# This file is the result of combining several RDB files, specifically # T0487.t2k.str2.rdb (weight 1.54425) # T0487.t2k.str4.rdb (weight 0.924988) # T0487.t2k.pb.rdb (weight 0.789901) # T0487.t2k.bys.rdb (weight 0.748322) # T0487.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 T0487.t2k.str2.rdb # ============================================ # TARGET T0487 # 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 T0487.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 7 # # ============================================ # Comments from T0487.t2k.str4.rdb # ============================================ # TARGET T0487 # 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 T0487.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 7 # # ============================================ # Comments from T0487.t2k.pb.rdb # ============================================ # TARGET T0487 # 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 T0487.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 7 # # ============================================ # Comments from T0487.t2k.bys.rdb # ============================================ # TARGET T0487 # 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 T0487.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 7 # # ============================================ # Comments from T0487.t2k.alpha.rdb # ============================================ # TARGET T0487 # 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 T0487.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 7 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 N 0.2828 0.1321 0.5850 2 R 0.3359 0.1535 0.5106 3 F 0.5301 0.1006 0.3693 4 A 0.6628 0.0683 0.2689 5 L 0.6448 0.0623 0.2929 6 R 0.6049 0.0396 0.3556 7 P 0.4018 0.0858 0.5124 8 L 0.3313 0.0560 0.6127 9 N 0.1767 0.0170 0.8062 10 P 0.0242 0.6583 0.3175 11 E 0.0208 0.6995 0.2796 12 E 0.0634 0.4154 0.5212 13 L 0.2433 0.1107 0.6461 14 R 0.2611 0.0589 0.6800 15 P 0.2936 0.1898 0.5167 16 W 0.4226 0.1246 0.4529 17 R 0.6282 0.0727 0.2991 18 L 0.7400 0.0236 0.2364 19 E 0.7669 0.0139 0.2192 20 V 0.7516 0.0117 0.2367 21 V 0.6512 0.0168 0.3320 22 L 0.5212 0.0312 0.4476 23 D 0.3382 0.0254 0.6364 24 P 0.2307 0.0805 0.6887 25 P 0.2005 0.0385 0.7610 26 P 0.1225 0.2035 0.6740 27 G 0.0847 0.1666 0.7488 28 R 0.1106 0.2431 0.6463 29 E 0.1050 0.2839 0.6111 30 E 0.1595 0.2780 0.5625 31 V 0.1494 0.4535 0.3971 32 Y 0.0879 0.6148 0.2973 33 P 0.0216 0.8513 0.1272 34 L 0.0099 0.9091 0.0810 35 L 0.0086 0.9139 0.0775 36 A 0.0084 0.9193 0.0724 37 Q 0.0083 0.9236 0.0681 38 V 0.0084 0.9207 0.0709 39 A 0.0085 0.9162 0.0753 40 R 0.0090 0.8964 0.0946 41 R 0.0202 0.7850 0.1948 42 A 0.0592 0.4507 0.4901 43 G 0.0591 0.1484 0.7925 44 G 0.2151 0.1356 0.6494 45 V 0.4960 0.1326 0.3714 46 T 0.6685 0.0921 0.2394 47 V 0.7182 0.0643 0.2175 48 R 0.6594 0.0666 0.2741 49 M 0.5114 0.0985 0.3902 50 G 0.3013 0.1147 0.5840 51 D 0.1860 0.1719 0.6421 52 G 0.1779 0.1725 0.6496 53 L 0.3063 0.1621 0.5316 54 A 0.3534 0.1260 0.5206 55 S 0.2871 0.0934 0.6195 56 W 0.2180 0.1280 0.6540 57 S 0.2585 0.0492 0.6923 58 P 0.2256 0.0491 0.7252 59 P 0.2369 0.1004 0.6626 60 E 0.2523 0.0882 0.6595 61 V 