# This file is the result of combining several RDB files, specifically # T0440.t04.dssp-ebghstl.rdb (weight 1.53986) # T0440.t04.stride-ebghtl.rdb (weight 1.24869) # T0440.t04.str2.rdb (weight 1.54758) # T0440.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 T0440.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0440 # 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 T0440.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 1471 # # ============================================ # Comments from T0440.t04.stride-ebghtl.rdb # ============================================ # TARGET T0440 # 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 T0440.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 1471 # # ============================================ # Comments from T0440.t04.str2.rdb # ============================================ # TARGET T0440 # 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 T0440.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 1471 # # ============================================ # Comments from T0440.t04.alpha.rdb # ============================================ # TARGET T0440 # 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 T0440.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 1471 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0787 0.0158 0.9056 2 K 0.1902 0.0253 0.7844 3 R 0.2650 0.0395 0.6955 4 D 0.3034 0.0517 0.6449 5 G 0.3142 0.0913 0.5945 6 H 0.4107 0.0587 0.5306 7 T 0.4124 0.0698 0.5178 8 H 0.3310 0.0745 0.5945 9 T 0.2665 0.0999 0.6336 10 E 0.2158 0.1289 0.6553 11 F 0.2289 0.1217 0.6494 12 C 0.1609 0.0779 0.7611 13 P 0.0662 0.1475 0.7864 14 H 0.0680 0.1030 0.8290 15 G 0.0741 0.0868 0.8390 16 T 0.0598 0.0684 0.8718 17 H 0.0590 0.0723 0.8688 18 D 0.0701 0.0299 0.9000 19 D 0.0816 0.0734 0.8450 20 V 0.0048 0.9543 0.0409 21 E 0.0047 0.9610 0.0344 22 E 0.0046 0.9616 0.0338 23 M 0.0047 0.9611 0.0343 24 V 0.0046 0.9610 0.0343 25 L 0.0046 0.9612 0.0342 26 K 0.0046 0.9614 0.0340 27 A 0.0047 0.9608 0.0345 28 I 0.0049 0.9507 0.0444 29 E 0.0054 0.9189 0.0757 30 L 0.0408 0.3827 0.5765 31 D 0.0498 0.0133 0.9370 32 F 0.0878 0.0076 0.9046 33 D 0.1307 0.0540 0.8153 34 E 0.8923 0.0082 0.0995 35 Y 0.9293 0.0037 0.0670 36 S 0.9273 0.0043 0.0684 37 I 0.8965 0.0075 0.0960 38 V 0.7403 0.0141 0.2456 39 E 0.3568 0.0489 0.5943 40 H 0.1136 0.0653 0.8212 41 A 0.0828 0.0663 0.8509 42 P 0.0543 0.1748 0.7709 43 L 0.0612 0.1660 0.7728 44 S 0.0551 0.1670 0.7779 45 S 0.0144 0.8472 0.1384 46 E 0.0052 0.9406 0.0542 47 F 0.0055 0.9438 0.0507 48 M 0.0063 0.9381 0.0556 49 K 0.0060 0.9390 0.0550 50 N 0.0073 0.9142 0.0785 51 T 0.0100 0.8629 0.1270 52 A 0.0287 0.7492 0.2222 53 G 0.0221 0.5853 0.3926 54 D 0.0322 0.4542 0.5136 55 K 0.0411 0.2855 0.6734 56 E 0.0517 0.0611 0.8871 57 A 0.2449 0.0188 0.7364 58 V 0.6243 0.0121 0.3636 59 T 0.8086 0.0099 0.1815 60 T 0.7365 0.0182 0.2453 61 A 0.6855 0.0421 