# This file is the result of combining several RDB files, specifically # T0441.t2k.str2.rdb (weight 1.54425) # T0441.t2k.str4.rdb (weight 0.924988) # T0441.t2k.pb.rdb (weight 0.789901) # T0441.t2k.bys.rdb (weight 0.748322) # T0441.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 T0441.t2k.str2.rdb # ============================================ # TARGET T0441 # 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 T0441.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 3458 # # ============================================ # Comments from T0441.t2k.str4.rdb # ============================================ # TARGET T0441 # 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 T0441.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 3458 # # ============================================ # Comments from T0441.t2k.pb.rdb # ============================================ # TARGET T0441 # 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 T0441.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 3458 # # ============================================ # Comments from T0441.t2k.bys.rdb # ============================================ # TARGET T0441 # 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 T0441.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 3458 # # ============================================ # Comments from T0441.t2k.alpha.rdb # ============================================ # TARGET T0441 # 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 T0441.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 3458 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2380 0.0996 0.6624 2 S 0.2157 0.0948 0.6895 3 E 0.2190 0.2387 0.5423 4 P 0.2375 0.2509 0.5116 5 R 0.3142 0.1962 0.4896 6 K 0.3700 0.1108 0.5192 7 R 0.3238 0.0825 0.5936 8 R 0.1882 0.2080 0.6038 9 S 0.1481 0.2098 0.6420 10 T 0.1014 0.1809 0.7177 11 G 0.0845 0.1209 0.7946 12 N 0.2155 0.0698 0.7147 13 V 0.2947 0.0524 0.6529 14 T 0.2057 0.0601 0.7342 15 L 0.0220 0.7229 0.2551 16 A 0.0141 0.8589 0.1270 17 D 0.0101 0.9156 0.0743 18 V 0.0100 0.9156 0.0744 19 A 0.0084 0.9188 0.0728 20 K 0.0085 0.9118 0.0797 21 Q 0.0168 0.8105 0.1727 22 A 0.0580 0.4144 0.5277 23 G 0.0504 0.0726 0.8771 24 V 0.1717 0.0676 0.7607 25 G 0.2304 0.0941 0.6755 26 T 0.2373 0.3065 0.4562 27 M 0.2468 0.3493 0.4039 28 T 0.2487 0.4070 0.3443 29 V 0.1675 0.5933 0.2392 30 S 0.0999 0.7097 0.1903 31 R 0.0550 0.7850 0.1601 32 A 0.0547 0.7369 0.2084 33 L 0.1028 0.5511 0.3461 34 R 0.1015 0.2883 0.6102 35 T 0.1526 0.1348 0.7126 36 P 0.0665 0.3272 0.6064 37 E 0.0503 0.4427 0.5070 38 L 0.1009 0.3439 0.5552 39 V 0.1661 0.2153 0.6186 40 S 0.1467 0.1727 0.6806 41 D 0.0107 0.7595 0.2298 42 K 0.0093 0.8696 0.1211 