# This file is the result of combining several RDB files, specifically # T0303.t06.dssp-ebghstl.rdb (weight 1.53986) # T0303.t06.stride-ebghtl.rdb (weight 1.24869) # T0303.t06.str2.rdb (weight 1.54758) # T0303.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 T0303.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0303 # Using neural net t06-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 T0303.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 4702 # # ============================================ # Comments from T0303.t06.stride-ebghtl.rdb # ============================================ # TARGET T0303 # Using neural net t06-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 T0303.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 4702 # # ============================================ # Comments from T0303.t06.str2.rdb # ============================================ # TARGET T0303 # Using neural net 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 T0303.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 4702 # # ============================================ # Comments from T0303.t06.alpha.rdb # ============================================ # TARGET T0303 # Using neural net 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 T0303.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 4702 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0577 0.0531 0.8892 2 T 0.0858 0.0984 0.8158 3 Q 0.1594 0.0626 0.7780 4 F 0.3041 0.0079 0.6880 5 K 0.4225 0.0316 0.5459 6 L 0.9221 0.0036 0.0743 7 I 0.9325 0.0032 0.0643 8 G 0.9324 0.0032 0.0644 9 F 0.9112 0.0043 0.0845 10 D 0.6434 0.0066 0.3500 11 L 0.1863 0.0786 0.7350 12 D 0.0706 0.0573 0.8721 13 G 0.0644 0.0740 0.8616 14 T 0.2612 0.0968 0.6421 15 L 0.5530 0.0984 0.3486 16 V 0.4519 0.1249 0.4232 17 N 0.2591 0.1070 0.6339 18 S 0.0948 0.1139 0.7913 19 L 0.0587 0.2415 0.6998 20 P 0.0142 0.7525 0.2332 21 D 0.0121 0.8800 0.1078 22 L 0.0055 0.9380 0.0565 23 A 0.0047 0.9505 0.0448 24 L 0.0047 0.9502 0.0451 25 S 0.0047 0.9474 0.0479 26 I 0.0047 0.9533 0.0420 27 N 0.0047 0.9590 0.0363 28 S 0.0048 0.9571 0.0381 29 A 0.0048 0.9561 0.0390 30 L 0.0049 0.9545 0.0406 31 K 0.0051 0.9394 0.0555 32 D 0.0061 0.8796 0.1143 33 V 0.0506 0.5292 0.4202 34 N 0.0426 0.0608 0.8966 35 L 0.0547 0.0173 0.9280 36 P 0.0564 0.0507 0.8929 37 Q 0.0539 0.1716 0.7745 38 A 0.0663 0.1941 0.7396 39 S 0.0599 0.3234 0.6167 40 E 0.0088 0.9100 0.0811 41 N 0.0107 0.9126 0.0767 42 L 0.0159 0.9174 0.0667 43 V 0.0253 0.9084 0.0663 44 M 0.0304 0.8948 0.0748 45 T 0.0269 0.8776 0.0956 46 W 0.0270 0.8411 0.1319 47 I 0.0387 0.6572 0.3040 48 G 0.0353 0.3084 0.6562 49 N 0.0473 0.2083 0.7444 50 G 0.0458 0.2330 0.7212 51 A 0.0333 0.6101 0.3566 52 D 0.0245 0.8167 0.1588 53 V 0.0195 0.8972 0.0833 54 L 0.0202 0.9072 0.0727 55 S 0.0155 0.9114 0.0730 56 Q 0.0112 0.9214 0.0673 57 R 0.0101 0.9161 0.0738 58 A 0.0096 0.9167 0.0737 59 V 0.0114 0.9151 0.0735 60 D 0.0108 0.9208 0.0685 61 W 0.0098 0.9208 0.0693 62 A 0.0094 0.9106 0.0799 63 C 0.0158 0.8791 0.1050 64 T 0.0177 0.8514 0.1308 65 Q 0.0179 0.8106 0.1715 66 A 0.0230 0.7185 0.2585 67 E 0.0295 0.5466 0.4239 68 K 0.0474 0.4146 0.5380 69 E 0.0567 0.2208 0.7225 70 L 0.0908 0.0498 0.8594 71 T 0.0531 0.0224 0.9245 72 E 0.0049 0.9404 0.0547 73 D 0.0048 0.9509 0.0444 74 E 0.0049 0.9514 0.0436 75 F 0.0050 0.9571 0.0380 76 K 0.0047 0.9571 0.0382 77 Y 0.0050 0.9540 0.0410 78 F 0.0048 0.9506 0.0446 79 K 0.0053 0.9500 0.0446 80 R 0.0057 0.9382 0.0561 81 Q 0.0080 0.9091 0.0829 82 F 0.0251 0.8462 0.1287 83 G 0.0260 0.7516 0.2224 84 F 0.0328 0.7443 0.2229 85 Y 0.0433 0.7400 0.2168 86 Y 0.0620 0.6078 0.3302 87 G 0.0570 0.4543 0.4887 88 E 0.0745 0.4806 0.4449 