# This file is the result of combining several RDB files, specifically # T0195.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0195.t2k.stride-ebghtl.rdb (weight 1.24869) # T0195.t2k.str.rdb (weight 1.53983) # T0195.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 T0195.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0195 # 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 T0195.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 45 # # ============================================ # Comments from T0195.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0195 # 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 T0195.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 45 # # ============================================ # Comments from T0195.t2k.str.rdb # ============================================ # TARGET T0195 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0195.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 45 # # ============================================ # Comments from T0195.t2k.alpha.rdb # ============================================ # TARGET T0195 # 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 T0195.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 45 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0948 0.0649 0.8403 2 K 0.3720 0.1408 0.4872 3 V 0.5188 0.1497 0.3315 4 V 0.4920 0.1722 0.3358 5 K 0.4772 0.1753 0.3475 6 E 0.4707 0.2103 0.3190 7 F 0.4689 0.1737 0.3574 8 S 0.5521 0.1290 0.3189 9 V 0.5295 0.1101 0.3604 10 C 0.3697 0.0894 0.5410 11 G 0.1498 0.0633 0.7869 12 G 0.1774 0.0534 0.7692 13 R 0.5538 0.0382 0.4080 14 L 0.8051 0.0139 0.1811 15 I 0.8605 0.0121 0.1274 16 K 0.8915 0.0103 0.0982 17 L 0.8838 0.0121 0.1040 18 S 0.8849 0.0088 0.1062 19 H 0.7743 0.0225 0.2031 20 N 0.5976 0.0368 0.3656 21 S 0.3412 0.1007 0.5582 22 N 0.1617 0.2904 0.5479 23 S 0.1697 0.3087 0.5216 24 T 0.1137 0.2206 0.6656 25 K 0.1085 0.0761 0.8154 26 T 0.2358 0.0399 0.7243 27 S 0.3247 0.0202 0.6551 28 M 0.5364 0.0104 0.4532 29 N 0.6604 0.0050 0.3346 30 V 0.8522 0.0043 0.1436 31 N 0.8999 0.0038 0.0963 32 I 0.9130 0.0036 0.0834 33 Y 0.8873 0.0044 0.1083 34 L 0.7061 0.0074 0.2865 35 P 0.2671 0.0189 0.7140 36 K 0.0678 0.1709 0.7613 37 H 0.0600 0.2222 0.7178 38 Y 0.0678 0.2073 0.7250 39 Y 0.1095 0.1363 0.7542 40 A 0.0767 0.2432 0.6801 41 Q 0.0733 0.2549 0.6717 42 D 0.0934 0.2200 0.6866 43 F 0.0741 0.2042 0.7218 44 P 0.0653 0.2467 0.6880 45 R 0.0573 0.2287 0.7140 46 N 0.0664 0.1564 0.7772 47 K 0.0775 0.0781 0.8444 48 R 0.0981 0.0581 0.8438 49 I 0.1501 0.0174 0.8325 50 P 0.2981 0.0136 0.6883 51 T 0.8732 0.0084 0.1184 52 V 0.9176 0.0096 0.0728 53 F 0.9131 0.0113 0.0756 54 Y 0.8963 0.0157 0.0880 55 L 0.7770 0.0277 0.1953 56 S 0.4110 0.0373 0.5516 57 G 0.1522 0.0412 0.8066 58 L 0.1691 0.0491 0.7818 59 T 0.1219 0.0653 0.8128 60 C 0.0894 0.0601 0.8505 61 T 0.0682 0.0595 0.8723 62 P 0.0157 0.6347 0.3496 63 D 0.0110 0.7319 0.2571 64 N 0.0268 0.7546 0.2185 65 A 0.0297 0.8118 0.1585 66 S 0.0268 0.8245 0.1487 67 E 0.0300 0.8094 0.1607 68 K 0.0237 0.7810 0.1953 69 A 0.0371 0.6748 0.2880 70 F 0.0209 0.6867 