# This file is the result of combining several RDB files, specifically # T0199.t04.dssp-ebghstl.rdb (weight 1.53986) # T0199.t04.stride-ebghtl.rdb (weight 1.24869) # T0199.t04.str2.rdb (weight 1.54758) # T0199.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 T0199.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0199 # 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 T0199.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 145 # # ============================================ # Comments from T0199.t04.stride-ebghtl.rdb # ============================================ # TARGET T0199 # 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 T0199.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 145 # # ============================================ # Comments from T0199.t04.str2.rdb # ============================================ # TARGET T0199 # 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 T0199.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 145 # # ============================================ # Comments from T0199.t04.alpha.rdb # ============================================ # TARGET T0199 # 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 T0199.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 145 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0803 0.2542 0.6654 2 R 0.1129 0.3830 0.5041 3 R 0.1107 0.4809 0.4084 4 L 0.1052 0.4169 0.4779 5 N 0.1068 0.3321 0.5610 6 R 0.0685 0.3767 0.5548 7 K 0.0655 0.3942 0.5403 8 N 0.0687 0.4516 0.4797 9 N 0.0201 0.7830 0.1969 10 E 0.0108 0.8858 0.1034 11 A 0.0147 0.8909 0.0945 12 L 0.0169 0.8716 0.1115 13 K 0.0128 0.8302 0.1571 14 K 0.0195 0.6467 0.3338 15 L 0.0451 0.5095 0.4454 16 N 0.0396 0.5081 0.4523 17 D 0.0049 0.9387 0.0564 18 R 0.0047 0.9557 0.0396 19 Q 0.0047 0.9602 0.0351 20 R 0.0046 0.9615 0.0339 21 K 0.0046 0.9614 0.0340 22 V 0.0046 0.9615 0.0338 23 L 0.0046 0.9609 0.0345 24 Y 0.0046 0.9614 0.0340 25 C 0.0046 0.9617 0.0337 26 I 0.0046 0.9605 0.0349 27 V 0.0047 0.9599 0.0354 28 R 0.0046 0.9607 0.0346 29 E 0.0047 0.9594 0.0359 30 Y 0.0048 0.9563 0.0389 31 I 0.0050 0.9442 0.0508 32 E 0.0066 0.9023 0.0911 33 N 0.0448 0.4570 0.4982 34 K 0.0386 0.1095 0.8519 35 K 0.0674 0.0166 0.9160 36 P 0.2075 0.0198 0.7727 37 V 0.2452 0.0817 0.6732 38 S 0.2132 0.1040 0.6828 39 S 0.0982 0.6220 0.2798 40 Q 0.0209 0.9106 0.0685 41 R 0.0284 0.9203 0.0513 42 V 0.0166 0.9338 0.0496 43 L 0.0177 0.9227 0.0596 44 E 0.0237 0.8949 0.0814 45 V 0.0249 0.8179 0.1572 46 S 0.0527 0.4857 0.4616 47 N 0.0489 0.0729 0.8782 48 I 0.0953 0.0398 0.8649 49 E 0.1461 0.0623 0.7917 50 F 0.1822 