# This file is the result of combining several RDB files, specifically # T0301.t04.dssp-ebghstl.rdb (weight 1.53986) # T0301.t04.stride-ebghtl.rdb (weight 1.24869) # T0301.t04.str2.rdb (weight 1.54758) # T0301.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 T0301.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0301 # 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 T0301.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 13.5211 # # ============================================ # Comments from T0301.t04.stride-ebghtl.rdb # ============================================ # TARGET T0301 # 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 T0301.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 13.5211 # # ============================================ # Comments from T0301.t04.str2.rdb # ============================================ # TARGET T0301 # 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 T0301.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 13.5211 # # ============================================ # Comments from T0301.t04.alpha.rdb # ============================================ # TARGET T0301 # 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 T0301.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 13.5211 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0654 0.0344 0.9002 2 A 0.0909 0.0449 0.8642 3 H 0.0881 0.0336 0.8783 4 P 0.0725 0.0448 0.8827 5 P 0.0902 0.1262 0.7836 6 Q 0.2280 0.1411 0.6309 7 I 0.4068 0.0776 0.5156 8 R 0.6029 0.0327 0.3644 9 I 0.6086 0.0174 0.3740 10 P 0.5341 0.0183 0.4476 11 A 0.6626 0.0689 0.2686 12 T 0.7361 0.0914 0.1725 13 Y 0.7801 0.0788 0.1410 14 L 0.7166 0.0629 0.2205 15 R 0.4947 0.0623 0.4430 16 G 0.2389 0.0581 0.7030 17 G 0.1436 0.0677 0.7887 18 T 0.1406 0.0726 0.7868 19 S 0.1218 0.0766 0.8016 20 K 0.0971 0.1580 0.7448 21 G 0.1541 0.2064 0.6395 22 V 0.3540 0.2435 0.4025 23 F 0.5795 0.1555 0.2650 24 F 0.5646 0.1242 0.3112 25 R 0.4202 0.0958 0.4840 26 L 0.0320 0.7077 0.2603 27 E 0.0157 0.6282 0.3561 28 D 0.0180 0.5526 0.4294 29 L 0.0738 0.1260 0.8002 30 P 0.0579 0.1911 0.7510 31 E 0.0220 0.5183 0.4597 32 S 0.0300 0.4533 0.5167 33 C 0.0753 0.2835 0.6412 34 R 0.0762 0.1439 0.7799 35 V 0.0654 0.0484 0.8861 36 P 0.0534 0.0952 0.8514 37 G 0.0242 0.4211 0.5547 38 E 0.0183 0.7094 0.2724 39 A 0.0111 0.8652 0.1238 40 R 0.0100 0.8820 0.1080 41 D 0.0108 0.8859 0.1033 