# This file is the result of combining several RDB files, specifically # T0294.t06.dssp-ebghstl.rdb (weight 1.53986) # T0294.t06.stride-ebghtl.rdb (weight 1.24869) # T0294.t06.str2.rdb (weight 1.54758) # T0294.t06.alpha.rdb (weight 0.659012) # T0294.t04.dssp-ebghstl.rdb (weight 1.53986) # T0294.t04.stride-ebghtl.rdb (weight 1.24869) # T0294.t04.str2.rdb (weight 1.54758) # T0294.t04.alpha.rdb (weight 0.659012) # T0294.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0294.t2k.stride-ebghtl.rdb (weight 1.24869) # T0294.t2k.str2.rdb (weight 1.54758) # T0294.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 T0294.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0294 # 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 T0294.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 2029 # # ============================================ # Comments from T0294.t06.stride-ebghtl.rdb # ============================================ # TARGET T0294 # 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 T0294.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 2029 # # ============================================ # Comments from T0294.t06.str2.rdb # ============================================ # TARGET T0294 # 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 T0294.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 2029 # # ============================================ # Comments from T0294.t06.alpha.rdb # ============================================ # TARGET T0294 # 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 T0294.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 2029 # # ============================================ # Comments from T0294.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0294 # 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 T0294.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 2028 # # ============================================ # Comments from T0294.t04.stride-ebghtl.rdb # ============================================ # TARGET T0294 # 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 T0294.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 2028 # # ============================================ # Comments from T0294.t04.str2.rdb # ============================================ # TARGET T0294 # 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 T0294.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 2028 # # ============================================ # Comments from T0294.t04.alpha.rdb # ============================================ # TARGET T0294 # 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 T0294.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 2028 # # ============================================ # Comments from T0294.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0294 # 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 T0294.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 1744 # # ============================================ # Comments from T0294.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0294 # 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 T0294.