# This file is the result of combining several RDB files, specifically # T0316.t04.dssp-ebghstl.rdb (weight 1.53986) # T0316.t04.stride-ebghtl.rdb (weight 1.24869) # T0316.t04.str2.rdb (weight 1.54758) # T0316.t04.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 T0316.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0316 # Using neural net t06-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0316.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1870 # # ============================================ # Comments from T0316.t04.stride-ebghtl.rdb # ============================================ # TARGET T0316 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0316.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1870 # # ============================================ # Comments from T0316.t04.str2.rdb # ============================================ # TARGET T0316 # Using neural net t06-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0316.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1870 # # ============================================ # Comments from T0316.t04.alpha.rdb # ============================================ # TARGET T0316 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0316.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1870 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0809 0.0381 0.8810 2 S 0.1379 0.0701 0.7920 3 D 0.1110 0.0942 0.7948 4 N 0.0852 0.1259 0.7889 5 S 0.0722 0.1258 0.8020 6 K 0.0730 0.0741 0.8529 7 T 0.1947 0.0259 0.7794 8 R 0.7859 0.0042 0.2099 9 V 0.9234 0.0034 0.0732 10 V 0.9335 0.0032 0.0633 11 V 0.9317 0.0033 0.0649 12 G 0.9187 0.0055 0.0758 13 M 0.8696 0.0082 0.1221 14 S 0.5690 0.0156 0.4154 15 G 0.1396 0.0343 0.8260 16 G 0.0744 0.0738 0.8518 17 V 0.0488 0.3987 0.5524 18 D 0.0256 0.6453 0.3291 19 S 0.0052 0.9290 0.0658 20 S 0.0048 0.9569 0.0384 21 V 0.0047 0.9600 0.0354 22 T 0.0047 0.9606 0.0347 23 A 0.0046 0.9614 0.0339 24 L 0.0046 0.9616 0.0337 25 L 0.0046 0.9615 0.0339 26 L 0.0047 0.9600 0.0353 27 K 0.0048 0.9544 0.0408 28 E 0.0056 0.9176 0.0768 29 Q 0.0407 0.3866 0.5727 30 G 0.0399 0.0154 0.9447 31 Y 0.0695 0.0080 0.9225 32 D 0.4506 0.0121 0.5373 33 V 0.8663 0.0032 0.1304 34 I 0.9083 0.0042 0.0876 35 G 0.9305 0.0033 0.0661 36 I 0.9253 0.0036 0.0711 37 F 0.8903 0.0055 0.1042 38 M 0.7719 0.0126 0.2154 39 K 0.6079 0.0387 0.3534 40 N 0.4033 0.0304 0.5663 41 W 0.1842 0.0588 0.7570 42 D 0.1297 0.0597 0.8106 43 D 0.1043 0.0882 0.8075 44 T 0.0748 0.1021 0.8231 45 D 0.0724 0.0939 0.8337 46 E 0.0452 0.1494 0.8054 47 N 0.0988 0.0828 0.8184 48 G 0.1037 0.0642 0.8321 49 V 0.2408 0.0554 0.7038 50 C 0.2550 0.0520 0.6931 51 T 0.1198 0.0601 0.8201 52 A 0.0675 0.1196 0.8129 53 T 0.0308 0.5915 0.3777 54 E 0.0270 0.6690 0.3040 55 D 0.0281 0.6788 0.2931 56 Y 0.0057 0.9149 0.0794 57 K 0.0049 0.9344 0.0607 58 D 0.0047 