# This file is the result of combining several RDB files, specifically # T0634.t04.dssp-ebghstl.rdb (weight 1.53986) # T0634.t04.stride-ebghtl.rdb (weight 1.24869) # T0634.t04.str2.rdb (weight 1.54758) # T0634.t04.alpha.rdb (weight 0.659012) # T0634.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0634.t2k.stride-ebghtl.rdb (weight 1.24869) # T0634.t2k.str2.rdb (weight 1.54758) # T0634.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 T0634.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0634 # 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 T0634.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 13.1379 # # ============================================ # Comments from T0634.t04.stride-ebghtl.rdb # ============================================ # TARGET T0634 # 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 T0634.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 13.1379 # # ============================================ # Comments from T0634.t04.str2.rdb # ============================================ # TARGET T0634 # 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 T0634.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 13.1379 # # ============================================ # Comments from T0634.t04.alpha.rdb # ============================================ # TARGET T0634 # 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 T0634.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 13.1379 # # ============================================ # Comments from T0634.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0634 # 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 T0634.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 5985 # # ============================================ # Comments from T0634.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0634 # 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 T0634.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 5985 # # ============================================ # Comments from T0634.t2k.str2.rdb # ============================================ # TARGET T0634 # 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 T0634.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 5985 # # ============================================ # Comments from T0634.t2k.alpha.rdb # ============================================ # TARGET T0634 # 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 T0634.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 5985 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0701 0.0351 0.8948 2 S 0.1216 0.0311 0.8473 3 L 0.1668 0.0346 0.7986 4 K 0.4548 0.0218 0.5233 5 K 0.8833 0.0038 0.1128 6 I 0.9171 0.0039 0.0790 7 L 0.9197 0.0040 0.0763 8 I 0.8482 0.0146 0.1373 9 I 0.4609 0.0101 0.5290 10 D 0.0915 0.0217 0.8868 11 Q 0.0469 0.1597 0.7934 12 Q 0.0066 0.8821 0.1114 13 D 0.0059 0.9209 0.0733 14 F 0.0050 0.9430 0.0519 15 S 0.0047 0.9562 0.0390 16 R 0.0048 0.9558 0.0394 17 I 0.0047 0.9578 0.0374 18 E 0.0050 0.9547 0.0403 19 L 0.0048 0.9553 0.0399 20 K 0.0048 0.9544 0.0408 21 N 0.0049 0.9494 0.0457 22 F 0.0060 0.9326 0.0614 23 