# This file is the result of combining several RDB files, specifically # T0291.t06.dssp-ebghstl.rdb (weight 1.53986) # T0291.t06.stride-ebghtl.rdb (weight 1.24869) # T0291.t06.str2.rdb (weight 1.54758) # T0291.t06.alpha.rdb (weight 0.659012) # T0291.t04.dssp-ebghstl.rdb (weight 1.53986) # T0291.t04.stride-ebghtl.rdb (weight 1.24869) # T0291.t04.str2.rdb (weight 1.54758) # T0291.t04.alpha.rdb (weight 0.659012) # T0291.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0291.t2k.stride-ebghtl.rdb (weight 1.24869) # T0291.t2k.str2.rdb (weight 1.54758) # T0291.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 T0291.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0291 # 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 T0291.t06-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 13482 # # ============================================ # Comments from T0291.t06.stride-ebghtl.rdb # ============================================ # TARGET T0291 # Using neural net t06-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 T0291.t06-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 13482 # # ============================================ # Comments from T0291.t06.str2.rdb # ============================================ # TARGET T0291 # 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 T0291.t06-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 13482 # # ============================================ # Comments from T0291.t06.alpha.rdb # ============================================ # TARGET T0291 # Using neural net t06-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 T0291.t06-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 13482 # # ============================================ # Comments from T0291.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0291 # 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 T0291.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 79.048 # # ============================================ # Comments from T0291.t04.stride-ebghtl.rdb # ============================================ # TARGET T0291 # 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 T0291.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 79.048 # # ============================================ # Comments from T0291.t04.str2.rdb # ============================================ # TARGET T0291 # 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 T0291.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 79.048 # # ============================================ # Comments from T0291.t04.alpha.rdb # ============================================ # TARGET T0291 # 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 T0291.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 79.048 # # ============================================ # Comments from T0291.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0291 # 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 T0291.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 4685 # # ============================================ # Comments from T0291.