# This file is the result of combining several RDB files, specifically # T0316.t04.dssp-ebghstl.rdb (weight 1.53986) # T0316.t04.stride-ebghtl.rdb (weight 1.24869) # T0316.t04.str2.rdb (weight 1.54758) # T0316.t04.alpha.rdb (weight 0.659012) # 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 T0316.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0316 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0316.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 23.8055 # # ============================================ # Comments from T0316.t04.stride-ebghtl.rdb # ============================================ # TARGET T0316 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0316.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 23.8055 # # ============================================ # Comments from T0316.t04.str2.rdb # ============================================ # TARGET T0316 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0316.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 23.8055 # # ============================================ # Comments from T0316.t04.alpha.rdb # ============================================ # TARGET T0316 # Using neural net t04-2621-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 T0316.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 23.8055 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.2333 0.0275 0.7392 2 R 0.5648 0.0226 0.4125 3 V 0.7136 0.0183 0.2681 4 A 0.7733 0.0127 0.2140 5 R 0.7250 0.0176 0.2574 6 D 0.2814 0.0412 0.6775 7 E 0.0670 0.1031 0.8299 8 D 0.0508 0.0218 0.9273 9 G 0.0817 0.0277 0.8906 10 T 0.3996 0.0165 0.5839 11 V 0.8513 0.0055 0.1432 12 H 0.8767 0.0090 0.1143 13 M 0.8944 0.0098 0.0958 14 L 0.8584 0.0186 0.1231 15 R 0.7772 0.0280 0.1948 16 G 0.6366 0.0305 0.3329 17 V 0.4538 0.0500 0.4962 18 D 0.2218 0.0419 0.7363 19 N 0.0354 0.1059 0.8587 20 G 0.0261 0.0892 0.8847 21 K 0.0747 0.1608 0.7645 22 D 0.1328 0.1651 0.7021 23 Q 0.2053 0.4636 0.3311 24 T 0.3418 0.5022 0.1559 25 Y 0.3630 0.5473 0.0898 26 F 0.3496 0.5591 0.0913 27 L 0.2658 0.5976 0.1366 28 S 0.1679 0.5617 0.2703 29 Q 0.1251 0.3605 0.5144 30 L 0.1053 0.1291 0.7656 31 S 0.0648 0.0661 0.8690 32 Q 0.0049 0.9236 0.0716 33 E 0.0047 0.9421 0.0532 34 Q 0.0048 0.9481 0.0471 35 L 0.0048 0.9500 0.0453 36 Q 0.0053 0.9307 0.0640 37 K 0.0106 0.8355 0.1538 38 T 0.0339 0.7065 0.2595 39 M 0.0919 0.4299 0.4782 40 F 0.0996 0.2183 0.6820 41 P 0.0873 0.1950 0.7177 42 L 0.0508 0.3712 0.5780 43 G 0.0396 0.2905 0.6699 44 H 0.0495 0.2518 0.6987 45 L 0.0749 0.1250 0.8001 46 E 0.0630 0.0921 0.8449 47 K 0.0274 0.5886 0.3840 48 P 0.0055 0.8634 0.1312 49 E 0.0066 