# This file is the result of combining several RDB files, specifically # T0326.t06.dssp-ebghstl.rdb (weight 1.53986) # T0326.t06.stride-ebghtl.rdb (weight 1.24869) # T0326.t06.str2.rdb (weight 1.54758) # T0326.t06.alpha.rdb (weight 0.659012) # T0326.t04.dssp-ebghstl.rdb (weight 1.53986) # T0326.t04.stride-ebghtl.rdb (weight 1.24869) # T0326.t04.str2.rdb (weight 1.54758) # T0326.t04.alpha.rdb (weight 0.659012) # T0326.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0326.t2k.stride-ebghtl.rdb (weight 1.24869) # T0326.t2k.str2.rdb (weight 1.54758) # T0326.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 T0326.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0326 # 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 T0326.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 378 # # ============================================ # Comments from T0326.t06.stride-ebghtl.rdb # ============================================ # TARGET T0326 # 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 T0326.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 378 # # ============================================ # Comments from T0326.t06.str2.rdb # ============================================ # TARGET T0326 # 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 T0326.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 378 # # ============================================ # Comments from T0326.t06.alpha.rdb # ============================================ # TARGET T0326 # 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 T0326.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 378 # # ============================================ # Comments from T0326.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0326 # 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 T0326.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 1929 # # ============================================ # Comments from T0326.t04.stride-ebghtl.rdb # ============================================ # TARGET T0326 # 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 T0326.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 1929 # # ============================================ # Comments from T0326.t04.str2.rdb # ============================================ # TARGET T0326 # 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 T0326.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 1929 # # ============================================ # Comments from T0326.t04.alpha.rdb # ============================================ # TARGET T0326 # 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 T0326.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 1929 # # ============================================ # Comments from T0326.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0326 # 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 T0326.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 124 # # ============================================ # Comments from T0326.