# This file is the result of combining several RDB files, specifically # T0441.t04.dssp-ebghstl.rdb (weight 1.53986) # T0441.t04.stride-ebghtl.rdb (weight 1.24869) # T0441.t04.str2.rdb (weight 1.54758) # T0441.t04.alpha.rdb (weight 0.659012) # T0441.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0441.t2k.stride-ebghtl.rdb (weight 1.24869) # T0441.t2k.str2.rdb (weight 1.54758) # T0441.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 T0441.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0441 # 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 T0441.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 215.306 # # ============================================ # Comments from T0441.t04.stride-ebghtl.rdb # ============================================ # TARGET T0441 # 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 T0441.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 215.306 # # ============================================ # Comments from T0441.t04.str2.rdb # ============================================ # TARGET T0441 # 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 T0441.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 215.306 # # ============================================ # Comments from T0441.t04.alpha.rdb # ============================================ # TARGET T0441 # 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 T0441.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 215.306 # # ============================================ # Comments from T0441.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0441 # 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 T0441.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 3489 # # ============================================ # Comments from T0441.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0441 # 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 T0441.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 3489 # # ============================================ # Comments from T0441.t2k.str2.rdb # ============================================ # TARGET T0441 # 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 T0441.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 3489 # # ============================================ # Comments from T0441.t2k.alpha.rdb # ============================================ # TARGET T0441 # 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 T0441.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 3489 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1463 0.0471 0.8065 2 S 0.1897 0.0534 0.7568 3 E 0.1640 0.0931 0.7430 4 P 0.1837 0.1138 0.7026 5 R 0.2948 0.0859 0.6193 6 K 0.3266 0.0449 0.6285 7 R 0.1556 0.0355 0.8089 8 R 0.0607 0.0917 0.8476 9 S 0.0376 0.0982 0.8643 10 T 0.0604 0.0772 0.8624 11 G 0.0847 0.0714 0.8439 12 N 0.1538 0.0218 0.8244 13 V 0.1894 0.0149 0.7957 14 T 0.1627 0.0215 0.8158 15 L 0.0054 0.9080 0.0867 