# This file is the result of combining several RDB files, specifically # T0561.t06.str2.rdb (weight 1.54425) # T0561.t06.str4.rdb (weight 0.924988) # T0561.t06.pb.rdb (weight 0.789901) # T0561.t06.bys.rdb (weight 0.748322) # T0561.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 T0561.t06.str2.rdb # ============================================ # TARGET T0561 # 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 T0561.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 2.79724 # # ============================================ # Comments from T0561.t06.str4.rdb # ============================================ # TARGET T0561 # 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 T0561.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 2.79724 # # ============================================ # Comments from T0561.t06.pb.rdb # ============================================ # TARGET T0561 # 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 T0561.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 2.79724 # # ============================================ # Comments from T0561.t06.bys.rdb # ============================================ # TARGET T0561 # 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 T0561.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 2.79724 # # ============================================ # Comments from T0561.t06.alpha.rdb # ============================================ # TARGET T0561 # 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 T0561.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 2.79724 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 V 0.2099 0.2212 0.5688 2 E 0.1615 0.3290 0.5095 3 K 0.1259 0.5760 0.2980 4 K 0.1034 0.6571 0.2395 5 K 0.1023 0.6462 0.2514 6 Y 0.1250 0.5699 0.3051 7 L 0.1401 0.5178 0.3421 8 D 0.1033 0.5320 0.3646 9 S 0.0173 0.7993 0.1833 10 E 0.0137 0.8432 0.1431 11 F 0.0138 0.8773 0.1089 12 L 0.0144 0.8849 0.1007 13 L 0.0108 0.8805 0.1088 14 H 0.0127 0.8688 0.1184 15 C 0.0218 0.8219 0.1563 16 I 0.0412 0.7372 0.2216 17 S 0.0356 0.7813 0.1831 18 A 0.0097 0.8762 0.1141 19 Q 0.0094 0.8922 0.0983 20 L 0.0101 0.9016 0.0883 21 L 0.0093 0.9048 0.0858 22 D 0.0086 0.9126 0.0788 23 M 0.0086 0.9161 0.0753 24 W 0.0084 0.9178 0.0738 25 K 0.0085 0.9152 0.0762 26 Q 0.0092 0.8945 0.0962 27 A 0.0110 0.8773 0.1117 28 R 0.0108 0.8794 0.1098 29 A 0.0116 0.8858 0.1025 30 R 0.0122 0.8906 0.0972 31 W 0.0188 0.8849 0.0963 32 L 0.0208 0.8894 0.0898 33 E 0.0188 0.8939 0.0874 34 L 0.0260 0.8539 0.1201 35 V 0.0390 0.7840 0.1770 36 G 0.0310 0.7844 0.1846 37 K 0.0216 0.8139 0.1645 38 E 0.0192 0.8346 0.1462 39 W 0.0125 0.8858 0.1017 40 A 0.0104 0.8916 0.0980 41 H 0.0127 0.8845 0.1028 42 M 0.0212 0.8451 0.1337 43 L 0.0300 0.7895 0.1805 44 A 0.0545 0.6137 0.3319 45 L 0.1178 0.3635 0.5187 46 N 0.1639 0.1077 0.7284 47 P 0.0390 0.4586 0.5023 48 E 0.0578 0.4012 0.5411 49 R 0.1413 0.3522 0.5065 50 K 0.1843 0.3535 0.4621 51 D 0.2775 0.2889 