# This file is the result of combining several RDB files, specifically # T0381.t04.dssp-ebghstl.rdb (weight 1.53986) # T0381.t04.stride-ebghtl.rdb (weight 1.24869) # T0381.t04.str2.rdb (weight 1.54758) # T0381.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 T0381.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0381 # Using neural net t06-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 T0381.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 1165 # # ============================================ # Comments from T0381.t04.stride-ebghtl.rdb # ============================================ # TARGET T0381 # 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 T0381.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 1165 # # ============================================ # Comments from T0381.t04.str2.rdb # ============================================ # TARGET T0381 # Using neural net t04-2621-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 T0381.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 1165 # # ============================================ # Comments from T0381.t04.alpha.rdb # ============================================ # TARGET T0381 # 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 T0381.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 1165 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0770 0.0184 0.9047 2 T 0.0764 0.0236 0.9000 3 A 0.0475 0.1173 0.8352 4 T 0.0520 0.1134 0.8345 5 E 0.0708 0.0829 0.8463 6 P 0.0699 0.1126 0.8175 7 T 0.0788 0.2341 0.6870 8 E 0.0428 0.4682 0.4890 9 K 0.0485 0.4134 0.5381 10 I 0.0791 0.2132 0.7077 11 L 0.0784 0.0479 0.8737 12 P 0.0626 0.0551 0.8823 13 S 0.0664 0.0297 0.9040 14 P 0.0198 0.4029 0.5772 15 D 0.0240 0.5088 0.4671 16 Y 0.0254 0.7320 0.2426 17 V 0.0195 0.8433 0.1372 18 Q 0.0114 0.8964 0.0923 19 S 0.0083 0.9309 0.0608 20 L 0.0047 0.9554 0.0399 21 A 0.0047 0.9603 0.0350 22 R 0.0047 0.9598 0.0355 23 G 0.0047 0.9603 0.0350 24 L 0.0047 0.9603 0.0350 25 A 0.0046 0.9612 0.0342 26 V 0.0046 0.9601 0.0352 27 I 0.0047 0.9585 0.0368 28 R 0.0047 0.9507 0.0446 29 C 0.0049 0.9362 0.0589 30 F 0.0081 0.8751 0.1168 31 D 0.0179 0.7323 0.2498 32 H 0.0214 0.5923 0.3864 33 R 0.0478 0.3634 0.5888 34 N 0.0371 0.1680 0.7949 35 Q 0.0471 0.1292 0.8237 36 R 0.1027 0.0863 0.8110 37 R 0.1665 0.0320 0.8015 38 T 0.1180 0.0296 0.8525 39 L 0.0048 0.9535 0.0417 40 S 0.0046 0.9611 0.0343 41 D 0.0046 0.9614 0.0340 42 V 0.0046 0.9614 0.0339 43 A 0.0047 0.9587 0.0366 44 R 0.0049 0.9450 0.0500 45 A 0.0056 0.8890 0.1054 46 T 0.0484 0.4608 0.4908 47 D 0.0390 0.0567 0.9042 48 L 0.0547 0.0260 0.9193 49 T 0.0503 0.0623 0.8874 50 R 0.0223 0.6133 0.3644 51 A 0.0129 0.8740 0.1131 52 T 0.0082 0.9118 0.0799 53 A 0.0047 0.9564 0.0389 54 R 0.0047 0.9609 0.0344 55 R 0.0046 0.9611 0.0343 56 F 0.0047 0.9598 0.0355 