# This file is the result of combining several RDB files, specifically # T0289.t04.dssp-ebghstl.rdb (weight 1.53986) # T0289.t04.stride-ebghtl.rdb (weight 1.24869) # T0289.t04.str2.rdb (weight 1.54758) # T0289.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 T0289.t04.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.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 13.7165 # # ============================================ # Comments from T0289.t04.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.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 13.7165 # # ============================================ # Comments from T0289.t04.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.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 13.7165 # # ============================================ # Comments from T0289.t04.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.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 13.7165 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.0184 0.5551 0.4265 2 L 0.0239 0.7360 0.2401 3 D 0.0258 0.8160 0.1581 4 F 0.0336 0.8606 0.1058 5 I 0.0324 0.8668 0.1008 6 Q 0.0406 0.8654 0.0940 7 R 0.0495 0.8417 0.1087 8 F 0.0384 0.7410 0.2206 9 N 0.0500 0.5612 0.3888 10 E 0.0480 0.2683 0.6837 11 G 0.0304 0.0532 0.9164 12 K 0.0937 0.0409 0.8653 13 E 0.3053 0.0232 0.6715 14 F 0.1603 0.0134 0.8263 15 P 0.0951 0.0147 0.8902 16 P 0.0869 0.2186 0.6946 17 C 0.0966 0.2607 0.6427 18 A 0.3560 0.2004 0.4435 19 I 0.6885 0.0381 0.2734 20 D 0.8438 0.0252 0.1310 21 V 0.8682 0.0394 0.0924 22 Y 0.8600 0.0430 0.0970 23 K 0.8449 0.0427 0.1124 24 I 0.7458 0.0659 0.1883 25 M 0.6179 0.0797 0.3024 26 E 0.5112 0.1180 0.3708 27 K 0.5687 0.0714 0.3599 28 V 0.6038 0.0266 0.3697 29 D 0.5324 0.0243 0.4433 30 Y 0.3565 0.0191 0.6244 31 P 0.3402 0.0237 0.6361 32 R 0.3669 0.0443 0.5888 33 N 0.1201 0.0365 0.8434 34 E 0.0444 0.1263 0.8293 35 S 0.0604 0.0262 0.9133 36 G 0.0673 0.0252 0.9076 37 D 0.2613 0.0159 0.7228 38 V 0.7267 0.0139 0.2594 39 A 0.8274 0.0203 0.1523 40 A 0.8983 0.0107 0.0910 41 V 0.9055 0.0097 0.0848 42 I 0.8541 0.0152 0.1308 43 H 0.4336 0.0238 0.5426 44 P 0.0960 0.2733 0.6307 45 N 0.0584 0.2560 0.6856 46 L 0.0860 0.3773 0.5367 47 Q 0.1444 0.2228 0.6327 48 D 0.0843 0.2468 0.6688 49 Q 0.0819 0.2303 0.6877 50 D 0.1322 0.1385 0.7293 51 W 0.1750 0.1649 0.6601 52 K 0.2949 0.0978 0.6073 53 P 0.4347 0.1016 0.4636 54 L 0.3021 0.0669 0.6310 55 H 0.1014 0.0246 0.8739 56 P 0.0313 0.0705 0.8982 57 G 0.0216 0.0407 0.9377 58 D 0.1098 0.0187 0.8715 59 P 0.2364 0.0429 0.7208 60 V 0.5705 0.0746 0.3549 61 F 0.7828 0.0408 0.1763 62 V 0.8208 0.0307 0.1485 63 S 0.6978 0.0240 0.2782 64 L 0.4042 0.0537 0.5422 65 D 0.0911 0.0308 0.8781 66 G 0.0851 0.0336 0.8813 67 K 0.4552 0.0149 0.5299 68 V 0.8458 0.0052 0.1490 69 I 0.8084 0.0072 0.1843 70 P 0.7203 0.0120 0.2677 71 L 0.4321 0.0461 0.5218 72 G 0.1432 0.0544 0.8023 73 G 0.0872 0.0543 0.8585 74 D 0.1170 0.0822 0.8008 75 C 0.2618 0.0628 0.6754 76 T 0.4686 0.0352 0.4962 77 V 0.5610 0.0391 0.3999 78 Y 0.5478 0.0462 0.4060 79 P 0.4719 0.1441 0.3840 80 V 0.6001 0.2088 0.1911 81 F 0.5442 0.3059 0.1499 82 V 0.3181 0.5674 0.1145 83 N 0.1367 0.6540 0.2093 84 E 0.0992 0.6896 0.2112 85 A 0.0270 0.8796 0.0933 86 A 0.0212 0.8933 0.0855 87 Y 0.0159 0.9019 0.0821 88 Y 0.0191 0.8852 0.0957 89 E 0.0179 0.8598 0.1223 90 K 0.0133 0.7536 0.2331 91 K 0.0179 0.6766 0.3056 92 E 0.0368 0.6883 0.2749 93 A 0.0775 0.6953 0.2271 94 F 0.1354 0.6496 0.2151 95 A 0.2410 0.5615 0.1975 96 K 0.2703 0.5054 0.2243 97 T 0.3986 0.3293 0.2721 98 T 0.4666 0.2372 0.2962 99 K 0.5297 0.1891 0.2811 100 L 0.5838 0.1609 0.2552 101 T 0.5935 0.1090 0.2975 102 L 0.5074 0.0701 0.4226 103 N 0.3032 0.0527 0.6441 104 A 0.0790 0.5016 0.4194 105 K 0.0279 0.7228 0.2493 106 S 0.0349 0.7193 0.2458 107 I 0.0406 0.7724 0.1870 108 R 0.0432 0.7619 0.1949 109 S 0.0324 0.7400 0.2276 110 T 0.0350 0.6261 0.3389 111 L 0.0645 0.4234 0.5121 112 H 0.0449 0.1832 0.7719