# This file is the result of combining several RDB files, specifically # T0443.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0443.t2k.stride-ebghtl.rdb (weight 1.24869) # T0443.t2k.str.rdb (weight 1.53983) # 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 T0443.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0443 # 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 T0443.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 56 # # ============================================ # Comments from T0443.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0443 # 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 T0443.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 56 # # ============================================ # Comments from T0443.t2k.str.rdb # ============================================ # TARGET T0443 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0443.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 56 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0126 0.0092 0.9782 2 Q 0.0208 0.0166 0.9626 3 P 0.0152 0.0810 0.9038 4 E 0.0050 0.7342 0.2608 5 T 0.0050 0.7728 0.2222 6 S 0.0041 0.8883 0.1076 7 A 0.0037 0.9390 0.0573 8 Q 0.0041 0.9549 0.0410 9 Y 0.0037 0.9627 0.0335 10 Q 0.0037 0.9684 0.0278 11 H 0.0037 0.9720 0.0243 12 R 0.0037 0.9674 0.0289 13 F 0.0037 0.9699 0.0264 14 S 0.0037 0.9663 0.0300 15 Q 0.0037 0.9402 0.0560 16 A 0.0038 0.9093 0.0869 17 I 0.0108 0.8216 0.1676 18 R 0.0309 0.6023 0.3668 19 G 0.0262 0.1583 0.8155 20 G 0.0229 0.0925 0.8846 21 E 0.0435 0.0698 0.8867 22 A 0.0458 0.0643 0.8899 23 A 0.0280 0.0653 0.9068 24 D 0.0130 0.0800 0.9070 25 G 0.0139 0.0625 0.9236 26 L 0.0290 0.1070 0.8639 27 P 0.0287 0.3665 0.6048 28 Q 0.0064 0.8881 0.1055 29 D 0.0071 0.9064 0.0865 30 R 0.0084 0.9386 0.0530 31 L 0.0087 0.9577 0.0336 32 N 0.0088 0.9623 0.0289 33 V 0.0182 0.9519 0.0299 34 Y 0.0126 0.9638 0.0236 35 I 0.0093 0.9682 0.0226 36 R 0.0098 0.9655 0.0247 37 L 0.0108 0.9529 0.0364 38 I 0.0113 0.9488 0.0399 39 R 0.0067 0.9349 0.0584 40 N 0.0051 0.8869 0.1080 41 N 0.0078 0.8746 0.1177 42 I 0.0045 0.9441 0.0515 43 H 0.0041 0.9410 0.0549 44 S 0.0048 0.9428 0.0524 45 F 0.0054 0.9487 0.0459 46 I 0.0082 0.9201 0.0716 47 D 0.0049 0.8297 0.1655 48 R 0.0054 0.7026 0.2919 49 C 0.0187 0.5643 0.4170 50 Y 0.0300 0.4314 0.5386 51 T 0.0624 0.6204 0.3172 52 E 0.0762 0.6785 0.2452 53 T 0.0719 0.6677 0.2604 54 R 0.0200 0.7638 0.2162 55 Q 0.0126 0.6995 0.2879 56 Y 0.0251 0.5098 0.4651 57 F 0.0603 0.1228 0.8168 58 D 0.0174 0.0563 0.9263 59 S 0.0047 0.8450 0.1503 