# This file is the result of combining several RDB files, specifically # T0270.t04.dssp-ebghstl.rdb (weight 1.53986) # T0270.t04.stride-ebghtl.rdb (weight 1.24869) # T0270.t04.str2.rdb (weight 1.54758) # T0270.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 T0270.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0270 # 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 T0270.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 30.5874 # # ============================================ # Comments from T0270.t04.stride-ebghtl.rdb # ============================================ # TARGET T0270 # 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 T0270.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 30.5874 # # ============================================ # Comments from T0270.t04.str2.rdb # ============================================ # TARGET T0270 # 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 T0270.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 30.5874 # # ============================================ # Comments from T0270.t04.alpha.rdb # ============================================ # TARGET T0270 # 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 T0270.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 30.5874 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0668 0.0413 0.8919 2 E 0.0817 0.1331 0.7853 3 R 0.1070 0.1343 0.7586 4 H 0.1294 0.1002 0.7704 5 V 0.1030 0.0218 0.8752 6 P 0.0828 0.0248 0.8924 7 E 0.0772 0.0366 0.8862 8 P 0.0825 0.0469 0.8706 9 T 0.1033 0.0478 0.8490 10 H 0.1260 0.0419 0.8321 11 T 0.1190 0.0359 0.8451 12 L 0.1050 0.1365 0.7584 13 E 0.0882 0.1829 0.7289 14 G 0.1824 0.2270 0.5906 15 W 0.3911 0.2386 0.3704 16 H 0.5694 0.2281 0.2025 17 V 0.5932 0.2189 0.1878 18 L 0.5046 0.2476 0.2478 19 H 0.3673 0.3412 0.2915 20 D 0.3034 0.3986 0.2980 21 F 0.3179 0.4297 0.2523 22 R 0.3645 0.3935 0.2421 23 L 0.3581 0.3586 0.2833 24 L 0.2893 0.2889 0.4218 25 D 0.2124 0.1688 0.6188 26 F 0.0485 0.6346 0.3169 27 A 0.0489 0.6514 0.2997 28 R 0.0879 0.6477 0.2644 29 W 0.2125 0.4435 0.3440 30 F 0.2640 0.2825 0.4535 31 S 0.2623 0.1488 0.5889 32 A 0.1169 0.0270 0.8561 33 P 0.0764 0.0293 0.8944 34 L 0.0081 0.8206 0.1713 35 E 0.0072 0.8649 0.1279 36 A 0.0077 0.8613 0.1310 37 R 0.0079 0.8644 0.1277 38 E 0.0072 0.9092 0.0836 39 D 0.0082 0.8796 0.1123 40 A 0.0063 0.9053 0.0884 41 W 0.0049 0.9512 0.0439 42 E 0.0048 0.9563 0.0389 43 E 0.0048 0.9568 0.0384 44 L 0.0048 0.9566 0.0386 45 K 0.0047 0.9577 0.0376 46 G 0.0047 0.9540 0.0413 47 L 0.0048 0.9503 0.0449 48 V 0.0049 0.9476 0.0475 49 R 0.0055 0.9382 0.0563 50 E 0.0065 0.9145 0.0790 51 W 0.0078 0.9168 0.0754 52 R 