# This file is the result of combining several RDB files, specifically # T0378.t06.dssp-ebghstl.rdb (weight 1.53986) # T0378.t06.stride-ebghtl.rdb (weight 1.24869) # T0378.t06.str2.rdb (weight 1.54758) # T0378.t06.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 T0378.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0378 # 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 T0378.t06-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 1350 # # ============================================ # Comments from T0378.t06.stride-ebghtl.rdb # ============================================ # TARGET T0378 # Using neural net t06-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 T0378.t06-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 1350 # # ============================================ # Comments from T0378.t06.str2.rdb # ============================================ # TARGET T0378 # Using neural net t06-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 T0378.t06-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 1350 # # ============================================ # Comments from T0378.t06.alpha.rdb # ============================================ # TARGET T0378 # Using neural net t06-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 T0378.t06-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 1350 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0752 0.0488 0.8760 2 L 0.0452 0.2318 0.7230 3 S 0.0378 0.2463 0.7159 4 A 0.0381 0.3535 0.6084 5 N 0.0199 0.5900 0.3901 6 Q 0.0250 0.7367 0.2384 7 I 0.0229 0.8567 0.1205 8 K 0.0136 0.9074 0.0790 9 F 0.0165 0.9118 0.0717 10 L 0.0095 0.9233 0.0673 11 R 0.0068 0.9335 0.0597 12 S 0.0075 0.9110 0.0815 13 L 0.0068 0.8893 0.1039 14 R 0.0100 0.8418 0.1482 15 E 0.0118 0.8052 0.1830 16 R 0.0208 0.7159 0.2632 17 K 0.0242 0.6510 0.3248 18 Y 0.0392 0.6327 0.3281 19 R 0.0494 0.6194 0.3312 20 L 0.0517 0.5745 0.3738 21 R 0.0554 0.5387 0.4058 22 E 0.0667 0.3500 0.5833 23 Q 0.0983 0.1861 0.7157 24 A 0.2301 0.1105 0.6594 25 F 0.6026 0.0800 0.3174 26 A 0.7972 0.0661 0.1367 27 V 0.7890 0.0754 0.1355 28 E 0.6388 0.0881 0.2730 29 G 0.1953 0.1122 0.6925 30 P 0.0414 0.4905 0.4681 31 K 0.0275 0.6713 0.3012 32 L 0.0217 0.8424 0.1359 33 V 0.0067 0.9294 0.0640 34 G 0.0057 0.9301 0.0642 35 E 0.0061 0.9029 0.0910 36 M 0.0091 0.8470 0.1438 37 L 0.0157 0.7429 0.2414 38 P 0.0118 0.5956 0.3926 39 F 0.0201 0.4210 0.5590 40 Y 0.1044 0.0586 0.8370 41 R 0.1741 0.0379 0.7880 42 C 0.4703 0.0253 0.5043 43 R 0.4469 0.0722 0.4810 44 M 0.8621 0.0281 0.1099 45 L 0.8972 0.0271 0.0756 46 V 0.8839 0.0283 0.0878 47 G 0.7619 0.0312 0.2069 48 T 0.2518 0.0783 0.6699 49 A 0.0238 0.7865 0.1897 50 A 0.0159 0.8301 0.1540 51 M 0.0135 0.8558 0.1307 52 L 