# This file is the result of combining several RDB files, specifically # T0301.t06.dssp-ebghstl.rdb (weight 1.53986) # T0301.t06.stride-ebghtl.rdb (weight 1.24869) # T0301.t06.str2.rdb (weight 1.54758) # T0301.t06.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 T0301.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0301 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0301.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 15.9436 # # ============================================ # Comments from T0301.t06.stride-ebghtl.rdb # ============================================ # TARGET T0301 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0301.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 15.9436 # # ============================================ # Comments from T0301.t06.str2.rdb # ============================================ # TARGET T0301 # 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 T0301.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 15.9436 # # ============================================ # Comments from T0301.t06.alpha.rdb # ============================================ # TARGET T0301 # Using neural net t04-2621-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 T0301.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 15.9436 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 F 0.0892 0.0476 0.8632 2 L 0.1637 0.0306 0.8056 3 D 0.1288 0.0120 0.8592 4 P 0.0731 0.0918 0.8351 5 S 0.0643 0.0827 0.8529 6 D 0.0667 0.1031 0.8302 7 D 0.0724 0.0966 0.8310 8 G 0.0661 0.1068 0.8271 9 E 0.0964 0.1463 0.7573 10 D 0.1974 0.1448 0.6578 11 G 0.1812 0.2154 0.6035 12 G 0.1638 0.2391 0.5971 13 A 0.3435 0.1728 0.4837 14 I 0.4265 0.1344 0.4391 15 F 0.2463 0.0494 0.7043 16 P 0.1372 0.0829 0.7800 17 T 0.1136 0.0384 0.8480 18 G 0.0921 0.0637 0.8442 19 N 0.1965 0.0541 0.7494 20 L 0.3592 0.1522 0.4886 21 V 0.4685 0.1199 0.4117 22 D 0.4747 0.1410 0.3843 23 D 0.6699 0.0786 0.2515 24 L 0.7722 0.0262 0.2016 25 E 0.7406 0.0186 0.2409 26 V 0.4780 0.0316 0.4904 27 P 0.1510 0.0873 0.7617 28 G 0.0808 0.0749 0.8443 29 V 0.1591 0.0619 0.7790 30 G 0.2214 0.0394 0.7392 31 T 0.5055 0.0235 0.4710 32 F 0.7341 0.0067 0.2593 33 K 0.8286 0.0060 0.1654 34 A 0.8875 0.0044 0.1081 35 T 0.9021 0.0054 0.0925 36 M 0.9024 0.0069 0.0907 37 I 0.8468 0.0173 0.1359 38 N 0.6150 0.0361 0.3489 39 A 0.2598 0.0896 0.6505 40 G 0.1727 0.0872 0.7401 41 I 0.1700 0.0998 0.7302 42 P 0.2844 0.1083 0.6073 43 T 0.6749 0.0860 0.2391 44 V 0.8614 0.0469 0.0916 45 F 0.8755 0.0344 0.0901 46 V 0.8025 0.0421 0.1554 47 N 0.4862 0.0310 0.4828 48 A 0.0445 0.6765 0.2790 49 E 0.0175 0.7836 0.1989 50 E 0.0347 0.7845 0.1809 51 I 0.1024 0.4557 0.4418 52 G 0.0646 0.1314 0.8039 53 Y 0.1141 0.1120 0.7739 54 R 0.1023 0.1133 0.7844 55 G 0.0862 0.1718 0.7421 56 T 0.1258 0.2358 0.6384 57 E 0.1913 0.2757 0.5330 58 L 0.0931 0.3947 0.5122 59 R 0.0174 0.8402 0.1423 60 E 0.0113 0.8793 0.1095 61 E 0.0148 0.8475 0.1377 62 I 0.0478 0.6118 0.3403 63 N 0.0459 0.2905 0.6636 64 G 0.0417 0.1564 0.8020 65 D 0.0851 0.0317 0.8832 66 P 0.0052 0.9192 0.0755 67 Q 0.0049 0.9237 0.0713 68 Q 0.0053 0.9465 0.0482 69 L 0.0048 0.9540 0.0412 70 A 0.0048 0.9514 0.0438 71 R 0.0050 0.9505 0.0446 72 F 0.0047 0.9580 0.0373 73 E 0.0047 0.9607 0.0347 74 R 0.0047 0.9611 0.0342 75 I 0.0047 0.9611 0.0343 76 R 0.0047 0.9602 0.0351 77 V 0.0047 0.9611 0.0342 78 A 0.0047 0.9598 0.0355 79 G 0.0047 0.9589 0.0364 80 A 0.0047 0.9579 0.0374 81 L 0.0051 0.9555 0.0394 82 R 0.0074 0.9348 0.0579 83 M 0.0355 0.7109 0.2536 84 G 0.0336 0.1747 0.7917 85 L 0.0575 0.0931 0.8494 86 I 0.1045 