0.9461 0.0491 59 V 0.0047 0.9562 0.0391 60 V 0.0046 0.9613 0.0341 61 A 0.0046 0.9613 0.0341 62 V 0.0046 0.9615 0.0339 63 A 0.0047 0.9603 0.0350 64 D 0.0048 0.9525 0.0427 65 Q 0.0055 0.9286 0.0660 66 I 0.0449 0.4637 0.4915 67 G 0.0468 0.0139 0.9394 68 I 0.0670 0.0079 0.9251 69 P 0.3029 0.0119 0.6852 70 Y 0.8581 0.0062 0.1356 71 Y 0.9108 0.0047 0.0845 72 S 0.9221 0.0037 0.0742 73 V 0.8449 0.0119 0.1432 74 N 0.4945 0.0068 0.4988 75 F 0.0844 0.4030 0.5126 76 E 0.0270 0.6468 0.3262 77 K 0.0117 0.8464 0.1420 78 E 0.0133 0.8822 0.1045 79 Y 0.0109 0.8963 0.0928 80 W 0.0068 0.9253 0.0679 81 D 0.0058 0.9263 0.0680 82 R 0.0067 0.9215 0.0718 83 V 0.0092 0.9135 0.0772 84 F 0.0112 0.9126 0.0761 85 E 0.0117 0.9175 0.0708 86 Y 0.0131 0.9093 0.0775 87 F 0.0138 0.8940 0.0922 88 L 0.0124 0.9072 0.0803 89 A 0.0079 0.9230 0.0691 90 E 0.0077 0.9258 0.0665 91 Y 0.0170 0.8912 0.0918 92 R 0.0227 0.8280 0.1493 93 A 0.0382 0.4126 0.5492 94 G 0.0274 0.0844 0.8881 95 R 0.0931 0.0308 0.8761 96 T 0.1367 0.0150 0.8484 97 P 0.1104 0.0324 0.8572 98 N 0.1139 0.0276 0.8585 99 P 0.0552 0.2206 0.7242 100 D 0.0627 0.3558 0.5815 101 V 0.0822 0.5452 0.3727 102 M 0.0871 0.4922 0.4207 103 C 0.0677 0.5087 0.4236 104 N 0.0336 0.5296 0.4368 105 K 0.0108 0.8337 0.1555 106 E 0.0115 0.8817 0.1068 107 I 0.0170 0.8963 0.0867 108 K 0.0150 0.8917 0.0933 109 F 0.0086 0.9292 0.0622 110 K 0.0069 0.9413 0.0519 111 A 0.0051 0.9549 0.0400 112 F 0.0048 0.9568 0.0384 113 L 0.0047 0.9603 0.0350 114 D 0.0047 0.9607 0.0346 115 Y 0.0047 0.9612 0.0341 116 A 0.0047 0.9602 0.0351 117 I 0.0048 0.9518 0.0433 118 T 0.0051 0.9267 0.0682 119 L 0.0405 0.4378 0.5217 120 G 0.0615 0.0126 0.9259 121 A 0.0854 0.0182 0.8964 122 D 0.0932 0.0587 0.8481 123 Y 0.8651 0.0152 0.1197 124 V 0.9172 0.0086 0.0741 125 A 0.9099 0.0094 0.0807 126 T 0.7646 0.0299 0.2056 127 G 0.3835 0.0424 0.5741 128 H 0.3550 0.0895 0.5556 129 Y 0.4213 0.1044 0.4743 130 A 0.5393 0.1078 0.3529 131 R 0.6484 0.0952 0.2564 132 V 0.6153 0.1132 0.2715 133 A 0.4705 0.1234 0.4060 134 R 0.2463 0.1188 0.6349 135 D 0.1418 0.1105 0.7476 136 E 0.0733 0.3280 0.5987 137 D 0.0836 0.2697 0.6467 138 G 0.1227 0.2724 0.6049 139 T 0.2804 0.3177 0.4020 140 V 0.2980 0.4214 0.2806 141 H 0.2537 0.4263 0.3200 142 M 0.2109 0.4102 0.3790 143 L 0.1593 0.2977 0.5430 144 R 0.0871 0.2374 0.6756 145 G 0.0781 0.1879 0.7341 146 V 0.1240 0.1650 0.7110 147 D 0.0860 0.1743 0.7397 148 N 0.0520 0.2452 0.7028 149 G 0.0531 0.2422 0.7047 150 K 0.0701 0.2673 0.6626 151 D 0.1017 0.2404 0.6579 152 Q 0.0967 0.3183 0.5850 153 T 0.0929 0.4554 0.4517 154 Y 0.1122 0.5525 0.3353 155 F 0.1171 0.5725 0.3105 156 L 0.1002 0.5272 0.3726 157 S 0.0581 0.5141 0.4278 158 Q 0.0438 0.5258 0.4304 159 L 0.0550 0.4748 0.4703 160 S 0.0513 0.4757 0.4730 161 Q 0.0070 0.8805 0.1125 162 E 0.0076 0.9044 0.0880 163 Q 0.0076 0.9094 0.0831 164 L 0.0125 0.8870 