43 L 0.0087 0.9175 0.0738 44 R 0.0084 0.9172 0.0745 45 E 0.0083 0.9244 0.0673 46 K 0.0082 0.9251 0.0667 47 I 0.0083 0.9216 0.0701 48 Q 0.0083 0.9245 0.0673 49 Q 0.0082 0.9253 0.0665 50 V 0.0083 0.9232 0.0685 51 V 0.0084 0.9194 0.0722 52 D 0.0085 0.9126 0.0789 53 E 0.0125 0.8203 0.1672 54 L 0.0567 0.4425 0.5009 55 G 0.0448 0.0851 0.8701 56 Y 0.1513 0.0918 0.7569 57 I 0.2296 0.0521 0.7184 58 P 0.2104 0.2429 0.5467 59 N 0.1494 0.4120 0.4386 60 K 0.0279 0.7605 0.2117 61 A 0.0279 0.7916 0.1805 62 A 0.0282 0.8469 0.1249 63 G 0.0207 0.8489 0.1304 64 A 0.0325 0.8202 0.1473 65 L 0.0465 0.7596 0.1939 66 A 0.0812 0.6111 0.3077 67 S 0.1009 0.4250 0.4741 68 A 0.1128 0.2849 0.6023 69 E 0.1831 0.1948 0.6222 70 S 0.3101 0.1130 0.5769 71 Y 0.4118 0.0652 0.5229 72 S 0.6733 0.0188 0.3079 73 I 0.7678 0.0099 0.2223 74 A 0.8033 0.0068 0.1899 75 L 0.8051 0.0055 0.1894 76 I 0.7930 0.0078 0.1992 77 I 0.6241 0.0128 0.3631 78 P 0.3219 0.0846 0.5935 79 S 0.1937 0.1506 0.6557 80 L 0.1003 0.3351 0.5647 81 F 0.1086 0.3155 0.5759 82 E 0.1190 0.3869 0.4940 83 K 0.0400 0.6891 0.2709 84 A 0.0425 0.7256 0.2318 85 C 0.0405 0.7965 0.1630 86 A 0.0162 0.8594 0.1244 87 H 0.0147 0.8438 0.1415 88 F 0.0182 0.8322 0.1496 89 L 0.0162 0.8578 0.1260 90 P 0.0088 0.8974 0.0939 91 S 0.0084 0.9206 0.0710 92 F 0.0084 0.9144 0.0771 93 Q 0.0083 0.9232 0.0686 94 Q 0.0083 0.9245 0.0672 95 A 0.0083 0.9225 0.0692 96 L 0.0084 0.9145 0.0770 97 N 0.0090 0.8873 0.1037 98 K 0.0133 0.8059 0.1808 99 A 0.0587 0.2114 0.7299 100 G 0.0540 0.0647 0.8813 101 Y 0.2538 0.0251 0.7211 102 Q 0.5947 0.0181 0.3872 103 L 0.7969 0.0070 0.1961 104 L 0.7989 0.0066 0.1945 105 L 0.7900 0.0080 0.2020 106 G 0.7118 0.0170 0.2712 107 Y 0.4837 0.0439 0.4723 108 S 0.2298 0.0977 0.6725 109 D 0.1241 0.2020 0.6739 110 Y 0.1213 0.2177 0.6609 111 S 0.1482 0.1543 0.6975 112 I 0.0186 0.7151 0.2662 113 E 0.0121 0.8405 0.1474 114 Q 0.0114 0.8997 0.0889 115 E 0.0086 0.9189 0.0726 116 E 0.0083 0.9226 0.0691 117 K 0.0083 0.9238 0.0679 118 L 0.0084 0.9204 0.0712 119 L 0.0084 0.9193 0.0724 120 S 0.0084 0.9201 0.0716 121 T 0.0087 0.9110 0.0803 122 F 0.0097 0.8888 0.1015 123 L 0.0115 0.8308 0.1577 124 E 0.0245 0.6845 0.2910 125 S 0.0700 0.2729 0.6571 126 R 0.2034 0.0597 0.7370 127 P 0.2408 0.0566 0.7026 128 A 0.3827 0.0594 0.5579 129 G 0.7548 0.0121 0.2331 130 V 0.7714 0.0060 0.2226 131 V 0.8026 0.0049 0.1926 132 L 0.7968 0.0061 0.1971 133 F 0.7080 0.0146 0.2774 134 G 0.3832 0.0362 0.5806 135 S 0.2037 0.1460 0.6502 136 E 0.1483 0.2095 0.6422 137 H 0.1492 0.2027 0.6481 138 S 0.1213 0.2631 0.6157 139 Q 0.0282 0.6641 0.3077 140 R 0.0183 0.7937 0.1880 141 T 0.0174 0.8601 0.1225 142 H 0.0122 0.8989 0.0889 143 Q 0.0094 0.9160 0.0746 144 L 