# This file is the result of combining several RDB files, specifically # T0427.t06.str2.rdb (weight 1.54425) # T0427.t06.str4.rdb (weight 0.924988) # T0427.t06.pb.rdb (weight 0.789901) # T0427.t06.bys.rdb (weight 0.748322) # T0427.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 T0427.t06.str2.rdb # ============================================ # TARGET T0427 # 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 T0427.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 2898 # # ============================================ # Comments from T0427.t06.str4.rdb # ============================================ # TARGET T0427 # 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 T0427.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 2898 # # ============================================ # Comments from T0427.t06.pb.rdb # ============================================ # TARGET T0427 # 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 T0427.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 2898 # # ============================================ # Comments from T0427.t06.bys.rdb # ============================================ # TARGET T0427 # 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 T0427.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 2898 # # ============================================ # Comments from T0427.t06.alpha.rdb # ============================================ # TARGET T0427 # 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 T0427.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 2898 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.5428 0.0276 0.4297 2 S 0.6655 0.0144 0.3200 3 V 0.7658 0.0095 0.2247 4 Q 0.7561 0.0091 0.2348 5 L 0.6532 0.0191 0.3277 6 V 0.3521 0.1514 0.4965 7 K 0.1508 0.1189 0.7303 8 G 0.1903 0.0606 0.7490 9 V 0.5357 0.0099 0.4545 10 N 0.6989 0.0102 0.2908 11 L 0.7950 0.0054 0.1996 12 H 0.7902 0.0081 0.2016 13 V 0.7630 0.0074 0.2296 14 I 0.7037 0.0107 0.2857 15 P 0.4172 0.0252 0.5576 16 T 0.2410 0.0741 0.6849 17 E 0.0693 0.3185 0.6122 18 K 0.1028 0.2565 0.6407 19 Y 0.2337 0.1078 0.6585 20 K 0.2911 0.1052 0.6036 21 T 0.6532 0.0257 0.3211 22 V 0.7771 0.0083 0.2146 23 R 0.8146 0.0056 0.1798 24 L 0.8272 0.0046 0.1681 25 L 0.8298 0.0043 0.1659 26 V 0.8266 0.0046 0.1687 27 R 0.8140 0.0051 0.1810 28 F 0.7517 0.0119 0.2364 29 N 0.5413 0.0356 0.4231 30 T 0.3075 0.0952 0.5973 31 R 0.2076 0.0998 0.6926 32 L 0.2069 0.1655 0.6276 33 N 0.1420 0.2463 0.6117 34 H 0.1529 0.2345 0.6127 35 E 0.1494 0.2505 0.6001 36 T 0.1393 0.3273 0.5335 37 I 0.0760 0.5192 0.4049 38 T 0.0764 0.5917 0.3319 