# This file is the result of combining several RDB files, specifically # T0405.t06.str2.rdb (weight 1.54425) # T0405.t06.str4.rdb (weight 0.924988) # T0405.t06.pb.rdb (weight 0.789901) # T0405.t06.bys.rdb (weight 0.748322) # T0405.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 T0405.t06.str2.rdb # ============================================ # TARGET T0405 # 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 T0405.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 3.05259 # # ============================================ # Comments from T0405.t06.str4.rdb # ============================================ # TARGET T0405 # 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 T0405.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 3.05259 # # ============================================ # Comments from T0405.t06.pb.rdb # ============================================ # TARGET T0405 # 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 T0405.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 3.05259 # # ============================================ # Comments from T0405.t06.bys.rdb # ============================================ # TARGET T0405 # 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 T0405.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 3.05259 # # ============================================ # Comments from T0405.t06.alpha.rdb # ============================================ # TARGET T0405 # 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 T0405.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 3.05259 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1695 0.1834 0.6471 2 N 0.1301 0.2288 0.6411 3 E 0.0666 0.5147 0.4187 4 T 0.0529 0.7030 0.2440 5 E 0.0176 0.8666 0.1158 6 K 0.0142 0.8972 0.0886 7 L 0.0146 0.9091 0.0763 8 V 0.0145 0.9129 0.0726 9 A 0.0120 0.9163 0.0717 10 A 0.0113 0.9138 0.0749 11 L 0.0149 0.9016 0.0836 12 L 0.0185 0.8816 0.0998 13 E 0.0280 0.8275 0.1445 14 R 0.0441 0.7504 0.2055 15 N 0.0621 0.5449 0.3930 16 F 0.0792 0.3054 0.6154 17 G 0.0905 0.1825 0.7270 18 K 0.1792 0.2438 0.5769 19 N 0.2243 0.1773 0.5984 20 I 0.2490 0.1749 0.5761 21 G 0.2848 0.1296 0.5856 22 T 0.4033 0.1036 0.4931 23 R 0.3954 0.0878 0.5168 24 Y 0.3249 0.0426 0.6325 25 P 0.1645 0.1490 0.6865 26 G 0.0850 0.1482 0.7668 27 N 0.1304 0.2189 0.6506 28 E 0.0667 0.5670 0.3663 29 A 0.0670 0.6735 0.2595 30 A 0.0881 0.6971 0.2148 31 Q 0.1085 0.6733 0.2182 32 M 0.1642 0.5585 0.2773 33 R 0.1373 0.5210 0.3417 34 A 0.0394 0.7602 0.2004 35 E 0.0192 0.8389 0.1419 36 E 0.0236 0.8665 0.1099 37 V 0.0392 0.8124 0.1484 38 I 0.0436 0.7824 0.1741 39 G 0.0416 0.7416 0.2168 40 E 0.1166 0.6491 0.2343 41 I 0.2922 0.4581 0.2497 42 A 0.4481 0.3283 0.2237 43 I 0.5452 0.2545 0.2003 44 V 0.5010 0.2707 0.2283 45 I 0.4046 0.3096 0.2859 46 A 0.2259 0.3931 0.3810 47 P 0.0634 0.7316 0.2049 48 L 0.0333 0.8134 0.1534 49 V 0.0254 0.8481 0.1265 50 E 0.0268 0.8264 0.1468 51 K 0.0457 0.7157 0.2386 52 L 0.0816 0.4233 0.4951 53 G 0.1001 0.2159 0.6840 54 I 0.2389 0.2085 0.5526 55 E 0.2292 0.3040 0.4668 56 