# This file is the result of combining several RDB files, specifically # T0322.t04.dssp-ebghstl.rdb (weight 1.53986) # T0322.t04.stride-ebghtl.rdb (weight 1.24869) # T0322.t04.str2.rdb (weight 1.54758) # T0322.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 T0322.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0322 # 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 T0322.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 2131 # # ============================================ # Comments from T0322.t04.stride-ebghtl.rdb # ============================================ # TARGET T0322 # 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 T0322.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 2131 # # ============================================ # Comments from T0322.t04.str2.rdb # ============================================ # TARGET T0322 # 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 T0322.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 2131 # # ============================================ # Comments from T0322.t04.alpha.rdb # ============================================ # TARGET T0322 # 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 T0322.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 2131 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0609 0.0208 0.9183 2 S 0.0812 0.0356 0.8832 3 D 0.0470 0.1241 0.8288 4 D 0.0564 0.1482 0.7953 5 L 0.0267 0.6260 0.3473 6 T 0.0222 0.7339 0.2438 7 D 0.0215 0.7980 0.1805 8 A 0.0184 0.8401 0.1416 9 Q 0.0178 0.8033 0.1789 10 T 0.0179 0.8244 0.1577 11 A 0.0174 0.7350 0.2476 12 A 0.0269 0.6289 0.3442 13 I 0.0629 0.2437 0.6934 14 P 0.0318 0.4153 0.5529 15 E 0.0228 0.4585 0.5187 16 G 0.0292 0.4407 0.5301 17 F 0.0554 0.4224 0.5222 18 S 0.0293 0.5856 0.3851 19 Q 0.0389 0.6196 0.3415 20 L 0.0678 0.5661 0.3661 21 N 0.0763 0.4227 0.5010 22 W 0.0586 0.3863 0.5551 23 S 0.0627 0.3182 0.6191 24 R 0.0528 0.3290 0.6182 25 G 0.0519 0.3953 0.5528 26 F 0.0690 0.5426 0.3883 27 G 0.0744 0.5490 0.3766 28 R 0.0870 0.5421 0.3708 29 Q 0.1126 0.4455 0.4419 30 I 0.1405 0.2483 0.6112 31 G 0.1023 0.0875 0.8102 32 P 0.1643 0.1146 0.7210 33 L 0.3543 0.0684 0.5773 34 F 0.6195 0.0357 0.3448 35 E 0.7431 0.0272 0.2297 36 H 0.7146 0.0361 0.2493 37 R 0.7420 0.0212 0.2368 38 E 0.5700 0.0284 0.4016 39 G 0.2940 0.0198 0.6862 40 P 0.0627 0.0547 0.8827 41 G 0.1161 0.0403 0.8436 42 Q 0.7997 0.0123 0.1880 43 A 0.9144 0.0035 0.0822 44 R 0.9254 0.0038 0.0708 45 L 0.9237 0.0034 0.0729 46 A 0.9044 0.0042 0.0914 47 F 0.8608 0.0049 0.1343 48 R 0.7504 0.0055 0.2441 49 V 0.5211 0.0167 0.4622 50 E 0.2988 0.0252 0.6760 51 E 0.1115 0.3303 0.5582 52 H 0.0819 0.3262 0.5919 53 H 0.1320 0.2806 0.5874 54 T 0.2063 0.1358 0.6578 55 N 0.0969 0.0921 