0.0844 0.7335 51 S 0.1227 0.0795 0.7978 52 S 0.0470 0.3992 0.5537 53 A 0.0625 0.5729 0.3646 54 T 0.0886 0.6492 0.2621 55 I 0.0400 0.8373 0.1226 56 R 0.0106 0.9046 0.0848 57 N 0.0066 0.9159 0.0775 58 D 0.0084 0.9141 0.0775 59 M 0.0049 0.9557 0.0394 60 K 0.0048 0.9585 0.0367 61 K 0.0048 0.9585 0.0368 62 L 0.0048 0.9578 0.0374 63 E 0.0049 0.9456 0.0495 64 Y 0.0057 0.8545 0.1398 65 L 0.0422 0.3604 0.5974 66 G 0.0304 0.0420 0.9276 67 Y 0.0812 0.0714 0.8474 68 I 0.3503 0.0391 0.6106 69 Y 0.3478 0.0474 0.6049 70 Q 0.3145 0.0164 0.6692 71 P 0.2749 0.0378 0.6873 72 H 0.3150 0.0312 0.6538 73 T 0.2150 0.0609 0.7241 74 S 0.1221 0.0641 0.8138 75 A 0.1450 0.0678 0.7872 76 G 0.1559 0.0502 0.7939 77 R 0.3651 0.0342 0.6007 78 I 0.2571 0.0166 0.7263 79 P 0.1920 0.0184 0.7896 80 T 0.0908 0.0308 0.8784 81 D 0.0143 0.5850 0.4007 82 K 0.0065 0.8081 0.1854 83 G 0.0106 0.8836 0.1058 84 L 0.0182 0.8983 0.0835 85 R 0.0185 0.9245 0.0571 86 F 0.0355 0.8916 0.0728 87 Y 0.0305 0.8824 0.0871 88 Y 0.0210 0.8976 0.0814 89 E 0.0202 0.8943 0.0855 90 E 0.0172 0.8561 0.1268 91 M 0.0318 0.7578 0.2104 92 L 0.0837 0.5158 0.4005 93 K 0.1026 0.2587 0.6387 94 I 0.0917 0.1425 0.7657 95 S 0.0675 0.0992 0.8333 96 K 0.0397 0.3191 0.6412 97 E 0.0465 0.3648 0.5886 98 T 0.0509 0.3805 0.5686 99 S 0.0146 0.7599 0.2255 100 E 0.0139 0.8661 0.1200 101 A 0.0152 0.8994 0.0854 102 D 0.0225 0.9040 0.0735 103 L 0.0384 0.8851 0.0766 104 A 0.0406 0.8715 0.0879 105 V 0.0361 0.8744 0.0895 106 E 0.0421 0.8501 0.1078 107 T 0.0440 0.7910 0.1650 108 F 0.0771 0.6423 0.2807 109 K 0.0901 0.4129 0.4970 110 S 0.0873 0.1833 0.7295 111 M 0.0840 0.0620 0.8540 112 P 0.0813 0.0883 0.8304 113 L 0.0884 0.1175 0.7941 114 A 0.1100 0.0686 0.8213 115 D 0.0964 0.0322 0.8714 116 P 0.0052 0.9348 0.0600 117 E 0.0048 0.9561 0.0391 118 K 0.0048 0.9578 0.0374 119 V 0.0047 0.9599 0.0354 120 L 0.0047 0.9595 0.0358 121 F 0.0047 0.9601 0.0352 122 L 0.0047 0.9592 0.0361 123 A 0.0047 0.9574 0.0379 124 G 0.0048 0.9586 0.0366 125 N 0.0048 0.9560 0.0392 126 L 0.0049 0.9454 0.0497 127 L 0.0051 0.9208 0.0741 128 A 0.0062 0.8274 0.1665 129 R 0.0092 0.6134 0.3774 130 L 0.0357 0.3979 0.5665 131 T 0.0559 0.2060 0.7381 132 E 0.0867 0.1335 0.7798 133 G 0.2734 0.0787 0.6479 134 Y 0.6130 0.0545 0.3325 135 V 0.8693 0.0238 0.1069 136 L 0.9018 0.0176 0.0806 137 I 0.8792 0.0152 0.1056 138 E 0.7051 0.0197 0.2752 139 R 0.2754 0.0120 0.7126 140 P 0.0943 0.0758 0.8299 141 N 0.0961 0.0724 0.8315 142 T 0.0836 0.1743 0.7421 143 R 0.1079 0.2071 0.6850 144 D 0.2179 0.1649 0.6171 145 L 0.4670 0.0751 0.4578 146 K 0.7474 0.0309 0.2217 147 I 0.8651 0.0109 