# This file is the result of combining several RDB files, specifically # T0395.t04.str2.rdb (weight 1.54425) # T0395.t04.str4.rdb (weight 0.924988) # T0395.t04.pb.rdb (weight 0.789901) # T0395.t04.bys.rdb (weight 0.748322) # T0395.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 T0395.t04.str2.rdb # ============================================ # TARGET T0395 # 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 T0395.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 1828 # # ============================================ # Comments from T0395.t04.str4.rdb # ============================================ # TARGET T0395 # 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 T0395.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 1828 # # ============================================ # Comments from T0395.t04.pb.rdb # ============================================ # TARGET T0395 # 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 T0395.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 1828 # # ============================================ # Comments from T0395.t04.bys.rdb # ============================================ # TARGET T0395 # 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 T0395.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 1828 # # ============================================ # Comments from T0395.t04.alpha.rdb # ============================================ # TARGET T0395 # 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 T0395.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 1828 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3121 0.0814 0.6066 2 R 0.2285 0.0755 0.6960 3 L 0.1304 0.3507 0.5189 4 G 0.0691 0.3882 0.5427 5 D 0.1187 0.4138 0.4675 6 A 0.1981 0.3882 0.4137 7 A 0.2091 0.4288 0.3621 8 E 0.1285 0.5915 0.2800 9 L 0.1249 0.5999 0.2752 10 C 0.1510 0.5006 0.3485 11 Y 0.1413 0.4423 0.4164 12 N 0.1463 0.3526 0.5011 13 L 0.1312 0.3842 0.4846 14 T 0.1300 0.3677 0.5023 15 S 0.0831 0.4891 0.4278 16 S 0.0741 0.5163 0.4096 17 Y 0.0921 0.5672 0.3407 18 L 0.1202 0.5903 0.2895 19 Q 0.1084 0.6506 0.2410 20 I 0.1245 0.6343 0.2413 21 A 0.1178 0.6082 0.2740 22 A 0.1141 0.5606 0.3253 23 E 0.1233 0.4926 0.3841 24 S 0.0600 0.6716 0.2684 25 D 0.0221 0.8057 0.1722 26 S 0.0164 0.8580 0.1256 27 I 0.0112 0.8938 0.0949 28 I 0.0106 0.9092 0.0802 29 A 0.0100 0.9129 0.0770 30 Q 0.0110 0.9006 0.0884 31 T 0.0114 0.8955 0.0931 32 Q 0.0096 0.8976 0.0928 33 