# This file is the result of combining several RDB files, specifically # T0628.t06.str2.rdb (weight 1.54425) # T0628.t06.str4.rdb (weight 0.924988) # T0628.t06.pb.rdb (weight 0.789901) # T0628.t06.bys.rdb (weight 0.748322) # T0628.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 T0628.t06.str2.rdb # ============================================ # TARGET T0628 # 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 T0628.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 43.6862 # # ============================================ # Comments from T0628.t06.str4.rdb # ============================================ # TARGET T0628 # 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 T0628.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 43.6862 # # ============================================ # Comments from T0628.t06.pb.rdb # ============================================ # TARGET T0628 # 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 T0628.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 43.6862 # # ============================================ # Comments from T0628.t06.bys.rdb # ============================================ # TARGET T0628 # 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 T0628.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 43.6862 # # ============================================ # Comments from T0628.t06.alpha.rdb # ============================================ # TARGET T0628 # 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 T0628.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 43.6862 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1474 0.2554 0.5972 2 N 0.1351 0.2761 0.5888 3 A 0.1730 0.2788 0.5482 4 M 0.2178 0.1967 0.5855 5 T 0.2805 0.1195 0.6000 6 A 0.2927 0.2130 0.4943 7 R 0.4335 0.1184 0.4480 8 Y 0.7489 0.0279 0.2232 9 I 0.7485 0.0208 0.2308 10 A 0.7886 0.0117 0.1996 11 I 0.7552 0.0196 0.2252 12 D 0.4784 0.0346 0.4870 13 W 0.2046 0.1982 0.5972 14 G 0.1677 0.2302 0.6022 15 S 0.2237 0.2561 0.5203 16 T 0.1954 0.2951 0.5095 17 N 0.2862 0.2517 0.4621 18 L 0.4606 0.2355 0.3039 19 R 0.6214 0.1670 0.2116 20 A 0.7407 0.0910 0.1683 21 W 0.7350 0.0765 0.1886 22 L 0.7335 0.0493 0.2172 23 Y 0.6652 0.0561 0.2786 24 Q 0.4194 0.0771 0.5036 25 G 0.1322 0.1045 0.7634 26 E 0.1516 0.1448 0.7036 27 E 0.3209 0.1733 0.5057 28 C 0.3425 0.2872 0.3703 29 L 0.2548 0.4457 0.2996 30 E 0.2405 0.5181 0.2414 31 S 0.1687 0.5687 0.2626 32 R 0.1894 0.4603 0.3503 33 Q 0.1826 0.3509 0.4665 34 S 0.1446 0.3587 0.4967 35 E 0.0550 0.5260 0.4190 36 A 0.0830 0.3490 0.5680 37 G 0.1240 0.2633 0.6127 38 V 0.2480 0.2952 0.4568 39 T 0.3358 0.2910 0.3731 40 R 0.3104 0.2470 0.4426 41 L 0.2421 0.1920 0.5659 42 N 0.1440 0.1707 0.6853 43 G 0.0837 0.1996 0.7167 44 R 0.1078 0.1608 0.7314 45 S 0.1636 0.0970 0.7394 46 P 0.0427 0.5841 0.3732 47 A 0.0140 0.8172 0.1689 48 A 0.0098 0.9037 0.0865 49 V 0.0095 0.9139 0.0766 50 L 0.0087 0.9151 0.0762 51 A 0.0085 0.9131 0.0785 52 E 0.0089 0.9066 0.0845 53 I 0.0112 0.8816 0.1072 54 T 0.0182 0.8355 0.1463 55 Q 0.0155 0.7913 0.1933 56 H 0.0233 0.6884 0.2884 57 W 0.0500 0.5569 0.3931 58 R 0.0706 0.4401 0.4892 59 D 0.0714 0.2681 0.6605 60 G 0.0609 0.1955 