# This file is the result of combining several RDB files, specifically # T0355.t04.dssp-ebghstl.rdb (weight 1.53986) # T0355.t04.stride-ebghtl.rdb (weight 1.24869) # T0355.t04.str2.rdb (weight 1.54758) # T0355.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 T0355.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0355 # 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 T0355.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 685 # # ============================================ # Comments from T0355.t04.stride-ebghtl.rdb # ============================================ # TARGET T0355 # 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 T0355.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 685 # # ============================================ # Comments from T0355.t04.str2.rdb # ============================================ # TARGET T0355 # 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 T0355.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 685 # # ============================================ # Comments from T0355.t04.alpha.rdb # ============================================ # TARGET T0355 # 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 T0355.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 685 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0779 0.1967 0.7255 2 Q 0.0898 0.2477 0.6625 3 T 0.1096 0.2475 0.6428 4 I 0.0892 0.1690 0.7418 5 S 0.0562 0.1836 0.7602 6 D 0.0249 0.5065 0.4686 7 N 0.0286 0.5217 0.4497 8 A 0.0237 0.6159 0.3604 9 A 0.0180 0.7680 0.2140 10 N 0.0126 0.8564 0.1309 11 A 0.0090 0.9154 0.0756 12 I 0.0061 0.9443 0.0496 13 Q 0.0066 0.9440 0.0495 14 E 0.0068 0.9407 0.0526 15 I 0.0094 0.9128 0.0778 16 F 0.0335 0.6869 0.2795 17 G 0.0274 0.1637 0.8089 18 R 0.0574 0.1161 0.8265 19 S 0.0807 0.1328 0.7864 20 K 0.1230 0.1469 0.7301 21 A 0.2378 0.1622 0.5999 22 L 0.5095 0.1931 0.2974 23 I 0.5736 0.1700 0.2564 24 G 0.6101 0.1333 0.2566 25 M 0.6719 0.1060 0.2221 26 I 0.6783 0.0898 0.2319 27 H 0.4986 0.0847 0.4167 28 C 0.1631 0.0426 0.7943 29 P 0.0698 0.0846 0.8456 30 A 0.0630 0.1054 0.8316 31 F 0.0700 0.0601 0.8699 32 P 0.0537 0.0916 0.8547 33 G 0.0919 0.0642 0.8439 34 A 0.1680 0.0299 0.8021 35 P 0.2566 0.0668 0.6766 36 R 0.5642 0.0732 0.3626 37 Y 0.5676 0.0785 0.3539 38 R 0.4640 0.1040 0.4320 39 N 0.2782 0.1198 0.6020 40 A 0.1402 0.1045 0.7553 41 S 0.1187 0.0591 0.8222 42 M 0.0229 0.5539 0.4231 43 D 0.0100 0.8130 0.1770 44 A 0.0059 0.9037 0.0904 45 I 0.0047 0.9330 0.0623 46 Y 0.0047 0.9474 0.0479 47 D 0.0048 0.9503 0.0450 48 A 0.0049 0.9346 0.0605 49 C 0.0050 0.9315 0.0635 50 M 0.0048 0.9538 0.0415 51 R 0.0047 0.9595 0.0359 52 D 0.0047 0.9580 0.0373 53 A 0.0047 0.9591 0.0362 54 E 0.0047 0.9595 0.0358 55 R 0.0047 0.9596 0.0358 56 L 0.0047 0.9580 0.0373 57 I 0.0049 0.9490 0.0461 58 E 0.0057 0.8969 0.0974 59 G 0.0412 0.4600 0.4989 60 G 0.0458 0.0330 0.9213 61 M 0.0875 0.0150 0.8975 62 H 0.0891 0.0601 0.8508 63 G 0.8954 0.0075 0.0971 64 L 0.9285 0.0046 0.0669 65 I 0.9286 0.0052 0.0662 66 V 