# This file is the result of combining several RDB files, specifically # T0289.t06.dssp-ebghstl.rdb (weight 1.53986) # T0289.t06.stride-ebghtl.rdb (weight 1.24869) # T0289.t06.str2.rdb (weight 1.54758) # T0289.t06.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 T0289.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0289 # Using neural net t04-2621-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 T0289.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 976 # # ============================================ # Comments from T0289.t06.stride-ebghtl.rdb # ============================================ # TARGET T0289 # 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 T0289.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 976 # # ============================================ # Comments from T0289.t06.str2.rdb # ============================================ # TARGET T0289 # 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 T0289.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 976 # # ============================================ # Comments from T0289.t06.alpha.rdb # ============================================ # TARGET T0289 # 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 T0289.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 976 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1018 0.0389 0.8592 2 T 0.2951 0.0241 0.6809 3 S 0.4273 0.0228 0.5499 4 C 0.3833 0.0273 0.5894 5 V 0.3372 0.0335 0.6293 6 A 0.1738 0.0772 0.7490 7 E 0.0976 0.1014 0.8011 8 E 0.0871 0.0828 0.8301 9 P 0.1110 0.0783 0.8108 10 I 0.1849 0.0196 0.7955 11 K 0.3036 0.0113 0.6851 12 K 0.7779 0.0054 0.2167 13 I 0.9267 0.0033 0.0700 14 A 0.9325 0.0032 0.0642 15 I 0.9287 0.0033 0.0679 16 F 0.8849 0.0054 0.1096 17 G 0.6256 0.0197 0.3547 18 G 0.3140 0.0310 0.6549 19 T 0.3017 0.0494 0.6489 20 H 0.1912 0.0612 0.7476 21 G 0.0518 0.2144 0.7338 22 N 0.0470 0.2215 0.7315 23 E 0.0681 0.4539 0.4780 24 L 0.0571 0.6648 0.2781 25 T 0.0284 0.7652 0.2064 26 G 0.0064 0.9412 0.0525 27 V 0.0047 0.9594 0.0359 28 F 0.0046 0.9613 0.0341 29 L 0.0046 0.9614 0.0340 30 V 0.0046 0.9613 0.0341 31 T 0.0046 0.9614 0.0339 32 H 0.0046 0.9604 0.0350 33 W 0.0047 0.9580 0.0374 34 L 0.0048 0.9518 0.0434 35 K 0.0053 0.9066 0.0882 36 N 0.0172 0.7344 0.2484 37 G 0.0185 0.5066 0.4749 38 A 0.0300 0.4544 0.5157 39 E 0.0346 0.5940 0.3714 40 V 0.0706 0.5165 0.4129 41 H 0.0894 0.4233 0.4873 42 R 0.1067 0.3071 0.5862 43 A 0.0479 0.1871 0.7649 44 G 0.0776 0.0547 0.8677 45 L 0.3669 0.0100 0.6231 46 E 0.8535 0.0040 0.1424 47 V 0.9267 0.0033 0.0700 48 K 0.9246 0.0038 0.0715 49 P 0.9273 0.0031 0.0696 50 F 0.8629 0.0185 0.1187 51 I 0.7765 0.0065 0.2170 52 T 0.3860 0.0169 0.5970 53 N 0.1987 0.0184 0.7830 54 P 0.0462 0.5191 0.4347 55 R 0.0257 0.6840 0.2903 56 A 0.0407 0.8058 0.1534 57 V 0.0887 0.7818 0.1295 58 E 0.0957 0.7405 0.1638 59 K 0.1108 0.5979 0.2913 60 C 0.1758 0.3405 0.4838 61 T 0.1959 0.1898 0.6143 62 R 0.2417 0.1562 0.6022 63 Y 0.2674 0.1319 0.6007 64 I 0.1701 0.1167 0.7132 65 D 0.1556 0.0647 0.7797 66 C 0.2400 0.0783 0.6817 67 D 0.3600 0.0758 0.5642 68 L 0.1516 0.3269 0.5215 69 N 0.1558 0.3424 0.5018 70 R 0.1834 0.3634 0.4532 71 V 0.2037 0.1877 0.6086 72 F 0.2010 0.0956 0.7033 73 D 0.1476 0.0975 0.7549 74 L 0.0381 0.5535 0.4084 75 E 0.0305 0.6020 0.3675 76 N 0.0414 0.5608 0.3977 77 L 0.0692 