# This file is the result of combining several RDB files, specifically # T0321.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0321.t2k.stride-ebghtl.rdb (weight 1.24869) # T0321.t2k.str2.rdb (weight 1.54758) # T0321.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 T0321.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0321 # 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 T0321.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 37 # # ============================================ # Comments from T0321.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0321 # 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 T0321.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 37 # # ============================================ # Comments from T0321.t2k.str2.rdb # ============================================ # TARGET T0321 # 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 T0321.t2k-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 37 # # ============================================ # Comments from T0321.t2k.alpha.rdb # ============================================ # TARGET T0321 # 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 T0321.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 37 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0129 0.4861 0.5010 2 W 0.0061 0.9138 0.0802 3 E 0.0050 0.9234 0.0716 4 I 0.0048 0.9339 0.0613 5 Y 0.0053 0.9343 0.0604 6 D 0.0059 0.9376 0.0565 7 A 0.0060 0.9240 0.0700 8 M 0.0066 0.9142 0.0792 9 I 0.0147 0.7856 0.1997 10 N 0.0136 0.5308 0.4556 11 G 0.0170 0.3866 0.5964 12 I 0.0420 0.2244 0.7336 13 P 0.0470 0.1884 0.7645 14 E 0.0286 0.2640 0.7073 15 D 0.0506 0.1963 0.7531 16 F 0.1694 0.0793 0.7513 17 L 0.4392 0.0612 0.4996 18 V 0.6609 0.0735 0.2656 19 D 0.6843 0.1195 0.1962 20 E 0.8116 0.0490 0.1394 21 L 0.8647 0.0377 0.0976 22 V 0.8792 0.0297 0.0911 23 C 0.8050 0.0368 0.1582 24 G 0.6198 0.0417 0.3384 25 T 0.4326 0.0558 0.5115 26 T 0.4774 0.0571 0.4656 27 H 0.7154 0.0440 0.2406 28 S 0.8636 0.0171 0.1192 29 V 0.9074 0.0083 0.0842 30 I 0.8994 0.0094 0.0912 31 R 0.8866 0.0076 0.1058 32 S 0.6772 0.0181 0.3047 33 G 0.3041 0.0805 0.6154 34 N 0.0851 0.0470 0.8679 35 G 0.1032 0.0610 0.8358 36 V 0.2829 0.0605 0.6567 37 G 0.5467 0.0481 0.4052 38 L 0.5889 0.0484 0.3626 39 G 0.5320 0.0491 0.4189 40 P 0.4163 0.0549 0.5289 41 N 0.3732 0.0405 0.5863 42 R 0.2117 0.0378 0.7505 43 P 0.1397 0.0538 0.8065 44 F 0.1204 0.0698 0.8098 45 E 0.0873 0.0723 0.8405 46 T 0.1075 0.0770 0.8156 47 R 0.1709 0.0954 0.7337 48 M 0.1986 0.0938 0.7076 49 P 0.1536 0.1152 0.7312 50 M 0.1066 0.1939 0.6995 51 L 0.0770 0.2678 0.6552 52 T 0.0539 0.3491 0.5970 53 Q 0.0517 0.3557 