# This file is the result of combining several RDB files, specifically # T0465.t06.str2.rdb (weight 1.54425) # T0465.t06.str4.rdb (weight 0.924988) # T0465.t06.pb.rdb (weight 0.789901) # T0465.t06.bys.rdb (weight 0.748322) # T0465.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 T0465.t06.str2.rdb # ============================================ # TARGET T0465 # 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 T0465.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 35.5806 # # ============================================ # Comments from T0465.t06.str4.rdb # ============================================ # TARGET T0465 # 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 T0465.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 35.5806 # # ============================================ # Comments from T0465.t06.pb.rdb # ============================================ # TARGET T0465 # 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 T0465.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 35.5806 # # ============================================ # Comments from T0465.t06.bys.rdb # ============================================ # TARGET T0465 # 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 T0465.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 35.5806 # # ============================================ # Comments from T0465.t06.alpha.rdb # ============================================ # TARGET T0465 # 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 T0465.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 35.5806 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2348 0.2650 0.5002 2 S 0.1842 0.3556 0.4602 3 E 0.1452 0.4450 0.4098 4 N 0.1365 0.3933 0.4702 5 Q 0.1186 0.3900 0.4913 6 N 0.1083 0.4426 0.4491 7 E 0.1471 0.4228 0.4300 8 K 0.1764 0.3764 0.4472 9 V 0.2365 0.3066 0.4569 10 Y 0.2423 0.2609 0.4968 11 D 0.2313 0.1964 0.5723 12 L 0.0665 0.6245 0.3090 13 S 0.0360 0.7538 0.2103 14 F 0.0388 0.7347 0.2265 15 F 0.0655 0.5671 0.3674 16 M 0.1353 0.3251 0.5396 17 P 0.0620 0.4621 0.4758 18 G 0.0410 0.3501 0.6089 19 Q 0.0902 0.3340 0.5758 20 T 0.1643 0.3221 0.5136 21 I 0.2007 0.3020 0.4973 22 D 0.2203 0.2596 0.5201 23 A 0.1929 0.3801 0.4271 24 E 0.2175 0.3197 0.4628 25 E 0.3299 0.2311 0.4390 26 V 0.4550 0.1004 0.4445 27 E 0.4699 0.0607 0.4694 28 V 0.4672 0.0250 0.5078 29 P 0.4038 0.0413 0.5549 30 I 0.4024 0.1447 0.4530 31 S 0.4185 0.1847 0.3968 32 K 0.5049 0.1703 0.3248 33 R 0.5579 0.1461 0.2960 34 F 0.6324 0.0944 0.2732 35 V 0.6088 0.0892 0.3020 36 D 0.3974 0.1104 0.4922 37 K 0.1455 0.3556 0.4989 38 E 0.0848 0.1858 0.7294 39 G 0.0706 0.0809 0.8486 40 N 0.2910 0.0378 0.6713 41 V 0.5211 0.0211 0.4578 42 V 0.5522 0.0162 0.4316 43 P 0.6355 0.0159 0.3486 44 F 0.7629 0.0116 0.2255 45 I 0.7864 0.0078 0.2058 46 F 0.7301 0.0108 0.2592 47 K 0.6269 0.0328 0.3403 48 A 0.4514 0.0510 0.4976 49 I 0.3765 0.0782 