# This file is the result of combining several RDB files, specifically # T0558.t04.str2.rdb (weight 1.54425) # T0558.t04.str4.rdb (weight 0.924988) # T0558.t04.pb.rdb (weight 0.789901) # T0558.t04.bys.rdb (weight 0.748322) # T0558.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 T0558.t04.str2.rdb # ============================================ # TARGET T0558 # 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 T0558.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 2888 # # ============================================ # Comments from T0558.t04.str4.rdb # ============================================ # TARGET T0558 # 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 T0558.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 2888 # # ============================================ # Comments from T0558.t04.pb.rdb # ============================================ # TARGET T0558 # 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 T0558.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 2888 # # ============================================ # Comments from T0558.t04.bys.rdb # ============================================ # TARGET T0558 # 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 T0558.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 2888 # # ============================================ # Comments from T0558.t04.alpha.rdb # ============================================ # TARGET T0558 # 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 T0558.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 2888 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1753 0.2400 0.5846 2 K 0.1475 0.3613 0.4913 3 N 0.1693 0.4693 0.3613 4 F 0.1804 0.5345 0.2850 5 I 0.2281 0.5489 0.2230 6 L 0.3028 0.5081 0.1892 7 L 0.3614 0.4331 0.2055 8 V 0.3471 0.4002 0.2527 9 A 0.2726 0.4049 0.3225 10 L 0.2383 0.3454 0.4163 11 F 0.2326 0.2830 0.4844 12 L 0.2115 0.2363 0.5522 13 V 0.2458 0.1361 0.6180 14 A 0.2926 0.0715 0.6359 15 P 0.2964 0.1640 0.5397 16 F 0.4069 0.1590 0.4341 17 A 0.4948 0.1367 0.3685 18 Q 0.5668 0.1072 0.3260 19 G 0.5774 0.0767 0.3459 20 S 0.5176 0.0557 0.4266 21 S 0.2929 0.0346 0.6725 22 P 0.0953 0.3365 0.5681 23 Q 0.1112 0.2130 0.6758 24 H 0.3206 0.1060 0.5734 25 L 0.6507 0.0253 0.3240 26 L 0.7431 0.0253 0.2317 27 V 0.7733 0.0148 0.2119 28 G 0.6529 0.0342 0.3129 29 G 0.5026 0.0465 0.4509 30 S 0.3187 0.0932 0.5880 31 G 0.1873 0.1385 0.6742 32 W 0.1805 0.1182 0.7013 33 N 0.3014 0.0656 0.6331 34 K 0.6916 0.0134 0.2950 35 I 0.7545 0.0071 0.2383 36 A 0.7959 0.0062 0.1979 37 I 0.8074 0.0059 0.1867 38 I 0.7752 0.0111 0.2137 39 N 0.6081 0.0084 0.3835 40 K 0.2126 0.2904 0.4970 41 D 0.1240 0.2765 0.5995 42 T 0.1039 0.1437 0.7525 43 K 0.1430 0.0923 0.7647 44 E 0.4474 0.0630 0.4896 45 I 0.6256 0.0416 0.3328 46 V 0.6332 0.0512 0.3156 47 W 0.7149 0.0290 0.2560 48 E 0.6839 0.0232 0.2929 49 Y 0.6229 0.0181 0.3590 50 P 0.3925 0.0378 0.5697 51 L 0.2161 0.2202 0.5637 52 E 0.1592 0.2025 0.6384 53 K 0.1772 0.1683 0.6545 54 G 0.1764 0.1188 0.7047 55 W 0.2805 0.1019 0.6177 56 E 0.3922 0.0731 0.5347 57 C 0.4665 0.0714 0.4621 58 N 0.4587 0.0817 0.4596 59 S 0.6954 0.0322 0.2724 60 V 0.7287 0.0195 