# This file is the result of combining several RDB files, specifically # T0413.t04.str2.rdb (weight 1.54425) # T0413.t04.str4.rdb (weight 0.924988) # T0413.t04.pb.rdb (weight 0.789901) # T0413.t04.bys.rdb (weight 0.748322) # T0413.t04.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 T0413.t04.str2.rdb # ============================================ # TARGET T0413 # Using neural net dunbrack-40pc-3157-t04-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 T0413.t04-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 2018 # # ============================================ # Comments from T0413.t04.str4.rdb # ============================================ # TARGET T0413 # Using neural net dunbrack-40pc-3157-t04-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 T0413.t04-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 2018 # # ============================================ # Comments from T0413.t04.pb.rdb # ============================================ # TARGET T0413 # Using neural net dunbrack-40pc-3157-t04-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 T0413.t04-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 2018 # # ============================================ # Comments from T0413.t04.bys.rdb # ============================================ # TARGET T0413 # Using neural net dunbrack-40pc-3157-t04-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 T0413.t04-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 2018 # # ============================================ # Comments from T0413.t04.alpha.rdb # ============================================ # TARGET T0413 # Using neural net dunbrack-40pc-3157-t04-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 T0413.t04-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 2018 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1743 0.2485 0.5771 2 N 0.1664 0.2365 0.5971 3 A 0.2195 0.1743 0.6062 4 M 0.2759 0.0882 0.6359 5 K 0.2555 0.0386 0.7060 6 P 0.1998 0.2009 0.5993 7 A 0.1627 0.3637 0.4736 8 D 0.1687 0.3205 0.5108 9 L 0.1203 0.4491 0.4305 10 T 0.1182 0.4486 0.4332 11 N 0.1219 0.4383 0.4398 12 A 0.0976 0.5469 0.3555 13 D 0.0751 0.6485 0.2765 14 R 0.0605 0.7268 0.2127 15 I 0.0686 0.7280 0.2033 16 A 0.0735 0.7119 0.2146 17 L 0.0735 0.6979 0.2286 18 E 0.0825 0.6013 0.3162 19 L 0.1101 0.4389 0.4510 20 G 0.1214 0.2516 0.6270 21 H 0.1847 0.1781 0.6373 22 A 0.1728 0.1626 0.6646 23 G 0.1450 0.1231 0.7318 24 R 0.1768 0.1463 0.6770 25 N 0.2447 0.0842 0.6711 26 A 0.3345 0.0656 