# This file is the result of combining several RDB files, specifically # T0209.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0209.t2k.stride-ebghtl.rdb (weight 1.24869) # T0209.t2k.str2.rdb (weight 1.54758) # T0209.t2k.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 T0209.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0209 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0209.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 83 # # ============================================ # Comments from T0209.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0209 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0209.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 83 # # ============================================ # Comments from T0209.t2k.str2.rdb # ============================================ # TARGET T0209 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0209.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 83 # # ============================================ # Comments from T0209.t2k.alpha.rdb # ============================================ # TARGET T0209 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0209.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 83 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1131 0.0250 0.8619 2 N 0.2954 0.0203 0.6843 3 D 0.5976 0.0139 0.3885 4 L 0.7156 0.0100 0.2745 5 T 0.7723 0.0066 0.2211 6 L 0.6951 0.0057 0.2991 7 S 0.6718 0.0080 0.3202 8 P 0.7344 0.0067 0.2589 9 I 0.7649 0.0166 0.2185 10 A 0.8495 0.0088 0.1418 11 I 0.8862 0.0057 0.1081 12 I 0.8368 0.0112 0.1520 13 H 0.6908 0.0205 0.2886 14 T 0.3604 0.0252 0.6144 15 P 0.2607 0.0956 0.6438 16 Y 0.1646 0.1718 0.6636 17 K 0.1471 0.2610 0.5918 18 E 0.1512 0.2296 0.6192 19 K 0.1425 0.2258 0.6317 20 F 0.1104 0.1348 0.7548 21 S 0.1023 0.0816 0.8161 22 V 0.1122 0.0374 0.8504 23 P 0.1053 0.0499 0.8448 24 R 0.1712 0.0945 0.7343 25 Q 0.1282 0.0760 0.7958 26 P 0.0923 0.1797 0.7281 27 N 0.1230 0.1764 0.7007 28 L 0.1974 0.1702 0.6323 29 V 0.2118 0.1073 0.6808 30 E 0.1639 0.1168 0.7193 31 D 0.1566 0.0881 0.7553 32 G 0.3495 0.0516 0.5989 33 V 0.6215 0.0256 0.3529 34 G 0.8256 0.0098 0.1646 35 I 0.9076 0.0047 0.0877 36 V 0.9178 0.0038 0.0784 37 E 0.9109 0.0046 0.0845 38 L 0.8225 0.0079 0.1696 39 L 0.4823 0.0173 0.5005 40 P 0.1604 0.1012 0.7384 41 P 0.0849 0.1146 0.8005 42 Y 0.1100 0.1158 0.7742 43 N 0.1033 0.0422 0.8546 44 S 0.0366 0.3190 0.6444 45 P 0.0103 0.7898 0.2000 46 E 0.0104 0.8120 0.1776 47 A 0.0129 0.8099 0.1773 48 V 0.0222 0.7511 0.2267 49 R 0.0233 0.6373 0.3394 