# This file is the result of combining several RDB files, specifically # T0217.t04.dssp-ebghstl.rdb (weight 1.53986) # T0217.t04.stride-ebghtl.rdb (weight 1.24869) # T0217.t04.str2.rdb (weight 1.54758) # T0217.t04.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.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0217 # 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 T0217.t04-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 66.4773 # # ============================================ # Comments from T0217.t04.stride-ebghtl.rdb # ============================================ # TARGET T0217 # 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 T0217.t04-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 66.4773 # # ============================================ # Comments from T0217.t04.str2.rdb # ============================================ # TARGET T0217 # Using neural net t04-2621-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 T0217.t04-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 66.4773 # # ============================================ # Comments from T0217.t04.alpha.rdb # ============================================ # TARGET T0217 # 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 T0217.t04-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 66.4773 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1989 0.0105 0.7906 2 V 0.6935 0.0061 0.3004 3 Y 0.8703 0.0046 0.1251 4 V 0.8827 0.0160 0.1013 5 G 0.8080 0.0144 0.1776 6 T 0.6341 0.0196 0.3463 7 S 0.4216 0.0592 0.5193 8 G 0.2944 0.0753 0.6303 9 F 0.3045 0.0851 0.6104 10 S 0.3109 0.0895 0.5996 11 F 0.1533 0.2390 0.6077 12 E 0.0635 0.4105 0.5260 13 D 0.0451 0.4180 0.5370 14 W 0.0829 0.3870 0.5301 15 K 0.0542 0.2082 0.7377 16 G 0.0544 0.1227 0.8229 17 V 0.2161 0.0847 0.6992 18 V 0.4548 0.0603 0.4849 19 Y 0.2633 0.0349 0.7018 20 P 0.0733 0.1669 0.7598 21 E 0.0185 0.2352 0.7462 22 H 0.0223 0.1511 0.8267 23 L 0.0909 0.0337 0.8754 24 K 0.0651 0.0220 0.9130 25 P 0.0214 0.6298 0.3488 26 S 0.0108 0.8136 0.1757 27 Q 0.0120 0.8582 0.1298 28 F 0.0120 0.8841 0.1039 29 L 0.0111 0.9187 0.0703 30 K 0.0082 0.9309 0.0609 31 Y 0.0125 0.9131 0.0745 32 Y 0.0131 0.8859 0.1010 33 W 0.0251 0.7904 0.1844 34 A 0.0392 0.6248 0.3360 35 V 0.0823 0.3458 0.5719 36 L 0.0476 0.1877 0.7646 37 G 0.0673 0.0482 0.8846 38 F 0.1743 0.0130 0.8126 39 R 0.3041 0.0146 0.6813 40 I 0.8700 0.0055 0.1246 41 V 0.9186 0.0042 0.0771 42 E 0.9262 0.0036 0.0702 43 L 0.8625 0.0138 0.1237 44 N 0.5213 0.0246 0.4541 45 F 0.3294 0.0545 0.6161 46 T 0.3270 0.0703 0.6027 47 Y 0.4107 0.0910 0.4983 48 Y 0.2475 0.0769 0.6756 49 T 0.1563 0.0646 0.7791 50 Q 0.0861 0.0278 0.8861 51 P 0.0733 0.0361 0.8906 52 S 0.0696 0.0452 0.8852 53 W 0.0063 0.9086 0.0851 54 R 0.0053 0.9452 0.0495 55 S 0.0066 