# This file is the result of combining several RDB files, specifically # T0313.t06.dssp-ebghstl.rdb (weight 1.53986) # T0313.t06.stride-ebghtl.rdb (weight 1.24869) # T0313.t06.str2.rdb (weight 1.54758) # T0313.t06.alpha.rdb (weight 0.659012) # T0313.t04.dssp-ebghstl.rdb (weight 1.53986) # T0313.t04.stride-ebghtl.rdb (weight 1.24869) # T0313.t04.str2.rdb (weight 1.54758) # T0313.t04.alpha.rdb (weight 0.659012) # T0313.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0313.t2k.stride-ebghtl.rdb (weight 1.24869) # T0313.t2k.str2.rdb (weight 1.54758) # T0313.t2k.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 T0313.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0313 # 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 T0313.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 90.4103 # # ============================================ # Comments from T0313.t06.stride-ebghtl.rdb # ============================================ # TARGET T0313 # Using neural net t06-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 T0313.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 90.4103 # # ============================================ # Comments from T0313.t06.str2.rdb # ============================================ # TARGET T0313 # Using neural net t06-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 T0313.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 90.4103 # # ============================================ # Comments from T0313.t06.alpha.rdb # ============================================ # TARGET T0313 # Using neural net t06-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 T0313.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 90.4103 # # ============================================ # Comments from T0313.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0313 # 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 T0313.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 90.7817 # # ============================================ # Comments from T0313.t04.stride-ebghtl.rdb # ============================================ # TARGET T0313 # 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 T0313.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 90.7817 # # ============================================ # Comments from T0313.t04.str2.rdb # ============================================ # TARGET T0313 # Using neural net t06-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 T0313.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 90.7817 # # ============================================ # Comments from T0313.t04.alpha.rdb # ============================================ # TARGET T0313 # 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 T0313.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 90.7817 # # ============================================ # Comments from T0313.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0313 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0313.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1285 # # ============================================ # Comments from T0313.