# This file is the result of combining several RDB files, specifically # T0384.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0384.t2k.stride-ebghtl.rdb (weight 1.24869) # T0384.t2k.str2.rdb (weight 1.54758) # T0384.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 T0384.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0384 # 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 T0384.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 1530 # # ============================================ # Comments from T0384.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0384 # 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 T0384.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 1530 # # ============================================ # Comments from T0384.t2k.str2.rdb # ============================================ # TARGET T0384 # 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 T0384.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 1530 # # ============================================ # Comments from T0384.t2k.alpha.rdb # ============================================ # TARGET T0384 # 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 T0384.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 1530 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0706 0.0291 0.9002 2 L 0.3630 0.0085 0.6285 3 K 0.7421 0.0169 0.2410 4 L 0.9049 0.0053 0.0898 5 G 0.9235 0.0034 0.0731 6 V 0.9255 0.0034 0.0711 7 I 0.8515 0.0256 0.1229 8 G 0.5186 0.0246 0.4568 9 T 0.1451 0.1057 0.7492 10 G 0.0659 0.2447 0.6894 11 A 0.0180 0.7681 0.2139 12 I 0.0116 0.8250 0.1634 13 S 0.0097 0.8699 0.1204 14 H 0.0071 0.9012 0.0917 15 H 0.0084 0.8698 0.1217 16 F 0.0114 0.8660 0.1226 17 I 0.0077 0.9076 0.0847 18 E 0.0074 0.9260 0.0666 19 A 0.0060 0.9284 0.0656 20 A 0.0065 0.9146 0.0789 21 H 0.0073 0.8342 0.1586 22 T 0.0146 0.6241 0.3613 23 S 0.0708 0.1401 0.7891 24 G 0.0168 0.1089 0.8743 25 E 0.0290 0.0530 0.9180 26 Y 0.4690 0.0099 0.5211 27 Q 0.8510 0.0048 0.1443 28 L 0.9306 0.0029 0.0665 29 V 0.8972 0.0119 0.0909 30 A 0.9178 0.0036 0.0786 31 I 0.8720 0.0045 0.1235 32 Y 0.7272 0.0117 0.2611 33 S 0.3587 0.0115 0.6298 34 R 0.0708 0.0617 0.8675 35 K 0.0941 0.0255 0.8804 36 L 0.0059 0.8373 0.1569 37 E 0.0057 0.9021 0.0921 38 T 0.0050 0.9272 0.0678 39 A 0.0048 0.9478 0.0475 40 A 0.0052 0.9491 0.0457 41 T 0.0048 0.9497 0.0455 42 F 0.0048 0.9492 0.0460 43 A 0.0049 0.9386 0.0565 44 S 0.0054 0.8998 0.0947 45 R 0.0084 0.8411 0.1505 46 Y 0.0498 0.4766 0.4735 47 Q 0.0386 