# This file is the result of combining several RDB files, specifically # T0342.t04.dssp-ebghstl.rdb (weight 1.53986) # T0342.t04.stride-ebghtl.rdb (weight 1.24869) # T0342.t04.str2.rdb (weight 1.54758) # T0342.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 T0342.t04.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.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 458 # # ============================================ # Comments from T0342.t04.stride-ebghtl.rdb # ============================================ # TARGET T0342 # 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 T0342.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 458 # # ============================================ # Comments from T0342.t04.str2.rdb # ============================================ # TARGET T0342 # 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 T0342.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 458 # # ============================================ # Comments from T0342.t04.alpha.rdb # ============================================ # TARGET T0342 # 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 T0342.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 458 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0747 0.0396 0.8856 2 A 0.0512 0.1957 0.7530 3 N 0.0617 0.1896 0.7488 4 S 0.0622 0.1993 0.7385 5 G 0.0590 0.1149 0.8260 6 C 0.1299 0.0961 0.7741 7 K 0.1646 0.1074 0.7280 8 D 0.1749 0.0797 0.7454 9 V 0.1249 0.0771 0.7981 10 T 0.1146 0.0531 0.8323 11 G 0.0751 0.0261 0.8987 12 P 0.0555 0.0697 0.8747 13 D 0.0549 0.0933 0.8518 14 E 0.0609 0.1864 0.7528 15 E 0.0678 0.1449 0.7872 16 S 0.1971 0.0599 0.7430 17 F 0.5883 0.0132 0.3985 18 L 0.8495 0.0058 0.1447 19 Y 0.9217 0.0048 0.0735 20 F 0.9238 0.0058 0.0704 21 A 0.9034 0.0099 0.0867 22 Y 0.7779 0.0319 0.1902 23 G 0.3616 0.0702 0.5681 24 S 0.1232 0.1931 0.6837 25 N 0.0730 0.2612 0.6658 26 L 0.0702 0.2451 0.6847 27 L 0.0798 0.1930 0.7272 28 T 0.0426 0.4729 0.4846 29 E 0.0200 0.7537 0.2263 30 R 0.0238 0.7949 0.1813 31 I 0.0367 0.7724 0.1908 32 H 0.0513 0.6983 0.2505 33 L 0.0661 0.6264 0.3076 34 R 0.0741 0.4331 0.4929 35 N 0.0950 0.0387 0.8662 36 P 0.0196 0.1522 0.8282 37 S 0.0475 0.1192 0.8334 38 A 0.1342 0.1440 0.7218 39 A 0.2593 0.1001 0.6406 40 F 0.6300 0.0462 0.3238 41 F 0.7564 0.0219 0.2217 42 C 0.8092 0.0118 0.1790 43 V 0.8167 0.0112 0.1721 44 A 0.8282 0.0093 0.1625 45 R 0.8490 0.0070 0.1440 46 L 0.5862 0.0168 0.3970 47 Q 0.2089 0.0594 0.7317 48 D 0.1306 0.0458 0.8236 49 F 0.5623 0.0369 0.4008 50 K 0.7214 0.0229 0.2557 51 L 0.7171 0.0249 0.2580 52 D 0.6005 0.0284 0.3712 53 F 0.4412 0.0546 0.5043 54 G 0.2547 0.0572 0.6881 55 N 0.1946 0.0713 0.7341 56 S 0.1512 0.1168 0.7321 57 Q 0.1383 0.0761 0.7855 58 G 0.1124 0.0731 0.8145 59 K 0.1136 0.0988 0.7875 60 T 0.1797 0.0959 0.7244 61 S 0.1853 0.1175 0.6972 62 Q 0.1204 0.2443 0.6353 63 T 0.1537 0.2529 0.5934 64 W 0.1893 0.1735 0.6371 65 H 0.1522 0.1171 0.7307 66 G 0.1663 0.0739 0.7598 67 G 0.4202 0.0464 0.5334 68 I 0.6771 0.0264 0.2966 69 A 0.7321 0.0258 0.2421 70 T 0.7653 0.0272 0.2075 71 I 0.7923 0.0223 0.1855 72 F 0.7200 0.0145 0.2655 