# This file is the result of combining several RDB files, specifically # T0209.t04.dssp-ebghstl.rdb (weight 1.53986) # T0209.t04.stride-ebghtl.rdb (weight 1.24869) # T0209.t04.str2.rdb (weight 1.54758) # T0209.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 T0209.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0209 # 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 T0209.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 54.2297 # # ============================================ # Comments from T0209.t04.stride-ebghtl.rdb # ============================================ # TARGET T0209 # 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 T0209.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 54.2297 # # ============================================ # Comments from T0209.t04.str2.rdb # ============================================ # TARGET T0209 # 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 T0209.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 54.2297 # # ============================================ # Comments from T0209.t04.alpha.rdb # ============================================ # TARGET T0209 # 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 T0209.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 54.2297 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1007 0.0294 0.8699 2 N 0.1228 0.0678 0.8093 3 D 0.2728 0.0792 0.6481 4 L 0.5001 0.0381 0.4618 5 T 0.6948 0.0125 0.2927 6 L 0.7369 0.0065 0.2567 7 S 0.6225 0.0106 0.3669 8 P 0.6569 0.0094 0.3337 9 I 0.8076 0.0109 0.1815 10 A 0.9041 0.0043 0.0916 11 I 0.9204 0.0041 0.0755 12 I 0.9141 0.0040 0.0819 13 H 0.7602 0.0220 0.2178 14 T 0.3473 0.0118 0.6409 15 P 0.1249 0.0860 0.7891 16 Y 0.1275 0.1133 0.7592 17 K 0.1799 0.1686 0.6515 18 E 0.2428 0.1679 0.5893 19 K 0.3012 0.1998 0.4990 20 F 0.2527 0.1245 0.6228 21 S 0.1939 0.0886 0.7175 22 V 0.1487 0.0339 0.8173 23 P 0.1177 0.0668 0.8155 24 R 0.1673 0.0597 0.7730 25 Q 0.1269 0.0445 0.8286 26 P 0.0690 0.2208 0.7102 27 N 0.1132 0.2751 0.6117 28 L 0.2131 0.2543 0.5326 29 V 0.2370 0.1329 0.6301 30 E 0.1761 0.1511 0.6728 31 D 0.1361 0.0811 0.7829 32 G 0.2973 0.0467 0.6560 33 V 0.7230 0.0171 0.2599 34 G 0.8874 0.0064 0.1062 35 I 0.9264 0.0042 0.0694 36 V 0.9277 0.0036 0.0687 37 E 0.9183 0.0041 0.0776 38 L 0.8380 0.0058 0.1562 39 L 0.3770 0.0129 0.6102 40 P 0.1054 0.0353 0.8593 41 P 0.0548 0.1228 0.8224 42 Y 0.0659 0.0993 0.8348 43 N 0.0661 0.0629 0.8710 44 S 0.0749 0.1266 0.7985 45 P 0.0072 0.8331 0.1597 46 E 0.0088 0.8605 0.1307 47 A 0.0091 0.8865 0.1045 48 V 0.0237 0.8372 