# This file is the result of combining several RDB files, specifically # T0582.t06.str2.rdb (weight 1.54425) # T0582.t06.str4.rdb (weight 0.924988) # T0582.t06.pb.rdb (weight 0.789901) # T0582.t06.bys.rdb (weight 0.748322) # T0582.t06.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.t06.str2.rdb # ============================================ # TARGET T0582 # Using neural net dunbrack-40pc-3157-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 T0582.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 2410 # # ============================================ # Comments from T0582.t06.str4.rdb # ============================================ # TARGET T0582 # Using neural net dunbrack-40pc-3157-t06-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.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 2410 # # ============================================ # Comments from T0582.t06.pb.rdb # ============================================ # TARGET T0582 # Using neural net dunbrack-40pc-3157-t06-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.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 2410 # # ============================================ # Comments from T0582.t06.bys.rdb # ============================================ # TARGET T0582 # Using neural net dunbrack-40pc-3157-t06-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.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 2410 # # ============================================ # Comments from T0582.t06.alpha.rdb # ============================================ # TARGET T0582 # Using neural net dunbrack-40pc-3157-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 T0582.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 2410 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3494 0.0700 0.5805 2 E 0.3326 0.0671 0.6003 3 I 0.3266 0.0770 0.5964 4 N 0.2311 0.0662 0.7027 5 A 0.1005 0.3760 0.5235 6 D 0.1238 0.2916 0.5846 7 F 0.1778 0.1743 0.6479 8 T 0.1964 0.0955 0.7080 9 K 0.2652 0.0601 0.6747 10 P 0.3060 0.0696 0.6244 11 V 0.5611 0.0544 0.3845 12 V 0.6133 0.0264 0.3604 13 I 0.5890 0.0224 0.3886 14 D 0.2981 0.0138 0.6881 15 T 0.0672 0.4828 0.4500 16 D 0.0451 0.5765 0.3785 17 Q 0.0854 0.4319 0.4827 18 L 0.2352 0.1837 0.5812 19 E 0.2428 0.1709 0.5863 20 W 0.3671 0.1047 0.5281 21 R 0.3919 0.0467 0.5614 22 P 0.3462 0.0543 0.5995 23 S 0.3084 0.0410 0.6505 24 P 0.1873 0.1327 0.6800 25 M 0.1867 0.1338 0.6795 26 K 0.1095 0.1839 0.7066 27 G 0.0923 0.1314 0.7762 28 V 0.3541 0.0745 0.5714 29 E 0.5350 0.0842 0.3808 30 R 0.6129 0.0946 0.2925 31 R 0.6232 