# This file is the result of combining several RDB files, specifically # T0287.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0287.t2k.stride-ebghtl.rdb (weight 1.24869) # T0287.t2k.str2.rdb (weight 1.54758) # T0287.t2k.alpha.rdb (weight 0.659012) # 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 T0287.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0287 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0287.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1 # # ============================================ # Comments from T0287.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0287 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0287.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1 # # ============================================ # Comments from T0287.t2k.str2.rdb # ============================================ # TARGET T0287 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0287.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 1 # # ============================================ # Comments from T0287.t2k.alpha.rdb # ============================================ # TARGET T0287 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0287.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0520 0.1123 0.8357 2 S 0.0491 0.2546 0.6963 3 N 0.0314 0.3654 0.6031 4 N 0.0359 0.4610 0.5032 5 M 0.0271 0.7363 0.2366 6 R 0.0211 0.8181 0.1608 7 K 0.0359 0.8232 0.1409 8 L 0.0520 0.8477 0.1003 9 F 0.0694 0.8206 0.1100 10 S 0.0512 0.8349 0.1139 11 M 0.0431 0.8268 0.1301 12 I 0.0634 0.7657 0.1709 13 A 0.0658 0.6220 0.3122 14 D 0.0609 0.3702 0.5689 15 S 0.0436 0.3523 0.6041 16 K 0.0274 0.4896 0.4830 17 D 0.0310 0.5376 0.4314 18 K 0.0263 0.6697 0.3040 19 K 0.0205 0.7533 0.2261 20 E 0.0212 0.8305 0.1484 21 K 0.0259 0.8465 0.1276 22 L 0.0283 0.8499 0.1218 23 I 0.0273 0.8698 0.1029 24 E 0.0275 0.8601 0.1124 25 S 0.0215 0.8396 0.1389 26 L 0.0290 0.7592 0.2118 27 Q 0.0353 0.7016 0.2631 28 E 0.0285 0.7219 0.2496 29 N 0.0374 0.5903 0.3723 30 E 0.0531 0.5710 0.3759 31 L 0.0921 0.5210 0.3869 32 L 0.0731 0.4289 0.4980 33 N 0.0889 0.2584 0.6527 34 T 0.0514 0.3421 0.6065 35 D 0.0379 0.4748 0.4873 36 E 0.0275 0.6596 0.3128 37 K 0.0280 0.7240 0.2481 38 K 0.0286 0.7500 0.2214 39 K 0.0655 0.7348 0.1997 40 I 0.0476 0.8133 0.1391 41 I 0.0315 0.8540 0.1145 42 D 0.0209 0.8769 0.1022 43 Q 0.0153 0.8880 0.0966 44 I 0.0220 0.8683 0.1097 45 K 0.0269 0.8336 0.1394 46 T 0.0302 0.7904 0.1794 47 M 0.0178 0.8498 0.1324 48 H 0.0145 0.8704 0.1151 49 D 0.0123 0.8904 0.0974 50 F 0.0095 0.9035 0.0870 51 F 0.0148 0.8801 0.1051 52 K 0.0128 0.8652 0.1220 53 Q 0.0174 0.8192 0.1634 54 M 0.0358 0.7352 0.2290 55 H 0.0535 0.5529 0.3936 56 T 0.0438 0.4457 0.5105 57 N 0.0458 0.3127 0.6414 58 K 0.0345 0.4718 0.4938 59 G 0.0286 0.5768 0.3946 60 A 0.0275 0.7488 0.2238 61 L 0.0149 0.8645 0.1206 62 D 0.0109 0.8966 0.0925 63 K 0.0086 0.9221 0.0693 64 V 0.0085 0.9269 0.0646 65 L 0.0084 0.9216 0.0699 66 R 0.0083 0.9037 0.0881 67 N 0.0111 0.8289 0.1599 68 Y 0.0114 0.8045 0.1841 69 M 0.0158 0.7730 0.2112 70 K 0.0097 0.8349 0.1554 71 D 0.0143 0.8037 0.1820 72 Y 0.0176 0.8583 0.1241 73 R 0.0156 0.8928 0.0916 74 A 0.0233 0.8915 0.0852 75 V 0.0285 0.8921 0.0794 76 I 0.0402 0.8654 0.0944 77 K 0.0410 0.8284 0.1306 78 S 0.0480 0.7244 