0.6000 27 I 0.4960 0.0275 0.4765 28 P 0.5920 0.0281 0.3799 29 Y 0.6418 0.0274 0.3309 30 L 0.6201 0.0239 0.3560 31 D 0.4534 0.0504 0.4962 32 D 0.3534 0.1153 0.5313 33 D 0.2768 0.1760 0.5472 34 R 0.1703 0.2532 0.5764 35 N 0.1663 0.1776 0.6562 36 A 0.1192 0.1838 0.6970 37 D 0.1284 0.1116 0.7600 38 R 0.3358 0.0348 0.6294 39 P 0.5331 0.0320 0.4349 40 F 0.7088 0.0197 0.2714 41 T 0.7399 0.0144 0.2457 42 L 0.7773 0.0090 0.2137 43 N 0.7806 0.0103 0.2091 44 T 0.7904 0.0086 0.2010 45 Y 0.7366 0.0149 0.2485 46 R 0.5697 0.0166 0.4137 47 P 0.3338 0.0393 0.6268 48 Y 0.1477 0.1791 0.6731 49 G 0.0806 0.1269 0.7925 50 Y 0.1778 0.0860 0.7362 51 T 0.1971 0.0372 0.7657 52 P 0.1327 0.2272 0.6401 53 D 0.1508 0.1375 0.7117 54 R 0.3076 0.0277 0.6647 55 P 0.4633 0.0189 0.5178 56 V 0.7987 0.0066 0.1947 57 V 0.8105 0.0046 0.1849 58 V 0.8118 0.0046 0.1836 59 V 0.7952 0.0069 0.1980 60 Q 0.6937 0.0237 0.2826 61 H 0.4461 0.0508 0.5031 62 G 0.2579 0.0793 0.6629 63 V 0.2300 0.1168 0.6532 64 L 0.1868 0.1794 0.6337 65 R 0.1591 0.2209 0.6200 66 N 0.1461 0.1801 0.6738 67 G 0.1178 0.2580 0.6242 68 A 0.1109 0.3548 0.5343 69 D 0.1428 0.3414 0.5158 70 Y 0.0959 0.4752 0.4289 71 R 0.0786 0.5247 0.3967 72 D 0.0727 0.5260 0.4013 73 F 0.0759 0.4873 0.4368 74 W 0.0869 0.4895 0.4236 75 I 0.0773 0.5652 0.3574 76 P 0.0350 0.7657 0.1993 77 A 0.0228 0.8377 0.1395 78 A 0.0224 0.8341 0.1435 79 D 0.0270 0.7651 0.2079 80 R 0.0559 0.5116 0.4326 81 H 0.0941 0.1724 0.7335 82 K 0.1133 0.0568 0.8298 83 L 0.4518 0.0094 0.5388 84 L 0.7039 0.0108 0.2853 85 I 0.8020 0.0047 0.1934 86 V 0.7852 0.0083 0.2066 87 A 0.6755 0.0081 0.3164 88 P 0.4191 0.0480 0.5329 89 T 0.2571 0.0886 0.6543 90 F 0.2184 0.0889 0.6928 91 S 0.1472 0.1667 0.6860 92 D 0.1290 0.1977 0.6733 93 E 0.1909 0.1670 0.6421 94 I 0.2259 0.1495 0.6246 95 W 0.2241 0.0982 0.6776 96 P 0.1500 0.2264 0.6236 97 G 0.1139 0.1645 0.7216 98 V 0.1807 0.2292 0.5901 99 E 0.1665 0.3072 0.5262 100 S 0.1650 0.3118 0.5232 101 Y 0.1403 0.2920 0.5677 102 N 0.1417 0.2555 0.6028 103 N 0.1221 0.1943 0.6836 104 G 0.1186 0.1471 0.7343 105 R 0.2224 0.2073 0.5703 106 A 0.3011 0.2496 0.4492 107 F 0.3647 0.2069 0.4283 108 T 0.3159 0.2257 0.4584 109 A 0.2257 0.3406 0.4338 110 A 0.1766 0.2456 0.5778 111 G 0.1673 0.1501 0.6825 112 N 0.1996 0.0557 0.7447 113 P 0.1379 0.2745 0.5876 114 R 0.1518 0.2629 0.5853 115 H 0.1673 0.1835 0.6492 116 V 0.1403 0.2473 0.6124 117 D 0.1094 0.1910 0.6996 118 G 0.0823 0.2313 0.6864 119 W 0.1458 0.3439 0.5103 120 T 0.1639 0.4297 0.4064 121 Y 