0.9463 0.0471 56 F 0.0059 0.9569 0.0372 57 V 0.0054 0.9582 0.0364 58 Q 0.0049 0.9598 0.0353 59 M 0.0049 0.9549 0.0402 60 L 0.0060 0.9360 0.0580 61 R 0.0092 0.8623 0.1285 62 K 0.0152 0.6358 0.3490 63 T 0.0701 0.0353 0.8945 64 P 0.0434 0.0239 0.9327 65 P 0.0152 0.1197 0.8652 66 D 0.0517 0.0811 0.8672 67 F 0.5220 0.0156 0.4625 68 Y 0.8755 0.0085 0.1160 69 F 0.9170 0.0038 0.0792 70 T 0.9143 0.0041 0.0816 71 V 0.8909 0.0043 0.1048 72 K 0.7579 0.0129 0.2291 73 T 0.4544 0.0141 0.5315 74 P 0.2373 0.0627 0.7000 75 G 0.2192 0.1311 0.6497 76 S 0.3758 0.1856 0.4386 77 V 0.4370 0.1586 0.4044 78 T 0.4227 0.1353 0.4420 79 H 0.1906 0.2434 0.5660 80 V 0.0860 0.5439 0.3701 81 L 0.0845 0.5823 0.3332 82 W 0.0788 0.5607 0.3606 83 K 0.0683 0.4752 0.4565 84 E 0.0579 0.3308 0.6114 85 G 0.0531 0.1716 0.7754 86 K 0.0580 0.1024 0.8396 87 D 0.0691 0.0296 0.9013 88 P 0.0272 0.3746 0.5982 89 K 0.0210 0.6964 0.2826 90 E 0.0211 0.7782 0.2007 91 D 0.0188 0.8335 0.1477 92 M 0.0048 0.9502 0.0450 93 E 0.0047 0.9561 0.0392 94 N 0.0048 0.9513 0.0439 95 F 0.0048 0.9495 0.0457 96 T 0.0049 0.9493 0.0459 97 R 0.0051 0.9329 0.0620 98 Q 0.0058 0.9074 0.0868 99 I 0.0078 0.8655 0.1267 100 E 0.0079 0.8186 0.1735 101 P 0.0066 0.8432 0.1503 102 L 0.0085 0.8143 0.1772 103 I 0.0103 0.8109 0.1788 104 E 0.0088 0.7186 0.2726 105 E 0.0115 0.5716 0.4170 106 Q 0.0273 0.4340 0.5387 107 R 0.0576 0.3766 0.5658 108 L 0.1243 0.1908 0.6849 109 K 0.1308 0.0929 0.7763 110 M 0.3687 0.0441 0.5872 111 T 0.6942 0.0298 0.2760 112 L 0.9028 0.0134 0.0838 113 A 0.8912 0.0125 0.0964 114 Q 0.8241 0.0133 0.1626 115 F 0.4482 0.0134 0.5384 116 P 0.1410 0.0378 0.8212 117 F 0.0591 0.1447 0.7962 118 S 0.0611 0.1861 0.7528 119 F 0.0869 0.1667 0.7464 120 K 0.0971 0.1262 0.7767 121 F 0.1336 0.0788 0.7876 122 S 0.0661 0.0438 0.8901 123 R 0.0066 0.8528 0.1406 124 K 0.0081 0.8316 0.1603 125 N 0.0104 0.8480 0.1415 126 V 0.0059 0.9389 0.0551 127 E 0.0049 0.9501 0.0450 128 Y 0.0050 0.9460 0.0489 129 L 0.0051 0.9480 0.0469 130 E 0.0048 0.9388 0.0564 131 K 0.0050 0.9010 0.0939 132 L 0.0063 0.8412 0.1525 133 R 0.0104 0.7917 0.1979 134 E 0.0084 0.6534 0.3382 135 S 0.0171 0.4327 0.5503 136 Y 0.0699 0.0430 0.8871 137 P 0.0454 0.0549 0.8997 138 Y 0.1463 0.0275 0.8263 139 E 0.3434 0.0240 0.6326 140 L 0.8767 0.0062 0.1170 141 A 0.9210 0.0034 0.0757 142 V 0.9280 0.0037 0.0684 143 E 0.9136 0.0047 0.0817 144 F 0.7715 0.0107 0.2178 145 R 0.4111 0.0219 0.5670 146 H 0.1421 0.0342 0.8237 147 Y 0.0378 0.2015 0.7608 148 S 0.0471 0.2302 0.7227 149 W 0.0524 0.2483 0.6992 150 D 0.0605 0.1239 0.8157 151 R 0.0394 0.2530 0.7076 152 E 0.0055 0.9005 0.0941 153 E 0.0052 0.9209 0.0739 154 T 0.0048 0.9501 0.0451 155 Y 0.0047 0.9593 0.0360 156 E 0.0047 0.9613 0.0341 157 F 0.0047 0.9612 0.0341 158 L 0.0047 0.9605 0.0348 159 R 0.0048 