# This file is the result of combining several RDB files, specifically # T0163.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0163.t2k.stride-ebghtl.rdb (weight 1.24869) # T0163.t2k.str.rdb (weight 1.53983) # T0163.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 T0163.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0163 # 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 T0163.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 570 # # ============================================ # Comments from T0163.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0163 # 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 T0163.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 570 # # ============================================ # Comments from T0163.t2k.str.rdb # ============================================ # TARGET T0163 # 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 T0163.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 570 # # ============================================ # Comments from T0163.t2k.alpha.rdb # ============================================ # TARGET T0163 # 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 T0163.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 570 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0467 0.0346 0.9187 2 K 0.0841 0.0576 0.8583 3 R 0.1358 0.0838 0.7804 4 H 0.1632 0.0584 0.7784 5 Y 0.2747 0.0120 0.7133 6 E 0.4348 0.0357 0.5295 7 A 0.9197 0.0041 0.0762 8 V 0.9318 0.0035 0.0647 9 V 0.9292 0.0035 0.0673 10 I 0.8427 0.0254 0.1319 11 G 0.2875 0.0271 0.6854 12 G 0.0624 0.0674 0.8702 13 G 0.0464 0.2716 0.6821 14 I 0.0069 0.8901 0.1030 15 I 0.0054 0.9348 0.0598 16 G 0.0051 0.9468 0.0481 17 S 0.0045 0.9557 0.0397 18 A 0.0044 0.9592 0.0364 19 I 0.0044 0.9589 0.0367 20 A 0.0044 0.9582 0.0374 21 Y 0.0044 0.9579 0.0376 22 Y 0.0044 0.9571 0.0385 23 L 0.0048 0.9542 0.0410 24 A 0.0049 0.9457 0.0494 25 K 0.0058 0.8836 0.1106 26 E 0.0414 0.3363 0.6223 27 N 0.0389 0.0173 0.9438 28 K 0.0837 0.0095 0.9067 29 N 0.4718 0.0086 0.5196 30 T 0.9062 0.0039 0.0899 31 A 0.9264 0.0038 0.0699 32 L 0.9296 0.0035 0.0669 33 F 0.8980 0.0097 0.0923 34 E 0.7294 0.0084 0.2622 35 S 0.2914 0.0481 0.6606 36 G 0.1167 0.0474 0.8359 37 T 0.1145 0.0796 0.8058 38 M 0.1124 0.1063 0.7813 39 G 0.0982 0.1103 0.7915 40 G 0.0980 0.1376 0.7643 41 R 0.1374 0.1610 0.7017 42 T 0.2371 0.1747 0.5882 43 T 0.3011 0.1767 0.5222 44 S 0.3146 0.1824 0.5030 45 A 0.2583 0.2271 0.5146 46 A 0.2438 0.2200 0.5361 47 A 0.2091 0.2163 0.5745 48 G 0.2347 0.1669 0.5984 49 M 0.4047 0.1417 0.4535 50 L 0.4623 0.1173 0.4204 51 G 0.3240 0.1161 0.5599 52 A 0.1531 0.2406 0.6064 53 H 0.1229 0.2266 0.6504 54 A 0.1672 0.2127 0.6201 55 E 0.1598 0.1842 0.6560 56 C 0.1059 0.1817 0.7124 57 E 0.0788 0.1904 0.7308 58 E 0.0487 0.2578 0.6934 