# This file is the result of combining several RDB files, specifically # T0275.t04.dssp-ebghstl.rdb (weight 1.53986) # T0275.t04.stride-ebghtl.rdb (weight 1.24869) # T0275.t04.str2.rdb (weight 1.54758) # T0275.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 T0275.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0275 # Using neural net t04-2621-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 T0275.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 1062 # # ============================================ # Comments from T0275.t04.stride-ebghtl.rdb # ============================================ # TARGET T0275 # 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 T0275.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 1062 # # ============================================ # Comments from T0275.t04.str2.rdb # ============================================ # TARGET T0275 # 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 T0275.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 1062 # # ============================================ # Comments from T0275.t04.alpha.rdb # ============================================ # TARGET T0275 # 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 T0275.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 1062 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0774 0.0391 0.8834 2 F 0.1736 0.0163 0.8101 3 K 0.2855 0.0187 0.6958 4 T 0.8148 0.0056 0.1796 5 I 0.9220 0.0035 0.0745 6 L 0.9315 0.0032 0.0653 7 L 0.9215 0.0039 0.0746 8 A 0.8442 0.0055 0.1503 9 Y 0.5264 0.0152 0.4584 10 D 0.1771 0.0205 0.8025 11 G 0.0394 0.0497 0.9109 12 S 0.0600 0.0909 0.8491 13 E 0.0061 0.8594 0.1345 14 H 0.0066 0.8903 0.1031 15 A 0.0050 0.9422 0.0528 16 R 0.0047 0.9582 0.0371 17 R 0.0047 0.9589 0.0364 18 A 0.0047 0.9587 0.0366 19 A 0.0047 0.9609 0.0344 20 E 0.0047 0.9614 0.0339 21 V 0.0047 0.9605 0.0348 22 A 0.0047 0.9584 0.0368 23 K 0.0047 0.9595 0.0358 24 A 0.0047 0.9593 0.0360 25 E 0.0048 0.9573 0.0380 26 A 0.0048 0.9541 0.0411 27 E 0.0049 0.9380 0.0571 28 A 0.0057 0.8730 0.1213 29 H 0.0419 0.3122 0.6459 30 G 0.0377 0.0168 0.9455 31 A 0.1093 0.0092 0.8815 32 R 0.6895 0.0069 0.3036 33 L 0.9180 0.0030 0.0790 34 I 0.9263 0.0037 0.0699 35 V 0.9335 0.0032 0.0634 36 V 0.9282 0.0033 0.0686 37 H 0.9183 0.0034 0.0783 38 A 0.7951 0.0089 0.1960 39 Y 0.5074 0.0145 0.4781 40 E 0.2184 0.0191 0.7625 41 P 0.1001 0.0366 0.8633 42 V 0.0737 0.0326 0.8937 43 P 0.0502 0.1387 0.8111 44 D 0.0459 0.2260 0.7281 45 Y 0.0541 0.2357 0.7102 46 L 0.0617 0.1805 0.7578 47 G 0.0475 0.1227 0.8298 48 E 0.0543 0.2250 0.7207 49 P 0.0258 0.6452 0.3290 50 F 0.0280 0.7520 0.2200 51 F 0.0133 0.8756 0.1111 52 E 0.0066 0.9407 0.0527 53 E 0.0052 0.9535 0.0413 54 A 0.0049 0.9531 0.0420 55 L 0.0047 0.9531 0.0422 56 R 0.0047 0.9558 0.0395 57 R 0.0047 0.9521 0.0432 58 R 0.0048 0.9435 0.0517 59 L 0.0047 0.9514 0.0439 60 E 0.0048 0.9541 0.0411 61 R 0.0049 0.9460 0.0491 62 A 0.0050 0.9424 0.0526 63 E 0.0050 0.9502 0.0448 64 G 0.0048 0.9513 0.0439 65 V 0.0048 0.9521 0.0432 66 L 0.0047 0.9571 0.0381 67 E 0.0047 0.9606 0.0347 68 E 0.0047 0.9604 0.0349 69 A 0.0047 0.9598 0.0355 70 R 0.0048 0.9566 0.0386 71 A 0.0052 0.9344 0.0604 72 L 0.0082 0.8513 0.1404 73 T 0.0464 0.4661 0.4875 74 G 0.0401 0.0375 0.9223 75 V 0.0566 0.0088 0.9346 76 P 0.0865 0.0144 0.8991 77 K 0.2205 0.1998 0.5797 78 E 0.3824 0.2161 0.4016 79 D 0.5682 0.1565 0.2753 80 A 0.7875 0.0555 0.1570 81 L 0.8577 0.0343 0.1080 82 L 0.8264 0.0512 0.1225 83 L 0.6406 0.0845 0.2749 84 E 0.2422 0.0752 0.6826 85 G 0.0517 0.0506 0.8977 86 V 0.0884 0.0636 0.8480 87 P 0.0477 0.7389 0.2135 88 A 0.0053 0.9472 0.0475 89 E 0.0047 0.9581 0.0372 90 A 0.0047 0.9581 0.0371 91 I 0.0049 0.9588 0.0362 92 L 0.0047 0.9602 0.0352 93 Q 0.0047 0.9609 0.0345 94 A 0.0046 0.9612 0.0341 95 A 0.0047 0.9590 0.0363 96 R 0.0050 0.9406 0.0544 97 A 0.0059 0.8585 0.1356 98 E 0.0447 0.3957 0.5596 99 K 0.0586 0.0360 0.9054 100 A 0.0939 0.0121 0.8941 101 D 0.1382 0.0454 0.8164 102 L 0.9165 0.0036 0.0799 103 I 0.9332 0.0032 0.0636 104 V 0.9313 0.0032 0.0655 105 M 0.8744 0.0109 0.1146 106 G 0.5225 0.0177 0.4598 107 T 0.2021 0.0457 0.7521 108 R 0.1050 0.0864 0.8086 109 G 0.0790 0.0927 0.8283 110 L 0.0724 0.1915 0.7360 111 G 0.0678 0.2528 0.6794 112 A 0.0663 0.4151 0.5186 113 L 0.0543 0.6257 0.3200 114 G 0.0415 0.6666 0.2920 115 S 0.0697 0.6800 0.2503 116 L 0.1041 0.6556 0.2403 117 F 0.1339 0.5499 0.3163 118 L 0.0887 0.4154 0.4959 119 G 0.0598 0.2318 0.7084 120 S 0.0549 0.4691 0.4760 121 Q 0.0149 0.8347 0.1504 122 S 0.0051 0.9442 0.0507 123 Q 0.0047 0.9545 0.0408 124 R 0.0052 0.9561 0.0387 125 V 0.0055 0.9521 0.0424 126 V 0.0065 0.9269 0.0665 127 A 0.0079 0.8354 0.1568 128 E 0.0179 0.4906 0.4915 129 A 0.0748 0.0475 0.8776 130 P 0.0633 0.0444 0.8923 131 C 0.1520 0.0100 0.8380 132 P 0.3559 0.0106 0.6334 133 V 0.9089 0.0037 0.0874 134 L 0.9277 0.0035 0.0688 135 L 0.9214 0.0035 0.0751 136 V 0.8026 0.0078 0.1896 137 R 0.3032 0.0124 0.6844