# This file is the result of combining several RDB files, specifically # T0457.t06.str2.rdb (weight 1.54425) # T0457.t06.str4.rdb (weight 0.924988) # T0457.t06.pb.rdb (weight 0.789901) # T0457.t06.bys.rdb (weight 0.748322) # T0457.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 T0457.t06.str2.rdb # ============================================ # TARGET T0457 # 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 T0457.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 1719 # # ============================================ # Comments from T0457.t06.str4.rdb # ============================================ # TARGET T0457 # 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 T0457.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 1719 # # ============================================ # Comments from T0457.t06.pb.rdb # ============================================ # TARGET T0457 # 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 T0457.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 1719 # # ============================================ # Comments from T0457.t06.bys.rdb # ============================================ # TARGET T0457 # 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 T0457.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 1719 # # ============================================ # Comments from T0457.t06.alpha.rdb # ============================================ # TARGET T0457 # 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 T0457.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 1719 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0238 0.8044 0.1718 2 V 0.0091 0.9017 0.0892 3 E 0.0084 0.9200 0.0716 4 I 0.0083 0.9218 0.0699 5 F 0.0084 0.9191 0.0726 6 N 0.0083 0.9237 0.0680 7 E 0.0083 0.9244 0.0673 8 I 0.0083 0.9238 0.0679 9 M 0.0084 0.9184 0.0732 10 Q 0.0083 0.9207 0.0710 11 R 0.0086 0.9115 0.0799 12 V 0.0098 0.9014 0.0888 13 K 0.0108 0.8461 0.1431 14 E 0.0220 0.5198 0.4583 15 A 0.0958 0.2459 0.6584 16 E 0.1469 0.1532 0.6998 17 T 0.5027 0.0426 0.4547 18 I 0.7639 0.0086 0.2274 19 I 0.8087 0.0062 0.1851 20 I 0.7919 0.0076 0.2005 21 H 0.7544 0.0177 0.2279 22 R 0.6245 0.0342 0.3413 23 H 0.4131 0.0540 0.5329 24 V 0.3017 0.0997 0.5986 25 R 0.2498 0.0509 0.6993 26 P 0.1230 0.1902 0.6867 27 D 0.1833 0.0895 0.7272 28 P 0.0275 0.4619 0.5106 29 D 0.0405 0.5960 0.3635 30 A 0.0248 0.8140 0.1612 31 Y 0.0124 0.8874 0.1002 32 G 0.0089 0.9180 0.0731 33 S 0.0083 0.9229 0.0688 34 Q 0.0083 0.9232 0.0685 35 L 0.0083 0.9241 0.0676 36 G 0.0083 0.9250 0.0667 37 L 