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 1744 # # ============================================ # Comments from T0294.t2k.str2.rdb # ============================================ # TARGET T0294 # 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 T0294.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 982.356 # # ============================================ # Comments from T0294.t2k.alpha.rdb # ============================================ # TARGET T0294 # 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 T0294.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 1744 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0961 0.0931 0.8108 2 R 0.0906 0.0506 0.8588 3 P 0.1175 0.0675 0.8150 4 V 0.1691 0.0839 0.7471 5 R 0.1929 0.0626 0.7445 6 L 0.1812 0.0904 0.7283 7 M 0.1757 0.0853 0.7390 8 K 0.2559 0.0424 0.7017 9 V 0.4402 0.0268 0.5330 10 F 0.6120 0.0125 0.3756 11 V 0.8250 0.0098 0.1652 12 T 0.8673 0.0086 0.1241 13 R 0.8769 0.0084 0.1147 14 R 0.7968 0.0133 0.1899 15 I 0.5317 0.0251 0.4432 16 P 0.1847 0.0763 0.7390 17 A 0.0897 0.0886 0.8218 18 E 0.0473 0.1678 0.7849 19 G 0.0580 0.2294 0.7125 20 R 0.0593 0.5234 0.4172 21 V 0.0672 0.7322 0.2006 22 A 0.0564 0.8178 0.1258 23 L 0.0379 0.8572 0.1049 24 A 0.0293 0.8703 0.1004 25 R 0.0221 0.8695 0.1084 26 A 0.0202 0.8082 0.1716 27 A 0.0182 0.6619 0.3199 28 D 0.0346 0.4512 0.5141 29 C 0.0664 0.1992 0.7344 30 E 0.1167 0.0539 0.8295 31 V 0.4336 0.0233 0.5431 32 E 0.7811 0.0128 0.2061 33 Q 0.8360 0.0097 0.1542 34 W 0.7247 0.0171 0.2582 35 D 0.5570 0.0246 0.4184 36 S 0.2934 0.0410 0.6656 37 D 0.1071 0.0766 0.8163 38 E 0.0770 0.0784 0.8447 39 P 0.0663 0.0860 0.8477 40 I 0.0702 0.0794 0.8504 41 P 0.0592 0.0798 0.8611 42 A 0.0255 0.6492 0.3253 43 K 0.0092 0.8519 0.1389 44 E 0.0077 0.8837 0.1086 45 L 0.0070 0.9090 0.0840 46 E 0.0078 0.9058 0.0864 47 R 0.0084 0.8873 0.1043 48 G 0.0104 0.8295 0.1600 49 V 0.0172 0.7155 0.2674 50 A 0.0276 0.5650 0.4075 51 G 0.0370 0.4237 0.5393 52 A 0.0629 0.3239 0.6132 53 H 0.1687 0.2111 0.6202 54 G 0.3847 0.1710 0.4444 55 L 0.7261 0.1027 0.1712 56 L 0.8243 0.0740 0.1017 57 C 0.8432 0.0603 0.0965 58 L 0.7798 0.0778 0.1424 59 L 0.5725 0.0892 0.3384 60 S 0.2397 0.0798 0.6805 61 D 0.1270 0.1083 0.7646 62 H 0.1301 0.1131 0.7568 63 V 0.1438 0.0999 0.7563 64 D 0.0901 0.1041 0.8058 65 K 0.0559 0.2846 0.6596 66 R 0.0071 0.8815 0.1115 67 I 0.0072 0.9019 0.0909 68 L 0.0063 0.9114 0.0823 69 D 0.0058 0.9170 0.0771 70 A 0.0075 0.8382 0.1543 71 A 0.0128 0.6735 0.3137 72 G 0.0500 0.1967 0.7534 73 A 0.0133 0.1854 0.8013 74 N 0.0268 0.0952 0.8780 75 L 0.3623 0.0302 0.6075 76 K 0.7855 0.0318 0.1826 77 V 0.9217 0.0064 0.0718 78 I 0.9115 0.0141 0.0743 79 S 0.9135 0.0107 0.0758 80 T 0.8596 0.0198 0.1206 81 M 0.6147 0.0547 0.3306 82 S 0.3478 0.0638 0.5884 83 V 0.2852 0.0738 0.6410 84 G 0.2435 0.0686 0.6879 85 I 0.2797 0.0912 0.6291 86 D 0.1924 0.1258 0.6817 87 H 0.2746 0.1225 0.6029 88 L 0.4442 0.0749 0.4809 89 A 0.2917 0.0962 0.6121 90 L 0.0066 0.9092 0.0842 91 D 0.0049 0.9425 0.0526 92 E 0.0050 0.9467 0.0483 93 I 0.0056 0.9455 0.0489 94 K 0.0077 0.9189 0.0735 95 K 0.0103 0.8308 0.1589 96 R 0.0475 0.2924 0.6602 97 G 