# This file is the result of combining several RDB files, specifically # T0316.t06.dssp-ebghstl.rdb (weight 1.53986) # T0316.t06.stride-ebghtl.rdb (weight 1.24869) # T0316.t06.str2.rdb (weight 1.54758) # T0316.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 T0316.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0316 # 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 T0316.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 18.0221 # # ============================================ # Comments from T0316.t06.stride-ebghtl.rdb # ============================================ # TARGET T0316 # 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 T0316.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 18.0221 # # ============================================ # Comments from T0316.t06.str2.rdb # ============================================ # TARGET T0316 # 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 T0316.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 18.0221 # # ============================================ # Comments from T0316.t06.alpha.rdb # ============================================ # TARGET T0316 # 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 T0316.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 18.0221 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 L 0.0843 0.1473 0.7684 2 G 0.0670 0.0936 0.8394 3 H 0.0864 0.1130 0.8006 4 L 0.0935 0.0870 0.8195 5 E 0.0622 0.0771 0.8608 6 K 0.0276 0.5372 0.4353 7 P 0.0062 0.8595 0.1343 8 E 0.0069 0.9308 0.0623 9 V 0.0061 0.9494 0.0445 10 R 0.0047 0.9560 0.0393 11 R 0.0046 0.9612 0.0341 12 L 0.0046 0.9617 0.0336 13 A 0.0047 0.9612 0.0342 14 E 0.0048 0.9566 0.0386 15 E 0.0052 0.9448 0.0500 16 A 0.0426 0.5649 0.3924 17 G 0.0426 0.0279 0.9296 18 L 0.0709 0.0177 0.9114 19 S 0.1532 0.0749 0.7718 20 T 0.3242 0.1659 0.5100 21 A 0.3329 0.1598 0.5073 22 K 0.2733 0.1236 0.6031 23 K 0.1715 0.1042 0.7244 24 K 0.0966 0.1978 0.7056 25 D 0.1026 0.1851 0.7124 26 S 0.2601 0.1250 0.6149 27 T 0.2520 0.0849 0.6631 28 G 0.4280 0.0522 0.5198 29 I 0.8165 0.0109 0.1727 30 C 0.8892 0.0095 0.1013 31 F 0.8713 0.0088 0.1199 32 I 0.6342 0.0243 0.3415 33 G 0.2097 0.0293 0.7610 34 E 0.0804 0.1197 0.7999 35 K 0.0452 0.2031 0.7516 36 N 0.0725 0.2654 0.6622 37 F 0.0163 0.8514 0.1323 38 K 0.0065 0.9089 0.0845 39 N 0.0072 0.9010 0.0918 40 F 0.0191 0.8936 0.0873 41 L 0.0164 0.8810 0.1026 42 S 0.0086 0.8600 0.1314 43 N 0.0159 0.6687 0.3154 44 Y 0.0514 0.3947 0.5540 45 L 0.0799 0.0427 0.8775 46 P 0.0833 0.0536 0.8631 47 A 0.1400 0.0343 0.8256 48 Q 0.1253 0.0230 0.8517 49 P 0.1075 0.0617 0.8308 50 G 0.2280 0.0351 0.7370 51 R 0.6430 0.0148 0.3423 52 M 0.8897 0.0047 0.1055 53 M 0.8770 0.0058 0.1172 54 T 0.6747 0.0076 0.3176 55 V 0.2194 0.0756 0.7050 56 D 0.0461 0.0327 0.9213 57 G 0.0631 0.0343 0.9026 58 R 0.4540 0.0206 0.5254 59 D 0.8361 0.0131 0.1508 60 M 0.7566 0.0427 0.2006 61 G 0.6623 0.0422 0.2955 62 E 0.5904 0.0663 0.3434 63 H 0.4751 0.0752 0.4497 64 A 0.2283 0.0887 0.6830 65 G 0.3649 0.0440 0.5911 66 L 0.6691 0.0395 0.2914 67 M 0.8402 0.0200 0.1399 68 Y 0.8608 0.0227 0.1165 69 Y 0.8454 0.0322 0.1223 70 T 0.7551 0.0566 0.1884 71 I 0.5450 0.1748 0.2802 72 G 0.4490 0.1384 0.4126 73 Q 0.4469 0.1891 0.3639 74 R 0.3898 0.1883 0.4219 75 G 0.2194 0.1865 0.5942 76 G 0.1992 0.1252 0.6756 77 L 0.2517 0.0924 0.6559 78 G 0.2916 0.0654 0.6430 79 I 0.2579 0.1059 0.6362 80 G 0.2170 0.0961 0.6869 81 G 0.1457 0.1052 0.7491 82 Q 0.1122 0.1569 0.7309 83 H 0.0877 0.1434 0.7690 84 G 0.0683 0.1134 0.8183 85 G 0.0580 0.0991 0.8429 86 D 0.0897 0.0898 0.8205 87 N 0.1280 0.0608 0.8112 88 A 0.1776 0.0162 0.8062 89 P 0.3150 0.0170 0.6680 90 W 0.7171 0.0197 0.2632 91 F 0.8864 0.0092 0.1044 92 V 0.9020 0.0066 0.0914 93 V 0.8350 0.0289 0.1361 94 G 0.7585 0.0197 0.2218 95 K 0.6255 0.0286 0.3459 96 D 0.4488 0.0384 0.5128 97 L 0.1143 0.2907 0.5950 98 S 0.0857 0.2801 0.6341 99 K 0.1152 0.1970 0.6877 100 N 0.1998 0.0351 0.7651 101 I 0.7898 0.0070 0.2032 102 L 0.9191 0.0035 0.0773 103 Y 0.9225 0.0040 0.0735 104 V 0.8728 0.0113 0.1158 105 G 0.4985 0.0148 0.4867 106 Q 0.1516 0.0432 0.8052 107 G 0.0694 0.0496 0.8810 108 F 0.0951 0.0710 0.8340 109 Y 0.0985 0.0921 0.8094 110 H 0.0739 0.2113 0.7148 111 D 0.0295 0.4909 0.4796 112 S 0.0383 0.6013 0.3604 113 L 0.1302 0.4899 0.3798 114 M 0.2160 0.3230 0.4610 115 S 0.2468 0.2324 0.5208 116 T 0.2485 0.1763 0.5752 117 S 0.5067 0.0967 0.3966 118 L 0.7211 0.0304 0.2485 119 E 0.7637 0.0274 0.2089 120 A 0.6600 0.0727 0.2673 121 S 0.4059 0.1398 0.4543 122 Q 0.3956 0.1286 0.4758 123 V 0.5195 0.0819 0.3986 124 H 0.5745 0.0874 0.3381 125 F 0.5523 0.1044 0.3433 126 T 0.4725 0.1142 0.4133 127 R 0.2993 0.1056 0.5951 128 E 0.1684 0.0696 0.7621 129 M 0.1062 0.0216 0.8722 130 P 0.0644 0.0335 0.9021