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0313 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0313.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1285 # # ============================================ # Comments from T0313.t2k.str2.rdb # ============================================ # TARGET T0313 # 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 T0313.t2k-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 145.95 # # ============================================ # Comments from T0313.t2k.alpha.rdb # ============================================ # TARGET T0313 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0313.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1285 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 N 0.1525 0.0371 0.8105 2 I 0.4997 0.0079 0.4924 3 R 0.7980 0.0047 0.1972 4 V 0.9180 0.0035 0.0785 5 I 0.9193 0.0045 0.0762 6 A 0.9105 0.0044 0.0851 7 R 0.8741 0.0057 0.1202 8 V 0.6941 0.0098 0.2962 9 R 0.3637 0.0132 0.6230 10 P 0.1297 0.0245 0.8458 11 V 0.0872 0.0493 0.8635 12 T 0.0689 0.0426 0.8885 13 K 0.0229 0.3534 0.6237 14 E 0.0288 0.4338 0.5373 15 D 0.0522 0.4456 0.5022 16 G 0.0612 0.4110 0.5278 17 E 0.0778 0.3316 0.5905 18 G 0.0712 0.2233 0.7055 19 P 0.0720 0.1153 0.8127 20 E 0.1559 0.1124 0.7317 21 A 0.3405 0.0717 0.5878 22 T 0.5442 0.0411 0.4147 23 N 0.7570 0.0184 0.2246 24 A 0.8291 0.0125 0.1584 25 V 0.8279 0.0102 0.1619 26 T 0.7346 0.0149 0.2505 27 F 0.4745 0.0308 0.4947 28 D 0.1580 0.0546 0.7874 29 A 0.0826 0.0869 0.8304 30 D 0.2207 0.0554 0.7240 31 D 0.4668 0.0327 0.5004 32 D 0.6771 0.0159 0.3070 33 S 0.8116 0.0133 0.1751 34 I 0.7865 0.0191 0.1944 35 I 0.6637 0.0336 0.3027 36 H 0.4549 0.0462 0.4989 37 L 0.2592 0.0855 0.6553 38 L 0.1619 0.0939 0.7441 39 H 0.1543 0.0909 0.7548 40 K 0.1405 0.0849 0.7746 41 G 0.1666 0.0711 0.7622 42 K 0.2088 0.0526 0.7386 43 P 0.3436 0.0443 0.6121 44 V 0.5988 0.0251 0.3761 45 S 0.7788 0.0121 0.2091 46 F 0.8562 0.0066 0.1372 47 E 0.8326 0.0080 0.1594 48 L 0.7918 0.0161 0.1922 49 D 0.6311 0.0484 0.3205 50 K 0.5787 0.0489 0.3724 51 V 0.5504 0.0381 0.4115 52 F 0.4188 0.0268 0.5544 53 S 0.1260 0.0231 0.8509 54 P 0.0256 0.1421 0.8323 55 Q 0.0336 0.0966 0.8699 56 A 0.1059 0.1067 0.7875 57 S 0.1230 0.1131 0.7639 58 Q 0.0296 0.7491 0.2213 59 Q 0.0124 0.8788 0.1088 60 D 0.0185 0.8973 0.0842 61 V 0.0122 0.9082 0.0795 62 F 0.0132 0.8947 0.0921 63 Q 0.0135 0.8840 0.1025 64 E 0.0117 0.8645 0.1238 65 V 0.0129 0.8532 0.1339 66 Q 0.0085 0.9132 0.0783 67 A 0.0058 0.9124 0.0817 68 L 0.0057 0.9263 0.0679 69 V 0.0075 0.9327 0.0599 70 T 0.0062 0.9415 0.0524 71 S 0.0073 0.9302 0.0625 72 C 0.0098 0.9121 0.0782 73 I 0.0222 0.8021 0.1757 74 D 0.0333 0.2925 0.6742 75 G 0.0348 0.0665 0.8988 76 F 0.1233 0.0466 0.8301 77 N 0.2746 0.0374 0.6880 78 V 0.7701 0.0157 0.2142 79 C 0.8987 0.0092 0.0921 80 I 0.9221 0.0064 0.0715 81 F 0.9085 0.0093 0.0822 82 A 0.8750 0.0121 0.1130 83 Y 0.6048 0.0353 0.3599 84 G 0.3180 0.0319 0.6502 85 Q 0.2210 0.0471 0.7318 86 T 0.1197 0.0735 0.8069 87 G 0.0662 0.0637 0.8701 88 A 0.0720 0.0489 0.8790 89 G 0.0862 0.0417 0.8721 90 K 0.2256 0.0608 0.7136 91 T 0.6047 0.0675 0.3277 92 