# This file is the result of combining several RDB files, specifically # T0301.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0301.t2k.stride-ebghtl.rdb (weight 1.24869) # T0301.t2k.str2.rdb (weight 1.54758) # T0301.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 T0301.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0301 # 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 T0301.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 112 # # ============================================ # Comments from T0301.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0301 # 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 T0301.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 112 # # ============================================ # Comments from T0301.t2k.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.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 16.7975 # # ============================================ # Comments from T0301.t2k.alpha.rdb # ============================================ # TARGET T0301 # 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 T0301.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 112 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 F 0.2246 0.0385 0.7370 2 L 0.2316 0.0373 0.7311 3 D 0.1771 0.0446 0.7782 4 P 0.1644 0.0632 0.7725 5 S 0.1253 0.0504 0.8243 6 D 0.0698 0.1326 0.7977 7 D 0.0656 0.1190 0.8155 8 G 0.0748 0.1139 0.8113 9 E 0.0985 0.1424 0.7591 10 D 0.1311 0.1811 0.6878 11 G 0.1143 0.1498 0.7360 12 G 0.1123 0.1240 0.7637 13 A 0.2387 0.1151 0.6462 14 I 0.3046 0.0901 0.6053 15 F 0.1989 0.0486 0.7524 16 P 0.1019 0.0597 0.8385 17 T 0.0898 0.0515 0.8588 18 G 0.0846 0.0384 0.8770 19 N 0.2254 0.0334 0.7412 20 L 0.4117 0.0658 0.5225 21 V 0.5520 0.0867 0.3614 22 D 0.6785 0.0654 0.2561 23 D 0.7628 0.0316 0.2055 24 L 0.8224 0.0151 0.1625 25 E 0.7881 0.0127 0.1992 26 V 0.5117 0.0333 0.4550 27 P 0.0983 0.0919 0.8099 28 G 0.0493 0.1255 0.8252 29 V 0.1095 0.0852 0.8053 30 G 0.1890 0.0431 0.7679 31 T 0.3477 0.0198 0.6324 32 F 0.6770 0.0057 0.3173 33 K 0.8501 0.0050 0.1448 34 A 0.8992 0.0042 0.0965 35 T 0.9112 0.0041 0.0847 36 M 0.9123 0.0042 0.0835 37 I 0.8473 0.0148 0.1379 38 N 0.6010 0.0260 0.3731 39 A 0.2486 0.0760 0.6754 40 G 0.1670 0.0687 0.7642 41 I 0.1623 0.0849 0.7528 42 P 0.2105 0.0930 0.6965 43 T 0.6635 0.0733 0.2631 44 V 0.8340 0.0470 0.1191 45 F 0.8681 0.0336 0.0983 46 V 0.8040 0.0332 0.1628 47 N 0.4862 0.0798 0.4339 48 A 0.0540 0.6729 0.2731 49 E 0.0208 0.7304 0.2489 50 E 0.0390 0.7272 0.2338 51 I 0.1066 0.4118 0.4816 52 G 0.0702 0.0958 0.8340 53 Y 0.0979 0.0770 0.8251 54 R 0.1132 0.0852 0.8016 55 G 0.1085 0.1721 0.7194 56 T 0.1572 0.1281 0.7146 57 E 0.1875 0.1400 0.6726 58 L 0.0884 0.1919 0.7197 59 R 0.0081 0.8561 0.1358 60 E 0.0063 0.8786 0.1151 61 E 0.0072 0.8723 0.1205 62 I 0.0151 0.7522 0.2327 63 N 0.0235 0.5047 0.4719 64 G 0.0281 0.3424 0.6295 65 D 0.0563 0.1047 0.8389 66 P 0.0055 0.9086 0.0860 67 Q 0.0053 0.9136 0.0811 68 Q 0.0052 0.9458 0.0490 69 L 0.0048 0.9557 0.0395 70 A 0.0048 0.9496 0.0456 71 R 0.0048 0.9534 0.0418 72 F 0.0047 0.9571 0.0382 73 E 0.0047 0.9582 0.0371 74 R 0.0047 0.9594 0.0359 75 I 0.0047 0.9601 0.0353 76 R 0.0047 0.9604 0.0350 77 V 0.0047 0.9594 0.0358 78 A 0.0049 0.9568 0.0383 79 G 0.0049 0.9551 0.0400 80 A 0.0048 0.9508 0.0443 81 L 0.0054 0.9428 0.0518 82 R 0.0071 0.9130 0.0800 83 M 0.0436 0.6333 0.3230 84 G 0.0324 0.1677 0.7999 85 L 0.0547 0.1960 0.7493 86 I 0.0727 0.2649 0.6624 87 K 0.0667 0.2721 0.6612 88 T 0.0683 0.2246 0.7070 