# This file is the result of combining several RDB files, specifically # T0325.t04.dssp-ebghstl.rdb (weight 1.53986) # T0325.t04.stride-ebghtl.rdb (weight 1.24869) # T0325.t04.str2.rdb (weight 1.54758) # T0325.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 T0325.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0325 # 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 T0325.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 107.175 # # ============================================ # Comments from T0325.t04.stride-ebghtl.rdb # ============================================ # TARGET T0325 # 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 T0325.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 107.175 # # ============================================ # Comments from T0325.t04.str2.rdb # ============================================ # TARGET T0325 # 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 T0325.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 107.175 # # ============================================ # Comments from T0325.t04.alpha.rdb # ============================================ # TARGET T0325 # 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 T0325.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 107.175 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0628 0.0475 0.8897 2 S 0.1039 0.0436 0.8525 3 N 0.1546 0.0523 0.7930 4 K 0.3678 0.0174 0.6149 5 K 0.7831 0.0054 0.2114 6 L 0.9234 0.0034 0.0732 7 I 0.9302 0.0033 0.0666 8 I 0.9160 0.0048 0.0792 9 N 0.7700 0.0070 0.2229 10 A 0.3024 0.0540 0.6437 11 D 0.1094 0.1224 0.7683 12 D 0.0979 0.1818 0.7203 13 F 0.0711 0.1803 0.7485 14 G 0.1010 0.1233 0.7758 15 Y 0.1651 0.0784 0.7565 16 T 0.0810 0.0376 0.8813 17 P 0.0083 0.5729 0.4188 18 A 0.0106 0.6805 0.3089 19 V 0.0147 0.8225 0.1628 20 T 0.0113 0.8895 0.0992 21 Q 0.0091 0.9314 0.0595 22 G 0.0142 0.9438 0.0420 23 I 0.0059 0.9589 0.0352 24 I 0.0050 0.9603 0.0347 25 E 0.0056 0.9575 0.0368 26 A 0.0061 0.9502 0.0437 27 H 0.0060 0.9344 0.0596 28 K 0.0091 0.8872 0.1037 29 R 0.0451 0.4287 0.5262 30 G 0.0416 0.0584 0.9000 31 V 0.2304 0.0544 0.7153 32 V 0.6089 0.0327 0.3585 33 T 0.5115 0.0659 0.4226 34 S 0.4740 0.1394 0.3867 35 T 0.4129 0.2198 0.3673 36 T 0.4250 0.2518 0.3232 37 A 0.4044 0.2650 0.3306 38 L 0.2563 0.2194 0.5243 39 P 0.1331 0.2359 0.6310 40 T 0.0629 0.1979 0.7392 41 S 0.0443 0.3051 0.6506 42 P 0.0088 0.6907 0.3005 43 Y 0.0112 0.7848 0.2040 44 F 0.0056 0.9135 0.0809 45 L 0.0051 0.9426 0.0523 46 E 0.0049 0.9460 0.0491 47 A 0.0049 0.9492 0.0459 48 M 0.0049 0.9491 0.0460 49 E 0.0053 0.9315 0.0632 50 S 0.0066 0.8597 0.1337 51 A 0.0172 0.7163 0.2666 52 R 0.0188 0.5122 0.4690 53 I 0.0222 0.4376 0.5402 54 S 0.0410 0.2709 0.6880 55 A 0.0870 0.0422 0.8708 56 P 0.0189 0.1708 