0.5925 54 N 0.0688 0.3573 0.5739 55 L 0.0618 0.3302 0.6080 56 L 0.0434 0.2417 0.7149 57 G 0.0446 0.1256 0.8298 58 L 0.0632 0.1369 0.8000 59 P 0.0915 0.2054 0.7031 60 L 0.0052 0.9454 0.0494 61 R 0.0048 0.9566 0.0386 62 V 0.0050 0.9571 0.0379 63 A 0.0047 0.9562 0.0391 64 A 0.0048 0.9504 0.0448 65 G 0.0048 0.9312 0.0640 66 C 0.0051 0.9044 0.0905 67 V 0.0130 0.8159 0.1711 68 K 0.0179 0.6792 0.3029 69 S 0.0508 0.4654 0.4838 70 W 0.0272 0.4695 0.5033 71 N 0.0387 0.4906 0.4706 72 Y 0.0074 0.8832 0.1094 73 V 0.0047 0.9476 0.0476 74 E 0.0047 0.9560 0.0393 75 A 0.0047 0.9567 0.0386 76 S 0.0048 0.9557 0.0396 77 I 0.0048 0.9541 0.0411 78 G 0.0047 0.9581 0.0372 79 L 0.0051 0.9582 0.0367 80 A 0.0047 0.9594 0.0358 81 A 0.0051 0.9579 0.0371 82 I 0.0053 0.9534 0.0413 83 N 0.0072 0.9432 0.0496 84 A 0.0075 0.9341 0.0584 85 Y 0.0099 0.8920 0.0981 86 Y 0.0266 0.7314 0.2420 87 N 0.0327 0.4988 0.4685 88 N 0.0503 0.2839 0.6658 89 P 0.0437 0.5023 0.4540 90 Q 0.0386 0.5666 0.3948 91 V 0.0619 0.5491 0.3890 92 A 0.1124 0.3957 0.4919 93 R 0.0822 0.2187 0.6991 94 E 0.0462 0.2752 0.6786 95 H 0.0515 0.1996 0.7489 96 G 0.0911 0.1598 0.7491 97 V 0.1796 0.1259 0.6946 98 I 0.2674 0.1579 0.5747 99 F 0.2180 0.1744 0.6076 100 S 0.1544 0.1694 0.6762 101 D 0.1148 0.1673 0.7178 102 A 0.1020 0.1935 0.7045 103 K 0.1100 0.1529 0.7371 104 R 0.1162 0.2297 0.6541 105 V 0.0932 0.2696 0.6372 106 E 0.0936 0.2904 0.6160 107 D 0.0856 0.3943 0.5201 108 R 0.0824 0.4480 0.4697 109 M 0.0928 0.4245 0.4827 110 N 0.0684 0.3946 0.5371 111 D 0.0561 0.3806 0.5633 112 P 0.0498 0.6430 0.3072 113 F 0.0910 0.6677 0.2413 114 I 0.1199 0.6697 0.2104 115 M 0.1812 0.6114 0.2074 116 S 0.2327 0.4880 0.2793 117 Q 0.2241 0.4465 0.3294 118 N 0.2609 0.3526 0.3865 119 E 0.2009 0.3037 0.4954 120 V 0.1181 0.1426 0.7392 121 K 0.0326 0.0990 0.8684 122 G 0.0323 0.0471 0.9206 123 K 0.2018 0.0170 0.7812 124 K 0.6347 0.0054 0.3599 125 V 0.9069 0.0044 0.0887 126 G 0.9250 0.0038 0.0712 127 V 0.9262 0.0034 0.0704 128 V 0.8715 0.0184 0.1101 129 G 0.6907 0.0186 0.2907 130 H 0.3606 0.0330 0.6064 131 F 0.1327 0.0481 0.8191 132 P 0.0507 0.3038 0.6455 133 H 0.0553 0.4259 0.5188 134 L 0.0340 0.7010 0.2650 135 E 0.0256 0.7505 0.2239 136 S 0.0158 0.7699 0.2143 137 L 0.0169 0.7342 0.2489 138 L 0.0299 0.6777 0.2925 139 E 0.0227 0.6677 0.3097 140 P 0.0288 0.5765 0.3948 141 I 0.0660 0.3902 0.5438 142 C 0.1338 0.1199 0.7463 143 D 0.2116 0.0709 0.7174 144 L 0.6042 0.0271 0.3687 145 S 0.8061 0.0143 0.1796 146 I 0.8934 0.0076 0.0990 147 L 0.8635 0.0146 0.1219 148 E 0.7796 0.0193 0.2011 149 W 0.5214 0.0344 0.4441 150 S 0.1845 0.0207 0.7949 151 P 0.0863 0.0726 0.8412 152 E 0.0654 0.0716 0.8629 153 E 0.0480 0.1590 