# This file is the result of combining several RDB files, specifically # T0489.t06.str2.rdb (weight 1.54425) # T0489.t06.str4.rdb (weight 0.924988) # T0489.t06.pb.rdb (weight 0.789901) # T0489.t06.bys.rdb (weight 0.748322) # T0489.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 T0489.t06.str2.rdb # ============================================ # TARGET T0489 # 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 T0489.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 48.473 # # ============================================ # Comments from T0489.t06.str4.rdb # ============================================ # TARGET T0489 # 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 T0489.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 48.473 # # ============================================ # Comments from T0489.t06.pb.rdb # ============================================ # TARGET T0489 # 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 T0489.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 48.473 # # ============================================ # Comments from T0489.t06.bys.rdb # ============================================ # TARGET T0489 # 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 T0489.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 48.473 # # ============================================ # Comments from T0489.t06.alpha.rdb # ============================================ # TARGET T0489 # 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 T0489.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 48.473 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3168 0.1819 0.5013 2 M 0.3376 0.1655 0.4970 3 F 0.3521 0.1551 0.4928 4 K 0.3226 0.1391 0.5383 5 W 0.2642 0.0956 0.6402 6 P 0.1445 0.3323 0.5232 7 W 0.1115 0.4776 0.4108 8 K 0.1407 0.4505 0.4088 9 A 0.1436 0.4151 0.4413 10 D 0.1319 0.3848 0.4832 11 D 0.0813 0.4874 0.4313 12 E 0.0651 0.4878 0.4471 13 S 0.0964 0.3069 0.5966 14 G 0.0943 0.2043 0.7014 15 N 0.1301 0.1619 0.7080 16 A 0.1819 0.1259 0.6922 17 E 0.1585 0.1577 0.6838 18 M 0.1860 0.1624 0.6516 19 P 0.1031 0.3841 0.5128 20 W 0.0237 0.7729 0.2034 21 E 0.0142 0.8590 0.1267 22 Q 0.0145 0.8634 0.1221 23 A 0.0279 0.7958 0.1763 24 L 0.0472 0.6661 0.2867 25 A 0.0725 0.4964 0.4311 26 I 0.1545 0.3023 0.5432 27 P 0.0925 0.5184 0.3891 28 V 0.0593 0.7253 0.2154 29 L 0.0459 0.7586 0.1955 30 A 0.0347 0.6501 0.3152 31 H 0.0576 0.3778 0.5646 32 L 0.1957 0.0841 0.7202 33 S 0.1570 0.0337 0.8094 34 S 0.0159 0.6941 0.2901 35 T 0.0109 0.8343 0.1548 36 E 0.0117 0.8890 0.0994 37 Q 0.0091 0.9160 0.0750 38 H 0.0084 0.9198 0.0719 39 K 0.0084 0.9212 0.0704 40 L 0.0083 0.9217 0.0699 41 T 0.0083 0.9219 0.0698 42 Q 0.0083 0.9242 0.0675 43 M 0.0083 0.9243 0.0674 44 A 0.0083 0.9239 0.0678 45 A 0.0083 0.9230 0.0687 46 R 0.0083 0.9226 0.0690 47 F 0.0085 0.9196 0.0719 48 L 0.0097 0.9026 0.0877 49 Q 0.0127 0.8547 0.1327 50 Q 0.0293 0.7442 