0.2923 71 W 0.0163 0.8649 0.1188 72 Q 0.0167 0.9132 0.0701 73 F 0.0143 0.9290 0.0567 74 Q 0.0130 0.9391 0.0479 75 A 0.0090 0.9395 0.0515 76 D 0.0093 0.9196 0.0711 77 K 0.0144 0.8159 0.1697 78 Y 0.0571 0.3176 0.6253 79 G 0.0676 0.0249 0.9074 80 F 0.5287 0.0059 0.4654 81 A 0.9094 0.0040 0.0867 82 I 0.9230 0.0035 0.0735 83 V 0.9038 0.0052 0.0910 84 F 0.7180 0.0069 0.2750 85 P 0.3585 0.0194 0.6221 86 D 0.2086 0.0308 0.7606 87 T 0.1613 0.0447 0.7940 88 S 0.0865 0.0355 0.8779 89 P 0.0466 0.1103 0.8431 90 R 0.0544 0.0828 0.8628 91 G 0.0752 0.0884 0.8365 92 D 0.1158 0.1140 0.7702 93 E 0.2188 0.1489 0.6323 94 V 0.2248 0.1378 0.6374 95 A 0.1311 0.1566 0.7123 96 N 0.1001 0.1347 0.7652 97 D 0.1069 0.1157 0.7774 98 P 0.0904 0.1582 0.7514 99 E 0.0895 0.2356 0.6749 100 G 0.0708 0.3104 0.6188 101 S 0.1032 0.2912 0.6056 102 W 0.2085 0.2368 0.5547 103 D 0.2704 0.1617 0.5679 104 F 0.1401 0.1907 0.6692 105 G 0.1164 0.1061 0.7774 106 Q 0.1382 0.0789 0.7829 107 G 0.2052 0.0570 0.7379 108 A 0.3013 0.0446 0.6541 109 G 0.4359 0.0471 0.5169 110 F 0.6572 0.0497 0.2931 111 Y 0.6741 0.0501 0.2758 112 L 0.5406 0.0786 0.3808 113 N 0.3060 0.1256 0.5685 114 A 0.0903 0.3225 0.5872 115 T 0.0745 0.3371 0.5884 116 Q 0.0810 0.3158 0.6033 117 E 0.0858 0.2321 0.6821 118 P 0.0775 0.3195 0.6030 119 Y 0.0629 0.3749 0.5621 120 A 0.0586 0.3900 0.5514 121 Q 0.0323 0.3033 0.6644 122 H 0.0427 0.1506 0.8067 123 Y 0.0550 0.3495 0.5955 124 Q 0.0906 0.4539 0.4555 125 M 0.0583 0.7349 0.2068 126 Y 0.0603 0.8131 0.1265 127 D 0.0554 0.8523 0.0923 128 Y 0.0511 0.8639 0.0850 129 I 0.0389 0.8859 0.0751 130 H 0.0299 0.8922 0.0779 131 K 0.0130 0.9102 0.0768 132 E 0.0115 0.9009 0.0876 133 L 0.0086 0.9179 0.0735 134 P 0.0056 0.9406 0.0538 135 Q 0.0052 0.9374 0.0574 136 T 0.0053 0.9319 0.0629 137 L 0.0082 0.8967 0.0951 138 D 0.0087 0.8091 0.1822 139 S 0.0135 0.6625 0.3240 140 H 0.0311 0.5191 0.4497 141 F 0.0910 0.2169 0.6922 142 N 0.0709 0.1866 0.7426 143 K 0.0698 0.2461 0.6841 144 N 0.0802 0.1911 0.7287 145 G 0.0483 0.3039 0.6478 146 D 0.0545 0.4839 0.4616 147 V 0.0727 0.5781 0.3492 148 K 0.1053 0.5884 0.3063 149 L 0.1821 0.5511 0.2668 150 D 0.1775 0.5104 0.3121 151 F 0.1747 0.4209 0.4044 152 L 0.1928 0.2575 0.5498 153 D 0.1371 0.1761 0.6868 154 N 0.2056 0.1812 0.6132 155 V 0.5208 0.0719 0.4073 156 A 0.6762 0.0449 0.2789 157 I 0.7790 0.0361 0.1849 158 T 0.6201 0.0479 0.3320 159 G 0.3501 0.0677 0.5823 160 H 0.2287 0.1290 0.6423 161 S 0.1495 0.1895 0.6610 162 M 0.0588 0.4442 0.4970 163 G 0.0328 0.5599 0.4073 164 G 0.0107 0.8743 0.1150 165 Y 0.0063 0.9389 0.0548 166 G 0.0055 0.9507 0.0439 167 A 0.0059 0.9554 0.0387 168 I 0.0060 0.9567 0.0373 169 C 0.0074 0.9531 0.0395 170 G 0.0099 0.9397 0.0504 171 Y 0.0151 0.9051 0.0798 172 L 0.0368 0.7843 0.1790 173 K 0.0542 0.5560 0.3898 174 G 0.0548 0.2335 0.7117 175 Y 0.0399 0.1115 0.8487 176 S 0.0699 0.0843 0.8458 177 G 0.0640 0.1778 0.7582 178 K 0.0852 0.2084 0.7065 179 R 0.2453 0.2319 0.5228 180 Y 0.5392 0.0877 0.3732 181 K 0.6116 0.0857 0.3027 182 S 0.7565 0.0813 0.1622 183 C 0.6890 0.1257 0.1854 184 S 0.6463 0.1448 0.2089 185 A 0.5590 0.1787 