# This file is the result of combining several RDB files, specifically # T0628.t04.str2.rdb (weight 1.54425) # T0628.t04.str4.rdb (weight 0.924988) # T0628.t04.pb.rdb (weight 0.789901) # T0628.t04.bys.rdb (weight 0.748322) # T0628.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 T0628.t04.str2.rdb # ============================================ # TARGET T0628 # 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 T0628.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 41.7256 # # ============================================ # Comments from T0628.t04.str4.rdb # ============================================ # TARGET T0628 # 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 T0628.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 41.7256 # # ============================================ # Comments from T0628.t04.pb.rdb # ============================================ # TARGET T0628 # 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 T0628.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 41.7256 # # ============================================ # Comments from T0628.t04.bys.rdb # ============================================ # TARGET T0628 # 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 T0628.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 41.7256 # # ============================================ # Comments from T0628.t04.alpha.rdb # ============================================ # TARGET T0628 # 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 T0628.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 41.7256 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1464 0.2535 0.6000 2 N 0.1383 0.2968 0.5649 3 A 0.1733 0.3176 0.5091 4 M 0.2301 0.2466 0.5233 5 T 0.2943 0.1401 0.5656 6 A 0.3351 0.1870 0.4780 7 R 0.4808 0.1369 0.3822 8 Y 0.7412 0.0320 0.2268 9 I 0.7732 0.0178 0.2090 10 A 0.7860 0.0107 0.2034 11 I 0.7387 0.0233 0.2379 12 D 0.5198 0.0391 0.4411 13 W 0.2610 0.1738 0.5653 14 G 0.1788 0.1546 0.6666 15 S 0.2041 0.1870 0.6090 16 T 0.2157 0.2098 0.5745 17 N 0.3195 0.1639 0.5166 18 L 0.5519 0.1230 0.3251 19 R 0.6979 0.0817 0.2204 20 A 0.7694 0.0309 0.1998 21 W 0.7943 0.0214 0.1843 22 L 0.7698 0.0220 0.2083 23 Y 0.6644 0.0588 0.2768 24 Q 0.3664 0.0779 0.5557 25 G 0.1273 0.1176 0.7551 26 E 0.1308 0.1743 0.6949 27 E 0.2834 0.2068 0.5098 28 C 0.3044 0.3698 0.3259 29 L 0.1938 0.5364 0.2698 30 E 0.1721 0.6015 0.2264 31 S 0.1572 0.5796 0.2631 32 R 0.1661 0.5118 0.3221 33 Q 0.1880 0.3285 0.4836 34 S 0.1538 0.2886 0.5576 35 E 0.0793 0.4470 0.4737 36 A 0.0982 0.3303 0.5715 37 G 0.1385 0.2390 0.6225 38 V 0.2570 0.2839 0.4591 39 T 0.3418 0.2740 0.3842 40 R 0.3472 0.2415 0.4113 41 L 0.2407 0.2423 0.5170 42 N 0.1618 0.1818 0.6563 43 G 0.0910 0.2196 0.6895 44 R 0.1059 0.1723 0.7218 45 S 0.1709 0.0987 0.7304 46 P 0.0401 0.5759 0.3840 47 A 0.0134 0.8269 0.1597 48 A 0.0101 0.9078 0.0820 49 V 0.0097 0.9130 0.0773 50 L 0.0090 0.9075 0.0834 51 A 0.0088 0.9116 0.0796 52 E 0.0088 0.9037 0.0875 53 I 0.0110 0.8748 0.1142 54 T 0.0154 0.8192 0.1654 55 Q 0.0163 0.7930 0.1907 56 H 0.0269 0.6970 0.2762 57 W 0.0511 0.5949 0.3540 58 R 0.0761 0.4408 0.4831 59 D 0.0863 0.3130 0.6007 60 G 0.0690 0.2203 