# This file is the result of combining several RDB files, specifically # T0323.t06.dssp-ebghstl.rdb (weight 1.53986) # T0323.t06.stride-ebghtl.rdb (weight 1.24869) # T0323.t06.str2.rdb (weight 1.54758) # T0323.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 T0323.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0323 # 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 T0323.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 1244 # # ============================================ # Comments from T0323.t06.stride-ebghtl.rdb # ============================================ # TARGET T0323 # 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 T0323.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 1244 # # ============================================ # Comments from T0323.t06.str2.rdb # ============================================ # TARGET T0323 # 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 T0323.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 1244 # # ============================================ # Comments from T0323.t06.alpha.rdb # ============================================ # TARGET T0323 # 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 T0323.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 1244 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0904 0.0248 0.8848 2 R 0.1939 0.0663 0.7397 3 Y 0.2235 0.0971 0.6794 4 F 0.1620 0.1129 0.7251 5 S 0.1031 0.1182 0.7787 6 T 0.0514 0.1384 0.8102 7 D 0.0477 0.1102 0.8421 8 S 0.0442 0.2461 0.7097 9 P 0.0213 0.6149 0.3638 10 E 0.0175 0.7923 0.1901 11 V 0.0251 0.8270 0.1479 12 K 0.0249 0.8383 0.1368 13 T 0.0260 0.8453 0.1287 14 I 0.0190 0.8668 0.1142 15 V 0.0190 0.8541 0.1269 16 A 0.0176 0.7947 0.1878 17 Q 0.0212 0.7048 0.2740 18 D 0.0425 0.6093 0.3482 19 S 0.0051 0.8545 0.1404 20 R 0.0053 0.8845 0.1102 21 L 0.0054 0.9295 0.0651 22 F 0.0047 0.9504 0.0449 23 Q 0.0047 0.9556 0.0397 24 F 0.0048 0.9541 0.0411 25 I 0.0053 0.9499 0.0447 26 E 0.0058 0.9215 0.0727 27 I 0.0130 0.7871 0.1999 28 A 0.0518 0.4319 0.5164 29 G 0.0333 0.1480 0.8187 30 E 0.0732 0.1033 0.8235 31 V 0.1616 0.0511 0.7873 32 Q 0.2027 0.0389 0.7584 33 L 0.1490 0.0238 0.8272 34 P 0.1075 0.0312 0.8613 35 T 0.0729 0.0600 0.8670 36 K 0.0706 0.0299 0.8996 37 P 0.0536 0.0413 0.9051 38 N 0.0805 0.0496 0.8698 39 P 0.0056 0.9222 0.0723 40 F 0.0047 0.9501 0.0451 41 Q 0.0047 0.9565 0.0388 42 S 0.0047 0.9597 0.0356 43 L 0.0047 0.9601 0.0352 44 V 0.0047 0.9609 0.0345 45 S 0.0047 0.9611 0.0343 46 S 0.0047 0.9601 0.0352 47 I 0.0049 0.9541 0.0410 48 V 0.0051 0.9429 0.0520 49 E 0.0058 0.9027 0.0915 50 Q 0.0091 0.8268 0.1642 51 Q 0.0176 0.7497 0.2327 52 L 0.0650 0.6021 0.3329 53 S 0.0809 0.4823 0.4368 54 I 0.0097 0.9358 0.0545 55 K 0.0071 0.9480 0.0449 56 A 0.0064 0.9466 0.0471 57 A 0.0057 0.9432 0.0511 58 S 0.0052 0.9517 0.0431 59 A 0.0052 0.9463 0.0485 60 I 0.0050 0.9396 0.0553 61 Y 0.0049 0.9451 0.0500 62 G 0.0047 0.9509 0.0444 63 R 0.0047 0.9528 0.0424 64 V 0.0048 0.9531 0.0421 65 E 0.0049 0.9547 0.0404 66 Q 0.0053 0.9453 0.0494 67 L 0.0090 0.9069 0.0840 68 V 0.0503 0.6645 0.2852 69 G 0.0316 0.1470 0.8215 70 G 0.0413 0.1259 0.8328 71 A 0.0810 0.1403 0.7787 72 L 0.1042 0.0572 0.8386 73 E 0.0781 0.0487 0.8732 74 K 0.0757 0.0244 0.8999 75 P 0.0052 0.9195 0.0753 76 E 0.0049 0.9402 0.0549 77 Q 0.0055 0.9297 0.0649 78 L 0.0087 0.8876 0.1037 79 Y 0.0120 0.6509 0.3370 80 R 0.0214 0.3028 0.6758 81 V 0.0633 0.0433 0.8934 82 S 0.0691 0.0298 0.9011 83 D 0.0050 0.9047 0.0902 84 E 0.0048 0.9219 0.0733 85 A 0.0049 0.9307 0.0643 86 L 0.0092 0.9197 0.0710 87 R 0.0116 0.8611 0.1273 88 Q 0.0120 0.8328 