# This file is the result of combining several RDB files, specifically # T0362.t06.dssp-ebghstl.rdb (weight 1.53986) # T0362.t06.stride-ebghtl.rdb (weight 1.24869) # T0362.t06.str2.rdb (weight 1.54758) # T0362.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 T0362.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0362 # 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 T0362.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 1472 # # ============================================ # Comments from T0362.t06.stride-ebghtl.rdb # ============================================ # TARGET T0362 # 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 T0362.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 1472 # # ============================================ # Comments from T0362.t06.str2.rdb # ============================================ # TARGET T0362 # 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 T0362.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 1472 # # ============================================ # Comments from T0362.t06.alpha.rdb # ============================================ # TARGET T0362 # 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 T0362.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 1472 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0762 0.0118 0.9119 2 N 0.0653 0.0094 0.9252 3 P 0.0295 0.1565 0.8140 4 E 0.0292 0.1555 0.8153 5 N 0.1108 0.1359 0.7533 6 W 0.3938 0.0421 0.5640 7 L 0.7654 0.0138 0.2208 8 L 0.8601 0.0081 0.1318 9 L 0.8600 0.0052 0.1348 10 R 0.8311 0.0073 0.1617 11 R 0.8388 0.0052 0.1560 12 V 0.8396 0.0050 0.1555 13 V 0.7149 0.0088 0.2763 14 R 0.4683 0.0107 0.5210 15 F 0.0953 0.3743 0.5304 16 G 0.0513 0.3623 0.5864 17 D 0.1261 0.3657 0.5082 18 T 0.2877 0.1088 0.6036 19 D 0.1391 0.0646 0.7963 20 A 0.0329 0.3277 0.6394 21 A 0.0468 0.1855 0.7677 22 G 0.0645 0.1639 0.7717 23 V 0.2396 0.1799 0.5804 24 M 0.4394 0.1634 0.3971 25 H 0.2195 0.2288 0.5517 26 F 0.0437 0.6810 0.2753 27 H 0.0122 0.9017 0.0861 28 Q 0.0118 0.9287 0.0596 29 L 0.0074 0.9476 0.0450 30 F 0.0062 0.9502 0.0436 31 R 0.0051 0.9514 0.0435 32 W 0.0048 0.9509 0.0444 33 C 0.0047 0.9553 0.0400 34 H 0.0047 0.9543 0.0409 35 E 0.0048 0.9504 0.0448 36 S 0.0048 0.9402 0.0550 37 W 0.0047 0.9468 0.0485 38 E 0.0047 0.9548 0.0405 39 E 0.0048 0.9548 0.0404 40 S 0.0048 0.9531 0.0421 41 L 0.0048 0.9510 0.0441 42 E 0.0050 0.9381 0.0570 43 S 0.0067 0.8721 0.1212 44 Y 0.0462 0.4365 0.5173 45 G 0.0441 0.0329 0.9230 46 L 0.0821 0.0163 0.9016 47 N 0.1046 0.0141 0.8812 48 P 0.0102 0.7748 0.2150 49 A 0.0061 0.8149 0.1789 50 D 0.0110 0.8001 0.1888 51 I 0.0686 0.5088 0.4226 52 F 0.1007 