0.1090 0.2678 32 M 0.5844 0.1340 0.2816 33 L 0.4805 0.1847 0.3348 34 D 0.3785 0.2411 0.3804 35 R 0.2501 0.2593 0.4906 36 I 0.1661 0.2294 0.6045 37 G 0.1219 0.1426 0.7355 38 G 0.1124 0.1553 0.7323 39 E 0.1938 0.1972 0.6090 40 V 0.2716 0.1759 0.5525 41 A 0.3357 0.1371 0.5272 42 R 0.4571 0.1445 0.3985 43 A 0.6116 0.0943 0.2941 44 T 0.7170 0.0467 0.2363 45 S 0.7217 0.0389 0.2394 46 I 0.7388 0.0356 0.2255 47 V 0.7244 0.0311 0.2445 48 R 0.7082 0.0284 0.2634 49 Y 0.5687 0.0307 0.4006 50 A 0.3027 0.0280 0.6693 51 P 0.1440 0.1461 0.7099 52 G 0.0755 0.1141 0.8104 53 S 0.1981 0.1163 0.6857 54 R 0.3129 0.0970 0.5901 55 F 0.3607 0.0577 0.5816 56 S 0.2814 0.0887 0.6299 57 A 0.2468 0.1739 0.5793 58 H 0.2957 0.0952 0.6091 59 T 0.2811 0.1306 0.5882 60 H 0.2531 0.0825 0.6644 61 D 0.1175 0.1865 0.6960 62 G 0.0838 0.1345 0.7817 63 G 0.2262 0.0737 0.7001 64 E 0.5536 0.0228 0.4236 65 E 0.7344 0.0153 0.2502 66 F 0.8076 0.0059 0.1864 67 I 0.8096 0.0061 0.1843 68 V 0.7549 0.0071 0.2380 69 L 0.7151 0.0237 0.2612 70 D 0.6172 0.0353 0.3474 71 G 0.5481 0.0302 0.4217 72 V 0.6983 0.0259 0.2759 73 F 0.7053 0.0252 0.2695 74 Q 0.6635 0.0311 0.3054 75 D 0.4905 0.0461 0.4634 76 E 0.2316 0.1971 0.5713 77 H 0.1554 0.1346 0.7100 78 G 0.1487 0.0989 0.7525 79 D 0.2803 0.0841 0.6356 80 Y 0.3360 0.0284 0.6356 81 P 0.2515 0.0290 0.7195 82 A 0.1437 0.1730 0.6833 83 G 0.1392 0.1047 0.7560 84 T 0.3900 0.0562 0.5538 85 Y 0.6611 0.0291 0.3098 86 V 0.7189 0.0237 0.2574 87 R 0.7106 0.0172 0.2723 88 N 0.5196 0.0159 0.4645 89 P 0.2738 0.0207 0.7055 90 P 0.1486 0.1793 0.6721 91 T 0.1505 0.1345 0.7151 92 T 0.2888 0.0794 0.6318 93 S 0.3187 0.0972 0.5840 94 H 0.3443 0.0768 0.5789 95 V 0.3234 0.0505 0.6261 96 P 0.2653 0.0964 0.6383 97 G 0.2408 0.0945 0.6648 98 S 0.2090 0.0811 0.7099 99 A 0.1028 0.2727 0.6245 100 E 0.1001 0.1918 0.7080 101 G 0.1364 0.1150 0.7486 102 C 0.3844 0.0762 0.5395 103 T 0.6654 0.0308 0.3038 104 I 0.7808 0.0189 0.2003 105 F 0.8063 0.0123 0.1814 106 V 0.8131 0.0112 0.1757 107 K 0.8018 0.0141 0.1841 108 L 0.7511 0.0251 0.2237 109 W 0.5949 0.0448 0.3603 110 Q 0.3767 0.0826 0.5407 111 F 0.2761 0.0691 0.6548 112 D 0.1947 0.0264 0.7789 113 P 0.0383 0.4587 0.5030 114 A 0.0385 0.4814 0.4801 115 D 0.0660 0.4439 0.4901 116 R 0.0914 0.3328 0.5758 117 T 0.1907 0.2479 0.5614 118 Q 0.2732 0.1434 0.5833 119 F 0.2765 0.1202 0.6033 120 S 0.2107 0.1134 0.6759 121 K 0.0777 0.4913 0.4310 122 N 0.0888 0.4633 0.4479 123 M 0.1266 0.4845 0.3889 124 E 0.1410 0.4664 0.3925 125 A 0.1361 0.4545 0.4094 126 E 0.1435 0.3465 0.5100 127 L 0.1347 0.2418 0.6235 128 G 0.1318 