# This file is the result of combining several RDB files, specifically # T0421.t04.str2.rdb (weight 1.54425) # T0421.t04.str4.rdb (weight 0.924988) # T0421.t04.pb.rdb (weight 0.789901) # T0421.t04.bys.rdb (weight 0.748322) # T0421.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 T0421.t04.str2.rdb # ============================================ # TARGET T0421 # 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 T0421.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 1166 # # ============================================ # Comments from T0421.t04.str4.rdb # ============================================ # TARGET T0421 # 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 T0421.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 1166 # # ============================================ # Comments from T0421.t04.pb.rdb # ============================================ # TARGET T0421 # 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 T0421.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 1166 # # ============================================ # Comments from T0421.t04.bys.rdb # ============================================ # TARGET T0421 # 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 T0421.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 1166 # # ============================================ # Comments from T0421.t04.alpha.rdb # ============================================ # TARGET T0421 # 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 T0421.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 1166 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2120 0.2683 0.5197 2 A 0.2097 0.2315 0.5588 3 L 0.2063 0.2658 0.5279 4 D 0.1915 0.2160 0.5925 5 E 0.1851 0.2464 0.5685 6 A 0.2148 0.1210 0.6641 7 P 0.1448 0.3009 0.5543 8 A 0.1436 0.3751 0.4814 9 E 0.1721 0.3246 0.5033 10 A 0.2053 0.2255 0.5692 11 R 0.2162 0.1269 0.6570 12 P 0.1249 0.3085 0.5666 13 G 0.0738 0.3914 0.5348 14 S 0.0684 0.6057 0.3258 15 R 0.0594 0.7266 0.2140 16 A 0.0443 0.8070 0.1488 17 V 0.0306 0.8577 0.1117 18 E 0.0286 0.8700 0.1014 19 L 0.0306 0.8486 0.1208 20 E 0.0605 0.7517 0.1878 21 I 0.0745 0.6510 0.2744 22 D 0.0946 0.4184 0.4870 23 G 0.0858 0.3269 0.5873 24 R 0.1016 0.3825 0.5159 25 S 0.1183 0.4068 0.4749 26 R 0.1708 0.3068 0.5224 27 I 0.2301 0.2314 0.5385 28 F 0.2320 0.1905 0.5775 29 D 0.2143 0.1442 0.6416 30 I 0.1378 0.2890 0.5732 31 D 0.1274 0.1938 0.6788 32 D 0.1957 0.1150 0.6892 33 P 0.0387 0.4758 0.4854 34 D 0.0615 0.3369 0.6016 35 L 0.1571 0.2316 0.6113 36 P 0.1644 0.2310 0.6046 37 K 0.2663 0.2133 0.5204 38 W 0.3145 0.1297 0.5557 39 I 0.2792 0.0917 0.6292 40 D 0.1727 0.1897 0.6377 41 E 0.0793 0.4045 0.5162 42 E 0.0886 0.4389 0.4725 43 A 0.1544 0.4058 0.4398 44 F 0.2513 0.2905 0.4582 45 R 0.2307 0.2465 0.5228 46 S 0.1616 0.2877 0.5507 47 D 0.0720 0.3529 0.5751 48 D 0.0947 0.2060 0.6993 49 Y 0.2321 0.0579 0.7100 50 P 0.1902 0.0815 0.7283 51 Y 0.1287 0.3470 0.5242 52 K 0.0929 0.3723 0.5348 53 K 0.1431 0.3031 0.5538 54 K 0.2020 0.1827 0.6153 55 L 0.2268 0.1590 0.6143 56 D 0.1702 0.0566 0.7732 57 R 0.0203 0.7308 0.2489 58 E 0.0104 0.8626 0.1271 59 E 0.0099 0.9091 0.0810 60 Y 0.0092 0.9169 0.0739 61 E 0.0085 0.9214 0.0701 62 E 0.0083 0.9229 