0.7436 61 A 0.1482 0.1174 0.7345 62 T 0.2827 0.0518 0.6655 63 P 0.4710 0.0408 0.4883 64 V 0.7838 0.0148 0.2015 65 V 0.7789 0.0172 0.2040 66 M 0.7708 0.0272 0.2020 67 A 0.6528 0.0523 0.2948 68 G 0.3630 0.0642 0.5728 69 M 0.3115 0.1095 0.5791 70 V 0.3087 0.1412 0.5500 71 G 0.2195 0.1670 0.6135 72 S 0.1383 0.3206 0.5411 73 N 0.1201 0.3393 0.5406 74 V 0.1466 0.2744 0.5790 75 G 0.1827 0.1934 0.6239 76 W 0.3303 0.2403 0.4294 77 K 0.4319 0.1977 0.3704 78 I 0.4665 0.1367 0.3968 79 A 0.3634 0.0760 0.5607 80 P 0.2561 0.1713 0.5726 81 Y 0.3170 0.1490 0.5340 82 L 0.3626 0.0629 0.5745 83 P 0.2995 0.0504 0.6501 84 L 0.3084 0.0543 0.6373 85 P 0.2437 0.1075 0.6488 86 A 0.2546 0.1495 0.5959 87 A 0.1977 0.0847 0.7176 88 F 0.0489 0.6262 0.3249 89 S 0.0188 0.7773 0.2039 90 D 0.0218 0.8101 0.1682 91 I 0.0264 0.8104 0.1632 92 G 0.0191 0.8374 0.1434 93 Q 0.0205 0.7988 0.1807 94 Q 0.0457 0.6693 0.2850 95 L 0.1497 0.4547 0.3956 96 T 0.2500 0.3155 0.4346 97 A 0.2931 0.2285 0.4784 98 V 0.2368 0.1327 0.6305 99 G 0.1755 0.0673 0.7572 100 D 0.2266 0.0916 0.6819 101 N 0.3699 0.0558 0.5743 102 I 0.7074 0.0150 0.2775 103 W 0.7467 0.0131 0.2402 104 I 0.7572 0.0096 0.2332 105 I 0.6425 0.0141 0.3434 106 P 0.3459 0.0396 0.6145 107 G 0.2440 0.0687 0.6873 108 L 0.3653 0.1048 0.5299 109 C 0.4172 0.0933 0.4896 110 V 0.4038 0.1040 0.4923 111 S 0.2721 0.1020 0.6260 112 R 0.1738 0.1736 0.6527 113 D 0.1502 0.1847 0.6651 114 D 0.1552 0.1592 0.6855 115 N 0.1648 0.1946 0.6406 116 H 0.1414 0.3235 0.5351 117 N 0.1774 0.2908 0.5318 118 V 0.2898 0.2529 0.4574 119 M 0.2559 0.2008 0.5433 120 R 0.1917 0.1569 0.6514 121 G 0.1390 0.1384 0.7226 122 E 0.2032 0.3596 0.4373 123 E 0.2172 0.5027 0.2801 124 T 0.2287 0.5454 0.2258 125 Q 0.2415 0.5771 0.1814 126 L 0.2376 0.5902 0.1723 127 L 0.1832 0.6052 0.2116 128 G 0.1775 0.5893 0.2332 129 A 0.1126 0.6959 0.1915 130 R 0.1174 0.6516 0.2310 131 A 0.1055 0.5070 0.3875 132 L 0.1462 0.2876 0.5662 133 A 0.1887 0.0845 0.7268 134 P 0.1260 0.1821 0.6919 135 S 0.1359 0.1286 0.7355 136 S 0.3561 0.0513 0.5926 137 V 0.7184 0.0129 0.2687 138 Y 0.7775 0.0091 0.2134 139 V 0.7647 0.0088 0.2265 140 M 0.5744 0.0154 0.4102 141 P 0.2849 0.0539 0.6612 142 G 0.1897 0.1055 0.7048 143 T 0.1904 0.1516 0.6580 144 H 0.2092 0.1790 0.6118 145 C 0.3589 0.1408 0.5003 146 K 0.4869 0.1516 0.3615 147 W 0.7104 0.0498 0.2399 148 V 0.7571 0.0208 0.2222 149 L 0.7720 0.0232 0.2048 150 A 0.7058 0.0452 0.2490 151 D 0.4840 0.0986 0.4175 152 R 0.2001 0.1802 0.6197 153 R 0.1655 0.1289 0.7057 154 Q 0.5051 0.0628 0.4320 155 I 0.5783 0.0541 0.3676 156 H 0.4928 0.1063 0.4009 157 D 0.5226 0.1081 0.3693 158 F 0.4289 0.2111 0.3600 159 R 0.3960 0.3190 0.2850 160 T 0.3312 0.4093 0.2595 161 V 0.2010 0.5656 0.2334 162 L 0.1186 0.6453 0.2361 163 T 0.0367 0.7860 0.1773 164 G 0.0224 0.8391 0.1386 165 E 0.0106 0.8986 0.0907 166 L 0.0084 0.9210 0.0706 167 H 0.0083 0.9204 0.0712 168 H 0.0083 0.9211 0.0706 169 L 0.0085 0.9133 0.0782 170 L 0.0091 0.9009 0.0900 171 L 0.0107 0.8484 0.1408 172 Q 0.0190 0.6774 0.3037 173 L 0.0554 0.5500 0.3946 174 S 0.0952 0.5178 0.3869 175 L 0.1417 0.5193 0.3391 176 V 0.1509 0.4219 0.4272 177 G 0.1230 0.3612 0.5158 178 A 0.1198 0.2923 0.5879 