# This file is the result of combining several RDB files, specifically # T0319.t04.dssp-ebghstl.rdb (weight 1.53986) # T0319.t04.stride-ebghtl.rdb (weight 1.24869) # T0319.t04.str2.rdb (weight 1.54758) # T0319.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 T0319.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0319 # 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 T0319.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 19.8416 # # ============================================ # Comments from T0319.t04.stride-ebghtl.rdb # ============================================ # TARGET T0319 # 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 T0319.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 19.8416 # # ============================================ # Comments from T0319.t04.str2.rdb # ============================================ # TARGET T0319 # 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 T0319.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 19.8416 # # ============================================ # Comments from T0319.t04.alpha.rdb # ============================================ # TARGET T0319 # 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 T0319.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 19.8416 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0913 0.1093 0.7994 2 K 0.2294 0.2735 0.4971 3 F 0.3132 0.4557 0.2311 4 L 0.2501 0.5603 0.1896 5 T 0.2007 0.6223 0.1770 6 T 0.1196 0.7145 0.1658 7 N 0.1228 0.6847 0.1925 8 F 0.1029 0.6896 0.2076 9 L 0.1421 0.6157 0.2422 10 K 0.1631 0.5029 0.3340 11 C 0.1343 0.3473 0.5184 12 S 0.1135 0.2360 0.6505 13 V 0.1550 0.2960 0.5490 14 K 0.1995 0.3114 0.4891 15 A 0.2833 0.2069 0.5098 16 C 0.3337 0.1195 0.5468 17 D 0.3529 0.0961 0.5509 18 T 0.3030 0.0822 0.6148 19 S 0.2401 0.0767 0.6832 20 N 0.1304 0.0841 0.7854 21 D 0.0995 0.0699 0.8306 22 N 0.1371 0.0499 0.8130 23 F 0.3150 0.0209 0.6641 24 P 0.4735 0.0200 0.5066 25 L 0.7038 0.0188 0.2773 26 Q 0.8477 0.0105 0.1418 27 Y 0.8378 0.0108 0.1513 28 D 0.7393 0.0124 0.2484 29 G 0.5068 0.0885 0.4047 30 S 0.4323 0.1403 0.4274 31 K 0.5644 0.1284 0.3072 32 C 0.6978 0.0748 0.2274 33 Q 0.7742 0.0555 0.1703 34 L 0.7909 0.0582 0.1509 35 V 0.6693 0.0805 0.2503 36 Q 0.5782 0.0885 0.3333 37 D 0.3078 0.1476 0.5446 38 E 0.1781 0.1665 0.6554 39 S 0.2023 0.1538 0.6439 40 I 0.3209 0.1266 0.5525 41 E 0.3059 0.1044 0.5897 42 F 0.1804 0.0563 0.7633 43 N 0.1072 0.0161 0.8766 44 P 0.0053 0.9046 0.0901 45 E 0.0049 0.9380 0.0571 46 F 0.0049 0.9460 0.0491 47 L 0.0057 0.9436 0.0507 48 L 0.0084 0.9189 0.0727 49 N 0.0085 0.8352 0.1563 50 I 0.0131 0.7656 0.2213 51 V 0.0404 0.5579 0.4017 52 D 0.0367 0.4797 0.4836 53 R 0.0634 0.5062 0.4304 54 V 0.1041 0.2353 0.6606 55 D 0.0849 0.1425 0.7726 56 W 0.0051 0.9436 0.0513 57 P 0.0047 0.9589 0.0363 58 A 0.0047 0.9593 0.0360 59 V 0.0047 0.9597 0.0356 60 L 0.0046 0.9611 0.0343 61 T 0.0047 0.9604 0.0349 62 V 0.0047 0.9594 0.0360 63 A 0.0047 0.9568 0.0385 64 A 0.0049 0.9470 0.0481 65 E 0.0061 0.8899 0.1040 66 L 0.0423 0.5147 0.4430 67 G 0.0356 0.1156 0.8488 68 N 0.0468 0.2490 0.7041 69 N 0.0513 0.3069 0.6419 70 A 0.0738 0.2423 0.6839 71 L 0.0978 0.0325 0.8697 72 P 0.0728 0.0257 0.9015 73 P 0.0454 0.1741 0.7805 74 T 0.0684 0.1451 0.7865 75 K 0.0838 0.0445 0.8717 76 P 0.0705 0.0486 0.8809 77 S 0.0811 0.0588 0.8601 78 F 0.0799 0.0324 0.8877 79 P 0.0655 0.0957 0.8388 80 S 0.0616 0.1970 0.7414 81 S 0.1151 0.2242 0.6607 82 I 0.1178 0.4802 0.4020 83 Q 0.1176 0.4951 0.3874 84 E 0.1234 0.4477 0.4289 85 L 0.1017 0.3668 0.5315 86 T 0.0693 0.2846 0.6461 87 D 0.0364 0.4257 0.5379 88 D 0.0190 0.4391 0.5419 89 D 0.0143 0.7332 0.2525 90 M 0.0064 0.9246 0.0690 91 A 0.0052 0.9478 0.0470 92 I 0.0050 0.9512 0.0438 93 L 0.0047 0.9545 0.0409 94 N 0.0047 0.9558 0.0395 95 D 0.0047 0.9566 0.0386 96 L 0.0047 0.9571 0.0382 97 H 0.0047 0.9575 0.0378 98 T 0.0047 0.9581 0.0372 99 L 0.0048 0.9504 0.0447 100 L 0.0055 0.9205 0.0741 101 L 0.0117 0.8156 0.1728 102 Q 0.0281 0.6844 0.2875 103 T 0.1151 0.5065 0.3784 104 S 0.3218 0.3233 0.3549 105 I 0.5499 0.2011 0.2490 106 A 0.6769 0.1040 0.2191 107 E 0.5841 0.0701 0.3459 108 G 0.5156 0.0267 0.4578 109 E 0.7695 0.0136 0.2169 110 M 0.8699 0.0060 0.1241 111 K 0.8201 0.0069 0.1730 112 C 0.5379 0.0175 0.4447 113 R 0.0368 0.1382 0.8250 114 N 0.0251 0.1022 0.8727 115 C 0.1053 0.0779 0.8168 116 G 0.1405 0.0329 0.8266 117 H 0.4585 0.0171 0.5243 118 I 0.8347 0.0088 0.1565 119 Y 0.8386 0.0107 0.1507 120 Y 0.7974 0.0130 0.1896 121 I 0.5911 0.0552 0.3536 122 K 0.3893 0.1108 0.4999 123 N 0.1128 0.1017 0.7855 124 G 0.1175 0.0629 0.8196 125 I 0.2158 0.0470 0.7372 126 P 0.2045 0.1848 0.6107 127 N 0.1324 0.3327 0.5349 128 L 0.1834 0.2842 0.5323 129 L 0.2253 0.1172 0.6576 130 L 0.1231 0.0352 0.8417 131 P 0.0731 0.0272 0.8997 132 P 0.0161 0.4888 0.4951 133 H 0.0193 0.4283 0.5523 134 L 0.0469 0.3203 0.6328 135 V 0.0408 0.0923 0.8669