# This file is the result of combining several RDB files, specifically # T0208.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0208.t2k.stride-ebghtl.rdb (weight 1.24869) # T0208.t2k.str2.rdb (weight 1.54758) # T0208.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 T0208.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0208 # 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 T0208.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 41 # # ============================================ # Comments from T0208.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0208 # 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 T0208.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 41 # # ============================================ # Comments from T0208.t2k.str2.rdb # ============================================ # TARGET T0208 # 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 T0208.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 41 # # ============================================ # Comments from T0208.t2k.alpha.rdb # ============================================ # TARGET T0208 # 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 T0208.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 41 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1184 0.0546 0.8270 2 K 0.2737 0.0600 0.6663 3 W 0.5274 0.0580 0.4146 4 G 0.6689 0.0830 0.2480 5 F 0.7586 0.0696 0.1719 6 R 0.7973 0.0577 0.1450 7 W 0.7583 0.0573 0.1844 8 Y 0.5105 0.0572 0.4323 9 G 0.1983 0.0333 0.7684 10 A 0.0677 0.0865 0.8458 11 A 0.0456 0.1223 0.8321 12 G 0.0594 0.0799 0.8607 13 D 0.0935 0.0352 0.8714 14 A 0.2438 0.0461 0.7101 15 I 0.4029 0.0251 0.5721 16 P 0.2869 0.0408 0.6723 17 L 0.0199 0.8927 0.0875 18 K 0.0094 0.9143 0.0763 19 H 0.0171 0.8869 0.0960 20 I 0.0323 0.8513 0.1164 21 R 0.0638 0.6988 0.2374 22 Q 0.0578 0.6325 0.3097 23 I 0.0681 0.2179 0.7140 24 P 0.0322 0.1878 0.7800 25 G 0.0415 0.1173 0.8411 26 I 0.0960 0.3638 0.5402 27 T 0.0920 0.4019 0.5061 28 G 0.1867 0.3972 0.4162 29 V 0.3112 0.5002 0.1886 30 V 0.3418 0.4717 0.1865 31 G 0.3220 0.4390 0.2390 32 T 0.2465 0.4839 0.2696 33 L 0.1353 0.4709 0.3938 34 L 0.0873 0.3608 0.5519 35 N 0.1031 0.1702 0.7268 36 K 0.1390 0.0570 0.8040 37 L 0.0885 0.0457 0.8659 38 P 0.0457 0.0841 0.8702 39 G 0.0349 0.0741 0.8911 40 D 0.1458 0.0430 0.8112 41 V 0.3586 0.0329 0.6085 42 W 0.2591 0.0212 0.7197 43 T 0.1093 0.0380 0.8526 44 V 0.0058 0.9062 0.0880 45 A 0.0050 0.9235 0.0714 46 E 0.0050 0.9413 0.0537 47 I 0.0047 0.9505 0.0448 48 Q 0.0052 0.9493 0.0454 49 A 0.0050 0.9459 0.0492 50 L 0.0052 0.9490 0.0457 51 K 0.0054 0.9509 0.0437 52 Q 0.0055 0.9465 0.0480 53 S 0.0053 0.9400 0.0547 54 V 0.0074 0.9302 0.0624 55 E 0.0107 0.9036 0.0857 