0.7106 61 A 0.1311 0.1454 0.7235 62 T 0.2847 0.0488 0.6665 63 P 0.4214 0.0553 0.5233 64 V 0.7621 0.0186 0.2193 65 V 0.7638 0.0207 0.2154 66 M 0.7383 0.0355 0.2262 67 A 0.5573 0.0740 0.3687 68 G 0.3445 0.0968 0.5587 69 M 0.2454 0.1877 0.5669 70 V 0.2205 0.1993 0.5803 71 G 0.1942 0.1632 0.6426 72 S 0.1394 0.3023 0.5583 73 N 0.1281 0.3147 0.5572 74 V 0.1951 0.2091 0.5959 75 G 0.2603 0.1426 0.5972 76 W 0.4594 0.1532 0.3874 77 K 0.5885 0.1001 0.3114 78 I 0.6087 0.0708 0.3205 79 A 0.5018 0.0541 0.4441 80 P 0.2950 0.1201 0.5849 81 Y 0.2778 0.1515 0.5707 82 L 0.2972 0.0754 0.6274 83 P 0.2694 0.0816 0.6489 84 L 0.3020 0.0472 0.6507 85 P 0.2255 0.0653 0.7092 86 A 0.2390 0.1669 0.5941 87 A 0.1644 0.1328 0.7028 88 F 0.0413 0.6426 0.3161 89 S 0.0173 0.7891 0.1936 90 D 0.0169 0.8391 0.1439 91 I 0.0178 0.8325 0.1497 92 G 0.0196 0.8066 0.1738 93 Q 0.0174 0.7745 0.2080 94 Q 0.0362 0.6762 0.2876 95 L 0.0975 0.5074 0.3951 96 T 0.1887 0.3342 0.4771 97 A 0.2113 0.2283 0.5604 98 V 0.1841 0.1504 0.6655 99 G 0.1481 0.0878 0.7641 100 D 0.2448 0.0891 0.6661 101 N 0.3942 0.0500 0.5558 102 I 0.6572 0.0205 0.3222 103 W 0.7310 0.0130 0.2559 104 I 0.7486 0.0105 0.2408 105 I 0.6051 0.0174 0.3775 106 P 0.3874 0.0668 0.5458 107 G 0.2580 0.0949 0.6471 108 L 0.3853 0.0744 0.5403 109 C 0.3943 0.0772 0.5285 110 V 0.3790 0.1346 0.4864 111 S 0.2432 0.1600 0.5968 112 R 0.1952 0.1917 0.6131 113 D 0.1404 0.2202 0.6394 114 D 0.1628 0.1868 0.6504 115 N 0.1694 0.2114 0.6191 116 H 0.1253 0.3651 0.5097 117 N 0.1639 0.3424 0.4937 118 V 0.2531 0.2803 0.4665 119 M 0.2681 0.2580 0.4739 120 R 0.2117 0.2819 0.5064 121 G 0.1571 0.3589 0.4840 122 E 0.1895 0.5447 0.2658 123 E 0.1881 0.6257 0.1863 124 T 0.1895 0.6384 0.1720 125 Q 0.1536 0.7005 0.1458 126 L 0.0981 0.7654 0.1365 127 L 0.0549 0.7929 0.1523 128 G 0.0804 0.7113 0.2082 129 A 0.0311 0.8264 0.1425 130 R 0.0447 0.7724 0.1829 131 A 0.0740 0.5933 0.3327 132 L 0.1254 0.3371 0.5375 133 A 0.1972 0.0875 0.7153 134 P 0.1426 0.1720 0.6854 135 S 0.1515 0.1411 0.7074 136 S 0.3931 0.0509 0.5560 137 V 0.7116 0.0135 0.2749 138 Y 0.7886 0.0061 0.2053 139 V 0.7634 0.0096 0.2270 140 M 0.4911 0.0129 0.4960 141 P 0.3007 0.0729 0.6264 142 G 0.2009 0.0828 0.7163 143 T 0.2309 0.1295 0.6396 144 H 0.3284 0.1098 0.5618 145 C 0.5196 0.0825 0.3980 146 K 0.6585 0.0791 0.2623 147 W 0.7822 0.0199 0.1979 148 V 0.7973 0.0128 0.1899 149 L 0.7789 0.0098 0.2113 150 A 0.7093 0.0531 0.2376 151 D 0.5436 0.1071 0.3492 152 R 0.1805 0.1756 0.6439 153 R 0.1686 0.1320 0.6994 154 Q 0.4691 0.0619 0.4690 155 I 0.5867 0.0690 0.3444 156 H 0.5151 0.1235 0.3613 157 D 0.5208 0.1681 0.3111 158 F 0.4354 0.2670 0.2975 159 R 0.3857 0.3702 0.2441 160 T 0.2649 0.5209 0.2142 161 V 0.1249 0.6970 0.1781 162 L 0.0972 0.6869 0.2159 163 T 0.0244 0.8319 0.1437 164 G 0.0130 0.8919 0.0951 165 E 0.0090 0.9166 0.0744 166 L 0.0085 0.9214 0.0701 167 H 0.0083 0.9215 0.0701 168 H 0.0083 0.9188 0.0729 169 L 0.0084 0.9150 0.0766 170 L 0.0089 0.8978 0.0933 171 L 0.0107 0.8459 0.1434 172 Q 0.0169 0.7030 0.2801 173 L 0.0536 0.5525 0.3938 174 S 0.0979 0.5438 0.3583 175 L 0.1083 0.5800 0.3117 176 V 0.1385 0.4959 0.3656 177 G 0.1406 0.4054 0.4540 178 A 0.1585 0.2702 0.5712 