# This file is the result of combining several RDB files, specifically # T0332.t06.dssp-ebghstl.rdb (weight 1.53986) # T0332.t06.stride-ebghtl.rdb (weight 1.24869) # T0332.t06.str2.rdb (weight 1.54758) # T0332.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 T0332.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0332 # 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 T0332.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 1412 # # ============================================ # Comments from T0332.t06.stride-ebghtl.rdb # ============================================ # TARGET T0332 # 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 T0332.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 1412 # # ============================================ # Comments from T0332.t06.str2.rdb # ============================================ # TARGET T0332 # 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 T0332.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 1412 # # ============================================ # Comments from T0332.t06.alpha.rdb # ============================================ # TARGET T0332 # 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 T0332.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 1412 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 L 0.0551 0.0472 0.8977 2 G 0.0555 0.0489 0.8956 3 K 0.0708 0.0949 0.8344 4 S 0.0743 0.1294 0.7963 5 I 0.1023 0.1551 0.7426 6 S 0.1248 0.0733 0.8019 7 R 0.3184 0.0282 0.6535 8 L 0.7955 0.0046 0.2000 9 I 0.9266 0.0034 0.0699 10 V 0.9330 0.0032 0.0638 11 V 0.9278 0.0036 0.0686 12 A 0.8969 0.0065 0.0967 13 S 0.6996 0.0365 0.2639 14 L 0.3902 0.0224 0.5874 15 I 0.2063 0.0477 0.7460 16 D 0.1320 0.0760 0.7921 17 K 0.0813 0.0480 0.8707 18 P 0.0481 0.2638 0.6881 19 T 0.0664 0.3647 0.5690 20 N 0.0544 0.6568 0.2888 21 L 0.0070 0.9007 0.0924 22 G 0.0055 0.9418 0.0527 23 G 0.0048 0.9542 0.0411 24 L 0.0047 0.9580 0.0373 25 C 0.0047 0.9592 0.0362 26 R 0.0047 0.9579 0.0374 27 T 0.0047 0.9583 0.0370 28 C 0.0047 0.9583 0.0370 29 E 0.0049 0.9478 0.0473 30 V 0.0051 0.9104 0.0844 31 F 0.0449 0.4346 0.5205 32 G 0.0585 0.0129 0.9287 33 A 0.0998 0.0083 0.8919 34 S 0.1319 0.0476 0.8205 35 V 0.8889 0.0069 0.1042 36 L 0.9267 0.0042 0.0691 37 V 0.9283 0.0040 0.0678 38 V 0.8763 0.0067 0.1170 39 G 0.5040 0.0158 0.4802 40 S 0.2549 0.0311 0.7140 41 L 0.1146 0.1334 0.7520 42 Q 0.1297 0.1498 0.7205 43 C 0.1471 0.1285 0.7244 44 I 0.1245 0.0788 0.7967 45 S 0.0806 0.0992 0.8202 46 D 0.0558 0.1357 0.8086 47 K 0.0097 0.8112 0.1791 48 Q 0.0155 0.8386 0.1459 49 F 0.0331 0.8687 0.0982 50 Q 0.0347 0.8846 0.0806 51 H 0.0557 0.8499 0.0944 52 L 0.0524 0.8075 0.1400 53 S 0.0849 0.6882 0.2269 54 V 0.0716 0.5923 0.3360 55 S 0.0949 0.3837 0.5214 56 A 0.0549 