# This file is the result of combining several RDB files, specifically # T0440.t06.str2.rdb (weight 1.54425) # T0440.t06.str4.rdb (weight 0.924988) # T0440.t06.pb.rdb (weight 0.789901) # T0440.t06.bys.rdb (weight 0.748322) # T0440.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 T0440.t06.str2.rdb # ============================================ # TARGET T0440 # 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 T0440.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 1615 # # ============================================ # Comments from T0440.t06.str4.rdb # ============================================ # TARGET T0440 # 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 T0440.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 1615 # # ============================================ # Comments from T0440.t06.pb.rdb # ============================================ # TARGET T0440 # 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 T0440.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 1615 # # ============================================ # Comments from T0440.t06.bys.rdb # ============================================ # TARGET T0440 # 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 T0440.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 1615 # # ============================================ # Comments from T0440.t06.alpha.rdb # ============================================ # TARGET T0440 # 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 T0440.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 1615 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3221 0.0723 0.6056 2 K 0.3853 0.0599 0.5548 3 R 0.4620 0.0532 0.4848 4 D 0.3855 0.0664 0.5481 5 G 0.4241 0.1457 0.4302 6 H 0.4876 0.1157 0.3967 7 T 0.5043 0.0923 0.4034 8 H 0.4416 0.0762 0.4822 9 T 0.3487 0.0899 0.5615 10 E 0.2871 0.1362 0.5767 11 F 0.3086 0.1034 0.5880 12 C 0.2425 0.0505 0.7070 13 P 0.0610 0.3589 0.5801 14 H 0.0778 0.2482 0.6740 15 G 0.1109 0.1724 0.7168 16 T 0.1222 0.1910 0.6868 17 H 0.1299 0.1998 0.6703 18 D 0.1231 0.1593 0.7176 19 D 0.1620 0.0686 0.7693 20 V 0.0126 0.7550 0.2324 21 E 0.0091 0.8731 0.1178 22 E 0.0083 0.9245 0.0673 23 M 0.0083 0.9242 0.0676 24 V 0.0083 0.9215 0.0702 25 L 0.0083 0.9244 0.0673 26 K 0.0083 0.9243 0.0674 27 A 0.0083 0.9239 0.0678 28 I 0.0084 0.9167 0.0748 29 E 0.0112 0.8351 0.1537 30 L 0.0549 0.2990 0.6462 31 D 0.0499 0.0789 0.8713 32 F 0.1759 0.0498 0.7744 33 D 0.2504 0.1061 0.6435 34 E 0.7338 0.0401 0.2260 35 Y 0.7502 0.0179 0.2319 36 S 0.7950 0.0115 0.1934 37 I 0.7653 0.0144 0.2203 38 V 0.6239 0.0314 0.3447 39 E 0.2931 0.1397 0.5672 40 H 0.1678 0.1530 0.6792 41 A 0.1752 0.1953 0.6295 42 P 0.1003 0.3504 0.5493 43 L 0.1030 0.4448 0.4522 44 S 0.0856 0.5946 0.3197 45 S 0.0322 0.7231 0.2448 46 E 0.0362 0.7190 0.2447 47 F 0.0510 0.7412 0.2078 48 M 0.0337 0.7993 0.1670 49 K 0.0396 0.7539 0.2065 50 N 0.0530 0.6560 0.2911 51 T 0.0796 0.5005 0.4199 52 A 0.0791 0.3656 0.5553 53 G 0.0904 0.2323 0.6773 54 