42 R 0.0073 0.9116 0.0811 43 L 0.0089 0.9072 0.0838 44 F 0.0104 0.9177 0.0718 45 M 0.0142 0.9148 0.0710 46 R 0.0195 0.8991 0.0814 47 V 0.0273 0.8633 0.1094 48 I 0.0768 0.6111 0.3121 49 G 0.0919 0.1712 0.7369 50 S 0.1192 0.0515 0.8293 51 P 0.0754 0.0700 0.8546 52 D 0.0896 0.0318 0.8785 53 P 0.0167 0.3929 0.5904 54 Y 0.0213 0.4438 0.5349 55 A 0.0374 0.5118 0.4509 56 A 0.0980 0.3639 0.5380 57 H 0.2157 0.2688 0.5155 58 I 0.3025 0.1858 0.5117 59 D 0.2187 0.1512 0.6301 60 G 0.1889 0.1120 0.6991 61 M 0.1994 0.1025 0.6981 62 G 0.1851 0.0845 0.7304 63 G 0.1424 0.0598 0.7978 64 A 0.1523 0.0617 0.7860 65 T 0.1334 0.0541 0.8125 66 S 0.0892 0.1269 0.7839 67 S 0.0773 0.1286 0.7941 68 T 0.1617 0.0749 0.7634 69 S 0.2840 0.0385 0.6775 70 K 0.6262 0.0211 0.3527 71 C 0.8791 0.0066 0.1144 72 V 0.9120 0.0051 0.0830 73 I 0.9130 0.0040 0.0830 74 L 0.8205 0.0093 0.1702 75 S 0.5377 0.0108 0.4515 76 K 0.1551 0.1152 0.7297 77 S 0.0731 0.0960 0.8308 78 S 0.0647 0.0835 0.8518 79 Q 0.0669 0.0265 0.9066 80 P 0.0366 0.1024 0.8610 81 G 0.0435 0.1662 0.7903 82 H 0.1502 0.1248 0.7250 83 D 0.2812 0.0803 0.6384 84 V 0.4730 0.1084 0.4186 85 D 0.5260 0.1202 0.3538 86 Y 0.7673 0.0623 0.1704 87 L 0.8112 0.0487 0.1401 88 Y 0.8395 0.0339 0.1265 89 G 0.8441 0.0276 0.1283 90 Q 0.8510 0.0178 0.1313 91 V 0.7755 0.0324 0.1922 92 S 0.7021 0.0137 0.2842 93 I 0.4532 0.0383 0.5085 94 D 0.2021 0.0475 0.7504 95 K 0.1427 0.0703 0.7870 96 P 0.1823 0.1047 0.7130 97 F 0.4778 0.0913 0.4309 98 V 0.6244 0.0348 0.3408 99 D 0.4484 0.0243 0.5273 100 W 0.1630 0.1260 0.7110 101 S 0.1180 0.0834 0.7986 102 G 0.0688 0.1097 0.8215 103 N 0.0755 0.1073 0.8173 104 C 0.1552 0.1583 0.6865 105 G 0.1341 0.2106 0.6553 106 N 0.1662 0.3186 0.5152 107 L 0.1648 0.4792 0.3560 108 S 0.1608 0.5658 0.2734 109 T 0.1879 0.5562 0.2559 110 G 0.1700 0.5593 0.2708 111 A 0.1241 0.6224 0.2535 112 G 0.0565 0.7290 0.2146 113 A 0.0170 0.8752 0.1078 114 F 0.0175 0.8985 0.0840 115 A 0.0212 0.9045 0.0743 116 L 0.0208 0.8793 0.0998 117 H 0.0196 0.8006 0.1799 118 A 0.0452 0.3672 0.5876 119 G 0.0343 0.0782 0.8875 120 L 0.1254 0.0527 0.8220 121 V 0.2437 0.0283 0.7280 122 D 0.1441 0.0229 0.8330 123 P 0.0302 0.5125 0.4573 124 A 0.0366 0.4623 0.5011 125 R 0.1291 0.3887 0.4823 126 I 0.2069 0.0240 0.7691 127 P 0.0983 0.0337 0.8680 128 E 0.0486 0.1333 0.8181 129 D 0.0516 0.0889 0.8595 130 G 0.0858 0.0619 0.8523 131 I 0.5607 0.0173 0.4220 