# This file is the result of combining several RDB files, specifically # T0369.t06.dssp-ebghstl.rdb (weight 1.53986) # T0369.t06.stride-ebghtl.rdb (weight 1.24869) # T0369.t06.str2.rdb (weight 1.54758) # T0369.t06.alpha.rdb (weight 0.659012) # T0369.t04.dssp-ebghstl.rdb (weight 1.53986) # T0369.t04.stride-ebghtl.rdb (weight 1.24869) # T0369.t04.str2.rdb (weight 1.54758) # T0369.t04.alpha.rdb (weight 0.659012) # T0369.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0369.t2k.stride-ebghtl.rdb (weight 1.24869) # T0369.t2k.str2.rdb (weight 1.54758) # T0369.t2k.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 T0369.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0369 # 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 T0369.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 142 # # ============================================ # Comments from T0369.t06.stride-ebghtl.rdb # ============================================ # TARGET T0369 # Using neural net t06-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 T0369.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 142 # # ============================================ # Comments from T0369.t06.str2.rdb # ============================================ # TARGET T0369 # Using neural net t06-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 T0369.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 142 # # ============================================ # Comments from T0369.t06.alpha.rdb # ============================================ # TARGET T0369 # Using neural net t06-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 T0369.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 142 # # ============================================ # Comments from T0369.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0369 # 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 T0369.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 124 # # ============================================ # Comments from T0369.t04.stride-ebghtl.rdb # ============================================ # TARGET T0369 # 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 T0369.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 124 # # ============================================ # Comments from T0369.t04.str2.rdb # ============================================ # TARGET T0369 # 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 T0369.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 124 # # ============================================ # Comments from T0369.t04.alpha.rdb # ============================================ # TARGET T0369 # 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 T0369.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 124 # # ============================================ # Comments from T0369.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0369 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0369.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 23 # # ============================================ # Comments from T0369.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0369 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0369.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 23 # # ============================================ # Comments from T0369.t2k.str2.rdb # ============================================ # TARGET T0369 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0369.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 23 # # ============================================ # Comments from T0369.t2k.alpha.rdb # ============================================ # TARGET T0369 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0369.