# This file is the result of combining several RDB files, specifically # T0413.t06.str2.rdb (weight 1.54425) # T0413.t06.str4.rdb (weight 0.924988) # T0413.t06.pb.rdb (weight 0.789901) # T0413.t06.bys.rdb (weight 0.748322) # T0413.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 T0413.t06.str2.rdb # ============================================ # TARGET T0413 # 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 T0413.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 17823 # # ============================================ # Comments from T0413.t06.str4.rdb # ============================================ # TARGET T0413 # 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 T0413.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 17823 # # ============================================ # Comments from T0413.t06.pb.rdb # ============================================ # TARGET T0413 # 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 T0413.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 17823 # # ============================================ # Comments from T0413.t06.bys.rdb # ============================================ # TARGET T0413 # 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 T0413.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 17823 # # ============================================ # Comments from T0413.t06.alpha.rdb # ============================================ # TARGET T0413 # 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 T0413.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 17823 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1803 0.1771 0.6426 2 N 0.1867 0.1395 0.6738 3 A 0.1787 0.1690 0.6523 4 M 0.2200 0.1149 0.6651 5 K 0.2336 0.0396 0.7268 6 P 0.2087 0.0941 0.6973 7 A 0.1683 0.2654 0.5662 8 D 0.1806 0.2359 0.5835 9 L 0.1422 0.3090 0.5488 10 T 0.1466 0.2821 0.5713 11 N 0.1417 0.2802 0.5781 12 A 0.1016 0.4298 0.4687 13 D 0.1034 0.4754 0.4212 14 R 0.1162 0.5109 0.3728 15 I 0.1384 0.4920 0.3696 16 A 0.1413 0.4784 0.3803 17 L 0.1369 0.4684 0.3948 18 E 0.1348 0.3959 0.4693 19 L 0.1699 0.2590 0.5710 20 G 0.2003 0.1654 0.6343 21 H 0.2923 0.1168 0.5910 22 A 0.2889 0.1180 0.5932 23 G 0.3242 0.0993 0.5765 24 R 0.4800 0.0703 0.4497 25 N 0.6204 0.0416 0.3380 26 A 0.6368 0.0282 0.3350 27 I 0.5966 0.0193 0.3840 28 P 0.4526 0.0360 0.5114 29 Y 0.3555 0.0623 0.5822 30 L 0.2458 0.1643 0.5899 31 D 0.2198 0.1280 0.6522 32 D 0.1101 0.2856 0.6043 