# This file is the result of combining several RDB files, specifically # T0216.t04.dssp-ebghstl.rdb (weight 1.53986) # T0216.t04.stride-ebghtl.rdb (weight 1.24869) # T0216.t04.str2.rdb (weight 1.54758) # T0216.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 T0216.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0216 # 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 T0216.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 110.98 # # ============================================ # Comments from T0216.t04.stride-ebghtl.rdb # ============================================ # TARGET T0216 # 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 T0216.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 110.98 # # ============================================ # Comments from T0216.t04.str2.rdb # ============================================ # TARGET T0216 # 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 T0216.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 110.98 # # ============================================ # Comments from T0216.t04.alpha.rdb # ============================================ # TARGET T0216 # 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 T0216.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 110.98 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 K 0.0907 0.0109 0.8984 2 T 0.1939 0.0101 0.7959 3 I 0.1465 0.0108 0.8427 4 P 0.0881 0.0157 0.8961 5 S 0.0452 0.1177 0.8370 6 G 0.0733 0.0741 0.8526 7 K 0.2697 0.0374 0.6928 8 Y 0.4553 0.0100 0.5347 9 P 0.5492 0.0090 0.4419 10 V 0.8511 0.0066 0.1423 11 L 0.8768 0.0094 0.1137 12 M 0.7221 0.0203 0.2577 13 R 0.2231 0.0287 0.7482 14 N 0.0322 0.5134 0.4543 15 T 0.0120 0.8537 0.1344 16 A 0.0091 0.8953 0.0956 17 L 0.0054 0.9390 0.0556 18 L 0.0047 0.9523 0.0430 19 D 0.0050 0.9527 0.0422 20 L 0.0048 0.9526 0.0426 21 M 0.0051 0.9468 0.0481 22 E 0.0058 0.9172 0.0770 23 M 0.0086 0.8233 0.1681 24 F 0.0181 0.7020 0.2798 25 I 0.0260 0.6373 0.3367 26 P 0.0243 0.6173 0.3584 27 M 0.0303 0.6770 0.2927 28 I 0.1019 0.5119 0.3862 29 S 0.1060 0.3906 0.5035 30 A 0.0064 0.8895 0.1041 31 E 0.0069 0.9057 0.0874 32 N 0.0072 0.9139 0.0788 33 V 0.0162 0.8924 0.0914 34 Q 0.0260 0.8069 0.1671 35 K 0.0345 0.5890 0.3765 36 N 0.0351 0.2227 0.7423 37 L 0.0813 0.1399 0.7788 38 S 0.0962 0.1480 0.7558 39 P 0.0417 0.5106 0.4477 40 L 0.0484 0.5364 0.4153 41 K 0.0557 0.4648 0.4795 42 G 0.0257 0.4117 0.5626 43 K 0.0831 0.3939 0.5230 44 L 0.0830 0.1868 0.7301 45 G 0.0601 0.0572 0.8827 46 E 0.2965 0.0438 0.6597 47 Q 0.6733 0.0263 0.3004 48 V 0.5882 0.0351 0.3766 49 G 0.3648 0.0244 0.6108 50 N 0.1817 0.0224 0.7959 51 P 0.0801 0.1026 0.8173 52 A 0.2028 0.0579 0.7393 53 V 0.6327 0.0174 0.3499 54 S 0.7019 0.0105 0.2876 55 I 0.6877 0.0559 0.2564 56 K 0.5561 0.0810 0.3628 57 D 0.4515 0.0805 0.4681 58 L 0.1985 0.0429 0.7586 59 P 0.0917 0.1292 0.7791 60 Y 0.1283 0.1027 0.7690 61 H 0.0817 0.0494 0.8689 62 P 0.0448 0.1506 0.8046 63 K 0.0517 0.1432 0.8050 64 G 0.1107 0.1331 0.7562 65 L 0.1649 0.1136 0.7215 66 S 0.2237 0.0762 0.7000 67 S 0.2084 0.0578 0.7338 68 T 0.1473 0.0333 0.8194 69 P 0.1439 0.0577 0.7983 70 F 0.2130 0.0802 0.7068 71 D 0.1282 0.0723 0.7995 72 D 0.0362 0.1816 0.7822 73 E 0.0740 0.0801 0.8458 74 G 0.1012 0.0729 0.8260 75 V 0.1164 0.0350 0.8486 76 P 0.1651 0.0361 0.7988 77 T 0.1824 0.0912 0.7264 78 T 0.2134 0.1839 0.6027 79 E 0.3589 0.2204 0.4207 80 K 0.5645 0.1463 0.2893 81 F 0.7976 0.0675 0.1349 82 V 0.8387 0.0621 0.0992 83 L 0.7369 0.1101 0.1530 84 E 0.4924 0.1641 0.3435 85 N 0.0693 0.1187 0.8120 86 G 0.1878 0.0374 0.7748 87 V 0.7595 0.0297 0.2108 88 