R 0.0101 0.8960 0.0939 34 A 0.0130 0.8748 0.1122 35 I 0.0163 0.8347 0.1490 36 N 0.0195 0.7948 0.1858 37 T 0.0334 0.7479 0.2187 38 T 0.0584 0.7178 0.2238 39 K 0.0136 0.8288 0.1575 40 S 0.0106 0.8854 0.1040 41 I 0.0093 0.9182 0.0724 42 L 0.0114 0.9126 0.0760 43 I 0.0103 0.9037 0.0860 44 N 0.0095 0.9031 0.0874 45 E 0.0113 0.8778 0.1109 46 T 0.0222 0.7843 0.1935 47 F 0.0378 0.6605 0.3016 48 P 0.0299 0.6206 0.3495 49 K 0.0564 0.4534 0.4903 50 W 0.1413 0.2196 0.6391 51 S 0.1777 0.1157 0.7066 52 P 0.1152 0.3027 0.5822 53 L 0.1116 0.2399 0.6485 54 N 0.0929 0.1113 0.7958 55 G 0.1281 0.0727 0.7992 56 E 0.3971 0.0192 0.5837 57 I 0.7263 0.0078 0.2659 58 S 0.7960 0.0066 0.1974 59 F 0.8131 0.0049 0.1820 60 S 0.7816 0.0081 0.2103 61 Y 0.6762 0.0218 0.3019 62 N 0.3747 0.0607 0.5646 63 G 0.1656 0.0948 0.7395 64 G 0.1226 0.1618 0.7157 65 K 0.0580 0.4946 0.4475 66 D 0.0341 0.7171 0.2488 67 C 0.0121 0.8843 0.1036 68 Q 0.0093 0.9064 0.0843 69 V 0.0083 0.9196 0.0721 70 L 0.0082 0.9252 0.0666 71 L 0.0082 0.9253 0.0664 72 L 0.0082 0.9253 0.0665 73 L 0.0082 0.9249 0.0668 74 Y 0.0083 0.9222 0.0695 75 L 0.0084 0.9183 0.0733 76 S 0.0088 0.9020 0.0892 77 C 0.0111 0.8435 0.1454 78 L 0.0184 0.7631 0.2186 79 W 0.0237 0.7591 0.2172 80 E 0.0366 0.6390 0.3244 81 Y 0.0903 0.4592 0.4506 82 Y 0.1030 0.3974 0.4996 83 I 0.1174 0.4780 0.4047 84 V 0.1849 0.4108 0.4042 85 K 0.2461 0.3440 0.4099 86 L 0.2643 0.2979 0.4378 87 S 0.2844 0.2569 0.4588 88 Q 0.2895 0.2536 0.4570 89 S 0.2951 0.2081 0.4968 90 Q 0.2421 0.1741 0.5837 91 F 0.1760 0.2637 0.5604 92 D 0.1546 0.1995 0.6459 93 G 0.0899 0.2738 0.6362 94 K 0.1546 0.2470 0.5984 95 F 0.2544 0.1449 0.6008 96 H 0.1714 0.2025 0.6261 97 R 0.1495 0.1578 0.6927 98 F 0.2346 0.0567 0.7087 99 P 0.2176 0.1159 0.6665 100 L 0.2516 0.1493 0.5991 101 T 0.3121 0.0752 0.6127 102 K 0.4060 0.0503 0.5437 103 L 0.4686 0.0179 0.5135 104 P 0.5527 0.0288 0.4185 105 T 0.7879 0.0071 0.2049 106 V 0.7994 0.0062 0.1944 107 F 0.7817 0.0057 0.2126 108 I 0.7343 0.0159 0.2498 109 D 0.4038 0.0307 0.5655 110 H 0.1632 0.1531 0.6837 111 D 0.0990 0.1820 0.7190 112 D 0.1183 0.2492 0.6325 113 T 0.1413 0.2809 0.5778 114 F 0.0959 0.4790 0.4251 115 K 0.0237 0.7888 0.1875 116 T 0.0202 0.8558 0.1240 117 L 0.0113 0.9057 0.0830 118 E 0.0086 0.9152 0.0762 119 N 0.0085 0.9215 0.0700 120 F 0.0090 0.9198 0.0712 121 I 0.0083 0.9224 0.0693 122 E 0.0083 0.9227 0.0690 123 E 0.0084 0.9224 0.0692 124 T 0.0086 0.9182 0.0732 125 S 