0.0097 0.9139 0.0764 145 L 0.0096 0.9084 0.0820 146 E 0.0107 0.8663 0.1231 147 A 0.0211 0.7498 0.2291 148 S 0.0586 0.2510 0.6904 149 N 0.0505 0.0729 0.8765 150 T 0.2405 0.0161 0.7435 151 P 0.4518 0.0204 0.5279 152 V 0.7785 0.0069 0.2146 153 L 0.8148 0.0050 0.1802 154 E 0.7934 0.0047 0.2019 155 I 0.7487 0.0129 0.2384 156 A 0.5710 0.0377 0.3912 157 E 0.3859 0.0847 0.5294 158 L 0.2644 0.1289 0.6067 159 S 0.2085 0.1551 0.6364 160 S 0.1218 0.2641 0.6140 161 K 0.1366 0.2141 0.6493 162 A 0.1486 0.2340 0.6173 163 S 0.1764 0.1718 0.6518 164 Y 0.2630 0.1236 0.6134 165 L 0.3096 0.1161 0.5743 166 N 0.5229 0.0704 0.4067 167 I 0.5753 0.0581 0.3666 168 G 0.5520 0.0579 0.3901 169 V 0.3685 0.1724 0.4591 170 D 0.1954 0.2131 0.5915 171 H 0.0860 0.4887 0.4253 172 F 0.0260 0.7707 0.2033 173 E 0.0122 0.8589 0.1289 174 V 0.0095 0.9069 0.0836 175 G 0.0083 0.9219 0.0697 176 K 0.0083 0.9214 0.0703 177 A 0.0082 0.9251 0.0667 178 C 0.0083 0.9225 0.0692 179 T 0.0083 0.9218 0.0699 180 R 0.0083 0.9240 0.0677 181 H 0.0083 0.9247 0.0670 182 L 0.0083 0.9218 0.0699 183 I 0.0085 0.9033 0.0882 184 E 0.0108 0.8307 0.1586 185 Q 0.0485 0.3201 0.6313 186 G 0.0461 0.0879 0.8661 187 F 0.1631 0.0915 0.7454 188 K 0.2880 0.1062 0.6058 189 N 0.5908 0.0558 0.3534 190 V 0.7515 0.0274 0.2211 191 G 0.7687 0.0202 0.2111 192 F 0.7688 0.0176 0.2136 193 I 0.7228 0.0261 0.2511 194 G 0.5905 0.0360 0.3735 195 A 0.3404 0.0551 0.6045 196 R 0.1888 0.1415 0.6698 197 G 0.1108 0.2122 0.6770 198 N 0.1153 0.1978 0.6869 199 H 0.1239 0.2661 0.6100 200 S 0.0919 0.4600 0.4480 201 T 0.0660 0.6650 0.2690 202 L 0.0324 0.8220 0.1456 203 Q 0.0170 0.8899 0.0931 204 R 0.0122 0.9051 0.0827 205 Q 0.0111 0.9059 0.0830 206 L 0.0100 0.9038 0.0862 207 H 0.0092 0.9035 0.0873 208 G 0.0093 0.9082 0.0825 209 W 0.0085 0.9125 0.0790 210 Q 0.0083 0.9231 0.0686 211 S 0.0083 0.9248 0.0669 212 A 0.0083 0.9242 0.0675 213 M 0.0083 0.9199 0.0717 214 I 0.0087 0.8923 0.0990 215 E 0.0116 0.8115 0.1768 216 N 0.0532 0.3273 0.6195 217 Y 0.0494 0.0929 0.8576 218 L 0.1666 0.0522 0.7811 219 T 0.2122 0.0285 0.7593 220 P 0.1822 0.1769 0.6410 221 D 0.1895 0.1582 0.6523 222 H 0.1967 0.2939 0.5094 223 F 0.3164 0.2111 0.4725 224 L 0.4779 0.1221 0.4000 225 T 0.5110 0.0879 0.4010 226 T 0.4301 0.0852 0.4847 227 H 0.2807 0.1183 0.6010 228 E 0.2177 0.1096 0.6726 229 A 0.2042 0.0776 0.7182 230 P 0.1460 0.1944 0.6596 231 S 0.1487 0.2490 0.6023 232 S 0.0465 0.5938 0.3597 233 Q 0.0315 0.6897 0.2788 234 L 0.0325 0.7273 0.2402 235 G 0.0189 0.8275 0.1536 236 A 0.0094 0.9053 0.0853 237 E 0.0084 0.9191 0.0725 238 G 0.0083 0.9225 0.0691 239 L 0.0084 0.9192 0.0724 240 A 0.0083 0.9218 0.0699 241 K 0.0084 0.9194 0.0722 242 L 0.0089 0.9026 0.0885 243 L 0.0102 0.8467 