# This file is the result of combining several RDB files, specifically # T0316.t06.dssp-ebghstl.rdb (weight 1.53986) # T0316.t06.stride-ebghtl.rdb (weight 1.24869) # T0316.t06.str2.rdb (weight 1.54758) # T0316.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 T0316.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0316 # 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 T0316.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 25.8903 # # ============================================ # Comments from T0316.t06.stride-ebghtl.rdb # ============================================ # TARGET T0316 # 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 T0316.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 25.8903 # # ============================================ # Comments from T0316.t06.str2.rdb # ============================================ # TARGET T0316 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0316.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 25.8903 # # ============================================ # Comments from T0316.t06.alpha.rdb # ============================================ # TARGET T0316 # 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 T0316.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 25.8903 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.2274 0.0255 0.7471 2 R 0.5897 0.0210 0.3893 3 V 0.7483 0.0149 0.2368 4 A 0.8069 0.0119 0.1812 5 R 0.7781 0.0150 0.2068 6 D 0.4354 0.0319 0.5327 7 E 0.1154 0.0971 0.7875 8 D 0.0546 0.0208 0.9246 9 G 0.0830 0.0274 0.8896 10 T 0.4256 0.0166 0.5578 11 V 0.8483 0.0059 0.1458 12 H 0.8771 0.0089 0.1140 13 M 0.8980 0.0090 0.0930 14 L 0.8649 0.0167 0.1184 15 R 0.7853 0.0263 0.1885 16 G 0.6442 0.0288 0.3270 17 V 0.4540 0.0494 0.4966 18 D 0.2199 0.0420 0.7381 19 N 0.0358 0.1064 0.8578 20 G 0.0259 0.0910 0.8831 21 K 0.0744 0.1615 0.7641 22 D 0.1327 0.1669 0.7004 23 Q 0.2114 0.4572 0.3314 24 T 0.3514 0.4923 0.1562 25 Y 0.3676 0.5420 0.0904 26 F 0.3528 0.5554 0.0919 27 L 0.2655 0.5945 0.1400 28 S 0.1675 0.5550 0.2775 29 Q 0.1248 0.3519 0.5233 30 L 0.1044 0.1264 0.7693 31 S 0.0650 0.0665 0.8685 32 Q 0.0049 0.9258 0.0693 33 E 0.0047 0.9433 0.0520 34 Q 0.0048 0.9491 0.0461 35 L 0.0048 0.9502 0.0451 36 Q 0.0053 0.9309 0.0638 37 K 0.0099 0.8366 0.1536 38 T 0.0311 0.7094 0.2595 39 M 0.0875 0.4343 0.4782 40 F 0.0963 0.2213 0.6824 41 P 0.0847 0.1996 0.7157 42 L 0.0495 0.3778 0.5727 43 G 0.0393 0.2975 0.6632 44 H 0.0477 0.2622 0.6901 45 L 0.0736 0.1299 0.7964 46 E 0.0626 0.0947 0.8428 47 K 0.0266 0.5970 0.3764 48 P 0.0054 0.8630 0.1316 49 E 0.0066 0.9296 0.0638 50 V 0.0053 0.9485 