# This file is the result of combining several RDB files, specifically # T0198.t04.dssp-ebghstl.rdb (weight 1.53986) # T0198.t04.stride-ebghtl.rdb (weight 1.24869) # T0198.t04.str2.rdb (weight 1.54758) # T0198.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 T0198.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0198 # Using neural net t04-2621-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 T0198.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 231 # # ============================================ # Comments from T0198.t04.stride-ebghtl.rdb # ============================================ # TARGET T0198 # 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 T0198.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 231 # # ============================================ # Comments from T0198.t04.str2.rdb # ============================================ # TARGET T0198 # 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 T0198.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 231 # # ============================================ # Comments from T0198.t04.alpha.rdb # ============================================ # TARGET T0198 # 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 T0198.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 231 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0313 0.1542 0.8145 2 N 0.0378 0.3002 0.6620 3 R 0.0299 0.5675 0.4026 4 L 0.0288 0.6390 0.3322 5 L 0.0208 0.7319 0.2473 6 N 0.0120 0.8458 0.1422 7 E 0.0061 0.9320 0.0619 8 K 0.0058 0.9339 0.0603 9 V 0.0048 0.9527 0.0425 10 E 0.0047 0.9592 0.0361 11 E 0.0047 0.9568 0.0385 12 F 0.0048 0.9560 0.0392 13 K 0.0047 0.9587 0.0366 14 K 0.0047 0.9579 0.0374 15 G 0.0047 0.9526 0.0427 16 V 0.0047 0.9534 0.0419 17 L 0.0047 0.9548 0.0405 18 K 0.0047 0.9490 0.0463 19 A 0.0047 0.9445 0.0508 20 G 0.0047 0.9542 0.0411 21 W 0.0046 0.9614 0.0339 22 F 0.0046 0.9614 0.0339 23 I 0.0047 0.9612 0.0342 24 E 0.0047 0.9611 0.0342 25 K 0.0047 0.9605 0.0348 26 M 0.0047 0.9583 0.0370 27 F 0.0047 0.9587 0.0366 28 R 0.0047 0.9588 0.0365 29 N 0.0047 0.9526 0.0428 30 S 0.0047 0.9544 0.0409 31 I 0.0047 0.9591 0.0362 32 S 0.0047 0.9605 0.0348 33 S 0.0047 0.9587 0.0366 34 L 0.0048 0.9517 0.0435 35 V 0.0052 0.9248 0.0700 36 E 0.0097 0.8257 0.1646 37 R 0.0241 0.5825 0.3934 38 N 0.0781 0.2662 0.6557 39 E 0.0055 0.9376 0.0570 40 S 0.0051 0.9530 0.0419 41 L 0.0051 0.9532 0.0417 42 A 0.0047 0.9583 0.0370 43 R 0.0047 0.9583 0.0370 44 E 0.0048 0.9534 0.0418 45 V 0.0049 0.9458 0.0493 46 I 0.0072 0.9012 0.0917 47 A 