# This file is the result of combining several RDB files, specifically # T0316.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0316.t2k.stride-ebghtl.rdb (weight 1.24869) # T0316.t2k.str2.rdb (weight 1.54758) # T0316.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 T0316.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0316 # 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 T0316.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 375 # # ============================================ # Comments from T0316.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0316 # 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 T0316.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 375 # # ============================================ # Comments from T0316.t2k.str2.rdb # ============================================ # TARGET T0316 # 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 T0316.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 31.7356 # # ============================================ # Comments from T0316.t2k.alpha.rdb # ============================================ # TARGET T0316 # 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 T0316.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 375 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.4702 0.0247 0.5050 2 R 0.7248 0.0148 0.2604 3 V 0.8281 0.0094 0.1625 4 A 0.8406 0.0076 0.1518 5 R 0.7996 0.0133 0.1870 6 D 0.5052 0.0311 0.4637 7 E 0.0993 0.0633 0.8374 8 D 0.0504 0.0229 0.9267 9 G 0.0561 0.0348 0.9091 10 T 0.4582 0.0119 0.5299 11 V 0.8730 0.0051 0.1220 12 H 0.8942 0.0069 0.0989 13 M 0.9146 0.0054 0.0800 14 L 0.8574 0.0148 0.1278 15 R 0.8234 0.0119 0.1647 16 G 0.6332 0.0254 0.3414 17 V 0.4506 0.0321 0.5173 18 D 0.2449 0.0338 0.7213 19 N 0.0258 0.1544 0.8198 20 G 0.0379 0.1021 0.8600 21 K 0.1043 0.1166 0.7790 22 D 0.2394 0.0896 0.6710 23 Q 0.3957 0.2056 0.3986 24 T 0.6153 0.2223 0.1624 25 Y 0.5956 0.2879 0.1164 26 F 0.5696 0.3041 0.1263 27 L 0.4807 0.3122 0.2071 28 S 0.3360 0.3246 0.3393 29 Q 0.2386 0.2559 0.5055 30 L 0.1839 0.0799 0.7362 31 S 0.0958 0.0623 0.8419 32 Q 0.0059 0.8895 0.1046 33 E 0.0051 0.9123 0.0825 34 Q 0.0054 0.9271 0.0675 35 L 0.0059 0.9290 0.0652 36 Q 0.0067 0.8943 0.0990 37 K 0.0095 0.8084 0.1821 38 T 0.0283 0.6520 0.3197 39 M 0.0567 0.4094 0.5339 40 F 0.0909 0.2092 0.6999 41 P 0.0875 0.1830 0.7295 42 L 0.0505 0.3452 0.6043 43 G 0.0427 0.2922 0.6651 44 H 0.0405 0.3539 0.6056 45 L 0.0648 0.2227 0.7125 46 E 0.0666 0.1510 0.7824 47 K 0.0356 0.5977 0.3667 48 P 0.0065 0.8543 0.1392 49 E 0.0068 0.9273 0.0660 50 V 0.0052 0.9490 0.0458 51 R 