39 K 0.0167 0.8386 0.1447 40 R 0.0092 0.8959 0.0949 41 T 0.0086 0.9189 0.0724 42 L 0.0085 0.9193 0.0722 43 L 0.0084 0.9177 0.0739 44 S 0.0083 0.9214 0.0703 45 S 0.0084 0.9175 0.0741 46 L 0.0089 0.9084 0.0827 47 M 0.0107 0.8821 0.1072 48 E 0.0194 0.7477 0.2329 49 T 0.0541 0.3965 0.5494 50 N 0.0501 0.1941 0.7558 51 S 0.1404 0.1819 0.6777 52 L 0.0859 0.3223 0.5918 53 N 0.1145 0.1952 0.6903 54 Y 0.2088 0.0777 0.7135 55 P 0.1528 0.1541 0.6931 56 N 0.1332 0.1597 0.7071 57 Q 0.0282 0.6944 0.2774 58 V 0.0141 0.8459 0.1400 59 K 0.0131 0.8912 0.0958 60 L 0.0110 0.9010 0.0881 61 S 0.0086 0.9160 0.0755 62 E 0.0083 0.9206 0.0710 63 R 0.0085 0.9169 0.0746 64 L 0.0089 0.9106 0.0805 65 A 0.0085 0.9088 0.0827 66 E 0.0098 0.8830 0.1072 67 L 0.0257 0.7403 0.2339 68 Y 0.0623 0.4069 0.5309 69 G 0.0803 0.2222 0.6975 70 A 0.2153 0.2475 0.5372 71 S 0.3406 0.2177 0.4417 72 F 0.3462 0.1687 0.4851 73 G 0.3193 0.1179 0.5629 74 I 0.3871 0.1053 0.5076 75 G 0.3851 0.0946 0.5202 76 V 0.3816 0.0880 0.5304 77 S 0.2865 0.0866 0.6269 78 K 0.1903 0.2406 0.5691 79 K 0.1729 0.1693 0.6578 80 G 0.1471 0.1053 0.7476 81 N 0.2034 0.1071 0.6895 82 Q 0.1756 0.2447 0.5797 83 H 0.2885 0.1846 0.5269 84 W 0.5408 0.0858 0.3734 85 F 0.6817 0.0423 0.2760 86 N 0.7596 0.0169 0.2235 87 I 0.7937 0.0102 0.1961 88 S 0.7800 0.0133 0.2067 89 M 0.7629 0.0158 0.2213 90 N 0.6955 0.0311 0.2734 91 I 0.5995 0.0452 0.3554 92 V 0.4221 0.0861 0.4917 93 N 0.2324 0.1234 0.6442 94 D 0.0786 0.3578 0.5636 95 H 0.0826 0.4165 0.5010 96 Y 0.1175 0.3989 0.4836 97 L 0.1090 0.3977 0.4932 98 Q 0.1006 0.3245 0.5749 99 D 0.1266 0.2885 0.5849 100 S 0.0273 0.6900 0.2828 101 Q 0.0227 0.7596 0.2177 102 V 0.0276 0.7912 0.1811 103 L 0.0143 0.8778 0.1079 104 A 0.0085 0.9157 0.0758 105 E 0.0083 0.9198 0.0718 106 A 0.0084 0.9178 0.0738 107 V 0.0084 0.9175 0.0741 108 D 0.0083 0.9225 0.0692 109 F 0.0083 0.9211 0.0705 110 L 0.0084 0.9208 0.0709 111 K 0.0085 0.9122 0.0793 112 E 0.0089 0.8965 0.0947 113 I 0.0136 0.8439 0.1424 114 I 0.0289 0.7371 0.2339 115 F 0.0680 0.5691 0.3629 116 A 0.1426 0.2975 0.5599 117 P 0.0702 0.4802 0.4496 118 N 0.0727 0.5210 0.4064 119 I 0.0854 0.5636 0.3510 120 Q 0.0886 0.4771 0.4342 121 A 0.0682 0.2964 0.6354 122 G 0.0520 0.1703 0.7777 123 Q 0.1911 0.1015 0.7074 124 F 0.2524 0.0553 0.6923 125 E 0.1718 0.0486 0.7796 126 A 0.0205 0.7186 0.2608 127 E 0.0124 0.8259 0.1617 128 T 0.0145 0.8847 0.1008 129 F 0.0138 0.8994 0.0867 130 Q 0.0095 0.9115 0.0790 131 R 0.0094 0.9121 0.0784 132 E 0.0097 0.9063 0.0840 133 K 0.0087 0.9131 0.0782 134 E 0.0084 0.9181 0.0735 135 N 0.0084 0.9213 0.0704 136 L 0.0084 