# This file is the result of combining several RDB files, specifically # T0425.t06.str2.rdb (weight 1.54425) # T0425.t06.str4.rdb (weight 0.924988) # T0425.t06.pb.rdb (weight 0.789901) # T0425.t06.bys.rdb (weight 0.748322) # T0425.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 T0425.t06.str2.rdb # ============================================ # TARGET T0425 # 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 T0425.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 256.974 # # ============================================ # Comments from T0425.t06.str4.rdb # ============================================ # TARGET T0425 # 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 T0425.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 256.974 # # ============================================ # Comments from T0425.t06.pb.rdb # ============================================ # TARGET T0425 # 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 T0425.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 256.974 # # ============================================ # Comments from T0425.t06.bys.rdb # ============================================ # TARGET T0425 # 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 T0425.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 256.974 # # ============================================ # Comments from T0425.t06.alpha.rdb # ============================================ # TARGET T0425 # 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 T0425.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 256.974 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2177 0.0947 0.6876 2 S 0.2999 0.0540 0.6462 3 K 0.6629 0.0159 0.3211 4 I 0.7720 0.0070 0.2210 5 I 0.8035 0.0050 0.1915 6 C 0.8056 0.0048 0.1896 7 L 0.7908 0.0066 0.2026 8 T 0.6320 0.0089 0.3591 9 A 0.2536 0.1370 0.6094 10 G 0.1543 0.1244 0.7213 11 H 0.1586 0.1367 0.7047 12 S 0.1338 0.1566 0.7096 13 N 0.1606 0.1551 0.6843 14 T 0.2357 0.1048 0.6595 15 D 0.2429 0.0483 0.7088 16 P 0.1053 0.3215 0.5731 17 G 0.1267 0.2677 0.6056 18 A 0.2522 0.2374 0.5104 19 V 0.2733 0.1842 0.5426 20 N 0.1864 0.1355 0.6780 21 G 0.1088 0.1089 0.7824 22 S 0.1560 0.1456 0.6984 23 D 0.1840 0.2481 0.5680 24 R 0.1483 0.4785 0.3732 25 E 0.0763 0.7256 0.1981 26 A 0.0444 0.8131 0.1426 27 D 0.0369 0.8383 0.1249 28 L 0.0263 0.8713 0.1024 29 A 0.0135 0.9033 0.0832 30 Q 0.0085 0.9190 0.0725 31 D 0.0083 0.9225 0.0691 32 M 0.0083 0.9209 0.0708 33 R 0.0083 0.9202 0.0714 34 N 0.0083 0.9238 0.0680 35 I 0.0083 0.9236 0.0681 36 V 0.0083 0.9233 0.0684 37 A 0.0083 0.9202 0.0715 38 S 0.0083 0.9212 0.0705 39 I 0.0085 0.9113 0.0801 40 L 0.0104 0.8838 0.1058 41 R 0.0120 0.8508 0.1372 42 N 0.0233 0.7496 0.2271 43 D 0.0511 0.4775 0.4714 44 Y 0.0728 0.1579 0.7693 45 G 0.0754 0.0734 0.8512 46 L 0.3293 0.0123 0.6584 47 T 0.6377 0.0144 0.3479 48 V 0.7612 0.0067 0.2321 49 K 0.7671 0.0099 0.2230 50 T 0.7123 0.0092 0.2786 51 D 0.4770 0.0279 0.4951 52 G 0.2744 0.0677 0.6579 53 T 0.1866 0.1003 0.7132 54 G 0.1051 0.1115 0.7834 55 K 0.1519 0.1272 0.7208 56 G 0.1732 0.1425 0.6844 57 N 0.2477 0.0916 0.6607 58 M 0.3146 0.0381 0.6473 59 P 0.1911 0.0358 0.7732 60 L 0.0355 0.6713 0.2932 61 R 0.0137 0.8306 0.1556 62 D 