# This file is the result of combining several RDB files, specifically # T0496.t04.str2.rdb (weight 1.54425) # T0496.t04.str4.rdb (weight 0.924988) # T0496.t04.pb.rdb (weight 0.789901) # T0496.t04.bys.rdb (weight 0.748322) # T0496.t04.alpha.rdb (weight 0.678173) # 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 T0496.t04.str2.rdb # ============================================ # TARGET T0496 # Using neural net dunbrack-40pc-3157-t04-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 T0496.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 20.6928 # # ============================================ # Comments from T0496.t04.str4.rdb # ============================================ # TARGET T0496 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-str4-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 21 (1 str4 ) # The input amino acid frequencies were determined from # alignment T0496.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 20.6928 # # ============================================ # Comments from T0496.t04.pb.rdb # ============================================ # TARGET T0496 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-pb-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 16 (1 pb ) # The input amino acid frequencies were determined from # alignment T0496.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 20.6928 # # ============================================ # Comments from T0496.t04.bys.rdb # ============================================ # TARGET T0496 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-bys-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 Bystroff ) # The input amino acid frequencies were determined from # alignment T0496.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 20.6928 # # ============================================ # Comments from T0496.t04.alpha.rdb # ============================================ # TARGET T0496 # Using neural net dunbrack-40pc-3157-t04-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 T0496.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 20.6928 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2379 0.1348 0.6273 2 N 0.2299 0.0907 0.6795 3 T 0.3442 0.0532 0.6025 4 P 0.3838 0.0951 0.5212 5 V 0.4607 0.0704 0.4688 6 S 0.3611 0.0546 0.5843 7 V 0.1647 0.4857 0.3496 8 N 0.1120 0.6182 0.2699 9 E 0.0628 0.7280 0.2092 10 K 0.0187 0.8615 0.1198 11 K 0.0092 0.8955 0.0953 12 D 0.0085 0.9154 0.0761 13 F 0.0087 0.9199 0.0714 14 V 0.0083 0.9208 0.0708 15 K 0.0083 0.9237 0.0679 16 W 0.0093 0.9205 0.0702 17 F 0.0103 0.9119 0.0778 18 L 0.0142 0.8763 0.1096 19 N 0.0177 0.7905 0.1917 20 N 0.0437 0.5148 0.4414 21 Y 0.1123 0.3862 0.5016 22 Q 0.1604 0.3121 0.5275 23 L 0.1747 0.3901 0.4352 24 K 0.1408 0.3913 0.4679 25 Q 0.0929 0.5986 0.3086 26 R 0.0216 0.7920 0.1864 27 E 0.0161 0.8453 0.1386 28 C 0.0176 0.8939 0.0884 29 V 0.0118 0.9148 0.0733 30 W 0.0117 0.9197 0.0686 31 I 0.0094 0.9216 0.0690 32 L 0.0094 0.9204 0.0702 33 N 0.0094 0.9169 0.0737 34 Y 0.0107 0.9030 0.0863 35 L 0.0149 0.8697 0.1155 36 M 0.0247 0.7711 0.2041 37 S 0.0499 0.5086 0.4415 38 H 0.0525 0.5294 0.4180 39 D 0.0145 0.7047 0.2808 40 Q 0.0134 0.8166 0.1700 41 L 0.0206 0.8167 0.1627 42 M 0.0452 0.7205 0.2343 43 H 0.0687 0.6037 0.3276 44 K 0.1652 0.3531 0.4817 45 V 0.3390 0.1319 0.5292 46 H 0.4179 0.1486 0.4335 47 F 0.5558 0.1376 0.3066 48 V 0.4456 0.2406 0.3138 49 E 0.3437 0.3178 0.3385 50 H 0.1978 