# This file is the result of combining several RDB files, specifically # T0355.t06.dssp-ebghstl.rdb (weight 1.53986) # T0355.t06.stride-ebghtl.rdb (weight 1.24869) # T0355.t06.str2.rdb (weight 1.54758) # T0355.t06.alpha.rdb (weight 0.659012) # T0355.t04.dssp-ebghstl.rdb (weight 1.53986) # T0355.t04.stride-ebghtl.rdb (weight 1.24869) # T0355.t04.str2.rdb (weight 1.54758) # T0355.t04.alpha.rdb (weight 0.659012) # T0355.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0355.t2k.stride-ebghtl.rdb (weight 1.24869) # T0355.t2k.str2.rdb (weight 1.54758) # T0355.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 T0355.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0355 # 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 T0355.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 972 # # ============================================ # Comments from T0355.t06.stride-ebghtl.rdb # ============================================ # TARGET T0355 # 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 T0355.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 972 # # ============================================ # Comments from T0355.t06.str2.rdb # ============================================ # TARGET T0355 # 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 T0355.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 972 # # ============================================ # Comments from T0355.t06.alpha.rdb # ============================================ # TARGET T0355 # 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 T0355.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 972 # # ============================================ # Comments from T0355.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0355 # 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 T0355.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 685 # # ============================================ # Comments from T0355.t04.stride-ebghtl.rdb # ============================================ # TARGET T0355 # 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 T0355.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 685 # # ============================================ # Comments from T0355.t04.str2.rdb # ============================================ # TARGET T0355 # 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 T0355.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 685 # # ============================================ # Comments from T0355.t04.alpha.rdb # ============================================ # TARGET T0355 # 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 T0355.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 685 # # ============================================ # Comments from T0355.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0355 # 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 T0355.