0.2275 79 I 0.0756 0.4817 0.4428 80 G 0.0817 0.1937 0.7246 81 V 0.0708 0.3390 0.5902 82 D 0.0527 0.4690 0.4783 83 K 0.0382 0.6410 0.3208 84 F 0.0411 0.7385 0.2204 85 K 0.0400 0.8133 0.1468 86 K 0.0592 0.8088 0.1320 87 V 0.0738 0.8201 0.1060 88 Y 0.0666 0.8283 0.1051 89 R 0.0616 0.8150 0.1233 90 L 0.0365 0.8189 0.1447 91 L 0.0408 0.7493 0.2099 92 E 0.0365 0.6788 0.2847 93 S 0.0252 0.7273 0.2474 94 E 0.0248 0.7406 0.2346 95 T 0.0258 0.8077 0.1665 96 M 0.0180 0.8746 0.1074 97 E 0.0199 0.8849 0.0952 98 L 0.0206 0.9031 0.0763 99 L 0.0201 0.9105 0.0694 100 H 0.0187 0.9083 0.0729 101 A 0.0154 0.9005 0.0841 102 I 0.0234 0.8645 0.1121 103 A 0.0344 0.7641 0.2015 104 E 0.0410 0.5588 0.4001 105 N 0.0743 0.1380 0.7878 106 P 0.0259 0.2944 0.6798 107 N 0.0384 0.2873 0.6743 108 F 0.1247 0.3807 0.4946 109 L 0.2183 0.3610 0.4207 110 F 0.2144 0.4207 0.3649 111 S 0.1239 0.4599 0.4162 112 K 0.0948 0.4666 0.4386 113 F 0.0946 0.3977 0.5077 114 D 0.0871 0.3767 0.5361 115 R 0.0586 0.5614 0.3801 116 S 0.0814 0.5711 0.3475 117 I 0.1235 0.5988 0.2777 118 L 0.1688 0.5412 0.2901 119 G 0.2295 0.4714 0.2991 120 I 0.2893 0.4662 0.2445 121 F 0.3043 0.4033 0.2924 122 L 0.2388 0.3632 0.3980 123 P 0.1487 0.3732 0.4781 124 F 0.1498 0.3436 0.5066 125 F 0.2017 0.2633 0.5350 126 S 0.1216 0.1923 0.6862 127 K 0.1115 0.1652 0.7234 128 P 0.1912 0.2100 0.5988 129 I 0.4500 0.2155 0.3346 130 M 0.5854 0.1659 0.2488 131 F 0.6055 0.1564 0.2382 132 K 0.5935 0.1460 0.2605 133 M 0.5265 0.1492 0.3242 134 S 0.4805 0.1501 0.3694 135 I 0.3222 0.3302 0.3475 136 R 0.2793 0.3707 0.3500 137 E 0.2537 0.3250 0.4212 138 M 0.2109 0.2858 0.5033 139 D 0.1579 0.2737 0.5684 140 S 0.1796 0.3239 0.4966 141 Q 0.2856 0.3336 0.3807 142 I 0.4720 0.2348 0.2932 143 E 0.5176 0.2384 0.2440 144 L 0.4665 0.2532 0.2803 145 Y 0.2564 0.2235 0.5200 146 G 0.1710 0.1651 0.6639 147 T 0.1283 0.1496 0.7222 148 N 0.1144 0.0986 0.7870 149 L 0.1399 0.1027 0.7574 150 P 0.1886 0.1525 0.6589 151 L 0.3542 0.2697 0.3761 152 L 0.5259 0.2367 0.2374 153 K 0.5969 0.2250 0.1781 154 L 0.6978 0.1658 0.1364 155 F 0.7315 0.1388 0.1297 156 V 0.7342 0.1114 0.1544 157 M 0.5924 0.1226 0.2849 158 T 0.2974 0.1154 0.5872 159 D 0.0972 0.2514 0.6514 160 E 0.0576 0.4399 0.5025 161 E 0.0988 0.5056 0.3956 162 V 0.1897 0.4540 0.3564 163 N 0.2091 0.4236 0.3674 164 F 0.1856 0.5452 0.2692 165 Y 0.1754 0.5556 0.2690 166 A 0.1430 0.5384 0.3186 167 N 0.1178 0.4331 0.4491 168 L 0.0832 0.5994 0.3175 169 K 0.0862 0.6337 0.2802 170 T 0.0766 0.6668 0.2566 171 I 0.0527 0.7545 0.1929 172 E 0.0394 0.7817 0.1789 173 Q 0.0400 0.7444 0.2156 174 Y 0.0363 0.7257 0.2380 175 N 0.0310 0.7298 0.2392 176 D 0.0166 0.8423 0.1411 177 Y 0.0161 0.8702 0.1137 178 V 0.0175 0.8934 0.0890 179 R 0.0110 0.9106 0.0784 180 D 0.0126 0.9047 0.0826 181 L 0.0121 0.9090 0.0789 182 L 0.0200 0.8680 0.1120 183 M 0.0266 0.8110 0.1624 184 K 0.0490 0.6700 0.2810 185 F 0.1005 0.4716 0.4280 186 D 0.1085 0.3448 0.5467 187 L 0.0158 0.8305 0.1537 188 E 0.0113 0.8697 0.1190 189 K 0.0136 0.8821 0.1044 190 Y 0.0164 0.8746 0.1090 191 M 0.0261 0.8351 0.1388 192 K 0.0236 0.8196 0.1568 193 E 0.0265 0.7696 0.2039 194 K 0.0434 0.5755 0.3811 195 G 0.0451 0.2168 0.7381 196 V 0.0947 0.1811 0.7242 197 Q 0.1185 0.1888 0.6927 198 N 0.0979 0.1319 0.7702 199 A 0.0520 0.0913 0.8567