0.1547 0.7135 129 A 0.2130 0.0924 0.6946 130 P 0.2413 0.1087 0.6500 131 V 0.2426 0.0710 0.6865 132 E 0.1204 0.1646 0.7151 133 G 0.0633 0.1101 0.8265 134 I 0.3469 0.0338 0.6193 135 S 0.6012 0.0273 0.3715 136 T 0.7328 0.0143 0.2529 137 S 0.7530 0.0148 0.2322 138 L 0.7369 0.0194 0.2438 139 L 0.6452 0.0346 0.3202 140 H 0.4164 0.0326 0.5510 141 E 0.1436 0.2472 0.6092 142 D 0.1311 0.1873 0.6817 143 E 0.1455 0.2161 0.6385 144 R 0.1669 0.2634 0.5696 145 E 0.2628 0.2875 0.4496 146 T 0.4494 0.2135 0.3371 147 V 0.6372 0.1117 0.2511 148 T 0.6464 0.1086 0.2450 149 H 0.6802 0.0701 0.2497 150 R 0.7033 0.0412 0.2555 151 K 0.6514 0.0375 0.3112 152 L 0.4806 0.0336 0.4858 153 E 0.2509 0.0261 0.7230 154 P 0.1070 0.1919 0.7010 155 G 0.0423 0.1160 0.8416 156 A 0.2311 0.0567 0.7122 157 N 0.4779 0.0423 0.4799 158 L 0.5127 0.0499 0.4374 159 T 0.5243 0.0553 0.4205 160 S 0.5015 0.0718 0.4267 161 E 0.3844 0.1183 0.4973 162 A 0.3035 0.1019 0.5947 163 A 0.1496 0.2033 0.6471 164 G 0.0862 0.1380 0.7758 165 G 0.1196 0.0862 0.7942 166 I 0.4367 0.0198 0.5435 167 E 0.7075 0.0129 0.2796 168 V 0.8154 0.0046 0.1799 169 L 0.8079 0.0057 0.1864 170 V 0.7683 0.0055 0.2262 171 L 0.7481 0.0154 0.2364 172 D 0.6828 0.0247 0.2925 173 G 0.6176 0.0242 0.3582 174 D 0.7154 0.0221 0.2624 175 V 0.7528 0.0124 0.2348 176 T 0.7176 0.0147 0.2677 177 V 0.6279 0.0349 0.3372 178 N 0.2957 0.0647 0.6396 179 D 0.2256 0.0879 0.6865 180 E 0.5397 0.0720 0.3883 181 V 0.6064 0.0592 0.3344 182 L 0.4995 0.0530 0.4474 183 G 0.3217 0.0470 0.6312 184 R 0.1433 0.2527 0.6039 185 N 0.1333 0.1332 0.7335 186 A 0.3631 0.0762 0.5607 187 W 0.6194 0.0435 0.3370 188 L 0.7302 0.0232 0.2466 189 R 0.7084 0.0172 0.2743 190 L 0.4967 0.0137 0.4896 191 P 0.2903 0.0256 0.6842 192 E 0.1050 0.2082 0.6868 193 G 0.0636 0.1174 0.8189 194 E 0.3054 0.0656 0.6291 195 A 0.5579 0.0452 0.3968 196 L 0.6985 0.0269 0.2746 197 S 0.7775 0.0128 0.2096 198 A 0.7622 0.0191 0.2187 199 T 0.7378 0.0257 0.2365 200 A 0.6071 0.0470 0.3459 201 G 0.3420 0.0529 0.6050 202 A 0.2564 0.1209 0.6227 203 R 0.1656 0.1521 0.6822 204 G 0.2062 0.0810 0.7127 205 A 0.5267 0.0169 0.4564 206 K 0.7654 0.0089 0.2257 207 I 0.8247 0.0048 0.1705 208 W 0.8148 0.0059 0.1794 209 M 0.7722 0.0099 0.2180 210 K 0.6794 0.0459 0.2748 211 T 0.4422 0.0694 0.4884 212 G 0.2135 0.0733 0.7132 213 H 0.2665 0.0690 0.6645 214 L 0.2679 0.1028 0.6293 215 R 0.2460 0.1660 0.5881 216 F 0.3148 0.2329 0.4523 217 V 0.3631 0.1647 0.4722 218 R 0.3640 0.1074 0.5285 219 T 0.2936 0.0340 0.6724 220 P 0.2083 0.1389 0.6527 221 E 0.2401 0.1650 0.5949 222 V 0.2855 0.1171 0.5975