0.0462 51 R 0.0047 0.9555 0.0398 52 R 0.0046 0.9615 0.0339 53 L 0.0046 0.9617 0.0336 54 A 0.0047 0.9612 0.0341 55 E 0.0048 0.9570 0.0383 56 E 0.0052 0.9457 0.0491 57 A 0.0425 0.5542 0.4033 58 G 0.0422 0.0265 0.9313 59 L 0.0697 0.0164 0.9139 60 S 0.1430 0.0760 0.7810 61 T 0.3244 0.1642 0.5115 62 A 0.3461 0.1525 0.5014 63 K 0.2857 0.1187 0.5956 64 K 0.1760 0.1042 0.7198 65 K 0.0980 0.1993 0.7027 66 D 0.1022 0.1924 0.7054 67 S 0.2540 0.1283 0.6177 68 T 0.2472 0.0794 0.6734 69 G 0.4132 0.0500 0.5367 70 I 0.8100 0.0106 0.1793 71 C 0.8875 0.0098 0.1027 72 F 0.8676 0.0092 0.1232 73 I 0.6249 0.0253 0.3499 74 G 0.2057 0.0300 0.7643 75 E 0.0839 0.1060 0.8101 76 K 0.0470 0.1901 0.7630 77 N 0.0745 0.2593 0.6662 78 F 0.0152 0.8591 0.1257 79 K 0.0065 0.9127 0.0808 80 N 0.0081 0.9045 0.0873 81 F 0.0204 0.8977 0.0819 82 L 0.0152 0.8876 0.0973 83 S 0.0076 0.8649 0.1276 84 N 0.0156 0.6706 0.3138 85 Y 0.0494 0.3916 0.5590 86 L 0.0775 0.0413 0.8812 87 P 0.0792 0.0521 0.8687 88 A 0.1342 0.0341 0.8316 89 Q 0.1176 0.0233 0.8591 90 P 0.0961 0.0650 0.8389 91 G 0.1884 0.0411 0.7705 92 R 0.5536 0.0195 0.4269 93 M 0.8731 0.0059 0.1209 94 M 0.8654 0.0060 0.1287 95 T 0.6145 0.0088 0.3768 96 V 0.1720 0.0833 0.7447 97 D 0.0461 0.0286 0.9254 98 G 0.0642 0.0344 0.9014 99 R 0.4577 0.0191 0.5231 100 D 0.8355 0.0119 0.1527 101 M 0.7484 0.0406 0.2110 102 G 0.6551 0.0394 0.3055 103 E 0.5817 0.0622 0.3561 104 H 0.4684 0.0726 0.4590 105 A 0.2288 0.0850 0.6861 106 G 0.3637 0.0430 0.5933 107 L 0.6644 0.0389 0.2967 108 M 0.8414 0.0197 0.1389 109 Y 0.8650 0.0217 0.1133 110 Y 0.8498 0.0315 0.1187 111 T 0.7561 0.0556 0.1883 112 I 0.5441 0.1868 0.2691 113 G 0.4537 0.1552 0.3911 114 Q 0.4389 0.2074 0.3537 115 R 0.3719 0.2046 0.4235 116 G 0.2041 0.1988 0.5971 117 G 0.1750 0.1329 0.6921 118 L 0.2162 0.1014 0.6824 119 G 0.2415 0.0735 0.6849 120 I 0.2184 0.1115 0.6701 121 G 0.1989 0.0940 0.7071 122 G 0.1430 0.1008 0.7562 123 Q 0.1141 0.1459 0.7399 124 H 0.0851 0.1307 0.7842 125 G 0.0661 0.1038 0.8300 126 G 0.0576 0.0927 0.8497 127 D 0.0911 0.0868 0.8220 128 N 0.1305 0.0596 0.8099 129 A 0.1771 0.0161 0.8068 130 P 0.3141 0.0165 0.6693 131 W 0.7170 0.0192 0.2638 132 F 0.8869 0.0095 0.1036 133 V 0.9026 0.0066 0.0908 134 V 0.8360 0.0278 0.1362 135 G 0.7620 0.0195 0.2185 136 K 0.6348 0.0277 0.3375 137 D 0.4566 0.0371 0.5063 138 L 0.1125 0.2876 0.6000 139 S 0.0797 0.2749 0.6454 140 K 0.1059 0.1942 0.6999 141 N 0.1860 0.0340 0.7800 142 I 0.7809 0.0075 0.2116 143 L 0.9191 0.0035 0.0774 144 Y 0.9225 0.0040 0.0735 145 V 0.8739 0.0110 0.1151 146 G 0.5015 0.0140 0.4844 147 Q 0.1479 0.0427 0.8094 148 G 0.0675 0.0489 