0.1005 165 Q 0.0195 0.8269 0.1535 166 K 0.0447 0.7052 0.2501 167 T 0.0700 0.6084 0.3216 168 M 0.2619 0.3456 0.3925 169 F 0.3328 0.1726 0.4946 170 P 0.2817 0.1676 0.5507 171 L 0.0882 0.3671 0.5447 172 G 0.0621 0.3001 0.6378 173 H 0.0721 0.2370 0.6909 174 L 0.1224 0.0523 0.8253 175 E 0.0700 0.0350 0.8950 176 K 0.0121 0.8998 0.0881 177 P 0.0047 0.9557 0.0396 178 E 0.0047 0.9585 0.0368 179 V 0.0047 0.9604 0.0349 180 R 0.0046 0.9610 0.0344 181 R 0.0046 0.9615 0.0338 182 L 0.0046 0.9618 0.0336 183 A 0.0047 0.9613 0.0341 184 E 0.0048 0.9557 0.0396 185 E 0.0053 0.9365 0.0581 186 A 0.0424 0.4564 0.5012 187 G 0.0425 0.0188 0.9387 188 L 0.0646 0.0099 0.9256 189 S 0.1109 0.0527 0.8364 190 T 0.2834 0.1390 0.5775 191 A 0.2024 0.1676 0.6300 192 K 0.1814 0.1740 0.6446 193 K 0.1452 0.0880 0.7667 194 K 0.0961 0.1111 0.7928 195 D 0.0950 0.0640 0.8410 196 S 0.1300 0.0987 0.7714 197 T 0.1719 0.0872 0.7409 198 G 0.3248 0.0723 0.6030 199 I 0.5869 0.0452 0.3679 200 C 0.7631 0.0333 0.2036 201 F 0.7363 0.0335 0.2302 202 I 0.4913 0.0570 0.4516 203 G 0.1885 0.0553 0.7562 204 E 0.0820 0.3038 0.6142 205 K 0.0548 0.5236 0.4216 206 N 0.0675 0.5619 0.3706 207 F 0.0343 0.7321 0.2336 208 K 0.0212 0.8060 0.1729 209 N 0.0217 0.7941 0.1842 210 F 0.0249 0.7972 0.1779 211 L 0.0378 0.7457 0.2165 212 S 0.0190 0.7761 0.2049 213 N 0.0205 0.6944 0.2851 214 Y 0.0643 0.5620 0.3737 215 L 0.1239 0.2757 0.6004 216 P 0.1218 0.2212 0.6570 217 A 0.1433 0.1710 0.6857 218 Q 0.1209 0.0334 0.8457 219 P 0.0404 0.0744 0.8853 220 G 0.0399 0.0495 0.9106 221 R 0.3796 0.0335 0.5869 222 M 0.6927 0.0231 0.2841 223 M 0.7051 0.0333 0.2616 224 T 0.6845 0.0267 0.2889 225 V 0.4788 0.0971 0.4241 226 D 0.3323 0.1021 0.5656 227 G 0.2138 0.2834 0.5028 228 R 0.1656 0.4405 0.3939 229 D 0.2504 0.4555 0.2940 230 M 0.1684 0.5369 0.2947 231 G 0.1460 0.4190 0.4350 232 E 0.1299 0.4838 0.3864 233 H 0.1492 0.4409 0.4099 234 A 0.0988 0.1864 0.7147 235 G 0.1051 0.0517 0.8431 236 L 0.3949 0.0358 0.5693 237 M 0.6894 0.0341 0.2765 238 Y 0.8178 0.0357 0.1465 239 Y 0.8080 0.0333 0.1587 240 T 0.7756 0.0337 0.1907 241 I 0.6871 0.0708 0.2421 242 G 0.5701 0.0637 0.3662 243 Q 0.5126 0.0914 0.3959 244 R 0.4288 0.0936 0.4777 245 G 0.3963 0.0846 0.5190 246 G 0.4795 0.0699 0.4506 247 L 0.6009 0.0546 0.3445 248 G 0.5774 0.0359 0.3868 249 I 0.4487 0.0568 0.4945 250 G 0.2922 0.0586 0.6492 251 G 0.1820 0.0685 0.7495 252 Q 0.1616 0.1095 0.7290 253 H 0.1789 0.1244 0.6967 254 G 0.1452 0.1178 0.7370 255 G 0.1110 0.1061 0.7828 256 D 0.1133 0.1095 0.7772 257 N 0.1440 0.0478 0.8082 258 A 0.1753 0.0306 0.7941 259 P 0.3833 0.0292 0.5875 260 W 0.8212 0.0203 0.1585 261 F 0.9036 0.0132 0.0832 262 V 0.9106 0.0127 0.0767 263 V 0.8599 0.0300 0.1101 264 G 0.7392 0.0276 0.2331 265 K 0.5401 0.0445 0.4154 266 D 0.4275 0.0381 0.5344 267 L 0.0779 0.5226 0.3996 268 S 0.0740 0.4700 0.4560 269 K 