# This file is the result of combining several RDB files, specifically # T0489.t04.str2.rdb (weight 1.54425) # T0489.t04.str4.rdb (weight 0.924988) # T0489.t04.pb.rdb (weight 0.789901) # T0489.t04.bys.rdb (weight 0.748322) # T0489.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 T0489.t04.str2.rdb # ============================================ # TARGET T0489 # 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 T0489.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 48.6216 # # ============================================ # Comments from T0489.t04.str4.rdb # ============================================ # TARGET T0489 # 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 T0489.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 48.6216 # # ============================================ # Comments from T0489.t04.pb.rdb # ============================================ # TARGET T0489 # 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 T0489.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 48.6216 # # ============================================ # Comments from T0489.t04.bys.rdb # ============================================ # TARGET T0489 # 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 T0489.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 48.6216 # # ============================================ # Comments from T0489.t04.alpha.rdb # ============================================ # TARGET T0489 # 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 T0489.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 48.6216 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3263 0.1700 0.5036 2 M 0.3616 0.1499 0.4885 3 F 0.3844 0.1284 0.4872 4 K 0.3387 0.1378 0.5235 5 W 0.2955 0.0896 0.6149 6 P 0.1926 0.3062 0.5012 7 W 0.1830 0.4371 0.3799 8 K 0.2104 0.3938 0.3958 9 A 0.2279 0.3628 0.4093 10 D 0.1703 0.3667 0.4630 11 D 0.1066 0.4907 0.4027 12 E 0.0842 0.5174 0.3984 13 S 0.1003 0.3711 0.5286 14 G 0.1057 0.2095 0.6848 15 N 0.1294 0.1543 0.7164 16 A 0.1946 0.0979 0.7075 17 E 0.1845 0.1113 0.7043 18 M 0.2097 0.1598 0.6304 19 P 0.1227 0.2816 0.5957 20 W 0.0246 0.7447 0.2308 21 E 0.0148 0.8382 0.1470 22 Q 0.0152 0.8539 0.1308 23 A 0.0271 0.7736 0.1994 24 L 0.0602 0.6366 0.3032 25 A 0.0822 0.4887 0.4292 26 I 0.1685 0.3202 0.5113 27 P 0.1287 0.4012 0.4702 28 V 0.0840 0.6736 0.2424 29 L 0.0858 0.6761 0.2381 30 A 0.0708 0.6390 0.2902 31 H 0.0984 0.3319 0.5697 32 L 0.1817 0.1331 0.6852 33 S 0.1552 0.0440 0.8009 34 S 0.0171 0.6860 0.2969 35 T 0.0105 0.8187 0.1708 36 E 0.0101 0.8875 0.1024 37 Q 0.0090 0.9117 0.0793 38 H 0.0091 0.9155 0.0754 39 K 0.0089 0.9162 0.0748 40 L 0.0085 0.9192 0.0724 41 T 0.0083 0.9228 0.0689 42 Q 0.0083 0.9243 0.0674 43 M 0.0083 0.9245 0.0673 44 A 0.0083 0.9235 0.0682 45 A 0.0083 0.9247 0.0671 46 R 0.0094 0.9202 0.0705 47 F 0.0084 0.9140 0.0776 48 L 0.0098 0.8992 0.0910 49 Q 0.0122 0.8667 0.1212 50 Q 0.0311 0.7120 