# This file is the result of combining several RDB files, specifically # T0296.t04.dssp-ebghstl.rdb (weight 1.53986) # T0296.t04.stride-ebghtl.rdb (weight 1.24869) # T0296.t04.str2.rdb (weight 1.54758) # T0296.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 T0296.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0296 # 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 T0296.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 4.62834 # # ============================================ # Comments from T0296.t04.stride-ebghtl.rdb # ============================================ # TARGET T0296 # 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 T0296.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 4.62834 # # ============================================ # Comments from T0296.t04.str2.rdb # ============================================ # TARGET T0296 # 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 T0296.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 4.62834 # # ============================================ # Comments from T0296.t04.alpha.rdb # ============================================ # TARGET T0296 # 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 T0296.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 4.62834 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0753 0.0180 0.9067 2 D 0.0826 0.0308 0.8866 3 I 0.0103 0.8855 0.1041 4 R 0.0078 0.9166 0.0756 5 Q 0.0103 0.9242 0.0655 6 V 0.0095 0.9402 0.0503 7 T 0.0065 0.9503 0.0431 8 E 0.0064 0.9392 0.0544 9 T 0.0066 0.9356 0.0577 10 I 0.0052 0.9399 0.0548 11 A 0.0057 0.9514 0.0430 12 M 0.0060 0.9487 0.0453 13 I 0.0096 0.9254 0.0650 14 E 0.0127 0.8931 0.0941 15 E 0.0233 0.7891 0.1876 16 Q 0.0524 0.4563 0.4913 17 N 0.0743 0.2240 0.7016 18 F 0.1324 0.0881 0.7795 19 D 0.2975 0.0575 0.6450 20 I 0.6296 0.1234 0.2470 21 R 0.7121 0.1106 0.1773 22 T 0.7744 0.1035 0.1221 23 I 0.7921 0.0880 0.1199 24 T 0.7294 0.1129 0.1578 25 M 0.5789 0.1504 0.2707 26 G 0.5597 0.0692 0.3711 27 I 0.6914 0.0407 0.2679 28 S 0.6260 0.0424 0.3316 29 L 0.2210 0.4150 0.3639 30 L 0.1046 0.5900 0.3054 31 D 0.0825 0.5880 0.3295 32 C 0.1131 0.3962 0.4907 33 I 0.1258 0.1941 0.6801 34 D 0.0771 0.0516 0.8713 35 P 0.0076 0.5557 0.4366 36 D 0.0254 0.5440 0.4305 37 I 0.0089 0.8591 0.1320 38 N 0.0057 0.9227 0.0717 39 R 0.0052 0.9354 0.0593 40 A 0.0053 0.9404 0.0543 41 A 0.0047 0.9509 0.0444 42 E 0.0047 0.9593 0.0360 43 K 0.0048 0.9565 0.0387 44 I 0.0047 0.9579 0.0374 45 Y 0.0047 0.9583 0.0370 46 Q 0.0048 0.9559 0.0394 47 K 0.0048 0.9507 0.0445 48 I 0.0057 0.9422 0.0521 49 T 0.0093 0.9117 0.0790 50 T 0.0065 0.9080 0.0855 51 K 0.0066 0.9082 0.0852 52 A 0.0069 0.9181 0.0750 53 A 0.0067 0.8964 0.0969 54 N 0.0068 0.8468 0.1464 55 L 0.0115 0.8788 0.1097 56 V 0.0095 0.8865 0.1040 57 A 0.0126 0.8813 0.1061 58 V 0.0091 0.9123 0.0785 59 G 0.0054 0.9421 0.0525 60 D 