0.0057 0.9299 0.0644 53 E 0.0064 0.9320 0.0616 54 L 0.0068 0.9256 0.0676 55 E 0.0081 0.9071 0.0847 56 E 0.0146 0.8310 0.1544 57 A 0.0476 0.3532 0.5992 58 G 0.0357 0.0424 0.9219 59 Q 0.1345 0.0437 0.8218 60 G 0.4135 0.0337 0.5528 61 S 0.5484 0.0319 0.4198 62 Y 0.5575 0.0472 0.3952 63 G 0.5989 0.0529 0.3482 64 I 0.7394 0.0681 0.1925 65 Y 0.7799 0.0530 0.1671 66 Q 0.7194 0.0792 0.2014 67 V 0.4636 0.2151 0.3213 68 V 0.2399 0.2385 0.5216 69 G 0.1296 0.2911 0.5793 70 H 0.1760 0.3240 0.5001 71 K 0.2080 0.3972 0.3948 72 A 0.2038 0.3126 0.4837 73 D 0.1685 0.2847 0.5468 74 L 0.6197 0.2656 0.1148 75 L 0.6159 0.3060 0.0781 76 F 0.6114 0.3093 0.0793 77 L 0.5440 0.3187 0.1373 78 N 0.3316 0.2547 0.4138 79 L 0.1753 0.1159 0.7088 80 R 0.0820 0.0660 0.8520 81 P 0.0221 0.2139 0.7640 82 G 0.0253 0.1599 0.8148 83 L 0.0385 0.4391 0.5224 84 D 0.0122 0.8563 0.1315 85 P 0.0068 0.9265 0.0667 86 L 0.0048 0.9522 0.0430 87 L 0.0049 0.9583 0.0368 88 E 0.0050 0.9562 0.0388 89 A 0.0047 0.9540 0.0412 90 E 0.0047 0.9539 0.0414 91 A 0.0049 0.9372 0.0579 92 R 0.0055 0.8964 0.0981 93 L 0.0135 0.8207 0.1659 94 S 0.0100 0.6883 0.3018 95 R 0.0114 0.7057 0.2830 96 S 0.0225 0.6663 0.3112 97 A 0.0252 0.6810 0.2938 98 F 0.0284 0.7719 0.1996 99 A 0.0254 0.8068 0.1678 100 R 0.0210 0.8134 0.1656 101 Y 0.0317 0.7271 0.2412 102 L 0.0896 0.4349 0.4755 103 G 0.0902 0.1182 0.7916 104 R 0.1022 0.1562 0.7416 105 S 0.1775 0.1541 0.6685 106 Y 0.3524 0.0856 0.5620 107 S 0.4916 0.0347 0.4736 108 F 0.7542 0.0392 0.2066 109 Y 0.8446 0.0189 0.1365 110 S 0.8912 0.0120 0.0967 111 V 0.8989 0.0123 0.0888 112 V 0.8573 0.0198 0.1229 113 E 0.8421 0.0123 0.1456 114 L 0.5416 0.0533 0.4051 115 G 0.2110 0.0556 0.7335 116 S 0.1170 0.0731 0.8099 117 Q 0.2061 0.0781 0.7157 118 E 0.2039 0.0528 0.7433 119 K 0.1652 0.0264 0.8084 120 P 0.1458 0.0465 0.8076 121 L 0.1655 0.0559 0.7786 122 D 0.0971 0.0249 0.8780 123 P 0.0184 0.1591 0.8224 124 E 0.0256 0.1005 0.8739 125 S 0.0776 0.0526 0.8698 126 P 0.0349 0.1728 0.7924 127 Y 0.0836 0.1748 0.7417 128 V 0.1257 0.1247 0.7495 129 K 0.0893 0.0999 0.8107 130 P 0.0371 0.4614 0.5015 131 R 0.0557 0.4232 0.5211 132 L 0.1438 0.2558 0.6004 133 T 0.0966 0.0718 0.8316 134 P 0.0679 0.1403 0.7918 135 R 0.1207 0.1079 0.7713 136 V 0.1394 0.0216 0.8391 137 P 0.0837 0.0347 0.8816 138 K 0.0809 0.1378 0.7813 139 S 0.0814 0.1516 0.7670 140 G 0.1217 0.0961 0.7822 141 Y 0.7040 0.0096 0.2864 142 V 0.9074 0.0039 0.0887 143 C 0.9295 0.0034 0.0672 144 F 0.9137 0.0060 0.0804 145 Y 0.8436 0.0069 0.1495 146 P 0.6120 0.0174 0.3706 147 M 0.3885 0.0252 0.5864 148 N 0.4440 0.0330 0.5230 149 K 0.3151 0.0561 0.6289 150 R 0.1943 0.0453 0.7604 151 R 0.1214 0.1067 0.7719 