60 K 0.0039 0.9258 0.0703 61 E 0.0038 0.9433 0.0528 62 W 0.0038 0.9644 0.0318 63 S 0.0037 0.9677 0.0285 64 R 0.0038 0.9683 0.0280 65 L 0.0038 0.9640 0.0322 66 K 0.0037 0.9705 0.0257 67 E 0.0041 0.9718 0.0241 68 G 0.0037 0.9673 0.0290 69 F 0.0041 0.9619 0.0340 70 V 0.0052 0.9495 0.0453 71 R 0.0059 0.9113 0.0828 72 D 0.0072 0.7716 0.2212 73 A 0.0188 0.3793 0.6019 74 R 0.0268 0.2031 0.7700 75 A 0.0453 0.1367 0.8180 76 Q 0.0348 0.1276 0.8376 77 T 0.0216 0.0943 0.8841 78 P 0.0229 0.5682 0.4089 79 Y 0.0414 0.6605 0.2982 80 F 0.0229 0.8219 0.1552 81 Q 0.0119 0.8664 0.1217 82 E 0.0123 0.8640 0.1237 83 I 0.0087 0.9025 0.0888 84 P 0.0038 0.9485 0.0477 85 G 0.0038 0.9619 0.0343 86 E 0.0037 0.9668 0.0295 87 F 0.0037 0.9738 0.0224 88 L 0.0037 0.9729 0.0234 89 Q 0.0037 0.9676 0.0287 90 Y 0.0038 0.9536 0.0426 91 C 0.0049 0.9092 0.0859 92 Q 0.0043 0.7763 0.2194 93 S 0.0071 0.4424 0.5505 94 P 0.0107 0.2576 0.7318 95 P 0.0158 0.1346 0.8496 96 L 0.0154 0.1078 0.8768 97 S 0.0127 0.1770 0.8104 98 D 0.0052 0.7385 0.2563 99 G 0.0073 0.7917 0.2010 100 I 0.0060 0.9277 0.0663 101 L 0.0046 0.9428 0.0526 102 A 0.0044 0.9430 0.0526 103 L 0.0060 0.9323 0.0617 104 M 0.0050 0.9074 0.0876 105 D 0.0083 0.8895 0.1022 106 F 0.0131 0.9086 0.0783 107 E 0.0237 0.9214 0.0549 108 Y 0.0276 0.9338 0.0386 109 T 0.0268 0.9407 0.0326 110 Q 0.0252 0.9455 0.0294 111 L 0.0442 0.9191 0.0368 112 L 0.0766 0.8698 0.0536 113 A 0.1300 0.7928 0.0772 114 E 0.1795 0.7085 0.1120 115 V 0.1841 0.5956 0.2203 116 A 0.1702 0.3700 0.4598 117 Q 0.1131 0.2249 0.6620 118 I 0.0796 0.1358 0.7847 119 P 0.0625 0.1005 0.8369 120 D 0.0511 0.0899 0.8590 121 I 0.0386 0.0786 0.8827 122 P 0.0285 0.0870 0.8845 123 D 0.0311 0.1165 0.8524 124 I 0.0270 0.3428 0.6301 125 H 0.0270 0.3725 0.6005 126 Y 0.0428 0.3835 0.5737 127 S 0.0331 0.4357 0.5313 128 N 0.0377 0.3612 0.6011 129 D 0.0424 0.2553 0.7023 130 S 0.0707 0.1274 0.8019 131 K 0.1543 0.0969 0.7488 132 Y 0.2755 0.0746 0.6499 133 T 0.3011 0.0811 0.6178 134 P 0.2610 0.0841 0.6549 135 S 0.0819 0.0631 0.8550 136 P 0.0355 0.6539 0.3106 137 A 0.0823 0.6866 0.2311 138 A 0.1546 0.6358 0.2096 139 F 0.1769 0.6208 0.2023 140 I 0.1946 0.6203 0.1851 141 R 0.2077 0.5515 0.2408 142 Q 0.2079 0.4605 0.3316 143 Y 0.2409 0.1985 0.5605 144 R 0.2418 0.0549 0.7033 145 Y 0.2393 0.0405 0.7202 146 D 0.4074 0.0490 0.5436 147 V 0.5678 0.0896 0.3426 148 T 0.6139 0.0947 0.2914 149 H 0.5327 0.1150 0.3523 150 D 0.3364 0.0767 0.5869 151 L 0.1625 0.0422 0.7953 152 Q 0.0873 0.0647 0.8479 153 E 0.0941 0.0505 0.8554 154 A 0.0997 0.0244 0.8759 155 E 