# This file is the result of combining several RDB files, specifically # T0399.t06.str2.rdb (weight 1.54425) # T0399.t06.str4.rdb (weight 0.924988) # T0399.t06.pb.rdb (weight 0.789901) # T0399.t06.bys.rdb (weight 0.748322) # T0399.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 T0399.t06.str2.rdb # ============================================ # TARGET T0399 # 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 T0399.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 145 # # ============================================ # Comments from T0399.t06.str4.rdb # ============================================ # TARGET T0399 # 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 T0399.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 145 # # ============================================ # Comments from T0399.t06.pb.rdb # ============================================ # TARGET T0399 # 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 T0399.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 145 # # ============================================ # Comments from T0399.t06.bys.rdb # ============================================ # TARGET T0399 # 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 T0399.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 145 # # ============================================ # Comments from T0399.t06.alpha.rdb # ============================================ # TARGET T0399 # 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 T0399.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 145 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1598 0.4388 0.4014 2 S 0.1148 0.5293 0.3559 3 M 0.0794 0.6293 0.2913 4 K 0.0555 0.7104 0.2341 5 K 0.0442 0.6953 0.2605 6 T 0.0503 0.7216 0.2282 7 K 0.0379 0.7971 0.1650 8 N 0.0206 0.8599 0.1195 9 W 0.0164 0.8956 0.0880 10 L 0.0128 0.9130 0.0742 11 L 0.0118 0.9180 0.0702 12 V 0.0099 0.9209 0.0692 13 F 0.0085 0.9235 0.0680 14 L 0.0083 0.9243 0.0674 15 T 0.0083 0.9247 0.0670 16 V 0.0083 0.9248 0.0670 17 T 0.0083 0.9247 0.0670 18 F 0.0083 0.9242 0.0675 19 C 0.0083 0.9226 0.0691 20 F 0.0084 0.9181 0.0735 21 L 0.0094 0.9028 0.0878 22 M 0.0137 0.8424 0.1439 23 L 0.0320 0.6853 0.2827 24 G 0.0770 0.4472 0.4758 25 C 0.1549 0.2885 0.5566 26 Q 0.1939 0.1868 0.6194 27 S 0.1552 0.1810 0.6637 28 K 0.1034 0.2496 0.6471 29 E 0.0933 0.3040 0.6027 30 D 0.1316 0.2723 0.5961 31 K 0.1536 0.2844 0.5620 32 K 0.1945 0.2344 0.5712 33 G 0.1744 0.1478 0.6777 34 G 0.1916 0.1039 0.7045 35 T 0.2815 0.0730 0.6455 36 K 0.2809 0.0446 0.6745 37 P 0.1940 0.1642 0.6418 38 S 0.1351 0.2280 0.6369 39 N 0.1188 0.2459 0.6353 40 E 0.1438 0.3387 0.5175 41 A 0.1367 0.4837 0.3796 42 A 0.1080 0.5832 0.3089 43 L 0.1207 0.5629 0.3164 44 T 0.1443 0.5045 0.3512 45 K 0.1435 0.4611 0.3954 46 T 0.1765 0.3736 0.4499 47 E 0.0951 0.4298 0.4751 48 N 0.1019 0.3283 0.5698 49 L 0.1170 0.4578 0.4252 50 D 0.1674 0.4023 0.4303 51 F 0.2481 0.3293 0.4226 52 R 0.3307 0.2547 0.4146 53 L 0.4207 0.1442 0.4351 54 S 0.3470 0.1395 0.5135 55 F 0.2042 0.4006 0.3952 56 N 0.1278 0.4780 0.3942 57 K 0.1768 0.4257 0.3975 58 I 0.3097 0.2474 0.4429 59 K 0.3108 0.1931 0.4961 60 V 0.2926 0.2301 0.4773 61 T 0.2090 0.2681 0.5229 62 T 0.1787 0.3501 0.4712 63 D 0.1540 0.3322 0.5137 64 Q 0.1313 0.3546 0.5140 65 N 0.1043 0.2685 0.6273 66 H 0.1572 0.1953 0.6475 67 F 0.2604 0.0761 0.6635 68 S 0.2116 0.0925 0.6958 69 G 0.1862 0.1214 0.6924 70 G 0.1681 0.0926 0.7393 71 T 0.2264 0.0691 0.7044 72 S 0.1952 0.0525 0.7523 73 I 0.0124 0.7491 0.2386 74 E 0.0092 0.8686 0.1222 75 Q 0.0084 