# This file is the result of combining several RDB files, specifically # T0427.t2k.str2.rdb (weight 1.54425) # T0427.t2k.str4.rdb (weight 0.924988) # T0427.t2k.pb.rdb (weight 0.789901) # T0427.t2k.bys.rdb (weight 0.748322) # T0427.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 T0427.t2k.str2.rdb # ============================================ # TARGET T0427 # 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 T0427.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 857 # # ============================================ # Comments from T0427.t2k.str4.rdb # ============================================ # TARGET T0427 # 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 T0427.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 857 # # ============================================ # Comments from T0427.t2k.pb.rdb # ============================================ # TARGET T0427 # 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 T0427.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 857 # # ============================================ # Comments from T0427.t2k.bys.rdb # ============================================ # TARGET T0427 # 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 T0427.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 857 # # ============================================ # Comments from T0427.t2k.alpha.rdb # ============================================ # TARGET T0427 # 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 T0427.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 857 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.6477 0.0271 0.3251 2 S 0.6806 0.0197 0.2997 3 V 0.7594 0.0106 0.2300 4 Q 0.7463 0.0113 0.2424 5 L 0.5387 0.0363 0.4250 6 V 0.3204 0.1273 0.5523 7 K 0.1524 0.0924 0.7552 8 G 0.1855 0.0595 0.7551 9 V 0.5204 0.0094 0.4702 10 N 0.7269 0.0077 0.2654 11 L 0.8024 0.0050 0.1927 12 H 0.8070 0.0062 0.1868 13 V 0.7756 0.0055 0.2189 14 I 0.6853 0.0130 0.3017 15 P 0.5028 0.0258 0.4714 16 T 0.2796 0.0382 0.6821 17 E 0.1067 0.2565 0.6368 18 K 0.1432 0.1940 0.6628 19 Y 0.3385 0.0489 0.6125 20 K 0.3989 0.0590 0.5421 21 T 0.6852 0.0216 0.2932 22 V 0.7487 0.0123 0.2391 23 R 0.8023 0.0059 0.1918 24 L 0.8135 0.0052 0.1813 25 L 0.8152 0.0048 0.1800 26 V 0.8121 0.0054 0.1826 27 R 0.7947 0.0058 0.1995 28 F 0.7409 0.0165 0.2426 29 N 0.5373 0.0349 0.4278 30 T 0.3079 0.1155 0.5766 31 R 0.1907 0.1326 0.6767 32 L 0.1929 0.1982 0.6088 33 N 0.1573 0.2788 0.5639 34 H 0.1475 0.3283 0.5242 35 E 0.1871 0.2677 0.5451 36 T 0.1805 0.2420 0.5775 37 I 0.0978 0.4223 0.4799 38 T 0.0619 0.4380 0.5001 