# This file is the result of combining several RDB files, specifically # T0327.t06.dssp-ebghstl.rdb (weight 1.53986) # T0327.t06.stride-ebghtl.rdb (weight 1.24869) # T0327.t06.str2.rdb (weight 1.54758) # T0327.t06.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 T0327.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0327 # 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 T0327.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 2 # # ============================================ # Comments from T0327.t06.stride-ebghtl.rdb # ============================================ # TARGET T0327 # 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 T0327.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 2 # # ============================================ # Comments from T0327.t06.str2.rdb # ============================================ # TARGET T0327 # 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 T0327.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 2 # # ============================================ # Comments from T0327.t06.alpha.rdb # ============================================ # TARGET T0327 # 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 T0327.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 2 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0579 0.0765 0.8656 2 N 0.0716 0.0733 0.8551 3 K 0.0180 0.5391 0.4429 4 D 0.0180 0.6634 0.3186 5 K 0.0121 0.8800 0.1079 6 L 0.0179 0.8979 0.0842 7 R 0.0153 0.9225 0.0622 8 Y 0.0190 0.9312 0.0497 9 A 0.0285 0.9238 0.0476 10 I 0.0279 0.9202 0.0519 11 L 0.0291 0.9081 0.0628 12 K 0.0306 0.8978 0.0716 13 E 0.0290 0.8902 0.0808 14 I 0.0261 0.8491 0.1248 15 F 0.0591 0.6953 0.2456 16 E 0.0779 0.4118 0.5103 17 G 0.0613 0.1297 0.8089 18 N 0.0645 0.0610 0.8744 19 T 0.0944 0.0242 0.8814 20 P 0.1365 0.0368 0.8268 21 L 0.1364 0.0641 0.7995 22 S 0.1098 0.0677 0.8226 23 E 0.0505 0.3667 0.5828 24 N 0.0713 0.2369 0.6919 25 D 0.1384 0.2146 0.6470 26 I 0.2294 0.1222 0.6484 27 G 0.2532 0.0640 0.6828 28 V 0.2878 0.0381 0.6742 29 T 0.2161 0.0389 0.7449 30 E 0.0320 0.6661 0.3019 31 D 0.0241 0.6509 0.3250 32 Q 0.0292 0.6967 0.2741 33 F 0.0427 0.6753 0.2820 34 D 0.0343 0.7023 0.2634 35 D 0.0418 0.7402 0.2180 36 A 0.0409 0.8291 0.1299 37 V 0.0555 0.8256 0.1189 38 N 0.0681 0.7880 0.1439 39 F 0.0739 0.7799 0.1463 40 L 0.0982 0.7424 0.1593 41 K 0.1372 0.6268 0.2360 42 R 0.1605 0.5239 0.3155 43 E 0.1430 0.2279 0.6291 44 G 0.1942 0.0546 0.7512 45 Y 0.6051 0.0222 0.3727 46 I 0.8742 0.0055 0.1204 47 I 0.8047 0.0246 0.1707 48 G 0.8293 0.0091 0.1616 49 V 0.8260 0.0098 0.1642 50 H 0.7832 0.0122 0.2047 51 Y 0.5283 0.0285 0.4433 52 S 0.1893 0.0547 0.7560 53 D 0.0658 0.0926 0.8416 54 D 0.0558 0.0749 0.8693 55 R 0.0894 0.0821 0.8285 56 P 0.1072 0.2344 0.6584 57 H 0.2237 0.2964 0.4798 58 L 0.3386 0.3652 0.2962 59 Y 0.3824 0.3322 0.2854 60 K 0.4029 0.2544 0.3427 61 L 0.2973 0.1761 0.5266 62 G 0.1158 0.0683 0.8158 63 P 0.0783 0.2753 0.6465 64 E 0.1377 0.3417 0.5206 65 L 0.2109 0.3313 0.4578 66 T 0.1698 0.2436 0.5866 67 E 0.1293 0.3893 0.4814 68 K 0.0760 0.2756 0.6484 69 G 0.0752 0.1880 0.7368 70 E 0.0942 0.3533 0.5525 71 N 0.1498 0.4198 0.4305 72 Y 0.2054 0.4637 0.3309 73 L 0.3073 0.3920 0.3007 74 K 0.1791 0.4140 0.4069 75 E 0.1090 0.3829 0.5081 76 N 0.0575 0.1381 0.8044 77 G 0.0613 0.0551 0.8835 78 T 0.1640 0.1006 0.7354 79 W 0.1936 0.3553 0.4511 80 S 