59 R 0.0498 0.2932 0.6570 60 D 0.0257 0.6934 0.2809 61 A 0.0196 0.8014 0.1790 62 F 0.0192 0.8454 0.1354 63 F 0.0163 0.8739 0.1099 64 D 0.0154 0.8823 0.1024 65 F 0.0112 0.8833 0.1054 66 A 0.0104 0.8888 0.1008 67 M 0.0059 0.9168 0.0773 68 H 0.0063 0.9036 0.0901 69 S 0.0057 0.8964 0.0979 70 Q 0.0061 0.9081 0.0857 71 R 0.0065 0.9120 0.0815 72 L 0.0059 0.9017 0.0924 73 Y 0.0077 0.8953 0.0970 74 K 0.0066 0.9033 0.0901 75 G 0.0076 0.8780 0.1144 76 L 0.0092 0.8563 0.1346 77 G 0.0163 0.8206 0.1631 78 E 0.0143 0.7988 0.1869 79 E 0.0206 0.7584 0.2210 80 L 0.0347 0.6540 0.3114 81 Y 0.0416 0.6338 0.3246 82 A 0.0518 0.5642 0.3840 83 L 0.0466 0.4788 0.4746 84 S 0.0682 0.3174 0.6143 85 G 0.0935 0.1831 0.7234 86 V 0.1329 0.1725 0.6947 87 D 0.1696 0.1385 0.6919 88 I 0.2361 0.1351 0.6288 89 R 0.3180 0.1166 0.5655 90 Q 0.4780 0.0943 0.4277 91 H 0.4805 0.0824 0.4371 92 N 0.3801 0.1040 0.5159 93 G 0.2289 0.0809 0.6901 94 G 0.1944 0.0641 0.7415 95 M 0.5228 0.0393 0.4379 96 F 0.7675 0.0183 0.2142 97 K 0.7908 0.0246 0.1846 98 L 0.7257 0.0380 0.2363 99 A 0.5291 0.0402 0.4306 100 F 0.2135 0.0504 0.7360 101 S 0.0927 0.0423 0.8650 102 E 0.0201 0.6363 0.3436 103 E 0.0146 0.7072 0.2782 104 D 0.0137 0.7724 0.2140 105 V 0.0133 0.8088 0.1779 106 L 0.0144 0.8088 0.1768 107 Q 0.0152 0.8226 0.1623 108 L 0.0189 0.8090 0.1721 109 R 0.0173 0.8207 0.1621 110 Q 0.0176 0.7811 0.2013 111 M 0.0232 0.6999 0.2769 112 D 0.0397 0.5636 0.3966 113 D 0.0423 0.3767 0.5809 114 L 0.0571 0.1960 0.7469 115 D 0.0749 0.1402 0.7849 116 S 0.1238 0.1415 0.7347 117 V 0.2193 0.1888 0.5918 118 S 0.3451 0.1663 0.4886 119 W 0.3731 0.1154 0.5115 120 Y 0.1875 0.0593 0.7532 121 S 0.0839 0.0402 0.8759 122 K 0.0056 0.8984 0.0960 123 E 0.0054 0.9093 0.0853 124 E 0.0063 0.9031 0.0906 125 V 0.0085 0.9023 0.0892 126 L 0.0098 0.8436 0.1466 127 E 0.0140 0.7227 0.2633 128 K 0.0357 0.5756 0.3887 129 E 0.0765 0.2939 0.6295 130 P 0.0638 0.2842 0.6520 131 Y 0.0728 0.2549 0.6723 132 A 0.0880 0.2060 0.7060 133 S 0.0863 0.1356 0.7781 134 G 0.0696 0.2129 0.7175 135 D 0.1033 0.1886 0.7081 136 I 0.2739 0.1614 0.5647 137 F 0.4233 0.1248 0.4519 138 G 0.5213 0.1086 0.3701 139 A 0.6075 0.0928 0.2997 140 S 0.6654 0.0724 0.2623 141 F 0.6671 0.0501 0.2828 142 I 0.4545 0.0350 0.5106 143 Q 0.1839 0.1124 0.7037 144 D 0.0953 0.1261 0.7786 145 D 0.1562 0.1423 0.7016 146 V 0.2938 0.1098 0.5964 147 H 0.4784 0.0700 0.4516 148 V 0.4345 0.0504 0.5151 149 E 0.1700 0.0307 0.7992 150 P 0.0110 0.8532 0.1358 151 Y 0.0051 0.9315 0.0634 152 F 0.0050 0.9425 0.0525 153 V 0.0048 0.9450 0.0502 154 C 0.0046 0.9539 0.0414 155 K 0.0045 0.9552 0.0403 156 A 0.0044 0.9579 0.0376 157 Y 0.0045 0.9573 0.0382 158 V 0.0045 0.9581 0.0374 159 K 0.0047 0.9578 0.0376 160 A 0.0045 0.9577 0.0378 161 A 0.0044 0.9559 0.0397 162 K 0.0046 0.9439 0.0514 163 M 0.0051 0.8751 