# This file is the result of combining several RDB files, specifically # T0286.t04.dssp-ebghstl.rdb (weight 1.53986) # T0286.t04.stride-ebghtl.rdb (weight 1.24869) # T0286.t04.str2.rdb (weight 1.54758) # T0286.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 T0286.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0286 # 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 T0286.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 1461 # # ============================================ # Comments from T0286.t04.stride-ebghtl.rdb # ============================================ # TARGET T0286 # 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 T0286.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 1461 # # ============================================ # Comments from T0286.t04.str2.rdb # ============================================ # TARGET T0286 # 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 T0286.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 1461 # # ============================================ # Comments from T0286.t04.alpha.rdb # ============================================ # TARGET T0286 # 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 T0286.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 1461 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0580 0.1023 0.8398 2 A 0.0648 0.1512 0.7840 3 S 0.0606 0.1551 0.7844 4 K 0.0711 0.0821 0.8468 5 T 0.2042 0.0240 0.7718 6 I 0.5481 0.0061 0.4458 7 K 0.8673 0.0041 0.1285 8 I 0.9256 0.0034 0.0711 9 M 0.9252 0.0036 0.0712 10 P 0.9062 0.0039 0.0898 11 V 0.7422 0.0348 0.2230 12 G 0.3527 0.0265 0.6208 13 D 0.1964 0.0715 0.7321 14 S 0.2050 0.1660 0.6290 15 C 0.1613 0.3357 0.5030 16 T 0.1779 0.3254 0.4967 17 E 0.1360 0.2862 0.5778 18 G 0.1109 0.1604 0.7287 19 M 0.1047 0.1319 0.7634 20 G 0.1116 0.0944 0.7940 21 G 0.1003 0.1331 0.7665 22 G 0.0750 0.1634 0.7616 23 E 0.0551 0.2223 0.7226 24 M 0.0431 0.2236 0.7332 25 G 0.0396 0.1973 0.7630 26 S 0.0691 0.3154 0.6155 27 Y 0.0498 0.6978 0.2524 28 R 0.0148 0.8823 0.1028 29 T 0.0056 0.9462 0.0483 30 E 0.0052 0.9484 0.0464 31 L 0.0050 0.9532 0.0418 32 Y 0.0047 0.9574 0.0379 33 R 0.0047 0.9586 0.0367 34 L 0.0048 0.9557 0.0395 35 L 0.0049 0.9472 0.0479 36 T 0.0056 0.9228 0.0716 37 Q 0.0081 0.8475 0.1444 38 A 0.0432 0.5170 0.4398 39 G 0.0411 0.0880 0.8709 40 L 0.0758 0.0449 0.8793 41 S 0.1790 0.0477 0.7733 42 I 0.4862 0.0207 0.4932 43 D 0.7684 0.0135 0.2181 44 F 0.8786 0.0130 0.1084 45 V 0.7764 0.0334 0.1901 46 G 0.5623 0.0299 0.4078 47 S 0.2850 0.0621 0.6528 48 Q 0.2318 0.1076 0.6606 49 R 0.1733 0.1078 0.7189 50 S 0.1325 0.0754 0.7921 51 G 0.1198 0.0600 0.8202 52 P 0.1266 0.1109 0.7625 53 S 0.1614 0.1131 0.7255 54 S 0.1705 0.0869 0.7427 55 L 0.1179 0.0652 0.8170 56 P 0.1042 0.1012 0.7946 57 D 0.1097 0.1233 0.7670 58 K 0.1181 0.1194 0.7624 59 D 0.1573 0.1250 0.7177 60 H 0.2374 0.1300 0.6326 61 E 0.2620 0.1281 0.6099 62 G 0.2926 0.0862 0.6212 63 H 0.2985 0.0733 0.6282 64 S 0.1951 0.0908 0.7141 65 G 0.1041 0.1048 0.7912 66 W 0.1472 0.1108 0.7420 67 T 0.1746 0.1302 0.6952 68 I 0.0546 0.6179 0.3275 69 P 0.0101 0.8568 0.1332 70 Q 0.0114 0.8589 0.1296 71 I 0.0108 0.8882 0.1010 72 A 0.0072 0.8823 0.1106 73 S 0.0058 0.8116 0.1826 74 N 0.0084 0.7731 0.2186 75 I 0.0102 0.8097 0.1801 76 N 0.0056 0.9024 0.0920 77 N 0.0049 0.9120 0.0831 78 W 0.0074 0.9129 0.0797 79 L 0.0081 0.8851 0.1068 80 N 0.0079 