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 56 # # ============================================ # Comments from T0355.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0355 # 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 T0355.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 56 # # ============================================ # Comments from T0355.t2k.str2.rdb # ============================================ # TARGET T0355 # 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 T0355.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 56 # # ============================================ # Comments from T0355.t2k.alpha.rdb # ============================================ # TARGET T0355 # 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 T0355.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 56 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0718 0.0348 0.8934 2 Q 0.1897 0.1248 0.6855 3 T 0.2650 0.1532 0.5818 4 I 0.1521 0.2683 0.5796 5 S 0.1087 0.2507 0.6407 6 D 0.0264 0.5378 0.4358 7 N 0.0285 0.4854 0.4861 8 A 0.0366 0.5119 0.4515 9 A 0.0116 0.7910 0.1974 10 N 0.0119 0.8385 0.1496 11 A 0.0094 0.8852 0.1054 12 I 0.0097 0.9106 0.0798 13 Q 0.0087 0.9117 0.0796 14 E 0.0095 0.8877 0.1028 15 I 0.0178 0.8043 0.1779 16 F 0.0665 0.5171 0.4164 17 G 0.0434 0.1872 0.7695 18 R 0.0809 0.0776 0.8415 19 S 0.0562 0.0566 0.8873 20 K 0.0995 0.0165 0.8840 21 A 0.3667 0.0104 0.6229 22 L 0.8432 0.0049 0.1520 23 I 0.8934 0.0122 0.0944 24 G 0.9093 0.0049 0.0858 25 M 0.8893 0.0050 0.1057 26 I 0.8212 0.0093 0.1695 27 H 0.6597 0.0156 0.3247 28 C 0.3557 0.0302 0.6141 29 P 0.2070 0.0407 0.7523 30 A 0.2020 0.0600 0.7380 31 F 0.1597 0.0461 0.7941 32 P 0.0650 0.0950 0.8400 33 G 0.0714 0.0919 0.8367 34 A 0.1010 0.0646 0.8344 35 P 0.0793 0.1643 0.7564 36 R 0.0722 0.1351 0.7927 37 Y 0.0901 0.1569 0.7529 38 R 0.0481 0.1121 0.8398 39 N 0.0438 0.0960 0.8603 40 A 0.0788 0.0809 0.8403 41 S 0.0965 0.1320 0.7715 42 M 0.0057 0.9260 0.0683 43 D 0.0048 0.9507 0.0445 44 A 0.0049 0.9530 0.0421 45 I 0.0048 0.9562 0.0391 46 Y 0.0048 0.9565 0.0388 47 D 0.0049 0.9533 0.0417 48 A 0.0050 0.9505 0.0446 49 C 0.0049 0.9535 0.0416 50 M 0.0049 0.9554 0.0397 51 R 0.0048 0.9563 0.0389 52 D 0.0048 0.9521 0.0431 53 A 0.0049 0.9560 0.0391 54 E 0.0047 0.9587 0.0366 55 R 0.0047 0.9585 0.0368 56 L 0.0048 0.9569 0.0383 57 I 0.0050 0.9440 0.0510 58 E 0.0075 0.8327 0.1598 59 G 0.0407 0.3540 0.6054 60 G 0.0456 0.0223 0.9321 61 M 0.0927 0.0092 0.8981 62 H 0.1318 0.0364 0.8318 63 G 0.9089 0.0048 0.0863 64 L 0.9297 0.0036 0.0668 65 I 0.9251 0.0044 0.0705 66 V 0.9090 0.0102 0.0807 67 E 0.7559 0.0226 0.2215 68 N 0.3486 0.0169 0.6345 69 H 0.0809 0.1251 0.7940 70 G 0.0640 0.0917 0.8444 71 D 0.1052 0.0835 0.8113 72 V 0.1425 0.0462 0.8113 73 P 0.2042 0.0719 0.7239 74 F 0.2676 0.0797 0.6527 75 S 0.2369 0.0751 0.6880 76 K 0.1282 0.0774 