0.2266 51 K 0.1122 0.5815 0.3064 52 R 0.1743 0.4784 0.3473 53 L 0.3349 0.2924 0.3728 54 V 0.3932 0.2433 0.3635 55 A 0.4013 0.1916 0.4071 56 L 0.2913 0.2080 0.5007 57 Q 0.1434 0.1400 0.7166 58 G 0.0957 0.0975 0.8068 59 L 0.3352 0.0306 0.6342 60 E 0.5233 0.0270 0.4497 61 L 0.5115 0.0351 0.4535 62 T 0.2467 0.0311 0.7221 63 P 0.0345 0.6567 0.3089 64 L 0.0324 0.7053 0.2624 65 H 0.0540 0.8080 0.1380 66 Q 0.0465 0.8463 0.1072 67 A 0.0392 0.8742 0.0866 68 R 0.0299 0.8939 0.0762 69 I 0.0256 0.8964 0.0780 70 A 0.0238 0.9003 0.0759 71 M 0.0179 0.9045 0.0776 72 L 0.0193 0.8884 0.0924 73 F 0.0336 0.8372 0.1292 74 C 0.0424 0.7926 0.1649 75 L 0.0857 0.7357 0.1786 76 P 0.0561 0.7602 0.1837 77 V 0.0586 0.7354 0.2061 78 L 0.0701 0.6705 0.2595 79 E 0.1226 0.4522 0.4252 80 L 0.1325 0.2403 0.6272 81 G 0.1099 0.1632 0.7268 82 I 0.1197 0.4133 0.4671 83 E 0.1215 0.4987 0.3799 84 W 0.1613 0.4683 0.3704 85 L 0.1910 0.3155 0.4935 86 D 0.0919 0.3731 0.5350 87 G 0.0653 0.2061 0.7286 88 F 0.2856 0.0734 0.6410 89 H 0.4112 0.0650 0.5239 90 E 0.7671 0.0138 0.2191 91 V 0.7666 0.0072 0.2262 92 L 0.7933 0.0065 0.2002 93 I 0.7532 0.0084 0.2384 94 Y 0.6373 0.0118 0.3509 95 P 0.3492 0.0374 0.6134 96 A 0.2659 0.0515 0.6826 97 P 0.2320 0.1865 0.5815 98 F 0.4092 0.1244 0.4664 99 I 0.5505 0.0574 0.3921 100 V 0.4447 0.0447 0.5106 101 D 0.3130 0.0830 0.6039 102 D 0.2299 0.1912 0.5789 103 E 0.3015 0.2133 0.4852 104 W 0.3443 0.1977 0.4580 105 E 0.3001 0.2290 0.4709 106 D 0.2246 0.2194 0.5560 107 D 0.1421 0.3397 0.5183 108 I 0.1425 0.2075 0.6500 109 G 0.1820 0.1029 0.7151 110 L 0.4339 0.0614 0.5047 111 V 0.5606 0.0664 0.3730 112 H 0.5158 0.0990 0.3852 113 N 0.4228 0.1870 0.3902 114 Q 0.3812 0.2478 0.3710 115 R 0.4550 0.2117 0.3333 116 V 0.4859 0.2135 0.3006 117 V 0.4337 0.2566 0.3098 118 Q 0.4040 0.2380 0.3580 119 S 0.2986 0.2035 0.4979 120 G 0.2312 0.1365 0.6323 121 Q 0.3634 0.1562 0.4804 122 S 0.3814 0.1733 0.4453 123 W 0.2375 0.2276 0.5349 124 Q 0.1640 0.2356 0.6003 125 Q 0.1581 0.1432 0.6987 126 G 0.2549 0.0482 0.6969 127 P 0.3784 0.0252 0.5964 128 V 0.7487 0.0139 0.2374 129 V 0.7537 0.0126 0.2337 130 L 0.7341 0.0134 0.2525 131 N 0.4592 0.0132 0.5276 132 W 0.1061 0.4525 0.4414 133 L 0.0449 0.6963 0.2588 134 D 0.0490 0.7389 0.2121 135 I 0.0500 0.7525 0.1974 136 Q 0.0481 0.7087 0.2432 137 D 0.0739 0.5568 0.3693 138 S 0.1181 0.3674 0.5145 139 F 0.1647 0.2450 0.5903 140 D 0.1468 0.2028 0.6504 141 A 0.0669 0.3453 0.5877 142 S 0.0621 0.2239 0.7140 143 G 0.0664 0.1200 0.8136 144 F 0.2666 0.0771 0.6563 145 N 0.4176 0.1040 0.4784 146 L 0.5874 0.1528 0.2598 147 V 0.5463 0.2540 0.1997 148 V 0.3874 0.4591 0.1536 149 H 0.1596 0.6909 0.1495 150 E 0.0476 0.8297 0.1227 151 V 0.0234 0.8664 0.1102 152 A 0.0184 0.8693 0.1123 153 H 0.0143 0.8843 0.1014 154 K 0.0216 0.8582 0.1202 155 L 0.0532 0.7534 0.1934 156 D 0.0611 0.6568 0.2821 157 T 0.0537 0.6319 0.3143 158 R 0.0592 0.4882 0.4526 159 N 0.0838 0.1862 