# This file is the result of combining several RDB files, specifically # T0405.t2k.str2.rdb (weight 1.54425) # T0405.t2k.str4.rdb (weight 0.924988) # T0405.t2k.pb.rdb (weight 0.789901) # T0405.t2k.bys.rdb (weight 0.748322) # T0405.t2k.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.t2k.str2.rdb # ============================================ # TARGET T0405 # Using neural net dunbrack-40pc-3157-t2k-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.t2k-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 2.99991 # # ============================================ # Comments from T0405.t2k.str4.rdb # ============================================ # TARGET T0405 # Using neural net dunbrack-40pc-3157-t2k-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.t2k-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 2.99991 # # ============================================ # Comments from T0405.t2k.pb.rdb # ============================================ # TARGET T0405 # Using neural net dunbrack-40pc-3157-t2k-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.t2k-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 2.99991 # # ============================================ # Comments from T0405.t2k.bys.rdb # ============================================ # TARGET T0405 # Using neural net dunbrack-40pc-3157-t2k-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.t2k-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 2.99991 # # ============================================ # Comments from T0405.t2k.alpha.rdb # ============================================ # TARGET T0405 # Using neural net dunbrack-40pc-3157-t2k-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.t2k-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 2.99991 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2151 0.2198 0.5651 2 N 0.1546 0.2788 0.5666 3 E 0.0745 0.5338 0.3917 4 T 0.0662 0.6209 0.3129 5 E 0.0325 0.7845 0.1831 6 K 0.0254 0.8554 0.1192 7 L 0.0249 0.8833 0.0918 8 V 0.0149 0.9038 0.0813 9 A 0.0160 0.9030 0.0810 10 A 0.0161 0.8976 0.0863 11 L 0.0219 0.8744 0.1037 12 L 0.0277 0.8504 0.1218 13 E 0.0332 0.8092 0.1576 14 R 0.0519 0.7075 0.2405 15 N 0.0726 0.5597 0.3677 16 F 0.0876 0.3123 0.6002 17 G 0.0992 0.1978 0.7030 18 K 0.1493 0.2243 0.6264 19 N 0.2184 0.1813 0.6002 20 I 0.2327 0.2003 0.5670 21 G 0.2453 0.1487 0.6060 22 T 0.3223 0.1221 0.5555 23 R 0.3482 0.0938 0.5580 24 Y 0.2496 0.0393 0.7111 25 P 0.1247 0.1808 0.6945 26 G 0.0684 0.1575 0.7741 27 N 0.1471 0.2063 0.6466 28 E 0.1057 0.4963 0.3980 29 A 0.1060 0.5818 0.3122 30 A 0.1270 0.6084 0.2647 31 Q 0.1708 0.5238 0.3054 32 M 0.2203 0.4667 0.3130 33 R 0.1540 0.4143 0.4317 34 A 0.0401 0.7681 0.1919 35 E 0.0177 0.8443 0.1380 36 E 0.0221 0.8664 0.1115 37 V 0.0324 0.8335 0.1341 38 I 0.0404 0.7956 0.1639 39 G 0.0425 0.7247 0.2328 40 E 0.0737 0.6963 0.2300 41 I 0.1644 0.5950 0.2405 42 A 0.2606 0.5195 0.2199 43 I 0.4034 0.3812 0.2154 44 V 0.3963 0.3317 0.2721 45 I 0.2896 0.3387 0.3717 46 A 0.1828 0.4057 0.4115 47 P 0.0596 0.7445 0.1959 48 L 0.0421 0.8097 0.1482 49 V 0.0273 0.8562 0.1165 50 E 0.0245 0.8428 0.1327 51 K 0.0452 