# This file is the result of combining several RDB files, specifically # T0321.t04.dssp-ebghstl.rdb (weight 1.53986) # T0321.t04.stride-ebghtl.rdb (weight 1.24869) # T0321.t04.str2.rdb (weight 1.54758) # T0321.t04.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 T0321.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0321 # 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 T0321.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 65 # # ============================================ # Comments from T0321.t04.stride-ebghtl.rdb # ============================================ # TARGET T0321 # 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 T0321.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 65 # # ============================================ # Comments from T0321.t04.str2.rdb # ============================================ # TARGET T0321 # 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 T0321.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 65 # # ============================================ # Comments from T0321.t04.alpha.rdb # ============================================ # TARGET T0321 # 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 T0321.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 65 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0171 0.2953 0.6876 2 W 0.0206 0.7522 0.2272 3 E 0.0155 0.8591 0.1254 4 I 0.0071 0.9338 0.0591 5 Y 0.0053 0.9448 0.0499 6 D 0.0053 0.9426 0.0521 7 A 0.0058 0.9351 0.0590 8 M 0.0067 0.9121 0.0812 9 I 0.0143 0.8223 0.1634 10 N 0.0163 0.6058 0.3779 11 G 0.0220 0.3376 0.6404 12 I 0.0618 0.0374 0.9008 13 P 0.0505 0.0749 0.8746 14 E 0.0277 0.2890 0.6833 15 D 0.0576 0.2439 0.6985 16 F 0.2402 0.0803 0.6796 17 L 0.4971 0.0310 0.4719 18 V 0.6179 0.0741 0.3080 19 D 0.5807 0.1090 0.3103 20 E 0.6767 0.1148 0.2085 21 L 0.7825 0.0684 0.1492 22 V 0.8285 0.0419 0.1296 23 C 0.7263 0.0426 0.2312 24 G 0.4551 0.0287 0.5161 25 T 0.3359 0.0260 0.6381 26 T 0.4020 0.0344 0.5636 27 H 0.5830 0.0262 0.3907 28 S 0.7888 0.0174 0.1938 29 V 0.8773 0.0125 0.1102 30 I 0.8802 0.0110 0.1088 31 R 0.7705 0.0261 0.2034 32 S 0.3836 0.0371 0.5793 33 G 0.0638 0.0496 0.8866 34 N 0.1075 0.0496 0.8429 35 G 0.5741 0.0340 0.3920 36 V 0.7878 0.0246 0.1876 37 G 0.8294 0.0163 0.1544 38 L 0.8299 0.0194 0.1507 39 G 0.6678 0.0149 0.3173 40 P 0.4742 0.0223 0.5035 41 N 0.2486 0.0243 0.7271 42 R 0.1133 0.0306 0.8560 43 P 0.0750 0.1013 0.8237 44 F 0.0761 0.1318 0.7921 45 E 0.0664 0.1769 0.7566 46 T 0.1013 0.1626 0.7360 47 R 0.1744 0.1528 0.6727 48 M 0.1746 0.1125 0.7130 49 P 0.1622 0.1557 0.6821 50 M 0.1133 0.2578 0.6289 51 L 0.1073 0.2915 0.6013 52 T 0.0638 0.4511 0.4851 53 Q 0.0476 