# This file is the result of combining several RDB files, specifically # T0457.t04.str2.rdb (weight 1.54425) # T0457.t04.str4.rdb (weight 0.924988) # T0457.t04.pb.rdb (weight 0.789901) # T0457.t04.bys.rdb (weight 0.748322) # T0457.t04.alpha.rdb (weight 0.678173) # 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 T0457.t04.str2.rdb # ============================================ # TARGET T0457 # Using neural net dunbrack-40pc-3157-t04-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 T0457.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 1664 # # ============================================ # Comments from T0457.t04.str4.rdb # ============================================ # TARGET T0457 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-str4-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 21 (1 str4 ) # The input amino acid frequencies were determined from # alignment T0457.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 1664 # # ============================================ # Comments from T0457.t04.pb.rdb # ============================================ # TARGET T0457 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-pb-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 16 (1 pb ) # The input amino acid frequencies were determined from # alignment T0457.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 1664 # # ============================================ # Comments from T0457.t04.bys.rdb # ============================================ # TARGET T0457 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-bys-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 Bystroff ) # The input amino acid frequencies were determined from # alignment T0457.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 1664 # # ============================================ # Comments from T0457.t04.alpha.rdb # ============================================ # TARGET T0457 # Using neural net dunbrack-40pc-3157-t04-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 T0457.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 1664 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0225 0.7626 0.2149 2 V 0.0097 0.8926 0.0977 3 E 0.0084 0.9187 0.0729 4 I 0.0084 0.9193 0.0723 5 F 0.0084 0.9192 0.0724 6 N 0.0083 0.9233 0.0684 7 E 0.0083 0.9235 0.0682 8 I 0.0083 0.9215 0.0701 9 M 0.0083 0.9217 0.0699 10 Q 0.0083 0.9130 0.0787 11 R 0.0084 0.9160 0.0757 12 V 0.0088 0.8997 0.0915 13 K 0.0100 0.7941 0.1960 14 E 0.0223 0.5159 0.4618 15 A 0.1126 0.2073 0.6801 16 E 0.1981 0.1521 0.6499 17 T 0.5595 0.0368 0.4036 18 I 0.7573 0.0087 0.2340 19 I 0.8028 0.0054 0.1918 20 I 0.7991 0.0078 0.1932 21 H 0.7487 0.0180 0.2333 22 R 