# This file is the result of combining several RDB files, specifically # T0305.t06.dssp-ebghstl.rdb (weight 1.53986) # T0305.t06.stride-ebghtl.rdb (weight 1.24869) # T0305.t06.str2.rdb (weight 1.54758) # T0305.t06.alpha.rdb (weight 0.659012) # T0305.t04.dssp-ebghstl.rdb (weight 1.53986) # T0305.t04.stride-ebghtl.rdb (weight 1.24869) # T0305.t04.str2.rdb (weight 1.54758) # T0305.t04.alpha.rdb (weight 0.659012) # T0305.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0305.t2k.stride-ebghtl.rdb (weight 1.24869) # T0305.t2k.str2.rdb (weight 1.54758) # T0305.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 T0305.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0305 # 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 T0305.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 1149 # # ============================================ # Comments from T0305.t06.stride-ebghtl.rdb # ============================================ # TARGET T0305 # 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 T0305.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 1149 # # ============================================ # Comments from T0305.t06.str2.rdb # ============================================ # TARGET T0305 # 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 T0305.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 1149 # # ============================================ # Comments from T0305.t06.alpha.rdb # ============================================ # TARGET T0305 # 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 T0305.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 1149 # # ============================================ # Comments from T0305.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0305 # 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 T0305.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 1132 # # ============================================ # Comments from T0305.t04.stride-ebghtl.rdb # ============================================ # TARGET T0305 # 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 T0305.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 1132 # # ============================================ # Comments from T0305.t04.str2.rdb # ============================================ # TARGET T0305 # 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 T0305.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 1132 # # ============================================ # Comments from T0305.t04.alpha.rdb # ============================================ # TARGET T0305 # 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 T0305.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 1132 # # ============================================ # Comments from T0305.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0305 # 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 T0305.