Y 0.6830 0.0852 0.2318 93 T 0.6678 0.0834 0.2488 94 M 0.6133 0.0943 0.2924 95 E 0.4298 0.0794 0.4908 96 G 0.2640 0.0430 0.6929 97 T 0.1043 0.0551 0.8406 98 A 0.0545 0.1258 0.8196 99 E 0.0414 0.1172 0.8414 100 N 0.0720 0.1244 0.8037 101 P 0.0453 0.2396 0.7152 102 G 0.0684 0.2094 0.7222 103 I 0.1516 0.3094 0.5391 104 N 0.0764 0.3882 0.5354 105 Q 0.0093 0.9087 0.0820 106 R 0.0059 0.9368 0.0573 107 A 0.0049 0.9473 0.0478 108 L 0.0048 0.9537 0.0415 109 Q 0.0048 0.9541 0.0410 110 L 0.0049 0.9511 0.0440 111 L 0.0049 0.9501 0.0451 112 F 0.0051 0.9411 0.0538 113 S 0.0050 0.9177 0.0773 114 E 0.0060 0.8865 0.1074 115 V 0.0177 0.8345 0.1478 116 Q 0.0188 0.7892 0.1919 117 E 0.0296 0.6227 0.3477 118 K 0.0629 0.3529 0.5842 119 A 0.0576 0.1317 0.8107 120 S 0.0314 0.1633 0.8053 121 D 0.0437 0.0914 0.8649 122 W 0.2341 0.0403 0.7256 123 E 0.6263 0.0102 0.3635 124 Y 0.8202 0.0044 0.1754 125 T 0.8850 0.0042 0.1108 126 I 0.9176 0.0032 0.0792 127 T 0.9183 0.0033 0.0784 128 V 0.9087 0.0036 0.0878 129 S 0.8757 0.0057 0.1186 130 A 0.8421 0.0146 0.1433 131 A 0.8584 0.0232 0.1183 132 E 0.8182 0.0544 0.1274 133 I 0.6121 0.1741 0.2138 134 Y 0.3449 0.2746 0.3805 135 N 0.2038 0.3880 0.4082 136 E 0.1487 0.5937 0.2576 137 V 0.2342 0.5645 0.2013 138 L 0.1460 0.7006 0.1534 139 R 0.0878 0.7524 0.1597 140 D 0.1070 0.7161 0.1770 141 L 0.0714 0.6790 0.2497 142 L 0.0771 0.3614 0.5615 143 G 0.0758 0.1789 0.7452 144 K 0.0410 0.2228 0.7363 145 E 0.0442 0.1985 0.7572 146 P 0.0516 0.2128 0.7356 147 Q 0.0623 0.2403 0.6974 148 E 0.0805 0.2399 0.6797 149 K 0.1285 0.1781 0.6934 150 L 0.2024 0.1343 0.6633 151 E 0.3789 0.0884 0.5326 152 I 0.6216 0.0406 0.3379 153 R 0.7455 0.0223 0.2321 154 L 0.8132 0.0167 0.1701 155 C 0.7454 0.0289 0.2257 156 P 0.6880 0.0281 0.2838 157 D 0.3118 0.0297 0.6585 158 G 0.0879 0.0969 0.8151 159 S 0.0368 0.0680 0.8953 160 G 0.0929 0.0368 0.8702 161 Q 0.2896 0.0169 0.6935 162 L 0.8079 0.0071 0.1850 163 Y 0.8468 0.0063 0.1469 164 V 0.7373 0.0120 0.2507 165 P 0.2870 0.0675 0.6455 166 G 0.1910 0.0347 0.7743 167 L 0.4318 0.0195 0.5487 168 T 0.6560 0.0277 0.3163 169 E 0.7761 0.0116 0.2123 170 F 0.7638 0.0080 0.2282 171 Q 0.7163 0.0082 0.2755 172 V 0.5386 0.0104 0.4510 173 Q 0.1580 0.0411 0.8010 174 S 0.0817 0.0147 0.9036 175 V 0.0053 0.9243 0.0704 176 D 0.0048 0.9493 0.0459 177 D 0.0050 0.9520 0.0430 178 I 0.0047 0.9580 0.0372 179 N 0.0047 0.9577 0.0376 180 K 0.0047 0.9559 0.0394 181 V 0.0048 0.9542 0.0410 182 F 0.0052 0.9504 0.0445 183 E 0.0055 0.9343 0.0602 184 F 0.0116 0.8661 0.1223 185 G 0.0135 0.7689 0.2176 186 H 0.0189 0.7183 0.2629 187 T 0.0256 0.6763 0.2981 188 N 0.0591 0.5511 0.3898 189 R 0.0966 0.4204 0.4830 190 T 0.1693 0.3992 0.4315 191 T 0.1673 0.3971 0.4355 192 E 0.1334 0.3497 0.5170 193 F 0.1772 0.3210 0.5018 194 T 0.1994 0.2721 0.5286 195 N 0.2023 0.2329 0.5648 196 L 0.1646 0.2447 0.5907 197 N 0.1133 0.1882 0.6985 198 E 0.0801 0.2735 0.6463 199 H 0.0971 0.2047 0.6982 200 S 0.1162 0.1245 0.7594 201 S 0.1443 0.1398 0.7159 202 R 0.2312 0.1561 0.6127 203 S 0.4253 0.1124 0.4623 204 H 0.5952 0.0502 0.3546 205 A 0.7762 0.0179 0.2059 206 L 0.8907 0.0057 0.1036 207 L 0.9113 0.0041 