# This file is the result of combining several RDB files, specifically # T0321.t06.dssp-ebghstl.rdb (weight 1.53986) # T0321.t06.stride-ebghtl.rdb (weight 1.24869) # T0321.t06.str2.rdb (weight 1.54758) # T0321.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 T0321.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0321 # 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 T0321.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 31.3761 # # ============================================ # Comments from T0321.t06.stride-ebghtl.rdb # ============================================ # TARGET T0321 # 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 T0321.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 31.3761 # # ============================================ # Comments from T0321.t06.str2.rdb # ============================================ # TARGET T0321 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0321.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 31.3761 # # ============================================ # Comments from T0321.t06.alpha.rdb # ============================================ # TARGET T0321 # 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 T0321.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 31.3761 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0192 0.3088 0.6720 2 W 0.0198 0.7036 0.2766 3 E 0.0217 0.8059 0.1725 4 I 0.0067 0.9348 0.0585 5 Y 0.0048 0.9561 0.0391 6 D 0.0048 0.9583 0.0370 7 A 0.0054 0.9525 0.0420 8 M 0.0060 0.9424 0.0516 9 I 0.0103 0.8838 0.1059 10 N 0.0287 0.5217 0.4496 11 G 0.0219 0.2085 0.7695 12 I 0.0584 0.0371 0.9045 13 P 0.0489 0.2305 0.7207 14 E 0.0267 0.3031 0.6702 15 D 0.0803 0.3105 0.6092 16 F 0.2629 0.0555 0.6816 17 L 0.4711 0.0244 0.5044 18 V 0.6081 0.0552 0.3367 19 D 0.4991 0.0868 0.4142 20 E 0.7939 0.0430 0.1631 21 L 0.8796 0.0227 0.0977 22 V 0.8877 0.0144 0.0979 23 C 0.7889 0.0254 0.1857 24 G 0.4743 0.0333 0.4923 25 T 0.3919 0.0277 0.5804 26 T 0.5709 0.0339 0.3953 27 H 0.8376 0.0173 0.1451 28 S 0.9046 0.0086 0.0868 29 V 0.9167 0.0064 0.0770 30 I 0.9072 0.0067 0.0861 31 R 0.8661 0.0104 0.1235 32 S 0.5051 0.0330 0.4619 33 G 0.0888 0.0600 0.8512 34 N 0.0690 0.0430 0.8880 35 G 0.2633 0.0630 0.6737 36 V 0.4264 0.0713 0.5024 37 G 0.5988 0.0564 0.3448 38 L 0.6468 0.0597 0.2936 39 G 0.5326 0.0392 0.4282 40 P 0.3649 0.0364 0.5987 41 N 0.2038 0.0287 0.7675 42 R 0.0995 0.0292 0.8713 43 P 0.0638 0.1106 0.8255 44 F 0.0654 0.1342 0.8003 45 E 0.0979 0.1261 0.7760 46 T 0.1430 0.0914 0.7656 47 R 0.1673 0.0888 0.7439 48 M 0.1329 0.0633 0.8038 49 P 0.1260 0.1244 0.7496 50 M 0.0767 0.2564 0.6669 51 L 0.0680 0.3235 0.6085 52 T 0.0504 0.4883 0.4612 53 Q 0.0468 0.5001 0.4531 54 N 0.0632 0.4583 0.4785 55 L 0.0748 0.3827 0.5425 56 L 0.0417 0.1998 0.7585 57 G 0.0250 0.0893 0.8856 58 L 0.0657 0.0803 0.8540 59 P 0.0977 0.1252 0.7771 60 L 0.0066 0.9406 0.0528 61 R 0.0091 0.9474 0.0435 62 V 0.0082 0.9487 0.0431 63 A 0.0117 0.9304 0.0579 64 A 0.0082 0.9189 0.0728 65 G 0.0098 0.8883 0.1019 66 C 0.0135 0.8551 0.1313 67 V 0.0334 0.7346 0.2320 68 K 0.0319 0.5999 0.3682 69 S 0.0445 0.4956 0.4599 70 W 0.0224 0.5717 0.4059 71 N 0.0285 0.7340 0.2376 72 Y 0.0049 0.9414 0.0537 73 V 0.0047 0.9585 0.0368 74 E 0.0047 0.9603 0.0350 75 A 0.0047 0.9605 0.0348 76 S 0.0047 0.9602 0.0351 77 I 0.0047 0.9604 0.0349 78 G 0.0046 0.9612 0.0342 79 L 0.0047 0.9608 0.0346 80 A 0.0047 0.9610 0.0344 81 A 0.0046 0.9604 0.0349 82 I 0.0047 0.9591 0.0362 83 N 0.0049 0.9502 0.0449 84 A 0.0062 0.9266 0.0672 85 Y 0.0159 0.7882 0.1958 86 Y 0.0592 0.5180 0.4228 87 N 0.0725 0.2040 0.7234 88 N 0.0752 0.0590 0.8658 89 P 0.0257 0.3706 0.6037 90 Q 0.0417 0.4497 0.5085 91 V 0.0681 0.5051 0.4269 92 A 0.0994 0.4522 0.4484 93 R 0.0573 0.4850 0.4577 94 E 0.0459 0.4979 0.4562 95 H 0.0613 0.2198 0.7189 96 G 0.0552 0.0635 0.8814 97 V 0.2561 0.0296 0.7143 98 I 0.5952 0.0271 0.3776 99 F 0.5946 0.0538 0.3516 100 S 0.4781 0.0786 0.4434 101 D 0.3130 0.1103 0.5767 102 A 0.1821 0.1687 0.6492 103 K 0.1358 0.1981 0.6661 104 R 0.1772 0.1406 0.6822 105 V 0.2737 0.0985 0.6277 106 E 0.4206 0.0842 0.4952 107 D 0.5748 0.1038 0.3215 108 R 0.6479 0.0934 0.2586 109 M 0.6735 0.0828 0.2437 110 N 0.5205 0.1056 0.3740 111 D 0.2314 0.1125 0.6561 112 P 0.1107 0.2332 0.6561 113 F 0.1183 0.3036 0.5781 114 I 0.0996 0.4629 0.4375 115 M 0.0671 0.5590 0.3739 116 S 0.0715 0.5942 0.3343 117 Q 0.0272 0.8133 0.1595 118 N 0.0162 0.8281 0.1557 119 E 0.0185 0.8093 0.1722 120 V 0.0470 0.6908 0.2622 121 K 0.0453 0.4400 0.5147 122 G 0.0386 0.1447 0.8167 123 K 0.0494 0.0500 0.9006