0.7154 0.2395 52 L 0.0792 0.3454 0.5754 53 G 0.0844 0.1062 0.8094 54 I 0.1997 0.1343 0.6659 55 E 0.2555 0.1655 0.5790 56 N 0.2595 0.1929 0.5476 57 K 0.2113 0.2784 0.5103 58 T 0.3005 0.2098 0.4897 59 V 0.3208 0.2678 0.4114 60 K 0.2661 0.3299 0.4040 61 K 0.2468 0.3233 0.4299 62 T 0.2678 0.2808 0.4514 63 I 0.3103 0.2526 0.4371 64 P 0.2181 0.4644 0.3175 65 F 0.1440 0.6313 0.2247 66 L 0.1030 0.7366 0.1604 67 Y 0.1052 0.7584 0.1364 68 E 0.1180 0.7289 0.1531 69 L 0.1038 0.7268 0.1694 70 Q 0.1062 0.6590 0.2348 71 K 0.0852 0.5448 0.3699 72 N 0.0712 0.3871 0.5417 73 Q 0.1093 0.3618 0.5289 74 F 0.1761 0.2904 0.5336 75 C 0.2338 0.2392 0.5270 76 D 0.2081 0.2169 0.5750 77 M 0.1791 0.3063 0.5145 78 S 0.1739 0.2734 0.5528 79 A 0.1859 0.2401 0.5740 80 Y 0.2534 0.1201 0.6266 81 P 0.2276 0.1684 0.6040 82 Y 0.3464 0.0939 0.5597 83 P 0.3459 0.1694 0.4848 84 L 0.5014 0.1536 0.3450 85 L 0.6918 0.0656 0.2426 86 L 0.7075 0.0357 0.2568 87 V 0.6328 0.0580 0.3093 88 N 0.3989 0.0664 0.5348 89 G 0.1944 0.0918 0.7138 90 T 0.2285 0.1088 0.6627 91 S 0.2233 0.1203 0.6564 92 T 0.1254 0.3090 0.5656 93 D 0.1300 0.2457 0.6243 94 T 0.1023 0.4635 0.4342 95 E 0.0466 0.7171 0.2363 96 K 0.0579 0.7367 0.2054 97 Y 0.0746 0.6933 0.2321 98 W 0.0910 0.6209 0.2881 99 R 0.1004 0.5326 0.3670 100 D 0.1231 0.2854 0.5915 101 L 0.2054 0.1106 0.6840 102 P 0.1754 0.1777 0.6469 103 T 0.2169 0.1987 0.5844 104 Y 0.3186 0.1851 0.4963 105 W 0.3860 0.1770 0.4370 106 T 0.3344 0.1745 0.4911 107 D 0.1872 0.3076 0.5052 108 D 0.1090 0.4160 0.4751 109 A 0.0945 0.4322 0.4733 110 N 0.0974 0.3319 0.5707 111 K 0.2179 0.2507 0.5314 112 I 0.4189 0.1517 0.4294 113 V 0.4820 0.1624 0.3556 114 L 0.3716 0.1745 0.4539 115 P 0.2024 0.4759 0.3217 116 Y 0.1622 0.5700 0.2678 117 V 0.1258 0.7041 0.1702 118 L 0.0842 0.7785 0.1373 119 E 0.0548 0.8081 0.1371 120 H 0.0725 0.7479 0.1796 121 I 0.0681 0.7206 0.2113 122 K 0.0609 0.6149 0.3242 123 N 0.0539 0.4194 0.5267 124 N 0.0513 0.4061 0.5426 125 K 0.0811 0.5103 0.4086 126 V 0.0799 0.6786 0.2416 127 R 0.0454 0.8211 0.1335 128 Q 0.0241 0.8796 0.0963 129 K 0.0164 0.8944 0.0893 130 L 0.0133 0.8976 0.0891 131 L 0.0119 0.8986 0.0895 132 A 0.0122 0.8928 0.0950 133 F 0.0178 0.8813 0.1010 134 H 0.0196 0.8866 0.0938 135 A 0.0164 0.8947 0.0889 136 W 0.0194 0.8893 0.0913 137 L 0.0336 0.8345 0.1319 138 L 0.0452 0.7507 0.2041 139 G 0.0462 0.7009 0.2529 140 E 0.0775 0.7293 0.1932 141 V 0.0820 0.7597 0.1583 142 V 0.0661 0.7896 0.1443 143 E 0.0906 0.7567 0.1527 144 M 0.1035 0.7009 0.1956 145 N 0.0888 0.6673 0.2438 146 E 0.0218 0.7672 0.2110 147 A 0.0337 0.6658 0.3005 148 L 0.0764 0.2722 0.6514 149 G 0.0725 0.1140 0.8135 150 A 0.2108 0.1391 0.6501 151 D 0.3791 0.1170 0.5039 152 F 0.5998 0.0559 0.3442 153 R 0.6987 0.0256 0.2758 154 V 0.7655 0.0156 0.2189 155 K 0.7814 0.0159 0.2027 156 L 0.7729 0.0117 0.2154 157 V 0.7597 0.0200 0.2203 158 F 0.6352 0.0296 0.3352 159 E 0.4044 0.1396 0.4560 160 S 0.2716 0.1953 0.5330 161 D 0.2289 0.1803 0.5907 162 M 0.3903 0.1424 0.4673 163 R 0.5596 0.0728 0.3676 164 I 0.6957 0.0471 0.2572 165 R 0.7377 0.0274 0.2349 166 L 0.7633 0.0216 0.2151 167 R 0.7426 0.0268 0.2306 