0.8109 56 G 0.0680 0.1093 0.8226 57 L 0.0726 0.1239 0.8035 58 G 0.1035 0.1017 0.7949 59 N 0.1900 0.1344 0.6756 60 C 0.2825 0.1771 0.5404 61 H 0.1447 0.3496 0.5056 62 G 0.0326 0.7562 0.2112 63 G 0.0084 0.9307 0.0608 64 M 0.0065 0.9516 0.0419 65 L 0.0054 0.9562 0.0383 66 M 0.0051 0.9566 0.0383 67 S 0.0049 0.9500 0.0451 68 F 0.0048 0.9417 0.0535 69 A 0.0048 0.9507 0.0446 70 D 0.0049 0.9545 0.0406 71 M 0.0047 0.9568 0.0385 72 A 0.0048 0.9540 0.0412 73 W 0.0047 0.9588 0.0365 74 G 0.0046 0.9605 0.0348 75 R 0.0047 0.9592 0.0362 76 I 0.0047 0.9543 0.0410 77 I 0.0052 0.9404 0.0544 78 S 0.0072 0.9001 0.0928 79 L 0.0139 0.7953 0.1908 80 Q 0.0387 0.5489 0.4124 81 K 0.0431 0.2593 0.6976 82 S 0.0470 0.1023 0.8507 83 Y 0.1003 0.0460 0.8537 84 S 0.2281 0.0282 0.7437 85 W 0.6600 0.0133 0.3268 86 V 0.8198 0.0073 0.1729 87 T 0.8874 0.0062 0.1063 88 V 0.8848 0.0067 0.1086 89 R 0.9112 0.0047 0.0841 90 L 0.8956 0.0058 0.0986 91 M 0.8526 0.0072 0.1401 92 C 0.8350 0.0085 0.1565 93 D 0.8353 0.0160 0.1487 94 F 0.7672 0.0250 0.2078 95 L 0.5376 0.0663 0.3961 96 S 0.3257 0.0539 0.6204 97 G 0.2375 0.0382 0.7244 98 A 0.2515 0.0126 0.7358 99 K 0.1669 0.0174 0.8157 100 L 0.0711 0.0821 0.8468 101 G 0.0599 0.0506 0.8895 102 D 0.2560 0.0245 0.7196 103 W 0.7589 0.0043 0.2369 104 V 0.8983 0.0041 0.0976 105 E 0.9234 0.0036 0.0730 106 G 0.9073 0.0055 0.0872 107 E 0.9074 0.0048 0.0879 108 G 0.9064 0.0046 0.0889 109 E 0.9105 0.0045 0.0850 110 L 0.9216 0.0031 0.0754 111 I 0.8520 0.0155 0.1325 112 S 0.8359 0.0055 0.1585 113 E 0.4549 0.0432 0.5019 114 E 0.1621 0.0470 0.7909 115 D 0.2165 0.0308 0.7527 116 M 0.6417 0.0097 0.3486 117 L 0.8892 0.0046 0.1062 118 F 0.9187 0.0038 0.0775 119 T 0.9288 0.0032 0.0680 120 V 0.9262 0.0034 0.0705 121 R 0.9207 0.0034 0.0759 122 G 0.9226 0.0036 0.0738 123 R 0.9297 0.0033 0.0670 124 I 0.9271 0.0034 0.0696 125 W 0.8847 0.0048 0.1105 126 A 0.6253 0.0179 0.3568 127 G 0.0626 0.0218 0.9156 128 E 0.0685 0.0355 0.8960 129 R 0.7935 0.0086 0.1979 130 T 0.9146 0.0033 0.0821 131 L 0.9152 0.0050 0.0798 132 I 0.9213 0.0050 0.0738 133 T 0.9183 0.0056 0.0761 134 G 0.9123 0.0052 0.0825 135 T 0.9010 0.0121 0.0869 136 G 0.9108 0.0048 0.0844 137 V 0.9200 0.0054 0.0746 138 F 0.9247 0.0041 0.0712 139 K 0.9062 0.0057 0.0881 140 A 0.8644 0.0065 0.1292 141 L 0.6012 0.0201 0.3787 142 S 0.3303 0.0305 0.6393 143 A 0.0607 0.1499 0.7894 144 R 0.0483 0.0944 0.8573 145 K 0.0740 0.0276 0.8984 146 P 0.0798 0.0167 0.9035 147 R 0.0702 0.0152 0.9145 148 P 0.0432 0.0701 0.8867 149 G 0.0471 0.1311 0.8218 150 E 0.0935 0.2793 0.6273 151 L 0.0992 0.3701 0.5307 152 A 0.1185 0.5341 0.3474 153 Y 0.1325 0.5597 0.3078 154 K 0.1130 0.5495 0.3375 155 E 0.0795 0.4814 0.4391 156 E 0.0635 0.3604 0.5761 157 A 0.0394 0.1123 0.8482