# This file is the result of combining several RDB files, specifically # T0283.t04.dssp-ebghstl.rdb (weight 1.53986) # T0283.t04.stride-ebghtl.rdb (weight 1.24869) # T0283.t04.str2.rdb (weight 1.54758) # T0283.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 T0283.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0283 # 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 T0283.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 7.04591 # # ============================================ # Comments from T0283.t04.stride-ebghtl.rdb # ============================================ # TARGET T0283 # 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 T0283.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 7.04591 # # ============================================ # Comments from T0283.t04.str2.rdb # ============================================ # TARGET T0283 # 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 T0283.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 7.04591 # # ============================================ # Comments from T0283.t04.alpha.rdb # ============================================ # TARGET T0283 # 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 T0283.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 7.04591 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0379 0.1088 0.8533 2 S 0.0369 0.3938 0.5694 3 F 0.0130 0.8586 0.1284 4 I 0.0069 0.9272 0.0659 5 E 0.0062 0.9419 0.0519 6 K 0.0078 0.9354 0.0568 7 M 0.0071 0.9203 0.0726 8 I 0.0135 0.8594 0.1271 9 G 0.0133 0.7197 0.2669 10 S 0.0175 0.6926 0.2899 11 L 0.0179 0.7429 0.2392 12 N 0.0179 0.6195 0.3626 13 D 0.0217 0.6424 0.3359 14 K 0.0124 0.8436 0.1440 15 R 0.0141 0.8770 0.1089 16 E 0.0168 0.8847 0.0986 17 W 0.0050 0.9380 0.0570 18 K 0.0047 0.9531 0.0422 19 A 0.0047 0.9509 0.0444 20 M 0.0047 0.9524 0.0429 21 E 0.0047 0.9585 0.0368 22 A 0.0047 0.9565 0.0388 23 R 0.0047 0.9501 0.0452 24 A 0.0049 0.9336 0.0615 25 K 0.0054 0.8545 0.1401 26 A 0.0099 0.5719 0.4183 27 L 0.0246 0.2219 0.7535 28 P 0.0262 0.2345 0.7394 29 K 0.0053 0.8816 0.1131 30 E 0.0054 0.9151 0.0795 31 Y 0.0051 0.9442 0.0507 32 H 0.0047 0.9582 0.0371 33 H 0.0047 0.9592 0.0362 34 A 0.0047 0.9584 0.0369 35 Y 0.0047 0.9596 0.0357 36 K 0.0046 0.9607 0.0347 37 A 0.0047 0.9596 0.0358 38 I 0.0048 0.9571 0.0381 39 Q 0.0049 0.9527 0.0425 40 K 0.0057 0.9370 0.0573 41 Y 0.0098 0.8844 0.1058 42 M 0.0264 0.7932 0.1804 43 W 0.0628 0.6453 0.2919 44 T 0.0573 0.5698 0.3729 45 S 0.0711 0.3125 0.6164 46 G 0.0825 0.0993 0.8183 47 G 0.0733 0.0520 0.8747 48 P 0.0883 0.1032 0.8085 49 T 0.1009 0.1212 0.7779 50 D 0.1081 0.1681 0.7238 51 W 0.0385 0.5908 0.3707 52 Q 0.0276 0.6648 0.3076 53 D 0.0369 0.6383 0.3248 54 T 0.0192 0.8338 0.1470 55 K 0.0138 0.8802 0.1060 56 R 0.0124 0.9086 0.0790 57 I 0.0083 0.9137 0.0780 58 F 0.0060 0.9213 0.0727 59 G 0.0049 0.9272 0.0679 60 G 0.0050 0.9356 0.0594 61 I 0.0049 0.9473 0.0478 62 L 0.0047 0.9555 0.0397 63 D 0.0047 0.9576 0.0377 64 L 0.0048 0.9560 0.0392 65 F 0.0050 0.9522 0.0428 66 E 0.0051 0.9479 0.0469 67 E 0.0070 0.9353 0.0577 68 G 0.0105 0.9078 0.0816 69 A 0.0161 0.8709 0.1129 70 A 0.0239 0.7900 0.1861 71 E 0.0383 0.2716 0.6901 72 G 0.0316 0.0618 0.9066 73 K 0.1514 0.0237 0.8249 74 K 0.3699 0.0349 0.5952 75 V 0.2398 0.3812 0.3789 76 T 0.1717 0.5521 0.2763 77 D 0.1808 0.5817 0.2375 78 L 0.2602 0.3811 0.3586 79 T 0.1555 0.3132 0.5313 80 G 0.0355 0.5106 0.4539 81 E 0.0093 0.7324 0.2583 82 D 0.0171 0.7916 0.1913 83 V 0.0048 0.9391 0.0560 84 A 0.0047 0.9531 0.0422 85 A 0.0047 0.9500 0.0453 86 F 0.0047 0.9471 0.0481 87 C 0.0048 0.9520 0.0432 88 D 0.0047 0.9545 0.0407 89 E 0.0048 0.9492 0.0461 90 L 0.0049 0.9314 0.0637 91 M 0.0054 0.8728 0.1218 92 K 0.0066 0.7161 0.2773 93 D 0.0246 0.4457 0.5298 94 T 0.0338 0.3479 0.6184 95 K 0.0191 0.3424 0.6385 96 T 0.0397 0.5582 0.4021 97 W 0.0177 0.8537 0.1286 98 M 0.0087 0.9188 0.0725 99 D 0.0059 0.9469 0.0472 100 K 0.0048 0.9530 0.0422 101 Y 0.0050 0.9515 0.0435 102 R 0.0048 0.9527 0.0425 103 T 0.0058 0.9500 0.0442 104 K 0.0062 0.9337 0.0601 105 L 0.0070 0.9068 0.0862 106 N 0.0129 0.8359 0.1512 107 D 0.0105 0.7824 0.2072 108 S 0.0148 0.7217 0.2635 109 I 0.0427 0.5266 0.4307 110 G 0.0581 0.2728 0.6692 111 R 0.0601 0.1561 0.7838 112 D 0.0518 0.0494 0.8988