# This file is the result of combining several RDB files, specifically # T0222.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0222.t2k.stride-ebghtl.rdb (weight 1.24869) # T0222.t2k.str2.rdb (weight 1.54758) # T0222.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 T0222.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0222 # 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 T0222.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 95 # # ============================================ # Comments from T0222.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0222 # 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 T0222.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 95 # # ============================================ # Comments from T0222.t2k.str2.rdb # ============================================ # TARGET T0222 # 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 T0222.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 95 # # ============================================ # Comments from T0222.t2k.alpha.rdb # ============================================ # TARGET T0222 # 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 T0222.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 95 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1088 0.0130 0.8782 2 A 0.4490 0.0125 0.5385 3 A 0.7743 0.0081 0.2176 4 F 0.8570 0.0070 0.1361 5 Q 0.8553 0.0043 0.1404 6 I 0.7017 0.0172 0.2811 7 A 0.1595 0.0308 0.8097 8 N 0.0879 0.0458 0.8663 9 K 0.5643 0.0149 0.4208 10 T 0.7206 0.0091 0.2702 11 V 0.5496 0.0251 0.4252 12 G 0.1615 0.0296 0.8089 13 K 0.0285 0.0942 0.8773 14 D 0.0367 0.0524 0.9109 15 A 0.1134 0.0249 0.8617 16 P 0.1426 0.0197 0.8377 17 V 0.5926 0.0085 0.3990 18 F 0.8872 0.0076 0.1052 19 I 0.9277 0.0041 0.0682 20 I 0.9190 0.0064 0.0745 21 A 0.8907 0.0118 0.0975 22 E 0.8121 0.0209 0.1671 23 A 0.4778 0.0498 0.4724 24 G 0.2272 0.0646 0.7082 25 I 0.1476 0.2019 0.6505 26 N 0.1046 0.2079 0.6875 27 H 0.0746 0.1720 0.7535 28 D 0.0439 0.1270 0.8291 29 G 0.0457 0.0805 0.8738 30 K 0.0629 0.1290 0.8081 31 L 0.0053 0.9481 0.0466 32 D 0.0050 0.9564 0.0387 33 Q 0.0048 0.9570 0.0382 34 A 0.0047 0.9598 0.0355 35 F 0.0047 0.9591 0.0362 36 A 0.0047 0.9586 0.0368 37 L 0.0047 0.9585 0.0368 38 I 0.0047 0.9603 0.0350 39 D 0.0047 0.9599 0.0354 40 A 0.0047 0.9598 0.0355 41 A 0.0048 0.9570 0.0382 42 A 0.0049 0.9472 0.0478 43 E 0.0057 0.8794 0.1148 44 A 0.0372 0.3664 0.5963 45 G 0.0431 0.0285 0.9284 46 A 0.0797 0.0205 0.8998 47 D 0.1418 0.0716 0.7866 48 A 0.7773 0.0405 0.1822 49 V 0.8220 0.0447 0.1333 50 K 0.8564 0.0253 0.1184 51 F 0.7762 0.0382 0.1856 52 Q 0.5507 0.0473 0.4020 53 M 0.4063 0.0495 0.5442 54 F 0.3632 0.0455 0.5914 55 Q 0.2369 0.0352 0.7279 56 A 0.0429 0.6856 0.2715 57 D 0.0233 0.7240 0.2527 58 R 0.0383 0.7460 0.2157 59 M 0.0997 0.5948 0.3055 60 