0.1240 148 L 0.8289 0.0278 0.1433 149 R 0.8679 0.0069 0.1252 150 V 0.8737 0.0038 0.1225 151 M 0.8958 0.0049 0.0993 152 L 0.9010 0.0035 0.0955 153 I 0.8658 0.0050 0.1293 154 P 0.7862 0.0039 0.2099 155 V 0.3509 0.0294 0.6197 156 S 0.1218 0.0442 0.8340 157 E 0.0180 0.1934 0.7885 158 D 0.0401 0.0955 0.8644 159 Y 0.4209 0.0334 0.5457 160 L 0.8418 0.0043 0.1539 161 I 0.9141 0.0033 0.0826 162 F 0.9321 0.0033 0.0646 163 S 0.9322 0.0032 0.0645 164 I 0.9285 0.0034 0.0680 165 L 0.9011 0.0043 0.0947 166 T 0.6039 0.0113 0.3849 167 E 0.1657 0.0812 0.7531 168 F 0.0609 0.0356 0.9035 169 G 0.1379 0.0375 0.8246 170 V 0.5105 0.0289 0.4606 171 S 0.7978 0.0130 0.1892 172 K 0.7645 0.0190 0.2165 173 V 0.6953 0.0195 0.2851 174 T 0.6082 0.0187 0.3731 175 P 0.6244 0.0283 0.3473 176 I 0.5406 0.0406 0.4189 177 K 0.4544 0.0514 0.4942 178 T 0.2518 0.0948 0.6534 179 Q 0.1341 0.2806 0.5852 180 E 0.1218 0.2892 0.5891 181 R 0.1505 0.1930 0.6565 182 L 0.2002 0.0443 0.7556 183 N 0.0980 0.0231 0.8790 184 W 0.0050 0.9437 0.0514 185 E 0.0047 0.9601 0.0353 186 E 0.0047 0.9598 0.0354 187 I 0.0049 0.9597 0.0354 188 E 0.0047 0.9598 0.0355 189 R 0.0048 0.9566 0.0387 190 Q 0.0048 0.9496 0.0456 191 L 0.0051 0.9482 0.0467 192 N 0.0057 0.9424 0.0519 193 F 0.0080 0.9311 0.0609 194 L 0.0120 0.9067 0.0813 195 L 0.0270 0.7879 0.1852 196 R 0.0410 0.3193 0.6397 197 G 0.0282 0.0541 0.9177 198 R 0.1262 0.0202 0.8536 199 T 0.1842 0.0162 0.7997 200 V 0.0493 0.7415 0.2092 201 G 0.0501 0.7460 0.2038 202 E 0.0658 0.7647 0.1694 203 V 0.1213 0.6532 0.2255 204 L 0.1483 0.5757 0.2760 205 M 0.1089 0.6589 0.2323 206 G 0.1082 0.5792 0.3126 207 K 0.1194 0.6300 0.2506 208 I 0.0732 0.7876 0.1393 209 E 0.0598 0.7987 0.1415 210 S 0.0408 0.8353 0.1239 211 L 0.0368 0.8015 0.1618 212 K 0.0229 0.8104 0.1667 213 G 0.0114 0.8358 0.1529 214 S 0.0078 0.8927 0.0996 215 G 0.0063 0.9342 0.0595 216 F 0.0047 0.9560 0.0393 217 L 0.0049 0.9592 0.0359 218 R 0.0052 0.9593 0.0355 219 L 0.0049 0.9578 0.0373 220 I 0.0048 0.9550 0.0402 221 E 0.0052 0.9502 0.0445 222 S 0.0084 0.9177 0.0739 223 L 0.0121 0.8335 0.1543 224 I 0.0335 0.6105 0.3560 225 G 0.0249 0.4644 0.5107 226 E 0.0332 0.5845 0.3823 227 T 0.0412 0.6685 0.2903 228 V 0.0258 0.8403 0.1340 229 E 0.0180 0.8998 0.0822 230 R 0.0255 0.9058 0.0688 231 Y 0.0488 0.8889 0.0624 232 L 0.0491 0.8780 0.0730 233 D 0.0317 0.8776 0.0906 234 A 0.0366 0.6282 0.3352 235 G 0.0399 0.2758 0.6842 236 L 0.0685 0.5466 0.3849 237 E 0.0590 0.7640 0.1770 238 N 0.0392 0.7739 0.1869 239 L 0.0392 0.7300 0.2308 240 L 0.0640 0.5125 0.4235 241 K 0.0510 0.3070 0.6420 242 D 0.0709 0.0946 0.8344 243 E 0.0260 