# This file is the result of combining several RDB files, specifically # T0357.t06.dssp-ebghstl.rdb (weight 1.53986) # T0357.t06.stride-ebghtl.rdb (weight 1.24869) # T0357.t06.str2.rdb (weight 1.54758) # T0357.t06.alpha.rdb (weight 0.659012) # T0357.t04.dssp-ebghstl.rdb (weight 1.53986) # T0357.t04.stride-ebghtl.rdb (weight 1.24869) # T0357.t04.str2.rdb (weight 1.54758) # T0357.t04.alpha.rdb (weight 0.659012) # T0357.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0357.t2k.stride-ebghtl.rdb (weight 1.24869) # T0357.t2k.str2.rdb (weight 1.54758) # T0357.t2k.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 T0357.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0357 # 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 T0357.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 15.1717 # # ============================================ # Comments from T0357.t06.stride-ebghtl.rdb # ============================================ # TARGET T0357 # 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 T0357.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 15.1717 # # ============================================ # Comments from T0357.t06.str2.rdb # ============================================ # TARGET T0357 # 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 T0357.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 15.1717 # # ============================================ # Comments from T0357.t06.alpha.rdb # ============================================ # TARGET T0357 # 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 T0357.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 15.1717 # # ============================================ # Comments from T0357.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0357 # 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 T0357.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 15.107 # # ============================================ # Comments from T0357.t04.stride-ebghtl.rdb # ============================================ # TARGET T0357 # 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 T0357.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 15.107 # # ============================================ # Comments from T0357.t04.str2.rdb # ============================================ # TARGET T0357 # 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 T0357.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 15.107 # # ============================================ # Comments from T0357.t04.alpha.rdb # ============================================ # TARGET T0357 # 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 T0357.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 15.107 # # ============================================ # Comments from T0357.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0357 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0357.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 39 # # ============================================ # Comments from T0357.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0357 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0357.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 39 # # ============================================ # Comments from T0357.t2k.str2.rdb # ============================================ # TARGET T0357 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0357.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 39 # # ============================================ # Comments from T0357.t2k.alpha.rdb # ============================================ # TARGET T0357 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0357.