# This file is the result of combining several RDB files, specifically # T0325.t06.dssp-ebghstl.rdb (weight 1.53986) # T0325.t06.stride-ebghtl.rdb (weight 1.24869) # T0325.t06.str2.rdb (weight 1.54758) # T0325.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 T0325.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0325 # 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 T0325.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 107.445 # # ============================================ # Comments from T0325.t06.stride-ebghtl.rdb # ============================================ # TARGET T0325 # 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 T0325.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 107.445 # # ============================================ # Comments from T0325.t06.str2.rdb # ============================================ # TARGET T0325 # 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 T0325.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 107.445 # # ============================================ # Comments from T0325.t06.alpha.rdb # ============================================ # TARGET T0325 # 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 T0325.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 107.445 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0518 0.0402 0.9080 2 S 0.0876 0.0348 0.8776 3 N 0.1439 0.0445 0.8115 4 K 0.3765 0.0188 0.6047 5 K 0.7918 0.0054 0.2029 6 L 0.9225 0.0034 0.0741 7 I 0.9296 0.0033 0.0671 8 I 0.9152 0.0051 0.0797 9 N 0.7849 0.0062 0.2089 10 A 0.3156 0.0473 0.6371 11 D 0.1167 0.1152 0.7680 12 D 0.0884 0.1823 0.7293 13 F 0.0757 0.1819 0.7424 14 G 0.0997 0.1334 0.7669 15 Y 0.1674 0.0745 0.7580 16 T 0.0752 0.0351 0.8897 17 P 0.0074 0.5644 0.4282 18 A 0.0102 0.6706 0.3192 19 V 0.0142 0.8175 0.1683 20 T 0.0115 0.8859 0.1026 21 Q 0.0091 0.9291 0.0618 22 G 0.0137 0.9449 0.0414 23 I 0.0059 0.9585 0.0356 24 I 0.0047 0.9600 0.0353 25 E 0.0054 0.9572 0.0375 26 A 0.0061 0.9495 0.0444 27 H 0.0055 0.9370 0.0575 28 K 0.0081 0.8948 0.0971 29 R 0.0450 0.4299 0.5251 30 G 0.0431 0.0402 0.9167 31 V 0.1903 0.0517 0.7580 32 V 0.6186 0.0294 0.3520 33 T 0.5737 0.0603 0.3660 34 S 0.5432 0.1362 0.3206 35 T 0.4645 0.2079 0.3277 36 T 0.4769 0.2198 0.3033 37 A 0.4276 0.2236 0.3488 38 L 0.2722 0.1708 0.5569 39 P 0.1558 0.1760 0.6682 40 T 0.0772 0.1421 0.7807 41 S 0.0524 0.2694 0.6781 42 P 0.0081 0.7238 0.2681 43 Y 0.0092 0.8131 0.1776 44 F 0.0050 0.9215 0.0735 45 L 0.0048 0.9501 0.0451 46 E 0.0048 0.9494 0.0458 47 A 0.0048 0.9531 0.0422 48 M 0.0048 0.9516 0.0436 49 E 0.0052 0.9341 0.0607 50 S 0.0056 0.8696 0.1248 51 A 0.0142 0.7433 0.2425 52 R 0.0208 0.5480 0.4312 53 I 0.0220 0.4707 0.5073 54 S 0.0380 0.3201 0.6420 55 A 0.0809 0.0670 0.8520 56 P 0.0202 0.1870 