Y 0.1954 0.3511 0.4535 61 Q 0.1908 0.2258 0.5834 62 K 0.0935 0.3007 0.6059 63 D 0.1073 0.2243 0.6684 64 P 0.0844 0.2679 0.6478 65 G 0.1265 0.2368 0.6367 66 L 0.2089 0.1978 0.5933 67 Y 0.2759 0.1670 0.5571 68 K 0.2495 0.1445 0.6059 69 T 0.1651 0.1141 0.7208 70 A 0.1167 0.1287 0.7546 71 A 0.0843 0.1450 0.7707 72 G 0.0823 0.1408 0.7770 73 K 0.0795 0.1476 0.7729 74 D 0.1119 0.0998 0.7882 75 V 0.2086 0.0727 0.7187 76 S 0.2685 0.0967 0.6348 77 I 0.0916 0.5896 0.3188 78 F 0.0623 0.7084 0.2293 79 S 0.0591 0.7555 0.1854 80 L 0.0340 0.8374 0.1286 81 V 0.0347 0.8412 0.1241 82 Q 0.0373 0.8031 0.1596 83 S 0.0344 0.6956 0.2699 84 M 0.0826 0.3380 0.5793 85 E 0.0896 0.1346 0.7758 86 M 0.0729 0.0272 0.8999 87 P 0.0589 0.0240 0.9171 88 A 0.0072 0.8767 0.1161 89 E 0.0052 0.9085 0.0863 90 W 0.0056 0.9152 0.0792 91 I 0.0049 0.9476 0.0475 92 L 0.0050 0.9539 0.0411 93 P 0.0049 0.9571 0.0381 94 L 0.0048 0.9563 0.0389 95 L 0.0048 0.9591 0.0361 96 D 0.0048 0.9591 0.0361 97 Y 0.0048 0.9593 0.0359 98 C 0.0048 0.9582 0.0369 99 R 0.0050 0.9480 0.0470 100 E 0.0052 0.9168 0.0780 101 K 0.0436 0.3393 0.6171 102 Q 0.0393 0.0190 0.9417 103 V 0.0980 0.0112 0.8908 104 I 0.5874 0.0110 0.4017 105 F 0.8868 0.0077 0.1056 106 L 0.8795 0.0112 0.1093 107 S 0.7774 0.0159 0.2068 108 T 0.4598 0.0158 0.5244 109 V 0.1442 0.0966 0.7592 110 C 0.0683 0.0806 0.8511 111 D 0.0809 0.0657 0.8534 112 E 0.0068 0.8436 0.1497 113 G 0.0061 0.8863 0.1076 114 S 0.0066 0.9219 0.0715 115 A 0.0057 0.9400 0.0543 116 D 0.0058 0.9443 0.0499 117 L 0.0053 0.9458 0.0490 118 L 0.0067 0.9408 0.0525 119 Q 0.0055 0.9202 0.0743 120 S 0.0067 0.8248 0.1685 121 T 0.0510 0.4414 0.5076 122 S 0.0576 0.0783 0.8641 123 P 0.0787 0.0318 0.8896 124 S 0.1490 0.0636 0.7874 125 A 0.5879 0.1613 0.2508 126 F 0.7137 0.1327 0.1537 127 K 0.7212 0.1405 0.1383 128 I 0.5927 0.1471 0.2602 129 A 0.3598 0.1380 0.5023 130 S 0.1725 0.1941 0.6334 131 Y 0.1135 0.3413 0.5453 132 E 0.1246 0.4071 0.4683 133 I 0.1094 0.3919 0.4987 134 N 0.0650 0.2226 0.7124 135 H 0.0540 0.1685 0.7775 136 L 0.0261 0.5606 0.4132 137 P 0.0104 0.8906 0.0991 138 L 0.0058 0.9410 0.0532 139 L 0.0051 0.9517 0.0433 140 K 0.0053 0.9527 0.0420 141 Y 0.0049 0.9558 0.0393 142 V 0.0051 0.9523 0.0426 143 A 0.0053 0.9438 0.0509 144 R 0.0073 0.8902 0.1026 145 L 0.0491 0.5077 0.4432 146 N 0.0371 0.0383 0.9246 147 R 0.0580 0.0091 0.9329 148 P 0.3121 0.0078 0.6801 149 M 0.8152 0.0105 0.1743 150 I 0.8831 0.0073 0.1096 151 F 0.8609 0.0153 0.1237 152 S 0.6634 0.0307 0.3059 153 T 0.2877 0.0490 0.6632 154 A 0.1469 0.0576 0.7955 155 G 0.1822 0.0911 0.7267 156 A 0.1972 0.0583 0.7445 157 E 0.0952 0.0364 0.8684 158 I 0.0050 0.9322 0.0628 159 S 0.0048 0.9486 0.0466 160 D 0.0048 0.9539 0.0413 161 V 0.0047 0.9591 0.0362 162 H 0.0047 0.9601 0.0352 163 E 0.0046 0.9600 0.0354 164 A 0.0047 0.9606 0.0348 165 W 0.0047 0.9605 