132 C 0.8276 0.0062 0.1662 133 E 0.9066 0.0045 0.0889 134 V 0.9197 0.0039 0.0763 135 R 0.9178 0.0062 0.0760 136 I 0.8981 0.0126 0.0892 137 W 0.8228 0.0330 0.1443 138 Q 0.7185 0.0495 0.2320 139 A 0.4316 0.1259 0.4426 140 N 0.3108 0.1142 0.5749 141 I 0.1997 0.0781 0.7222 142 G 0.1189 0.0592 0.8219 143 K 0.4932 0.0328 0.4739 144 T 0.8273 0.0106 0.1621 145 I 0.8936 0.0067 0.0997 146 I 0.9051 0.0083 0.0866 147 A 0.8750 0.0084 0.1166 148 H 0.8618 0.0076 0.1306 149 V 0.8238 0.0057 0.1706 150 P 0.7387 0.0043 0.2571 151 V 0.4225 0.0177 0.5597 152 S 0.1493 0.0645 0.7863 153 G 0.0541 0.0458 0.9001 154 G 0.1793 0.0335 0.7872 155 Q 0.6437 0.0149 0.3414 156 V 0.8571 0.0085 0.1344 157 Q 0.7630 0.0153 0.2217 158 E 0.7353 0.0248 0.2398 159 T 0.4599 0.0329 0.5072 160 G 0.3270 0.0289 0.6442 161 D 0.5472 0.0254 0.4274 162 F 0.7825 0.0214 0.1961 163 E 0.7869 0.0203 0.1927 164 L 0.7050 0.0343 0.2607 165 D 0.3485 0.0645 0.5870 166 G 0.1743 0.0359 0.7898 167 V 0.3487 0.0236 0.6277 168 T 0.3235 0.0257 0.6508 169 F 0.1583 0.0410 0.8007 170 P 0.0997 0.0903 0.8100 171 A 0.1029 0.1740 0.7230 172 A 0.2135 0.1196 0.6669 173 E 0.4586 0.0543 0.4872 174 I 0.7870 0.0152 0.1978 175 V 0.8695 0.0106 0.1199 176 L 0.8742 0.0118 0.1139 177 E 0.8619 0.0118 0.1263 178 F 0.8050 0.0139 0.1811 179 L 0.5693 0.0183 0.4124 180 D 0.2733 0.0107 0.7160 181 P 0.0943 0.0938 0.8118 182 S 0.0527 0.0833 0.8639 183 D 0.0510 0.0994 0.8496 184 D 0.0631 0.0665 0.8704 185 G 0.0802 0.0565 0.8632 186 E 0.0832 0.1437 0.7731 187 D 0.1919 0.1269 0.6813 188 G 0.2012 0.1508 0.6480 189 G 0.1810 0.1269 0.6921 190 A 0.3685 0.0837 0.5478 191 I 0.6126 0.0675 0.3199 192 F 0.2946 0.0440 0.6614 193 P 0.1579 0.0800 0.7621 194 T 0.1328 0.0475 0.8198 195 G 0.0790 0.0818 0.8392 196 N 0.1183 0.0638 0.8179 197 L 0.3228 0.1295 0.5477 198 V 0.4200 0.1014 0.4786 199 D 0.4378 0.1340 0.4281 200 D 0.6670 0.0723 0.2607 201 L 0.8020 0.0245 0.1735 202 E 0.7568 0.0149 0.2283 203 V 0.4674 0.0157 0.5169 204 P 0.1398 0.0562 0.8040 205 G 0.0879 0.0365 0.8757 206 V 0.1982 0.0577 0.7441 207 G 0.2069 0.0535 0.7397 208 T 0.4399 0.0460 0.5141 209 F 0.5807 0.0177 0.4016 210 K 0.6424 0.0215 0.3360 211 A 0.8478 0.0209 0.1312 212 T 0.8819 0.0216 0.0966 213 M 0.8627 0.0413 0.0960 214 I 0.7367 0.1210 0.1424 215 N 0.5095 0.1305 0.3600 216 A 0.2219 0.1459 0.6322 217 G 0.1779 0.1035 0.7187 218 I 0.1813 0.0760 0.7428 219 P 0.2732 0.0709 0.6559 