# This file is the result of combining several RDB files, specifically # T0162.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0162.t2k.stride-ebghtl.rdb (weight 1.24869) # T0162.t2k.str.rdb (weight 1.53983) # T0162.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 T0162.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0162 # 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 T0162.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 21 # # ============================================ # Comments from T0162.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0162 # 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 T0162.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 21 # # ============================================ # Comments from T0162.t2k.str.rdb # ============================================ # TARGET T0162 # 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 T0162.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 21 # # ============================================ # Comments from T0162.t2k.alpha.rdb # ============================================ # TARGET T0162 # 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 T0162.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 21 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0524 0.1125 0.8351 2 A 0.0757 0.2091 0.7151 3 D 0.0865 0.1666 0.7470 4 F 0.0345 0.4518 0.5137 5 E 0.0347 0.4538 0.5115 6 D 0.0493 0.3724 0.5783 7 R 0.1085 0.3061 0.5854 8 V 0.1021 0.1623 0.7356 9 S 0.0606 0.1127 0.8267 10 D 0.0096 0.8810 0.1094 11 E 0.0050 0.9468 0.0482 12 E 0.0054 0.9476 0.0469 13 K 0.0044 0.9560 0.0396 14 V 0.0044 0.9568 0.0388 15 R 0.0044 0.9562 0.0394 16 I 0.0044 0.9550 0.0406 17 A 0.0045 0.9545 0.0410 18 A 0.0045 0.9544 0.0411 19 K 0.0048 0.9490 0.0462 20 F 0.0054 0.9334 0.0611 21 I 0.0092 0.8884 0.1024 22 T 0.0154 0.7356 0.2491 23 H 0.0257 0.4835 0.4907 24 A 0.0482 0.1522 0.7996 25 P 0.0413 0.0380 0.9207 26 P 0.0227 0.2853 0.6920 27 G 0.0366 0.4087 0.5547 28 E 0.0767 0.6573 0.2660 29 F 0.0507 0.7941 0.1553 30 N 0.0359 0.8329 0.1312 31 E 0.0349 0.8607 0.1044 32 V 0.0171 0.8794 0.1035 33 F 0.0139 0.9039 0.0822 34 N 0.0096 0.9238 0.0667 35 D 0.0082 0.9295 0.0622 36 V 0.0047 0.9484 0.0469 37 R 0.0047 0.9492 0.0461 38 L 0.0053 0.9355 0.0592 39 L 0.0073 0.8895 0.1032 40 L 0.0259 0.7368 0.2373 41 N 0.0209 0.4241 0.5550 42 N 0.0411 0.2573 0.7016 43 D 0.0123 0.7277 0.2600 44 N 0.0062 0.8304 0.1634 45 L 0.0058 0.8684 0.1258 46 L 0.0071 0.8514 0.1416 47 R 0.0075 0.8238 0.1687 48 E 0.0122 0.8109 0.1769 49 G 0.0106 0.7768 0.2126 50 A 0.0064 0.8582 0.1353 51 A 0.0053 0.9136 0.0810 52 H 0.0046 0.9143 0.0811 53 A 0.0045 0.9193 0.0762 54 F 0.0052 0.9187 0.0761 55 A 0.0051 0.9052 0.0897 56 Q 0.0079 0.8512 0.1409 57 Y 0.0302 0.7075 0.2624 58 N 0.0593 0.3664 0.5742 59 M 0.0203 0.3203 0.6594 60 D 0.0305 0.1625 0.8070 61 Q 0.1435 0.0962 0.7603 62 F 0.2586 0.0350 0.7064 63 T 0.4924 0.0172 0.4904 64 P 0.7103 0.0107 0.2790 65 V 0.8121 0.0082 0.1797 