0.9200 0.0716 137 K 0.0084 0.9181 0.0735 138 A 0.0085 0.9170 0.0746 139 Y 0.0091 0.9106 0.0803 140 L 0.0113 0.8979 0.0909 141 E 0.0098 0.8826 0.1076 142 S 0.0154 0.8160 0.1686 143 I 0.0394 0.7184 0.2422 144 V 0.0510 0.6127 0.3363 145 E 0.0686 0.4258 0.5056 146 D 0.1362 0.2360 0.6278 147 K 0.0145 0.7389 0.2465 148 Q 0.0109 0.8356 0.1535 149 T 0.0109 0.9060 0.0831 150 Y 0.0094 0.9152 0.0754 151 A 0.0087 0.9145 0.0769 152 S 0.0084 0.9189 0.0727 153 L 0.0084 0.9205 0.0711 154 A 0.0084 0.9184 0.0732 155 L 0.0089 0.9122 0.0789 156 Q 0.0089 0.8996 0.0915 157 S 0.0111 0.8614 0.1274 158 V 0.0218 0.7534 0.2248 159 Y 0.0556 0.5155 0.4290 160 F 0.1172 0.2675 0.6153 161 N 0.1144 0.2543 0.6313 162 Q 0.0551 0.3854 0.5595 163 S 0.0840 0.2721 0.6438 164 E 0.1569 0.1840 0.6591 165 D 0.1154 0.3023 0.5823 166 Q 0.1320 0.2705 0.5975 167 K 0.2174 0.1437 0.6389 168 I 0.2787 0.0530 0.6683 169 P 0.2104 0.1034 0.6861 170 S 0.1711 0.2311 0.5978 171 F 0.1625 0.2012 0.6362 172 G 0.1904 0.1086 0.7010 173 T 0.1958 0.0921 0.7121 174 V 0.0291 0.6947 0.2762 175 A 0.0178 0.8008 0.1815 176 A 0.0257 0.7980 0.1764 177 L 0.0371 0.7632 0.1997 178 A 0.0213 0.6958 0.2829 179 E 0.0354 0.6125 0.3522 180 E 0.1145 0.3244 0.5611 181 T 0.1505 0.0988 0.7507 182 A 0.0125 0.7506 0.2369 183 A 0.0093 0.8697 0.1210 184 S 0.0085 0.9196 0.0718 185 L 0.0083 0.9224 0.0693 186 A 0.0084 0.9198 0.0719 187 A 0.0083 0.9220 0.0697 188 Y 0.0084 0.9213 0.0704 189 Y 0.0084 0.9166 0.0749 190 Q 0.0086 0.9101 0.0813 191 K 0.0111 0.8525 0.1364 192 M 0.0290 0.7091 0.2618 193 L 0.0883 0.4772 0.4345 194 A 0.1380 0.2681 0.5939 195 E 0.0359 0.4706 0.4935 196 D 0.0476 0.3091 0.6433 197 Q 0.1320 0.1414 0.7266 198 V 0.4725 0.0193 0.5082 199 D 0.6993 0.0116 0.2891 200 I 0.8169 0.0048 0.1784 201 F 0.8088 0.0061 0.1851 202 V 0.7838 0.0077 0.2085 203 L 0.6995 0.0255 0.2750 204 G 0.4213 0.0414 0.5374 205 D 0.2654 0.0571 0.6774 206 V 0.2397 0.0737 0.6866 207 N 0.1785 0.0237 0.7977 208 E 0.0142 0.7224 0.2634 209 A 0.0097 0.8278 0.1626 210 E 0.0097 0.8993 0.0909 211 L 0.0106 0.9035 0.0859 212 V 0.0091 0.9065 0.0845 213 P 0.0089 0.9036 0.0875 214 L 0.0100 0.8947 0.0954 215 F 0.0151 0.8677 0.1172 216 K 0.0162 0.7340 0.2498 217 Q 0.0384 0.4335 0.5281 218 L 0.1332 0.1473 0.7195 219 P 0.0870 0.2665 0.6465 220 F 0.1320 0.1726 0.6954 221 T 0.2071 0.0556 0.7373 222 P 0.1767 0.1072 0.7161 223 R 0.1512 0.2040 0.6448 224 E 0.1326 0.2590 0.6084 225 E 0.1246 0.2191 0.6564 226 G 0.1431 0.1369 0.7200 227 K 0.1999 0.1287 0.6714 228 A 0.2596 0.1552 0.5852 229 A 0.2891 0.1853 0.5256 230 I 0.3245 0.1690 0.5066 231 F 0.3053 0.1374 0.5574 