0.0049 0.9547 0.0404 52 R 0.0048 0.9602 0.0350 53 L 0.0048 0.9604 0.0348 54 A 0.0047 0.9590 0.0363 55 E 0.0050 0.9524 0.0426 56 E 0.0055 0.9322 0.0623 57 A 0.0420 0.5197 0.4383 58 G 0.0326 0.0314 0.9360 59 L 0.0645 0.0288 0.9067 60 S 0.2215 0.0788 0.6998 61 T 0.3589 0.1784 0.4627 62 A 0.3849 0.1458 0.4693 63 K 0.3023 0.0674 0.6303 64 K 0.1904 0.0680 0.7416 65 K 0.0948 0.2137 0.6915 66 D 0.1125 0.1641 0.7234 67 S 0.2615 0.1102 0.6283 68 T 0.2608 0.0707 0.6685 69 G 0.3488 0.0582 0.5930 70 I 0.6902 0.0302 0.2796 71 C 0.7401 0.0243 0.2355 72 F 0.7368 0.0173 0.2459 73 I 0.5270 0.0252 0.4478 74 G 0.1974 0.0317 0.7710 75 E 0.0666 0.1314 0.8020 76 K 0.0547 0.1657 0.7796 77 N 0.1001 0.2198 0.6801 78 F 0.0220 0.8339 0.1441 79 K 0.0067 0.9134 0.0799 80 N 0.0077 0.9067 0.0856 81 F 0.0184 0.8975 0.0841 82 L 0.0144 0.8779 0.1078 83 S 0.0077 0.8178 0.1745 84 N 0.0153 0.7132 0.2716 85 Y 0.0437 0.4677 0.4886 86 L 0.0641 0.0883 0.8475 87 P 0.0710 0.0406 0.8884 88 A 0.1016 0.0594 0.8390 89 Q 0.1237 0.0344 0.8419 90 P 0.2287 0.0418 0.7295 91 G 0.3655 0.0285 0.6061 92 R 0.6823 0.0090 0.3088 93 M 0.8247 0.0055 0.1698 94 M 0.8389 0.0051 0.1560 95 T 0.4483 0.0110 0.5408 96 V 0.1035 0.1078 0.7887 97 D 0.0519 0.0171 0.9310 98 G 0.0570 0.0269 0.9161 99 R 0.4251 0.0082 0.5667 100 D 0.8785 0.0031 0.1184 101 M 0.8258 0.0175 0.1567 102 G 0.8165 0.0140 0.1695 103 E 0.6758 0.0303 0.2939 104 H 0.5370 0.0417 0.4214 105 A 0.3203 0.0727 0.6070 106 G 0.4138 0.0696 0.5165 107 L 0.6494 0.0585 0.2921 108 M 0.7079 0.0649 0.2272 109 Y 0.7312 0.0664 0.2025 110 Y 0.6766 0.0629 0.2605 111 T 0.5732 0.0726 0.3542 112 I 0.4447 0.2014 0.3539 113 G 0.3647 0.2110 0.4243 114 Q 0.3177 0.2686 0.4137 115 R 0.2888 0.2712 0.4400 116 G 0.1665 0.2558 0.5778 117 G 0.1416 0.1469 0.7114 118 L 0.1944 0.0995 0.7061 119 G 0.2460 0.0634 0.6906 120 I 0.2395 0.1120 0.6485 121 G 0.1761 0.1309 0.6930 122 G 0.1378 0.1080 0.7542 123 Q 0.1136 0.1305 0.7559 124 H 0.0787 0.1438 0.7774 125 G 0.0629 0.1428 0.7942 126 G 0.0661 0.1403 0.7936 127 D 0.0992 0.1160 0.7848 128 N 0.1410 0.0662 0.7928 129 A 0.2006 0.0236 0.7758 130 P 0.3938 0.0180 0.5882 131 W 0.7667 0.0191 0.2142 132 F 0.8839 0.0081 0.1080 133 V 0.9015 0.0057 0.0928 134 V 0.8345 0.0256 0.1398 135 G 0.8297 0.0097 0.1605 136 K 0.6796 0.0154 0.3049 137 D 0.4890 0.0245 0.4865 138 L 0.0922 0.2996 0.6082 139 S 0.0669 0.2428 0.6903 140 K 0.1012 0.1886 0.7102 141 N 0.1883 0.0336 0.7781 142 I 0.7876 0.0068 0.2056 143 L 0.9223 0.0034 0.0743 144 Y 0.9232 0.0033 0.0735 145 V 0.8725 0.0101 0.1174 146 G 0.5691 0.0076 0.4233 147 Q 0.1701 0.0438 0.7862 148 G 0.0344 0.2161 0.7496 