# 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 1665 # # ============================================ # 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 1665 # # ============================================ # 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 1665 # # ============================================ # 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 1665 # # ============================================ # 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 1665 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0232 0.7574 0.2194 2 V 0.0099 0.8918 0.0983 3 E 0.0084 0.9185 0.0731 4 I 0.0084 0.9191 0.0726 5 F 0.0084 0.9188 0.0728 6 N 0.0083 0.9233 0.0684 7 E 0.0083 0.9234 0.0683 8 I 0.0083 0.9214 0.0702 9 M 0.0083 0.9217 0.0700 10 Q 0.0083 0.9130 0.0787 11 R 0.0084 0.9159 0.0757 12 V 0.0088 0.9001 0.0912 13 K 0.0099 0.7960 0.1940 14 E 0.0220 0.5226 0.4553 15 A 0.1117 0.2125 0.6759 16 E 0.1958 0.1555 0.6486 17 T 0.5557 0.0382 0.4061 18 I 0.7557 0.0088 0.2355 19 I 0.8021 0.0054 0.1925 20 I 0.7989 0.0079 0.1932 21 H 0.7474 0.0182 0.2344 22 R 0.6168 0.0321 0.3510 23 H 0.4237 0.0449 0.5315 24 V 0.2987 0.0971 0.6043 25 R 0.2446 0.0440 0.7113 26 P 0.1227 0.2384 0.6389 27 D 0.1706 0.1299 0.6994 28 P 0.0249 0.4600 0.5151 29 D 0.0350 0.5334 0.4316 30 A 0.0358 0.7778 0.1864 31 Y 0.0205 0.8751 0.1044 32 G 0.0114 0.9103 0.0783 33 S 0.0087 0.9211 0.0702 34 Q 0.0083 0.9243 0.0674 35 L 0.0083 0.9250 0.0667 36 G 0.0083 0.9249 0.0669 37 L 0.0083 0.9241 0.0676 38 K 0.0083 0.9236 0.0681 39 L 0.0083 0.9231 0.0686 40 Y 0.0084 0.9202 0.0715 41 L 0.0087 0.9053 0.0860 42 E 0.0095 0.8659 0.1246 43 R 0.0175 0.7114 0.2711 44 K 0.0549 0.3579 0.5871 45 F 0.1423 0.1218 0.7359 46 P 0.0977 0.2648 0.6375 47 E 0.1571 0.1494 0.6935 48 K 0.3607 0.0339 0.6054 49 N 0.5886 0.0231 0.3882 50 I 0.7562 0.0099 0.2339 51 Y 0.7277 0.0167 0.2556 52 A 0.6494 0.0189 0.3317 53 T 0.3793 0.0770 0.5437 54 G 0.1532 0.1032 0.7436 55 E 0.2156 0.0976 0.6868 56 A 0.2532 0.0863 0.6606 57 E 0.2112 0.0673 0.7215 58 P 0.0641 0.4756 0.4603 59 S 0.0695 0.3631 0.5674 60 L 0.1850 0.2840 0.5310 61 S 0.2101 0.2708 0.5191 62 F 0.2142 0.3095 0.4763 63 I 0.1942 0.2673 0.5385 64 G 0.1111 0.3721 0.5167 65 D 0.1265 0.3600 0.5136 66 L 0.1957 0.2760 0.5283 67 D 0.1706 