0.7929 57 T 0.0371 0.1440 0.8189 58 L 0.1484 0.0504 0.8012 59 A 0.2410 0.0294 0.7296 60 I 0.7585 0.0124 0.2291 61 G 0.8479 0.0088 0.1433 62 V 0.9028 0.0045 0.0927 63 H 0.9208 0.0042 0.0750 64 L 0.9164 0.0059 0.0777 65 T 0.9021 0.0099 0.0880 66 L 0.7957 0.0180 0.1863 67 T 0.5178 0.0249 0.4573 68 L 0.1660 0.1415 0.6925 69 N 0.0551 0.2046 0.7403 70 Q 0.0602 0.1899 0.7499 71 A 0.1189 0.0846 0.7965 72 K 0.1624 0.0424 0.7952 73 P 0.2969 0.0406 0.6625 74 I 0.2693 0.0477 0.6830 75 L 0.1408 0.0341 0.8251 76 P 0.0896 0.0788 0.8316 77 R 0.0165 0.6516 0.3319 78 E 0.0226 0.6393 0.3381 79 M 0.0428 0.5604 0.3969 80 V 0.1305 0.1191 0.7504 81 P 0.0723 0.2629 0.6648 82 S 0.1166 0.3097 0.5736 83 L 0.2054 0.2674 0.5272 84 V 0.3803 0.1037 0.5161 85 D 0.0920 0.0338 0.8742 86 E 0.0134 0.1484 0.8382 87 A 0.0471 0.0399 0.9130 88 G 0.0848 0.0564 0.8588 89 Y 0.2504 0.0572 0.6924 90 F 0.4647 0.0675 0.4678 91 W 0.2262 0.1236 0.6501 92 H 0.1441 0.2598 0.5961 93 Q 0.1014 0.3718 0.5268 94 S 0.0748 0.5391 0.3860 95 I 0.0919 0.5486 0.3595 96 F 0.0964 0.5193 0.3842 97 E 0.0794 0.4565 0.4641 98 E 0.0735 0.2941 0.6324 99 K 0.0899 0.1928 0.7173 100 V 0.1243 0.0591 0.8166 101 N 0.0793 0.0279 0.8928 102 L 0.0049 0.9429 0.0522 103 E 0.0047 0.9569 0.0384 104 E 0.0047 0.9575 0.0377 105 V 0.0047 0.9591 0.0362 106 Y 0.0047 0.9600 0.0353 107 N 0.0047 0.9599 0.0354 108 E 0.0047 0.9601 0.0352 109 W 0.0047 0.9602 0.0351 110 D 0.0047 0.9602 0.0351 111 A 0.0046 0.9610 0.0343 112 Q 0.0046 0.9610 0.0343 113 I 0.0046 0.9614 0.0340 114 I 0.0046 0.9610 0.0343 115 S 0.0046 0.9609 0.0344 116 F 0.0047 0.9603 0.0351 117 M 0.0048 0.9545 0.0407 118 K 0.0057 0.9056 0.0888 119 S 0.0439 0.4449 0.5112 120 G 0.0327 0.0295 0.9377 121 R 0.0601 0.0125 0.9273 122 R 0.1053 0.0120 0.8827 123 P 0.1109 0.2044 0.6847 124 D 0.0917 0.2518 0.6565 125 H 0.3064 0.2657 0.4279 126 I 0.4400 0.1041 0.4558 127 D 0.3201 0.0904 0.5895 128 S 0.1424 0.2396 0.6180 129 H 0.1231 0.2643 0.6126 130 H 0.1330 0.3215 0.5455 131 N 0.1581 0.2961 0.5458 132 V 0.1590 0.3325 0.5085 133 H 0.0903 0.3172 0.5925 134 G 0.0430 0.3404 0.6166 135 K 0.0476 0.3946 0.5577 136 N 0.0521 0.4620 0.4858 137 K 0.0132 0.8047 0.1821 138 K 0.0186 0.8549 0.1265 139 L 0.0097 0.9152 0.0751 140 L 0.0056 0.9474 0.0470 141 G 0.0047 0.9568 0.0385 142 V 0.0047 0.9604 0.0349 143 A 0.0047 0.9607 0.0346 144 L 0.0047 0.9605 0.0348 145 A 0.0047 0.9596 0.0357 146 L 0.0047 0.9569 0.0384 147 A 0.0048 0.9535 0.0417 148 R 0.0053 0.9374 0.0573 149 K 0.0084 0.8880 0.1036 150 Y 0.0482 0.5646 0.3872 151 Q 0.0560 0.0379 0.9060 152 L 0.0773 0.0132 0.9095 153 P 0.2008 0.0287 0.7705 154 L 0.4518 0.0986 0.4496 155 R 0.4963 0.1252 0.3785 156 N 0.4504 0.1041 0.4455 157 A 0.2817 0.1421 0.5762 158 S 0.1908 0.1726 0.6366 159 R 0.1605 0.2115 0.6280 160 S 0.1734 0.2176 