# This file is the result of combining several RDB files, specifically # T0457.t06.str2.rdb (weight 1.54425) # T0457.t06.str4.rdb (weight 0.924988) # T0457.t06.pb.rdb (weight 0.789901) # T0457.t06.bys.rdb (weight 0.748322) # T0457.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 T0457.t06.str2.rdb # ============================================ # TARGET T0457 # 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 T0457.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 1677 # # ============================================ # Comments from T0457.t06.str4.rdb # ============================================ # TARGET T0457 # 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 T0457.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 1677 # # ============================================ # Comments from T0457.t06.pb.rdb # ============================================ # TARGET T0457 # 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 T0457.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 1677 # # ============================================ # Comments from T0457.t06.bys.rdb # ============================================ # TARGET T0457 # 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 T0457.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 1677 # # ============================================ # Comments from T0457.t06.alpha.rdb # ============================================ # TARGET T0457 # 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 T0457.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 1677 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0248 0.8030 0.1722 2 V 0.0094 0.9007 0.0899 3 E 0.0084 0.9195 0.0721 4 I 0.0083 0.9213 0.0704 5 F 0.0084 0.9186 0.0730 6 N 0.0083 0.9234 0.0683 7 E 0.0083 0.9243 0.0674 8 I 0.0083 0.9237 0.0680 9 M 0.0084 0.9180 0.0737 10 Q 0.0083 0.9202 0.0714 11 R 0.0087 0.9106 0.0807 12 V 0.0099 0.8992 0.0909 13 K 0.0112 0.8372 0.1515 14 E 0.0234 0.4906 0.4859 15 A 0.1016 0.2272 0.6711 16 E 0.1593 0.1370 0.7036 17 T 0.5243 0.0358 0.4399 18 I 0.7684 0.0080 0.2236 19 I 0.8111 0.0057 0.1832 20 I 0.7916 0.0069 0.2014 21 H 0.7519 0.0165 0.2316 22 R 0.5989 0.0350 0.3660 23 H 0.3665 0.0587 0.5748 24 V 0.2652 0.1222 0.6126 25 R 0.2459 0.0595 0.6946 26 P 0.1332 0.1653 0.7015 27 D 0.1834 0.0880 0.7287 28 P 0.0276 0.4980 0.4744 29 D 0.0395 0.5970 0.3634 30 A 0.0259 0.8067 0.1674 31 Y 0.0127 0.8842 0.1031 32 G 0.0089 0.9179 0.0732 33 S 0.0083 0.9228 0.0689 34 Q 0.0083 0.9231 0.0686 35 L 0.0083 0.9241 0.0676 36 G 0.0083 0.9251 0.0667 37 L 