152 Q 0.0909 0.0815 0.8275 153 G 0.0583 0.0740 0.8676 154 Q 0.0763 0.0918 0.8318 155 D 0.1197 0.1221 0.7581 156 N 0.2076 0.0956 0.6967 157 W 0.2920 0.1841 0.5238 158 Y 0.3578 0.1652 0.4770 159 M 0.3552 0.1091 0.5356 160 L 0.1395 0.0131 0.8474 161 P 0.0671 0.0144 0.9185 162 A 0.0051 0.9283 0.0666 163 K 0.0047 0.9567 0.0386 164 E 0.0047 0.9572 0.0381 165 R 0.0047 0.9583 0.0370 166 A 0.0047 0.9584 0.0370 167 S 0.0047 0.9537 0.0416 168 L 0.0047 0.9508 0.0445 169 M 0.0047 0.9511 0.0442 170 K 0.0049 0.9478 0.0474 171 A 0.0056 0.9230 0.0714 172 H 0.0136 0.8668 0.1196 173 G 0.0079 0.8652 0.1269 174 E 0.0070 0.8802 0.1127 175 T 0.0080 0.8759 0.1161 176 G 0.0117 0.8330 0.1553 177 R 0.0144 0.8069 0.1787 178 K 0.0175 0.7621 0.2205 179 Y 0.0307 0.5944 0.3749 180 Q 0.0262 0.6407 0.3331 181 G 0.0170 0.6553 0.3277 182 E 0.0256 0.7267 0.2477 183 V 0.0681 0.7771 0.1547 184 M 0.1164 0.7179 0.1657 185 Q 0.1945 0.6876 0.1179 186 V 0.2667 0.6172 0.1161 187 I 0.3846 0.4931 0.1223 188 S 0.3458 0.4670 0.1872 189 G 0.2896 0.3416 0.3688 190 A 0.2274 0.2486 0.5240 191 Q 0.1977 0.1692 0.6331 192 G 0.1442 0.0741 0.7817 193 L 0.1016 0.0962 0.8022 194 D 0.0877 0.1014 0.8110 195 D 0.0896 0.1727 0.7377 196 W 0.1817 0.1898 0.6285 197 E 0.4222 0.2211 0.3567 198 W 0.7438 0.1016 0.1546 199 G 0.8306 0.0727 0.0966 200 V 0.8295 0.0714 0.0991 201 D 0.7953 0.0780 0.1267 202 L 0.6914 0.0855 0.2230 203 F 0.4261 0.0961 0.4778 204 S 0.1852 0.0924 0.7224 205 E 0.0626 0.1083 0.8291 206 D 0.0936 0.0444 0.8619 207 P 0.0070 0.8401 0.1529 208 V 0.0065 0.9167 0.0768 209 Q 0.0052 0.9434 0.0513 210 F 0.0058 0.9444 0.0498 211 K 0.0048 0.9576 0.0376 212 K 0.0049 0.9593 0.0358 213 I 0.0052 0.9569 0.0379 214 V 0.0052 0.9538 0.0410 215 Y 0.0055 0.9476 0.0469 216 E 0.0071 0.9073 0.0856 217 M 0.0234 0.8060 0.1705 218 R 0.0377 0.4551 0.5073 219 F 0.0334 0.4916 0.4751 220 D 0.0311 0.6290 0.3399 221 E 0.0465 0.7644 0.1891 222 V 0.1068 0.7175 0.1757 223 S 0.1277 0.6703 0.2020 224 A 0.1442 0.6733 0.1825 225 R 0.2396 0.5503 0.2100 226 Y 0.3199 0.4665 0.2136 227 G 0.3327 0.3390 0.3284 228 E 0.2909 0.2293 0.4798 229 F 0.2912 0.1724 0.5363 230 G 0.1876 0.0515 0.7609 231 P 0.2781 0.0607 0.6612 232 F 0.6743 0.0514 0.2744 233 F 0.7862 0.0416 0.1722 234 V 0.6991 0.0523 0.2486 235 G 0.5241 0.0497 0.4262 236 K 0.4320 0.0700 0.4980 237 Y 0.4262 0.0439 0.5299 238 L 0.2347 0.0157 0.7496 239 D 0.1022 0.0107 0.8871 240 E 0.0049 0.9429 0.0522 241 E 0.0047 0.9592 0.0361 242 A 0.0047 0.9607 0.0346 243 L 0.0047 0.9594 0.0359 244 R 0.0048 0.9557 0.0395 245 A 0.0055 0.9334 0.0611 246 F 0.0080 0.8654 0.1266 247 L 0.0362 0.5086 0.4552 248 G 0.0391 0.1525 0.8084 249 L 0.0429 0.0650 0.8921