# This file is the result of combining several RDB files, specifically # T0241.t04.dssp-ebghstl.rdb (weight 1.53986) # T0241.t04.stride-ebghtl.rdb (weight 1.24869) # T0241.t04.str2.rdb (weight 1.54758) # T0241.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 T0241.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0241 # 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 T0241.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 16.6698 # # ============================================ # Comments from T0241.t04.stride-ebghtl.rdb # ============================================ # TARGET T0241 # 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 T0241.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 16.6698 # # ============================================ # Comments from T0241.t04.str2.rdb # ============================================ # TARGET T0241 # 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 T0241.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 16.6698 # # ============================================ # Comments from T0241.t04.alpha.rdb # ============================================ # TARGET T0241 # 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 T0241.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 16.6698 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 P 0.0598 0.0526 0.8876 2 K 0.0797 0.1360 0.7843 3 N 0.1485 0.1392 0.7123 4 V 0.5317 0.1878 0.2805 5 L 0.6660 0.2235 0.1104 6 F 0.6083 0.2828 0.1089 7 Q 0.3560 0.4843 0.1597 8 Y 0.1060 0.6841 0.2099 9 S 0.0613 0.7371 0.2016 10 T 0.0202 0.8811 0.0987 11 I 0.0061 0.9495 0.0444 12 N 0.0049 0.9530 0.0420 13 A 0.0047 0.9454 0.0499 14 L 0.0061 0.9192 0.0747 15 M 0.0121 0.8512 0.1367 16 L 0.0332 0.6494 0.3173 17 G 0.0398 0.3325 0.6277 18 Q 0.1060 0.2822 0.6118 19 F 0.2421 0.2052 0.5527 20 E 0.1473 0.1532 0.6995 21 G 0.0997 0.0882 0.8121 22 D 0.2650 0.0640 0.6710 23 L 0.4754 0.0204 0.5041 24 T 0.3659 0.0296 0.6045 25 L 0.0080 0.9419 0.0501 26 K 0.0059 0.9546 0.0396 27 D 0.0054 0.9546 0.0400 28 L 0.0083 0.9469 0.0447 29 K 0.0091 0.9116 0.0793 30 L 0.0163 0.7837 0.2000 31 R 0.0577 0.2949 0.6474 32 G 0.0459 0.0676 0.8865 33 D 0.0933 0.0603 0.8463 34 M 0.2430 0.0935 0.6635 35 G 0.3446 0.0918 0.5637 36 L 0.3648 0.1174 0.5178 37 G 0.3417 0.0978 0.5606 38 T 0.2892 0.0943 0.6165 39 I 0.1942 0.2148 0.5910 40 N 0.1284 0.2407 0.6308 41 D 0.1303 0.2248 0.6450 42 L 0.1575 0.1268 0.7157 43 D 0.1030 0.0550 0.8420 44 G 0.1975 0.0717 0.7307 45 E 0.6141 0.0420 0.3439 46 M 0.8620 0.0286 0.1094 47 I 0.8800 0.0180 0.1020 