0.0047 0.9573 0.0380 61 E 0.0048 0.9590 0.0363 62 I 0.0048 0.9573 0.0380 63 A 0.0051 0.9530 0.0419 64 A 0.0056 0.9406 0.0539 65 E 0.0113 0.8917 0.0970 66 L 0.0460 0.6451 0.3089 67 G 0.0452 0.0748 0.8800 68 I 0.1523 0.0428 0.8048 69 P 0.4668 0.0405 0.4927 70 I 0.7194 0.0789 0.2017 71 V 0.7330 0.0604 0.2066 72 N 0.6195 0.0570 0.3235 73 K 0.5767 0.0433 0.3799 74 R 0.5787 0.0289 0.3924 75 V 0.7017 0.0185 0.2797 76 S 0.7405 0.0123 0.2472 77 V 0.6438 0.0210 0.3351 78 T 0.4385 0.0266 0.5349 79 P 0.3287 0.2371 0.4342 80 I 0.2629 0.5261 0.2110 81 S 0.2746 0.5877 0.1377 82 L 0.3014 0.5818 0.1168 83 I 0.3128 0.5055 0.1817 84 G 0.2702 0.4512 0.2786 85 A 0.2434 0.3423 0.4143 86 A 0.1396 0.2734 0.5870 87 T 0.0997 0.1871 0.7132 88 D 0.0690 0.1347 0.7963 89 A 0.0263 0.4168 0.5569 90 T 0.0244 0.5326 0.4430 91 D 0.0349 0.6194 0.3457 92 Y 0.0227 0.8856 0.0917 93 V 0.0124 0.9407 0.0470 94 V 0.0126 0.9436 0.0438 95 L 0.0073 0.9504 0.0423 96 A 0.0059 0.9492 0.0449 97 K 0.0055 0.9286 0.0659 98 A 0.0048 0.9272 0.0680 99 L 0.0048 0.9355 0.0596 100 D 0.0047 0.9549 0.0404 101 K 0.0047 0.9577 0.0376 102 A 0.0047 0.9588 0.0365 103 A 0.0047 0.9551 0.0402 104 K 0.0049 0.9432 0.0518 105 E 0.0066 0.8965 0.0969 106 I 0.0465 0.4477 0.5058 107 G 0.0619 0.0285 0.9096 108 V 0.2005 0.0177 0.7819 109 D 0.5447 0.0545 0.4008 110 F 0.8028 0.0328 0.1644 111 I 0.7937 0.0418 0.1645 112 G 0.6650 0.0533 0.2817 113 G 0.4240 0.0782 0.4978 114 F 0.3614 0.1987 0.4398 115 S 0.3121 0.4357 0.2523 116 A 0.3316 0.4999 0.1685 117 L 0.3860 0.4745 0.1396 118 V 0.3998 0.4570 0.1432 119 Q 0.3130 0.4102 0.2768 120 K 0.1352 0.2174 0.6474 121 G 0.0691 0.0586 0.8723 122 Y 0.1470 0.0458 0.8072 123 Q 0.1626 0.0528 0.7846 124 K 0.0596 0.2288 0.7116 125 G 0.0426 0.2940 0.6634 126 D 0.0550 0.5974 0.3476 127 E 0.0426 0.8293 0.1280 128 I 0.0519 0.8489 0.0992 129 L 0.0306 0.8949 0.0745 130 I 0.0257 0.8867 0.0877 131 N 0.0189 0.8030 0.1781 132 S 0.0201 0.7690 0.2109 133 I 0.0105 0.8004 0.1891 134 P 0.0060 0.9256 0.0684 135 R 0.0050 0.9347 0.0603 136 A 0.0067 0.9332 0.0601 137 L 0.0088 0.8912 0.1000 138 A 0.0066 0.7925 0.2009 139 E 0.0129 0.5709 0.4162 140 T 0.0723 0.2657 0.6620 141 D 0.0409 0.2596 0.6995 142 K 0.3049 0.2460 0.4492 143 V 0.5566 0.1719 0.2715 144 C 0.5892 0.1348 0.2759 145 S 0.5680 0.1195 0.3125 146 S 0.6378 0.0809 0.2813 147 V 0.7001 0.0455 0.2544 148 N 0.6613 0.0348 0.3039 149 I 0.5275 0.1092 0.3633 150 G 0.3987 0.0973 0.5040 151 S 0.3105 0.1076 0.5819 152 T 0.1487 0.1370 0.7142 153 K 0.0782 0.2727 0.6491 154 S 0.0741 0.2905 0.6354 155 G 0.1263 0.2631 0.6106 156 I 0.2488 0.2737 0.4775 157 N 0.2090 0.3176 0.4733 158 M 0.0435 0.8063 0.1502 159 T 0.0276 0.8583 0.1141 160 A 0.0229 0.8772 0.0999 161 V 0.0182 0.8901 0.0916 162 A 0.0062 0.9363 0.0575 163 D 0.0062 0.9261 0.0677 164 M 0.0073 0.9170 0.0757 165 G 0.0076 0.8824 0.1100 166 R 0.0106 0.8962 0.0931 167 I 0.0218 