66 K 0.8274 0.0065 0.1662 67 I 0.6883 0.0131 0.2987 68 E 0.3454 0.0655 0.5891 69 G 0.0946 0.0967 0.8086 70 Y 0.1288 0.1151 0.7562 71 D 0.1572 0.0744 0.7684 72 D 0.1598 0.0463 0.7939 73 Q 0.4612 0.0188 0.5200 74 V 0.8692 0.0056 0.1252 75 L 0.9101 0.0043 0.0856 76 I 0.8950 0.0052 0.0998 77 T 0.6328 0.0123 0.3550 78 E 0.3016 0.0754 0.6230 79 H 0.1489 0.0886 0.7625 80 G 0.1318 0.0860 0.7822 81 D 0.1876 0.1023 0.7101 82 L 0.1692 0.1008 0.7299 83 G 0.0825 0.0702 0.8473 84 N 0.0922 0.0456 0.8622 85 G 0.2727 0.0494 0.6779 86 R 0.6810 0.0179 0.3011 87 F 0.8029 0.0099 0.1872 88 L 0.7614 0.0121 0.2265 89 D 0.4290 0.0146 0.5564 90 P 0.0576 0.1904 0.7520 91 R 0.0448 0.1869 0.7683 92 N 0.2205 0.1399 0.6396 93 K 0.2982 0.1137 0.5881 94 I 0.6543 0.0594 0.2863 95 S 0.8474 0.0326 0.1199 96 F 0.8732 0.0221 0.1047 97 K 0.8562 0.0300 0.1138 98 F 0.6942 0.1206 0.1851 99 D 0.5022 0.2372 0.2606 100 H 0.4510 0.3551 0.1939 101 L 0.3648 0.4560 0.1792 102 R 0.3377 0.4805 0.1817 103 K 0.2263 0.5227 0.2510 104 E 0.1964 0.5064 0.2971 105 A 0.1487 0.4933 0.3579 106 S 0.0844 0.3881 0.5276 107 D 0.0925 0.1565 0.7510 108 P 0.1005 0.1524 0.7471 109 Q 0.0922 0.1161 0.7917 110 P 0.0800 0.2025 0.7175 111 E 0.0609 0.2539 0.6852 112 D 0.0638 0.2286 0.7077 113 T 0.0540 0.3160 0.6300 114 E 0.0340 0.4676 0.4984 115 S 0.0288 0.5250 0.4462 116 A 0.0312 0.6228 0.3460 117 L 0.0237 0.7910 0.1853 118 K 0.0158 0.8676 0.1165 119 Q 0.0139 0.8785 0.1075 120 W 0.0074 0.9000 0.0926 121 R 0.0053 0.9343 0.0604 122 D 0.0047 0.9474 0.0478 123 A 0.0045 0.9493 0.0462 124 C 0.0046 0.9466 0.0488 125 D 0.0044 0.9562 0.0394 126 S 0.0045 0.9573 0.0382 127 A 0.0045 0.9552 0.0404 128 L 0.0045 0.9561 0.0394 129 R 0.0045 0.9572 0.0383 130 A 0.0048 0.9540 0.0411 131 Y 0.0063 0.9449 0.0489 132 V 0.0087 0.9286 0.0627 133 K 0.0084 0.9126 0.0790 134 D 0.0140 0.8045 0.1815 135 H 0.0432 0.6212 0.3356 136 Y 0.0805 0.0838 0.8357 137 P 0.0328 0.1141 0.8532 138 N 0.0380 0.0640 0.8980 139 G 0.0705 0.0637 0.8657 140 F 0.2975 0.0523 0.6502 141 C 0.6020 0.0440 0.3540 142 T 0.7228 0.0284 0.2488 143 V 0.8045 0.0179 0.1776 144 Y 0.8578 0.0124 0.1298 145 G 0.8332 0.0113 0.1555 146 K 0.8153 0.0161 0.1686 147 S 0.6849 0.0136 0.3015 148 I 0.3441 0.0717 0.5843 149 D 0.0902 0.0789 0.8310 150 G 0.0935 0.0791 0.8274 151 Q 0.3659 0.0323 0.6018 152 Q 0.7422 0.0068 0.2510 153 T 0.9007 0.0037 0.0956 154 I 0.9245 0.0036 0.0718 155 I 0.9287 0.0035 0.0678 156 A 0.9277 0.0036 0.0687 157 C 0.9193 0.0036 0.0771 158 I 0.8950 0.0041 0.1009 159 E 0.7780 0.0188 0.2032 160 S 0.5440 0.0330 0.4230 161 H 0.3666 0.0702 0.5632 162 Q 0.3361 0.0664 0.5975 163 F 0.3562 0.0534 0.5904 164 Q 0.1631 0.0236 0.8132 165 P 0.0608 0.1529 0.7863 166 K 0.0452 0.1806 0.7742 167 N 0.1423 0.1993 0.6584 168 F 0.2492 0.1108 0.6400 169 W 0.3006 0.0934 0.6060 170 N 0.2365 0.0482 0.7153 171 G 0.2298 0.0460 0.7242 172 R 0.4914 0.0258 0.4828 173 W 0.7398 0.0136 0.2466 174 R 0.7407 0.0173 0.2420 175 S 0.8391 0.0104 0.1505 176 E 0.8863 0.0103 0.1034 177 