# This file is the result of combining several RDB files, specifically # T0217.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0217.t2k.stride-ebghtl.rdb (weight 1.24869) # T0217.t2k.str2.rdb (weight 1.54758) # T0217.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 T0217.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0217 # 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 T0217.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 111 # # ============================================ # Comments from T0217.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0217 # 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 T0217.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 111 # # ============================================ # Comments from T0217.t2k.str2.rdb # ============================================ # TARGET T0217 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0217.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 111 # # ============================================ # Comments from T0217.t2k.alpha.rdb # ============================================ # TARGET T0217 # 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 T0217.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 111 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1253 0.0214 0.8533 2 V 0.4929 0.0147 0.4925 3 Y 0.7027 0.0149 0.2824 4 V 0.7283 0.0312 0.2405 5 G 0.6802 0.0283 0.2915 6 T 0.5315 0.0418 0.4267 7 S 0.2818 0.0840 0.6342 8 G 0.2302 0.1137 0.6561 9 F 0.2109 0.1396 0.6495 10 S 0.2033 0.1083 0.6885 11 F 0.1108 0.1685 0.7207 12 E 0.0683 0.3666 0.5651 13 D 0.0415 0.4556 0.5029 14 W 0.0552 0.5076 0.4371 15 K 0.0885 0.4172 0.4943 16 G 0.1220 0.2949 0.5831 17 V 0.2526 0.1537 0.5937 18 V 0.4346 0.0738 0.4916 19 Y 0.3464 0.0399 0.6136 20 P 0.1179 0.0870 0.7952 21 E 0.0303 0.1251 0.8446 22 H 0.0320 0.0819 0.8861 23 L 0.0645 0.0529 0.8826 24 K 0.0743 0.0641 0.8616 25 P 0.0366 0.5360 0.4274 26 S 0.0146 0.7064 0.2790 27 Q 0.0193 0.7999 0.1808 28 F 0.0297 0.8393 0.1311 29 L 0.0133 0.9062 0.0804 30 K 0.0122 0.9161 0.0717 31 Y 0.0112 0.9138 0.0751 32 Y 0.0157 0.8773 0.1070 33 W 0.0238 0.7975 0.1787 34 A 0.0313 0.6577 0.3110 35 V 0.0520 0.3511 0.5970 36 L 0.0495 0.1679 0.7826 37 G 0.0396 0.0818 0.8786 38 F 0.0985 0.0282 0.8733 39 R 0.1883 0.0284 0.7833 40 I 0.6650 0.0246 0.3104 41 V 0.8554 0.0150 0.1295 42 E 0.8853 0.0087 0.1060 43 L 0.7654 0.0184 0.2163 44 N 0.4671 0.0415 0.4914 45 F 0.2605 0.1175 0.6220 46 T 0.2926 0.1515 0.5559 47 Y 0.3573 0.1784 0.4643 48 Y 0.2950 0.1462 0.5589 49 T 0.1891 0.0890 0.7219 50 Q 0.1173 0.0422 0.8406 51 P 0.0788 0.0301 0.8910 52 S 0.0678 0.0350 0.8972 53 W 0.0091 0.8445 0.1464 54 R 0.0059 0.9000 0.0940 55 S 0.0058 0.9249 0.0693 56 F 0.0048 0.9520 0.0433 57 V 0.0048 