0.2518 61 A 0.7580 0.0118 0.2302 62 A 0.7320 0.0123 0.2556 63 T 0.4085 0.0153 0.5762 64 K 0.1258 0.2903 0.5839 65 A 0.0887 0.1684 0.7428 66 G 0.1295 0.0814 0.7891 67 E 0.5786 0.0141 0.4073 68 I 0.7464 0.0066 0.2471 69 L 0.7818 0.0095 0.2087 70 F 0.8065 0.0063 0.1872 71 S 0.7275 0.0130 0.2596 72 Y 0.5464 0.0504 0.4032 73 S 0.3487 0.0776 0.5737 74 K 0.3531 0.0699 0.5770 75 G 0.6177 0.0267 0.3557 76 A 0.7551 0.0081 0.2368 77 K 0.7916 0.0064 0.2020 78 M 0.8029 0.0065 0.1905 79 I 0.7800 0.0147 0.2052 80 T 0.5558 0.0149 0.4293 81 R 0.2142 0.2329 0.5529 82 D 0.1039 0.1493 0.7469 83 G 0.1181 0.0803 0.8016 84 R 0.4171 0.0315 0.5514 85 E 0.6334 0.0258 0.3408 86 L 0.6617 0.0431 0.2952 87 W 0.7143 0.0324 0.2533 88 N 0.6828 0.0261 0.2912 89 I 0.5758 0.0565 0.3677 90 A 0.3929 0.0677 0.5394 91 A 0.2576 0.0910 0.6514 92 P 0.1672 0.1929 0.6398 93 A 0.1561 0.1736 0.6704 94 G 0.1468 0.1154 0.7379 95 C 0.2516 0.0904 0.6579 96 E 0.3955 0.0600 0.5445 97 M 0.5160 0.0539 0.4301 98 Q 0.5324 0.0716 0.3960 99 T 0.6736 0.0418 0.2846 100 A 0.7167 0.0247 0.2586 101 R 0.7489 0.0145 0.2365 102 I 0.7280 0.0108 0.2613 103 L 0.3794 0.0143 0.6063 104 P 0.1130 0.2956 0.5914 105 D 0.0915 0.1665 0.7420 106 G 0.1078 0.0901 0.8021 107 N 0.4290 0.0302 0.5408 108 A 0.7398 0.0079 0.2523 109 L 0.7772 0.0102 0.2125 110 V 0.8166 0.0055 0.1780 111 A 0.7731 0.0101 0.2168 112 W 0.6317 0.0361 0.3322 113 C 0.4026 0.0531 0.5443 114 G 0.2432 0.0601 0.6967 115 H 0.2642 0.0463 0.6895 116 P 0.2011 0.1927 0.6062 117 S 0.2848 0.1470 0.5682 118 T 0.6682 0.0268 0.3050 119 I 0.7650 0.0107 0.2243 120 L 0.8064 0.0087 0.1849 121 E 0.8091 0.0081 0.1829 122 V 0.7900 0.0121 0.1979 123 N 0.6435 0.0152 0.3413 124 M 0.3575 0.2022 0.4403 125 K 0.1659 0.1378 0.6964 126 G 0.1470 0.0947 0.7583 127 E 0.4152 0.0517 0.5331 128 V 0.5799 0.0563 0.3639 129 L 0.5429 0.0934 0.3637 130 S 0.5268 0.0853 0.3878 131 K 0.5651 0.0721 0.3627 132 T 0.6235 0.0422 0.3343 133 E 0.5768 0.0398 0.3834 134 F 0.4622 0.0758 0.4620 135 E 0.2994 0.1545 0.5460 136 T 0.2076 0.1441 0.6483 137 G 0.1792 0.1288 0.6920 138 I 0.2071 0.1687 0.6243 139 E 0.2152 0.1524 0.6324 140 R 0.2219 0.1096 0.6685 141 P 0.1307 0.3446 0.5247 142 H 0.1520 0.2808 0.5672 143 A 0.1877 0.2339 0.5785 144 Q 0.2980 0.1514 0.5506 145 F 0.3931 0.1027 0.5042 146 R 0.4362 0.1177 0.4461 147 Q 0.6614 0.0615 0.2772 148 I 0.6873 0.0419 0.2708 149 N 0.7074 0.0229 0.2698 150 K 0.6850 0.0193 0.2956 151 N 0.3106 0.0162 0.6733 152 K 0.0862 0.3331 0.5808 153 K 0.0786 0.1691 0.7522 154 G 0.0972 0.0903 0.8125 155 N 0.4099 0.0203 0.5698 156 Y 0.7100 0.0099 0.2801 157 L 0.7609 0.0144 0.2247 158 V 0.7754 0.0101 0.2144 159 P 0.6591 0.0198 0.3211 160 L 0.5484 0.0842 0.3674 161 F 0.4412 0.0981 0.4607 162 A 0.2604 0.1759 0.5637 163 T 0.2234 0.1148 0.6618 164 S 0.4051 0.0754 0.5195 165 E 0.6729 0.0220 0.3050 166 V 0.7494 0.0083 0.2423 167 R 0.7881 0.0079 0.2040 168 E 0.8044 0.0066 0.1890 169 I 0.7724 0.0129 0.2147 170 A 0.5470 0.0117 0.4413 171 P 0.1422 0.3004 0.5574 172 N 0.0816 0.1753 0.7431 173 G 0.0975 0.0850 0.8174 174 Q 0.3675 0.0391 0.5934 175 L 0.6020 0.0499 0.3481 176 L 0.6183 0.0844 0.2973 177 N 0.6448 0.0839 0.2713 178 S 0.6204 