56 Q 0.0122 0.8062 0.1816 57 E 0.0433 0.3948 0.5619 58 G 0.0476 0.0399 0.9125 59 L 0.1767 0.0200 0.8033 60 A 0.6771 0.0134 0.3095 61 L 0.8610 0.0084 0.1306 62 L 0.8739 0.0098 0.1163 63 G 0.8901 0.0070 0.1029 64 I 0.7970 0.0285 0.1745 65 E 0.6783 0.0286 0.2932 66 S 0.4534 0.0384 0.5083 67 V 0.2672 0.0256 0.7072 68 A 0.1562 0.0405 0.8033 69 I 0.0407 0.3366 0.6227 70 H 0.0365 0.4648 0.4987 71 D 0.0417 0.6004 0.3579 72 A 0.0666 0.5999 0.3335 73 I 0.1260 0.5970 0.2770 74 K 0.1382 0.5252 0.3365 75 A 0.0931 0.3621 0.5448 76 G 0.0726 0.1348 0.7926 77 T 0.0591 0.0713 0.8695 78 D 0.0281 0.3092 0.6628 79 Q 0.0319 0.4639 0.5042 80 R 0.0118 0.8247 0.1635 81 D 0.0057 0.9228 0.0715 82 H 0.0057 0.9365 0.0578 83 Y 0.0049 0.9451 0.0500 84 I 0.0048 0.9529 0.0423 85 D 0.0048 0.9539 0.0413 86 N 0.0048 0.9493 0.0459 87 Y 0.0047 0.9528 0.0425 88 R 0.0047 0.9558 0.0395 89 Q 0.0047 0.9557 0.0396 90 T 0.0047 0.9563 0.0390 91 L 0.0047 0.9561 0.0392 92 R 0.0048 0.9544 0.0409 93 N 0.0048 0.9501 0.0450 94 L 0.0049 0.9431 0.0519 95 G 0.0051 0.9210 0.0739 96 K 0.0062 0.8470 0.1469 97 C 0.0445 0.4658 0.4897 98 G 0.0492 0.0428 0.9080 99 I 0.0769 0.0155 0.9076 100 S 0.2357 0.0478 0.7165 101 L 0.8427 0.0220 0.1354 102 V 0.9007 0.0159 0.0834 103 C 0.8896 0.0230 0.0874 104 Y 0.7761 0.0500 0.1739 105 S 0.5165 0.0677 0.4158 106 F 0.2163 0.1109 0.6729 107 K 0.1696 0.1365 0.6939 108 P 0.1827 0.2286 0.5887 109 I 0.2255 0.3048 0.4697 110 F 0.2271 0.2699 0.5030 111 G 0.1853 0.2799 0.5348 112 W 0.1817 0.3119 0.5064 113 A 0.2307 0.2330 0.5363 114 K 0.2620 0.1628 0.5752 115 T 0.2162 0.1091 0.6746 116 D 0.1824 0.1438 0.6738 117 L 0.1332 0.3066 0.5603 118 A 0.1973 0.2777 0.5250 119 Y 0.3365 0.1800 0.4834 120 E 0.4505 0.0850 0.4645 121 N 0.1432 0.0449 0.8119 122 E 0.0221 0.1230 0.8549 123 D 0.0474 0.0420 0.9106 124 G 0.0569 0.0663 0.8768 125 S 0.1757 0.1146 0.7097 126 L 0.4106 0.2237 0.3657 127 S 0.4135 0.2816 0.3048 128 L 0.3823 0.3168 0.3009 129 L 0.3611 0.3140 0.3250 130 F 0.3448 0.3019 0.3533 131 D 0.2137 0.3629 0.4235 132 Q 0.0256 0.8544 0.1200 133 A 0.0184 0.8735 0.1082 134 V 0.0135 0.8799 0.1066 135 V 0.0147 0.8623 0.1230 136 E 0.0104 0.7610 0.2287 137 N 0.0171 0.5890 0.3938 138 M 0.0757 0.3009 0.6233 139 Q 0.0864 0.0755 0.8381 140 P 0.0182 0.7482 0.2336 141 E 0.0146 0.8211 0.1643 142 D 0.0270 0.8452 0.1278 143 M 0.0581 0.7998 0.1421 144 Y 0.0787 0.7440 0.1774 145 Q 0.0779 0.7472 0.1749 146 L 0.0980 0.6773 0.2247 147 I 0.1156 0.6260 0.2584 148 H 0.1357 0.5674 0.2970 149 S 0.1438 0.4967 0.3595 150 Q 0.1756 0.3465 0.4778 151 S 0.2056 0.1998 0.5946 152 K 0.1755 0.2173 0.6072 153 G 0.1686 0.2026 0.6288 154 F 0.1336 0.1674 0.6990 155 R 0.1322 0.1105 0.7574 156 L 0.1191 0.0916 0.7893 157 P 0.0889 0.1527 