0.0858 0.8756 48 N 0.0667 0.0725 0.8608 49 I 0.1060 0.1278 0.7662 50 Q 0.1988 0.1571 0.6440 51 L 0.2850 0.1420 0.5730 52 F 0.3107 0.0869 0.6024 53 D 0.1875 0.1115 0.7010 54 Q 0.1515 0.0908 0.7577 55 L 0.0116 0.7692 0.2191 56 E 0.0097 0.7847 0.2056 57 V 0.0098 0.8120 0.1782 58 F 0.0157 0.7317 0.2526 59 F 0.0420 0.4661 0.4920 60 K 0.0492 0.2158 0.7350 61 S 0.0188 0.2555 0.7257 62 S 0.0580 0.1181 0.8239 63 F 0.2412 0.0111 0.7477 64 D 0.3687 0.0343 0.5970 65 L 0.9247 0.0035 0.0718 66 V 0.9334 0.0031 0.0634 67 Y 0.9292 0.0033 0.0675 68 I 0.8963 0.0044 0.0993 69 A 0.4848 0.0153 0.4999 70 S 0.1326 0.0160 0.8514 71 P 0.0818 0.0694 0.8488 72 N 0.0594 0.1798 0.7608 73 S 0.0220 0.5440 0.4340 74 L 0.0172 0.5620 0.4208 75 H 0.0232 0.6574 0.3194 76 F 0.0052 0.9213 0.0735 77 A 0.0047 0.9561 0.0392 78 Q 0.0047 0.9572 0.0381 79 A 0.0047 0.9598 0.0355 80 K 0.0047 0.9601 0.0352 81 A 0.0050 0.9599 0.0351 82 A 0.0049 0.9570 0.0382 83 L 0.0062 0.9444 0.0495 84 S 0.0061 0.8511 0.1428 85 A 0.0390 0.3470 0.6140 86 G 0.0381 0.0286 0.9333 87 K 0.0793 0.0280 0.8927 88 H 0.5159 0.0179 0.4662 89 V 0.8225 0.0133 0.1643 90 I 0.8747 0.0095 0.1157 91 L 0.8163 0.0108 0.1728 92 E 0.6113 0.0162 0.3724 93 K 0.2325 0.0212 0.7464 94 P 0.1650 0.0449 0.7902 95 A 0.1688 0.1116 0.7196 96 V 0.2217 0.0832 0.6952 97 S 0.1216 0.0501 0.8283 98 Q 0.0820 0.0215 0.8965 99 P 0.0051 0.9148 0.0801 100 Q 0.0047 0.9408 0.0544 101 E 0.0049 0.9472 0.0479 102 W 0.0047 0.9587 0.0366 103 F 0.0047 0.9582 0.0371 104 D 0.0047 0.9579 0.0374 105 L 0.0048 0.9578 0.0375 106 I 0.0050 0.9586 0.0364 107 Q 0.0049 0.9571 0.0379 108 T 0.0051 0.9566 0.0384 109 A 0.0049 0.9543 0.0408 110 E 0.0053 0.9329 0.0618 111 K 0.0058 0.8994 0.0948 112 N 0.0449 0.4084 0.5467 113 N 0.0325 0.0279 0.9396 114 C 0.1136 0.0155 0.8709 115 F 0.5918 0.0098 0.3984 116 I 0.7859 0.0199 0.1942 117 F 0.8410 0.0221 0.1369 118 E 0.8080 0.0333 0.1587 119 A 0.6111 0.1005 0.2885 120 A 0.4472 0.1803 0.3725 121 R 0.2689 0.2887 0.4424 122 N 0.2067 0.3211 0.4722 123 Y 0.1305 0.2864 0.5831 124 H 0.0741 0.2360 0.6899 125 E 0.0589 0.1978 0.7433 126 K 0.0080 0.9056 0.0864 127 A 0.0063 0.9317 0.0620 128 F 0.0049 0.9533 0.0418 129 T 0.0047 0.9580 0.0373 130 T 0.0047 0.9588 0.0365 131 I 0.0047 0.9586 0.0368 132 K 0.0047 0.9598 0.0355 133 N 0.0047 0.9577 0.0376 134 F 0.0048 0.9514 0.0438 135 L 0.0058 0.9344 0.0598 136 A 0.0068 0.8713 0.1219 137 D 0.0441 0.3683 0.5877 138 K 0.0349 0.0390 0.9261 139 Q 0.0966 0.0483 0.8551 140 V 0.2786 0.0484 0.6730 141 L 0.2022 