0.7968 0.1953 81 T 0.0121 0.6144 0.3735 82 H 0.0537 0.3560 0.5903 83 N 0.0835 0.0234 0.8930 84 P 0.0843 0.0534 0.8623 85 D 0.1159 0.0679 0.8162 86 V 0.8817 0.0053 0.1130 87 V 0.9313 0.0032 0.0654 88 F 0.9338 0.0031 0.0630 89 L 0.9249 0.0038 0.0713 90 W 0.8822 0.0044 0.1134 91 I 0.5562 0.0319 0.4119 92 G 0.2343 0.0401 0.7256 93 G 0.1456 0.1962 0.6583 94 N 0.0956 0.4103 0.4942 95 D 0.0920 0.5609 0.3471 96 L 0.0581 0.6328 0.3091 97 L 0.0701 0.5453 0.3846 98 L 0.0881 0.3985 0.5134 99 N 0.0630 0.2073 0.7297 100 G 0.0540 0.1387 0.8073 101 N 0.0737 0.1496 0.7768 102 L 0.0690 0.1783 0.7527 103 N 0.0525 0.1428 0.8047 104 A 0.0215 0.5946 0.3840 105 T 0.0173 0.7154 0.2673 106 G 0.0233 0.7619 0.2148 107 L 0.0050 0.9501 0.0449 108 S 0.0047 0.9588 0.0365 109 N 0.0047 0.9588 0.0365 110 L 0.0047 0.9603 0.0350 111 I 0.0047 0.9608 0.0346 112 D 0.0046 0.9609 0.0344 113 Q 0.0048 0.9573 0.0379 114 I 0.0049 0.9447 0.0504 115 F 0.0057 0.9138 0.0805 116 T 0.0080 0.7828 0.2091 117 V 0.0288 0.5804 0.3907 118 K 0.0816 0.0594 0.8590 119 P 0.0121 0.1521 0.8358 120 N 0.0245 0.0695 0.9060 121 V 0.2495 0.0159 0.7346 122 T 0.7473 0.0042 0.2485 123 L 0.9308 0.0031 0.0661 124 F 0.9304 0.0034 0.0662 125 V 0.9258 0.0034 0.0708 126 A 0.8214 0.0116 0.1670 127 D 0.4719 0.0129 0.5152 128 Y 0.2020 0.0393 0.7587 129 Y 0.1279 0.0492 0.8228 130 P 0.0987 0.0524 0.8488 131 W 0.0557 0.0422 0.9021 132 P 0.0280 0.4701 0.5018 133 E 0.0128 0.6983 0.2889 134 A 0.0215 0.7327 0.2457 135 I 0.0125 0.8557 0.1318 136 K 0.0063 0.9045 0.0892 137 Q 0.0058 0.9123 0.0820 138 Y 0.0066 0.9139 0.0795 139 N 0.0085 0.8940 0.0976 140 A 0.0063 0.8674 0.1263 141 V 0.0085 0.8490 0.1425 142 I 0.0069 0.9143 0.0788 143 P 0.0054 0.9487 0.0460 144 G 0.0047 0.9588 0.0365 145 I 0.0047 0.9593 0.0360 146 V 0.0047 0.9589 0.0364 147 Q 0.0047 0.9595 0.0358 148 Q 0.0047 0.9583 0.0369 149 K 0.0050 0.9520 0.0431 150 A 0.0076 0.9245 0.0679 151 N 0.0085 0.8289 0.1626 152 A 0.0283 0.5205 0.4512 153 G 0.0445 0.0991 0.8564 154 K 0.0366 0.0821 0.8813 155 K 0.0883 0.0583 0.8534 156 V 0.4080 0.0168 0.5752 157 Y 0.8213 0.0051 0.1736 158 F 0.9113 0.0036 0.0851 159 V 0.8767 0.0057 0.1176 160 K 0.7351 0.0047 0.2602 161 L 0.2360 0.2257 0.5383 162 S 0.1270 0.3789 0.4942 163 E 0.0932 0.5355 0.3712 164 I 0.1569 0.4357 0.4073 165 Q 0.1836 0.3082 0.5082 166 F 0.1695 0.1933 0.6372 167 D 0.0999 0.0740 0.8261 168 R 0.0581 0.1368 0.8051 169 N 0.0615 0.1886 0.7498 170 T 0.0822 0.2475 0.6704 171 D 0.1761 0.1966 0.6273 172 I 0.2904 0.1363 0.5732 173 S 0.2298 0.0926 0.6777 174 W 0.1770 0.1322 0.6909 175 D 0.1265 0.0986 0.7749 176 G 0.1449 0.0954 0.7596 177 L 0.2963 0.0666 0.6371 178 H 0.3534 0.0615 0.5851 179 L 0.1358 0.1300 0.7342 180 S 0.0673 0.1027 0.8300 181 E 0.0054 0.8962 0.0984 182 I 0.0047 0.9329 0.0623 183 G 0.0050 0.9485 0.0465 184 Y 0.0047 0.9590 0.0363 185 K 0.0047 0.9609 0.0344 186 K 0.0047 0.9601 0.0352 187 I 0.0047 0.9593 0.0360 188 A 0.0047 0.9594 0.0360 189 N 0.0047 0.9574 0.0379 190 I 0.0048 0.9520 0.0433 191 W 0.0049 0.9487 0.0464 192 Y 0.0047 0.9540 0.0413 193 K 0.0047 0.9521 0.0432 194 Y 0.0049 0.9392 0.0559 195 T 0.0052 0.9286 0.0661 196 I 0.0051 0.9439 0.0510 197 D 0.0048 0.9481 0.0471 198 I 0.0050 0.9334 0.0616 199 L 0.0080 0.8944 0.0977 200 R 0.0087 0.8770 0.1143 201 A 0.0132 0.8382 0.1486 202 L 0.0288 0.6647 0.3064 203 A 0.0419 0.3693 0.5888 204 G 0.0379 0.1460 0.8161 205 E 0.0444 0.0748 0.8808