# This file is the result of combining several RDB files, specifically # T0385.t04.dssp-ebghstl.rdb (weight 1.53986) # T0385.t04.stride-ebghtl.rdb (weight 1.24869) # T0385.t04.str2.rdb (weight 1.54758) # T0385.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 T0385.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0385 # 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 T0385.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 24.9235 # # ============================================ # Comments from T0385.t04.stride-ebghtl.rdb # ============================================ # TARGET T0385 # 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 T0385.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 24.9235 # # ============================================ # Comments from T0385.t04.str2.rdb # ============================================ # TARGET T0385 # 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 T0385.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 24.9235 # # ============================================ # Comments from T0385.t04.alpha.rdb # ============================================ # TARGET T0385 # 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 T0385.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 24.9235 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1474 0.0455 0.8071 2 T 0.1819 0.0685 0.7496 3 S 0.1657 0.0723 0.7620 4 S 0.1384 0.1058 0.7558 5 E 0.0981 0.0962 0.8057 6 P 0.0794 0.1748 0.7458 7 A 0.0874 0.2159 0.6966 8 H 0.0828 0.1986 0.7185 9 G 0.0703 0.1257 0.8041 10 A 0.1077 0.0726 0.8196 11 T 0.1030 0.0478 0.8492 12 P 0.0760 0.2103 0.7137 13 K 0.0714 0.2172 0.7115 14 R 0.1040 0.1261 0.7698 15 S 0.0820 0.0265 0.8914 16 P 0.0512 0.0700 0.8788 17 S 0.0606 0.0617 0.8777 18 E 0.0450 0.1169 0.8381 19 G 0.0438 0.1245 0.8317 20 S 0.0539 0.3643 0.5818 21 A 0.0383 0.6722 0.2896 22 D 0.0188 0.8603 0.1209 23 N 0.0059 0.9356 0.0585 24 A 0.0053 0.9487 0.0460 25 A 0.0052 0.9533 0.0414 26 L 0.0047 0.9586 0.0367 27 C 0.0047 0.9608 0.0345 28 D 0.0047 0.9590 0.0363 29 A 0.0047 0.9592 0.0361 30 L 0.0047 0.9589 0.0364 31 A 0.0047 0.9581 0.0371 32 V 0.0047 0.9567 0.0385 33 E 0.0048 0.9554 0.0398 34 H 0.0048 0.9514 0.0438 35 A 0.0056 0.9405 0.0540 36 T 0.0070 0.9304 0.0625 37 I 0.0136 0.9102 0.0762 38 Y 0.0260 0.8603 0.1136 39 G 0.0392 0.8156 0.1452 40 Y 0.0432 0.7487 0.2080 41 G 0.0917 0.5584 0.3499 42 I 0.1534 0.5493 0.2974 43 V 0.1936 0.5291 0.2773 44 S 0.1546 0.4377 0.4077 45 A 0.1027 0.2880 0.6094 46 L 0.1207 0.1366 0.7426 47 S 0.0805 0.0511 0.8684 48 P 0.0491 0.0798 0.8711 49 P 0.0209 0.3059 0.6731 50 G 0.0276 0.3420 0.6304 51 V 0.0266 0.7240 0.2494 52 N 0.0090 0.8782 0.1128 53 F 0.0060 0.9388 0.0553 54 L 0.0061 0.9484 0.0456 55 V 0.0047 0.9578 0.0375 56 A 0.0047 0.9595 0.0359 57 D 0.0047 0.9567 0.0386 