# This file is the result of combining several RDB files, specifically # T0295.t06.dssp-ebghstl.rdb (weight 1.53986) # T0295.t06.stride-ebghtl.rdb (weight 1.24869) # T0295.t06.str2.rdb (weight 1.54758) # T0295.t06.alpha.rdb (weight 0.659012) # T0295.t04.dssp-ebghstl.rdb (weight 1.53986) # T0295.t04.stride-ebghtl.rdb (weight 1.24869) # T0295.t04.str2.rdb (weight 1.54758) # T0295.t04.alpha.rdb (weight 0.659012) # T0295.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0295.t2k.stride-ebghtl.rdb (weight 1.24869) # T0295.t2k.str2.rdb (weight 1.54758) # T0295.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 T0295.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0295 # 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 T0295.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 2966 # # ============================================ # Comments from T0295.t06.stride-ebghtl.rdb # ============================================ # TARGET T0295 # 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 T0295.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 2966 # # ============================================ # Comments from T0295.t06.str2.rdb # ============================================ # TARGET T0295 # 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 T0295.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 2966 # # ============================================ # Comments from T0295.t06.alpha.rdb # ============================================ # TARGET T0295 # 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 T0295.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 2966 # # ============================================ # Comments from T0295.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0295 # 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 T0295.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 2062 # # ============================================ # Comments from T0295.t04.stride-ebghtl.rdb # ============================================ # TARGET T0295 # 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 T0295.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 2062 # # ============================================ # Comments from T0295.t04.str2.rdb # ============================================ # TARGET T0295 # 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 T0295.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 2062 # # ============================================ # Comments from T0295.t04.alpha.rdb # ============================================ # TARGET T0295 # 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 T0295.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 2062 # # ============================================ # Comments from T0295.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0295 # 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 T0295.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 1990 # # ============================================ # Comments from T0295.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0295 # 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 T0295.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 1990 # # ============================================ # Comments from T0295.t2k.str2.rdb # ============================================ # TARGET T0295 # 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 T0295.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 1990 # # ============================================ # Comments from T0295.t2k.alpha.rdb # ============================================ # TARGET T0295 # 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 T0295.