33 D 0.1087 0.2968 0.5945 34 R 0.1243 0.2784 0.5973 35 N 0.1161 0.2050 0.6789 36 A 0.1189 0.1986 0.6825 37 D 0.1143 0.0997 0.7860 38 R 0.3524 0.0309 0.6167 39 P 0.5405 0.0295 0.4299 40 F 0.6958 0.0236 0.2807 41 T 0.7527 0.0153 0.2320 42 L 0.7772 0.0120 0.2108 43 N 0.7643 0.0165 0.2191 44 T 0.7732 0.0163 0.2105 45 Y 0.7192 0.0241 0.2566 46 R 0.6168 0.0159 0.3673 47 P 0.4196 0.0487 0.5317 48 Y 0.1856 0.1783 0.6361 49 G 0.1207 0.1316 0.7476 50 Y 0.1997 0.1138 0.6865 51 T 0.2244 0.0546 0.7211 52 P 0.1326 0.1828 0.6845 53 D 0.1485 0.1165 0.7351 54 R 0.2863 0.0363 0.6773 55 P 0.3595 0.0284 0.6122 56 V 0.7645 0.0076 0.2279 57 V 0.8142 0.0049 0.1809 58 V 0.8101 0.0048 0.1851 59 V 0.8026 0.0058 0.1917 60 Q 0.7221 0.0159 0.2620 61 H 0.4798 0.0386 0.4816 62 G 0.2541 0.0660 0.6799 63 V 0.2257 0.1323 0.6420 64 L 0.1870 0.1690 0.6440 65 R 0.1677 0.1758 0.6564 66 N 0.1558 0.1435 0.7007 67 G 0.0871 0.3188 0.5940 68 A 0.0690 0.4762 0.4547 69 D 0.0943 0.4767 0.4290 70 Y 0.0733 0.6021 0.3247 71 R 0.0505 0.6881 0.2614 72 D 0.0382 0.6995 0.2623 73 F 0.0433 0.6857 0.2710 74 W 0.0534 0.6813 0.2653 75 I 0.0452 0.7549 0.1999 76 P 0.0199 0.8381 0.1420 77 A 0.0180 0.8357 0.1463 78 A 0.0226 0.7901 0.1872 79 D 0.0227 0.7028 0.2745 80 R 0.0376 0.5533 0.4092 81 H 0.0878 0.1985 0.7137 82 K 0.1309 0.0832 0.7859 83 L 0.4582 0.0104 0.5314 84 L 0.6993 0.0119 0.2888 85 I 0.7987 0.0055 0.1958 86 V 0.7880 0.0080 0.2040 87 A 0.7298 0.0078 0.2624 88 P 0.4757 0.0593 0.4649 89 T 0.3050 0.0706 0.6245 90 F 0.2212 0.0955 0.6833 91 S 0.1463 0.1559 0.6978 92 D 0.1252 0.1819 0.6929 93 E 0.1618 0.2095 0.6287 94 I 0.2054 0.1754 0.6192 95 W 0.2297 0.0768 0.6934 96 P 0.1530 0.1740 0.6730 97 G 0.1242 0.1766 0.6993 98 V 0.2106 0.1740 0.6154 99 E 0.2095 0.2158 0.5747 100 S 0.2022 0.2477 0.5502 101 Y 0.1324 0.3384 0.5292 102 N 0.1239 0.3256 0.5505 103 N 0.1135 0.2691 0.6173 104 G 0.0985 0.2534 0.6481 105 R 0.1734 0.2832 0.5433 106 A 0.1993 0.3310 0.4697 107 F 0.2199 0.3239 0.4562 108 T 0.2054 0.2877 0.5069 109 A 0.1360 0.3748 0.4891 110 A 0.1109 0.2602 0.6289 111 G 0.1013 0.1635 0.7351 112 N 0.1923 0.0722 0.7354 113 P 0.1329 0.2377 0.6293 114 R 0.1496 0.2439 0.6065 115 H 0.1670 0.1806 0.6523 116 V 0.1429 0.2507 0.6065 117 D 0.1143 0.2321 0.6536 118 G 0.0700 0.4546 0.4754 119 W 0.0845 0.5534 0.3621 120 T 0.0938 0.5946 0.3117 121 Y 0.0153 0.8183 0.1664 122 A 0.0088 0.8942 0.0970 123 L 0.0083 0.9232 0.0685 124 V 0.0083 0.9234 0.0683 125 A 