0.4337 52 F 0.4157 0.2034 0.3809 53 L 0.4332 0.2048 0.3620 54 W 0.3733 0.2070 0.4197 55 K 0.2356 0.2438 0.5206 56 N 0.1836 0.1371 0.6793 57 Q 0.1144 0.3233 0.5622 58 S 0.1138 0.4626 0.4236 59 E 0.0497 0.6280 0.3223 60 M 0.0669 0.6175 0.3156 61 N 0.0762 0.6104 0.3134 62 S 0.0773 0.6975 0.2252 63 A 0.0904 0.7161 0.1936 64 F 0.0915 0.7443 0.1641 65 F 0.0722 0.7874 0.1404 66 D 0.0557 0.7720 0.1723 67 L 0.0176 0.8386 0.1438 68 C 0.0124 0.8711 0.1165 69 E 0.0092 0.9091 0.0816 70 V 0.0087 0.9087 0.0826 71 G 0.0085 0.9173 0.0741 72 K 0.0083 0.9177 0.0739 73 Q 0.0087 0.9142 0.0771 74 V 0.0125 0.8962 0.0912 75 M 0.0275 0.8506 0.1220 76 L 0.0448 0.7257 0.2295 77 G 0.0624 0.5785 0.3591 78 L 0.0977 0.5321 0.3702 79 L 0.1246 0.3017 0.5737 80 G 0.1031 0.1541 0.7428 81 K 0.1739 0.1670 0.6591 82 E 0.2542 0.1755 0.5703 83 V 0.2998 0.1340 0.5662 84 A 0.2630 0.0885 0.6484 85 L 0.2402 0.0450 0.7148 86 P 0.1584 0.1390 0.7025 87 K 0.0463 0.5936 0.3602 88 E 0.0386 0.7275 0.2340 89 E 0.0415 0.7692 0.1894 90 Q 0.0452 0.8003 0.1545 91 A 0.0405 0.8240 0.1355 92 F 0.0464 0.8482 0.1054 93 W 0.0516 0.8578 0.0906 94 I 0.0411 0.8747 0.0842 95 M 0.0287 0.8885 0.0828 96 Y 0.0287 0.8840 0.0873 97 A 0.0309 0.8691 0.1000 98 V 0.0400 0.8273 0.1327 99 H 0.0593 0.7554 0.1853 100 L 0.0352 0.7687 0.1962 101 S 0.0261 0.7655 0.2083 102 A 0.0163 0.8116 0.1721 103 A 0.0250 0.8166 0.1583 104 C 0.0337 0.8117 0.1547 105 A 0.0171 0.8596 0.1233 106 E 0.0178 0.8403 0.1419 107 E 0.0271 0.7826 0.1903 108 L 0.0604 0.6472 0.2924 109 H 0.0722 0.4623 0.4655 110 M 0.1452 0.3915 0.4633 111 E 0.1228 0.4671 0.4102 112 V 0.1212 0.5076 0.3713 113 A 0.1639 0.4786 0.3574 114 M 0.1764 0.4852 0.3384 115 S 0.2210 0.4203 0.3587 116 L 0.2249 0.4745 0.3006 117 R 0.2467 0.4320 0.3213 118 K 0.3909 0.2812 0.3279 119 L 0.4297 0.1576 0.4127 120 N 0.4455 0.0865 0.4680 121 V 0.5946 0.0351 0.3703 122 K 0.5801 0.0449 0.3750 123 L 0.5083 0.0813 0.4104 124 K 0.3534 0.1687 0.4780 125 D 0.3314 0.1286 0.5400 126 F 0.3499 0.1219 0.5282 127 N 0.3374 0.1406 0.5220 128 F 0.2501 0.1746 0.5753 129 G 0.1958 0.1466 0.6576 130 G 0.2408 0.2112 0.5480 131 T 0.2750 0.3314 0.3937 132 R 0.2726 0.4214 0.3060 133 Y 0.2547 0.3887 0.3566 134 F 0.1855 0.4173 0.3972 135 K 0.1071 0.3896 0.5032 136 D 0.0937 0.1979 0.7084 137 M 0.2095 0.0384 0.7521 138 P 0.1637 0.0292 0.8071 139 P 0.0527 0.5518 0.3956 140 E 0.0201 0.7614 0.2185 141 E 0.0315 0.8181 0.1504 142 K 0.0382 0.8152 0.1466 143 K 0.0473 0.8126 0.1401 144 R 0.0545 0.8103 0.1351 145 R 0.0528 0.8119 0.1353 146 M 0.0350 0.8396 0.1254 147 E 0.0376 0.8318 0.1306 148 R 0.0358 0.8295 0.1347 149 K 0.0319 0.8321 0.1360 150 Q 0.0355 0.8430 0.1215 151 R 0.0336 0.8414 0.1250 152 I 0.0160 0.8859 0.0981 153 E 0.0108 0.9017 0.0875 154 E 0.0119 0.9012 0.0869 155 A 0.0206 0.8650 0.1145 156 R 0.0278 0.8149 0.1572 157 R 0.0431 0.6613 0.2956 158 H 0.0724 0.3689 0.5587 159 G 0.0956 0.1467 0.7576 160 M 0.1777 0.0644 0.7579 161 P 0.1532 0.1262 0.7206