57 L 0.0047 0.9604 0.0349 58 L 0.0046 0.9607 0.0347 59 T 0.0046 0.9611 0.0343 60 L 0.0047 0.9603 0.0351 61 V 0.0048 0.9532 0.0420 62 E 0.0053 0.9248 0.0698 63 L 0.0413 0.5260 0.4327 64 G 0.0289 0.0745 0.8966 65 Y 0.1623 0.0611 0.7766 66 V 0.6715 0.0432 0.2852 67 A 0.7115 0.0289 0.2595 68 T 0.6652 0.0331 0.3017 69 D 0.2702 0.0271 0.7027 70 G 0.0406 0.0596 0.8998 71 S 0.0749 0.0536 0.8715 72 A 0.3384 0.0512 0.6103 73 F 0.5490 0.0260 0.4250 74 W 0.5726 0.0237 0.4038 75 L 0.3723 0.0356 0.5922 76 T 0.1016 0.0615 0.8369 77 P 0.0089 0.9041 0.0871 78 R 0.0069 0.9344 0.0587 79 V 0.0058 0.9510 0.0431 80 L 0.0074 0.9475 0.0450 81 E 0.0077 0.9413 0.0510 82 L 0.0082 0.9083 0.0835 83 G 0.0087 0.8966 0.0947 84 Y 0.0100 0.9036 0.0865 85 S 0.0106 0.8942 0.0952 86 Y 0.0121 0.8551 0.1327 87 L 0.0210 0.7841 0.1948 88 S 0.0154 0.6281 0.3565 89 S 0.0230 0.4365 0.5405 90 L 0.0567 0.1788 0.7644 91 S 0.0488 0.1258 0.8254 92 L 0.0395 0.5820 0.3785 93 P 0.0233 0.8145 0.1622 94 E 0.0091 0.8842 0.1067 95 V 0.0105 0.8546 0.1349 96 A 0.0126 0.8190 0.1684 97 Q 0.0085 0.8501 0.1414 98 P 0.0054 0.9146 0.0800 99 H 0.0048 0.9432 0.0519 100 L 0.0047 0.9573 0.0380 101 E 0.0047 0.9592 0.0362 102 K 0.0047 0.9569 0.0384 103 L 0.0049 0.9510 0.0441 104 S 0.0051 0.9394 0.0555 105 H 0.0060 0.8782 0.1158 106 K 0.0104 0.7324 0.2572 107 V 0.0691 0.3582 0.5727 108 H 0.0445 0.1150 0.8405 109 E 0.1705 0.0877 0.7418 110 S 0.4699 0.0434 0.4867 111 S 0.7268 0.0244 0.2488 112 S 0.8433 0.0124 0.1442 113 V 0.9029 0.0082 0.0889 114 S 0.9167 0.0058 0.0775 115 I 0.9052 0.0066 0.0882 116 L 0.8246 0.0132 0.1622 117 D 0.2933 0.0283 0.6784 118 G 0.0621 0.0390 0.8989 119 A 0.1437 0.0520 0.8044 120 D 0.6144 0.0193 0.3664 121 I 0.9085 0.0033 0.0881 122 V 0.9272 0.0036 0.0693 123 Y 0.9287 0.0035 0.0678 124 V 0.9193 0.0041 0.0765 125 A 0.8763 0.0076 0.1162 126 R 0.7813 0.0080 0.2107 127 V 0.5362 0.0084 0.4554 128 P 0.3102 0.0171 0.6727 129 V 0.1266 0.0976 0.7758 130 S 0.0855 0.1568 0.7577 131 R 0.1557 0.1274 0.7169 132 I 0.3636 0.0710 0.5653 133 M 0.5806 0.0417 0.3778 134 T 0.7371 0.0319 0.2310 135 V 0.7195 0.0349 0.2456 136 G 0.6567 0.0251 0.3182 137 I 0.5270 0.0253 0.4477 138 T 0.4232 0.0349 0.5419 139 I 0.1974 0.1169 0.6857 140 G 0.1072 0.0870 0.8057 141 T 0.2340 0.0964 0.6697 142 R 0.3651 0.0708 0.5640 143 L 0.2606 0.0731 0.6663 144 P 0.1966 0.1553 0.6482 145 A 0.1245 0.4790 0.3965 146 Y 0.1308 0.5368 0.3324 147 A 0.1321 0.5404 0.3275 148 T 0.0555 0.6205 0.3240 149 S 0.0351 0.7347 0.2302 150 M 0.0112 0.8829 0.1059 151 G 0.0084 0.9287 0.0629 152 R 0.0107 0.9413 0.0480 153 V 0.0110 0.9450 0.0439 154 L 0.0110 0.9367 0.0524 155 L 0.0160 0.8617 0.1223 156 A 0.0371 0.5769 0.3859 157 G 0.0256 0.3044 0.6700 158 L 0.0598 0.0201 0.9201 159 P 0.0534 0.0146 0.9320 160 D 0.0050 0.8912 0.1038 161 D 0.0047 0.9443 0.0509 162 E 