# This file is the result of combining several RDB files, specifically # T0371.t04.dssp-ebghstl.rdb (weight 1.53986) # T0371.t04.stride-ebghtl.rdb (weight 1.24869) # T0371.t04.str2.rdb (weight 1.54758) # T0371.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 T0371.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0371 # 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 T0371.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 2160 # # ============================================ # Comments from T0371.t04.stride-ebghtl.rdb # ============================================ # TARGET T0371 # 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 T0371.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 2160 # # ============================================ # Comments from T0371.t04.str2.rdb # ============================================ # TARGET T0371 # 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 T0371.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 2160 # # ============================================ # Comments from T0371.t04.alpha.rdb # ============================================ # TARGET T0371 # 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 T0371.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 2160 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1162 0.0187 0.8650 2 Q 0.1382 0.0359 0.8259 3 I 0.0466 0.6884 0.2650 4 E 0.0267 0.7777 0.1955 5 S 0.0289 0.7834 0.1877 6 F 0.0305 0.7898 0.1797 7 K 0.0215 0.8015 0.1770 8 S 0.0235 0.7362 0.2403 9 L 0.0287 0.5971 0.3742 10 L 0.0658 0.2372 0.6970 11 P 0.0238 0.3121 0.6641 12 K 0.0433 0.1683 0.7883 13 Y 0.2772 0.0231 0.6997 14 K 0.4957 0.0385 0.4658 15 C 0.9240 0.0035 0.0725 16 I 0.9324 0.0033 0.0644 17 F 0.9330 0.0032 0.0637 18 F 0.9098 0.0051 0.0851 19 D 0.6792 0.0078 0.3130 20 A 0.2827 0.0683 0.6490 21 F 0.1507 0.1009 0.7484 22 G 0.1475 0.1569 0.6956 23 V 0.3213 0.1883 0.4904 24 L 0.5652 0.1754 0.2593 25 K 0.4939 0.1788 0.3272 26 T 0.2939 0.1376 0.5685 27 Y 0.0740 0.1997 0.7263 28 N 0.0518 0.2053 0.7429 29 G 0.0514 0.2466 0.7019 30 L 0.0757 0.1989 0.7254 31 L 0.0698 0.1362 0.7941 32 P 0.0142 0.5517 0.4341 33 G 0.0188 0.6030 0.3782 34 I 0.0098 0.8685 0.1218 35 E 0.0051 0.9387 0.0562 36 N 0.0052 0.9381 0.0568 37 T 0.0054 0.9433 0.0513 38 F 0.0047 0.9575 0.0378 39 D 0.0047 0.9601 0.0352 40 Y 0.0047 0.9609 0.0344 41 L 0.0047 0.9599 0.0354 42 K 0.0048 0.9541 0.0411 43 A 0.0059 0.9047 0.0895 44 Q 0.0421 0.3361 0.6218 45 G 0.0371 0.0149 0.9479 46 Q 0.0919 0.0081 0.9000 47 D 0.6408 0.0060 0.3532 48 Y 0.9209 0.0036 0.0756 49 Y 0.9305 0.0033 0.0662 50 I 0.9278 0.0032 0.0690 51 V 0.8500 0.0060 0.1440 52 T 0.4951 0.0123 0.4925 53 N 0.1500 0.0442 0.8058 54 D 0.0868 0.0932 0.8200 55 A 0.0568 0.1431 0.8000 56 S 0.0518 0.0922 0.8559 57 R 0.0914 0.0263 0.8824 58 S 0.0671 0.0177 0.9151 59 P 0.0049 0.9354 0.0597 60 E 0.0047 0.9544 0.0409 61 Q 0.0047 0.9570 0.0382 62 L 0.0047 0.9572 0.0380 63 A 0.0047 0.9571 0.0382 64 D 0.0047 