# This file is the result of combining several RDB files, specifically # T0154.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0154.t2k.stride-ebghtl.rdb (weight 1.24869) # T0154.t2k.str.rdb (weight 1.53983) # T0154.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 T0154.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0154 # 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 T0154.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 44 # # ============================================ # Comments from T0154.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0154 # 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 T0154.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 44 # # ============================================ # Comments from T0154.t2k.str.rdb # ============================================ # TARGET T0154 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0154.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 44 # # ============================================ # Comments from T0154.t2k.alpha.rdb # ============================================ # TARGET T0154 # 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 T0154.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 44 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0865 0.0192 0.8943 2 T 0.2249 0.0292 0.7459 3 I 0.2123 0.0487 0.7390 4 P 0.1978 0.0805 0.7216 5 A 0.2565 0.0957 0.6478 6 F 0.2621 0.0640 0.6739 7 H 0.1557 0.0335 0.8108 8 P 0.0796 0.1274 0.7930 9 G 0.0887 0.1265 0.7848 10 E 0.1471 0.1540 0.6989 11 L 0.2734 0.0936 0.6329 12 N 0.5068 0.1145 0.3787 13 V 0.6621 0.1360 0.2019 14 Y 0.6481 0.1004 0.2515 15 S 0.4215 0.1288 0.4497 16 A 0.1361 0.1042 0.7597 17 P 0.0055 0.9084 0.0861 18 G 0.0045 0.9348 0.0606 19 D 0.0046 0.9492 0.0462 20 V 0.0044 0.9572 0.0384 21 A 0.0044 0.9585 0.0371 22 D 0.0044 0.9555 0.0401 23 V 0.0045 0.9492 0.0462 24 S 0.0047 0.9481 0.0473 25 R 0.0046 0.9470 0.0484 26 A 0.0048 0.9450 0.0502 27 L 0.0056 0.9409 0.0535 28 R 0.0066 0.9243 0.0691 29 L 0.0070 0.8547 0.1383 30 T 0.0421 0.3695 0.5884 31 G 0.0262 0.0280 0.9458 32 R 0.1095 0.0121 0.8785 33 R 0.5781 0.0078 0.4141 34 V 0.8277 0.0112 0.1611 35 M 0.8517 0.0097 0.1386 36 L 0.8660 0.0111 0.1229 37 V 0.6666 0.0190 0.3144 38 P 0.3299 0.1248 0.5453 39 T 0.1396 0.2357 0.6247 40 M 0.0443 0.4538 0.5019 41 G 0.0241 0.5745 0.4014 42 A 0.0249 0.6940 0.2811 43 L 0.0266 0.7503 0.2231 44 H 0.0263 0.7801 0.1936 45 E 0.0177 0.8239 0.1584 46 G 0.0209 0.8310 0.1481 47 H 0.0068 0.9412 0.0521 48 L 0.0051 0.9565 0.0384 49 A 0.0050 0.9581 0.0369 50 L 0.0044 0.9585 0.0370 51 V 0.0044 0.9596 0.0360 52 R 0.0045 0.9569 0.0386 53 A 0.0047 0.9492 0.0461 54 A 0.0063 0.9301 0.0636 55 K 0.0074 0.8496 0.1429 56 R 0.0142 0.6320 0.3539 57 V 0.0620 0.3530 0.5850 58 P 0.0480 0.1402 0.8118 59 G 0.0551 0.0573 0.8877 60 S 0.0879 0.0426 0.8695 61 V 0.7261 0.0045 0.2694 62 V 0.9193 0.0036 0.0771 63 V 0.9268 0.0034 0.0697 64 V 0.9180 0.0042 0.0779 65 S 0.8891 0.0065 0.1044 66 I 0.7833 0.0100 0.2067 67 F 0.7042 0.0128 0.2830 68 V 0.4652 0.0197 0.5150 69 N 0.2072 0.0251 0.7678 70 P 0.0432 0.4129 0.5439 71 M 0.0954 0.4331 0.4714 72 Q 0.1806 0.3969 0.4225 73 F 0.1228 0.1288 0.7484 74 