0.9039 0.0121 0.0840 67 E 0.7187 0.0365 0.2448 68 N 0.4212 0.0458 0.5330 69 H 0.2113 0.0787 0.7099 70 G 0.0934 0.0722 0.8344 71 D 0.0663 0.0574 0.8762 72 V 0.1214 0.0272 0.8514 73 P 0.1970 0.0511 0.7519 74 F 0.2076 0.0641 0.7283 75 S 0.1568 0.0477 0.7955 76 K 0.0810 0.0442 0.8748 77 P 0.0551 0.1919 0.7531 78 D 0.0384 0.3541 0.6075 79 D 0.0499 0.3536 0.5965 80 I 0.0687 0.2955 0.6358 81 G 0.0394 0.3495 0.6111 82 P 0.0139 0.8759 0.1102 83 E 0.0120 0.9305 0.0574 84 T 0.0077 0.9518 0.0405 85 S 0.0069 0.9562 0.0369 86 A 0.0060 0.9558 0.0382 87 F 0.0057 0.9532 0.0411 88 M 0.0053 0.9571 0.0376 89 S 0.0053 0.9577 0.0369 90 V 0.0051 0.9563 0.0386 91 V 0.0059 0.9436 0.0505 92 T 0.0088 0.9163 0.0750 93 D 0.0081 0.8432 0.1486 94 R 0.0219 0.5778 0.4003 95 I 0.0545 0.2139 0.7316 96 V 0.1914 0.0707 0.7380 97 R 0.2850 0.0557 0.6593 98 T 0.1433 0.2719 0.5848 99 A 0.0550 0.2226 0.7224 100 G 0.0573 0.1738 0.7689 101 V 0.1355 0.1109 0.7536 102 P 0.1729 0.2387 0.5884 103 V 0.1891 0.4731 0.3378 104 G 0.2179 0.4871 0.2950 105 I 0.1523 0.6891 0.1586 106 N 0.0954 0.7917 0.1128 107 V 0.1109 0.7859 0.1032 108 L 0.0850 0.7712 0.1437 109 A 0.0700 0.6743 0.2557 110 N 0.0427 0.3995 0.5578 111 A 0.0713 0.0809 0.8478 112 P 0.0671 0.1001 0.8328 113 I 0.0825 0.1420 0.7755 114 P 0.1431 0.1991 0.6578 115 A 0.2274 0.4501 0.3224 116 F 0.4113 0.4214 0.1673 117 A 0.4015 0.4852 0.1133 118 I 0.2963 0.5994 0.1043 119 A 0.2668 0.6182 0.1150 120 K 0.1494 0.7061 0.1445 121 A 0.1182 0.5923 0.2895 122 G 0.0875 0.2510 0.6615 123 G 0.1027 0.0390 0.8583 124 A 0.1593 0.0328 0.8079 125 K 0.4180 0.0787 0.5033 126 F 0.7646 0.0507 0.1847 127 I 0.6797 0.0637 0.2566 128 R 0.5029 0.0391 0.4581 129 V 0.1144 0.6942 0.1914 130 N 0.0556 0.7945 0.1498 131 Q 0.0357 0.8241 0.1402 132 W 0.0446 0.8093 0.1461 133 A 0.0347 0.8454 0.1199 134 N 0.0154 0.9027 0.0819 135 A 0.0107 0.9274 0.0619 136 Y 0.0087 0.9404 0.0509 137 V 0.0119 0.9328 0.0553 138 A 0.0118 0.9098 0.0784 139 N 0.0108 0.8594 0.1298 140 E 0.0488 0.4072 0.5441 141 G 0.0490 0.0462 0.9048 142 F 0.1471 0.0303 0.8226 143 M 0.2303 0.0743 0.6954 144 E 0.5427 0.0755 0.3818 145 G 0.6268 0.0498 0.3234 146 R 0.7335 0.0514 0.2151 147 A 0.6001 0.1035 0.2964 148 A 0.3246 0.1986 0.4767 149 E 0.1742 0.2715 0.5543 150 A 0.1232 0.4232 0.4536 151 M 0.0652 0.5529 0.3818 152 R 0.0470 0.6851 0.2680 153 Y 0.0317 0.7775 0.1907 154 R 0.0135 0.8773 0.1092 155 S 0.0079 0.9049 0.0872 156 L 0.0057 0.9185 0.0759 157 L 0.0091 0.9065 0.0844 158 R 0.0093 0.8765 0.1142 159 A 0.0072 0.8412 0.1515 160 E 0.0398 0.5371 0.4232 161 H 0.0298 0.1486 0.8216 162 I 0.1497 0.0800 0.7703 163 K 0.3230 0.1195 0.5575 164 V 0.7335 0.0945 0.1720 165 F 0.7727 0.0831 0.1442 166 A 0.7485 0.0840 0.1675 167 D 0.6073 0.0801 0.3127 168 S 0.4340 0.0661 0.4999 169 H 0.2595 0.0426 0.6979 170 V 0.1730 0.0991 0.7280 171 K 0.1474 0.0933 0.7593 172 H 0.1291 0.0709 0.8000 173 G 0.0840 0.1552 0.7607 174 A 0.0324 0.6120 0.3556 175 H 0.0448 0.6237 0.3315 176 A 0.0557 0.6244 0.3199 177 I 0.0978 0.3834 0.5188 178 T 