0.0048 0.9522 0.0430 163 L 0.0047 0.9577 0.0376 164 D 0.0047 0.9574 0.0379 165 A 0.0047 0.9530 0.0423 166 Y 0.0047 0.9487 0.0465 167 L 0.0052 0.9333 0.0615 168 E 0.0054 0.8746 0.1200 169 K 0.0093 0.6547 0.3361 170 L 0.0559 0.3210 0.6231 171 D 0.0687 0.1258 0.8055 172 I 0.0698 0.3302 0.6000 173 Q 0.0832 0.4146 0.5021 174 R 0.1206 0.4137 0.4657 175 L 0.1369 0.2486 0.6145 176 T 0.0927 0.0912 0.8161 177 E 0.0169 0.3346 0.6485 178 R 0.0356 0.2584 0.7059 179 T 0.0811 0.2413 0.6777 180 I 0.1071 0.1770 0.7159 181 T 0.1323 0.0983 0.7694 182 A 0.0813 0.0739 0.8449 183 R 0.0050 0.9406 0.0544 184 D 0.0047 0.9582 0.0371 185 E 0.0047 0.9596 0.0358 186 L 0.0047 0.9591 0.0362 187 K 0.0047 0.9606 0.0347 188 A 0.0047 0.9605 0.0348 189 A 0.0047 0.9597 0.0356 190 I 0.0047 0.9601 0.0352 191 L 0.0047 0.9604 0.0349 192 A 0.0047 0.9608 0.0346 193 V 0.0047 0.9581 0.0372 194 R 0.0050 0.9439 0.0511 195 A 0.0081 0.8035 0.1884 196 D 0.0404 0.3120 0.6476 197 G 0.0490 0.0890 0.8620 198 I 0.2581 0.0716 0.6702 199 C 0.6901 0.0441 0.2658 200 V 0.6346 0.0484 0.3170 201 L 0.4160 0.0579 0.5261 202 D 0.0844 0.3782 0.5374 203 Q 0.0494 0.5808 0.3698 204 E 0.0873 0.6381 0.2745 205 L 0.1350 0.5798 0.2852 206 E 0.1162 0.5039 0.3799 207 A 0.0576 0.3319 0.6106 208 G 0.0772 0.0814 0.8414 209 L 0.3931 0.0308 0.5761 210 R 0.6470 0.0450 0.3080 211 S 0.8826 0.0110 0.1064 212 M 0.8965 0.0073 0.0962 213 A 0.8996 0.0063 0.0941 214 A 0.8378 0.0069 0.1554 215 P 0.7916 0.0070 0.2014 216 I 0.7499 0.0110 0.2390 217 R 0.6314 0.0233 0.3453 218 G 0.1803 0.0393 0.7805 219 A 0.0347 0.1263 0.8389 220 S 0.0500 0.0338 0.9162 221 G 0.0620 0.0313 0.9067 222 L 0.2827 0.0091 0.7082 223 T 0.8217 0.0034 0.1749 224 V 0.8906 0.0095 0.0999 225 A 0.9255 0.0038 0.0707 226 A 0.9311 0.0034 0.0655 227 V 0.9274 0.0038 0.0688 228 N 0.9112 0.0047 0.0841 229 I 0.8239 0.0116 0.1645 230 S 0.5726 0.0251 0.4023 231 T 0.2443 0.0284 0.7274 232 P 0.1501 0.0919 0.7579 233 A 0.0891 0.3687 0.5423 234 A 0.0922 0.3539 0.5539 235 R 0.1433 0.2277 0.6290 236 Y 0.1921 0.0348 0.7731 237 S 0.1041 0.0237 0.8722 238 L 0.0050 0.9121 0.0829 239 E 0.0050 0.9375 0.0575 240 D 0.0048 0.9385 0.0566 241 L 0.0048 0.9325 0.0627 242 H 0.0051 0.9220 0.0729 243 S 0.0058 0.8832 0.1110 244 D 0.0054 0.8347 0.1599 245 L 0.0078 0.8725 0.1197 246 I 0.0049 0.9282 0.0669 247 P 0.0047 0.9580 0.0373 248 S 0.0047 0.9609 0.0344 249 L 0.0047 0.9605 0.0348 250 R 0.0046 0.9612 0.0342 251 V 0.0046 0.9608 0.0345 252 T 0.0047 0.9581 0.0373 253 A 0.0047 0.9564 0.0389 254 T 0.0047 0.9538 0.0415 255 D 0.0049 0.9452 0.0499 256 I 0.0052 0.9366 0.0583 257 E 0.0058 0.9206 0.0736 258 Q 0.0064 0.8793 0.1143 259 D 0.0103 0.8034 0.1863 260 L 0.0350 0.6673 0.2976 261 A 0.0320 0.3576 0.6104 262 T 0.0464 0.2593 0.6943 263 V 0.0585 0.1938 0.7477 264 N 0.0542 0.0748 0.8710 265 R 0.0371 0.0609 0.9020