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 1990 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 H 0.1341 0.1737 0.6922 2 L 0.1924 0.2048 0.6028 3 L 0.2054 0.1729 0.6217 4 K 0.1342 0.1101 0.7557 5 N 0.0946 0.0416 0.8639 6 P 0.0053 0.8745 0.1202 7 G 0.0060 0.9096 0.0845 8 I 0.0052 0.9475 0.0473 9 L 0.0047 0.9578 0.0374 10 D 0.0047 0.9576 0.0377 11 K 0.0048 0.9575 0.0377 12 I 0.0047 0.9562 0.0390 13 I 0.0049 0.9516 0.0435 14 Y 0.0057 0.9227 0.0716 15 A 0.0081 0.8592 0.1327 16 A 0.0642 0.5576 0.3782 17 K 0.0683 0.1996 0.7321 18 I 0.1042 0.1379 0.7579 19 K 0.0656 0.0504 0.8840 20 S 0.0255 0.1079 0.8666 21 S 0.0330 0.0619 0.9051 22 D 0.2141 0.0259 0.7600 23 I 0.7926 0.0045 0.2029 24 V 0.9105 0.0043 0.0851 25 L 0.9125 0.0052 0.0823 26 E 0.9068 0.0039 0.0893 27 I 0.6625 0.0312 0.3062 28 G 0.3427 0.0214 0.6360 29 C 0.1420 0.0584 0.7996 30 G 0.0816 0.0787 0.8397 31 T 0.0536 0.2303 0.7161 32 G 0.0376 0.3946 0.5678 33 N 0.0195 0.8730 0.1075 34 L 0.0132 0.9241 0.0627 35 T 0.0108 0.9372 0.0520 36 V 0.0061 0.9472 0.0468 37 K 0.0070 0.9279 0.0650 38 L 0.0066 0.8914 0.1021 39 L 0.0115 0.8443 0.1442 40 P 0.0100 0.7044 0.2857 41 L 0.0208 0.5000 0.4792 42 A 0.0735 0.1107 0.8157 43 K 0.0742 0.0833 0.8426 44 K 0.4784 0.0313 0.4903 45 V 0.8400 0.0073 0.1526 46 I 0.8934 0.0125 0.0942 47 T 0.9064 0.0069 0.0867 48 I 0.8647 0.0123 0.1229 49 D 0.6558 0.0158 0.3284 50 I 0.1554 0.0345 0.8101 51 D 0.0824 0.0189 0.8987 52 S 0.0057 0.8578 0.1365 53 R 0.0053 0.8993 0.0954 54 M 0.0053 0.9322 0.0626 55 I 0.0048 0.9557 0.0396 56 S 0.0047 0.9559 0.0394 57 E 0.0047 0.9557 0.0396 58 V 0.0048 0.9538 0.0414 59 K 0.0049 0.9525 0.0426 60 K 0.0056 0.9412 0.0533 61 R 0.0071 0.9167 0.0762 62 C 0.0097 0.8942 0.0960 63 L 0.0075 0.8682 0.1243 64 Y 0.0134 0.7721 0.2146 65 E 0.0474 0.3636 0.5890 66 G 0.0494 0.0736 0.8770 67 Y 0.0996 0.0385 0.8619 68 N 0.1012 0.0870 0.8118 69 N 0.3672 0.0471 0.5857 70 L 0.8027 0.0080 0.1893 71 E 0.8969 0.0054 0.0977 72 V 0.9142 0.0046 0.0811 73 Y 0.8540 0.0175 0.1286 74 E 0.6983 0.0277 0.2739 75 G 0.2954 0.0733 0.6313 76 D 0.2097 0.1060 0.6842 77 A 0.1272 0.3902 0.4826 78 I 0.1512 0.3701 0.4787 79 K 0.1377 0.3066 0.5557 80 T 0.1339 0.1010 0.7651 81 V 0.1081 0.0733 0.8186 82 F 0.0780 0.1745 0.7475 83 P 0.0486 0.2073 0.7441 84 K 0.0820 0.2014 0.7166 85 F 0.1763 0.0775 0.7462 86 D 0.2490 0.0696 0.6814 87 V 0.7838 0.0211 0.1951 88 C 0.8902 0.0117 0.0982 89 T 0.8594 0.0229 0.1177 90 A 0.7959 0.0260 0.1781 91 N 0.5510 0.0354 0.4136 92 I 0.2277 0.0431 0.7292 93 P 0.1395 0.1041 0.7564 94 Y 0.1665 0.1646 0.6689 95 K 0.1942 0.1969 0.6088 96 I 0.1231 0.2618 0.6150 97 S 0.0752 0.2818 0.6431 98 S 0.0331 0.4894 0.4775 99 P 0.0118 0.8954 0.0929 100 L 0.0086 0.9335 0.0578 101 I 0.0071 0.9468 0.0461 102 F 0.0089 0.9461 0.0450 103 K 0.0080 0.9417 0.0504 104 L 0.0079 0.9238 0.0683 105 I 0.0130 0.8422 0.1448 106 S 0.0164 0.6277 0.3559 107 H 0.0313 0.3966 0.5722 108 R 0.0496 0.1662 0.7843 109 P 0.0438 0.1862 0.7700 110 L 0.0597 0.2035 0.7369 111 F 0.1036 0.2072 0.6892 112 K 0.1321 0.2519 0.6161 113 C 0.1661 0.4096 0.4243 114 A 0.2163 0.5508 0.2329 115 V 0.2060 0.6860 0.1081 116 L 0.1532 0.7723 0.0746 117 M 0.1058 0.8227 0.0716 118 F 0.0828 0.8340 0.0832 119 Q 0.0459 0.8727 0.0814 120 K 0.0200 0.9100 0.0699 121 E 0.0170 0.9101 0.0729 122 F 0.0169 0.9129 0.0701 123 A 0.0211 0.8949 0.0840 124 E 0.0241 0.8664 0.1095 125 R 0.0385 0.8222 0.1393 126 M 0.0707 0.7419 0.1874 127 L 0.0980 0.5752 0.3268 128 A 0.1128 0.3289 0.5583 129 N 0.0788 0.1227 0.7985 130 V 0.0461 0.1412 0.8127 131 G 0.0453 0.0733 0.8814 132 D 0.0872 0.1132 0.7996 133 S 0.0848 0.2008 0.7145 134 N 0.0809 0.2487 0.6704 135 Y 0.2111 0.2355 0.5533 136 S 0.3682 0.2339 0.3979 137 R 0.4066 0.3910 0.2024 138 L 0.4419 0.4313 0.1267 139 T 