0.0131 0.8068 0.1801 122 A 0.0090 0.8825 0.1085 123 L 0.0084 0.9199 0.0717 124 V 0.0083 0.9214 0.0702 125 A 0.0083 0.9235 0.0682 126 R 0.0083 0.9218 0.0700 127 V 0.0083 0.9236 0.0681 128 L 0.0083 0.9227 0.0690 129 A 0.0083 0.9225 0.0692 130 N 0.0084 0.9169 0.0746 131 I 0.0085 0.9155 0.0760 132 R 0.0091 0.8866 0.1043 133 A 0.0114 0.7967 0.1919 134 A 0.0357 0.5134 0.4509 135 E 0.0769 0.2603 0.6628 136 I 0.1481 0.1876 0.6643 137 A 0.2531 0.1087 0.6382 138 D 0.2189 0.0403 0.7408 139 C 0.0627 0.4707 0.4666 140 E 0.1209 0.3818 0.4973 141 Q 0.4130 0.1351 0.4519 142 V 0.7023 0.0254 0.2723 143 Y 0.7420 0.0221 0.2359 144 L 0.7536 0.0238 0.2226 145 F 0.5725 0.0615 0.3661 146 G 0.3422 0.0936 0.5642 147 H 0.1910 0.2286 0.5804 148 S 0.1213 0.3468 0.5319 149 A 0.0404 0.6024 0.3572 150 G 0.0271 0.7669 0.2061 151 G 0.0115 0.8986 0.0899 152 Q 0.0093 0.9193 0.0714 153 F 0.0087 0.9231 0.0682 154 V 0.0086 0.9235 0.0679 155 H 0.0085 0.9233 0.0682 156 R 0.0086 0.9210 0.0704 157 L 0.0091 0.9093 0.0817 158 M 0.0117 0.8681 0.1202 159 S 0.0214 0.7425 0.2360 160 S 0.0513 0.4427 0.5060 161 Q 0.1493 0.1392 0.7115 162 P 0.0583 0.3624 0.5794 163 H 0.0783 0.2426 0.6792 164 A 0.1997 0.1863 0.6140 165 P 0.2443 0.2026 0.5531 166 F 0.3417 0.2541 0.4042 167 H 0.4620 0.2319 0.3061 168 A 0.7053 0.0769 0.2178 169 V 0.7224 0.0556 0.2220 170 T 0.7206 0.0494 0.2300 171 A 0.5806 0.0951 0.3243 172 A 0.3935 0.1252 0.4812 173 N 0.2525 0.0882 0.6593 174 P 0.1523 0.2294 0.6183 175 G 0.1453 0.2318 0.6229 176 W 0.1666 0.2181 0.6153 177 Y 0.1851 0.1397 0.6752 178 T 0.1653 0.2122 0.6225 179 L 0.2107 0.1256 0.6637 180 P 0.1625 0.2769 0.5606 181 T 0.1539 0.3641 0.4820 182 F 0.1645 0.3692 0.4663 183 E 0.1443 0.3700 0.4857 184 H 0.1874 0.2946 0.5179 185 R 0.2385 0.1764 0.5852 186 F 0.2464 0.0705 0.6831 187 P 0.1740 0.1309 0.6951 188 E 0.1235 0.1957 0.6808 189 G 0.0942 0.1198 0.7860 190 L 0.1840 0.1051 0.7109 191 D 0.1497 0.1809 0.6694 192 G 0.1095 0.2192 0.6713 193 V 0.1562 0.1862 0.6576 194 G 0.1776 0.1341 0.6883 195 L 0.2117 0.0998 0.6886 196 T 0.1795 0.0306 0.7899 197 E 0.0262 0.6402 0.3336 198 D 0.0142 0.7935 0.1923 199 H 0.0172 0.8516 0.1313 200 L 0.0172 0.8525 0.1302 201 A 0.0229 0.8300 0.1471 202 R 0.0189 0.7233 0.2578 203 L 0.0418 0.5261 0.4321 204 L 0.1197 0.2941 0.5863 205 A 0.1542 0.1634 0.6824 206 Y 0.2640 0.0547 0.6813 207 P 0.3618 0.0749 0.5633 208 M 0.7540 0.0260 0.2201 209 T 0.7806 0.0184 0.2010 210 I 0.7845 0.0168 0.1986 211 L 0.7217 0.0311 0.2472 212 A 0.4838 0.0553 0.4608 213 