0.1912 0.7828 244 T 0.0749 0.1281 0.7970 245 L 0.1742 0.0298 0.7960 246 T 0.0857 0.0152 0.8992 247 L 0.0050 0.9330 0.0620 248 E 0.0047 0.9515 0.0438 249 D 0.0047 0.9518 0.0434 250 I 0.0047 0.9554 0.0398 251 R 0.0047 0.9573 0.0380 252 N 0.0047 0.9507 0.0446 253 L 0.0048 0.9485 0.0467 254 L 0.0048 0.9537 0.0415 255 E 0.0048 0.9556 0.0396 256 E 0.0049 0.9518 0.0432 257 V 0.0051 0.9365 0.0584 258 K 0.0063 0.8524 0.1413 259 D 0.0181 0.6794 0.3024 260 Q 0.0263 0.7682 0.2055 261 K 0.0098 0.8399 0.1503 262 F 0.0165 0.8755 0.1079 263 L 0.0158 0.9208 0.0634 264 E 0.0159 0.9259 0.0581 265 S 0.0160 0.9144 0.0696 266 L 0.0241 0.8714 0.1045 267 V 0.0352 0.7629 0.2019 268 G 0.0448 0.3926 0.5626 269 E 0.0395 0.0795 0.8810 270 G 0.0603 0.0279 0.9118 271 I 0.4281 0.0070 0.5648 272 T 0.8634 0.0038 0.1328 273 V 0.9116 0.0034 0.0850 274 R 0.9004 0.0053 0.0943 275 I 0.7614 0.0262 0.2124 276 G 0.3434 0.0510 0.6056 277 R 0.1707 0.2627 0.5666 278 E 0.1284 0.3902 0.4814 279 I 0.1069 0.2814 0.6116 280 G 0.0660 0.1414 0.7926 281 R 0.0881 0.2779 0.6340 282 K 0.0882 0.4190 0.4927 283 K 0.0885 0.4124 0.4991 284 L 0.1019 0.3942 0.5039 285 E 0.0702 0.4416 0.4882 286 K 0.1238 0.2594 0.6168 287 F 0.4900 0.0817 0.4283 288 A 0.8129 0.0188 0.1683 289 V 0.9086 0.0069 0.0844 290 F 0.9111 0.0056 0.0833 291 S 0.8417 0.0129 0.1454 292 G 0.7148 0.0178 0.2674 293 K 0.6810 0.0274 0.2916 294 Y 0.6355 0.0440 0.3205 295 F 0.4590 0.0554 0.4856 296 K 0.1809 0.0569 0.7622 297 G 0.0549 0.0327 0.9124 298 E 0.0705 0.0404 0.8891 299 S 0.2668 0.0162 0.7170 300 P 0.4920 0.0235 0.4845 301 I 0.7042 0.0248 0.2710 302 G 0.8141 0.0093 0.1766 303 S 0.8955 0.0055 0.0990 304 V 0.9294 0.0032 0.0674 305 Y 0.9305 0.0034 0.0661 306 L 0.9292 0.0032 0.0677 307 F 0.8471 0.0102 0.1427 308 T 0.5002 0.0109 0.4889 309 S 0.3026 0.0467 0.6507 310 K 0.3230 0.0940 0.5830 311 V 0.3404 0.1184 0.5413 312 T 0.1882 0.1502 0.6616 313 K 0.1511 0.1901 0.6588 314 Y 0.0549 0.4374 0.5077 315 D 0.0166 0.6576 0.3259 316 R 0.0132 0.6555 0.3313 317 N 0.0170 0.7327 0.2503 318 H 0.0125 0.8029 0.1846 319 R 0.0161 0.8897 0.0942 320 V 0.0075 0.9449 0.0477 321 F 0.0047 0.9598 0.0355 322 E 0.0046 0.9615 0.0338 323 Y 0.0046 0.9617 0.0337 324 I 0.0047 0.9602 0.0351 325 L 0.0047 0.9603 0.0351 326 N 0.0048 0.9575 0.0378 327 R 0.0049 0.9482 0.0469 328 L 0.0050 0.9447 0.0502 329 S 0.0050 0.9442 0.0509 330 E 0.0052 0.9268 0.0680 331 Y 0.0070 0.8950 0.0981 332 F 0.0178 0.7773 0.2049 333 T 0.0226 0.5890 0.3884 334 S 0.0204 0.4917 0.4879 335 T 0.0343 0.4148 0.5510 336 S 0.0550 0.2908 0.6543 337 R 0.0560 0.1483 0.7957 338 R 0.0517 0.0624 0.8860