# This file is the result of combining several RDB files, specifically # T0173.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0173.t2k.stride-ebghtl.rdb (weight 1.24869) # T0173.t2k.str.rdb (weight 1.53983) # T0173.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 T0173.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0173 # 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 T0173.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 64 # # ============================================ # Comments from T0173.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0173 # 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 T0173.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 64 # # ============================================ # Comments from T0173.t2k.str.rdb # ============================================ # TARGET T0173 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0173.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 64 # # ============================================ # Comments from T0173.t2k.alpha.rdb # ============================================ # TARGET T0173 # 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 T0173.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 64 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0439 0.0440 0.9120 2 S 0.0659 0.0487 0.8855 3 E 0.0813 0.0733 0.8453 4 T 0.1095 0.0867 0.8037 5 P 0.1601 0.0617 0.7782 6 R 0.7090 0.0106 0.2804 7 L 0.9078 0.0041 0.0881 8 L 0.9229 0.0043 0.0728 9 F 0.9272 0.0035 0.0693 10 V 0.8833 0.0112 0.1055 11 H 0.7538 0.0083 0.2379 12 A 0.4001 0.0146 0.5852 13 H 0.1455 0.0180 0.8365 14 P 0.0498 0.1522 0.7980 15 D 0.0402 0.1783 0.7815 16 D 0.0480 0.5262 0.4257 17 E 0.0157 0.7363 0.2480 18 S 0.0116 0.7667 0.2217 19 L 0.0175 0.7134 0.2692 20 S 0.0238 0.6509 0.3253 21 N 0.0204 0.7581 0.2215 22 G 0.0114 0.9005 0.0880 23 A 0.0050 0.9502 0.0448 24 T 0.0045 0.9585 0.0370 25 I 0.0044 0.9594 0.0362 26 A 0.0044 0.9599 0.0357 27 H 0.0044 0.9606 0.0350 28 Y 0.0045 0.9591 0.0364 29 T 0.0050 0.9493 0.0456 30 S 0.0060 0.8998 0.0942 31 R 0.0408 0.3536 0.6056 32 G 0.0363 0.0167 0.9469 33 A 0.0740 0.0099 0.9161 34 Q 0.5468 0.0047 0.4485 35 V 0.8912 0.0039 0.1049 36 H 0.9315 0.0035 0.0649 37 V 0.9331 0.0035 0.0635 38 V 0.9302 0.0036 0.0662 39 T 0.9161 0.0036 0.0803 40 C 0.7466 0.0095 0.2439 41 T 0.4448 0.0127 0.5425 42 L 0.1661 0.0776 0.7562 43 G 0.0903 0.0945 0.8153 44 E 0.1272 0.1467 0.7261 45 E 0.1140 0.1396 0.7464 46 G 0.1130 0.1058 0.7812 47 E 0.1240 0.1213 0.7547 48 V 0.1933 0.1404 0.6664 49 I 0.1239 0.1545 0.7216 50 G 0.0945 0.1393 0.7662 51 D 0.0569 0.4902 0.4529 52 R 0.0657 0.5665 0.3678 53 W 0.0949 0.5348 0.3703 54 A 0.0890 0.4316 0.4794 55 Q 0.0877 0.2941 0.6182 56 L 0.0804 0.1734 0.7462 57 T 0.0772 0.1589 0.7639 58 A 0.0636 0.1876 0.7487 59 D 0.0696 0.1701 0.7603 60 H 0.0676 0.1103 0.8221 61 A 0.0139 0.6515 0.3346 62 D 0.0132 0.6178 0.3690 63 Q 0.0163 0.6362 0.3475 64 L 0.0207 0.6528 0.3266 65 G 0.0109 0.7948 0.1943 66 G 0.0086 0.8659 0.1255 67 Y 0.0088 0.8824 0.1087 68 R 0.0084 0.8888 0.1027 69 I 0.0049 0.9480 0.0472 70 G 0.0054 0.9503 0.0443 71 E 0.0045 0.9548 0.0407 