16 A 0.0047 0.9407 0.0545 17 D 0.0050 0.9501 0.0449 18 V 0.0052 0.9570 0.0378 19 A 0.0050 0.9565 0.0385 20 K 0.0056 0.9441 0.0502 21 Q 0.0058 0.9143 0.0799 22 A 0.0455 0.4917 0.4628 23 G 0.0339 0.0650 0.9011 24 V 0.0672 0.0354 0.8975 25 G 0.0773 0.0333 0.8894 26 T 0.0077 0.8586 0.1337 27 M 0.0053 0.9141 0.0806 28 T 0.0066 0.9345 0.0589 29 V 0.0062 0.9486 0.0452 30 S 0.0063 0.9504 0.0433 31 R 0.0056 0.9490 0.0454 32 A 0.0055 0.9362 0.0582 33 L 0.0118 0.8489 0.1393 34 R 0.0396 0.4468 0.5136 35 T 0.0447 0.0951 0.8602 36 P 0.0673 0.0732 0.8595 37 E 0.0258 0.1828 0.7914 38 L 0.0503 0.1486 0.8011 39 V 0.1090 0.0341 0.8568 40 S 0.0556 0.0257 0.9187 41 D 0.0051 0.9276 0.0672 42 K 0.0048 0.9452 0.0500 43 L 0.0053 0.9489 0.0459 44 R 0.0047 0.9590 0.0363 45 E 0.0047 0.9596 0.0357 46 K 0.0047 0.9593 0.0360 47 I 0.0047 0.9599 0.0354 48 Q 0.0047 0.9605 0.0349 49 Q 0.0047 0.9610 0.0343 50 V 0.0047 0.9604 0.0349 51 V 0.0048 0.9573 0.0379 52 D 0.0050 0.9468 0.0482 53 E 0.0054 0.9186 0.0760 54 L 0.0447 0.4594 0.4959 55 G 0.0420 0.0310 0.9270 56 Y 0.0763 0.0210 0.9027 57 I 0.1328 0.0160 0.8512 58 P 0.0811 0.0758 0.8431 59 N 0.0676 0.1072 0.8252 60 K 0.0071 0.8921 0.1008 61 A 0.0061 0.9242 0.0698 62 A 0.0057 0.9352 0.0591 63 G 0.0063 0.9325 0.0611 64 A 0.0081 0.9076 0.0844 65 L 0.0107 0.8732 0.1161 66 A 0.0191 0.7868 0.1940 67 S 0.0398 0.5005 0.4596 68 A 0.0457 0.1546 0.7997 69 E 0.0816 0.0726 0.8458 70 S 0.1856 0.0396 0.7748 71 Y 0.2882 0.0413 0.6704 72 S 0.7533 0.0103 0.2364 73 I 0.8789 0.0048 0.1163 74 A 0.9081 0.0040 0.0879 75 L 0.9147 0.0036 0.0817 76 I 0.8873 0.0052 0.1075 77 I 0.7208 0.0084 0.2707 78 P 0.3796 0.0520 0.5684 79 S 0.1107 0.0593 0.8300 80 L 0.0542 0.1381 0.8077 81 F 0.0370 0.1361 0.8270 82 E 0.0619 0.1642 0.7739 83 K 0.0113 0.7744 0.2143 84 A 0.0144 0.8296 0.1561 85 C 0.0052 0.9345 0.0602 86 A 0.0047 0.9562 0.0391 87 H 0.0047 0.9575 0.0378 88 F 0.0047 0.9578 0.0375 89 L 0.0047 0.9584 0.0369 90 P 0.0048 0.9542 0.0410 91 S 0.0048 0.9477 0.0475 92 F 0.0047 0.9536 0.0417 93 Q 0.0047 0.9577 0.0376 94 Q 0.0047 0.9587 0.0366 95 A 0.0048 0.9582 0.0370 96 L 0.0048 0.9558 0.0394 97 N 0.0051 0.9403 0.0546 98 K 0.0066 0.8714 0.1221 99 A 0.0405 0.3351 0.6244 100 G 0.0390 0.0186 0.9424 101 Y 0.1328 0.0102 0.8570 102 Q 0.7292 0.0064 0.2644 103 L 0.9159 0.0032 0.0809 104 L 0.9237 0.0036 0.0727 105 L 0.9200 0.0033 0.0767 106 G 0.8454 0.0077 0.1469 107 Y 0.5113 0.0157 0.4730 108 S 0.1370 0.0445 0.8185 109 D 0.0591 0.0667 0.8741 110 Y 0.0472 0.0671 0.8857 111 S 0.0728 0.0895 0.8376 112 I 0.0089 0.7842 0.2069 113 E 0.0074 0.8537 0.1389 114 Q 0.0072 0.8926 0.1002 115 E 0.0053 0.9378 0.0569 116 E 0.0059 0.9446 0.0495 117 K 0.0052 0.9476 0.0472 118 L 0.0048 0.9531 0.0421 119 L 0.0047 0.9556 0.0397 120 S 0.0047 0.9547 0.0406 121 T 0.0048 0.9516 0.0436 122 F 0.0050 0.9448 0.0502 123 L 0.0054 0.9149 0.0797 124 E 0.0084 0.6977 0.2940 125 S 0.0360 0.3250 0.6390 126 R 0.0735 0.0373 0.8892 