48 Q 0.8663 0.0194 0.1143 49 M 0.7435 0.0313 0.2252 50 G 0.2224 0.0225 0.7551 51 T 0.2164 0.0353 0.7483 52 K 0.7636 0.0143 0.2221 53 F 0.8829 0.0084 0.1087 54 Y 0.8663 0.0082 0.1255 55 Q 0.8947 0.0044 0.1009 56 I 0.8280 0.0088 0.1632 57 D 0.4613 0.0209 0.5178 58 S 0.0997 0.1053 0.7950 59 T 0.0643 0.0273 0.9084 60 G 0.1656 0.0258 0.8086 61 K 0.5124 0.0104 0.4773 62 L 0.8757 0.0058 0.1184 63 S 0.8263 0.0121 0.1615 64 E 0.8445 0.0076 0.1479 65 L 0.4088 0.0086 0.5826 66 P 0.1409 0.0221 0.8370 67 E 0.0264 0.2684 0.7052 68 S 0.0328 0.2021 0.7651 69 V 0.2259 0.1176 0.6565 70 K 0.4012 0.0324 0.5664 71 T 0.3155 0.0146 0.6699 72 P 0.2966 0.0396 0.6637 73 F 0.7023 0.0270 0.2707 74 A 0.8410 0.0122 0.1468 75 V 0.8907 0.0071 0.1022 76 T 0.8837 0.0082 0.1080 77 T 0.7581 0.0226 0.2193 78 H 0.5534 0.0248 0.4218 79 F 0.3490 0.0302 0.6209 80 E 0.2591 0.0195 0.7214 81 P 0.1618 0.1135 0.7246 82 K 0.1587 0.2011 0.6401 83 E 0.3061 0.1744 0.5195 84 K 0.4827 0.0900 0.4273 85 T 0.5774 0.0461 0.3764 86 T 0.6085 0.0496 0.3419 87 L 0.4222 0.1108 0.4670 88 T 0.2530 0.1481 0.5989 89 N 0.2129 0.1312 0.6559 90 V 0.1885 0.1751 0.6364 91 Q 0.1813 0.0966 0.7221 92 D 0.1089 0.0679 0.8233 93 Y 0.0049 0.9360 0.0591 94 N 0.0047 0.9582 0.0371 95 Q 0.0047 0.9591 0.0362 96 L 0.0047 0.9589 0.0364 97 T 0.0047 0.9604 0.0349 98 K 0.0047 0.9601 0.0352 99 M 0.0047 0.9585 0.0368 100 L 0.0049 0.9501 0.0450 101 E 0.0051 0.9353 0.0595 102 E 0.0064 0.8780 0.1156 103 K 0.0113 0.7826 0.2061 104 F 0.0474 0.4407 0.5119 105 E 0.0251 0.3165 0.6584 106 N 0.0384 0.2383 0.7232 107 K 0.0772 0.2352 0.6875 108 N 0.2118 0.0824 0.7058 109 V 0.5000 0.0697 0.4303 110 F 0.7845 0.0246 0.1909 111 Y 0.8491 0.0212 0.1297 112 A 0.9059 0.0099 0.0842 113 V 0.9117 0.0071 0.0812 114 K 0.9157 0.0065 0.0778 115 L 0.8671 0.0187 0.1142 116 T 0.6689 0.0396 0.2916 117 G 0.7010 0.0187 0.2804 118 T 0.7747 0.0195 0.2058 119 F 0.7626 0.0217 0.2157 120 K 0.6835 0.0546 0.2619 121 M 0.8365 0.0166 0.1469 122 V 0.8664 0.0086 0.1250 123 K 0.8949 0.0071 0.0980 124 A 0.8887 0.0080 0.1033 125 R 0.8450 0.0128 0.1422 126 T 0.7541 0.0123 0.2336 127 V 0.3907 0.0203 0.5890 128 P 0.2134 0.0800 0.7066 129 K 0.1515 0.1501 0.6984 130 Q 0.1954 0.1077 0.6969 131 T 0.1795 0.0684 0.7521 132 R 0.1402 0.0291 0.8307 133 P 0.1075 0.0429 0.8496 134 Y 0.0831 0.1106 0.8063 135 P 0.0525 0.5091 0.4385 136 Q 0.0500 0.6653 0.2847 137 L 0.0102 0.9050 0.0848 138 T 0.0085 0.9300 0.0615 139 E 0.0082 0.9294 0.0625 140 V 0.0128 0.9104 0.0768 141 T 0.0130 0.8625 0.1244 142 K 0.0106 0.7262 0.2632 143 K 0.0161 0.4192 0.5647 