0.8103 57 T 0.0353 0.1316 0.8331 58 L 0.1723 0.0508 0.7769 59 A 0.2998 0.0273 0.6729 60 I 0.7887 0.0148 0.1965 61 G 0.8584 0.0095 0.1321 62 V 0.9061 0.0049 0.0890 63 H 0.9211 0.0045 0.0744 64 L 0.9103 0.0050 0.0846 65 T 0.8901 0.0066 0.1033 66 L 0.7666 0.0144 0.2190 67 T 0.4880 0.0224 0.4895 68 L 0.1652 0.1679 0.6668 69 N 0.0772 0.1872 0.7356 70 Q 0.0727 0.1708 0.7565 71 A 0.1144 0.0668 0.8188 72 K 0.1585 0.0367 0.8048 73 P 0.2600 0.0440 0.6960 74 I 0.2515 0.0483 0.7002 75 L 0.1525 0.0357 0.8118 76 P 0.0954 0.0947 0.8099 77 R 0.0128 0.6942 0.2930 78 E 0.0214 0.6732 0.3055 79 M 0.0464 0.5656 0.3881 80 V 0.1309 0.1447 0.7244 81 P 0.0612 0.2827 0.6561 82 S 0.1259 0.2746 0.5995 83 L 0.2334 0.2194 0.5471 84 V 0.3857 0.0954 0.5188 85 D 0.0839 0.0291 0.8870 86 E 0.0124 0.1480 0.8396 87 A 0.0474 0.0382 0.9144 88 G 0.0771 0.0565 0.8664 89 Y 0.2002 0.0589 0.7408 90 F 0.4397 0.0755 0.4849 91 W 0.2151 0.1284 0.6565 92 H 0.1684 0.2463 0.5854 93 Q 0.0907 0.4751 0.4342 94 S 0.0769 0.6018 0.3213 95 I 0.0706 0.6455 0.2839 96 F 0.0686 0.6047 0.3267 97 E 0.0575 0.5308 0.4117 98 E 0.0422 0.3367 0.6211 99 K 0.0725 0.1847 0.7428 100 V 0.1262 0.0392 0.8346 101 N 0.0806 0.0225 0.8968 102 L 0.0049 0.9463 0.0488 103 E 0.0047 0.9593 0.0360 104 E 0.0047 0.9602 0.0352 105 V 0.0047 0.9606 0.0348 106 Y 0.0047 0.9606 0.0347 107 N 0.0047 0.9609 0.0344 108 E 0.0047 0.9606 0.0347 109 W 0.0047 0.9603 0.0350 110 D 0.0047 0.9605 0.0348 111 A 0.0046 0.9614 0.0340 112 Q 0.0046 0.9613 0.0341 113 I 0.0046 0.9613 0.0340 114 I 0.0046 0.9614 0.0340 115 S 0.0046 0.9610 0.0344 116 F 0.0047 0.9601 0.0352 117 M 0.0049 0.9534 0.0417 118 K 0.0061 0.9035 0.0903 119 S 0.0424 0.4505 0.5071 120 G 0.0323 0.0310 0.9367 121 R 0.0580 0.0125 0.9295 122 R 0.1000 0.0114 0.8886 123 P 0.1043 0.1720 0.7237 124 D 0.1060 0.2294 0.6647 125 H 0.3413 0.2212 0.4376 126 I 0.4472 0.0987 0.4541 127 D 0.3215 0.0839 0.5946 128 S 0.1399 0.2519 0.6083 129 H 0.1187 0.2523 0.6291 130 H 0.1155 0.3319 0.5526 131 N 0.1385 0.2897 0.5717 132 V 0.1263 0.3421 0.5316 133 H 0.0816 0.3092 0.6091 134 G 0.0412 0.3384 0.6205 135 K 0.0472 0.3278 0.6250 136 N 0.0620 0.4205 0.5175 137 K 0.0144 0.8164 0.1692 138 K 0.0165 0.8715 0.1119 139 L 0.0109 0.9190 0.0701 140 L 0.0058 0.9470 0.0471 141 G 0.0047 0.9585 0.0368 142 V 0.0047 0.9607 0.0347 143 A 0.0047 0.9610 0.0343 144 L 0.0046 0.9610 0.0344 145 A 0.0047 0.9600 0.0353 146 L 0.0047 0.9574 0.0379 147 A 0.0049 0.9526 0.0425 148 R 0.0054 0.9333 0.0613 149 K 0.0079 0.8870 0.1050 150 Y 0.0470 0.5246 0.4284 151 Q 0.0533 0.0287 0.9180 152 L 0.0863 0.0095 0.9042 153 P 0.2784 0.0158 0.7058 154 L 0.5668 0.0429 0.3903 155 R 0.6017 0.0586 0.3397 156 N 0.5336 0.0573 0.4091 157 A 0.2860 0.0973 0.6167 158 S 0.1559 0.1540 0.6901 159 R 0.1205 0.1895 0.6900 160 S 0.1310 0.2298 