0.0893 0.8062 87 K 0.0749 0.0749 0.8502 88 T 0.0745 0.0227 0.9029 89 P 0.0066 0.8587 0.1347 90 E 0.0054 0.9032 0.0914 91 E 0.0075 0.9050 0.0875 92 A 0.0147 0.8768 0.1086 93 A 0.0173 0.7516 0.2311 94 T 0.0237 0.5802 0.3961 95 R 0.0547 0.3626 0.5826 96 Q 0.0720 0.2005 0.7275 97 H 0.1347 0.0835 0.7818 98 T 0.1994 0.0185 0.7820 99 P 0.1727 0.0140 0.8134 100 K 0.7228 0.0135 0.2638 101 I 0.9085 0.0048 0.0867 102 A 0.9147 0.0057 0.0796 103 F 0.9124 0.0050 0.0826 104 V 0.7973 0.0106 0.1921 105 A 0.3890 0.0148 0.5962 106 P 0.1430 0.0169 0.8401 107 P 0.0857 0.1817 0.7326 108 R 0.0597 0.3486 0.5916 109 D 0.0937 0.3923 0.5140 110 Y 0.1413 0.4036 0.4551 111 R 0.2253 0.3486 0.4261 112 T 0.2170 0.2867 0.4962 113 A 0.1643 0.2258 0.6099 114 S 0.0893 0.1245 0.7862 115 G 0.1044 0.0753 0.8203 116 K 0.3504 0.0806 0.5690 117 L 0.6686 0.0653 0.2661 118 V 0.5299 0.1235 0.3466 119 A 0.4048 0.1413 0.4539 120 A 0.1181 0.2742 0.6077 121 G 0.0737 0.1644 0.7620 122 D 0.1641 0.1466 0.6894 123 I 0.3182 0.1169 0.5649 124 D 0.3990 0.1033 0.4976 125 L 0.7601 0.0910 0.1489 126 L 0.8132 0.0937 0.0931 127 V 0.8327 0.0853 0.0820 128 R 0.7559 0.1308 0.1133 129 A 0.6476 0.1624 0.1900 130 L 0.4261 0.2052 0.3687 131 S 0.2712 0.1224 0.6064 132 M 0.0646 0.2114 0.7240 133 G 0.0365 0.1426 0.8209 134 K 0.0795 0.1775 0.7430 135 L 0.1055 0.2728 0.6217 136 H 0.1045 0.3311 0.5644 137 H 0.0590 0.4605 0.4806 138 A 0.0894 0.5776 0.3331 139 M 0.0766 0.6327 0.2907 140 M 0.0381 0.7808 0.1812 141 G 0.0138 0.9024 0.0838 142 T 0.0056 0.9474 0.0470 143 A 0.0047 0.9586 0.0367 144 A 0.0047 0.9597 0.0356 145 V 0.0047 0.9602 0.0352 146 A 0.0047 0.9604 0.0349 147 I 0.0047 0.9597 0.0355 148 G 0.0052 0.9562 0.0386 149 T 0.0058 0.9439 0.0503 150 A 0.0077 0.9120 0.0803 151 A 0.0221 0.8221 0.1558 152 A 0.0559 0.5877 0.3563 153 I 0.0662 0.1768 0.7570 154 P 0.0286 0.2147 0.7566 155 G 0.0454 0.1581 0.7964 156 T 0.2183 0.3217 0.4600 157 L 0.2584 0.5527 0.1889 158 V 0.1214 0.7537 0.1248 159 N 0.1254 0.7242 0.1504 160 L 0.0930 0.7405 0.1665 161 A 0.0913 0.6574 0.2513 162 A 0.0858 0.4615 0.4527 163 G 0.0728 0.1667 0.7606 164 G 0.0620 0.1066 0.8314 165 G 0.0684 0.0894 0.8422 166 E 0.1400 0.1165 0.7435 167 R 0.1973 0.1102 0.6925 168 S 0.2436 0.0488 0.7076 169 A 0.6929 0.0201 0.2870 170 V 0.8642 0.0073 0.1285 171 R 0.8911 0.0072 0.1017 172 F 0.8067 0.0203 0.1731 173 G 0.4222 0.0248 0.5530 174 H 0.1861 0.0183 0.7956 175 P 0.1586 0.0768 0.7646 176 S 0.1640 0.0593 0.7767 177 G 0.3115 0.0348 0.6537 178 T 0.6652 0.0199 0.3150 179 L 0.8771 0.0072 0.1157 180 R 0.9109 0.0059 0.0832 181 V 0.9080 0.0074 0.0846 182 G 0.8892 0.0085 0.1023 183 A 0.8692 0.0076 0.1232 184 E 0.8886 0.0080 0.1034 185 A 0.8612 0.0147 0.1241 186 S 0.7228 0.0241 0.2531 187 Q 0.4277 0.1059 0.4664 188 A 0.2263 0.1197 0.6540 189 N 0.0830 0.0567 0.8603 190 G 0.0741 0.0429 0.8831 191 E 0.3172 0.0443 0.6386 192 W 0.6932 0.0126 0.2942 193 T 0.7810 0.0185 0.2005 194 V 0.8294 0.0211 0.1495 195 T 0.6232 0.1117 0.2652 196 K 0.6297 0.2386 0.1317 197 A 0.5173 0.3817 0.1010 198 I 0.3997 0.5255 0.0748 199 M 0.2705 0.6484 0.0811 200 S 0.2206 0.6701 0.1093 201 R 0.0949 0.7350 0.1702 202 S 0.0775 0.7407 0.1818 203 A 0.0151 0.9237 0.0612 204 R 0.0185 0.9120 0.0695 205 I 0.0268 0.9086 0.0646 206 L 0.0383 0.8682 0.0935 207 M 0.1301 0.6558 0.2141 208 E 0.1643 0.4185 0.4171 209 G 0.2321 0.1716 0.5963 210 W 0.5423 0.0961 0.3616 211 V 0.7339 0.0393 0.2268 212 R 0.7150 0.0268 0.2582 213 V 0.4938 0.0172 0.4890 214 P 0.2068 0.0413 0.7520 215 G 0.0676 0.1840 0.7484 216 D 0.0822 0.2126 0.7051 217 A 0.1141 0.2314 0.6545 218 F 0.0873 0.0853 0.8274