0.9294 0.0639 50 V 0.0056 0.9481 0.0464 51 R 0.0047 0.9555 0.0398 52 R 0.0046 0.9615 0.0339 53 L 0.0046 0.9617 0.0336 54 A 0.0047 0.9612 0.0342 55 E 0.0048 0.9567 0.0385 56 E 0.0052 0.9452 0.0496 57 A 0.0425 0.5545 0.4030 58 G 0.0421 0.0274 0.9305 59 L 0.0693 0.0175 0.9132 60 S 0.1488 0.0770 0.7742 61 T 0.3307 0.1680 0.5013 62 A 0.3546 0.1557 0.4897 63 K 0.2963 0.1207 0.5830 64 K 0.1833 0.0992 0.7175 65 K 0.1028 0.1918 0.7054 66 D 0.1037 0.1809 0.7154 67 S 0.2605 0.1227 0.6168 68 T 0.2578 0.0803 0.6619 69 G 0.4311 0.0509 0.5180 70 I 0.8139 0.0109 0.1753 71 C 0.8881 0.0098 0.1021 72 F 0.8682 0.0092 0.1226 73 I 0.6308 0.0243 0.3449 74 G 0.2084 0.0289 0.7627 75 E 0.0814 0.1132 0.8054 76 K 0.0447 0.2007 0.7547 77 N 0.0706 0.2709 0.6585 78 F 0.0153 0.8581 0.1266 79 K 0.0068 0.9125 0.0807 80 N 0.0081 0.9035 0.0884 81 F 0.0198 0.8967 0.0835 82 L 0.0155 0.8865 0.0981 83 S 0.0076 0.8632 0.1292 84 N 0.0158 0.6706 0.3136 85 Y 0.0493 0.3959 0.5548 86 L 0.0787 0.0409 0.8805 87 P 0.0815 0.0508 0.8677 88 A 0.1382 0.0330 0.8287 89 Q 0.1199 0.0228 0.8573 90 P 0.0995 0.0646 0.8359 91 G 0.2007 0.0396 0.7597 92 R 0.5787 0.0176 0.4037 93 M 0.8793 0.0054 0.1153 94 M 0.8694 0.0058 0.1248 95 T 0.6367 0.0083 0.3550 96 V 0.1868 0.0784 0.7348 97 D 0.0449 0.0311 0.9239 98 G 0.0620 0.0346 0.9034 99 R 0.4482 0.0194 0.5324 100 D 0.8343 0.0123 0.1534 101 M 0.7475 0.0423 0.2103 102 G 0.6504 0.0430 0.3066 103 E 0.5720 0.0667 0.3613 104 H 0.4530 0.0750 0.4720 105 A 0.2152 0.0888 0.6960 106 G 0.3506 0.0451 0.6043 107 L 0.6573 0.0407 0.3020 108 M 0.8372 0.0210 0.1418 109 Y 0.8631 0.0230 0.1140 110 Y 0.8463 0.0335 0.1202 111 T 0.7497 0.0601 0.1903 112 I 0.5411 0.1858 0.2731 113 G 0.4531 0.1478 0.3991 114 Q 0.4415 0.2027 0.3558 115 R 0.3756 0.2047 0.4198 116 G 0.2128 0.1987 0.5885 117 G 0.1877 0.1329 0.6795 118 L 0.2515 0.1021 0.6464 119 G 0.3055 0.0761 0.6184 120 I 0.2786 0.1275 0.5940 121 G 0.2665 0.1098 0.6237 122 G 0.2067 0.1169 0.6764 123 Q 0.1647 0.1237 0.7116 124 H 0.1224 0.1150 0.7626 125 G 0.0689 0.0934 0.8377 126 G 0.0572 0.1149 0.8279 127 D 0.0833 0.0928 0.8238 128 N 0.1107 0.0553 0.8341 129 A 0.1783 0.0140 0.8076 130 P 0.3514 0.0135 0.6350 131 W 0.7238 0.0174 0.2587 132 F 0.8837 0.0088 0.1075 133 V 0.8996 0.0061 0.0943 134 V 0.8296 0.0274 0.1431 135 G 0.7543 0.0201 0.2255 136 K 0.6246 0.0294 0.3460 137 D 0.4451 0.0383 0.5167 138 L 0.1056 0.2797 0.6147 139 S 0.0727 0.2652 0.6621 140 K 0.0946 0.1976 0.7078 141 N 0.1811 0.0346 0.7843 142 I 0.7727 0.0074 0.2198 143 L 0.9194 0.0035 0.0770 144 Y 0.9232 0.0038 0.0730 145 V 0.8689 0.0112 0.1199 146 G 0.4890 0.0128 0.4981 147 Q 0.1226 0.0549 0.8225 148 