0.9206 0.0710 76 L 0.0086 0.9208 0.0706 77 K 0.0085 0.9100 0.0815 78 Q 0.0091 0.8926 0.0982 79 W 0.0175 0.7531 0.2294 80 F 0.0611 0.2619 0.6770 81 G 0.0491 0.1094 0.8416 82 D 0.1610 0.0385 0.8005 83 P 0.1542 0.1598 0.6860 84 N 0.1576 0.1670 0.6754 85 K 0.2265 0.1659 0.6076 86 S 0.3299 0.1726 0.4975 87 E 0.3938 0.1764 0.4299 88 Q 0.3962 0.1747 0.4290 89 R 0.3619 0.1706 0.4675 90 N 0.3034 0.1706 0.5260 91 A 0.1610 0.1512 0.6878 92 G 0.1260 0.0906 0.7834 93 N 0.3620 0.0452 0.5928 94 I 0.6277 0.0233 0.3490 95 T 0.7199 0.0196 0.2605 96 L 0.7310 0.0260 0.2430 97 D 0.7000 0.0444 0.2556 98 S 0.7203 0.0379 0.2419 99 Y 0.6573 0.0626 0.2801 100 T 0.6793 0.0455 0.2752 101 W 0.6380 0.0464 0.3156 102 V 0.4687 0.0837 0.4476 103 K 0.1897 0.1879 0.6224 104 D 0.1105 0.1194 0.7701 105 G 0.1853 0.0632 0.7515 106 A 0.5807 0.0223 0.3970 107 V 0.7532 0.0073 0.2396 108 I 0.8127 0.0058 0.1815 109 N 0.8203 0.0047 0.1750 110 A 0.8216 0.0049 0.1735 111 Q 0.8058 0.0062 0.1880 112 L 0.7469 0.0141 0.2390 113 Y 0.4939 0.0399 0.4662 114 K 0.1714 0.2320 0.5966 115 N 0.1151 0.1659 0.7190 116 S 0.1965 0.1472 0.6563 117 T 0.3921 0.1629 0.4450 118 V 0.4973 0.1767 0.3260 119 A 0.4839 0.2085 0.3076 120 R 0.5324 0.2004 0.2672 121 S 0.5115 0.2022 0.2863 122 I 0.4890 0.1892 0.3218 123 S 0.3835 0.2105 0.4060 124 N 0.3095 0.1827 0.5078 125 F 0.3425 0.1533 0.5042 126 S 0.3680 0.1850 0.4470 127 F 0.3472 0.2408 0.4120 128 S 0.2271 0.3034 0.4695 129 R 0.1699 0.2572 0.5729 130 E 0.1785 0.2456 0.5759 131 A 0.2142 0.1927 0.5931 132 K 0.2443 0.1278 0.6279 133 I 0.3125 0.0514 0.6361 134 G 0.1936 0.0269 0.7795 135 K 0.0357 0.6365 0.3278 136 E 0.0279 0.6958 0.2763 137 D 0.0518 0.6391 0.3090 138 Y 0.0668 0.6497 0.2835 139 D 0.0410 0.6388 0.3202 140 E 0.0652 0.4985 0.4363 141 L 0.1947 0.3056 0.4997 142 K 0.1926 0.2122 0.5951 143 I 0.1482 0.1713 0.6804 144 G 0.0908 0.1100 0.7992 145 E 0.1616 0.1268 0.7116 146 S 0.1822 0.0951 0.7227 147 Y 0.0153 0.7436 0.2411 148 K 0.0095 0.8682 0.1223 149 K 0.0087 0.9193 0.0720 150 V 0.0095 0.9192 0.0712 151 V 0.0088 0.9145 0.0767 152 E 0.0105 0.8962 0.0933 153 K 0.0193 0.7683 0.2124 154 L 0.0629 0.2892 0.6478 155 G 0.0492 0.0971 0.8537 156 E 0.1679 0.0396 0.7925 157 P 0.1785 0.0954 0.7260 158 D 0.1964 0.1872 0.6164 159 V 0.3810 0.2000 0.4190 160 L 0.4634 0.1659 0.3706 161 S 0.4808 0.1558 0.3635 162 Q 0.4446 0.1620 0.3935 163 S 0.3578 0.1503 0.4919 164 M 0.2516 0.1922 0.5562 165 S 0.1937 0.1701 0.6361 166 S 0.1479 0.1572 0.6950 167 D 0.1509 0.1317 0.7173 168 K 0.2889 0.1691 0.5420 169 E 0.4749 0.1459 0.3792 170 E 0.6014 0.0928 0.3058 171 M 0.6767 0.0669 0.2564 172 Q 0.7226 0.0477 0.2297 173 T 0.7734 0.0252 0.2015 174 V 0.7499 0.0341 0.2160 175 W 0.6819 0.0548 0.2633 176 S 0.5495 0.1260 0.3245 177 S 0.3254 0.1414 0.5332 178 G 0.2139 0.1169 0.6693 179 I 0.2552 0.1209 0.6238 180 K 0.2459 0.1202 0.6339 181 T 0.2462 0.1071 0.6467 182 K 0.2445 0.1131 0.6425 183 S 0.2864 0.0948 0.6189 184 S 0.2677 0.1335 0.5989 185 S 0.3409 0.0899 0.5693 186 A 0.5931 0.0515 0.3554 187 T 0.7587 0.0123 0.2290 188 I 0.8170 0.0050 0.1780 189 E 0.8202 0.0045 0.1753 190 L 0.8206 0.0046 0.1748 191 Y 0.8144 0.0055 0.1801 192 F 0.7189 0.0128 0.2683 193 E 0.4965 0.1304 0.3731 194 N 0.1539 0.0940 0.7520 195 G 0.1296 0.0567 0.8137 196 L 0.5135 0.0213 0.4652 197 L 0.6607 0.0166 0.3227 198 K 0.6315 0.0376 0.3309 199 N 0.6125 0.0423 0.3452 200 K 0.5390 0.0941 0.3669 201 T 0.4502 0.0978 0.4520 202 Q 0.2798 0.2375 0.4827 203 K 0.1732 0.3062 0.5206 204 D 0.1364 0.2329 0.6307 205 L 0.1680 0.2094 0.6225 206 E 0.1536 0.2186 0.6278