# This file is the result of combining several RDB files, specifically # T0320.t06.dssp-ebghstl.rdb (weight 1.53986) # T0320.t06.stride-ebghtl.rdb (weight 1.24869) # T0320.t06.str2.rdb (weight 1.54758) # T0320.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 T0320.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0320 # 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 T0320.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 2603 # # ============================================ # Comments from T0320.t06.stride-ebghtl.rdb # ============================================ # TARGET T0320 # 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 T0320.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 2603 # # ============================================ # Comments from T0320.t06.str2.rdb # ============================================ # TARGET T0320 # 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 T0320.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 2603 # # ============================================ # Comments from T0320.t06.alpha.rdb # ============================================ # TARGET T0320 # 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 T0320.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 2603 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0893 0.0585 0.8522 2 Q 0.1400 0.1002 0.7598 3 L 0.1421 0.2188 0.6390 4 S 0.1325 0.1855 0.6819 5 K 0.1622 0.2936 0.5442 6 A 0.2025 0.3728 0.4247 7 A 0.3167 0.3543 0.3289 8 E 0.3965 0.3239 0.2796 9 M 0.3585 0.2696 0.3719 10 C 0.2424 0.2088 0.5488 11 Y 0.1644 0.3562 0.4795 12 E 0.2165 0.3427 0.4408 13 I 0.3072 0.3125 0.3804 14 T 0.3031 0.2806 0.4163 15 N 0.2592 0.2689 0.4719 16 S 0.2637 0.3188 0.4175 17 Y 0.3094 0.3113 0.3793 18 L 0.2598 0.2526 0.4876 19 H 0.1947 0.1848 0.6205 20 I 0.0980 0.3428 0.5592 21 D 0.0866 0.3659 0.5475 22 Q 0.0301 0.6018 0.3680 23 K 0.0277 0.6812 0.2911 24 S 0.0447 0.7246 0.2307 25 Q 0.0480 0.7297 0.2223 26 I 0.0556 0.7622 0.1822 27 I 0.0528 0.7614 0.1858 28 A 0.0244 0.8364 0.1392 29 S 0.0264 0.7842 0.1894 30 T 0.0116 0.8424 0.1460 31 Q 0.0054 0.9265 0.0681 32 E 0.0048 0.9457 0.0495 33 A 0.0047 0.9504 0.0449 34 I 0.0048 0.9506 0.0446 35 R 0.0048 0.9564 0.0388 36 L 0.0050 0.9545 0.0405 37 T 0.0049 0.9486 0.0465 38 R 0.0048 0.9544 0.0408 39 K 0.0052 0.9540 0.0407 40 Y 0.0056 0.9356 0.0588 41 L 0.0049 0.9312 0.0639 42 L 0.0047 0.9544 0.0409 43 S 0.0048 0.9567 0.0385 44 E 0.0051 0.9542 0.0408 45 I 0.0053 0.9485 0.0462 46 F 0.0061 0.9351 0.0588 47 V 0.0079 0.9044 0.0877 48 R 0.0140 0.8080 0.1780 49 W 0.0583 0.6775 0.2643 50 S 0.0951 0.3998 0.5050 51 P 0.0256 0.4616 0.5128 52 L 0.0333 0.2589 0.7078 53 N 0.0660 0.0598 0.8742 54 G 0.0742 0.0303 0.8955 55 E 0.3819 0.0129 0.6052 56 I 0.8862 0.0035 0.1103 57 S 0.9273 0.0036 0.0691 58 F 0.9306 0.0033 0.0661 59 S 0.9212 0.0043 0.0745 60 Y 0.8535 0.0108 0.1357 61 N 0.5707 0.0171 0.4121 62 G 0.1726 0.0414 0.7860 63 G 0.1086 0.0876 0.8037 64 K 0.0546 0.3730 0.5724 65 D 0.0269 0.6271 0.3460 66 C 0.0061 0.9317 0.0622 67 Q 0.0048 0.9564 0.0388 68 V 0.0047 0.9608 0.0345 69 L 0.0047 0.9606 0.0347 70 L 0.0047 0.9610 0.0343 71 L 0.0047 0.9611 0.0343 72 L 0.0047 