73 Q 0.5684 0.0140 0.4177 74 S 0.1390 0.0169 0.8441 75 P 0.0298 0.0727 0.8976 76 G 0.0284 0.0488 0.9229 77 D 0.1181 0.0397 0.8422 78 E 0.4982 0.0183 0.4834 79 V 0.8209 0.0092 0.1699 80 W 0.8265 0.0145 0.1590 81 G 0.8627 0.0082 0.1291 82 V 0.8909 0.0072 0.1019 83 V 0.9085 0.0066 0.0849 84 W 0.8916 0.0085 0.0999 85 K 0.8134 0.0069 0.1797 86 M 0.5197 0.0102 0.4701 87 N 0.1308 0.0092 0.8600 88 K 0.0058 0.8661 0.1280 89 S 0.0053 0.8959 0.0988 90 N 0.0066 0.8845 0.1089 91 L 0.0071 0.8975 0.0954 92 N 0.0067 0.8727 0.1206 93 S 0.0084 0.8441 0.1474 94 L 0.0214 0.7760 0.2026 95 D 0.0228 0.7214 0.2558 96 E 0.0174 0.7662 0.2165 97 Q 0.0246 0.7159 0.2595 98 E 0.0666 0.3883 0.5451 99 G 0.0661 0.0904 0.8435 100 V 0.1257 0.0381 0.8362 101 K 0.1661 0.0545 0.7794 102 S 0.1182 0.1066 0.7752 103 G 0.1477 0.0663 0.7861 104 M 0.4440 0.0446 0.5114 105 Y 0.7507 0.0061 0.2432 106 V 0.8875 0.0045 0.1080 107 V 0.9108 0.0030 0.0862 108 I 0.9042 0.0047 0.0911 109 E 0.9211 0.0032 0.0757 110 V 0.8882 0.0041 0.1077 111 K 0.8972 0.0034 0.0994 112 V 0.8764 0.0042 0.1193 113 A 0.8654 0.0057 0.1289 114 T 0.6000 0.0185 0.3815 115 Q 0.1394 0.0784 0.7822 116 E 0.0560 0.0244 0.9196 117 G 0.0485 0.0294 0.9220 118 K 0.2645 0.0106 0.7249 119 E 0.8056 0.0040 0.1904 120 I 0.8616 0.0052 0.1331 121 T 0.8874 0.0040 0.1086 122 C 0.9085 0.0037 0.0878 123 R 0.9228 0.0034 0.0739 124 S 0.9283 0.0034 0.0683 125 Y 0.9208 0.0041 0.0751 126 L 0.9055 0.0043 0.0902 127 M 0.7370 0.0134 0.2496 128 T 0.3369 0.0253 0.6378 129 N 0.1334 0.0536 0.8130 130 Y 0.0785 0.1067 0.8147 131 E 0.0608 0.1265 0.8127 132 S 0.0574 0.0782 0.8643 133 A 0.0647 0.0243 0.9110 134 P 0.0688 0.0116 0.9197 135 P 0.0763 0.0121 0.9116 136 S 0.0557 0.0650 0.8793 137 P 0.0056 0.9227 0.0717 138 Q 0.0059 0.9423 0.0518 139 Y 0.0054 0.9455 0.0490 140 K 0.0047 0.9573 0.0380 141 K 0.0052 0.9570 0.0378 142 I 0.0063 0.9546 0.0391 143 I 0.0085 0.9528 0.0387 144 C 0.0101 0.9409 0.0490 145 M 0.0158 0.8915 0.0927 146 G 0.0257 0.7714 0.2029 147 A 0.0367 0.7193 0.2440 148 K 0.0424 0.6032 0.3544 149 E 0.0403 0.4628 0.4969 150 N 0.0560 0.1968 0.7472 151 G 0.0416 0.0620 0.8964 152 L 0.0676 0.0168 0.9156 153 P 0.0700 0.1432 0.7868 154 L 0.0052 0.9294 0.0655 155 E 0.0048 0.9482 0.0470 156 Y 0.0050 0.9502 0.0448 157 Q 0.0059 0.9515 0.0426 158 E 0.0060 0.9358 0.0582 159 K 0.0063 0.9056 0.0881 160 L 0.0111 0.8527 0.1362 161 K 0.0124 0.7122 0.2754 162 A 0.0223 0.4563 0.5214 163 I 0.0835 0.1761 0.7404 164 E 0.0819 0.0706 0.8475 165 P 0.0555 0.1413 0.8033 166 N 0.0483 0.1441 0.8077 167 D 0.0535 0.1346 0.8119 168 Y 0.0856 0.1306 0.7838 169 T 0.0720 0.1308 0.7971 170 G 0.0467 0.1488 0.8046 171 K 0.0366 0.4522 0.5112 172 V 0.0490 0.5437 0.4072 173 S 0.0215 0.7885 0.1900 174 E 0.0071 0.9310 0.0619 175 E 0.0078 0.9365 0.0557 176 I 0.0048 0.9545 0.0407 177 E 0.0047 0.9586 0.0367 178 D 0.0047 0.9593 0.0360 179 I 0.0048 0.9548 0.0404 180 I 0.0055 0.9447 0.0498 181 K 0.0068 0.8951 0.0981 182 K 0.0258 0.6151 0.3590 183 G 0.0312 0.2235 0.7453 184 E 0.0524 0.1011 0.8465 185 T 0.0590 0.1275 0.8135 186 Q 0.0969 0.1269 0.7762 187 T 0.1133 0.0760 0.8107 188 L 0.0635 0.0415 0.8949