# This file is the result of combining several RDB files, specifically # T0462.t06.str2.rdb (weight 1.54425) # T0462.t06.str4.rdb (weight 0.924988) # T0462.t06.pb.rdb (weight 0.789901) # T0462.t06.bys.rdb (weight 0.748322) # T0462.t06.alpha.rdb (weight 0.678173) # 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 T0462.t06.str2.rdb # ============================================ # TARGET T0462 # Using neural net dunbrack-40pc-3157-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 T0462.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 71.0371 # # ============================================ # Comments from T0462.t06.str4.rdb # ============================================ # TARGET T0462 # Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-str4-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 21 (1 str4 ) # The input amino acid frequencies were determined from # alignment T0462.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 71.0371 # # ============================================ # Comments from T0462.t06.pb.rdb # ============================================ # TARGET T0462 # Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-pb-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 16 (1 pb ) # The input amino acid frequencies were determined from # alignment T0462.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 71.0371 # # ============================================ # Comments from T0462.t06.bys.rdb # ============================================ # TARGET T0462 # Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-bys-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 Bystroff ) # The input amino acid frequencies were determined from # alignment T0462.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 71.0371 # # ============================================ # Comments from T0462.t06.alpha.rdb # ============================================ # TARGET T0462 # Using neural net dunbrack-40pc-3157-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 T0462.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 71.0371 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3799 0.0266 0.5934 2 K 0.2860 0.0247 0.6893 3 L 0.1912 0.3415 0.4673 4 S 0.1275 0.4817 0.3908 5 R 0.1788 0.3718 0.4494 6 L 0.3142 0.0845 0.6013 7 V 0.2285 0.0376 0.7339 8 P 0.1245 0.1726 0.7029 9 G 0.0503 0.1017 0.8480 10 V 0.2705 0.0221 0.7074 11 P 0.5219 0.0238 0.4543 12 A 0.7413 0.0109 0.2478 13 R 0.7916 0.0073 0.2011 14 I 0.7320 0.0064 0.2616 15 K 0.6890 0.0181 0.2930 16 R 0.7559 0.0104 0.2337 17 L 0.6862 0.0167 0.2971 18 E 0.5486 0.0353 0.4161 19 V 0.3434 0.0998 0.5569 20 S 0.1251 0.2236 0.6512 21 G 0.0472 0.4196 0.5332 22 E 0.0404 0.7202 0.2394 23 L 0.0287 0.8365 0.1348 24 H 0.0127 0.8958 0.0915 25 E 0.0092 0.9119 0.0788 26 K 0.0091 0.9099 0.0810 27 L 0.0137 0.8900 0.0962 28 V 0.0246 0.8303 0.1451 29 G 0.0396 0.6247 0.3357 30 M 0.1003 0.2612 0.6385 31 G 0.1583 0.1141 0.7276 32 F 0.3556 0.0498 0.5946 33 V 0.3215 0.0287 0.6498 34 P 0.1623 0.1279 0.7098 35 G 0.0772 0.0915 0.8313 36 E 0.3615 0.0309 0.6076 37 E 0.6482 0.0160 0.3358 38 I 