0.0083 0.9244 0.0673 38 K 0.0083 0.9235 0.0682 39 L 0.0083 0.9218 0.0699 40 Y 0.0084 0.9194 0.0722 41 L 0.0087 0.9068 0.0845 42 E 0.0100 0.8568 0.1332 43 R 0.0212 0.6442 0.3347 44 K 0.0564 0.3014 0.6423 45 F 0.1369 0.0942 0.7689 46 P 0.0977 0.2591 0.6433 47 E 0.1602 0.1567 0.6831 48 K 0.4197 0.0521 0.5282 49 N 0.6239 0.0243 0.3518 50 I 0.7649 0.0102 0.2250 51 Y 0.7382 0.0157 0.2460 52 A 0.6011 0.0214 0.3775 53 T 0.2722 0.0898 0.6380 54 G 0.1255 0.0921 0.7824 55 E 0.2103 0.1068 0.6830 56 A 0.2531 0.1144 0.6324 57 E 0.2080 0.1093 0.6826 58 P 0.0782 0.4350 0.4868 59 S 0.0845 0.4007 0.5147 60 L 0.1473 0.4092 0.4435 61 S 0.1643 0.3581 0.4776 62 F 0.1610 0.3925 0.4465 63 I 0.1394 0.4300 0.4306 64 G 0.0590 0.5992 0.3418 65 D 0.0705 0.5673 0.3622 66 L 0.0943 0.5628 0.3429 67 D 0.0683 0.5920 0.3397 68 E 0.0841 0.5755 0.3404 69 I 0.1347 0.4112 0.4540 70 D 0.1313 0.3130 0.5556 71 D 0.0523 0.5058 0.4418 72 S 0.0642 0.4642 0.4717 73 V 0.1421 0.2981 0.5598 74 Y 0.1739 0.1722 0.6540 75 S 0.1654 0.1534 0.6812 76 D 0.1965 0.1477 0.6558 77 A 0.3716 0.0616 0.5668 78 L 0.7221 0.0145 0.2634 79 V 0.7766 0.0067 0.2167 80 I 0.8045 0.0056 0.1898 81 V 0.7869 0.0070 0.2062 82 C 0.7390 0.0159 0.2451 83 D 0.4295 0.0442 0.5263 84 T 0.1856 0.1513 0.6631 85 A 0.1317 0.1937 0.6745 86 N 0.1423 0.1560 0.7017 87 A 0.1752 0.1483 0.6765 88 P 0.1203 0.3050 0.5747 89 R 0.1433 0.3241 0.5327 90 I 0.1650 0.3065 0.5285 91 D 0.1194 0.4381 0.4425 92 D 0.0320 0.7383 0.2297 93 Q 0.0306 0.7760 0.1934 94 R 0.0392 0.7677 0.1931 95 Y 0.0636 0.6919 0.2445 96 L 0.0607 0.5568 0.3824 97 N 0.0765 0.3012 0.6223 98 G 0.1166 0.1569 0.7265 99 Q 0.2331 0.0678 0.6992 100 S 0.5876 0.0162 0.3961 101 L 0.7620 0.0082 0.2298 102 I 0.8090 0.0052 0.1858 103 K 0.7869 0.0068 0.2063 104 I 0.7479 0.0164 0.2357 105 D 0.5513 0.0602 0.3884 106 H 0.2847 0.0816 0.6337 107 H 0.2511 0.0400 0.7089 108 P 0.1116 0.2095 0.6789 109 A 0.1038 0.2618 0.6344 110 T 0.0922 0.3447 0.5631 111 D 0.0928 0.3557 0.5515 112 Q 0.1281 0.3189 0.5530 113 Y 0.1680 0.1586 0.6734 114 G 0.1504 0.1424 0.7072 115 D 0.2057 0.1403 0.6541 116 V 0.3258 0.1179 0.5562 117 N 0.4792 0.0984 0.4225 118 F 0.6123 0.0618 0.3258 119 V 0.5756 0.0413 0.3831 120 N 0.3308 0.0290 0.6402 121 T 0.1180 0.2903 0.5917 122 E 0.1082 0.2885 0.6033 123 A 0.1374 0.2861 0.5765 124 S 0.1091 0.4058 0.4851 125 S 0.0816 0.6012 0.3172 126 T 0.0370 0.7968 0.1662 127 S 0.0135 0.8961 0.0903 128 E 0.0104 0.9170 0.0726 129 I 0.0092 0.9215 0.0692 130 I 0.0083 0.9238 0.0679 131 F 0.0083 0.9225 0.0692 132 D 0.0083 0.9238 0.0679 133 F 