39 K 0.0246 0.7648 0.2105 40 R 0.0170 0.8009 0.1821 41 T 0.0254 0.7695 0.2051 42 L 0.0377 0.6843 0.2780 43 L 0.0347 0.7214 0.2439 44 S 0.0159 0.8411 0.1430 45 S 0.0162 0.8464 0.1375 46 L 0.0235 0.8348 0.1417 47 M 0.0322 0.8187 0.1491 48 E 0.0485 0.7107 0.2408 49 T 0.0760 0.4718 0.4521 50 N 0.1040 0.2760 0.6200 51 S 0.1362 0.2545 0.6093 52 L 0.0694 0.4073 0.5233 53 N 0.0809 0.3558 0.5633 54 Y 0.1058 0.3986 0.4955 55 P 0.0450 0.6759 0.2791 56 N 0.0216 0.8121 0.1663 57 Q 0.0133 0.8862 0.1005 58 V 0.0096 0.9110 0.0794 59 K 0.0085 0.9175 0.0740 60 L 0.0083 0.9211 0.0706 61 S 0.0084 0.9193 0.0724 62 E 0.0084 0.9169 0.0747 63 R 0.0087 0.9025 0.0888 64 L 0.0095 0.8769 0.1136 65 A 0.0133 0.8313 0.1554 66 E 0.0275 0.6960 0.2765 67 L 0.0653 0.5108 0.4238 68 Y 0.0897 0.3626 0.5476 69 G 0.0757 0.3310 0.5934 70 A 0.1047 0.3549 0.5404 71 S 0.1317 0.3138 0.5545 72 F 0.1137 0.3746 0.5117 73 G 0.0667 0.6584 0.2748 74 I 0.0334 0.7852 0.1815 75 G 0.0296 0.8283 0.1422 76 V 0.0222 0.8656 0.1122 77 S 0.0144 0.8812 0.1045 78 K 0.0139 0.8760 0.1101 79 K 0.0230 0.7699 0.2071 80 G 0.0414 0.6424 0.3161 81 N 0.0549 0.5854 0.3597 82 Q 0.1037 0.4341 0.4622 83 H 0.1740 0.2805 0.5456 84 W 0.3292 0.1708 0.5000 85 F 0.5195 0.1159 0.3646 86 N 0.6253 0.0696 0.3052 87 I 0.6417 0.0658 0.2925 88 S 0.5541 0.0528 0.3931 89 M 0.5012 0.0870 0.4118 90 N 0.4699 0.0927 0.4374 91 I 0.4326 0.1065 0.4609 92 V 0.2965 0.1226 0.5809 93 N 0.2276 0.2152 0.5572 94 D 0.1732 0.3004 0.5264 95 H 0.3039 0.2586 0.4374 96 Y 0.4562 0.1745 0.3693 97 L 0.4747 0.1984 0.3269 98 Q 0.4231 0.2241 0.3528 99 D 0.3765 0.2423 0.3812 100 S 0.2147 0.4891 0.2962 101 Q 0.1956 0.5040 0.3003 102 V 0.1478 0.5435 0.3087 103 L 0.0711 0.6594 0.2695 104 A 0.0148 0.8300 0.1552 105 E 0.0104 0.8601 0.1295 106 A 0.0145 0.8316 0.1538 107 V 0.0129 0.8739 0.1132 108 D 0.0085 0.9169 0.0746 109 F 0.0086 0.9149 0.0766 110 L 0.0088 0.9125 0.0788 111 K 0.0085 0.9160 0.0755 112 E 0.0086 0.9109 0.0805 113 I 0.0118 0.8811 0.1071 114 I 0.0245 0.8054 0.1701 115 F 0.0510 0.6359 0.3131 116 A 0.0823 0.6140 0.3037 117 P 0.0380 0.6461 0.3159 118 N 0.0483 0.5626 0.3891 119 I 0.0877 0.5428 0.3694 120 Q 0.1254 0.4156 0.4590 121 A 0.1232 0.2608 0.6160 122 G 0.0834 0.3014 0.6152 123 Q 0.1200 0.1984 0.6816 124 F 0.2153 0.0728 0.7119 125 E 0.1613 0.0664 0.7724 126 A 0.0150 0.7149 0.2701 127 E 0.0108 0.8374 0.1518 128 T 0.0133 0.8855 0.1013 129 F 0.0129 0.9012 0.0859 130 Q 0.0103 0.9112 0.0784 131 R 0.0096 0.9131 0.0773 132 E 0.0099 0.9115 0.0786 133 K 0.0087 0.9143 0.0770 134 E 0.0084 0.9175 0.0741 135 N 0.0087 0.9168 0.0745 136 L 0.0084 0.9187 