0.0143 0.8907 0.0950 63 A 0.0149 0.8939 0.0912 64 V 0.0149 0.8955 0.0896 65 K 0.0120 0.8840 0.1041 66 L 0.0177 0.8146 0.1677 67 I 0.0605 0.5914 0.3480 68 R 0.0661 0.2666 0.6673 69 G 0.0574 0.1128 0.8298 70 S 0.2127 0.0574 0.7299 71 D 0.2984 0.0465 0.6550 72 V 0.7275 0.0190 0.2535 73 A 0.7652 0.0093 0.2255 74 I 0.8135 0.0054 0.1812 75 E 0.8108 0.0068 0.1825 76 F 0.7489 0.0200 0.2311 77 H 0.6089 0.0578 0.3333 78 T 0.4256 0.1213 0.4531 79 N 0.2588 0.1530 0.5883 80 A 0.1599 0.3100 0.5300 81 A 0.1704 0.2531 0.5764 82 A 0.1216 0.3002 0.5782 83 N 0.1428 0.1581 0.6991 84 K 0.1057 0.2655 0.6288 85 T 0.2088 0.1676 0.6236 86 A 0.3012 0.1157 0.5831 87 T 0.3320 0.0727 0.5953 88 G 0.4957 0.0420 0.4623 89 I 0.6648 0.0175 0.3176 90 E 0.7788 0.0099 0.2113 91 A 0.8007 0.0063 0.1930 92 L 0.7892 0.0083 0.2026 93 S 0.7474 0.0109 0.2417 94 T 0.5692 0.0157 0.4151 95 P 0.2360 0.1102 0.6537 96 K 0.0890 0.2438 0.6672 97 N 0.0981 0.2041 0.6978 98 K 0.0907 0.3827 0.5267 99 R 0.0578 0.6254 0.3168 100 W 0.0370 0.7511 0.2120 101 C 0.0204 0.8545 0.1251 102 Q 0.0095 0.9048 0.0857 103 V 0.0087 0.9147 0.0766 104 L 0.0084 0.9209 0.0708 105 G 0.0083 0.9221 0.0696 106 K 0.0083 0.9237 0.0680 107 A 0.0083 0.9242 0.0676 108 V 0.0083 0.9236 0.0682 109 A 0.0084 0.9190 0.0726 110 K 0.0086 0.9098 0.0815 111 K 0.0103 0.8689 0.1209 112 T 0.0221 0.7910 0.1869 113 G 0.0232 0.7774 0.1994 114 W 0.0389 0.7347 0.2263 115 K 0.0823 0.5866 0.3311 116 L 0.1490 0.3208 0.5302 117 R 0.1678 0.2018 0.6305 118 G 0.1241 0.1811 0.6948 119 E 0.1121 0.2129 0.6750 120 D 0.1070 0.1566 0.7364 121 G 0.1613 0.0962 0.7424 122 F 0.3724 0.0416 0.5859 123 K 0.4012 0.0238 0.5750 124 P 0.3434 0.0871 0.5694 125 D 0.2095 0.1792 0.6113 126 N 0.1800 0.1404 0.6796 127 A 0.1139 0.2251 0.6610 128 G 0.0991 0.1940 0.7069 129 Q 0.2231 0.1286 0.6483 130 H 0.4635 0.0605 0.4761 131 S 0.6631 0.0560 0.2809 132 R 0.7223 0.0490 0.2287 133 L 0.6653 0.0769 0.2578 134 A 0.5309 0.1401 0.3290 135 Y 0.4038 0.1656 0.4306 136 A 0.2409 0.2084 0.5507 137 Q 0.1862 0.1453 0.6685 138 A 0.2340 0.0935 0.6725 139 G 0.2820 0.1513 0.5667 140 G 0.6171 0.0587 0.3242 141 I 0.7446 0.0297 0.2257 142 V 0.7604 0.0254 0.2142 143 F 0.7356 0.0336 0.2308 144 E 0.6768 0.0326 0.2906 145 P 0.5026 0.1172 0.3802 146 F 0.5011 0.1040 0.3949 147 F 0.5268 0.0903 0.3829 148 I 0.4535 0.0799 0.4665 149 S 0.3249 0.0823 0.5928 150 N 0.1965 0.0422 0.7613 151 D 0.0176 0.6631 0.3194 152 T 0.0137 0.8088 0.1775 153 D 0.0167 0.8679 0.1153 154 L 0.0105 0.8960 0.0935 155 A 0.0097 0.8833 0.1070 156 L 0.0131 0.8394 0.1475 157 F 0.0448 0.7170 0.2382 158 K 0.0707 0.5407 0.3886 159 T 0.1131 0.3293 0.5576 160 T 0.0407 0.4789 0.4804 161 K 0.0324 0.5649 0.4028 162 W 0.0481 0.6390 0.3129 163 G 0.0418 0.7416 0.2166 164 I 0.0298 0.8352 0.1350 165 C 0.0122 0.8998 0.0880 166 R 0.0089 0.9205 0.0705 167 A 0.0088 0.9208 0.0703 168 I 0.0087 0.9224 0.0689 169 A 0.0092 0.9170 0.0738 170 D 0.0116 0.8775 0.1109 171 A 0.0251 0.8442 0.1307 172 I 0.0601 0.7937 0.1462 173 A 0.0766 0.7204 0.2030 174 M 0.0955 0.6581 0.2464 175 E 0.1143 0.5110 0.3746 176 L 0.1308 0.2933 0.5759 177 G 0.1113 0.1406 0.7481 178 A 0.1733 0.1404 0.6862 179 A 0.1999 0.1462 0.6538 180 K 0.2280 0.1326 0.6394 181 V 0.2358 0.1234 0.6408