232 Y 0.2691 0.1378 0.5931 233 N 0.2346 0.1133 0.6521 234 Q 0.2674 0.0571 0.6755 235 P 0.2318 0.0845 0.6836 236 I 0.2164 0.1747 0.6089 237 R 0.2060 0.1886 0.6054 238 N 0.2248 0.1679 0.6073 239 V 0.3323 0.1442 0.5235 240 I 0.4293 0.1492 0.4214 241 E 0.5453 0.1321 0.3225 242 E 0.6224 0.0986 0.2790 243 R 0.6068 0.0990 0.2942 244 T 0.6133 0.0830 0.3037 245 E 0.5250 0.1091 0.3659 246 R 0.4504 0.1335 0.4161 247 E 0.3253 0.1748 0.4999 248 V 0.2430 0.2672 0.4898 249 L 0.2278 0.2565 0.5156 250 A 0.2117 0.2890 0.4993 251 Q 0.2443 0.3065 0.4492 252 S 0.3257 0.2531 0.4212 253 K 0.5676 0.1424 0.2900 254 L 0.7205 0.0614 0.2181 255 N 0.7322 0.0582 0.2095 256 L 0.7339 0.0547 0.2114 257 A 0.6762 0.0644 0.2594 258 Y 0.5964 0.0508 0.3528 259 N 0.4128 0.0653 0.5220 260 T 0.3102 0.0777 0.6121 261 D 0.2311 0.1273 0.6416 262 I 0.1852 0.2198 0.5950 263 Y 0.1609 0.2527 0.5864 264 Y 0.1575 0.1859 0.6566 265 G 0.1277 0.1276 0.7448 266 D 0.1466 0.1989 0.6545 267 S 0.0280 0.6373 0.3347 268 Y 0.0239 0.7231 0.2529 269 Y 0.0292 0.8202 0.1506 270 F 0.0155 0.8913 0.0932 271 A 0.0091 0.9159 0.0750 272 L 0.0084 0.9215 0.0701 273 Q 0.0083 0.9233 0.0684 274 V 0.0086 0.9210 0.0705 275 F 0.0089 0.9153 0.0758 276 N 0.0100 0.8955 0.0945 277 G 0.0146 0.8591 0.1262 278 I 0.0303 0.7695 0.2003 279 F 0.0515 0.5703 0.3783 280 G 0.0577 0.2530 0.6892 281 G 0.0758 0.1982 0.7260 282 F 0.1611 0.1265 0.7123 283 P 0.0845 0.3456 0.5699 284 H 0.0802 0.4183 0.5016 285 S 0.0662 0.6343 0.2995 286 K 0.0310 0.7728 0.1962 287 L 0.0261 0.8259 0.1479 288 F 0.0224 0.8683 0.1093 289 M 0.0175 0.8859 0.0965 290 N 0.0223 0.8788 0.0988 291 V 0.0344 0.8572 0.1083 292 R 0.0447 0.8240 0.1313 293 E 0.0509 0.7836 0.1655 294 K 0.0589 0.6649 0.2762 295 E 0.0713 0.3953 0.5334 296 H 0.1128 0.2970 0.5902 297 L 0.2873 0.2563 0.4564 298 A 0.4103 0.2141 0.3756 299 Y 0.5006 0.1657 0.3337 300 Y 0.5226 0.1319 0.3456 301 A 0.4911 0.1659 0.3429 302 S 0.4691 0.1481 0.3828 303 S 0.4116 0.1697 0.4187 304 S 0.3202 0.1814 0.4984 305 I 0.3018 0.2039 0.4943 306 D 0.2591 0.2001 0.5408 307 T 0.1959 0.2780 0.5261 308 F 0.1854 0.2269 0.5877 309 R 0.2205 0.1390 0.6405 310 G 0.3265 0.0846 0.5888 311 F 0.5908 0.0444 0.3648 312 M 0.7561 0.0156 0.2282 313 T 0.7968 0.0096 0.1936 314 V 0.7958 0.0090 0.1952 315 Q 0.7686 0.0144 0.2171 316 T 0.6916 0.0269 0.2815 317 G 0.4614 0.0439 0.4947 318 I 0.3570 0.0653 0.5778 319 D 0.1923 0.0538 0.7539 320 G 0.0493 0.3949 0.5557 321 K 0.0434 0.4434 0.5132 322 N 0.0800 0.4143 0.5056 323 R 0.0160 0.7980 0.1861 324 N 0.0089 0.8965 0.0946 325 Q 0.0084 0.9220 0.0696 326 V 0.0083 0.9230 0.0687 327 L 0.0083 