0.7944 77 P 0.0636 0.1417 0.7947 78 D 0.0415 0.1382 0.8203 79 D 0.0563 0.1078 0.8359 80 I 0.0991 0.0628 0.8381 81 G 0.0697 0.0871 0.8433 82 P 0.0119 0.9087 0.0794 83 E 0.0060 0.9398 0.0541 84 T 0.0068 0.9488 0.0444 85 S 0.0053 0.9568 0.0379 86 A 0.0047 0.9587 0.0366 87 F 0.0047 0.9589 0.0365 88 M 0.0047 0.9590 0.0363 89 S 0.0047 0.9599 0.0353 90 V 0.0048 0.9594 0.0359 91 V 0.0047 0.9584 0.0369 92 T 0.0047 0.9571 0.0382 93 D 0.0049 0.9486 0.0465 94 R 0.0051 0.9282 0.0667 95 I 0.0056 0.9185 0.0758 96 V 0.0075 0.8881 0.1044 97 R 0.0092 0.8235 0.1673 98 T 0.0168 0.7388 0.2444 99 A 0.0862 0.3721 0.5417 100 G 0.0725 0.1157 0.8118 101 V 0.1757 0.0720 0.7524 102 P 0.2422 0.1061 0.6517 103 V 0.4303 0.1763 0.3934 104 G 0.6248 0.1549 0.2203 105 I 0.6495 0.2299 0.1206 106 N 0.5633 0.3163 0.1204 107 V 0.4380 0.3842 0.1778 108 L 0.2623 0.4369 0.3008 109 A 0.1399 0.3708 0.4893 110 N 0.0638 0.3636 0.5726 111 A 0.0486 0.3474 0.6040 112 P 0.0111 0.7626 0.2263 113 I 0.0061 0.9175 0.0765 114 P 0.0056 0.9417 0.0527 115 A 0.0047 0.9560 0.0393 116 F 0.0047 0.9598 0.0355 117 A 0.0047 0.9604 0.0349 118 I 0.0047 0.9606 0.0348 119 A 0.0047 0.9600 0.0353 120 K 0.0048 0.9499 0.0453 121 A 0.0059 0.9020 0.0921 122 G 0.0398 0.5284 0.4318 123 G 0.0444 0.1330 0.8226 124 A 0.0776 0.1160 0.8063 125 K 0.1320 0.2879 0.5801 126 F 0.5399 0.2610 0.1991 127 I 0.6300 0.2458 0.1241 128 R 0.7058 0.1846 0.1096 129 V 0.6338 0.2197 0.1464 130 N 0.4870 0.2432 0.2698 131 Q 0.3665 0.2969 0.3367 132 W 0.4624 0.2742 0.2634 133 A 0.4391 0.2720 0.2890 134 N 0.4175 0.2257 0.3568 135 A 0.4470 0.2284 0.3246 136 Y 0.4945 0.2096 0.2959 137 V 0.4147 0.1942 0.3911 138 A 0.2404 0.1463 0.6133 139 N 0.1028 0.1871 0.7101 140 E 0.0587 0.2032 0.7381 141 G 0.0556 0.1893 0.7551 142 F 0.1094 0.1880 0.7026 143 M 0.1146 0.1963 0.6892 144 E 0.0526 0.3157 0.6317 145 G 0.0163 0.6918 0.2920 146 R 0.0167 0.7840 0.1993 147 A 0.0054 0.9413 0.0533 148 A 0.0048 0.9520 0.0432 149 E 0.0047 0.9566 0.0387 150 A 0.0047 0.9585 0.0368 151 M 0.0047 0.9586 0.0367 152 R 0.0047 0.9553 0.0400 153 Y 0.0047 0.9527 0.0426 154 R 0.0049 0.9440 0.0511 155 S 0.0055 0.9147 0.0798 156 L 0.0075 0.8313 0.1613 157 L 0.0450 0.4931 0.4619 158 R 0.0582 0.0818 0.8600 159 A 0.0727 0.1099 0.8174 160 E 0.0493 0.2215 0.7292 161 H 0.1851 0.1745 0.6403 162 I 0.6565 0.0266 0.3169 163 K 0.7872 0.0205 0.1922 164 V 0.8880 0.0166 0.0954 165 F 0.8263 0.0392 0.1346 166 A 0.7139 0.0438 0.2422 167 D 0.5272 0.0406 0.4322 168 S 0.4215 0.0619 0.5167 169 H 0.3829 0.0775 0.5396 170 V 0.2762 0.2672 0.4566 171 K 0.1802 0.2717 0.5482 172 H 0.1535 0.2385 0.6080 173 G 0.1511 0.2178 0.6310 174 A 0.1575 0.2231 0.6194 175 H 0.1659 0.2421 0.5921 176 A 0.1637 0.1858 0.6505 177 I 0.1575 0.1453 0.6973 178 T 0.1380 0.1344 0.7277 179 A 0.1225 0.1736 0.7039 180 D 0.1402 0.1543 0.7055 181 R 0.2815 0.1821 0.5364 182 S 0.3273 0.2241 0.4485 183 I 