N 0.2099 0.3289 0.4612 57 K 0.2191 0.3304 0.4506 58 T 0.3128 0.2699 0.4173 59 V 0.3002 0.3482 0.3516 60 K 0.2207 0.4298 0.3496 61 K 0.2601 0.3546 0.3853 62 T 0.2555 0.2870 0.4575 63 I 0.2078 0.3127 0.4794 64 P 0.1220 0.5706 0.3074 65 F 0.0944 0.7409 0.1647 66 L 0.0644 0.8220 0.1137 67 Y 0.0528 0.8449 0.1023 68 E 0.0595 0.8186 0.1219 69 L 0.0638 0.7787 0.1575 70 Q 0.0825 0.6998 0.2176 71 K 0.0863 0.5976 0.3161 72 N 0.0893 0.4439 0.4668 73 Q 0.1282 0.4153 0.4565 74 F 0.2024 0.3310 0.4666 75 C 0.2438 0.2595 0.4966 76 D 0.2122 0.2331 0.5547 77 M 0.1533 0.3693 0.4774 78 S 0.1690 0.3176 0.5134 79 A 0.1814 0.2647 0.5538 80 Y 0.2615 0.1012 0.6374 81 P 0.2230 0.1049 0.6721 82 Y 0.3107 0.0636 0.6257 83 P 0.3272 0.1415 0.5313 84 L 0.6426 0.0819 0.2755 85 L 0.7487 0.0385 0.2128 86 L 0.7316 0.0307 0.2377 87 V 0.6395 0.0463 0.3142 88 N 0.3554 0.0574 0.5872 89 G 0.1937 0.0623 0.7441 90 T 0.2436 0.0786 0.6777 91 S 0.2249 0.1232 0.6519 92 T 0.1205 0.2789 0.6006 93 D 0.1330 0.2389 0.6281 94 T 0.1314 0.3864 0.4821 95 E 0.0864 0.6329 0.2807 96 K 0.1294 0.6181 0.2525 97 Y 0.1610 0.5478 0.2912 98 W 0.1736 0.5055 0.3209 99 R 0.1626 0.4203 0.4171 100 D 0.1795 0.2332 0.5872 101 L 0.2213 0.1012 0.6775 102 P 0.1948 0.1681 0.6371 103 T 0.3057 0.1355 0.5588 104 Y 0.3989 0.1338 0.4673 105 W 0.4430 0.1210 0.4360 106 T 0.3544 0.1522 0.4934 107 D 0.1923 0.2670 0.5407 108 D 0.1240 0.3205 0.5556 109 A 0.0822 0.4223 0.4954 110 N 0.1003 0.3205 0.5792 111 K 0.2382 0.2688 0.4931 112 I 0.4588 0.1454 0.3958 113 V 0.4714 0.1333 0.3953 114 L 0.2978 0.1805 0.5217 115 P 0.1080 0.6072 0.2848 116 Y 0.1369 0.6463 0.2168 117 V 0.1267 0.7258 0.1476 118 L 0.0532 0.8319 0.1149 119 E 0.0331 0.8455 0.1214 120 H 0.0356 0.8076 0.1569 121 I 0.0469 0.7796 0.1735 122 K 0.0351 0.7432 0.2217 123 N 0.0405 0.5713 0.3882 124 N 0.0424 0.5757 0.3819 125 K 0.0469 0.7278 0.2253 126 V 0.0379 0.8206 0.1415 127 R 0.0144 0.8953 0.0903 128 Q 0.0107 0.9141 0.0752 129 K 0.0100 0.9158 0.0743 130 L 0.0102 0.9140 0.0758 131 L 0.0100 0.9119 0.0781 132 A 0.0100 0.9107 0.0793 133 F 0.0126 0.9048 0.0826 134 H 0.0157 0.8983 0.0860 135 A 0.0142 0.8975 0.0882 136 W 0.0165 0.8880 0.0955 137 L 0.0305 0.8277 0.1418 138 L 0.0373 0.7215 0.2412 139 G 0.0431 0.5465 0.4104 140 E 0.0648 0.7055 0.2298 141 V 0.0853 0.7628 0.1519 142 V 0.0691 0.7884 0.1424 143 E 0.0815 0.7355 0.1830 144 M 0.0995 0.6440 0.2565 145 N 0.0721 0.6313 0.2966 146 E 0.0333 0.7440 0.2227 147 A 0.0372 0.6756 0.2872 148 L 0.0786 0.3191 0.6023 149 G 0.0866 0.1215 0.7919 150 A 0.2505 0.1282 0.6213 151 D 0.3937 0.1091 0.4972 152 F 0.6081 0.0542 0.3376 153 R 0.6844 0.0239 0.2917 154 V 0.7793 0.0116 0.2091 155 K 0.7654 0.0167 0.2179 156 L 0.7728 0.0130 0.2142 157 V 0.7577 0.0190 0.2233 158 F 0.6734 0.0296 0.2970 159 E 0.4968 0.1108 0.3923 160 S 0.3413 0.1936 0.4651 161 D 0.3146 0.1528 0.5326 162 M 0.4601 0.1291 0.4108 163 R 0.6446 0.0481 0.3073 164 I 0.7426 0.0290 0.2283 165 R 0.7430 0.0257 0.2313 166 L 0.7804 0.0139 0.2057 167 R 0.7622 0.0187 0.2191 168 V 0.7468 0.0194 0.2338 169 Y 0.6799 0.0418 0.2783 170 E 0.6523 