G 0.0562 0.0588 0.8850 149 F 0.0862 0.0906 0.8232 150 Y 0.1013 0.0942 0.8046 151 H 0.0733 0.1918 0.7349 152 D 0.0230 0.4983 0.4787 153 S 0.0321 0.6231 0.3449 154 L 0.1086 0.5063 0.3851 155 M 0.1761 0.3390 0.4850 156 S 0.2043 0.2333 0.5624 157 T 0.2058 0.1733 0.6209 158 S 0.5027 0.0824 0.4149 159 L 0.7287 0.0228 0.2486 160 E 0.7801 0.0214 0.1985 161 A 0.6820 0.0651 0.2529 162 S 0.4193 0.1348 0.4459 163 Q 0.4149 0.1240 0.4610 164 V 0.5355 0.0714 0.3930 165 H 0.6015 0.0751 0.3234 166 F 0.5660 0.0943 0.3397 167 T 0.4812 0.1026 0.4162 168 R 0.3010 0.1057 0.5932 169 E 0.2224 0.0830 0.6946 170 M 0.1503 0.0282 0.8215 171 P 0.0949 0.0487 0.8563 172 E 0.0549 0.2514 0.6937 173 E 0.0599 0.2047 0.7354 174 F 0.1456 0.1030 0.7514 175 T 0.2912 0.0408 0.6680 176 L 0.5914 0.0195 0.3891 177 E 0.7804 0.0117 0.2079 178 C 0.8852 0.0040 0.1108 179 T 0.9130 0.0041 0.0829 180 A 0.9165 0.0037 0.0798 181 K 0.9201 0.0038 0.0761 182 F 0.8995 0.0042 0.0964 183 R 0.8156 0.0116 0.1728 184 Y 0.6837 0.0138 0.3025 185 R 0.3581 0.0235 0.6184 186 Q 0.1529 0.0231 0.8240 187 P 0.1020 0.0581 0.8399 188 D 0.1193 0.0617 0.8190 189 S 0.2854 0.0207 0.6939 190 K 0.5733 0.0100 0.4167 191 V 0.8469 0.0050 0.1481 192 T 0.9168 0.0034 0.0798 193 V 0.9239 0.0033 0.0728 194 H 0.9150 0.0038 0.0812 195 V 0.8652 0.0075 0.1273 196 K 0.4950 0.0278 0.4772 197 G 0.1088 0.0369 0.8543 198 E 0.1293 0.0650 0.8057 199 K 0.5989 0.0198 0.3813 200 T 0.8661 0.0044 0.1295 201 E 0.9163 0.0038 0.0799 202 V 0.9244 0.0032 0.0724 203 I 0.9062 0.0040 0.0897 204 F 0.8349 0.0071 0.1579 205 A 0.4439 0.0278 0.5282 206 E 0.1997 0.0239 0.7764 207 P 0.2215 0.0609 0.7176 208 Q 0.4059 0.0917 0.5023 209 R 0.6157 0.0677 0.3166 210 A 0.7009 0.0340 0.2651 211 I 0.6042 0.0319 0.3639 212 T 0.2668 0.0215 0.7117 213 P 0.0688 0.0620 0.8692 214 G 0.0859 0.0273 0.8869 215 Q 0.5806 0.0120 0.4074 216 A 0.8710 0.0052 0.1238 217 V 0.9219 0.0033 0.0748 218 V 0.9307 0.0032 0.0661 219 F 0.9110 0.0049 0.0840 220 Y 0.8166 0.0103 0.1731 221 D 0.3214 0.0222 0.6564 222 G 0.0678 0.0300 0.9022 223 E 0.1888 0.0689 0.7424 224 E 0.6252 0.0361 0.3387 225 C 0.7920 0.0261 0.1819 226 L 0.7282 0.0470 0.2247 227 G 0.5769 0.0532 0.3699 228 G 0.5310 0.0815 0.3875 229 G 0.6607 0.0893 0.2500 230 L 0.7414 0.1066 0.1520 231 I 0.6602 0.1972 0.1427 232 D 0.4872 0.2523 0.2605 233 N 0.3027 0.2731 0.4243 234 A 0.2671 0.2605 0.4724 235 Y 0.2230 0.2077 0.5693 236 R 0.1668 0.2065 0.6267 237 D 0.1073 0.2279 0.6648 238 G 0.1125 0.1960 0.6915 239 Q 0.2541 0.2100 0.5358 240 V 0.3674 0.2607 0.3719 241 C 0.3704 0.2411 0.3884 242 Q 0.3320 0.2257 0.4424 243 Y 0.2573 0.1738 0.5689 244 I 0.1259 0.0791 0.7950