 G 0.1155 0.1462 0.7383 422 D 0.0790 0.1999 0.7211 423 N 0.0430 0.4768 0.4802 424 E 0.0416 0.4751 0.4834 425 A 0.0552 0.4790 0.4658 426 H 0.0711 0.3855 0.5434 427 R 0.0765 0.3051 0.6185 428 W 0.0739 0.1939 0.7322 429 T 0.0637 0.0839 0.8524 430 Z 0.0462 0.0488 0.9051