0.0083 0.9244 0.0673 38 K 0.0083 0.9235 0.0682 39 L 0.0083 0.9217 0.0700 40 Y 0.0084 0.9195 0.0721 41 L 0.0086 0.9075 0.0839 42 E 0.0100 0.8615 0.1285 43 R 0.0204 0.6571 0.3225 44 K 0.0555 0.3128 0.6317 45 F 0.1383 0.0936 0.7681 46 P 0.0973 0.2563 0.6464 47 E 0.1583 0.1529 0.6888 48 K 0.4230 0.0510 0.5259 49 N 0.6398 0.0228 0.3374 50 I 0.7725 0.0097 0.2179 51 Y 0.7497 0.0138 0.2364 52 A 0.6098 0.0200 0.3702 53 T 0.2757 0.0853 0.6390 54 G 0.1268 0.0912 0.7820 55 E 0.2111 0.1037 0.6852 56 A 0.2535 0.1133 0.6332 57 E 0.2071 0.1125 0.6804 58 P 0.0765 0.4417 0.4818 59 S 0.0817 0.4072 0.5110 60 L 0.1481 0.4161 0.4358 61 S 0.1642 0.3642 0.4716 62 F 0.1600 0.3946 0.4454 63 I 0.1395 0.4326 0.4280 64 G 0.0584 0.6002 0.3413 65 D 0.0707 0.5723 0.3570 66 L 0.0905 0.5811 0.3285 67 D 0.0637 0.6112 0.3251 68 E 0.0794 0.5901 0.3305 69 I 0.1333 0.4211 0.4456 70 D 0.1272 0.3281 0.5446 71 D 0.0600 0.4764 0.4637 72 S 0.0730 0.4360 0.4911 73 V 0.1456 0.2850 0.5693 74 Y 0.1746 0.1697 0.6557 75 S 0.1651 0.1538 0.6810 76 D 0.1965 0.1447 0.6589 77 A 0.3732 0.0596 0.5673 78 L 0.7249 0.0136 0.2615 79 V 0.7784 0.0066 0.2150 80 I 0.8056 0.0056 0.1889 81 V 0.7883 0.0068 0.2049 82 C 0.7397 0.0155 0.2447 83 D 0.4290 0.0437 0.5273 84 T 0.1874 0.1504 0.6622 85 A 0.1312 0.1949 0.6740 86 N 0.1405 0.1564 0.7030 87 A 0.1742 0.1503 0.6755 88 P 0.1186 0.3116 0.5698 89 R 0.1420 0.3323 0.5257 90 I 0.1618 0.3212 0.5170 91 D 0.1173 0.4519 0.4308 92 D 0.0315 0.7454 0.2232 93 Q 0.0304 0.7796 0.1899 94 R 0.0400 0.7648 0.1953 95 Y 0.0647 0.6897 0.2456 96 L 0.0602 0.5603 0.3794 97 N 0.0762 0.3052 0.6185 98 G 0.1108 0.1583 0.7309 99 Q 0.2264 0.0678 0.7058 100 S 0.5727 0.0165 0.4107 101 L 0.7611 0.0082 0.2306 102 I 0.8085 0.0053 0.1862 103 K 0.7864 0.0068 0.2068 104 I 0.7497 0.0158 0.2345 105 D 0.5571 0.0588 0.3841 106 H 0.2889 0.0804 0.6307 107 H 0.2523 0.0404 0.7073 108 P 0.1132 0.2059 0.6809 109 A 0.1076 0.2524 0.6400 110 T 0.0907 0.3500 0.5593 111 D 0.0919 0.3578 0.5503 112 Q 0.1287 0.3165 0.5548 113 Y 0.1670 0.1572 0.6758 114 G 0.1484 0.1446 0.7070 115 D 0.2061 0.1404 0.6534 116 V 0.3339 0.1146 0.5515 117 N 0.4805 0.0984 0.4211 118 F 0.6122 0.0625 0.3253 119 V 0.5751 0.0426 0.3823 120 N 0.3334 0.0304 0.6363 121 T 0.1242 0.2746 0.6012 122 E 0.1102 0.2866 0.6033 123 A 0.1346 0.2937 0.5716 124 S 0.1060 0.4200 0.4741 125 S 0.0795 0.6085 0.3120 126 T 0.0355 0.8014 0.1631 127 S 0.0134 0.8972 0.0894 128 E 0.0103 0.9176 0.0721 129 I 0.0092 0.9215 0.0692 130 I 0.0083 0.9238 0.0679 131 F 0.0083 0.9226 0.0691 132 D 0.0083 0.9238 0.0679 133 F 