127 P 0.0984 0.0073 0.8943 128 A 0.1335 0.0359 0.8305 129 G 0.9064 0.0049 0.0887 130 V 0.9309 0.0035 0.0657 131 V 0.9319 0.0033 0.0648 132 L 0.9129 0.0051 0.0820 133 F 0.6765 0.0155 0.3080 134 G 0.2283 0.0233 0.7484 135 S 0.0954 0.0781 0.8265 136 E 0.0713 0.0916 0.8371 137 H 0.0552 0.0894 0.8554 138 S 0.0491 0.1065 0.8445 139 Q 0.0153 0.7794 0.2053 140 R 0.0068 0.8778 0.1153 141 T 0.0085 0.9025 0.0889 142 H 0.0084 0.9200 0.0716 143 Q 0.0093 0.9303 0.0605 144 L 0.0063 0.9425 0.0512 145 L 0.0066 0.9375 0.0559 146 E 0.0061 0.9243 0.0696 147 A 0.0087 0.8246 0.1667 148 S 0.0475 0.3191 0.6333 149 N 0.0393 0.0251 0.9356 150 T 0.0777 0.0087 0.9135 151 P 0.2987 0.0066 0.6947 152 V 0.8982 0.0036 0.0982 153 L 0.9279 0.0034 0.0687 154 E 0.9263 0.0035 0.0702 155 I 0.8695 0.0092 0.1213 156 A 0.4470 0.0193 0.5337 157 E 0.1571 0.0460 0.7969 158 L 0.1206 0.0756 0.8038 159 S 0.0908 0.1247 0.7845 160 S 0.0479 0.1714 0.7806 161 K 0.0595 0.1724 0.7680 162 A 0.0636 0.1672 0.7692 163 S 0.1090 0.1141 0.7768 164 Y 0.2585 0.0473 0.6941 165 L 0.3193 0.0765 0.6043 166 N 0.6801 0.0441 0.2758 167 I 0.7935 0.0256 0.1809 168 G 0.6847 0.0306 0.2847 169 V 0.3773 0.0800 0.5427 170 D 0.1079 0.1092 0.7828 171 H 0.0218 0.5732 0.4050 172 F 0.0069 0.9128 0.0804 173 E 0.0057 0.9435 0.0509 174 V 0.0048 0.9512 0.0440 175 G 0.0047 0.9582 0.0371 176 K 0.0047 0.9604 0.0349 177 A 0.0046 0.9611 0.0342 178 C 0.0047 0.9607 0.0346 179 T 0.0047 0.9608 0.0345 180 R 0.0047 0.9608 0.0346 181 H 0.0047 0.9595 0.0358 182 L 0.0047 0.9576 0.0376 183 I 0.0049 0.9449 0.0501 184 E 0.0059 0.8744 0.1197 185 Q 0.0387 0.2670 0.6943 186 G 0.0411 0.0323 0.9266 187 F 0.0881 0.0202 0.8916 188 K 0.2880 0.0339 0.6781 189 N 0.7496 0.0101 0.2403 190 V 0.9146 0.0046 0.0808 191 G 0.9238 0.0042 0.0721 192 F 0.9183 0.0047 0.0770 193 I 0.8379 0.0130 0.1491 194 G 0.4492 0.0243 0.5265 195 A 0.1382 0.0323 0.8296 196 R 0.0922 0.0811 0.8267 197 G 0.0459 0.1750 0.7790 198 N 0.0446 0.1764 0.7790 199 H 0.0569 0.2346 0.7086 200 S 0.0379 0.4956 0.4665 201 T 0.0254 0.6876 0.2870 202 L 0.0097 0.8912 0.0991 203 Q 0.0066 0.9328 0.0606 204 R 0.0062 0.9397 0.0541 205 Q 0.0059 0.9453 0.0488 206 L 0.0057 0.9488 0.0455 207 H 0.0077 0.9431 0.0492 208 G 0.0055 0.9463 0.0481 209 W 0.0047 0.9580 0.0373 210 Q 0.0047 0.9600 0.0353 211 S 0.0048 0.9601 0.0352 212 A 0.0047 0.9595 0.0358 213 M 0.0048 0.9575 0.0377 214 I 0.0050 0.9466 0.0484 215 E 0.0059 0.9001 0.0940 216 N 0.0426 0.4263 0.5311 217 Y 0.0345 0.0378 0.9278 218 L 0.0655 0.0207 0.9138 219 T 0.1263 0.0238 0.8499 220 P 0.1549 0.0606 0.7845 221 D 0.1364 0.0653 0.7983 222 H 0.1115 0.4583 0.4303 223 F 0.1680 0.4614 0.3706 224 L 0.2752 0.4028 0.3219 225 T 0.3873 0.2654 0.3473 226 T 0.3625 0.2012 0.4363 227 H 0.2559 0.1617 0.5823 228 E 0.1082 0.1103 0.7815 229 A 0.0824 0.1056 0.8120 230 P 0.0718 0.1184 0.8098 231 S 0.0737 0.1055 0.8208 232 S 0.0183 0.7177 0.2641 233 Q 0.0106 0.8377 0.1518 234 L 0.0115 0.8619 0.1267 