# This file is the result of combining several RDB files, specifically # T0413.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0413.t2k.stride-ebghtl.rdb (weight 1.24869) # T0413.t2k.str2.rdb (weight 1.54758) # T0413.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 T0413.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0413 # 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 T0413.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 320 # # ============================================ # Comments from T0413.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0413 # 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 T0413.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 320 # # ============================================ # Comments from T0413.t2k.str2.rdb # ============================================ # TARGET T0413 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0413.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 320 # # ============================================ # Comments from T0413.t2k.alpha.rdb # ============================================ # TARGET T0413 # 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 T0413.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 320 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0617 0.3324 0.6059 2 N 0.0477 0.5052 0.4471 3 A 0.0341 0.7385 0.2274 4 M 0.0319 0.8385 0.1296 5 K 0.0453 0.8618 0.0929 6 P 0.0335 0.8962 0.0702 7 A 0.0292 0.8985 0.0724 8 D 0.0259 0.9034 0.0706 9 L 0.0238 0.8975 0.0788 10 T 0.0169 0.8885 0.0946 11 N 0.0141 0.8669 0.1190 12 A 0.0189 0.8208 0.1602 13 D 0.0243 0.7475 0.2282 14 R 0.0296 0.6862 0.2842 15 I 0.0242 0.6764 0.2994 16 A 0.0273 0.6801 0.2926 17 L 0.0392 0.6237 0.3371 18 E 0.0427 0.5992 0.3580 19 L 0.0652 0.5100 0.4248 20 G 0.0838 0.3941 0.5222 21 H 0.1022 0.2936 0.6043 22 A 0.1036 0.2195 0.6769 23 G 0.0970 0.2020 0.7011 24 R 0.1281 0.1851 0.6868 25 N 0.1836 0.1249 0.6915 26 A 0.3713 0.0829 0.5458 27 I 0.6436 0.0380 0.3184 28 P 0.7221 0.0283 0.2496 29 Y 0.7186 0.0246 0.2568 30 L 0.6571 0.0299 0.3130 31 D 0.5108 0.0424 0.4468 32 D 0.3594 0.0641 0.5766 33 D 0.2132 0.0792 0.7076 34 R 0.1134 0.0855 0.8011 35 N 0.0936 0.0716 0.8348 36 A 0.1104 0.0644 0.8252 37 D 0.1733 0.0728 0.7539 38 R 0.3559 0.0415 0.6025 39 P 0.6237 0.0177 0.3586 40 F 0.8185 0.0099 0.1716 41 T 0.8814 0.0065 0.1121 42 L 0.8862 0.0066 0.1072 43 N 0.8820 0.0063 0.1117 44 T 0.8150 0.0081 0.1769 45 Y 0.6469 0.0121 0.3410 46 R 0.3673 0.0285 0.6041 47 P 0.1737 0.0468 0.7794 48 Y 0.0788 0.1322 0.7889 49 G 0.0672 0.1087 0.8241 50 Y 0.0815 0.1117 0.8067 51 T 0.0823 0.0905 0.8271 52 P 0.0724 0.0707 0.8569 53 D 0.0977 0.0366 0.8657 54 R 0.1665 0.0110 0.8226 55 P 0.3783 0.0056 0.6160 56 V 0.9142 0.0035 0.0823 57 V 0.9329 0.0033 0.0638 58 V 0.9328 0.0033 0.0639 59 V 0.9256 0.0036 0.0708 60 Q 0.8521 0.0064 0.1414 61 H 0.4413 0.0264 0.5323 62 G 0.1610 0.0498 0.7892 63 V 0.0949 0.1253 0.7798 64 L 0.0756 0.1427 0.7816 65 R 0.0712 0.1261 0.8028 66 N 0.0755 0.1223 0.8022 67 G 0.0184 0.7165 0.2651 68 A 0.0108 0.7698 0.2194 69 D 0.0144 0.7808 0.2048 70 Y 0.0167 0.7808 0.2025 71 R 0.0170 0.7667 0.2163 72 D 