# This file is the result of combining several RDB files, specifically # T0421.t06.str2.rdb (weight 1.54425) # T0421.t06.str4.rdb (weight 0.924988) # T0421.t06.pb.rdb (weight 0.789901) # T0421.t06.bys.rdb (weight 0.748322) # T0421.t06.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.t06.str2.rdb # ============================================ # TARGET T0421 # Using neural net dunbrack-40pc-3157-t06-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.t06-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 905 # # ============================================ # Comments from T0421.t06.str4.rdb # ============================================ # TARGET T0421 # Using neural net dunbrack-40pc-3157-t06-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.t06-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 905 # # ============================================ # Comments from T0421.t06.pb.rdb # ============================================ # TARGET T0421 # Using neural net dunbrack-40pc-3157-t06-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.t06-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 905 # # ============================================ # Comments from T0421.t06.bys.rdb # ============================================ # TARGET T0421 # Using neural net dunbrack-40pc-3157-t06-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.t06-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 905 # # ============================================ # Comments from T0421.t06.alpha.rdb # ============================================ # TARGET T0421 # Using neural net dunbrack-40pc-3157-t06-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.t06-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 905 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2939 0.1865 0.5196 2 A 0.2568 0.2047 0.5385 3 L 0.2162 0.2763 0.5076 4 D 0.1851 0.2648 0.5500 5 E 0.1704 0.2952 0.5345 6 A 0.2038 0.1687 0.6275 7 P 0.1319 0.3220 0.5461 8 A 0.0982 0.4556 0.4462 9 E 0.1071 0.4317 0.4612 10 A 0.1441 0.3012 0.5548 11 R 0.1821 0.1249 0.6930 12 P 0.1162 0.2613 0.6225 13 G 0.0761 0.2849 0.6391 14 S 0.1123 0.3653 0.5223 15 R 0.1080 0.5236 0.3684 16 A 0.0954 0.6582 0.2465 17 V 0.0914 0.7218 0.1868 18 E 0.0982 0.7252 0.1766 19 L 0.0999 0.7079 0.1922 20 E 0.0967 0.6771 0.2262 21 I 0.1141 0.5856 0.3003 22 D 0.0891 0.3909 0.5200 23 G 0.0717 0.2643 0.6640 24 R 0.1540 0.2547 0.5913 25 S 0.1681 0.3051 0.5268 26 R 0.1703 0.2881 