# This file is the result of combining several RDB files, specifically # T0356.t04.dssp-ebghstl.rdb (weight 1.53986) # T0356.t04.stride-ebghtl.rdb (weight 1.24869) # T0356.t04.str2.rdb (weight 1.54758) # T0356.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 T0356.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0356 # 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 T0356.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 51.5882 # # ============================================ # Comments from T0356.t04.stride-ebghtl.rdb # ============================================ # TARGET T0356 # 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 T0356.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 51.5882 # # ============================================ # Comments from T0356.t04.str2.rdb # ============================================ # TARGET T0356 # 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 T0356.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 51.5882 # # ============================================ # Comments from T0356.t04.alpha.rdb # ============================================ # TARGET T0356 # 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 T0356.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 51.5882 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0665 0.1423 0.7912 2 D 0.0602 0.2163 0.7235 3 A 0.0470 0.2515 0.7014 4 M 0.0672 0.1210 0.8117 5 K 0.0639 0.1451 0.7910 6 Y 0.0350 0.4590 0.5060 7 N 0.0273 0.5098 0.4629 8 D 0.0447 0.5311 0.4241 9 L 0.0050 0.9396 0.0553 10 R 0.0048 0.9545 0.0407 11 D 0.0047 0.9581 0.0372 12 F 0.0047 0.9608 0.0345 13 L 0.0047 0.9606 0.0347 14 T 0.0046 0.9605 0.0349 15 L 0.0047 0.9608 0.0345 16 L 0.0047 0.9580 0.0373 17 E 0.0049 0.9216 0.0736 18 Q 0.0083 0.7716 0.2200 19 Q 0.0449 0.3123 0.6427 20 G 0.0264 0.0270 0.9466 21 E 0.1019 0.0240 0.8741 22 L 0.6897 0.0097 0.3005 23 K 0.8315 0.0083 0.1602 24 R 0.9013 0.0048 0.0939 25 I 0.8558 0.0062 0.1380 26 T 0.6424 0.0286 0.3290 27 L 0.3680 0.0107 0.6212 28 P 0.2650 0.0122 0.7228 29 V 0.1726 0.0239 0.8034 30 D 0.0952 0.0198 0.8849 31 P 0.0102 0.4606 0.5292 32 H 0.0120 0.5815 0.4065 33 L 0.0246 0.7617 0.2137 34 E 0.0294 0.8019 0.1688 35 I 0.0088 0.9255 0.0657 36 T 0.0054 0.9522 0.0424 37 E 0.0049 0.9571 0.0380 38 I 0.0050 0.9571 0.0379 39 A 0.0047 0.9568 0.0385 40 D 0.0047 0.9562 0.0392 41 R 0.0047 0.9569 0.0384 42 T 0.0047 0.9556 0.0397 43 L 0.0059 0.9446 0.0495 44 R 0.0068 0.9014 0.0918 45 A 0.0386 0.4912 0.4701 46 G 0.0360 0.0432 0.9208 47 G 0.0528 0.0173 0.9299 48 P 0.1534 0.0275 0.8191 49 A 0.4711 0.0570 0.4720 50 L 0.6580 0.0646 0.2774 51 L 0.8081 0.0476 0.1443 52 F 0.7437 0.0432 0.2131 53 E 0.5418 0.0742 0.3840 54 N 0.1662 0.0259 0.8079 55 P 0.0659 0.1059 0.8282 56 K 0.0532 0.1287 0.8181 57 G 0.0494 0.1354 0.8151 58 Y 0.0804 0.1056 0.8140 59 S 0.1119 0.0909 0.7972 60 M 0.1658 0.0726 0.7616 61 P 0.2777 0.0751 0.6473 62 V 0.7035 0.0901 0.2064 63 L 0.7656 0.0992 0.1352 64 C 0.7099 0.1295 0.1606 65 N 0.5543 0.1637 0.2820 66 L 0.3457 0.2095 0.4448 67 F 0.2379 