G 0.2483 0.0713 0.6804 214 D 0.1821 0.1857 0.6322 215 Q 0.1524 0.2701 0.5775 216 D 0.1882 0.2249 0.5869 217 I 0.1619 0.2854 0.5527 218 A 0.2267 0.1858 0.5876 219 T 0.3014 0.0671 0.6315 220 D 0.2108 0.0566 0.7326 221 D 0.1684 0.2165 0.6151 222 P 0.0454 0.4735 0.4811 223 N 0.0569 0.2980 0.6451 224 L 0.1343 0.1776 0.6880 225 P 0.0676 0.4280 0.5043 226 S 0.0818 0.4820 0.4362 227 E 0.0757 0.5663 0.3581 228 P 0.0163 0.8262 0.1574 229 A 0.0100 0.8917 0.0983 230 A 0.0100 0.8936 0.0964 231 L 0.0184 0.8295 0.1521 232 R 0.0246 0.7173 0.2580 233 Q 0.0733 0.3433 0.5834 234 G 0.0939 0.1583 0.7478 235 P 0.1059 0.2927 0.6013 236 H 0.1502 0.2305 0.6193 237 R 0.1677 0.2425 0.5898 238 Y 0.1880 0.2914 0.5206 239 A 0.1809 0.3230 0.4962 240 R 0.1936 0.3202 0.4862 241 A 0.2188 0.2506 0.5305 242 R 0.2116 0.2832 0.5052 243 H 0.2100 0.2550 0.5349 244 Y 0.2069 0.2513 0.5418 245 Y 0.1959 0.2373 0.5668 246 E 0.1674 0.2604 0.5722 247 A 0.1925 0.2208 0.5867 248 G 0.1922 0.2315 0.5764 249 Q 0.2611 0.2992 0.4397 250 R 0.3053 0.3378 0.3568 251 A 0.2786 0.4124 0.3089 252 A 0.2307 0.4426 0.3267 253 A 0.1678 0.4761 0.3561 254 Q 0.1495 0.4142 0.4364 255 R 0.1314 0.3084 0.5602 256 G 0.1315 0.1719 0.6966 257 L 0.2258 0.0831 0.6912 258 P 0.2427 0.0702 0.6871 259 F 0.3660 0.0433 0.5907 260 G 0.4353 0.0289 0.5357 261 W 0.6605 0.0121 0.3274 262 Q 0.7282 0.0118 0.2601 263 L 0.7817 0.0055 0.2129 264 Q 0.7668 0.0100 0.2232 265 V 0.7319 0.0088 0.2593 266 V 0.5094 0.0170 0.4736 267 P 0.2209 0.0767 0.7023 268 G 0.1133 0.0838 0.8029 269 I 0.1921 0.1087 0.6992 270 G 0.1945 0.1045 0.7010 271 H 0.2184 0.1307 0.6510 272 D 0.2254 0.1618 0.6128 273 G 0.2384 0.1919 0.5697 274 Q 0.2179 0.2570 0.5251 275 A 0.1759 0.3510 0.4732 276 M 0.1083 0.5085 0.3831 277 S 0.0662 0.6505 0.2833 278 Q 0.0526 0.7266 0.2208 279 V 0.0492 0.7778 0.1730 280 C 0.0360 0.8291 0.1349 281 A 0.0221 0.8671 0.1108 282 S 0.0226 0.8732 0.1042 283 L 0.0233 0.8739 0.1028 284 W 0.0301 0.8462 0.1237 285 F 0.0418 0.7638 0.1944 286 D 0.0488 0.6400 0.3112 287 G 0.0514 0.4490 0.4996 288 R 0.0986 0.3031 0.5983 289 M 0.1448 0.2116 0.6436 290 P 0.0456 0.5490 0.4054 291 D 0.0499 0.5570 0.3931 292 A 0.0360 0.7164 0.2477 293 A 0.0339 0.7574 0.2088 294 E 0.0498 0.7375 0.2126 295 L 0.0391 0.7709 0.1901 296 A 0.0281 0.8075 0.1643 297 R 0.0381 0.7749 0.1869 298 L 0.0569 0.6452 0.2979 299 A 0.0826 0.4334 0.4840 300 G 0.0750 0.2763 0.6486 301 S 0.1242 0.2441 0.6318 302 Q 0.1440 0.2835 0.5725 303 S 0.1680 0.2422 0.5898 304 A 0.1900 0.1992 0.6108