# This file is the result of combining several RDB files, specifically # T0373.t06.dssp-ebghstl.rdb (weight 1.53986) # T0373.t06.stride-ebghtl.rdb (weight 1.24869) # T0373.t06.str2.rdb (weight 1.54758) # T0373.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 T0373.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0373 # 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 T0373.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 3196 # # ============================================ # Comments from T0373.t06.stride-ebghtl.rdb # ============================================ # TARGET T0373 # 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 T0373.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 3196 # # ============================================ # Comments from T0373.t06.str2.rdb # ============================================ # TARGET T0373 # 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 T0373.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 3196 # # ============================================ # Comments from T0373.t06.alpha.rdb # ============================================ # TARGET T0373 # 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 T0373.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 3196 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0551 0.0136 0.9313 2 P 0.0578 0.0384 0.9038 3 T 0.0439 0.0981 0.8580 4 N 0.0417 0.2141 0.7442 5 Q 0.0169 0.6136 0.3694 6 D 0.0174 0.7650 0.2175 7 L 0.0095 0.8788 0.1117 8 Q 0.0085 0.9117 0.0798 9 L 0.0053 0.9405 0.0542 10 A 0.0049 0.9516 0.0435 11 A 0.0047 0.9582 0.0371 12 H 0.0047 0.9583 0.0371 13 L 0.0047 0.9589 0.0364 14 R 0.0047 0.9601 0.0352 15 S 0.0047 0.9587 0.0366 16 Q 0.0047 0.9574 0.0379 17 V 0.0047 0.9590 0.0363 18 T 0.0047 0.9587 0.0366 19 T 0.0047 0.9575 0.0378 20 L 0.0047 0.9553 0.0400 21 T 0.0047 0.9566 0.0387 22 R 0.0047 0.9547 0.0406 23 R 0.0048 0.9492 0.0460 24 L 0.0051 0.9411 0.0538 25 R 0.0054 0.9295 0.0651 26 R 0.0052 0.9235 0.0713 27 E 0.0060 0.8851 0.1089 28 A 0.0150 0.8214 0.1637 29 Q 0.0195 0.6642 0.3163 30 A 0.0221 0.4661 0.5118 31 D 0.0568 0.1167 0.8265 32 P 0.0344 0.0758 0.8899 33 V 0.0962 0.0289 0.8749 34 Q 0.0717 0.0282 0.9001 35 F 0.0049 0.9339 0.0612 36 S 0.0048 0.9490 0.0462 37 Q 0.0048 0.9558 0.0394 38 L 0.0047 0.9602 0.0351 39 V 0.0047 0.9601 0.0352 40 V 0.0047 0.9609 0.0345 41 L 0.0047 0.9606 0.0347 42 G 0.0047 0.9587 0.0366 43 A 0.0048 0.9558 0.0394 44 I 0.0053 0.9477 0.0470 45 D 0.0069 0.9241 0.0690 46 R 0.0097 0.8243 0.1659 47 L 0.0480 0.3821 0.5699 48 G 0.0343 0.0402 0.9256 49 G 0.0485 0.0304 0.9211 50 D 0.1661 