0.1430 0.6191 68 G 0.1345 0.0727 0.7928 69 T 0.0741 0.0567 0.8692 70 P 0.0054 0.9296 0.0650 71 K 0.0047 0.9498 0.0455 72 R 0.0051 0.9540 0.0409 73 V 0.0058 0.9534 0.0409 74 A 0.0074 0.9371 0.0555 75 M 0.0091 0.8741 0.1168 76 G 0.0147 0.7410 0.2443 77 M 0.0536 0.3682 0.5782 78 G 0.0429 0.0744 0.8827 79 Q 0.0501 0.1216 0.8283 80 E 0.0517 0.1664 0.7819 81 D 0.0650 0.2256 0.7095 82 V 0.0090 0.8563 0.1347 83 S 0.0064 0.9093 0.0844 84 A 0.0056 0.9296 0.0648 85 L 0.0050 0.9458 0.0492 86 R 0.0050 0.9535 0.0415 87 E 0.0050 0.9540 0.0411 88 V 0.0047 0.9547 0.0406 89 G 0.0047 0.9561 0.0392 90 K 0.0047 0.9505 0.0448 91 L 0.0047 0.9428 0.0525 92 L 0.0049 0.9353 0.0599 93 A 0.0056 0.8616 0.1328 94 F 0.0069 0.7835 0.2096 95 L 0.0334 0.5331 0.4335 96 K 0.0355 0.2826 0.6819 97 E 0.0623 0.0475 0.8902 98 P 0.0535 0.0424 0.9041 99 E 0.0652 0.0325 0.9023 100 P 0.0536 0.0203 0.9261 101 P 0.0543 0.1121 0.8336 102 K 0.0399 0.3649 0.5953 103 G 0.0518 0.4277 0.5205 104 F 0.0222 0.8069 0.1708 105 R 0.0119 0.8959 0.0922 106 D 0.0112 0.8983 0.0905 107 L 0.0060 0.9200 0.0741 108 F 0.0070 0.8879 0.1051 109 D 0.0069 0.7732 0.2199 110 K 0.0114 0.6401 0.3485 111 L 0.0350 0.3716 0.5934 112 P 0.0095 0.7219 0.2686 113 Q 0.0125 0.7934 0.1941 114 F 0.0132 0.8547 0.1320 115 K 0.0145 0.8620 0.1235 116 Q 0.0175 0.8038 0.1787 117 V 0.0290 0.6934 0.2776 118 L 0.0674 0.4296 0.5030 119 N 0.0576 0.1386 0.8037 120 M 0.0758 0.0283 0.8959 121 P 0.0985 0.0259 0.8756 122 T 0.2178 0.0929 0.6893 123 K 0.4090 0.1368 0.4542 124 R 0.6010 0.1271 0.2719 125 L 0.4252 0.1065 0.4683 126 R 0.1720 0.0805 0.7475 127 G 0.0792 0.0422 0.8786 128 A 0.1364 0.0408 0.8227 129 P 0.3061 0.0514 0.6425 130 C 0.5033 0.0718 0.4249 131 Q 0.6009 0.0660 0.3331 132 Q 0.7300 0.0539 0.2161 133 K 0.8102 0.0381 0.1518 134 I 0.8328 0.0308 0.1363 135 V 0.7221 0.0382 0.2397 136 S 0.3434 0.0479 0.6087 137 G 0.0859 0.0423 0.8718 138 D 0.0972 0.0843 0.8186 139 D 0.2991 0.0549 0.6459 140 V 0.3596 0.0229 0.6175 141 D 0.2653 0.0195 0.7152 142 L 0.0431 0.6997 0.2572 143 N 0.0434 0.6024 0.3542 144 R 0.0560 0.5117 0.4322 145 I 0.1432 0.0267 0.8301 146 P 0.1741 0.0296 0.7963 147 I 0.3391 0.0578 0.6031 148 M 0.3564 0.0664 0.5772 149 T 0.3887 0.0826 0.5286 150 C 0.3162 0.0452 0.6386 151 W 0.1132 0.0254 0.8614 152 P 0.0241 0.1820 0.7938 153 E 0.0250 0.1359 0.8391 154 D 0.0878 0.1632 0.7490 155 A 0.1247 0.2042 0.6711 156 A 0.1211 0.2481 0.6308 157 P 0.1213 0.3442 0.5345 158 L 0.2464 0.2898 0.4638 159 I 0.4205 0.1202 0.4594 160 T 0.3792 0.0693 0.5515 161 W 0.2443 0.1419 0.6138 162 G 0.3414 0.1119 0.5467 163 L 0.6706 0.0673 0.2622 164 T 0.7872 0.0391 0.1737 165 V 0.8103 0.0355 0.1542 166 T 0.7682 0.0234 0.2083 167 R 0.6227 0.0308 0.3466 168 G 0.2274 0.0172 0.7555 169 P 0.0520 0.0823 0.8657 170 H 0.0509 0.0659 0.8832 171 K 0.0614 0.0755 0.8631 172 E 0.1292 0.0631 0.8077 173 R 0.5017 0.0307 0.4676 174 Q 0.7174 0.0246 0.2580 175 N 0.7714 0.0173 0.2114 176 L 0.7331 0.0338 0.2331 177 G 0.7457 0.0273 0.2270 178 I 0.7583 0.0262 0.2155 179 Y 0.5702 0.0237 0.4061 180 R 0.2910 0.0246 0.6844