0.6157 0.0320 0.3523 23 H 0.4203 0.0449 0.5348 24 V 0.2964 0.0976 0.6060 25 R 0.2444 0.0436 0.7120 26 P 0.1269 0.2338 0.6393 27 D 0.1732 0.1255 0.7013 28 P 0.0248 0.4555 0.5197 29 D 0.0359 0.5254 0.4387 30 A 0.0395 0.7653 0.1952 31 Y 0.0239 0.8689 0.1072 32 G 0.0130 0.9074 0.0796 33 S 0.0094 0.9200 0.0706 34 Q 0.0083 0.9243 0.0674 35 L 0.0083 0.9249 0.0668 36 G 0.0083 0.9245 0.0672 37 L 0.0083 0.9241 0.0676 38 K 0.0083 0.9238 0.0679 39 L 0.0083 0.9232 0.0685 40 Y 0.0083 0.9206 0.0711 41 L 0.0087 0.9062 0.0851 42 E 0.0095 0.8695 0.1211 43 R 0.0170 0.7190 0.2641 44 K 0.0541 0.3687 0.5772 45 F 0.1451 0.1202 0.7347 46 P 0.0914 0.2794 0.6292 47 E 0.1491 0.1564 0.6945 48 K 0.3621 0.0362 0.6018 49 N 0.5875 0.0243 0.3882 50 I 0.7592 0.0097 0.2311 51 Y 0.7260 0.0171 0.2569 52 A 0.6402 0.0208 0.3390 53 T 0.3589 0.0794 0.5617 54 G 0.1435 0.1059 0.7506 55 E 0.2133 0.1004 0.6863 56 A 0.2524 0.0858 0.6618 57 E 0.2086 0.0670 0.7244 58 P 0.0631 0.4821 0.4548 59 S 0.0682 0.3732 0.5586 60 L 0.1788 0.2974 0.5238 61 S 0.2009 0.2824 0.5167 62 F 0.2056 0.3193 0.4751 63 I 0.1882 0.2779 0.5339 64 G 0.1078 0.3796 0.5126 65 D 0.1220 0.3696 0.5084 66 L 0.1914 0.2831 0.5255 67 D 0.1680 0.2713 0.5606 68 E 0.1936 0.3167 0.4897 69 I 0.2198 0.2639 0.5163 70 D 0.1999 0.2486 0.5515 71 D 0.1037 0.4667 0.4297 72 S 0.1003 0.4612 0.4385 73 V 0.1476 0.3268 0.5255 74 Y 0.1795 0.1741 0.6464 75 S 0.1834 0.1513 0.6653 76 D 0.2296 0.1137 0.6568 77 A 0.3963 0.0524 0.5514 78 L 0.7289 0.0151 0.2560 79 V 0.7914 0.0057 0.2029 80 I 0.8183 0.0042 0.1775 81 V 0.8078 0.0046 0.1877 82 C 0.7683 0.0113 0.2204 83 D 0.5160 0.0213 0.4626 84 T 0.2548 0.1466 0.5986 85 A 0.1584 0.1880 0.6536 86 N 0.1570 0.1477 0.6953 87 A 0.1755 0.1617 0.6628 88 P 0.1170 0.3458 0.5372 89 R 0.1410 0.3394 0.5197 90 I 0.1326 0.4045 0.4629 91 D 0.0662 0.6089 0.3248 92 D 0.0234 0.8043 0.1723 93 Q 0.0194 0.8424 0.1383 94 R 0.0221 0.8511 0.1268 95 Y 0.0283 0.7859 0.1859 96 L 0.0435 0.6921 0.2644 97 N 0.0704 0.1999 0.7297 98 G 0.0534 0.0727 0.8740 99 Q 0.2346 0.0144 0.7510 100 S 0.5171 0.0232 0.4597 101 L 0.8069 0.0050 0.1881 102 I 0.8092 0.0050 0.1858 103 K 0.7891 0.0048 0.2061 104 I 0.7586 0.0112 0.2302 105 D 0.5936 0.0314 0.3750 106 H 0.3288 0.0697 0.6014 107 H 0.2352 0.0578 0.7070 108 P 0.1584 0.1610 0.6806 109 A 0.1193 0.2411 0.6397 110 T 0.1028 0.3112 0.5860 111 D 0.1004 0.3168 0.5828 112 Q 0.1368 0.2979 0.5652 113 Y 0.1828 0.1827 0.6345 114 G 0.1587 0.1325 0.7088 115 D 0.2175 0.1269 0.6556 116 V 0.2981 0.1453 0.5566 117 N 0.4439 0.1301 0.4260 118 F 0.6148 0.0655 0.3198 119 V 0.6173 0.0444 0.3383 120 N 0.3413 0.0270 0.6317 121 T 0.1019 0.3431 0.5550 122 E 0.0863 0.2907 0.6230 123 A 0.1256 0.2788 