0.0847 208 I 0.9255 0.0032 0.0714 209 V 0.9272 0.0033 0.0696 210 T 0.9232 0.0036 0.0732 211 V 0.9228 0.0031 0.0740 212 R 0.8748 0.0123 0.1129 213 G 0.8231 0.0087 0.1682 214 V 0.7102 0.0276 0.2622 215 D 0.6004 0.0279 0.3717 216 C 0.3476 0.0723 0.5801 217 S 0.2074 0.0644 0.7282 218 T 0.1215 0.0575 0.8210 219 G 0.1071 0.0507 0.8422 220 L 0.2944 0.0382 0.6674 221 R 0.6487 0.0158 0.3355 222 T 0.7911 0.0128 0.1961 223 T 0.7976 0.0113 0.1910 224 G 0.7862 0.0104 0.2034 225 K 0.8721 0.0072 0.1207 226 L 0.9021 0.0035 0.0944 227 N 0.9097 0.0056 0.0846 228 L 0.9072 0.0067 0.0862 229 V 0.8547 0.0113 0.1340 230 D 0.6405 0.0286 0.3308 231 L 0.2483 0.0908 0.6609 232 A 0.1554 0.0795 0.7651 233 G 0.1036 0.0910 0.8054 234 S 0.1343 0.1483 0.7173 235 E 0.1330 0.3467 0.5204 236 R 0.1336 0.3589 0.5075 237 V 0.1263 0.4336 0.4401 238 G 0.0885 0.3922 0.5194 239 K 0.0842 0.3589 0.5569 240 S 0.0791 0.2639 0.6569 241 G 0.0620 0.1091 0.8289 242 A 0.0789 0.1075 0.8136 243 E 0.0697 0.1486 0.7817 244 G 0.0491 0.2229 0.7280 245 S 0.1209 0.3384 0.5407 246 R 0.1736 0.4654 0.3611 247 L 0.0893 0.7568 0.1538 248 R 0.0765 0.7995 0.1240 249 E 0.0475 0.8405 0.1120 250 A 0.0339 0.8509 0.1152 251 Q 0.0320 0.8400 0.1280 252 H 0.0355 0.8205 0.1440 253 I 0.0244 0.8677 0.1079 254 N 0.0268 0.8444 0.1287 255 K 0.0148 0.8452 0.1400 256 S 0.0218 0.8294 0.1488 257 L 0.0051 0.9400 0.0549 258 S 0.0051 0.9387 0.0562 259 A 0.0054 0.9294 0.0652 260 L 0.0049 0.9473 0.0478 261 G 0.0048 0.9538 0.0414 262 D 0.0047 0.9553 0.0400 263 V 0.0047 0.9597 0.0356 264 I 0.0047 0.9586 0.0367 265 A 0.0047 0.9540 0.0412 266 A 0.0049 0.9425 0.0525 267 L 0.0081 0.8875 0.1044 268 R 0.0131 0.7659 0.2211 269 S 0.0329 0.4466 0.5205 270 R 0.0402 0.1868 0.7730 271 Q 0.0652 0.1180 0.8168 272 G 0.1013 0.0950 0.8036 273 H 0.2023 0.0540 0.7437 274 V 0.2665 0.0270 0.7065 275 P 0.2046 0.0370 0.7584 276 F 0.1049 0.1083 0.7868 277 R 0.0590 0.1491 0.7919 278 N 0.0468 0.1720 0.7812 279 S 0.0541 0.2939 0.6519 280 K 0.0353 0.6922 0.2725 281 L 0.0308 0.8220 0.1472 282 T 0.0260 0.8984 0.0756 283 Y 0.0409 0.8971 0.0620 284 L 0.0161 0.9206 0.0633 285 L 0.0107 0.9147 0.0746 286 Q 0.0085 0.8974 0.0941 287 D 0.0125 0.8180 0.1695 288 S 0.0225 0.6558 0.3217 289 L 0.0597 0.3032 0.6371 290 S 0.0609 0.1252 0.8139 291 G 0.0521 0.0857 0.8622 292 D 0.0819 0.0748 0.8433 293 S 0.2947 0.0592 0.6461 294 K 0.5533 0.0263 0.4205 295 T 0.8697 0.0061 0.1242 296 L 0.9180 0.0042 0.0778 297 M 0.9284 0.0032 0.0684 298 V 0.9273 0.0033 0.0694 299 V 0.9099 0.0054 0.0847 300 Q 0.8609 0.0074 0.1317 301 V 0.6837 0.0180 0.2984 302 S 0.3601 0.0133 0.6266 303 P 0.0750 0.3374 0.5877 304 V 0.0410 0.4214 0.5376 305 E 0.0309 0.5661 0.4030 306 K 0.0330 0.3723 0.5947 307 N 0.0688 0.2804 0.6509 308 T 0.0104 0.8124 0.1773 309 S 0.0069 0.8886 0.1045 310 E 0.0074 0.8975 0.0951 311 T 0.0082 0.9192 0.0727 312 L 0.0060 0.9402 0.0538 313 Y 0.0053 0.9367 0.0579 314 S 0.0056 0.9406 0.0539 315 L 0.0058 0.9418 0.0523 316 K 0.0067 0.9273 0.0661 317 F 0.0058 0.9235 0.0708 318 A 0.0078 0.8979 0.0944 319 E 0.0095 0.8219 0.1687 320 R 0.0130 0.6804 0.3066 321 V 0.0441 0.4278 0.5281 322 R 0.0281 0.2446 0.7272