# This file is the result of combining several RDB files, specifically # T0514.t04.dssp-ebghstl.rdb (weight 1.53986) # T0514.t04.stride-ebghtl.rdb (weight 1.24869) # T0514.t04.str2.rdb (weight 1.54758) # T0514.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 T0514.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0514 # 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 T0514.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 205 # # ============================================ # Comments from T0514.t04.stride-ebghtl.rdb # ============================================ # TARGET T0514 # 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 T0514.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 205 # # ============================================ # Comments from T0514.t04.str2.rdb # ============================================ # TARGET T0514 # 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 T0514.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 205 # # ============================================ # Comments from T0514.t04.alpha.rdb # ============================================ # TARGET T0514 # 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 T0514.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 205 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0704 0.0442 0.8854 2 S 0.1610 0.0538 0.7852 3 L 0.2721 0.0719 0.6560 4 T 0.2994 0.0798 0.6208 5 E 0.3883 0.0659 0.5458 6 T 0.5156 0.0679 0.4165 7 Y 0.4175 0.0612 0.5213 8 G 0.3116 0.0372 0.6512 9 L 0.4641 0.0333 0.5026 10 W 0.7588 0.0231 0.2181 11 S 0.8883 0.0109 0.1008 12 I 0.9124 0.0088 0.0788 13 N 0.9049 0.0091 0.0860 14 C 0.8437 0.0159 0.1403 15 G 0.7328 0.0163 0.2509 16 I 0.5955 0.0393 0.3652 17 Q 0.3173 0.0645 0.6183 18 E 0.0766 0.0763 0.8471 19 G 0.0636 0.0439 0.8926 20 K 0.2380 0.0248 0.7372 21 K 0.6016 0.0150 0.3834 22 V 0.8603 0.0078 0.1319 23 C 0.8843 0.0098 0.1059 24 F 0.9016 0.0086 0.0899 25 M 0.8904 0.0131 0.0965 26 H 0.8578 0.0186 0.1236 27 R 0.8345 0.0223 0.1432 28 Q 0.7954 0.0224 0.1822 29 E 0.8025 0.0286 0.1689 30 V 0.7161 0.0396 0.2443 31 N 0.2304 0.0599 0.7097 32 D 0.0402 0.1256 0.8342 33 Q 0.0528 0.0550 0.8922 34 N 0.0719 0.0438 0.8843 35 R 0.2779 0.0123 0.7098 36 V 0.7241 0.0043 0.2716 37 V 0.8933 0.0047 0.1020 38 V 0.9251 0.0036 0.0713 39 A 0.9329 0.0031 0.0640 40 M 0.9317 0.0032 0.0651 41 S 0.9262 0.0032 0.0706 42 V 0.9188 0.0035 0.0777 43 V 0.9082 0.0043 0.0874 44 L 0.8727 0.0059 0.1214 45 N 0.3334 0.0163 0.6503 46 A 0.0333 0.0846 0.8820 47 D 0.0442 0.0234 0.9324 48 G 0.0511 0.0339 0.9149 49 V 0.3791 0.0113 0.6097 50 V 0.8569 0.0040 0.1391 51 S 0.8355 0.0207 0.1437 52 G 0.8683 0.0077 0.1239 53 N 0.9160 0.0055 0.0785 54 L 0.9208 0.0038 0.0754 55 T 0.9112 0.0042 0.0846 56 V 0.8059 0.0068 0.1874 57 P 0.6163 0.0149 0.3689 58 F 0.2814 0.0805 0.6381 59 G 0.2750 0.0642 0.6609 60 I 0.5583 0.0322 0.4095 61 L 0.6757 0.0181 0.3062 62 V 0.4845 0.0226 0.4928 63 S 0.2316 0.0447 0.7237 64 K 0.0955 0.0808 0.8237 65 P 0.1675 0.0444 0.7881 66 V 0.6203 0.0086 0.3711 67 R 0.8659 0.0051 0.1291 68 L 0.9091 0.0036 0.0873 69 Q 0.9164 0.0036 0.0800 70 V 0.8420 0.0066 0.1514 71 D 0.4474 0.0128 0.5398 72 E 0.0676 0.0578 0.8745 73 G 0.0367 0.0431 0.9203 74 K 0.2037 0.0342 0.7621 75 A 0.4615 0.0360 0.5025 76 V 0.6537 0.0505 0.2958 77 I 0.7175 0.0406 0.2419 78 E 0.7518 0.0269 0.2213 79 T 0.6298 0.0247 0.3455 80 G 0.5419 0.0290 0.4291 81 I 0.5870 0.0502 0.3628 82 R 0.6191 0.1010 0.2799 83 T 0.6247 0.0700 0.3053 84 C 0.5005 0.0702 0.4293 85 V 0.2255 0.0483 0.7262 86 P 0.0671 0.1346 0.7982 87 A 0.0739 0.1180 0.8081 88 G 0.2973 0.0928 0.6099 89 C 0.5542 0.0390 0.4068 90 I 0.6779 0.0384 0.2837 91 V 0.5646 0.0339 0.4015 92 P 0.4786 0.0453 0.4761 93 I 0.3018 0.0935 0.6047 94 V 0.2486 0.0861 0.6653 95 F 0.1130 0.0651 0.8219 96 D 0.0738 0.0505 0.8756 97 K 0.0052 0.9280 0.0668 98 N 0.0050 0.9452 0.0498 99 Y 0.0049 0.9532 0.0419 100 V 0.0047 0.9594 0.0359 101 A 0.0047 0.9596 0.0357 102 A 0.0047 0.9558 0.0395 103 L 0.0058 0.9305 0.0637 104 R 0.0083 0.7723 0.2193 105 A 0.0234 0.2907 0.6859 106 G 0.0372 0.0409 0.9219 107 K 0.0811 0.0341 0.8848 108 H 0.4494 0.0146 0.5359 109 L 0.8180 0.0049 0.1771 110 K 0.9170 0.0034 0.0796 111 L 0.9265 0.0031 0.0704 112 A 0.9135 0.0037 0.0827 113 M 0.8976 0.0036 0.0989 114 T 0.8440 0.0053 0.1507 115 I 0.7240 0.0067 0.2693 116 A 0.3081 0.0247 0.6672 117 A 0.1149 0.0303 0.8548 118 P 0.0372 0.0625 0.9003 119 G 0.0340 0.0516 0.9144 120 E 0.0954 0.0279 0.8767 121 P 0.1455 0.0188 0.8357 122 P 0.1660 0.0309 0.8031 123 L 0.2240 0.0787 0.6973 124 N 0.2634 0.0635 0.6731 125 D 0.2418 0.0541 0.7041 126 L 0.4178 0.0295 0.5527 127 F 0.5950 0.0349 0.3701 128 V 0.6417 0.0307 0.3276 129 Q 0.4649 0.0441 0.4910 130 L 0.1399 0.4440 0.4161 131 N 0.0570 0.4347 0.5083 132 G 0.0358 0.5022 0.4620 133 F 0.0123 0.8345 0.1533 134 S 0.0062 0.9361 0.0577 135 N 0.0051 0.9506 0.0444 136 A 0.0051 0.9500 0.0450 137 L 0.0048 0.9486 0.0466 138 N 0.0048 0.9474 0.0477 139 R 0.0054 0.9399 0.0548 140 L 0.0051 0.9316 0.0633 141 I 0.0054 0.9251 0.0696 142 A 0.0060 0.8984 0.0956 143 L 0.0095 0.7718 0.2187 144 Q 0.0296 0.4601 0.5104 145 K 0.0223 0.1741 0.8036