L 0.8778 0.0262 0.0961 89 K 0.7550 0.0926 0.1525 90 T 0.6399 0.1267 0.2334 91 F 0.5306 0.2240 0.2455 92 L 0.4161 0.2857 0.2982 93 H 0.2282 0.3559 0.4159 94 N 0.1322 0.3090 0.5588 95 L 0.0106 0.8897 0.0998 96 K 0.0074 0.9155 0.0772 97 T 0.0060 0.9375 0.0565 98 A 0.0071 0.9407 0.0522 99 R 0.0087 0.9263 0.0650 100 K 0.0115 0.8885 0.1000 101 E 0.0449 0.4492 0.5059 102 G 0.0385 0.0356 0.9259 103 V 0.0913 0.0122 0.8965 104 E 0.1729 0.0150 0.8122 105 P 0.2032 0.0507 0.7461 106 T 0.2262 0.0545 0.7193 107 G 0.2109 0.1008 0.6883 108 N 0.1931 0.0827 0.7242 109 G 0.1370 0.0917 0.7713 110 F 0.1571 0.0756 0.7673 111 V 0.1262 0.0793 0.7944 112 G 0.0980 0.0881 0.8139 113 G 0.1437 0.0701 0.7861 114 I 0.2198 0.0705 0.7097 115 R 0.2272 0.0420 0.7308 116 P 0.3082 0.0852 0.6066 117 V 0.3889 0.0963 0.5148 118 N 0.5649 0.0694 0.3657 119 L 0.7159 0.0436 0.2405 120 M 0.7817 0.0237 0.1946 121 L 0.7038 0.0194 0.2769 122 M 0.2972 0.0158 0.6870 123 P 0.0713 0.0848 0.8439 124 G 0.0320 0.0498 0.9182 125 E 0.1078 0.0356 0.8565 126 K 0.1316 0.0218 0.8467 127 S 0.1207 0.0235 0.8557 128 F 0.0048 0.9483 0.0468 129 E 0.0047 0.9595 0.0359 130 E 0.0049 0.9575 0.0376 131 L 0.0052 0.9560 0.0388 132 L 0.0053 0.9430 0.0517 133 K 0.0062 0.8695 0.1242 134 E 0.0087 0.7257 0.2657 135 M 0.0769 0.3289 0.5942 136 D 0.0258 0.2650 0.7092 137 R 0.0847 0.1655 0.7498 138 G 0.4745 0.0459 0.4796 139 V 0.8710 0.0062 0.1227 140 V 0.9177 0.0047 0.0776 141 I 0.9094 0.0049 0.0856 142 T 0.7565 0.0373 0.2061 143 E 0.5983 0.0247 0.3771 144 V 0.4775 0.0630 0.4595 145 E 0.3452 0.1164 0.5384 146 G 0.2432 0.1473 0.6095 147 M 0.2914 0.1746 0.5340 148 H 0.3008 0.1522 0.5470 149 A 0.1903 0.1322 0.6775 150 G 0.2392 0.0890 0.6718 151 A 0.3975 0.0801 0.5224 152 N 0.3588 0.0584 0.5828 153 S 0.1929 0.1632 0.6439 154 I 0.2269 0.1482 0.6249 155 S 0.2232 0.0873 0.6895 156 G 0.2491 0.0506 0.7003 157 E 0.5361 0.0445 0.4194 158 F 0.8100 0.0226 0.1674 159 S 0.8532 0.0188 0.1280 160 L 0.8639 0.0170 0.1190 161 F 0.8347 0.0117 0.1536 162 A 0.7852 0.0131 0.2017 163 K 0.6597 0.0235 0.3169 164 G 0.7952 0.0113 0.1935 165 Y 0.9088 0.0045 0.0867 166 W 0.9242 0.0037 0.0721 167 V 0.8957 0.0066 0.0977 168 E 0.7211 0.0249 0.2540 169 N 0.0670 0.0302 0.9028 170 G 0.0896 0.0308 0.8796 171 E 0.8060 0.0092 0.1848 172 I 0.9135 0.0033 0.0831 173 A 0.8102 0.0242 0.1656 174 H 0.6938 0.0175 0.2887 175 G 0.5834 0.0211 0.3955 176 V 0.5399 0.0308 0.4294 177 E 0.4235 0.0742 0.5023 178 D 0.4673 0.0628 0.4699 179 I 0.6259 0.0451 0.3290 180 T 0.8048 0.0385 0.1567 181 I 0.7260 0.0693 0.2047 182 S 0.4041 0.1330 0.4629 183 G 0.1233 0.1253 0.7514 184 N 0.1306 0.2354 0.6340 185 F 0.0067 0.9308 0.0625 186 L 0.0055 0.9532 0.0413 187 D 0.0047 0.9580 0.0373 188 L 0.0051 0.9546 0.0404 189 L 0.0057 0.9422 0.0521 190 R 0.0059 0.9053 0.0887 191 K 0.0088 0.8125 0.1787 192 I 0.0448 0.7817 0.1734 193 V 0.0703 0.7230 0.2067 194 L 0.1893 0.5726 0.2381 195 V 0.2300 0.3844 0.3856 196 G 0.1532 0.1783 0.6685 197 N 0.0899 0.1801 0.7300 198 D 0.1644 0.1542 0.6815 199 V 0.4582 0.0898 0.4520 200 K 0.6701 0.0445 0.2854 201 V 0.6885 0.0468 0.2647 202 S 0.4514 0.0501 0.4985 203 Q 0.1673 0.1094 0.7233 204 H 0.1683 0.0821 0.7496 205 T 0.3715 0.0605 0.5680 206 I 0.4272 0.0360 0.5368 207 A 0.2788 0.0286 0.6926 208 P 0.2380 0.0609 0.7011 209 S 0.4274 0.0747 0.4979 210 V 0.6839 0.0235 0.2926 211 L 0.7468 0.0116 0.2416 212 V 0.7566 0.0215 0.2218 213 E 0.6567 0.0615 0.2818 214 V 0.7245 0.0348 0.2407 215 L 0.7989 0.0165 0.1846 216 D 0.7919 0.0233 0.1848 217 V 0.6507 0.0416 0.3077 218 A 0.2886 0.0535 0.6579 219 G 0.1392 0.0306 0.8302 220 K 0.0763 0.0315 0.8922