0.5416 27 I 0.2322 0.2039 0.5639 28 F 0.2806 0.0965 0.6229 29 D 0.2108 0.0754 0.7138 30 I 0.0819 0.3468 0.5713 31 D 0.1084 0.2401 0.6514 32 D 0.1663 0.1395 0.6943 33 P 0.0785 0.3430 0.5785 34 D 0.1288 0.2516 0.6196 35 L 0.2007 0.1006 0.6987 36 P 0.1478 0.2121 0.6401 37 K 0.1076 0.3536 0.5388 38 W 0.1169 0.3763 0.5068 39 I 0.1395 0.3740 0.4865 40 D 0.1342 0.3674 0.4984 41 E 0.0787 0.5591 0.3623 42 E 0.0505 0.6705 0.2790 43 A 0.0593 0.6492 0.2915 44 F 0.0949 0.5054 0.3997 45 R 0.1394 0.3298 0.5308 46 S 0.1409 0.2447 0.6144 47 D 0.0475 0.4080 0.5445 48 D 0.0735 0.2420 0.6846 49 Y 0.2196 0.0687 0.7117 50 P 0.1685 0.1182 0.7133 51 Y 0.1071 0.3712 0.5217 52 K 0.0805 0.4699 0.4495 53 K 0.1107 0.4652 0.4241 54 K 0.1545 0.3259 0.5196 55 L 0.1970 0.2052 0.5978 56 D 0.1616 0.1023 0.7361 57 R 0.0153 0.7369 0.2479 58 E 0.0102 0.8638 0.1260 59 E 0.0102 0.9100 0.0798 60 Y 0.0109 0.9134 0.0757 61 E 0.0084 0.9190 0.0726 62 E 0.0084 0.9200 0.0716 63 T 0.0085 0.9181 0.0734 64 L 0.0088 0.9162 0.0750 65 T 0.0084 0.9196 0.0720 66 K 0.0084 0.9207 0.0709 67 L 0.0090 0.9166 0.0744 68 Q 0.0086 0.9190 0.0725 69 I 0.0086 0.9220 0.0694 70 E 0.0084 0.9229 0.0687 71 L 0.0086 0.9206 0.0708 72 V 0.0083 0.9223 0.0694 73 K 0.0083 0.9219 0.0697 74 V 0.0083 0.9217 0.0700 75 Q 0.0084 0.9201 0.0715 76 F 0.0083 0.9226 0.0691 77 W 0.0084 0.9204 0.0713 78 M 0.0092 0.9125 0.0783 79 Q 0.0109 0.8859 0.1031 80 A 0.0154 0.7596 0.2249 81 T 0.0556 0.2460 0.6984 82 G 0.0453 0.0748 0.8799 83 K 0.2147 0.0273 0.7580 84 R 0.4655 0.0219 0.5126 85 V 0.7933 0.0072 0.1995 86 M 0.8147 0.0047 0.1806 87 A 0.8102 0.0050 0.1848 88 V 0.7914 0.0056 0.2030 89 F 0.7642 0.0089 0.2269 90 E 0.6558 0.0200 0.3241 91 G 0.3921 0.0367 0.5713 92 R 0.2216 0.1501 0.6283 93 D 0.1565 0.1872 0.6564 94 A 0.0910 0.3274 0.5817 95 A 0.1049 0.2562 0.6390 96 G 0.0987 0.2079 0.6934 97 K 0.0901 0.4053 0.5046 98 G 0.0583 0.6192 0.3224 99 G 0.0341 0.7986 0.1672 100 A 0.0245 0.8699 0.1056 101 I 0.0144 0.9026 0.0830 102 H 0.0092 0.9172 0.0736 103 A 0.0092 0.9141 0.0768 104 T 0.0120 0.8931 0.0950 105 T 0.0157 0.8426 0.1417 106 A 0.0172 0.6816 0.3012 107 N 0.0372 0.4054 0.5574 108 M 0.1398 0.1725 0.6877 109 N 0.1704 0.0595 0.7701 110 P 0.0456 0.5233 0.4311 111 R 0.0662 0.3803 0.5535 112 S 0.2439 0.2060 0.5501 113 A 0.5838 0.0271 0.3891 114 R 0.7266 0.0140 0.2594 115 V 0.7780 0.0069 0.2151 116 V 0.7591 0.0136 0.2273 117 A 0.7043 0.0190 0.2767 118 L 0.5241 0.0450 0.4309 119 T 0.3623 0.0500 0.5876 