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 23 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0215 0.3162 0.6623 2 T 0.0124 0.8346 0.1530 3 D 0.0107 0.8700 0.1193 4 W 0.0067 0.9132 0.0801 5 Q 0.0057 0.9406 0.0537 6 Q 0.0051 0.9466 0.0483 7 A 0.0048 0.9493 0.0459 8 L 0.0048 0.9438 0.0513 9 D 0.0049 0.9386 0.0564 10 R 0.0051 0.9187 0.0762 11 H 0.0054 0.9037 0.0908 12 V 0.0087 0.9127 0.0786 13 G 0.0078 0.9034 0.0889 14 V 0.0084 0.8959 0.0957 15 G 0.0110 0.8895 0.0995 16 V 0.0084 0.9205 0.0711 17 R 0.0064 0.9342 0.0594 18 T 0.0060 0.9339 0.0601 19 T 0.0056 0.9461 0.0483 20 R 0.0047 0.9559 0.0393 21 D 0.0048 0.9549 0.0403 22 L 0.0048 0.9518 0.0434 23 I 0.0052 0.9342 0.0606 24 R 0.0060 0.8603 0.1336 25 L 0.0127 0.6348 0.3526 26 I 0.0628 0.1212 0.8160 27 Q 0.0627 0.0491 0.8882 28 P 0.0109 0.6638 0.3252 29 E 0.0109 0.6763 0.3129 30 D 0.0267 0.7401 0.2332 31 W 0.0953 0.3480 0.5567 32 D 0.1147 0.1480 0.7373 33 K 0.2698 0.0655 0.6647 34 R 0.2537 0.0285 0.7178 35 P 0.2054 0.0366 0.7581 36 I 0.1101 0.0991 0.7909 37 S 0.0439 0.2138 0.7422 38 G 0.0449 0.1808 0.7743 39 K 0.1016 0.1159 0.7825 40 R 0.1954 0.0650 0.7396 41 S 0.1827 0.0832 0.7341 42 V 0.0054 0.9402 0.0544 43 Y 0.0047 0.9569 0.0384 44 E 0.0047 0.9587 0.0366 45 V 0.0047 0.9600 0.0353 46 A 0.0047 0.9590 0.0363 47 V 0.0047 0.9560 0.0392 48 H 0.0048 0.9522 0.0430 49 L 0.0049 0.9450 0.0501 50 A 0.0053 0.9116 0.0831 51 V 0.0073 0.8447 0.1480 52 L 0.0202 0.8227 0.1571 53 L 0.0172 0.8231 0.1597 54 E 0.0155 0.8317 0.1528 55 A 0.0220 0.8560 0.1220 56 D 0.0251 0.8635 0.1114 57 L 0.0370 0.8341 0.1290 58 R 0.0513 0.7902 0.1585 59 I 0.0823 0.6879 0.2298 60 A 0.1444 0.4416 0.4140 61 T 0.1173 0.3056 0.5771 62 G 0.0573 0.4904 0.4524 63 A 0.0688 0.5597 0.3715 64 T 0.0715 0.6062 0.3223 65 A 0.0415 0.6631 0.2954 66 D 0.0484 0.5910 0.3605 67 E 0.0454 0.5760 0.3785 68 M 0.0617 0.4233 0.5150 69 A 0.0501 0.2860 0.6640 70 Q 0.0582 0.1975 0.7444 71 F 0.0582 0.1307 0.8111 72 Y 0.0552 0.1331 0.8118 73 A 0.0594 0.1655 0.7751 74 V 0.0717 0.3054 0.6230 75 P 0.0571 0.6642 0.2788 76 V 0.0558 0.7041 0.2401 77 L 0.0357 0.7783 0.1860 78 P 0.0055 0.9249 0.0696 79 E 0.0052 0.9363 0.0585 80 Q 0.0049 0.9408 0.0543 81 L 0.0051 0.9403 0.0546 82 V 0.0048 0.9493 0.0459 83 D 0.0048 0.9474 0.0478 84 R 0.0049 0.9434 0.0517 85 L 0.0049 0.9442 0.0509 86 D 0.0049 0.9459 0.0492 87 Q 0.0053 0.9366 0.0582 88 S 0.0052 0.9268 0.0680 89 W 0.0053 0.9281 0.0666 90 Q 0.0056 0.9247 0.0697 91 Y 0.0055 0.9159 0.0786 92 Y 0.0078 0.8776 0.1146 93 Q 0.0106 0.8616 0.1278 94 D 0.0105 0.8245 0.1650 95 R 0.0189 0.7480 0.2331 96 L 0.0302 0.6772 0.2926 97 M 0.0174 0.7022 0.2804 98 A 0.0273 0.6516 0.3211 99 D 0.0369 0.5961 0.3670 100 F 0.0737 0.3582 0.5681 101 S 0.0613 0.2530 0.6857 102 T 0.0996 0.1977 0.7027 103 E 0.1299 0.1279 0.7423 104 T 0.1810 0.1018 0.7172 105 T 0.2004 0.0955 0.7041 106 Y 0.2828 0.0982 0.6190 107 W 0.2746 0.1242 0.6012 108 G 0.2245 0.1145 0.6610 109 V 0.1693 0.1262 0.7045 110 T 0.1321 0.1196 0.7483 111 D 0.0827 0.2940 0.6233 112 S 0.0781 0.3753 0.5466 113 T 0.0103 0.8971 0.0926 114 T 0.0060 0.9470 0.0470 115 G 0.0059 0.9537 0.0404 116 W 0.0059 0.9550 0.0390 117 L 0.0059 0.9532 0.0408 118 L 0.0053 0.9530 0.0416 119 E 0.0054 0.9470 0.0476 120 A 0.0050 0.9510 0.0440 121 A 0.0049 0.9510 0.0441 122 V 0.0051 0.9445 0.0504 123 H 0.0055 0.9295 0.0649 124 L 0.0061 0.9260 0.0680 125 Y 0.0072 0.9105 0.0823 126 H 0.0159 0.8506 0.1335 127 H 0.0291 0.8228 0.1480 128 R 0.0065 0.9205 0.0731 129 S 0.0065 0.9346 0.0590 130 Q 0.0048 0.9539 0.0413 131 L 0.0056 0.9586 0.0357 132 L 0.0081 0.9559 0.0360 133 D 0.0106 0.9533 0.0361 134 Y 0.0124 0.9504 0.0372 135 L 0.0153 0.9432 0.0415 136 N 0.0094 0.9361 0.0545 137 L 0.0154 0.8506 0.1340 138 L 0.0478 0.4266 0.5256 139 G 0.0447 0.0602 0.8951 140 Y 0.0804 0.0324 0.8872 141 D 0.0975 0.0338 0.8687 142 I 0.0877 0.0971 0.8151 143 K 0.1081 0.1125 0.7794 144 L 0.1738 0.1011 0.7251 145 D 0.2554 0.1224 0.6222 146 L 0.1994 0.1816 0.6189 147 F 0.1854 0.1131 0.7015 148 E 0.0507 0.0439 0.9054