# This file is the result of combining several RDB files, specifically # T0342.t06.dssp-ebghstl.rdb (weight 1.53986) # T0342.t06.stride-ebghtl.rdb (weight 1.24869) # T0342.t06.str2.rdb (weight 1.54758) # T0342.t06.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 T0342.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0342 # Using neural net t06-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 T0342.t06-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 461 # # ============================================ # Comments from T0342.t06.stride-ebghtl.rdb # ============================================ # TARGET T0342 # Using neural net t06-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 T0342.t06-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 461 # # ============================================ # Comments from T0342.t06.str2.rdb # ============================================ # TARGET T0342 # Using neural net t06-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 T0342.t06-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 461 # # ============================================ # Comments from T0342.t06.alpha.rdb # ============================================ # TARGET T0342 # Using neural net t06-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 T0342.t06-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 461 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0722 0.0319 0.8959 2 A 0.0585 0.1643 0.7773 3 N 0.0638 0.1769 0.7593 4 S 0.0632 0.2412 0.6956 5 G 0.0743 0.1871 0.7386 6 C 0.1263 0.1448 0.7289 7 K 0.1369 0.1568 0.7064 8 D 0.1700 0.1085 0.7215 9 V 0.1541 0.0933 0.7527 10 T 0.1194 0.0651 0.8155 11 G 0.0788 0.0296 0.8917 12 P 0.0571 0.0595 0.8835 13 D 0.0513 0.0903 0.8584 14 E 0.0484 0.1776 0.7740 15 E 0.0669 0.1254 0.8077 16 S 0.1924 0.0509 0.7567 17 F 0.5956 0.0095 0.3949 18 L 0.8728 0.0041 0.1230 19 Y 0.9242 0.0040 0.0718 20 F 0.9271 0.0048 0.0681 21 A 0.9063 0.0101 0.0836 22 Y 0.7767 0.0338 0.1895 23 G 0.3532 0.0749 0.5720 24 S 0.1306 0.1982 0.6712 25 N 0.0846 0.2871 0.6283 26 L 0.0821 0.3368 0.5811 27 L 0.0819 0.3004 0.6177 28 T 0.0332 0.5898 0.3770 29 E 0.0316 0.7251 0.2434 30 R 0.0373 0.7659 0.1968 31 I 0.0467 0.7032 0.2501 32 H 0.0672 0.5393 0.3936 33 L 0.0874 0.2651 0.6475 34 R 0.0806 0.1528 0.7666 35 N 0.0872 0.0326 0.8802 36 P 0.0436 0.1095 0.8468 37 S 0.0736 0.0995 0.8269 38 A 0.1263 0.1866 0.6872 39 A 0.2409 0.1194 0.6397 40 F 0.6126 0.0574 0.3300 41 F 0.7341 0.0180 0.2479 42 C 0.8082 0.0102 0.1816 43 V 0.8394 0.0104 0.1503 44 A 0.8565 0.0076 0.1359 45 R 0.8742 0.0075 0.1183 46 L 0.7173 0.0162 0.2666 47 Q 0.3113 0.0630 0.6257 48 D 0.1841 0.0491 0.7668 49 F 0.6328 0.0371 0.3301 50 K 0.7427 0.0365 0.2208 51 L 0.7443 0.0385 0.2172 52 D 0.6616 0.0457 0.2927 53 F 0.4584 0.0601 0.4815 54 G 0.2376 0.0573 0.7051 55 N 0.1443 0.0988 0.7570 56 S 0.1297 0.1282 0.7421 57 Q 0.1151 0.0953 0.7897 58 G 0.1138 0.0713 0.8149 59 K 0.1678 0.0989 0.7333 60 T 0.2221 0.0959 0.6821 61 S 0.1945 0.1179 0.6876 62 Q 0.1419 0.2471 0.6110 63 T 0.1531 0.2469 0.6000 64 W 0.1927 0.1521 0.6552 65 H 0.1631 0.1189 0.7180 66 G 0.1786 0.0758 0.7456 67 G 0.3739 0.0520 0.5740 68 I 0.6207 0.0349 0.3443 69 A 0.7236 0.0316 