0.0349 166 R 0.0047 0.9607 0.0347 167 T 0.0047 0.9583 0.0370 168 I 0.0047 0.9560 0.0393 169 R 0.0049 0.9449 0.0502 170 A 0.0058 0.8926 0.1015 171 E 0.0392 0.3194 0.6414 172 G 0.0460 0.0318 0.9222 173 N 0.0834 0.0244 0.8922 174 N 0.1002 0.0421 0.8577 175 Q 0.3965 0.0407 0.5628 176 I 0.8849 0.0057 0.1094 177 A 0.9241 0.0039 0.0720 178 I 0.9286 0.0032 0.0682 179 M 0.8704 0.0067 0.1229 180 H 0.6303 0.0109 0.3588 181 C 0.4737 0.0366 0.4897 182 V 0.3397 0.0689 0.5914 183 A 0.2294 0.0996 0.6709 184 K 0.1396 0.0946 0.7658 185 Y 0.1154 0.0407 0.8439 186 P 0.1001 0.0406 0.8593 187 A 0.1136 0.0237 0.8628 188 P 0.0678 0.0263 0.9059 189 P 0.0171 0.6523 0.3306 190 E 0.0105 0.7131 0.2764 191 Y 0.0225 0.7705 0.2070 192 S 0.0664 0.6049 0.3287 193 N 0.0730 0.5473 0.3798 194 L 0.0136 0.8496 0.1368 195 S 0.0136 0.8899 0.0966 196 V 0.0118 0.9027 0.0855 197 I 0.0076 0.9394 0.0530 198 P 0.0054 0.9424 0.0522 199 M 0.0048 0.9490 0.0462 200 L 0.0048 0.9436 0.0516 201 A 0.0050 0.9276 0.0674 202 A 0.0066 0.8593 0.1341 203 A 0.0127 0.7332 0.2541 204 F 0.0796 0.3127 0.6077 205 P 0.0330 0.1240 0.8430 206 E 0.0496 0.1025 0.8479 207 A 0.1398 0.0318 0.8284 208 V 0.3421 0.0200 0.6379 209 I 0.6017 0.0276 0.3707 210 G 0.5653 0.0226 0.4120 211 F 0.4643 0.0365 0.4992 212 S 0.2590 0.0733 0.6677 213 D 0.1500 0.1261 0.7239 214 H 0.0846 0.1328 0.7826 215 S 0.0814 0.1584 0.7602 216 E 0.0643 0.1755 0.7603 217 H 0.0523 0.1241 0.8236 218 P 0.0475 0.5043 0.4482 219 T 0.0389 0.7142 0.2468 220 E 0.0196 0.8902 0.0903 221 A 0.0101 0.9358 0.0541 222 P 0.0087 0.9484 0.0429 223 C 0.0080 0.9528 0.0392 224 A 0.0131 0.9495 0.0375 225 A 0.0087 0.9517 0.0396 226 V 0.0090 0.9403 0.0507 227 R 0.0126 0.8908 0.0966 228 L 0.0454 0.4752 0.4794 229 G 0.0561 0.0310 0.9129 230 A 0.1047 0.0092 0.8861 231 K 0.3167 0.0404 0.6429 232 L 0.8879 0.0072 0.1048 233 I 0.9045 0.0095 0.0860 234 E 0.9143 0.0041 0.0815 235 K 0.8072 0.0152 0.1777 236 H 0.5158 0.0164 0.4678 237 F 0.3683 0.0229 0.6088 238 T 0.3610 0.0243 0.6147 239 I 0.2319 0.0417 0.7264 240 D 0.1126 0.0392 0.8481 241 K 0.0209 0.2238 0.7553 242 N 0.0314 0.1782 0.7904 243 L 0.0729 0.1283 0.7988 244 P 0.0847 0.1028 0.8124 245 G 0.0994 0.0679 0.8327 246 A 0.0932 0.1148 0.7920 247 D 0.0906 0.1342 0.7752 248 H 0.0751 0.2787 0.6463 249 S 0.0862 0.3998 0.5140 250 F 0.1143 0.3655 0.5203 251 A 0.1687 0.2464 0.5849 252 L 0.1585 0.1260 0.7156 253 N 0.0797 0.0460 0.8742 254 P 0.0062 0.9057 0.0882 255 D 0.0050 0.9362 0.0589 256 E 0.0052 0.9402 0.0546 257 L 0.0047 0.9568 0.0385 258 K 0.0047 0.9588 0.0365 259 E 0.0047 0.9577 0.0376 260 M 0.0047 0.9574 0.0379 261 V 0.0047 0.9580 0.0372 262 D 0.0047 0.9562 0.0391 263 G 0.0048 0.9524 0.0428 264 I 0.0047 0.9574 0.0379 265 R 0.0047 0.9581 0.0372 266 K 0.0047 0.9568 0.0384 267 T 0.0047 0.9562 0.0391 268 E 0.0049 0.9518 0.0434 269 A 0.0056 0.9344 