L 0.0068 0.8887 0.1046 24 D 0.0113 0.7463 0.2424 25 S 0.0415 0.2931 0.6654 26 E 0.0427 0.0243 0.9331 27 Y 0.2256 0.0097 0.7647 28 L 0.7722 0.0052 0.2226 29 V 0.8995 0.0030 0.0975 30 I 0.8810 0.0080 0.1110 31 E 0.8549 0.0042 0.1409 32 S 0.5577 0.0152 0.4271 33 K 0.1605 0.0465 0.7930 34 N 0.0788 0.0280 0.8932 35 E 0.0141 0.6737 0.3122 36 K 0.0068 0.9288 0.0644 37 E 0.0051 0.9505 0.0444 38 A 0.0047 0.9551 0.0401 39 L 0.0048 0.9550 0.0401 40 E 0.0048 0.9508 0.0444 41 Q 0.0049 0.9485 0.0466 42 I 0.0053 0.9379 0.0567 43 D 0.0058 0.9105 0.0837 44 H 0.0096 0.7391 0.2513 45 H 0.0388 0.4193 0.5420 46 H 0.0759 0.0413 0.8827 47 P 0.0856 0.0202 0.8942 48 D 0.1206 0.0479 0.8315 49 L 0.9157 0.0050 0.0793 50 V 0.9297 0.0040 0.0663 51 I 0.9256 0.0040 0.0704 52 L 0.8927 0.0100 0.0973 53 D 0.6762 0.0202 0.3036 54 M 0.3455 0.0848 0.5697 55 D 0.2203 0.0934 0.6863 56 I 0.1490 0.0732 0.7778 57 I 0.0548 0.1162 0.8290 58 G 0.0507 0.0815 0.8678 59 E 0.0512 0.1097 0.8391 60 N 0.0593 0.1179 0.8228 61 S 0.0262 0.6680 0.3058 62 P 0.0069 0.9349 0.0581 63 N 0.0065 0.9518 0.0418 64 L 0.0054 0.9540 0.0407 65 C 0.0057 0.9536 0.0407 66 L 0.0065 0.9486 0.0450 67 K 0.0064 0.9393 0.0542 68 L 0.0110 0.9093 0.0797 69 K 0.0143 0.8151 0.1706 70 R 0.0186 0.6469 0.3345 71 S 0.0601 0.2345 0.7055 72 K 0.0163 0.2444 0.7393 73 G 0.0238 0.2209 0.7553 74 L 0.0689 0.2413 0.6898 75 K 0.0508 0.1960 0.7532 76 N 0.0867 0.0831 0.8302 77 V 0.1945 0.0126 0.7929 78 P 0.4740 0.0060 0.5199 79 L 0.9184 0.0033 0.0784 80 I 0.9287 0.0034 0.0679 81 L 0.9242 0.0039 0.0720 82 L 0.8871 0.0066 0.1063 83 F 0.6479 0.0169 0.3352 84 S 0.3334 0.0536 0.6130 85 S 0.1131 0.1225 0.7644 86 E 0.0670 0.1084 0.8246 87 H 0.0612 0.1586 0.7802 88 K 0.0109 0.8780 0.1111 89 E 0.0063 0.9204 0.0733 90 A 0.0066 0.9333 0.0601 91 I 0.0076 0.9429 0.0494 92 V 0.0119 0.9339 0.0542 93 N 0.0125 0.9127 0.0748 94 G 0.0095 0.9059 0.0846 95 L 0.0168 0.8817 0.1016 96 H 0.0343 0.7613 0.2044 97 S 0.0554 0.3834 0.5612 98 G 0.0771 0.0652 0.8577 99 A 0.1001 0.0722 0.8278 100 D 0.0984 0.1343 0.7673 101 D 0.3869 0.1565 0.4566 102 Y 0.5475 0.1097 0.3427 103 L 0.6031 0.0778 0.3191 104 T 0.4200 0.0432 0.5368 105 K 0.1674 0.0435 0.7891 106 P 0.1482 0.0318 0.8200 107 F 0.1257 0.0275 0.8468 108 N 0.0798 0.0327 0.8875 109 R 0.0053 0.9200 0.0747 110 N 0.0049 0.9509 0.0442 111 D 0.0048 0.9558 0.0394 112 L 0.0047 0.9600 0.0354 113 L 0.0047 0.9593 0.0360 114 S 0.0047 0.9599 0.0354 115 R 0.0047 0.9601 0.0353 116 I 0.0047 0.9607 0.0346 117 E 0.0047 0.9607 0.0346 118 I 0.0047 0.9596 0.0357 119 H 0.0047 0.9576 0.0377 120 L 0.0048 0.9520 0.0432 121 R 0.0052 0.9204 0.0743 122 T 0.0062 0.8778 0.1160 123 Q 0.0092 0.8395 0.1513 124 N 0.0106 0.7613 0.2282 125 Y 0.0107 0.7499 0.2394 126 Y 0.0127 0.7958 0.1915 127 S 0.0108 0.8142 0.1750 128 D 0.0130 0.8214 0.1656 129 L 0.0168 0.7977 0.1854 130 R 0.0236 0.7635 0.2129 131 K 0.0227 0.6960 0.2814 132 N 0.0341 0.4776 0.4883 133 E 0.0527 0.2879 0.6594 134 G 0.0519 0.2085 0.7396 135 H 0.1171 0.2064 0.6765 136 H 0.2073 0.1867 0.6060 137 H 0.2277 0.1722 0.6001 138 H 0.1955 0.1258 0.6787 139 H 0.1381 0.0810 0.7809 140 H 0.0554 0.0376 0.9070