0.0084 0.9208 0.0708 134 I 0.0087 0.9093 0.0820 135 S 0.0090 0.8851 0.1058 136 H 0.0136 0.7637 0.2227 137 F 0.0536 0.4752 0.4713 138 N 0.0471 0.2933 0.6596 139 D 0.0873 0.2943 0.6184 140 L 0.1107 0.3347 0.5545 141 S 0.1537 0.2788 0.5675 142 I 0.2107 0.1699 0.6194 143 I 0.2340 0.1323 0.6337 144 D 0.1641 0.1458 0.6902 145 E 0.0129 0.7488 0.2384 146 H 0.0102 0.8459 0.1439 147 V 0.0093 0.9072 0.0835 148 A 0.0084 0.9197 0.0720 149 R 0.0084 0.9197 0.0720 150 V 0.0095 0.9159 0.0745 151 L 0.0130 0.9068 0.0802 152 Y 0.0317 0.8667 0.1017 153 L 0.0706 0.7555 0.1740 154 G 0.1340 0.6586 0.2073 155 I 0.2099 0.5433 0.2469 156 V 0.2872 0.3432 0.3696 157 G 0.2116 0.2638 0.5246 158 D 0.1762 0.2110 0.6128 159 T 0.0857 0.2652 0.6491 160 G 0.0858 0.2896 0.6246 161 R 0.1568 0.3817 0.4615 162 F 0.2221 0.3224 0.4555 163 L 0.2667 0.2249 0.5084 164 F 0.2439 0.1559 0.6001 165 S 0.1604 0.2268 0.6129 166 N 0.1493 0.1723 0.6784 167 T 0.2265 0.0959 0.6777 168 S 0.2007 0.0489 0.7504 169 P 0.0445 0.5267 0.4288 170 H 0.0323 0.6769 0.2908 171 T 0.0281 0.8082 0.1637 172 M 0.0116 0.8910 0.0973 173 E 0.0096 0.9126 0.0778 174 V 0.0092 0.9197 0.0711 175 A 0.0084 0.9192 0.0724 176 S 0.0085 0.9138 0.0777 177 Q 0.0093 0.8975 0.0933 178 L 0.0150 0.8259 0.1591 179 L 0.0241 0.6990 0.2769 180 A 0.0376 0.4629 0.4995 181 Y 0.1229 0.1869 0.6902 182 P 0.0702 0.3553 0.5745 183 F 0.0797 0.3690 0.5513 184 N 0.0843 0.3322 0.5834 185 H 0.0242 0.7555 0.2204 186 N 0.0136 0.8583 0.1281 187 A 0.0101 0.9093 0.0806 188 E 0.0098 0.9106 0.0797 189 L 0.0095 0.9060 0.0845 190 N 0.0088 0.9003 0.0908 191 K 0.0109 0.8693 0.1198 192 M 0.0268 0.7547 0.2185 193 S 0.0327 0.6517 0.3156 194 E 0.0422 0.5149 0.4429 195 K 0.1030 0.2774 0.6195 196 D 0.1703 0.0725 0.7572 197 P 0.0178 0.6174 0.3648 198 K 0.0241 0.5780 0.3978 199 L 0.0585 0.5647 0.3768 200 M 0.1243 0.4524 0.4233 201 P 0.0742 0.5828 0.3430 202 F 0.0333 0.7834 0.1833 203 Q 0.0138 0.8708 0.1154 204 G 0.0098 0.9024 0.0879 205 Y 0.0108 0.9064 0.0828 206 V 0.0126 0.8971 0.0903 207 L 0.0112 0.8937 0.0951 208 Q 0.0132 0.8462 0.1406 209 N 0.0215 0.7524 0.2261 210 F 0.0411 0.7457 0.2132 211 E 0.0520 0.7324 0.2156 212 L 0.0917 0.6359 0.2723 213 S 0.1353 0.4836 0.3811 214 D 0.1230 0.4035 0.4734 215 S 0.0882 0.3790 0.5328 216 H 0.1016 0.2496 0.6488 217 E 0.1610 0.2159 0.6230 218 Y 0.3532 0.1556 0.4912 219 C 0.4938 0.1304 0.3758 220 Q 0.6370 0.0931 0.2699 221 I 0.6522 0.0862 0.2616 222 K 0.6253 0.0932 0.2815 223 I 0.5668 0.1070 0.3262 224 T 0.4348 0.1718 0.3933 225 N 0.3075 0.3426 0.3499 226 D 0.2943 0.4358 0.2699 227 