# This file is the result of combining several RDB files, specifically # T0326.t04.dssp-ebghstl.rdb (weight 1.53986) # T0326.t04.stride-ebghtl.rdb (weight 1.24869) # T0326.t04.str2.rdb (weight 1.54758) # T0326.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 T0326.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0326 # 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 T0326.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 1929 # # ============================================ # Comments from T0326.t04.stride-ebghtl.rdb # ============================================ # TARGET T0326 # 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 T0326.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 1929 # # ============================================ # Comments from T0326.t04.str2.rdb # ============================================ # TARGET T0326 # 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 T0326.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 1929 # # ============================================ # Comments from T0326.t04.alpha.rdb # ============================================ # TARGET T0326 # 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 T0326.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 1929 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1043 0.0151 0.8806 2 P 0.2364 0.0136 0.7500 3 I 0.4560 0.0150 0.5290 4 N 0.5654 0.0229 0.4117 5 V 0.2338 0.0317 0.7345 6 P 0.0815 0.1919 0.7267 7 S 0.0378 0.1471 0.8151 8 G 0.0485 0.0984 0.8530 9 L 0.0692 0.1665 0.7643 10 P 0.0648 0.5686 0.3666 11 A 0.0135 0.9103 0.0761 12 V 0.0084 0.9468 0.0448 13 K 0.0077 0.9503 0.0420 14 V 0.0085 0.9483 0.0432 15 L 0.0090 0.9393 0.0517 16 A 0.0102 0.8917 0.0982 17 K 0.0099 0.7975 0.1925 18 E 0.0448 0.3636 0.5916 19 G 0.0424 0.0460 0.9117 20 I 0.2336 0.0260 0.7405 21 F 0.7060 0.0284 0.2655 22 V 0.7000 0.0465 0.2535 23 M 0.4709 0.0718 0.4573 24 T 0.2026 0.0933 0.7041 25 E 0.0204 0.8207 0.1588 26 K 0.0176 0.8455 0.1368 27 R 0.0222 0.8219 0.1559 28 A 0.0342 0.7658 0.2000 29 I 0.0310 0.6629 0.3061 30 H 0.0318 0.4889 0.4793 31 Q 0.0462 0.3314 0.6223 32 D 0.0675 0.2464 0.6861 33 I 0.1035 0.1455 0.7510 34 R 0.0879 0.0735 0.8386 35 P 0.0798 0.2707 0.6495 36 L 0.1586 0.2396 0.6018 37 E 0.5641 0.1750 0.2609 38 I 0.7569 0.1129 0.1303 39 L 0.7834 0.1157 0.1009 40 I 0.7561 0.1230 0.1209 41 L 0.6381 0.1138 0.2482 42 N 0.3590 0.0988 0.5422 43 L 0.1842 0.0855 0.7304 44 M 0.1029 0.0380 0.8591 45 P 0.0706 0.1632 0.7662 46 D 0.0543 0.2591 0.6866 47 K 0.0832 0.3361 0.5807 48 I 0.1496 0.4079 0.4424 49 K 0.1859 0.4527 0.3614 50 T 0.1826 0.5153 0.3020 51 E 0.1551 0.6279 0.2170 52 I 0.1349 0.6211 0.2441 53 Q 0.1161 0.5824 0.3015 54 L 0.1294 0.5722 0.2984 55 L 0.1580 0.5318 0.3103 56 R 0.1576 0.4651 0.3773 57 L 0.3279 0.4021 0.2701 58 L 0.5484 0.2238 0.2278 59 G 0.5755 0.1465 0.2780 60 N 0.5965 0.0916 0.3119 61 T 0.4751 0.0511 0.4738 62 P 0.2977 0.0767 0.6257 63 L 0.1735 0.1770 0.6495 64 Q 0.1301 0.2138 0.6560 65 V 0.1116 0.2066 0.6818 66 N 0.1368 0.2121 0.6511 67 V 0.2258 0.3659 0.4083 68 T 0.2669 0.5051 0.2280 69 L 0.2838 0.5601 0.1561 70 L 0.2975 0.5614 0.1411 71 Y 0.2489 0.6218 