0.6352 0.3099 57 E 0.0375 0.7201 0.2425 58 Q 0.0758 0.6236 0.3006 59 W 0.1531 0.4284 0.4185 60 L 0.3661 0.0644 0.5695 61 P 0.4281 0.0572 0.5147 62 L 0.7104 0.0693 0.2203 63 V 0.7936 0.0524 0.1540 64 E 0.8316 0.0218 0.1466 65 V 0.6443 0.0128 0.3429 66 K 0.2549 0.0141 0.7309 67 P 0.0723 0.2535 0.6742 68 P 0.0178 0.4384 0.5437 69 Q 0.0354 0.4600 0.5046 70 L 0.0049 0.9397 0.0554 71 I 0.0047 0.9573 0.0380 72 D 0.0047 0.9581 0.0372 73 Y 0.0047 0.9586 0.0367 74 L 0.0048 0.9536 0.0417 75 Q 0.0048 0.9329 0.0622 76 Q 0.0053 0.8840 0.1107 77 K 0.0090 0.8485 0.1425 78 K 0.0107 0.7628 0.2265 79 T 0.0109 0.6933 0.2958 80 E 0.0411 0.2721 0.6868 81 G 0.0399 0.0194 0.9407 82 Y 0.2602 0.0071 0.7327 83 T 0.8181 0.0041 0.1777 84 I 0.9071 0.0034 0.0895 85 I 0.8897 0.0059 0.1044 86 G 0.8639 0.0051 0.1310 87 V 0.7232 0.0122 0.2646 88 E 0.4875 0.0185 0.4940 89 Q 0.2155 0.1048 0.6796 90 T 0.1394 0.1790 0.6816 91 A 0.0670 0.4368 0.4962 92 K 0.0600 0.2779 0.6622 93 S 0.1116 0.1651 0.7232 94 L 0.2040 0.0521 0.7438 95 D 0.2337 0.0401 0.7262 96 L 0.0545 0.6476 0.2979 97 T 0.0561 0.6528 0.2911 98 Q 0.0840 0.6538 0.2621 99 Y 0.1917 0.2803 0.5280 100 C 0.1878 0.0992 0.7130 101 F 0.1225 0.0406 0.8370 102 P 0.0760 0.0583 0.8657 103 E 0.0697 0.0942 0.8361 104 K 0.1388 0.0491 0.8121 105 S 0.6688 0.0087 0.3225 106 L 0.9226 0.0036 0.0737 107 L 0.9325 0.0032 0.0644 108 L 0.9268 0.0033 0.0699 109 L 0.8237 0.0227 0.1537 110 G 0.4016 0.0144 0.5840 111 N 0.1690 0.0332 0.7978 112 E 0.0731 0.1843 0.7426 113 R 0.0505 0.2525 0.6969 114 E 0.0435 0.1959 0.7607 115 G 0.0529 0.0877 0.8594 116 I 0.0931 0.0213 0.8856 117 P 0.0738 0.0547 0.8715 118 A 0.0051 0.9363 0.0586 119 N 0.0050 0.9477 0.0473 120 L 0.0052 0.9417 0.0531 121 I 0.0059 0.9392 0.0549 122 Q 0.0079 0.8722 0.1199 123 Q 0.0158 0.5530 0.4312 124 L 0.0962 0.1828 0.7209 125 D 0.0893 0.1084 0.8023 126 V 0.6530 0.0376 0.3094 127 C 0.8792 0.0163 0.1045 128 V 0.9092 0.0103 0.0805 129 E 0.8898 0.0077 0.1025 130 I 0.6947 0.0085 0.2967 131 P 0.3933 0.0161 0.5906 132 Q 0.1710 0.0579 0.7711 133 Q 0.0772 0.1374 0.7854 134 G 0.0512 0.1374 0.8114 135 I 0.1374 0.2015 0.6611 136 I 0.2300 0.2949 0.4751 137 R 0.1685 0.4003 0.4312 138 S 0.2081 0.4680 0.3240 139 L 0.0731 0.7579 0.1690 140 N 0.0200 0.8778 0.1022 141 V 0.0051 0.9527 0.0423 142 H 0.0047 0.9586 0.0367 143 V 0.0047 0.9585 0.0368 144 S 0.0047 0.9599 0.0355 145 G 0.0047 0.9603 0.0350 146 A 0.0047 0.9607 0.0347 147 L 0.0047 0.9611 0.0342 148 L 0.0047 0.9609 0.0345 149 I 0.0046 0.9612 0.0341 150 W 0.0047 0.9611 0.0342 151 E 0.0047 0.9605 0.0349 152 Y 0.0047 0.9570 0.0383 153 T 0.0048 0.9497 0.0455 154 R 0.0050 0.9339 0.0611 155 Q 0.0065 0.8934 0.1000 156 Q 0.0137 0.7833 0.2030 157 L 0.0233 0.5162 0.4604 158 L 0.0431 0.1686 0.7883 159 S 0.0409 0.0356 0.9235