0.1391 49 R 0.0270 0.7239 0.2491 50 G 0.0427 0.5158 0.4415 51 L 0.0462 0.5984 0.3554 52 E 0.0523 0.5599 0.3877 53 Q 0.0611 0.4131 0.5258 54 F 0.1312 0.1873 0.6815 55 S 0.1153 0.1380 0.7467 56 H 0.4454 0.0813 0.4734 57 L 0.8293 0.0121 0.1586 58 W 0.9195 0.0056 0.0749 59 L 0.9252 0.0047 0.0701 60 I 0.9197 0.0090 0.0714 61 F 0.9017 0.0133 0.0850 62 Q 0.8696 0.0199 0.1106 63 F 0.6822 0.0538 0.2639 64 D 0.4002 0.0744 0.5255 65 Q 0.2685 0.1852 0.5463 66 I 0.2067 0.1969 0.5964 67 Q 0.1077 0.1983 0.6940 68 Q 0.0578 0.1197 0.8225 69 G 0.0423 0.0660 0.8917 70 K 0.1119 0.0485 0.8396 71 W 0.3166 0.0196 0.6638 72 Q 0.4290 0.0163 0.5547 73 P 0.5175 0.0221 0.4605 74 T 0.6582 0.0236 0.3182 75 V 0.6436 0.0123 0.3441 76 R 0.4428 0.0113 0.5458 77 P 0.2559 0.0149 0.7293 78 P 0.1842 0.0739 0.7419 79 R 0.1583 0.0920 0.7497 80 L 0.1016 0.0993 0.7991 81 G 0.0670 0.0595 0.8735 82 G 0.0662 0.0517 0.8821 83 N 0.1341 0.0393 0.8267 84 Q 0.3037 0.0434 0.6529 85 R 0.6420 0.0237 0.3343 86 V 0.7942 0.0283 0.1776 87 G 0.8494 0.0143 0.1363 88 V 0.8759 0.0152 0.1088 89 F 0.8657 0.0167 0.1177 90 A 0.7465 0.0214 0.2321 91 S 0.5115 0.0338 0.4547 92 R 0.2433 0.0500 0.7067 93 A 0.1493 0.0507 0.8001 94 T 0.0864 0.1150 0.7986 95 H 0.1088 0.0863 0.8049 96 R 0.1112 0.0416 0.8472 97 P 0.0967 0.0573 0.8459 98 N 0.1247 0.0355 0.8398 99 P 0.1342 0.2461 0.6197 100 L 0.2293 0.2238 0.5469 101 G 0.5027 0.1177 0.3796 102 L 0.6104 0.0493 0.3403 103 S 0.6268 0.0396 0.3336 104 K 0.7760 0.0271 0.1969 105 V 0.8663 0.0076 0.1260 106 E 0.8982 0.0064 0.0954 107 L 0.8984 0.0054 0.0962 108 R 0.8295 0.0281 0.1425 109 Q 0.8888 0.0061 0.1051 110 V 0.8964 0.0047 0.0988 111 E 0.9012 0.0045 0.0943 112 C 0.8472 0.0078 0.1450 113 I 0.4962 0.0388 0.4650 114 N 0.0999 0.0308 0.8693 115 G 0.0546 0.0300 0.9154 116 N 0.2615 0.0225 0.7161 117 I 0.7734 0.0048 0.2219 118 F 0.9111 0.0036 0.0854 119 L 0.9242 0.0034 0.0724 120 H 0.9227 0.0035 0.0739 121 L 0.8521 0.0051 0.1428 122 G 0.5625 0.0324 0.4051 123 A 0.5274 0.0237 0.4489 124 V 0.5891 0.0345 0.3764 125 D 0.6850 0.0426 0.2725 126 L 0.5825 0.1221 0.2954 127 V 0.4446 0.1252 0.4302 128 D 0.1537 0.0755 0.7708 129 G 0.1067 0.0392 0.8541 130 T 0.2324 0.0169 0.7507 131 P 0.5217 0.0145 0.4638 132 I 0.7411 0.0310 0.2279 133 F 0.7672 0.0282 0.2046 134 D 0.7333 0.0205 0.2463 135 I 0.5840 0.0375 0.3786 136 K 0.3856 0.0724 0.5420 137 P 0.3381 0.0989 0.5630 138 Y 0.2665 0.1188 0.6148 139 I 0.2682 0.1289 0.6029 140 A 0.2026 0.2160 0.5814 141 Y 0.1346 0.3580 0.5074 142 A 0.1595 0.2536 0.5869 143 D 0.1037 0.1531 0.7432 144 S 0.0733 0.1023 0.8243 145 E 0.0622 