0.1198 164 L 0.0433 0.2435 0.7133 165 G 0.0413 0.0147 0.9440 166 A 0.1285 0.0094 0.8620 167 E 0.7555 0.0068 0.2377 168 I 0.8348 0.0103 0.1549 169 F 0.7672 0.0146 0.2182 170 E 0.4983 0.0354 0.4662 171 H 0.1922 0.0319 0.7760 172 T 0.2482 0.0147 0.7370 173 P 0.5519 0.0146 0.4335 174 V 0.7869 0.0147 0.1984 175 L 0.8116 0.0258 0.1626 176 H 0.8614 0.0105 0.1281 177 V 0.8703 0.0079 0.1217 178 E 0.8488 0.0105 0.1408 179 R 0.7432 0.0313 0.2256 180 D 0.3983 0.0425 0.5593 181 G 0.0964 0.0445 0.8591 182 E 0.2193 0.0478 0.7330 183 A 0.7700 0.0090 0.2210 184 L 0.8872 0.0060 0.1068 185 F 0.9170 0.0042 0.0788 186 I 0.9188 0.0039 0.0773 187 K 0.9082 0.0048 0.0870 188 T 0.7388 0.0066 0.2546 189 P 0.1377 0.0846 0.7776 190 S 0.0567 0.0241 0.9192 191 G 0.1813 0.0368 0.7819 192 D 0.7299 0.0120 0.2582 193 V 0.8746 0.0049 0.1205 194 W 0.8283 0.0091 0.1627 195 A 0.7888 0.0132 0.1980 196 N 0.6951 0.0476 0.2572 197 H 0.8825 0.0126 0.1049 198 V 0.9237 0.0065 0.0699 199 V 0.9215 0.0076 0.0709 200 V 0.8932 0.0136 0.0932 201 A 0.5827 0.0474 0.3699 202 S 0.1976 0.0550 0.7474 203 G 0.1005 0.0721 0.8274 204 V 0.0850 0.2650 0.6500 205 W 0.0662 0.3833 0.5505 206 S 0.0312 0.6023 0.3665 207 G 0.0153 0.7106 0.2741 208 M 0.0170 0.7324 0.2505 209 F 0.0213 0.7665 0.2122 210 F 0.0212 0.7688 0.2101 211 K 0.0204 0.7472 0.2324 212 Q 0.0223 0.7179 0.2598 213 L 0.0534 0.4219 0.5246 214 G 0.0472 0.1163 0.8365 215 L 0.0825 0.0935 0.8240 216 N 0.1007 0.0838 0.8155 217 N 0.1173 0.0655 0.8172 218 A 0.1758 0.0453 0.7789 219 F 0.3348 0.0311 0.6341 220 L 0.4240 0.0204 0.5555 221 P 0.3764 0.0353 0.5883 222 V 0.4189 0.0416 0.5395 223 K 0.3908 0.0509 0.5583 224 G 0.4814 0.0284 0.4902 225 E 0.7901 0.0086 0.2014 226 C 0.9038 0.0041 0.0922 227 L 0.9081 0.0043 0.0875 228 S 0.8992 0.0048 0.0961 229 V 0.8083 0.0086 0.1830 230 W 0.5432 0.0142 0.4426 231 N 0.2586 0.0286 0.7128 232 D 0.1222 0.0607 0.8172 233 D 0.0904 0.1033 0.8063 234 I 0.0968 0.1032 0.8000 235 P 0.1591 0.1022 0.7388 236 L 0.2556 0.0786 0.6658 237 T 0.3651 0.0658 0.5691 238 K 0.5379 0.0555 0.4066 239 T 0.6458 0.0346 0.3196 240 L 0.6557 0.0279 0.3164 241 Y 0.3590 0.0401 0.6009 242 H 0.0965 0.1147 0.7888 243 D 0.0685 0.0737 0.8578 244 H 0.2630 0.0503 0.6867 245 C 0.6674 0.0130 0.3195 246 Y 0.8706 0.0063 0.1232 247 I 0.9012 0.0049 0.0939 248 V 0.8877 0.0056 0.1067 249 P 0.8337 0.0067 0.1596 250 R 0.4823 0.0357 0.4820 251 K 0.0911 0.0755 0.8334 252 S 0.0494 0.0407 0.9099 253 G 0.0551 0.0451 0.8998 254 R 0.5123 0.0181 0.4696 255 L 0.8564 0.0050 0.1386 256 V 0.8907 0.0057 0.1036 257 V 0.8558 0.0131 0.1311 258 G 0.6901 0.0171 0.2928 259 A 0.4849 0.0346 0.4805 260 T 0.3509 0.0559 0.5932 261 M 0.3074 0.0972 0.5954 262 K 0.2828 0.1176 0.5996 263 P 0.2170 0.1198 0.6631 264 G 0.1197 0.1020 0.7783 265 D 0.0811 0.0965 0.8224 266 W 0.0721 0.1164 