0.4934 0.4591 54 N 0.0596 0.4904 0.4500 55 L 0.0931 0.4158 0.4911 56 L 0.0577 0.2087 0.7336 57 G 0.0387 0.0773 0.8840 58 L 0.1063 0.0478 0.8459 59 P 0.1717 0.0567 0.7716 60 L 0.0070 0.9333 0.0597 61 R 0.0074 0.9515 0.0411 62 V 0.0077 0.9512 0.0410 63 A 0.0105 0.9426 0.0469 64 A 0.0084 0.9143 0.0773 65 G 0.0131 0.7784 0.2085 66 C 0.0191 0.6980 0.2829 67 V 0.0362 0.6134 0.3504 68 K 0.0362 0.4650 0.4989 69 S 0.0570 0.3284 0.6147 70 W 0.0257 0.4491 0.5252 71 N 0.0527 0.5020 0.4453 72 Y 0.0061 0.9149 0.0790 73 V 0.0048 0.9547 0.0406 74 E 0.0047 0.9593 0.0360 75 A 0.0047 0.9584 0.0368 76 S 0.0047 0.9593 0.0360 77 I 0.0047 0.9603 0.0350 78 G 0.0047 0.9607 0.0347 79 L 0.0047 0.9606 0.0348 80 A 0.0047 0.9611 0.0343 81 A 0.0046 0.9606 0.0348 82 I 0.0047 0.9581 0.0372 83 N 0.0048 0.9510 0.0442 84 A 0.0050 0.9284 0.0666 85 Y 0.0075 0.8560 0.1365 86 Y 0.0240 0.6158 0.3602 87 N 0.0421 0.3422 0.6156 88 N 0.0818 0.1189 0.7993 89 P 0.0178 0.6205 0.3618 90 Q 0.0300 0.6628 0.3072 91 V 0.0604 0.7151 0.2245 92 A 0.1225 0.5802 0.2973 93 R 0.0955 0.4581 0.4464 94 E 0.0646 0.3518 0.5836 95 H 0.0578 0.1526 0.7896 96 G 0.0913 0.0610 0.8477 97 V 0.3581 0.0366 0.6053 98 I 0.6213 0.0316 0.3470 99 F 0.5011 0.0563 0.4427 100 S 0.2962 0.0994 0.6044 101 D 0.1292 0.1548 0.7159 102 A 0.1029 0.1999 0.6972 103 K 0.0965 0.2194 0.6841 104 R 0.1498 0.2263 0.6239 105 V 0.1617 0.3569 0.4814 106 E 0.1103 0.5066 0.3831 107 D 0.0955 0.5704 0.3341 108 R 0.0811 0.5013 0.4176 109 M 0.1032 0.3521 0.5446 110 N 0.0716 0.2316 0.6968 111 D 0.1032 0.0815 0.8153 112 P 0.0303 0.6666 0.3031 113 F 0.0551 0.6972 0.2477 114 I 0.1143 0.6649 0.2207 115 M 0.1961 0.5405 0.2634 116 S 0.2606 0.4113 0.3282 117 Q 0.2161 0.3796 0.4043 118 N 0.2120 0.3565 0.4315 119 E 0.1756 0.3335 0.4908 120 V 0.1950 0.1956 0.6093 121 K 0.0588 0.0825 0.8586 122 G 0.0437 0.0370 0.9193 123 K 0.2422 0.0139 0.7439 124 K 0.8072 0.0039 0.1888 125 V 0.9184 0.0039 0.0777 126 G 0.9311 0.0034 0.0655 127 V 0.9294 0.0032 0.0673 128 V 0.8584 0.0231 0.1185 129 G 0.5651 0.0165 0.4184 130 H 0.1987 0.0379 0.7634 131 F 0.0842 0.1096 0.8062 132 P 0.0472 0.2862 0.6666 133 H 0.0694 0.4707 0.4599 134 L 0.0151 0.8330 0.1518 135 E 0.0100 0.8770 0.1130 136 S 0.0141 0.8387 0.1472 137 L 0.0287 0.7553 0.2160 138 L 0.0683 0.5499 0.3818 139 E 0.0727 0.4034 0.5239 140 P 0.0658 0.3101 0.6242 141 I 0.1416 0.1834 0.6750 142 C 0.2203 0.0553 0.7244 143 D 0.5592 0.0215 0.4193 144 L 0.8332 0.0046 0.1622 145 S 0.9062 0.0044 0.0894 146 I 0.9214 0.0034 0.0752 147 L 0.8973 0.0061 0.0965 148 E 0.8169 0.0053 0.1778 149 W 0.4481 0.0162 0.5357 150 S 0.1659 0.0105 0.8236 151 P 0.0442 0.0998 0.8560 152 E 0.0494 0.1041 0.8464 153 E 0.0643 