0.0353 0.7625 142 G 0.4226 0.0164 0.5610 143 A 0.8004 0.0043 0.1953 144 D 0.8522 0.0192 0.1286 145 F 0.9146 0.0038 0.0817 146 N 0.9092 0.0052 0.0856 147 Y 0.9112 0.0050 0.0838 148 A 0.8856 0.0089 0.1055 149 K 0.8206 0.0207 0.1587 150 Y 0.6892 0.0363 0.2745 151 S 0.3927 0.0684 0.5389 152 S 0.2754 0.0655 0.6591 153 K 0.1832 0.0972 0.7196 154 M 0.1528 0.1163 0.7309 155 P 0.1155 0.1458 0.7387 156 D 0.0840 0.2175 0.6985 157 L 0.0789 0.2520 0.6691 158 L 0.0687 0.2787 0.6527 159 A 0.0692 0.2506 0.6803 160 G 0.0700 0.2158 0.7142 161 Q 0.0640 0.2956 0.6405 162 T 0.0694 0.3455 0.5851 163 P 0.0907 0.3503 0.5590 164 N 0.1223 0.3689 0.5088 165 V 0.1323 0.3547 0.5130 166 F 0.1206 0.3242 0.5552 167 S 0.1130 0.2720 0.6149 168 D 0.0743 0.4087 0.5169 169 R 0.0848 0.3585 0.5568 170 F 0.0925 0.2636 0.6439 171 A 0.0936 0.1496 0.7569 172 G 0.1162 0.1195 0.7643 173 G 0.2071 0.1371 0.6558 174 A 0.4224 0.2191 0.3585 175 L 0.4708 0.2821 0.2471 176 M 0.4045 0.3179 0.2776 177 D 0.3094 0.3102 0.3804 178 L 0.1627 0.3562 0.4811 179 G 0.1453 0.2860 0.5687 180 I 0.1187 0.4365 0.4448 181 Y 0.1108 0.4680 0.4211 182 P 0.0222 0.9033 0.0745 183 L 0.0048 0.9544 0.0408 184 Y 0.0048 0.9584 0.0369 185 A 0.0047 0.9587 0.0366 186 A 0.0047 0.9593 0.0360 187 V 0.0049 0.9536 0.0416 188 R 0.0063 0.9294 0.0643 189 L 0.0120 0.8621 0.1259 190 F 0.0489 0.5643 0.3868 191 G 0.0396 0.0792 0.8812 192 K 0.0586 0.0397 0.9017 193 A 0.1290 0.0585 0.8125 194 N 0.1970 0.0977 0.7053 195 D 0.4381 0.1111 0.4508 196 A 0.6821 0.0875 0.2304 197 T 0.7457 0.0800 0.1742 198 Y 0.7585 0.0720 0.1694 199 H 0.7329 0.0733 0.1938 200 A 0.6587 0.0869 0.2544 201 Q 0.5489 0.0725 0.3786 202 Q 0.4225 0.0592 0.5183 203 L 0.2776 0.0575 0.6650 204 D 0.2041 0.0623 0.7336 205 N 0.1582 0.0701 0.7716 206 S 0.1600 0.0580 0.7821 207 I 0.2464 0.0648 0.6888 208 D 0.2915 0.0743 0.6342 209 L 0.4070 0.0548 0.5382 210 N 0.7192 0.0148 0.2660 211 G 0.8761 0.0053 0.1186 212 D 0.9208 0.0033 0.0759 213 G 0.9295 0.0033 0.0672 214 I 0.9321 0.0031 0.0648 215 L 0.9270 0.0034 0.0696 216 F 0.9223 0.0037 0.0740 217 Y 0.7444 0.0075 0.2481 218 P 0.1073 0.0737 0.8190 219 D 0.0471 0.0219 0.9310 220 Y 0.1361 0.0341 0.8299 221 Q 0.7196 0.0091 0.2713 222 V 0.9131 0.0043 0.0825 223 H 0.9118 0.0051 0.0831 224 I 0.9274 0.0033 0.0693 225 K 0.9150 0.0045 0.0805 226 A 0.8997 0.0059 0.0943 227 G 0.8421 0.0158 0.1421 228 K 0.7431 0.0350 0.2219 229 N 0.6352 0.0604 0.3044 230 I 0.4629 0.0625 0.4746 231 T 0.2509 0.0623 0.6867 232 S 0.1248 0.0752 0.8000 233 N 0.1149 0.0572 