72 L 0.0044 0.9588 0.0368 73 T 0.0044 0.9590 0.0365 74 A 0.0044 0.9580 0.0375 75 A 0.0044 0.9585 0.0371 76 L 0.0045 0.9571 0.0384 77 R 0.0048 0.9459 0.0493 78 A 0.0057 0.9059 0.0884 79 L 0.0434 0.4082 0.5484 80 G 0.0437 0.0241 0.9322 81 V 0.0800 0.0192 0.9009 82 S 0.0786 0.0703 0.8512 83 A 0.1762 0.1951 0.6287 84 P 0.3339 0.2155 0.4506 85 I 0.4640 0.1977 0.3383 86 Y 0.5271 0.1399 0.3330 87 L 0.3196 0.1145 0.5659 88 G 0.1685 0.0928 0.7387 89 G 0.0891 0.2120 0.6989 90 A 0.0799 0.2747 0.6454 91 G 0.0814 0.2428 0.6758 92 R 0.1314 0.1838 0.6847 93 W 0.1536 0.1005 0.7459 94 R 0.1278 0.1203 0.7519 95 D 0.1405 0.1192 0.7403 96 S 0.1199 0.1693 0.7109 97 G 0.1907 0.1583 0.6509 98 M 0.3057 0.1350 0.5593 99 A 0.3392 0.1417 0.5191 100 G 0.2604 0.1402 0.5994 101 T 0.1941 0.1070 0.6989 102 D 0.1485 0.1055 0.7460 103 Q 0.1386 0.1273 0.7341 104 R 0.0990 0.1159 0.7851 105 S 0.0548 0.1493 0.7959 106 Q 0.0595 0.1459 0.7945 107 R 0.0728 0.1192 0.8079 108 R 0.1240 0.1735 0.7025 109 F 0.1972 0.2369 0.5659 110 V 0.2157 0.2136 0.5707 111 D 0.2050 0.1447 0.6503 112 A 0.1745 0.0784 0.7472 113 D 0.0923 0.0536 0.8540 114 P 0.0082 0.9084 0.0834 115 R 0.0048 0.9433 0.0519 116 Q 0.0047 0.9519 0.0433 117 T 0.0045 0.9563 0.0392 118 V 0.0044 0.9595 0.0361 119 G 0.0044 0.9594 0.0362 120 A 0.0044 0.9584 0.0372 121 L 0.0044 0.9593 0.0363 122 V 0.0044 0.9594 0.0362 123 A 0.0044 0.9578 0.0378 124 I 0.0045 0.9554 0.0401 125 I 0.0051 0.9463 0.0486 126 R 0.0053 0.9234 0.0712 127 E 0.0097 0.7829 0.2073 128 L 0.0506 0.4228 0.5266 129 R 0.0855 0.0234 0.8911 130 P 0.0690 0.0423 0.8886 131 H 0.1042 0.0697 0.8260 132 V 0.8510 0.0054 0.1436 133 V 0.9241 0.0038 0.0720 134 V 0.9198 0.0039 0.0763 135 T 0.8481 0.0063 0.1456 136 Y 0.5429 0.0115 0.4456 137 D 0.1642 0.0166 0.8192 138 P 0.0294 0.1108 0.8598 139 N 0.0432 0.0607 0.8961 140 G 0.0480 0.0628 0.8892 141 G 0.0756 0.0896 0.8349 142 Y 0.1276 0.0877 0.7847 143 G 0.0795 0.1049 0.8157 144 H 0.0916 0.1007 0.8077 145 P 0.0414 0.4503 0.5083 146 D 0.0332 0.5866 0.3802 147 H 0.0090 0.9083 0.0827 148 V 0.0045 0.9537 0.0418 149 H 0.0045 0.9558 0.0397 150 T 0.0044 0.9580 0.0376 151 H 0.0044 0.9600 0.0356 152 T 0.0044 0.9609 0.0347 153 V 0.0043 0.9609 0.0347 154 T 0.0044 0.9608 0.0349 155 T 0.0044 0.9598 0.0359 156 A 0.0044 0.9577 0.0379 157 A 0.0044 0.9544 0.0412 158 V 0.0046 0.9432 0.0523 159 A 0.0049 0.9045 0.0907 160 A 0.0084 0.7848 0.2068 161 A 0.0430 0.5594 0.3976 162 G 0.0394 0.2986 0.6619 163 V 0.0529 0.2982 0.6489 164 G 0.0490 0.3961 0.5548 165 S 0.0625 0.3876 0.5498 166 G 0.0999 0.3094 0.5907 167 T 0.1297 0.2300 0.6403 168 A 0.1101 0.2719 0.6180 169 D 0.0862 0.3200 0.5939 170 H 0.0895 0.2932 0.6173 171 P 0.0820 0.2084 0.7096 172 G 0.0896 0.1645 0.7459 173 D 0.1062 0.1204 0.7734 174 P 0.1315 0.1318 0.7367 175 W 0.1411 0.1584 0.7005 176 T 0.1686 0.1352 0.6962 177 V 0.2642 0.1285 0.6073 178 P 0.3527 0.1181 0.5293 179 K 0.6298 0.1026 0.2677 180 F 0.7773 0.0809 0.1418 181 Y 0.7628 0.0981 0.1390 182 W 0.7685 0.0914 0.1401 183 T 0.6728 0.1100 0.2172 184 V 0.4778 0.1465 0.3757 185 L 0.2467 0.1499 0.6034 186 G 0.1397 0.1374 0.7229 187 L 0.0637 0.2478 0.6885 188 S 0.0438 