0.8836 149 F 0.0967 0.0697 0.8336 150 Y 0.1016 0.0924 0.8060 151 H 0.0730 0.2219 0.7051 152 D 0.0246 0.5336 0.4419 153 S 0.0304 0.6349 0.3348 154 L 0.1095 0.5189 0.3716 155 M 0.1852 0.3385 0.4763 156 S 0.2139 0.2282 0.5579 157 T 0.2124 0.1673 0.6203 158 S 0.5073 0.0805 0.4122 159 L 0.7305 0.0227 0.2468 160 E 0.7817 0.0210 0.1973 161 A 0.6806 0.0654 0.2540 162 S 0.4206 0.1331 0.4463 163 Q 0.4163 0.1244 0.4593 164 V 0.5402 0.0725 0.3873 165 H 0.6088 0.0748 0.3164 166 F 0.5848 0.0900 0.3253 167 T 0.4934 0.0967 0.4099 168 R 0.2994 0.1010 0.5996 169 E 0.2135 0.0834 0.7030 170 M 0.1407 0.0339 0.8254 171 P 0.0941 0.0745 0.8314 172 E 0.0603 0.2708 0.6689 173 E 0.0642 0.2297 0.7061 174 F 0.1386 0.0999 0.7615 175 T 0.2745 0.0428 0.6827 176 L 0.5674 0.0205 0.4121 177 E 0.7724 0.0130 0.2146 178 C 0.8863 0.0040 0.1097 179 T 0.9149 0.0040 0.0811 180 A 0.9172 0.0037 0.0791 181 K 0.9198 0.0038 0.0764 182 F 0.8971 0.0041 0.0988 183 R 0.8078 0.0116 0.1806 184 Y 0.6742 0.0141 0.3117 185 R 0.3514 0.0234 0.6252 186 Q 0.1513 0.0235 0.8252 187 P 0.1019 0.0568 0.8413 188 D 0.1180 0.0612 0.8208 189 S 0.2876 0.0206 0.6918 190 K 0.5667 0.0100 0.4233 191 V 0.8426 0.0052 0.1522 192 T 0.9103 0.0037 0.0860 193 V 0.9176 0.0034 0.0789 194 H 0.9046 0.0037 0.0917 195 V 0.8176 0.0110 0.1714 196 K 0.3849 0.0318 0.5833 197 G 0.0858 0.0380 0.8762 198 E 0.1466 0.0639 0.7894 199 K 0.6718 0.0174 0.3108 200 T 0.8736 0.0042 0.1222 201 E 0.9167 0.0037 0.0795 202 V 0.9234 0.0032 0.0734 203 I 0.9037 0.0040 0.0923 204 F 0.8306 0.0070 0.1624 205 A 0.4353 0.0287 0.5361 206 E 0.1980 0.0246 0.7775 207 P 0.2250 0.0633 0.7117 208 Q 0.4042 0.0956 0.5002 209 R 0.6113 0.0709 0.3178 210 A 0.6972 0.0349 0.2679 211 I 0.5983 0.0328 0.3689 212 T 0.2635 0.0217 0.7148 213 P 0.0692 0.0619 0.8688 214 G 0.0864 0.0271 0.8865 215 Q 0.5776 0.0123 0.4101 216 A 0.8699 0.0052 0.1249 217 V 0.9216 0.0033 0.0751 218 V 0.9307 0.0032 0.0660 219 F 0.9107 0.0049 0.0844 220 Y 0.8144 0.0103 0.1753 221 D 0.3185 0.0221 0.6594 222 G 0.0674 0.0298 0.9028 223 E 0.1878 0.0687 0.7435 224 E 0.6273 0.0354 0.3373 225 C 0.7939 0.0255 0.1806 226 L 0.7303 0.0469 0.2228 227 G 0.5802 0.0524 0.3675 228 G 0.5367 0.0785 0.3848 229 G 0.6669 0.0867 0.2464 230 L 0.7440 0.1047 0.1513 231 I 0.6641 0.1935 0.1424 232 D 0.4922 0.2463 0.2615 233 N 0.3107 0.2654 0.4239 234 A 0.2742 0.2545 0.4713 235 Y 0.2296 0.2063 0.5641 236 R 0.1753 0.2057 0.6191 237 D 0.1142 0.2242 0.6616 238 G 0.1253 0.1866 0.6880 239 Q 0.2749 0.1998 0.5254 240 V 0.3961 0.2493 0.3546 241 C 0.4070 0.2291 0.3639 242 Q 0.3695 0.2110 0.4195 243 Y 0.2765 0.1646 0.5590 244 I 0.1309 0.0765 0.7927