0.9491 0.0461 58 Q 0.0050 0.9461 0.0488 59 M 0.0056 0.9399 0.0546 60 L 0.0058 0.9285 0.0657 61 R 0.0083 0.8325 0.1593 62 K 0.0192 0.5966 0.3842 63 T 0.0705 0.1509 0.7786 64 P 0.0425 0.0797 0.8778 65 P 0.0183 0.1288 0.8529 66 D 0.0823 0.0957 0.8220 67 F 0.6373 0.0093 0.3535 68 Y 0.8810 0.0088 0.1102 69 F 0.9149 0.0044 0.0807 70 T 0.9154 0.0049 0.0797 71 V 0.8851 0.0060 0.1089 72 K 0.8023 0.0086 0.1891 73 T 0.5315 0.0172 0.4513 74 P 0.3199 0.0781 0.6020 75 G 0.1996 0.2015 0.5989 76 S 0.2716 0.2101 0.5183 77 V 0.2989 0.1727 0.5284 78 T 0.2052 0.1397 0.6551 79 H 0.0920 0.1970 0.7110 80 V 0.0672 0.3567 0.5761 81 L 0.0447 0.3830 0.5723 82 W 0.0456 0.3984 0.5560 83 K 0.0450 0.3828 0.5722 84 E 0.0473 0.4937 0.4590 85 G 0.0388 0.5515 0.4097 86 K 0.0247 0.5850 0.3903 87 D 0.0338 0.5483 0.4179 88 P 0.0110 0.7591 0.2299 89 K 0.0079 0.8671 0.1250 90 E 0.0071 0.9178 0.0752 91 D 0.0053 0.9379 0.0568 92 M 0.0048 0.9519 0.0433 93 E 0.0047 0.9556 0.0396 94 N 0.0048 0.9545 0.0408 95 F 0.0048 0.9519 0.0434 96 T 0.0049 0.9434 0.0517 97 R 0.0050 0.9098 0.0852 98 Q 0.0055 0.8402 0.1543 99 I 0.0232 0.7642 0.2127 100 E 0.0119 0.7742 0.2138 101 P 0.0187 0.7854 0.1959 102 L 0.0209 0.7650 0.2141 103 I 0.0304 0.6904 0.2792 104 E 0.0250 0.5277 0.4473 105 E 0.0388 0.2093 0.7519 106 Q 0.0429 0.1298 0.8273 107 R 0.0976 0.1171 0.7854 108 L 0.2036 0.0389 0.7574 109 K 0.1954 0.0352 0.7694 110 M 0.6485 0.0158 0.3357 111 T 0.8748 0.0102 0.1151 112 L 0.9005 0.0088 0.0908 113 A 0.8734 0.0093 0.1174 114 Q 0.7060 0.0135 0.2805 115 F 0.3145 0.0126 0.6728 116 P 0.1493 0.0255 0.8253 117 F 0.0512 0.1860 0.7628 118 S 0.0717 0.2426 0.6857 119 F 0.0812 0.2065 0.7123 120 K 0.0958 0.1259 0.7783 121 F 0.0934 0.0872 0.8194 122 S 0.0650 0.0447 0.8903 123 R 0.0084 0.7646 0.2270 124 K 0.0061 0.8010 0.1928 125 N 0.0090 0.8457 0.1454 126 V 0.0052 0.9364 0.0584 127 E 0.0049 0.9453 0.0498 128 Y 0.0049 0.9473 0.0478 129 L 0.0048 0.9510 0.0442 130 E 0.0049 0.9407 0.0543 131 K 0.0055 0.8936 0.1009 132 L 0.0086 0.8129 0.1785 133 R 0.0292 0.6915 0.2793 134 E 0.0102 0.6343 0.3555 135 S 0.0186 0.4612 0.5203 136 Y 0.0683 0.1545 0.7773 137 P 0.0540 0.0583 0.8877 138 Y 0.1812 0.0234 0.7954 139 E 0.4528 0.0240 0.5232 140 L 0.7793 0.0142 0.2065 141 A 0.8735 0.0085 0.1180 142 V 0.8680 0.0073 0.1246 143 E 0.7770 0.0087 0.2143 144 F 0.5335 0.0159 0.4506 145 R 0.2187 0.0353 0.7460 146 H 0.1060 0.0582 0.8358 147 Y 0.0251 0.4298 0.5451 148 S 0.0362 0.4517 0.5121 149 W 0.0444 0.4421 0.5134 150 D 0.0592 0.1958 0.7450 151 R 0.0549 0.1218 0.8233 152 E 0.0077 0.8434 0.1490 153 E 0.0059 0.8759 0.1182 154 T 0.0052 0.9305 0.0644 155 Y 0.0049 0.9542 0.0408 156 E 0.0050 0.9557 0.0393 157 F 0.0048 0.9579 0.0373 158 L 0.0048 0.9562 0.0390 159 R 0.0050 0.9444 0.0506 160 N 0.0061 