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0326 # 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 T0326.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 124 # # ============================================ # Comments from T0326.t2k.str2.rdb # ============================================ # TARGET T0326 # 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 T0326.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 29.467 # # ============================================ # Comments from T0326.t2k.alpha.rdb # ============================================ # TARGET T0326 # 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 T0326.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 124 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0863 0.0183 0.8954 2 P 0.1868 0.0135 0.7998 3 I 0.4511 0.0100 0.5389 4 N 0.5416 0.0095 0.4489 5 V 0.2680 0.0171 0.7149 6 P 0.0888 0.1442 0.7670 7 S 0.0197 0.2348 0.7455 8 G 0.0489 0.1236 0.8275 9 L 0.0810 0.0733 0.8457 10 P 0.0751 0.2022 0.7227 11 A 0.0308 0.6439 0.3252 12 V 0.0209 0.8203 0.1588 13 K 0.0190 0.8709 0.1101 14 V 0.0214 0.8783 0.1003 15 L 0.0269 0.8671 0.1060 16 A 0.0261 0.8089 0.1650 17 K 0.0245 0.6730 0.3025 18 E 0.0518 0.2792 0.6690 19 G 0.0500 0.0443 0.9057 20 I 0.1891 0.0460 0.7649 21 F 0.4965 0.0522 0.4513 22 V 0.4991 0.0714 0.4295 23 M 0.3350 0.0739 0.5911 24 T 0.1296 0.0707 0.7997 25 E 0.0135 0.8240 0.1625 26 K 0.0105 0.8220 0.1675 27 R 0.0160 0.8291 0.1549 28 A 0.0253 0.7594 0.2154 29 I 0.0191 0.6491 0.3318 30 H 0.0230 0.4935 0.4835 31 Q 0.0487 0.3299 0.6214 32 D 0.0698 0.2667 0.6635 33 I 0.0890 0.2162 0.6948 34 R 0.0852 0.1191 0.7957 35 P 0.1097 0.2760 0.6143 36 L 0.2178 0.2489 0.5333 37 E 0.5419 0.1649 0.2932 38 I 0.8118 0.0838 0.1044 39 L 0.8317 0.0699 0.0984 40 I 0.8596 0.0457 0.0946 41 L 0.7279 0.0703 0.2018 42 N 0.4571 0.0662 0.4767 43 L 0.2032 0.0945 0.7023 44 M 0.1352 0.0773 0.7875 45 P 0.0585 0.2462 0.6953 46 D 0.0466 0.3278 0.6256 47 K 0.0378 0.4875 0.4746 48 I 0.0506 0.6009 0.3485 49 K 0.0413 0.6818 0.2769 50 T 0.0376 0.7795 0.1829 51 E 0.0078 0.9330 0.0592 52 I 0.0063 0.9486 0.0451 53 Q 0.0054 0.9487 0.0459 54 L 0.0056 0.9517 0.0427 55 L 0.0057 0.9516 0.0428 56 R 0.0049 0.9418 0.0534 57 L 0.0053 0.9194 0.0754 58 L 0.0115 0.7695 0.2191 59 G 0.0157 0.3962 0.5881 60 N 0.0291 0.1984 0.7725 61 T 0.0774 0.0676 0.8550 62 P 0.0585 0.1158 0.8257 63 L 0.1283 0.0878 0.7839 64 Q 0.4474 0.0317 0.5210 65 V 0.6761 0.0074 0.3165 66 N 0.7817 0.0063 0.2120 67 V 0.8792 0.0045 0.1163 68 T 0.8791 0.0107 0.1102 69 L 0.8904 0.0070 0.1027 70 L 0.8438 0.0067 0.1496 71 Y 0.6981 0.0088 0.2930 72 T 0.4089 0.0570 0.5341 73 E 0.1642 0.1629 0.6729 74 T 0.1222 0.1658 0.7121 75 H 0.1688 0.0922 0.7390 76 K 0.1462 0.0958 0.7580 77 P 0.1049 0.1089 0.7862 78 K 0.0621 0.1171 0.8207 79 H 0.0738 0.0816 0.8445 80 T 0.0911 0.0609 0.8480 81 P 0.0565 0.3316 0.6119 82 I 0.0097 0.8239 0.1664 83 E 0.0077 0.8704 0.1219 84 H 0.0144 0.8454 0.1402 