0.0953 0.0099 0.8948 156 T 0.5882 0.0063 0.4055 157 A 0.9245 0.0026 0.0729 158 L 0.9683 0.0024 0.0292 159 L 0.9772 0.0024 0.0203 160 I 0.9741 0.0024 0.0234 161 W 0.9503 0.0026 0.0471 162 R 0.8449 0.0031 0.1520 163 N 0.2949 0.0107 0.6944 164 A 0.0298 0.0640 0.9062 165 E 0.0139 0.0821 0.9040 166 D 0.0889 0.0972 0.8139 167 D 0.4789 0.0298 0.4913 168 V 0.8731 0.0086 0.1183 169 M 0.8907 0.0121 0.0972 170 Y 0.8669 0.0259 0.1072 171 Q 0.8216 0.0290 0.1494 172 T 0.6452 0.0317 0.3231 173 L 0.2366 0.0319 0.7315 174 D 0.0700 0.0702 0.8598 175 G 0.0048 0.9321 0.0631 176 F 0.0038 0.9593 0.0370 177 D 0.0037 0.9719 0.0244 178 M 0.0041 0.9752 0.0208 179 M 0.0048 0.9727 0.0225 180 L 0.0041 0.9727 0.0232 181 L 0.0037 0.9707 0.0255 182 E 0.0038 0.9594 0.0368 183 I 0.0037 0.9449 0.0514 184 M 0.0038 0.9159 0.0803 185 G 0.0047 0.8379 0.1574 186 S 0.0060 0.7085 0.2855 187 S 0.0074 0.4972 0.4954 188 A 0.0088 0.4282 0.5631 189 L 0.0144 0.4240 0.5616 190 S 0.0162 0.4676 0.5162 191 F 0.0098 0.6611 0.3292 192 D 0.0077 0.8299 0.1624 193 T 0.0070 0.8956 0.0975 194 L 0.0051 0.9295 0.0654 195 A 0.0047 0.9491 0.0461 196 Q 0.0048 0.9562 0.0391 197 T 0.0045 0.9530 0.0425 198 L 0.0045 0.9455 0.0499 199 V 0.0046 0.9302 0.0652 200 E 0.0047 0.8833 0.1120 201 F 0.0042 0.7879 0.2079 202 M 0.0078 0.6269 0.3653 203 P 0.0068 0.5590 0.4341 204 K 0.0061 0.5523 0.4415 205 A 0.0076 0.4991 0.4934 206 D 0.0093 0.4506 0.5401 207 N 0.0136 0.4555 0.5309 208 W 0.0058 0.8415 0.1527 209 K 0.0049 0.9224 0.0727 210 N 0.0057 0.9306 0.0637 211 I 0.0049 0.9447 0.0504 212 L 0.0046 0.9349 0.0605 213 L 0.0040 0.9165 0.0796 214 G 0.0059 0.8656 0.1285 215 K 0.0082 0.8463 0.1455 216 W 0.0119 0.8305 0.1576 217 S 0.0087 0.8265 0.1648 218 G 0.0155 0.7639 0.2206 219 W 0.0507 0.6775 0.2718 220 I 0.1446 0.6002 0.2552 221 E 0.2199 0.5671 0.2131 222 Q 0.2963 0.5265 0.1772 223 R 0.3947 0.3950 0.2103 224 I 0.5427 0.2299 0.2274 225 I 0.5787 0.1717 0.2496 226 I 0.4031 0.0990 0.4979 227 P 0.1423 0.1009 0.7568 228 S 0.0883 0.0647 0.8471 229 L 0.1536 0.1115 0.7349 230 S 0.1798 0.1162 0.7040 231 A 0.1697 0.2407 0.5896 232 I 0.1341 0.2407 0.6252 233 S 0.0952 0.2081 0.6967 234 E 0.0507 0.2032 0.7461 235 N 0.0510 0.1267 0.8223 236 M 0.0842 0.1045 0.8113 237 E 0.0671 0.1029 0.8300 238 G 0.0488 0.0956 0.8557 239 N 0.0602 0.0404 0.8994 240 S 0.0814 0.0421 0.8765 241 P 0.0713 0.1718 0.7569 242 S 0.0690 0.2195 0.7115 243 Q 0.0714 0.3462 0.5824 244 N 0.0771 0.3453 0.5777 245 H 0.1654 0.2920 0.5426 246 L 0.1434 0.2158 0.6408 247 S 0.0956 0.1586 0.7458 248 A 0.0261 0.1885 0.7854