# This file is the result of combining several RDB files, specifically # T0493.t06.str2.rdb (weight 1.54425) # T0493.t06.str4.rdb (weight 0.924988) # T0493.t06.pb.rdb (weight 0.789901) # T0493.t06.bys.rdb (weight 0.748322) # T0493.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 T0493.t06.str2.rdb # ============================================ # TARGET T0493 # 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 T0493.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 3116 # # ============================================ # Comments from T0493.t06.str4.rdb # ============================================ # TARGET T0493 # 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 T0493.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 3116 # # ============================================ # Comments from T0493.t06.pb.rdb # ============================================ # TARGET T0493 # 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 T0493.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 3116 # # ============================================ # Comments from T0493.t06.bys.rdb # ============================================ # TARGET T0493 # 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 T0493.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 3116 # # ============================================ # Comments from T0493.t06.alpha.rdb # ============================================ # TARGET T0493 # 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 T0493.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 3116 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1655 0.1797 0.6548 2 N 0.1557 0.1253 0.7190 3 A 0.2056 0.2494 0.5450 4 S 0.2567 0.2360 0.5073 5 Y 0.3023 0.2181 0.4797 6 R 0.3096 0.1707 0.5197 7 S 0.2207 0.1633 0.6161 8 T 0.0849 0.4843 0.4308 9 Q 0.0212 0.7654 0.2135 10 Q 0.0151 0.8632 0.1217 11 I 0.0123 0.8984 0.0893 12 T 0.0090 0.9109 0.0801 13 D 0.0086 0.9126 0.0788 14 F 0.0088 0.9134 0.0778 15 T 0.0087 0.9138 0.0775 16 K 0.0086 0.9133 0.0781 17 E 0.0090 0.9083 0.0827 18 I 0.0143 0.8837 0.1020 19 L 0.0239 0.8345 0.1416 20 V 0.0380 0.6698 0.2923 21 N 0.0489 0.3468 0.6043 22 G 0.0733 0.1484 0.7783 23 E 0.1505 0.1472 0.7023 24 A 0.2199 0.1260 0.6541 25 V 0.2673 0.1179 0.6148 26 T 0.3159 0.1130 0.5710 27 A 0.3313 0.1527 0.5160 28 F 0.3024 0.1849 0.5127 29 D 0.2227 0.1530 0.6244 30 R 0.1359 0.2750 0.5890 31 Q 0.1059 0.1718 0.7223 32 G 0.0947 0.0965 0.8088 33 D 0.2172 0.0488 0.7340 34 L 0.3307 0.0305 0.6388 35 P 0.3968 0.0438 0.5594 36 N 0.6604 0.0288 0.3107 37 V 0.7344 0.0158 0.2498 38 V 0.7239 0.0184 0.2576 39 V 0.6462 0.0216 0.3322 40 T 0.3573 0.0211 0.6216 41 P 0.1207 0.2214 0.6579 42 N 0.1282 0.1922 0.6796 43 F 0.0474 0.5895 0.3631 44 E 0.0247 0.7535 0.2218 45 A 0.0199 0.8213 0.1588 46 G 0.0179 0.8489 0.1332 47 V 0.0111 0.8988 0.0900 48 D 0.0087 0.9149 0.0765 49 Q 0.0083 0.9233 0.0684 50 V 0.0083 0.9229 0.0688 51 V 0.0084 0.9205 0.0712 52 D 0.0083 0.9223 0.0694 53 Q 0.0085 0.9191 0.0725 54 L 0.0100 0.9093 0.0808 55 A 0.0110 0.8712 0.1178 56 M 0.0225 0.6899 0.2875 57 N 0.0647 0.3134 0.6219 58 D 0.0631 0.1373 