0.7554 0.0096 0.2349 39 E 0.7694 0.0093 0.2213 40 I 0.7557 0.0074 0.2369 41 V 0.7508 0.0180 0.2313 42 Q 0.7521 0.0197 0.2282 43 V 0.6569 0.0377 0.3054 44 A 0.4428 0.0279 0.5293 45 P 0.2930 0.0956 0.6113 46 L 0.1349 0.1664 0.6987 47 G 0.0843 0.0896 0.8260 48 D 0.2284 0.0228 0.7487 49 P 0.4050 0.0371 0.5579 50 I 0.7029 0.0324 0.2646 51 V 0.7767 0.0089 0.2144 52 C 0.7974 0.0079 0.1947 53 K 0.7687 0.0071 0.2242 54 I 0.6515 0.0216 0.3268 55 G 0.3150 0.0529 0.6320 56 N 0.2314 0.0636 0.7051 57 R 0.5139 0.0401 0.4459 58 N 0.6762 0.0376 0.2862 59 I 0.7260 0.0380 0.2360 60 T 0.7132 0.0533 0.2335 61 L 0.6347 0.0929 0.2724 62 R 0.4101 0.1519 0.4380 63 K 0.1541 0.5097 0.3363 64 R 0.0878 0.5900 0.3221 65 E 0.0886 0.5398 0.3716 66 A 0.1758 0.4437 0.3805 67 D 0.1923 0.3494 0.4584 68 L 0.4521 0.1264 0.4215 69 I 0.6652 0.0255 0.3093 70 E 0.7057 0.0171 0.2771 71 V 0.7516 0.0111 0.2373 72 E 0.7196 0.0200 0.2604 73 V 0.6409 0.0274 0.3318 74 V 0.4597 0.0813 0.4589 75 G 0.2300 0.0693 0.7007 76 G 0.1905 0.1003 0.7093 77 E 0.2967 0.0990 0.6043 78 L 0.3968 0.0425 0.5606 79 P 0.4262 0.0841 0.4897 80 L 0.5486 0.1156 0.3358 81 I 0.6248 0.0789 0.2962 82 L 0.5829 0.0842 0.3330 83 A 0.4266 0.1200 0.4534 84 D 0.2566 0.1926 0.5508 85 D 0.1304 0.1336 0.7359 86 G 0.1253 0.0891 0.7856 87 T 0.4283 0.0547 0.5170 88 Y 0.5906 0.0380 0.3714 89 E 0.6423 0.0366 0.3211 90 I 0.6887 0.0343 0.2769 91 T 0.6340 0.0621 0.3039 92 K 0.5903 0.0815 0.3281 93 L 0.4829 0.1414 0.3757 94 N 0.2305 0.1563 0.6133 95 G 0.1455 0.1354 0.7191 96 G 0.1949 0.1489 0.6562 97 R 0.2628 0.2662 0.4711 98 R 0.2793 0.4087 0.3120 99 F 0.1990 0.5697 0.2314 100 L 0.1451 0.6897 0.1652 101 F 0.1209 0.7362 0.1429 102 R 0.1000 0.7442 0.1558 103 M 0.0883 0.7343 0.1774 104 K 0.0842 0.6906 0.2252 105 N 0.0978 0.5472 0.3550 106 L 0.2355 0.2523 0.5122 107 G 0.2680 0.1947 0.5372 108 I 0.2793 0.1494 0.5712 109 E 0.2193 0.2179 0.5628 110 S 0.1022 0.1579 0.7398 111 G 0.0592 0.0730 0.8677 112 K 0.3345 0.0186 0.6469 113 K 0.6738 0.0106 0.3156 114 I 0.7608 0.0082 0.2311 115 Q 0.7784 0.0075 0.2141 116 V 0.7453 0.0076 0.2471 117 S 0.6121 0.0279 0.3600 118 G 0.2892 0.0346 0.6763 119 R 0.2774 0.0460 0.6767 120 R 0.2844 0.1209 0.5947 121 Y 0.3929 0.1069 0.5002 122 Y 0.5852 0.0736 0.3412 123 I 0.5996 0.0801 0.3203 124 E 0.5568 0.0806 0.3626 125 G 0.4625 0.0955 0.4421 126 R 0.4194 0.1657 0.4149 127 E 0.4601 0.2453 0.2945 128 I 0.4278 0.2243 0.3479 129 D 0.3075 0.2549 0.4376 130 L 0.1852 0.3569 0.4579 131 G 0.1756 0.2949 0.5295 132 Y 0.1872 0.1958 0.6170 133 G 0.1645 0.1415 0.6940 134 E 0.1989 0.2396 0.5614 135 A 0.2525 0.2047 0.5428 136 T 0.3924 0.1286 0.4790 137 K 0.6172 0.0496 0.3331 138 I 0.7081 0.0183 0.2736 139 W 0.6969 0.0192 0.2839 140 V 0.5867 0.0269 0.3864 141 R 0.3783 0.0913 0.5303 142 R 0.3241 0.0581 0.6178 143 V 0.5067 0.0324 0.4609 144 S 0.4803 0.0334 0.4862 145 D 0.3561 0.1876 0.4563 146 A 0.2586 0.1687 0.5727 147 G 0.2027 0.2607 0.5366 148 E 0.1744 0.2893 0.5364 149 E 0.1763 0.2148 0.6089 150 S 0.1901 0.1378 0.6721 151 H 0.2751 0.0784 0.6465 152 P 0.2361 0.1420 0.6219 153 Q 0.1986 0.1770 0.6244 154 K 0.1860 0.1635 0.6505