0.0729 137 K 0.0084 0.9193 0.0723 138 A 0.0083 0.9234 0.0683 139 Y 0.0084 0.9202 0.0715 140 L 0.0086 0.9124 0.0789 141 E 0.0102 0.9026 0.0872 142 S 0.0127 0.8548 0.1325 143 I 0.0252 0.7590 0.2157 144 V 0.0369 0.6979 0.2652 145 E 0.0572 0.4946 0.4482 146 D 0.1281 0.2431 0.6288 147 K 0.0152 0.7106 0.2742 148 Q 0.0117 0.8295 0.1587 149 T 0.0120 0.8958 0.0923 150 Y 0.0105 0.9099 0.0796 151 A 0.0092 0.9151 0.0757 152 S 0.0084 0.9215 0.0701 153 L 0.0083 0.9214 0.0703 154 A 0.0084 0.9203 0.0713 155 L 0.0085 0.9164 0.0751 156 Q 0.0087 0.9097 0.0817 157 S 0.0090 0.8978 0.0932 158 V 0.0140 0.8391 0.1469 159 Y 0.0519 0.6941 0.2540 160 F 0.1158 0.4479 0.4363 161 N 0.1051 0.3011 0.5938 162 Q 0.0579 0.3442 0.5979 163 S 0.0806 0.1992 0.7202 164 E 0.1661 0.1346 0.6993 165 D 0.1409 0.2724 0.5867 166 Q 0.1423 0.3036 0.5541 167 K 0.1908 0.1744 0.6348 168 I 0.3018 0.0674 0.6308 169 P 0.2482 0.0970 0.6547 170 S 0.2271 0.2234 0.5495 171 F 0.2084 0.2237 0.5679 172 G 0.1865 0.1385 0.6750 173 T 0.2020 0.1240 0.6740 174 V 0.0312 0.6956 0.2733 175 A 0.0230 0.8074 0.1696 176 A 0.0294 0.8262 0.1445 177 L 0.0195 0.8472 0.1333 178 A 0.0182 0.7828 0.1990 179 E 0.0228 0.6541 0.3232 180 E 0.0722 0.4589 0.4689 181 T 0.1221 0.2254 0.6525 182 A 0.0108 0.7931 0.1962 183 A 0.0091 0.8776 0.1133 184 S 0.0084 0.9208 0.0708 185 L 0.0084 0.9165 0.0751 186 A 0.0083 0.9239 0.0679 187 A 0.0083 0.9244 0.0674 188 Y 0.0083 0.9228 0.0688 189 Y 0.0084 0.9196 0.0720 190 Q 0.0086 0.9100 0.0814 191 K 0.0105 0.8568 0.1326 192 M 0.0348 0.6804 0.2847 193 L 0.0944 0.4433 0.4623 194 A 0.1300 0.2134 0.6565 195 E 0.0651 0.3810 0.5539 196 D 0.0747 0.2011 0.7241 197 Q 0.2138 0.0693 0.7169 198 V 0.4951 0.0101 0.4948 199 D 0.7513 0.0070 0.2417 200 I 0.8210 0.0043 0.1747 201 F 0.8227 0.0044 0.1729 202 V 0.7599 0.0056 0.2345 203 L 0.6930 0.0196 0.2874 204 G 0.4702 0.0353 0.4945 205 D 0.2618 0.0591 0.6791 206 V 0.2473 0.0891 0.6635 207 N 0.1643 0.0281 0.8076 208 E 0.0118 0.7278 0.2604 209 A 0.0096 0.8437 0.1466 210 E 0.0112 0.8839 0.1048 211 L 0.0117 0.9034 0.0849 212 V 0.0088 0.9053 0.0859 213 P 0.0083 0.9229 0.0688 214 L 0.0084 0.9192 0.0724 215 F 0.0088 0.9013 0.0900 216 K 0.0094 0.8536 0.1370 217 Q 0.0203 0.6210 0.3587 218 L 0.1212 0.2634 0.6154 219 P 0.0886 0.2720 0.6395 220 F 0.1192 0.1732 0.7076 221 T 0.1868 0.0798 0.7335 222 P 0.1501 0.2348 0.6151 223 R 0.1213 0.3028 0.5759 224 E 0.0982 0.3899 0.5119 225 E 0.1112 0.2280 0.6608 226 G 0.1171 0.1690 0.7139 227 K 0.1981 0.1423 0.6596 228 A 0.2452 0.1477 0.6072 229 A 0.2711 0.1579 0.5711 230 I 0.2676 0.1721 0.5603 231 F 0.2627 0.1344 0.6029 232 