0.0408 0.0185 0.9406 98 I 0.1178 0.0085 0.8737 99 R 0.6522 0.0075 0.3404 100 V 0.8509 0.0101 0.1390 101 G 0.8340 0.0227 0.1433 102 Y 0.7225 0.0165 0.2611 103 T 0.2566 0.0237 0.7196 104 P 0.0612 0.0909 0.8479 105 D 0.0479 0.0960 0.8561 106 V 0.0848 0.1192 0.7960 107 L 0.0971 0.1116 0.7913 108 T 0.0214 0.6337 0.3450 109 D 0.0055 0.8961 0.0984 110 T 0.0048 0.9456 0.0496 111 T 0.0047 0.9554 0.0399 112 A 0.0047 0.9597 0.0357 113 E 0.0047 0.9608 0.0345 114 L 0.0046 0.9612 0.0342 115 A 0.0047 0.9610 0.0344 116 V 0.0047 0.9611 0.0343 117 S 0.0046 0.9613 0.0340 118 L 0.0046 0.9608 0.0345 119 L 0.0047 0.9597 0.0356 120 L 0.0047 0.9568 0.0384 121 T 0.0049 0.9492 0.0459 122 T 0.0052 0.9339 0.0609 123 C 0.0064 0.8748 0.1188 124 R 0.0133 0.5839 0.4027 125 R 0.0215 0.4141 0.5645 126 L 0.0497 0.2838 0.6665 127 P 0.0272 0.5063 0.4665 128 E 0.0104 0.7833 0.2064 129 A 0.0090 0.8231 0.1679 130 I 0.0099 0.9048 0.0854 131 E 0.0108 0.9305 0.0587 132 E 0.0115 0.9238 0.0647 133 V 0.0131 0.9118 0.0751 134 K 0.0138 0.8836 0.1027 135 N 0.0389 0.4731 0.4880 136 G 0.0307 0.1296 0.8397 137 G 0.0854 0.1075 0.8072 138 W 0.2104 0.1596 0.6299 139 T 0.1398 0.2446 0.6155 140 S 0.1164 0.2472 0.6364 141 W 0.0940 0.1861 0.7199 142 K 0.0642 0.1478 0.7880 143 P 0.0567 0.3360 0.6073 144 L 0.0671 0.3522 0.5806 145 W 0.0848 0.3566 0.5586 146 L 0.1118 0.2925 0.5957 147 C 0.1361 0.2090 0.6549 148 G 0.1625 0.1327 0.7049 149 Y 0.3005 0.1065 0.5930 150 G 0.3760 0.0870 0.5369 151 L 0.2977 0.1091 0.5932 152 T 0.1211 0.1065 0.7724 153 Q 0.0836 0.0616 0.8548 154 S 0.3902 0.0165 0.5933 155 T 0.7626 0.0066 0.2308 156 V 0.8742 0.0210 0.1049 157 G 0.8996 0.0111 0.0892 158 I 0.9192 0.0076 0.0732 159 I 0.8470 0.0345 0.1184 160 G 0.6198 0.0270 0.3531 161 L 0.2073 0.0974 0.6954 162 G 0.0686 0.1648 0.7666 163 R 0.0122 0.8831 0.1047 164 I 0.0050 0.9476 0.0474 165 G 0.0047 0.9568 0.0384 166 Q 0.0048 0.9594 0.0358 167 A 0.0047 0.9605 0.0348 168 I 0.0047 0.9593 0.0360 169 A 0.0047 0.9561 0.0392 170 R 0.0048 0.9463 0.0489 171 R 0.0048 0.9196 0.0756 172 L 0.0063 0.8098 0.1840 173 K 0.0058 0.7668 0.2274 174 P 0.0071 0.7006 0.2923 175 F 0.0494 0.4050 0.5456 176 G 0.0834 0.0319 0.8847 177 V 0.2781 0.0080 0.7138 178 Q 0.7616 0.0048 0.2335 179 R 0.9248 0.0030 0.0722 180 F 0.9203 0.0050 0.0747 181 L 0.9065 0.0039 0.0896 182 Y 0.7375 0.0145 0.2480 183 T 0.2830 0.0116 0.7054 184 G 0.0499 0.0917 0.8584 185 R 0.0746 0.0765 0.8489 186 Q 0.0530 0.1269 0.8200 187 P 0.0512 0.1060 0.8428 188 R 0.0412 0.2526 0.7062 189 P 0.0294 0.4098 0.5607 190 E 0.0204 0.6362 0.3434 191 E 0.0172 0.6842 0.2986 192 A 0.0180 0.7257 0.2563 193 A 0.0297 0.6608 0.3095 194 E 0.0424 0.5038 0.4538 195 F 0.0589 0.2885 0.6526 196 Q 0.1115 0.1732 0.7153 197 A 0.2327 0.1312 0.6361 198 E 0.3702 0.1016 0.5281 199 F 0.3645 0.0609 0.5745 200 V 0.2119 0.0635 0.7246 201 S 0.1749 0.0429 0.7822 202 T 0.0074 0.8985 0.0941 203 P 0.0055 0.9348 0.0598 204 E 0.0056 0.9387 0.0557 205 L 0.0057 0.9285 0.0658 206 A 0.0076 0.8551 0.1373 207 A 0.0059 0.5243 0.4698 208 Q 0.0183 0.3185 0.6632 209 S 0.1062 0.0807 0.8132 210 D 0.0803 0.0751 0.8447 211 F 0.8595 0.0097 0.1309 212 I 0.9301 0.0035 0.0664 213 