# 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 15.0528 # # ============================================ # 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 15.0528 # # ============================================ # Comments from T0301.t04.str2.rdb # ============================================ # TARGET T0301 # Using neural net t04-2621-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 15.0528 # # ============================================ # 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 15.0528 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 D 0.0479 0.0709 0.8812 2 G 0.0824 0.0443 0.8733 3 V 0.1979 0.0223 0.7798 4 T 0.2509 0.0230 0.7261 5 F 0.1527 0.0532 0.7941 6 P 0.1166 0.1032 0.7802 7 A 0.1614 0.1606 0.6779 8 A 0.2897 0.1000 0.6103 9 E 0.5234 0.0417 0.4349 10 I 0.8064 0.0147 0.1789 11 V 0.8850 0.0086 0.1064 12 L 0.8825 0.0104 0.1071 13 E 0.8477 0.0104 0.1419 14 F 0.7815 0.0134 0.2052 15 L 0.5367 0.0188 0.4446 16 D 0.2745 0.0111 0.7144 17 P 0.0950 0.0984 0.8066 18 S 0.0561 0.0892 0.8547 19 D 0.0526 0.0935 0.8538 20 D 0.0643 0.0596 0.8761 21 G 0.0760 0.0562 0.8679 22 E 0.0842 0.1072 0.8086 23 D 0.1784 0.1084 0.7131 24 G 0.2090 0.1411 0.6499 25 G 0.1888 0.1389 0.6723 26 A 0.3355 0.0909 0.5736 27 I 0.5074 0.0784 0.4142 28 F 0.2735 0.0459 0.6806 29 P 0.1601 0.0832 0.7567 30 T 0.1492 0.0481 0.8027 31 G 0.0903 0.0947 0.8151 32 N 0.1505 0.0779 0.7715 33 L 0.2749 0.1435 0.5816 34 V 0.4054 0.0959 0.4986 35 D 0.4326 0.1193 0.4480 36 D 0.6459 0.0616 0.2925 37 L 0.7904 0.0215 0.1881 38 E 0.7651 0.0141 0.2208 39 V 0.4519 0.0137 0.5344 40 P 0.1273 0.0545 0.8182 41 G 0.0785 0.0350 0.8865 42 V 0.2051 0.0616 0.7332 43 G 0.2161 0.0520 0.7319 44 T 0.4447 0.0442 0.5111 45 F 0.5910 0.0117 0.3972 46 K 0.6814 0.0127 0.3059 47 A 0.8758 0.0097 0.1145 48 T 0.8849 0.0136 0.1016 49 M 0.8745 0.0179 0.1076 50 I 0.7988 0.0390 0.1622 51 N 0.5292 0.0937 0.3771 52 A 0.2173 0.1309 0.6518 53 G 0.1593 0.0948 0.7458 54 I 0.1676 0.0550 0.7774 55 P 0.2397 0.0489 0.7114 56 T 0.6479 0.0540 0.2981 57 V 0.8822 0.0202 0.0976 58 F 0.9108 0.0121 0.0771 59 V 0.8328 0.0255 0.1417 60 N 0.5970 0.0093 0.3937 61 A 0.0511 0.6667 0.2822 62 E 0.0155 0.7796 0.2049 63 E 0.0146 0.8189 0.1665 64 I 0.0806 0.4924 0.4270 65 G 0.0693 0.1433 0.7874 66 Y 0.1281 0.1504 0.7215 67 R 0.1172 0.1425 0.7403 68 G 0.0817 0.1382 0.7801 69 T 0.1169 0.2843 0.5988 70 E 0.1756 0.3626 0.4619 71 L 0.0901 0.5006 0.4092 72 R 0.0194 0.8581 0.1226 73 E 0.0109 0.8793 0.1098 74 E 0.0125 0.8516 0.1360 75 I 0.0375 0.6326 0.3299 76 N 0.0426 0.2578 0.6997 77 G 0.0377 0.1111 0.8512 78 D 0.0829 0.0204 0.8966 79 P 0.0052 0.9219 0.0729 80 Q 0.0049 0.9435 0.0516 81 Q 0.0050 0.9498 0.0453 82 L 0.0048 0.9530 0.0422 83 A 0.0048 0.9536 0.0415 84 R 0.0050 0.9503 0.0448 85 F 0.0047 0.9571 0.0382 86 E 0.0047 0.9606 0.0347 87 R 0.0047 0.9611 0.0342 88 I 0.0047 0.9607 0.0346 89 R 0.0047 0.9602 0.0351 90 V 0.0047 0.9605 0.0348 91 A 0.0048 0.9577 0.0375 92 G 0.0047 0.9567 0.0386 93 A 0.0047 0.9560 0.0393 94 L 0.0060 0.9517 0.0423 95 R 0.0078 0.9312 0.0610 96 M 0.0364 0.6145 0.3491 97 G 0.0335 0.1108 0.8557 98 L 0.0680 0.1258 0.8062 99 I 0.1222 0.0757 0.8020 100 K 0.0840 0.0564 0.8596 101 T 0.0784 0.0149 0.9066 102 P 0.0074 0.8508 0.1418 103 E 0.0056 0.8902 0.1042 104 E 0.0081 0.8976 0.0943 105 A 0.0205 0.8394 0.1401 106 A 0.0299 0.7142 0.2558 107 T 0.0371 0.5597 