0.2597 0.5697 68 E 0.1971 0.3027 0.5002 69 I 0.2220 0.2567 0.5212 70 D 0.1986 0.2485 0.5529 71 D 0.1044 0.4719 0.4237 72 S 0.1034 0.4689 0.4277 73 V 0.1492 0.3359 0.5150 74 Y 0.1787 0.1780 0.6433 75 S 0.1828 0.1531 0.6642 76 D 0.2260 0.1145 0.6595 77 A 0.3893 0.0527 0.5579 78 L 0.7260 0.0155 0.2585 79 V 0.7910 0.0058 0.2033 80 I 0.8179 0.0043 0.1778 81 V 0.8078 0.0046 0.1876 82 C 0.7698 0.0111 0.2191 83 D 0.5194 0.0208 0.4598 84 T 0.2557 0.1485 0.5958 85 A 0.1585 0.1896 0.6519 86 N 0.1558 0.1483 0.6959 87 A 0.1772 0.1603 0.6625 88 P 0.1210 0.3351 0.5438 89 R 0.1478 0.3267 0.5255 90 I 0.1402 0.3833 0.4766 91 D 0.0717 0.5877 0.3407 92 D 0.0240 0.7986 0.1773 93 Q 0.0200 0.8384 0.1416 94 R 0.0226 0.8487 0.1288 95 Y 0.0292 0.7820 0.1888 96 L 0.0441 0.6910 0.2648 97 N 0.0703 0.1994 0.7304 98 G 0.0533 0.0734 0.8734 99 Q 0.2353 0.0145 0.7502 100 S 0.5176 0.0230 0.4594 101 L 0.8072 0.0048 0.1879 102 I 0.8089 0.0050 0.1861 103 K 0.7892 0.0048 0.2060 104 I 0.7579 0.0113 0.2308 105 D 0.5939 0.0317 0.3744 106 H 0.3300 0.0700 0.6000 107 H 0.2357 0.0580 0.7063 108 P 0.1585 0.1610 0.6805 109 A 0.1187 0.2430 0.6383 110 T 0.1026 0.3101 0.5874 111 D 0.1010 0.3124 0.5866 112 Q 0.1384 0.2942 0.5675 113 Y 0.1824 0.1827 0.6349 114 G 0.1570 0.1335 0.7095 115 D 0.2156 0.1279 0.6565 116 V 0.2959 0.1466 0.5575 117 N 0.4436 0.1313 0.4251 118 F 0.6146 0.0662 0.3192 119 V 0.6175 0.0447 0.3379 120 N 0.3396 0.0268 0.6336 121 T 0.1005 0.3436 0.5559 122 E 0.0859 0.2914 0.6227 123 A 0.1248 0.2784 0.5968 124 S 0.1035 0.4009 0.4956 125 S 0.0722 0.6244 0.3034 126 T 0.0357 0.7810 0.1833 127 S 0.0138 0.8885 0.0977 128 E 0.0096 0.9202 0.0702 129 I 0.0098 0.9218 0.0684 130 I 0.0086 0.9241 0.0673 131 F 0.0084 0.9237 0.0679 132 D 0.0084 0.9237 0.0680 133 F 0.0084 0.9211 0.0706 134 I 0.0086 0.9154 0.0759 135 S 0.0089 0.9068 0.0842 136 H 0.0122 0.8500 0.1378 137 F 0.0282 0.7065 0.2654 138 N 0.0287 0.5480 0.4233 139 D 0.0417 0.5074 0.4509 140 L 0.0820 0.4383 0.4797 141 S 0.1452 0.2720 0.5828 142 I 0.1824 0.1723 0.6453 143 I 0.1946 0.1209 0.6844 144 D 0.1589 0.1026 0.7384 145 E 0.0112 0.7517 0.2371 146 H 0.0095 0.8547 0.1359 147 V 0.0086 0.9141 0.0773 148 A 0.0084 0.9197 0.0720 149 R 0.0084 0.9198 0.0718 150 V 0.0096 0.9186 0.0718 151 L 0.0125 0.9092 0.0783 152 Y 0.0241 0.8755 