0.4795 0.4197 0.1007 140 I 0.4881 0.4361 0.0758 141 N 0.4707 0.4513 0.0780 142 V 0.4664 0.4487 0.0849 143 K 0.4811 0.4147 0.1041 144 L 0.4605 0.4140 0.1255 145 F 0.4977 0.3300 0.1723 146 C 0.5507 0.2071 0.2422 147 K 0.6261 0.1013 0.2726 148 V 0.7483 0.0610 0.1907 149 T 0.7385 0.0748 0.1868 150 K 0.7557 0.0642 0.1800 151 V 0.7278 0.0682 0.2041 152 C 0.7197 0.0418 0.2384 153 N 0.6510 0.0326 0.3165 154 V 0.3357 0.0258 0.6384 155 N 0.1345 0.0343 0.8311 156 R 0.0223 0.3365 0.6412 157 S 0.0230 0.3374 0.6396 158 S 0.0928 0.2450 0.6622 159 F 0.1940 0.0482 0.7578 160 N 0.1201 0.0250 0.8549 161 P 0.1629 0.0200 0.8171 162 P 0.1078 0.0206 0.8717 163 P 0.1174 0.0286 0.8540 164 K 0.2284 0.0303 0.7413 165 V 0.4287 0.0182 0.5531 166 D 0.4760 0.0284 0.4956 167 S 0.7248 0.0133 0.2619 168 V 0.8484 0.0078 0.1438 169 I 0.9148 0.0032 0.0820 170 V 0.9108 0.0037 0.0855 171 K 0.9036 0.0037 0.0927 172 L 0.8771 0.0050 0.1180 173 I 0.7598 0.0064 0.2338 174 P 0.4707 0.0140 0.5153 175 K 0.1548 0.0385 0.8067 176 E 0.0860 0.0377 0.8763 177 S 0.0691 0.0304 0.9006 178 S 0.0656 0.0407 0.8937 179 F 0.0721 0.0717 0.8562 180 L 0.1010 0.1060 0.7930 181 T 0.0719 0.0995 0.8287 182 N 0.0759 0.0672 0.8569 183 F 0.0069 0.8911 0.1020 184 D 0.0052 0.9298 0.0651 185 E 0.0056 0.9398 0.0546 186 W 0.0048 0.9529 0.0422 187 D 0.0047 0.9584 0.0369 188 N 0.0047 0.9585 0.0367 189 L 0.0047 0.9596 0.0357 190 L 0.0047 0.9594 0.0359 191 R 0.0047 0.9573 0.0380 192 I 0.0048 0.9547 0.0405 193 C 0.0049 0.9377 0.0573 194 F 0.0054 0.8877 0.1069 195 S 0.0080 0.8168 0.1752 196 R 0.0121 0.7459 0.2420 197 K 0.0096 0.8039 0.1865 198 R 0.0076 0.8510 0.1413 199 K 0.0056 0.9112 0.0833 200 T 0.0082 0.9143 0.0775 201 L 0.0051 0.9429 0.0520 202 H 0.0048 0.9449 0.0503 203 A 0.0049 0.9327 0.0624 204 I 0.0049 0.9211 0.0739 205 F 0.0067 0.8732 0.1201 206 K 0.0064 0.8056 0.1880 207 R 0.0095 0.6902 0.3003 208 N 0.0279 0.5036 0.4685 209 A 0.0722 0.1812 0.7466 210 V 0.0579 0.1733 0.7688 211 L 0.0093 0.7964 0.1942 212 N 0.0074 0.8728 0.1198 213 M 0.0058 0.9223 0.0719 214 L 0.0052 0.9385 0.0563 215 E 0.0049 0.9486 0.0464 216 H 0.0048 0.9471 0.0481 217 N 0.0048 0.9198 0.0754 218 Y 0.0055 0.8741 0.1204 219 K 0.0052 0.8303 0.1646 220 N 0.0061 0.7466 0.2473 221 W 0.0547 0.4403 0.5050 222 C 0.0734 0.0672 0.8594 223 T 0.1096 0.0307 0.8596 224 L 0.1082 0.0267 0.8651 225 N 0.0468 0.3298 0.6234 226 K 0.0571 0.2977 0.6453 227 Q 0.1952 0.1873 0.6174 228 V 0.2044 0.0737 0.7219 229 P 0.1099 0.3421 0.5480 230 V 0.0571 0.4403 0.5026 231 N 0.1495 0.3063 0.5441 232 F 0.1956 0.0398 0.7646 233 P 0.1081 0.0251 0.8668 234 F 0.0051 0.9243 0.0706 235 K 0.0048 0.9417 0.0535 236 K 0.0049 0.9479 0.0472 237 Y 0.0051 0.9548 0.0401 238 C 0.0047 0.9551 0.0402 239 L 0.0048 0.9525 0.0427 240 D 0.0048 0.9507 0.0445 241 V 0.0051 0.9494 0.0455 242 L 0.0051 0.9411 0.0538 243 E 0.0060 0.9256 0.0684 244 H 0.0081 0.8898 0.1022 245 L 0.0200 0.7956 0.1844 246 D 0.0157 0.6876 0.2968 247 M 0.0278 0.5918 0.3803 248 C 0.0540 0.4082 0.5378 249 E 0.0482 0.3626 0.5892 250 K 0.0466 0.4270 0.5264 251 R 0.0688 0.2869 0.6443 252 S 0.0628 0.2370 0.7002 253 I 0.0770 0.2353 0.6877 254 N 0.0805 0.2012 0.7183 255 L 0.0738 0.2498 0.6765 256 D 0.0751 0.2108 0.7141 257 E 0.0500 0.3249 0.6251 258 N 0.0444 0.3043 0.6513 259 D 0.0342 0.4840 0.4818 260 F 0.0246 0.6639 0.3115 261 L 0.0364 0.6907 0.2728 262 K 0.0401 0.7132 0.2468 263 L 0.0434 0.6795 0.2771 264 L 0.0380 0.6542 0.3078 265 L 0.0472 0.5588 0.3939 266 E 0.0410 0.4734 0.4856 267 F 0.0665 0.3384 0.5952 268 N 0.0789 0.1807 0.7405 269 K 0.0412 0.3227 0.6361 270 K 0.0519 0.2071 0.7410 271 G 0.1201 0.1464 0.7334 272 I 0.3337 0.0986 0.5677 273 H 0.5186 0.0944 0.3871 274 F 0.4761 0.1095 0.4144 275 F 0.1772 0.0563 0.7665