50 G 0.0299 0.4360 0.5341 51 L 0.0461 0.4380 0.5159 52 E 0.0435 0.4532 0.5033 53 Q 0.0419 0.3834 0.5747 54 F 0.1299 0.1284 0.7417 55 S 0.1383 0.0895 0.7722 56 H 0.5976 0.0317 0.3707 57 L 0.8957 0.0084 0.0960 58 W 0.9237 0.0063 0.0700 59 L 0.9295 0.0043 0.0661 60 I 0.9147 0.0093 0.0760 61 F 0.8994 0.0089 0.0917 62 Q 0.8559 0.0178 0.1262 63 F 0.7840 0.0394 0.1765 64 D 0.5652 0.0692 0.3656 65 Q 0.3160 0.1327 0.5513 66 I 0.1933 0.1113 0.6955 67 Q 0.0725 0.1432 0.7842 68 Q 0.0590 0.1475 0.7935 69 G 0.0730 0.1434 0.7836 70 K 0.1328 0.0675 0.7998 71 W 0.3493 0.0321 0.6185 72 Q 0.5722 0.0211 0.4067 73 P 0.6158 0.0221 0.3621 74 T 0.6621 0.0221 0.3158 75 V 0.6533 0.0140 0.3327 76 R 0.5085 0.0109 0.4806 77 P 0.3035 0.0125 0.6840 78 P 0.1842 0.0560 0.7598 79 R 0.1360 0.0719 0.7921 80 L 0.0786 0.1231 0.7983 81 G 0.0429 0.0922 0.8649 82 G 0.0571 0.0647 0.8782 83 N 0.0727 0.0530 0.8743 84 Q 0.1461 0.0792 0.7747 85 R 0.3370 0.0648 0.5981 86 V 0.5592 0.0338 0.4070 87 G 0.6685 0.0237 0.3078 88 V 0.8346 0.0148 0.1506 89 F 0.8282 0.0150 0.1569 90 A 0.7213 0.0161 0.2627 91 S 0.5216 0.0232 0.4552 92 R 0.2509 0.0267 0.7223 93 A 0.1480 0.0222 0.8298 94 T 0.0650 0.0945 0.8405 95 H 0.0859 0.0688 0.8453 96 R 0.0965 0.0341 0.8694 97 P 0.1009 0.0411 0.8580 98 N 0.1122 0.0392 0.8486 99 P 0.1253 0.1051 0.7696 100 L 0.2502 0.0860 0.6638 101 G 0.4872 0.0599 0.4529 102 L 0.6787 0.0272 0.2941 103 S 0.7467 0.0201 0.2333 104 K 0.8600 0.0113 0.1287 105 V 0.8639 0.0115 0.1246 106 E 0.8897 0.0068 0.1035 107 L 0.8816 0.0065 0.1119 108 R 0.8295 0.0247 0.1458 109 Q 0.8685 0.0106 0.1209 110 V 0.8531 0.0156 0.1313 111 E 0.8343 0.0194 0.1463 112 C 0.7157 0.0413 0.2430 113 I 0.3179 0.0760 0.6062 114 N 0.0885 0.0855 0.8260 115 G 0.0672 0.0522 0.8806 116 N 0.0983 0.0380 0.8637 117 I 0.3457 0.0134 0.6409 118 F 0.8736 0.0040 0.1224 119 L 0.9169 0.0037 0.0794 120 H 0.9214 0.0035 0.0751 121 L 0.8746 0.0068 0.1186 122 G 0.6206 0.0343 0.3451 123 A 0.5072 0.0351 0.4577 124 V 0.5146 0.0467 0.4386 125 D 0.6187 0.0524 0.3289 126 L 0.5021 0.1002 0.3977 127 V 0.3392 0.1087 0.5522 128 D 0.1493 0.0843 0.7664 129 G 0.1227 0.0461 0.8312 130 T 0.2345 0.0183 0.7472 131 P 0.4230 0.0220 0.5550 132 I 0.6205 0.0415 0.3380 133 F 0.6817 0.0376 0.2807 134 D 0.5860 0.0382 0.3759 135 I 0.3814 0.0533 0.5653 136 K 0.2376 0.0566 0.7057 137 P 0.1336 0.1095 0.7569 138 Y 0.1146 0.1231 0.7623 139 I 0.1181 0.0901 0.7918 140 A 0.0640 0.1915 0.7444 141 Y 0.0675 0.2684 0.6642 142 A 0.0906 0.2607 0.6487 143 D 0.0756 0.2133 0.7111 144 S 0.0930 0.1309 0.7761 145 E 0.0623 0.2705 0.6672 