0.8115 267 S 0.0819 0.1021 0.8160 268 E 0.0650 0.1407 0.7943 269 T 0.0851 0.0908 0.8241 270 P 0.0842 0.0632 0.8526 271 D 0.0643 0.0540 0.8818 272 L 0.0074 0.8791 0.1134 273 G 0.0051 0.9050 0.0899 274 G 0.0055 0.9189 0.0755 275 L 0.0045 0.9422 0.0533 276 E 0.0045 0.9443 0.0511 277 S 0.0045 0.9420 0.0534 278 V 0.0046 0.9418 0.0536 279 M 0.0045 0.9494 0.0460 280 K 0.0046 0.9474 0.0480 281 K 0.0046 0.9435 0.0519 282 A 0.0047 0.9366 0.0586 283 K 0.0049 0.9234 0.0717 284 T 0.0057 0.8715 0.1227 285 M 0.0122 0.7819 0.2058 286 L 0.0564 0.5136 0.4299 287 P 0.0186 0.5226 0.4588 288 A 0.0298 0.4767 0.4935 289 I 0.0550 0.4111 0.5339 290 Q 0.0440 0.3306 0.6254 291 N 0.0620 0.3085 0.6295 292 M 0.1152 0.2222 0.6626 293 K 0.2100 0.2182 0.5719 294 V 0.4119 0.2412 0.3469 295 D 0.5087 0.2266 0.2648 296 R 0.5925 0.1909 0.2165 297 F 0.5394 0.2133 0.2473 298 W 0.5228 0.1854 0.2918 299 A 0.4638 0.1021 0.4341 300 G 0.4332 0.0429 0.5239 301 L 0.4908 0.0360 0.4732 302 R 0.5071 0.0237 0.4693 303 P 0.3660 0.0350 0.5990 304 G 0.3192 0.0418 0.6390 305 T 0.1431 0.0329 0.8240 306 K 0.0615 0.1014 0.8370 307 D 0.0639 0.0702 0.8658 308 G 0.0860 0.0629 0.8511 309 K 0.1901 0.0376 0.7722 310 P 0.4259 0.0457 0.5285 311 Y 0.5807 0.0653 0.3540 312 I 0.5469 0.0810 0.3721 313 G 0.3835 0.0872 0.5293 314 R 0.3487 0.1047 0.5466 315 H 0.2214 0.0865 0.6921 316 P 0.0686 0.1630 0.7684 317 E 0.0537 0.0939 0.8523 318 D 0.1593 0.0466 0.7940 319 S 0.0681 0.0971 0.8348 320 R 0.1192 0.0652 0.8156 321 I 0.6833 0.0221 0.2946 322 L 0.8771 0.0115 0.1113 323 F 0.8866 0.0132 0.1002 324 A 0.8330 0.0206 0.1464 325 A 0.6024 0.0377 0.3599 326 G 0.3138 0.0401 0.6461 327 H 0.2148 0.0648 0.7205 328 F 0.1269 0.0880 0.7851 329 R 0.0987 0.1643 0.7370 330 N 0.0800 0.2183 0.7018 331 G 0.1019 0.3423 0.5558 332 I 0.1418 0.5083 0.3499 333 L 0.1277 0.5350 0.3373 334 L 0.0741 0.6138 0.3121 335 A 0.0208 0.7338 0.2454 336 P 0.0058 0.9297 0.0646 337 A 0.0049 0.9477 0.0474 338 T 0.0045 0.9526 0.0428 339 G 0.0044 0.9575 0.0381 340 A 0.0043 0.9601 0.0356 341 L 0.0044 0.9604 0.0352 342 I 0.0044 0.9600 0.0357 343 S 0.0044 0.9593 0.0363 344 D 0.0044 0.9580 0.0376 345 L 0.0049 0.9505 0.0446 346 I 0.0062 0.9238 0.0700 347 M 0.0244 0.6863 0.2893 348 N 0.0368 0.2299 0.7333 349 K 0.0438 0.0597 0.8965 350 E 0.0951 0.0462 0.8586 351 V 0.1015 0.0796 0.8188 352 N 0.0923 0.1321 0.7755 353 Q 0.1097 0.2804 0.6099 354 D 0.1000 0.3152 0.5848 355 W 0.1121 0.3456 0.5424 356 L 0.1052 0.3182 0.5767 357 H 0.1270 0.2231 0.6498 358 A 0.1506 0.1880 0.6615 359 F 0.1723 0.0750 0.7527 360 R 0.1258 0.0530 0.8212 361 I 0.0395 0.4474 0.5130 362 D 0.0255 0.4773 0.4971 363 R 0.0498 0.4680 0.4821 364 K 0.0893 0.1571 0.7536 365 E 0.0981 0.0710 0.8309 366 A 0.0641 0.2784 0.6575 367 V 0.0938 0.2443 0.6619 368 Q 0.1320 0.1593 0.7087 369 I 0.0624 0.0278 0.9098