0.0084 0.9210 0.0706 134 I 0.0086 0.9108 0.0806 135 S 0.0089 0.8903 0.1008 136 H 0.0118 0.8009 0.1873 137 F 0.0380 0.5967 0.3653 138 N 0.0359 0.4612 0.5029 139 D 0.0578 0.4215 0.5206 140 L 0.0986 0.3595 0.5419 141 S 0.1500 0.2488 0.6012 142 I 0.2008 0.1472 0.6520 143 I 0.2215 0.1202 0.6583 144 D 0.1671 0.1093 0.7236 145 E 0.0128 0.7480 0.2392 146 H 0.0101 0.8467 0.1432 147 V 0.0093 0.9086 0.0820 148 A 0.0084 0.9199 0.0717 149 R 0.0085 0.9193 0.0723 150 V 0.0099 0.9150 0.0750 151 L 0.0139 0.9046 0.0815 152 Y 0.0368 0.8583 0.1049 153 L 0.0776 0.7430 0.1794 154 G 0.1429 0.6448 0.2124 155 I 0.2168 0.5341 0.2492 156 V 0.2992 0.3301 0.3707 157 G 0.2161 0.2573 0.5265 158 D 0.1785 0.2065 0.6150 159 T 0.0853 0.2641 0.6506 160 G 0.0848 0.2891 0.6260 161 R 0.1560 0.3836 0.4604 162 F 0.2188 0.3269 0.4542 163 L 0.2624 0.2277 0.5099 164 F 0.2420 0.1553 0.6027 165 S 0.1608 0.2262 0.6131 166 N 0.1480 0.1701 0.6819 167 T 0.2242 0.0928 0.6830 168 S 0.1992 0.0480 0.7529 169 P 0.0453 0.5207 0.4340 170 H 0.0332 0.6703 0.2965 171 T 0.0296 0.7996 0.1708 172 M 0.0128 0.8864 0.1008 173 E 0.0098 0.9131 0.0771 174 V 0.0092 0.9197 0.0711 175 A 0.0084 0.9193 0.0723 176 S 0.0087 0.9127 0.0786 177 Q 0.0093 0.8961 0.0946 178 L 0.0153 0.8216 0.1631 179 L 0.0245 0.6892 0.2863 180 A 0.0381 0.4574 0.5045 181 Y 0.1226 0.1870 0.6904 182 P 0.0696 0.3545 0.5759 183 F 0.0824 0.3559 0.5617 184 N 0.0893 0.3125 0.5982 185 H 0.0241 0.7520 0.2239 186 N 0.0137 0.8553 0.1309 187 A 0.0103 0.9086 0.0811 188 E 0.0100 0.9100 0.0801 189 L 0.0097 0.9047 0.0856 190 N 0.0089 0.8974 0.0937 191 K 0.0119 0.8592 0.1289 192 M 0.0314 0.7269 0.2417 193 S 0.0400 0.6175 0.3425 194 E 0.0458 0.4995 0.4548 195 K 0.1010 0.2754 0.6236 196 D 0.1697 0.0769 0.7534 197 P 0.0189 0.6075 0.3736 198 K 0.0260 0.5821 0.3919 199 L 0.0616 0.5686 0.3697 200 M 0.1217 0.4705 0.4078 201 P 0.0736 0.5979 0.3285 202 F 0.0356 0.7804 0.1840 203 Q 0.0150 0.8651 0.1200 204 G 0.0103 0.8970 0.0927 205 Y 0.0115 0.9022 0.0863 206 V 0.0145 0.8910 0.0945 207 L 0.0133 0.8867 0.1000 208 Q 0.0156 0.8335 0.1509 209 N 0.0260 0.7240 0.2500 210 F 0.0551 0.7048 0.2401 211 E 0.0766 0.6762 0.2472 212 L 0.1295 0.5645 0.3060 213 S 0.1578 0.4277 0.4145 214 D 0.1294 0.3777 0.4929 215 S 0.0950 0.3586 0.5464 216 H 0.1091 0.2469 0.6439 217 E 0.1763 0.2154 0.6083 218 Y 0.3802 0.1512 0.4685 219 C 0.5089 0.1285 0.3626 220 Q 0.6391 0.0943 0.2666 221 I 0.6455 0.0897 0.2648 222 K 0.6123 0.0958 0.2919 223 I 0.5450 0.1111 0.3439 224 T 0.4007 0.1827 0.4166 225 N 0.2691 0.3775 0.3534 226 D 0.2614 0.4791 0.2595 227 