# This file is the result of combining several RDB files, specifically # T0373.t04.dssp-ebghstl.rdb (weight 1.53986) # T0373.t04.stride-ebghtl.rdb (weight 1.24869) # T0373.t04.str2.rdb (weight 1.54758) # T0373.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 T0373.t04.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.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 2372 # # ============================================ # Comments from T0373.t04.stride-ebghtl.rdb # ============================================ # TARGET T0373 # 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 T0373.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 2372 # # ============================================ # Comments from T0373.t04.str2.rdb # ============================================ # TARGET T0373 # 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 T0373.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 2372 # # ============================================ # Comments from T0373.t04.alpha.rdb # ============================================ # TARGET T0373 # 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 T0373.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 2372 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0622 0.0152 0.9226 2 P 0.0629 0.0405 0.8966 3 T 0.0476 0.1060 0.8463 4 N 0.0525 0.2205 0.7270 5 Q 0.0160 0.6715 0.3125 6 D 0.0156 0.8065 0.1779 7 L 0.0083 0.9065 0.0852 8 Q 0.0067 0.9338 0.0595 9 L 0.0047 0.9476 0.0476 10 A 0.0047 0.9569 0.0384 11 A 0.0047 0.9602 0.0351 12 H 0.0047 0.9604 0.0349 13 L 0.0047 0.9604 0.0350 14 R 0.0047 0.9611 0.0343 15 S 0.0047 0.9606 0.0348 16 Q 0.0047 0.9595 0.0358 17 V 0.0047 0.9603 0.0350 18 T 0.0046 0.9602 0.0351 19 T 0.0047 0.9595 0.0358 20 L 0.0047 0.9581 0.0372 21 T 0.0047 0.9587 0.0367 22 R 0.0047 0.9573 0.0380 23 R 0.0048 0.9543 0.0409 24 L 0.0049 0.9483 0.0468 25 R 0.0051 0.9419 0.0530 26 R 0.0051 0.9341 0.0608 27 E 0.0059 0.9130 0.0812 28 A 0.0153 0.8499 0.1348 29 Q 0.0152 0.6796 0.3052 30 A 0.0216 0.4499 0.5285 31 D 0.0600 0.1051 0.8349 32 P 0.0377 0.0577 0.9047 33 V 0.1062 0.0203 0.8735 34 Q 0.0821 0.0255 0.8923 35 F 0.0053 0.9213 0.0733 36 S 0.0047 0.9475 0.0478 37 Q 0.0049 0.9551 0.0401 38 L 0.0047 0.9602 0.0351 39 V 0.0047 0.9606 0.0348 40 V 0.0047 0.9607 0.0347 41 L 0.0047 0.9609 0.0344 42 G 0.0047 0.9595 0.0359 43 A 0.0047 0.9562 0.0390 44 I 0.0050 0.9481 0.0470 45 D 0.0064 0.9197 0.0739 46 R 0.0095 0.7913 0.1993 47 L 0.0500 0.3807 0.5693 48 G 0.0375 0.0474 0.9151 49 G 0.0468 0.0318 0.9214 50 D 0.1132 0.0323 0.8545 51 V 0.1514 0.0098 