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0291 # 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 T0291.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 4685 # # ============================================ # Comments from T0291.t2k.str2.rdb # ============================================ # TARGET T0291 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0291.t2k-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 4685 # # ============================================ # Comments from T0291.t2k.alpha.rdb # ============================================ # TARGET T0291 # 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 T0291.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 4685 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 T 0.3809 0.0373 0.5818 2 Y 0.5155 0.0249 0.4596 3 V 0.5450 0.0173 0.4377 4 D 0.2508 0.0193 0.7299 5 P 0.0805 0.1345 0.7851 6 H 0.0905 0.1150 0.7945 7 T 0.1837 0.1022 0.7141 8 Y 0.1913 0.0934 0.7153 9 E 0.2538 0.0993 0.6470 10 D 0.1351 0.0681 0.7968 11 P 0.0763 0.1753 0.7484 12 T 0.0814 0.1926 0.7261 13 Q 0.1114 0.1866 0.7020 14 A 0.1426 0.1649 0.6924 15 V 0.1967 0.1516 0.6517 16 H 0.2012 0.1397 0.6591 17 E 0.1046 0.5699 0.3256 18 F 0.0836 0.6472 0.2692 19 A 0.0925 0.6755 0.2320 20 K 0.1529 0.5708 0.2762 21 E 0.1661 0.5320 0.3019 22 L 0.1457 0.4099 0.4445 23 D 0.1191 0.3492 0.5318 24 A 0.0562 0.4761 0.4676 25 T 0.0451 0.3708 0.5841 26 N 0.1117 0.2117 0.6766 27 I 0.3591 0.1030 0.5379 28 S 0.4868 0.0820 0.4312 29 I 0.4632 0.1867 0.3501 30 D 0.4393 0.1846 0.3761 31 K 0.4879 0.1342 0.3779 32 V 0.6762 0.0665 0.2574 33 V 0.5999 0.0616 0.3384 34 G 0.4748 0.0432 0.4821 35 A 0.3307 0.0531 0.6162 36 G 0.1766 0.0424 0.7810 37 E 0.1801 0.0732 0.7467 38 F 0.3813 0.0571 0.5615 39 G 0.5274 0.0390 0.4336 40 E 0.7933 0.0214 0.1853 41 V 0.8749 0.0103 0.1148 42 C 0.8769 0.0128 0.1104 43 S 0.8848 0.0102 0.1050 44 G 0.8680 0.0108 0.1212 45 R 0.8769 0.0112 0.1119 46 L 0.7926 0.0155 0.1919 47 K 0.3942 0.0555 0.5503 48 L 0.1196 0.0517 0.8286 49 P 0.0585 0.0603 0.8812 50 S 0.0918 0.0605 0.8477 51 K 0.4472 0.0664 0.4864 52 K 0.7745 0.0407 0.1848 53 E 0.8279 0.0448 0.1273 54 I 0.8421 0.0571 0.1008 55 S 0.8709 0.0509 0.0782 56 V 0.8718 0.0513 0.0769 57 A 0.8664 0.0591 0.0744 58 I 0.8313 0.0836 0.0851 59 K 0.7663 0.1301 0.1037 60 T 0.6215 0.2055 0.1731 61 L 0.3947 0.2317 0.3737 62 K 0.2003 0.2146 0.5851 63 V 0.0746 0.2189 0.7065 64 G 0.0543 0.1647 0.7810 65 Y 0.0534 0.1761 0.7705 66 T 0.0547 0.1683 0.7770 67 E 0.0128 0.7849 0.2023 68 K 0.0100 0.8432 0.1467 69 Q 0.0091 0.8900 0.1008 70 R 0.0057 0.9323 0.0620 71 R 0.0049 0.9470 0.0481 72 D 0.0049 0.9518 0.0433 73 F 0.0048 0.9549 0.0403 74 L 0.0047 0.9585 0.0368 75 G 0.0047 0.9571 0.0382 76 E 0.0047 0.9573 0.0380 77 A 0.0047 0.9581 0.0372 78 S 0.0047 0.9562 0.0390 79 I 0.0048 0.9544 0.0408 80 M 0.0051 0.9431 0.0519 81 G 0.0059 0.8447 0.1494 82 Q 0.0083 0.7236 0.2681 83 F 0.0486 0.4332 0.5182 84 D 0.0549 0.1576 0.7875 85 H 0.0757 0.0707 0.8536 86 P 0.0180 