# This file is the result of combining several RDB files, specifically # T0338.t06.dssp-ebghstl.rdb (weight 1.53986) # T0338.t06.stride-ebghtl.rdb (weight 1.24869) # T0338.t06.str2.rdb (weight 1.54758) # T0338.t06.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 T0338.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0338 # 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 T0338.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 986 # # ============================================ # Comments from T0338.t06.stride-ebghtl.rdb # ============================================ # TARGET T0338 # Using neural net t06-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 T0338.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 986 # # ============================================ # Comments from T0338.t06.str2.rdb # ============================================ # TARGET T0338 # Using neural net 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 T0338.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 986 # # ============================================ # Comments from T0338.t06.alpha.rdb # ============================================ # TARGET T0338 # Using neural net 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 T0338.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 986 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.0537 0.1565 0.7898 2 S 0.0776 0.2077 0.7147 3 S 0.0699 0.2972 0.6329 4 R 0.0494 0.4109 0.5397 5 W 0.0748 0.4610 0.4641 6 F 0.1142 0.4306 0.4552 7 F 0.1677 0.3538 0.4785 8 T 0.1674 0.3644 0.4682 9 R 0.0465 0.7420 0.2116 10 E 0.0423 0.7492 0.2085 11 Q 0.0441 0.7081 0.2479 12 L 0.0609 0.5571 0.3820 13 E 0.0679 0.3760 0.5561 14 N 0.0745 0.1704 0.7550 15 T 0.0661 0.0369 0.8970 16 P 0.0456 0.1969 0.7575 17 S 0.0510 0.2873 0.6618 18 R 0.0652 0.3813 0.5535 19 R 0.0965 0.3696 0.5339 20 C 0.0923 0.2450 0.6627 21 G 0.0802 0.1141 0.8057 22 V 0.1428 0.0957 0.7615 23 E 0.1431 0.1212 0.7358 24 A 0.0650 0.3808 0.5543 25 D 0.0564 0.4193 0.5243 26 K 0.0558 0.4696 0.4745 27 E 0.0445 0.4934 0.4620 28 L 0.0133 0.8139 0.1728 29 S 0.0118 0.8568 0.1314 30 C 0.0057 0.9286 0.0657 31 R 0.0047 0.9507 0.0446 32 Q 0.0047 0.9587 0.0366 33 Q 0.0047 0.9575 0.0378 34 A 0.0047 0.9582 0.0371 35 A 0.0047 0.9605 0.0349 36 N 0.0047 0.9609 0.0344 37 L 0.0046 0.9607 0.0346 38 I 0.0047 0.9598 0.0355 39 Q 0.0047 0.9606 0.0348 40 E 0.0047 0.9587 0.0367 41 M 0.0047 0.9551 0.0402 42 G 0.0048 0.9485 0.0467 43 Q 0.0052 0.9371 0.0577 44 R 0.0060 0.9052 0.0888 45 L 0.0482 0.6042 0.3475 46 N 0.0565 0.0944 0.8491 47 V 0.0593 0.0691 0.8717 48 S 0.0546 0.1891 0.7564 49 Q 0.0061 0.8748 0.1192 50 L 0.0070 0.9183 0.0746 51 T 0.0064 0.9410 0.0526 52 I 0.0047 0.9570 0.0383 53 N 0.0047 0.9598 