0.9527 0.0425 65 S 0.0047 0.9552 0.0401 66 Y 0.0047 0.9548 0.0405 67 H 0.0049 0.9416 0.0535 68 K 0.0060 0.8919 0.1021 69 L 0.0439 0.4282 0.5280 70 G 0.0343 0.0306 0.9351 71 L 0.0662 0.0247 0.9092 72 F 0.0887 0.0554 0.8558 73 S 0.1360 0.0414 0.8227 74 I 0.1423 0.0220 0.8357 75 T 0.0952 0.0206 0.8842 76 A 0.0157 0.7441 0.2402 77 D 0.0237 0.7286 0.2478 78 K 0.0682 0.7148 0.2170 79 I 0.2770 0.5225 0.2005 80 I 0.3112 0.4452 0.2436 81 S 0.2132 0.3684 0.4183 82 S 0.0858 0.3611 0.5532 83 G 0.0528 0.3838 0.5634 84 M 0.0846 0.5645 0.3510 85 I 0.1161 0.6659 0.2180 86 T 0.1266 0.7078 0.1656 87 K 0.1068 0.7632 0.1300 88 E 0.1044 0.7392 0.1564 89 Y 0.1091 0.6884 0.2025 90 I 0.1366 0.5709 0.2925 91 D 0.1170 0.4542 0.4287 92 L 0.1806 0.3842 0.4352 93 K 0.2449 0.3068 0.4483 94 V 0.2285 0.1901 0.5814 95 D 0.1081 0.1316 0.7603 96 G 0.0616 0.0742 0.8642 97 G 0.1917 0.0547 0.7536 98 I 0.5552 0.0455 0.3993 99 V 0.7222 0.0452 0.2326 100 A 0.6664 0.0820 0.2517 101 Y 0.5535 0.1251 0.3214 102 L 0.2843 0.1666 0.5490 103 G 0.1323 0.1356 0.7321 104 T 0.0842 0.4553 0.4604 105 A 0.0298 0.8001 0.1701 106 N 0.0239 0.8505 0.1256 107 S 0.0146 0.9059 0.0795 108 A 0.0080 0.9408 0.0512 109 N 0.0063 0.9459 0.0479 110 Y 0.0058 0.9482 0.0460 111 L 0.0077 0.9427 0.0496 112 V 0.0085 0.9270 0.0645 113 S 0.0105 0.8813 0.1082 114 D 0.0411 0.4420 0.5169 115 G 0.0322 0.0503 0.9175 116 I 0.1144 0.0350 0.8506 117 K 0.3169 0.0569 0.6262 118 M 0.4079 0.0917 0.5004 119 L 0.2821 0.0723 0.6456 120 P 0.2473 0.1252 0.6275 121 V 0.1837 0.2088 0.6075 122 S 0.1449 0.2418 0.6132 123 A 0.1085 0.3362 0.5553 124 I 0.0743 0.4532 0.4725 125 D 0.0490 0.4955 0.4555 126 D 0.0441 0.5438 0.4120 127 S 0.0609 0.4734 0.4656 128 N 0.0648 0.3804 0.5548 129 I 0.0496 0.4270 0.5235 130 G 0.0588 0.4064 0.5348 131 E 0.0930 0.4606 0.4464 132 V 0.0942 0.6388 0.2670 133 N 0.1221 0.6531 0.2248 134 A 0.2590 0.6021 0.1389 135 L 0.4052 0.4941 0.1007 136 V 0.5210 0.3716 0.1074 137 L 0.5250 0.3004 0.1746 138 L 0.3474 0.2693 0.3833 139 D 0.1821 0.1716 0.6464 140 D 0.0652 0.3129 0.6219 141 E 0.0418 0.2613 0.6969 142 G 0.0450 0.1895 0.7655 143 F 0.1366 0.1252 0.7382 144 N 0.1748 0.1418 0.6833 145 W 0.1462 0.2487 0.6051 146 F 0.0633 0.3643 0.5724 147 H 0.0158 0.7174 0.2668 148 D 0.0187 0.7215 0.2599 149 L 0.0064 0.9194 0.0742 150 N 0.0056 0.9433 0.0510 151 K 0.0050 0.9516 0.0434 152 T 0.0047 0.9560 0.0393 153 V 0.0047 0.9594 0.0359 154 N 0.0047 0.9574 0.0379 155 L 0.0048 0.9539 0.0413 156 L 0.0049 0.9435 0.0515 157 R 0.0056 0.9048 0.0896 158 K 0.0099 0.7411 0.2490 159 R 0.0388 0.2320 0.7292 160 T 0.0602 0.0221 0.9177 161 I 0.0961 0.0084 0.8955 162 P 0.3428 0.0137 0.6435 163 A 0.8969 0.0050 0.0982 164 I 0.9249 0.0035 0.0716 165 V 0.9156 0.0039 0.0804 166 A 0.7531 0.0122 0.2348 167 N 0.2225 0.0153 0.7622 168 T 0.0823 0.0747 0.8430 169 D 0.0757 0.1017 0.8226 170 N 0.0750 0.1308 0.7942 171 T 0.1357 0.1371 0.7272 172 Y 0.2010 0.1048 0.6942 173 P 0.2338 0.1354 0.6308 174 L 0.2422 0.1703 