0.7583 158 G 0.0873 0.1346 0.7781 159 W 0.1118 0.1288 0.7593 160 E 0.1102 0.1220 0.7677 161 E 0.1292 0.1694 0.7014 162 E 0.1495 0.1012 0.7493 163 R 0.1151 0.0788 0.8061 164 L 0.0059 0.8857 0.1084 165 Q 0.0048 0.9190 0.0762 166 Q 0.0048 0.9311 0.0641 167 F 0.0051 0.9439 0.0510 168 Q 0.0053 0.9470 0.0477 169 E 0.0051 0.9405 0.0545 170 L 0.0051 0.9296 0.0653 171 K 0.0062 0.9186 0.0752 172 A 0.0053 0.9034 0.0913 173 M 0.0071 0.8637 0.1292 174 Y 0.0284 0.6728 0.2988 175 A 0.0244 0.3092 0.6664 176 G 0.0335 0.1430 0.8235 177 V 0.0941 0.0475 0.8584 178 T 0.0681 0.0193 0.9127 179 E 0.0049 0.9161 0.0790 180 E 0.0047 0.9360 0.0592 181 D 0.0049 0.9444 0.0507 182 L 0.0048 0.9524 0.0428 183 V 0.0049 0.9535 0.0416 184 E 0.0053 0.9442 0.0505 185 N 0.0058 0.9311 0.0631 186 L 0.0049 0.9488 0.0463 187 R 0.0048 0.9553 0.0399 188 Y 0.0049 0.9529 0.0422 189 F 0.0050 0.9494 0.0456 190 L 0.0053 0.9414 0.0533 191 E 0.0053 0.9133 0.0814 192 R 0.0055 0.8494 0.1451 193 V 0.0161 0.8149 0.1690 194 I 0.0177 0.7386 0.2437 195 P 0.0171 0.8232 0.1597 196 V 0.0112 0.9154 0.0734 197 C 0.0130 0.9146 0.0724 198 E 0.0220 0.8795 0.0985 199 E 0.0468 0.7550 0.1981 200 E 0.0636 0.2963 0.6402 201 N 0.0795 0.0207 0.8998 202 I 0.3260 0.0112 0.6629 203 K 0.7732 0.0127 0.2141 204 M 0.8710 0.0073 0.1217 205 G 0.8515 0.0096 0.1388 206 I 0.7325 0.0082 0.2592 207 H 0.2764 0.0153 0.7083 208 P 0.0313 0.0966 0.8721 209 D 0.0253 0.0621 0.9126 210 D 0.0592 0.0458 0.8951 211 P 0.0596 0.0729 0.8675 212 P 0.0836 0.1426 0.7738 213 W 0.0858 0.3220 0.5922 214 E 0.0714 0.4532 0.4753 215 I 0.0645 0.4912 0.4443 216 F 0.0790 0.2308 0.6902 217 G 0.0784 0.0705 0.8510 218 L 0.1192 0.0391 0.8417 219 P 0.1816 0.0674 0.7511 220 R 0.5473 0.1207 0.3320 221 I 0.6399 0.1303 0.2298 222 T 0.6087 0.0837 0.3077 223 K 0.2841 0.0500 0.6660 224 N 0.1156 0.0387 0.8457 225 L 0.0060 0.8955 0.0986 226 A 0.0050 0.9277 0.0673 227 D 0.0058 0.9394 0.0548 228 L 0.0048 0.9536 0.0416 229 K 0.0050 0.9522 0.0427 230 R 0.0049 0.9396 0.0555 231 I 0.0063 0.9216 0.0721 232 L 0.0113 0.8714 0.1173 233 S 0.0123 0.6983 0.2895 234 L 0.0284 0.5358 0.4358 235 V 0.1202 0.1963 0.6835 236 D 0.1075 0.0824 0.8101 237 S 0.1001 0.0574 0.8426 238 P 0.0199 0.2848 0.6953 239 A 0.0376 0.2386 0.7238 240 N 0.0639 0.2000 0.7360 241 G 0.1386 0.1396 0.7218 242 I 0.4659 0.0921 0.4420 243 T 0.6175 0.0862 0.2963 244 F 0.5747 0.1033 0.3220 245 C 0.4994 0.0902 0.4104 246 T 0.3211 0.1193 0.5595 247 G 0.2476 0.0802 0.6722 248 S 0.2187 0.1261 0.6552 249 L 0.1468 0.2053 0.6479 250 G 0.1224 0.1771 0.7006 251 A 0.1200 0.1580 0.7219 252 D 0.0799 0.1012 0.8189 253 P 0.0443 0.2537 0.7020 254 T 0.0352 0.3059 0.6589 255 N 0.0406 0.2865 0.6729 256 D 0.0791 0.2511 0.6698 257 L 0.0076 0.7919 