0.2725 62 S 0.5989 0.0408 0.3603 63 M 0.6678 0.0290 0.3032 64 A 0.7260 0.0283 0.2457 65 M 0.5524 0.0757 0.3719 66 S 0.2627 0.1130 0.6243 67 D 0.1750 0.1367 0.6884 68 L 0.1476 0.1426 0.7098 69 P 0.0791 0.4807 0.4402 70 Y 0.0504 0.5986 0.3510 71 Y 0.0581 0.6515 0.2904 72 F 0.0639 0.7072 0.2289 73 K 0.0438 0.7720 0.1841 74 K 0.0555 0.7985 0.1461 75 M 0.0307 0.8729 0.0964 76 N 0.0273 0.8603 0.1124 77 H 0.0322 0.8700 0.0978 78 I 0.0334 0.8580 0.1086 79 K 0.0318 0.8150 0.1532 80 K 0.0308 0.7758 0.1934 81 K 0.0304 0.6929 0.2768 82 Y 0.0529 0.4947 0.4525 83 A 0.0490 0.2790 0.6720 84 S 0.0204 0.4022 0.5774 85 D 0.0315 0.2767 0.6918 86 L 0.2006 0.2945 0.5049 87 L 0.4514 0.2123 0.3364 88 I 0.6253 0.1923 0.1824 89 H 0.5398 0.2884 0.1717 90 I 0.4014 0.2523 0.3462 91 G 0.2605 0.1256 0.6139 92 F 0.5254 0.1073 0.3673 93 E 0.7185 0.0962 0.1853 94 V 0.6123 0.1304 0.2574 95 D 0.3980 0.1457 0.4563 96 Y 0.3545 0.1701 0.4754 97 L 0.2718 0.2233 0.5049 98 I 0.1054 0.3022 0.5924 99 G 0.0607 0.2772 0.6621 100 Y 0.0603 0.5162 0.4234 101 E 0.0394 0.6977 0.2629 102 D 0.0233 0.7558 0.2210 103 F 0.0149 0.8260 0.1591 104 T 0.0089 0.9109 0.0802 105 R 0.0054 0.9484 0.0462 106 D 0.0051 0.9531 0.0418 107 F 0.0050 0.9493 0.0458 108 L 0.0057 0.9405 0.0539 109 N 0.0061 0.8982 0.0957 110 E 0.0106 0.7941 0.1953 111 Y 0.0414 0.5030 0.4555 112 G 0.0391 0.0883 0.8725 113 P 0.0206 0.3761 0.6033 114 Q 0.0360 0.4130 0.5510 115 T 0.0866 0.2645 0.6490 116 D 0.0917 0.1782 0.7301 117 D 0.1095 0.2325 0.6580 118 G 0.4051 0.1630 0.4320 119 V 0.6560 0.0980 0.2460 120 L 0.6526 0.0807 0.2667 121 S 0.6796 0.0739 0.2465 122 L 0.6813 0.0926 0.2260 123 H 0.6549 0.0878 0.2573 124 F 0.5712 0.1090 0.3198 125 L 0.3801 0.1372 0.4827 126 E 0.2307 0.1233 0.6459 127 G 0.1688 0.1348 0.6964 128 Q 0.1987 0.1679 0.6334 129 G 0.1667 0.1714 0.6619 130 G 0.1519 0.1654 0.6827 131 F 0.1816 0.1690 0.6494 132 R 0.1517 0.1872 0.6612 133 S 0.1280 0.1948 0.6772 134 I 0.1182 0.2180 0.6638 135 D 0.1396 0.1889 0.6716 136 F 0.1342 0.1700 0.6959 137 S 0.1010 0.1483 0.7507 138 A 0.0581 0.3145 0.6274 139 E 0.0275 0.5698 0.4027 140 D 0.0290 0.6673 0.3036 141 Y 0.0215 0.8093 0.1692 142 N 0.0183 0.8425 0.1391 143 E 0.0082 0.8943 0.0975 144 G 0.0102 0.9006 0.0892 145 I 0.0128 0.9093 0.0779 146 V 0.0151 0.9003 0.0845 147 Q 0.0147 0.8667 0.1186 148 F 0.0199 0.7104 0.2697 149 Y 0.0620 0.3277 0.6103 150 G 0.0474 0.1325 0.8200 151 G 0.0622 0.1170 0.8208 152 F 0.0082 0.9047 0.0871 153 E 0.0051 0.9542 0.0408 154 Q 0.0047 0.9591 0.0362 155 A 0.0047 0.9584 0.0370 156 Q 0.0047 0.9548 0.0405 157 L 0.0048 0.9544 0.0409 158 A 0.0053 0.9379 0.0568 159 Y 0.0060 0.9213 0.0727 160 L 0.0084 0.9035 0.0881 161 E 0.0060 0.8856 0.1084 162 G 0.0064 0.8440 0.1496 163 V 0.0104 0.8464 0.1432 164 K 0.0124 0.8883 0.0994 165 Q 0.0150 0.8958 0.0892 166 S 0.0221 0.8853 0.0926 167 I 0.0313 0.8741 0.0946 168 E 0.0509 0.8181 0.1310 169 A 0.0378 