168 V 0.6832 0.0642 0.2525 169 Y 0.5791 0.0997 0.3212 170 E 0.5339 0.1365 0.3295 171 V 0.3792 0.3170 0.3039 172 E 0.3452 0.3886 0.2662 173 Q 0.4106 0.3667 0.2227 174 I 0.4727 0.3044 0.2229 175 A 0.5980 0.1837 0.2183 176 I 0.6978 0.0986 0.2036 177 E 0.7025 0.0702 0.2273 178 V 0.7223 0.0557 0.2220 179 H 0.6788 0.0649 0.2563 180 F 0.6017 0.0757 0.3226 181 L 0.3748 0.1280 0.4972 182 D 0.2136 0.1498 0.6366 183 N 0.1395 0.1603 0.7002 184 H 0.1383 0.1876 0.6741 185 D 0.1451 0.1882 0.6667 186 T 0.1144 0.4375 0.4481 187 E 0.1061 0.5773 0.3166 188 Q 0.1522 0.5743 0.2734 189 Q 0.1904 0.4959 0.3137 190 H 0.2443 0.3253 0.4304 191 L 0.1871 0.1828 0.6301 192 G 0.1820 0.1027 0.7152 193 Y 0.3200 0.0741 0.6059 194 D 0.4415 0.0580 0.5005 195 V 0.5331 0.0825 0.3845 196 S 0.4927 0.0819 0.4254 197 L 0.3952 0.1450 0.4597 198 D 0.2696 0.1263 0.6041 199 A 0.1269 0.4782 0.3949 200 D 0.1019 0.5006 0.3975 201 F 0.0758 0.6298 0.2944 202 T 0.0455 0.7621 0.1924 203 E 0.0161 0.8685 0.1154 204 K 0.0149 0.8842 0.1009 205 A 0.0198 0.8908 0.0894 206 R 0.0150 0.9078 0.0772 207 L 0.0207 0.8990 0.0803 208 L 0.0234 0.8841 0.0925 209 L 0.0322 0.8379 0.1299 210 R 0.0470 0.7167 0.2363 211 Q 0.0711 0.3970 0.5318 212 G 0.0876 0.2354 0.6770 213 I 0.2302 0.2719 0.4979 214 L 0.3151 0.2707 0.4142 215 T 0.2171 0.3583 0.4245 216 E 0.0687 0.6217 0.3097 217 N 0.0729 0.5520 0.3750 218 L 0.0708 0.5218 0.4074 219 G 0.0529 0.5752 0.3719 220 L 0.0209 0.8250 0.1541 221 E 0.0105 0.8938 0.0958 222 A 0.0091 0.9167 0.0742 223 L 0.0083 0.9208 0.0709 224 K 0.0084 0.9166 0.0750 225 A 0.0084 0.9133 0.0782 226 Y 0.0092 0.9022 0.0887 227 M 0.0120 0.8647 0.1233 228 K 0.0142 0.8258 0.1600 229 S 0.0230 0.7428 0.2342 230 V 0.0402 0.6831 0.2767 231 L 0.0854 0.5949 0.3197 232 P 0.0682 0.6569 0.2749 233 I 0.0487 0.7323 0.2190 234 A 0.0423 0.7339 0.2238 235 H 0.0564 0.6479 0.2958 236 S 0.0802 0.5475 0.3723 237 L 0.0563 0.6045 0.3392 238 K 0.0654 0.5965 0.3381 239 N 0.0683 0.5037 0.4280 240 L 0.0683 0.6058 0.3258 241 E 0.0704 0.6149 0.3147 242 H 0.0963 0.4483 0.4553 243 L 0.2107 0.2034 0.5859 244 T 0.1839 0.1405 0.6757 245 F 0.0468 0.6897 0.2635 246 E 0.0191 0.8146 0.1663 247 E 0.0211 0.8367 0.1422 248 T 0.0284 0.8281 0.1435 249 K 0.0229 0.8501 0.1270 250 K 0.0247 0.8393 0.1360 251 L 0.0252 0.8311 0.1436 252 T 0.0254 0.8248 0.1498 253 K 0.0354 0.7754 0.1892 254 L 0.0692 0.6624 0.2683 255 L 0.1317 0.4699 0.3984 256 T 0.1431 0.3251 0.5319 257 Q 0.1006 0.3904 0.5091 258 E 0.1368 0.3156 0.5476 259 E 0.2476 0.1280 0.6244 260 P 0.2493 0.2100 0.5407 261 K 0.3526 0.2044 0.4430 262 I 0.3642 0.2540 0.3818 263 M 0.3364 0.1970 0.4666 264 E 0.2286 0.2901 0.4813 265 D 0.1759 0.2342 0.5899 266 T 0.1461 0.2981 0.5558 267 D 0.1277 0.3301 0.5422 268 L 0.0969 0.4769 0.4262 269 T 0.0834 0.4965 0.4201 270 S 0.0318 0.7559 0.2123 271 K 0.0121 0.8390 0.1489 272 A 0.0107 0.8723 0.1170 273 L 0.0098 0.9069 0.0833 274 D 0.0085 0.9153 0.0763 275 F 0.0086 0.9118 0.0796 276 L 0.0089 0.9143 0.0768 277 Q 0.0085 0.9148 0.0767 278 K 0.0087 0.9072 0.0841 279 A 0.0120 0.8682 0.1199 280 A 0.0187 0.8116 0.1697 281 Q 0.0364 0.6392 0.3244 282 Q 0.0799 0.3985 0.5217