0.7930 154 G 0.0445 0.1057 0.8498 155 D 0.1000 0.0957 0.8043 156 Y 0.1535 0.0344 0.8121 157 P 0.0766 0.0436 0.8798 158 L 0.0096 0.6827 0.3078 159 P 0.0067 0.7747 0.2185 160 A 0.0078 0.8200 0.1722 161 S 0.0111 0.8188 0.1702 162 E 0.0086 0.7265 0.2649 163 F 0.0108 0.6135 0.3757 164 I 0.0287 0.5669 0.4043 165 L 0.0321 0.3765 0.5914 166 P 0.0169 0.3809 0.6022 167 E 0.0298 0.3186 0.6516 168 C 0.1174 0.0648 0.8178 169 D 0.1745 0.0982 0.7273 170 Y 0.9074 0.0097 0.0829 171 V 0.9301 0.0057 0.0642 172 Y 0.9273 0.0077 0.0650 173 I 0.8890 0.0201 0.0909 174 T 0.5595 0.0545 0.3860 175 C 0.1816 0.3631 0.4553 176 A 0.0815 0.6222 0.2963 177 S 0.0658 0.7441 0.1900 178 V 0.0828 0.7457 0.1715 179 V 0.0724 0.6958 0.2319 180 D 0.0398 0.6265 0.3337 181 K 0.0209 0.6214 0.3577 182 T 0.0329 0.7223 0.2448 183 L 0.0052 0.9406 0.0542 184 P 0.0048 0.9549 0.0404 185 R 0.0048 0.9534 0.0418 186 L 0.0048 0.9483 0.0469 187 L 0.0050 0.9244 0.0706 188 E 0.0052 0.8195 0.1754 189 L 0.0087 0.6726 0.3187 190 S 0.0690 0.3593 0.5716 191 R 0.0269 0.3339 0.6393 192 N 0.0454 0.2352 0.7195 193 A 0.1358 0.1629 0.7013 194 R 0.4393 0.0829 0.4777 195 R 0.8228 0.0161 0.1611 196 I 0.9149 0.0110 0.0741 197 T 0.9238 0.0050 0.0712 198 L 0.9157 0.0049 0.0794 199 V 0.7713 0.0280 0.2007 200 G 0.2840 0.0238 0.6922 201 P 0.1233 0.0418 0.8349 202 G 0.0949 0.0669 0.8382 203 T 0.0903 0.0756 0.8341 204 P 0.1345 0.0952 0.7704 205 L 0.1603 0.1529 0.6868 206 A 0.1349 0.1374 0.7277 207 P 0.0746 0.5438 0.3816 208 V 0.0761 0.6029 0.3210 209 L 0.0731 0.6500 0.2769 210 F 0.0612 0.5622 0.3766 211 E 0.0534 0.3894 0.5572 212 H 0.0674 0.1567 0.7758 213 G 0.0784 0.0444 0.8772 214 L 0.2621 0.0270 0.7109 215 Q 0.5901 0.0416 0.3683 216 E 0.8335 0.0234 0.1431 217 L 0.8553 0.0167 0.1281 218 S 0.7920 0.0183 0.1896 219 G 0.7830 0.0147 0.2023 220 F 0.8038 0.0097 0.1865 221 M 0.7962 0.0103 0.1935 222 V 0.6115 0.0165 0.3720 223 K 0.3098 0.0370 0.6532 224 D 0.1346 0.0182 0.8472 225 N 0.0053 0.9056 0.0891 226 A 0.0049 0.9437 0.0514 227 R 0.0049 0.9536 0.0416 228 A 0.0047 0.9577 0.0376 229 F 0.0047 0.9559 0.0394 230 R 0.0051 0.9567 0.0382 231 I 0.0048 0.9563 0.0389 232 V 0.0058 0.9495 0.0447 233 A 0.0060 0.9085 0.0855 234 G 0.0197 0.6523 0.3279 235 A 0.0307 0.3602 0.6092 236 E 0.0552 0.1843 0.7605 237 K 0.1009 0.1645 0.7346 238 V 0.2516 0.2128 0.5356 239 K 0.4638 0.2061 0.3301 240 I 0.4981 0.1988 0.3031 241 Y 0.4191 0.1587 0.4222 242 S 0.3066 0.1527 0.5407 243 A 0.1328 0.1773 0.6899 244 G 0.1994 0.1375 0.6632 245 Q 0.4783 0.0826 0.4391 246 K 0.7006 0.0568 0.2427 247 V 0.8020 0.0383 0.1597 248 T 0.8233 0.0281 0.1486 249 I 0.7414 0.0269 0.2316 250 K 0.5127 0.0405 0.4468 251 K 0.1980 0.0333 0.7687