D 0.1054 0.1348 0.7598 55 K 0.2550 0.0725 0.6726 56 E 0.4420 0.0524 0.5056 57 A 0.5888 0.0339 0.3773 58 V 0.5645 0.0312 0.4043 59 T 0.4767 0.0509 0.4723 60 T 0.4953 0.0754 0.4293 61 A 0.5851 0.0695 0.3454 62 S 0.6342 0.0513 0.3145 63 M 0.6354 0.0434 0.3213 64 A 0.5322 0.0480 0.4198 65 M 0.4140 0.1342 0.4518 66 S 0.2402 0.2083 0.5515 67 D 0.1678 0.1634 0.6688 68 L 0.1791 0.1615 0.6593 69 P 0.0944 0.4385 0.4671 70 Y 0.1099 0.5381 0.3520 71 Y 0.1295 0.6263 0.2443 72 F 0.0909 0.7568 0.1523 73 K 0.0850 0.7940 0.1211 74 K 0.0802 0.7996 0.1201 75 M 0.0580 0.8066 0.1353 76 N 0.0378 0.8078 0.1545 77 H 0.0323 0.7984 0.1693 78 I 0.0522 0.7317 0.2161 79 K 0.0628 0.6664 0.2707 80 K 0.0540 0.6860 0.2599 81 K 0.0504 0.6253 0.3242 82 Y 0.0832 0.4695 0.4473 83 A 0.1136 0.4012 0.4852 84 S 0.0711 0.4809 0.4480 85 D 0.1237 0.3698 0.5065 86 L 0.3502 0.2447 0.4051 87 L 0.4826 0.2003 0.3171 88 I 0.6054 0.1487 0.2460 89 H 0.4974 0.1895 0.3131 90 I 0.3077 0.1976 0.4947 91 G 0.2301 0.1195 0.6505 92 F 0.3388 0.1253 0.5358 93 E 0.4132 0.1670 0.4197 94 V 0.3467 0.2582 0.3952 95 D 0.2878 0.2741 0.4381 96 Y 0.2714 0.3130 0.4155 97 L 0.2460 0.3177 0.4363 98 I 0.1206 0.4074 0.4719 99 G 0.0774 0.4331 0.4895 100 Y 0.0811 0.5410 0.3779 101 E 0.0382 0.7281 0.2337 102 D 0.0271 0.7753 0.1976 103 F 0.0278 0.7887 0.1835 104 T 0.0267 0.8298 0.1435 105 R 0.0120 0.8854 0.1025 106 D 0.0103 0.8940 0.0958 107 F 0.0121 0.8829 0.1050 108 L 0.0153 0.8587 0.1259 109 N 0.0155 0.7756 0.2089 110 E 0.0240 0.5945 0.3815 111 Y 0.0808 0.2910 0.6282 112 G 0.0903 0.1173 0.7924 113 P 0.1327 0.1835 0.6838 114 Q 0.1408 0.2146 0.6446 115 T 0.1247 0.2556 0.6197 116 D 0.1366 0.2310 0.6324 117 D 0.2193 0.1909 0.5897 118 G 0.4113 0.1609 0.4278 119 V 0.5101 0.1210 0.3689 120 L 0.5056 0.0960 0.3984 121 S 0.4595 0.0887 0.4517 122 L 0.3196 0.2262 0.4541 123 H 0.3506 0.2487 0.4007 124 F 0.3489 0.2624 0.3887 125 L 0.2843 0.2335 0.4822 126 E 0.2155 0.2049 0.5796 127 G 0.1436 0.2523 0.6041 128 Q 0.1469 0.2506 0.6025 129 G 0.1432 0.1947 0.6621 130 G 0.1574 0.1811 0.6615 131 F 0.2110 0.1557 0.6333 132 R 0.2078 0.1886 0.6036 133 S 0.2541 0.1971 0.5488 134 I 0.2606 0.1964 0.5430 135 D 0.1950 0.2469 0.5581 136 F 0.1709 0.2948 0.5344 137 S 0.1217 0.4293 0.4491 138 A 0.0703 0.5995 0.3303 139 E 0.0486 0.6869 0.2646 140 D 0.0494 0.6730 0.2777 141 Y 0.0607 0.6619 0.2774 142 N 0.0440 0.7143 0.2417 143 E 0.0326 0.7391 0.2283 144 G 0.0379 0.7408 0.2213 145 I 0.0632 0.7399 0.1969 146 V 0.0701 0.7332 0.1966 147 Q 0.0796 0.6615 0.2589 148 F 0.0951 0.5119 0.3930 149 Y 0.0833 0.3477 0.5690 150 G 0.0684 0.2129 0.7187 151 G 0.0933 0.1667 0.7400 152 F 0.1413 0.2846 0.5741 153 E 0.0667 0.6022 0.3311 154 Q 0.0589 0.7311 0.2100 155 A 0.0528 0.7807 0.1665 156 Q 0.0353 0.8383 0.1263 157 L 0.0161 0.8831 0.1008 158 A 0.0168 0.8615 0.1217 159 Y 0.0218 0.8214 0.1568 160 L 0.0210 0.8368 0.1423 161 E 0.0114 0.8575 0.1311 162 G 0.0115 0.8659 0.1225 163 V 0.0097 0.8918 0.0985 164 K 0.0088 0.9149 0.0764 165 Q 0.0087 0.9197 0.0716 