0.4380 0.5182 189 A 0.0266 0.6322 0.3412 190 L 0.0178 0.7191 0.2631 191 I 0.0234 0.6911 0.2855 192 S 0.0270 0.6390 0.3340 193 G 0.0382 0.5918 0.3700 194 A 0.0456 0.6252 0.3292 195 R 0.0461 0.6508 0.3031 196 A 0.0556 0.6749 0.2696 197 L 0.0666 0.6375 0.2959 198 V 0.0834 0.5507 0.3659 199 P 0.0686 0.4792 0.4522 200 D 0.0586 0.4051 0.5364 201 D 0.0552 0.2875 0.6573 202 L 0.0729 0.1892 0.7380 203 R 0.0893 0.1349 0.7757 204 P 0.0876 0.1740 0.7384 205 E 0.0804 0.2056 0.7140 206 W 0.0815 0.2693 0.6493 207 V 0.0928 0.2793 0.6279 208 L 0.1004 0.3072 0.5924 209 P 0.0896 0.3957 0.5148 210 R 0.0920 0.4112 0.4968 211 A 0.0990 0.3443 0.5567 212 D 0.0902 0.2425 0.6672 213 E 0.1050 0.2441 0.6510 214 I 0.1114 0.2188 0.6697 215 A 0.1075 0.1573 0.7352 216 F 0.0657 0.2843 0.6499 217 G 0.0672 0.2594 0.6735 218 Y 0.1053 0.2379 0.6568 219 S 0.1096 0.2270 0.6634 220 D 0.0919 0.2190 0.6891 221 D 0.1095 0.1756 0.7149 222 G 0.1613 0.1170 0.7217 223 I 0.2626 0.0710 0.6664 224 D 0.3676 0.0795 0.5529 225 A 0.5657 0.0734 0.3609 226 V 0.7870 0.0474 0.1656 227 V 0.8361 0.0382 0.1256 228 E 0.7831 0.0474 0.1695 229 A 0.4752 0.0657 0.4591 230 D 0.0719 0.3617 0.5664 231 E 0.0199 0.6381 0.3420 232 Q 0.0085 0.8231 0.1683 233 A 0.0070 0.8907 0.1024 234 R 0.0062 0.9313 0.0625 235 A 0.0047 0.9430 0.0523 236 A 0.0048 0.9463 0.0489 237 K 0.0044 0.9571 0.0385 238 V 0.0044 0.9591 0.0365 239 A 0.0044 0.9592 0.0364 240 A 0.0044 0.9566 0.0389 241 L 0.0046 0.9523 0.0431 242 A 0.0048 0.9343 0.0609 243 A 0.0074 0.8699 0.1227 244 H 0.0313 0.7460 0.2227 245 A 0.0310 0.6156 0.3535 246 T 0.0563 0.4633 0.4804 247 Q 0.1175 0.3513 0.5312 248 V 0.2352 0.2736 0.4913 249 V 0.2457 0.1949 0.5594 250 V 0.1762 0.1477 0.6761 251 G 0.1245 0.0990 0.7765 252 P 0.0943 0.2462 0.6595 253 T 0.1761 0.2583 0.5656 254 G 0.3350 0.2422 0.4227 255 R 0.4706 0.1993 0.3301 256 A 0.5469 0.1627 0.2904 257 A 0.5917 0.1196 0.2886 258 A 0.5557 0.1089 0.3353 259 L 0.4545 0.0900 0.4556 260 S 0.2474 0.1062 0.6464 261 N 0.0661 0.3941 0.5398 262 N 0.0579 0.3932 0.5490 263 L 0.1662 0.4261 0.4077 264 A 0.2687 0.3527 0.3786 265 L 0.2979 0.2872 0.4150 266 P 0.3252 0.2615 0.4133 267 I 0.3051 0.2005 0.4944 268 L 0.3003 0.1523 0.5474 269 A 0.2596 0.2119 0.5286 270 D 0.2717 0.2530 0.4753 271 E 0.3336 0.2563 0.4101 272 H 0.3832 0.2381 0.3787 273 Y 0.4977 0.1824 0.3199 274 V 0.5471 0.1766 0.2762 275 L 0.4756 0.1888 0.3357 276 A 0.2821 0.2153 0.5026 277 G 0.1563 0.1952 0.6485 278 G 0.1229 0.1518 0.7253 279 S 0.1747 0.1040 0.7213 280 A 0.2076 0.1036 0.6887 281 G 0.1618 0.1061 0.7320 282 A 0.1475 0.1382 0.7143 283 R 0.1326 0.1456 0.7218 284 D 0.1283 0.1443 0.7273 285 E 0.1534 0.1128 0.7339 286 R 0.2214 0.0774 0.7012 287 G 0.1897 0.0568 0.7535 288 W 0.1032 0.1012 0.7957 289 E 0.0518 0.4133 0.5349 290 T 0.0461 0.4147 0.5392 291 D 0.0830 0.3515 0.5654 292 L 0.2544 0.2192 0.5265 293 L 0.4832 0.1425 0.3743 294 A 0.4773 0.1375 0.3852 295 G 0.5428 0.0898 0.3674 296 L 0.5873 0.0812 0.3315 297 G 0.5329 0.0640 0.4032 298 F 0.4321 0.0821 0.4858 299 T 0.2204 0.0903 0.6893 300 A 0.0955 0.1312 0.7733 301 S 0.0786 0.1061 0.8153 302 G 0.0720 0.0645 0.8634 303 T 0.0434 0.0367 0.9200