0.2623 186 F 0.4080 0.1847 0.4073 187 A 0.2900 0.1812 0.5288 188 P 0.2332 0.2211 0.5457 189 I 0.2410 0.1901 0.5688 190 V 0.2276 0.1037 0.6687 191 N 0.1466 0.0490 0.8044 192 P 0.0353 0.5206 0.4441 193 S 0.0206 0.4992 0.4802 194 N 0.0272 0.4582 0.5146 195 V 0.0633 0.1274 0.8093 196 P 0.0425 0.3428 0.6147 197 W 0.0200 0.6124 0.3676 198 G 0.0196 0.7078 0.2725 199 Q 0.0129 0.8361 0.1510 200 K 0.0125 0.8326 0.1549 201 A 0.0134 0.8419 0.1446 202 F 0.0145 0.8289 0.1566 203 K 0.0133 0.8236 0.1632 204 G 0.0169 0.7778 0.2053 205 Y 0.0328 0.6745 0.2927 206 L 0.0585 0.4397 0.5018 207 G 0.0455 0.2047 0.7498 208 E 0.0510 0.2551 0.6939 209 E 0.0481 0.3402 0.6117 210 K 0.0287 0.5807 0.3906 211 A 0.0252 0.6222 0.3526 212 Q 0.0274 0.6280 0.3445 213 W 0.0266 0.6377 0.3357 214 E 0.0248 0.6177 0.3575 215 A 0.0328 0.5864 0.3808 216 Y 0.0391 0.4843 0.4766 217 D 0.0612 0.3872 0.5516 218 P 0.0087 0.8645 0.1268 219 C 0.0085 0.8948 0.0968 220 L 0.0099 0.9063 0.0838 221 L 0.0132 0.8953 0.0915 222 I 0.0171 0.8621 0.1208 223 K 0.0233 0.7828 0.1939 224 N 0.0332 0.5988 0.3679 225 I 0.0574 0.4074 0.5352 226 R 0.0555 0.2767 0.6678 227 H 0.0699 0.1845 0.7456 228 V 0.0435 0.2790 0.6776 229 G 0.0501 0.1923 0.7577 230 D 0.0963 0.1879 0.7158 231 D 0.1428 0.1398 0.7174 232 R 0.3209 0.0832 0.5960 233 I 0.7531 0.0436 0.2033 234 L 0.8514 0.0309 0.1177 235 I 0.8366 0.0392 0.1242 236 H 0.7826 0.0457 0.1718 237 V 0.4864 0.0536 0.4600 238 G 0.1859 0.0689 0.7451 239 D 0.0908 0.1595 0.7497 240 S 0.0541 0.2625 0.6834 241 D 0.0474 0.4046 0.5480 242 P 0.0248 0.5372 0.4380 243 F 0.0348 0.4989 0.4663 244 L 0.0267 0.5781 0.3952 245 E 0.0183 0.6458 0.3359 246 E 0.0156 0.6222 0.3622 247 H 0.0282 0.4887 0.4831 248 L 0.0603 0.2389 0.7008 249 K 0.0648 0.0949 0.8402 250 P 0.0114 0.7649 0.2237 251 E 0.0074 0.8329 0.1597 252 L 0.0077 0.8872 0.1051 253 L 0.0053 0.9330 0.0618 254 L 0.0063 0.9410 0.0526 255 E 0.0062 0.9383 0.0555 256 A 0.0060 0.9318 0.0622 257 V 0.0096 0.9145 0.0758 258 K 0.0087 0.8794 0.1118 259 A 0.0164 0.7705 0.2132 260 T 0.0353 0.5342 0.4305 261 S 0.0489 0.2263 0.7248 262 W 0.0542 0.1208 0.8251 263 Q 0.0497 0.0518 0.8985 264 D 0.1557 0.0185 0.8258 265 Y 0.3912 0.0114 0.5974 266 V 0.8020 0.0062 0.1918 267 E 0.8968 0.0042 0.0990 268 I 0.8909 0.0039 0.1052 269 K 0.8675 0.0048 0.1278 270 K 0.6493 0.0123 0.3384 271 V 0.2726 0.0179 0.7094 272 H 0.0826 0.0520 0.8654 273 G 0.0728 0.0406 0.8866 274 F 0.1045 0.0986 0.7969 275 D 0.1494 0.1160 0.7346 276 H 0.1460 0.2625 0.5915 277 S 0.1624 0.4792 0.3585 278 Y 0.1141 0.7475 0.1384 279 Y 0.1138 0.7959 0.0903 280 F 0.1018 0.8226 0.0756 281 V 0.0683 0.8546 0.0771 282 S 0.0546 0.8560 0.0895 283 T 0.0287 0.8448 0.1265 284 F 0.0274 0.7757 0.1969 285 V 0.0087 0.8827 0.1086 286 P 0.0049 0.9406 0.0546 287 E 0.0048 0.9451 0.0501 288 H 0.0045 0.9484 0.0471 289 A 0.0044 0.9558 0.0398 290 E 0.0044 0.9581 0.0375 291 F 0.0045 0.9523 0.0432 292 H 0.0046 0.9495 0.0460 293 A 0.0047 0.9400 0.0553 294 R 0.0056 0.9069 0.0875 295 N 0.0089 0.8206 0.1705 296 L 0.0492 0.5476 0.4032 297 G 0.0302 0.3668 0.6031 298 L 0.0364 0.2759 0.6877 299 I 0.0419 0.0459 0.9121