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 1058 # # ============================================ # Comments from T0305.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0305 # 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 T0305.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 1058 # # ============================================ # Comments from T0305.t2k.str2.rdb # ============================================ # TARGET T0305 # 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 T0305.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 1058 # # ============================================ # Comments from T0305.t2k.alpha.rdb # ============================================ # TARGET T0305 # 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 T0305.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 1058 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 Y 0.3026 0.1386 0.5588 2 F 0.4037 0.1186 0.4777 3 Q 0.3760 0.1124 0.5116 4 S 0.2494 0.1559 0.5947 5 M 0.1249 0.5061 0.3690 6 K 0.0960 0.6247 0.2793 7 Q 0.0518 0.7974 0.1509 8 F 0.0459 0.8531 0.1010 9 V 0.0389 0.8585 0.1027 10 K 0.0489 0.8461 0.1050 11 H 0.0498 0.8415 0.1088 12 I 0.0267 0.8476 0.1256 13 G 0.0334 0.7861 0.1805 14 E 0.0480 0.7418 0.2103 15 L 0.0430 0.7098 0.2472 16 Y 0.0472 0.5964 0.3563 17 S 0.0516 0.4891 0.4592 18 N 0.0396 0.4926 0.4678 19 N 0.0234 0.5337 0.4429 20 Q 0.0320 0.4500 0.5180 21 H 0.0423 0.4041 0.5536 22 G 0.0331 0.4189 0.5481 23 F 0.0356 0.5401 0.4242 24 S 0.0353 0.6744 0.2903 25 E 0.0290 0.8010 0.1699 26 D 0.0255 0.8546 0.1199 27 F 0.0262 0.9022 0.0716 28 E 0.0245 0.9086 0.0669 29 E 0.0229 0.9072 0.0698 30 V 0.0309 0.8719 0.0972 31 Q 0.0431 0.7959 0.1610 32 R 0.0572 0.6661 0.2767 33 C 0.0755 0.3869 0.5376 34 T 0.0930 0.2655 0.6415 35 A 0.0713 0.2731 0.6555 36 D 0.0658 0.2177 0.7165 37 M 0.0864 0.1827 0.7308 38 N 0.0909 0.1778 0.7313 39 I 0.0972 0.1508 0.7519 40 T 0.1599 0.1802 0.6599 41 A 0.2076 0.2717 0.5207 42 E 0.1940 0.3346 0.4714 43 H 0.1653 0.4034 0.4313 44 S 0.1266 0.3492 0.5242 45 N 0.1127 0.2594 0.6279 46 H 0.0937 0.1800 0.7262 47 P 0.0609 0.3755 0.5635 48 E 0.0582 0.3927 0.5490 49 N 0.0775 0.3202 0.6024 50 K 0.0604 0.4455 0.4941 51 H 0.0700 0.4289 0.5011 52 K 0.1095 0.3606 0.5299 53 N 0.1476 0.2156 0.6367 54 R 0.1588 0.2197 0.6215 55 Y 0.1912 0.1601 0.6487 56 I 0.1582 0.1550 0.6868 57 N 0.1565 0.0837 0.7598 58 I 0.2171 0.0430 0.7399 59 L 0.2356 0.0257 0.7387 60 A 0.1731 0.0671 0.7598 61 Y 0.1248 0.1193 0.7559 62 D 0.1090 0.1614 0.7296 63 H 0.0919 0.1854 0.7227 64 S 0.1768 0.1114 0.7118 65 R 0.4327 0.0516 0.5157 66 V 0.6035 0.0273 0.3692 67 K 0.6597 0.0206 0.3197 68 L 0.4833 0.0319 0.4848 69 R 0.2610 0.0389 0.7001 70 P 0.1464 0.0575 0.7961 71 L 0.1288 0.0661 0.8051 72 P 0.0942 0.0874 0.8183 73 G 0.0878 0.0999 0.8123 74 K 0.0859 0.1081 0.8060 75 D 0.1094 0.0883 0.8022 76 S 0.0756 0.0621 0.8623 77 K 0.0730 0.0894 0.8376 78 H 0.0894 0.1114 0.7992 79 S 0.1051 0.0863 0.8087 80 D 0.2009 0.0834 0.7157 81 