0.0600 270 E 0.0099 0.8679 0.1222 271 L 0.0401 0.5848 0.3751 272 K 0.0378 0.1302 0.8320 273 Q 0.0591 0.1104 0.8304 274 G 0.0990 0.1802 0.7208 275 I 0.2071 0.1652 0.6277 276 T 0.3537 0.1791 0.4672 277 K 0.3826 0.1480 0.4694 278 P 0.3830 0.2278 0.3891 279 V 0.3005 0.2412 0.4582 280 S 0.2497 0.2693 0.4811 281 E 0.1048 0.5825 0.3127 282 K 0.1098 0.5557 0.3345 283 L 0.1439 0.4590 0.3971 284 L 0.1257 0.2707 0.6036 285 G 0.0823 0.1268 0.7909 286 S 0.0511 0.1972 0.7516 287 S 0.0476 0.2310 0.7213 288 Y 0.1034 0.2968 0.5998 289 K 0.1595 0.2892 0.5513 290 T 0.2222 0.2656 0.5122 291 T 0.1579 0.2395 0.6026 292 T 0.0885 0.1307 0.7809 293 A 0.0315 0.4957 0.4728 294 I 0.0368 0.5862 0.3770 295 E 0.0317 0.6565 0.3118 296 G 0.0425 0.6881 0.2693 297 E 0.0467 0.6723 0.2810 298 I 0.0541 0.6172 0.3287 299 R 0.0537 0.6661 0.2802 300 N 0.0603 0.6962 0.2435 301 F 0.0713 0.6793 0.2494 302 A 0.0861 0.6320 0.2819 303 Y 0.1269 0.5439 0.3292 304 R 0.2408 0.4505 0.3087 305 G 0.3969 0.3630 0.2402 306 I 0.6051 0.2468 0.1481 307 F 0.6952 0.1905 0.1143 308 T 0.6869 0.1716 0.1415 309 T 0.7028 0.1363 0.1609 310 A 0.6662 0.1055 0.2283 311 P 0.5846 0.0968 0.3186 312 I 0.3329 0.0584 0.6088 313 Q 0.1487 0.0576 0.7937 314 K 0.0441 0.1175 0.8384 315 G 0.0610 0.0590 0.8801 316 E 0.3788 0.0276 0.5936 317 A 0.7612 0.0154 0.2234 318 F 0.6672 0.0195 0.3133 319 S 0.4060 0.0202 0.5738 320 E 0.0547 0.5952 0.3502 321 D 0.0358 0.5386 0.4257 322 N 0.1210 0.5181 0.3608 323 I 0.5686 0.0437 0.3877 324 A 0.8073 0.0415 0.1512 325 V 0.8603 0.0214 0.1183 326 L 0.7690 0.0253 0.2057 327 R 0.3946 0.0341 0.5713 328 P 0.0772 0.1280 0.7948 329 G 0.0375 0.1059 0.8566 330 Q 0.1054 0.0966 0.7980 331 K 0.1085 0.0516 0.8400 332 P 0.0807 0.1134 0.8059 333 Q 0.0550 0.1034 0.8416 334 G 0.0783 0.0845 0.8372 335 L 0.1297 0.0455 0.8247 336 H 0.1089 0.0509 0.8403 337 P 0.0542 0.5264 0.4194 338 R 0.0315 0.6094 0.3591 339 F 0.0470 0.5958 0.3572 340 F 0.0525 0.7418 0.2057 341 E 0.0430 0.7396 0.2174 342 L 0.0654 0.7314 0.2032 343 L 0.1163 0.6783 0.2054 344 T 0.1787 0.5715 0.2498 345 S 0.1150 0.4732 0.4118 346 G 0.1003 0.2960 0.6037 347 V 0.2235 0.3604 0.4161 348 R 0.3558 0.3544 0.2897 349 A 0.2442 0.4249 0.3310 350 V 0.2589 0.4254 0.3157 351 R 0.2090 0.4298 0.3611 352 D 0.1917 0.3330 0.4752 353 I 0.1567 0.1442 0.6991 354 P 0.0954 0.0867 0.8179 355 A 0.0309 0.1028 0.8663 356 D 0.0206 0.0410 0.9384 357 T 0.1072 0.0210 0.8718 358 G 0.3365 0.0138 0.6497 359 I 0.4995 0.0138 0.4868 360 V 0.2446 0.0176 0.7378 361 W 0.0144 0.7264 0.2592 362 D 0.0087 0.7565 0.2347 363 D 0.0167 0.7822 0.2011 364 I 0.0622 0.6213 0.3165 365 L 0.0979 0.4752 0.4269 366 L 0.0580 0.3563 0.5857 367 K 0.0600 0.1814 0.7586 368 D 0.0522 0.0781 0.8697 369 S 0.1174 0.0562 0.8265 370 P 0.2072 0.0789 0.7139 371 F 0.2314 0.0764 0.6922 372 H 0.1592 0.0637 0.7770 373 E 0.0455 0.0382 0.9163