0.9603 0.0350 73 Y 0.0048 0.9568 0.0384 74 L 0.0057 0.9431 0.0511 75 S 0.0071 0.8865 0.1064 76 C 0.0203 0.7497 0.2299 77 L 0.0309 0.5508 0.4183 78 W 0.0318 0.6018 0.3664 79 E 0.0364 0.6204 0.3432 80 Y 0.0580 0.6073 0.3347 81 F 0.0666 0.5718 0.3616 82 F 0.1115 0.5703 0.3182 83 I 0.1233 0.5788 0.2980 84 K 0.1141 0.5622 0.3237 85 A 0.1019 0.5083 0.3898 86 Q 0.1000 0.3345 0.5655 87 N 0.0857 0.1783 0.7359 88 S 0.0952 0.1989 0.7058 89 Q 0.1317 0.2367 0.6316 90 F 0.1857 0.1711 0.6432 91 D 0.2245 0.1488 0.6267 92 F 0.3000 0.1604 0.5396 93 E 0.4472 0.1272 0.4256 94 F 0.4900 0.1454 0.3646 95 Q 0.4320 0.1328 0.4352 96 S 0.3385 0.1095 0.5520 97 F 0.1827 0.0858 0.7314 98 P 0.1047 0.2502 0.6452 99 M 0.1060 0.3953 0.4988 100 Q 0.1264 0.2911 0.5825 101 R 0.2224 0.0877 0.6900 102 L 0.2559 0.0090 0.7351 103 P 0.5482 0.0109 0.4409 104 T 0.9082 0.0038 0.0880 105 V 0.9245 0.0035 0.0720 106 F 0.9242 0.0034 0.0723 107 I 0.8565 0.0079 0.1356 108 D 0.4755 0.0123 0.5122 109 Q 0.1098 0.0966 0.7935 110 E 0.0433 0.1711 0.7856 111 E 0.0777 0.1987 0.7237 112 T 0.0779 0.1480 0.7742 113 F 0.0657 0.0789 0.8554 114 P 0.0091 0.7668 0.2241 115 T 0.0115 0.7983 0.1902 116 L 0.0083 0.8868 0.1049 117 E 0.0062 0.9390 0.0548 118 N 0.0054 0.9501 0.0446 119 F 0.0048 0.9532 0.0420 120 V 0.0047 0.9587 0.0366 121 L 0.0047 0.9604 0.0350 122 E 0.0047 0.9595 0.0359 123 T 0.0047 0.9592 0.0361 124 S 0.0048 0.9550 0.0401 125 E 0.0051 0.9402 0.0546 126 R 0.0069 0.8886 0.1045 127 Y 0.0498 0.5478 0.4025 128 C 0.0549 0.0243 0.9208 129 L 0.0957 0.0081 0.8962 130 S 0.3664 0.0115 0.6222 131 L 0.6991 0.0153 0.2856 132 Y 0.8180 0.0147 0.1673 133 E 0.7560 0.0260 0.2180 134 S 0.4684 0.0418 0.4898 135 Q 0.3332 0.0847 0.5821 136 R 0.3563 0.1276 0.5161 137 Q 0.3727 0.1474 0.4799 138 S 0.2555 0.1572 0.5873 139 G 0.1511 0.1374 0.7115 140 A 0.1435 0.1104 0.7461 141 S 0.1249 0.1071 0.7680 142 V 0.1073 0.1570 0.7357 143 N 0.0925 0.1462 0.7613 144 M 0.0588 0.2526 0.6886 145 A 0.0280 0.5152 0.4568 146 D 0.0108 0.7608 0.2285 147 A 0.0090 0.8307 0.1602 148 F 0.0058 0.9189 0.0752 149 R 0.0060 0.9333 0.0607 150 D 0.0052 0.9373 0.0575 151 F 0.0054 0.9387 0.0559 152 I 0.0058 0.9048 0.0894 153 K 0.0060 0.7668 0.2272 154 I 0.0149 0.5531 0.4320 155 Y 0.0828 0.0661 0.8511 156 P 0.0130 0.1950 0.7920 157 E 0.0242 0.0951 0.8807 158 T 0.1775 0.0426 0.7798 159 E 0.2689 0.0587 0.6724 160 A 0.8973 0.0056 0.0971 161 I 0.9253 0.0045 0.0703 162 V 0.9190 0.0060 0.0750 163 I 0.8366 0.0165 0.1469 164 G 0.6313 0.0209 0.3478 165 I 0.3955 0.0402 0.5643 166 R 0.2351 0.0628 0.7021 167 H 0.1261 0.1093 0.7647 168 T 0.0731 0.0969 0.8299 169 D 0.0777 0.0989 0.8234 170 P 0.0292 0.4211 0.5498 171 F 0.0430 0.4469 0.5101 172 G 0.0845 0.4920 0.4235 173 E 0.1144 0.4876 0.3980 174 A 0.1727 0.3781 0.4492 175 L 0.1767 0.2952 0.5281 176 K 0.1629 0.1936 0.6435 177 P 0.1423 0.3154 0.5423 178 I 0.1962 0.3389 0.4649 179 Q 0.3125 0.2677 0.4198 180 R 0.3114 0.2248 0.4638 181 T 0.2235 0.1629 0.6136 182 D 0.1005 0.0748 0.8246 183 S 0.0258 0.1401 0.8341 184 N 0.0395 0.1038 0.8568 185 W 0.0710 0.1045 0.8246 186 P 0.0386 0.1822 0.7792 187 D 0.0490 0.1399 0.8111 188 F 0.2493 0.0789 0.6717 189 M 0.5500 0.0477 0.4022 190 