# This file is the result of combining several RDB files, specifically # T0381.t06.dssp-ebghstl.rdb (weight 1.53986) # T0381.t06.stride-ebghtl.rdb (weight 1.24869) # T0381.t06.str2.rdb (weight 1.54758) # T0381.t06.alpha.rdb (weight 0.659012) # T0381.t04.dssp-ebghstl.rdb (weight 1.53986) # T0381.t04.stride-ebghtl.rdb (weight 1.24869) # T0381.t04.str2.rdb (weight 1.54758) # T0381.t04.alpha.rdb (weight 0.659012) # T0381.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0381.t2k.stride-ebghtl.rdb (weight 1.24869) # T0381.t2k.str2.rdb (weight 1.54758) # T0381.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 T0381.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0381 # 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 T0381.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 1132 # # ============================================ # Comments from T0381.t06.stride-ebghtl.rdb # ============================================ # TARGET T0381 # 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 T0381.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 1132 # # ============================================ # Comments from T0381.t06.str2.rdb # ============================================ # TARGET T0381 # 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 T0381.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 1132 # # ============================================ # Comments from T0381.t06.alpha.rdb # ============================================ # TARGET T0381 # 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 T0381.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 1132 # # ============================================ # Comments from T0381.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0381 # 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 T0381.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 1165 # # ============================================ # Comments from T0381.t04.stride-ebghtl.rdb # ============================================ # TARGET T0381 # 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 T0381.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 1165 # # ============================================ # Comments from T0381.t04.str2.rdb # ============================================ # TARGET T0381 # 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 T0381.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 1165 # # ============================================ # Comments from T0381.t04.alpha.rdb # ============================================ # TARGET T0381 # 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 T0381.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 1165 # # ============================================ # Comments from T0381.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0381 # 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 T0381.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 840 # # ============================================ # Comments from T0381.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0381 # 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 T0381.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 840 # # ============================================ # Comments from T0381.t2k.str2.rdb # ============================================ # TARGET T0381 # 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 T0381.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 840 # # ============================================ # Comments from T0381.t2k.alpha.rdb # ============================================ # TARGET T0381 # 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 T0381.