0.9232 0.0685 328 R 0.0083 0.9243 0.0675 329 L 0.0083 0.9236 0.0681 330 I 0.0083 0.9208 0.0709 331 S 0.0084 0.9178 0.0738 332 T 0.0084 0.9221 0.0695 333 E 0.0085 0.9200 0.0715 334 L 0.0084 0.9195 0.0721 335 E 0.0085 0.9133 0.0782 336 N 0.0087 0.9074 0.0839 337 I 0.0136 0.8847 0.1017 338 R 0.0180 0.8119 0.1701 339 L 0.0416 0.5122 0.4462 340 G 0.0498 0.1950 0.7552 341 K 0.0926 0.1191 0.7883 342 I 0.1789 0.0656 0.7554 343 R 0.1621 0.0478 0.7902 344 E 0.0146 0.7340 0.2515 345 L 0.0097 0.8663 0.1240 346 E 0.0094 0.9166 0.0739 347 I 0.0087 0.9200 0.0713 348 E 0.0083 0.9217 0.0700 349 Q 0.0083 0.9233 0.0684 350 T 0.0083 0.9237 0.0681 351 K 0.0083 0.9221 0.0696 352 A 0.0083 0.9209 0.0707 353 M 0.0084 0.9162 0.0753 354 L 0.0087 0.9160 0.0753 355 K 0.0089 0.9069 0.0841 356 N 0.0104 0.8705 0.1191 357 Q 0.0141 0.8470 0.1389 358 Y 0.0216 0.8424 0.1360 359 I 0.0358 0.8105 0.1537 360 L 0.0538 0.7378 0.2084 361 A 0.0816 0.5835 0.3349 362 L 0.0911 0.4658 0.4431 363 D 0.0911 0.3776 0.5313 364 N 0.1239 0.2449 0.6313 365 A 0.0390 0.6524 0.3086 366 G 0.0273 0.7465 0.2262 367 A 0.0223 0.8504 0.1273 368 W 0.0159 0.8862 0.0980 369 L 0.0146 0.8885 0.0969 370 E 0.0113 0.9015 0.0872 371 K 0.0106 0.9037 0.0857 372 E 0.0119 0.8915 0.0967 373 Y 0.0156 0.8685 0.1159 374 L 0.0157 0.8586 0.1257 375 N 0.0192 0.8291 0.1517 376 E 0.0305 0.7556 0.2139 377 L 0.0733 0.5638 0.3630 378 M 0.1509 0.2750 0.5741 379 P 0.0947 0.2805 0.6248 380 Q 0.1284 0.2031 0.6685 381 T 0.1539 0.1845 0.6616 382 M 0.0741 0.4932 0.4328 383 L 0.0673 0.5622 0.3705 384 T 0.0860 0.5731 0.3408 385 A 0.0147 0.8161 0.1691 386 E 0.0089 0.8900 0.1012 387 E 0.0084 0.9210 0.0706 388 W 0.0084 0.9211 0.0706 389 I 0.0084 0.9183 0.0733 390 A 0.0085 0.9151 0.0764 391 R 0.0094 0.8962 0.0944 392 I 0.0199 0.8402 0.1399 393 N 0.0187 0.6331 0.3482 394 A 0.0374 0.3312 0.6313 395 V 0.2047 0.0802 0.7151 396 T 0.1637 0.0265 0.8098 397 I 0.0256 0.6888 0.2856 398 P 0.0096 0.8593 0.1311 399 E 0.0086 0.9140 0.0774 400 I 0.0084 0.9201 0.0714 401 Q 0.0084 0.9187 0.0729 402 E 0.0083 0.9239 0.0678 403 V 0.0084 0.9213 0.0702 404 A 0.0086 0.9108 0.0806 405 K 0.0092 0.8822 0.1085 406 R 0.0185 0.6796 0.3019 407 L 0.1191 0.2498 0.6311 408 E 0.1100 0.1601 0.7300 409 L 0.2389 0.0930 0.6681 410 Q 0.5211 0.0464 0.4325 411 A 0.7677 0.0108 0.2215 412 I 0.8041 0.0062 0.1897 413 F 0.8042 0.0062 0.1897 414 F 0.7519 0.0093 0.2388 415 L 0.5593 0.0195 0.4213 416 E 0.2524 0.0563 0.6913 417 G 0.1335 0.0798 0.7867 418 E 0.1570 0.1797 0.6632 419 T 0.1673 0.2299 0.6028 420 E 0.1661 0.2577 0.5762 421 N 0.1693 0.2138 0.6169 422 D 0.1537 0.2075 0.6388