0.7995 59 S 0.1452 0.1008 0.7540 60 E 0.1615 0.1055 0.7331 61 R 0.1168 0.2839 0.5993 62 D 0.1276 0.2382 0.6341 63 T 0.3312 0.1097 0.5591 64 T 0.6541 0.0282 0.3177 65 A 0.7766 0.0125 0.2109 66 I 0.7968 0.0091 0.1941 67 I 0.7654 0.0139 0.2208 68 G 0.5929 0.0277 0.3795 69 K 0.3232 0.1416 0.5352 70 S 0.1737 0.2025 0.6237 71 L 0.0450 0.5738 0.3812 72 A 0.0176 0.7406 0.2418 73 E 0.0165 0.8183 0.1652 74 C 0.0102 0.8887 0.1010 75 E 0.0085 0.9136 0.0779 76 A 0.0083 0.9213 0.0704 77 L 0.0084 0.9205 0.0711 78 T 0.0083 0.9209 0.0707 79 K 0.0083 0.9237 0.0681 80 A 0.0083 0.9224 0.0692 81 L 0.0084 0.9186 0.0730 82 K 0.0086 0.9079 0.0835 83 A 0.0120 0.8085 0.1795 84 R 0.0567 0.3066 0.6367 85 G 0.0476 0.0735 0.8789 86 E 0.1661 0.0302 0.8037 87 Q 0.2669 0.0819 0.6512 88 V 0.4603 0.0716 0.4682 89 T 0.5834 0.0744 0.3421 90 L 0.5762 0.0890 0.3347 91 I 0.4702 0.1193 0.4105 92 Q 0.3034 0.1312 0.5654 93 T 0.2142 0.1779 0.6078 94 E 0.1580 0.3330 0.5090 95 N 0.1661 0.3241 0.5098 96 Q 0.1842 0.3376 0.4783 97 R 0.2417 0.2463 0.5121 98 L 0.2425 0.1774 0.5801 99 A 0.2393 0.0759 0.6848 100 P 0.1743 0.1627 0.6630 101 G 0.2420 0.0928 0.6652 102 V 0.6058 0.0162 0.3781 103 I 0.7061 0.0153 0.2785 104 V 0.7487 0.0142 0.2372 105 V 0.6688 0.0228 0.3084 106 P 0.5234 0.0558 0.4208 107 S 0.3199 0.2479 0.4322 108 F 0.2240 0.4105 0.3655 109 L 0.1578 0.4949 0.3473 110 A 0.1388 0.4276 0.4337 111 K 0.1066 0.2406 0.6527 112 G 0.1286 0.1252 0.7462 113 L 0.2776 0.0913 0.6311 114 E 0.3988 0.0670 0.5343 115 F 0.4021 0.0304 0.5675 116 D 0.3951 0.0563 0.5487 117 A 0.7786 0.0096 0.2118 118 V 0.7696 0.0078 0.2226 119 I 0.7946 0.0059 0.1995 120 V 0.7532 0.0082 0.2386 121 W 0.5902 0.0302 0.3796 122 N 0.3672 0.0346 0.5982 123 A 0.1522 0.2574 0.5904 124 N 0.1171 0.2488 0.6341 125 Q 0.0975 0.3407 0.5619 126 E 0.0875 0.3652 0.5473 127 N 0.1202 0.2695 0.6102 128 Y 0.2034 0.1262 0.6704 129 Q 0.1575 0.1477 0.6948 130 R 0.1467 0.2080 0.6453 131 E 0.0458 0.6206 0.3337 132 D 0.0390 0.7068 0.2542 133 E 0.0642 0.7225 0.2133 134 R 0.0740 0.7602 0.1658 135 Q 0.0843 0.7669 0.1488 136 L 0.1214 0.7512 0.1274 137 L 0.1351 0.7424 0.1225 138 Y 0.1948 0.6840 0.1212 139 T 0.1603 0.7204 0.1193 140 I 0.1537 0.7058 0.1405 141 C 0.1449 0.6832 0.1719 142 S 0.1023 0.6876 0.2101 143 R 0.0591 0.7426 0.1983 144 A 0.0521 0.7290 0.2188 145 M 0.0678 0.7093 0.2230 146 H 0.1277 0.5603 0.3120 147 E 0.3404 0.2410 0.4187 148 L 0.6839 0.0421 0.2740 149 T 0.7704 0.0152 0.2143 150 L 0.7846 0.0104 0.2050 151 V 0.7488 0.0198 0.2314 152 A 0.6031 0.0361 0.3608 153 V 0.3265 0.0936 0.5799 154 G 0.1708 0.1274 0.7018 155 S 0.1786 0.1082 0.7132 156 L 0.1252 0.2287 0.6461 157 S 0.1414 0.3020 0.5566 158 P 0.0208 0.7169 0.2623 159 L 0.0214 0.7756 0.2031 160 L 0.0207 0.8435 0.1358 161 A 0.0142 0.8337 0.1521 162 R 0.0216 0.7321 0.2463 163 V 0.0643 0.6082 0.3275 164 N 0.0486 0.6124 0.3391 165 H 0.0294 0.7161 0.2545 166 A 0.0381 0.7172 0.2447 167 L 0.0803 0.6468 0.2729 168 Y 0.1526 0.5273 0.3201 169 T 0.2060 0.4052 0.3889 170 L 0.1907 0.3456 0.4637 171 N 0.1615 0.2662 0.5723 172 E 0.1841 0.1850 0.6308 173 A 0.1840 0.1482 0.6678 174 K 0.1650 0.1534 0.6815