0.0980 0.8398 146 P 0.0258 0.3473 0.6269 147 N 0.0350 0.3074 0.6576 148 A 0.0689 0.3272 0.6039 149 Q 0.0671 0.2814 0.6514 150 S 0.0395 0.5282 0.4323 151 S 0.0300 0.6094 0.3606 152 F 0.0365 0.7045 0.2590 153 A 0.0423 0.6704 0.2873 154 Q 0.0367 0.6467 0.3166 155 E 0.0560 0.4790 0.4651 156 K 0.0776 0.2462 0.6762 157 L 0.0924 0.0370 0.8705 158 P 0.0956 0.0531 0.8513 159 V 0.2579 0.0923 0.6498 160 K 0.5465 0.0664 0.3871 161 L 0.6969 0.0342 0.2689 162 T 0.7881 0.0264 0.1855 163 V 0.7604 0.0323 0.2074 164 E 0.6838 0.0359 0.2802 165 F 0.4658 0.0718 0.4624 166 T 0.1919 0.1993 0.6088 167 E 0.0202 0.8531 0.1266 168 Q 0.0145 0.8839 0.1016 169 A 0.0100 0.9020 0.0880 170 K 0.0083 0.9231 0.0686 171 S 0.0066 0.9116 0.0819 172 A 0.0068 0.9044 0.0889 173 V 0.0084 0.8971 0.0945 174 K 0.0094 0.8637 0.1269 175 K 0.0094 0.8529 0.1376 176 R 0.0153 0.8211 0.1636 177 E 0.0155 0.7868 0.1977 178 E 0.0186 0.7162 0.2652 179 K 0.0310 0.5421 0.4269 180 R 0.0642 0.1608 0.7750 181 P 0.0210 0.5436 0.4355 182 H 0.0316 0.6480 0.3204 183 L 0.0067 0.9156 0.0777 184 S 0.0053 0.9487 0.0460 185 R 0.0050 0.9577 0.0373 186 F 0.0059 0.9578 0.0363 187 I 0.0054 0.9601 0.0345 188 R 0.0049 0.9608 0.0343 189 Q 0.0047 0.9610 0.0343 190 V 0.0051 0.9554 0.0395 191 L 0.0078 0.9396 0.0526 192 E 0.0097 0.8825 0.1078 193 Q 0.0274 0.6584 0.3142 194 D 0.0911 0.0670 0.8419 195 P 0.0328 0.1207 0.8465 196 R 0.0693 0.0539 0.8768 197 P 0.0653 0.2381 0.6966 198 A 0.0490 0.4975 0.4535 199 Y 0.1017 0.4657 0.4325 200 Q 0.1387 0.3172 0.5441 201 Q 0.0980 0.1302 0.7717 202 G 0.0634 0.0459 0.8907 203 K 0.0841 0.0173 0.8986 204 P 0.0931 0.0410 0.8659 205 S 0.0722 0.1163 0.8116 206 D 0.1229 0.1035 0.7737 207 R 0.5156 0.0383 0.4461 208 I 0.8309 0.0111 0.1580 209 Y 0.8823 0.0111 0.1066 210 G 0.9059 0.0076 0.0865 211 M 0.9087 0.0054 0.0859 212 S 0.8995 0.0059 0.0946 213 L 0.8676 0.0146 0.1178 214 Y 0.7890 0.0365 0.1744 215 E 0.8308 0.0195 0.1497 216 F 0.8515 0.0093 0.1393 217 N 0.8510 0.0071 0.1418 218 V 0.8587 0.0071 0.1343 219 K 0.8784 0.0092 0.1124 220 W 0.8913 0.0055 0.1032 221 R 0.8889 0.0072 0.1039 222 I 0.8191 0.0206 0.1603 223 K 0.5876 0.0458 0.3666 224 A 0.1431 0.0453 0.8116 225 G 0.1045 0.0400 0.8555 226 T 0.5771 0.0236 0.3993 227 V 0.8313 0.0046 0.1641 228 N 0.8942 0.0061 0.0998 229 C 0.9212 0.0043 0.0744 230 V 0.8942 0.0125 0.0933 231 E 0.9130 0.0060 0.0810 232 V 0.9073 0.0070 0.0857 233 I 0.8679 0.0122 0.1199 234 E 0.8150 0.0149 0.1701 235 I 0.5477 0.0666 0.3857 236 E 0.4216 0.0954 0.4830 237 K 0.1917 0.1116 0.6967 238 D 0.1170 0.0641 0.8189 239 K 0.1072 0.0572 0.8355