0.8694 0.1245 161 H 0.0434 0.2792 0.6774 162 G 0.0485 0.0175 0.9340 163 I 0.2284 0.0069 0.7647 164 T 0.7902 0.0129 0.1970 165 F 0.9221 0.0032 0.0747 166 V 0.9255 0.0033 0.0712 167 V 0.9082 0.0038 0.0881 168 V 0.7306 0.0079 0.2614 169 D 0.2562 0.0226 0.7212 170 E 0.0832 0.0727 0.8440 171 P 0.0568 0.1889 0.7542 172 K 0.0659 0.2169 0.7172 173 L 0.0810 0.1646 0.7544 174 P 0.0689 0.1839 0.7472 175 G 0.0751 0.1735 0.7514 176 L 0.1186 0.1464 0.7350 177 F 0.1556 0.1149 0.7295 178 P 0.1910 0.1124 0.6966 179 Y 0.2652 0.1287 0.6061 180 R 0.2871 0.1025 0.6104 181 P 0.3210 0.1354 0.5436 182 I 0.3223 0.1170 0.5606 183 T 0.3065 0.0924 0.6011 184 T 0.2107 0.0704 0.7190 185 T 0.0927 0.0894 0.8179 186 D 0.1273 0.0653 0.8075 187 Y 0.4434 0.0165 0.5401 188 A 0.7146 0.0118 0.2736 189 Y 0.9107 0.0049 0.0843 190 F 0.9249 0.0042 0.0709 191 R 0.9090 0.0064 0.0846 192 F 0.8469 0.0126 0.1405 193 H 0.4586 0.0352 0.5062 194 G 0.1548 0.0408 0.8045 195 R 0.0898 0.0655 0.8447 196 N 0.0659 0.1659 0.7682 197 E 0.0425 0.3413 0.6162 198 R 0.0459 0.4916 0.4625 199 W 0.0450 0.5228 0.4321 200 F 0.0424 0.5879 0.3697 201 E 0.0392 0.5832 0.3776 202 A 0.0434 0.5195 0.4371 203 E 0.0535 0.4526 0.4939 204 G 0.0630 0.3725 0.5645 205 E 0.0828 0.3947 0.5225 206 E 0.1480 0.3578 0.4941 207 R 0.1905 0.2921 0.5175 208 Y 0.2340 0.2604 0.5057 209 D 0.1920 0.2014 0.6066 210 Y 0.1486 0.1727 0.6788 211 L 0.1296 0.0916 0.7788 212 Y 0.0973 0.0432 0.8594 213 S 0.0631 0.0243 0.9126 214 E 0.0056 0.8965 0.0979 215 E 0.0050 0.9221 0.0729 216 E 0.0056 0.9278 0.0666 217 L 0.0049 0.9480 0.0471 218 K 0.0050 0.9471 0.0478 219 T 0.0050 0.9468 0.0481 220 L 0.0049 0.9473 0.0478 221 F 0.0047 0.9538 0.0414 222 E 0.0047 0.9468 0.0485 223 D 0.0048 0.9410 0.0542 224 V 0.0051 0.9403 0.0545 225 V 0.0048 0.9432 0.0520 226 E 0.0050 0.9341 0.0609 227 L 0.0059 0.9169 0.0772 228 S 0.0086 0.8756 0.1158 229 R 0.0132 0.6354 0.3514 230 R 0.0322 0.2374 0.7304 231 V 0.0560 0.0511 0.8929 232 K 0.0639 0.0428 0.8932 233 E 0.2915 0.0116 0.6970 234 T 0.7713 0.0048 0.2238 235 Y 0.9141 0.0036 0.0823 236 V 0.9304 0.0032 0.0664 237 F 0.9217 0.0037 0.0747 238 F 0.8774 0.0067 0.1160 239 N 0.5462 0.0151 0.4387 240 N 0.1295 0.0303 0.8402 241 C 0.0532 0.0827 0.8641 242 Y 0.0307 0.2464 0.7229 243 K 0.0282 0.2840 0.6878 244 G 0.0357 0.3571 0.6072 245 Q 0.0494 0.2980 0.6527 246 A 0.0443 0.3379 0.6178 247 A 0.0090 0.8546 0.1364 248 I 0.0072 0.9148 0.0780 249 N 0.0063 0.9348 0.0589 250 A 0.0047 0.9587 0.0366 251 L 0.0052 0.9598 0.0351 252 Q 0.0047 0.9592 0.0361 253 F 0.0047 0.9594 0.0359 254 K 0.0047 0.9577 0.0376 255 K 0.0049 0.9463 0.0488 256 M 0.0057 0.9060 0.0882 257 L 0.0453 0.5546 0.4001 258 E 0.0328 0.1142 0.8531 259 E 0.0853 0.0795 0.8352 260 R 0.1455 0.0637 0.7909 261 V 0.0606 0.0281 0.9113