0.0083 0.9225 0.0692 126 R 0.0083 0.9246 0.0671 127 V 0.0083 0.9236 0.0681 128 L 0.0083 0.9234 0.0683 129 A 0.0083 0.9205 0.0711 130 N 0.0084 0.9197 0.0719 131 I 0.0088 0.9125 0.0787 132 R 0.0094 0.8983 0.0923 133 A 0.0132 0.8255 0.1613 134 A 0.0384 0.6262 0.3355 135 E 0.0654 0.3629 0.5717 136 I 0.0948 0.2367 0.6685 137 A 0.1869 0.1213 0.6918 138 D 0.1745 0.0534 0.7721 139 C 0.0731 0.4442 0.4827 140 E 0.1343 0.3088 0.5569 141 Q 0.4819 0.0896 0.4286 142 V 0.7308 0.0155 0.2537 143 Y 0.7853 0.0130 0.2017 144 L 0.7914 0.0109 0.1977 145 F 0.7444 0.0227 0.2330 146 G 0.5821 0.0375 0.3804 147 H 0.3022 0.1293 0.5685 148 S 0.1884 0.2565 0.5550 149 A 0.0348 0.6546 0.3106 150 G 0.0217 0.7885 0.1898 151 G 0.0109 0.8967 0.0924 152 Q 0.0085 0.9166 0.0749 153 F 0.0084 0.9225 0.0691 154 V 0.0083 0.9244 0.0674 155 H 0.0083 0.9238 0.0680 156 R 0.0083 0.9226 0.0691 157 L 0.0087 0.9109 0.0804 158 M 0.0107 0.8599 0.1293 159 S 0.0151 0.7374 0.2475 160 S 0.0342 0.4606 0.5052 161 Q 0.1351 0.1493 0.7157 162 P 0.0638 0.3468 0.5894 163 H 0.0698 0.1952 0.7351 164 A 0.1792 0.0740 0.7468 165 P 0.1993 0.1118 0.6888 166 F 0.3128 0.1253 0.5619 167 H 0.4423 0.0858 0.4719 168 A 0.7725 0.0277 0.1998 169 V 0.7711 0.0139 0.2150 170 T 0.8027 0.0143 0.1830 171 A 0.7338 0.0264 0.2399 172 A 0.5728 0.0497 0.3775 173 N 0.3639 0.0258 0.6103 174 P 0.1688 0.1823 0.6490 175 G 0.1495 0.2252 0.6253 176 W 0.1782 0.2324 0.5894 177 Y 0.1910 0.1901 0.6189 178 T 0.2258 0.1542 0.6200 179 L 0.2297 0.1004 0.6699 180 P 0.1590 0.2321 0.6089 181 T 0.1658 0.2713 0.5628 182 F 0.1570 0.3216 0.5214 183 E 0.1345 0.3497 0.5158 184 H 0.1652 0.2722 0.5625 185 R 0.1981 0.1873 0.6146 186 F 0.2227 0.0695 0.7078 187 P 0.1404 0.2123 0.6474 188 E 0.0979 0.2711 0.6310 189 G 0.0795 0.2298 0.6907 190 L 0.1785 0.1770 0.6445 191 D 0.1559 0.1458 0.6982 192 G 0.1147 0.1945 0.6908 193 V 0.1519 0.1803 0.6679 194 G 0.1485 0.1229 0.7287 195 L 0.2055 0.0915 0.7030 196 T 0.1829 0.0504 0.7667 197 E 0.0250 0.6742 0.3009 198 D 0.0185 0.7964 0.1852 199 H 0.0212 0.8468 0.1320 200 L 0.0266 0.8350 0.1384 201 A 0.0265 0.8176 0.1559 202 R 0.0213 0.7349 0.2439 203 L 0.0352 0.5885 0.3763 204 L 0.1330 0.2734 0.5936 205 A 0.1436 0.1442 0.7122 206 Y 0.2770 0.0608 0.6622 207 P 0.3322 0.0883 0.5795 208 M 0.7462 0.0289 0.2249 209 T 0.7945 0.0131 0.1924 210 I 0.8034 0.0086 0.1880 211 L 0.7692 0.0163 0.2145 212 A 0.6729 0.0267 0.3004 213 G 0.3404 0.0489 0.6107 214 D 0.1983 0.1737 0.6279 215 