0.8388 52 T 0.0917 0.0111 0.8973 53 P 0.0049 0.9464 0.0487 54 S 0.0047 0.9607 0.0346 55 E 0.0047 0.9608 0.0345 56 L 0.0047 0.9595 0.0358 57 A 0.0048 0.9546 0.0407 58 A 0.0053 0.9351 0.0595 59 A 0.0070 0.8759 0.1171 60 E 0.0430 0.5248 0.4322 61 R 0.0312 0.1698 0.7991 62 M 0.0774 0.0767 0.8458 63 R 0.0463 0.0957 0.8579 64 S 0.0222 0.6488 0.3290 65 S 0.0160 0.7298 0.2541 66 N 0.0226 0.7693 0.2081 67 L 0.0066 0.9308 0.0626 68 A 0.0047 0.9530 0.0423 69 A 0.0047 0.9575 0.0378 70 L 0.0047 0.9581 0.0372 71 L 0.0047 0.9596 0.0357 72 R 0.0047 0.9599 0.0354 73 E 0.0047 0.9597 0.0356 74 L 0.0049 0.9549 0.0402 75 E 0.0051 0.9301 0.0647 76 R 0.0103 0.7323 0.2574 77 G 0.0445 0.1654 0.7901 78 G 0.0394 0.0233 0.9373 79 L 0.2147 0.0196 0.7656 80 I 0.7675 0.0073 0.2252 81 V 0.8456 0.0081 0.1463 82 R 0.8422 0.0086 0.1492 83 H 0.6717 0.0095 0.3188 84 A 0.5370 0.0136 0.4495 85 D 0.1674 0.0115 0.8211 86 P 0.0140 0.1837 0.8023 87 Q 0.0192 0.1305 0.8503 88 D 0.0800 0.1287 0.7913 89 G 0.0922 0.0942 0.8135 90 R 0.3897 0.0532 0.5571 91 R 0.7689 0.0139 0.2173 92 T 0.8531 0.0109 0.1361 93 R 0.9141 0.0058 0.0801 94 V 0.9181 0.0071 0.0748 95 S 0.9020 0.0144 0.0836 96 L 0.7553 0.0176 0.2271 97 S 0.2034 0.0195 0.7771 98 S 0.0103 0.7451 0.2446 99 E 0.0066 0.8323 0.1611 100 G 0.0056 0.9119 0.0825 101 R 0.0069 0.9403 0.0528 102 R 0.0061 0.9461 0.0478 103 N 0.0053 0.9389 0.0559 104 L 0.0056 0.9204 0.0739 105 Y 0.0066 0.8609 0.1325 106 G 0.0083 0.7896 0.2021 107 N 0.0164 0.6955 0.2880 108 R 0.0125 0.7781 0.2094 109 A 0.0061 0.9037 0.0902 110 K 0.0058 0.9284 0.0658 111 R 0.0065 0.9233 0.0702 112 E 0.0051 0.9317 0.0632 113 E 0.0050 0.9402 0.0548 114 W 0.0050 0.9477 0.0473 115 L 0.0050 0.9534 0.0417 116 V 0.0047 0.9570 0.0383 117 R 0.0050 0.9553 0.0397 118 A 0.0049 0.9501 0.0450 119 M 0.0054 0.9310 0.0635 120 H 0.0065 0.8677 0.1258 121 A 0.0148 0.6600 0.3252 122 C 0.0214 0.2703 0.7083 123 L 0.0696 0.0221 0.9083 124 D 0.0559 0.0119 0.9322 125 E 0.0049 0.9423 0.0527 126 S 0.0047 0.9573 0.0380 127 E 0.0047 0.9594 0.0359 128 R 0.0046 0.9610 0.0344 129 A 0.0047 0.9582 0.0371 130 L 0.0047 0.9499 0.0454 131 L 0.0047 0.9434 0.0519 132 A 0.0052 0.9330 0.0618 133 A 0.0059 0.8734 0.1207 134 A 0.0093 0.8549 0.1358 135 G 0.0064 0.8806 0.1130 136 P 0.0050 0.9076 0.0874 137 L 0.0048 0.9361 0.0591 138 L 0.0047 0.9544 0.0409 139 T 0.0047 0.9581 0.0373 140 R 0.0047 0.9547 0.0405 141 L 0.0049 0.9446 0.0505 142 A 0.0053 0.9230 0.0717 143 Q 0.0076 0.8089 0.1835 144 F 0.0167 0.5437 0.4396 145 E 0.0476 0.2047 0.7477 146 E 0.0456 0.0687 0.8857 147 P 0.0276 0.0689 0.9035