0.5875 175 T 0.2134 0.1612 0.6254 176 K 0.1345 0.3956 0.4699 177 T 0.1320 0.4219 0.4462 178 D 0.1226 0.4782 0.3992 179 V 0.1406 0.4886 0.3708 180 A 0.1383 0.4825 0.3792 181 I 0.1196 0.3736 0.5068 182 A 0.0797 0.2709 0.6493 183 I 0.0587 0.4676 0.4737 184 G 0.0493 0.4573 0.4934 185 G 0.0659 0.5839 0.3502 186 V 0.0412 0.8012 0.1576 187 A 0.0259 0.8606 0.1134 188 T 0.0263 0.8556 0.1181 189 M 0.0237 0.8667 0.1096 190 I 0.0304 0.8726 0.0971 191 E 0.0316 0.8706 0.0977 192 S 0.0462 0.8703 0.0835 193 I 0.0800 0.8209 0.0992 194 L 0.0992 0.7028 0.1980 195 G 0.1201 0.3823 0.4976 196 R 0.1223 0.3327 0.5450 197 R 0.1791 0.2772 0.5436 198 F 0.3056 0.2704 0.4239 199 I 0.3397 0.2446 0.4156 200 R 0.3153 0.2391 0.4457 201 F 0.1654 0.1735 0.6611 202 G 0.0889 0.0731 0.8380 203 K 0.0811 0.0286 0.8903 204 P 0.0926 0.0336 0.8739 205 D 0.0781 0.0525 0.8694 206 S 0.0063 0.9107 0.0829 207 Q 0.0049 0.9468 0.0483 208 M 0.0048 0.9553 0.0399 209 F 0.0047 0.9595 0.0358 210 M 0.0047 0.9598 0.0356 211 F 0.0049 0.9576 0.0375 212 A 0.0048 0.9567 0.0385 213 Y 0.0047 0.9577 0.0376 214 D 0.0047 0.9550 0.0403 215 M 0.0048 0.9527 0.0425 216 L 0.0048 0.9445 0.0508 217 R 0.0049 0.9311 0.0640 218 Q 0.0063 0.8773 0.1164 219 K 0.0114 0.7547 0.2339 220 M 0.0518 0.2448 0.7034 221 E 0.0442 0.0334 0.9224 222 I 0.0996 0.0105 0.8898 223 S 0.0851 0.0109 0.9040 224 K 0.0289 0.7006 0.2705 225 R 0.0746 0.5578 0.3676 226 E 0.3142 0.3445 0.3412 227 I 0.8596 0.0192 0.1211 228 L 0.8937 0.0179 0.0884 229 M 0.9107 0.0083 0.0810 230 V 0.8137 0.0404 0.1459 231 G 0.4575 0.0289 0.5136 232 D 0.1537 0.0420 0.8043 233 T 0.0922 0.0929 0.8149 234 L 0.0235 0.5705 0.4060 235 H 0.0157 0.7877 0.1966 236 T 0.0191 0.8228 0.1581 237 D 0.0112 0.8519 0.1369 238 I 0.0057 0.9481 0.0462 239 L 0.0051 0.9490 0.0459 240 G 0.0053 0.9525 0.0422 241 G 0.0064 0.9462 0.0473 242 N 0.0071 0.9289 0.0640 243 K 0.0122 0.8679 0.1199 244 F 0.0534 0.4180 0.5286 245 G 0.0520 0.0290 0.9190 246 L 0.1079 0.0117 0.8804 247 D 0.2315 0.0488 0.7197 248 T 0.8559 0.0128 0.1313 249 A 0.9255 0.0041 0.0704 250 L 0.9276 0.0037 0.0687 251 V 0.8933 0.0068 0.0999 252 L 0.6152 0.0151 0.3697 253 T 0.2156 0.0330 0.7513 254 G 0.0934 0.0558 0.8508 255 N 0.1099 0.0780 0.8121 256 T 0.0992 0.0958 0.8049 257 R 0.1197 0.1241 0.7562 258 I 0.0622 0.4763 0.4615 259 D 0.0329 0.6345 0.3326 260 D 0.0259 0.7355 0.2385 261 A 0.0246 0.7981 0.1773 262 E 0.0240 0.7948 0.1811 263 T 0.0289 0.7275 0.2435 264 K 0.0540 0.6661 0.2798 265 I 0.1305 0.5018 0.3677 266 K 0.0995 0.4129 0.4875 267 S 0.0837 0.3872 0.5291 268 T 0.0697 0.1909 0.7394 269 G 0.0508 0.0700 0.8791 270 I 0.1524 0.0394 0.8081 271 V 0.1945 0.0207 0.7849 272 P 0.1916 0.0639 0.7445 273 T 0.3047 0.0932 0.6020 274 H 0.6864 0.0714 0.2423 275 I 0.7445 0.0946 0.1608 276 C 0.6361 0.1286 0.2353 277 E 0.2767 0.2518 0.4714 278 S 0.0952 0.4047 0.5001 279 A 0.0534 0.6495 0.2971 280 V 0.0271 0.7712 0.2017 281 I 0.0258 0.7181 0.2561 282 E 0.0199 0.6076 0.3724 283 L 0.0313 0.2300 0.7387