# This file is the result of combining several RDB files, specifically # T0454.t04.dssp-ebghstl.rdb (weight 1.53986) # T0454.t04.stride-ebghtl.rdb (weight 1.24869) # T0454.t04.str2.rdb (weight 1.54758) # T0454.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 T0454.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0454 # 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 T0454.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 2180 # # ============================================ # Comments from T0454.t04.stride-ebghtl.rdb # ============================================ # TARGET T0454 # 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 T0454.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 2180 # # ============================================ # Comments from T0454.t04.str2.rdb # ============================================ # TARGET T0454 # 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 T0454.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 2180 # # ============================================ # Comments from T0454.t04.alpha.rdb # ============================================ # TARGET T0454 # 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 T0454.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 2180 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0648 0.0106 0.9246 2 T 0.0552 0.0218 0.9230 3 R 0.0085 0.7585 0.2330 4 A 0.0049 0.9091 0.0860 5 D 0.0063 0.9252 0.0685 6 C 0.0060 0.9222 0.0718 7 R 0.0047 0.9598 0.0355 8 S 0.0047 0.9610 0.0343 9 R 0.0046 0.9614 0.0340 10 L 0.0047 0.9609 0.0344 11 M 0.0047 0.9611 0.0343 12 E 0.0047 0.9614 0.0339 13 V 0.0047 0.9609 0.0344 14 A 0.0047 0.9604 0.0349 15 T 0.0047 0.9611 0.0342 16 E 0.0046 0.9614 0.0340 17 L 0.0046 0.9608 0.0345 18 F 0.0047 0.9588 0.0366 19 A 0.0050 0.9460 0.0491 20 Q 0.0069 0.8861 0.1071 21 K 0.0407 0.4532 0.5060 22 G 0.0291 0.0974 0.8735 23 F 0.0567 0.1159 0.8274 24 Y 0.0644 0.1998 0.7358 25 G 0.1308 0.1664 0.7028 26 V 0.2903 0.0511 0.6585 27 S 0.2215 0.0745 0.7040 28 I 0.0067 0.9531 0.0402 29 R 0.0054 0.9602 0.0344 30 E 0.0046 0.9616 0.0338 31 L 0.0046 0.9617 0.0337 32 A 0.0047 0.9609 0.0344 33 Q 0.0048 0.9564 0.0388 34 A 0.0053 0.9369 0.0579 35 A 0.0435 0.5013 0.4553 36 G 0.0374 0.0362 0.9264 37 A 0.0649 0.0139 0.9212 38 S 0.0615 0.0401 0.8984 39 I 0.0608 0.6012 0.3380 40 S 0.1154 0.6192 0.2654 41 M 0.1483 0.7011 0.1506 42 I 0.1869 0.6914 0.1217 43 S 0.2128 0.6424 0.1448 44 Y 0.1537 0.6062 0.2401 45 H 0.1347 0.4509 0.4144 46 F 0.1039 0.1574 0.7387 47 G 0.0499 0.1311 0.8190 48 G 0.0486 0.1533 0.7981 49 K 0.0088 0.9260 0.0652 50 E 0.0070 0.9474 0.0456 51 G 0.0059 0.9518 0.0423 52 L 0.0048 0.9591 0.0362 53 Y 0.0047 0.9607 0.0346 54 A 0.0046 0.9615 0.0339 55 A 0.0047 0.9616 0.0338 56 V 0.0047 0.9609 0.0345 57 L 0.0047 0.9586 0.0367 58 Q 0.0048 0.9575 0.0377 59 E 0.0050 0.9443 0.0507 60 Q 0.0055 0.9209 0.0737 61 F 0.0079 0.8948 0.0972 62 A 0.0077 0.8125 0.1798 63 C 0.0102 0.7196 0.2702 64 F 0.0215 0.6260 0.3525 65 G 0.0153 0.5153 0.4694 66 Q 0.0248 0.5601 0.4151 67 L 0.0182 0.7899 0.1918 68 D 0.0146 0.8222 0.1632 69 D 0.0159 0.8315 0.1525 70 I 0.0209 0.7780 0.2011 71 R 0.0346 0.6724 0.2929 72 G 0.0363 0.4024 0.5612 73 Q 0.0395 0.2231 0.7374 74 A 0.0557 0.1311 0.8132 75 G 0.0503 0.0610 0.8887 76 D 0.0758 0.0316 0.8925 77 P 0.0058 0.9373 0.0569 78 L 0.0047 0.9588 0.0365 79 A 0.0047 