0.1552 89 A 0.0476 0.5256 0.4268 90 G 0.0435 0.1650 0.7915 91 V 0.0735 0.1455 0.7810 92 S 0.0551 0.2785 0.6664 93 K 0.0106 0.8296 0.1598 94 R 0.0097 0.8784 0.1119 95 K 0.0061 0.9309 0.0630 96 I 0.0058 0.9514 0.0427 97 E 0.0049 0.9579 0.0373 98 Y 0.0047 0.9577 0.0376 99 I 0.0047 0.9602 0.0351 100 R 0.0046 0.9611 0.0343 101 H 0.0046 0.9606 0.0347 102 V 0.0047 0.9589 0.0365 103 C 0.0047 0.9587 0.0366 104 E 0.0047 0.9573 0.0381 105 H 0.0047 0.9526 0.0427 106 V 0.0051 0.9405 0.0544 107 E 0.0063 0.8849 0.1088 108 S 0.0418 0.5293 0.4288 109 G 0.0290 0.1236 0.8474 110 R 0.0659 0.0758 0.8584 111 L 0.1595 0.0593 0.7812 112 D 0.1640 0.0692 0.7668 113 F 0.0310 0.6729 0.2960 114 T 0.0222 0.7150 0.2628 115 E 0.0324 0.7215 0.2461 116 L 0.0609 0.5036 0.4355 117 E 0.0321 0.2791 0.6889 118 G 0.0371 0.1408 0.8221 119 A 0.0788 0.0296 0.8916 120 E 0.0841 0.0410 0.8749 121 A 0.0110 0.8077 0.1813 122 T 0.0054 0.9097 0.0849 123 T 0.0049 0.9403 0.0548 124 V 0.0047 0.9531 0.0421 125 I 0.0047 0.9565 0.0388 126 E 0.0048 0.9579 0.0373 127 K 0.0050 0.9496 0.0453 128 L 0.0052 0.9302 0.0646 129 T 0.0058 0.8542 0.1400 130 A 0.0091 0.6600 0.3309 131 I 0.0731 0.2201 0.7068 132 K 0.0251 0.2421 0.7328 133 G 0.0523 0.1614 0.7864 134 I 0.0975 0.1927 0.7099 135 G 0.0622 0.2695 0.6684 136 Q 0.0103 0.8481 0.1416 137 W 0.0075 0.9162 0.0763 138 T 0.0055 0.9462 0.0483 139 A 0.0047 0.9575 0.0378 140 E 0.0047 0.9600 0.0353 141 M 0.0046 0.9605 0.0348 142 F 0.0047 0.9597 0.0356 143 M 0.0047 0.9601 0.0352 144 M 0.0048 0.9570 0.0382 145 F 0.0055 0.9436 0.0509 146 S 0.0066 0.8973 0.0961 147 L 0.0446 0.4842 0.4712 148 G 0.0282 0.0541 0.9177 149 R 0.0585 0.0551 0.8865 150 L 0.1258 0.0799 0.7943 151 D 0.1786 0.1089 0.7125 152 V 0.5008 0.0458 0.4534 153 L 0.6072 0.0280 0.3648 154 S 0.4867 0.0379 0.4754 155 V 0.2129 0.2510 0.5361 156 G 0.0955 0.2201 0.6844 157 D 0.0559 0.5231 0.4210 158 V 0.0278 0.7520 0.2202 159 G 0.0244 0.8565 0.1191 160 L 0.0177 0.9252 0.0571 161 Q 0.0154 0.9397 0.0450 162 R 0.0122 0.9439 0.0439 163 G 0.0094 0.9474 0.0432 164 A 0.0133 0.9374 0.0493 165 K 0.0196 0.9198 0.0606 166 W 0.0172 0.8922 0.0906 167 L 0.0374 0.7528 0.2098 168 Y 0.0470 0.4377 0.5153 169 G 0.0671 0.2225 0.7104 170 N 0.0807 0.1372 0.7820 171 G 0.0522 0.1025 0.8453 172 E 0.0514 0.0988 0.8498 173 G 0.0547 0.0800 0.8653 174 D 0.0498 0.1575 0.7926 175 G 0.0536 0.1720 0.7745 176 K 0.0136 0.8703 0.1161 177 K 0.0083 0.9368 0.0549 178 L 0.0087 0.9436 0.0477 179 L 0.0097 0.9439 0.0464 180 I 0.0123 0.9399 0.0478 181 Y 0.0125 0.9216 0.0659 182 H 0.0082 0.8978 0.0940 183 G 0.0102 0.8550 0.1347 184 K 0.0106 0.8173 0.1721 185 A 0.0125 0.7232 0.2643 186 W 0.0289 0.5322 0.4389 187 A 0.0601 0.0802 0.8597 188 P 0.0525 0.0791 0.8684 189 Y 0.0251 0.6188 0.3561 190 E 0.0198 0.7810 0.1992 191 T 0.0328 0.8270 0.1402 192 V 0.0671 0.8494 0.0835 193 A 0.0906 0.8293 0.0801 194 C 0.1209 0.8001 0.0790 195 L 0.1296 0.7852 0.0852 196 Y 0.1699 0.7038 0.1263 197 L 0.1930 0.5919 0.2151 198 W 0.2133 0.4100 0.3767 199 K 0.1150 0.2163 0.6688 200 A 0.0603 0.2202 0.7195 201 A 0.0452 0.2040 0.7508 202 G 0.0548 0.0947 0.8505 203 T 0.0654 0.1423 0.7922 204 F 0.0946 0.2023 0.7032 205 A 0.0554 0.4356 0.5091 206 E 0.0168 0.6042 0.3790 207 E 0.0246 0.5786 0.3969 208 Y 0.0679 0.3593 0.5729 209 R 0.0437 0.4181 0.5382 210 S 0.0457 0.4866 0.4677 211 L 0.0251 0.6164 0.3585 212 E 0.0089 0.8140 0.1771 213 E 0.0104 0.8082 0.1814 214 L 0.0251 0.7582 0.2167 215 L 0.0236 0.7103 0.2661 216 H 0.0251 0.6110 0.3639 217 H 0.0530 0.4188 0.5283 218 G 0.0434 0.1802 0.7763 219 N 0.0475 0.1385 0.8140 220 Q 0.0673 0.0791 0.8536 221 C 0.0583 0.0386 0.9031