# This file is the result of combining several RDB files, specifically # T0357.t06.dssp-ebghstl.rdb (weight 1.53986) # T0357.t06.stride-ebghtl.rdb (weight 1.24869) # T0357.t06.str2.rdb (weight 1.54758) # T0357.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 T0357.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0357 # 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 T0357.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 15.1717 # # ============================================ # Comments from T0357.t06.stride-ebghtl.rdb # ============================================ # TARGET T0357 # 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 T0357.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 15.1717 # # ============================================ # Comments from T0357.t06.str2.rdb # ============================================ # TARGET T0357 # 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 T0357.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 15.1717 # # ============================================ # Comments from T0357.t06.alpha.rdb # ============================================ # TARGET T0357 # 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 T0357.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 15.1717 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1097 0.0370 0.8533 2 V 0.3214 0.0261 0.6525 3 K 0.6173 0.0323 0.3504 4 F 0.7155 0.0313 0.2532 5 A 0.6968 0.0317 0.2715 6 C 0.7140 0.0311 0.2550 7 R 0.7664 0.0443 0.1892 8 A 0.8107 0.0415 0.1478 9 I 0.7680 0.0539 0.1781 10 T 0.7090 0.0465 0.2446 11 R 0.3296 0.0780 0.5924 12 G 0.2310 0.0568 0.7122 13 R 0.6342 0.0449 0.3209 14 A 0.8170 0.0238 0.1592 15 E 0.8022 0.0286 0.1692 16 G 0.8225 0.0109 0.1666 17 E 0.8470 0.0209 0.1321 18 A 0.8965 0.0141 0.0895 19 L 0.8889 0.0154 0.0956 20 V 0.8432 0.0231 0.1337 21 T 0.6342 0.0337 0.3321 22 K 0.2799 0.0936 0.6265 23 E 0.2645 0.1207 0.6148 24 Y 0.3417 0.1470 0.5112 25 I 0.4504 0.1431 0.4065 26 S 0.4547 0.1435 0.4019 27 F 0.3445 0.2465 0.4090 28 L 0.2442 0.2244 0.5314 29 G 0.1814 0.1089 0.7098 30 G 0.2839 0.0616 0.6545 31 I 0.4921 0.0218 0.4862 32 D 0.2144 0.0158 0.7697 33 K 0.0123 0.2113 0.7764 34 E 0.0161 0.1668 0.8171 35 T 0.1042 0.1967 0.6991 36 G 0.2208 0.0555 0.7237 37 I 0.5426 0.0219 0.4355 38 V 0.6842 0.0169 0.2989 39 K 0.3358 0.0210 0.6432 40 E 0.0435 0.1463 0.8103 41 D 0.0457 0.1028 0.8515 42 C 0.1328 0.0633 0.8039 43 E 0.0947 0.2013 0.7041 44 I 0.1425 0.2382 0.6194 45 K 0.1071 0.1899 0.7030 46 G 0.1181 0.0889 0.7930 47 E 0.3859 0.0450 0.5691 48 S 0.5880 0.0406 0.3714 49 V 0.4789 0.0979 0.4231 50 A 0.2037 0.0789 0.7174 51 G 0.1789 0.0426 0.7785 52 R 0.6524 0.0113 0.3363 53 I 0.9113 0.0034 0.0853 54 L 0.9210 0.0035 0.0755 55 V 0.8985 0.0042 0.0973 56 F 0.6296 0.0075 0.3629 57 P 0.2231 0.0441 0.7327 58 G 0.0899 0.0475 0.8627 59 G 0.1479 0.0491 0.8029 60 K 0.1646 0.0700 0.7654 61 G 0.1580 0.0661 0.7758 62 S 0.1270 0.1150 0.7580 63 T 0.1275 0.1885 0.6840 64 V 0.0605 0.4987 0.4408 65 G 0.0249 0.7603 0.2148 66 S 0.0075 0.9282 0.0643 67 Y 0.0081 0.9480 0.0439 68 V 0.0102 0.9507 0.0391 69 L 0.0080 0.9528 0.0392 70 L 0.0073 0.9505 0.0422 71 N 0.0076 0.9453 0.0471 72 L 0.0089 0.9364 0.0547 73 R 0.0081 0.9218 0.0701 74 K 0.0130 0.8139 0.1731 75 N 0.0471 0.2369 0.7160 76 G 0.0378 0.0382 0.9240 77 V 0.1050 0.0341 0.8609 78 A 0.1990 0.0357 0.7653 79 P 0.2061 0.1458 0.6480 80 K 0.4285 0.2154 0.3561 81 A 0.6844 0.1565 0.1592 82 I 0.7842 0.1184 0.0974 83 I 0.7804 0.0971 0.1225 84 N 0.6286 0.0892 0.2823 85 K 0.3263 0.1367 0.5370 86 K 0.2042 0.1324 0.6634 87 T 0.1470 0.1864 0.6666 88 E 0.1695 0.1837 0.6468 89 T 0.3643 0.1515 0.4842 90 I 0.7179 0.1080 0.1741 91 I 0.8283 0.0586 0.1131 92 A 0.8344 0.0537 0.1119 93 V 0.7375 0.1156 0.1469 94 G 0.7079 0.0974 0.1947 95 A 0.7567 0.1093 0.1341 96 A 0.8133 0.0819 0.1048 97 M 0.7795 0.0802 0.1403 98 A 0.5806 0.0644 0.3550 99 E 0.3265 0.0662 0.6073 100 I 0.2939 0.0144 0.6917 101 P 0.3516 0.0169 0.6315 102 L 0.7073 0.0339 0.2587 103 V 0.7890 0.0261 0.1848 104 E 0.7668 0.0267 0.2065 105 V 0.4993 0.0475 0.4532 106 R 0.2217 0.0524 0.7259 107 D 0.1103 0.1447 0.7450 108 E 0.0144 0.8413 0.1443 109 K 0.0194 0.8607 0.1200 110 F 0.0104 0.9139 0.0757 111 F 0.0192 0.9057 0.0751 112 E 0.0347 0.8798 0.0855 113 A 0.0425 0.8603 0.0971 114 V 0.0704 0.7385 0.1911 115 K 0.0742 0.5161 0.4097 116 T 0.0576 0.1548 0.7875 117 G 0.0377 0.0328 0.9295 118 D 0.1091 0.0265 0.8644 119 R 0.7160 0.0085 0.2755 120 V 0.8912 0.0039 0.1050 121 V 0.9134 0.0039 0.0827 122 V 0.8889 0.0045 0.1066 123 N 0.6444 0.0077 0.3479 124 A 0.1313 0.0902 0.7785 125 D 0.0459 0.1244 0.8297 126 E 0.0839 0.1147 0.8014 127 G 0.2788 0.0538 0.6674 128 Y 0.7396 0.0312 0.2292 129 V 0.8546 0.0154 0.1299 130 E 0.8630 0.0191 0.1179 131 L 0.8532 0.0317 0.1151 132 I 0.7306 0.0511 0.2183 133 E 0.6186 0.0630 0.3183 134 L 0.3556 0.1612 0.4832 135 E 0.2226 0.1747 0.6026 136 H 0.1560 0.2154 0.6286 137 H 0.1413 0.1657 0.6930 138 H 0.1082 0.1359 0.7559 139 H 0.0814 0.1294 0.7892 140 H 0.0587 0.0778 0.8634 141 H 0.0441 0.0338 0.9221