0.1431 244 L 0.0197 0.6711 0.3091 245 R 0.0613 0.4272 0.5115 246 D 0.1230 0.2083 0.6688 247 S 0.0899 0.2368 0.6732 248 S 0.1908 0.1026 0.7066 249 L 0.3221 0.0804 0.5975 250 N 0.5028 0.0529 0.4444 251 A 0.7921 0.0087 0.1992 252 L 0.7735 0.0065 0.2201 253 V 0.8008 0.0069 0.1924 254 C 0.7260 0.0192 0.2548 255 S 0.4155 0.0883 0.4962 256 H 0.1627 0.2606 0.5768 257 E 0.0280 0.7215 0.2505 258 E 0.0124 0.8464 0.1411 259 I 0.0117 0.9063 0.0819 260 A 0.0094 0.9147 0.0759 261 I 0.0083 0.9204 0.0712 262 G 0.0083 0.9231 0.0686 263 A 0.0083 0.9211 0.0706 264 L 0.0083 0.9239 0.0679 265 F 0.0083 0.9241 0.0676 266 E 0.0083 0.9239 0.0678 267 C 0.0084 0.9170 0.0746 268 H 0.0088 0.8898 0.1013 269 R 0.0109 0.8174 0.1717 270 R 0.0412 0.3661 0.5926 271 V 0.0523 0.1224 0.8252 272 L 0.1961 0.0589 0.7450 273 K 0.2957 0.0417 0.6626 274 V 0.3432 0.0298 0.6271 275 P 0.2620 0.0540 0.6840 276 T 0.2277 0.2403 0.5320 277 D 0.3498 0.0994 0.5508 278 I 0.5982 0.0220 0.3798 279 A 0.7440 0.0115 0.2445 280 I 0.8014 0.0066 0.1921 281 I 0.7864 0.0098 0.2038 282 C 0.7198 0.0122 0.2679 283 L 0.5287 0.0591 0.4122 284 E 0.2549 0.0909 0.6542 285 G 0.1313 0.0872 0.7815 286 S 0.1959 0.1370 0.6671 287 S 0.1818 0.2869 0.5314 288 M 0.1636 0.3991 0.4372 289 G 0.1417 0.4782 0.3801 290 E 0.1394 0.4740 0.3866 291 H 0.2032 0.3246 0.4722 292 A 0.2587 0.1842 0.5571 293 Y 0.2713 0.0831 0.6456 294 P 0.1970 0.1413 0.6617 295 S 0.2155 0.1609 0.6236 296 L 0.2881 0.1875 0.5244 297 T 0.3462 0.1316 0.5222 298 S 0.3666 0.1454 0.4879 299 A 0.3164 0.2060 0.4775 300 E 0.3392 0.1934 0.4674 301 F 0.3075 0.1374 0.5551 302 D 0.1891 0.1605 0.6503 303 Y 0.0184 0.7446 0.2371 304 E 0.0099 0.8609 0.1293 305 R 0.0093 0.9066 0.0841 306 M 0.0087 0.9132 0.0781 307 G 0.0083 0.9207 0.0709 308 T 0.0083 0.9220 0.0697 309 K 0.0083 0.9247 0.0671 310 A 0.0083 0.9245 0.0672 311 A 0.0083 0.9245 0.0672 312 E 0.0083 0.9242 0.0675 313 K 0.0083 0.9247 0.0671 314 L 0.0083 0.9197 0.0720 315 L 0.0084 0.9188 0.0728 316 H 0.0084 0.9148 0.0768 317 A 0.0101 0.8565 0.1333 318 I 0.0238 0.7270 0.2493 319 K 0.0534 0.3432 0.6035 320 G 0.0447 0.1159 0.8395 321 E 0.1658 0.0410 0.7932 322 P 0.1727 0.0998 0.7275 323 E 0.2056 0.1571 0.6373 324 E 0.2276 0.1225 0.6499 325 R 0.2602 0.0531 0.6867 326 P 0.2603 0.1063 0.6334 327 T 0.3666 0.0967 0.5367 328 S 0.4405 0.0633 0.4962 329 M 0.4430 0.0647 0.4923 330 G 0.4024 0.0546 0.5431 331 F 0.3885 0.0733 0.5382 332 K 0.4102 0.0851 0.5047 333 L 0.5048 0.0604 0.4348 334 K 0.6564 0.0349 0.3087 335 R 0.7088 0.0301 0.2610 336 R 0.6654 0.0390 0.2955 337 A 0.5258 0.0830 0.3912 338 S 0.3673 0.1218 0.5109 339 T 0.3113 0.1064 0.5823 340 A 0.2920 0.1037 0.6043 341 I 0.2895 0.0813 0.6292 342 N 0.2272 0.0885 0.6843