V 0.2762 0.4868 0.2370 228 L 0.2763 0.4246 0.2991 229 K 0.2161 0.3881 0.3958 230 Q 0.1664 0.3342 0.4994 231 F 0.1330 0.2809 0.5861 232 D 0.1394 0.2007 0.6598 233 I 0.2352 0.1252 0.6396 234 Q 0.2058 0.0454 0.7488 235 P 0.0606 0.4416 0.4978 236 N 0.0600 0.4355 0.5045 237 E 0.0746 0.6208 0.3047 238 A 0.0380 0.7889 0.1731 239 S 0.0219 0.8611 0.1171 240 Q 0.0193 0.8852 0.0955 241 F 0.0189 0.8889 0.0922 242 V 0.0151 0.8928 0.0921 243 N 0.0125 0.8885 0.0990 244 T 0.0129 0.8866 0.1005 245 V 0.0219 0.8540 0.1242 246 A 0.0243 0.8209 0.1547 247 D 0.0304 0.7698 0.1998 248 I 0.0412 0.6657 0.2931 249 S 0.0639 0.2366 0.6995 250 G 0.0423 0.0882 0.8694 251 L 0.2179 0.0176 0.7645 252 K 0.4184 0.0260 0.5557 253 I 0.7724 0.0070 0.2206 254 W 0.8111 0.0057 0.1832 255 M 0.8210 0.0044 0.1746 256 F 0.8038 0.0061 0.1901 257 G 0.7772 0.0073 0.2155 258 V 0.6384 0.0133 0.3482 259 D 0.4412 0.0364 0.5224 260 E 0.1802 0.1267 0.6930 261 G 0.1021 0.0820 0.8158 262 D 0.2103 0.0663 0.7234 263 Q 0.5881 0.0168 0.3952 264 I 0.7640 0.0074 0.2286 265 R 0.8089 0.0051 0.1860 266 C 0.8233 0.0045 0.1722 267 R 0.8089 0.0051 0.1860 268 I 0.7643 0.0109 0.2248 269 R 0.5895 0.0360 0.3744 270 S 0.4240 0.0566 0.5195 271 K 0.1625 0.1439 0.6936 272 G 0.0860 0.1197 0.7943 273 I 0.2387 0.0384 0.7228 274 T 0.1893 0.0358 0.7749 275 I 0.0227 0.7317 0.2456 276 N 0.0149 0.8491 0.1359 277 D 0.0144 0.9007 0.0849 278 V 0.0105 0.9123 0.0772 279 A 0.0097 0.9061 0.0843 280 N 0.0121 0.8695 0.1184 281 Q 0.0221 0.7318 0.2461 282 F 0.0743 0.3573 0.5684 283 G 0.0580 0.2082 0.7338 284 G 0.0924 0.1817 0.7259 285 G 0.1336 0.1875 0.6789 286 G 0.1847 0.1870 0.6283 287 H 0.2031 0.1574 0.6395 288 P 0.0843 0.4897 0.4260 289 N 0.1091 0.4237 0.4672 290 A 0.2084 0.3655 0.4261 291 S 0.2905 0.2329 0.4766 292 G 0.3602 0.1367 0.5030 293 V 0.5342 0.0464 0.4194 294 S 0.5460 0.0393 0.4147 295 V 0.3887 0.0585 0.5528 296 Y 0.2291 0.1292 0.6418 297 S 0.1848 0.1722 0.6429 298 W 0.0481 0.6065 0.3454 299 D 0.0284 0.6917 0.2798 300 E 0.0361 0.7340 0.2299 301 F 0.0111 0.8538 0.1351 302 E 0.0084 0.9139 0.0776 303 E 0.0083 0.9243 0.0674 304 L 0.0083 0.9239 0.0678 305 A 0.0083 0.9204 0.0713 306 Q 0.0083 0.9239 0.0678 307 A 0.0083 0.9218 0.0699 308 L 0.0083 0.9208 0.0709 309 R 0.0085 0.9129 0.0786 310 Q 0.0085 0.9125 0.0791 311 K 0.0093 0.8887 0.1020 312 L 0.0148 0.8378 0.1474 313 L 0.0174 0.8044 0.1783 314 E 0.0296 0.7222 0.2481 315 H 0.0650 0.5483 0.3867 316 H 0.1020 0.3875 0.5104 317 H 0.1460 0.2569 0.5971 318 H 0.1579 0.2057 0.6364 319 H 0.1680 0.1595 0.6725 320 H 0.1645 0.1583 0.6772