0.2190 0.6803 53 P 0.0535 0.2588 0.6877 54 G 0.0646 0.2026 0.7329 55 S 0.0756 0.2386 0.6858 56 R 0.0820 0.2933 0.6247 57 K 0.0816 0.2344 0.6840 58 S 0.0901 0.1580 0.7519 59 E 0.1364 0.1301 0.7335 60 V 0.2030 0.0965 0.7005 61 T 0.1215 0.0438 0.8348 62 P 0.0708 0.1236 0.8056 63 E 0.1083 0.1160 0.7757 64 V 0.3686 0.0853 0.5460 65 A 0.5218 0.0371 0.4411 66 L 0.7393 0.0173 0.2434 67 P 0.8151 0.0147 0.1702 68 I 0.8816 0.0156 0.1028 69 I 0.8745 0.0290 0.0965 70 H 0.9067 0.0104 0.0830 71 C 0.8887 0.0112 0.1001 72 Q 0.8291 0.0201 0.1508 73 A 0.7969 0.0132 0.1900 74 D 0.8311 0.0099 0.1590 75 F 0.7957 0.0115 0.1928 76 R 0.5732 0.0368 0.3900 77 R 0.4492 0.0113 0.5395 78 P 0.4426 0.0141 0.5432 79 I 0.4003 0.0169 0.5828 80 H 0.1739 0.0193 0.8068 81 T 0.0464 0.0639 0.8897 82 G 0.0369 0.0454 0.9177 83 D 0.2528 0.0197 0.7276 84 A 0.7505 0.0040 0.2455 85 L 0.9022 0.0036 0.0942 86 A 0.9281 0.0032 0.0686 87 M 0.9216 0.0037 0.0747 88 E 0.9167 0.0038 0.0795 89 L 0.9014 0.0042 0.0944 90 R 0.8313 0.0062 0.1625 91 P 0.7797 0.0200 0.2003 92 E 0.6607 0.0580 0.2813 93 R 0.8026 0.0241 0.1734 94 L 0.7337 0.0216 0.2447 95 N 0.4577 0.0172 0.5251 96 P 0.0694 0.0871 0.8434 97 N 0.1436 0.0618 0.7945 98 S 0.7904 0.0095 0.2002 99 F 0.9061 0.0037 0.0902 100 Q 0.9302 0.0032 0.0666 101 V 0.9315 0.0031 0.0654 102 H 0.9245 0.0033 0.0722 103 F 0.9263 0.0034 0.0703 104 E 0.9274 0.0032 0.0694 105 F 0.9229 0.0037 0.0734 106 R 0.8929 0.0041 0.1030 107 C 0.7084 0.0133 0.2783 108 E 0.0760 0.0357 0.8882 109 E 0.0681 0.0416 0.8903 110 Q 0.7770 0.0104 0.2126 111 I 0.9019 0.0036 0.0945 112 A 0.9026 0.0063 0.0911 113 A 0.9181 0.0045 0.0774 114 H 0.9213 0.0047 0.0740 115 A 0.9233 0.0036 0.0731 116 L 0.9274 0.0033 0.0693 117 I 0.9267 0.0032 0.0701 118 R 0.9165 0.0070 0.0765 119 H 0.9290 0.0034 0.0676 120 L 0.9243 0.0044 0.0713 121 A 0.9186 0.0043 0.0771 122 I 0.8681 0.0072 0.1247 123 N 0.5993 0.0076 0.3931 124 A 0.0441 0.2202 0.7357 125 Q 0.0234 0.1991 0.7775 126 T 0.0646 0.1641 0.7712 127 R 0.0878 0.0658 0.8464 128 H 0.2365 0.0280 0.7355 129 R 0.4729 0.0279 0.4992 130 C 0.3868 0.0209 0.5923 131 A 0.2409 0.0200 0.7390 132 L 0.0968 0.0151 0.8881 133 P 0.0606 0.0357 0.9036 134 E 0.0103 0.7210 0.2687 135 G 0.0105 0.7664 0.2231 136 I 0.0087 0.8847 0.1067 137 D 0.0058 0.9312 0.0630 138 R 0.0052 0.9433 0.0515 139 W 0.0051 0.9422 0.0526 140 L 0.0064 0.9325 0.0612 141 E 0.0069 0.9127 0.0804 142 A 0.0098 0.8402 0.1501 143 S 0.0408 0.6010 0.3582 144 G 0.0360 0.2631 0.7009 145 V 0.0542 0.1670 0.7788 146 G 0.0557 0.1440 0.8004 147 K 0.0751 0.1609 0.7640 148 I 0.0854 0.1550 0.7597 149 G 0.0809 0.1168 0.8023 150 S 0.0802 0.0756 0.8441 151 I 0.0522 0.0416 0.9062