85 I 0.0292 0.7978 0.1730 86 L 0.0235 0.7520 0.2244 87 K 0.0232 0.6306 0.3462 88 F 0.0468 0.5021 0.4510 89 Y 0.1064 0.2232 0.6704 90 T 0.1068 0.1428 0.7504 91 T 0.0863 0.0980 0.8157 92 F 0.0071 0.9144 0.0785 93 S 0.0052 0.9376 0.0572 94 A 0.0054 0.9334 0.0612 95 V 0.0065 0.9307 0.0628 96 K 0.0076 0.8857 0.1067 97 D 0.0145 0.6641 0.3213 98 R 0.0579 0.3280 0.6141 99 K 0.1102 0.0713 0.8185 100 F 0.1210 0.0116 0.8674 101 D 0.1216 0.0420 0.8363 102 G 0.8762 0.0055 0.1183 103 F 0.9290 0.0035 0.0675 104 I 0.9307 0.0034 0.0658 105 I 0.8951 0.0095 0.0954 106 T 0.5460 0.0343 0.4197 107 G 0.2255 0.0217 0.7528 108 A 0.1799 0.0174 0.8026 109 P 0.1724 0.0530 0.7746 110 V 0.1333 0.3965 0.4702 111 E 0.1581 0.4312 0.4108 112 L 0.1287 0.3685 0.5028 113 L 0.1400 0.0732 0.7868 114 P 0.0907 0.0734 0.8358 115 F 0.0252 0.5741 0.4007 116 E 0.0154 0.6451 0.3396 117 E 0.0265 0.5966 0.3769 118 V 0.0802 0.3621 0.5578 119 D 0.0699 0.2971 0.6330 120 Y 0.0518 0.5881 0.3602 121 W 0.0076 0.9013 0.0911 122 E 0.0049 0.9443 0.0508 123 E 0.0050 0.9483 0.0467 124 L 0.0048 0.9551 0.0401 125 T 0.0047 0.9592 0.0361 126 E 0.0047 0.9578 0.0376 127 I 0.0047 0.9582 0.0371 128 M 0.0047 0.9595 0.0358 129 E 0.0047 0.9586 0.0367 130 W 0.0048 0.9559 0.0393 131 S 0.0051 0.9441 0.0508 132 R 0.0060 0.9149 0.0792 133 H 0.0183 0.7387 0.2431 134 N 0.0330 0.4469 0.5200 135 V 0.0788 0.2285 0.6927 136 Y 0.1003 0.2441 0.6556 137 S 0.1183 0.3934 0.4883 138 T 0.2015 0.4804 0.3180 139 M 0.1900 0.6142 0.1958 140 F 0.1878 0.6329 0.1793 141 I 0.0955 0.7941 0.1104 142 C 0.0345 0.8463 0.1192 143 W 0.0080 0.9351 0.0570 144 A 0.0069 0.9484 0.0447 145 A 0.0047 0.9561 0.0392 146 Q 0.0047 0.9581 0.0372 147 A 0.0047 0.9591 0.0362 148 G 0.0047 0.9593 0.0361 149 L 0.0047 0.9595 0.0359 150 Y 0.0049 0.9547 0.0405 151 Y 0.0057 0.9325 0.0618 152 F 0.0096 0.8225 0.1679 153 Y 0.0430 0.3589 0.5981 154 G 0.0392 0.0348 0.9259 155 I 0.0904 0.0207 0.8890 156 P 0.1974 0.0235 0.7791 157 K 0.2736 0.0721 0.6544 158 Y 0.3086 0.0706 0.6208 159 E 0.2180 0.0695 0.7125 160 L 0.1582 0.1249 0.7170 161 P 0.1028 0.2194 0.6778 162 Q 0.1552 0.2785 0.5662 163 K 0.3070 0.1984 0.4946 164 L 0.4302 0.1447 0.4250 165 S 0.4959 0.0862 0.4178 166 G 0.4949 0.0461 0.4590 167 V 0.6700 0.0310 0.2990 168 Y 0.6764 0.0232 0.3004 169 K 0.6220 0.0329 0.3451 170 H 0.6189 0.0594 0.3218 171 R 0.6751 0.0537 0.2712 172 V 0.6077 0.0637 0.3286 173 A 0.3193 0.0621 0.6187 174 K 0.1083 0.0590 0.8327 175 D 0.0555 0.1148 0.8298 176 S 0.0752 0.1038 0.8210 177 V 0.0427 0.3614 0.5959 178 L 0.0708 0.4483 0.4809 179 F 0.1230 0.4510 0.4260 180 R 0.0883 0.2722 0.6394 181 G 0.0912 0.0966 0.8121 182 H 0.1250 0.0378 0.8372 183 D 0.0922 0.0608 0.8470 184 D 0.0479 0.2365 0.7155 185 F 0.1708 0.2720 0.5572 186 F 0.4242 0.1380 0.4378 187 W 0.5177 0.0753 0.4070 188 A 0.3862 0.0516 0.5623 189 P 0.2364 0.0898 0.6738 190 H 0.1511 0.1564 0.6925 191 S 0.1284 0.2016 0.6701 192 R 0.1130 0.2848 0.6022 193 Y 0.0744 0.4399 0.4857 194 T 0.0743 0.3607 0.5650 195 E 