0.1293 72 T 0.2068 0.6513 0.1420 73 E 0.1347 0.6814 0.1840 74 T 0.1263 0.6017 0.2720 75 H 0.1797 0.4189 0.4014 76 K 0.1050 0.3142 0.5808 77 P 0.0672 0.3816 0.5512 78 K 0.0374 0.2697 0.6929 79 H 0.0601 0.0487 0.8912 80 T 0.1884 0.0105 0.8011 81 P 0.4181 0.0072 0.5747 82 I 0.7939 0.0098 0.1963 83 E 0.8731 0.0125 0.1144 84 H 0.8810 0.0136 0.1054 85 I 0.8067 0.0205 0.1728 86 L 0.5509 0.0260 0.4230 87 K 0.2278 0.0803 0.6919 88 F 0.1229 0.0970 0.7801 89 Y 0.1444 0.0722 0.7834 90 T 0.1640 0.0528 0.7832 91 T 0.1508 0.0505 0.7987 92 F 0.0337 0.7609 0.2054 93 S 0.0195 0.8409 0.1396 94 A 0.0141 0.8803 0.1057 95 V 0.0205 0.8547 0.1248 96 K 0.0251 0.7745 0.2004 97 D 0.0281 0.6597 0.3122 98 R 0.0491 0.3107 0.6402 99 K 0.0912 0.0657 0.8432 100 F 0.1412 0.0154 0.8434 101 D 0.2009 0.0369 0.7622 102 G 0.8764 0.0052 0.1184 103 F 0.9312 0.0033 0.0655 104 I 0.9319 0.0032 0.0649 105 I 0.8993 0.0066 0.0941 106 T 0.6111 0.0130 0.3759 107 G 0.2305 0.0232 0.7463 108 A 0.1284 0.0169 0.8546 109 P 0.1441 0.0422 0.8136 110 V 0.1643 0.0828 0.7529 111 E 0.1892 0.0824 0.7284 112 L 0.1382 0.1537 0.7081 113 L 0.1465 0.1163 0.7372 114 P 0.1082 0.1286 0.7631 115 F 0.0098 0.7821 0.2081 116 E 0.0134 0.7720 0.2146 117 E 0.0156 0.7227 0.2617 118 V 0.0360 0.5531 0.4110 119 D 0.0247 0.5109 0.4644 120 Y 0.0288 0.5515 0.4197 121 W 0.0195 0.6246 0.3559 122 E 0.0052 0.9309 0.0640 123 E 0.0048 0.9336 0.0616 124 L 0.0048 0.9534 0.0418 125 T 0.0047 0.9599 0.0354 126 E 0.0047 0.9601 0.0352 127 I 0.0047 0.9604 0.0349 128 M 0.0047 0.9600 0.0353 129 E 0.0047 0.9598 0.0355 130 W 0.0048 0.9573 0.0379 131 S 0.0050 0.9491 0.0459 132 R 0.0059 0.9151 0.0789 133 H 0.0132 0.7499 0.2369 134 N 0.0314 0.2370 0.7316 135 V 0.0446 0.0630 0.8924 136 Y 0.0848 0.0177 0.8975 137 S 0.2147 0.0291 0.7562 138 T 0.6895 0.0401 0.2704 139 M 0.8053 0.0424 0.1523 140 F 0.8282 0.0698 0.1020 141 I 0.7173 0.1627 0.1201 142 C 0.2700 0.3486 0.3814 143 W 0.0274 0.8055 0.1670 144 A 0.0051 0.9350 0.0599 145 A 0.0049 0.9537 0.0414 146 Q 0.0047 0.9599 0.0355 147 A 0.0047 0.9588 0.0365 148 G 0.0047 0.9548 0.0405 149 L 0.0048 0.9469 0.0483 150 Y 0.0051 0.9285 0.0663 151 Y 0.0075 0.8854 0.1071 152 F 0.0267 0.7192 0.2541 153 Y 0.0405 0.3835 0.5760 154 G 0.0405 0.0419 0.9176 155 I 0.0859 0.0208 0.8933 156 P 0.1983 0.0240 0.7777 157 K 0.5010 0.0519 0.4471 158 Y 0.5904 0.0364 0.3732 159 E 0.4656 0.0334 0.5010 160 L 0.2225 0.0331 0.7444 161 P 0.1239 0.1226 0.7534 162 Q 0.1534 0.1486 0.6980 163 K 0.2829 0.1257 0.5915 164 L 0.5177 0.0767 0.4055 165 S 0.5557 0.0510 0.3933 166 G 0.5153 0.0321 0.4527 167 V 0.7427 0.0198 0.2375 168 Y 0.8005 0.0108 0.1887 169 K 0.8014 0.0101 0.1885 170 H 0.8429 0.0085 0.1486 171 R 0.8774 0.0085 0.1141 172 V 0.8198 0.0140 0.1662 173 A 0.4693 0.0300 0.5007 174 K 0.0722 0.0902 0.8376 175 D 0.0414 0.0651 0.8934 176 S 0.1296 0.0979 0.7724 177 V 0.2056 0.2209 0.5735 178 L 0.2567 0.3551 0.3882 179 F 0.2455 0.3669 0.3876 180 R 0.1423 0.2667 0.5910 181 G 0.0908 0.1138 0.7954 182 H 0.1228 0.0419 0.8353 183 D 0.0950 0.1022 0.8029 184 D 0.0852 0.1187 0.7961 185 F 0.1774 0.1145 0.7081 186 F 0.4270 0.0487 0.5243 187 W 0.4824 0.0282 0.4894 188 A 0.2693 0.0221 