89 P 0.0198 0.7560 0.2242 90 E 0.0100 0.8770 0.1130 91 E 0.0072 0.9031 0.0897 92 A 0.0110 0.8886 0.1003 93 A 0.0117 0.7360 0.2523 94 T 0.0193 0.4943 0.4864 95 R 0.0599 0.2623 0.6777 96 Q 0.0541 0.1222 0.8237 97 H 0.0955 0.0560 0.8485 98 T 0.1960 0.0160 0.7880 99 P 0.2233 0.0109 0.7658 100 K 0.8165 0.0068 0.1768 101 I 0.9072 0.0044 0.0884 102 A 0.9094 0.0056 0.0850 103 F 0.9141 0.0043 0.0816 104 V 0.8093 0.0145 0.1762 105 A 0.5540 0.0088 0.4372 106 P 0.2738 0.0148 0.7115 107 P 0.1456 0.0771 0.7773 108 R 0.0864 0.1438 0.7698 109 D 0.0895 0.1506 0.7598 110 Y 0.1129 0.1203 0.7668 111 R 0.2137 0.1212 0.6651 112 T 0.2299 0.1153 0.6548 113 A 0.1694 0.1060 0.7246 114 S 0.0765 0.0762 0.8472 115 G 0.0815 0.0467 0.8718 116 K 0.3090 0.0301 0.6609 117 L 0.6506 0.0223 0.3270 118 V 0.5447 0.0456 0.4097 119 A 0.3685 0.0585 0.5729 120 A 0.1097 0.3488 0.5415 121 G 0.0390 0.2856 0.6754 122 D 0.1134 0.1877 0.6989 123 I 0.3771 0.0304 0.5926 124 D 0.5218 0.0343 0.4439 125 L 0.8900 0.0146 0.0954 126 L 0.8939 0.0239 0.0823 127 V 0.9122 0.0120 0.0757 128 R 0.8608 0.0241 0.1151 129 A 0.6823 0.0532 0.2646 130 L 0.5124 0.0918 0.3959 131 S 0.3239 0.0629 0.6131 132 M 0.1073 0.1355 0.7572 133 G 0.0613 0.0904 0.8482 134 K 0.1213 0.1385 0.7402 135 L 0.1007 0.3322 0.5671 136 H 0.0627 0.3667 0.5706 137 H 0.0403 0.5314 0.4283 138 A 0.0653 0.6326 0.3021 139 M 0.0445 0.7490 0.2064 140 M 0.0228 0.8681 0.1091 141 G 0.0094 0.9383 0.0523 142 T 0.0066 0.9531 0.0403 143 A 0.0062 0.9562 0.0375 144 A 0.0053 0.9592 0.0355 145 V 0.0050 0.9596 0.0354 146 A 0.0047 0.9593 0.0360 147 I 0.0051 0.9549 0.0400 148 G 0.0051 0.9526 0.0423 149 T 0.0054 0.9452 0.0495 150 A 0.0069 0.9169 0.0762 151 A 0.0120 0.8254 0.1626 152 A 0.0300 0.6572 0.3129 153 I 0.0723 0.2257 0.7019 154 P 0.0343 0.2015 0.7642 155 G 0.0351 0.1828 0.7822 156 T 0.1561 0.3051 0.5388 157 L 0.1602 0.6872 0.1525 158 V 0.0388 0.8808 0.0804 159 N 0.0236 0.8943 0.0821 160 L 0.0336 0.8676 0.0988 161 A 0.0465 0.7615 0.1921 162 A 0.0728 0.5132 0.4140 163 G 0.0688 0.1483 0.7829 164 G 0.0740 0.0919 0.8341 165 G 0.0676 0.1101 0.8223 166 E 0.0825 0.1314 0.7860 167 R 0.1023 0.1122 0.7855 168 S 0.1850 0.0505 0.7645 169 A 0.5266 0.0227 0.4507 170 V 0.8034 0.0094 0.1872 171 R 0.8576 0.0080 0.1344 172 F 0.7615 0.0174 0.2211 173 G 0.5403 0.0202 0.4395 174 H 0.2846 0.0163 0.6991 175 P 0.1821 0.0550 0.7629 176 S 0.2588 0.0556 0.6857 177 G 0.4225 0.0305 0.5470 178 T 0.7432 0.0130 0.2438 179 L 0.8852 0.0070 0.1078 180 R 0.9161 0.0050 0.0788 181 V 0.9007 0.0071 0.0922 182 G 0.9042 0.0053 0.0904 183 A 0.9026 0.0054 0.0920 184 E 0.9073 0.0045 0.0882 185 A 0.8885 0.0057 0.1058 186 S 0.7899 0.0113 0.1988 187 Q 0.4650 0.0787 0.4562 188 A 0.1543 0.0645 0.7812 189 N 0.0631 0.0531 0.8838 190 G 0.0578 0.0549 0.8873 191 E 0.2792 0.0308 0.6900 192 W 0.6843 0.0075 0.3082 193 T 0.7959 0.0085 0.1956 194 V 0.8803 0.0093 0.1104 195 T 0.7086 0.0702 0.2212 196 K 0.6746 0.1969 0.1285 197 A 0.5387 0.3387 0.1226 198 I 0.4920 0.3994 0.1085 199 M 0.3738 0.5223 0.1040 200 S 0.2157 0.6889 0.0954 201 R 0.1034 0.8038 0.0928 202 S 0.0351 0.8933 0.0716 203 A 0.0215 0.9115 0.0669 204 R 0.0145 0.9083 0.0773 205 I 0.0193 0.8650 0.1157 206 L 0.0202 0.7653 0.2145 207 M 0.0783 0.5347 0.3871 208 E 0.1488 0.3200 0.5312 209 G 0.2853 0.1072 0.6075 210 W 0.5152 0.0814 0.4034 211 V 0.6668 0.0394 0.2938 212 R 0.6358 0.0265 0.3377 213 V 0.4379 0.0257 0.5363 214 P 0.1753 0.1049 0.7198 215 G 0.0338 0.4792 0.4871 216 D 0.0502 0.4864 0.4634 217 A 0.1038 0.3964 0.4998 218 F 0.0826 0.0808 0.8366