0.7578 0.2043 170 D 0.0511 0.5338 0.4151 171 L 0.0610 0.3051 0.6338 172 G 0.0400 0.1545 0.8055 173 L 0.0891 0.1518 0.7590 174 F 0.1148 0.0606 0.8246 175 K 0.1006 0.0384 0.8609 176 P 0.0249 0.6192 0.3559 177 R 0.0295 0.6608 0.3097 178 R 0.0482 0.7275 0.2243 179 M 0.0492 0.7170 0.2337 180 G 0.0501 0.6070 0.3428 181 H 0.0273 0.7329 0.2398 182 I 0.0115 0.9010 0.0875 183 S 0.0069 0.9260 0.0672 184 L 0.0058 0.9432 0.0510 185 C 0.0062 0.9389 0.0549 186 Q 0.0063 0.9341 0.0596 187 K 0.0081 0.8992 0.0927 188 F 0.0263 0.7082 0.2655 189 Q 0.0376 0.3111 0.6513 190 Q 0.0700 0.2315 0.6985 191 F 0.1443 0.1763 0.6795 192 F 0.1576 0.1713 0.6711 193 G 0.1202 0.2225 0.6573 194 E 0.0995 0.2881 0.6124 195 D 0.0932 0.2465 0.6603 196 T 0.0648 0.1788 0.7565 197 S 0.0195 0.5815 0.3990 198 D 0.0192 0.6493 0.3315 199 F 0.0292 0.6864 0.2844 200 S 0.0401 0.6898 0.2701 201 E 0.0077 0.8723 0.1200 202 E 0.0079 0.8931 0.0990 203 V 0.0079 0.9071 0.0850 204 M 0.0063 0.9393 0.0545 205 E 0.0052 0.9532 0.0416 206 K 0.0049 0.9532 0.0419 207 F 0.0047 0.9585 0.0368 208 R 0.0047 0.9602 0.0351 209 V 0.0046 0.9614 0.0340 210 I 0.0047 0.9607 0.0346 211 L 0.0047 0.9611 0.0342 212 A 0.0046 0.9615 0.0338 213 L 0.0046 0.9611 0.0342 214 V 0.0047 0.9595 0.0359 215 K 0.0048 0.9443 0.0509 216 K 0.0056 0.8600 0.1344 217 R 0.0435 0.2868 0.6697 218 D 0.0449 0.0197 0.9354 219 Y 0.1190 0.0119 0.8692 220 E 0.6773 0.0079 0.3148 221 L 0.8789 0.0070 0.1141 222 D 0.8897 0.0081 0.1022 223 F 0.8452 0.0135 0.1413 224 N 0.5950 0.0263 0.3788 225 T 0.2759 0.0590 0.6651 226 A 0.0984 0.1919 0.7097 227 G 0.0585 0.2699 0.6716 228 L 0.1176 0.2650 0.6173 229 F 0.1825 0.1771 0.6404 230 K 0.1548 0.1062 0.7390 231 P 0.0850 0.2103 0.7047 232 L 0.0832 0.2612 0.6556 233 C 0.1031 0.1690 0.7279 234 G 0.0605 0.0930 0.8465 235 E 0.0887 0.0693 0.8421 236 T 0.1323 0.0666 0.8011 237 Y 0.0846 0.0298 0.8855 238 P 0.0568 0.0360 0.9073 239 P 0.0222 0.7722 0.2056 240 K 0.0057 0.9385 0.0558 241 K 0.0048 0.9538 0.0414 242 I 0.0049 0.9561 0.0390 243 V 0.0047 0.9602 0.0351 244 T 0.0047 0.9612 0.0341 245 L 0.0047 0.9611 0.0342 246 A 0.0047 0.9594 0.0358 247 S 0.0049 0.9533 0.0417 248 E 0.0058 0.9259 0.0683 249 L 0.0461 0.4643 0.4896 250 Q 0.0472 0.0154 0.9374 251 I 0.0819 0.0074 0.9107 252 P 0.3090 0.0079 0.6832 253 F 0.7966 0.0073 0.1961 254 V 0.8609 0.0074 0.1317 255 Y 0.8043 0.0213 0.1745 256 G 0.5050 0.0247 0.4703 257 S 0.2176 0.0745 0.7080 258 D 0.1445 0.1541 0.7014 259 S 0.0827 0.1798 0.7375 260 H 0.0852 0.1534 0.7614 261 G 0.0694 0.1334 0.7972 262 V 0.0534 0.4136 0.5330 263 Q 0.0552 0.4619 0.4829 264 D 0.0832 0.4772 0.4396 265 I 0.0634 0.4454 0.4912 266 G 0.0565 0.2674 0.6760 267 R 0.0692 0.2915 0.6394 268 G 0.0897 0.2499 0.6603 269 Y 0.0893 0.4103 0.5003 270 S 0.0875 0.4949 0.4176 271 T 0.1362 0.5115 0.3523 272 Y 0.1726 0.4045 0.4229 273 C 0.1612 0.2594 0.5794 274 Q 0.1055 0.1788 0.7157 275 K 0.0586 0.0989 0.8425