0.8279 234 L 0.3270 0.0283 0.6447 235 P 0.7221 0.0102 0.2677 236 C 0.9018 0.0042 0.0940 237 E 0.9229 0.0034 0.0737 238 I 0.9152 0.0037 0.0812 239 Y 0.8478 0.0111 0.1411 240 T 0.5597 0.0137 0.4266 241 T 0.1873 0.0865 0.7262 242 D 0.1768 0.0366 0.7866 243 G 0.4071 0.0256 0.5673 244 T 0.7881 0.0083 0.2036 245 L 0.9006 0.0051 0.0944 246 T 0.8931 0.0065 0.1004 247 L 0.8100 0.0120 0.1780 248 N 0.4578 0.0415 0.5007 249 T 0.1962 0.0628 0.7410 250 I 0.1129 0.1214 0.7658 251 E 0.1334 0.1210 0.7456 252 H 0.1419 0.1668 0.6913 253 I 0.2056 0.1797 0.6147 254 R 0.3070 0.2138 0.4792 255 S 0.4089 0.1965 0.3946 256 A 0.4721 0.1906 0.3373 257 I 0.4432 0.1941 0.3627 258 F 0.3685 0.1903 0.4412 259 T 0.2914 0.1791 0.5294 260 D 0.2238 0.1411 0.6351 261 H 0.1845 0.1210 0.6946 262 Q 0.1586 0.1074 0.7340 263 G 0.1703 0.1063 0.7235 264 N 0.2101 0.0986 0.6913 265 Q 0.2694 0.0954 0.6352 266 V 0.3245 0.1103 0.5652 267 Q 0.3394 0.1277 0.5329 268 L 0.3060 0.1263 0.5677 269 P 0.2394 0.1308 0.6297 270 I 0.1668 0.1423 0.6909 271 Q 0.1069 0.1852 0.7080 272 Q 0.0735 0.1984 0.7281 273 A 0.0565 0.2572 0.6863 274 P 0.0385 0.3903 0.5712 275 H 0.0372 0.5213 0.4415 276 T 0.0204 0.7191 0.2604 277 M 0.0134 0.8628 0.1238 278 T 0.0052 0.9451 0.0497 279 E 0.0048 0.9546 0.0406 280 E 0.0048 0.9563 0.0390 281 V 0.0047 0.9595 0.0358 282 A 0.0047 0.9607 0.0346 283 A 0.0046 0.9604 0.0349 284 F 0.0047 0.9603 0.0350 285 A 0.0047 0.9597 0.0356 286 H 0.0047 0.9590 0.0363 287 M 0.0048 0.9578 0.0374 288 I 0.0051 0.9475 0.0474 289 Q 0.0067 0.8896 0.1037 290 Q 0.0417 0.4328 0.5254 291 P 0.0318 0.0546 0.9136 292 D 0.0618 0.0201 0.9182 293 L 0.1090 0.0242 0.8668 294 N 0.0933 0.0355 0.8712 295 L 0.1115 0.0344 0.8541 296 Y 0.1046 0.0375 0.8579 297 Q 0.0811 0.0331 0.8857 298 T 0.0108 0.8671 0.1221 299 W 0.0054 0.9156 0.0790 300 L 0.0053 0.9344 0.0602 301 Y 0.0048 0.9473 0.0479 302 D 0.0047 0.9538 0.0415 303 A 0.0047 0.9547 0.0405 304 G 0.0047 0.9573 0.0380 305 S 0.0047 0.9602 0.0351 306 V 0.0047 0.9605 0.0348 307 H 0.0047 0.9607 0.0346 308 E 0.0047 0.9605 0.0348 309 L 0.0047 0.9606 0.0347 310 L 0.0047 0.9599 0.0354 311 Y 0.0047 0.9589 0.0364 312 T 0.0048 0.9546 0.0406 313 M 0.0053 0.9442 0.0505 314 R 0.0064 0.9274 0.0662 315 Q 0.0071 0.8463 0.1466 316 T 0.0089 0.7680 0.2231 317 A 0.0450 0.3473 0.6077 318 G 0.0301 0.0321 0.9377 319 I 0.1329 0.0120 0.8551 320 R 0.5630 0.0062 0.4307 321 F 0.6508 0.0108 0.3384 322 E 0.6290 0.0090 0.3620 323 A 0.4211 0.0174 0.5615 324 E 0.1475 0.0176 0.8349 325 K 0.0292 0.0886 0.8821