Y 0.2546 0.1208 0.6246 233 N 0.2213 0.0965 0.6822 234 Q 0.2610 0.0591 0.6799 235 P 0.2336 0.0926 0.6738 236 I 0.2489 0.1589 0.5922 237 R 0.2373 0.1946 0.5681 238 N 0.2759 0.1548 0.5692 239 V 0.3152 0.1427 0.5421 240 I 0.3608 0.1599 0.4794 241 E 0.4394 0.1624 0.3982 242 E 0.5377 0.1335 0.3287 243 R 0.5731 0.1125 0.3143 244 T 0.5851 0.0979 0.3170 245 E 0.5183 0.1197 0.3621 246 R 0.4030 0.1742 0.4228 247 E 0.2391 0.3282 0.4327 248 V 0.1852 0.3337 0.4812 249 L 0.1647 0.4299 0.4053 250 A 0.1535 0.4353 0.4112 251 Q 0.2572 0.3172 0.4256 252 S 0.3906 0.2359 0.3735 253 K 0.5837 0.1462 0.2701 254 L 0.7077 0.0798 0.2126 255 N 0.6983 0.0783 0.2234 256 L 0.7092 0.0683 0.2226 257 A 0.6478 0.0719 0.2804 258 Y 0.5635 0.0630 0.3735 259 N 0.3682 0.0853 0.5465 260 T 0.2601 0.1550 0.5849 261 D 0.2499 0.1289 0.6212 262 I 0.2087 0.2045 0.5868 263 Y 0.2014 0.2032 0.5954 264 Y 0.1599 0.2214 0.6187 265 G 0.1105 0.1611 0.7284 266 D 0.1652 0.1176 0.7172 267 S 0.0225 0.5982 0.3794 268 Y 0.0203 0.7221 0.2576 269 Y 0.0211 0.8452 0.1337 270 F 0.0116 0.9011 0.0873 271 A 0.0093 0.9128 0.0779 272 L 0.0084 0.9205 0.0711 273 Q 0.0083 0.9222 0.0695 274 V 0.0084 0.9177 0.0738 275 F 0.0096 0.9069 0.0835 276 N 0.0124 0.8764 0.1112 277 G 0.0174 0.8190 0.1636 278 I 0.0388 0.6768 0.2843 279 F 0.0684 0.4254 0.5062 280 G 0.0768 0.2570 0.6662 281 G 0.0821 0.2009 0.7171 282 F 0.1408 0.1962 0.6630 283 P 0.0653 0.4401 0.4947 284 H 0.0713 0.4900 0.4387 285 S 0.0383 0.7087 0.2530 286 K 0.0160 0.8235 0.1606 287 L 0.0167 0.8344 0.1490 288 F 0.0183 0.8644 0.1173 289 M 0.0196 0.8717 0.1086 290 N 0.0383 0.8352 0.1265 291 V 0.0596 0.8077 0.1327 292 R 0.0897 0.7574 0.1530 293 E 0.0799 0.7391 0.1809 294 K 0.1008 0.6065 0.2927 295 E 0.1219 0.4035 0.4746 296 H 0.1611 0.2474 0.5915 297 L 0.3781 0.2244 0.3975 298 A 0.5106 0.1843 0.3051 299 Y 0.5596 0.1609 0.2795 300 Y 0.5780 0.1291 0.2929 301 A 0.4776 0.2123 0.3101 302 S 0.4529 0.2067 0.3405 303 S 0.3669 0.2460 0.3871 304 S 0.3025 0.2296 0.4679 305 I 0.2779 0.2522 0.4699 306 D 0.2332 0.2516 0.5153 307 T 0.1594 0.3294 0.5112 308 F 0.1810 0.2472 0.5719 309 R 0.1993 0.1704 0.6303 310 G 0.2534 0.0962 0.6504 311 F 0.5734 0.0474 0.3792 312 M 0.7365 0.0236 0.2400 313 T 0.7860 0.0151 0.1989 314 V 0.7743 0.0186 0.2071 315 Q 0.7367 0.0244 0.2388 316 T 0.6572 0.0438 0.2991 317 G 0.4277 0.0602 0.5121 318 I 0.2985 0.0795 0.6221 319 D 0.1789 0.0707 0.7504 320 G 0.0608 0.3557 0.5835 321 K 0.0518 0.4441 0.5041 322 N 0.0812 0.3891 0.5297 323 R 0.0169 0.7755 0.2076 324 N 0.0095 0.8810 0.1095 325 Q 0.0084 0.9216 0.0700 326 V 0.0083 0.9213 0.0704 327 L 0.0083 