V 0.9270 0.0038 0.0692 214 V 0.9119 0.0052 0.0829 215 A 0.6479 0.0177 0.3344 216 C 0.2456 0.0136 0.7408 217 S 0.1256 0.0170 0.8573 218 L 0.1338 0.0395 0.8267 219 T 0.0602 0.0232 0.9166 220 P 0.0075 0.5969 0.3956 221 A 0.0089 0.5645 0.4266 222 T 0.0212 0.6180 0.3608 223 E 0.0221 0.6943 0.2836 224 G 0.0332 0.5635 0.4033 225 L 0.0973 0.5129 0.3898 226 C 0.1878 0.2435 0.5686 227 N 0.0894 0.1318 0.7787 228 K 0.0061 0.9291 0.0648 229 D 0.0053 0.9423 0.0525 230 F 0.0052 0.9403 0.0545 231 F 0.0066 0.9276 0.0657 232 Q 0.0089 0.8369 0.1542 233 K 0.0147 0.5647 0.4206 234 M 0.0708 0.2147 0.7145 235 K 0.0728 0.0812 0.8460 236 E 0.0453 0.1076 0.8471 237 T 0.1407 0.0475 0.8118 238 A 0.8133 0.0074 0.1794 239 V 0.9264 0.0033 0.0703 240 F 0.9308 0.0033 0.0660 241 I 0.9123 0.0055 0.0821 242 N 0.8360 0.0060 0.1580 243 I 0.4539 0.0493 0.4968 244 S 0.1983 0.0696 0.7322 245 R 0.1258 0.1200 0.7542 246 G 0.0957 0.1534 0.7509 247 D 0.1652 0.2164 0.6184 248 V 0.3942 0.1457 0.4601 249 V 0.4111 0.0711 0.5178 250 N 0.2000 0.0608 0.7392 251 Q 0.0084 0.9063 0.0853 252 D 0.0052 0.9493 0.0455 253 D 0.0049 0.9535 0.0416 254 L 0.0048 0.9542 0.0410 255 Y 0.0050 0.9554 0.0396 256 Q 0.0050 0.9497 0.0453 257 A 0.0050 0.9468 0.0483 258 L 0.0066 0.9354 0.0581 259 A 0.0065 0.8872 0.1063 260 S 0.0439 0.2965 0.6596 261 G 0.0283 0.0394 0.9323 262 K 0.0943 0.0344 0.8714 263 I 0.4883 0.0196 0.4921 264 A 0.6493 0.0329 0.3178 265 A 0.8559 0.0109 0.1332 266 A 0.8802 0.0093 0.1104 267 G 0.8801 0.0092 0.1107 268 L 0.8113 0.0129 0.1758 269 D 0.7078 0.0200 0.2723 270 V 0.5573 0.0549 0.3878 271 T 0.3502 0.0588 0.5910 272 S 0.2248 0.0670 0.7081 273 P 0.1283 0.0642 0.8074 274 E 0.0852 0.0380 0.8769 275 P 0.1147 0.0370 0.8483 276 L 0.1587 0.0475 0.7938 277 P 0.0679 0.0770 0.8550 278 T 0.0471 0.1220 0.8308 279 N 0.0443 0.1187 0.8371 280 H 0.0662 0.1386 0.7952 281 P 0.0542 0.3332 0.6126 282 L 0.0581 0.4727 0.4692 283 L 0.0690 0.4198 0.5112 284 T 0.1312 0.2075 0.6614 285 L 0.0913 0.0429 0.8658 286 K 0.0273 0.1222 0.8505 287 N 0.1282 0.0571 0.8147 288 C 0.8164 0.0079 0.1757 289 V 0.8855 0.0085 0.1060 290 I 0.8716 0.0085 0.1199 291 L 0.7099 0.0177 0.2724 292 P 0.4632 0.0528 0.4841 293 H 0.2899 0.1063 0.6038 294 I 0.1974 0.2257 0.5770 295 G 0.1282 0.2587 0.6132 296 S 0.1066 0.2726 0.6207 297 A 0.0923 0.2257 0.6821 298 T 0.0592 0.2129 0.7280 299 H 0.0051 0.9259 0.0689 300 R 0.0048 0.9460 0.0492 301 T 0.0048 0.9490 0.0462 302 R 0.0047 0.9550 0.0403 303 N 0.0048 0.9517 0.0435 304 T 0.0049 0.9466 0.0485 305 M 0.0048 0.9501 0.0451 306 S 0.0047 0.9555 0.0397 307 L 0.0048 0.9568 0.0384 308 L 0.0047 0.9585 0.0368 309 A 0.0047 0.9592 0.0361 310 A 0.0047 0.9584 0.0369 311 N 0.0047 0.9581 0.0372 312 N 0.0048 0.9555 0.0397 313 L 0.0047 0.9573 0.0380 314 L 0.0047 0.9583 0.0370 315 A 0.0049 0.9431 0.0520 316 G 0.0059 0.9182 0.0759 317 L 0.0106 0.7982 0.1912 318 R 0.0320 0.4662 0.5017 319 G 0.0303 0.0795 0.8901 320 E 0.0659 0.0208 0.9133 321 P 0.1334 0.0216 0.8449 322 M 0.1147 0.0399 0.8453 323 P 0.0737 0.1110 0.8153 324 S 0.1012 0.1642 0.7347 325 E 0.1645 0.1680 0.6675 326 L 0.2255 0.0723 0.7023 327 K 0.1979 0.0431 0.7591 328 L 0.0596 0.1216 0.8188