220 T 0.6732 0.0684 0.2584 221 V 0.8855 0.0205 0.0940 222 F 0.9076 0.0124 0.0800 223 V 0.8304 0.0282 0.1414 224 N 0.5739 0.0098 0.4163 225 A 0.0387 0.7014 0.2599 226 E 0.0120 0.7995 0.1885 227 E 0.0138 0.8245 0.1616 228 I 0.0830 0.4912 0.4257 229 G 0.0723 0.1679 0.7598 230 Y 0.1349 0.1631 0.7020 231 R 0.1181 0.1577 0.7242 232 G 0.0798 0.1582 0.7619 233 T 0.1044 0.3574 0.5382 234 E 0.1584 0.4461 0.3954 235 L 0.0975 0.5628 0.3397 236 R 0.0214 0.8470 0.1316 237 E 0.0132 0.8630 0.1238 238 E 0.0134 0.8327 0.1539 239 I 0.0410 0.6187 0.3403 240 N 0.0447 0.2883 0.6670 241 G 0.0394 0.1258 0.8348 242 D 0.0824 0.0250 0.8926 243 P 0.0052 0.9205 0.0743 244 Q 0.0049 0.9415 0.0536 245 Q 0.0050 0.9493 0.0458 246 L 0.0048 0.9546 0.0406 247 A 0.0048 0.9540 0.0412 248 R 0.0049 0.9509 0.0442 249 F 0.0047 0.9571 0.0381 250 E 0.0047 0.9606 0.0347 251 R 0.0047 0.9611 0.0342 252 I 0.0047 0.9607 0.0347 253 R 0.0047 0.9600 0.0353 254 V 0.0047 0.9596 0.0357 255 A 0.0048 0.9567 0.0386 256 G 0.0047 0.9537 0.0416 257 A 0.0051 0.9525 0.0424 258 L 0.0065 0.9473 0.0463 259 R 0.0084 0.9173 0.0743 260 M 0.0376 0.6373 0.3250 261 G 0.0337 0.1721 0.7942 262 L 0.0840 0.1783 0.7377 263 I 0.1342 0.1018 0.7640 264 K 0.0972 0.0655 0.8373 265 T 0.0750 0.0229 0.9021 266 P 0.0199 0.6061 0.3740 267 E 0.0102 0.7560 0.2338 268 E 0.0159 0.7889 0.1952 269 A 0.0330 0.7515 0.2156 270 A 0.0474 0.6432 0.3094 271 T 0.0448 0.4597 0.4955 272 R 0.0614 0.2418 0.6968 273 Q 0.0773 0.1541 0.7687 274 H 0.1359 0.0686 0.7956 275 T 0.1644 0.0177 0.8179 276 P 0.1937 0.0134 0.7929 277 K 0.5993 0.0170 0.3837 278 I 0.8641 0.0087 0.1273 279 A 0.9025 0.0079 0.0897 280 F 0.9151 0.0053 0.0796 281 V 0.8380 0.0072 0.1548 282 A 0.4952 0.0139 0.4908 283 P 0.1889 0.0140 0.7971 284 P 0.1033 0.1461 0.7506 285 R 0.0712 0.3299 0.5989 286 D 0.1037 0.3748 0.5215 287 Y 0.1722 0.3995 0.4283 288 R 0.3101 0.2982 0.3916 289 T 0.2926 0.2757 0.4317 290 A 0.2227 0.2407 0.5366 291 S 0.0979 0.1184 0.7837 292 G 0.1210 0.0598 0.8191 293 K 0.5391 0.0668 0.3941 294 L 0.7324 0.0547 0.2129 295 V 0.5167 0.0908 0.3925 296 A 0.4382 0.0936 0.4682 297 A 0.1401 0.2485 0.6114 298 G 0.0862 0.1339 0.7799 299 D 0.1827 0.1038 0.7134 300 I 0.3658 0.0620 0.5721 301 D 0.5221 0.0661 0.4118 302 L 0.8593 0.0336 0.1071 303 L 0.8853 0.0364 0.0783 304 V 0.8843 0.0349 0.0808 305 R 0.8297 0.0707 0.0996 306 A 0.7614 0.0672 0.1714 307 L 0.5339 0.0756 0.3906 