0.7300 160 G 0.0797 0.1216 0.7986 161 D 0.1667 0.1860 0.6473 162 R 0.1915 0.2757 0.5329 163 A 0.1545 0.2933 0.5522 164 S 0.1402 0.1752 0.6846 165 G 0.1053 0.1130 0.7817 166 V 0.2680 0.0401 0.6919 167 P 0.2989 0.0517 0.6493 168 L 0.3106 0.0729 0.6166 169 I 0.2993 0.0454 0.6553 170 P 0.2048 0.0756 0.7196 171 L 0.0941 0.4003 0.5056 172 R 0.1054 0.4713 0.4232 173 E 0.1264 0.4535 0.4201 174 V 0.0888 0.5910 0.3201 175 A 0.0414 0.6974 0.2613 176 G 0.0320 0.7417 0.2263 177 W 0.0215 0.8311 0.1474 178 E 0.0105 0.8972 0.0923 179 H 0.0088 0.9118 0.0795 180 D 0.0092 0.9054 0.0854 181 L 0.0097 0.9079 0.0824 182 H 0.0085 0.9161 0.0754 183 A 0.0084 0.9179 0.0737 184 A 0.0087 0.9089 0.0824 185 M 0.0097 0.9077 0.0826 186 N 0.0087 0.8993 0.0920 187 N 0.0092 0.8853 0.1055 188 I 0.0121 0.8825 0.1054 189 Q 0.0096 0.9059 0.0845 190 D 0.0093 0.9023 0.0884 191 E 0.0122 0.8783 0.1095 192 I 0.0228 0.8624 0.1147 193 D 0.0195 0.8526 0.1279 194 L 0.0319 0.7301 0.2380 195 V 0.0739 0.4169 0.5092 196 G 0.0615 0.2226 0.7159 197 E 0.1094 0.2460 0.6446 198 S 0.1693 0.2217 0.6090 199 A 0.1433 0.3241 0.5325 200 A 0.1632 0.3204 0.5164 201 S 0.2185 0.2458 0.5358 202 I 0.2931 0.1822 0.5247 203 D 0.2281 0.1350 0.6369 204 A 0.0396 0.6285 0.3319 205 Y 0.0503 0.5751 0.3747 206 A 0.0923 0.5365 0.3712 207 A 0.1351 0.3979 0.4669 208 T 0.1915 0.2420 0.5665 209 D 0.1608 0.1178 0.7214 210 P 0.0150 0.6889 0.2960 211 A 0.0147 0.7681 0.2172 212 E 0.0202 0.8766 0.1032 213 C 0.0272 0.8784 0.0944 214 F 0.0498 0.8470 0.1031 215 A 0.0905 0.7948 0.1148 216 V 0.1276 0.7504 0.1220 217 L 0.1621 0.6817 0.1562 218 S 0.0861 0.7441 0.1698 219 E 0.0683 0.7624 0.1693 220 Y 0.0797 0.7119 0.2084 221 F 0.1009 0.6090 0.2902 222 F 0.1077 0.5251 0.3673 223 S 0.1489 0.3979 0.4533 224 A 0.1886 0.1843 0.6271 225 P 0.0544 0.4864 0.4592 226 E 0.0197 0.7105 0.2698 227 L 0.0234 0.7088 0.2677 228 F 0.0552 0.5813 0.3635 229 A 0.0541 0.6107 0.3352 230 P 0.0181 0.6498 0.3322 231 R 0.0290 0.5740 0.3970 232 F 0.0505 0.4787 0.4709 233 P 0.0100 0.8648 0.1252 234 A 0.0083 0.9194 0.0723 235 L 0.0083 0.9227 0.0690 236 W 0.0083 0.9226 0.0691 237 Q 0.0083 0.9242 0.0675 238 R 0.0083 0.9220 0.0697 239 F 0.0083 0.9222 0.0695 240 C 0.0084 0.9158 0.0758 241 H 0.0086 0.9099 0.0816 242 F 0.0123 0.8501 0.1376 243 Y 0.0206 0.7482 0.2313 244 R 0.0334 0.6124 0.3543 245 Q 0.1105 0.4544 0.4351 246 D 0.1607 0.1345 0.7048 247 P 0.0169 0.6792 0.3039 248 L 0.0151 0.7680 0.2169 249 A 0.0240 0.8156 0.1604 250 R 0.0435 0.7567 0.1998 251 R 0.0771 0.6379 0.2851 252 R 0.0815 0.6020 0.3165 253 E 0.0694 0.5465 0.3841 254 N 0.0789 0.3370 0.5841 255 G 0.0812 0.2476 0.6712 256 L 0.1736 0.1923 0.6342 257 Q 0.1972 0.1758 0.6270 258 D 0.1741 0.1537 0.6722 259 E 0.1061 0.2826 0.6114 260 G 0.1121 0.2558 0.6321 261 D 0.1747 0.2269 0.5983 262 R 0.2149 0.2375 0.5476 263 R 0.2244 0.2278 0.5478 264 I 0.2810 0.1718 0.5472 265 V 0.2905 0.1482 0.5613 266 H 0.2650 0.1305 0.6045