0.0145 0.7398 0.2457 73 F 0.0158 0.7380 0.2462 74 W 0.0125 0.8231 0.1644 75 I 0.0070 0.9020 0.0910 76 P 0.0062 0.9248 0.0689 77 A 0.0058 0.9358 0.0584 78 A 0.0063 0.9310 0.0626 79 D 0.0062 0.8971 0.0967 80 R 0.0106 0.7719 0.2175 81 H 0.0501 0.2403 0.7096 82 K 0.0479 0.0206 0.9315 83 L 0.3737 0.0070 0.6192 84 L 0.8739 0.0038 0.1223 85 I 0.9225 0.0031 0.0743 86 V 0.9135 0.0043 0.0823 87 A 0.8281 0.0049 0.1671 88 P 0.5062 0.0311 0.4627 89 T 0.1758 0.0642 0.7600 90 F 0.1326 0.0844 0.7830 91 S 0.1011 0.1343 0.7647 92 D 0.0979 0.1358 0.7663 93 E 0.1030 0.1326 0.7643 94 I 0.1175 0.1617 0.7207 95 W 0.1165 0.1811 0.7024 96 P 0.0916 0.2447 0.6636 97 G 0.0887 0.2797 0.6315 98 V 0.1007 0.3147 0.5845 99 E 0.1043 0.3415 0.5541 100 S 0.1168 0.3418 0.5414 101 Y 0.1155 0.3128 0.5716 102 N 0.1082 0.2590 0.6328 103 N 0.0929 0.2861 0.6210 104 G 0.0872 0.2677 0.6451 105 R 0.1139 0.2572 0.6289 106 A 0.1187 0.3154 0.5659 107 F 0.1345 0.2915 0.5740 108 T 0.1297 0.2585 0.6118 109 A 0.1014 0.2931 0.6055 110 A 0.0944 0.3037 0.6018 111 G 0.0941 0.2809 0.6250 112 N 0.0936 0.2535 0.6530 113 P 0.0883 0.2412 0.6704 114 R 0.0734 0.2214 0.7051 115 H 0.0611 0.2139 0.7250 116 V 0.0559 0.2240 0.7201 117 D 0.0491 0.2269 0.7241 118 G 0.0440 0.4158 0.5402 119 W 0.0370 0.4443 0.5187 120 T 0.0334 0.5888 0.3777 121 Y 0.0076 0.9029 0.0894 122 A 0.0065 0.9226 0.0709 123 L 0.0055 0.9350 0.0595 124 V 0.0048 0.9539 0.0414 125 A 0.0047 0.9565 0.0388 126 R 0.0047 0.9569 0.0384 127 V 0.0047 0.9563 0.0390 128 L 0.0047 0.9563 0.0390 129 A 0.0048 0.9533 0.0420 130 N 0.0049 0.9462 0.0489 131 I 0.0051 0.9359 0.0590 132 R 0.0060 0.8996 0.0944 133 A 0.0093 0.7789 0.2118 134 A 0.0246 0.5796 0.3958 135 E 0.0565 0.2546 0.6889 136 I 0.0676 0.0797 0.8527 137 A 0.0905 0.0544 0.8551 138 D 0.1016 0.0302 0.8682 139 C 0.0274 0.4345 0.5381 140 E 0.0466 0.3504 0.6029 141 Q 0.3084 0.2399 0.4517 142 V 0.7772 0.0210 0.2018 143 Y 0.8827 0.0157 0.1016 144 L 0.9107 0.0109 0.0784 145 F 0.8402 0.0421 0.1177 146 G 0.6628 0.0545 0.2826 147 H 0.3021 0.1140 0.5838 148 S 0.1014 0.1708 0.7279 149 A 0.0155 0.6842 0.3003 150 G 0.0062 0.8625 0.1314 151 G 0.0048 0.9468 0.0484 152 Q 0.0047 0.9588 0.0365 153 F 0.0047 0.9602 0.0352 154 V 0.0047 0.9601 0.0352 155 H 0.0047 0.9597 0.0356 156 R 0.0047 0.9583 0.0369 157 L 0.0050 0.9515 0.0435 158 M 0.0055 0.9297 0.0648 159 S 0.0076 0.8196 0.1728 160 S 0.0242 0.6124 0.3635 161 Q 0.0693 0.1350 0.7956 162 P 0.0314 0.3145 0.6541 163 H 0.0387 0.3353 0.6261 164 A 0.0948 0.3976 0.5076 165 P 0.3385 0.2636 0.3979 166 F 0.5689 0.1772 0.2539 167 H 0.7315 0.1159 0.1526 168 A 0.8088 0.0809 0.1103 169 V 0.8309 0.0628 0.1063 170 T 0.8072 0.0661 0.1267 171 A 0.6538 0.0774 0.2688 172 A 0.3743 0.0761 0.5496 173 N 0.2074 0.0795 0.7131 174 P 0.1494 0.1515 0.6990 175 G 0.1286 0.2144 0.6570 176 W 0.1339 0.2545 0.6116 177 Y 0.1664 0.2366 0.5970 178 T 0.2033 0.2060 0.5908 179 L 0.2044 0.1521 0.6435 180 P 0.1430 0.1679 0.6891 181 T 0.1240 0.1805 0.6956 182 F 0.0754 0.3334 0.5912 183 E 0.0765 0.3568 0.5667 184 H 0.0964 0.3138 0.5898 185 R 0.0919 0.3206 0.5874 186 F 0.0967 0.2969 0.6064 187 P 0.0836 0.3528 0.5636 188 E 0.0693 0.4294 0.5013 189 