R 0.7554 0.0338 0.2107 191 L 0.7027 0.0467 0.2506 192 Q 0.5476 0.0410 0.4114 193 P 0.3215 0.1122 0.5663 194 L 0.2078 0.2250 0.5672 195 L 0.1759 0.2008 0.6234 196 H 0.1719 0.0939 0.7343 197 W 0.2094 0.0360 0.7545 198 D 0.1035 0.0323 0.8641 199 L 0.0049 0.9280 0.0671 200 T 0.0047 0.9474 0.0479 201 N 0.0047 0.9565 0.0388 202 I 0.0047 0.9609 0.0345 203 W 0.0047 0.9608 0.0345 204 S 0.0047 0.9614 0.0339 205 F 0.0047 0.9607 0.0346 206 L 0.0048 0.9580 0.0372 207 L 0.0051 0.9509 0.0440 208 Y 0.0072 0.9135 0.0793 209 S 0.0467 0.5156 0.4376 210 N 0.0354 0.0303 0.9343 211 E 0.0598 0.0113 0.9289 212 P 0.1339 0.0394 0.8267 213 I 0.2390 0.1407 0.6203 214 C 0.2547 0.1672 0.5781 215 G 0.2112 0.2115 0.5773 216 L 0.2262 0.2112 0.5626 217 Y 0.1480 0.1593 0.6927 218 G 0.1099 0.0917 0.7984 219 K 0.1194 0.0569 0.8237 220 G 0.1332 0.0512 0.8156 221 F 0.2576 0.0417 0.7007 222 T 0.2944 0.0606 0.6450 223 S 0.2590 0.0545 0.6865 224 I 0.1693 0.1045 0.7262 225 G 0.1203 0.0698 0.8099 226 G 0.1549 0.0747 0.7704 227 I 0.1822 0.1043 0.7135 228 N 0.2171 0.1296 0.6533 229 N 0.1811 0.1143 0.7045 230 S 0.1564 0.1089 0.7347 231 L 0.1421 0.0441 0.8139 232 P 0.1280 0.0547 0.8173 233 N 0.0862 0.0575 0.8563 234 P 0.0255 0.3324 0.6421 235 H 0.0336 0.3452 0.6212 236 L 0.0758 0.3542 0.5700 237 R 0.0847 0.2522 0.6631 238 K 0.0875 0.2547 0.6577 239 D 0.0542 0.2102 0.7355 240 S 0.0341 0.2323 0.7336 241 N 0.0494 0.1664 0.7842 242 N 0.0861 0.0759 0.8380 243 P 0.0217 0.4330 0.5453 244 A 0.0337 0.5604 0.4059 245 L 0.0817 0.6082 0.3101 246 H 0.1205 0.5750 0.3046 247 F 0.1269 0.5856 0.2875 248 E 0.0919 0.6514 0.2567 249 W 0.0626 0.7289 0.2085 250 E 0.0554 0.8096 0.1351 251 I 0.0602 0.8296 0.1103 252 I 0.0978 0.7882 0.1139 253 H 0.1106 0.7679 0.1215 254 A 0.1061 0.7188 0.1751 255 F 0.0891 0.5356 0.3753 256 G 0.1155 0.1771 0.7074 257 K 0.1777 0.1649 0.6573 258 D 0.1488 0.1589 0.6923 259 A 0.0568 0.2468 0.6964 260 E 0.0606 0.1473 0.7921 261 G 0.0825 0.1426 0.7749 262 E 0.2000 0.1667 0.6332 263 R 0.3678 0.1722 0.4600 264 S 0.2952 0.1870 0.5178 265 S 0.2324 0.2944 0.4732 266 A 0.2878 0.3419 0.3703 267 I 0.3462 0.2700 0.3838 268 N 0.3829 0.1720 0.4451 269 T 0.3235 0.1156 0.5609 270 S 0.1758 0.0615 0.7628 271 P 0.1418 0.1284 0.7298 272 I 0.3923 0.1213 0.4865 273 S 0.5311 0.0968 0.3721 274 V 0.5124 0.0935 0.3941 275 V 0.4179 0.0885 0.4936 276 D 0.2211 0.0753 0.7037 277 K 0.1659 0.1208 0.7133 278 E 0.2532 0.1045 0.6423 279 R 0.3343 0.1063 0.5594 280 F 0.3830 0.1103 0.5068 281 S 0.5986 0.0963 0.3051 282 K 0.7190 0.0724 0.2085 283 Y 0.6540 0.0665 0.2794 284 H 0.5066 0.0775 0.4160 285 D 0.2583 0.1719 0.5698 286 N 0.1596 0.1314 0.7090 287 Y 0.1280 0.1290 0.7429 288 Y 0.1486 0.0494 0.8020 289 P 0.0689 0.0735 0.8576 290 G 0.1068 0.0482 0.8450 291 W 0.6936 0.0109 0.2956 292 Y 0.8726 0.0063 0.1211 293 L 0.8769 0.0063 0.1168 294 V 0.6609 0.0266 0.3124 295 D 0.1933 0.0515 0.7552 296 D 0.0576 0.1857 0.7567 297 T 0.0795 0.4316 0.4889 298 L 0.1628 0.5588 0.2784 299 E 0.1869 0.5306 0.2825 300 R 0.2040 0.5094 0.2866 301 A 0.1616 0.5247 0.3137 302 G 0.2186 0.3325 0.4490 303 R 0.3071 0.2634 0.4295 304 I 0.2901 0.2274 0.4825 305 K 0.1492 0.1446 0.7062 306 N 0.0663 0.0396 0.8941