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 39 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1030 0.0140 0.8830 2 V 0.4932 0.0111 0.4956 3 K 0.7556 0.0077 0.2367 4 F 0.8179 0.0095 0.1726 5 A 0.7740 0.0235 0.2025 6 C 0.7453 0.0185 0.2362 7 R 0.7465 0.0235 0.2300 8 A 0.7729 0.0184 0.2087 9 I 0.6946 0.0369 0.2685 10 T 0.6227 0.0239 0.3535 11 R 0.3448 0.0599 0.5953 12 G 0.3090 0.0473 0.6437 13 R 0.6339 0.0357 0.3304 14 A 0.7773 0.0188 0.2039 15 E 0.8009 0.0262 0.1729 16 G 0.7995 0.0126 0.1879 17 E 0.8317 0.0133 0.1551 18 A 0.8847 0.0082 0.1071 19 L 0.9030 0.0071 0.0899 20 V 0.8615 0.0134 0.1251 21 T 0.6438 0.0199 0.3364 22 K 0.2408 0.0631 0.6961 23 E 0.2144 0.0371 0.7485 24 Y 0.3029 0.0649 0.6322 25 I 0.4699 0.0747 0.4554 26 S 0.5416 0.0932 0.3652 27 F 0.4832 0.1592 0.3576 28 L 0.3790 0.1180 0.5030 29 G 0.2638 0.0770 0.6592 30 G 0.2728 0.0459 0.6813 31 I 0.4162 0.0260 0.5579 32 D 0.2470 0.0278 0.7252 33 K 0.0241 0.2932 0.6827 34 E 0.0187 0.2143 0.7670 35 T 0.0844 0.1574 0.7583 36 G 0.1612 0.0414 0.7975 37 I 0.4588 0.0280 0.5131 38 V 0.6441 0.0297 0.3261 39 K 0.2082 0.0353 0.7565 40 E 0.0517 0.1313 0.8169 41 D 0.0380 0.0933 0.8687 42 C 0.1116 0.1283 0.7601 43 E 0.0502 0.3318 0.6179 44 I 0.0502 0.3039 0.6459 45 K 0.0753 0.2456 0.6791 46 G 0.0872 0.0875 0.8253 47 E 0.3063 0.0389 0.6548 48 S 0.4877 0.0449 0.4674 49 V 0.3755 0.0921 0.5324 50 A 0.1556 0.0713 0.7732 51 G 0.1434 0.0392 0.8174 52 R 0.5780 0.0104 0.4116 53 I 0.8780 0.0047 0.1173 54 L 0.9031 0.0045 0.0924 55 V 0.8824 0.0101 0.1075 56 F 0.6695 0.0095 0.3209 57 P 0.3075 0.0516 0.6410 58 G 0.1121 0.0498 0.8381 59 G 0.1225 0.0675 0.8099 60 K 0.0641 0.1096 0.8264 61 G 0.0599 0.1182 0.8219 62 S 0.0716 0.1898 0.7385 63 T 0.0505 0.4108 0.5387 64 V 0.0270 0.6218 0.3512 65 G 0.0110 0.8209 0.1680 66 S 0.0054 0.9367 0.0579 67 Y 0.0050 0.9537 0.0413 68 V 0.0047 0.9584 0.0369 69 L 0.0047 0.9585 0.0368 70 L 0.0050 0.9586 0.0364 71 N 0.0047 0.9592 0.0361 72 L 0.0052 0.9545 0.0403 73 R 0.0054 0.9374 0.0572 74 K 0.0085 0.8380 0.1535 75 N 0.0423 0.3292 0.6285 76 G 0.0372 0.0411 0.9218 77 V 0.0833 0.0437 0.8731 78 A 0.1544 0.0371 0.8085 79 P 0.1539 0.0856 0.7605 80 K 0.4102 0.2045 0.3854 81 A 0.5904 0.2204 0.1891 82 I 0.6341 0.2256 0.1403 83 I 0.6389 0.1937 0.1674 84 N 0.4953 0.1654 0.3393 85 K 0.2216 0.2019 0.5765 86 K 0.1095 0.2131 0.6774 87 T 0.0825 0.3384 0.5791 88 E 0.0681 0.4168 0.5151 89 T 0.1314 0.5824 0.2863 90 I 0.2152 0.6617 0.1232 91 I 0.3009 0.6202 0.0789 92 A 0.2674 0.6596 0.0730 93 V 0.2354 0.6707 0.0940 94 G 0.2103 0.6946 0.0950 95 A 0.2370 0.6726 0.0904 96 A 0.1972 0.7058 0.0970 97 M 0.1880 0.6641 0.1480 98 A 0.1159 0.5637 0.3203 99 E 0.1017 0.3111 0.5872 100 I 0.1204 0.1633 0.7163 101 P 0.1755 0.1932 0.6313 102 L 0.1479 0.2872 0.5648 103 V 0.1471 0.2696 0.5833 104 E 0.1309 0.2280 0.6411 105 V 0.1408 0.1226 0.7366 106 R 0.1896 0.0511 0.7593 107 D 0.2341 0.0323 0.7336 108 E 0.3632 0.0853 0.5515 109 K 0.4405 0.0835 0.4760 110 F 0.4501 0.1057 0.4442 111 F 0.4104 0.1147 0.4749 112 E 0.4130 0.0890 0.4980 113 A 0.4265 0.2059 0.3676 114 V 0.3352 0.2080 0.4568 115 K 0.3134 0.2009 0.4857 116 T 0.2221 0.1231 0.6548 117 G 0.1421 0.0740 0.7839 118 D 0.3253 0.0533 0.6215 119 R 0.7237 0.0198 0.2565 120 V 0.8378 0.0120 0.1501 121 V 0.8620 0.0081 0.1299 122 V 0.7787 0.0139 0.2074 123 N 0.4798 0.0231 0.4971 124 A 0.1161 0.1803 0.7036 125 D 0.0765 0.2390 0.6845 126 E 0.2397 0.2115 0.5489 127 G 0.4463 0.1204 0.4332 128 Y 0.6594 0.0851 0.2556 129 V 0.7374 0.1081 0.1545 130 E 0.7269 0.1330 0.1401 131 L 0.7254 0.1470 0.1277 132 I 0.6443 0.1971 0.1585 133 E 0.5505 0.2072 0.2423 134 L 0.3724 0.2556 0.3720 135 E 0.1978 0.1623 0.6399 136 H 0.1210 0.0790 0.8000 137 H 0.0798 0.1150 0.8052 138 H 0.0501 0.2070 0.7429 139 H 0.0673 0.1734 0.7593 140 H 0.0689 0.1184 0.8127 141 H 0.0461 0.0396 0.9143