0.2005 258 P 0.0048 0.9421 0.0531 259 T 0.0048 0.9522 0.0430 260 M 0.0048 0.9553 0.0399 261 I 0.0050 0.9487 0.0463 262 R 0.0055 0.9321 0.0624 263 E 0.0081 0.8690 0.1229 264 I 0.0266 0.6954 0.2780 265 G 0.0390 0.3348 0.6262 266 H 0.0239 0.1942 0.7819 267 R 0.1402 0.1647 0.6952 268 I 0.3552 0.0479 0.5969 269 N 0.4933 0.0499 0.4568 270 F 0.8254 0.0237 0.1509 271 V 0.8203 0.0320 0.1477 272 H 0.8210 0.0306 0.1485 273 F 0.7425 0.0601 0.1975 274 R 0.6331 0.0782 0.2886 275 N 0.6050 0.0686 0.3263 276 V 0.6213 0.0632 0.3154 277 K 0.6585 0.0611 0.2804 278 Y 0.5245 0.0861 0.3895 279 L 0.2099 0.0788 0.7113 280 G 0.0619 0.0798 0.8583 281 E 0.0592 0.0450 0.8959 282 H 0.1209 0.0490 0.8300 283 R 0.2799 0.0309 0.6892 284 F 0.5866 0.0309 0.3826 285 E 0.6461 0.0393 0.3147 286 E 0.5474 0.0775 0.3751 287 T 0.3373 0.1075 0.5551 288 A 0.2552 0.1033 0.6415 289 H 0.1689 0.0806 0.7505 290 P 0.1482 0.0993 0.7525 291 S 0.0933 0.0980 0.8087 292 V 0.0321 0.2133 0.7546 293 A 0.0416 0.2006 0.7578 294 G 0.0421 0.2302 0.7276 295 S 0.0607 0.2788 0.6605 296 L 0.1440 0.4318 0.4242 297 D 0.1160 0.4996 0.3844 298 M 0.0053 0.9396 0.0550 299 A 0.0047 0.9577 0.0376 300 E 0.0047 0.9603 0.0350 301 L 0.0047 0.9603 0.0351 302 M 0.0047 0.9604 0.0350 303 Q 0.0047 0.9600 0.0354 304 A 0.0047 0.9581 0.0372 305 L 0.0049 0.9524 0.0427 306 V 0.0054 0.9306 0.0640 307 D 0.0068 0.8670 0.1263 308 V 0.0344 0.4821 0.4836 309 G 0.0460 0.1098 0.8441 310 Y 0.0744 0.0431 0.8825 311 E 0.1058 0.0497 0.8445 312 G 0.2586 0.0370 0.7044 313 V 0.2044 0.0216 0.7740 314 I 0.4561 0.0231 0.5208 315 R 0.3426 0.0177 0.6397 316 P 0.1748 0.0662 0.7590 317 D 0.1154 0.1013 0.7833 318 H 0.1351 0.1330 0.7319 319 G 0.1297 0.1915 0.6788 320 R 0.1808 0.2752 0.5441 321 A 0.2177 0.3014 0.4809 322 I 0.2303 0.2722 0.4975 323 W 0.1500 0.1704 0.6796 324 D 0.0796 0.0890 0.8314 325 E 0.0739 0.1175 0.8085 326 K 0.1293 0.0821 0.7886 327 A 0.1057 0.0898 0.8045 328 M 0.0898 0.0562 0.8540 329 P 0.0635 0.1664 0.7700 330 G 0.0568 0.1669 0.7763 331 Y 0.0776 0.4012 0.5212 332 G 0.0603 0.5077 0.4320 333 L 0.0203 0.8554 0.1244 334 Y 0.0220 0.8845 0.0935 335 D 0.0145 0.8932 0.0923 336 R 0.0094 0.9242 0.0664 337 A 0.0096 0.9374 0.0530 338 M 0.0069 0.9413 0.0518 339 G 0.0054 0.9517 0.0428 340 L 0.0048 0.9582 0.0370 341 T 0.0048 0.9588 0.0364 342 Y 0.0048 0.9573 0.0380 343 I 0.0050 0.9546 0.0404 344 Q 0.0056 0.9528 0.0417 345 G 0.0051 0.9508 0.0441 346 L 0.0048 0.9564 0.0388 347 Y 0.0047 0.9582 0.0370 348 E 0.0048 0.9565 0.0387 349 A 0.0051 0.9510 0.0438 350 T 0.0053 0.9406 0.0541 351 K 0.0065 0.8954 0.0981 352 A 0.0091 0.7300 0.2609 353 K 0.0170 0.5808 0.4022 354 Q 0.0319 0.4680 0.5001 355 N 0.0422 0.3537 0.6041 356 R 0.0542 0.1652 0.7806 357 K 0.0347 0.0522 0.9132