Y 0.5970 0.0517 0.3514 82 I 0.7152 0.0302 0.2546 83 N 0.7155 0.0272 0.2574 84 A 0.6331 0.0414 0.3256 85 N 0.5887 0.0550 0.3562 86 Y 0.5921 0.0693 0.3386 87 V 0.5871 0.0458 0.3672 88 D 0.3676 0.0614 0.5710 89 G 0.1650 0.0672 0.7678 90 Y 0.0951 0.1000 0.8049 91 N 0.0889 0.0884 0.8227 92 K 0.1203 0.0705 0.8092 93 A 0.1627 0.1132 0.7241 94 K 0.2732 0.1150 0.6118 95 A 0.6335 0.0648 0.3017 96 Y 0.8206 0.0313 0.1481 97 I 0.8476 0.0301 0.1224 98 A 0.8010 0.0434 0.1557 99 T 0.6650 0.0476 0.2874 100 Q 0.3724 0.0337 0.5939 101 G 0.1650 0.0209 0.8140 102 P 0.1321 0.0263 0.8416 103 L 0.1070 0.0663 0.8266 104 K 0.0368 0.2768 0.6864 105 S 0.0496 0.2854 0.6651 106 T 0.0764 0.3446 0.5790 107 F 0.0071 0.9130 0.0799 108 E 0.0050 0.9370 0.0580 109 D 0.0051 0.9475 0.0474 110 F 0.0047 0.9562 0.0391 111 W 0.0047 0.9574 0.0379 112 R 0.0051 0.9574 0.0375 113 M 0.0056 0.9561 0.0384 114 I 0.0086 0.9503 0.0411 115 W 0.0115 0.9229 0.0656 116 E 0.0645 0.7384 0.1971 117 Q 0.0433 0.4031 0.5536 118 N 0.0564 0.0575 0.8860 119 T 0.1197 0.0145 0.8658 120 G 0.3132 0.0496 0.6373 121 I 0.8893 0.0055 0.1051 122 I 0.9284 0.0035 0.0681 123 V 0.9192 0.0076 0.0733 124 M 0.8957 0.0088 0.0955 125 I 0.7168 0.0196 0.2636 126 T 0.3583 0.0305 0.6113 127 N 0.2069 0.1066 0.6865 128 L 0.2217 0.2501 0.5282 129 V 0.2051 0.3042 0.4906 130 E 0.1701 0.3583 0.4715 131 K 0.0851 0.2471 0.6678 132 G 0.0506 0.0984 0.8510 133 R 0.1847 0.0753 0.7400 134 R 0.4514 0.0674 0.4812 135 K 0.4207 0.1036 0.4758 136 C 0.3052 0.1815 0.5132 137 D 0.2537 0.2343 0.5119 138 Q 0.2327 0.1939 0.5735 139 Y 0.3066 0.1079 0.5855 140 W 0.2314 0.0302 0.7385 141 P 0.1267 0.0417 0.8317 142 T 0.0729 0.0784 0.8487 143 E 0.0715 0.0591 0.8694 144 N 0.1340 0.0447 0.8212 145 S 0.3977 0.0501 0.5523 146 E 0.6419 0.0465 0.3115 147 E 0.7060 0.0360 0.2581 148 Y 0.5543 0.0353 0.4104 149 G 0.2872 0.0454 0.6674 150 N 0.5556 0.0245 0.4199 151 I 0.8633 0.0043 0.1324 152 I 0.9141 0.0034 0.0825 153 V 0.9193 0.0031 0.0775 154 T 0.8913 0.0060 0.1026 155 L 0.8815 0.0045 0.1140 156 K 0.7823 0.0202 0.1975 157 S 0.7245 0.0176 0.2578 158 T 0.6726 0.0346 0.2928 159 K 0.6859 0.0325 0.2815 160 I 0.6184 0.0470 0.3346 161 H 0.4465 0.0498 0.5037 162 A 0.2895 0.1045 0.6060 163 C 0.3463 0.0779 0.5758 164 Y 0.6338 0.0303 0.3359 165 T 0.8010 0.0151 0.1839 166 V 0.8774 0.0071 0.1154 167 R 0.8800 0.0096 0.1104 168 R 0.8973 0.0069 0.0958 169 F 0.8987 0.0063 0.0950 170 S 0.9075 0.0054 0.0871 171 I 0.8978 0.0075 0.0948 172 R 0.8386 0.0177 0.1437 173 N 0.7707 0.0176 0.2117 174 T 0.6097 0.0263 0.3640 175 K 0.6280 0.0285 0.3435 176 V 0.6618 0.0376 0.3006 177 K 0.6419 0.0442 0.3139 178 K 0.6442 0.0563 0.2995 179 G 0.5925 0.0614 0.3461 180 Q 0.5731 0.0661 0.3608 181 K 0.5332 0.0733 0.3935 182 G 0.4085 0.0681 0.5234 183 N 0.3368 0.0548 0.6084 184 P 0.2759 0.0796 0.6445 185 K 0.1963 0.0854 0.7183 186 G 0.1426 0.0889 0.7685 187 R 0.1401 0.0769 0.7830 188 Q 0.1396 0.0690 0.7914 189 N 0.2566 0.0494 0.6940 