# This file is the result of combining several RDB files, specifically # YEL009C.t2k.dssp-ebghstl.rdb (weight 1.53986) # YEL009C.t2k.stride-ebghtl.rdb (weight 1.24869) # YEL009C.t2k.str2.rdb (weight 1.54758) # YEL009C.t2k.alpha.rdb (weight 0.659012) # 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 YEL009C.t2k.dssp-ebghstl.rdb # ============================================ # TARGET YEL009C # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment YEL009C.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 323 # # ============================================ # Comments from YEL009C.t2k.stride-ebghtl.rdb # ============================================ # TARGET YEL009C # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment YEL009C.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 323 # # ============================================ # Comments from YEL009C.t2k.str2.rdb # ============================================ # TARGET YEL009C # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment YEL009C.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 323 # # ============================================ # Comments from YEL009C.t2k.alpha.rdb # ============================================ # TARGET YEL009C # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment YEL009C.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 323 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0854 0.0892 0.8254 2 S 0.1177 0.1195 0.7628 3 E 0.0972 0.1350 0.7678 4 Y 0.0678 0.2589 0.6733 5 Q 0.0619 0.3444 0.5937 6 P 0.0621 0.3828 0.5552 7 S 0.0907 0.3205 0.5888 8 L 0.1130 0.2730 0.6140 9 F 0.0950 0.2597 0.6453 10 A 0.0835 0.1844 0.7321 11 L 0.0557 0.2615 0.6828 12 N 0.0655 0.2731 0.6614 13 P 0.0561 0.4072 0.5367 14 M 0.0486 0.3808 0.5706 15 G 0.0672 0.3205 0.6123 16 F 0.0808 0.2579 0.6613 17 S 0.0621 0.2668 0.6711 18 P 0.0502 0.3340 0.6159 19 L 0.0695 0.2740 0.6565 20 D 0.0716 0.2826 0.6458 21 G 0.0511 0.2704 0.6786 22 S 0.0724 0.2557 0.6719 23 K 0.1171 0.2094 0.6735 24 S 0.1242 0.1851 0.6907 25 T 0.1120 0.1802 0.7078 26 N 0.0990 0.1433 0.7577 27 E 0.0817 0.2079 0.7104 28 N 0.0910 0.1837 0.7253 29 V 0.1224 0.1875 0.6900 30 S 0.1375 0.1867 0.6758 31 A 0.1479 0.1949 0.6572 32 S 0.1947 0.1405 0.6648 33 T 0.1736 0.1058 0.7206 34 S 0.1356 0.1205 0.7439 35 T 0.0676 0.2388 0.6936 36 A 0.0661 0.2270 0.7070 37 K 0.1083 0.2176 0.6741 38 P 0.1292 0.2283 0.6425 39 M 0.1150 0.1978 0.6871 40 V 0.0923 0.2042 0.7035 41 G 0.0641 0.3956 0.5403 42 Q 0.0376 0.6050 0.3574 43 L 0.0424 0.6195 0.3382 44 I 0.0608 0.5417 0.3974 45 F 0.0851 0.3915 0.5233 46 D 0.0757 0.3602 0.5641 47 K 0.0972 0.3674 0.5354 48 F 0.1163 0.3833 0.5004 49 I 0.1344 0.3422 0.5234 50 K 0.1139 0.3615 0.5246 51 T 0.1340 0.3376 0.5284 52 E 0.1714 0.2744 0.5542 53 E 0.1734 0.2004 0.6262 54 D 0.1445 0.1556 0.6998 55 P 0.1135 0.1385 0.7480 56 I 0.1189 0.1130 0.7681 57 I 0.0992 0.1695 0.7314 58 K 0.1026 0.1292 0.7682 59 Q 0.2118 0.0788 0.7094 60 D 0.2778 0.0558 0.6663 61 T 