0.0087 0.9086 0.0827 126 L 0.0098 0.8935 0.0967 127 R 0.0236 0.7432 0.2332 128 Y 0.0737 0.3134 0.6129 129 S 0.0763 0.0939 0.8299 130 L 0.2286 0.0319 0.7395 131 S 0.3006 0.0489 0.6505 132 L 0.4369 0.1206 0.4425 133 Y 0.4274 0.0935 0.4790 134 E 0.3231 0.0757 0.6012 135 S 0.2027 0.1006 0.6967 136 D 0.1506 0.1533 0.6961 137 R 0.0429 0.5373 0.4198 138 D 0.0306 0.7216 0.2478 139 K 0.0375 0.7556 0.2069 140 C 0.0310 0.8109 0.1581 141 E 0.0174 0.8554 0.1272 142 T 0.0175 0.8358 0.1467 143 M 0.0186 0.8305 0.1509 144 A 0.0137 0.8690 0.1172 145 E 0.0115 0.8874 0.1011 146 A 0.0104 0.8846 0.1050 147 F 0.0092 0.8969 0.0939 148 E 0.0086 0.9160 0.0754 149 T 0.0084 0.9152 0.0764 150 F 0.0093 0.8936 0.0971 151 L 0.0101 0.8748 0.1150 152 Q 0.0120 0.7885 0.1994 153 V 0.0321 0.6081 0.3598 154 F 0.1444 0.2230 0.6325 155 P 0.0384 0.4187 0.5429 156 E 0.0574 0.2152 0.7275 157 T 0.1928 0.1468 0.6605 158 K 0.3573 0.1429 0.4999 159 A 0.7577 0.0242 0.2181 160 I 0.7369 0.0251 0.2380 161 V 0.7787 0.0159 0.2054 162 I 0.7183 0.0375 0.2442 163 G 0.6079 0.0401 0.3520 164 I 0.4489 0.0804 0.4707 165 R 0.3074 0.1103 0.5823 166 H 0.2142 0.1932 0.5925 167 T 0.1481 0.1957 0.6562 168 D 0.1781 0.1714 0.6505 169 P 0.0816 0.4455 0.4729 170 F 0.0784 0.4993 0.4223 171 G 0.0920 0.5255 0.3825 172 E 0.1354 0.5149 0.3497 173 H 0.2117 0.3840 0.4044 174 L 0.2652 0.2174 0.5175 175 K 0.3217 0.0975 0.5808 176 P 0.2956 0.1460 0.5583 177 I 0.3026 0.2241 0.4733 178 Q 0.3338 0.2109 0.4553 179 K 0.2938 0.2155 0.4906 180 T 0.2168 0.1924 0.5908 181 D 0.1872 0.1405 0.6723 182 A 0.0778 0.3125 0.6097 183 N 0.0922 0.1902 0.7175 184 W 0.1939 0.1054 0.7007 185 P 0.1323 0.2098 0.6579 186 D 0.1082 0.2431 0.6487 187 F 0.2350 0.1592 0.6058 188 Y 0.4219 0.0914 0.4866 189 R 0.5876 0.0644 0.3480 190 L 0.5838 0.0633 0.3529 191 Q 0.4904 0.0597 0.4499 192 P 0.3332 0.2174 0.4494 193 L 0.1782 0.4263 0.3955 194 L 0.1769 0.3612 0.4620 195 H 0.1683 0.2441 0.5876 196 W 0.1901 0.2853 0.5246 197 N 0.1760 0.1379 0.6861 198 L 0.0138 0.7458 0.2405 199 A 0.0093 0.8691 0.1216 200 N 0.0089 0.9183 0.0728 201 I 0.0083 0.9233 0.0684 202 W 0.0083 0.9230 0.0687 203 S 0.0083 0.9243 0.0674 204 F 0.0083 0.9235 0.0682 205 L 0.0084 0.9196 0.0720 206 L 0.0091 0.8990 0.0919 207 Y 0.0149 0.8019 0.1832 208 S 0.0568 0.3165 0.6267 209 N 0.0474 0.0939 0.8587 210 E 0.1788 0.0305 0.7907 211 P 0.2112 0.0646 0.7242 212 I 0.3091 0.1547 0.5362 213 C 0.2787 0.1572 0.5642 214 E 0.1536 0.4829 0.3634 215 