G 0.0664 0.4287 0.5049 190 L 0.0715 0.4406 0.4879 191 D 0.0622 0.4175 0.5203 192 G 0.0619 0.3717 0.5664 193 V 0.0607 0.3910 0.5484 194 G 0.0560 0.4811 0.4629 195 L 0.0440 0.5390 0.4171 196 T 0.0447 0.5291 0.4262 197 E 0.0395 0.5746 0.3859 198 D 0.0420 0.5671 0.3909 199 H 0.0398 0.5498 0.4103 200 L 0.0356 0.5654 0.3990 201 A 0.0380 0.5057 0.4563 202 R 0.0336 0.4290 0.5374 203 L 0.0504 0.2779 0.6717 204 L 0.0828 0.1383 0.7789 205 A 0.0913 0.0570 0.8517 206 Y 0.1364 0.0183 0.8453 207 P 0.4076 0.0133 0.5791 208 M 0.8981 0.0052 0.0967 209 T 0.9254 0.0040 0.0706 210 I 0.9236 0.0041 0.0723 211 L 0.8979 0.0052 0.0969 212 A 0.6068 0.0195 0.3737 213 G 0.2901 0.0241 0.6859 214 D 0.1763 0.0880 0.7356 215 Q 0.1278 0.1387 0.7335 216 D 0.1134 0.1255 0.7611 217 I 0.0766 0.1706 0.7528 218 A 0.1037 0.1349 0.7613 219 T 0.0961 0.1008 0.8031 220 D 0.0911 0.0958 0.8131 221 D 0.0426 0.4687 0.4887 222 P 0.0195 0.5948 0.3857 223 N 0.0253 0.6136 0.3611 224 L 0.0271 0.6510 0.3219 225 P 0.0188 0.7674 0.2137 226 S 0.0176 0.7694 0.2130 227 E 0.0171 0.8046 0.1783 228 P 0.0088 0.8913 0.0999 229 A 0.0070 0.9145 0.0785 230 A 0.0065 0.9163 0.0772 231 L 0.0079 0.9016 0.0906 232 R 0.0112 0.8254 0.1634 233 Q 0.0214 0.6067 0.3719 234 G 0.0434 0.3355 0.6211 235 P 0.0499 0.3132 0.6369 236 H 0.0620 0.3373 0.6008 237 R 0.0544 0.5096 0.4361 238 Y 0.0385 0.6027 0.3587 239 A 0.0331 0.5803 0.3865 240 R 0.0387 0.5362 0.4252 241 A 0.0288 0.6269 0.3443 242 R 0.0206 0.7952 0.1842 243 H 0.0136 0.8732 0.1131 244 Y 0.0102 0.9087 0.0811 245 Y 0.0095 0.9319 0.0586 246 E 0.0081 0.9384 0.0535 247 A 0.0074 0.9425 0.0502 248 G 0.0078 0.9395 0.0527 249 Q 0.0089 0.9322 0.0589 250 R 0.0107 0.9135 0.0758 251 A 0.0135 0.8814 0.1051 252 A 0.0247 0.7999 0.1754 253 A 0.0243 0.6938 0.2819 254 Q 0.0337 0.4921 0.4743 255 R 0.0478 0.2471 0.7051 256 G 0.0502 0.1049 0.8449 257 L 0.0773 0.0655 0.8571 258 P 0.1049 0.0481 0.8470 259 F 0.2979 0.0479 0.6542 260 G 0.5784 0.0256 0.3960 261 W 0.8385 0.0092 0.1523 262 Q 0.8927 0.0061 0.1012 263 L 0.9058 0.0042 0.0900 264 Q 0.8826 0.0063 0.1111 265 V 0.8576 0.0058 0.1366 266 V 0.6144 0.0113 0.3743 267 P 0.1755 0.0592 0.7653 268 G 0.0785 0.0454 0.8761 269 I 0.1385 0.0725 0.7889 270 G 0.1206 0.0920 0.7874 271 H 0.1068 0.1308 0.7624 272 D 0.0646 0.1889 0.7465 273 G 0.0263 0.4459 0.5278 274 Q 0.0272 0.5833 0.3895 275 A 0.0283 0.6885 0.2832 276 M 0.0330 0.7253 0.2417 277 S 0.0354 0.7572 0.2074 278 Q 0.0245 0.7955 0.1800 279 V 0.0172 0.8347 0.1481 280 C 0.0083 0.9134 0.0783 281 A 0.0078 0.9262 0.0660 282 S 0.0094 0.9191 0.0716 283 L 0.0092 0.9243 0.0664 284 W 0.0127 0.9012 0.0861 285 F 0.0168 0.8631 0.1201 286 D 0.0399 0.7464 0.2138 287 G 0.0762 0.4423 0.4815 288 R 0.0754 0.1133 0.8114 289 M 0.0787 0.0758 0.8455 290 P 0.0815 0.0975 0.8210 291 D 0.0800 0.1414 0.7786 292 A 0.0572 0.2903 0.6525 293 A 0.0480 0.3021 0.6499 294 E 0.0739 0.2723 0.6538 295 L 0.0779 0.2123 0.7098 296 A 0.0774 0.2110 0.7116 297 R 0.0964 0.2209 0.6827 298 L 0.1006 0.2371 0.6623 299 A 0.1026 0.2188 0.6786 300 G 0.0905 0.1950 0.7145 301 S 0.0962 0.1372 0.7666 302 Q 0.0918 0.0966 0.8115 303 S 0.0716 0.0677 0.8607 304 A 0.0329 0.0577 0.9094