0.0185 0.8533 0.1282 53 R 0.0173 0.7906 0.1921 54 A 0.0199 0.6821 0.2980 55 V 0.0396 0.4565 0.5040 56 S 0.0825 0.2584 0.6591 57 T 0.0644 0.0716 0.8641 58 P 0.0517 0.2010 0.7473 59 H 0.0574 0.1640 0.7785 60 D 0.0875 0.0802 0.8323 61 A 0.2981 0.0114 0.6905 62 E 0.7293 0.0063 0.2644 63 V 0.8957 0.0039 0.1003 64 V 0.8828 0.0063 0.1109 65 E 0.8618 0.0042 0.1339 66 L 0.4852 0.0086 0.5063 67 P 0.1436 0.0200 0.8364 68 E 0.0311 0.2479 0.7209 69 S 0.0441 0.3100 0.6459 70 F 0.0709 0.2582 0.6709 71 D 0.1394 0.3271 0.5335 72 F 0.0517 0.7028 0.2454 73 K 0.0317 0.7778 0.1905 74 R 0.0384 0.7827 0.1789 75 I 0.0598 0.6751 0.2651 76 S 0.0912 0.4035 0.5053 77 T 0.0568 0.2487 0.6945 78 Q 0.0771 0.1178 0.8051 79 T 0.1234 0.0671 0.8095 80 T 0.1244 0.0334 0.8423 81 P 0.1211 0.0444 0.8345 82 Q 0.1860 0.0724 0.7416 83 P 0.4590 0.0252 0.5158 84 L 0.8128 0.0102 0.1771 85 M 0.9143 0.0053 0.0804 86 A 0.9151 0.0056 0.0793 87 V 0.9099 0.0073 0.0828 88 F 0.7772 0.0073 0.2155 89 D 0.4220 0.0131 0.5649 90 L 0.1338 0.0199 0.8462 91 P 0.0873 0.0391 0.8736 92 A 0.0719 0.0644 0.8637 93 E 0.0732 0.0291 0.8977 94 P 0.0800 0.0352 0.8849 95 E 0.0659 0.2341 0.7000 96 P 0.0596 0.3469 0.5935 97 V 0.0794 0.3769 0.5437 98 V 0.1617 0.1322 0.7061 99 E 0.1056 0.1055 0.7889 100 G 0.1708 0.0384 0.7908 101 L 0.7355 0.0056 0.2589 102 T 0.9228 0.0035 0.0737 103 L 0.9320 0.0032 0.0648 104 L 0.9254 0.0035 0.0711 105 L 0.8704 0.0071 0.1225 106 D 0.5597 0.0434 0.3969 107 G 0.2337 0.0253 0.7410 108 V 0.2230 0.0430 0.7340 109 Q 0.2284 0.0480 0.7235 110 D 0.1023 0.0257 0.8720 111 P 0.0269 0.2095 0.7636 112 G 0.0498 0.2378 0.7124 113 N 0.0558 0.5978 0.3464 114 V 0.0077 0.8920 0.1003 115 G 0.0056 0.9423 0.0521 116 T 0.0052 0.9549 0.0400 117 I 0.0048 0.9574 0.0378 118 L 0.0047 0.9580 0.0373 119 R 0.0048 0.9544 0.0408 120 T 0.0047 0.9538 0.0415 121 A 0.0047 0.9513 0.0440 122 D 0.0055 0.9332 0.0612 123 W 0.0057 0.8881 0.1062 124 F 0.0482 0.4096 0.5422 125 G 0.0593 0.0144 0.9263 126 I 0.1132 0.0085 0.8783 127 R 0.1440 0.0429 0.8131 128 H 0.8922 0.0053 0.1024 129 V 0.9271 0.0035 0.0694 130 W 0.9268 0.0042 0.0690 131 L 0.8713 0.0073 0.1214 132 G 0.4341 0.0199 0.5460 133 T 0.1547 0.0383 0.8070 134 G 0.0727 0.0596 0.8677 135 S 0.1090 0.1034 0.7876 136 A 0.1082 0.1660 0.7258 137 D 0.1115 0.1621 0.7264 138 V 0.0889 0.1879 0.7232 139 F 0.0967 0.1247 0.7786 140 S 0.0740 0.0514 0.8747 141 P 0.0058 0.8815 0.1127 142 K 0.0080 0.9095 0.0825 143 V 0.0157 0.9224 0.0619 144 V 0.0229 0.9252 0.0518 145 Q 0.0409 0.8919 0.0672 146 A 0.0486 0.8530 0.0984 147 S 0.0584 0.8088 0.1328 148 M 0.0389 0.7787 0.1825 149 G 0.0542 0.6026 0.3433 150 A 0.0845 0.6058 0.3096 151 L 0.1198 0.6034 0.2767 152 A 0.1438 0.4804 0.3758 153 R 0.2085 0.3035 0.4880 154 V 0.2766 