L 0.1102 0.5877 0.3021 216 Y 0.1254 0.5379 0.3366 217 R 0.1214 0.4125 0.4660 218 Y 0.1296 0.2140 0.6564 219 G 0.1024 0.1204 0.7772 220 F 0.2159 0.0962 0.6879 221 T 0.2712 0.1378 0.5910 222 S 0.3308 0.1159 0.5533 223 L 0.2648 0.1775 0.5578 224 G 0.2434 0.1234 0.6333 225 N 0.2664 0.1097 0.6239 226 V 0.2897 0.1477 0.5625 227 E 0.2595 0.2087 0.5318 228 E 0.2471 0.2089 0.5440 229 T 0.2752 0.1346 0.5902 230 L 0.2905 0.0627 0.6468 231 P 0.2518 0.0979 0.6504 232 N 0.2279 0.0624 0.7097 233 P 0.0649 0.4673 0.4678 234 H 0.1145 0.4138 0.4717 235 L 0.2550 0.2399 0.5051 236 R 0.2794 0.1332 0.5873 237 K 0.2339 0.2363 0.5298 238 D 0.1493 0.2053 0.6453 239 K 0.1189 0.2949 0.5862 240 N 0.1357 0.2033 0.6610 241 S 0.1814 0.1537 0.6649 242 T 0.2322 0.0703 0.6975 243 P 0.1809 0.2343 0.5848 244 L 0.1755 0.3831 0.4415 245 K 0.2097 0.3972 0.3931 246 L 0.2401 0.3535 0.4064 247 N 0.1685 0.3910 0.4405 248 F 0.1254 0.4250 0.4497 249 E 0.1385 0.5171 0.3444 250 W 0.1802 0.5602 0.2596 251 E 0.2070 0.5637 0.2292 252 I 0.2437 0.5227 0.2336 253 E 0.3009 0.3681 0.3310 254 N 0.2725 0.2441 0.4834 255 R 0.2808 0.1466 0.5726 256 Y 0.4024 0.0844 0.5132 257 K 0.4450 0.0798 0.4752 258 H 0.4280 0.1153 0.4567 259 N 0.3412 0.1553 0.5035 260 E 0.3193 0.1319 0.5488 261 V 0.2484 0.1925 0.5591 262 T 0.2070 0.1943 0.5987 263 K 0.2325 0.1445 0.6230 264 A 0.2854 0.0812 0.6334 265 E 0.2641 0.0537 0.6821 266 P 0.2259 0.1494 0.6246 267 I 0.2770 0.1035 0.6195 268 P 0.2592 0.1216 0.6192 269 I 0.2754 0.1796 0.5451 270 A 0.2209 0.1795 0.5996 271 D 0.1437 0.3468 0.5095 272 E 0.0814 0.4909 0.4277 273 D 0.0880 0.4648 0.4471 274 L 0.0826 0.5655 0.3520 275 V 0.0968 0.5576 0.3456 276 K 0.1231 0.5106 0.3663 277 I 0.0390 0.7340 0.2271 278 E 0.0173 0.8285 0.1542 279 N 0.0205 0.8426 0.1369 280 L 0.0372 0.8057 0.1571 281 H 0.0497 0.7483 0.2020 282 E 0.0537 0.7137 0.2326 283 D 0.1032 0.5146 0.3822 284 Y 0.1497 0.2739 0.5764 285 Y 0.1999 0.1155 0.6846 286 P 0.1584 0.2149 0.6267 287 G 0.2402 0.1623 0.5975 288 W 0.5209 0.0777 0.4014 289 Y 0.6285 0.0611 0.3104 290 L 0.6498 0.0652 0.2850 291 V 0.5622 0.0888 0.3490 292 D 0.3843 0.1293 0.4864 293 D 0.2150 0.3027 0.4822 294 K 0.2429 0.3938 0.3633 295 L 0.2398 0.4972 0.2630 296 E 0.1776 0.6075 0.2150 297 R 0.1953 0.5279 0.2767 298 A 0.2082 0.3903 0.4015 299 G 0.2421 0.2872 0.4707 300 R 0.3431 0.2879 0.3690 301 I 0.3129 0.3659 0.3213 302 K 0.2553 0.3500 0.3947 303 K 0.1913 0.2578 0.5509 304 K 0.1611 0.2242 0.6147