0.3521 0.4502 51 A 0.1527 0.4171 0.4302 52 K 0.1351 0.3894 0.4755 53 Y 0.1584 0.2536 0.5880 54 C 0.2149 0.0856 0.6995 55 P 0.1531 0.2526 0.5942 56 R 0.2286 0.1646 0.6068 57 G 0.4958 0.0579 0.4463 58 L 0.7427 0.0199 0.2374 59 V 0.7991 0.0126 0.1883 60 M 0.7801 0.0155 0.2045 61 S 0.6787 0.0371 0.2843 62 A 0.5022 0.1429 0.3549 63 N 0.3412 0.1723 0.4865 64 C 0.2658 0.1493 0.5848 65 V 0.2236 0.1984 0.5780 66 K 0.1581 0.2138 0.6281 67 D 0.1939 0.1405 0.6656 68 T 0.2832 0.0600 0.6567 69 P 0.3382 0.1235 0.5383 70 F 0.4858 0.1360 0.3783 71 H 0.5978 0.1272 0.2750 72 F 0.6225 0.1119 0.2656 73 F 0.5932 0.1170 0.2898 74 K 0.4721 0.1650 0.3628 75 Q 0.2584 0.2081 0.5336 76 N 0.2241 0.1592 0.6166 77 V 0.3738 0.1036 0.5227 78 M 0.4652 0.0973 0.4375 79 T 0.4051 0.1145 0.4804 80 T 0.3092 0.1331 0.5576 81 D 0.2178 0.0946 0.6876 82 A 0.0291 0.6477 0.3231 83 E 0.0197 0.7812 0.1991 84 K 0.0241 0.8353 0.1406 85 S 0.0384 0.7904 0.1712 86 F 0.0503 0.7461 0.2036 87 H 0.0511 0.7480 0.2009 88 D 0.0853 0.6833 0.2314 89 I 0.1912 0.5430 0.2658 90 R 0.2633 0.3990 0.3377 91 L 0.3104 0.2346 0.4549 92 N 0.2126 0.0851 0.7022 93 R 0.0664 0.3403 0.5932 94 D 0.0998 0.1962 0.7040 95 E 0.2032 0.1613 0.6355 96 D 0.3671 0.0994 0.5335 97 I 0.6742 0.0420 0.2838 98 Y 0.7593 0.0136 0.2271 99 I 0.8156 0.0066 0.1778 100 Q 0.8050 0.0090 0.1860 101 L 0.7899 0.0108 0.1993 102 N 0.7030 0.0247 0.2722 103 F 0.4898 0.0907 0.4195 104 K 0.2281 0.2384 0.5335 105 S 0.1330 0.3691 0.4979 106 S 0.1102 0.4185 0.4713 107 F 0.1180 0.3910 0.4910 108 Q 0.1332 0.3306 0.5363 109 N 0.1485 0.3075 0.5441 110 A 0.0274 0.6993 0.2733 111 N 0.0254 0.7682 0.2065 112 Y 0.0325 0.8234 0.1440 113 V 0.0391 0.8474 0.1135 114 A 0.0596 0.8312 0.1092 115 V 0.0507 0.8256 0.1237 116 L 0.1135 0.7143 0.1722 117 E 0.0863 0.6466 0.2671 118 E 0.0978 0.3671 0.5352 119 N 0.1744 0.1363 0.6893 120 P 0.0489 0.3947 0.5563 121 Y 0.0833 0.2379 0.6788 122 L 0.1908 0.0916 0.7177 123 P 0.1632 0.1553 0.6816 124 K 0.1653 0.2992 0.5355 125 H 0.2282 0.2493 0.5225 126 I 0.2514 0.3432 0.4054 127 E 0.2253 0.4204 0.3543 128 V 0.1654 0.5185 0.3161 129 N 0.1116 0.5332 0.3552 130 E 0.0386 0.6987 0.2627 131 K 0.0305 0.7654 0.2041 132 D 0.0203 0.8522 0.1275 133 R 0.0096 0.9056 0.0848 134 L 0.0091 0.9141 0.0768 135 L 0.0085 0.9207 0.0708 136 A 0.0084 0.9199 0.0717 137 E 0.0083 0.9217 0.0699 138 R 0.0084 0.9185 0.0731 139 F 0.0092 0.9088 0.0820 140 L 0.0097 0.8990 0.0913 141 E 0.0098 0.9035 0.0867 142 E 0.0113 0.8926 0.0961 143 S 0.0145 0.8822 0.1033 144 V 0.0116 0.8929 0.0955 145 F 0.0102 0.9079 0.0820 146 S 0.0104 0.9106 0.0791 147 F 0.0102 0.9111 0.0786 148 R 0.0102 0.9122 0.0776 149 R 0.0084 0.9188 0.0728 150 E 0.0083 0.9202 0.0715 151 R 0.0084 0.9173 0.0744 152 L 0.0084 0.9100 0.0816 153 L 0.0085 0.9006 0.0909 154 K 0.0084 0.9014 0.0902 155 Q 0.0103 0.8646 0.1251 156 I 0.0162 0.8112 0.1726 157 D 0.0105 0.7999 0.1896 158 E 0.0088 0.8758 0.1154 159 A 0.0108 0.8563 0.1329 160 L 0.0199 0.7150 0.2651 161 D 0.0373 0.5850 0.3777 162 K 0.0302 0.5223 0.4474 163 Q 0.0460 0.3783 0.5757 164 D 0.0891 0.3638 0.5471 165 K 0.0111 0.8148 0.1741 166 E 0.0094 0.8933 0.0974 167 A 0.0089 0.9108 0.0803 168 F 0.0085 0.9137 0.0778 169 H 0.0088 0.9182 0.0730 170 R 0.0091 0.9113 0.0796 171 L 0.0091 0.9086 0.0823 172 T 0.0085 0.9142 0.0773 173 A 0.0083 0.9146 0.0771 174 E 0.0088 0.9006 0.0906 175 L 0.0100 0.8878 0.1023 176 K 0.0139 0.8289 0.1572 177 M 0.0323 0.7116 0.2561 178 L 0.0695 0.4973 0.4332