179 G 0.1609 0.1348 0.7043 180 L 0.2188 0.0421 0.7392 181 P 0.1636 0.0291 0.8073 182 P 0.0967 0.3392 0.5641 183 Q 0.0763 0.3680 0.5557 184 E 0.1048 0.3716 0.5236 185 T 0.1296 0.2960 0.5744 186 S 0.1396 0.2640 0.5964 187 A 0.0107 0.7736 0.2157 188 A 0.0095 0.8649 0.1257 189 A 0.0088 0.9154 0.0758 190 F 0.0086 0.9160 0.0754 191 A 0.0086 0.9112 0.0802 192 A 0.0085 0.9056 0.0859 193 G 0.0093 0.9019 0.0888 194 L 0.0089 0.9086 0.0824 195 Q 0.0098 0.8988 0.0915 196 R 0.0132 0.8545 0.1323 197 G 0.0208 0.7748 0.2044 198 I 0.0338 0.6177 0.3485 199 N 0.0600 0.3905 0.5495 200 N 0.1430 0.1928 0.6642 201 P 0.0269 0.5480 0.4251 202 A 0.0274 0.5772 0.3954 203 V 0.0450 0.5830 0.3721 204 L 0.0454 0.6084 0.3461 205 P 0.0188 0.7757 0.2055 206 Q 0.0137 0.8482 0.1382 207 L 0.0188 0.8639 0.1174 208 F 0.0251 0.8664 0.1085 209 E 0.0247 0.8826 0.0927 210 V 0.0247 0.8872 0.0881 211 R 0.0342 0.8628 0.1030 212 A 0.0170 0.8801 0.1029 213 S 0.0143 0.8810 0.1047 214 H 0.0167 0.8585 0.1247 215 V 0.0259 0.7683 0.2058 216 L 0.0589 0.5747 0.3664 217 G 0.0519 0.2984 0.6498 218 A 0.0958 0.2041 0.7001 219 L 0.1925 0.0553 0.7522 220 P 0.1531 0.0395 0.8073 221 R 0.0158 0.7033 0.2809 222 E 0.0101 0.8372 0.1526 223 Q 0.0101 0.8973 0.0926 224 V 0.0092 0.8961 0.0946 225 S 0.0093 0.8889 0.1018 226 E 0.0088 0.8897 0.1015 227 F 0.0098 0.8798 0.1104 228 L 0.0143 0.8279 0.1578 229 S 0.0121 0.8393 0.1486 230 G 0.0180 0.8304 0.1516 231 L 0.0193 0.8817 0.0989 232 L 0.0320 0.8500 0.1181 233 I 0.0298 0.8443 0.1259 234 G 0.0208 0.8507 0.1285 235 A 0.0147 0.8923 0.0930 236 E 0.0137 0.8996 0.0867 237 V 0.0105 0.8932 0.0963 238 A 0.0103 0.8843 0.1054 239 T 0.0119 0.8401 0.1480 240 L 0.0228 0.7661 0.2110 241 S 0.0372 0.6853 0.2775 242 D 0.0311 0.6802 0.2887 243 T 0.0451 0.6164 0.3385 244 F 0.0909 0.4434 0.4657 245 A 0.0944 0.2565 0.6491 246 G 0.0754 0.1276 0.7970 247 Q 0.1824 0.0986 0.7190 248 Q 0.3067 0.0561 0.6372 249 A 0.5719 0.0359 0.3922 250 I 0.7674 0.0086 0.2241 251 S 0.8044 0.0055 0.1900 252 L 0.8030 0.0063 0.1907 253 V 0.7402 0.0203 0.2395 254 A 0.4779 0.0390 0.4831 255 G 0.1907 0.1337 0.6756 256 S 0.0694 0.4001 0.5304 257 S 0.0331 0.5912 0.3758 258 L 0.0192 0.7224 0.2584 259 T 0.0102 0.8589 0.1309 260 S 0.0085 0.9068 0.0847 261 R 0.0084 0.9153 0.0763 262 Y 0.0084 0.9204 0.0712 263 Q 0.0083 0.9228 0.0689 264 Q 0.0083 0.9236 0.0681 265 A 0.0083 0.9215 0.0701 266 F 0.0084 0.9166 0.0750 267 A 0.0089 0.8927 0.0984 268 A 0.0133 0.8018 0.1848 269 I 0.0559 0.2944 0.6497 270 G 0.0490 0.0916 0.8594 271 R 0.1883 0.0447 0.7670 272 E 0.2721 0.0607 0.6672 273 V 0.4507 0.1208 0.4285 274 S 0.5063 0.1015 0.3922 275 A 0.5409 0.0801 0.3789 276 V 0.3773 0.0766 0.5461 277 A 0.1879 0.1178 0.6943 278 G 0.0611 0.4810 0.4579 279 D 0.0261 0.7227 0.2512 280 T 0.0154 0.8512 0.1334 281 A 0.0133 0.8837 0.1030 282 F 0.0096 0.9005 0.0899 283 Q 0.0093 0.8899 0.1008 284 T 0.0096 0.9055 0.0849 285 G 0.0110 0.8988 0.0902 286 I 0.0084 0.9183 0.0733 287 R 0.0084 0.9226 0.0690 288 S 0.0084 0.9214 0.0703 289 I 0.0084 0.9193 0.0724 290 A 0.0084 0.9144 0.0772 291 Y 0.0087 0.9047 0.0866 292 A 0.0110 0.8637 0.1253 293 V 0.0294 0.6644 0.3061 294 A 0.0463 0.4385 0.5152 295 N 0.0689 0.2740 0.6571