308 S 0.2998 0.0657 0.6345 309 M 0.0824 0.2144 0.7032 310 G 0.0503 0.1674 0.7823 311 K 0.0901 0.1820 0.7278 312 L 0.1275 0.2672 0.6054 313 H 0.0959 0.3330 0.5710 314 H 0.0446 0.5463 0.4091 315 A 0.0522 0.6023 0.3456 316 M 0.0510 0.6376 0.3114 317 M 0.0329 0.7341 0.2330 318 G 0.0196 0.8243 0.1561 319 T 0.0102 0.9135 0.0762 320 A 0.0050 0.9532 0.0418 321 A 0.0047 0.9593 0.0360 322 V 0.0047 0.9598 0.0355 323 A 0.0047 0.9594 0.0359 324 I 0.0048 0.9577 0.0376 325 G 0.0054 0.9486 0.0460 326 T 0.0061 0.9348 0.0591 327 A 0.0093 0.8912 0.0995 328 A 0.0252 0.7789 0.1959 329 A 0.0541 0.5731 0.3728 330 I 0.0758 0.1516 0.7727 331 P 0.0308 0.1930 0.7763 332 G 0.0474 0.1754 0.7772 333 T 0.1428 0.4183 0.4389 334 L 0.1025 0.7312 0.1663 335 V 0.0706 0.7766 0.1527 336 N 0.1044 0.6978 0.1978 337 L 0.0737 0.7224 0.2039 338 A 0.0816 0.5692 0.3492 339 A 0.0796 0.3673 0.5531 340 G 0.0631 0.1336 0.8034 341 G 0.0611 0.0902 0.8487 342 G 0.0772 0.0741 0.8487 343 E 0.1601 0.1112 0.7287 344 R 0.2489 0.1060 0.6451 345 S 0.3440 0.0604 0.5955 346 A 0.7484 0.0181 0.2335 347 V 0.8766 0.0065 0.1169 348 R 0.8978 0.0051 0.0971 349 F 0.8185 0.0180 0.1636 350 G 0.5888 0.0209 0.3903 351 H 0.2524 0.0207 0.7269 352 P 0.1155 0.0843 0.8002 353 S 0.1559 0.0543 0.7898 354 G 0.3836 0.0364 0.5800 355 T 0.7401 0.0153 0.2446 356 L 0.8933 0.0063 0.1004 357 R 0.9068 0.0064 0.0868 358 V 0.9003 0.0089 0.0907 359 G 0.8806 0.0114 0.1080 360 A 0.8726 0.0102 0.1173 361 E 0.8794 0.0106 0.1100 362 A 0.8467 0.0185 0.1348 363 S 0.7500 0.0242 0.2258 364 Q 0.5268 0.0973 0.3758 365 A 0.2727 0.1148 0.6125 366 N 0.0804 0.0451 0.8745 367 G 0.0788 0.0375 0.8837 368 E 0.3778 0.0417 0.5804 369 W 0.7358 0.0144 0.2498 370 T 0.8058 0.0192 0.1750 371 V 0.8472 0.0250 0.1278 372 T 0.7418 0.0801 0.1780 373 K 0.7455 0.1031 0.1515 374 A 0.6783 0.2055 0.1162 375 I 0.5968 0.3234 0.0798 376 M 0.4241 0.4866 0.0893 377 S 0.2608 0.6281 0.1111 378 R 0.1041 0.7295 0.1663 379 S 0.0832 0.7519 0.1649 380 A 0.0333 0.8823 0.0843 381 R 0.0456 0.8794 0.0750 382 I 0.0543 0.8778 0.0679 383 L 0.0938 0.8025 0.1038 384 M 0.1962 0.6182 0.1856 385 E 0.1842 0.4276 0.3882 386 G 0.2710 0.2237 0.5052 387 W 0.5874 0.1225 0.2901 388 V 0.7985 0.0322 0.1693 389 R 0.7703 0.0188 0.2109 390 V 0.4735 0.0138 0.5127 391 P 0.1731 0.0401 0.7868 392 G 0.0536 0.1938 0.7526 393 D 0.0666 0.2149 0.7185 394 A 0.0812 0.2035 0.7152 395 F 0.0643 0.0529 0.8828