Q 0.1534 0.2719 0.5747 216 D 0.1637 0.2583 0.5780 217 I 0.1061 0.3682 0.5256 218 A 0.1681 0.2703 0.5616 219 T 0.2594 0.0999 0.6407 220 D 0.2178 0.0655 0.7167 221 D 0.1395 0.1763 0.6842 222 P 0.0333 0.4912 0.4755 223 N 0.0598 0.3695 0.5707 224 L 0.1291 0.2472 0.6238 225 P 0.0659 0.4162 0.5180 226 S 0.0878 0.4028 0.5094 227 E 0.0699 0.4814 0.4487 228 P 0.0165 0.8381 0.1454 229 A 0.0108 0.8854 0.1038 230 A 0.0137 0.8516 0.1346 231 L 0.0448 0.7494 0.2058 232 R 0.0403 0.6228 0.3370 233 Q 0.0669 0.4735 0.4596 234 G 0.1150 0.2287 0.6563 235 P 0.0961 0.3365 0.5674 236 H 0.1085 0.2817 0.6097 237 R 0.1639 0.3642 0.4719 238 Y 0.2069 0.3568 0.4363 239 A 0.2116 0.3215 0.4669 240 R 0.2259 0.2714 0.5027 241 A 0.1753 0.3353 0.4893 242 R 0.1618 0.3820 0.4562 243 H 0.1627 0.3851 0.4522 244 Y 0.1536 0.4178 0.4286 245 Y 0.1372 0.4301 0.4328 246 E 0.1176 0.4573 0.4251 247 A 0.1215 0.4567 0.4218 248 G 0.1117 0.4796 0.4087 249 Q 0.1414 0.5361 0.3225 250 R 0.1620 0.5686 0.2694 251 A 0.1571 0.5898 0.2531 252 A 0.1644 0.5401 0.2955 253 A 0.1154 0.5212 0.3634 254 Q 0.0958 0.4070 0.4972 255 R 0.1143 0.2609 0.6248 256 G 0.1035 0.1648 0.7317 257 L 0.2093 0.0658 0.7249 258 P 0.2121 0.0831 0.7047 259 F 0.2781 0.0709 0.6510 260 G 0.3447 0.0513 0.6039 261 W 0.5582 0.0143 0.4274 262 Q 0.7036 0.0112 0.2852 263 L 0.7615 0.0071 0.2314 264 Q 0.7720 0.0099 0.2181 265 V 0.7296 0.0079 0.2625 266 V 0.4982 0.0155 0.4863 267 P 0.2101 0.0892 0.7007 268 G 0.0920 0.1148 0.7932 269 I 0.1849 0.1092 0.7059 270 G 0.1871 0.1101 0.7028 271 H 0.2271 0.1703 0.6025 272 D 0.1922 0.1994 0.6084 273 G 0.1602 0.2501 0.5896 274 Q 0.1645 0.2963 0.5391 275 A 0.1306 0.3941 0.4753 276 M 0.1142 0.4296 0.4562 277 S 0.1228 0.4615 0.4157 278 Q 0.0373 0.7320 0.2307 279 V 0.0247 0.8303 0.1449 280 C 0.0220 0.8725 0.1055 281 A 0.0144 0.8895 0.0960 282 S 0.0112 0.9047 0.0841 283 L 0.0103 0.9067 0.0830 284 W 0.0127 0.8945 0.0928 285 F 0.0215 0.8536 0.1249 286 D 0.0170 0.8191 0.1639 287 G 0.0193 0.6987 0.2820 288 R 0.0388 0.5968 0.3645 289 M 0.1076 0.3539 0.5385 290 P 0.0426 0.5147 0.4427 291 D 0.0604 0.4709 0.4687 292 A 0.0530 0.5931 0.3539 293 A 0.0306 0.7364 0.2329 294 E 0.0542 0.6811 0.2647 295 L 0.0884 0.6109 0.3007 296 A 0.0824 0.6286 0.2890 297 R 0.1119 0.5895 0.2986 298 L 0.1388 0.4656 0.3956 299 A 0.1242 0.3346 0.5412 300 G 0.1191 0.2272 0.6536 301 S 0.1909 0.2012 0.6079 302 Q 0.2517 0.1787 0.5696 303 S 0.2603 0.1540 0.5856 304 A 0.2100 0.1791 0.6109