0.1170 0.7651 0.1178 184 D 0.0591 0.8623 0.0786 185 E 0.0374 0.8859 0.0767 186 L 0.0206 0.9119 0.0675 187 T 0.0150 0.9210 0.0640 188 R 0.0109 0.9313 0.0577 189 D 0.0077 0.9396 0.0528 190 L 0.0070 0.9355 0.0575 191 A 0.0071 0.9134 0.0795 192 F 0.0145 0.6942 0.2913 193 F 0.0340 0.3022 0.6638 194 D 0.0665 0.0747 0.8588 195 A 0.1056 0.0159 0.8786 196 D 0.1082 0.0465 0.8453 197 G 0.8972 0.0050 0.0977 198 V 0.9291 0.0035 0.0674 199 I 0.9264 0.0037 0.0698 200 A 0.8845 0.0070 0.1085 201 T 0.5218 0.0221 0.4561 202 G 0.2351 0.0424 0.7225 203 Q 0.1412 0.1915 0.6673 204 R 0.1500 0.2147 0.6353 205 T 0.0836 0.1445 0.7719 206 G 0.0504 0.0538 0.8958 207 N 0.0730 0.0332 0.8938 208 S 0.1161 0.0316 0.8523 209 A 0.0995 0.0403 0.8602 210 S 0.0795 0.0376 0.8829 211 L 0.0052 0.9288 0.0660 212 E 0.0048 0.9474 0.0478 213 E 0.0049 0.9496 0.0455 214 I 0.0047 0.9542 0.0411 215 E 0.0065 0.9457 0.0478 216 E 0.0062 0.9273 0.0665 217 I 0.0094 0.9073 0.0834 218 G 0.0122 0.8715 0.1163 219 A 0.0143 0.7228 0.2629 220 A 0.0382 0.4024 0.5594 221 T 0.0565 0.0820 0.8615 222 H 0.0365 0.0469 0.9166 223 L 0.1123 0.0111 0.8767 224 P 0.4114 0.0119 0.5767 225 L 0.8965 0.0064 0.0971 226 L 0.9211 0.0039 0.0750 227 V 0.8700 0.0154 0.1146 228 G 0.6216 0.0228 0.3556 229 S 0.2262 0.0479 0.7259 230 G 0.1304 0.0514 0.8181 231 V 0.1931 0.0258 0.7812 232 N 0.1153 0.0187 0.8660 233 E 0.0092 0.7678 0.2231 234 G 0.0066 0.8032 0.1903 235 N 0.0112 0.8505 0.1383 236 I 0.0051 0.9443 0.0505 237 V 0.0049 0.9511 0.0441 238 E 0.0053 0.9490 0.0457 239 I 0.0054 0.9406 0.0540 240 L 0.0088 0.9082 0.0830 241 K 0.0063 0.8097 0.1840 242 R 0.0187 0.6155 0.3659 243 T 0.0942 0.1061 0.7997 244 S 0.0517 0.0595 0.8888 245 G 0.7062 0.0159 0.2779 246 V 0.9202 0.0038 0.0760 247 I 0.9271 0.0037 0.0693 248 V 0.8741 0.0091 0.1168 249 A 0.5875 0.0277 0.3848 250 S 0.3791 0.0945 0.5264 251 S 0.4405 0.1358 0.4237 252 L 0.5686 0.0903 0.3410 253 K 0.3839 0.0765 0.5396 254 E 0.1890 0.1179 0.6930 255 G 0.0613 0.0423 0.8964 256 G 0.0857 0.0429 0.8715 257 V 0.3756 0.0412 0.5832 258 W 0.5142 0.0551 0.4307 259 W 0.2504 0.1051 0.6445 260 N 0.1429 0.0739 0.7831 261 P 0.1400 0.1059 0.7541 262 V 0.2041 0.0466 0.7493 263 E 0.1291 0.0595 0.8113 264 L 0.0054 0.9248 0.0698 265 A 0.0052 0.9420 0.0529 266 R 0.0052 0.9479 0.0469 267 V 0.0047 0.9582 0.0370 268 R 0.0047 0.9600 0.0353 269 S 0.0047 0.9588 0.0365 270 F 0.0047 0.9580 0.0373 271 V 0.0047 0.9588 0.0366 272 A 0.0047 0.9573 0.0380 273 A 0.0047 0.9550 0.0403 274 A 0.0049 0.9521 0.0430 275 R 0.0050 0.9488 0.0462 276 P 0.0055 0.9296 0.0649 277 G 0.0073 0.9010 0.0917 278 L 0.0116 0.8832 0.1052 279 E 0.0113 0.8407 0.1480 280 A 0.0160 0.7462 0.2378 281 L 0.0309 0.5506 0.4185 282 E 0.0351 0.3437 0.6211 283 H 0.0515 0.3239 0.6246 284 H 0.0760 0.2653 0.6588 285 H 0.1310 0.2162 0.6528 286 H 0.1589 0.1493 0.6918 287 H 0.1173 0.0909 0.7919 288 H 0.0479 0.0371 0.9150