# This file is the result of combining several RDB files, specifically # T0367.t06.dssp-ebghstl.rdb (weight 1.53986) # T0367.t06.stride-ebghtl.rdb (weight 1.24869) # T0367.t06.str2.rdb (weight 1.54758) # T0367.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 T0367.t06.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.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 66 # # ============================================ # Comments from T0367.t06.stride-ebghtl.rdb # ============================================ # TARGET T0367 # 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 T0367.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 66 # # ============================================ # Comments from T0367.t06.str2.rdb # ============================================ # TARGET T0367 # 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 T0367.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 66 # # ============================================ # Comments from T0367.t06.alpha.rdb # ============================================ # TARGET T0367 # 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 T0367.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 66 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0458 0.0400 0.9142 2 D 0.0519 0.3223 0.6258 3 E 0.0176 0.8620 0.1204 4 L 0.0087 0.9271 0.0642 5 E 0.0065 0.9492 0.0443 6 L 0.0089 0.9428 0.0482 7 R 0.0062 0.9491 0.0446 8 I 0.0047 0.9578 0.0375 9 R 0.0047 0.9591 0.0362 10 K 0.0048 0.9560 0.0393 11 A 0.0048 0.9533 0.0419 12 E 0.0048 0.9540 0.0412 13 K 0.0049 0.9405 0.0546 14 L 0.0051 0.9245 0.0704 15 V 0.0049 0.9358 0.0593 16 Q 0.0048 0.9490 0.0462 17 D 0.0049 0.9430 0.0521 18 A 0.0049 0.9396 0.0555 19 K 0.0048 0.9445 0.0507 20 K 0.0049 0.9353 0.0597 21 E 0.0054 0.9287 0.0659 22 F 0.0060 0.9077 0.0863 23 E 0.0065 0.8620 0.1315 24 M 0.0422 0.6349 0.3229 25 G 0.0212 0.4132 0.5656 26 L 0.0202 0.6074 0.3724 27 Y 0.0092 0.8847 0.1061 28 E 0.0051 0.9430 0.0520 29 R 0.0047 0.9525 0.0428 30 C 0.0047 0.9528 0.0425 31 C 0.0047 0.9530 0.0423 32 S 0.0047 0.9535 0.0418 33 T 0.0047 0.9563 0.0390 34 A 0.0046 0.9589 0.0364 35 Y 0.0047 0.9604 0.0349 36 Y 0.0047 0.9608 0.0345 37 A 0.0047 0.9601 0.0353 38 M 0.0047 0.9601 0.0353 39 F 0.0046 0.9606 0.0347 40 H 0.0047 0.9597 0.0356 41 A 0.0047 0.9595 0.0359 42 A 0.0047 0.9584 0.0369 43 K 0.0047 0.9604 0.0349 44 A 0.0047 0.9599 0.0354 45 M 0.0047 0.9587 0.0365 46 L 0.0048 0.9538 0.0414 47 L 0.0071 0.9228 0.0701 48 G 0.0102 0.7985 0.1912 49 Y 0.0473 0.3208 0.6319 50 G 0.0365 0.0439 0.9196 51 R 0.0757 0.0325 0.8919 52 D 0.1271 0.0372 0.8358 53 S 0.0612 0.2734 0.6654 54 K 0.0440 0.3518 0.6042 55 T 0.0592 0.3488 0.5921 56 H 0.0556 0.4005 0.5439 57 R 0.0194 0.6707 0.3099 58 G 0.0230 0.7533 0.2237 59 T 0.0139 0.9094 0.0767 60 I 0.0104 0.9365 0.0530 61 Y 0.0084 0.9414 0.0502 62 L 0.0079 0.9357 0.0564 63 I 0.0088 0.9311 0.0600 64 W 0.0082 0.9234 0.0684 65 E 0.0090 0.9083 0.0827 66 C 0.0136 0.8862 0.1002 67 R 0.0239 0.8368 0.1393 68 E 0.0169 0.8405 0.1426 69 E 0.0164 0.7937 0.1899 70 L 0.0549 0.5111 0.4340 71 G 0.0438 0.0999 0.8564 72 L 0.0695 0.0839 0.8466 73 S 0.0743 0.0864 0.8392 74 D 0.0190 0.4976 0.4834 75 D 0.0102 0.7011 0.2887 76 D 0.0126 0.7646 0.2228 77 C 0.0189 0.7770 0.2040 78 S 0.0150 0.7970 0.1881 79 K 0.0182 0.8148 0.1670 80 L 0.0288 0.7694 0.2019 81 S 0.0175 0.8264 0.1562 82 R 0.0228 0.7798 0.1974 83 A 0.0322 0.7261 0.2417 84 F 0.0545 0.6139 0.3316 85 D 0.0643 0.5499 0.3858 86 L 0.0484 0.5602 0.3914 87 R 0.0747 0.4081 0.5172 88 E 0.0787 0.2939 0.6274 89 E 0.0539 0.3674 0.5787 90 S 0.0502 0.3318 0.6180 91 D 0.0615 0.3144 0.6241 92 Y 0.1033 0.1941 0.7025 93 G 0.0885 0.1176 0.7939 94 I 0.1236 0.1346 0.7418 95 Y 0.1297 0.1030 0.7673 96 K 0.1532 0.0719 0.7749 97 E 0.1516 0.0362 0.8122 98 V 0.1519 0.0208 0.8273 99 S 0.0704 0.0190 0.9106 100 K 0.0048 0.9511 0.0440 101 D 0.0047 0.9567 0.0386 102 L 0.0048 0.9565 0.0388 103 A 0.0047 0.9596 0.0358 104 I 0.0047 0.9603 0.0350 105 K 0.0047 0.9579 0.0374 106 I 0.0048 0.9550 0.0402 107 L 0.0047 0.9575 0.0378 108 K 0.0049 0.9542 0.0409 109 D 0.0049 0.9472 0.0478 110 A 0.0047 0.9571 0.0381 111 E 0.0047 0.9605 0.0349 112 I 0.0047 0.9602 0.0351 113 F 0.0047 0.9598 0.0355 114 V 0.0047 0.9611 0.0343 115 Q 0.0046 0.9611 0.0342 116 K 0.0046 0.9604 0.0350 117 A 0.0047 0.9576 0.0377 118 K 0.0047 0.9547 0.0406 119 N 0.0049 0.9446 0.0505 120 A 0.0057 0.9197 0.0745 121 V 0.0111 0.8617 0.1272 122 N 0.0172 0.6748 0.3080 123 K 0.0239 0.4417 0.5344 124 N 0.0477 0.0965 0.8559 125 R 0.0375 0.0456 0.9169