0.2447 70 T 0.7719 0.0302 0.1979 71 I 0.8269 0.0176 0.1556 72 F 0.8179 0.0100 0.1721 73 Q 0.6953 0.0106 0.2942 74 S 0.1485 0.0150 0.8365 75 P 0.0272 0.0688 0.9040 76 G 0.0246 0.0450 0.9304 77 D 0.1258 0.0380 0.8362 78 E 0.5484 0.0113 0.4403 79 V 0.8547 0.0057 0.1395 80 W 0.8430 0.0120 0.1450 81 G 0.8721 0.0070 0.1209 82 V 0.9165 0.0051 0.0784 83 V 0.9214 0.0046 0.0740 84 W 0.9084 0.0061 0.0855 85 K 0.8675 0.0044 0.1281 86 M 0.5424 0.0090 0.4486 87 N 0.1464 0.0102 0.8433 88 K 0.0056 0.8468 0.1476 89 S 0.0051 0.8737 0.1212 90 N 0.0063 0.8742 0.1195 91 L 0.0072 0.8892 0.1035 92 N 0.0057 0.8792 0.1150 93 S 0.0082 0.8551 0.1367 94 L 0.0203 0.8059 0.1738 95 D 0.0271 0.7787 0.1942 96 E 0.0235 0.7871 0.1894 97 Q 0.0280 0.7200 0.2520 98 E 0.0645 0.4535 0.4820 99 G 0.0710 0.1104 0.8185 100 V 0.1196 0.0492 0.8312 101 K 0.1540 0.0615 0.7845 102 S 0.0945 0.1009 0.8046 103 G 0.1488 0.0543 0.7969 104 M 0.4659 0.0238 0.5104 105 Y 0.7774 0.0047 0.2179 106 V 0.8881 0.0046 0.1073 107 V 0.8942 0.0031 0.1027 108 I 0.8982 0.0048 0.0970 109 E 0.9169 0.0032 0.0799 110 V 0.8767 0.0046 0.1187 111 K 0.8830 0.0035 0.1135 112 V 0.8662 0.0038 0.1300 113 A 0.8549 0.0051 0.1400 114 T 0.5623 0.0122 0.4255 115 Q 0.0934 0.0858 0.8208 116 E 0.0497 0.0238 0.9265 117 G 0.0452 0.0299 0.9249 118 K 0.3055 0.0087 0.6858 119 E 0.8224 0.0038 0.1738 120 I 0.8724 0.0046 0.1230 121 T 0.9011 0.0046 0.0943 122 C 0.9140 0.0036 0.0824 123 R 0.9300 0.0032 0.0668 124 S 0.9305 0.0033 0.0663 125 Y 0.9226 0.0038 0.0737 126 L 0.8945 0.0050 0.1005 127 M 0.7103 0.0147 0.2749 128 T 0.3327 0.0286 0.6386 129 N 0.1512 0.0519 0.7969 130 Y 0.0953 0.1032 0.8015 131 E 0.0611 0.1314 0.8074 132 S 0.0505 0.0943 0.8552 133 A 0.0579 0.0393 0.9028 134 P 0.0696 0.0217 0.9087 135 P 0.0759 0.0225 0.9016 136 S 0.0598 0.0527 0.8875 137 P 0.0061 0.9196 0.0744 138 Q 0.0057 0.9370 0.0573 139 Y 0.0053 0.9475 0.0471 140 K 0.0048 0.9571 0.0381 141 K 0.0048 0.9581 0.0370 142 I 0.0054 0.9578 0.0369 143 I 0.0063 0.9571 0.0366 144 C 0.0071 0.9489 0.0440 145 M 0.0106 0.9164 0.0730 146 G 0.0147 0.8552 0.1301 147 A 0.0307 0.7948 0.1745 148 K 0.0273 0.6957 0.2770 149 E 0.0237 0.5624 0.4138 150 N 0.0468 0.2706 0.6826 151 G 0.0390 0.0513 0.9097 152 L 0.0606 0.0179 0.9215 153 P 0.0824 0.1404 0.7772 154 L 0.0055 0.9248 0.0697 155 E 0.0051 0.9435 0.0514 156 Y 0.0049 0.9507 0.0444 157 Q 0.0048 0.9523 0.0429 158 E 0.0048 0.9346 0.0605 159 K 0.0052 0.9025 0.0923 160 L 0.0104 0.8542 0.1354 161 K 0.0100 0.7268 0.2632 162 A 0.0165 0.5345 0.4490 163 I 0.0690 0.2309 0.7001 164 E 0.0787 0.0993 0.8220 165 P 0.0634 0.2227 0.7138 166 N 0.0617 0.1893 0.7490 167 D 0.0589 0.1247 0.8164 168 Y 0.0950 0.1255 0.7795 169 T 0.0822 0.1431 0.7747 170 G 0.0517 0.1700 0.7783 171 K 0.0477 0.4500 0.5023 172 V 0.0539 0.5917 0.3544 173 S 0.0195 0.8231 0.1574 174 E 0.0068 0.9321 0.0612 175 E 0.0066 0.9397 0.0537 176 I 0.0047 0.9550 0.0402 177 E 0.0047 0.9592 0.0361 178 D 0.0047 0.9589 0.0365 179 I 0.0047 0.9547 0.0406 180 I 0.0049 0.9466 0.0485 181 K 0.0057 0.8965 0.0978 182 K 0.0192 0.7010 0.2798 183 G 0.0222 0.4636 0.5143 184 E 0.0352 0.3152 0.6496 185 T 0.0551 0.2822 0.6626 186 Q 0.0662 0.2732 0.6607 187 T 0.0756 0.1629 0.7615 188 L 0.0414 0.0640 0.8946