120 K 0.2830 0.0288 0.6882 121 P 0.2099 0.0557 0.7344 122 T 0.1888 0.0575 0.7537 123 E 0.0813 0.4070 0.5117 124 T 0.1329 0.4058 0.4614 125 E 0.1824 0.4211 0.3964 126 R 0.1701 0.3783 0.4516 127 G 0.1614 0.3665 0.4720 128 Q 0.1635 0.5192 0.3173 129 W 0.1190 0.6465 0.2345 130 Y 0.0965 0.7078 0.1958 131 F 0.0713 0.7767 0.1520 132 Q 0.0605 0.8107 0.1289 133 R 0.0581 0.8200 0.1219 134 Y 0.0789 0.7538 0.1673 135 V 0.0806 0.7248 0.1946 136 A 0.0711 0.6344 0.2945 137 T 0.1359 0.3779 0.4862 138 F 0.2103 0.1347 0.6550 139 P 0.1292 0.2471 0.6238 140 T 0.0846 0.3609 0.5545 141 A 0.0891 0.1569 0.7540 142 G 0.0733 0.0957 0.8311 143 E 0.3828 0.0165 0.6008 144 F 0.7306 0.0079 0.2614 145 V 0.7898 0.0079 0.2023 146 L 0.8007 0.0058 0.1936 147 F 0.7043 0.0152 0.2805 148 D 0.4104 0.0387 0.5509 149 R 0.2115 0.1671 0.6215 150 S 0.2293 0.2180 0.5527 151 W 0.1679 0.3905 0.4416 152 Y 0.1884 0.3095 0.5022 153 N 0.2082 0.2353 0.5565 154 R 0.3188 0.1762 0.5050 155 A 0.3803 0.1664 0.4534 156 G 0.4935 0.1221 0.3844 157 V 0.5983 0.0876 0.3141 158 E 0.5989 0.0812 0.3199 159 P 0.5516 0.1398 0.3086 160 V 0.3923 0.2074 0.4003 161 M 0.2504 0.1970 0.5525 162 G 0.1257 0.1565 0.7178 163 F 0.1905 0.1316 0.6779 164 C 0.2356 0.0658 0.6986 165 T 0.1742 0.0307 0.7951 166 P 0.0176 0.7092 0.2733 167 D 0.0113 0.8338 0.1549 168 Q 0.0113 0.8984 0.0903 169 Y 0.0095 0.9141 0.0764 170 E 0.0084 0.9173 0.0743 171 Q 0.0085 0.9188 0.0727 172 F 0.0092 0.9093 0.0814 173 L 0.0102 0.8873 0.1025 174 K 0.0099 0.8292 0.1608 175 E 0.0185 0.6869 0.2946 176 A 0.0498 0.6040 0.3462 177 P 0.0122 0.7841 0.2036 178 R 0.0120 0.8283 0.1597 179 F 0.0124 0.8946 0.0930 180 E 0.0105 0.9085 0.0811 181 E 0.0151 0.9013 0.0837 182 M 0.0194 0.8444 0.1362 183 I 0.0442 0.7411 0.2146 184 A 0.0397 0.6934 0.2668 185 N 0.0379 0.5337 0.4284 186 E 0.0741 0.1913 0.7346 187 G 0.0649 0.0890 0.8461 188 I 0.3471 0.0294 0.6234 189 H 0.6398 0.0216 0.3386 190 L 0.7432 0.0163 0.2405 191 F 0.7943 0.0100 0.1957 192 K 0.8079 0.0071 0.1851 193 F 0.8040 0.0077 0.1883 194 W 0.7526 0.0180 0.2294 195 I 0.6113 0.0303 0.3584 196 N 0.3516 0.0299 0.6186 197 I 0.2052 0.1051 0.6897 198 G 0.1713 0.0385 0.7902 199 R 0.0112 0.7508 0.2380 200 E 0.0091 0.8698 0.1210 201 M 0.0083 0.9225 0.0692 202 Q 0.0083 0.9216 0.0701 203 L 0.0084 0.9188 0.0728 204 K 0.0084 0.9121 0.0795 205 R 0.0093 0.8977 0.0929 206 F 0.0121 0.8705 0.1174 207 H 0.0165 0.8248 0.1587 208 D 0.0259 0.6970 0.2771 209 R 0.0608 0.5436 0.3956 210 R 0.0759 