0.9612 0.0341 80 V 0.0047 0.9612 0.0341 81 M 0.0047 0.9606 0.0347 82 T 0.0046 0.9613 0.0340 83 A 0.0047 0.9615 0.0338 84 Y 0.0046 0.9611 0.0343 85 L 0.0047 0.9607 0.0347 86 R 0.0046 0.9615 0.0339 87 W 0.0046 0.9611 0.0343 88 T 0.0047 0.9585 0.0368 89 I 0.0047 0.9586 0.0367 90 Q 0.0047 0.9559 0.0394 91 R 0.0051 0.9439 0.0510 92 H 0.0088 0.8978 0.0934 93 R 0.0106 0.7997 0.1897 94 N 0.0198 0.5595 0.4207 95 N 0.0826 0.1572 0.7602 96 P 0.0072 0.8061 0.1867 97 Q 0.0076 0.8767 0.1158 98 L 0.0071 0.9360 0.0569 99 L 0.0095 0.9439 0.0465 100 R 0.0151 0.9411 0.0438 101 F 0.0222 0.9331 0.0448 102 Y 0.0174 0.9338 0.0488 103 T 0.0236 0.9135 0.0629 104 S 0.0249 0.8843 0.0908 105 E 0.0328 0.8107 0.1565 106 L 0.0519 0.6043 0.3438 107 T 0.0510 0.3395 0.6095 108 N 0.0610 0.0730 0.8661 109 P 0.0445 0.0694 0.8861 110 T 0.0466 0.1350 0.8184 111 P 0.0087 0.8151 0.1762 112 C 0.0106 0.8684 0.1210 113 F 0.0087 0.8989 0.0925 114 A 0.0087 0.9160 0.0754 115 A 0.0087 0.8939 0.0974 116 I 0.0113 0.8586 0.1301 117 V 0.0151 0.8345 0.1505 118 S 0.0100 0.8674 0.1225 119 P 0.0049 0.9330 0.0622 120 A 0.0050 0.9341 0.0609 121 I 0.0050 0.9482 0.0469 122 A 0.0047 0.9590 0.0363 123 S 0.0047 0.9600 0.0354 124 V 0.0047 0.9605 0.0348 125 I 0.0047 0.9612 0.0342 126 R 0.0046 0.9617 0.0337 127 L 0.0046 0.9617 0.0336 128 L 0.0047 0.9611 0.0343 129 A 0.0046 0.9614 0.0339 130 E 0.0046 0.9617 0.0336 131 S 0.0046 0.9612 0.0342 132 I 0.0047 0.9599 0.0354 133 E 0.0047 0.9571 0.0382 134 A 0.0047 0.9434 0.0519 135 G 0.0048 0.9150 0.0802 136 M 0.0062 0.8671 0.1267 137 T 0.0104 0.8043 0.1853 138 R 0.0435 0.3755 0.5810 139 G 0.0313 0.0706 0.8980 140 L 0.1176 0.0626 0.8199 141 F 0.3082 0.0472 0.6446 142 R 0.1294 0.0547 0.8159 143 R 0.0372 0.2044 0.7584 144 D 0.0484 0.1294 0.8222 145 L 0.1117 0.0949 0.7934 146 H 0.0946 0.0990 0.8064 147 A 0.0049 0.9451 0.0500 148 V 0.0047 0.9598 0.0355 149 N 0.0047 0.9603 0.0350 150 S 0.0047 0.9602 0.0351 151 A 0.0047 0.9608 0.0346 152 L 0.0046 0.9614 0.0340 153 A 0.0046 0.9613 0.0341 154 L 0.0047 0.9600 0.0353 155 A 0.0047 0.9598 0.0355 156 G 0.0047 0.9585 0.0367 157 M 0.0049 0.9530 0.0421 158 V 0.0060 0.9444 0.0496 159 N 0.0065 0.9314 0.0621 160 Y 0.0100 0.9164 0.0737 161 F 0.0148 0.8943 0.0909 162 F 0.0378 0.8338 0.1284 163 L 0.0534 0.7642 0.1823 164 S 0.0618 0.6488 0.2895 165 T 0.0369 0.7177 0.2453 166 L 0.0682 0.6558 0.2760 167 A 0.1123 0.5934 0.2943 168 T 0.1259 0.5416 0.3325 169 E 0.1100 0.4125 0.4775 170 G 0.1226 0.2611 0.6163 171 L 0.1865 0.1851 0.6284 172 T 0.1625 0.1192 0.7183 173 S 0.0824 0.1069 0.8107 174 H 0.0605 0.0723 0.8672 175 S 0.0668 0.0250 0.9082 176 P 0.0291 0.2194 0.7516 177 D 0.0464 0.2012 0.7523 178 Q 0.0658 0.1992 0.7350 179 D 0.0091 0.8639 0.1270 180 E 0.0049 0.9566 0.0386 181 E 0.0047 0.9606 0.0347 182 L 0.0047 0.9602 0.0351 183 I 0.0047 0.9606 0.0347 184 R 0.0046 0.9612 0.0342 185 Q 0.0047 0.9600 0.0353 186 Y 0.0047 0.9599 0.0354 187 V 0.0047 0.9601 0.0353 188 A 0.0046 0.9613 0.0341 189 I 0.0047 0.9592 0.0362 190 F 0.0047 0.9542 0.0410 191 T 0.0049 0.9476 0.0475 192 R 0.0069 0.9012 0.0919 193 G 0.0109 0.7749 0.2141 194 I 0.0462 0.6549 0.2988 195 M 0.0998 0.3755 0.5247 196 A 0.0872 0.2515 0.6613 197 D 0.0687 0.1386 0.7927 198 G 0.0500 0.1597 0.7903 199 G 0.0528 0.1300 0.8173 200 A 0.1103 0.0841 0.8056 201 A 0.0855 0.0287 0.8858 202 P 0.0617 0.0151 0.9232 203 A 0.0432 0.0397 0.9171