0.0529 0.3004 0.6467 179 A 0.0224 0.4833 0.4944 180 D 0.0370 0.3576 0.6054 181 R 0.0698 0.3502 0.5800 182 S 0.0928 0.3910 0.5162 183 I 0.0381 0.7752 0.1866 184 D 0.0315 0.8009 0.1677 185 E 0.0298 0.7969 0.1733 186 L 0.0339 0.7218 0.2443 187 T 0.0897 0.4973 0.4130 188 R 0.0415 0.3378 0.6208 189 D 0.1038 0.1582 0.7380 190 L 0.5176 0.0494 0.4329 191 A 0.6979 0.0387 0.2634 192 F 0.8760 0.0175 0.1065 193 F 0.8256 0.0261 0.1483 194 D 0.7559 0.0142 0.2299 195 A 0.6121 0.0213 0.3666 196 D 0.4218 0.0400 0.5382 197 G 0.4812 0.0448 0.4740 198 V 0.6189 0.0457 0.3354 199 I 0.7158 0.0410 0.2433 200 A 0.5970 0.0498 0.3532 201 T 0.3485 0.0673 0.5842 202 G 0.1950 0.0678 0.7372 203 Q 0.1729 0.1223 0.7048 204 R 0.1770 0.1461 0.6769 205 T 0.1091 0.1307 0.7602 206 G 0.0631 0.0966 0.8403 207 N 0.0782 0.0629 0.8589 208 S 0.0800 0.1379 0.7821 209 A 0.0742 0.1417 0.7841 210 S 0.0676 0.1018 0.8306 211 L 0.0084 0.8969 0.0947 212 E 0.0053 0.9399 0.0548 213 E 0.0059 0.9362 0.0579 214 I 0.0072 0.9435 0.0493 215 E 0.0071 0.9469 0.0460 216 E 0.0086 0.9351 0.0563 217 I 0.0093 0.9263 0.0644 218 G 0.0109 0.9075 0.0816 219 A 0.0119 0.8490 0.1390 220 A 0.0270 0.6502 0.3228 221 T 0.0871 0.3022 0.6107 222 H 0.0603 0.0743 0.8654 223 L 0.1063 0.0116 0.8821 224 P 0.3061 0.0100 0.6839 225 L 0.8706 0.0065 0.1228 226 L 0.9012 0.0053 0.0935 227 V 0.8362 0.0291 0.1347 228 G 0.5632 0.0305 0.4063 229 S 0.2302 0.0561 0.7136 230 G 0.1401 0.0368 0.8232 231 V 0.1410 0.0173 0.8417 232 N 0.0617 0.0120 0.9263 233 E 0.0052 0.9261 0.0687 234 G 0.0052 0.9338 0.0610 235 N 0.0053 0.9415 0.0532 236 I 0.0047 0.9593 0.0360 237 V 0.0047 0.9604 0.0350 238 E 0.0047 0.9601 0.0353 239 I 0.0050 0.9543 0.0407 240 L 0.0061 0.9312 0.0628 241 K 0.0068 0.8518 0.1415 242 R 0.0137 0.5046 0.4818 243 T 0.0842 0.0738 0.8419 244 S 0.0476 0.0543 0.8981 245 G 0.6992 0.0146 0.2861 246 V 0.9196 0.0062 0.0742 247 I 0.9254 0.0061 0.0685 248 V 0.8747 0.0297 0.0957 249 A 0.5798 0.0819 0.3384 250 S 0.2335 0.3930 0.3735 251 S 0.1905 0.5332 0.2763 252 L 0.1890 0.6129 0.1981 253 K 0.1986 0.5832 0.2183 254 E 0.1463 0.4587 0.3950 255 G 0.0748 0.2997 0.6255 256 G 0.0632 0.2631 0.6737 257 V 0.0753 0.3612 0.5635 258 W 0.0948 0.3058 0.5993 259 W 0.0931 0.1302 0.7766 260 N 0.0621 0.0674 0.8705 261 P 0.0066 0.9006 0.0929 262 V 0.0063 0.9286 0.0651 263 E 0.0059 0.9338 0.0604 264 L 0.0050 0.9548 0.0402 265 A 0.0048 0.9576 0.0377 266 R 0.0047 0.9556 0.0397 267 V 0.0047 0.9575 0.0378 268 R 0.0047 0.9607 0.0347 269 S 0.0047 0.9595 0.0358 270 F 0.0047 0.9571 0.0382 271 V 0.0048 0.9548 0.0404 272 A 0.0052 0.9383 0.0565 273 A 0.0061 0.8691 0.1248 274 A 0.0109 0.8020 0.1870 275 R 0.0076 0.8678 0.1246 276 P 0.0071 0.8587 0.1342 277 G 0.0078 0.8716 0.1206 278 L 0.0102 0.8768 0.1130 279 E 0.0094 0.8382 0.1524 280 A 0.0110 0.7792 0.2098 281 L 0.0285 0.6668 0.3046 282 E 0.0467 0.5524 0.4009 283 H 0.0629 0.5042 0.4329 284 H 0.0897 0.3980 0.5123 285 H 0.1240 0.2712 0.6048 286 H 0.1177 0.1893 0.6930 287 H 0.0933 0.1014 0.8053 288 H 0.0661 0.0418 0.8922