0.5957 124 S 0.1038 0.4033 0.4930 125 S 0.0712 0.6258 0.3030 126 T 0.0355 0.7811 0.1835 127 S 0.0138 0.8883 0.0979 128 E 0.0097 0.9201 0.0702 129 I 0.0099 0.9217 0.0684 130 I 0.0086 0.9241 0.0673 131 F 0.0084 0.9236 0.0680 132 D 0.0084 0.9237 0.0680 133 F 0.0084 0.9213 0.0704 134 I 0.0086 0.9155 0.0759 135 S 0.0089 0.9069 0.0842 136 H 0.0123 0.8485 0.1392 137 F 0.0293 0.6949 0.2758 138 N 0.0312 0.5227 0.4461 139 D 0.0452 0.4970 0.4578 140 L 0.0821 0.4355 0.4824 141 S 0.1450 0.2763 0.5786 142 I 0.1861 0.1712 0.6426 143 I 0.1973 0.1193 0.6835 144 D 0.1599 0.0994 0.7407 145 E 0.0112 0.7511 0.2378 146 H 0.0096 0.8540 0.1365 147 V 0.0086 0.9142 0.0771 148 A 0.0084 0.9197 0.0719 149 R 0.0084 0.9200 0.0716 150 V 0.0096 0.9188 0.0716 151 L 0.0124 0.9100 0.0777 152 Y 0.0242 0.8765 0.0993 153 L 0.0617 0.7959 0.1424 154 G 0.1315 0.6597 0.2088 155 I 0.2050 0.5246 0.2704 156 V 0.2621 0.3743 0.3637 157 G 0.2565 0.2611 0.4824 158 D 0.1938 0.2169 0.5893 159 T 0.1396 0.1953 0.6650 160 G 0.1357 0.1641 0.7002 161 R 0.2468 0.1752 0.5780 162 F 0.3606 0.1299 0.5094 163 L 0.3651 0.1217 0.5132 164 F 0.3114 0.1020 0.5866 165 S 0.1860 0.2388 0.5751 166 N 0.1683 0.1616 0.6701 167 T 0.2152 0.0982 0.6867 168 S 0.1950 0.0452 0.7598 169 P 0.0628 0.5089 0.4284 170 H 0.0500 0.6226 0.3274 171 T 0.0628 0.7023 0.2349 172 M 0.0330 0.8237 0.1433 173 E 0.0284 0.8693 0.1023 174 V 0.0227 0.8793 0.0980 175 A 0.0116 0.8996 0.0888 176 S 0.0091 0.9075 0.0835 177 Q 0.0093 0.8955 0.0952 178 L 0.0109 0.8645 0.1246 179 L 0.0166 0.7226 0.2608 180 A 0.0282 0.5499 0.4219 181 Y 0.1165 0.2189 0.6646 182 P 0.1079 0.2036 0.6885 183 F 0.1379 0.2213 0.6408 184 N 0.1554 0.1293 0.7152 185 H 0.0331 0.6625 0.3044 186 N 0.0215 0.7930 0.1855 187 A 0.0149 0.8690 0.1160 188 E 0.0135 0.8825 0.1039 189 L 0.0121 0.8944 0.0935 190 N 0.0125 0.8842 0.1033 191 K 0.0180 0.8264 0.1557 192 M 0.0384 0.6785 0.2830 193 S 0.0677 0.4661 0.4662 194 E 0.0577 0.3792 0.5631 195 K 0.0846 0.2108 0.7046 196 D 0.1605 0.1141 0.7254 197 P 0.0133 0.6692 0.3175 198 K 0.0137 0.6590 0.3273 199 L 0.0251 0.6558 0.3191 200 M 0.0323 0.6912 0.2765 201 P 0.0193 0.7972 0.1835 202 F 0.0161 0.8330 0.1509 203 Q 0.0120 0.8621 0.1259 204 G 0.0093 0.8972 0.0935 205 Y 0.0092 0.9100 0.0807 206 V 0.0116 0.8973 0.0911 207 L 0.0157 0.8595 0.1248 208 Q 0.0180 0.7972 0.1848 209 N 0.0492 0.5523 0.3984 210 F 0.1103 0.4753 0.4144 211 E 0.1475 0.4873 0.3652 212 L 0.2253 0.4443 0.3304 213 S 0.2431 0.3402 0.4166 214 D 0.1892 0.3262 0.4846 215 S 0.1254 0.3412 0.5334 216 H 0.1382 0.2895 0.5723 217 E 0.2558 0.2491 0.4950 218 Y 0.4395 0.2106 0.3499 219 C 0.5870 0.1642 0.2488 220 Q 0.6844 0.1198 0.1958 221 I 0.7283 0.0791 0.1926 222 K 