0.2221 0.7598 87 N 0.0779 0.1882 0.7339 88 I 0.5953 0.1507 0.2540 89 I 0.7462 0.0971 0.1567 90 R 0.7689 0.0914 0.1396 91 L 0.7840 0.0762 0.1397 92 E 0.6930 0.0812 0.2258 93 G 0.6359 0.0688 0.2953 94 V 0.6895 0.0619 0.2486 95 V 0.7138 0.0540 0.2321 96 T 0.5971 0.0652 0.3377 97 K 0.2379 0.0640 0.6981 98 S 0.0785 0.0637 0.8578 99 K 0.1031 0.0483 0.8486 100 P 0.3305 0.0200 0.6495 101 V 0.8023 0.0051 0.1927 102 M 0.9203 0.0038 0.0759 103 I 0.9283 0.0033 0.0684 104 V 0.9224 0.0041 0.0736 105 T 0.8989 0.0066 0.0945 106 E 0.8431 0.0088 0.1482 107 Y 0.6692 0.0141 0.3167 108 M 0.2852 0.0294 0.6855 109 E 0.0484 0.0886 0.8630 110 N 0.0461 0.0368 0.9171 111 G 0.1200 0.0199 0.8601 112 S 0.2721 0.0244 0.7035 113 L 0.0661 0.7887 0.1452 114 D 0.0120 0.9083 0.0796 115 S 0.0108 0.9104 0.0788 116 F 0.0217 0.8762 0.1021 117 L 0.0499 0.7363 0.2138 118 R 0.0311 0.6259 0.3430 119 K 0.0350 0.4495 0.5155 120 H 0.0445 0.2189 0.7367 121 D 0.0361 0.0853 0.8786 122 A 0.0763 0.0678 0.8559 123 Q 0.1310 0.0563 0.8127 124 F 0.1207 0.0484 0.8309 125 T 0.0977 0.0504 0.8519 126 V 0.0065 0.9410 0.0525 127 I 0.0047 0.9561 0.0392 128 Q 0.0048 0.9566 0.0386 129 L 0.0047 0.9592 0.0361 130 V 0.0047 0.9601 0.0352 131 G 0.0047 0.9597 0.0356 132 M 0.0047 0.9599 0.0354 133 L 0.0047 0.9592 0.0361 134 R 0.0047 0.9586 0.0367 135 G 0.0047 0.9573 0.0380 136 I 0.0047 0.9567 0.0385 137 A 0.0048 0.9533 0.0419 138 S 0.0048 0.9249 0.0703 139 G 0.0049 0.9326 0.0625 140 M 0.0049 0.9308 0.0642 141 K 0.0050 0.9073 0.0877 142 Y 0.0059 0.8342 0.1599 143 L 0.0119 0.8358 0.1523 144 S 0.0134 0.7300 0.2567 145 D 0.0285 0.5532 0.4182 146 M 0.0645 0.1719 0.7636 147 G 0.1030 0.0723 0.8247 148 Y 0.4406 0.0447 0.5147 149 V 0.5856 0.0459 0.3685 150 H 0.4731 0.0965 0.4304 151 R 0.2710 0.1115 0.6175 152 D 0.2113 0.0941 0.6945 153 L 0.2121 0.1205 0.6674 154 A 0.1820 0.0854 0.7326 155 A 0.1442 0.3637 0.4921 156 R 0.1243 0.3537 0.5220 157 N 0.2614 0.2911 0.4475 158 I 0.6097 0.0888 0.3014 159 L 0.7536 0.0367 0.2096 160 I 0.7232 0.0243 0.2525 161 N 0.2148 0.0302 0.7551 162 S 0.0388 0.1233 0.8379 163 N 0.0697 0.0388 0.8915 164 L 0.2452 0.0362 0.7186 165 V 0.5336 0.0092 0.4572 166 C 0.8253 0.0047 0.1699 167 K 0.8466 0.0075 0.1459 168 V 0.7794 0.0198 0.2008 169 S 0.5782 0.0438 0.3780 170 D 0.3937 0.0537 0.5527 171 F 0.1881 0.0894 0.7225 172 G 0.1939 0.1549 0.6511 173 L 0.1638 0.4225 0.4137 174 G 0.1810 0.4952 0.3238 175 R 0.2379 0.5084 0.2538 176 V 0.2715 0.3937 0.3348 177 L 0.2527 0.1996 0.5477 178 E 0.1691 0.1302 0.7007 179 D 0.0958 0.1374 0.7668 180 D 0.0804 0.1122 0.8074 181 P 0.0731 0.2335 0.6935 182 E 0.0892 0.2903 0.6205 183 A 0.1030 0.3569 0.5400 184 A 0.1590 0.3200 0.5210 185 Y 0.2568 0.2598 0.4834 186 T 0.2695 0.1960 0.5344 187 T 0.2630 0.1330 0.6040 188 R 0.2634 0.0866 0.6500 189 G 0.2958 0.0558 0.6484 190 G 0.4110 0.0457 0.5433 191 K 0.4318 0.0572 0.5110 192 I 0.3532 0.0408 0.6060 193 P 0.2301 0.0789 0.6910 194 I 0.1232 0.3338 0.5430 195 R 0.1398 0.3901 0.4702 196 W 0.1275 0.3831 0.4894 197 T 0.1545 0.2197 0.6257 198 S 0.0943 0.2076 0.6982 