0.1004 153 L 0.0617 0.7937 0.1446 154 G 0.1294 0.6604 0.2103 155 I 0.2015 0.5258 0.2727 156 V 0.2577 0.3745 0.3678 157 G 0.2525 0.2621 0.4854 158 D 0.1924 0.2176 0.5900 159 T 0.1406 0.1973 0.6621 160 G 0.1380 0.1681 0.6940 161 R 0.2492 0.1793 0.5714 162 F 0.3657 0.1306 0.5037 163 L 0.3731 0.1223 0.5046 164 F 0.3183 0.1001 0.5816 165 S 0.1917 0.2331 0.5752 166 N 0.1701 0.1580 0.6719 167 T 0.2152 0.0979 0.6868 168 S 0.1960 0.0455 0.7585 169 P 0.0652 0.4995 0.4352 170 H 0.0527 0.6112 0.3361 171 T 0.0643 0.6929 0.2428 172 M 0.0305 0.8231 0.1464 173 E 0.0244 0.8741 0.1014 174 V 0.0193 0.8854 0.0953 175 A 0.0112 0.9020 0.0869 176 S 0.0089 0.9082 0.0828 177 Q 0.0091 0.8958 0.0951 178 L 0.0109 0.8653 0.1237 179 L 0.0165 0.7232 0.2602 180 A 0.0277 0.5472 0.4251 181 Y 0.1178 0.2115 0.6707 182 P 0.1088 0.1981 0.6931 183 F 0.1390 0.2140 0.6470 184 N 0.1556 0.1267 0.7177 185 H 0.0335 0.6589 0.3076 186 N 0.0225 0.7870 0.1905 187 A 0.0154 0.8650 0.1197 188 E 0.0140 0.8793 0.1067 189 L 0.0129 0.8928 0.0943 190 N 0.0124 0.8831 0.1045 191 K 0.0183 0.8227 0.1590 192 M 0.0389 0.6693 0.2918 193 S 0.0695 0.4472 0.4832 194 E 0.0590 0.3682 0.5728 195 K 0.0894 0.1999 0.7107 196 D 0.1635 0.0997 0.7369 197 P 0.0125 0.6814 0.3061 198 K 0.0125 0.6893 0.2982 199 L 0.0232 0.6858 0.2909 200 M 0.0293 0.7295 0.2412 201 P 0.0177 0.8273 0.1550 202 F 0.0156 0.8564 0.1279 203 Q 0.0122 0.8727 0.1151 204 G 0.0096 0.9003 0.0902 205 Y 0.0104 0.9070 0.0826 206 V 0.0159 0.8846 0.0996 207 L 0.0292 0.8089 0.1619 208 Q 0.0389 0.6639 0.2971 209 N 0.0743 0.3544 0.5714 210 F 0.1361 0.3200 0.5439 211 E 0.1975 0.3051 0.4975 212 L 0.2514 0.3506 0.3980 213 S 0.2425 0.2953 0.4623 214 D 0.2198 0.3003 0.4799 215 S 0.1480 0.3640 0.4880 216 H 0.1457 0.3218 0.5325 217 E 0.2092 0.2902 0.5006 218 Y 0.4239 0.2006 0.3755 219 C 0.6318 0.1085 0.2597 220 Q 0.7124 0.0836 0.2040 221 I 0.7409 0.0726 0.1865 222 K 0.7043 0.0920 0.2036 223 I 0.6467 0.0989 0.2544 224 T 0.4378 0.2159 0.3464 225 N 0.2450 0.4078 0.3472 226 D 0.1910 0.4976 0.3114 227 V 0.2234 0.5095 0.2671 228 L 0.1818 0.5213 0.2969 229 K 0.1577 0.5140 0.3283 230 Q 0.1544 0.3956 0.4500 231 F 0.1499 0.2829 0.5672 232 D 0.1505 0.1754 0.6741 233 I 0.2009 0.1426 0.6565 234 Q 0.1979 0.0569 0.7452 235 P 0.0664 0.4323 0.5013 236 N 0.0483 0.5282 0.4235 