# 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 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 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 16.0615 # # ============================================ # 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 16.0615 # # ============================================ # Comments from T0301.t04.str2.rdb # ============================================ # TARGET T0301 # 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 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 16.0615 # # ============================================ # 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 16.0615 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 F 0.0850 0.0468 0.8682 2 L 0.1536 0.0318 0.8146 3 D 0.1241 0.0125 0.8634 4 P 0.0629 0.1147 0.8225 5 S 0.0556 0.1127 0.8317 6 D 0.0666 0.1292 0.8042 7 D 0.0792 0.0995 0.8213 8 G 0.0657 0.1138 0.8205 9 E 0.0897 0.1575 0.7529 10 D 0.1700 0.1689 0.6611 11 G 0.1656 0.2421 0.5923 12 G 0.1495 0.2651 0.5854 13 A 0.3244 0.1965 0.4791 14 I 0.4086 0.1526 0.4388 15 F 0.2384 0.0530 0.7086 16 P 0.1341 0.0847 0.7812 17 T 0.1135 0.0381 0.8484 18 G 0.0930 0.0637 0.8434 19 N 0.2059 0.0539 0.7402 20 L 0.3716 0.1424 0.4860 21 V 0.4951 0.1074 0.3975 22 D 0.4910 0.1329 0.3761 23 D 0.7012 0.0612 0.2377 24 L 0.8199 0.0160 0.1641 25 E 0.7995 0.0118 0.1887 26 V 0.4858 0.0239 0.4903 27 P 0.1068 0.0870 0.8062 28 G 0.0668 0.0665 0.8667 29 V 0.1302 0.0819 0.7879 30 G 0.1444 0.0476 0.8080 31 T 0.3354 0.0290 0.6355 32 F 0.6118 0.0070 0.3813 33 K 0.7750 0.0059 0.2191 34 A 0.8860 0.0039 0.1101 35 T 0.9056 0.0050 0.0894 36 M 0.9108 0.0062 0.0830 37 I 0.8561 0.0163 0.1276 38 N 0.6060 0.0332 0.3608 39 A 0.2628 0.0878 0.6494 40 G 0.1753 0.0891 0.7356 41 I 0.1695 0.1057 0.7247 42 P 0.2834 0.1122 0.6044 43 T 0.6747 0.0878 0.2375 44 V 0.8597 0.0480 0.0923 45 F 0.8741 0.0358 0.0901 46 V 0.8005 0.0431 0.1564 47 N 0.4784 0.0319 0.4897 48 A 0.0443 0.6783 0.2773 49 E 0.0185 0.7796 0.2019 50 E 0.0359 0.7819 0.1822 51 I 0.0991 0.4579 0.4430 52 G 0.0629 0.1222 0.8149 53 Y 0.1119 0.0978 0.7903 54 R 0.1050 0.1047 0.7903 55 G 0.0857 0.1951 0.7192 56 T 0.1201 0.2760 0.6039 57 E 0.1833 0.3131 0.5036 58 L 0.0921 0.4314 0.4765 59 R 0.0184 0.8394 0.1422 60 E 0.0123 0.8754 0.1123 61 E 0.0157 0.8415 0.1428 62 I 0.0471 0.6105 0.3424 63 N 0.0469 0.2814 0.6716 64 G 0.0425 0.1528 0.8047 65 D 0.0858 0.0321 0.8822 66 P 0.0052 0.9212 0.0735 67 Q 0.0049 0.9259 0.0692 68 Q 0.0053 0.9473 0.0474 69 L 0.0048 0.9533 0.0419 70 A 0.0048 0.9490 0.0461 71 R 0.0049 0.9500 0.0451 72 F 0.0047 0.9586 0.0367 73 E 0.0047 0.9607 0.0347 74 R 0.0047 0.9611 0.0342 75 I 0.0047 0.9611 0.0343 76 R 0.0047 0.9602 0.0351 77 V 0.0047 0.9611 0.0342 78 A 0.0047 0.9598 0.0355 79 G 0.0047 0.9586 0.0367 80 A 0.0047 0.9579 0.0374 81 L 0.0051 0.9555 0.0394 82 R 0.0074 0.9351 0.0576 83 M 0.0358 0.7096 0.2546 84 G 0.0337 0.1725 0.7939 85 L 0.0585 0.0926 0.8490 86 I 0.1043 0.0882 0.8075 87 K 0.0768 0.0728 0.8504 88 T 0.0755 0.0221 0.9023 89 P 0.0081 0.8164 0.1755 90 E 0.0062 0.8796 0.1142 91 E 0.0086 0.8970 0.0944 92 A 0.0176 0.8632 0.1192 93 A 0.0302 0.7390 0.2308 94 T 0.0315 0.5867 0.3818 95 R 0.0549 0.3930 0.5521 96 Q 0.0599 0.2533 0.6868 97 H 0.1027 0.1045 0.7928 98 T 0.1557 0.0192 