0.2569 51 K 0.0873 0.5184 0.3943 52 R 0.1754 0.3776 0.4470 53 L 0.3243 0.2617 0.4140 54 V 0.4082 0.1892 0.4026 55 A 0.4235 0.1540 0.4225 56 L 0.3219 0.1826 0.4955 57 Q 0.1561 0.1472 0.6968 58 G 0.1047 0.0890 0.8063 59 L 0.3571 0.0307 0.6122 60 E 0.5446 0.0296 0.4258 61 L 0.4659 0.0537 0.4803 62 T 0.2362 0.0476 0.7162 63 P 0.0257 0.6775 0.2968 64 L 0.0139 0.8034 0.1827 65 H 0.0237 0.8620 0.1143 66 Q 0.0280 0.8795 0.0924 67 A 0.0314 0.8874 0.0812 68 R 0.0344 0.8890 0.0766 69 I 0.0313 0.8931 0.0756 70 A 0.0209 0.9049 0.0742 71 M 0.0312 0.8863 0.0824 72 L 0.0329 0.8710 0.0961 73 F 0.0576 0.8041 0.1383 74 C 0.0683 0.7357 0.1961 75 L 0.0928 0.7180 0.1892 76 P 0.0439 0.7838 0.1723 77 V 0.0810 0.7167 0.2023 78 L 0.0853 0.6795 0.2352 79 E 0.0952 0.5505 0.3543 80 L 0.1119 0.3410 0.5471 81 G 0.1038 0.2464 0.6498 82 I 0.1046 0.4355 0.4599 83 E 0.1166 0.5206 0.3628 84 W 0.1531 0.4867 0.3602 85 L 0.1820 0.3395 0.4785 86 D 0.1245 0.2463 0.6292 87 G 0.0841 0.1419 0.7740 88 F 0.2948 0.0620 0.6432 89 H 0.4269 0.0686 0.5046 90 E 0.7390 0.0110 0.2499 91 V 0.7636 0.0069 0.2295 92 L 0.8011 0.0053 0.1937 93 I 0.7890 0.0077 0.2033 94 Y 0.6127 0.0099 0.3774 95 P 0.3589 0.0408 0.6003 96 A 0.2358 0.0425 0.7217 97 P 0.2205 0.1763 0.6033 98 F 0.3672 0.1135 0.5193 99 I 0.4820 0.0682 0.4498 100 V 0.4442 0.0580 0.4978 101 D 0.2922 0.1050 0.6028 102 D 0.1885 0.2615 0.5500 103 E 0.2455 0.2768 0.4777 104 W 0.3063 0.2643 0.4294 105 E 0.3068 0.2498 0.4434 106 D 0.2313 0.2568 0.5119 107 D 0.1323 0.3412 0.5265 108 I 0.1440 0.1838 0.6723 109 G 0.2111 0.1050 0.6839 110 L 0.4729 0.0657 0.4614 111 V 0.5875 0.0693 0.3433 112 H 0.5451 0.0840 0.3710 113 N 0.4276 0.1643 0.4081 114 Q 0.3433 0.2513 0.4054 115 R 0.3641 0.2777 0.3582 116 V 0.4199 0.2645 0.3156 117 V 0.4030 0.2878 0.3092 118 Q 0.3578 0.2755 0.3668 119 S 0.2753 0.2076 0.5171 120 G 0.2245 0.1726 0.6028 121 Q 0.3483 0.2182 0.4335 122 S 0.4000 0.2088 0.3912 123 W 0.3080 0.2395 0.4524 124 Q 0.2049 0.2870 0.5080 125 Q 0.2088 0.1274 0.6638 126 G 0.2622 0.0401 0.6977 127 P 0.3974 0.0379 0.5647 128 V 0.7604 0.0127 0.2269 129 V 0.7674 0.0089 0.2237 130 L 0.7358 0.0151 0.2491 131 N 0.4194 0.0161 0.5645 132 W 0.1503 0.3776 0.4720 133 L 0.0818 0.5936 0.3247 134 D 0.0698 0.6717 0.2586 135 I 0.0489 0.7054 0.2457 136 Q 0.0524 0.6692 0.2784 137 D 0.0600 0.4955 0.4446 138 S 0.0881 0.3081 0.6037 139 F 0.1617 0.1739 0.6645 140 D 0.1602 0.1366 0.7031 141 A 0.0753 0.3503 0.5744 142 S 0.0821 0.2287 0.6893 143 G 0.0890 0.1523 0.7587 144 F 0.2357 0.1521 0.6122 145 N 0.3836 0.2083 0.4081 146 L 0.5723 0.1804 0.2473 147 V 0.6175 0.1665 0.2160 148 V 0.4876 0.3126 0.1998 149 H 0.2355 0.6005 0.1640 150 E 0.1040 0.7641 0.1319 151 V 0.0617 0.8022 0.1361 152 A 0.0376 0.7894 0.1730 153 H 0.0388 0.7606 0.2006 154 K 0.0519 0.7194 0.2287 155 L 0.0990 0.6142 0.2867 156 D 0.1239 0.4883 0.3878 157 T 0.0684 0.5749 0.3567 158 R 0.0866 0.4466 0.4668 159 N 0.0945 0.1829 