199 P 0.0261 0.7956 0.1783 200 E 0.0259 0.8452 0.1289 201 A 0.0336 0.8352 0.1312 202 I 0.0470 0.7864 0.1666 203 A 0.0481 0.5889 0.3631 204 Y 0.0601 0.2594 0.6805 205 R 0.0795 0.0713 0.8492 206 K 0.1115 0.0666 0.8219 207 F 0.1922 0.0520 0.7557 208 T 0.1107 0.0448 0.8445 209 S 0.0804 0.2691 0.6506 210 A 0.0802 0.3987 0.5212 211 S 0.1526 0.3403 0.5072 212 D 0.1958 0.3869 0.4173 213 V 0.1886 0.5885 0.2229 214 W 0.1818 0.6234 0.1948 215 S 0.1261 0.6946 0.1793 216 Y 0.0565 0.8087 0.1348 217 G 0.0322 0.8562 0.1117 218 I 0.0368 0.9033 0.0599 219 V 0.0615 0.8906 0.0479 220 L 0.0436 0.9101 0.0463 221 W 0.0622 0.8879 0.0499 222 E 0.0751 0.8568 0.0681 223 V 0.0713 0.8178 0.1109 224 M 0.0873 0.6730 0.2397 225 S 0.1305 0.4044 0.4651 226 Y 0.0586 0.0988 0.8426 227 G 0.0690 0.0437 0.8873 228 E 0.1068 0.0363 0.8569 229 R 0.0897 0.0427 0.8676 230 P 0.0743 0.0791 0.8466 231 Y 0.0649 0.1722 0.7629 232 W 0.0421 0.2708 0.6871 233 E 0.0475 0.2229 0.7296 234 M 0.0721 0.1433 0.7846 235 S 0.0609 0.2666 0.6725 236 N 0.0350 0.6063 0.3587 237 Q 0.0341 0.7779 0.1880 238 D 0.0441 0.8245 0.1314 239 V 0.0616 0.8302 0.1082 240 I 0.0723 0.8143 0.1134 241 K 0.0867 0.7715 0.1418 242 A 0.0950 0.7149 0.1900 243 V 0.0974 0.5729 0.3297 244 D 0.0833 0.2953 0.6214 245 E 0.0488 0.2041 0.7471 246 G 0.0547 0.1191 0.8263 247 Y 0.1307 0.0996 0.7697 248 R 0.1714 0.0734 0.7551 249 L 0.0987 0.0656 0.8357 250 P 0.0855 0.0613 0.8532 251 P 0.0826 0.0477 0.8697 252 P 0.0655 0.0936 0.8408 253 M 0.0230 0.2823 0.6947 254 D 0.0328 0.2509 0.7163 255 C 0.0542 0.1331 0.8127 256 P 0.0473 0.1859 0.7668 257 A 0.0056 0.9162 0.0782 258 A 0.0050 0.9352 0.0598 259 L 0.0049 0.9537 0.0414 260 Y 0.0047 0.9596 0.0358 261 Q 0.0047 0.9589 0.0364 262 L 0.0048 0.9575 0.0377 263 M 0.0047 0.9563 0.0390 264 L 0.0049 0.9466 0.0484 265 D 0.0056 0.9270 0.0674 266 C 0.0064 0.9037 0.0899 267 W 0.0190 0.7789 0.2021 268 Q 0.0329 0.5898 0.3774 269 K 0.0653 0.2883 0.6464 270 D 0.0855 0.0461 0.8684 271 R 0.0077 0.4308 0.5615 272 N 0.0088 0.4171 0.5741 273 N 0.0195 0.4024 0.5781 274 R 0.0784 0.0563 0.8653 275 P 0.0976 0.0624 0.8399 276 K 0.1412 0.0385 0.8202 277 F 0.0080 0.9232 0.0688 278 E 0.0054 0.9466 0.0480 279 Q 0.0050 0.9537 0.0413 280 I 0.0047 0.9541 0.0412 281 V 0.0050 0.9371 0.0579 282 S 0.0053 0.8949 0.0998 283 I 0.0085 0.8585 0.1330 284 L 0.0097 0.8616 0.1287 285 D 0.0081 0.8678 0.1240 286 K 0.0103 0.8391 0.1506 287 L 0.0211 0.7816 0.1972 288 I 0.0537 0.5909 0.3554 289 R 0.0472 0.3488 0.6039 290 N 0.0605 0.1395 0.8001 291 P 0.0539 0.1304 0.8157 292 G 0.0588 0.1397 0.8015 293 S 0.0749 0.1402 0.7849 294 L 0.1066 0.1280 0.7654 295 K 0.1647 0.1044 0.7310 296 I 0.1590 0.0964 0.7446 297 I 0.1496 0.1475 0.7030 298 T 0.1323 0.2014 0.6663 299 S 0.0698 0.3700 0.5603 300 A 0.0512 0.4697 0.4791 301 A 0.0619 0.4164 0.5217 302 A 0.0688 0.3045 0.6267 303 R 0.0674 0.1524 0.7802 304 P 0.0559 0.1887 0.7554 305 S 0.0584 0.2514 0.6902 306 N 0.0395 0.3399 0.6207 307 L 0.0381 0.3785 0.5833 308 L 0.0421 0.3432 0.6147 309 L 0.0508 0.1816 0.7676 310 D 0.0620 0.0401 0.8979