G 0.0792 0.0589 0.8619 75 A 0.0685 0.1517 0.7798 76 G 0.0505 0.2132 0.7363 77 E 0.0838 0.2020 0.7142 78 D 0.1081 0.2284 0.6634 79 L 0.0275 0.6522 0.3203 80 D 0.0180 0.5377 0.4443 81 A 0.0291 0.4092 0.5617 82 Y 0.0753 0.1114 0.8134 83 P 0.0654 0.1141 0.8205 84 R 0.0885 0.0992 0.8123 85 T 0.0733 0.0859 0.8408 86 P 0.0140 0.8217 0.1643 87 D 0.0060 0.9319 0.0621 88 D 0.0051 0.9397 0.0552 89 D 0.0067 0.9397 0.0536 90 L 0.0046 0.9520 0.0434 91 A 0.0044 0.9533 0.0423 92 Q 0.0044 0.9526 0.0429 93 L 0.0046 0.9535 0.0420 94 R 0.0048 0.9441 0.0512 95 A 0.0059 0.9058 0.0883 96 E 0.0417 0.3801 0.5781 97 G 0.0460 0.0172 0.9368 98 V 0.1109 0.0084 0.8807 99 E 0.4566 0.0235 0.5199 100 I 0.9114 0.0045 0.0841 101 A 0.9157 0.0058 0.0786 102 F 0.9011 0.0053 0.0936 103 T 0.7687 0.0075 0.2237 104 P 0.2100 0.0241 0.7659 105 T 0.1110 0.0217 0.8673 106 T 0.0202 0.7466 0.2332 107 A 0.0197 0.7936 0.1867 108 A 0.0286 0.7866 0.1848 109 M 0.0875 0.4833 0.4292 110 Y 0.1136 0.1464 0.7400 111 P 0.0695 0.1404 0.7902 112 D 0.0477 0.0960 0.8564 113 G 0.0563 0.0652 0.8785 114 L 0.1967 0.0306 0.7727 115 R 0.4760 0.0235 0.5005 116 T 0.7020 0.0119 0.2861 117 T 0.7978 0.0095 0.1927 118 V 0.7543 0.0086 0.2370 119 Q 0.5554 0.0115 0.4331 120 P 0.1950 0.1009 0.7041 121 G 0.0668 0.2070 0.7262 122 P 0.0605 0.3133 0.6262 123 L 0.0629 0.4495 0.4876 124 A 0.0633 0.4860 0.4507 125 A 0.0764 0.5101 0.4136 126 E 0.0883 0.5377 0.3740 127 L 0.1299 0.3702 0.4999 128 E 0.1174 0.2056 0.6770 129 G 0.0882 0.0953 0.8165 130 G 0.1053 0.0660 0.8287 131 P 0.1195 0.0667 0.8138 132 R 0.1028 0.0623 0.8349 133 P 0.0646 0.1495 0.7858 134 T 0.0793 0.1870 0.7337 135 H 0.1053 0.3189 0.5758 136 F 0.1021 0.4092 0.4887 137 A 0.0478 0.5742 0.3780 138 G 0.0449 0.6795 0.2757 139 V 0.0695 0.8205 0.1100 140 L 0.0736 0.8507 0.0757 141 T 0.0843 0.8453 0.0704 142 V 0.0709 0.8615 0.0676 143 V 0.0393 0.8961 0.0645 144 L 0.0251 0.9121 0.0628 145 K 0.0188 0.9080 0.0732 146 L 0.0208 0.8710 0.1082 147 L 0.0283 0.8164 0.1553 148 Q 0.0268 0.6406 0.3327 149 I 0.0466 0.4875 0.4660 150 V 0.1245 0.1692 0.7063 151 R 0.1068 0.0380 0.8553 152 P 0.0737 0.1747 0.7516 153 D 0.0979 0.2249 0.6772 154 R 0.3698 0.2629 0.3673 155 V 0.4626 0.2758 0.2616 156 F 0.4601 0.2839 0.2560 157 F 0.2466 0.2049 0.5486 158 G 0.0869 0.1436 0.7695 159 E 0.0837 0.3176 0.5987 160 K 0.0531 0.4400 0.5069 161 D 0.0333 0.7548 0.2120 162 Y 0.0129 0.8755 0.1116 163 Q 0.0072 0.9255 0.0674 164 Q 0.0086 0.9431 0.0483 165 L 0.0054 0.9579 0.0367 166 V 0.0046 0.9591 0.0363 167 L 0.0049 0.9603 0.0349 168 I 0.0049 0.9588 0.0363 169 R 0.0044 0.9587 0.0369 170 Q 0.0045 0.9571 0.0384 171 L 0.0046 0.9529 0.0425 172 V 0.0051 0.9413 0.0536 173 A 0.0059 0.8926 0.1016 174 D 0.0084 0.7487 0.2430 175 F 0.0644 0.4207 0.5150 176 N 0.0631 0.0755 0.8614 177 L 0.1130 0.0225 0.8645 178 D 0.2460 0.0327 0.7214 179 V 0.6666 0.0102 0.3232 180 A 0.8838 0.0049 0.1114 181 V 0.8904 0.0059 0.1037 182 V 0.8208 0.0116 0.1675 183 G 0.6897 0.0105 0.2998 184 V 0.4441 0.0139 0.5420 185 P 0.4229 0.0554 0.5217 186 T 0.6118 0.0454 0.3428 187 V 0.7098 0.0339 0.2563 188 R 0.6768 0.0233 0.2999 189 E 0.3122 0.0953 0.5926 190 A 0.0738 0.1659 0.7602 191 D 0.0565 0.0663 0.8772 192 G 0.0986 