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 840 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1548 0.0348 0.8104 2 T 0.2499 0.0346 0.7155 3 A 0.1707 0.0517 0.7777 4 T 0.1243 0.0531 0.8226 5 E 0.1070 0.0590 0.8340 6 P 0.0954 0.0812 0.8234 7 T 0.0787 0.1266 0.7947 8 E 0.0405 0.3089 0.6506 9 K 0.0425 0.3249 0.6326 10 I 0.0520 0.3242 0.6239 11 L 0.0446 0.2808 0.6746 12 P 0.0459 0.2537 0.7003 13 S 0.0544 0.2257 0.7199 14 P 0.0264 0.4311 0.5426 15 D 0.0245 0.4919 0.4836 16 Y 0.0245 0.6421 0.3335 17 V 0.0188 0.8432 0.1379 18 Q 0.0079 0.9093 0.0828 19 S 0.0059 0.9422 0.0520 20 L 0.0047 0.9574 0.0379 21 A 0.0047 0.9598 0.0355 22 R 0.0047 0.9582 0.0371 23 G 0.0047 0.9590 0.0363 24 L 0.0047 0.9606 0.0348 25 A 0.0047 0.9602 0.0352 26 V 0.0047 0.9591 0.0363 27 I 0.0047 0.9574 0.0379 28 R 0.0047 0.9521 0.0431 29 C 0.0050 0.9337 0.0613 30 F 0.0086 0.8952 0.0962 31 D 0.0113 0.7785 0.2102 32 H 0.0148 0.5448 0.4403 33 R 0.0420 0.2632 0.6948 34 N 0.0463 0.1334 0.8202 35 Q 0.0452 0.1180 0.8368 36 R 0.0802 0.0858 0.8340 37 R 0.1388 0.0401 0.8211 38 T 0.1162 0.0315 0.8522 39 L 0.0055 0.9353 0.0592 40 S 0.0047 0.9558 0.0395 41 D 0.0047 0.9580 0.0373 42 V 0.0047 0.9593 0.0360 43 A 0.0048 0.9576 0.0377 44 R 0.0053 0.9440 0.0507 45 A 0.0067 0.9072 0.0862 46 T 0.0468 0.4870 0.4662 47 D 0.0343 0.0357 0.9300 48 L 0.0505 0.0106 0.9389 49 T 0.0574 0.0150 0.9276 50 R 0.0158 0.8274 0.1567 51 A 0.0050 0.9198 0.0753 52 T 0.0050 0.9450 0.0501 53 A 0.0047 0.9579 0.0374 54 R 0.0047 0.9599 0.0354 55 R 0.0047 0.9610 0.0343 56 F 0.0047 0.9610 0.0343 57 L 0.0047 0.9605 0.0349 58 L 0.0047 0.9603 0.0350 59 T 0.0047 0.9598 0.0355 60 L 0.0047 0.9590 0.0363 61 V 0.0052 0.9457 0.0491 62 E 0.0053 0.8972 0.0975 63 L 0.0434 0.3399 0.6168 64 G 0.0392 0.0481 0.9127 65 Y 0.2100 0.0805 0.7096 66 V 0.7319 0.0469 0.2212 67 A 0.7630 0.0401 0.1969 68 T 0.6980 0.0371 0.2650 69 D 0.3697 0.0282 0.6020 70 G 0.0599 0.0800 0.8601 71 S 0.0311 0.0883 0.8806 72 A 0.3500 0.0728 0.5772 73 F 0.5974 0.0348 0.3677 74 W 0.5575 0.0373 0.4051 75 L 0.3693 0.1005 0.5302 76 T 0.1198 0.2446 0.6356 77 P 0.0116 0.8924 0.0961 78 R 0.0104 0.9201 0.0695 79 V 0.0097 0.9336 0.0567 80 L 0.0075 0.9455 0.0470 81 E 0.0067 0.9429 0.0505 82 L 0.0058 0.9333 0.0608 83 G 0.0053 0.9326 0.0621 84 Y 0.0053 0.9314 0.0633 85 S 0.0052 0.9194 0.0754 86 Y 0.0058 0.8995 0.0947 87 L 0.0087 0.8017 0.1895 88 S 0.0094 0.6448 0.3458 89 S 0.0201 0.4379 0.5419 90 L 0.0567 0.2208 0.7225 91 S 0.0570 0.2113 0.7317 92 L 0.0122 0.8003 0.1876 93 P 0.0073 0.8735 0.1192 94 E 0.0069 0.8909 0.1022 95 V 0.0078 0.8666 0.1256 96 A 0.0114 0.8168 0.1718 97 Q 0.0088 0.8543 0.1369 98 P 0.0054 0.9300 0.0646 99 H 0.0049 0.9476 0.0475 100 L 0.0048 0.9546 0.0406 101 E 0.0048 0.9563 0.0389 102 K 0.0048 0.9564 0.0388 103 L 0.0048 0.9530 0.0422 104 S 0.0049 0.9461 0.0490 105 H 0.0053 0.8932 0.1015 106 K 0.0078 0.8003 0.1919 107 V 0.0499 0.4728 0.4772 108 H 0.0356 0.0589 0.9055 109 E 0.1357 0.0510 0.8133 110 S 0.5578 0.0288 0.4133 111 S 0.7849 0.0186 0.1965 112 S 0.8707 0.0141 0.1152 113 V 0.8814 0.0141 0.1045 114 S 0.8744 0.0165 0.1091 115 I 0.8834 0.0107 0.1059 116 L 0.7861 0.0272 0.1867 117 D 0.4115 0.0376 0.5509 118 G 0.0664 0.0680 0.8656 119 A 0.0855 0.0533 0.8612 120 D 0.6326 0.0136 0.3538 121 I 0.9041 0.0034 0.0925 122 V 0.9263 0.0034 0.0703 123 Y 0.9299 0.0032 0.0669 124 V 0.9217 0.0039 0.0744 125 A 0.8902 0.0062 0.1037 126 R 0.8333 0.0086 0.1582 127 V 0.7321 0.0128 0.2550 128 P 0.4932 0.0257 0.4811 129 V 0.2557 0.0353 0.7090 130 S 0.1602 0.0715 0.7683 131 R 0.1855 0.0422 0.7723 132 I 0.3688 0.0346 