0.1874 0.0541 0.7584 62 P 0.1254 0.2665 0.6081 63 S 0.0824 0.3638 0.5539 64 N 0.0921 0.4007 0.5071 65 L 0.1050 0.3667 0.5283 66 D 0.1346 0.2990 0.5665 67 F 0.1010 0.4025 0.4966 68 D 0.0923 0.4033 0.5044 69 F 0.0841 0.3796 0.5363 70 A 0.1029 0.2726 0.6244 71 L 0.1159 0.1602 0.7239 72 P 0.1051 0.1641 0.7308 73 Q 0.0853 0.2619 0.6529 74 T 0.0702 0.3274 0.6023 75 A 0.0742 0.2978 0.6280 76 T 0.1013 0.2181 0.6805 77 A 0.1049 0.1539 0.7411 78 P 0.0959 0.1847 0.7194 79 D 0.0979 0.1795 0.7227 80 A 0.1085 0.1978 0.6937 81 K 0.1339 0.1949 0.6712 82 T 0.1592 0.2193 0.6215 83 V 0.1481 0.2202 0.6317 84 L 0.1303 0.2047 0.6650 85 P 0.1092 0.2485 0.6423 86 I 0.0860 0.2540 0.6599 87 P 0.0631 0.3780 0.5589 88 E 0.0539 0.4446 0.5015 89 L 0.0650 0.4320 0.5030 90 D 0.0683 0.3806 0.5512 91 D 0.0736 0.3094 0.6170 92 A 0.0919 0.2581 0.6500 93 V 0.1166 0.2054 0.6779 94 V 0.1025 0.2025 0.6950 95 E 0.0807 0.2171 0.7023 96 S 0.0864 0.1847 0.7289 97 F 0.1131 0.2026 0.6843 98 F 0.1470 0.1992 0.6539 99 S 0.1173 0.2350 0.6477 100 S 0.0966 0.2658 0.6375 101 S 0.1046 0.2728 0.6227 102 T 0.1091 0.2496 0.6414 103 D 0.1056 0.2135 0.6808 104 S 0.1204 0.2037 0.6759 105 T 0.1283 0.1948 0.6770 106 P 0.1355 0.2155 0.6490 107 M 0.1620 0.1981 0.6399 108 F 0.1487 0.2147 0.6367 109 E 0.1282 0.1935 0.6783 110 Y 0.1146 0.1894 0.6960 111 E 0.0984 0.1974 0.7042 112 N 0.1021 0.1693 0.7286 113 L 0.0841 0.2110 0.7049 114 E 0.0904 0.1833 0.7263 115 D 0.0924 0.1940 0.7136 116 N 0.0874 0.1718 0.7407 117 S 0.0553 0.3099 0.6348 118 K 0.0534 0.3840 0.5625 119 E 0.0630 0.4083 0.5286 120 W 0.0935 0.3768 0.5296 121 T 0.1139 0.3290 0.5571 122 S 0.1231 0.2702 0.6066 123 L 0.1164 0.2306 0.6530 124 F 0.1269 0.1523 0.7208 125 D 0.0934 0.1667 0.7400 126 N 0.0707 0.1979 0.7315 127 D 0.0863 0.1794 0.7343 128 I 0.0991 0.1509 0.7501 129 P 0.1171 0.1577 0.7253 130 V 0.1152 0.2034 0.6813 131 T 0.0889 0.2452 0.6659 132 T 0.0965 0.2568 0.6466 133 D 0.1053 0.2460 0.6486 134 D 0.0938 0.3047 0.6015 135 V 0.1051 0.2915 0.6034 136 S 0.1334 0.2367 0.6299 137 L 0.1506 0.2285 0.6209 138 A 0.1448 0.1934 0.6618 139 D 0.1188 0.2161 0.6651 140 K 0.1284 0.1922 0.6794 141 A 0.1622 0.1807 0.6572 142 I 0.1998 0.1451 0.6551 143 E 0.1994 0.1412 0.6594 144 S 0.1771 0.2159 0.6070 145 T 0.1649 0.2354 0.5997 146 E 0.1782 0.2207 0.6011 147 E 0.1652 0.2356 0.5992 148 V 0.1322 0.2448 0.6230 149 S 0.1247 0.2336 0.6417 150 L 0.1455 0.2172 0.6373 151 V 0.1701 0.1468 0.6831 152 P 0.1693 0.1417 0.6890 153 S 0.1614 0.1349 0.7038 154 N 0.1496 0.1197 0.7307 155 L 0.1413 0.0976 0.7611 156 E 0.1558 0.1007 0.7435 157 V 0.1565 0.0928 0.7507 158 S 0.1416 0.0883 0.7700 159 T 0.1445 0.1086 0.7469 160 T 0.1508 0.1208 0.7284 161 S 0.1542 0.1004 0.7453 162 F 0.1645 0.0972 0.7383 163 L 0.1598 0.0815 0.7587 164 P 0.1768 0.0841 0.7391 165 T 0.1541 0.0855 0.7604 166 P 0.1556 0.1175 0.7269 167 V 0.1765 0.1197 0.7038 168 L 0.1606 0.1088 0.7306 169 E 0.1504 0.1032 0.7464 170 D 0.1353 0.1500 0.7147 171 A 0.1340 0.1462 0.7198 172 K 