237 E 0.0730 0.6447 0.2823 238 A 0.0557 0.7596 0.1847 239 S 0.0255 0.8666 0.1079 240 Q 0.0250 0.8858 0.0892 241 F 0.0209 0.8930 0.0861 242 V 0.0145 0.8987 0.0868 243 N 0.0118 0.8967 0.0915 244 T 0.0135 0.8883 0.0982 245 V 0.0161 0.8699 0.1140 246 A 0.0203 0.8212 0.1585 247 D 0.0306 0.7296 0.2399 248 I 0.0533 0.6483 0.2984 249 S 0.0713 0.1893 0.7394 250 G 0.0494 0.0840 0.8666 251 L 0.2335 0.0171 0.7494 252 K 0.4913 0.0277 0.4810 253 I 0.7923 0.0061 0.2016 254 W 0.8041 0.0055 0.1905 255 M 0.8211 0.0043 0.1747 256 F 0.8191 0.0048 0.1761 257 G 0.7713 0.0069 0.2218 258 V 0.6939 0.0149 0.2912 259 D 0.4601 0.0374 0.5026 260 E 0.2017 0.0959 0.7024 261 G 0.1143 0.0724 0.8134 262 D 0.1977 0.0692 0.7331 263 Q 0.6158 0.0149 0.3693 264 I 0.7471 0.0085 0.2444 265 R 0.8119 0.0054 0.1827 266 C 0.8182 0.0045 0.1773 267 R 0.8076 0.0057 0.1867 268 I 0.7810 0.0081 0.2109 269 R 0.6739 0.0258 0.3003 270 S 0.4157 0.0437 0.5406 271 K 0.1400 0.1655 0.6945 272 G 0.0875 0.1022 0.8103 273 I 0.2281 0.0648 0.7071 274 T 0.2394 0.0414 0.7193 275 I 0.0321 0.6770 0.2908 276 N 0.0121 0.8349 0.1530 277 D 0.0104 0.9017 0.0879 278 V 0.0116 0.8995 0.0889 279 A 0.0121 0.8857 0.1022 280 N 0.0115 0.8536 0.1348 281 Q 0.0160 0.7819 0.2021 282 F 0.0674 0.4338 0.4987 283 G 0.0687 0.2606 0.6707 284 G 0.0907 0.1973 0.7120 285 G 0.1098 0.2005 0.6897 286 G 0.1535 0.1881 0.6583 287 H 0.1931 0.1714 0.6355 288 P 0.0593 0.5370 0.4037 289 N 0.0868 0.4000 0.5132 290 A 0.1868 0.3058 0.5074 291 S 0.2372 0.1858 0.5770 292 G 0.3810 0.1184 0.5006 293 V 0.5144 0.0590 0.4266 294 S 0.5574 0.0530 0.3895 295 V 0.4611 0.0959 0.4430 296 Y 0.2796 0.1443 0.5760 297 S 0.2021 0.1315 0.6664 298 W 0.0531 0.5213 0.4256 299 D 0.0312 0.6192 0.3496 300 E 0.0374 0.7258 0.2369 301 F 0.0094 0.8753 0.1153 302 E 0.0085 0.9100 0.0815 303 E 0.0083 0.9234 0.0683 304 L 0.0083 0.9231 0.0686 305 A 0.0083 0.9232 0.0685 306 Q 0.0083 0.9235 0.0683 307 A 0.0083 0.9239 0.0678 308 L 0.0083 0.9208 0.0709 309 R 0.0083 0.9194 0.0723 310 Q 0.0083 0.9193 0.0724 311 K 0.0086 0.9107 0.0807 312 L 0.0096 0.8870 0.1034 313 L 0.0104 0.8294 0.1602 314 E 0.0195 0.6842 0.2963 315 H 0.0815 0.3743 0.5442 316 H 0.0943 0.2537 0.6520 317 H 0.1572 0.2479 0.5949 318 H 0.2008 0.1965 0.6028 319 H 0.2160 0.1595 0.6244 320 H 0.1998 0.1494 0.6508