0.0623 0.2854 171 V 0.5232 0.2028 0.2740 172 E 0.4695 0.2757 0.2548 173 Q 0.6141 0.1685 0.2174 174 I 0.5899 0.1691 0.2411 175 A 0.7039 0.0812 0.2149 176 I 0.7418 0.0528 0.2055 177 E 0.7539 0.0421 0.2040 178 V 0.7628 0.0287 0.2085 179 H 0.7067 0.0525 0.2408 180 F 0.6347 0.0683 0.2970 181 L 0.4718 0.1023 0.4259 182 D 0.2841 0.1228 0.5931 183 N 0.1316 0.1619 0.7065 184 H 0.1357 0.1793 0.6850 185 D 0.1329 0.1958 0.6712 186 T 0.1087 0.4021 0.4892 187 E 0.0873 0.5957 0.3169 188 Q 0.1603 0.5462 0.2935 189 Q 0.2319 0.4669 0.3012 190 H 0.2935 0.3267 0.3798 191 L 0.2641 0.1895 0.5464 192 G 0.2350 0.0941 0.6709 193 Y 0.3722 0.0547 0.5731 194 D 0.4554 0.0552 0.4893 195 V 0.5572 0.0661 0.3767 196 S 0.5194 0.0551 0.4255 197 L 0.4324 0.1220 0.4456 198 D 0.3234 0.1308 0.5458 199 A 0.1820 0.3908 0.4272 200 D 0.1453 0.4544 0.4004 201 F 0.0908 0.6195 0.2897 202 T 0.0572 0.7370 0.2058 203 E 0.0216 0.8527 0.1256 204 K 0.0179 0.8724 0.1097 205 A 0.0203 0.8943 0.0854 206 R 0.0175 0.9027 0.0799 207 L 0.0227 0.8925 0.0847 208 L 0.0218 0.8740 0.1042 209 L 0.0330 0.8402 0.1268 210 R 0.0495 0.7358 0.2147 211 Q 0.0760 0.4395 0.4846 212 G 0.0972 0.3027 0.6001 213 I 0.1809 0.4180 0.4011 214 L 0.2093 0.4895 0.3012 215 T 0.1695 0.5118 0.3187 216 E 0.1019 0.5867 0.3114 217 N 0.0884 0.5150 0.3966 218 L 0.0758 0.4998 0.4243 219 G 0.0672 0.5699 0.3629 220 L 0.0178 0.8413 0.1408 221 E 0.0089 0.8955 0.0955 222 A 0.0087 0.9191 0.0722 223 L 0.0084 0.9201 0.0714 224 K 0.0084 0.9183 0.0733 225 A 0.0085 0.9120 0.0795 226 Y 0.0099 0.8963 0.0938 227 M 0.0139 0.8599 0.1263 228 K 0.0145 0.8308 0.1547 229 S 0.0254 0.7561 0.2185 230 V 0.0441 0.7065 0.2495 231 L 0.0768 0.5781 0.3450 232 P 0.0697 0.5881 0.3423 233 I 0.0427 0.7255 0.2318 234 A 0.0484 0.7198 0.2318 235 H 0.0648 0.6273 0.3078 236 S 0.0960 0.5123 0.3917 237 L 0.0622 0.6218 0.3160 238 K 0.0400 0.6325 0.3275 239 N 0.0550 0.5095 0.4355 240 L 0.0587 0.5796 0.3617 241 E 0.0503 0.6063 0.3435 242 H 0.1000 0.4709 0.4291 243 L 0.2480 0.1682 0.5839 244 T 0.2275 0.1313 0.6412 245 F 0.0927 0.5655 0.3418 246 E 0.0460 0.7324 0.2216 247 E 0.0497 0.7331 0.2172 248 T 0.0544 0.7576 0.1880 249 K 0.0532 0.7593 0.1874 250 K 0.0489 0.7639 0.1872 251 L 0.0332 0.8107 0.1560 252 T 0.0369 0.8143 0.1488 253 K 0.0511 0.8261 0.1228 254 L 0.0654 0.7709 0.1636 255 L 0.1048 0.6210 0.2741 256 T 0.1257 0.4759 0.3984 257 Q 0.1305 0.3400 0.5295 258 E 0.1463 0.2168 0.6369 259 E 0.2187 0.1022 0.6791 260 P 0.2002 0.1980 0.6017 261 K 0.3028 0.2305 0.4667 262 I 0.4341 0.1803 0.3855 263 M 0.3819 0.1885 0.4296 264 E 0.3252 0.2003 0.4745 265 D 0.1982 0.2083 0.5935 266 T 0.1367 0.2707 0.5926 267 D 0.1307 0.3211 0.5481 268 L 0.0844 0.4960 0.4196 269 T 0.0762 0.5638 0.3600 270 S 0.0321 0.7724 0.1955 271 K 0.0132 0.8405 0.1463 272 A 0.0125 0.8824 0.1051 273 L 0.0099 0.9083 0.0818 274 D 0.0087 0.9155 0.0758 275 F 0.0085 0.9166 0.0749 276 L 0.0085 0.9166 0.0749 277 Q 0.0085 0.9129 0.0786 278 K 0.0089 0.8986 0.0925 279 A 0.0129 0.8448 0.1422 280 A 0.0241 0.7623 0.2135 281 Q 0.0366 0.6372 0.3262 282 Q 0.0745 0.3888 0.5368