0.1466 0.1462 0.7072 173 L 0.1492 0.1094 0.7414 174 T 0.1411 0.1221 0.7369 175 Q 0.1454 0.1099 0.7447 176 T 0.1316 0.1657 0.7027 177 R 0.1318 0.1556 0.7126 178 K 0.1371 0.1359 0.7270 179 V 0.1387 0.1440 0.7173 180 K 0.1428 0.1368 0.7204 181 K 0.1236 0.1113 0.7651 182 P 0.1128 0.1324 0.7547 183 N 0.1297 0.1247 0.7456 184 S 0.1471 0.1312 0.7217 185 V 0.1582 0.1256 0.7162 186 V 0.1410 0.1472 0.7117 187 K 0.1351 0.1365 0.7284 188 K 0.1150 0.1368 0.7482 189 S 0.1134 0.1483 0.7383 190 H 0.1149 0.1781 0.7070 191 H 0.1384 0.1551 0.7065 192 V 0.1479 0.1265 0.7256 193 G 0.1204 0.1242 0.7554 194 K 0.0857 0.1772 0.7370 195 D 0.0794 0.1954 0.7252 196 D 0.0995 0.2040 0.6965 197 E 0.1047 0.2450 0.6503 198 S 0.1241 0.2357 0.6402 199 R 0.1224 0.2251 0.6525 200 L 0.1173 0.1949 0.6878 201 D 0.0889 0.2103 0.7008 202 H 0.0859 0.2324 0.6817 203 L 0.1263 0.2038 0.6700 204 G 0.1562 0.1716 0.6722 205 V 0.1919 0.1416 0.6665 206 V 0.1754 0.1600 0.6646 207 A 0.1615 0.1645 0.6740 208 Y 0.1217 0.2264 0.6518 209 N 0.1153 0.2185 0.6662 210 R 0.1078 0.2525 0.6398 211 K 0.1028 0.2371 0.6601 212 Q 0.0886 0.2241 0.6873 213 R 0.0991 0.2000 0.7009 214 S 0.1101 0.1721 0.7178 215 I 0.1048 0.1482 0.7470 216 P 0.1031 0.1416 0.7554 217 L 0.1160 0.1369 0.7470 218 S 0.0922 0.1181 0.7897 219 P 0.0889 0.1980 0.7130 220 I 0.0856 0.2262 0.6881 221 V 0.0716 0.2185 0.7099 222 P 0.0548 0.2716 0.6735 223 E 0.0331 0.5216 0.4453 224 S 0.0225 0.6052 0.3723 225 S 0.0210 0.6635 0.3155 226 D 0.0086 0.8259 0.1655 227 P 0.0068 0.8883 0.1049 228 A 0.0052 0.9220 0.0728 229 A 0.0051 0.9396 0.0553 230 L 0.0050 0.9450 0.0501 231 K 0.0049 0.9420 0.0530 232 R 0.0050 0.9389 0.0561 233 A 0.0053 0.9342 0.0605 234 R 0.0073 0.9099 0.0829 235 N 0.0142 0.8679 0.1180 236 T 0.0096 0.8867 0.1038 237 E 0.0068 0.9229 0.0703 238 A 0.0061 0.9257 0.0682 239 A 0.0054 0.9256 0.0690 240 R 0.0065 0.9333 0.0602 241 R 0.0063 0.9134 0.0803 242 S 0.0120 0.9003 0.0876 243 R 0.0054 0.9234 0.0712 244 A 0.0056 0.9387 0.0557 245 R 0.0057 0.9425 0.0518 246 K 0.0056 0.9485 0.0460 247 L 0.0058 0.9503 0.0438 248 Q 0.0059 0.9493 0.0448 249 R 0.0057 0.9459 0.0484 250 M 0.0053 0.9517 0.0430 251 K 0.0052 0.9515 0.0433 252 Q 0.0049 0.9513 0.0439 253 L 0.0047 0.9553 0.0399 254 E 0.0048 0.9577 0.0375 255 D 0.0047 0.9573 0.0379 256 K 0.0047 0.9575 0.0378 257 V 0.0047 0.9600 0.0353 258 E 0.0047 0.9592 0.0361 259 E 0.0047 0.9563 0.0390 260 L 0.0047 0.9559 0.0394 261 L 0.0048 0.9549 0.0404 262 S 0.0049 0.9502 0.0449 263 K 0.0060 0.9339 0.0601 264 N 0.0054 0.9348 0.0598 265 Y 0.0049 0.9361 0.0590 266 H 0.0049 0.9422 0.0530 267 L 0.0048 0.9500 0.0452 268 E 0.0047 0.9585 0.0368 269 N 0.0047 0.9588 0.0364 270 E 0.0047 0.9586 0.0367 271 V 0.0047 0.9595 0.0358 272 A 0.0047 0.9567 0.0386 273 R 0.0048 0.9491 0.0462 274 L 0.0048 0.9504 0.0448 275 K 0.0050 0.9475 0.0475 276 K 0.0052 0.9273 0.0676 277 L 0.0057 0.9047 0.0896 278 V 0.0084 0.8437 0.1479 279 G 0.0101 0.5837 0.4062 280 E 0.0159 0.4363 0.5478 281 R 0.0272 0.1292 0.8436