0.0245 0.8093 51 V 0.2143 0.0102 0.7754 52 T 0.0931 0.0103 0.8966 53 P 0.0049 0.9471 0.0480 54 S 0.0047 0.9585 0.0368 55 E 0.0047 0.9590 0.0363 56 L 0.0047 0.9586 0.0367 57 A 0.0047 0.9524 0.0429 58 A 0.0051 0.9217 0.0732 59 A 0.0066 0.8564 0.1370 60 E 0.0467 0.5568 0.3965 61 R 0.0315 0.1784 0.7901 62 M 0.0819 0.0572 0.8609 63 R 0.0568 0.0566 0.8866 64 S 0.0162 0.7093 0.2745 65 S 0.0089 0.7772 0.2139 66 N 0.0132 0.8353 0.1515 67 L 0.0049 0.9407 0.0544 68 A 0.0047 0.9558 0.0395 69 A 0.0047 0.9583 0.0370 70 L 0.0047 0.9577 0.0376 71 L 0.0047 0.9586 0.0367 72 R 0.0047 0.9591 0.0362 73 E 0.0047 0.9579 0.0373 74 L 0.0049 0.9522 0.0428 75 E 0.0051 0.9263 0.0686 76 R 0.0120 0.7647 0.2234 77 G 0.0434 0.2226 0.7340 78 G 0.0403 0.0254 0.9344 79 L 0.2161 0.0255 0.7584 80 I 0.7970 0.0080 0.1950 81 V 0.8506 0.0092 0.1402 82 R 0.8416 0.0108 0.1476 83 H 0.7345 0.0081 0.2574 84 A 0.6181 0.0115 0.3705 85 D 0.2247 0.0101 0.7652 86 P 0.0119 0.1652 0.8229 87 Q 0.0190 0.1063 0.8747 88 D 0.0715 0.1145 0.8140 89 G 0.0677 0.0612 0.8711 90 R 0.3323 0.0258 0.6419 91 R 0.6912 0.0110 0.2979 92 T 0.8475 0.0053 0.1472 93 R 0.9134 0.0033 0.0833 94 V 0.9230 0.0044 0.0727 95 S 0.9051 0.0070 0.0879 96 L 0.7145 0.0114 0.2741 97 S 0.1480 0.0128 0.8391 98 S 0.0067 0.7846 0.2088 99 E 0.0056 0.8353 0.1591 100 G 0.0052 0.9191 0.0757 101 R 0.0062 0.9410 0.0527 102 R 0.0061 0.9356 0.0583 103 N 0.0056 0.9205 0.0739 104 L 0.0074 0.8940 0.0986 105 Y 0.0075 0.8440 0.1486 106 G 0.0079 0.7874 0.2048 107 N 0.0108 0.7512 0.2380 108 R 0.0077 0.8539 0.1383 109 A 0.0052 0.9221 0.0728 110 K 0.0050 0.9388 0.0562 111 R 0.0050 0.9487 0.0463 112 E 0.0047 0.9554 0.0399 113 E 0.0047 0.9585 0.0368 114 W 0.0047 0.9584 0.0369 115 L 0.0047 0.9580 0.0373 116 V 0.0047 0.9563 0.0390 117 R 0.0049 0.9424 0.0528 118 A 0.0052 0.9141 0.0808 119 M 0.0071 0.8640 0.1290 120 H 0.0076 0.7329 0.2595 121 A 0.0235 0.4676 0.5089 122 C 0.0273 0.1973 0.7754 123 L 0.0784 0.0332 0.8884 124 D 0.0518 0.0210 0.9272 125 E 0.0048 0.9510 0.0442 126 S 0.0047 0.9574 0.0379 127 E 0.0048 0.9586 0.0366 128 R 0.0047 0.9609 0.0345 129 A 0.0047 0.9589 0.0364 130 L 0.0047 0.9532 0.0421 131 L 0.0048 0.9477 0.0475 132 A 0.0055 0.9355 0.0590 133 A 0.0062 0.8596 0.1341 134 A 0.0099 0.8437 0.1465 135 G 0.0057 0.8914 0.1029 136 P 0.0048 0.9315 0.0638 137 L 0.0047 0.9445 0.0508 138 L 0.0047 0.9541 0.0412 139 T 0.0047 0.9537 0.0416 140 R 0.0048 0.9472 0.0480 141 L 0.0049 0.9304 0.0647 142 A 0.0058 0.8895 0.1047 143 Q 0.0079 0.7434 0.2487 144 F 0.0166 0.5335 0.4499 145 E 0.0503 0.2326 0.7171 146 E 0.0448 0.0665 0.8887 147 P 0.0279 0.0623 0.9098