0.3894 0.5348 211 H 0.1408 0.2181 0.6411 212 D 0.1668 0.0825 0.7508 213 P 0.0377 0.5527 0.4096 214 L 0.0371 0.6535 0.3094 215 K 0.0900 0.6261 0.2840 216 I 0.2224 0.4389 0.3387 217 W 0.2733 0.2887 0.4379 218 K 0.3247 0.1756 0.4998 219 L 0.3613 0.0617 0.5770 220 S 0.1910 0.0157 0.7933 221 P 0.0230 0.6392 0.3378 222 M 0.0204 0.7254 0.2542 223 D 0.0437 0.7379 0.2184 224 I 0.0130 0.8473 0.1398 225 A 0.0092 0.8662 0.1246 226 A 0.0113 0.8621 0.1266 227 L 0.0173 0.8672 0.1155 228 S 0.0134 0.8193 0.1673 229 K 0.0199 0.7343 0.2458 230 W 0.0292 0.7789 0.1919 231 D 0.0136 0.8374 0.1490 232 D 0.0138 0.8212 0.1650 233 Y 0.0219 0.8052 0.1728 234 T 0.0188 0.8580 0.1232 235 G 0.0139 0.8887 0.0974 236 K 0.0155 0.8928 0.0918 237 R 0.0126 0.9017 0.0857 238 D 0.0095 0.9064 0.0841 239 R 0.0098 0.8969 0.0933 240 M 0.0116 0.8789 0.1094 241 L 0.0173 0.8609 0.1217 242 K 0.0178 0.8366 0.1456 243 E 0.0353 0.7116 0.2532 244 T 0.1116 0.4104 0.4781 245 H 0.1203 0.2404 0.6394 246 T 0.1788 0.1769 0.6443 247 E 0.0771 0.3664 0.5565 248 H 0.1240 0.1750 0.7009 249 G 0.2273 0.0509 0.7219 250 P 0.2759 0.0554 0.6687 251 W 0.5065 0.0314 0.4621 252 A 0.7366 0.0132 0.2502 253 V 0.7454 0.0078 0.2468 254 I 0.7426 0.0118 0.2455 255 R 0.5447 0.0243 0.4310 256 G 0.2771 0.1417 0.5812 257 N 0.1319 0.2115 0.6567 258 D 0.1203 0.2648 0.6149 259 K 0.0598 0.6191 0.3211 260 R 0.0523 0.7210 0.2267 261 R 0.0535 0.7725 0.1741 262 S 0.0402 0.8301 0.1298 263 R 0.0307 0.8560 0.1133 264 I 0.0321 0.8778 0.0901 265 N 0.0100 0.9175 0.0726 266 V 0.0086 0.9221 0.0693 267 I 0.0084 0.9234 0.0682 268 R 0.0083 0.9238 0.0679 269 H 0.0083 0.9237 0.0680 270 M 0.0084 0.9224 0.0693 271 L 0.0085 0.9123 0.0792 272 T 0.0093 0.8890 0.1016 273 K 0.0140 0.7755 0.2105 274 L 0.0766 0.6540 0.2694 275 D 0.0512 0.5682 0.3806 276 Y 0.0439 0.5459 0.4102 277 D 0.0576 0.2762 0.6662 278 G 0.0452 0.1528 0.8020 279 K 0.1618 0.1003 0.7379 280 D 0.1859 0.1046 0.7095 281 E 0.1960 0.2449 0.5591 282 A 0.1483 0.3727 0.4790 283 A 0.1528 0.3742 0.4729 284 I 0.1822 0.2492 0.5686 285 G 0.1437 0.1702 0.6861 286 E 0.1737 0.1724 0.6539 287 V 0.1652 0.2431 0.5917 288 D 0.1587 0.2637 0.5776 289 E 0.0336 0.7090 0.2574 290 K 0.0379 0.7450 0.2171 291 I 0.0748 0.6668 0.2584 292 L 0.1218 0.4859 0.3924 293 G 0.0978 0.3196 0.5825 294 S 0.1560 0.1998 0.6443 295 G 0.1774 0.0855 0.7372 296 P 0.1392 0.1995 0.6613 297 G 0.1597 0.1937 0.6466 298 F 0.2364 0.1580 0.6056 299 L 0.2504 0.1616 0.5880 300 R 0.2303 0.1617 0.6080