0.0460 0.6774 155 Q 0.2103 0.0190 0.7707 156 P 0.2990 0.0525 0.6485 157 T 0.4445 0.0401 0.5153 158 P 0.4497 0.0505 0.4998 159 L 0.2229 0.0930 0.6841 160 K 0.1016 0.1507 0.7476 161 N 0.1156 0.1075 0.7769 162 T 0.0052 0.9147 0.0801 163 V 0.0047 0.9546 0.0407 164 D 0.0047 0.9566 0.0387 165 T 0.0048 0.9571 0.0382 166 L 0.0047 0.9581 0.0372 167 A 0.0047 0.9558 0.0396 168 Y 0.0047 0.9566 0.0387 169 F 0.0048 0.9553 0.0399 170 R 0.0048 0.9495 0.0457 171 R 0.0057 0.9086 0.0857 172 Q 0.0407 0.3437 0.6156 173 G 0.0380 0.0141 0.9479 174 I 0.0817 0.0079 0.9104 175 P 0.5385 0.0045 0.4569 176 V 0.9236 0.0033 0.0732 177 Y 0.9280 0.0038 0.0682 178 G 0.9277 0.0036 0.0688 179 A 0.8992 0.0062 0.0946 180 F 0.7136 0.0062 0.2803 181 L 0.3077 0.0399 0.6524 182 D 0.1415 0.0380 0.8205 183 G 0.0613 0.1642 0.7745 184 Q 0.0734 0.1879 0.7388 185 S 0.1812 0.1897 0.6291 186 L 0.2942 0.1467 0.5591 187 Y 0.2994 0.1210 0.5796 188 E 0.2287 0.1306 0.6407 189 A 0.1281 0.0857 0.7862 190 P 0.1347 0.0926 0.7727 191 L 0.1132 0.0863 0.8005 192 P 0.1029 0.1007 0.7963 193 N 0.1000 0.0946 0.8054 194 F 0.0947 0.0673 0.8380 195 T 0.0644 0.0600 0.8757 196 E 0.0831 0.0302 0.8867 197 P 0.1698 0.0176 0.8126 198 A 0.7726 0.0059 0.2215 199 I 0.9260 0.0034 0.0706 200 L 0.9328 0.0031 0.0641 201 V 0.9259 0.0034 0.0706 202 L 0.8269 0.0189 0.1542 203 G 0.3997 0.0148 0.5856 204 S 0.1612 0.0376 0.8012 205 E 0.0883 0.1432 0.7686 206 G 0.0551 0.1502 0.7947 207 R 0.0503 0.1347 0.8150 208 G 0.0664 0.0739 0.8597 209 I 0.1016 0.0265 0.8719 210 S 0.0658 0.0312 0.9030 211 P 0.0049 0.9448 0.0502 212 E 0.0048 0.9544 0.0409 213 V 0.0051 0.9478 0.0471 214 A 0.0057 0.9475 0.0467 215 A 0.0061 0.8976 0.0963 216 E 0.0104 0.6510 0.3386 217 I 0.0767 0.3103 0.6130 218 T 0.0938 0.1679 0.7382 219 D 0.4108 0.1206 0.4686 220 R 0.7477 0.0567 0.1956 221 L 0.8711 0.0138 0.1151 222 T 0.8696 0.0062 0.1242 223 I 0.6860 0.0061 0.3078 224 P 0.3366 0.0119 0.6516 225 A 0.1226 0.0685 0.8088 226 S 0.0512 0.1238 0.8250 227 G 0.0414 0.1500 0.8086 228 L 0.0994 0.1322 0.7684 229 S 0.1640 0.0988 0.7372 230 V 0.1645 0.0960 0.7395 231 K 0.1251 0.1294 0.7455 232 G 0.0764 0.1136 0.8101 233 H 0.1465 0.1618 0.6916 234 T 0.1923 0.2718 0.5360 235 E 0.1464 0.3898 0.4638 236 S 0.1666 0.4815 0.3519 237 L 0.0543 0.7951 0.1506 238 N 0.0162 0.9007 0.0832 239 V 0.0053 0.9545 0.0402 240 A 0.0047 0.9592 0.0361 241 I 0.0047 0.9593 0.0361 242 A 0.0047 0.9601 0.0352 243 T 0.0047 0.9606 0.0348 244 A 0.0047 0.9608 0.0346 245 I 0.0047 0.9610 0.0343 246 L 0.0047 0.9604 0.0350 247 C 0.0047 0.9597 0.0356 248 S 0.0047 0.9572 0.0381 249 E 0.0049 0.9510 0.0441 250 W 0.0052 0.9317 0.0631 251 R 0.0088 0.8700 0.1211 252 R 0.0180 0.7067 0.2753 253 R 0.0414 0.3213 0.6373 254 S 0.0568 0.0230 0.9202