0.0673 0.8340 193 L 0.3250 0.0727 0.6022 194 A 0.5594 0.0881 0.3525 195 M 0.5202 0.1199 0.3600 196 S 0.4278 0.1147 0.4576 197 S 0.3485 0.1310 0.5205 198 R 0.2282 0.1711 0.6006 199 N 0.2145 0.1673 0.6181 200 R 0.2058 0.1609 0.6333 201 Y 0.2421 0.0768 0.6811 202 L 0.0972 0.0254 0.8774 203 D 0.0503 0.0395 0.9102 204 P 0.0053 0.9023 0.0924 205 A 0.0051 0.9088 0.0860 206 Q 0.0054 0.9214 0.0732 207 R 0.0046 0.9407 0.0546 208 A 0.0046 0.9296 0.0658 209 A 0.0050 0.9069 0.0881 210 A 0.0048 0.9097 0.0855 211 V 0.0046 0.9258 0.0696 212 A 0.0045 0.9308 0.0646 213 L 0.0045 0.9488 0.0468 214 S 0.0044 0.9551 0.0405 215 A 0.0044 0.9551 0.0405 216 A 0.0044 0.9562 0.0394 217 L 0.0044 0.9571 0.0385 218 T 0.0044 0.9539 0.0417 219 A 0.0044 0.9498 0.0458 220 A 0.0044 0.9492 0.0464 221 A 0.0044 0.9510 0.0446 222 H 0.0044 0.9509 0.0447 223 A 0.0045 0.9457 0.0498 224 A 0.0050 0.9326 0.0624 225 T 0.0055 0.8579 0.1366 226 A 0.0409 0.4338 0.5253 227 G 0.0287 0.1278 0.8435 228 A 0.0555 0.1792 0.7652 229 Q 0.0605 0.2748 0.6647 230 A 0.0576 0.2797 0.6627 231 A 0.0063 0.8790 0.1147 232 L 0.0049 0.9349 0.0602 233 D 0.0050 0.9463 0.0487 234 A 0.0047 0.9510 0.0442 235 A 0.0047 0.9514 0.0439 236 R 0.0045 0.9493 0.0462 237 A 0.0047 0.9403 0.0551 238 V 0.0048 0.9298 0.0654 239 L 0.0053 0.9083 0.0864 240 D 0.0071 0.7836 0.2093 241 A 0.0167 0.6611 0.3222 242 A 0.0516 0.2838 0.6646 243 P 0.0247 0.2091 0.7662 244 G 0.0294 0.1056 0.8650 245 V 0.1427 0.0410 0.8163 246 A 0.4136 0.0101 0.5763 247 V 0.4803 0.0047 0.5150 248 D 0.6367 0.0297 0.3336 249 Y 0.8800 0.0047 0.1153 250 L 0.9152 0.0039 0.0809 251 E 0.9168 0.0044 0.0788 252 L 0.9143 0.0039 0.0817 253 R 0.7729 0.0161 0.2110 254 D 0.4417 0.0080 0.5503 255 I 0.0437 0.2774 0.6789 256 G 0.0201 0.2507 0.7292 257 L 0.0589 0.2615 0.6796 258 G 0.0795 0.0718 0.8488 259 P 0.1349 0.0401 0.8251 260 M 0.2050 0.0621 0.7329 261 P 0.1810 0.0833 0.7357 262 L 0.1355 0.1042 0.7604 263 N 0.1144 0.0931 0.7925 264 G 0.1166 0.0691 0.8143 265 S 0.1962 0.0682 0.7356 266 G 0.6192 0.0101 0.3707 267 R 0.8590 0.0070 0.1340 268 L 0.9125 0.0075 0.0800 269 L 0.9059 0.0117 0.0825 270 V 0.8990 0.0158 0.0852 271 A 0.8472 0.0212 0.1317 272 A 0.8085 0.0399 0.1516 273 R 0.7025 0.0683 0.2292 274 L 0.4770 0.0764 0.4465 275 G 0.1442 0.0644 0.7914 276 T 0.1320 0.0870 0.7810 277 T 0.4639 0.0349 0.5011 278 R 0.6973 0.0241 0.2785 279 L 0.7620 0.0273 0.2106 280 L 0.7099 0.0385 0.2516 281 D 0.5667 0.0404 0.3929 282 N 0.4101 0.0569 0.5330 283 I 0.5257 0.0340 0.4403 284 A 0.6672 0.0229 0.3099 285 I 0.5756 0.0191 0.4054 286 E 0.3038 0.0232 0.6729 287 I 0.1052 0.1635 0.7313 288 G 0.0847 0.1931 0.7222 289 T 0.2248 0.1965 0.5788 290 F 0.3383 0.1196 0.5421 291 A 0.2676 0.1030 0.6294 292 G 0.1665 0.0773 0.7562 293 T 0.1424 0.0731 0.7846 294 D 0.1405 0.0663 0.7932 295 R 0.0885 0.0458 0.8658 296 P 0.0565 0.2480 0.6956 297 D 0.0470 0.3642 0.5887 298 G 0.0376 0.5870 0.3754 299 Y 0.0664 0.7564 0.1772 300 R 0.0906 0.8118 0.0976 301 A 0.0963 0.8275 0.0762 302 I 0.1065 0.8130 0.0805 303 L 0.1070 0.7945 0.0985 304 E 0.1042 0.7604 0.1354 305 S 0.1040 0.6814 0.2146 306 H 0.1325 0.5421 0.3254 307 W 0.1426 0.4051 0.4522 308 R 0.0869 0.2104 0.7027 309 N 0.0466 0.0382 0.9152