0.2252 0.3683 0.4065 62 L 0.2690 0.3595 0.3715 63 V 0.2543 0.3512 0.3944 64 L 0.1383 0.4539 0.4079 65 E 0.0824 0.6199 0.2977 66 G 0.0613 0.5994 0.3393 67 T 0.0813 0.7222 0.1965 68 L 0.0956 0.7277 0.1767 69 A 0.0778 0.7459 0.1762 70 R 0.1197 0.5942 0.2861 71 M 0.1198 0.3200 0.5602 72 G 0.1073 0.1371 0.7556 73 Q 0.2136 0.1005 0.6858 74 T 0.2827 0.0780 0.6393 75 Y 0.3298 0.1260 0.5442 76 A 0.4777 0.1165 0.4058 77 Y 0.6227 0.0735 0.3038 78 R 0.6833 0.0426 0.2741 79 L 0.6514 0.0517 0.2969 80 Y 0.5007 0.0567 0.4426 81 P 0.2682 0.2333 0.4985 82 K 0.1457 0.1882 0.6660 83 G 0.1345 0.1204 0.7451 84 R 0.2543 0.0825 0.6632 85 R 0.3251 0.0421 0.6328 86 P 0.2972 0.1024 0.6003 87 L 0.2907 0.0783 0.6310 88 D 0.2314 0.0467 0.7219 89 P 0.1312 0.2410 0.6278 90 K 0.1501 0.2099 0.6400 91 D 0.1774 0.0777 0.7449 92 P 0.0263 0.5524 0.4213 93 G 0.0223 0.5566 0.4212 94 E 0.0266 0.7914 0.1820 95 R 0.0178 0.8807 0.1015 96 S 0.0149 0.8953 0.0898 97 V 0.0087 0.9056 0.0857 98 L 0.0083 0.9199 0.0718 99 S 0.0083 0.9218 0.0699 100 A 0.0083 0.9230 0.0686 101 L 0.0084 0.9186 0.0730 102 A 0.0084 0.9183 0.0733 103 R 0.0084 0.9172 0.0744 104 R 0.0086 0.9130 0.0783 105 L 0.0088 0.9021 0.0891 106 L 0.0092 0.8951 0.0957 107 Q 0.0092 0.8941 0.0967 108 E 0.0097 0.8777 0.1126 109 R 0.0144 0.8321 0.1535 110 L 0.0281 0.7741 0.1978 111 R 0.0373 0.7451 0.2175 112 R 0.0609 0.5930 0.3460 113 L 0.1076 0.4358 0.4566 114 E 0.1203 0.2912 0.5885 115 G 0.1441 0.1807 0.6752 116 V 0.3585 0.1619 0.4797 117 W 0.4890 0.1443 0.3667 118 V 0.5160 0.1503 0.3338 119 E 0.4867 0.1443 0.3690 120 G 0.5241 0.0997 0.3762 121 L 0.6131 0.0946 0.2923 122 A 0.6312 0.1006 0.2682 123 V 0.6083 0.1211 0.2705 124 Y 0.5182 0.1428 0.3390 125 R 0.3996 0.2060 0.3944 126 R 0.3412 0.2060 0.4527 127 E 0.3423 0.2512 0.4065 128 H 0.3193 0.1958 0.4850 129 A 0.2444 0.1974 0.5583 130 R 0.1873 0.1384 0.6744 131 G 0.1564 0.0811 0.7625 132 P 0.1953 0.1417 0.6630 133 G 0.2700 0.1227 0.6073 134 W 0.5523 0.0735 0.3742 135 R 0.6514 0.0583 0.2903 136 V 0.6307 0.0808 0.2885 137 L 0.5397 0.0724 0.3880 138 G 0.3752 0.0707 0.5542 139 G 0.3910 0.0603 0.5487 140 A 0.6216 0.0289 0.3495 141 V 0.7226 0.0163 0.2611 142 L 0.7716 0.0124 0.2160 143 D 0.7487 0.0091 0.2422 144 L 0.7754 0.0136 0.2110 145 W 0.7487 0.0116 0.2397 146 V 0.7048 0.0179 0.2773 147 S 0.4310 0.0286 0.5404 148 D 0.2238 0.1944 0.5818 149 S 0.1251 0.1473 0.7275 150 G 0.1593 0.0875 0.7533 151 A 0.4796 0.0240 0.4964 152 F 0.7060 0.0149 0.2791 153 L 0.7441 0.0180 0.2379 154 L 0.7770 0.0141 0.2089 155 E 0.7538 0.0155 0.2308 156 V 0.6987 0.0208 0.2805 157 D 0.4441 0.0182 0.5377 158 P 0.0866 0.5065 0.4069 159 A 0.0630 0.4636 0.4734 160 Y 0.1892 0.4731 0.3377 161 R 0.2705 0.4102 0.3193 162 I 0.3488 0.3079 0.3433 163 L 0.2939 0.2408 0.4652 164 C 0.2027 0.1649 0.6324 165 E 0.0893 0.4522 0.4585 166 M 0.1235 0.4162 0.4604 167 S 0.1412 0.4489 0.4099 168 L 0.0197 0.7795 0.2009 169 E 0.0100 0.8813 0.1087 170 A 0.0095 0.9180 0.0725 171 W 0.0092 0.9144 0.0764 172 L 0.0102 0.8842 0.1056 173 A 0.0135 0.7841 0.2024 174 Q 0.0403 0.3366 0.6231 175 G 0.0632 0.1149 0.8219 176 H 0.1402 0.1065 0.7533 177 P 0.1265 0.1560 0.7175 178 L 0.2067 0.1129 0.6803 179 P 