0.0689 63 T 0.0084 0.9184 0.0732 64 L 0.0084 0.9171 0.0746 65 T 0.0083 0.9208 0.0709 66 K 0.0083 0.9195 0.0722 67 L 0.0084 0.9168 0.0747 68 Q 0.0083 0.9232 0.0685 69 I 0.0083 0.9246 0.0672 70 E 0.0084 0.9226 0.0690 71 L 0.0083 0.9225 0.0692 72 V 0.0083 0.9233 0.0684 73 K 0.0083 0.9235 0.0683 74 V 0.0083 0.9240 0.0678 75 Q 0.0083 0.9240 0.0677 76 F 0.0083 0.9245 0.0673 77 W 0.0087 0.9223 0.0691 78 M 0.0088 0.9175 0.0736 79 Q 0.0098 0.8963 0.0939 80 A 0.0162 0.7931 0.1907 81 T 0.0583 0.2244 0.7173 82 G 0.0506 0.0811 0.8683 83 K 0.2074 0.0265 0.7661 84 R 0.4141 0.0238 0.5621 85 V 0.7969 0.0052 0.1979 86 M 0.8163 0.0044 0.1793 87 A 0.8189 0.0041 0.1770 88 V 0.8183 0.0043 0.1774 89 F 0.7862 0.0067 0.2071 90 E 0.6694 0.0252 0.3055 91 G 0.3641 0.0365 0.5994 92 R 0.2220 0.1675 0.6104 93 D 0.1640 0.1961 0.6398 94 A 0.1389 0.2929 0.5682 95 A 0.1285 0.2144 0.6571 96 G 0.1095 0.1729 0.7175 97 K 0.0906 0.3447 0.5646 98 G 0.0696 0.5323 0.3981 99 G 0.0543 0.7292 0.2165 100 A 0.0568 0.8083 0.1350 101 I 0.0327 0.8791 0.0882 102 H 0.0199 0.9049 0.0752 103 A 0.0150 0.9109 0.0741 104 T 0.0143 0.8980 0.0877 105 T 0.0192 0.8582 0.1226 106 A 0.0223 0.7660 0.2117 107 N 0.0446 0.4185 0.5370 108 M 0.1247 0.1921 0.6832 109 N 0.1769 0.0831 0.7400 110 P 0.0542 0.4161 0.5296 111 R 0.0891 0.3073 0.6036 112 S 0.2742 0.1463 0.5795 113 A 0.5583 0.0316 0.4101 114 R 0.7275 0.0162 0.2562 115 V 0.7665 0.0088 0.2247 116 V 0.7403 0.0166 0.2430 117 A 0.7038 0.0191 0.2771 118 L 0.5170 0.0391 0.4439 119 T 0.4122 0.0354 0.5523 120 K 0.3078 0.0226 0.6697 121 P 0.2259 0.0456 0.7285 122 T 0.1664 0.0559 0.7776 123 E 0.0805 0.3483 0.5711 124 T 0.1138 0.4038 0.4824 125 E 0.1889 0.3958 0.4154 126 R 0.2509 0.3149 0.4342 127 G 0.1902 0.3181 0.4916 128 Q 0.2089 0.4377 0.3534 129 W 0.1414 0.6264 0.2322 130 Y 0.1021 0.7308 0.1672 131 F 0.0895 0.7615 0.1490 132 Q 0.0685 0.8059 0.1256 133 R 0.0561 0.8274 0.1165 134 Y 0.0467 0.8036 0.1498 135 V 0.0577 0.7478 0.1945 136 A 0.0678 0.6628 0.2694 137 T 0.1470 0.3365 0.5165 138 F 0.2425 0.0627 0.6948 139 P 0.1510 0.1465 0.7025 140 T 0.0975 0.3065 0.5960 141 A 0.0904 0.1925 0.7170 142 G 0.1547 0.0843 0.7610 143 E 0.4651 0.0317 0.5032 144 F 0.7527 0.0123 0.2350 145 V 0.8036 0.0080 0.1885 146 L 0.8055 0.0075 0.1871 147 F 0.7517 0.0202 0.2281 148 D 0.5018 0.0476 0.4505 149 R 0.2631 0.2564 0.4805 150 S 0.1838 0.3282 0.4879 151 W 0.1323 0.4688 0.3989 152 Y 0.1544 0.3590 0.4867 153 N 0.1520 0.2779 0.5701 154 R 0.2079 0.1997 0.5924 155 A 0.2467 0.1699 0.5834 156 G 0.3029 0.1411 0.5560 157 V 0.4044 0.1152 0.4804 158 E 0.4357 0.1115 0.4528 159 P 0.3757 0.2149 0.4094 160 V 0.2851 0.3179 0.3969 161 M 0.2014 0.3152 0.4833 162 G 0.1548 0.2383 0.6069 163 F 0.1732 0.1730 0.6538 164 C 0.1917 0.1051 0.7033 165 T 0.1776 0.0525 0.7699 166 P 0.0418 0.5970 0.3611 167 D 0.0234 0.7873 0.1893 168 Q 0.0273 0.8484 0.1243 169 Y 0.0181 0.8866 0.0953 170 E 0.0124 0.9047 0.0829 171 Q 0.0105 0.9053 0.0842 172 F 0.0148 0.8755 0.1097 173 L 0.0166 0.8144 0.1690 174 K 0.0166 0.7372 0.2462 175 E 0.0356 0.5782 0.3862 176 A 0.0524 0.4959 0.4517 177 P 0.0226 0.6947 0.2827 178 R 0.0209 0.8267 0.1524 179 F 0.0222 0.8635 0.1143 180 E 0.0152 0.8925 0.0923 181 E 0.0226 0.8881 0.0894 182 M 0.0362 