166 S 0.0090 0.9194 0.0716 167 I 0.0091 0.9176 0.0732 168 E 0.0101 0.9132 0.0768 169 A 0.0115 0.8957 0.0928 170 D 0.0175 0.8330 0.1495 171 L 0.0256 0.7061 0.2683 172 G 0.0340 0.4488 0.5172 173 L 0.0760 0.2442 0.6798 174 F 0.0905 0.1170 0.7925 175 K 0.2387 0.0443 0.7171 176 P 0.3793 0.0473 0.5733 177 R 0.5783 0.0403 0.3814 178 R 0.7434 0.0311 0.2255 179 M 0.6750 0.0495 0.2755 180 G 0.6286 0.0467 0.3247 181 H 0.3311 0.0389 0.6300 182 I 0.0614 0.5423 0.3963 183 S 0.0404 0.6468 0.3128 184 L 0.0392 0.7446 0.2162 185 C 0.0444 0.7779 0.1776 186 Q 0.0272 0.8247 0.1481 187 K 0.0333 0.7828 0.1840 188 F 0.0531 0.7049 0.2420 189 Q 0.0654 0.6831 0.2516 190 Q 0.0733 0.6296 0.2972 191 F 0.0960 0.4736 0.4304 192 F 0.1214 0.2541 0.6245 193 G 0.0946 0.2019 0.7035 194 E 0.1281 0.2530 0.6189 195 D 0.1421 0.2194 0.6385 196 T 0.0923 0.4194 0.4883 197 S 0.0684 0.4879 0.4437 198 D 0.0773 0.4435 0.4793 199 F 0.0902 0.4594 0.4504 200 S 0.0596 0.6303 0.3101 201 E 0.0218 0.7770 0.2012 202 E 0.0209 0.8174 0.1617 203 V 0.0270 0.8075 0.1655 204 M 0.0191 0.8625 0.1183 205 E 0.0124 0.8774 0.1102 206 K 0.0126 0.8804 0.1071 207 F 0.0101 0.9001 0.0897 208 R 0.0084 0.9188 0.0729 209 V 0.0083 0.9230 0.0687 210 I 0.0083 0.9210 0.0707 211 L 0.0084 0.9194 0.0722 212 A 0.0083 0.9230 0.0687 213 L 0.0083 0.9231 0.0686 214 V 0.0085 0.9200 0.0715 215 K 0.0088 0.9012 0.0900 216 K 0.0140 0.7727 0.2132 217 R 0.0576 0.2924 0.6501 218 D 0.0577 0.0902 0.8522 219 Y 0.2344 0.0459 0.7197 220 E 0.6112 0.0297 0.3591 221 L 0.7683 0.0110 0.2207 222 D 0.7821 0.0103 0.2076 223 F 0.7734 0.0124 0.2142 224 N 0.5774 0.0398 0.3829 225 T 0.3130 0.1079 0.5791 226 A 0.1554 0.2156 0.6290 227 G 0.1163 0.2629 0.6209 228 L 0.1660 0.2681 0.5660 229 F 0.2196 0.1969 0.5835 230 K 0.2275 0.1616 0.6108 231 P 0.1652 0.2606 0.5743 232 L 0.1401 0.3479 0.5119 233 C 0.1443 0.2295 0.6262 234 G 0.1070 0.1479 0.7451 235 E 0.1870 0.1300 0.6830 236 T 0.2006 0.1500 0.6494 237 Y 0.2385 0.0625 0.6990 238 P 0.1623 0.0951 0.7426 239 P 0.0477 0.6342 0.3181 240 K 0.0113 0.8419 0.1468 241 K 0.0093 0.9089 0.0818 242 I 0.0085 0.9200 0.0715 243 V 0.0084 0.9196 0.0720 244 T 0.0083 0.9224 0.0693 245 L 0.0084 0.9204 0.0713 246 A 0.0086 0.9162 0.0752 247 S 0.0088 0.9003 0.0909 248 E 0.0136 0.8010 0.1854 249 L 0.0624 0.3022 0.6355 250 Q 0.0542 0.0811 0.8646 251 I 0.2371 0.0145 0.7484 252 P 0.3816 0.0287 0.5898 253 F 0.7507 0.0169 0.2323 254 V 0.7644 0.0179 0.2177 255 Y 0.7072 0.0254 0.2674 256 G 0.5695 0.0496 0.3809 257 S 0.2981 0.1018 0.6001 258 D 0.1872 0.2015 0.6113 259 S 0.1143 0.3506 0.5351 260 H 0.1484 0.2257 0.6258 261 G 0.1610 0.1708 0.6682 262 V 0.1178 0.3848 0.4974 263 Q 0.1058 0.4540 0.4401 264 D 0.1333 0.3971 0.4696 265 I 0.1369 0.3283 0.5348 266 G 0.1166 0.2479 0.6355 267 R 0.1151 0.3240 0.5608 268 G 0.1144 0.3111 0.5745 269 Y 0.1355 0.4484 0.4161 270 S 0.1164 0.5630 0.3206 271 T 0.1328 0.5428 0.3244 272 Y 0.1754 0.3723 0.4523 273 C 0.2449 0.2222 0.5329 274 Q 0.2119 0.1669 0.6211 275 K 0.1821 0.1341 0.6839