146 P 0.0256 0.3806 0.5938 147 N 0.0398 0.3333 0.6269 148 A 0.0973 0.2625 0.6402 149 Q 0.1032 0.2885 0.6082 150 S 0.0608 0.4334 0.5059 151 S 0.0531 0.4260 0.5209 152 F 0.0538 0.5324 0.4139 153 A 0.0532 0.5587 0.3882 154 Q 0.0427 0.5018 0.4555 155 E 0.0486 0.3873 0.5641 156 K 0.0632 0.2342 0.7026 157 L 0.0751 0.2464 0.6785 158 P 0.0816 0.3281 0.5904 159 V 0.1121 0.3660 0.5219 160 K 0.1450 0.3650 0.4900 161 L 0.2544 0.3017 0.4439 162 T 0.4099 0.2388 0.3512 163 V 0.5117 0.1773 0.3110 164 E 0.3949 0.1415 0.4636 165 F 0.1818 0.1481 0.6700 166 T 0.0465 0.4808 0.4727 167 E 0.0081 0.8673 0.1246 168 Q 0.0069 0.8922 0.1009 169 A 0.0065 0.9017 0.0919 170 K 0.0073 0.8960 0.0967 171 S 0.0081 0.8821 0.1097 172 A 0.0085 0.8751 0.1164 173 V 0.0097 0.8765 0.1138 174 K 0.0087 0.8712 0.1201 175 K 0.0103 0.8403 0.1494 176 R 0.0095 0.8226 0.1680 177 E 0.0094 0.7763 0.2143 178 E 0.0139 0.6617 0.3244 179 K 0.0190 0.5564 0.4247 180 R 0.0239 0.5810 0.3950 181 P 0.0092 0.7800 0.2108 182 H 0.0082 0.8420 0.1498 183 L 0.0055 0.9126 0.0819 184 S 0.0054 0.9422 0.0524 185 R 0.0050 0.9524 0.0426 186 F 0.0050 0.9551 0.0399 187 I 0.0047 0.9584 0.0369 188 R 0.0047 0.9593 0.0360 189 Q 0.0048 0.9563 0.0389 190 V 0.0049 0.9511 0.0439 191 L 0.0063 0.9304 0.0633 192 E 0.0087 0.8461 0.1452 193 Q 0.0261 0.5651 0.4089 194 D 0.0717 0.0861 0.8422 195 P 0.0346 0.2064 0.7591 196 R 0.0561 0.2192 0.7246 197 P 0.0692 0.2822 0.6486 198 A 0.0639 0.5057 0.4304 199 Y 0.1111 0.5258 0.3631 200 Q 0.1573 0.4341 0.4086 201 Q 0.1357 0.2942 0.5701 202 G 0.1247 0.1441 0.7311 203 K 0.1107 0.0783 0.8110 204 P 0.0988 0.0671 0.8342 205 S 0.0713 0.1362 0.7925 206 D 0.0905 0.1053 0.8042 207 R 0.4550 0.0449 0.5001 208 I 0.7931 0.0078 0.1991 209 Y 0.8764 0.0065 0.1171 210 G 0.9163 0.0035 0.0803 211 M 0.9107 0.0039 0.0854 212 S 0.8988 0.0041 0.0971 213 L 0.8375 0.0122 0.1503 214 Y 0.6486 0.0498 0.3016 215 E 0.5951 0.0419 0.3630 216 F 0.7215 0.0102 0.2682 217 N 0.8467 0.0067 0.1466 218 V 0.9148 0.0034 0.0819 219 K 0.9240 0.0040 0.0721 220 W 0.9245 0.0035 0.0720 221 R 0.9188 0.0037 0.0774 222 I 0.8643 0.0078 0.1279 223 K 0.4816 0.0434 0.4750 224 A 0.0718 0.0356 0.8927 225 G 0.0470 0.0669 0.8861 226 T 0.4794 0.0303 0.4902 227 V 0.8167 0.0057 0.1776 228 N 0.9056 0.0050 0.0893 229 C 0.9278 0.0031 0.0691 230 V 0.9056 0.0062 0.0882 231 E 0.9009 0.0050 0.0941 232 V 0.9122 0.0043 0.0835 233 I 0.8697 0.0118 0.1185 234 E 0.8520 0.0055 0.1424 235 I 0.6075 0.0323 0.3601 236 E 0.4013 0.0442 0.5544 237 K 0.1618 0.0689 0.7693 238 D 0.0878 0.0467 0.8655 239 K 0.0342 0.0463 0.9195