# This file is the result of combining several RDB files, specifically # T0434.t2k.str2.rdb (weight 1.54425) # T0434.t2k.str4.rdb (weight 0.924988) # T0434.t2k.pb.rdb (weight 0.789901) # T0434.t2k.bys.rdb (weight 0.748322) # T0434.t2k.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 T0434.t2k.str2.rdb # ============================================ # TARGET T0434 # Using neural net dunbrack-40pc-3157-t2k-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 T0434.t2k-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 181 # # ============================================ # Comments from T0434.t2k.str4.rdb # ============================================ # TARGET T0434 # Using neural net dunbrack-40pc-3157-t2k-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 T0434.t2k-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 181 # # ============================================ # Comments from T0434.t2k.pb.rdb # ============================================ # TARGET T0434 # Using neural net dunbrack-40pc-3157-t2k-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 T0434.t2k-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 181 # # ============================================ # Comments from T0434.t2k.bys.rdb # ============================================ # TARGET T0434 # Using neural net dunbrack-40pc-3157-t2k-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 T0434.t2k-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 181 # # ============================================ # Comments from T0434.t2k.alpha.rdb # ============================================ # TARGET T0434 # Using neural net dunbrack-40pc-3157-t2k-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 T0434.t2k-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 181 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2823 0.0897 0.6280 2 G 0.2408 0.0805 0.6787 3 S 0.2690 0.1314 0.5996 4 S 0.2802 0.1543 0.5654 5 H 0.3014 0.1874 0.5112 6 H 0.3314 0.1785 0.4901 7 H 0.3637 0.1264 0.5099 8 H 0.3227 0.0910 0.5864 9 H 0.2621 0.1077 0.6301 10 H 0.1978 0.1056 0.6966 11 S 0.1123 0.2829 0.6048 12 S 0.0956 0.2741 0.6303 13 G 0.1173 0.2152 0.6674 14 L 0.2260 0.1383 0.6357 15 V 0.2540 0.0697 0.6763 16 P 0.1839 0.1959 0.6202 17 R 0.1516 0.2330 0.6154 18 G 0.1224 0.1459 0.7317 19 S 0.1454 0.2409 0.6137 20 K 0.1502 0.2753 0.5745 21 M 0.1788 0.2794 0.5418 22 D 0.1642 0.2199 0.6159 23 M 0.1248 0.3481 0.5271 24 E 0.1178 0.3867 0.4955 25 D 0.1465 0.3512 0.5023 26 A 0.1607 0.3565 0.4828 27 D 0.1727 0.2961 0.5312 28 M 0.2277 0.2746 0.4977 29 T 0.2599 0.2342 0.5059 30 L 0.2364 0.3288 0.4348 31 W 0.2511 0.2954 0.4535 32 T 0.2260 0.3403 0.4337 33 E 0.2084 0.3493 0.4423 34 A 0.2239 0.3200 0.4561 35 E 0.1894 0.3072 0.5033 36 F 0.1796 0.3062 0.5142 37 E 0.1638 0.3046 0.5316 38 E 0.1367 0.3523 0.5110 39 K 0.1893 0.1980 0.6127 40 C 0.2025 0.1936 0.6039 41 T 0.2112 0.2092 0.5796 42 Y 0.3028 0.1706 0.5267 43 I 0.3195 0.0981 0.5824 44 V 0.2745 0.1356 0.5899 45 N 0.2290 0.1642 0.6067 46 D 0.2428 0.1193 0.6379 47 H 0.2557 0.0422 0.7021 48 P 0.2231 0.1008 0.6761 49 W 0.2093 0.1795 0.6112 50 D 0.2062 0.1524 0.6414 51 S 0.1956 0.1386 0.6658 52 G 0.1938 0.1498 0.6564 53 A 0.1843 0.1810 0.6346 54 D 0.1514 0.1629 0.6857 55 G 0.1223 0.1307 0.7470 56 G 0.1252 0.1108 0.7640 57 T 0.2543 0.0799 0.6658 58 S 0.2993 0.1275 0.5732 59 V 0.2815 0.1858 0.5326 60 Q 0.1999 0.3732 0.4269 61 A 0.1325 0.5000 0.3676 62 E 0.1874 0.3632 0.4494 63 A 0.3018 0.1779 0.5202 64 S 0.3120 0.0933 0.5947 65 L 0.2939 0.0403 0.6658 66 P 0.2065 0.0570 0.7365 67 R 0.1071 0.2949 0.5979 68 N 0.1689 0.1483 0.6829 69 L 0.4647 0.0366 0.4987 70 L 0.6926 0.0196 