# This file is the result of combining several RDB files, specifically # T0582.t04.str2.rdb (weight 1.54425) # T0582.t04.str4.rdb (weight 0.924988) # T0582.t04.pb.rdb (weight 0.789901) # T0582.t04.bys.rdb (weight 0.748322) # T0582.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 T0582.t04.str2.rdb # ============================================ # TARGET T0582 # 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 T0582.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 1685 # # ============================================ # Comments from T0582.t04.str4.rdb # ============================================ # TARGET T0582 # 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 T0582.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 1685 # # ============================================ # Comments from T0582.t04.pb.rdb # ============================================ # TARGET T0582 # 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 T0582.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 1685 # # ============================================ # Comments from T0582.t04.bys.rdb # ============================================ # TARGET T0582 # 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 T0582.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 1685 # # ============================================ # Comments from T0582.t04.alpha.rdb # ============================================ # TARGET T0582 # 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 T0582.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 1685 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3298 0.0681 0.6021 2 E 0.3210 0.0614 0.6176 3 I 0.3411 0.1146 0.5443 4 N 0.2501 0.0932 0.6567 5 A 0.1390 0.3742 0.4869 6 D 0.1510 0.2594 0.5895 7 F 0.2021 0.2059 0.5920 8 T 0.2143 0.1013 0.6844 9 K 0.2828 0.0649 0.6523 10 P 0.3485 0.0565 0.5949 11 V 0.5743 0.0570 0.3686 12 V 0.6627 0.0223 0.3150 13 I 0.6170 0.0237 0.3593 14 D 0.2932 0.0160 0.6908 15 T 0.0993 0.3897 0.5109 16 D 0.0607 0.3986 0.5407 17 Q 0.1054 0.2794 0.6152 18 L 0.2726 0.1130 0.6143 19 E 0.2834 0.1299 0.5867 20 W 0.3572 0.1202 0.5227 21 R 0.3864 0.0477 0.5659 22 P 0.3334 0.0691 0.5975 23 S 0.2835 0.0422 0.6742 24 P 0.1895 0.1529 0.6576 25 M 0.1904 0.1524 0.6573 26 K 0.1288 0.1862 0.6850 27 G 0.1405 0.1311 0.7284 28 V 0.4395 0.1057 0.4548 29 E 0.5856 0.1069 0.3075 30 R 0.6550 0.1034 0.2416 31 R 0.6595 0.0930 0.2475 32 M 0.6202 0.1132 0.2666 33 L 0.4634 0.1917 0.3449 34 D 0.3042 0.2417 0.4541 35 R 0.2240 0.2425 0.5335 36 I 0.1702 0.1783 0.6514 37 G 0.1226 0.1364 0.7410 38 G 0.1265 0.1625 0.7110 39 E 0.1889 0.2477 0.5634 40 V 0.2564 0.2678 0.4758 41 A 0.3324 0.2374 0.4302 42 R 0.4411 0.2152 0.3437 43 A 0.6232 0.1040 0.2728 44 T 0.6989 0.0679 0.2333 45 S 0.7536 0.0367 0.2098 46 I 0.7735 0.0250 0.2015 47 V 0.7756 0.0152 0.2092 48 R 0.7391 0.0162 0.2447 49 Y 0.5872 0.0295 0.3833 50 A 0.3121 0.0275 0.6604 51 P 0.1489 0.1663 0.6848 52 G 0.0808 0.1109 0.8083 53 S 0.2328 0.1041 0.6630 54 R 0.3357 0.0890 0.5753 55 F 0.3864 0.0527 0.5609 56 S 0.2845 0.0822 0.6333 57 A 0.2655 0.2142 0.5203 58 H 0.3017 0.1464 0.5519 59 T 0.3009 0.1038 0.5953 60 H 0.2485 0.0596 0.6919 61 D 0.1542 0.1499 0.6959 62 G 0.1080 0.1188 0.7731 63 G 0.2865 0.0591 0.6544 64 E 0.6419 0.0250 0.3331 65 E 0.7788 0.0084 0.2128 66 F 0.8229 0.0045 0.1725 67 I 0.8259 0.0044 0.1697 68 V 0.8120 0.0046 0.1834 69 L 0.7834 0.0121 0.2045 70 D 0.6724 0.0295 0.2981 71 G 0.5638 0.0265 0.4097 72 V 0.6851 0.0357 0.2793 73 F 0.7041 0.0248 0.2711 74 Q 0.6671 0.0359 0.2970 75 D 0.5072 0.0801 0.4127 76 E 0.2653 0.2165 0.5181 77 H 0.1593 0.1509 0.6898 78 G 0.1386 0.1033 0.7581 79 D 0.2305 0.0669 0.7026 80 Y 0.3013 0.0281 0.6706 81 P 0.2246 0.0329 0.7425 82 A 0.1784 0.1745 0.6471 83 G 0.1464 0.1278 