0.0748 0.3048 179 V 0.5442 0.0800 0.3758 180 K 0.3653 0.0868 0.5479 181 L 0.2644 0.1361 0.5995 182 S 0.1739 0.1225 0.7035 183 G 0.1611 0.0760 0.7629 184 T 0.2737 0.0293 0.6969 185 P 0.3904 0.0543 0.5553 186 F 0.4950 0.0543 0.4507 187 S 0.6933 0.0274 0.2793 188 S 0.7374 0.0241 0.2385 189 A 0.7706 0.0136 0.2157 190 F 0.7454 0.0123 0.2423 191 L 0.4373 0.0166 0.5461 192 D 0.1476 0.2782 0.5742 193 N 0.0992 0.1587 0.7421 194 G 0.1296 0.0779 0.7925 195 D 0.4686 0.0311 0.5003 196 C 0.7454 0.0086 0.2460 197 L 0.7656 0.0144 0.2200 198 V 0.8127 0.0068 0.1805 199 A 0.7688 0.0117 0.2195 200 C 0.6470 0.0320 0.3210 201 G 0.4195 0.0631 0.5174 202 D 0.2285 0.1670 0.6045 203 A 0.2071 0.1119 0.6809 204 H 0.3380 0.0688 0.5932 205 C 0.6760 0.0151 0.3090 206 F 0.7511 0.0091 0.2397 207 V 0.8043 0.0074 0.1883 208 Q 0.8100 0.0064 0.1836 209 L 0.7869 0.0097 0.2034 210 N 0.6456 0.0081 0.3463 211 L 0.3619 0.2646 0.3735 212 E 0.1981 0.2839 0.5180 213 S 0.1161 0.1398 0.7441 214 N 0.1314 0.0804 0.7882 215 R 0.4817 0.0316 0.4868 216 I 0.6666 0.0255 0.3080 217 V 0.6926 0.0443 0.2631 218 R 0.7526 0.0298 0.2176 219 R 0.7394 0.0206 0.2401 220 V 0.6954 0.0314 0.2733 221 N 0.4989 0.0567 0.4444 222 A 0.3328 0.1124 0.5548 223 N 0.2269 0.1343 0.6388 224 D 0.2043 0.1392 0.6565 225 I 0.1808 0.1940 0.6252 226 E 0.1466 0.2213 0.6321 227 G 0.1256 0.2069 0.6674 228 V 0.2491 0.2138 0.5370 229 Q 0.3351 0.2037 0.4612 230 L 0.3480 0.2115 0.4405 231 F 0.3572 0.1645 0.4783 232 F 0.4475 0.1160 0.4365 233 V 0.4171 0.1240 0.4589 234 A 0.4297 0.1296 0.4407 235 Q 0.6387 0.0595 0.3018 236 L 0.6446 0.0434 0.3120 237 F 0.6677 0.0198 0.3125 238 P 0.5662 0.0295 0.4043 239 L 0.3072 0.0240 0.6689 240 Q 0.1106 0.3055 0.5840 241 N 0.0970 0.1668 0.7362 242 G 0.1223 0.0891 0.7887 243 G 0.4224 0.0239 0.5537 244 L 0.7501 0.0068 0.2431 245 Y 0.7931 0.0073 0.1996 246 I 0.8109 0.0059 0.1832 247 C 0.7375 0.0153 0.2472 248 N 0.5877 0.0331 0.3792 249 W 0.4120 0.0807 0.5073 250 Q 0.2195 0.1172 0.6633 251 G 0.1613 0.0934 0.7453 252 H 0.2606 0.0773 0.6621 253 D 0.5636 0.0279 0.4085 254 R 0.7191 0.0127 0.2682 255 E 0.7535 0.0103 0.2362 256 A 0.7457 0.0221 0.2322 257 G 0.6421 0.0427 0.3152 258 K 0.5555 0.0481 0.3964 259 G 0.3573 0.0837 0.5590 260 K 0.2575 0.0866 0.6559 261 H 0.2853 0.0495 0.6652 262 P 0.3101 0.1043 0.5856 263 Q 0.5084 0.0825 0.4091 264 L 0.6556 0.0373 0.3071 265 V 0.7323 0.0245 0.2432 266 E 0.7449 0.0132 0.2419 267 I 0.6952 0.0268 0.2780 268 D 0.4787 0.0581 0.4632 269 S 0.2888 0.1367 0.5745 270 E 0.1840 0.1310 0.6850 271 G 0.1742 0.0970 0.7288 272 K 0.3220 0.0859 0.5922 273 V 0.5730 0.0585 0.3685 274 V 0.6185 0.0779 0.3036 275 W 0.6314 0.0673 0.3012 276 Q 0.6361 0.0448 0.3191 277 L 0.4535 0.0614 0.4850 278 N 0.2847 0.1166 0.5988 279 D 0.1396 0.1274 0.7329 280 K 0.1473 0.0863 0.7664 281 V 0.4837 0.0238 0.4925 282 K 0.7263 0.0120 0.2617 283 F 0.7943 0.0088 0.1969 284 G 0.7889 0.0090 0.2021 285 M 0.7695 0.0094 0.2212 286 I 0.6689 0.0244 0.3067 287 S 0.4866 0.0602 0.4532 288 T 0.2612 0.1881 0.5506 289 I 0.1909 0.1434 0.6657 290 C 0.2929 0.0847 0.6224 291 P 0.3385 0.1117 0.5498 292 I 0.3939 0.1196 0.4865 293 R 0.3246 0.1002 0.5752 294 E 0.2528 0.1227 0.6246