0.4032 108 R 0.0647 0.2524 0.6829 109 Q 0.0672 0.1321 0.8007 110 H 0.1218 0.0584 0.8198 111 T 0.1742 0.0148 0.8110 112 P 0.2046 0.0122 0.7833 113 K 0.6816 0.0128 0.3056 114 I 0.8829 0.0051 0.1120 115 A 0.9147 0.0044 0.0808 116 F 0.9194 0.0037 0.0769 117 V 0.8502 0.0063 0.1436 118 A 0.5162 0.0131 0.4707 119 P 0.1995 0.0137 0.7868 120 P 0.0983 0.1520 0.7497 121 R 0.0626 0.3969 0.5405 122 D 0.0904 0.4538 0.4558 123 Y 0.1509 0.4644 0.3848 124 R 0.2807 0.3265 0.3928 125 T 0.2498 0.3005 0.4496 126 A 0.1956 0.2574 0.5470 127 S 0.0927 0.1486 0.7587 128 G 0.1079 0.0850 0.8071 129 K 0.4011 0.0857 0.5133 130 L 0.6881 0.0665 0.2454 131 V 0.4774 0.1032 0.4194 132 A 0.3097 0.1059 0.5844 133 A 0.1124 0.2572 0.6305 134 G 0.0744 0.1451 0.7805 135 D 0.1554 0.1149 0.7297 136 I 0.2447 0.0669 0.6884 137 D 0.3521 0.0664 0.5815 138 L 0.7762 0.0711 0.1527 139 L 0.8513 0.0644 0.0843 140 V 0.8628 0.0551 0.0821 141 R 0.8036 0.0871 0.1094 142 A 0.7397 0.0829 0.1775 143 L 0.5161 0.0948 0.3891 144 S 0.2987 0.0800 0.6213 145 M 0.0911 0.2140 0.6949 146 G 0.0602 0.1806 0.7592 147 K 0.1037 0.2032 0.6931 148 L 0.1249 0.3123 0.5628 149 H 0.0945 0.3813 0.5242 150 H 0.0457 0.5530 0.4013 151 A 0.0555 0.6091 0.3354 152 M 0.0552 0.6313 0.3134 153 M 0.0336 0.7284 0.2379 154 G 0.0172 0.8424 0.1404 155 T 0.0079 0.9267 0.0654 156 A 0.0050 0.9551 0.0398 157 A 0.0047 0.9594 0.0359 158 V 0.0047 0.9598 0.0355 159 A 0.0047 0.9598 0.0355 160 I 0.0048 0.9591 0.0362 161 G 0.0052 0.9533 0.0415 162 T 0.0060 0.9418 0.0522 163 A 0.0085 0.9133 0.0783 164 A 0.0226 0.8428 0.1346 165 A 0.0462 0.6737 0.2801 166 I 0.0738 0.2167 0.7096 167 P 0.0299 0.2745 0.6955 168 G 0.0462 0.3117 0.6421 169 T 0.1305 0.4849 0.3846 170 L 0.0918 0.7618 0.1464 171 V 0.0650 0.7912 0.1439 172 N 0.0970 0.7203 0.1826 173 L 0.0684 0.7431 0.1885 174 A 0.0873 0.6015 0.3112 175 A 0.0940 0.3973 0.5087 176 G 0.0764 0.1537 0.7699 177 G 0.0644 0.0958 0.8398 178 G 0.0733 0.0756 0.8511 179 E 0.1507 0.1027 0.7466 180 R 0.2336 0.0924 0.6740 181 S 0.3068 0.0510 0.6422 182 A 0.7214 0.0167 0.2619 183 V 0.8694 0.0067 0.1239 184 R 0.8959 0.0047 0.0994 185 F 0.8194 0.0173 0.1632 186 G 0.5952 0.0207 0.3841 187 H 0.2705 0.0204 0.7091 188 P 0.1312 0.0826 0.7862 189 S 0.1730 0.0479 0.7791 190 G 0.4482 0.0300 0.5217 191 T 0.7665 0.0125 0.2210 192 L 0.8977 0.0054 0.0969 193 R 0.9128 0.0053 0.0819 194 V 0.9046 0.0079 0.0875 195 G 0.8884 0.0094 0.1022 196 A 0.8795 0.0080 0.1126 197 E 0.8851 0.0090 0.1060 198 A 0.8557 0.0150 0.1293 199 S 0.7495 0.0198 0.2307 200 Q 0.5258 0.0836 0.3907 201 A 0.3223 0.1007 0.5770 202 N 0.0810 0.0427 0.8763 203 G 0.0757 0.0379 0.8864 204 E 0.3795 0.0419 0.5786 205 W 0.7102 0.0141 0.2757 206 T 0.8098 0.0181 0.1720 207 V 0.8650 0.0165 0.1185 208 T 0.7461 0.0690 0.1849 209 K 0.7913 0.0748 0.1340 210 A 0.7556 0.1359 0.1085 211 I 0.6668 0.2547 0.0785 212 M 0.4649 0.4459 0.0892 213 S 0.2714 0.6114 0.1172 214 R 0.1099 0.7195 0.1706 215 S 0.0942 0.7289 0.1769 216 A 0.0410 0.8684 0.0905 217 R 0.0576 0.8590 0.0833 218 I 0.0705 0.8543 0.0752 219 L 0.1162 0.7719 0.1119 220 M 0.2282 0.5759 0.1959 221 E 0.2063 0.4086 0.3851 222 G 0.3069 0.1956 0.4975 223 W 0.6215 0.0844 0.2941 224 V 0.8231 0.0232 0.1538 225 R 0.8049 0.0180 0.1771 226 V 0.5306 0.0146 0.4548 227 P 0.2229 0.0344 0.7427 228 G 0.0697 0.1797 0.7505 229 D 0.0877 0.2104 0.7019 230 A 0.0904 0.1990 0.7106 231 F 0.0675 0.0592 0.8734