0.7023 0.0966 0.2011 223 I 0.6567 0.0991 0.2442 224 T 0.4699 0.1946 0.3355 225 N 0.2948 0.3527 0.3525 226 D 0.2273 0.4589 0.3138 227 V 0.2411 0.4987 0.2602 228 L 0.1917 0.5175 0.2908 229 K 0.1732 0.5020 0.3248 230 Q 0.1696 0.3849 0.4455 231 F 0.1653 0.2777 0.5570 232 D 0.1668 0.1639 0.6693 233 I 0.2131 0.1370 0.6499 234 Q 0.1998 0.0517 0.7485 235 P 0.0663 0.4281 0.5056 236 N 0.0465 0.5141 0.4394 237 E 0.0729 0.6329 0.2942 238 A 0.0578 0.7514 0.1908 239 S 0.0272 0.8615 0.1114 240 Q 0.0264 0.8825 0.0911 241 F 0.0219 0.8909 0.0871 242 V 0.0147 0.8987 0.0867 243 N 0.0122 0.8960 0.0918 244 T 0.0136 0.8879 0.0985 245 V 0.0163 0.8691 0.1146 246 A 0.0210 0.8213 0.1577 247 D 0.0305 0.7371 0.2324 248 I 0.0500 0.6597 0.2903 249 S 0.0701 0.1917 0.7382 250 G 0.0495 0.0825 0.8681 251 L 0.2316 0.0171 0.7513 252 K 0.4897 0.0278 0.4825 253 I 0.7907 0.0061 0.2032 254 W 0.8039 0.0055 0.1906 255 M 0.8212 0.0043 0.1746 256 F 0.8188 0.0049 0.1763 257 G 0.7730 0.0068 0.2202 258 V 0.6988 0.0152 0.2860 259 D 0.4600 0.0361 0.5039 260 E 0.1987 0.0976 0.7038 261 G 0.1131 0.0731 0.8137 262 D 0.1990 0.0688 0.7322 263 Q 0.6161 0.0152 0.3688 264 I 0.7466 0.0087 0.2447 265 R 0.8113 0.0054 0.1832 266 C 0.8172 0.0046 0.1783 267 R 0.8061 0.0059 0.1880 268 I 0.7773 0.0086 0.2141 269 R 0.6678 0.0272 0.3051 270 S 0.4082 0.0468 0.5450 271 K 0.1373 0.1691 0.6936 272 G 0.0872 0.1028 0.8100 273 I 0.2293 0.0634 0.7073 274 T 0.2383 0.0409 0.7208 275 I 0.0320 0.6765 0.2915 276 N 0.0119 0.8355 0.1526 277 D 0.0104 0.9021 0.0876 278 V 0.0115 0.8998 0.0887 279 A 0.0120 0.8861 0.1019 280 N 0.0114 0.8551 0.1335 281 Q 0.0159 0.7839 0.2001 282 F 0.0673 0.4348 0.4979 283 G 0.0686 0.2601 0.6712 284 G 0.0908 0.1975 0.7117 285 G 0.1100 0.2020 0.6880 286 G 0.1548 0.1877 0.6574 287 H 0.1933 0.1715 0.6353 288 P 0.0603 0.5359 0.4038 289 N 0.0922 0.3905 0.5173 290 A 0.1929 0.2910 0.5162 291 S 0.2387 0.1694 0.5919 292 G 0.3666 0.1164 0.5171 293 V 0.4765 0.0621 0.4614 294 S 0.5273 0.0493 0.4234 295 V 0.4199 0.0597 0.5204 296 Y 0.2437 0.0875 0.6688 297 S 0.1901 0.0457 0.7642 298 W 0.0281 0.6562 0.3156 299 D 0.0134 0.8104 0.1762 300 E 0.0119 0.8749 0.1132 301 F 0.0087 0.9020 0.0892 302 E 0.0085 0.9170 0.0745 303 E 0.0083 0.9193 0.0724 304 L 0.0084 0.9182 0.0734 305 A 0.0083 0.9229 0.0688 306 Q 0.0083 0.9239 0.0678 307 A 0.0083 0.9225 0.0692 308 L 0.0084 0.9151 0.0765 309 R 0.0085 0.9038 0.0876 310 Q 0.0095 0.8844 0.1060 311 K 0.0211 0.7569 0.2220 312 L 0.0464 0.6283 0.3253 313 L 0.0606 0.5486 0.3908 314 E 0.1169 0.4664 0.4166 315 H 0.1882 0.3285 0.4833 316 H 0.2139 0.2818 0.5043 317 H 0.2209 0.2537 0.5253 318 H 0.1851 0.1935 0.6214 319 H 0.1505 0.2242 0.6253 320 H 0.1780 0.1843 0.6377