0.1646 0.7711 154 G 0.0934 0.0861 0.8205 155 D 0.2035 0.0726 0.7239 156 Y 0.1511 0.0385 0.8104 157 P 0.0932 0.0466 0.8602 158 L 0.0491 0.2703 0.6806 159 P 0.0204 0.4995 0.4800 160 A 0.0165 0.6731 0.3105 161 S 0.0325 0.6527 0.3148 162 E 0.0204 0.6311 0.3485 163 F 0.0361 0.5242 0.4397 164 I 0.0715 0.4663 0.4622 165 L 0.0636 0.3197 0.6167 166 P 0.0146 0.4829 0.5026 167 E 0.0263 0.4028 0.5709 168 C 0.2008 0.0945 0.7046 169 D 0.1180 0.0891 0.7929 170 Y 0.8443 0.0345 0.1211 171 V 0.9012 0.0270 0.0719 172 Y 0.8862 0.0429 0.0709 173 I 0.7566 0.0913 0.1521 174 T 0.3249 0.1694 0.5056 175 C 0.0986 0.5122 0.3892 176 A 0.0558 0.7189 0.2254 177 S 0.0449 0.8441 0.1111 178 V 0.0340 0.8511 0.1149 179 V 0.0272 0.7704 0.2024 180 D 0.0430 0.5381 0.4189 181 K 0.0136 0.4079 0.5785 182 T 0.0259 0.5209 0.4532 183 L 0.0049 0.9187 0.0764 184 P 0.0048 0.9496 0.0456 185 R 0.0048 0.9528 0.0424 186 L 0.0048 0.9511 0.0441 187 L 0.0049 0.9310 0.0641 188 E 0.0053 0.8171 0.1775 189 L 0.0092 0.7100 0.2809 190 S 0.0298 0.4188 0.5514 191 R 0.0173 0.3740 0.6087 192 N 0.0236 0.2289 0.7475 193 A 0.0915 0.1226 0.7859 194 R 0.1866 0.0268 0.7866 195 R 0.6904 0.0087 0.3010 196 I 0.9148 0.0039 0.0814 197 T 0.9301 0.0034 0.0665 198 L 0.9263 0.0035 0.0701 199 V 0.8321 0.0132 0.1547 200 G 0.3769 0.0181 0.6050 201 P 0.1050 0.0607 0.8343 202 G 0.0663 0.1181 0.8156 203 T 0.0476 0.2403 0.7121 204 P 0.0419 0.4289 0.5292 205 L 0.0492 0.5387 0.4121 206 A 0.0393 0.6392 0.3215 207 P 0.0173 0.8145 0.1683 208 V 0.0247 0.8393 0.1360 209 L 0.0211 0.8634 0.1155 210 F 0.0175 0.8144 0.1681 211 E 0.0119 0.7368 0.2513 212 H 0.0428 0.5217 0.4355 213 G 0.0626 0.1425 0.7949 214 L 0.1798 0.1690 0.6512 215 Q 0.3264 0.1792 0.4943 216 E 0.7247 0.1296 0.1457 217 L 0.6993 0.1222 0.1785 218 S 0.6205 0.0751 0.3044 219 G 0.5628 0.0509 0.3862 220 F 0.6359 0.0272 0.3369 221 M 0.7578 0.0227 0.2195 222 V 0.6818 0.0207 0.2975 223 K 0.4364 0.0422 0.5213 224 D 0.1985 0.0409 0.7606 225 N 0.0076 0.8572 0.1352 226 A 0.0082 0.9170 0.0748 227 R 0.0071 0.9316 0.0613 228 A 0.0071 0.9474 0.0455 229 F 0.0092 0.9494 0.0414 230 R 0.0093 0.9495 0.0412 231 I 0.0114 0.9453 0.0432 232 V 0.0120 0.9277 0.0603 233 A 0.0206 0.8452 0.1343 234 G 0.0325 0.5784 0.3891 235 A 0.0677 0.2542 0.6781 236 E 0.0643 0.1926 0.7431 237 K 0.2025 0.1970 0.6005 238 V 0.4746 0.1319 0.3935 239 K 0.6568 0.1041 0.2390 240 I 0.6863 0.1017 0.2121 241 Y 0.5640 0.1047 0.3313 242 S 0.3891 0.1089 0.5021 243 A 0.2610 0.0991 0.6399 244 G 0.3942 0.0403 0.5654 245 Q 0.7201 0.0188 0.2611 246 K 0.8734 0.0081 0.1184 247 V 0.8887 0.0067 0.1046 248 T 0.9042 0.0067 0.0891 249 I 0.8488 0.0098 0.1414 250 K 0.5264 0.0164 0.4573 251 K 0.1510 0.0172 0.8318