0.9155 0.0626 168 I 0.0224 0.9138 0.0638 169 K 0.0228 0.9098 0.0674 170 E 0.0264 0.8946 0.0790 171 T 0.0225 0.8278 0.1497 172 A 0.0449 0.5810 0.3741 173 N 0.0727 0.2979 0.6294 174 L 0.0695 0.1830 0.7474 175 S 0.0461 0.1692 0.7847 176 D 0.0476 0.2474 0.7050 177 M 0.0975 0.2717 0.6308 178 G 0.1300 0.2117 0.6582 179 V 0.2902 0.1749 0.5349 180 A 0.5882 0.0596 0.3521 181 K 0.8085 0.0256 0.1659 182 L 0.9192 0.0062 0.0746 183 V 0.9258 0.0065 0.0677 184 V 0.9214 0.0092 0.0695 185 F 0.8576 0.0213 0.1211 186 A 0.5891 0.0304 0.3805 187 N 0.3205 0.0452 0.6343 188 A 0.1994 0.0901 0.7105 189 V 0.1197 0.2527 0.6275 190 E 0.0748 0.2503 0.6749 191 D 0.0639 0.1484 0.7877 192 N 0.0988 0.0721 0.8292 193 P 0.0593 0.2548 0.6859 194 F 0.1356 0.2633 0.6011 195 M 0.2306 0.2389 0.5305 196 A 0.2276 0.2485 0.5239 197 G 0.1756 0.2661 0.5583 198 A 0.2385 0.2860 0.4755 199 F 0.3096 0.2322 0.4582 200 H 0.2384 0.1617 0.5999 201 G 0.1375 0.0791 0.7833 202 V 0.1731 0.0790 0.7479 203 G 0.1366 0.0649 0.7985 204 E 0.1347 0.1144 0.7509 205 A 0.1658 0.1031 0.7311 206 D 0.2363 0.0795 0.6842 207 V 0.7787 0.0156 0.2058 208 I 0.9127 0.0052 0.0821 209 I 0.9116 0.0068 0.0817 210 N 0.8775 0.0067 0.1158 211 V 0.7213 0.0287 0.2500 212 G 0.5596 0.0307 0.4097 213 V 0.4215 0.0515 0.5269 214 S 0.1517 0.0628 0.7855 215 G 0.0585 0.1500 0.7915 216 P 0.0197 0.6607 0.3196 217 G 0.0163 0.8600 0.1238 218 V 0.0156 0.9232 0.0612 219 V 0.0091 0.9459 0.0450 220 K 0.0080 0.9523 0.0398 221 R 0.0069 0.9535 0.0395 222 A 0.0068 0.9502 0.0430 223 L 0.0062 0.9395 0.0543 224 E 0.0085 0.9161 0.0754 225 K 0.0119 0.8275 0.1605 226 V 0.0405 0.5129 0.4467 227 R 0.0316 0.2686 0.6998 228 G 0.0258 0.1393 0.8349 229 Q 0.0708 0.1194 0.8098 230 S 0.1008 0.1767 0.7225 231 F 0.0239 0.8478 0.1283 232 D 0.0093 0.9215 0.0693 233 V 0.0120 0.9291 0.0589 234 V 0.0072 0.9442 0.0486 235 A 0.0051 0.9562 0.0388 236 E 0.0048 0.9586 0.0367 237 T 0.0047 0.9574 0.0378 238 V 0.0051 0.9531 0.0418 239 K 0.0051 0.9508 0.0442 240 K 0.0059 0.9326 0.0616 241 T 0.0098 0.8747 0.1155 242 A 0.0250 0.8333 0.1416 243 F 0.0954 0.6807 0.2239 244 K 0.1655 0.6366 0.1979 245 I 0.2044 0.5857 0.2099 246 T 0.1327 0.4323 0.4350 247 R 0.1266 0.4032 0.4702 248 I 0.0462 0.5779 0.3759 249 G 0.0361 0.5464 0.4176 250 Q 0.0699 0.6838 0.2463 251 L 0.0923 0.7886 0.1191 252 V 0.0388 0.8669 0.0943 253 G 0.0269 0.8930 0.0802 254 Q 0.0075 0.9464 0.0461 255 M 0.0066 0.9520 0.0414 256 A 0.0054 0.9547 0.0399 257 S 0.0058 0.9519 0.0424 258 E 0.0055 0.9431 0.0514 259 R 0.0069 0.9042 0.0889 260 L 0.0493 0.5719 0.3787 261 G 0.0528 0.0387 0.9085 262 V 0.0852 0.0129 0.9019 263 E 0.1870 0.0307 0.7823 264 F 0.3842 0.0540 0.5619 265 G 0.6633 0.0329 0.3038 266 I 0.8734 0.0173 0.1094 267 V 0.8607 0.0235 0.1158 268 D 0.7943 0.0204 0.1852 269 L 0.5893 0.0864 0.3244 270 S 0.3957 0.1195 0.4848 271 L 0.2195 0.2254 0.5551 272 A 0.1270 0.1690 0.7040