0.0115 0.7776 0.2110 48 D 0.0318 0.6303 0.3379 49 E 0.0149 0.8269 0.1582 50 E 0.0058 0.8865 0.1077 51 V 0.0069 0.9108 0.0823 52 V 0.0086 0.9172 0.0742 53 D 0.0063 0.9235 0.0702 54 Q 0.0052 0.9410 0.0538 55 M 0.0050 0.9484 0.0466 56 E 0.0048 0.9570 0.0383 57 V 0.0050 0.9583 0.0367 58 E 0.0049 0.9577 0.0374 59 I 0.0050 0.9561 0.0389 60 Q 0.0050 0.9568 0.0383 61 E 0.0048 0.9597 0.0355 62 K 0.0049 0.9581 0.0370 63 A 0.0047 0.9594 0.0359 64 M 0.0047 0.9603 0.0350 65 E 0.0047 0.9603 0.0349 66 V 0.0049 0.9558 0.0393 67 L 0.0056 0.9384 0.0561 68 G 0.0067 0.8654 0.1279 69 L 0.0109 0.6977 0.2913 70 F 0.0262 0.5014 0.4724 71 S 0.0567 0.0738 0.8695 72 P 0.0520 0.2013 0.7466 73 I 0.0576 0.2850 0.6574 74 G 0.0353 0.5544 0.4103 75 K 0.0240 0.8269 0.1491 76 P 0.0140 0.9008 0.0852 77 L 0.0061 0.9424 0.0515 78 L 0.0050 0.9561 0.0389 79 T 0.0047 0.9597 0.0356 80 V 0.0047 0.9594 0.0359 81 T 0.0047 0.9604 0.0349 82 A 0.0046 0.9612 0.0342 83 G 0.0047 0.9612 0.0342 84 I 0.0047 0.9609 0.0345 85 R 0.0047 0.9573 0.0380 86 V 0.0048 0.9484 0.0468 87 A 0.0048 0.9486 0.0467 88 E 0.0049 0.9446 0.0505 89 L 0.0050 0.9400 0.0551 90 I 0.0048 0.9473 0.0479 91 E 0.0048 0.9362 0.0590 92 N 0.0048 0.9223 0.0729 93 I 0.0050 0.9154 0.0795 94 A 0.0052 0.9280 0.0669 95 D 0.0050 0.9432 0.0518 96 K 0.0049 0.9467 0.0484 97 C 0.0048 0.9501 0.0451 98 H 0.0047 0.9520 0.0432 99 D 0.0047 0.9527 0.0427 100 I 0.0048 0.9543 0.0409 101 A 0.0047 0.9593 0.0360 102 K 0.0046 0.9613 0.0341 103 N 0.0047 0.9596 0.0357 104 V 0.0047 0.9567 0.0386 105 L 0.0048 0.9515 0.0436 106 E 0.0055 0.9351 0.0594 107 L 0.0101 0.8625 0.1274 108 M 0.0466 0.5681 0.3853 109 E 0.0313 0.2181 0.7506 110 E 0.0531 0.0511 0.8958 111 P 0.0594 0.0342 0.9064 112 P 0.0648 0.0580 0.8772 113 L 0.0750 0.0411 0.8840 114 K 0.0593 0.0584 0.8823 115 P 0.0494 0.1106 0.8400 116 L 0.0383 0.5268 0.4349 117 E 0.0288 0.5911 0.3800 118 D 0.0290 0.5678 0.4032 119 I 0.0099 0.7617 0.2284 120 P 0.0050 0.9438 0.0512 121 A 0.0047 0.9503 0.0449 122 M 0.0047 0.9491 0.0462 123 A 0.0047 0.9534 0.0420 124 N 0.0047 0.9582 0.0372 125 Q 0.0047 0.9575 0.0378 126 T 0.0047 0.9585 0.0368 127 S 0.0047 0.9605 0.0349 128 E 0.0046 0.9611 0.0343 129 M 0.0046 0.9605 0.0349 130 L 0.0047 0.9608 0.0346 131 K 0.0046 0.9617 0.0337 132 F 0.0046 0.9610 0.0344 133 A 0.0047 0.9600 0.0353 134 L 0.0047 0.9602 0.0351 135 R 0.0047 0.9600 0.0353 136 M 0.0048 0.9574 0.0378 137 F 0.0050 0.9404 0.0546 138 A 0.0073 0.8795 0.1133 139 D 0.0307 0.6981 0.2712 140 V 0.0343 0.4853 0.4803 141 N 0.0876 0.2332 0.6791 142 V 0.0060 