89 N 0.1275 0.4787 0.3938 90 L 0.1500 0.4486 0.4015 91 C 0.1421 0.3803 0.4775 92 N 0.1224 0.3604 0.5172 93 I 0.1192 0.3548 0.5259 94 S 0.1563 0.2754 0.5682 95 R 0.1867 0.2048 0.6085 96 L 0.1574 0.1268 0.7158 97 Y 0.0813 0.0646 0.8541 98 P 0.0119 0.5370 0.4511 99 N 0.0149 0.5140 0.4710 100 V 0.0053 0.9101 0.0845 101 K 0.0047 0.9566 0.0387 102 E 0.0047 0.9588 0.0366 103 T 0.0047 0.9600 0.0353 104 L 0.0047 0.9610 0.0344 105 E 0.0046 0.9605 0.0348 106 A 0.0046 0.9608 0.0346 107 L 0.0047 0.9593 0.0360 108 K 0.0048 0.9527 0.0425 109 A 0.0056 0.9102 0.0843 110 Q 0.0425 0.2741 0.6834 111 G 0.0343 0.0156 0.9501 112 Y 0.0892 0.0079 0.9029 113 I 0.7582 0.0036 0.2382 114 L 0.9260 0.0041 0.0699 115 A 0.9329 0.0033 0.0638 116 V 0.9319 0.0032 0.0649 117 V 0.8964 0.0050 0.0986 118 T 0.5354 0.0101 0.4545 119 N 0.0801 0.0380 0.8819 120 K 0.0711 0.0341 0.8948 121 P 0.0673 0.1243 0.8084 122 T 0.0293 0.5242 0.4464 123 K 0.0206 0.6893 0.2901 124 H 0.0219 0.7502 0.2279 125 V 0.0150 0.8706 0.1144 126 Q 0.0061 0.9389 0.0550 127 P 0.0049 0.9529 0.0422 128 I 0.0047 0.9583 0.0370 129 L 0.0047 0.9568 0.0385 130 T 0.0049 0.9448 0.0503 131 A 0.0055 0.9138 0.0808 132 F 0.0436 0.5130 0.4433 133 G 0.0446 0.0279 0.9275 134 I 0.0541 0.0600 0.8859 135 D 0.0467 0.2955 0.6579 136 H 0.0644 0.5396 0.3960 137 L 0.0746 0.5902 0.3352 138 F 0.1448 0.4731 0.3821 139 S 0.1344 0.5002 0.3655 140 E 0.3105 0.4518 0.2377 141 M 0.4764 0.3503 0.1733 142 L 0.4793 0.2712 0.2495 143 G 0.3188 0.1111 0.5701 144 G 0.1408 0.0916 0.7677 145 Q 0.0966 0.1107 0.7927 146 S 0.1279 0.1224 0.7497 147 L 0.1070 0.1007 0.7922 148 P 0.0807 0.1511 0.7682 149 E 0.0989 0.1556 0.7455 150 I 0.1355 0.0938 0.7707 151 K 0.1045 0.0367 0.8588 152 P 0.0816 0.0535 0.8650 153 H 0.0767 0.0476 0.8756 154 P 0.0222 0.6876 0.2903 155 A 0.0164 0.8867 0.0969 156 P 0.0055 0.9443 0.0501 157 F 0.0047 0.9578 0.0374 158 Y 0.0047 0.9605 0.0348 159 Y 0.0047 0.9599 0.0354 160 L 0.0047 0.9597 0.0356 161 C 0.0048 0.9577 0.0375 162 G 0.0051 0.9472 0.0478 163 K 0.0065 0.9055 0.0880 164 F 0.0448 0.4569 0.4983 165 G 0.0389 0.0201 0.9410 166 L 0.0719 0.0084 0.9197 167 Y 0.0984 0.0095 0.8921 168 P 0.0422 0.5590 0.3987 169 K 0.0848 0.5184 0.3968 170 Q 0.2320 0.4001 0.3679 171 I 0.8495 0.0147 0.1358 172 L 0.9045 0.0066 0.0890 173 F 0.9133 0.0052 0.0815 174 V 0.8158 0.0396 0.1446 175 G 0.5055 0.0177 0.4767 176 D 0.1852 0.0312 0.7836 177 S 0.0855 0.0678 0.8467 178 Q 0.0139 0.6087 0.3774 179 N 0.0185 0.6549 0.3266 180 D 0.0245 0.7310 0.2445 181 I 0.0078 0.9344 0.0579 182 F 0.0058 0.9479 0.0463 183 A 0.0050 0.9540 0.0410 184 A 0.0051 0.9537 0.0413 185 H 0.0050 0.9450 0.0500 186 S 0.0056 0.8913 0.1031 187 A 0.0443 0.3848 0.5709 188 G 0.0403 0.0194 0.9403 189 C 0.1067 0.0078 0.8856 190 A 0.3812 0.0165 0.6023 191 V 0.9051 0.0044 0.0904 192 V 0.9193 0.0062 0.0746 193 G 0.9185 0.0055 0.0760 194 L 0.8600 0.0116 0.1284 195 T 0.5390 0.0217 0.4393 196 Y 0.2055 0.0509 0.7436 197 G 0.0921 0.0568 0.8510 198 Y 0.1016 0.0975 0.8009 199 N 0.1163 0.1042 0.7796 200 Y 0.1142 0.1351 0.7507 201 N 0.1332 0.1305 0.7363 202 I 0.1909 0.1433 0.6657 203 P 0.2162 0.1854 0.5984 204 I 0.1171 0.4946 0.3883 205 A 0.0751 0.5204 0.4045 206 Q 0.0623 0.4380 0.4996 207 S 0.0891 0.1644 0.7465 208 K 0.0928 0.0389 0.8683 209 P 0.0980 0.0694 0.8325 210 D 0.2115 0.1226 0.6658 211 W 0.6856 0.0679 0.2464 212 I 0.7730 0.0573 0.1697 213 F 0.6090 0.0580 0.3330 214 D 0.2300 0.0948 0.6753 215 D 0.1344 0.0588 0.8068 216 F 0.0071 0.8763 0.1166 217 A 0.0059 0.9112 0.0828 218 D 0.0072 0.9073 0.0854 219 I 0.0099 0.8940 0.0961 220 L 0.0116 0.8724 0.1160 221 K 0.0257 0.7721 0.2021 222 I 0.0477 0.6212 0.3311 223 T 0.0625 0.3551 0.5825 224 Q 0.0401 0.0620 0.8979