149 F 0.0274 0.3619 0.6108 150 Y 0.0403 0.3279 0.6318 151 H 0.0685 0.2825 0.6490 152 D 0.0218 0.5304 0.4478 153 S 0.0375 0.5918 0.3706 154 L 0.0852 0.5614 0.3534 155 M 0.1778 0.4224 0.3999 156 S 0.2107 0.3593 0.4301 157 T 0.1785 0.3708 0.4507 158 S 0.3279 0.2560 0.4162 159 L 0.4785 0.1757 0.3458 160 E 0.5373 0.1358 0.3269 161 A 0.3826 0.2226 0.3949 162 S 0.1968 0.2670 0.5362 163 Q 0.2066 0.2367 0.5567 164 V 0.3626 0.1500 0.4873 165 H 0.4406 0.1131 0.4463 166 F 0.4361 0.1364 0.4275 167 T 0.3956 0.1152 0.4892 168 R 0.2809 0.1022 0.6170 169 E 0.1826 0.0801 0.7373 170 M 0.1347 0.0559 0.8094 171 P 0.0888 0.0633 0.8479 172 E 0.0650 0.1501 0.7849 173 E 0.0558 0.1427 0.8015 174 F 0.1162 0.0618 0.8220 175 T 0.2616 0.0396 0.6988 176 L 0.5900 0.0173 0.3927 177 E 0.8265 0.0051 0.1684 178 C 0.8919 0.0037 0.1044 179 T 0.9192 0.0032 0.0776 180 A 0.9218 0.0033 0.0748 181 K 0.9181 0.0035 0.0784 182 F 0.9031 0.0033 0.0936 183 R 0.8160 0.0102 0.1738 184 Y 0.6864 0.0141 0.2996 185 R 0.3397 0.0331 0.6272 186 Q 0.1366 0.0272 0.8363 187 P 0.1028 0.0386 0.8587 188 D 0.1276 0.0394 0.8330 189 S 0.2447 0.0145 0.7408 190 K 0.5513 0.0089 0.4398 191 V 0.8432 0.0053 0.1514 192 T 0.9197 0.0033 0.0771 193 V 0.9210 0.0033 0.0757 194 H 0.9115 0.0043 0.0842 195 V 0.8725 0.0078 0.1197 196 K 0.5484 0.0252 0.4264 197 G 0.0588 0.0425 0.8987 198 E 0.0688 0.0670 0.8642 199 K 0.6031 0.0209 0.3760 200 T 0.8922 0.0035 0.1043 201 E 0.9216 0.0035 0.0749 202 V 0.9264 0.0031 0.0705 203 I 0.8821 0.0067 0.1112 204 F 0.7416 0.0077 0.2507 205 A 0.3240 0.0415 0.6345 206 E 0.1749 0.0220 0.8032 207 P 0.2049 0.0628 0.7323 208 Q 0.4445 0.0673 0.4882 209 R 0.6439 0.0596 0.2965 210 A 0.6760 0.0350 0.2889 211 I 0.5840 0.0227 0.3933 212 T 0.2541 0.0227 0.7232 213 P 0.0634 0.0667 0.8699 214 G 0.0806 0.0315 0.8879 215 Q 0.5133 0.0117 0.4750 216 A 0.8567 0.0042 0.1391 217 V 0.9190 0.0035 0.0775 218 V 0.9250 0.0035 0.0715 219 F 0.9182 0.0039 0.0779 220 Y 0.8689 0.0082 0.1229 221 D 0.3404 0.0298 0.6298 222 G 0.0454 0.0506 0.9041 223 E 0.1772 0.0649 0.7579 224 E 0.7649 0.0190 0.2161 225 C 0.8235 0.0250 0.1514 226 L 0.7409 0.0492 0.2099 227 G 0.5193 0.0746 0.4061 228 G 0.3313 0.2262 0.4425 229 G 0.3579 0.3372 0.3050 230 L 0.3280 0.4936 0.1784 231 I 0.1873 0.6861 0.1266 232 D 0.1578 0.6886 0.1536 233 N 0.1634 0.6449 0.1918 234 A 0.1429 0.6167 0.2405 235 Y 0.1755 0.5057 0.3188 236 R 0.1096 0.4109 0.4795 237 D 0.0535 0.1947 0.7518 238 G 0.0405 0.1023 0.8571 239 Q 0.1834 0.1260 0.6905 240 V 0.4570 0.1168 0.4262 241 C 0.4516 0.1264 0.4220 242 Q 0.4644 0.1096 0.4260 243 Y 0.3689 0.0889 0.5422 244 I 0.1205 0.0341 0.8454