0.7086 189 P 0.2791 0.0550 0.6659 190 H 0.3156 0.0910 0.5934 191 S 0.3473 0.1117 0.5409 192 R 0.3372 0.1517 0.5111 193 Y 0.3427 0.1757 0.4816 194 T 0.3416 0.1624 0.4960 195 E 0.2955 0.1401 0.5644 196 V 0.2240 0.1147 0.6612 197 K 0.1445 0.0928 0.7627 198 K 0.0998 0.4326 0.4676 199 E 0.1084 0.4561 0.4355 200 D 0.1295 0.4755 0.3949 201 I 0.0825 0.6339 0.2836 202 D 0.0645 0.5621 0.3734 203 K 0.0857 0.3423 0.5720 204 V 0.1270 0.0323 0.8407 205 P 0.0783 0.0817 0.8400 206 E 0.2121 0.0964 0.6915 207 L 0.5697 0.0301 0.4002 208 E 0.8357 0.0124 0.1519 209 I 0.9019 0.0079 0.0902 210 L 0.8636 0.0153 0.1211 211 A 0.8428 0.0096 0.1476 212 E 0.6640 0.0156 0.3204 213 S 0.2509 0.0179 0.7312 214 D 0.0461 0.0996 0.8543 215 E 0.0408 0.0764 0.8828 216 A 0.1460 0.0442 0.8098 217 G 0.4243 0.0438 0.5319 218 V 0.8156 0.0304 0.1540 219 Y 0.8525 0.0407 0.1068 220 V 0.8877 0.0304 0.0819 221 V 0.8945 0.0210 0.0845 222 A 0.8492 0.0292 0.1216 223 N 0.5914 0.0353 0.3733 224 K 0.1066 0.1184 0.7751 225 S 0.0789 0.1009 0.8202 226 E 0.1454 0.0480 0.8067 227 R 0.2808 0.0240 0.6952 228 Q 0.7720 0.0130 0.2150 229 I 0.8923 0.0063 0.1014 230 F 0.9128 0.0051 0.0821 231 V 0.8942 0.0058 0.1000 232 T 0.7457 0.0216 0.2327 233 G 0.3770 0.0207 0.6024 234 H 0.1565 0.0250 0.8185 235 P 0.0907 0.1894 0.7199 236 E 0.1323 0.1916 0.6760 237 Y 0.2202 0.1383 0.6415 238 D 0.1784 0.0778 0.7438 239 R 0.0747 0.3923 0.5330 240 Y 0.0615 0.4446 0.4938 241 T 0.0505 0.6014 0.3481 242 L 0.0382 0.6919 0.2698 243 R 0.0242 0.7541 0.2217 244 D 0.0153 0.8497 0.1351 245 E 0.0226 0.8762 0.1012 246 Y 0.0278 0.8824 0.0898 247 Y 0.0285 0.8658 0.1057 248 R 0.0245 0.8488 0.1267 249 D 0.0248 0.7901 0.1851 250 I 0.0273 0.7072 0.2656 251 G 0.0420 0.5823 0.3757 252 R 0.0630 0.4968 0.4403 253 N 0.0831 0.3463 0.5706 254 L 0.1644 0.1856 0.6500 255 K 0.1510 0.0929 0.7561 256 V 0.1148 0.0510 0.8342 257 P 0.1122 0.0499 0.8379 258 I 0.1167 0.0278 0.8555 259 P 0.0911 0.0783 0.8305 260 A 0.0293 0.5493 0.4213 261 N 0.0404 0.4410 0.5187 262 Y 0.1011 0.3059 0.5931 263 F 0.0971 0.0475 0.8554 264 P 0.0511 0.1503 0.7987 265 N 0.0479 0.1413 0.8109 266 D 0.0729 0.1269 0.8003 267 D 0.0960 0.0484 0.8557 268 P 0.0270 0.3196 0.6533 269 T 0.0338 0.2866 0.6796 270 K 0.0680 0.2699 0.6620 271 T 0.0767 0.1255 0.7978 272 P 0.0763 0.3596 0.5641 273 I 0.1079 0.6124 0.2797 274 L 0.1101 0.6767 0.2132 275 T 0.0879 0.7255 0.1866 276 W 0.0283 0.8695 0.1022 277 W 0.0137 0.9085 0.0778 278 S 0.0089 0.9289 0.0622 279 H 0.0049 0.9490 0.0460 280 A 0.0047 0.9567 0.0385 281 H 0.0047 0.9568 0.0385 282 L 0.0048 0.9540 0.0412 283 F 0.0048 0.9489 0.0464 284 F 0.0052 0.9458 0.0490 285 S 0.0057 0.9382 0.0561 286 N 0.0069 0.9211 0.0720 287 W 0.0069 0.9221 0.0710 288 L 0.0098 0.9205 0.0697 289 N 0.0126 0.9101 0.0773 290 Y 0.0329 0.8806 0.0865 291 C 0.0742 0.8129 0.1129 292 I 0.1688 0.6720 0.1592 293 Y 0.2521 0.5014 0.2465 294 Q 0.3060 0.2560 0.4380 295 K 0.2295 0.1278 0.6426 296 T 0.1285 0.0336 0.8379 297 P 0.0810 0.2449 0.6740 298 Y 0.1167 0.2408 0.6425 299 R 0.1379 0.2544 0.6077 300 L 0.0344 0.7088 0.2568 301 E 0.0265 0.7138 0.2597 302 D 0.0357 0.6177 0.3467 303 I 0.0772 0.3769 0.5459 304 H 0.0481 0.1864 0.7655