0.3822 0.5486 78 S 0.0751 0.2696 0.6553 79 K 0.0748 0.2762 0.6490 80 E 0.0913 0.2074 0.7013 81 M 0.1103 0.1807 0.7091 82 S 0.0826 0.1273 0.7901 83 E 0.0542 0.1122 0.8336 84 D 0.0693 0.1060 0.8247 85 L 0.0739 0.0746 0.8515 86 P 0.0337 0.4164 0.5499 87 Y 0.0243 0.5580 0.4177 88 E 0.0204 0.7175 0.2621 89 V 0.0131 0.8732 0.1138 90 R 0.0088 0.9230 0.0682 91 R 0.0067 0.9457 0.0476 92 A 0.0060 0.9533 0.0408 93 Q 0.0053 0.9547 0.0400 94 E 0.0050 0.9553 0.0397 95 I 0.0049 0.9517 0.0433 96 N 0.0055 0.9448 0.0496 97 H 0.0068 0.8923 0.1010 98 L 0.0123 0.8287 0.1590 99 F 0.0399 0.6120 0.3481 100 G 0.0407 0.1724 0.7870 101 P 0.0349 0.2808 0.6843 102 K 0.0304 0.3383 0.6313 103 N 0.0425 0.2811 0.6763 104 S 0.0548 0.2203 0.7249 105 D 0.0495 0.2021 0.7485 106 D 0.0788 0.1276 0.7936 107 A 0.2117 0.0448 0.7435 108 Y 0.4979 0.0096 0.4925 109 D 0.6747 0.0114 0.3139 110 V 0.9241 0.0033 0.0726 111 V 0.9328 0.0032 0.0640 112 F 0.9269 0.0040 0.0691 113 D 0.8873 0.0036 0.1091 114 L 0.5467 0.0327 0.4206 115 H 0.2616 0.0509 0.6875 116 N 0.1310 0.1058 0.7632 117 T 0.1067 0.1214 0.7719 118 T 0.1205 0.1794 0.7001 119 S 0.0999 0.2504 0.6497 120 N 0.1319 0.2457 0.6224 121 M 0.1636 0.1891 0.6473 122 G 0.2038 0.0779 0.7183 123 C 0.3647 0.0510 0.5843 124 T 0.5792 0.0569 0.3639 125 L 0.6875 0.0631 0.2494 126 I 0.6887 0.0628 0.2485 127 L 0.6117 0.0745 0.3138 128 E 0.4038 0.0834 0.5128 129 D 0.1402 0.1274 0.7324 130 S 0.0683 0.1676 0.7641 131 R 0.0600 0.1505 0.7895 132 N 0.0526 0.2416 0.7057 133 D 0.0223 0.5870 0.3907 134 F 0.0150 0.7565 0.2285 135 L 0.0089 0.8462 0.1449 136 I 0.0059 0.9314 0.0626 137 Q 0.0064 0.9332 0.0604 138 M 0.0055 0.9409 0.0537 139 F 0.0056 0.9382 0.0562 140 H 0.0054 0.9267 0.0678 141 Y 0.0067 0.9059 0.0875 142 I 0.0155 0.8610 0.1235 143 K 0.0205 0.7997 0.1797 144 T 0.0370 0.7365 0.2264 145 C 0.0565 0.6060 0.3375 146 M 0.1068 0.3602 0.5331 147 A 0.0981 0.1758 0.7260 148 P 0.0877 0.0950 0.8173 149 L 0.1111 0.0334 0.8554 150 P 0.1554 0.0581 0.7865 151 C 0.3177 0.1229 0.5594 152 S 0.4939 0.1301 0.3760 153 V 0.5316 0.1562 0.3122 154 Y 0.5097 0.1280 0.3623 155 L 0.3904 0.1191 0.4906 156 I 0.2683 0.1031 0.6286 157 E 0.1614 0.1010 0.7376 158 H 0.0900 0.0792 0.8309 159 P 0.0495 0.1622 0.7883 160 S 0.0578 0.1657 0.7765 161 L 0.1119 0.2066 0.6815 162 K 0.1205 0.3171 0.5623 163 Y 0.0950 0.5296 0.3754 164 A 0.0664 0.7015 0.2320 165 T 0.0580 0.7734 0.1687 166 T 0.0583 0.7976 0.1441 167 R 0.0488 0.7753 0.1759 168 S 0.0526 0.6339 0.3135 169 I 0.0625 0.3227 0.6148 170 A 0.0710 0.0763 0.8526 171 K 0.1343 0.0406 0.8251 172 Y 0.1996 0.0144 0.7860 173 P 0.5444 0.0219 0.4337 174 V 0.8390 0.0209 0.1401 175 G 0.8948 0.0142 0.0910 176 I 0.9007 0.0107 0.0886 177 E 0.8500 0.0105 0.1394 178 V 0.4896 0.0289 0.4815 179 G 0.1963 0.0188 0.7849 180 P 0.1219 0.0435 0.8346 181 Q 0.0950 0.0253 0.8797 182 P 0.0747 0.0566 0.8688 183 H 0.0541 0.1210 0.8249 184 G 0.0520 0.1254 0.8226 185 V 0.0988 0.2925 0.6087 186 L 0.1407 0.2625 0.5968 187 R 0.0679 0.4958 0.4363 188 A 0.0101 0.9125 0.0774 189 D 0.0097 0.9172 0.0732 190 I 0.0049 0.9491 0.0460 191 L 0.0048 0.9575 0.0378 192 D 0.0047 0.9603 0.0351 193 Q 0.0047 0.9596 0.0358 194 M 0.0047 0.9592 0.0362 195 R 0.0047 0.9590 0.0363 196 R 0.0047 0.9494 0.0459 197 M 0.0051 0.9229 0.0720 198 L 0.0077 0.8289 0.1634 199 K 0.0180 0.5679 0.4141 200 H 0.0305 0.1884 0.7811