# This file is the result of combining several RDB files, specifically # T0367.t04.dssp-ebghstl.rdb (weight 1.53986) # T0367.t04.stride-ebghtl.rdb (weight 1.24869) # T0367.t04.str2.rdb (weight 1.54758) # T0367.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 T0367.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0367 # 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 T0367.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 60 # # ============================================ # Comments from T0367.t04.stride-ebghtl.rdb # ============================================ # TARGET T0367 # 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 T0367.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 60 # # ============================================ # Comments from T0367.t04.str2.rdb # ============================================ # TARGET T0367 # 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 T0367.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 60 # # ============================================ # Comments from T0367.t04.alpha.rdb # ============================================ # TARGET T0367 # 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 T0367.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 60 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0532 0.0448 0.9020 2 D 0.0453 0.4095 0.5452 3 E 0.0077 0.9222 0.0700 4 L 0.0051 0.9512 0.0437 5 E 0.0050 0.9574 0.0377 6 L 0.0056 0.9542 0.0402 7 R 0.0050 0.9554 0.0396 8 I 0.0047 0.9598 0.0355 9 R 0.0047 0.9604 0.0350 10 K 0.0047 0.9579 0.0373 11 A 0.0047 0.9558 0.0395 12 E 0.0047 0.9541 0.0411 13 K 0.0048 0.9430 0.0521 14 L 0.0051 0.9250 0.0699 15 V 0.0049 0.9362 0.0589 16 Q 0.0048 0.9478 0.0474 17 D 0.0050 0.9387 0.0563 18 A 0.0050 0.9387 0.0563 19 K 0.0049 0.9425 0.0526 20 K 0.0052 0.9243 0.0705 21 E 0.0063 0.9059 0.0878 22 F 0.0089 0.8878 0.1033 23 E 0.0076 0.8476 0.1448 24 M 0.0430 0.5903 0.3667 25 G 0.0251 0.3925 0.5825 26 L 0.0302 0.5646 0.4052 27 Y 0.0155 0.8735 0.1110 28 E 0.0070 0.9386 0.0544 29 R 0.0056 0.9480 0.0465 30 C 0.0050 0.9498 0.0452 31 C 0.0051 0.9496 0.0453 32 S 0.0048 0.9501 0.0451 33 T 0.0047 0.9535 0.0418 34 A 0.0047 0.9585 0.0369 35 Y 0.0047 0.9600 0.0353 36 Y 0.0046 0.9611 0.0342 37 A 0.0046 0.9603 0.0350 38 M 0.0047 0.9600 0.0353 39 F 0.0047 0.9605 0.0348 40 H 0.0047 0.9598 0.0355 41 A 0.0047 0.9586 0.0367 42 A 0.0047 0.9588 0.0365 43 K 0.0047 0.9593 0.0360 44 A 0.0047 0.9585 0.0368 45 M 0.0049 0.9574 0.0377 46 L 0.0055 0.9515 0.0431 47 L 0.0075 0.9244 0.0681 48 G 0.0129 0.7706 0.2165 49 Y 0.0471 0.2939 0.6590 50 G 0.0320 0.0413 0.9266 51 R 0.0768 0.0268 0.8963 52 D 0.1103 0.0278 0.8619 53 S 0.0373 0.2937 0.6690 54 K 0.0329 0.3672 0.5999 55 T 0.0504 0.3823 0.5673 56 H 0.0531 0.4171 0.5298 57 R 0.0155 0.7697 0.2148 58 G 0.0175 0.8581 0.1244 59 T 0.0122 0.9285 0.0593 60 I 0.0104 0.9439 0.0457 61 Y 0.0098 0.9441 0.0461 62 L 0.0104 0.9322 0.0574 63 I 0.0126 0.9166 0.0707 64 W 0.0131 0.8955 0.0913 65 E 0.0142 0.8783 0.1076 66 C 0.0279 0.8358 0.1363 67 R 0.0428 0.7800 0.1772 68 E 0.0348 0.8010 0.1641 69 E 0.0351 0.7793 0.1856 70 L 0.0565 0.5064 0.4371 71 G 0.0427 0.1113 0.8460 72 L 0.0831 0.0760 0.8409 73 S 0.0816 0.0651 0.8533 74 D 0.0282 0.3089 0.6629 75 D 0.0100 0.6418 0.3482 76 D 0.0146 0.7060 0.2794 77 C 0.0246 0.7076 0.2678 78 S 0.0254 0.6849 0.2898 79 K 0.0284 0.7146 0.2570 80 L 0.0436 0.6358 0.3206 81 S 0.0245 0.7096 0.2658 82 R 0.0332 0.6562 0.3106 83 A 0.0514 0.5933 0.3554 84 F 0.0786 0.4159 0.5055 85 D 0.0730 0.3372 0.5898 86 L 0.0803 0.3525 0.5672 87 R 0.0985 0.2547 0.6468 88 E 0.0790 0.1781 0.7430 89 E 0.0425 0.4028 0.5548 90 S 0.0497 0.3888 0.5615 91 D 0.0552 0.3877 0.5571 92 Y 0.0850 0.2494 0.6656 93 G 0.0717 0.1558 0.7725 94 I 0.1006 0.1716 0.7278 95 Y 0.1201 0.1176 0.7623 96 K 0.1118 0.0873 0.8009 97 E 0.1170 0.0634 0.8196 98 V 0.1314 0.0353 0.8333 99 S 0.0628 0.0233 0.9140 100 K 0.0048 0.9515 0.0437 101 D 0.0047 0.9594 0.0359 102 L 0.0047 0.9599 0.0354 103 A 0.0047 0.9609 0.0344 104 I 0.0047 0.9611 0.0342 105 K 0.0046 0.9605 0.0349 106 I 0.0047 0.9575 0.0378 107 L 0.0047 0.9577 0.0376 108 K 0.0050 0.9559 0.0391 109 D 0.0050 0.9490 0.0460 110 A 0.0047 0.9585 0.0368 111 E 0.0047 0.9612 0.0342 112 I 0.0046 0.9614 0.0339 113 F 0.0046 0.9610 0.0343 114 V 0.0047 0.9611 0.0342 115 Q 0.0046 0.9617 0.0336 116 K 0.0046 0.9610 0.0344 117 A 0.0047 0.9590 0.0363 118 K 0.0047 0.9578 0.0375 119 N 0.0049 0.9517 0.0434 120 A 0.0054 0.9322 0.0623 121 V 0.0089 0.8858 0.1053 122 N 0.0127 0.7268 0.2604 123 K 0.0224 0.5071 0.4704 124 N 0.0452 0.0987 0.8561 125 R 0.0398 0.0494 0.9108