0.6090 161 I 0.1305 0.2736 0.5958 162 E 0.1100 0.2611 0.6289 163 T 0.0705 0.3802 0.5493 164 K 0.0317 0.6033 0.3650 165 D 0.0347 0.6442 0.3211 166 Y 0.0289 0.7911 0.1800 167 L 0.0417 0.7879 0.1705 168 E 0.0476 0.7791 0.1733 169 L 0.0425 0.7444 0.2131 170 Y 0.0627 0.5971 0.3403 171 Q 0.0413 0.3676 0.5912 172 D 0.0551 0.1474 0.7975 173 V 0.1280 0.0524 0.8196 174 R 0.1529 0.0619 0.7853 175 T 0.1377 0.0519 0.8104 176 P 0.0717 0.3224 0.6059 177 D 0.0271 0.6591 0.3139 178 E 0.0391 0.7648 0.1961 179 M 0.0751 0.7520 0.1729 180 L 0.1176 0.7081 0.1743 181 Y 0.1551 0.6492 0.1957 182 Q 0.1874 0.5847 0.2279 183 F 0.2173 0.4699 0.3128 184 Y 0.1731 0.3246 0.5023 185 D 0.0940 0.2044 0.7017 186 K 0.0270 0.2277 0.7452 187 A 0.0509 0.1618 0.7872 188 I 0.1633 0.0457 0.7911 189 S 0.0775 0.0274 0.8952 190 T 0.0050 0.9445 0.0505 191 E 0.0047 0.9563 0.0390 192 T 0.0047 0.9578 0.0375 193 I 0.0047 0.9592 0.0361 194 L 0.0047 0.9586 0.0367 195 Q 0.0048 0.9519 0.0433 196 L 0.0049 0.9438 0.0513 197 L 0.0052 0.9310 0.0638 198 D 0.0056 0.8768 0.1177 199 M 0.0069 0.8462 0.1469 200 V 0.0206 0.7697 0.2097 201 V 0.0414 0.5817 0.3769 202 C 0.0641 0.3321 0.6039 203 S 0.0693 0.0776 0.8532 204 E 0.0392 0.1301 0.8307 205 G 0.0364 0.0739 0.8897 206 E 0.1352 0.0450 0.8198 207 V 0.6184 0.0084 0.3732 208 F 0.8298 0.0068 0.1634 209 E 0.9195 0.0038 0.0767 210 I 0.9207 0.0044 0.0749 211 N 0.8957 0.0052 0.0992 212 C 0.7228 0.0127 0.2644 213 H 0.2862 0.0176 0.6962 214 P 0.1154 0.1929 0.6917 215 A 0.1246 0.2453 0.6301 216 F 0.1687 0.3314 0.4999 217 I 0.1298 0.3640 0.5062 218 D 0.0836 0.4057 0.5107 219 T 0.0197 0.8178 0.1625 220 I 0.0196 0.8414 0.1389 221 L 0.0253 0.8192 0.1554 222 Q 0.0327 0.7278 0.2394 223 N 0.0355 0.5267 0.4378 224 Q 0.0488 0.2971 0.6541 225 S 0.0569 0.1447 0.7984 226 G 0.0355 0.2198 0.7447 227 Y 0.0570 0.2444 0.6986 228 C 0.0735 0.3052 0.6213 229 M 0.0534 0.4734 0.4733 230 P 0.0546 0.6487 0.2967 231 R 0.0470 0.8117 0.1413 232 I 0.0374 0.8787 0.0839 233 R 0.0366 0.8887 0.0747 234 E 0.0160 0.9313 0.0527 235 V 0.0095 0.9372 0.0533 236 E 0.0092 0.9338 0.0570 237 I 0.0095 0.8868 0.1037 238 L 0.0239 0.7145 0.2616 239 T 0.0283 0.3839 0.5878 240 S 0.0543 0.2688 0.6769 241 Q 0.0048 0.9261 0.0691 242 E 0.0047 0.9397 0.0555 243 V 0.0048 0.9538 0.0414 244 K 0.0047 0.9605 0.0349 245 E 0.0046 0.9607 0.0347 246 A 0.0046 0.9612 0.0342 247 I 0.0047 0.9607 0.0347 248 E 0.0048 0.9524 0.0428 249 E 0.0055 0.9193 0.0752 250 R 0.0428 0.3402 0.6169 251 G 0.0389 0.0161 0.9450 252 I 0.1147 0.0068 0.8785 253 L 0.6578 0.0071 0.3351 254 L 0.8097 0.0061 0.1842 255 A 0.6292 0.0308 0.3400 256 N 0.4057 0.0177 0.5766 257 Y 0.0784 0.5364 0.3853 258 E 0.0433 0.6260 0.3307 259 S 0.0478 0.6455 0.3067 260 L 0.0816 0.3636 0.5548 261 A 0.0596 0.1860 0.7544 262 M 0.0310 0.0633 0.9057