0.5966 133 M 0.6179 0.0197 0.3624 134 T 0.7678 0.0161 0.2161 135 V 0.7790 0.0173 0.2038 136 G 0.7337 0.0162 0.2500 137 I 0.5891 0.0195 0.3914 138 T 0.3710 0.0296 0.5994 139 I 0.1813 0.0746 0.7441 140 G 0.1104 0.0547 0.8348 141 T 0.2711 0.0420 0.6869 142 R 0.4820 0.0467 0.4713 143 L 0.4085 0.0522 0.5393 144 P 0.3053 0.1059 0.5888 145 A 0.2117 0.3066 0.4817 146 Y 0.2000 0.3631 0.4369 147 A 0.1599 0.4007 0.4394 148 T 0.1073 0.4159 0.4768 149 S 0.0659 0.6365 0.2977 150 M 0.0383 0.7608 0.2008 151 G 0.0518 0.7671 0.1811 152 R 0.0659 0.8260 0.1081 153 V 0.0919 0.8214 0.0867 154 L 0.0871 0.8197 0.0932 155 L 0.0867 0.7649 0.1485 156 A 0.0664 0.5446 0.3890 157 G 0.0644 0.2521 0.6835 158 L 0.0628 0.0266 0.9105 159 P 0.0547 0.0294 0.9159 160 D 0.0058 0.9002 0.0940 161 D 0.0051 0.9298 0.0652 162 E 0.0051 0.9453 0.0497 163 L 0.0048 0.9526 0.0426 164 D 0.0052 0.9457 0.0490 165 A 0.0049 0.9344 0.0607 166 Y 0.0054 0.9174 0.0772 167 L 0.0069 0.8904 0.1028 168 E 0.0067 0.7781 0.2152 169 K 0.0136 0.6073 0.3791 170 L 0.0607 0.3174 0.6220 171 D 0.0526 0.2048 0.7426 172 I 0.0665 0.2417 0.6918 173 Q 0.0679 0.2470 0.6852 174 R 0.0772 0.2305 0.6923 175 L 0.0923 0.1504 0.7573 176 T 0.0801 0.0757 0.8442 177 E 0.0300 0.2426 0.7274 178 R 0.0374 0.1958 0.7668 179 T 0.0840 0.1415 0.7745 180 I 0.1016 0.1825 0.7159 181 T 0.1053 0.1505 0.7442 182 A 0.0823 0.1145 0.8031 183 R 0.0053 0.9268 0.0679 184 D 0.0050 0.9400 0.0550 185 E 0.0049 0.9477 0.0474 186 L 0.0048 0.9535 0.0417 187 K 0.0047 0.9572 0.0380 188 A 0.0047 0.9556 0.0397 189 A 0.0048 0.9542 0.0410 190 I 0.0048 0.9545 0.0408 191 L 0.0047 0.9539 0.0414 192 A 0.0048 0.9501 0.0451 193 V 0.0049 0.9419 0.0531 194 R 0.0059 0.9257 0.0684 195 A 0.0068 0.8613 0.1319 196 D 0.0419 0.4861 0.4719 197 G 0.0397 0.0946 0.8658 198 I 0.1523 0.0686 0.7791 199 C 0.4573 0.0463 0.4964 200 V 0.4723 0.0555 0.4722 201 L 0.3615 0.0483 0.5902 202 D 0.0784 0.4442 0.4774 203 Q 0.0560 0.4718 0.4722 204 E 0.1290 0.4415 0.4295 205 L 0.1829 0.2978 0.5193 206 E 0.2042 0.1766 0.6192 207 A 0.1078 0.1860 0.7062 208 G 0.1214 0.0838 0.7949 209 L 0.4566 0.0265 0.5169 210 R 0.7032 0.0369 0.2600 211 S 0.8689 0.0119 0.1192 212 M 0.8868 0.0093 0.1039 213 A 0.8798 0.0076 0.1126 214 A 0.8328 0.0068 0.1604 215 P 0.8190 0.0049 0.1760 216 I 0.7338 0.0142 0.2520 217 R 0.7365 0.0110 0.2525 218 G 0.2303 0.0174 0.7522 219 A 0.0214 0.1075 0.8712 220 S 0.0486 0.0220 0.9294 221 G 0.0508 0.0277 0.9215 222 L 0.2903 0.0086 0.7011 223 T 0.8540 0.0031 0.1430 224 V 0.8800 0.0113 0.1087 225 A 0.9225 0.0036 0.0739 226 A 0.9241 0.0033 0.0727 227 V 0.9197 0.0039 0.0765 228 N 0.9097 0.0047 0.0856 229 I 0.8158 0.0151 0.1691 230 S 0.5877 0.0346 0.3777 231 T 0.3097 0.0408 0.6494 232 P 0.2180 0.1154 0.6666 233 A 0.1134 0.3259 0.5607 234 A 0.1130 0.3223 0.5648 235 R 0.1189 0.2335 0.6475 236 Y 0.1212 0.0604 0.8184 237 S 0.0692 0.0346 0.8962 238 L 0.0069 0.8187 0.1744 239 E 0.0060 0.8532 0.1408 240 D 0.0055 0.8857 0.1088 241 L 0.0063 0.8866 0.1070 242 H 0.0057 0.8749 0.1194 243 S 0.0064 0.8233 0.1703 244 D 0.0090 0.7811 0.2100 245 L 0.0104 0.8153 0.1742 246 I 0.0060 0.9035 0.0905 247 P 0.0053 0.9370 0.0578 248 S 0.0049 0.9463 0.0487 249 L 0.0048 0.9538 0.0413 250 R 0.0049 0.9522 0.0429 251 V 0.0048 0.9535 0.0417 252 T 0.0048 0.9533 0.0420 253 A 0.0047 0.9567 0.0386 254 T 0.0048 0.9554 0.0399 255 D 0.0048 0.9540 0.0412 256 I 0.0049 0.9510 0.0441 257 E 0.0053 0.9381 0.0566 258 Q 0.0075 0.9021 0.0904 259 D 0.0168 0.7965 0.1867 260 L 0.0420 0.4091 0.5489 261 A 0.0402 0.2112 0.7486 262 T 0.0718 0.1385 0.7897 263 V 0.0873 0.0943 0.8184 264 N 0.0799 0.0527 0.8674 265 R 0.0343 0.0477 0.9180