# This file is the result of combining several RDB files, specifically # T0377.t04.dssp-ebghstl.rdb (weight 1.53986) # T0377.t04.stride-ebghtl.rdb (weight 1.24869) # T0377.t04.str2.rdb (weight 1.54758) # T0377.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 T0377.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0377 # 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 T0377.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 70.9037 # # ============================================ # Comments from T0377.t04.stride-ebghtl.rdb # ============================================ # TARGET T0377 # 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 T0377.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 70.9037 # # ============================================ # Comments from T0377.t04.str2.rdb # ============================================ # TARGET T0377 # 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 T0377.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 70.9037 # # ============================================ # Comments from T0377.t04.alpha.rdb # ============================================ # TARGET T0377 # 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 T0377.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 70.9037 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1551 0.0636 0.7813 2 A 0.2760 0.0733 0.6507 3 M 0.5798 0.0211 0.3991 4 L 0.8752 0.0041 0.1207 5 Y 0.9298 0.0032 0.0670 6 L 0.9325 0.0032 0.0643 7 I 0.9319 0.0032 0.0650 8 F 0.9200 0.0034 0.0765 9 Y 0.8677 0.0050 0.1273 10 D 0.6229 0.0061 0.3711 11 I 0.1640 0.0373 0.7987 12 T 0.0725 0.0485 0.8790 13 D 0.0534 0.1696 0.7770 14 D 0.0094 0.7560 0.2346 15 N 0.0094 0.8872 0.1034 16 L 0.0053 0.9414 0.0534 17 R 0.0047 0.9579 0.0374 18 N 0.0047 0.9604 0.0349 19 R 0.0047 0.9607 0.0347 20 V 0.0047 0.9606 0.0347 21 A 0.0046 0.9614 0.0340 22 E 0.0046 0.9618 0.0336 23 F 0.0046 0.9617 0.0336 24 L 0.0047 0.9598 0.0355 25 K 0.0048 0.9509 0.0443 26 K 0.0058 0.9026 0.0917 27 K 0.0379 0.5265 0.4356 28 G 0.0317 0.1283 0.8401 29 L 0.0713 0.1494 0.7792 30 D 0.1230 0.3584 0.5186 31 R 0.2742 0.4429 0.2829 32 I 0.3978 0.3745 0.2276 33 Q 0.4115 0.3488 0.2397 34 Y 0.3474 0.2932 0.3594 35 S 0.4128 0.1231 0.4641 36 V 0.4872 0.1119 0.4009 37 F 0.6281 0.0617 0.3103 38 M 0.6640 0.0727 0.2633 39 G 0.6409 0.0480 0.3111 40 D 0.5754 0.0322 0.3925 41 L 0.3094 0.0285 0.6621 42 N 0.0889 0.0157 0.8955 43 S 0.0052 0.9161 0.0786 44 S 0.0049 0.9367 0.0584 45 R 0.0050 0.9442 0.0508 46 L 0.0047 0.9565 0.0388 47 K 0.0047 0.9590 0.0363 48 D 0.0048 0.9567 0.0386 49 V 0.0047 0.9566 0.0387 50 E 0.0047 0.9583 0.0370 51 A 0.0049 0.9488 0.0464 52 G 0.0050 0.9189 0.0761 53 L 0.0078 0.9145 0.0777 54 K 0.0152 0.8819 0.1030 55 I 0.0212 0.8749 0.1039 56 I 0.0361 0.8258 0.1380 57 G 0.0457 0.6435 0.3108 58 N 0.0413 0.5019 0.4567 59 R 0.0466 0.5484 0.4050 60 K 0.0895 0.4631 0.4474 61 K 0.1253 0.3550 0.5197 62 L 0.1979 0.2801 0.5220 63 Q 0.2454 0.1283 0.6264 64 E 0.1397 0.0701 0.7902 65 D 0.0430 0.2291 0.7279 66 E 0.0711 0.2515 0.6773 67 R 0.2544 0.1295 0.6161 68 F 0.3911 0.0358 0.5731 69 F 0.7338 0.0143 0.2518 70 I 0.9174 0.0034 0.0792 71 L 0.9267 0.0035 0.0699 72 I 0.9237 0.0032 0.0731 73 V 0.8839 0.0050 0.1111 74 P 0.7642 0.0050 0.2308 75 I 0.3364 0.0269 0.6367 76 T 0.1505 0.0240 0.8255 77 E 0.0181 0.4646 0.5173 78 N 0.0215 0.4838 0.4947 79 Q 0.0655 0.5052 0.4294 80 F 0.2188 0.3238 0.4574 81 R 0.3740 0.1939 0.4321 82 E 0.6218 0.1333 0.2449 83 R 0.7923 0.0727 0.1350 84 I 0.8510 0.0509 0.0982 85 V 0.8378 0.0618 0.1004 86 I 0.6328 0.0912 0.2760 87 G 0.2787 0.0388 0.6825 88 Y 0.1907 0.0570 0.7522 89 S 0.1409 0.0570 0.8021 90 G 0.0869 0.0599 0.8532 91 S 0.0883 0.0657 0.8460 92 E 0.0945 0.2522 0.6533 93 R 0.1095 0.3199 0.5705 94 E 0.1296 0.2783 0.5921 95 E 0.1545 0.2497 0.5957 96 K 0.1629 0.1910 0.6462 97 S 0.1890 0.1292 0.6818 98 N 0.3855 0.0776 0.5370 99 V 0.6720 0.0336 0.2944 100 V 0.5968 0.0182 0.3850 101 W 0.2878 0.0189 0.6933