V 0.3056 0.4410 0.2535 228 L 0.2966 0.3851 0.3184 229 K 0.2307 0.3595 0.4098 230 Q 0.1716 0.3237 0.5047 231 F 0.1328 0.2847 0.5825 232 D 0.1407 0.2041 0.6552 233 I 0.2259 0.1390 0.6351 234 Q 0.2070 0.0511 0.7419 235 P 0.0562 0.4627 0.4811 236 N 0.0541 0.4617 0.4842 237 E 0.0635 0.6537 0.2827 238 A 0.0301 0.8155 0.1544 239 S 0.0164 0.8795 0.1041 240 Q 0.0144 0.8978 0.0878 241 F 0.0143 0.8993 0.0864 242 V 0.0124 0.9011 0.0865 243 N 0.0110 0.8979 0.0911 244 T 0.0110 0.8961 0.0929 245 V 0.0183 0.8683 0.1134 246 A 0.0212 0.8393 0.1395 247 D 0.0267 0.7965 0.1768 248 I 0.0360 0.6978 0.2662 249 S 0.0632 0.2376 0.6992 250 G 0.0415 0.0846 0.8739 251 L 0.2150 0.0173 0.7676 252 K 0.4151 0.0254 0.5595 253 I 0.7682 0.0071 0.2246 254 W 0.8104 0.0057 0.1839 255 M 0.8198 0.0045 0.1757 256 F 0.8034 0.0061 0.1905 257 G 0.7715 0.0076 0.2209 258 V 0.6335 0.0128 0.3537 259 D 0.4197 0.0291 0.5512 260 E 0.1619 0.1457 0.6923 261 G 0.0923 0.0939 0.8138 262 D 0.2024 0.0653 0.7324 263 Q 0.5991 0.0161 0.3847 264 I 0.7672 0.0071 0.2257 265 R 0.8113 0.0050 0.1838 266 C 0.8242 0.0045 0.1713 267 R 0.8105 0.0049 0.1846 268 I 0.7683 0.0099 0.2218 269 R 0.6023 0.0327 0.3650 270 S 0.4358 0.0532 0.5109 271 K 0.1788 0.1355 0.6856 272 G 0.1123 0.1206 0.7671 273 I 0.2522 0.0443 0.7034 274 T 0.1942 0.0400 0.7659 275 I 0.0213 0.7348 0.2440 276 N 0.0146 0.8507 0.1347 277 D 0.0135 0.9028 0.0837 278 V 0.0104 0.9122 0.0774 279 A 0.0095 0.9063 0.0842 280 N 0.0119 0.8696 0.1185 281 Q 0.0215 0.7331 0.2454 282 F 0.0741 0.3629 0.5630 283 G 0.0585 0.2110 0.7304 284 G 0.0912 0.1839 0.7249 285 G 0.1337 0.1889 0.6774 286 G 0.1840 0.1883 0.6278 287 H 0.2032 0.1585 0.6383 288 P 0.0855 0.4870 0.4275 289 N 0.1113 0.4207 0.4680 290 A 0.2124 0.3607 0.4269 291 S 0.2937 0.2315 0.4747 292 G 0.3653 0.1361 0.4986 293 V 0.5373 0.0463 0.4164 294 S 0.5462 0.0396 0.4142 295 V 0.3890 0.0587 0.5523 296 Y 0.2270 0.1316 0.6414 297 S 0.1821 0.1779 0.6400 298 W 0.0474 0.6025 0.3502 299 D 0.0282 0.6889 0.2829 300 E 0.0337 0.7410 0.2254 301 F 0.0110 0.8574 0.1316 302 E 0.0084 0.9143 0.0773 303 E 0.0083 0.9243 0.0674 304 L 0.0083 0.9240 0.0678 305 A 0.0083 0.9204 0.0712 306 Q 0.0083 0.9239 0.0678 307 A 0.0083 0.9222 0.0695 308 L 0.0083 0.9214 0.0702 309 R 0.0085 0.9124 0.0791 310 Q 0.0085 0.9113 0.0802 311 K 0.0096 0.8841 0.1063 312 L 0.0163 0.8352 0.1485 313 L 0.0158 0.8074 0.1768 314 E 0.0274 0.7320 0.2406 315 H 0.0578 0.5575 0.3847 316 H 0.0847 0.4137 0.5017 317 H 0.1324 0.2635 0.6041 318 H 0.1422 0.2127 0.6451 319 H 0.1581 0.1711 0.6708 320 H 0.1677 0.1559 0.6765