W 0.9006 0.0056 0.0938 178 K 0.9001 0.0052 0.0948 179 F 0.8895 0.0051 0.1054 180 T 0.8370 0.0058 0.1572 181 I 0.6544 0.0171 0.3286 182 T 0.3196 0.0253 0.6551 183 P 0.0604 0.0862 0.8534 184 P 0.0588 0.0811 0.8601 185 T 0.2398 0.0708 0.6894 186 A 0.4497 0.0614 0.4889 187 Q 0.7579 0.0190 0.2231 188 V 0.8588 0.0060 0.1352 189 A 0.8294 0.0200 0.1506 190 A 0.8626 0.0070 0.1304 191 V 0.9146 0.0040 0.0814 192 L 0.9226 0.0035 0.0739 193 K 0.9235 0.0040 0.0725 194 I 0.9177 0.0035 0.0788 195 Q 0.8971 0.0038 0.0991 196 V 0.9002 0.0038 0.0960 197 H 0.8517 0.0050 0.1433 198 Y 0.8264 0.0088 0.1649 199 Y 0.6635 0.0216 0.3149 200 E 0.3475 0.0489 0.6037 201 D 0.1764 0.0424 0.7811 202 G 0.2049 0.0404 0.7547 203 N 0.5029 0.0258 0.4713 204 V 0.8555 0.0073 0.1372 205 Q 0.8801 0.0074 0.1125 206 L 0.8881 0.0084 0.1035 207 V 0.8288 0.0191 0.1521 208 S 0.6872 0.0198 0.2931 209 H 0.4213 0.0407 0.5380 210 K 0.2974 0.0567 0.6459 211 D 0.3857 0.0584 0.5559 212 I 0.3960 0.1467 0.4574 213 Q 0.3362 0.1359 0.5279 214 D 0.3437 0.1466 0.5096 215 S 0.3904 0.0847 0.5249 216 V 0.5306 0.0986 0.3708 217 Q 0.5829 0.1073 0.3098 218 V 0.4388 0.1531 0.4081 219 S 0.1969 0.1592 0.6438 220 S 0.0850 0.1486 0.7663 221 D 0.0225 0.5190 0.4585 222 V 0.0156 0.6864 0.2979 223 Q 0.0147 0.7456 0.2397 224 T 0.0142 0.8073 0.1785 225 A 0.0045 0.9328 0.0627 226 K 0.0044 0.9511 0.0445 227 E 0.0044 0.9542 0.0414 228 F 0.0044 0.9580 0.0376 229 I 0.0044 0.9601 0.0356 230 K 0.0044 0.9578 0.0378 231 I 0.0044 0.9568 0.0388 232 I 0.0044 0.9558 0.0398 233 E 0.0045 0.9506 0.0449 234 N 0.0048 0.9248 0.0704 235 A 0.0056 0.9136 0.0808 236 E 0.0060 0.9170 0.0771 237 N 0.0059 0.9263 0.0678 238 E 0.0053 0.9301 0.0646 239 Y 0.0044 0.9392 0.0564 240 Q 0.0044 0.9493 0.0463 241 T 0.0048 0.9501 0.0451 242 A 0.0049 0.9414 0.0537 243 I 0.0064 0.9334 0.0603 244 S 0.0088 0.9055 0.0857 245 E 0.0120 0.8507 0.1373 246 N 0.0225 0.7351 0.2424 247 Y 0.0468 0.6145 0.3387 248 Q 0.0709 0.5538 0.3753 249 T 0.0980 0.4086 0.4934 250 M 0.1080 0.2317 0.6602 251 S 0.0754 0.2626 0.6620 252 D 0.0126 0.7011 0.2863 253 T 0.0133 0.7597 0.2270 254 T 0.0337 0.7600 0.2063 255 F 0.0384 0.8131 0.1486 256 K 0.0348 0.8616 0.1036 257 A 0.0219 0.8733 0.1048 258 L 0.0220 0.8504 0.1276 259 R 0.0217 0.8272 0.1511 260 R 0.0210 0.6848 0.2942 261 Q 0.0338 0.4764 0.4898 262 L 0.0830 0.0756 0.8415 263 P 0.0899 0.0506 0.8595 264 V 0.2619 0.0910 0.6470 265 T 0.4100 0.0939 0.4961 266 R 0.4346 0.1637 0.4017 267 T 0.4354 0.1441 0.4205 268 K 0.5070 0.1140 0.3791 269 I 0.4559 0.0554 0.4887 270 D 0.2581 0.0354 0.7064 271 W 0.0281 0.4985 0.4734 272 N 0.0244 0.4316 0.5439 273 K 0.0557 0.4706 0.4737 274 I 0.3150 0.1284 0.5565 275 L 0.4715 0.1091 0.4193 276 S 0.7056 0.0848 0.2095 277 Y 0.7170 0.0894 0.1937 278 K 0.6876 0.1037 0.2088 279 I 0.4849 0.2163 0.2988 280 G 0.2125 0.3183 0.4692 281 K 0.1225 0.4931 0.3843 282 E 0.1239 0.4997 0.3764 283 M 0.1157 0.4498 0.4345 284 Q 0.0734 0.3422 0.5844 285 N 0.0615 0.1381 0.8004 286 A 0.0410 0.0434 0.9156