179 G 0.1295 0.1650 0.7056 180 L 0.2159 0.0398 0.7443 181 P 0.1742 0.0281 0.7977 182 P 0.0750 0.3277 0.5973 183 Q 0.0641 0.3764 0.5595 184 E 0.1098 0.3212 0.5690 185 T 0.1446 0.2602 0.5952 186 S 0.1234 0.3032 0.5735 187 A 0.0120 0.8110 0.1769 188 A 0.0095 0.8807 0.1098 189 A 0.0088 0.9163 0.0750 190 F 0.0086 0.9200 0.0714 191 A 0.0084 0.9173 0.0743 192 A 0.0087 0.9108 0.0805 193 G 0.0092 0.9127 0.0781 194 L 0.0091 0.9138 0.0771 195 Q 0.0095 0.9025 0.0880 196 R 0.0135 0.8354 0.1511 197 G 0.0244 0.7175 0.2580 198 I 0.0413 0.6056 0.3531 199 N 0.0691 0.3835 0.5474 200 N 0.1340 0.2021 0.6638 201 P 0.0266 0.6099 0.3635 202 A 0.0256 0.6187 0.3557 203 V 0.0412 0.6483 0.3105 204 L 0.0323 0.7643 0.2034 205 P 0.0117 0.8778 0.1105 206 Q 0.0123 0.8768 0.1109 207 L 0.0182 0.8769 0.1048 208 F 0.0196 0.8766 0.1039 209 E 0.0294 0.8717 0.0989 210 V 0.0358 0.8637 0.1006 211 R 0.0311 0.8650 0.1038 212 A 0.0204 0.8746 0.1050 213 S 0.0165 0.8732 0.1103 214 H 0.0210 0.8571 0.1219 215 V 0.0308 0.7785 0.1908 216 L 0.0409 0.5283 0.4308 217 G 0.0396 0.3018 0.6585 218 A 0.0877 0.2284 0.6839 219 L 0.2089 0.0401 0.7510 220 P 0.1578 0.0281 0.8141 221 R 0.0156 0.7141 0.2702 222 E 0.0104 0.8081 0.1815 223 Q 0.0115 0.8695 0.1190 224 V 0.0113 0.8803 0.1083 225 S 0.0089 0.8952 0.0959 226 E 0.0091 0.8602 0.1307 227 F 0.0105 0.8403 0.1492 228 L 0.0180 0.8096 0.1724 229 S 0.0220 0.7568 0.2212 230 G 0.0324 0.7680 0.1996 231 L 0.0521 0.8253 0.1226 232 L 0.1483 0.7294 0.1223 233 I 0.0961 0.7484 0.1556 234 G 0.0284 0.8370 0.1347 235 A 0.0114 0.8903 0.0983 236 E 0.0123 0.9043 0.0833 237 V 0.0104 0.9047 0.0849 238 A 0.0094 0.8824 0.1082 239 T 0.0126 0.8286 0.1588 240 L 0.0322 0.7397 0.2280 241 S 0.0538 0.6450 0.3011 242 D 0.0283 0.6555 0.3162 243 T 0.0409 0.5832 0.3759 244 F 0.0911 0.3870 0.5219 245 A 0.0860 0.2899 0.6240 246 G 0.0743 0.1685 0.7572 247 Q 0.1812 0.1068 0.7120 248 Q 0.3025 0.0603 0.6372 249 A 0.5616 0.0313 0.4071 250 I 0.7758 0.0091 0.2151 251 S 0.8077 0.0070 0.1853 252 L 0.7908 0.0086 0.2006 253 V 0.7552 0.0145 0.2303 254 A 0.5172 0.0344 0.4484 255 G 0.2145 0.1136 0.6719 256 S 0.0657 0.4064 0.5280 257 S 0.0305 0.6247 0.3448 258 L 0.0188 0.7857 0.1956 259 T 0.0105 0.8820 0.1075 260 S 0.0084 0.9166 0.0750 261 R 0.0084 0.9195 0.0721 262 Y 0.0083 0.9211 0.0705 263 Q 0.0083 0.9220 0.0697 264 Q 0.0083 0.9236 0.0681 265 A 0.0083 0.9209 0.0708 266 F 0.0084 0.9184 0.0732 267 A 0.0086 0.9086 0.0827 268 A 0.0133 0.7984 0.1883 269 I 0.0573 0.2923 0.6504 270 G 0.0493 0.0833 0.8675 271 R 0.1905 0.0324 0.7771 272 E 0.3009 0.0500 0.6491 273 V 0.4569 0.0500 0.4931 274 S 0.5770 0.0529 0.3700 275 A 0.6119 0.0423 0.3458 276 V 0.5523 0.0405 0.4072 277 A 0.2512 0.0693 0.6795 278 G 0.0594 0.4874 0.4532 279 D 0.0293 0.6984 0.2723 280 T 0.0238 0.8049 0.1714 281 A 0.0183 0.8572 0.1245 282 F 0.0151 0.8801 0.1048 283 Q 0.0105 0.8913 0.0982 284 T 0.0132 0.8756 0.1112 285 G 0.0113 0.8945 0.0942 286 I 0.0084 0.9154 0.0762 287 R 0.0083 0.9220 0.0697 288 S 0.0083 0.9221 0.0696 289 I 0.0084 0.9208 0.0708 290 A 0.0085 0.9139 0.0776 291 Y 0.0087 0.8945 0.0967 292 A 0.0125 0.8274 0.1600 293 V 0.0393 0.6251 0.3356 294 A 0.0604 0.4192 0.5204 295 N 0.0754 0.2675 0.6571