0.0355 54 T 0.0047 0.9584 0.0368 55 A 0.0047 0.9603 0.0350 56 I 0.0047 0.9601 0.0352 57 V 0.0047 0.9587 0.0366 58 Y 0.0047 0.9494 0.0459 59 M 0.0047 0.9503 0.0450 60 H 0.0054 0.9445 0.0502 61 R 0.0073 0.9308 0.0620 62 F 0.0143 0.8927 0.0930 63 Y 0.0333 0.8022 0.1645 64 M 0.0668 0.6570 0.2762 65 H 0.0789 0.4889 0.4323 66 H 0.1187 0.2119 0.6694 67 S 0.1703 0.1226 0.7072 68 F 0.2001 0.1185 0.6814 69 T 0.1774 0.1594 0.6632 70 K 0.0946 0.3705 0.5349 71 F 0.0683 0.3517 0.5800 72 N 0.0748 0.2914 0.6337 73 K 0.0226 0.7083 0.2691 74 N 0.0249 0.8271 0.1481 75 I 0.0397 0.9011 0.0592 76 I 0.0153 0.9390 0.0457 77 S 0.0092 0.9490 0.0418 78 S 0.0049 0.9584 0.0367 79 T 0.0047 0.9590 0.0364 80 A 0.0047 0.9596 0.0357 81 L 0.0049 0.9581 0.0370 82 F 0.0049 0.9568 0.0383 83 L 0.0052 0.9521 0.0426 84 A 0.0056 0.9390 0.0554 85 A 0.0078 0.9084 0.0838 86 K 0.0111 0.8915 0.0974 87 V 0.0272 0.8409 0.1319 88 E 0.0259 0.7994 0.1747 89 E 0.0470 0.6964 0.2566 90 Q 0.0633 0.5749 0.3618 91 A 0.0770 0.4532 0.4698 92 R 0.1247 0.3505 0.5248 93 K 0.1365 0.2667 0.5968 94 L 0.0133 0.8850 0.1016 95 E 0.0087 0.9122 0.0791 96 H 0.0146 0.9131 0.0722 97 V 0.0201 0.9184 0.0615 98 I 0.0417 0.8821 0.0762 99 K 0.0658 0.8290 0.1053 100 V 0.0615 0.8002 0.1384 101 A 0.0909 0.6896 0.2196 102 H 0.1199 0.5056 0.3745 103 A 0.1976 0.2953 0.5071 104 C 0.2254 0.1712 0.6033 105 L 0.1750 0.1130 0.7120 106 H 0.1133 0.0872 0.7995 107 P 0.1147 0.1338 0.7515 108 L 0.0711 0.3706 0.5584 109 E 0.0565 0.4533 0.4902 110 P 0.0517 0.5919 0.3564 111 L 0.0733 0.6175 0.3092 112 L 0.1645 0.4765 0.3590 113 D 0.1908 0.3861 0.4231 114 T 0.1873 0.3313 0.4814 115 K 0.1510 0.2963 0.5527 116 C 0.0631 0.4613 0.4756 117 D 0.0292 0.6173 0.3536 118 A 0.0352 0.7232 0.2416 119 Y 0.0544 0.7196 0.2260 120 L 0.0475 0.6880 0.2645 121 Q 0.0390 0.6612 0.2998 122 Q 0.0225 0.6653 0.3122 123 T 0.0063 0.9179 0.0758 124 R 0.0049 0.9495 0.0456 125 E 0.0048 0.9567 0.0385 126 L 0.0047 0.9598 0.0355 127 V 0.0047 0.9602 0.0351 128 I 0.0047 0.9603 0.0351 129 L 0.0047 0.9600 0.0353 130 E 0.0047 0.9607 0.0347 131 T 0.0046 0.9613 0.0341 132 I 0.0046 0.9603 0.0351 133 M 0.0047 0.9595 0.0359 134 L 0.0047 0.9582 0.0371 135 Q 0.0055 0.9454 0.0492 136 T 0.0062 0.8991 0.0947 137 L 0.0547 0.4654 0.4800 138 G 0.0588 0.0516 0.8897 139 F 0.2049 0.0321 0.7630 140 E 0.5654 0.0296 0.4050 141 I 0.7219 0.0121 0.2659 142 T 0.6755 0.0165 0.3080 143 I 0.5730 0.0148 0.4122 144 E 0.2815 0.0487 0.6698 145 H 0.1282 0.0268 0.8451 146 P 0.0539 0.1811 0.7650 147 H 0.0420 0.3335 0.6246 148 T 0.0252 0.6852 0.2895 149 D 0.0181 0.8596 0.1223 150 V 0.0081 0.9415 0.0504 151 V 0.0067 0.9533 0.0400 152 K 0.0066 0.9530 0.0403 153 C 0.0065 0.9507 0.0428 154 T 0.0077 0.9435 0.0487 155 Q 0.0086 0.9196 0.0718 156 