0.1374 0.2813 0.5813 180 K 0.1091 0.5239 0.3670 181 R 0.1713 0.4945 0.3342 182 V 0.2250 0.4804 0.2946 183 R 0.2172 0.4657 0.3171 184 N 0.1886 0.4199 0.3915 185 A 0.1545 0.4030 0.4425 186 Y 0.2005 0.2727 0.5268 187 D 0.1812 0.2375 0.5813 188 R 0.1968 0.2624 0.5408 189 R 0.3146 0.2160 0.4694 190 T 0.4604 0.1676 0.3719 191 W 0.5186 0.1806 0.3008 192 E 0.5163 0.2152 0.2685 193 L 0.5284 0.2179 0.2537 194 L 0.4640 0.2578 0.2782 195 R 0.4065 0.2203 0.3732 196 L 0.2362 0.2063 0.5574 197 G 0.1619 0.1546 0.6835 198 E 0.1508 0.2410 0.6082 199 E 0.2192 0.1642 0.6166 200 D 0.2029 0.0616 0.7355 201 P 0.0798 0.4146 0.5056 202 K 0.0817 0.4392 0.4791 203 E 0.1765 0.2520 0.5714 204 L 0.3138 0.0442 0.6421 205 P 0.2530 0.0512 0.6959 206 L 0.2179 0.0521 0.7301 207 P 0.1280 0.2033 0.6688 208 G 0.0959 0.1592 0.7449 209 G 0.1318 0.1047 0.7635 210 L 0.3441 0.0712 0.5847 211 S 0.3879 0.1040 0.5081 212 L 0.2505 0.4077 0.3418 213 L 0.1887 0.5623 0.2490 214 D 0.1899 0.5818 0.2283 215 Y 0.2190 0.5418 0.2392 216 H 0.1942 0.5278 0.2780 217 A 0.0792 0.6622 0.2586 218 S 0.0857 0.5359 0.3784 219 K 0.0800 0.2422 0.6778 220 G 0.0817 0.1334 0.7850 221 R 0.2170 0.0866 0.6963 222 L 0.2783 0.1095 0.6122 223 Q 0.2541 0.1335 0.6124 224 G 0.2146 0.1397 0.6457 225 R 0.2645 0.1046 0.6309 226 E 0.3198 0.0899 0.5903 227 G 0.2888 0.0592 0.6520 228 G 0.3936 0.0423 0.5641 229 R 0.6784 0.0119 0.3097 230 V 0.7724 0.0065 0.2211 231 A 0.7994 0.0064 0.1941 232 W 0.8041 0.0053 0.1906 233 V 0.7706 0.0089 0.2205 234 A 0.6593 0.0193 0.3213 235 D 0.3367 0.0185 0.6448 236 P 0.1075 0.2394 0.6531 237 K 0.1036 0.2289 0.6675 238 D 0.1904 0.0660 0.7436 239 P 0.0862 0.3214 0.5924 240 R 0.1136 0.2259 0.6605 241 K 0.2516 0.0653 0.6831 242 P 0.2676 0.1220 0.6105 243 I 0.3041 0.1266 0.5692 244 P 0.1655 0.4452 0.3892 245 H 0.1517 0.5193 0.3290 246 L 0.1031 0.6220 0.2749 247 T 0.0862 0.5629 0.3509 248 G 0.0754 0.5307 0.3939 249 L 0.1287 0.4440 0.4273 250 L 0.1952 0.3501 0.4547 251 V 0.2722 0.2883 0.4394 252 P 0.2667 0.3901 0.3432 253 V 0.3547 0.3484 0.2968 254 L 0.4550 0.2615 0.2835 255 T 0.3753 0.2661 0.3587 256 L 0.1674 0.5294 0.3032 257 E 0.0902 0.6370 0.2728 258 D 0.0725 0.6392 0.2882 259 L 0.0436 0.7280 0.2284 260 H 0.0423 0.7305 0.2272 261 E 0.0428 0.7444 0.2128 262 E 0.0562 0.6853 0.2584 263 E 0.0688 0.5280 0.4033 264 G 0.0579 0.3898 0.5523 265 S 0.0941 0.4264 0.4796 266 L 0.1579 0.3561 0.4859 267 A 0.1856 0.3453 0.4691 268 L 0.1996 0.2870 0.5134 269 S 0.1861 0.1615 0.6524 270 L 0.2289 0.0779 0.6933 271 P 0.1690 0.1365 0.6945 272 W 0.1133 0.4226 0.4641 273 E 0.0941 0.5783 0.3276 274 E 0.0815 0.6577 0.2608 275 R 0.0933 0.6578 0.2489 276 R 0.0966 0.6935 0.2099 277 R 0.0622 0.7498 0.1881 278 R 0.0406 0.7851 0.1743 279 T 0.0262 0.8478 0.1260 280 R 0.0121 0.8940 0.0939 281 E 0.0132 0.8971 0.0897 282 I 0.0167 0.8947 0.0886 283 A 0.0107 0.9022 0.0871 284 S 0.0094 0.9064 0.0842 285 W 0.0145 0.8749 0.1106 286 I 0.0265 0.8227 0.1508 287 G 0.0280 0.7636 0.2084 288 R 0.0521 0.7107 0.2372 289 R 0.1153 0.5244 0.3603 290 L 0.1545 0.3029 0.5426 291 G 0.1524 0.1612 0.6864 292 L 0.2131 0.1387 0.6482 293 G 0.2421 0.0913 0.6666 294 T 0.2212 0.0429 0.7359 295 P 0.1170 0.2135 0.6695