0.1064 0.2371 0.6564 196 V 0.1194 0.0729 0.8077 197 K 0.0715 0.0306 0.8978 198 K 0.0066 0.8466 0.1467 199 E 0.0067 0.8736 0.1197 200 D 0.0079 0.8863 0.1058 201 I 0.0222 0.8506 0.1272 202 D 0.0207 0.7065 0.2728 203 K 0.0316 0.4614 0.5069 204 V 0.0665 0.1229 0.8106 205 P 0.0410 0.1787 0.7803 206 E 0.0673 0.1604 0.7724 207 L 0.2733 0.1303 0.5965 208 E 0.6246 0.0895 0.2859 209 I 0.8030 0.0598 0.1372 210 L 0.7234 0.0913 0.1853 211 A 0.6813 0.0695 0.2493 212 E 0.4822 0.0488 0.4689 213 S 0.1898 0.0611 0.7491 214 D 0.0611 0.1721 0.7668 215 E 0.0796 0.1464 0.7740 216 A 0.3163 0.0688 0.6149 217 G 0.4505 0.0391 0.5103 218 V 0.8190 0.0145 0.1665 219 Y 0.9014 0.0106 0.0880 220 V 0.9197 0.0062 0.0741 221 V 0.9088 0.0082 0.0830 222 A 0.8552 0.0101 0.1347 223 N 0.4769 0.0171 0.5060 224 K 0.0314 0.1224 0.8463 225 S 0.0451 0.0552 0.8997 226 E 0.1921 0.0485 0.7594 227 R 0.4526 0.0197 0.5276 228 Q 0.8417 0.0049 0.1534 229 I 0.9103 0.0039 0.0858 230 F 0.9107 0.0043 0.0850 231 V 0.8950 0.0060 0.0989 232 T 0.7425 0.0277 0.2298 233 G 0.3852 0.0291 0.5856 234 H 0.1650 0.0396 0.7954 235 P 0.0980 0.2076 0.6945 236 E 0.1309 0.2474 0.6217 237 Y 0.1883 0.1744 0.6373 238 D 0.1421 0.1223 0.7356 239 R 0.0197 0.7051 0.2752 240 Y 0.0144 0.7500 0.2356 241 T 0.0161 0.7969 0.1870 242 L 0.0124 0.8568 0.1308 243 R 0.0061 0.9123 0.0816 244 D 0.0052 0.9394 0.0554 245 E 0.0052 0.9429 0.0519 246 Y 0.0051 0.9458 0.0491 247 Y 0.0055 0.9432 0.0513 248 R 0.0061 0.9422 0.0517 249 D 0.0074 0.9287 0.0639 250 I 0.0061 0.8970 0.0969 251 G 0.0087 0.7577 0.2335 252 R 0.0451 0.4085 0.5464 253 N 0.0455 0.0908 0.8637 254 L 0.0893 0.0448 0.8659 255 K 0.1242 0.0371 0.8387 256 V 0.0925 0.0723 0.8352 257 P 0.0972 0.0828 0.8200 258 I 0.1192 0.0561 0.8247 259 P 0.1074 0.0587 0.8339 260 A 0.1571 0.0791 0.7638 261 N 0.1123 0.0535 0.8343 262 Y 0.1291 0.0493 0.8216 263 F 0.1394 0.0419 0.8187 264 P 0.0815 0.0786 0.8399 265 N 0.0567 0.0979 0.8454 266 D 0.0977 0.0875 0.8148 267 D 0.1046 0.0439 0.8514 268 P 0.0269 0.1999 0.7732 269 T 0.0278 0.1682 0.8040 270 K 0.0647 0.1022 0.8331 271 T 0.0885 0.0442 0.8673 272 P 0.1327 0.0642 0.8031 273 I 0.2705 0.1452 0.5844 274 L 0.3943 0.1867 0.4190 275 T 0.3379 0.2067 0.4554 276 W 0.1930 0.6134 0.1936 277 W 0.1620 0.6430 0.1949 278 S 0.0968 0.6749 0.2283 279 H 0.0354 0.7215 0.2431 280 A 0.0128 0.8572 0.1299 281 H 0.0138 0.8609 0.1252 282 L 0.0161 0.8616 0.1224 283 F 0.0312 0.8297 0.1392 284 F 0.0265 0.8404 0.1330 285 S 0.0415 0.8211 0.1374 286 N 0.0426 0.7815 0.1760 287 W 0.0219 0.8670 0.1110 288 L 0.0120 0.8903 0.0976 289 N 0.0189 0.8740 0.1072 290 Y 0.1220 0.7846 0.0933 291 C 0.1895 0.7182 0.0922 292 I 0.2171 0.6410 0.1419 293 Y 0.3003 0.5075 0.1921 294 Q 0.2935 0.4041 0.3024 295 K 0.2111 0.2520 0.5369 296 T 0.1512 0.0645 0.7843 297 P 0.1010 0.1944 0.7046 298 Y 0.1361 0.1991 0.6648 299 R 0.1314 0.1845 0.6841 300 L 0.0129 0.7635 0.2236 301 E 0.0141 0.7664 0.2194 302 D 0.0251 0.7382 0.2367 303 I 0.0881 0.3857 0.5262 304 H 0.0616 0.1992 0.7393