0.0741 0.5750 0.3509 81 K 0.0388 0.7945 0.1666 82 A 0.0366 0.8085 0.1549 83 Y 0.0453 0.8032 0.1515 84 K 0.0600 0.7756 0.1643 85 T 0.0666 0.7726 0.1608 86 I 0.0217 0.8962 0.0821 87 K 0.0152 0.9161 0.0686 88 E 0.0220 0.8961 0.0820 89 I 0.0155 0.8987 0.0859 90 K 0.0210 0.8804 0.0986 91 D 0.0316 0.8353 0.1331 92 W 0.0463 0.8133 0.1404 93 I 0.1262 0.6980 0.1757 94 K 0.1710 0.5929 0.2361 95 L 0.1446 0.5731 0.2823 96 E 0.1171 0.4820 0.4009 97 H 0.1239 0.3762 0.4998 98 H 0.1303 0.2921 0.5775 99 H 0.1297 0.2546 0.6157 100 H 0.1283 0.2686 0.6030 101 H 0.1363 0.2500 0.6136 102 H 0.1531 0.2255 0.6214 103 M 0.1501 0.1810 0.6688 104 N 0.1021 0.1298 0.7682 105 K 0.0213 0.5667 0.4120 106 D 0.0205 0.6664 0.3132 107 K 0.0185 0.8405 0.1410 108 L 0.0395 0.8511 0.1094 109 R 0.0386 0.8788 0.0826 110 Y 0.0457 0.8932 0.0612 111 A 0.0540 0.8874 0.0586 112 I 0.0575 0.8791 0.0634 113 L 0.0395 0.8896 0.0709 114 K 0.0332 0.8963 0.0705 115 E 0.0304 0.8954 0.0743 116 I 0.0264 0.8710 0.1026 117 F 0.0616 0.7300 0.2084 118 E 0.0645 0.4673 0.4682 119 G 0.0492 0.1402 0.8107 120 N 0.0593 0.0611 0.8796 121 T 0.0977 0.0231 0.8792 122 P 0.1619 0.0353 0.8028 123 L 0.1724 0.0607 0.7669 124 S 0.1320 0.0653 0.8027 125 E 0.0603 0.3585 0.5812 126 N 0.0771 0.2402 0.6827 127 D 0.1445 0.2266 0.6289 128 I 0.2548 0.1199 0.6253 129 G 0.2755 0.0667 0.6578 130 V 0.3100 0.0452 0.6448 131 T 0.2507 0.0507 0.6987 132 E 0.0479 0.6420 0.3102 133 D 0.0319 0.6425 0.3255 134 Q 0.0372 0.6895 0.2733 135 F 0.0521 0.6543 0.2936 136 D 0.0374 0.6838 0.2788 137 D 0.0429 0.7001 0.2570 138 A 0.0573 0.7738 0.1689 139 V 0.0838 0.7577 0.1585 140 N 0.1047 0.7148 0.1805 141 F 0.1139 0.7259 0.1602 142 L 0.1587 0.6695 0.1718 143 K 0.1815 0.5638 0.2547 144 R 0.1795 0.4894 0.3311 145 E 0.1296 0.2088 0.6616 146 G 0.1789 0.0521 0.7690 147 Y 0.5956 0.0241 0.3802 148 I 0.8610 0.0073 0.1317 149 I 0.7969 0.0244 0.1787 150 G 0.7979 0.0126 0.1895 151 V 0.8012 0.0120 0.1868 152 H 0.7588 0.0146 0.2266 153 Y 0.5130 0.0319 0.4551 154 S 0.1900 0.0617 0.7483 155 D 0.0634 0.1028 0.8338 156 D 0.0524 0.0882 0.8594 157 R 0.0905 0.0869 0.8225 158 P 0.1009 0.2626 0.6365 159 H 0.2014 0.3441 0.4545 160 L 0.3080 0.3990 0.2930 161 Y 0.3440 0.3584 0.2976 162 K 0.3625 0.2862 0.3513 163 L 0.2579 0.2216 0.5205 164 G 0.1099 0.0741 0.8160 165 P 0.0627 0.3478 0.5895 166 E 0.1088 0.4314 0.4598 167 L 0.1650 0.4404 0.3946 168 T 0.1497 0.3676 0.4826 169 E 0.1088 0.4842 0.4070 170 K 0.0772 0.3370 0.5858 171 G 0.0775 0.2112 0.7112 172 E 0.0818 0.4066 0.5115 173 N 0.1346 0.4812 0.3842 174 Y 0.1845 0.5426 0.2729 175 L 0.2763 0.4602 0.2636 176 K 0.1761 0.4686 0.3553 177 E 0.0962 0.4278 0.4760 178 N 0.0574 0.1479 0.7947 179 G 0.0620 0.0653 0.8726 180 T 0.1771 0.1179 0.7051 181 W 0.2153 0.3542 0.4305 182 S 0.0887 0.5752 0.3361 183 K 0.0567 0.7551 0.1882 184 A 0.0536 0.7752 0.1712 185 Y 0.0611 0.7690 0.1700 186 K 0.0706 0.7498 0.1795 187 T 0.0710 0.7657 0.1634 188 I 0.0269 0.8807 0.0924 189 K 0.0188 0.9068 0.0745 190 E 0.0286 0.8789 0.0925 191 I 0.0179 0.8881 0.0940 192 K 0.0244 0.8671 0.1085 193 D 0.0347 0.8188 0.1466 194 W 0.0491 0.7990 0.1519 195 I 0.1409 0.6705 0.1886 196 K 0.1905 0.5692 0.2403 197 L 0.1607 0.5408 0.2985 198 E 0.1296 0.4581 0.4123 199 H 0.1307 0.3945 0.4748 200 H 0.1298 0.3179 0.5524 201 H 0.1171 0.2577 0.6252 202 H 0.1063 0.1890 0.7046 203 H 0.0898 0.1232 0.7870 204 H 0.0582 0.0394 0.9024