58 A 0.0047 0.9478 0.0475 59 L 0.0047 0.9441 0.0511 60 K 0.0048 0.9315 0.0637 61 Q 0.0050 0.9003 0.0947 62 H 0.0057 0.8845 0.1098 63 R 0.0059 0.8780 0.1161 64 H 0.0075 0.8188 0.1737 65 R 0.0079 0.8411 0.1510 66 R 0.0049 0.9432 0.0519 67 D 0.0047 0.9598 0.0355 68 D 0.0047 0.9605 0.0348 69 V 0.0047 0.9606 0.0348 70 I 0.0046 0.9614 0.0339 71 V 0.0046 0.9618 0.0336 72 M 0.0046 0.9617 0.0337 73 L 0.0047 0.9606 0.0347 74 S 0.0048 0.9510 0.0442 75 A 0.0052 0.9092 0.0856 76 R 0.0429 0.4078 0.5493 77 G 0.0415 0.0232 0.9353 78 V 0.0797 0.0127 0.9075 79 T 0.2017 0.0277 0.7706 80 A 0.1706 0.0462 0.7833 81 P 0.1818 0.0759 0.7423 82 I 0.1885 0.1828 0.6287 83 A 0.1409 0.2469 0.6123 84 A 0.0996 0.3516 0.5488 85 A 0.0932 0.2634 0.6434 86 G 0.1088 0.1328 0.7584 87 Y 0.3255 0.0374 0.6371 88 Q 0.3902 0.0269 0.5829 89 L 0.3689 0.0158 0.6153 90 P 0.2872 0.0236 0.6892 91 M 0.2783 0.0391 0.6826 92 Q 0.2602 0.0392 0.7006 93 V 0.1775 0.0551 0.7674 94 S 0.1035 0.0495 0.8470 95 S 0.0704 0.0709 0.8588 96 A 0.0048 0.9537 0.0415 97 A 0.0047 0.9603 0.0350 98 D 0.0047 0.9601 0.0353 99 A 0.0047 0.9605 0.0349 100 A 0.0046 0.9607 0.0346 101 R 0.0046 0.9608 0.0346 102 L 0.0047 0.9605 0.0348 103 A 0.0047 0.9585 0.0368 104 V 0.0048 0.9533 0.0419 105 R 0.0052 0.9248 0.0700 106 M 0.0060 0.8819 0.1121 107 E 0.0086 0.8632 0.1282 108 N 0.0086 0.8685 0.1229 109 D 0.0177 0.8611 0.1211 110 G 0.0143 0.9200 0.0656 111 A 0.0102 0.9409 0.0489 112 T 0.0096 0.9463 0.0441 113 A 0.0086 0.9411 0.0503 114 W 0.0103 0.9342 0.0555 115 R 0.0083 0.9326 0.0591 116 A 0.0099 0.9019 0.0882 117 V 0.0132 0.8720 0.1149 118 V 0.0175 0.8709 0.1116 119 E 0.0111 0.8361 0.1528 120 H 0.0173 0.7440 0.2387 121 A 0.0512 0.5206 0.4282 122 E 0.0412 0.3106 0.6482 123 T 0.0526 0.0990 0.8484 124 A 0.0088 0.6252 0.3659 125 D 0.0132 0.7597 0.2271 126 D 0.0076 0.9101 0.0823 127 R 0.0057 0.9466 0.0477 128 V 0.0063 0.9483 0.0455 129 F 0.0069 0.9413 0.0517 130 A 0.0056 0.9380 0.0565 131 S 0.0057 0.9346 0.0598 132 T 0.0056 0.9104 0.0840 133 A 0.0074 0.8555 0.1371 134 L 0.0129 0.7562 0.2309 135 T 0.0217 0.7491 0.2292 136 E 0.0049 0.9272 0.0679 137 S 0.0050 0.9506 0.0443 138 A 0.0047 0.9581 0.0371 139 V 0.0047 0.9602 0.0351 140 M 0.0047 0.9588 0.0365 141 A 0.0047 0.9584 0.0368 142 T 0.0047 0.9578 0.0375 143 R 0.0048 0.9537 0.0415 144 W 0.0048 0.9542 0.0411 145 N 0.0052 0.9509 0.0438 146 R 0.0056 0.9407 0.0537 147 V 0.0092 0.9007 0.0902 148 L 0.0429 0.6825 0.2746 149 G 0.0287 0.2450 0.7263 150 A 0.0486 0.1736 0.7778 151 W 0.0857 0.0370 0.8774 152 P 0.1216 0.0430 0.8354 153 I 0.2095 0.0617 0.7288 154 T 0.2280 0.1051 0.6669 155 A 0.2960 0.1371 0.5669 156 A 0.3789 0.0949 0.5262 157 F 0.2873 0.0425 0.6702 158 P 0.1725 0.0506 0.7769 159 G 0.0962 0.0500 0.8538 160 G 0.0694 0.0547 0.8759 161 D 0.0552 0.0801 0.8647 162 E 0.0515 0.1412 0.8073