0.7259 84 T 0.4331 0.0651 0.5017 85 Y 0.6820 0.0320 0.2860 86 V 0.7538 0.0176 0.2286 87 R 0.7449 0.0153 0.2398 88 N 0.6004 0.0158 0.3839 89 P 0.3118 0.0224 0.6658 90 P 0.1536 0.1836 0.6628 91 T 0.1107 0.1272 0.7620 92 T 0.2500 0.0759 0.6741 93 S 0.2821 0.1191 0.5988 94 H 0.3320 0.0897 0.5783 95 V 0.3243 0.0580 0.6176 96 P 0.2579 0.1254 0.6167 97 G 0.2388 0.1259 0.6353 98 S 0.2020 0.0865 0.7115 99 A 0.1475 0.2196 0.6329 100 E 0.1293 0.1855 0.6852 101 G 0.1682 0.0965 0.7353 102 C 0.4925 0.0354 0.4721 103 T 0.7311 0.0276 0.2413 104 I 0.8081 0.0122 0.1798 105 F 0.8113 0.0130 0.1757 106 V 0.8121 0.0125 0.1754 107 K 0.7837 0.0255 0.1908 108 L 0.6650 0.0672 0.2677 109 W 0.5010 0.0774 0.4216 110 Q 0.2977 0.0926 0.6097 111 F 0.2145 0.1139 0.6716 112 D 0.1976 0.0277 0.7747 113 P 0.0340 0.4925 0.4734 114 A 0.0418 0.4309 0.5273 115 D 0.0945 0.3103 0.5952 116 R 0.1523 0.2302 0.6174 117 T 0.2422 0.1919 0.5659 118 Q 0.2528 0.2815 0.4656 119 F 0.3221 0.2638 0.4140 120 S 0.3229 0.2882 0.3889 121 K 0.3183 0.2717 0.4099 122 N 0.2641 0.1594 0.5764 123 M 0.1771 0.3175 0.5054 124 E 0.1129 0.4618 0.4253 125 A 0.0867 0.5631 0.3503 126 E 0.1323 0.4202 0.4476 127 L 0.1946 0.2487 0.5567 128 G 0.2080 0.1290 0.6630 129 A 0.2713 0.0637 0.6649 130 P 0.2690 0.0806 0.6504 131 V 0.2417 0.0796 0.6787 132 E 0.1189 0.1752 0.7059 133 G 0.0680 0.1236 0.8084 134 I 0.2517 0.0585 0.6898 135 S 0.3537 0.0668 0.5795 136 T 0.4530 0.1096 0.4373 137 S 0.4871 0.1024 0.4104 138 L 0.5247 0.1246 0.3507 139 L 0.4659 0.1436 0.3905 140 H 0.3659 0.1335 0.5006 141 E 0.2489 0.1883 0.5627 142 D 0.2125 0.1655 0.6219 143 E 0.1102 0.3640 0.5259 144 R 0.1488 0.2762 0.5750 145 E 0.2297 0.2936 0.4768 146 T 0.4277 0.1725 0.3999 147 V 0.6120 0.1077 0.2803 148 T 0.6564 0.0898 0.2538 149 H 0.7087 0.0568 0.2345 150 R 0.7276 0.0304 0.2420 151 K 0.6729 0.0258 0.3013 152 L 0.4999 0.0334 0.4667 153 E 0.2695 0.0293 0.7012 154 P 0.1324 0.1746 0.6929 155 G 0.0668 0.1180 0.8151 156 A 0.2537 0.0911 0.6552 157 N 0.4328 0.0685 0.4988 158 L 0.5429 0.0514 0.4057 159 T 0.4135 0.0910 0.4956 160 S 0.3781 0.1740 0.4479 161 E 0.3101 0.2204 0.4694 162 A 0.2878 0.1651 0.5470 163 A 0.2101 0.1665 0.6234 164 G 0.1424 0.1113 0.7463 165 G 0.2065 0.0640 0.7295 166 I 0.5089 0.0245 0.4666 167 E 0.7144 0.0155 0.2701 168 V 0.8118 0.0054 0.1829 169 L 0.8106 0.0054 0.1840 170 V 0.8096 0.0044 0.1860 171 L 0.7757 0.0112 0.2131 172 D 0.6601 0.0250 0.3149 173 G 0.5622 0.0224 0.4154 174 D 0.7132 0.0182 0.2685 175 V 0.7737 0.0081 0.2182 176 T 0.7281 0.0107 0.2612 177 V 0.6315 0.0439 0.3246 178 N 0.2990 0.0830 0.6180 179 D 0.2346 0.1122 0.6532 180 E 0.6017 0.0539 0.3444 181 V 0.6465 0.0416 0.3119 182 L 0.5893 0.0580 0.3526 183 G 0.3872 0.0458 0.5669 184 R 0.2474 0.1690 0.5836 185 N 0.1766 0.1250 0.6983 186 A 0.3772 0.0785 0.5442 187 W 0.6076 0.0461 0.3463 188 L 0.7351 0.0178 0.2470 189 R 0.7316 0.0118 0.2567 190 L 0.5357 0.0168 0.4476 191 P 0.2767 0.0497 0.6736 192 E 0.1133 0.2100 0.6767 193 G 0.0782 0.1595 0.7624 194 E 0.2352 0.1258 0.6389 195 A 0.3514 0.1413 0.5073 196 L 0.4971 0.0972 0.4057 197 S 0.5434 0.0885 0.3681 198 A 0.5105 0.1591 0.3304 199 T 0.4772 0.1533 0.3695 200 A 0.3545 0.1519 0.4936 201 G 0.2216 0.1029 0.6754 202 A 0.1820 0.2136 0.6044 203 R 0.2041 0.1828 0.6131 204 G 0.3561 0.1090 0.5349 205 A 0.6122 0.0633 0.3246 206 K 0.7817 0.0175 0.2008 207 I 0.8189 0.0079 0.1733 208 W 0.8076 0.0076 0.1849 209 M 0.7909 0.0159 0.1932 210 K 0.6257 0.0572 0.3171 211 T 0.3026 0.1147 0.5827 212 G 0.1385 0.0959 0.7657 213 H 0.2139 0.0979 0.6883 214 L 0.2730 0.1462 0.5809 215 R 0.3093 0.1932 0.4976 216 F 0.3798 0.1832 0.4370 217 V 0.3878 0.1010 0.5112 218 R 0.3131 0.0921 0.5948 219 T 0.2256 0.0501 0.7243 220 P 0.0938 0.3244 0.5818 221 E 0.1255 0.3248 0.5497 222 V 0.2466 0.1741 0.5794