0.0874 0.3701 0.5425 270 N 0.2356 0.0971 0.6673 271 I 0.6875 0.0363 0.2762 272 L 0.8227 0.0221 0.1551 273 Y 0.8111 0.0226 0.1664 274 V 0.6615 0.0567 0.2818 275 G 0.3628 0.0471 0.5902 276 Q 0.1957 0.1021 0.7022 277 G 0.1189 0.1413 0.7398 278 F 0.1156 0.1960 0.6884 279 Y 0.1045 0.2979 0.5976 280 H 0.0661 0.4417 0.4922 281 D 0.0243 0.6720 0.3037 282 S 0.0339 0.6874 0.2787 283 L 0.0669 0.6229 0.3101 284 M 0.1056 0.4930 0.4013 285 S 0.1206 0.4457 0.4337 286 T 0.1540 0.4403 0.4057 287 S 0.3542 0.3098 0.3360 288 L 0.5561 0.1756 0.2684 289 E 0.6656 0.1493 0.1851 290 A 0.6899 0.1394 0.1707 291 S 0.5866 0.1536 0.2598 292 Q 0.5559 0.1409 0.3031 293 V 0.4622 0.1491 0.3887 294 H 0.3993 0.1120 0.4887 295 F 0.4759 0.0886 0.4354 296 T 0.4912 0.0992 0.4096 297 R 0.3469 0.0929 0.5601 298 E 0.1855 0.0760 0.7385 299 M 0.1090 0.0463 0.8447 300 P 0.0799 0.0770 0.8431 301 E 0.0444 0.3895 0.5661 302 E 0.0562 0.4087 0.5351 303 F 0.1107 0.3250 0.5642 304 T 0.1917 0.2805 0.5277 305 L 0.3698 0.2664 0.3638 306 E 0.4859 0.2889 0.2252 307 C 0.6407 0.2029 0.1564 308 T 0.6997 0.1889 0.1115 309 A 0.7507 0.1344 0.1149 310 K 0.7303 0.1331 0.1365 311 F 0.7175 0.1112 0.1712 312 R 0.7024 0.1052 0.1924 313 Y 0.7045 0.0516 0.2439 314 R 0.5301 0.0391 0.4308 315 Q 0.1847 0.0179 0.7974 316 P 0.0684 0.0478 0.8838 317 D 0.0615 0.0514 0.8871 318 S 0.3457 0.0132 0.6411 319 K 0.6327 0.0054 0.3619 320 V 0.8973 0.0037 0.0990 321 T 0.9264 0.0033 0.0703 322 V 0.9298 0.0031 0.0671 323 H 0.9173 0.0039 0.0787 324 V 0.8902 0.0037 0.1061 325 K 0.5500 0.0180 0.4320 326 G 0.0905 0.0264 0.8831 327 E 0.0763 0.0707 0.8530 328 K 0.4215 0.0251 0.5534 329 T 0.8641 0.0040 0.1319 330 E 0.9182 0.0039 0.0780 331 V 0.9264 0.0031 0.0705 332 I 0.8962 0.0077 0.0961 333 F 0.8245 0.0056 0.1699 334 A 0.5148 0.0157 0.4695 335 E 0.2331 0.0207 0.7462 336 P 0.1368 0.0474 0.8159 337 Q 0.0661 0.3593 0.5746 338 R 0.0961 0.3787 0.5252 339 A 0.2126 0.2636 0.5239 340 I 0.3482 0.0592 0.5926 341 T 0.1745 0.0234 0.8021 342 P 0.0578 0.0648 0.8773 343 G 0.0661 0.0427 0.8912 344 Q 0.3722 0.0191 0.6087 345 A 0.7962 0.0054 0.1984 346 V 0.9148 0.0035 0.0817 347 V 0.9252 0.0034 0.0714 348 F 0.8908 0.0061 0.1031 349 Y 0.6790 0.0115 0.3095 350 D 0.2109 0.0278 0.7613 351 G 0.0691 0.0374 0.8935 352 E 0.3190 0.0554 0.6256 353 E 0.7319 0.0314 0.2367 354 C 0.7578 0.0285 0.2137 355 L 0.5391 0.0427 0.4182 356 G 0.3420 0.0717 0.5863 357 G 0.2977 0.1246 0.5777 358 G 0.5187 0.1369 0.3444 359 L 0.6809 0.1756 0.1435 360 I 0.6540 0.2161 0.1298 361 D 0.5402 0.2778 0.1820 362 N 0.3214 0.3476 0.3311 363 A 0.1766 0.3101 0.5134 364 Y 0.1389 0.2220 0.6391 365 R 0.1087 0.2107 0.6806 366 D 0.0821 0.2959 0.6221 367 G 0.0903 0.3035 0.6062 368 Q 0.1987 0.3790 0.4222 369 V 0.2746 0.4778 0.2476 370 C 0.2518 0.4548 0.2934 371 Q 0.1853 0.4222 0.3924 372 Y 0.1571 0.3027 0.5402 373 I 0.0930 0.0657 0.8413