190 E 0.5145 0.0389 0.4465 191 R 0.7488 0.0097 0.2415 192 V 0.8799 0.0043 0.1158 193 V 0.9038 0.0035 0.0928 194 I 0.9045 0.0051 0.0903 195 Q 0.9159 0.0033 0.0808 196 Y 0.9086 0.0037 0.0877 197 H 0.8879 0.0051 0.1070 198 Y 0.7547 0.0125 0.2328 199 T 0.4670 0.0463 0.4866 200 Q 0.2351 0.0364 0.7285 201 W 0.1484 0.0320 0.8196 202 P 0.0727 0.1110 0.8163 203 D 0.0694 0.1482 0.7824 204 M 0.0539 0.1178 0.8282 205 G 0.0609 0.0650 0.8740 206 V 0.1033 0.0519 0.8448 207 P 0.1083 0.0879 0.8039 208 E 0.0502 0.2492 0.7006 209 Y 0.0729 0.2144 0.7126 210 A 0.0260 0.5931 0.3809 211 L 0.0127 0.7768 0.2105 212 P 0.0109 0.8514 0.1377 213 V 0.0049 0.9527 0.0424 214 L 0.0047 0.9584 0.0369 215 T 0.0047 0.9589 0.0364 216 F 0.0047 0.9594 0.0359 217 V 0.0047 0.9599 0.0355 218 R 0.0047 0.9580 0.0373 219 R 0.0048 0.9535 0.0417 220 S 0.0053 0.9443 0.0504 221 S 0.0073 0.9183 0.0744 222 A 0.0096 0.8379 0.1526 223 A 0.0258 0.6763 0.2979 224 R 0.0688 0.2695 0.6617 225 M 0.0602 0.1156 0.8242 226 P 0.0579 0.1246 0.8175 227 E 0.0582 0.1010 0.8408 228 T 0.0783 0.0532 0.8685 229 G 0.1302 0.0183 0.8515 230 P 0.2575 0.0086 0.7340 231 V 0.8845 0.0037 0.1118 232 L 0.9286 0.0032 0.0682 233 V 0.9241 0.0038 0.0721 234 H 0.8832 0.0052 0.1116 235 C 0.5550 0.0228 0.4223 236 S 0.2448 0.0756 0.6796 237 A 0.0790 0.1074 0.8137 238 G 0.0580 0.0953 0.8467 239 V 0.0801 0.1087 0.8112 240 G 0.0858 0.1311 0.7831 241 R 0.0471 0.5762 0.3767 242 T 0.0174 0.8549 0.1278 243 G 0.0069 0.9356 0.0576 244 T 0.0050 0.9578 0.0372 245 Y 0.0047 0.9597 0.0356 246 I 0.0048 0.9603 0.0349 247 V 0.0047 0.9600 0.0353 248 I 0.0047 0.9595 0.0358 249 D 0.0047 0.9589 0.0363 250 S 0.0048 0.9586 0.0365 251 M 0.0048 0.9565 0.0388 252 L 0.0049 0.9532 0.0420 253 Q 0.0051 0.9446 0.0503 254 Q 0.0054 0.9236 0.0710 255 I 0.0093 0.8844 0.1063 256 K 0.0099 0.8273 0.1627 257 D 0.0163 0.6178 0.3660 258 K 0.0449 0.2622 0.6929 259 S 0.0358 0.0625 0.9017 260 T 0.1708 0.0324 0.7968 261 V 0.2938 0.0291 0.6771 262 N 0.2437 0.0371 0.7192 263 V 0.0067 0.9352 0.0581 264 L 0.0047 0.9558 0.0395 265 G 0.0047 0.9589 0.0364 266 F 0.0047 0.9602 0.0351 267 L 0.0047 0.9589 0.0365 268 K 0.0047 0.9566 0.0387 269 H 0.0047 0.9567 0.0386 270 I 0.0049 0.9506 0.0446 271 R 0.0052 0.9334 0.0613 272 T 0.0071 0.8226 0.1703 273 Q 0.0179 0.5704 0.4117 274 R 0.0728 0.1744 0.7528 275 N 0.0365 0.1865 0.7770 276 Y 0.0527 0.1578 0.7895 277 L 0.2275 0.1396 0.6329 278 V 0.3549 0.0508 0.5943 279 Q 0.2518 0.0429 0.7053 280 T 0.0787 0.0577 0.8637 281 E 0.0050 0.8712 0.1238 282 E 0.0048 0.9345 0.0607 283 Q 0.0048 0.9563 0.0390 284 Y 0.0047 0.9594 0.0359 285 I 0.0049 0.9593 0.0358 286 F 0.0054 0.9586 0.0360 287 I 0.0049 0.9591 0.0360 288 H 0.0047 0.9596 0.0357 289 D 0.0047 0.9576 0.0377 290 A 0.0047 0.9601 0.0352 291 L 0.0047 0.9584 0.0369 292 L 0.0047 0.9558 0.0394 293 E 0.0049 0.9468 0.0482 294 A 0.0059 0.9194 0.0746 295 I 0.0149 0.8388 0.1463 296 L 0.0284 0.5760 0.3957 297 G 0.0344 0.1500 0.8156