0.9536 0.0415 160 N 0.0055 0.9243 0.0702 161 H 0.0424 0.3731 0.5845 162 G 0.0476 0.0116 0.9408 163 I 0.1142 0.0056 0.8802 164 T 0.5825 0.0145 0.4030 165 F 0.9241 0.0032 0.0727 166 V 0.9305 0.0033 0.0662 167 V 0.9261 0.0034 0.0705 168 V 0.8168 0.0083 0.1750 169 D 0.2861 0.0133 0.7005 170 E 0.0782 0.0854 0.8365 171 P 0.0323 0.1991 0.7686 172 K 0.0574 0.1927 0.7498 173 L 0.0720 0.0769 0.8511 174 P 0.0460 0.1368 0.8172 175 G 0.0491 0.1022 0.8487 176 L 0.1265 0.0775 0.7960 177 F 0.1256 0.0341 0.8403 178 P 0.1456 0.0425 0.8119 179 Y 0.2152 0.0482 0.7366 180 R 0.2238 0.0394 0.7368 181 P 0.2314 0.0774 0.6912 182 I 0.2513 0.0978 0.6509 183 T 0.2423 0.0793 0.6784 184 T 0.1712 0.0550 0.7738 185 T 0.1054 0.0817 0.8129 186 D 0.1249 0.0689 0.8062 187 Y 0.4888 0.0294 0.4818 188 A 0.7511 0.0137 0.2351 189 Y 0.9101 0.0055 0.0844 190 F 0.9174 0.0068 0.0758 191 R 0.9092 0.0105 0.0803 192 F 0.8319 0.0237 0.1444 193 H 0.5074 0.0241 0.4685 194 G 0.1849 0.0330 0.7822 195 R 0.1158 0.0449 0.8393 196 N 0.0807 0.1301 0.7891 197 E 0.0311 0.5671 0.4018 198 R 0.0489 0.6552 0.2959 199 W 0.0774 0.6746 0.2479 200 F 0.1224 0.5676 0.3099 201 E 0.1044 0.4739 0.4216 202 A 0.0672 0.3784 0.5544 203 E 0.0656 0.2280 0.7065 204 G 0.0620 0.1502 0.7878 205 E 0.1062 0.2193 0.6745 206 E 0.1787 0.2454 0.5760 207 R 0.2055 0.3133 0.4812 208 Y 0.1917 0.3334 0.4749 209 D 0.1691 0.3216 0.5092 210 Y 0.1633 0.3123 0.5244 211 L 0.1841 0.1711 0.6448 212 Y 0.1688 0.0571 0.7741 213 S 0.0712 0.0231 0.9057 214 E 0.0051 0.9254 0.0695 215 E 0.0047 0.9512 0.0441 216 E 0.0048 0.9514 0.0438 217 L 0.0047 0.9568 0.0385 218 K 0.0047 0.9578 0.0375 219 T 0.0049 0.9519 0.0432 220 L 0.0050 0.9431 0.0519 221 F 0.0048 0.9479 0.0473 222 E 0.0048 0.9473 0.0479 223 D 0.0049 0.9406 0.0545 224 V 0.0048 0.9430 0.0522 225 V 0.0047 0.9506 0.0446 226 E 0.0048 0.9483 0.0469 227 L 0.0056 0.9317 0.0627 228 S 0.0079 0.8802 0.1119 229 R 0.0094 0.7474 0.2433 230 R 0.0186 0.4331 0.5483 231 V 0.0892 0.1382 0.7725 232 K 0.1000 0.0902 0.8098 233 E 0.5402 0.0198 0.4400 234 T 0.8315 0.0057 0.1628 235 Y 0.9272 0.0033 0.0695 236 V 0.9322 0.0032 0.0646 237 F 0.9284 0.0039 0.0677 238 F 0.8883 0.0080 0.1037 239 N 0.5850 0.0144 0.4006 240 N 0.1994 0.0391 0.7616 241 C 0.0870 0.0970 0.8160 242 Y 0.0584 0.2168 0.7249 243 K 0.0471 0.2562 0.6967 244 G 0.0518 0.3665 0.5817 245 Q 0.0591 0.5598 0.3811 246 A 0.0384 0.7201 0.2415 247 A 0.0130 0.8723 0.1147 248 I 0.0089 0.9126 0.0785 249 N 0.0086 0.9061 0.0853 250 A 0.0048 0.9528 0.0424 251 L 0.0047 0.9595 0.0358 252 Q 0.0047 0.9593 0.0360 253 F 0.0047 0.9565 0.0388 254 K 0.0047 0.9586 0.0367 255 K 0.0047 0.9566 0.0387 256 M 0.0049 0.9466 0.0485 257 L 0.0054 0.8945 0.1001 258 E 0.0069 0.7086 0.2845 259 E 0.0164 0.5626 0.4210 260 R 0.0296 0.2922 0.6782 261 V 0.0440 0.0617 0.8942