0.9242 0.0676 328 R 0.0083 0.9248 0.0670 329 L 0.0083 0.9236 0.0681 330 I 0.0083 0.9218 0.0699 331 S 0.0083 0.9200 0.0716 332 T 0.0083 0.9232 0.0685 333 E 0.0083 0.9231 0.0686 334 L 0.0084 0.9151 0.0765 335 E 0.0083 0.9212 0.0705 336 N 0.0084 0.9126 0.0789 337 I 0.0094 0.8963 0.0944 338 R 0.0139 0.8022 0.1839 339 L 0.0419 0.5271 0.4311 340 G 0.0424 0.2255 0.7321 341 K 0.1030 0.1483 0.7487 342 I 0.1604 0.1258 0.7139 343 R 0.1508 0.1369 0.7123 344 E 0.0132 0.7589 0.2279 345 L 0.0091 0.8745 0.1164 346 E 0.0084 0.9213 0.0704 347 I 0.0083 0.9207 0.0709 348 E 0.0083 0.9237 0.0680 349 Q 0.0083 0.9243 0.0675 350 T 0.0083 0.9213 0.0704 351 K 0.0083 0.9230 0.0687 352 A 0.0083 0.9231 0.0686 353 M 0.0084 0.9190 0.0726 354 L 0.0086 0.9116 0.0798 355 K 0.0100 0.8720 0.1180 356 N 0.0124 0.7998 0.1878 357 Q 0.0223 0.7301 0.2476 358 Y 0.0570 0.7266 0.2164 359 I 0.0834 0.7299 0.1867 360 L 0.1332 0.6375 0.2292 361 A 0.1531 0.5307 0.3161 362 L 0.1303 0.4905 0.3792 363 D 0.1127 0.3817 0.5056 364 N 0.1241 0.2351 0.6408 365 A 0.0265 0.5808 0.3927 366 G 0.0171 0.7591 0.2238 367 A 0.0149 0.8716 0.1135 368 W 0.0138 0.8938 0.0924 369 L 0.0098 0.9069 0.0833 370 E 0.0088 0.9134 0.0778 371 K 0.0088 0.9108 0.0804 372 E 0.0094 0.9042 0.0864 373 Y 0.0131 0.8827 0.1042 374 L 0.0159 0.8618 0.1223 375 N 0.0227 0.8209 0.1564 376 E 0.0537 0.6900 0.2564 377 L 0.1260 0.4413 0.4326 378 M 0.1755 0.1902 0.6343 379 P 0.1002 0.2759 0.6239 380 Q 0.1084 0.2196 0.6720 381 T 0.1495 0.1761 0.6744 382 M 0.1171 0.3472 0.5357 383 L 0.1312 0.3242 0.5446 384 T 0.1428 0.2717 0.5855 385 A 0.0148 0.7680 0.2172 386 E 0.0093 0.8716 0.1191 387 E 0.0084 0.9206 0.0710 388 W 0.0088 0.9183 0.0729 389 I 0.0083 0.9218 0.0699 390 A 0.0083 0.9207 0.0710 391 R 0.0088 0.9058 0.0854 392 I 0.0116 0.8789 0.1096 393 N 0.0133 0.7936 0.1931 394 A 0.0314 0.4968 0.4718 395 V 0.1741 0.2218 0.6041 396 T 0.1645 0.0475 0.7880 397 I 0.0132 0.7347 0.2521 398 P 0.0094 0.8610 0.1297 399 E 0.0085 0.9200 0.0715 400 I 0.0086 0.9052 0.0863 401 Q 0.0083 0.9238 0.0679 402 E 0.0082 0.9253 0.0664 403 V 0.0083 0.9236 0.0681 404 A 0.0084 0.9184 0.0733 405 K 0.0085 0.9120 0.0795 406 R 0.0102 0.8639 0.1259 407 L 0.0256 0.7537 0.2207 408 E 0.0456 0.5499 0.4045 409 L 0.0936 0.3250 0.5814 410 Q 0.1094 0.2780 0.6126 411 A 0.1867 0.1949 0.6183 412 I 0.4088 0.0677 0.5236 413 F 0.6847 0.0186 0.2967 414 F 0.7863 0.0076 0.2061 415 L 0.7973 0.0063 0.1964 416 E 0.7942 0.0085 0.1973 417 G 0.7434 0.0123 0.2443 418 E 0.6378 0.0257 0.3366 419 T 0.3762 0.0205 0.6033 420 E 0.2107 0.1460 0.6434 421 N 0.1230 0.2343 0.6427 422 D 0.1279 0.1698 0.7023