# This file is the result of combining several RDB files, specifically # T0289.t06.dssp-ebghstl.rdb (weight 1.53986) # T0289.t06.stride-ebghtl.rdb (weight 1.24869) # T0289.t06.str2.rdb (weight 1.54758) # T0289.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 T0289.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0289 # 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 T0289.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 12.0665 # # ============================================ # Comments from T0289.t06.stride-ebghtl.rdb # ============================================ # TARGET T0289 # 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 T0289.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 12.0665 # # ============================================ # Comments from T0289.t06.str2.rdb # ============================================ # TARGET T0289 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0289.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 12.0665 # # ============================================ # Comments from T0289.t06.alpha.rdb # ============================================ # TARGET T0289 # 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 T0289.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 12.0665 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 P 0.0626 0.0154 0.9220 2 P 0.0751 0.0653 0.8596 3 C 0.0995 0.1008 0.7997 4 A 0.3991 0.0922 0.5087 5 I 0.6491 0.0305 0.3203 6 D 0.8412 0.0184 0.1403 7 V 0.8737 0.0314 0.0949 8 Y 0.8562 0.0383 0.1055 9 K 0.8424 0.0384 0.1192 10 I 0.7355 0.0636 0.2010 11 M 0.6163 0.0808 0.3029 12 E 0.5124 0.1236 0.3640 13 K 0.5613 0.0766 0.3621 14 V 0.5907 0.0283 0.3809 15 D 0.5187 0.0260 0.4553 16 Y 0.3458 0.0198 0.6344 17 P 0.3291 0.0246 0.6463 18 R 0.3555 0.0477 0.5968 19 N 0.1222 0.0400 0.8378 20 E 0.0481 0.1283 0.8235 21 S 0.0618 0.0267 0.9115 22 G 0.0688 0.0250 0.9062 23 D 0.2667 0.0159 0.7174 24 V 0.7315 0.0134 0.2551 25 A 0.8287 0.0195 0.1518 26 A 0.8998 0.0098 0.0903 27 V 0.9066 0.0091 0.0843 28 I 0.8563 0.0145 0.1293 29 H 0.4352 0.0226 0.5422 30 P 0.0951 0.2653 0.6395 31 N 0.0587 0.2468 0.6945 32 L 0.0889 0.3630 0.5481 33 Q 0.1463 0.2172 0.6364 34 D 0.0861 0.2457 0.6682 35 Q 0.0804 0.2314 0.6882 36 D 0.1313 0.1384 0.7303 37 W 0.1767 0.1650 0.6583 38 K 0.2979 0.0975 0.6046 39 P 0.4420 0.1012 0.4568 40 L 0.3076 0.0669 0.6255 41 H 0.1029 0.0246 0.8725 42 P 0.0316 0.0699 0.8985 43 G 0.0216 0.0400 0.9384 44 D 0.1093 0.0183 0.8724 45 P 0.2435 0.0389 0.7177 46 V 0.5945 0.0656 0.3399 47 F 0.7982 0.0351 0.1667 48 V 0.8328 0.0272 0.1399 49 S 0.7163 0.0222 0.2615 50 L 0.4269 0.0516 0.5215 51 D 0.0926 0.0304 0.8769 52 G 0.0848 0.0337 0.8815 53 K 0.4651 0.0148 0.5201 54 V 0.8476 0.0050 0.1475 55 I 0.8077 0.0072 0.1851 56 P 0.7186 0.0120 0.2694 57 L 0.4266 0.0470 0.5264 58 G 0.1398 0.0547 0.8054 59 G 0.0853 0.0552 0.8595 60 D 0.1165 0.0828 0.8007 61 C 0.2593 0.0642 0.6766 62 T 0.4660 0.0363 0.4977 63 V 0.5556 0.0410 0.4035 64 Y 0.5397 0.0486 0.4117 65 P 0.4611 0.1517 0.3873 66 V 0.5930 0.2132 0.1939 67 F 0.5415 0.3075 0.1510 68 V 0.3237 0.5599 0.1163 69 N 0.1459 0.6412 0.2130 70 E 0.1054 0.6805 0.2142 71 A 0.0294 0.8718 0.0988 72 A 0.0226 0.8864 0.0910 73 Y 0.0180 0.8935 0.0885 74 Y 0.0223 0.8721 0.1056 75 E 0.0205 0.8426 0.1369 76 K 0.0145 0.7385 0.2470 77 K 0.0203 0.6682 0.3115 78 E 0.0398 0.6791 0.2810 79 A 0.0840 0.6883 0.2277 80 F 0.1436 0.6439 0.2126 81 A 0.2505 0.5576 0.1919 82 K 0.2778 0.5026 0.2195 83 T 0.3989 0.3353 0.2659 84 T 0.4624 0.2464 0.2912 85 K 0.5223 0.1996 0.2781 86 L 0.5768 0.1684 0.2548 87 T 0.5848 0.1181 0.2970 88 L 0.4946 0.0799 0.4255 89 N 0.2933 0.0583 0.6484 90 A 0.0805 0.4926 0.4269 91 K 0.0330 0.6948 0.2722 92 S 0.0404 0.6950 0.2646 93 I 0.0532 0.7408 0.2060 94 R 0.0544 0.7383 0.2073 95 S 0.0443 0.7050 0.2506 96 T 0.0420 0.5917 0.3663 97 L 0.0690 0.3902 0.5409 98 H 0.0445 0.1434 0.8121