L 0.0091 0.8837 0.1072 157 V 0.0383 0.7117 0.2501 158 R 0.0412 0.4721 0.4867 159 A 0.0407 0.3979 0.5614 160 S 0.0501 0.4123 0.5377 161 K 0.0123 0.8119 0.1758 162 D 0.0137 0.8516 0.1347 163 L 0.0051 0.9303 0.0646 164 A 0.0049 0.9486 0.0465 165 Q 0.0048 0.9528 0.0425 166 T 0.0047 0.9546 0.0406 167 S 0.0047 0.9577 0.0376 168 Y 0.0047 0.9596 0.0358 169 F 0.0047 0.9593 0.0360 170 M 0.0048 0.9547 0.0406 171 A 0.0048 0.9497 0.0455 172 T 0.0063 0.9230 0.0707 173 N 0.0086 0.8527 0.1386 174 S 0.0187 0.7818 0.1995 175 L 0.0414 0.6381 0.3205 176 H 0.0828 0.4462 0.4710 177 L 0.1367 0.3400 0.5233 178 T 0.1308 0.2758 0.5934 179 T 0.1320 0.4317 0.4363 180 F 0.1917 0.4602 0.3482 181 C 0.2745 0.4498 0.2757 182 L 0.2926 0.3597 0.3477 183 Q 0.2526 0.2649 0.4825 184 Y 0.1785 0.1880 0.6335 185 K 0.0897 0.1372 0.7731 186 P 0.0103 0.8856 0.1041 187 T 0.0058 0.9351 0.0592 188 V 0.0050 0.9574 0.0376 189 I 0.0047 0.9598 0.0355 190 A 0.0047 0.9608 0.0345 191 C 0.0047 0.9608 0.0346 192 V 0.0047 0.9610 0.0344 193 C 0.0046 0.9610 0.0344 194 I 0.0047 0.9605 0.0349 195 H 0.0046 0.9604 0.0349 196 L 0.0047 0.9587 0.0367 197 A 0.0047 0.9571 0.0382 198 C 0.0049 0.9486 0.0465 199 K 0.0055 0.9150 0.0795 200 W 0.0083 0.8369 0.1548 201 S 0.0448 0.4427 0.5125 202 N 0.0362 0.0887 0.8751 203 W 0.0837 0.0417 0.8746 204 E 0.1539 0.0406 0.8055 205 I 0.1496 0.0223 0.8282 206 P 0.1424 0.0293 0.8283 207 V 0.1747 0.0815 0.7439 208 S 0.1531 0.0924 0.7546 209 T 0.1082 0.1360 0.7558 210 D 0.0743 0.1310 0.7947 211 G 0.1134 0.1286 0.7580 212 K 0.2613 0.1448 0.5940 213 H 0.4090 0.1597 0.4313 214 W 0.5792 0.1698 0.2511 215 W 0.6121 0.1648 0.2232 216 E 0.6556 0.1432 0.2013 217 Y 0.6474 0.1024 0.2502 218 V 0.4398 0.0779 0.4823 219 D 0.1435 0.0327 0.8239 220 P 0.0171 0.1276 0.8554 221 T 0.0377 0.0593 0.9031 222 V 0.1845 0.0195 0.7960 223 T 0.1035 0.0109 0.8856 224 L 0.0050 0.9284 0.0666 225 E 0.0048 0.9392 0.0560 226 L 0.0049 0.9409 0.0541 227 L 0.0050 0.9485 0.0464 228 D 0.0047 0.9566 0.0387 229 E 0.0047 0.9550 0.0403 230 L 0.0047 0.9546 0.0407 231 T 0.0047 0.9597 0.0357 232 H 0.0047 0.9602 0.0351 233 E 0.0046 0.9588 0.0366 234 F 0.0047 0.9578 0.0375 235 L 0.0047 0.9584 0.0369 236 Q 0.0048 0.9573 0.0380 237 I 0.0050 0.9480 0.0471 238 L 0.0054 0.9149 0.0797 239 E 0.0075 0.7955 0.1970 240 K 0.0170 0.5816 0.4014 241 T 0.0662 0.0520 0.8818 242 P 0.0141 0.4295 0.5564 243 N 0.0221 0.4628 0.5152 244 R 0.0307 0.6251 0.3442 245 L 0.0340 0.7311 0.2349 246 K 0.0589 0.7514 0.1898 247 K 0.0720 0.7408 0.1872 248 I 0.0840 0.6876 0.2284 249 R 0.1167 0.6125 0.2707 250 N 0.1207 0.5014 0.3779 251 W 0.1045 0.5523 0.3432 252 R 0.0982 0.5543 0.3475 253 A 0.0715 0.4719 0.4566 254 N 0.0552 0.3019 0.6428 255 Q 0.0555 0.1288 0.8158 256 A 0.0379 0.0453 0.9168