0.8357 0.1281 183 I 0.0761 0.6873 0.2366 184 A 0.0438 0.6147 0.3415 185 N 0.0496 0.4732 0.4772 186 E 0.0661 0.1621 0.7718 187 G 0.0706 0.0889 0.8404 188 I 0.3074 0.0331 0.6596 189 H 0.5546 0.0229 0.4225 190 L 0.7318 0.0190 0.2492 191 F 0.8047 0.0064 0.1889 192 K 0.8020 0.0062 0.1918 193 F 0.8063 0.0062 0.1875 194 W 0.7821 0.0100 0.2079 195 I 0.7126 0.0172 0.2702 196 N 0.4345 0.0186 0.5469 197 I 0.2241 0.1282 0.6477 198 G 0.1574 0.0602 0.7824 199 R 0.0126 0.7381 0.2493 200 E 0.0092 0.8669 0.1239 201 M 0.0084 0.9171 0.0746 202 Q 0.0087 0.9211 0.0703 203 L 0.0086 0.9182 0.0733 204 K 0.0085 0.9203 0.0713 205 R 0.0091 0.9126 0.0783 206 F 0.0107 0.8967 0.0926 207 H 0.0116 0.8711 0.1173 208 D 0.0201 0.7841 0.1958 209 R 0.0582 0.6082 0.3336 210 R 0.0758 0.4216 0.5026 211 H 0.1065 0.2699 0.6236 212 D 0.1796 0.0994 0.7210 213 P 0.0590 0.4793 0.4616 214 L 0.0487 0.5732 0.3781 215 K 0.0784 0.6277 0.2939 216 I 0.2050 0.4676 0.3274 217 W 0.3858 0.2575 0.3567 218 K 0.4320 0.1460 0.4219 219 L 0.3698 0.0911 0.5391 220 S 0.1843 0.0223 0.7934 221 P 0.0247 0.6532 0.3221 222 M 0.0201 0.7570 0.2229 223 D 0.0406 0.7923 0.1671 224 I 0.0139 0.8445 0.1416 225 A 0.0101 0.8823 0.1076 226 A 0.0124 0.8598 0.1278 227 L 0.0140 0.8557 0.1303 228 S 0.0168 0.8229 0.1603 229 K 0.0274 0.7825 0.1902 230 W 0.0224 0.8079 0.1698 231 D 0.0147 0.8477 0.1376 232 D 0.0114 0.8632 0.1254 233 Y 0.0154 0.8280 0.1565 234 T 0.0138 0.8619 0.1243 235 G 0.0120 0.8876 0.1004 236 K 0.0128 0.8958 0.0914 237 R 0.0110 0.8957 0.0933 238 D 0.0094 0.8980 0.0926 239 R 0.0087 0.9044 0.0869 240 M 0.0102 0.8882 0.1016 241 L 0.0133 0.8594 0.1273 242 K 0.0153 0.8270 0.1576 243 E 0.0371 0.6719 0.2910 244 T 0.1053 0.3908 0.5039 245 H 0.1196 0.2631 0.6172 246 T 0.1335 0.2456 0.6209 247 E 0.0823 0.3670 0.5507 248 H 0.1186 0.1862 0.6951 249 G 0.2238 0.0627 0.7135 250 P 0.2608 0.0870 0.6523 251 W 0.4974 0.0387 0.4639 252 A 0.7163 0.0165 0.2672 253 V 0.7507 0.0106 0.2387 254 I 0.7174 0.0222 0.2604 255 R 0.6015 0.0318 0.3666 256 G 0.3492 0.0992 0.5516 257 N 0.1809 0.1715 0.6476 258 D 0.1339 0.2436 0.6225 259 K 0.0657 0.5551 0.3791 260 R 0.0531 0.6885 0.2585 261 R 0.0429 0.7892 0.1679 262 S 0.0395 0.8221 0.1384 263 R 0.0410 0.8261 0.1329 264 I 0.0189 0.8920 0.0891 265 N 0.0117 0.9131 0.0753 266 V 0.0101 0.9197 0.0702 267 I 0.0083 0.9223 0.0694 268 R 0.0083 0.9237 0.0680 269 H 0.0083 0.9231 0.0686 270 M 0.0084 0.9185 0.0731 271 L 0.0086 0.9096 0.0819 272 T 0.0089 0.8918 0.0993 273 K 0.0136 0.7829 0.2034 274 L 0.0637 0.6178 0.3185 275 D 0.0539 0.5671 0.3790 276 Y 0.0412 0.6251 0.3337 277 D 0.0663 0.2750 0.6588 278 G 0.0489 0.1316 0.8195 279 K 0.1620 0.0935 0.7445 280 D 0.2017 0.1007 0.6975 281 E 0.2043 0.2899 0.5058 282 A 0.1767 0.3187 0.5047 283 A 0.1740 0.3273 0.4987 284 I 0.1800 0.2484 0.5716 285 G 0.1528 0.1700 0.6772 286 E 0.1923 0.1755 0.6322 287 V 0.1839 0.2942 0.5219 288 D 0.1730 0.3546 0.4723 289 E 0.0385 0.6948 0.2667 290 K 0.0587 0.6903 0.2509 291 I 0.1167 0.5636 0.3197 292 L 0.1632 0.3976 0.4393 293 G 0.1318 0.2794 0.5888 294 S 0.1648 0.1695 0.6657 295 G 0.1649 0.0944 0.7407 296 P 0.1153 0.3135 0.5712 297 G 0.1349 0.2871 0.5780 298 F 0.2083 0.2257 0.5660 299 L 0.2042 0.2147 0.5811 300 R 0.1711 0.2136 0.6153