0.8251 99 P 0.1441 0.0142 0.8416 100 K 0.6901 0.0152 0.2947 101 I 0.9067 0.0050 0.0882 102 A 0.9138 0.0057 0.0805 103 F 0.9124 0.0050 0.0826 104 V 0.8002 0.0103 0.1895 105 A 0.3869 0.0148 0.5983 106 P 0.1390 0.0168 0.8442 107 P 0.0868 0.1807 0.7325 108 R 0.0609 0.3490 0.5900 109 D 0.0982 0.3968 0.5050 110 Y 0.1492 0.4001 0.4508 111 R 0.2402 0.3362 0.4235 112 T 0.2237 0.2784 0.4979 113 A 0.1650 0.2253 0.6097 114 S 0.0911 0.1235 0.7854 115 G 0.0998 0.0801 0.8201 116 K 0.3382 0.0876 0.5742 117 L 0.6573 0.0760 0.2668 118 V 0.5146 0.1459 0.3394 119 A 0.3912 0.1662 0.4426 120 A 0.1313 0.2553 0.6134 121 G 0.0815 0.1417 0.7768 122 D 0.1644 0.1157 0.7199 123 I 0.3109 0.1086 0.5805 124 D 0.4072 0.0990 0.4939 125 L 0.7761 0.0792 0.1446 126 L 0.8228 0.0824 0.0949 127 V 0.8384 0.0782 0.0834 128 R 0.7651 0.1212 0.1137 129 A 0.6589 0.1521 0.1890 130 L 0.4358 0.1977 0.3665 131 S 0.2765 0.1191 0.6045 132 M 0.0667 0.2072 0.7261 133 G 0.0365 0.1411 0.8223 134 K 0.0802 0.1762 0.7436 135 L 0.1071 0.2725 0.6204 136 H 0.1050 0.3313 0.5637 137 H 0.0591 0.4600 0.4810 138 A 0.0898 0.5775 0.3327 139 M 0.0763 0.6339 0.2898 140 M 0.0374 0.7828 0.1797 141 G 0.0138 0.9038 0.0825 142 T 0.0056 0.9475 0.0469 143 A 0.0047 0.9586 0.0367 144 A 0.0047 0.9597 0.0356 145 V 0.0047 0.9602 0.0352 146 A 0.0047 0.9604 0.0349 147 I 0.0047 0.9594 0.0358 148 G 0.0052 0.9562 0.0386 149 T 0.0058 0.9435 0.0506 150 A 0.0077 0.9121 0.0802 151 A 0.0224 0.8216 0.1560 152 A 0.0558 0.5871 0.3572 153 I 0.0660 0.1750 0.7590 154 P 0.0282 0.2105 0.7613 155 G 0.0449 0.1556 0.7996 156 T 0.2187 0.3194 0.4619 157 L 0.2583 0.5518 0.1899 158 V 0.1217 0.7492 0.1291 159 N 0.1233 0.7242 0.1525 160 L 0.0962 0.7345 0.1693 161 A 0.0970 0.6465 0.2564 162 A 0.0952 0.4594 0.4454 163 G 0.0789 0.1726 0.7485 164 G 0.0620 0.1250 0.8131 165 G 0.0701 0.1075 0.8224 166 E 0.1525 0.1400 0.7076 167 R 0.2141 0.1250 0.6609 168 S 0.2417 0.0551 0.7032 169 A 0.6932 0.0210 0.2859 170 V 0.8671 0.0067 0.1262 171 R 0.8929 0.0067 0.1004 172 F 0.8098 0.0189 0.1712 173 G 0.4247 0.0245 0.5508 174 H 0.1865 0.0187 0.7949 175 P 0.1560 0.0767 0.7672 176 S 0.1656 0.0586 0.7758 177 G 0.3165 0.0343 0.6493 178 T 0.6714 0.0189 0.3096 179 L 0.8779 0.0069 0.1152 180 R 0.9112 0.0059 0.0829 181 V 0.9073 0.0074 0.0852 182 G 0.8892 0.0086 0.1023 183 A 0.8706 0.0073 0.1221 184 E 0.8879 0.0077 0.1043 185 A 0.8596 0.0142 0.1263 186 S 0.7155 0.0242 0.2603 187 Q 0.4124 0.1091 0.4784 188 A 0.2136 0.1226 0.6638 189 N 0.0830 0.0573 0.8597 190 G 0.0754 0.0437 0.8809 191 E 0.3126 0.0459 0.6416 192 W 0.6853 0.0139 0.3009 193 T 0.7736 0.0194 0.2070 194 V 0.8265 0.0208 0.1527 195 T 0.6214 0.1082 0.2704 196 K 0.6350 0.2279 0.1371 197 A 0.5243 0.3735 0.1022 198 I 0.4099 0.5141 0.0760 199 M 0.2824 0.6364 0.0812 200 S 0.2280 0.6635 0.1086 201 R 0.1023 0.7264 0.1714 202 S 0.0830 0.7344 0.1826 203 A 0.0164 0.9215 0.0621 204 R 0.0197 0.9091 0.0712 205 I 0.0281 0.9064 0.0655 206 L 0.0405 0.8664 0.0931 207 M 0.1355 0.6513 0.2132 208 E 0.1670 0.4166 0.4165 209 G 0.2317 0.1745 0.5937 210 W 0.5415 0.0979 0.3606 211 V 0.7351 0.0395 0.2254 212 R 0.7144 0.0275 0.2582 213 V 0.4880 0.0169 0.4952 214 P 0.1976 0.0445 0.7579 215 G 0.0636 0.1768 0.7596 216 D 0.0826 0.2013 0.7160 217 A 0.1196 0.2221 0.6583 218 F 0.0894 0.0852 0.8253