0.6393 161 I 0.0938 0.3303 0.5759 162 E 0.0894 0.3289 0.5817 163 T 0.0687 0.4499 0.4814 164 K 0.0365 0.6329 0.3306 165 D 0.0426 0.6601 0.2973 166 Y 0.0392 0.7793 0.1815 167 L 0.0523 0.7606 0.1871 168 E 0.0569 0.7289 0.2142 169 L 0.0623 0.6547 0.2831 170 Y 0.0806 0.4777 0.4417 171 Q 0.0533 0.2896 0.6570 172 D 0.0676 0.1219 0.8104 173 V 0.1485 0.0490 0.8026 174 R 0.1742 0.0523 0.7735 175 T 0.1408 0.0433 0.8158 176 P 0.0716 0.3292 0.5991 177 D 0.0242 0.6475 0.3283 178 E 0.0522 0.7361 0.2117 179 M 0.0978 0.7113 0.1909 180 L 0.1503 0.6445 0.2053 181 Y 0.1695 0.6014 0.2291 182 Q 0.1812 0.5502 0.2686 183 F 0.2213 0.4609 0.3178 184 Y 0.1841 0.3544 0.4615 185 D 0.1205 0.2126 0.6669 186 K 0.0370 0.2007 0.7623 187 A 0.0590 0.1077 0.8333 188 I 0.1551 0.0296 0.8153 189 S 0.0730 0.0195 0.9076 190 T 0.0049 0.9460 0.0491 191 E 0.0047 0.9584 0.0369 192 T 0.0047 0.9591 0.0362 193 I 0.0047 0.9594 0.0360 194 L 0.0047 0.9589 0.0364 195 Q 0.0048 0.9531 0.0421 196 L 0.0049 0.9451 0.0499 197 L 0.0050 0.9347 0.0603 198 D 0.0056 0.8941 0.1003 199 M 0.0072 0.8590 0.1337 200 V 0.0186 0.7874 0.1940 201 V 0.0440 0.6334 0.3225 202 C 0.0638 0.3832 0.5530 203 S 0.0598 0.1244 0.8158 204 E 0.0403 0.1465 0.8132 205 G 0.0372 0.0841 0.8787 206 E 0.1295 0.0611 0.8094 207 V 0.6246 0.0125 0.3629 208 F 0.8205 0.0078 0.1718 209 E 0.9158 0.0047 0.0795 210 I 0.9174 0.0051 0.0774 211 N 0.8954 0.0047 0.0999 212 C 0.7076 0.0154 0.2770 213 H 0.2895 0.0220 0.6885 214 P 0.1191 0.1973 0.6836 215 A 0.1119 0.2407 0.6475 216 F 0.1722 0.3081 0.5197 217 I 0.1143 0.3643 0.5214 218 D 0.0700 0.4069 0.5231 219 T 0.0103 0.8619 0.1278 220 I 0.0138 0.8670 0.1192 221 L 0.0188 0.8426 0.1386 222 Q 0.0269 0.7506 0.2225 223 N 0.0289 0.5036 0.4675 224 Q 0.0468 0.2769 0.6763 225 S 0.0496 0.1597 0.7906 226 G 0.0342 0.2135 0.7523 227 Y 0.0615 0.2278 0.7107 228 C 0.0789 0.3063 0.6148 229 M 0.0591 0.4636 0.4772 230 P 0.0490 0.6721 0.2788 231 R 0.0438 0.8111 0.1451 232 I 0.0303 0.8917 0.0780 233 R 0.0309 0.8967 0.0725 234 E 0.0131 0.9348 0.0521 235 V 0.0084 0.9389 0.0527 236 E 0.0091 0.9321 0.0587 237 I 0.0097 0.8829 0.1073 238 L 0.0254 0.6781 0.2965 239 T 0.0360 0.3407 0.6233 240 S 0.0609 0.2539 0.6852 241 Q 0.0048 0.9243 0.0709 242 E 0.0047 0.9417 0.0536 243 V 0.0048 0.9555 0.0397 244 K 0.0047 0.9609 0.0344 245 E 0.0046 0.9614 0.0339 246 A 0.0046 0.9617 0.0336 247 I 0.0047 0.9609 0.0345 248 E 0.0048 0.9547 0.0405 249 E 0.0055 0.9175 0.0770 250 R 0.0433 0.3406 0.6162 251 G 0.0393 0.0158 0.9449 252 I 0.1177 0.0077 0.8746 253 L 0.7026 0.0065 0.2909 254 L 0.8179 0.0055 0.1766 255 A 0.6408 0.0337 0.3255 256 N 0.4422 0.0183 0.5395 257 Y 0.0849 0.5438 0.3713 258 E 0.0486 0.6000 0.3514 259 S 0.0518 0.6080 0.3402 260 L 0.0890 0.2978 0.6132 261 A 0.0591 0.1711 0.7698 262 M 0.0364 0.0839 0.8796