0.2879 71 F 0.7534 0.0137 0.2329 72 K 0.6911 0.0212 0.2877 73 Y 0.5836 0.0489 0.3674 74 A 0.3869 0.0780 0.5350 75 T 0.2720 0.1231 0.6049 76 N 0.2261 0.0936 0.6803 77 S 0.1594 0.1981 0.6425 78 E 0.1363 0.2613 0.6023 79 E 0.2629 0.2001 0.5369 80 V 0.4328 0.1217 0.4456 81 I 0.5452 0.0819 0.3729 82 G 0.6337 0.0517 0.3146 83 V 0.6905 0.0497 0.2598 84 M 0.6966 0.0488 0.2546 85 S 0.5931 0.0720 0.3349 86 K 0.4956 0.1609 0.3435 87 E 0.4679 0.1692 0.3628 88 Y 0.4966 0.0968 0.4066 89 I 0.4659 0.0350 0.4991 90 P 0.3089 0.0852 0.6059 91 K 0.1479 0.1998 0.6523 92 G 0.1005 0.1248 0.7747 93 T 0.3230 0.0611 0.6159 94 R 0.5096 0.0584 0.4320 95 F 0.4987 0.0650 0.4363 96 G 0.4428 0.0492 0.5080 97 P 0.4035 0.0796 0.5168 98 L 0.4737 0.0812 0.4451 99 I 0.4869 0.0822 0.4309 100 G 0.5232 0.0550 0.4218 101 E 0.6362 0.0394 0.3244 102 I 0.6584 0.0325 0.3091 103 Y 0.5955 0.0337 0.3708 104 T 0.3501 0.0553 0.5946 105 N 0.1831 0.2260 0.5909 106 D 0.1344 0.3128 0.5528 107 T 0.2450 0.1738 0.5812 108 V 0.2815 0.0646 0.6539 109 P 0.2173 0.1337 0.6490 110 K 0.1260 0.3745 0.4995 111 N 0.1201 0.3276 0.5523 112 A 0.0926 0.3892 0.5182 113 N 0.1117 0.2720 0.6164 114 R 0.1362 0.3045 0.5593 115 K 0.1880 0.2987 0.5133 116 Y 0.3546 0.2266 0.4188 117 F 0.4995 0.1743 0.3261 118 W 0.6644 0.1027 0.2329 119 R 0.7184 0.0595 0.2221 120 I 0.7052 0.0490 0.2457 121 Y 0.6333 0.0661 0.3006 122 S 0.4295 0.1217 0.4488 123 R 0.1546 0.1193 0.7261 124 G 0.0840 0.0890 0.8270 125 E 0.3277 0.0471 0.6252 126 L 0.5276 0.0433 0.4291 127 H 0.6255 0.0416 0.3329 128 H 0.7480 0.0219 0.2301 129 F 0.7455 0.0167 0.2378 130 I 0.7306 0.0231 0.2463 131 D 0.5746 0.0389 0.3865 132 G 0.3049 0.1515 0.5436 133 F 0.2152 0.1609 0.6240 134 N 0.2123 0.0983 0.6894 135 E 0.0756 0.4243 0.5001 136 E 0.0956 0.3742 0.5301 137 K 0.1217 0.4032 0.4751 138 S 0.1332 0.4684 0.3985 139 N 0.2130 0.4417 0.3453 140 W 0.3103 0.4100 0.2797 141 M 0.3496 0.3697 0.2807 142 R 0.3484 0.3634 0.2882 143 Y 0.4574 0.2039 0.3387 144 V 0.5237 0.1028 0.3735 145 N 0.3177 0.0646 0.6177 146 P 0.1759 0.3195 0.5046 147 A 0.1429 0.2822 0.5749 148 H 0.1554 0.1542 0.6905 149 S 0.1619 0.0479 0.7901 150 P 0.0297 0.4778 0.4924 151 R 0.0314 0.5716 0.3970 152 E 0.0721 0.6175 0.3104 153 Q 0.1308 0.6049 0.2642 154 N 0.2318 0.5104 0.2578 155 L 0.3385 0.4842 0.1773 156 A 0.4411 0.3899 0.1690 157 A 0.4601 0.3544 0.1855 158 C 0.4391 0.3079 0.2531 159 Q 0.4374 0.2015 0.3611 160 N 0.1960 0.1219 0.6821 161 G 0.0966 0.0876 0.8158 162 M 0.2567 0.0754 0.6680 163 N 0.5164 0.0207 0.4629 164 I 0.7521 0.0069 0.2410 165 Y 0.7941 0.0065 0.1994 166 F 0.8120 0.0046 0.1834 167 Y 0.7838 0.0087 0.2075 168 T 0.7811 0.0072 0.2117 169 I 0.7395 0.0127 0.2478 170 K 0.6637 0.0142 0.3222 171 P 0.5498 0.0172 0.4330 172 I 0.3557 0.0174 0.6269 173 P 0.1954 0.0225 0.7821 174 A 0.0984 0.2105 0.6912 175 N 0.0473 0.1381 0.8146 176 Q 0.3179 0.0599 0.6222 177 E 0.5774 0.0411 0.3814 178 L 0.7329 0.0174 0.2497 179 L 0.7625 0.0130 0.2245 180 V 0.7856 0.0184 0.1961 181 W 0.7236 0.0341 0.2423 182 Y 0.5657 0.0881 0.3462 183 C 0.2736 0.1844 0.5420 184 R 0.0647 0.6888 0.2465 185 D 0.0275 0.7954 0.1772 186 F 0.0239 0.8575 0.1186 187 A 0.0147 0.8871 0.0981 188 E 0.0133 0.8702 0.1165 189 R 0.0364 0.7323 0.2313 190 L 0.0857 0.3311 0.5832 191 H 0.0675 0.0917 0.8408 192 Y 0.2067 0.0301 0.7632 193 P 0.2336 0.0484 0.7180 194 Y 0.2742 0.0379 0.6879 195 P 0.1507 0.1527 0.6966 196 G 0.1088 0.3185 0.5727 197 E 0.1809 0.3856 0.4335 198 L 0.2510 0.4072 0.3418 199 T 0.2783 0.4154 0.3063 200 M 0.3079 0.3758 0.3163 201 M 0.2673 0.3378 0.3950 202 N 0.2308 0.2468 0.5224 203 L 0.1561 0.2293 0.6147 204 T 0.1621 0.1428 0.6951 205 Q 0.2098 0.1465 0.6437