144 Q 0.0738 0.0618 0.8644 145 S 0.0619 0.1331 0.8050 146 E 0.2365 0.2421 0.5214 147 F 0.4290 0.1694 0.4016 148 E 0.5285 0.1165 0.3550 149 F 0.4072 0.1671 0.4257 150 K 0.2424 0.1519 0.6057 151 N 0.2127 0.0709 0.7164 152 V 0.4890 0.0327 0.4784 153 K 0.5518 0.0333 0.4149 154 G 0.7991 0.0093 0.1915 155 T 0.8545 0.0069 0.1385 156 L 0.9100 0.0039 0.0861 157 I 0.8446 0.0230 0.1324 158 G 0.7995 0.0150 0.1855 159 F 0.6555 0.0317 0.3128 160 Y 0.4666 0.0395 0.4939 161 T 0.1754 0.0350 0.7896 162 P 0.0578 0.4571 0.4851 163 N 0.0481 0.5628 0.3891 164 Y 0.0556 0.6396 0.3048 165 A 0.0992 0.5493 0.3514 166 A 0.0738 0.4700 0.4562 167 A 0.0956 0.3199 0.5845 168 L 0.1919 0.1751 0.6329 169 N 0.1746 0.0944 0.7310 170 V 0.1414 0.0699 0.7888 171 P 0.1133 0.1355 0.7512 172 G 0.1814 0.1369 0.6817 173 F 0.3954 0.1198 0.4849 174 H 0.5390 0.0962 0.3648 175 L 0.6154 0.1068 0.2778 176 H 0.6684 0.0840 0.2476 177 F 0.7291 0.0503 0.2207 178 I 0.6130 0.0402 0.3468 179 T 0.2976 0.0339 0.6685 180 E 0.0654 0.2604 0.6742 181 D 0.0685 0.2077 0.7237 182 K 0.0909 0.2038 0.7053 183 T 0.1456 0.1340 0.7204 184 S 0.2336 0.1036 0.6628 185 G 0.2694 0.0732 0.6574 186 G 0.4253 0.0474 0.5273 187 H 0.6898 0.0261 0.2841 188 V 0.7587 0.0440 0.1972 189 L 0.7971 0.0323 0.1706 190 N 0.8270 0.0205 0.1525 191 L 0.8661 0.0109 0.1230 192 Q 0.8848 0.0082 0.1070 193 F 0.8655 0.0123 0.1222 194 D 0.6252 0.0484 0.3263 195 N 0.4900 0.0308 0.4793 196 A 0.8524 0.0059 0.1417 197 N 0.9182 0.0042 0.0775 198 L 0.9141 0.0036 0.0824 199 E 0.9032 0.0040 0.0927 200 I 0.8613 0.0047 0.1340 201 S 0.5833 0.0106 0.4061 202 P 0.4569 0.0601 0.4830 203 I 0.3409 0.1165 0.5426 204 H 0.2860 0.1099 0.6042 205 E 0.6010 0.0550 0.3439 206 F 0.7561 0.0163 0.2276 207 D 0.8422 0.0088 0.1491 208 V 0.8608 0.0068 0.1325 209 Q 0.8019 0.0089 0.1892 210 L 0.4171 0.0100 0.5729 211 P 0.1974 0.0190 0.7836 212 H 0.1069 0.0524 0.8407 213 T 0.0839 0.0874 0.8287 214 D 0.0341 0.2661 0.6998 215 D 0.0345 0.4239 0.5416 216 F 0.0565 0.5014 0.4421 217 A 0.0492 0.4591 0.4918 218 H 0.0542 0.3849 0.5608 219 S 0.0730 0.2822 0.6448 220 D 0.0713 0.2305 0.6982 221 L 0.0510 0.3043 0.6447 222 T 0.0327 0.4083 0.5590 223 Q 0.0145 0.7132 0.2723 224 V 0.0218 0.6948 0.2834 225 T 0.0213 0.7272 0.2515 226 T 0.0096 0.8799 0.1105 227 S 0.0069 0.9025 0.0906 228 Q 0.0090 0.9116 0.0794 229 V 0.0130 0.9167 0.0703 230 H 0.0134 0.9172 0.0694 231 Q 0.0186 0.9011 0.0803 232 A 0.0240 0.8658 0.1102 233 E 0.0323 0.7948 0.1729 234 S 0.0442 0.6112 0.3446 235 E 0.0398 0.4164 0.5438 236 R 0.0549 0.2066 0.7385 237 K 0.0487 0.0989 0.8524