235 G 0.0067 0.9090 0.0843 236 A 0.0056 0.9420 0.0523 237 E 0.0050 0.9533 0.0418 238 G 0.0047 0.9555 0.0398 239 L 0.0047 0.9552 0.0401 240 A 0.0048 0.9558 0.0394 241 K 0.0049 0.9513 0.0438 242 L 0.0054 0.9381 0.0565 243 L 0.0072 0.8982 0.0946 244 L 0.0104 0.7750 0.2146 245 R 0.0375 0.4818 0.4807 246 D 0.0468 0.1047 0.8485 247 S 0.0509 0.0745 0.8746 248 S 0.0888 0.0355 0.8757 249 L 0.1629 0.0157 0.8214 250 N 0.4334 0.0319 0.5346 251 A 0.9169 0.0042 0.0789 252 L 0.9283 0.0037 0.0680 253 V 0.9245 0.0039 0.0716 254 C 0.8536 0.0060 0.1404 255 S 0.3539 0.0337 0.6124 256 H 0.0800 0.0742 0.8458 257 E 0.0222 0.6990 0.2787 258 E 0.0077 0.9156 0.0768 259 I 0.0067 0.9332 0.0601 260 A 0.0050 0.9518 0.0432 261 I 0.0048 0.9572 0.0380 262 G 0.0047 0.9579 0.0374 263 A 0.0047 0.9597 0.0356 264 L 0.0047 0.9600 0.0354 265 F 0.0047 0.9605 0.0348 266 E 0.0047 0.9601 0.0352 267 C 0.0047 0.9586 0.0367 268 H 0.0049 0.9482 0.0469 269 R 0.0053 0.9080 0.0867 270 R 0.0423 0.3261 0.6315 271 V 0.0358 0.0238 0.9404 272 L 0.0885 0.0170 0.8945 273 K 0.2627 0.0169 0.7204 274 V 0.2326 0.0249 0.7426 275 P 0.1479 0.0757 0.7764 276 T 0.1263 0.1336 0.7401 277 D 0.3508 0.0618 0.5874 278 I 0.7512 0.0112 0.2376 279 A 0.8644 0.0087 0.1269 280 I 0.9108 0.0058 0.0834 281 I 0.8742 0.0144 0.1114 282 C 0.7702 0.0110 0.2188 283 L 0.4982 0.0376 0.4642 284 E 0.1574 0.0430 0.7996 285 G 0.0644 0.1303 0.8053 286 S 0.0590 0.3748 0.5662 287 S 0.0517 0.5747 0.3735 288 M 0.0287 0.6905 0.2809 289 G 0.0462 0.7011 0.2528 290 E 0.0534 0.6423 0.3043 291 H 0.0771 0.4987 0.4242 292 A 0.1302 0.2629 0.6069 293 Y 0.1007 0.0760 0.8233 294 P 0.0997 0.0770 0.8233 295 S 0.1546 0.0971 0.7483 296 L 0.3377 0.0817 0.5805 297 T 0.4815 0.0743 0.4442 298 S 0.6166 0.0588 0.3247 299 A 0.5803 0.0814 0.3383 300 E 0.4247 0.0755 0.4998 301 F 0.2648 0.0585 0.6767 302 D 0.1211 0.0467 0.8321 303 Y 0.0083 0.8480 0.1437 304 E 0.0058 0.9175 0.0767 305 R 0.0056 0.9382 0.0562 306 M 0.0049 0.9451 0.0500 307 G 0.0047 0.9482 0.0471 308 T 0.0047 0.9552 0.0400 309 K 0.0047 0.9576 0.0377 310 A 0.0047 0.9599 0.0355 311 A 0.0047 0.9604 0.0349 312 E 0.0047 0.9605 0.0348 313 K 0.0047 0.9604 0.0350 314 L 0.0047 0.9592 0.0361 315 L 0.0047 0.9573 0.0379 316 H 0.0048 0.9446 0.0505 317 A 0.0058 0.9130 0.0812 318 I 0.0111 0.8470 0.1418 319 K 0.0269 0.5243 0.4487 320 G 0.0429 0.1166 0.8405 321 E 0.0547 0.0630 0.8824 322 P 0.0799 0.0702 0.8499 323 E 0.0800 0.0641 0.8559 324 E 0.0840 0.0575 0.8585 325 R 0.1359 0.0607 0.8033 326 P 0.2258 0.0509 0.7232 327 T 0.4748 0.0331 0.4922 328 S 0.6539 0.0155 0.3306 329 M 0.6254 0.0127 0.3619 330 G 0.4686 0.0128 0.5186 331 F 0.2688 0.0174 0.7139 332 K 0.3209 0.0392 0.6400 333 L 0.6876 0.0297 0.2827 334 K 0.8448 0.0147 0.1405 335 R 0.8300 0.0175 0.1525 336 R 0.7367 0.0276 0.2357 337 A 0.3801 0.0774 0.5426 338 S 0.2046 0.0843 0.7112 339 T 0.1408 0.0908 0.7684 340 A 0.0989 0.0582 0.8429 341 I 0.0733 0.0342 0.8925 342 N 0.0523 0.0259 0.9219