0.9175 0.0764 143 E 0.0056 0.9420 0.0524 144 K 0.0071 0.9281 0.0648 145 S 0.0071 0.9430 0.0500 146 F 0.0063 0.9447 0.0489 147 E 0.0070 0.9405 0.0525 148 V 0.0078 0.9354 0.0568 149 C 0.0120 0.9177 0.0703 150 R 0.0157 0.8739 0.1104 151 M 0.0158 0.8170 0.1672 152 D 0.0338 0.7811 0.1851 153 S 0.0058 0.8759 0.1184 154 K 0.0066 0.8967 0.0967 155 V 0.0057 0.9322 0.0622 156 D 0.0049 0.9427 0.0524 157 D 0.0047 0.9546 0.0407 158 L 0.0047 0.9576 0.0377 159 Y 0.0047 0.9584 0.0370 160 E 0.0047 0.9604 0.0349 161 K 0.0047 0.9600 0.0353 162 V 0.0047 0.9584 0.0369 163 R 0.0047 0.9602 0.0351 164 E 0.0047 0.9610 0.0343 165 E 0.0047 0.9604 0.0350 166 L 0.0047 0.9594 0.0359 167 L 0.0047 0.9586 0.0367 168 L 0.0048 0.9565 0.0387 169 Y 0.0054 0.9411 0.0535 170 M 0.0084 0.8853 0.1064 171 M 0.0153 0.7130 0.2717 172 E 0.0282 0.4875 0.4843 173 S 0.0712 0.0433 0.8855 174 P 0.0094 0.5741 0.4165 175 K 0.0177 0.6989 0.2834 176 Y 0.0246 0.8269 0.1485 177 V 0.0106 0.9375 0.0518 178 K 0.0065 0.9523 0.0412 179 R 0.0061 0.9554 0.0385 180 A 0.0047 0.9595 0.0358 181 L 0.0047 0.9603 0.0350 182 L 0.0047 0.9600 0.0353 183 L 0.0047 0.9585 0.0367 184 L 0.0047 0.9591 0.0362 185 E 0.0047 0.9557 0.0396 186 I 0.0049 0.9495 0.0456 187 A 0.0059 0.9316 0.0625 188 G 0.0069 0.8618 0.1313 189 N 0.0062 0.8344 0.1594 190 I 0.0060 0.9168 0.0772 191 E 0.0061 0.9245 0.0693 192 I 0.0096 0.9268 0.0635 193 I 0.0094 0.9138 0.0767 194 A 0.0107 0.8844 0.1049 195 D 0.0078 0.9157 0.0765 196 Y 0.0071 0.9212 0.0717 197 A 0.0127 0.9200 0.0672 198 T 0.0134 0.9166 0.0700 199 N 0.0148 0.9008 0.0844 200 I 0.0059 0.9392 0.0549 201 V 0.0074 0.9458 0.0468 202 E 0.0107 0.9447 0.0446 203 V 0.0197 0.9282 0.0521 204 S 0.0503 0.8939 0.0557 205 V 0.1241 0.8221 0.0538 206 Y 0.1920 0.7396 0.0685 207 M 0.1282 0.7487 0.1231 208 V 0.1777 0.5683 0.2540 209 Q 0.0644 0.1558 0.7799 210 G 0.0556 0.0546 0.8898 211 E 0.3529 0.0674 0.5797 212 A 0.6084 0.0642 0.3274 213 Y 0.4122 0.0886 0.4992 214 K 0.2893 0.1030 0.6077 215 C 0.1739 0.1293 0.6969 216 Y 0.1115 0.1165 0.7719 217 H 0.0830 0.2421 0.6749 218 D 0.0474 0.6503 0.3023 219 E 0.0492 0.8071 0.1437 220 L 0.0719 0.8035 0.1246 221 L 0.0865 0.7662 0.1473 222 L 0.0869 0.7364 0.1767 223 F 0.1192 0.6172 0.2636 224 K 0.1126 0.5609 0.3265 225 K 0.1037 0.4926 0.4037 226 S 0.0914 0.4096 0.4991 227 G 0.0657 0.3309 0.6034 228 G 0.0900 0.3360 0.5739 229 V 0.1689 0.4573 0.3739 230 L 0.1794 0.4923 0.3284 231 F 0.1575 0.4563 0.3862 232 E 0.1173 0.4153 0.4674 233 S 0.0988 0.2999 0.6013 234 S 0.0830 0.1387 0.7784 235 D 0.0570 0.0739 0.8692