0.5453 50 T 0.2387 0.0413 0.7200 51 T 0.0391 0.6195 0.3414 52 D 0.0290 0.7399 0.2310 53 R 0.0422 0.7647 0.1931 54 I 0.0166 0.8513 0.1321 55 D 0.0091 0.9075 0.0834 56 E 0.0093 0.9129 0.0779 57 L 0.0153 0.8957 0.0889 58 E 0.0159 0.8865 0.0976 59 K 0.0213 0.8311 0.1477 60 E 0.0433 0.6434 0.3133 61 N 0.0928 0.3462 0.5610 62 T 0.1994 0.2288 0.5719 63 T 0.4023 0.1479 0.4498 64 Y 0.5134 0.1163 0.3703 65 K 0.5570 0.1206 0.3224 66 N 0.5276 0.1102 0.3622 67 V 0.3920 0.1187 0.4893 68 K 0.1819 0.1488 0.6693 69 G 0.0906 0.1257 0.7837 70 R 0.1765 0.1086 0.7149 71 G 0.2476 0.0886 0.6638 72 R 0.3954 0.0910 0.5135 73 V 0.4676 0.1340 0.3984 74 K 0.3793 0.2421 0.3785 75 E 0.3840 0.2124 0.4035 76 L 0.3459 0.1570 0.4972 77 D 0.2000 0.1238 0.6762 78 S 0.0316 0.6769 0.2915 79 Q 0.0153 0.8094 0.1753 80 R 0.0166 0.8645 0.1189 81 F 0.0175 0.8850 0.0975 82 Y 0.0161 0.8988 0.0851 83 A 0.0132 0.9071 0.0796 84 R 0.0201 0.8958 0.0841 85 I 0.0526 0.8519 0.0955 86 A 0.0985 0.7881 0.1134 87 V 0.1632 0.6720 0.1648 88 E 0.2330 0.5088 0.2582 89 T 0.2811 0.3442 0.3747 90 T 0.4019 0.1923 0.4059 91 V 0.4133 0.1421 0.4446 92 Y 0.3183 0.0599 0.6218 93 P 0.1458 0.2649 0.5893 94 T 0.1058 0.2669 0.6273 95 F 0.0955 0.2810 0.6234 96 K 0.0962 0.2698 0.6339 97 A 0.1105 0.4423 0.4472 98 K 0.0120 0.8034 0.1846 99 E 0.0102 0.8865 0.1034 100 L 0.0135 0.8929 0.0936 101 R 0.0112 0.8972 0.0916 102 E 0.0125 0.8647 0.1228 103 A 0.0212 0.7025 0.2763 104 Y 0.0640 0.2952 0.6408 105 K 0.0614 0.1484 0.7901 106 T 0.1725 0.0890 0.7385 107 E 0.1532 0.1017 0.7451 108 D 0.1703 0.0316 0.7982 109 P 0.0132 0.7438 0.2430 110 V 0.0092 0.8661 0.1247 111 E 0.0084 0.9204 0.0712 112 V 0.0085 0.9197 0.0718 113 A 0.0092 0.9078 0.0829 114 K 0.0088 0.9001 0.0911 115 R 0.0118 0.8737 0.1145 116 V 0.0456 0.7069 0.2475 117 L 0.0982 0.5226 0.3792 118 S 0.1278 0.3078 0.5644 119 V 0.0803 0.3628 0.5568 120 G 0.0637 0.2874 0.6489 121 G 0.0762 0.2430 0.6808 122 E 0.1247 0.4581 0.4172 123 Y 0.0810 0.6958 0.2232 124 A 0.0300 0.8201 0.1498 125 N 0.0204 0.8591 0.1205 126 W 0.0126 0.8900 0.0974 127 L 0.0104 0.8974 0.0923 128 N 0.0099 0.8993 0.0908 129 K 0.0117 0.8936 0.0948 130 A 0.0200 0.8785 0.1015 131 I 0.0310 0.8116 0.1574 132 E 0.0731 0.7252 0.2017 133 I 0.1409 0.5217 0.3374 134 N 0.1370 0.2505 0.6124 135 G 0.0928 0.1283 0.7789 136 F 0.1599 0.1383 0.7018 137 D 0.1468 0.1658 0.6873 138 D 0.0644 0.3405 0.5951 139 D 0.1013 0.3058 0.5929 140 L 0.0278 0.7172 0.2550 141 E 0.0143 0.8473 0.1385 142 D 0.0159 0.8871 0.0970 143 L 0.0150 0.8993 0.0857 144 E 0.0091 0.9161 0.0747 145 E 0.0090 0.9185 0.0725 146 A 0.0101 0.9128 0.0771 147 A 0.0168 0.8868 0.0964 148 K 0.0206 0.8158 0.1636 149 N 0.0436 0.5997 0.3567 150 L 0.0641 0.4425 0.4935 151 E 0.0821 0.3388 0.5790 152 H 0.1015 0.2531 0.6454 153 H 0.1061 0.2240 0.6699 154 H 0.1221 0.2173 0.6606 155 H 0.1519 0.1960 0.6521 156 H 0.1579 0.1862 0.6559 157 H 0.1824 0.1642 0.6535