0.7226 160 G 0.0837 0.1395 0.7768 161 D 0.1625 0.1863 0.6512 162 R 0.2102 0.2214 0.5685 163 A 0.1940 0.2545 0.5515 164 S 0.1349 0.1556 0.7095 165 G 0.1090 0.0911 0.7998 166 V 0.2495 0.0379 0.7126 167 P 0.2685 0.0472 0.6842 168 L 0.2842 0.1087 0.6071 169 I 0.2640 0.0562 0.6798 170 P 0.1765 0.1081 0.7154 171 L 0.1085 0.3110 0.5805 172 R 0.1124 0.3847 0.5029 173 E 0.1311 0.3837 0.4852 174 V 0.0680 0.6252 0.3068 175 A 0.0475 0.7064 0.2461 176 G 0.0322 0.7734 0.1943 177 W 0.0195 0.8500 0.1305 178 E 0.0100 0.8961 0.0939 179 H 0.0088 0.9143 0.0770 180 D 0.0090 0.9135 0.0774 181 L 0.0085 0.9144 0.0771 182 H 0.0085 0.9196 0.0719 183 A 0.0083 0.9214 0.0703 184 A 0.0084 0.9184 0.0732 185 M 0.0085 0.9140 0.0775 186 N 0.0087 0.9039 0.0874 187 N 0.0094 0.8793 0.1113 188 I 0.0106 0.8866 0.1028 189 Q 0.0097 0.8868 0.1035 190 D 0.0099 0.8777 0.1124 191 E 0.0142 0.8520 0.1338 192 I 0.0259 0.8116 0.1624 193 D 0.0349 0.7597 0.2053 194 L 0.0619 0.6237 0.3145 195 V 0.1007 0.3126 0.5867 196 G 0.0727 0.2119 0.7154 197 E 0.1153 0.2318 0.6529 198 S 0.1763 0.2059 0.6178 199 A 0.1598 0.3467 0.4935 200 A 0.1823 0.3552 0.4625 201 S 0.2439 0.3189 0.4372 202 I 0.3167 0.2476 0.4357 203 D 0.2573 0.2083 0.5344 204 A 0.0502 0.6331 0.3167 205 Y 0.0519 0.5740 0.3741 206 A 0.1083 0.5358 0.3559 207 A 0.1444 0.4224 0.4332 208 T 0.2168 0.2306 0.5526 209 D 0.2039 0.0691 0.7270 210 P 0.0271 0.5225 0.4504 211 A 0.0325 0.7043 0.2632 212 E 0.0430 0.8005 0.1566 213 C 0.0838 0.7586 0.1577 214 F 0.0824 0.7845 0.1331 215 A 0.1461 0.7352 0.1186 216 V 0.1291 0.7669 0.1041 217 L 0.1190 0.7595 0.1215 218 S 0.0929 0.7769 0.1302 219 E 0.0949 0.7728 0.1323 220 Y 0.1154 0.7064 0.1782 221 F 0.1368 0.5796 0.2836 222 F 0.1558 0.4528 0.3914 223 S 0.1802 0.2570 0.5628 224 A 0.1611 0.1470 0.6919 225 P 0.0603 0.4433 0.4964 226 E 0.0228 0.6731 0.3041 227 L 0.0224 0.7302 0.2475 228 F 0.0404 0.5944 0.3652 229 A 0.0510 0.5206 0.4284 230 P 0.0186 0.6141 0.3673 231 R 0.0264 0.5286 0.4450 232 F 0.0560 0.4789 0.4651 233 P 0.0102 0.8631 0.1267 234 A 0.0084 0.9171 0.0745 235 L 0.0084 0.9207 0.0709 236 W 0.0083 0.9233 0.0684 237 Q 0.0083 0.9231 0.0686 238 R 0.0085 0.9187 0.0728 239 F 0.0088 0.9139 0.0773 240 C 0.0088 0.9093 0.0819 241 H 0.0105 0.8900 0.0995 242 F 0.0171 0.8208 0.1621 243 Y 0.0412 0.6995 0.2593 244 R 0.0495 0.5890 0.3614 245 Q 0.0911 0.4191 0.4898 246 D 0.1648 0.1316 0.7036 247 P 0.0171 0.6609 0.3219 248 L 0.0163 0.7667 0.2171 249 A 0.0241 0.8104 0.1655 250 R 0.0412 0.7568 0.2020 251 R 0.0709 0.6888 0.2402 252 R 0.0777 0.6387 0.2835 253 E 0.0593 0.6060 0.3348 254 N 0.0790 0.3761 0.5450 255 G 0.0880 0.2402 0.6718 256 L 0.1759 0.2020 0.6222 257 Q 0.2158 0.1823 0.6019 258 D 0.1813 0.1823 0.6364 259 E 0.1190 0.2875 0.5935 260 G 0.1205 0.2317 0.6478 261 D 0.1770 0.2184 0.6046 262 R 0.2227 0.2185 0.5588 263 R 0.2333 0.2389 0.5279 264 I 0.2663 0.1819 0.5518 265 V 0.2522 0.1617 0.5861 266 H 0.2206 0.1304 0.6490